Find a specific motif or a sequence of motifs within genomic sequences.
motif.count(seq.file, motif, as.ratio = FALSE)
| seq.file | path to the genomic sequecne file of interest (e.g. LTR TE seqs predicted by
|
|---|---|
| motif | a character string or vector of strings which shall be counted within each sequence. |
| as.ratio | shall count values be returned as asbolute frequency (count value) or as relative frequency (percentage). |
Hajk-Georg Drost
# find number of "CG" motifs in predicted LTR transposons motif.count(seq.file = system.file("LTRseqs.fas",package = "LTRpred"), motif = "CG") #> [1] 245 186 235 116 129 118 98 180 236 75 81 105 127 56 214 77 152 172 #> [19] 115 581 459 196 129 70 165 84 84 169 124 216 179 263 166 107 133 79 #> [37] 117 664 113 81 152 102 191 77 146 92 156 116 140 297 104 108 116 204 #> [55] 173 85 133 260 119 129 291 274 134 113 655 169 224 189 62 67 81 210 #> [73] 605 75 437 347 178 106 93 146 585 67 96 191 147 159 83 163 79 190 #> [91] 150 102 109 119 181 135 150 130 216 122 117 131 80 234 188 176 91 187 #> [109] 224 152 124 627 157 367 146 130 66 145 405 265 56 110 63 165 88 300 #> [127] 164 86 110 96 99 239 92 87 164 117 136 83 611 686 576 973 445 112 #> [145] 151 66 91 396 80 111 130 300 191 136 409 62 172 369 84 192 326 190 #> [163] 129 140 88 139 206 203 112 81 82 96 328 229 334 206 89 235 116 165 #> [181] 124 291 100 200 81 177 154 522 154 174 205 124 194 120 397 198 459 615 #> [199] 142 90 173 147 117 108 99 93 125 87 176 77 170 208 64 121 116 318 #> [217] 185 189 112 206 123 124 287 218 103 117 318 564 114 212 304 211 327 223 #> [235] 302 333 401 116 116 129 113 518 204 741 226 137 310 162 120 149 98 225 #> [253] 532 81 169 76 144 218 66 98 452 83 247 418 156 91 254 69 222 128 #> [271] 89 151 134 77 482 94 102 78 95 159 128 126 157 385 385 211 91 145 #> [289] 111 125 247 207 522 117 111 151 186 148 194 125 122 659 660 66 138 101 #> [307] 527 145 88 132 91 147 190 309 115 498 108 187 653 104 257 327 301 147 #> [325] 162 187 134 146 101 240 84 162 168 235 80 114 75 132 111 93 117 132 #> [343] 235 139 78 70 79 188 74 69 350 399 79 131 108 88 181 72 258 122 #> [361] 132 643 74 104 143 137 316 236 368 239 215 177 701 82 176 119 121 176 #> [379] 115 93 73 99 199 171 113 114 219 108 289 119 238 274 76 62 108 207 #> [397] 178 193 116 155 57 592 97 177 310 373 93 308 262 276 162 77 181 71 #> [415] 75 97 77 77 176 130 80 130 128 182 105 128 232 111 116 138 76 143 #> [433] 215 395 214 74 107 199 117 140 100 128 179 109 206 126 117 128 154 78 #> [451] 204 131 191 94 240 96 580 686 # find number of "CG" motifs in predicted LTR transposons: rel. frequency motif.count(seq.file = system.file("LTRseqs.fas",package = "LTRpred"), motif = "CG", as.ratio = TRUE) #> 1_CHROMOSOME_dumped__149500_155909 1_CHROMOSOME_dumped__249531_259127 #> 0.03822153 0.01938106 #> 1_CHROMOSOME_dumped__428932_438092 1_CHROMOSOME_dumped__2659374_2663971 #> 0.02565222 0.02522836 #> 1_CHROMOSOME_dumped__3357954_3363283 1_CHROMOSOME_dumped__3780765_3785720 #> 0.02420263 0.02380952 #> 1_CHROMOSOME_dumped__3907118_3911673 1_CHROMOSOME_dumped__4081628_4091086 #> 0.02151010 0.01902950 #> 1_CHROMOSOME_dumped__4119030_4126617 1_CHROMOSOME_dumped__4405997_4411118 #> 0.03110174 0.01464272 #> 1_CHROMOSOME_dumped__5691759_5696703 1_CHROMOSOME_dumped__5897842_5902839 #> 0.01638018 