#### The actual repeat library file is in binary format #### ==> SegmentalDups <== #bin chrom chromStart chromEnd name score strand otherChrom otherStart otherEnd otherSize uid posBasesHit testResult verdict chits ccov alignfile alignL indelN indelS alignB matchB mismatchB transitionsB transversionsB fracMatch fracMatchIndel jcK k2K 585 chr1 465 30596 No.1139,chr2:114046528 570211 - chr2 114046528 114076216 243018229 1139 1000 N/A Filtered N/A N/A build35/align_both/0012//both064929 30176 43 531 29645 29282 363 128 235 0.987755 0.986324 0.012346 0.0123574 585 chr1 486 9707 No.11420,chr16:427 226883 + chr16 427 9533 88827254 11420 1000 N/A Filtered N/A N/A build35/align_both/0008//both044902 9240 14 151 9089 8966 123 49 74 0.986467 0.98495 0.0136564 0.0136667 585 chr1 486 76975 No.8735,chr15:100263879 0 - chr15 100263879 100338121 100338915 8735 1000 N/A Filtered N/A N/A build35/align_both/0008//both044358 75852 59 2108 73744 73271 473 166 307 0.993586 0.992792 0.00644167 0.00644479 585 chr1 486 9707 No.2448,chrY:57691013 223952 - chrY 57691013 57700310 57701691 2448 1000 N/A Filtered N/A N/A build35/align_both/0013//both065202 9312 13 104 9208 9044 164 64 100 0.982189 0.980805 0.0180255 0.0180445 585 chr1 486 9707 No.2344,chrX:154813586 223952 - chrX 154813586 154822883 154824264 2344 1000 N/A Filtered N/A N/A build35/align_both/0013//both065193 9312 13 104 9208 9044 164 64 100 0.982189 0.980805 0.0180255 0.0180445 585 chr1 486 30596 No.2251,chr9:844 582086 + chr9 844 30515 138429268 2251 1000 N/A Filtered N/A N/A build35/align_both/0013//both065185 30137 14 491 29646 29474 172 64 108 0.994198 0.993729 0.00582435 0.00582657 585 chr1 8256 76975 No.15309,chr19:11001 1165312 + chr19 11001 79672 63811651 15309 1000 N/A Filtered N/A N/A build35/align_both/0011//both058776 68799 42 206 68593 68280 313 124 189 0.995437 0.994828 0.00457709 0.00457824 585 chr1 23908 30596 No.5889,chr12:17641 78493 + chr12 17641 24322 132449811 5889 1000 N/A Filtered N/A N/A build35/align_both/0003//both015094 6697 10 23 6674 6548 126 38 88 0.981121 0.979653 0.0191209 0.0191582 585 chr1 59871 76975 No.1772,chr6:5001 118641 + chr6 5001 22075 170975699 1772 1000 N/A Filtered N/A N/A build35/align_both/0012//both064992 17136 19 92 17044 16908 136 51 85 0.992021 0.990916 0.0080221 0.00802624 ==> RepeatMsk <== #bin swScore milliDiv milliDel milliIns genoName genoStart genoEnd genoLeft strand repName repClass repFamily repStart repEnd repLeft id 585 1504 13 4 13 chr1 0 468 -245522379 + (CCCTAA)n Simple_repeat Simple_repeat 1 464 0 1 585 2833 129 82 21 chr1 468 1310 -245521537 + TAR1 Satellite telo 1 893 0 2 585 437 235 186 35 chr1 1366 1538 -245521309 - L1MC/D LINE L1 -2162 5646 5449 3 585 253 294 19 10 chr1 1540 1643 -245521204 - MER5B DNA MER1_type -74 104 1 4 585 318 230 38 0 chr1 5127 5218 -245517629 - MIR SINE MIR -65 143 49 5 585 203 162 0 0 chr1 6575 6612 -245516235 + (TGG)n Simple_repeat Simple_repeat 1 37 0 6 585 280 322 147 0 chr1 8769 8912 -245513935 + L2 LINE L2 2836 2999 -314 7 585 1652 296 122 22 chr1 9834 10590 -245512257 + L3 LINE CR1 3083 3913 -589 8 585 347 315 129 10 chr1 11811 12013 -245510834 + MLT1K LTR MaLR 15 240 -351 9 ==> simpleRepeat <== #bin chrom chromStart chromEnd name period copyNum consensusSize perMatch perIndel score A C G T entropy sequence 3 chr1 176160458 176160783 trf 4 78.2 4 75 16 150 0 31 0 68 0.95 CTTT 9 chr1 2096808 2097302 trf 31 15.5 31 75 8 305 6 49 23 20 1.72 CCCCCAGCTGTGCGTCCGTCCCTCGGCTCCG 14 chr1 44039523 44041456 trf 12 161.2 12 63 16 263 4 55 5 35 1.41 CCTCTTCCTGCT 14 chr1 44039713 44041312 trf 36 44.4 36 83 6 1484 4 55 5 34 1.41 GCCACTCTTCCTCCCCCTCCTCCTGTTCCTCTTCCC 26 chr1 148897457 148897827 trf 36 9.9 39 93 3 509 3 48 23 24 1.66 CTGCTCGCGCCTCTCCTCCTGCTGCTCGCGCCTCAGCTG 26 chr1 148897478 148897806 trf 18 17.7 18 88 5 458 3 47 24 24 1.67 CTGCTCGCGCCTCAGCTG 26 chr1 148897637 148897847 trf 21 10.7 21 77 14 225 1 50 20 27 1.56 CTGCTGCTCGCGCCTCTCCTC 32 chr1 198180750 198180913 trf 81 2 81 90 0 254 39 11 19 29 1.87 TGTGACAATTAAATGAGTTAATACATTAAAGGTCTTCAAACAGTCTATAGCATATAGTAAGCACACAAGATGGATGAATAA 75 chr1 2613436 2666377 trf 40 1318 40 80 5 35504 26 37 24 11 1.89 GCACCCACACCCACAGGTGAGCATCTGACAGCCTGAAACA