Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009603.1 Hibiscus syriacus cultivar Beakdansim tig00116983_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1462390
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 7
Found at i:1103734 original size:64 final size:64
Alignment explanation
Indices: 1103666--1103787 Score: 158
Period size: 64 Copynumber: 1.9 Consensus size: 64
1103656 ACATAAATCT
* **
1103666 CATTCGATGTTTGTATTCT-AAGCGGGTGCATCGAT-GCACTACTTGTGCATCGATACACTGATG
1 CATTCGATGTTTGTATTCTAAAG-GAGTGCATCGATAG-ACTACAGGTGCATCGATACACTGATG
1103729 G
64 G
* * *
1103730 CATTCGATGTTTTTATTTTAAAGGAGTGCATCGATAGACTTCAGGTGCATCGATACAC
1 CATTCGATGTTTGTATTCTAAAGGAGTGCATCGATAGACTACAGGTGCATCGATACAC
1103788 CTTGAACAAT
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
64 46 0.92
65 4 0.08
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.34
Consensus pattern (64 bp):
CATTCGATGTTTGTATTCTAAAGGAGTGCATCGATAGACTACAGGTGCATCGATACACTGATGG
Found at i:1109740 original size:18 final size:18
Alignment explanation
Indices: 1109717--1109787 Score: 97
Period size: 18 Copynumber: 3.9 Consensus size: 18
1109707 CTGAATATTT
1109717 TATCCCGAAGGACCACTA
1 TATCCCGAAGGACCACTA
*
1109735 TATCCCAAAGGACCACTA
1 TATCCCGAAGGACCACTA
*
1109753 TGTCCCGAAGGACCACTA
1 TATCCCGAAGGACCACTA
* * *
1109771 TGTCTCGAAAGACCACT
1 TATCCCGAAGGACCACT
1109788 GATAATCCCT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 48 1.00
ACGTcount: A:0.32, C:0.32, G:0.17, T:0.18
Consensus pattern (18 bp):
TATCCCGAAGGACCACTA
Found at i:1110422 original size:64 final size:65
Alignment explanation
Indices: 1110350--1110513 Score: 174
Period size: 64 Copynumber: 2.6 Consensus size: 65
1110340 CATCCCTTGA
*
1110350 CGGGTGCATCGATGCACTA-TCTATGCATCGGTACA-TAAATCACATTCGATGTTTATATTCT-A
1 CGGGTGCATCGATGCACTACT-TATGCATCGATACACT-AATCACATTCGATGTTTATATTCTAA
1110412 AG
64 AG
* * * * *
1110414 CGGGTGCATCGATGCACTACTTGTGCATCGATACACTGATGACATTCGATGTTTTTATTTTAAAG
1 CGGGTGCATCGATGCACTACTTATGCATCGATACACTAATCACATTCGATGTTTATATTCTAAAG
* * * ***
1110479 -GAGTGCATCGATACACTTCAGGTGCATCGATACAC
1 CGGGTGCATCGATGCACTACTTATGCATCGATACAC
1110514 CTTGAACAAT
Statistics
Matches: 86, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
64 81 0.94
65 5 0.06
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.32
Consensus pattern (65 bp):
CGGGTGCATCGATGCACTACTTATGCATCGATACACTAATCACATTCGATGTTTATATTCTAAAG
Found at i:1111817 original size:21 final size:23
Alignment explanation
Indices: 1111774--1111822 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
1111764 CTTAAGAAGT
*
1111774 AAAAATTAAAAAATAAAGAAAAG
1 AAAACTTAAAAAATAAAGAAAAG
*
1111797 AAAACTTAAAAAA-AAA-TAAAG
1 AAAACTTAAAAAATAAAGAAAAG
1111818 AAAAC
1 AAAAC
1111823 AAAGAACAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 9 0.38
22 3 0.12
23 12 0.50
ACGTcount: A:0.78, C:0.04, G:0.06, T:0.12
Consensus pattern (23 bp):
AAAACTTAAAAAATAAAGAAAAG
Found at i:1113382 original size:2 final size:2
Alignment explanation
Indices: 1113375--1113400 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1113365 ACTTTTCATA
1113375 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1113401 CTTGGGTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1115445 original size:19 final size:18
Alignment explanation
Indices: 1115409--1115453 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
1115399 CAATTCCCAC
*
1115409 AAAAACATTAATTTCGGG
1 AAAAATATTAATTTCGGG
*
1115427 AAAAATATTCATTTACGGG
1 AAAAATATTAATTT-CGGG
1115446 AAAAATAT
1 AAAAATAT
1115454 ATAACTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 12 0.50
19 12 0.50
ACGTcount: A:0.49, C:0.09, G:0.13, T:0.29
Consensus pattern (18 bp):
AAAAATATTAATTTCGGG
Found at i:1115546 original size:29 final size:30
Alignment explanation
Indices: 1115477--1115547 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 30
1115467 ATTATATTTT
* *
1115477 TTTTGTTC-CTAAACTTTTCAAAATTTACA
1 TTTTGGTCACTAAACTTTTCAAAACTTACA
* **
1115506 CTTTGGGAACTAAAC-TTTCAAAACTTACA
1 TTTTGGTCACTAAACTTTTCAAAACTTACA
1115535 TTTTGGTCACTAA
1 TTTTGGTCACTAA
1115548 GCAAAATTTG
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
29 27 0.82
30 6 0.18
ACGTcount: A:0.32, C:0.18, G:0.08, T:0.41
Consensus pattern (30 bp):
TTTTGGTCACTAAACTTTTCAAAACTTACA
Found at i:1115648 original size:103 final size:103
Alignment explanation
Indices: 1115521--1115727 Score: 414
Period size: 103 Copynumber: 2.0 Consensus size: 103
1115511 GGAACTAAAC
1115521 TTTCAAAACTTACATTTTGGTCACTAAGCAAAATTTGGGGTATTACACCCACTTTTATAAATACC
1 TTTCAAAACTTACATTTTGGTCACTAAGCAAAATTTGGGGTATTACACCCACTTTTATAAATACC
1115586 GTTGGAATTATATTTTCCCTTTGCAAAATTTACATTTT
66 GTTGGAATTATATTTTCCCTTTGCAAAATTTACATTTT
1115624 TTTCAAAACTTACATTTTGGTCACTAAGCAAAATTTGGGGTATTACACCCACTTTTATAAATACC
1 TTTCAAAACTTACATTTTGGTCACTAAGCAAAATTTGGGGTATTACACCCACTTTTATAAATACC
1115689 GTTGGAATTATATTTTCCCTTTGCAAAATTTACATTTT
66 GTTGGAATTATATTTTCCCTTTGCAAAATTTACATTTT
1115727 T
1 T
1115728 CTTTATTTTT
Statistics
Matches: 104, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
103 104 1.00
ACGTcount: A:0.31, C:0.17, G:0.11, T:0.41
Consensus pattern (103 bp):
TTTCAAAACTTACATTTTGGTCACTAAGCAAAATTTGGGGTATTACACCCACTTTTATAAATACC
GTTGGAATTATATTTTCCCTTTGCAAAATTTACATTTT