0.02100840 #> 1_CHROMOSOME_dumped__5920835_5927113 1_CHROMOSOME_dumped__6009304_6014076 #> 0.02022615 0.01173266 #> 1_CHROMOSOME_dumped__6191403_6197517 1_CHROMOSOME_dumped__6538418_6543536 #> 0.03499591 0.01504200 #> 1_CHROMOSOME_dumped__6719067_6724311 1_CHROMOSOME_dumped__6767255_6773967 #> 0.02897998 0.02562193 #> 1_CHROMOSOME_dumped__6825176_6830220 1_CHROMOSOME_dumped__7025897_7047012 #> 0.02279485 0.02751468 #> 1_CHROMOSOME_dumped__8445394_8466734 1_CHROMOSOME_dumped__8578711_8588761 #> 0.02150790 0.01950055 #> 1_CHROMOSOME_dumped__8643650_8649288 1_CHROMOSOME_dumped__9368344_9373311 #> 0.02287640 0.01409018 #> 1_CHROMOSOME_dumped__9476002_9480634 1_CHROMOSOME_dumped__10121579_10125768 #> 0.03561407 0.02004773 #> 1_CHROMOSOME_dumped__10696719_10701589 1_CHROMOSOME_dumped__11125145_11133104 #> 0.01724492 0.02123116 #> 1_CHROMOSOME_dumped__11148084_11152830 1_CHROMOSOME_dumped__11284903_11295619 #> 0.02612176 0.02015489 #> 1_CHROMOSOME_dumped__11339006_11344662 1_CHROMOSOME_dumped__11346530_11355061 #> 0.03164221 0.03082513 #> 1_CHROMOSOME_dumped__11697950_11705480 1_CHROMOSOME_dumped__11789447_11794074 #> 0.02204223 0.02312014 #> 1_CHROMOSOME_dumped__11890866_11900756 1_CHROMOSOME_dumped__12194788_12199420 #> 0.01344657 0.01705159 #> 1_CHROMOSOME_dumped__12541821_12546900 1_CHROMOSOME_dumped__12664511_12673933 #> 0.02303150 0.07046588 #> 1_CHROMOSOME_dumped__12871512_12878779 1_CHROMOSOME_dumped__12969459_12975236 #> 0.01554761 0.01401869 #> 1_CHROMOSOME_dumped__13324761_13329591 1_CHROMOSOME_dumped__13334465_13339870 #> 0.03146347 0.01886792 #> 1_CHROMOSOME_dumped__13388869_13396650 1_CHROMOSOME_dumped__13398499_13402662 #> 0.02454382 0.01849183 #> 1_CHROMOSOME_dumped__13439443_13448531 1_CHROMOSOME_dumped__13559843_13564825 #> 0.01606337 0.01846277 #> 1_CHROMOSOME_dumped__13593058_13599710 1_CHROMOSOME_dumped__13676498_13682108 #> 0.02344807 0.02067368 #> 1_CHROMOSOME_dumped__13818567_13823889 1_CHROMOSOME_dumped__13883095_13890935 #> 0.02630096 0.03787782 #> 1_CHROMOSOME_dumped__13912841_13919010 1_CHROMOSOME_dumped__14019278_14024519 #> 0.01685575 0.02060282 #> 1_CHROMOSOME_dumped__14179555_14183988 1_CHROMOSOME_dumped__14214740_14225657 #> 0.02616148 0.01868474 #> 1_CHROMOSOME_dumped__14282118_14286791 1_CHROMOSOME_dumped__14745962_14750821 #> 0.03701326 0.01748971 #> 1_CHROMOSOME_dumped__15610250_15615956 1_CHROMOSOME_dumped__16012601_16019700 #> 0.02330471 0.03661972 #> 1_CHROMOSOME_dumped__16117817_16124067 1_CHROMOSOME_dumped__16176836_16181678 #> 0.01903695 0.02663638 #> 1_CHROMOSOME_dumped__16387793_16398190 1_CHROMOSOME_dumped__16537640_16548760 #> 0.02798615 0.02463807 #> 1_CHROMOSOME_dumped__16551721_16557069 1_CHROMOSOME_dumped__16569870_16575240 #> 0.02505141 0.02103891 #> 1_CHROMOSOME_dumped__16626036_16637234 1_CHROMOSOME_dumped__16638793_16645558 #> 0.05848736 0.02497783 #> 1_CHROMOSOME_dumped__16674908_16683328 1_CHROMOSOME_dumped__16853317_16858040 #> 0.02660017 0.04000847 #> 1_CHROMOSOME_dumped__17023916_17029257 1_CHROMOSOME_dumped__17054990_17060023 #> 0.01160614 0.01330950 #> 1_CHROMOSOME_dumped__17156581_17161059 1_CHROMOSOME_dumped__17247721_17252580 #> 0.01808439 0.04320988 #> 1_CHROMOSOME_dumped__17255285_17265290 1_CHROMOSOME_dumped__17520596_17525126 #> 0.06046372 0.01655264 #> 1_CHROMOSOME_dumped__17528667_17536139 1_CHROMOSOME_dumped__17574998_17592212 #> 0.05847718 0.02015684 #> 1_CHROMOSOME_dumped__17606460_17612336 1_CHROMOSOME_dumped__18198315_18206598 #> 0.03028756 0.01279575 #> 1_CHROMOSOME_dumped__18552993_18557995 1_CHROMOSOME_dumped__18639849_18648168 #> 0.01858885 0.01754808 #> 1_CHROMOSOME_dumped__18962095_18971496 1_CHROMOSOME_dumped__18996885_19001831 #> 0.06222080 0.01354356 #> 1_CHROMOSOME_dumped__20085162_20090239 1_CHROMOSOME_dumped__21244323_21249201 #> 0.01890508 0.03914737 #> 1_CHROMOSOME_dumped__21318903_21325509 1_CHROMOSOME_dumped__21346162_21351041 #> 0.02224913 0.03258197 #> 1_CHROMOSOME_dumped__21438251_21442649 1_CHROMOSOME_dumped__21930876_21937598 #> 0.01886792 0.02424513 #> 1_CHROMOSOME_dumped__21947272_21951934 1_CHROMOSOME_dumped__22100643_22105329 #> 0.01694188 0.04053766 #> 1_CHROMOSOME_dumped__22272951_22280403 1_CHROMOSOME_dumped__22619338_22624555 #> 0.02012612 0.01954772 #> 1_CHROMOSOME_dumped__22831590_22837366 1_CHROMOSOME_dumped__22941592_22946917 #> 0.01886792 0.02234322 #> 1_CHROMOSOME_dumped__23000655_23008290 1_CHROMOSOME_dumped__23118242_23123215 #> 0.02370351 0.02714113 #> 1_CHROMOSOME_dumped__23569996_23575851 1_CHROMOSOME_dumped__23646949_23653338 #> 0.02561475 0.02034429 #> 1_CHROMOSOME_dumped__24506842_24514619 1_CHROMOSOME_dumped__24873949_24879663 #> 0.02777064 0.02134733 #> 1_CHROMOSOME_dumped__24938566_24945901 1_CHROMOSOME_dumped__25265020_25271109 #> 0.01594875 0.02151067 #> 1_CHROMOSOME_dumped__26366608_26371676 1_CHROMOSOME_dumped__27199829_27210847 #> 0.01578221 0.02123605 #> 1_CHROMOSOME_dumped__27829437_27835759 1_CHROMOSOME_dumped__27930411_27936476 #> 0.02973272 0.02901418 #> 1_CHROMOSOME_dumped__28501879_28506082 1_CHROMOSOME_dumped__29587846_29595895 #> 0.02164605 0.02322981 #> 1_CHROMOSOME_dumped__29642083_29647526 1_CHROMOSOME_dumped__29700884_29707698 #> 0.04114622 0.02230374 #> 1_CHROMOSOME_dumped__30419866_30424328 2_CHROMOSOME_dumped__2080_10521 #> 0.02778400 0.07427150 #> 2_CHROMOSOME_dumped__167975_174024 2_CHROMOSOME_dumped__593307_610013 #> 0.02595041 0.02196684 #> 2_CHROMOSOME_dumped__611690_617410 2_CHROMOSOME_dumped__775782_782412 #> 0.02552001 0.01960489 #> 2_CHROMOSOME_dumped__909733_914339 2_CHROMOSOME_dumped__959966_964731 #> 0.01432603 0.03042384 #> 2_CHROMOSOME_dumped__975729_990317 2_CHROMOSOME_dumped__1235983_1250415 #> 0.02776064 0.01836070 #> 2_CHROMOSOME_dumped__1292790_1297013 2_CHROMOSOME_dumped__1388832_1393901 #> 0.01325758 0.02169625 #> 2_CHROMOSOME_dumped__1395261_1399523 2_CHROMOSOME_dumped__1523655_1531024 #> 0.01477833 0.02238806 #> 2_CHROMOSOME_dumped__1557140_1562062 2_CHROMOSOME_dumped__1629671_1637490 #> 0.01787528 0.03836317 #> 2_CHROMOSOME_dumped__1882607_1887821 2_CHROMOSOME_dumped__1970254_1974960 #> 0.03144775 0.01827066 #> 2_CHROMOSOME_dumped__2075307_2080607 2_CHROMOSOME_dumped__2274202_2280048 #> 0.02075080 0.01641868 #> 2_CHROMOSOME_dumped__2302464_2307170 2_CHROMOSOME_dumped__2745600_2752272 #> 0.02103250 0.03581597 #> 2_CHROMOSOME_dumped__2844749_2849616 2_CHROMOSOME_dumped__2858551_2864192 #> 0.01889893 0.01542006 #> 2_CHROMOSOME_dumped__2902330_2907117 2_CHROMOSOME_dumped__2911997_2919582 #> 0.03425230 0.01542315 #> 2_CHROMOSOME_dumped__3083903_3089468 2_CHROMOSOME_dumped__3160549_3166281 #> 0.02443406 0.01447759 #> 2_CHROMOSOME_dumped__3221681_3238915 