Found at i:1122735 original size:37 final size:37
Alignment explanation
Indices: 1122669--1122774 Score: 162
Period size: 36 Copynumber: 2.9 Consensus size: 37
1122659 AAGATAACGT
* *
1122669 TAGAGTTTTATTAGGATT-AAACTCCTAAAAATATGA
1 TAGAGTTTTACTATGATTCAAACTCCTAAAAATATGA
*
1122705 TAGAGTTTTACTATGATTCAAACTCTTAAAAATATGA
1 TAGAGTTTTACTATGATTCAAACTCCTAAAAATATGA
*
1122742 TAGA-TTTTACTATAATTCAAACTCCTAAAAATA
1 TAGAGTTTTACTATGATTCAAACTCCTAAAAATA
1122775 GGATCTATAA
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
36 43 0.67
37 21 0.33
ACGTcount: A:0.42, C:0.11, G:0.09, T:0.37
Consensus pattern (37 bp):
TAGAGTTTTACTATGATTCAAACTCCTAAAAATATGA
Found at i:1123481 original size:3 final size:3
Alignment explanation
Indices: 1123473--1123513 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
1123463 ATTACTGTTT
*
1123473 TTA TTA TTA TTA GTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1123514 CTATTTTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:1123528 original size:9 final size:10
Alignment explanation
Indices: 1123472--1123527 Score: 64
Period size: 9 Copynumber: 5.6 Consensus size: 10
1123462 AATTACTGTT
1123472 TTTATTATTA
1 TTTATTATTA
1123482 TTAGTATTATTA
1 TT--TATTATTA
1123494 -TTATTATTA
1 TTTATTATTA
1123503 -TTATTATTA
1 TTTATTATTA
1123512 TTCTATT-TTA
1 TT-TATTATTA
1123522 TTTATT
1 TTTATT
1123528 TCTATTTACC
Statistics
Matches: 42, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
9 21 0.50
10 8 0.19
11 5 0.12
12 8 0.19
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.68
Consensus pattern (10 bp):
TTTATTATTA
Found at i:1125347 original size:22 final size:22
Alignment explanation
Indices: 1125319--1125363 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
1125309 ATTATTTATA
1125319 ATAACAGACATGTTTTCGGATC
1 ATAACAGACATGTTTTCGGATC
1125341 ATAACAGACATGTTTTCGGATC
1 ATAACAGACATGTTTTCGGATC
1125363 A
1 A
1125364 AGAACTCAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (22 bp):
ATAACAGACATGTTTTCGGATC
Found at i:1126540 original size:12 final size:12
Alignment explanation
Indices: 1126507--1126549 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
1126497 CAATCAGAAC
1126507 AAAAAAA-AAAG
1 AAAAAAACAAAG
1126518 AAAAAAACAAAG
1 AAAAAAACAAAG
* *
1126530 GAAAAAGCAAAG
1 AAAAAAACAAAG
1126542 TAAAAAAA
1 -AAAAAAA
1126550 TAAAAAGCAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
11 7 0.27
12 14 0.54
13 5 0.19
ACGTcount: A:0.81, C:0.05, G:0.12, T:0.02
Consensus pattern (12 bp):
AAAAAAACAAAG
Found at i:1126568 original size:20 final size:20
Alignment explanation
Indices: 1126502--1126560 Score: 52
Period size: 20 Copynumber: 3.0 Consensus size: 20
1126492 AGATCCAATC
*
1126502 AGAACAAAAA-AAAAAG-AA
1 AGAAAAAAAATAAAAAGCAA
**
1126520 A-AAAACAAAGGAAAAAGCAA
1 AGAAAA-AAAATAAAAAGCAA
*
1126540 AGTAAAAAAATAAAAAGCAA
1 AGAAAAAAAATAAAAAGCAA
1126560 A
1 A
1126561 AACAAAAACC
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
17 3 0.09
18 4 0.12
19 6 0.19
20 16 0.50
21 3 0.09
ACGTcount: A:0.78, C:0.07, G:0.12, T:0.03
Consensus pattern (20 bp):
AGAAAAAAAATAAAAAGCAA
Found at i:1127688 original size:32 final size:32
Alignment explanation
Indices: 1127651--1127714 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
1127641 TGGGAGCACC
* * *
1127651 TTTGAAGATTCAACTTCAAATGTTGGGGCATT
1 TTTGAAAATTCAACATCAAATATTGGGGCATT
*
1127683 TTTGAAAATTCAACATCGAATATTGGGGCATT
1 TTTGAAAATTCAACATCAAATATTGGGGCATT
1127715 CGGGGATTCA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.31, C:0.12, G:0.20, T:0.36
Consensus pattern (32 bp):
TTTGAAAATTCAACATCAAATATTGGGGCATT
Found at i:1128542 original size:110 final size:110
Alignment explanation
Indices: 1128238--1128532 Score: 509
Period size: 110 Copynumber: 2.7 Consensus size: 110
1128228 TCGAGACAAG
* *
1128238 CTGACTGTCAATAAACAAGTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAACAAAGGATA
1 CTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAACAAAGGATA
* *
1128303 TTGGACTCGAGACAACACAAGTTCAACTTCACAGCGAAGGGGCGA
66 TTGGACTCGAGACAACACAAGCTCAACTTCACAACGAAGGGGCGA
* *
1128348 CTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAACGAAGGGTA
1 CTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAACAAAGGATA
1128413 TTGGACTCGAGACAACACAAGCTCAACTTCACAACGAAGGGGCGA
66 TTGGACTCGAGACAACACAAGCTCAACTTCACAACGAAGGGGCGA
* *
1128458 CTGACTGTCAACAAACAACATTTCAGTTTCATTCAGAGTCAATTTCAACTTCACATCAAAGGATA
1 CTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAACAAAGGATA
*
1128523 TTGAACTCGA
66 TTGGACTCGA
1128533 AGTGACACAA
Statistics
Matches: 174, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
110 174 1.00
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.25
Consensus pattern (110 bp):
CTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAACAAAGGATA
TTGGACTCGAGACAACACAAGCTCAACTTCACAACGAAGGGGCGA
Found at i:1129720 original size:37 final size:37
Alignment explanation
Indices: 1129670--1129775 Score: 185
Period size: 37 Copynumber: 2.9 Consensus size: 37
1129660 AACATAACGT
*
1129670 TAGAGTTTTACTATGATTCAGACTCCTAAAAATATGA
1 TAGAGTTTTACTATGATTCAAACTCCTAAAAATATGA
1129707 TAGAGTTTTACTATGATTCAAACTCCTAAAAATATGA
1 TAGAGTTTTACTATGATTCAAACTCCTAAAAATATGA
* *
1129744 TAGAGTTTTATTATGGTTCAAACTCCTAAAAA
1 TAGAGTTTTACTATGATTCAAACTCCTAAAAA
1129776 AAGGATTCAT