2_CHROMOSOME_dumped__3270279_3289109 #> 0.03545112 0.03642929 #> 2_CHROMOSOME_dumped__3367929_3386289 2_CHROMOSOME_dumped__3426174_3451000 #> 0.03137084 0.03919120 #> 2_CHROMOSOME_dumped__3539977_3559406 2_CHROMOSOME_dumped__4080728_4088155 #> 0.02290273 0.01507808 #> 2_CHROMOSOME_dumped__4090709_4096103 2_CHROMOSOME_dumped__4110947_4115696 #> 0.02798888 0.01389474 #> 2_CHROMOSOME_dumped__4116023_4120740 2_CHROMOSOME_dumped__4161050_4173975 #> 0.01928783 0.03063593 #> 2_CHROMOSOME_dumped__4230743_4236513 2_CHROMOSOME_dumped__4408338_4413617 #> 0.01386242 0.02102273 #> 2_CHROMOSOME_dumped__4542920_4547698 2_CHROMOSOME_dumped__4558517_4566125 #> 0.02720234 0.03942699 #> 2_CHROMOSOME_dumped__4682601_4690775 2_CHROMOSOME_dumped__4693482_4698777 #> 0.02336391 0.02567976 #> 2_CHROMOSOME_dumped__4737963_4753533 2_CHROMOSOME_dumped__4775685_4780521 #> 0.02626678 0.01281786 #> 2_CHROMOSOME_dumped__4818686_4826103 2_CHROMOSOME_dumped__5040989_5048393 #> 0.02318684 0.04983120 #> 2_CHROMOSOME_dumped__5073848_5078420 2_CHROMOSOME_dumped__5394710_5399650 #> 0.01836869 0.03885853 #> 2_CHROMOSOME_dumped__6023868_6032902 2_CHROMOSOME_dumped__6256496_6260935 #> 0.03608190 0.04279279 #> 2_CHROMOSOME_dumped__6422229_6427295 2_CHROMOSOME_dumped__6819006_6823730 #> 0.02545885 0.02962963 #> 2_CHROMOSOME_dumped__6837314_6843322 2_CHROMOSOME_dumped__6894106_6899938 #> 0.01464470 0.02382993 #> 2_CHROMOSOME_dumped__7157625_7166649 2_CHROMOSOME_dumped__7224084_7229138 #> 0.02282548 0.04015826 #> 2_CHROMOSOME_dumped__7373364_7379268 2_CHROMOSOME_dumped__7448762_7454290 #> 0.01896698 0.01465003 #> 2_CHROMOSOME_dumped__8697239_8702070 2_CHROMOSOME_dumped__8816049_8820894 #> 0.01697020 0.01981015 #> 2_CHROMOSOME_dumped__8873017_8891285 2_CHROMOSOME_dumped__9187492_9195280 #> 0.01795391 0.02940044 #> 2_CHROMOSOME_dumped__9306572_9319034 2_CHROMOSOME_dumped__9927681_9932559 #> 0.02679933 0.04222177 #> 2_CHROMOSOME_dumped__10464648_10471481 2_CHROMOSOME_dumped__10483666_10492018 #> 0.01302312 0.02813360 #> 2_CHROMOSOME_dumped__10637411_10647335 2_CHROMOSOME_dumped__11435732_11443090 #> 0.01168766 0.02242152 #> 2_CHROMOSOME_dumped__11721105_11726615 2_CHROMOSOME_dumped__12445635_12457164 #> 0.02250045 0.02523851 #> 2_CHROMOSOME_dumped__12620243_12625077 2_CHROMOSOME_dumped__13508554_13515938 #> 0.02068252 0.02708192 #> 2_CHROMOSOME_dumped__13664992_13669870 2_CHROMOSOME_dumped__14026300_14032819 #> 0.01660176 0.02714724 #> 2_CHROMOSOME_dumped__14406571_14412855 2_CHROMOSOME_dumped__16280712_16302420 #> 0.02450278 0.02404533 #> 2_CHROMOSOME_dumped__17136148_17141211 2_CHROMOSOME_dumped__17252349_17258537 #> 0.03041074 0.02811440 #> 2_CHROMOSOME_dumped__17270937_17278587 2_CHROMOSOME_dumped__17676479_17684201 #> 0.02679388 0.01605594 #> 2_CHROMOSOME_dumped__18347446_18355355 2_CHROMOSOME_dumped__18659187_18664902 #> 0.02452592 0.02099370 #> 3_CHROMOSOME_dumped__780904_798849 3_CHROMOSOME_dumped__1526151_1535730 #> 0.02212192 0.02066806 #> 3_CHROMOSOME_dumped__1657651_1681989 3_CHROMOSOME_dumped__3110405_3124906 #> 0.01885862 0.04240794 #> 3_CHROMOSOME_dumped__3807306_3812643 3_CHROMOSOME_dumped__6188741_6193283 #> 0.02660172 0.01981070 #> 3_CHROMOSOME_dumped__6372409_6378607 3_CHROMOSOME_dumped__7354085_7359059 #> 0.02790773 0.02954774 #> 3_CHROMOSOME_dumped__7728276_7733244 3_CHROMOSOME_dumped__7760615_7765156 #> 0.02354599 0.02377807 #> 3_CHROMOSOME_dumped__8046323_8051045 3_CHROMOSOME_dumped__8537355_8543559 #> 0.02096125 0.01498791 #> 3_CHROMOSOME_dumped__8632393_8638600 3_CHROMOSOME_dumped__9226633_9231377 #> 0.02013531 0.01833509 #> 3_CHROMOSOME_dumped__9243115_9251762 3_CHROMOSOME_dumped__9387852_9393276 #> 0.02035153 0.01419355 #> 3_CHROMOSOME_dumped__9404664_9410413 3_CHROMOSOME_dumped__9604460_9613216 #> 0.02956522 0.02375243 #> 3_CHROMOSOME_dumped__9692211_9697532 3_CHROMOSOME_dumped__10494353_10500970 #> 0.01202555 0.01828347 #> 3_CHROMOSOME_dumped__10577158_10581825 3_CHROMOSOME_dumped__10711160_10725823 #> 0.02485004 0.02168576 #> 3_CHROMOSOME_dumped__11016111_11020804 3_CHROMOSOME_dumped__11122707_11127675 #> 0.03941202 0.03803582 #> 3_CHROMOSOME_dumped__11387801_11394402 3_CHROMOSOME_dumped__11652697_11657743 #> 0.01696456 0.04081633 #> 3_CHROMOSOME_dumped__11664969_11669787 3_CHROMOSOME_dumped__11853471_11859849 #> 0.02552397 0.01943878 #> 3_CHROMOSOME_dumped__12056081_12071267 3_CHROMOSOME_dumped__12275508_12287360 #> 0.01889774 0.01839197 #> 3_CHROMOSOME_dumped__12303477_12308746 3_CHROMOSOME_dumped__12314647_12319070 #> 0.01954459 0.02644665 #> 3_CHROMOSOME_dumped__12478086_12486327 3_CHROMOSOME_dumped__12491757_12502106 #> 0.03858287 0.05449275 #> 3_CHROMOSOME_dumped__12502664_12508397 3_CHROMOSOME_dumped__12549509_12555919 #> 0.01988141 0.03306816 #> 3_CHROMOSOME_dumped__12613331_12620941 3_CHROMOSOME_dumped__12636500_12644002 #> 0.03994219 0.02812208 #> 3_CHROMOSOME_dumped__12674274_12684173 3_CHROMOSOME_dumped__12695928_12704543 #> 0.03303030 0.02588208 #> 3_CHROMOSOME_dumped__12960389_12968468 3_CHROMOSOME_dumped__13087350_13092790 #> 0.03737624 0.06120198 #> 3_CHROMOSOME_dumped__13096163_13112097 3_CHROMOSOME_dumped__13318010_13323173 #> 0.02516473 0.02246321 #> 3_CHROMOSOME_dumped__13334612_13342566 3_CHROMOSOME_dumped__13360109_13368309 #> 0.01458202 0.01572979 #> 3_CHROMOSOME_dumped__13369174_13374107 3_CHROMOSOME_dumped__13440036_13449242 #> 0.02290231 0.05626154 #> 3_CHROMOSOME_dumped__14073146_14081964 3_CHROMOSOME_dumped__14117876_14141561 #> 0.02313187 0.03128430 #> 3_CHROMOSOME_dumped__14272824_14285579 3_CHROMOSOME_dumped__14329874_14334136 #> 0.01771715 0.03213699 #> 3_CHROMOSOME_dumped__14504089_14511689 3_CHROMOSOME_dumped__14579222_14584089 #> 0.04078411 0.03327855 #> 3_CHROMOSOME_dumped__14608928_14615360 3_CHROMOSOME_dumped__14616107_14623209 #> 0.01865382 0.02097705 #> 3_CHROMOSOME_dumped__14671141_14675856 3_CHROMOSOME_dumped__14729381_14734607 #> 0.02078032 0.04304572 #> 3_CHROMOSOME_dumped__14762490_14785730 3_CHROMOSOME_dumped__14860990_14866191 #> 0.02289058 0.01557093 #> 3_CHROMOSOME_dumped__14890955_14900038 3_CHROMOSOME_dumped__14956986_14962254 #> 0.01860414 0.01442399 #> 3_CHROMOSOME_dumped__15540529_15549180 3_CHROMOSOME_dumped__15591669_15600822 #> 0.01664355 0.02381473 #> 3_CHROMOSOME_dumped__15621872_15626854 3_CHROMOSOME_dumped__15768786_15773747 #> 0.01324503 0.01975010 #> 3_CHROMOSOME_dumped__15779153_15801235 3_CHROMOSOME_dumped__15919026_15924075 #> 0.02046823 0.01643564 #> 3_CHROMOSOME_dumped__16172247_16183071 3_CHROMOSOME_dumped__16243296_16256896 #> 0.02281755 0.03073303 #> 3_CHROMOSOME_dumped__16809187_16814152 3_CHROMOSOME_dumped__16826414_16832203 #> 0.03141361 0.01571675 #> 3_CHROMOSOME_dumped__16885889_16894261 3_CHROMOSOME_dumped__16957465_16962731 #> 0.03033560 0.01310044 #> 3_CHROMOSOME_dumped__17031074_17041106 3_CHROMOSOME_dumped__17235380_17239718 #> 0.02212698 0.02949988 #> 3_CHROMOSOME_dumped__17354612_17359635 3_CHROMOSOME_dumped__17403584_17414141 #> 0.01771497 0.01430195 #> 3_CHROMOSOME_dumped__17447389_17451847 3_CHROMOSOME_dumped__17978754_17983948 #> 0.03005158 0.01482194 #> 3_CHROMOSOME_dumped__18151296_18168081 3_CHROMOSOME_dumped__18169847_18174127 #> 0.02871440 0.02195749 #> 3_CHROMOSOME_dumped__18536569_18541113 3_CHROMOSOME_dumped__18734248_18739393 #> 0.02244224 0.01515740 #> 3_CHROMOSOME_dumped__18791152_18796089 3_CHROMOSOME_dumped__19290470_19296623 #> 0.01923856 0.02583685 #> 3_CHROMOSOME_dumped__19759349_19765040 3_CHROMOSOME_dumped__20304946_20310167 #> 0.02248770 0.02412869 #> 3_CHROMOSOME_dumped__21485038_21491983 3_CHROMOSOME_dumped__21576037_21593706 #> 0.02260294 0.02178834 #> 3_CHROMOSOME_dumped__21642929_21660064 3_CHROMOSOME_dumped__21894821_21904623 #> 0.02246732 0.02152402 #> 3_CHROMOSOME_dumped__21971055_21975268 3_CHROMOSOME_dumped__22015001_22020670 #> 0.02159468 0.02557319 #> 3_CHROMOSOME_dumped__22059535_22064329 3_CHROMOSOME_dumped__22232190_22236820 #> 0.02314911 0.02699201 #> 3_CHROMOSOME_dumped__22237229_22242466 3_CHROMOSOME_dumped__22334467_22341333 #> 0.04715540 0.03014417 #> 3_CHROMOSOME_dumped__22513587_22521224 3_CHROMOSOME_dumped__22695566_22700521 #> 0.06834250 0.02360775 #> 3_CHROMOSOME_dumped__23100313_23104853 4_CHROMOSOME_dumped__178046_186886 #> 0.02444396 0.01707952 #> 4_CHROMOSOME_dumped__1340159_1351874 4_CHROMOSOME_dumped__1473821_1478344 #> 0.01587573 0.03271441 #> 4_CHROMOSOME_dumped__1619054_1624381 4_CHROMOSOME_dumped__1749269_1755807 #> 0.03641141 0.01911607 #> 4_CHROMOSOME_dumped__1814108_1818633 4_CHROMOSOME_dumped__1943797_1955321 #> 0.02695537 0.05718004 #> 4_CHROMOSOME_dumped__2001193_2010885 4_CHROMOSOME_dumped__2064089_2068818 #> 0.06809037 0.01395349 #> 4_CHROMOSOME_dumped__2188978_2194314 4_CHROMOSOME_dumped__2198167_2203996 #> 0.02585722 0.01732419 #> 4_CHROMOSOME_dumped__2243443_2261156 4_CHROMOSOME_dumped__2279948_2286705 #> 0.02975048 0.02145605 #> 4_CHROMOSOME_dumped__2302657_2307843 4_CHROMOSOME_dumped__2442384_2446881 #> 0.01696549 0.02934638 #> 4_CHROMOSOME_dumped__2597020_2602180 4_CHROMOSOME_dumped__2615229_2622565 #> 0.01763224 0.02003544 #> 4_CHROMOSOME_dumped__2763293_2771367 4_CHROMOSOME_dumped__2867762_2875913 #> 0.02352941 0.03790481 #> 4_CHROMOSOME_dumped__2989830_2994788 4_CHROMOSOME_dumped__3704587_3716723 #> 0.02319016 0.04103156 #> 4_CHROMOSOME_dumped__3881650_3886431 4_CHROMOSOME_dumped__3907466_3915200 #> 0.02258469 0.02417582 #> 4_CHROMOSOME_dumped__4464332_4482516 4_CHROMOSOME_dumped__4623486_4628226 #> 0.03590872 0.02193630 #> 4_CHROMOSOME_dumped__4677141_4684195 4_CHROMOSOME_dumped__4958195_4969598 #> 0.03642807 0.02867415 #> 4_CHROMOSOME_dumped__5127101_5135153 4_CHROMOSOME_dumped__5291921_5296999 #> 0.03737737 0.02894271 #> 4_CHROMOSOME_dumped__5591440_5596425 4_CHROMOSOME_dumped__5822426_5827300 #> 0.03249097 0.03835897 #> 4_CHROMOSOME_dumped__5987008_5991992 4_CHROMOSOME_dumped__6588726_6593808 #> 0.02688064 0.02872319 #> 4_CHROMOSOME_dumped__6594136_6598635 4_CHROMOSOME_dumped__6659028_6672586 #> 0.02244444 0.01770042 #> 4_CHROMOSOME_dumped__6723347_6728791 