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 66 1.00
ACGTcount: A:0.39, C:0.13, G:0.12, T:0.36
Consensus pattern (37 bp):
TAGAGTTTTACTATGATTCAAACTCCTAAAAATATGA
Found at i:1130179 original size:19 final size:18
Alignment explanation
Indices: 1130154--1130204 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 18
1130144 ATTATTATTA
1130154 TTATTATTATTTTTTATAT
1 TTATTATTATTTTTTA-AT
1130173 GTT-TTATCT-TTTTTTAAT
1 -TTATTAT-TATTTTTTAAT
1130191 TTATTATTATTTTT
1 TTATTATTATTTTT
1130205 AAAACATTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
17 3 0.11
18 11 0.39
19 11 0.39
20 3 0.11
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.75
Consensus pattern (18 bp):
TTATTATTATTTTTTAAT
Found at i:1130254 original size:19 final size:21
Alignment explanation
Indices: 1130232--1130286 Score: 60
Period size: 24 Copynumber: 2.6 Consensus size: 21
1130222 TACATATTCA
1130232 TTATTTTTTT-TATC-TTATT
1 TTATTTTTTTCTATCATTATT
1130251 TTATTTCATTTATCTATCATTATT
1 TTATTT--TTT-TCTATCATTATT
*
1130275 ATATTTTTTTCT
1 TTATTTTTTTCT
1130287 CTCTCTATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
19 6 0.20
21 6 0.20
22 4 0.13
23 4 0.13
24 10 0.33
ACGTcount: A:0.20, C:0.09, G:0.00, T:0.71
Consensus pattern (21 bp):
TTATTTTTTTCTATCATTATT
Found at i:1130318 original size:44 final size:42
Alignment explanation
Indices: 1130226--1130322 Score: 108
Period size: 42 Copynumber: 2.3 Consensus size: 42
1130216 TTTATATACA
*
1130226 TATTCATTAT-TTTTTTTATCTTATTTTATTTCATTTATCTAT
1 TATT-ATTATATTTTTTTATCTTATATTATTTCATTTATCTAT
* * *
1130268 CATTATTATATTTTTTTCTCTCTCTATTATTT-ATTTATACGTAT
1 TATTATTATATTTTTTTATCT-TATATTATTTCATTTAT-C-TAT
1130312 TATTATTATAT
1 TATTATTATAT
1130323 ATATACATTT
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
41 5 0.11
42 19 0.41
43 9 0.20
44 13 0.28
ACGTcount: A:0.24, C:0.10, G:0.01, T:0.65
Consensus pattern (42 bp):
TATTATTATATTTTTTTATCTTATATTATTTCATTTATCTAT
Found at i:1130370 original size:2 final size:2
Alignment explanation
Indices: 1130365--1130424 Score: 81
Period size: 2 Copynumber: 31.5 Consensus size: 2
1130355 TAATATTTTT
*
1130365 TA TA TA TA TA TA TT TA T- TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
1130406 TA TA T- TA TA T- TA TT TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
1130425 TCTTATACAC
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
1 3 0.06
2 48 0.94
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (2 bp):
TA
Found at i:1130385 original size:29 final size:29
Alignment explanation
Indices: 1130353--1130424 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 29
1130343 TTTTTATTTG
* *
1130353 TATAATATTTTTTATATATATATATTTAT
1 TATAATATTTTATATATATATATATATAT
*
1130382 TAT-ATATATATATATATATATATATATAT
1 TATAATAT-TTTATATATATATATATATAT
*
1130411 TATATTA-TTTATAT
1 TATAATATTTTATAT
1130425 TCTTATACAC
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
28 10 0.28
29 24 0.67
30 2 0.06
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (29 bp):
TATAATATTTTATATATATATATATATAT
Found at i:1130547 original size:41 final size:41
Alignment explanation
Indices: 1130502--1130617 Score: 112
Period size: 42 Copynumber: 2.8 Consensus size: 41
1130492 TATTATTCTA
* *
1130502 TTTTATTTATATTTATTTATCTTT-TTTTTTCTCTAT-TTTAT
1 TTTTATTT-TATTTATTTATCTTTATTTTTTATCT-TCTTCAT
*
1130543 TTTTATTTTTATTT-TTTATTTTTAATTTTTTATCTTCTTCAT
1 TTTTA-TTTTATTTATTTATCTTT-ATTTTTTATCTTCTTCAT
* * *
1130585 ATTTATTTTATTTATTTGTATTTATTTTATTAT
1 TTTTATTTTATTTATTTATCTTTATTTT-TTAT
1130618 TTTTTATTTA
Statistics
Matches: 63, Mismatches: 6, Indels: 11
0.79 0.08 0.14
Matches are distributed among these distances:
40 8 0.13
41 24 0.38
42 31 0.49
ACGTcount: A:0.19, C:0.05, G:0.01, T:0.75
Consensus pattern (41 bp):
TTTTATTTTATTTATTTATCTTTATTTTTTATCTTCTTCAT
Found at i:1130552 original size:12 final size:12
Alignment explanation
Indices: 1130470--1130572 Score: 55
Period size: 13 Copynumber: 7.9 Consensus size: 12
1130460 TTTTACTTAC
*
1130470 TTTTTATTATTA
1 TTTTTATTTTTA
* * *
1130482 GTATTATTATTA
1 TTTTTATTTTTA
1130494 TTATTCTA-TTTTA
1 TT-TT-TATTTTTA
*
1130507 TTTATATTTATTTA
1 TTTTTA-TT-TTTA
* *
1130521 TCTTTTTTTTTCTC
1 T-TTTTATTTT-TA
1130535 TATTTTATTTTTA
1 T-TTTTATTTTTA
1130548 TTTTTATTTTTTA
1 TTTTTA-TTTTTA
1130561 TTTTTAATTTTT
1 TTTTT-ATTTTT
1130573 TATCTTCTTC
Statistics
Matches: 70, Mismatches: 12, Indels: 17
0.71 0.12 0.17
Matches are distributed among these distances:
11 2 0.03
12 17 0.24
13 28 0.40
14 20 0.29
15 3 0.04
ACGTcount: A:0.20, C:0.04, G:0.01, T:0.75
Consensus pattern (12 bp):
TTTTTATTTTTA
Found at i:1130559 original size:19 final size:20
Alignment explanation
Indices: 1130485--1130626 Score: 89
Period size: 21 Copynumber: 7.0 Consensus size: 20
1130475 ATTATTAGTA
*
1130485 TTATTATTA-TTATTCTA-TT
1 TTATTTTTATTTATT-TATTT
*
1130504 TTATTTATATTTATTTATCTT
1 TTATTTTTATTTATTTAT-TT
* *
1130525 TT-TTTTTCTCTATTTTATTT
1 TTATTTTTATTTA-TTTATTT
1130545 TTATTTTTATTT-TTTATTT
1 TTATTTTTATTTATTTATTT
* * *
1130564 TTAATTTTTTATCTTCTTCATAT
1 TT-A-TTTTTAT-TTATTTATTT
* *
1130587 TTA-TTTTATTTATTTGTAT
1 TTATTTTTATTTATTTATTT
1130606 TTATTTTATTATTT-TTTATTT
1 TTA-TTT-TTATTTATTTATTT
1130627 ATTCATTTAT
Statistics
Matches: 97, Mismatches: 14, Indels: 22
0.73 0.11 0.17