4_CHROMOSOME_dumped__6826682_6833259 #> 0.01542700 0.02462755 #> 4_CHROMOSOME_dumped__6914662_6919598 4_CHROMOSOME_dumped__7298372_7305107 #> 0.03402876 0.03488717 #> 4_CHROMOSOME_dumped__7359462_7364591 4_CHROMOSOME_dumped__7522904_7527330 #> 0.01559454 0.02575107 #> 4_CHROMOSOME_dumped__7816826_7821792 4_CHROMOSOME_dumped__8086223_8092247 #> 0.01509966 0.02190871 #> 4_CHROMOSOME_dumped__8202631_8206965 4_CHROMOSOME_dumped__8313595_8319066 #> 0.02560554 0.01699561 #> 4_CHROMOSOME_dumped__8589987_8597164 4_CHROMOSOME_dumped__8852913_8857290 #> 0.01629980 0.03015075 #> 4_CHROMOSOME_dumped__9163509_9172988 4_CHROMOSOME_dumped__9182952_9188015 #> 0.02478903 0.02744866 #> 4_CHROMOSOME_dumped__9570498_9575604 4_CHROMOSOME_dumped__9732605_9737731 #> 0.01527315 0.01365321 #> 4_CHROMOSOME_dumped__9908989_9914046 4_CHROMOSOME_dumped__9950615_9958242 #> 0.01561882 0.02464604 #> 4_CHROMOSOME_dumped__10899527_10904693 4_CHROMOSOME_dumped__10992996_10998058 #> 0.01432166 0.01362828 #> 4_CHROMOSOME_dumped__11040514_11046715 4_CHROMOSOME_dumped__11206541_11211219 #> 0.05643341 0.08527463 #> 4_CHROMOSOME_dumped__11481824_11486753 4_CHROMOSOME_dumped__11703299_11707622 #> 0.01602434 0.03029602 #> 4_CHROMOSOME_dumped__11734522_11739041 4_CHROMOSOME_dumped__12211784_12218169 #> 0.02389381 0.01378014 #> 4_CHROMOSOME_dumped__13336302_13341644 4_CHROMOSOME_dumped__14258825_14263830 #> 0.03387610 0.01438274 #> 4_CHROMOSOME_dumped__14503006_14512023 4_CHROMOSOME_dumped__14684005_14688751 #> 0.02860945 0.02570044 #> 4_CHROMOSOME_dumped__15027814_15033127 4_CHROMOSOME_dumped__15551901_15565729 #> 0.02484005 0.04649649 #> 4_CHROMOSOME_dumped__15840427_15844699 4_CHROMOSOME_dumped__16320863_16325954 #> 0.01731804 0.02042419 #> 4_CHROMOSOME_dumped__17225299_17230933 4_CHROMOSOME_dumped__17712151_17716968 #> 0.02537711 0.02843504 #> 4_CHROMOSOME_dumped__18381613_18390512 5_CHROMOSOME_dumped__64772_71199 #> 0.03550562 0.03671437 #> 5_CHROMOSOME_dumped__211336_219089 5_CHROMOSOME_dumped__1331310_1337190 #> 0.04745938 0.04063935 #> 5_CHROMOSOME_dumped__1961367_1970365 5_CHROMOSOME_dumped__2373775_2379810 #> 0.02389154 0.02932406 #> 5_CHROMOSOME_dumped__2380969_2405489 5_CHROMOSOME_dumped__2510278_2515356 #> 0.02858774 0.01614491 #> 5_CHROMOSOME_dumped__3247646_3253022 5_CHROMOSOME_dumped__3904675_3909862 #> 0.03273201 0.02293755 #> 5_CHROMOSOME_dumped__4208083_4213084 5_CHROMOSOME_dumped__5603823_5608721 #> 0.02419032 0.03592570 #> 5_CHROMOSOME_dumped__6064597_6068747 5_CHROMOSOME_dumped__6403057_6408054 #> 0.02770417 0.01860744 #> 5_CHROMOSOME_dumped__6433629_6438777 5_CHROMOSOME_dumped__6468251_6472831 #> 0.01417751 0.02161100 #> 5_CHROMOSOME_dumped__7170326_7177335 5_CHROMOSOME_dumped__7210794_7219564 #> 0.02838802 0.01949607 #> 5_CHROMOSOME_dumped__7505453_7511007 5_CHROMOSOME_dumped__7511425_7516841 #> 0.02034203 0.02104486 #> 5_CHROMOSOME_dumped__7820047_7826629 5_CHROMOSOME_dumped__7858641_7864260 #> 0.03326751 0.01921708 #> 5_CHROMOSOME_dumped__8204176_8218846 5_CHROMOSOME_dumped__8245442_8252558 #> 0.01969873 0.01672053 #> 5_CHROMOSOME_dumped__8927997_8934328 5_CHROMOSOME_dumped__9181894_9189365 #> 0.03758686 0.03667024 #> 5_CHROMOSOME_dumped__9381694_9386622 5_CHROMOSOME_dumped__9949175_9954432 #> 0.01541895 0.01179156 #> 5_CHROMOSOME_dumped__10026369_10030633 5_CHROMOSOME_dumped__10128753_10133863 #> 0.02532239 0.04050088 #> 5_CHROMOSOME_dumped__10359352_10364274 5_CHROMOSOME_dumped__10638480_10643372 #> 0.03615681 0.03944410 #> 5_CHROMOSOME_dumped__10808404_10812940 5_CHROMOSOME_dumped__11159506_11166120 #> 0.02556756 0.02343159 #> 5_CHROMOSOME_dumped__11491567_11496131 5_CHROMOSOME_dumped__11503488_11512862 #> 0.01248631 0.06314667 #> 5_CHROMOSOME_dumped__11515554_11521087 5_CHROMOSOME_dumped__11621561_11635005 #> 0.01752801 0.01316475 #> 5_CHROMOSOME_dumped__11980554_11994151 5_CHROMOSOME_dumped__12189060_12194348 #> 0.02279747 0.07052373 #> 5_CHROMOSOME_dumped__13253687_13258453 5_CHROMOSOME_dumped__13261021_13272510 #> 0.01950913 0.02680592 #> 5_CHROMOSOME_dumped__13344204_13354020 5_CHROMOSOME_dumped__13607605_13621821 #> 0.02668840 0.01941338 #> 5_CHROMOSOME_dumped__13712934_13721136 5_CHROMOSOME_dumped__13736102_13741134 #> 0.01974887 0.01529903 #> 5_CHROMOSOME_dumped__13948926_13953982 5_CHROMOSOME_dumped__14083253_14088531 #> 0.03579197 0.01344952 #> 5_CHROMOSOME_dumped__14113154_14118424 5_CHROMOSOME_dumped__14203867_14209072 #> 0.01422880 0.01863235 #> 5_CHROMOSOME_dumped__14409576_14414448 5_CHROMOSOME_dumped__14468876_14473748 #> 0.01580135 0.01580135 #> 5_CHROMOSOME_dumped__14756546_14764119 5_CHROMOSOME_dumped__14873452_14880646 #> 0.02323739 0.01806810 #> 5_CHROMOSOME_dumped__15175722_15180975 5_CHROMOSOME_dumped__15277978_15284587 #> 0.01522649 0.01966717 #> 5_CHROMOSOME_dumped__15320410_15326088 5_CHROMOSOME_dumped__15377478_15384917 #> 0.02253918 0.02446237 #> 5_CHROMOSOME_dumped__15411867_15416287 5_CHROMOSOME_dumped__15646198_15651172 #> 0.02375028 0.02572864 #> 5_CHROMOSOME_dumped__15813256_15821248 5_CHROMOSOME_dumped__16509654_16515435 #> 0.02902540 0.01919751 #> 5_CHROMOSOME_dumped__16615185_16620067 5_CHROMOSOME_dumped__16882616_16889700 #> 0.02375589 0.01947777 #> 5_CHROMOSOME_dumped__17090770_17095675 5_CHROMOSOME_dumped__17394157_17400642 #> 0.01549124 0.02204749 #> 5_CHROMOSOME_dumped__17596764_17605847 5_CHROMOSOME_dumped__18119049_18132012 #> 0.02366799 0.03046899 #> 5_CHROMOSOME_dumped__18142156_18146897 5_CHROMOSOME_dumped__18233616_18238203 #> 0.04512864 0.01612903 #> 5_CHROMOSOME_dumped__18490606_18495233 5_CHROMOSOME_dumped__18511248_18518552 #> 0.02312014 0.02724162 #> 5_CHROMOSOME_dumped__18551370_18557055 5_CHROMOSOME_dumped__18673108_18678357 #> 0.02057686 0.02666667 #> 5_CHROMOSOME_dumped__18933102_18938947 5_CHROMOSOME_dumped__19345986_19351107 #> 0.01710571 0.02499024 #> 5_CHROMOSOME_dumped__19700784_19710576 5_CHROMOSOME_dumped__19987111_19992585 #> 0.01827836 0.01990868 #> 5_CHROMOSOME_dumped__20391919_20401644 5_CHROMOSOME_dumped__21384430_21390116 #> 0.02118034 0.02215579 #> 5_CHROMOSOME_dumped__21800243_21805138 5_CHROMOSOME_dumped__21915762_21920415 #> 0.02389706 0.02750322 #> 5_CHROMOSOME_dumped__22002013_22006896 5_CHROMOSOME_dumped__22911048_22916161 #> 0.03153153 0.01525225 #> 5_CHROMOSOME_dumped__24129974_24138730 5_CHROMOSOME_dumped__24526077_24530973 #> 0.02329565 0.02675107 #> 5_CHROMOSOME_dumped__25509002_25517288 5_CHROMOSOME_dumped__25992308_25997851 #> 0.02304815 0.01695527 #> 5_CHROMOSOME_dumped__26207873_26219365 5_CHROMOSOME_dumped__26587592_26591987 #> 0.02088228 0.02183803 #> mitochondria_CHROMOS_111563_129916 mitochondria_CHROMOS_241879_260732 #> 0.03160074 0.03638485