Matches are distributed among these distances:
19 28 0.29
20 23 0.24
21 30 0.31
22 9 0.09
23 7 0.07
ACGTcount: A:0.20, C:0.05, G:0.01, T:0.75
Consensus pattern (20 bp):
TTATTTTTATTTATTTATTT
Found at i:1130606 original size:15 final size:15
Alignment explanation
Indices: 1130587--1130689 Score: 56
Period size: 15 Copynumber: 6.9 Consensus size: 15
1130577 TTCTTCATAT
1130587 TTATTTTATTTATT-
1 TTATTTTATTTATTA
1130601 TGTA-TTTATTTTATTA
1 T-TATTTTA-TTTATTA
1130617 TT-TTTTATTTATTCA
1 TTATTTTATTTATT-A
* *
1130632 TT-TATTATGTATATA
1 TTATTTTATTTAT-TA
*
1130647 TTATTATCA-TTATTA
1 TTATT-TTATTTATTA
* *
1130662 TTCTTTTTTTTCATT-
1 TTATTTTATTT-ATTA
*
1130677 TTATTTTTTTTAT
1 TTATTTTATTTAT
1130690 CATATTCATT
Statistics
Matches: 70, Mismatches: 9, Indels: 20
0.71 0.09 0.20
Matches are distributed among these distances:
14 14 0.20
15 45 0.64
16 9 0.13
17 2 0.03
ACGTcount: A:0.22, C:0.04, G:0.02, T:0.72
Consensus pattern (15 bp):
TTATTTTATTTATTA
Found at i:1130627 original size:19 final size:19
Alignment explanation
Indices: 1130440--1130629 Score: 79
Period size: 19 Copynumber: 9.6 Consensus size: 19
1130430 TACACTTCTA
* *
1130440 TTTTATTTTCTTTTATTACT
1 TTTTA-TTTATTTTATTATT
*
1130460 TTTTACTTACTTTTTATTATT
1 TTTTATTTA--TTTTATTATT
* * *
1130481 AGTATTA-TTATTATTATTCTA
1 --TTTTATTTATT-TTATTATT
1130502 TTTTATTTATATTTATTTATCT
1 TTTTATTTAT-TTTA-TTAT-T
* *
1130524 TTTTTTTTCTCTATT-TTATT
1 TTTTATTTAT-T-TTATTATT
*
1130544 TTTATTTTTATTTT-TTA-T
1 TTT-TATTTATTTTATTATT
*
1130562 TTTTAATT-TTTTATCT-TCT
1 TTTTATTTATTTTAT-TAT-T
**
1130581 TCATATTTATTTTATT-TAT
1 TTTTATTTATTTTATTAT-T
*
1130600 TTGTATTTATTTTATTATT
1 TTTTATTTATTTTATTATT
1130619 TTTTATTTATT
1 TTTTATTTATT
1130630 CATTTATTAT
Statistics
Matches: 131, Mismatches: 22, Indels: 35
0.70 0.12 0.19
Matches are distributed among these distances:
16 4 0.03
17 4 0.03
18 5 0.04
19 45 0.34
20 26 0.20
21 29 0.22
22 12 0.09
23 6 0.05
ACGTcount: A:0.20, C:0.06, G:0.01, T:0.73
Consensus pattern (19 bp):
TTTTATTTATTTTATTATT
Found at i:1130634 original size:8 final size:7
Alignment explanation
Indices: 1130451--1130663 Score: 56
Period size: 6 Copynumber: 29.3 Consensus size: 7
1130441 TTTATTTTCT
1130451 TTTATTA
1 TTTATTA
1130458 CTTT-TTA
1 -TTTATTA
*
1130465 CTTACTT-
1 TTTA-TTA
1130472 TTTATTA
1 TTTATTA
*
1130479 -TTAGTA
1 TTTATTA
1130485 -TTATTA
1 TTTATTA
1130491 -TTATTA
1 TTTATTA
1130497 TTCTATTTTA
1 TT-TA--TTA
1130507 TTTA-TA
1 TTTATTA
1130513 TTTATTTA
1 TTTA-TTA
* *
1130521 TCTTTTTT
1 T-TTATTA
*
1130529 TTTCTCTA
1 TTTAT-TA
1130537 TTTTATT-
1 -TTTATTA
1130544 TTTATT-
1 TTTATTA
*
1130550 TTTATTT
1 TTTATTA
1130557 TTTATT-
1 TTTATTA
*
1130563 TTTAATTT
1 TTT-ATTA
1130571 TTTATCT-
1 TTTAT-TA
1130578 TCTTCA-TA
1 T-TT-ATTA
1130586 TTTATTTTA
1 TTTA--TTA
1130595 TTTATT-
1 TTTATTA
*
1130601 TGTATTTA
1 TTTA-TTA
1130609 TTTTATTA
1 -TTTATTA
*
1130617 TTTTTTA
1 TTTATTA
1130624 TTTATTCA
1 TTTATT-A
1130632 TTTATTA
1 TTTATTA
*
1130639 TGTA-TA
1 TTTATTA
1130645 TATTATTA
1 T-TTATTA
1130653 TCATTATTA
1 T--TTATTA
1130662 TT
1 TT
1130664 CTTTTTTTTC
Statistics
Matches: 161, Mismatches: 15, Indels: 59
0.69 0.06 0.25
Matches are distributed among these distances:
6 48 0.30
7 47 0.29
8 35 0.22
9 26 0.16
10 5 0.03
ACGTcount: A:0.23, C:0.06, G:0.01, T:0.70
Consensus pattern (7 bp):
TTTATTA
Found at i:1130636 original size:19 final size:18
Alignment explanation
Indices: 1130592--1130651 Score: 59
Period size: 19 Copynumber: 3.3 Consensus size: 18
1130582 CATATTTATT
1130592 TTATTTA-TTTGTATTTA
1 TTATTTATTTTGTATTTA
* *
1130609 TTTTATTATTTTTTATTTA
1 TTAT-TTATTTTGTATTTA
* *
1130628 TTCATTTATTATGTATATA
1 TT-ATTTATTTTGTATTTA
1130647 TTATT
1 TTATT
1130652 ATCATTATTA
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
17 3 0.09
18 6 0.18
19 24 0.71
20 1 0.03
ACGTcount: A:0.25, C:0.02, G:0.03, T:0.70
Consensus pattern (18 bp):
TTATTTATTTTGTATTTA
Found at i:1130639 original size:11 final size:10
Alignment explanation
Indices: 1130452--1130663 Score: 68
Period size: 10 Copynumber: 21.8 Consensus size: 10
1130442 TTATTTTCTT
1130452 TTATTACTTT-
1 TTATTA-TTTA
1130462 TTACTTACTTT-
1 TTA-TTA-TTTA
1130473 TTATTA-TTA
1 TTATTATTTA
*
1130482 GTATTA-TTA
1 TTATTATTTA
1130491 TTATTATTCTA
1 TTATTATT-TA
1130502 TT-TTATTTA
1 TTATTATTTA
1130511 -TATTTATTTA
1 TTA-TTATTTA
*
1130521 TCT-TT-TTTT
1 T-TATTATTTA
*
1130530 TTCTCTATTTTA
1 TTAT-TA-TTTA
*
1130542 TTTTTATTT-
1 TTATTATTTA
*
1130551 TTATTTTTTA
1 TTATTATTTA
* *
1130561 TTTTTAATT-
1 TTATTATTTA
*
1130570 TT-TTATCTTC
1 TTATTAT-TTA
1130580 TTCA-TATTTA
1 TT-ATTATTTA
1130590 TT-TTATTTA
1 TTATTATTTA
1130599 TT-TGTATTTA
1 TTAT-TATTTA
1130609 TT-TTA-TTA
1 TTATTATTTA
1130617 -T-TT-TTTA
1 TTATTATTTA
1130624 TTTATTCATTTA
1 -TTATT-ATTTA
*
1130636 TTATGTATATA
1 TTAT-TATTTA
*
1130647 TTATTA-TCA
1 TTATTATTTA
1130656 TTATTATT
1 TTATTATT
1130664 CTTTTTTTTC
Statistics
Matches: 160, Mismatches: 15, Indels: 54
0.70 0.07 0.24
Matches are distributed among these distances:
7 6 0.04
8 10 0.06
9 50 0.31
10 51 0.32
11 31 0.19
12 12 0.08
ACGTcount: A:0.23, C:0.06, G:0.01, T:0.70
Consensus pattern (10 bp):
TTATTATTTA
Found at i:1130700 original size:18 final size:17
Alignment explanation
Indices: 1130650--1130702 Score: 61
Period size: 17 Copynumber: 2.9 Consensus size: 17
1130640 GTATATATTA
1130650 TTATCATTATTATTCTTTT
1 TTATCA-TATTATT-TTTT
* *
1130669 TTTTCATTTTATTTTTT
1 TTATCATATTATTTTTT
1130686 TTATCATATTCATTTTT
1 TTATCATATT-ATTTTT
1130703 ATTTTCACTC
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
17 12 0.41
18 12 0.41
19 5 0.17
ACGTcount: A:0.19, C:0.09, G:0.00, T:0.72
Consensus pattern (17 bp):
TTATCATATTATTTTTT
Found at i:1130702 original size:19 final size:18
Alignment explanation
Indices: 1130650--1130707 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 18
1130640 GTATATATTA
1130650 TTATCATTATTATTCTTTTT
1 TTATCA-TATTATT-TTTTT
*
1130670 TT-TCATTTTA-TTTTTT
1 TTATCATATTATTTTTTT
1130686 TTATCATATTCATTTTTATT
1 TTATCATATT-ATTTTT-TT
1130706 TT
1 TT
1130708 CACTCTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
16 7 0.22
17 7 0.22
18 5 0.16
19 7 0.22
20 6 0.19
ACGTcount: A:0.19, C:0.09, G:0.00, T:0.72
Consensus pattern (18 bp):
TTATCATATTATTTTTTT
Found at i:1139518 original size:16 final size:16
Alignment explanation
Indices: 1139497--1139530 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1139487 TAGTTCAAAA
1139497 TTACTTTATTTTAATT
1 TTACTTTATTTTAATT
*
1139513 TTACTTTATTTTACTT
1 TTACTTTATTTTAATT
1139529 TT
1 TT
1139531 CAAACAATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.21, C:0.09, G:0.00, T:0.71
Consensus pattern (16 bp):
TTACTTTATTTTAATT
Found at i:1149563 original size:24 final size:24
Alignment explanation
Indices: 1149531--1149581 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
1149521 TGGATTAGAT
1149531 TAAAGAAATCATGCTTCATATGAG
1 TAAAGAAATCATGCTTCATATGAG
* * *
1149555 TAAAGAAATCCTGCTTTATCTGAG
1 TAAAGAAATCATGCTTCATATGAG
1149579 TAA
1 TAA
1149582 TAAACTACTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.31
Consensus pattern (24 bp):
TAAAGAAATCATGCTTCATATGAG
Found at i:1159436 original size:12 final size:12
Alignment explanation
Indices: 1159416--1159449 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
1159406 TAAAGAGACA
*
1159416 CGACTCTCCTCC
1 CGACCCTCCTCC
1159428 CGACCCTCCTCC
1 CGACCCTCCTCC
1159440 CGACCCTCCT
1 CGACCCTCCT
1159450 AACTGTGAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.09, C:0.62, G:0.09, T:0.21
Consensus pattern (12 bp):
CGACCCTCCTCC
Found at i:1160893 original size:19 final size:20
Alignment explanation
Indices: 1160852--1160903 Score: 88
Period size: 19 Copynumber: 2.6 Consensus size: 20
1160842 TTTGGGTTCT
*
1160852 TGAGTATCGATATTAGCCCC
1 TGAGTATCGATACTAGCCCC
1160872 TGAGTATCGATACTAG-CCC
1 TGAGTATCGATACTAGCCCC
1160891 TGAGTATCGATAC
1 TGAGTATCGATAC
1160904 CATACTATCA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 16 0.52
20 15 0.48
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (20 bp):
TGAGTATCGATACTAGCCCC
Found at i:1163535 original size:63 final size:63
Alignment explanation
Indices: 1163435--1163553 Score: 159
Period size: 63 Copynumber: 1.9 Consensus size: 63
1163425 ATTTATTATC
* *
1163435 TATTTAACTTTGAATATTAAAGATAACTATATACTTTTGAACGTTTCAAATTAAAATAATATA
1 TATTTAACTTTGAATATAAAAGATAACTATATACTTTTGAACATTTCAAATTAAAATAATATA
* * ** *
1163498 TATTTAAGTTTGAATAGTAAAAGGTGTCTATAT-CTTTTGAATATTTCAAATTAAAA
1 TATTTAACTTTGAATA-TAAAAGATAACTATATACTTTTGAACATTTCAAATTAAAA
1163554 GATATTATTA
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
63 36 0.75
64 12 0.25
ACGTcount: A:0.42, C:0.07, G:0.09, T:0.42
Consensus pattern (63 bp):
TATTTAACTTTGAATATAAAAGATAACTATATACTTTTGAACATTTCAAATTAAAATAATATA
Found at i:1166171 original size:241 final size:242
Alignment explanation
Indices: 1165918--1166401 Score: 945
Period size: 241 Copynumber: 2.0 Consensus size: 242
1165908 TACGGTGGAT
1165918 ACTTAATTTTTTTTTTACCTTTAAAATTTTAATTTCCTATAGATTTTAGCTTTCACTCTAAGTTT
1 ACTTAATTTTTTTTTTACCTTTAAAATTTTAATTTCCTATAGATTTTAGCTTTCACTCTAAGTTT
1165983 ACTATATGATTAGTTAAAATACTTAGTAATATTAATTGGAATAGCAATAAAAATCAGAGACGGAT
66 ACTATATGATTAGTTAAAATACTTAGTAATATTAATTGGAATAGCAATAAAAATCAGAGACGGAT
1166048 CTCTATCGATTG-TGTTGGC-TTGGTGTTTTTGCAGTAGTAAATAGCAGTCATCAGGTTTTGTGG
131 CTCTATCGATTGTTGTTGGCTTTGGTGTTTTTGCAGTAGTAAATAGCAGTCATCAGGTTTTGTGG
1166111 TGTTCAAAAACGGCTTTTACTATTTGTAGTATTAGAAAGAAATGAAAG
196 TGTTCAAAAACGGC-TTTACTATTTGTAGTATTAGAAAGAAATGAAAG
1166159 ACTTAATTTTTTTTTTACCTTTAAAATTTTAATTTCCTATAGATTTTAGCTTTCACTCTAAGTTT
1 ACTTAATTTTTTTTTTACCTTTAAAATTTTAATTTCCTATAGATTTTAGCTTTCACTCTAAGTTT
1166224 ACTATATGATTAGTTAAAATACTTAGTAATATTAATTGGAATAGCAATAAAAATCAGAGACGGAT
66 ACTATATGATTAGTTAAAATACTTAGTAATATTAATTGGAATAGCAATAAAAATCAGAGACGGAT
1166289 CTCTATCGATTGTTGTTGGCTTTGGTGTTTTTGCAGTAGTAAATAGCAGTCATCAGGTTTTGTGG
131 CTCTATCGATTGTTGTTGGCTTTGGTGTTTTTGCAGTAGTAAATAGCAGTCATCAGGTTTTGTGG
1166354 TGTTCAAAAACGGCTTTACTATTTGTAGTATTAGAAAGAAATGAAAG
196 TGTTCAAAAACGGCTTTACTATTTGTAGTATTAGAAAGAAATGAAAG
1166401 A
1 A
1166402 AGGTTTGTGT
Statistics
Matches: 241, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
241 142 0.59
242 41 0.17
243 58 0.24
ACGTcount: A:0.32, C:0.11, G:0.17, T:0.41
Consensus pattern (242 bp):
ACTTAATTTTTTTTTTACCTTTAAAATTTTAATTTCCTATAGATTTTAGCTTTCACTCTAAGTTT
ACTATATGATTAGTTAAAATACTTAGTAATATTAATTGGAATAGCAATAAAAATCAGAGACGGAT
CTCTATCGATTGTTGTTGGCTTTGGTGTTTTTGCAGTAGTAAATAGCAGTCATCAGGTTTTGTGG
TGTTCAAAAACGGCTTTACTATTTGTAGTATTAGAAAGAAATGAAAG
Found at i:1168931 original size:75 final size:74
Alignment explanation
Indices: 1168811--1168958 Score: 255
Period size: 75 Copynumber: 2.0 Consensus size: 74
1168801 AAAAAATAAA
1168811 GCTACACCGATCCTCTTTTTCCACATAAAGGACAAAGAATGTCGGCTCCTA-TGGT-AACCTCTC
1 GCTACACCGATCCTCTTTTTCCACATAAAGGACAAAGAATGTCGGCTCCTAGTGGTAAACCTCTC
1168874 TTAACCAAT
66 TTAACCAAT
1168883 GCTACACCGATTCCTCTTTTTCCTTACATAAAGGACAAAGAATGTCGGCTCCTAGTGGTAAACCT
1 GCTACACCGA-TCCTCTTTTTCC--ACATAAAGGACAAAGAATGTCGGCTCCTAGTGGTAAACCT
1168948 CTCTTAACCAA
63 CTCTTAACCAA
1168959 CTCAGCTTTG
Statistics
Matches: 71, Mismatches: 0, Indels: 5
0.93 0.00 0.07
Matches are distributed among these distances:
72 10 0.14
73 12 0.17
75 29 0.41
76 4 0.06
77 16 0.23
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.28
Consensus pattern (74 bp):
GCTACACCGATCCTCTTTTTCCACATAAAGGACAAAGAATGTCGGCTCCTAGTGGTAAACCTCTC
TTAACCAAT
Found at i:1174611 original size:16 final size:14
Alignment explanation
Indices: 1174589--1174630 Score: 57
Period size: 16 Copynumber: 2.9 Consensus size: 14
1174579 GCCACCTATG
1174589 ACACTCTCTCTCTCA
1 ACACTCTCTCTCT-A
*
1174604 CCCACTCTCTCTCTA
1 -ACACTCTCTCTCTA
1174619 ACACTCTCTCTC
1 ACACTCTCTCTC
1174631 ATGTTTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 11 0.46
15 1 0.04
16 12 0.50
ACGTcount: A:0.17, C:0.50, G:0.00, T:0.33
Consensus pattern (14 bp):
ACACTCTCTCTCTA
Found at i:1184468 original size:3 final size:3
Alignment explanation
Indices: 1184457--1184524 Score: 75
Period size: 3 Copynumber: 22.0 Consensus size: 3
1184447 TCAATTTTTT
** *
1184457 TTA TT- TTA TTA TTA TTA TTA AAA TTA TCA TTA TTA TTA TGTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA
1184502 TATA TATA TTA TTA TTA TTA TTA
1 T-TA T-TA TTA TTA TTA TTA TTA
1184525 AAAAAAATAA
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
2 2 0.04
3 44 0.79
4 10 0.18
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:1185442 original size:8 final size:8
Alignment explanation
Indices: 1185431--1185486 Score: 55
Period size: 8 Copynumber: 7.1 Consensus size: 8
1185421 TTATTTACAA
1185431 TATTATTT
1 TATTATTT
1185439 TATT-TTT
1 TATTATTT
*
1185446 T-TTA-AT
1 TATTATTT
1185452 TATTACTTT
1 TATTA-TTT
*
1185461 CATTATTAT
1 TATTATT-T
1185470 TATTATTT
1 TATTATTT
1185478 TATTATTT
1 TATTATTT
1185486 T
1 T
1185487 CATCTTAATA
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
6 4 0.10
7 7 0.18
8 16 0.41
9 12 0.31
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.71
Consensus pattern (8 bp):
TATTATTT
Found at i:1185471 original size:18 final size:17
Alignment explanation
Indices: 1185421--1185484 Score: 53
Period size: 17 Copynumber: 3.8 Consensus size: 17
1185411 TTTTATATGT
*
1185421 TTATTTACAATATTATT-
1 TTATTT-CATTATTATTA
*
1185438 TTATTT--TTTTTAATTA
1 TTATTTCATTATT-ATTA
1185454 TTACTTTCATTATTATTA
1 TTA-TTTCATTATTATTA
*
1185472 TTATTTTATTATT
1 TTATTTCATTATT
1185485 TTCATCTTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
14 3 0.08
15 3 0.08
16 3 0.08
17 18 0.47
18 7 0.18
19 4 0.11
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (17 bp):
TTATTTCATTATTATTA
Found at i:1185504 original size:2 final size:2
Alignment explanation
Indices: 1185497--1185522 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1185487 CATCTTAATA
1185497 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1185523 GTTTAAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1185799 original size:29 final size:28
Alignment explanation
Indices: 1185746--1185803 Score: 66
Period size: 29 Copynumber: 2.0 Consensus size: 28
1185736 ATATTTCTAA
*
1185746 ATAAATAAATATTTTATTTATAAATATAT
1 ATAAATAAATATTTTACTTATAAAT-TAT
1185775 ATAAATAAATAGATTTT-CTTA-AAATTAT
1 ATAAATAAAT--ATTTTACTTATAAATTAT
1185803 A
1 A
1185804 AATTTGAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
28 4 0.15
29 14 0.54
30 3 0.12
31 5 0.19
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (28 bp):
ATAAATAAATATTTTACTTATAAATTAT
Found at i:1195745 original size:22 final size:22
Alignment explanation
Indices: 1195716--1195770 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
1195706 ATCTACACTC
1195716 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
1195738 TTTAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
1195760 TTCAAAGATGA
1 TTCAAAGATGA
1195771 AAGCTTTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.40
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:1196799 original size:73 final size:73
Alignment explanation
Indices: 1196647--1197361 Score: 1213
Period size: 73 Copynumber: 9.8 Consensus size: 73
1196637 GTTTTCACAT
1196647 AAATTTATCTCACTTGAGATTGTTTTTCTTAAAAC-AAATTTGTCTCGCTTGAGA-AGGTTTCAC
1 AAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACA-GTTTCAC
1196710 TCGAAACAG
65 TCGAAACAG
* *
1196719 AACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTTTACT
1 AAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTTCACT
1196784 CGAAACAG
66 CGAAACAG
*
1196792 AAATTTATCTCACTTGAGATTGTTTTTCTTAAAAC-AAATTTGTCTCGCTTGAGATAGTTTCACT
1 AAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTTCACT
1196856 CGAAACAG
66 CGAAACAG
* *
1196864 AACTTTATCTCACTTGAGATTGTTTTTCTTTAAACAAAATTTGTCTCGCTTGAGACAGTTTCACT
1 AAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTTCACT
*
1196929 CGAAACAT
66 CGAAACAG
* *
1196937 AAATTTATCTCACTTGAGATTGTTTTTCTTGAAACAAATTTTGTCTCGCTTGAGACAGTTTCACT
1 AAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTTCACT
1197002 CGAAACAG
66 CGAAACAG
* *
1197010 AACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTTTACT
1 AAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTTCACT
*
1197075 TGAAACAG
66 CGAAACAG
*
1197083 AAATTTATCTCACTTGAGATTGTTTTTTTTAAAAC-AAATTTGTCTCGCTTGAGACAGTTTCACT
1 AAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTTCACT
1197147 CGAAACAG
66 CGAAACAG
* * * *
1197155 AACTTTATCTCACTTGAGATTATTTTTCTTAAAACAAAATTTGTCTCGTTTGAGACAATTTCACT
1 AAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTTCACT
1197220 CGAAACAG
66 CGAAACAG
*
1197228 AAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAATTTTGTCTCGCTTGAGACAGTTTCACT
1 AAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTTCACT
* *
1197293 TGAAACAA
66 CGAAACAG
1197301 AAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAGATTTGTCTCGCTTGAGACAGTT
1 AAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAA-ATTTGTCTCGCTTGAGACAGTT
1197362 ATTTCGAGTT
Statistics
Matches: 603, Mismatches: 35, Indels: 8
0.93 0.05 0.01
Matches are distributed among these distances:
72 169 0.28
73 412 0.68
74 22 0.04
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.39
Consensus pattern (73 bp):
AAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTTCACT
CGAAACAG
Found at i:1197027 original size:218 final size:218
Alignment explanation
Indices: 1196647--1197361 Score: 1229
Period size: 218 Copynumber: 3.3 Consensus size: 218
1196637 GTTTTCACAT
1196647 AAATTTATCTCACTTGAGATTGTTTTTCTTAAAAC-AAATTTGTCTCGCTTGAGA-AGGTTTCAC
1 AAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACA-GTTTCAC
1196710 TCGAAACAGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGAC
65 TCGAAACAGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGAC
*
1196775 AGTTTTACTCGAAACAGAAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAATTTGTCTCGC
130 AGTTTCACTCGAAACAGAAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAATTTGTCTCGC
* *
1196840 TTGAGATAGTTTCACTCGAAACAG
195 TTGAGACAGTTTCACTTGAAACAG
* *
1196864 AACTTTATCTCACTTGAGATTGTTTTTCTTTAAACAAAATTTGTCTCGCTTGAGACAGTTTCACT
1 AAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTTCACT
* * * *
1196929 CGAAACATAAATTTATCTCACTTGAGATTGTTTTTCTTGAAACAAATTTTGTCTCGCTTGAGACA
66 CGAAACAGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACA
*
1196994 GTTTCACTCGAAACAGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGC
131 GTTTCACTCGAAACAGAAATTTATCTCACTTGAGATTGTTTTTCTTAAAAC-AAATTTGTCTCGC
*
1197059 TTGAGACAGTTTTACTTGAAACAG
195 TTGAGACAGTTTCACTTGAAACAG
*
1197083 AAATTTATCTCACTTGAGATTGTTTTTTTTAAAAC-AAATTTGTCTCGCTTGAGACAGTTTCACT
1 AAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTTCACT
* *
1197147 CGAAACAGAACTTTATCTCACTTGAGATTATTTTTCTTAAAACAAAATTTGTCTCGTTTGAGACA
66 CGAAACAGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACA
*
1197212 ATTTCACTCGAAACAGAAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAATTTTGTCTCGC
131 GTTTCACTCGAAACAGAAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAA-TTTGTCTCGC
*
1197277 TTGAGACAGTTTCACTTGAAACAA
195 TTGAGACAGTTTCACTTGAAACAG
1197301 AAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAGATTTGTCTCGCTTGAGACAGTT
1 AAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAA-ATTTGTCTCGCTTGAGACAGTT
1197362 ATTTCGAGTT
Statistics
Matches: 467, Mismatches: 25, Indels: 9
0.93 0.05 0.02
Matches are distributed among these distances:
217 36 0.08
218 340 0.73
219 69 0.15
220 22 0.05
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.39
Consensus pattern (218 bp):
AAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTTCACT
CGAAACAGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACA
GTTTCACTCGAAACAGAAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAATTTGTCTCGCT
TGAGACAGTTTCACTTGAAACAG
Found at i:1197166 original size:291 final size:291
Alignment explanation
Indices: 1196643--1197361 Score: 1298
Period size: 291 Copynumber: 2.5 Consensus size: 291
1196633 GGATGTTTTC
1196643 ACATAAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAA-TTTGTCTCGCTTGAGA-AGGTT
1 ACATAAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAATTTTGTCTCGCTTGAGACA-GTT
1196706 TCACTCGAAACAGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTG
65 TCACTCGAAACAGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTG
1196771 AGACAGTTTTACTCGAAACAGAAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAATTTGTC
130 AGACAGTTTTACTCGAAACAGAAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAATTTGTC
* * *
1196836 TCGCTTGAGATAGTTTCACTCGAAACAGAACTTTATCTCACTTGAGATTGTTTTTCTTTAAACAA
195 TCGCTTGAGACAGTTTCACTCGAAACAGAACTTTATCTCACTTGAGATTATTTTTCTTAAAACAA
*
1196901 AATTTGTCTCGCTTGAGACAGTTTCACTCGAA
260 AATTTGTCTCGCTTGAGACAATTTCACTCGAA
*
1196933 ACATAAATTTATCTCACTTGAGATTGTTTTTCTTGAAACAAATTTTGTCTCGCTTGAGACAGTTT
1 ACATAAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAATTTTGTCTCGCTTGAGACAGTTT
1196998 CACTCGAAACAGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGA
66 CACTCGAAACAGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGA
* *
1197063 GACAGTTTTACTTGAAACAGAAATTTATCTCACTTGAGATTGTTTTTTTTAAAACAAATTTGTCT
131 GACAGTTTTACTCGAAACAGAAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAATTTGTCT
1197128 CGCTTGAGACAGTTTCACTCGAAACAGAACTTTATCTCACTTGAGATTATTTTTCTTAAAACAAA
196 CGCTTGAGACAGTTTCACTCGAAACAGAACTTTATCTCACTTGAGATTATTTTTCTTAAAACAAA
*
1197193 ATTTGTCTCGTTTGAGACAATTTCACTCGAA
261 ATTTGTCTCGCTTGAGACAATTTCACTCGAA
*
1197224 ACAGAAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAATTTTGTCTCGCTTGAGACAGTTT
1 ACATAAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAATTTTGTCTCGCTTGAGACAGTTT
* * *
1197289 CACTTGAAACAAAAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAGATTTGTCTCGCTTG
66 CACTCGAAACAGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAA-ATTTGTCTCGCTTG
1197354 AGACAGTT
130 AGACAGTT
1197362 ATTTCGAGTT
Statistics
Matches: 413, Mismatches: 13, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
290 41 0.10
291 349 0.85
292 23 0.06
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.39
Consensus pattern (291 bp):
ACATAAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAATTTTGTCTCGCTTGAGACAGTTT
CACTCGAAACAGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGA
GACAGTTTTACTCGAAACAGAAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAATTTGTCT
CGCTTGAGACAGTTTCACTCGAAACAGAACTTTATCTCACTTGAGATTATTTTTCTTAAAACAAA
ATTTGTCTCGCTTGAGACAATTTCACTCGAA
Found at i:1197769 original size:3 final size:3
Alignment explanation
Indices: 1197758--1197823 Score: 73
Period size: 3 Copynumber: 22.0 Consensus size: 3
1197748 ATCAATTTTT
** *
1197758 TTA TT- TTA TTA TTA TTA TTA AAA TTA TCA TTA TTA TTA TGTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA
1197803 -TA TATA TTA TTA TTA TTA TTA
1 TTA T-TA TTA TTA TTA TTA TTA
1197824 AAAAAATAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
2 4 0.08
3 43 0.81
4 6 0.11
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:1199167 original size:18 final size:17
Alignment explanation
Indices: 1199144--1199178 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1199134 TATTTTTTAA
1199144 ATTATTACTTTCATTATT
1 ATTATTA-TTTCATTATT
*
1199162 ATTATTATTTTATTATT
1 ATTATTATTTCATTATT
1199179 TTCATCTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.66
Consensus pattern (17 bp):
ATTATTATTTCATTATT
Found at i:1199489 original size:29 final size:28
Alignment explanation
Indices: 1199436--1199493 Score: 66
Period size: 29 Copynumber: 2.0 Consensus size: 28
1199426 ATATTTCTAA
*
1199436 ATAAATAAATATTTTATTTATAAATATAT
1 ATAAATAAATATTTTACTTATAAAT-TAT
1199465 ATAAATAAATAGATTTT-CTTA-AAATTAT
1 ATAAATAAAT--ATTTTACTTATAAATTAT
1199493 A
1 A
1199494 AATTTGAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
28 4 0.15
29 14 0.54
30 3 0.12
31 5 0.19
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (28 bp):
ATAAATAAATATTTTACTTATAAATTAT
Found at i:1202039 original size:25 final size:25
Alignment explanation
Indices: 1202007--1202065 Score: 109
Period size: 25 Copynumber: 2.4 Consensus size: 25
1201997 TTTGTAGTAC
*
1202007 AAAAATAATATTTATTATAATGACG
1 AAAAATAATATTTATTATAATGACA
1202032 AAAAATAATATTTATTATAATGACA
1 AAAAATAATATTTATTATAATGACA
1202057 AAAAATAAT
1 AAAAATAAT
1202066 GTCACCATTA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.58, C:0.03, G:0.05, T:0.34
Consensus pattern (25 bp):
AAAAATAATATTTATTATAATGACA
Found at i:1202297 original size:25 final size:25
Alignment explanation
Indices: 1202264--1202311 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
1202254 TAGAATTTTT
*
1202264 TTATTATAATGACGAAAAATAATAA
1 TTATTATAATGACAAAAAATAATAA
*
1202289 TTATTATAATTACAAAAAATAAT
1 TTATTATAATGACAAAAAATAAT
1202312 GACACAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.35
Consensus pattern (25 bp):
TTATTATAATGACAAAAAATAATAA
Found at i:1202360 original size:38 final size:38
Alignment explanation
Indices: 1202318--1202414 Score: 158
Period size: 38 Copynumber: 2.6 Consensus size: 38
1202308 TAATGACACA
* *
1202318 ATTAATTATCTATTAATAATCCGGGTATGTTGGTGGTT
1 ATTAATTATCTATTAATAATCCGAGTAGGTTGGTGGTT
* *
1202356 ATTAATTATCCATTAATAACCCGAGTAGGTTGGTGGTT
1 ATTAATTATCTATTAATAATCCGAGTAGGTTGGTGGTT
1202394 ATTAATTATCTATTAATAATC
1 ATTAATTATCTATTAATAATC
1202415 AAGGTAAGTT
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 53 1.00
ACGTcount: A:0.31, C:0.10, G:0.16, T:0.42
Consensus pattern (38 bp):
ATTAATTATCTATTAATAATCCGAGTAGGTTGGTGGTT
Found at i:1202431 original size:38 final size:38
Alignment explanation
Indices: 1202318--1202431 Score: 149
Period size: 38 Copynumber: 3.0 Consensus size: 38
1202308 TAATGACACA
* *
1202318 ATTAATTATCTATTAATAATCCGGGTATGTTGGTGGTT
1 ATTAATTATCTATTAATAATCCAGGTAAGTTGGTGGTT
* * *
1202356 ATTAATTATCCATTAATAA-CCCGAGTAGGTTGGTGGTT
1 ATTAATTATCTATTAATAATCCAG-GTAAGTTGGTGGTT
* *
1202394 ATTAATTATCTATTAATAATCAAGGTAAGTTGATGGTT
1 ATTAATTATCTATTAATAATCCAGGTAAGTTGGTGGTT
1202432 GGTGGTTGAA
Statistics
Matches: 66, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
37 3 0.05
38 61 0.92
39 2 0.03
ACGTcount: A:0.31, C:0.09, G:0.19, T:0.41
Consensus pattern (38 bp):
ATTAATTATCTATTAATAATCCAGGTAAGTTGGTGGTT
Found at i:1204809 original size:27 final size:27
Alignment explanation
Indices: 1204737--1204863 Score: 164
Period size: 27 Copynumber: 4.7 Consensus size: 27
1204727 TGTTGACGCT
* * * * *
1204737 ATATTTTAATGAATGTGAATAGTGTTA
1 ATATTTGAATGAATGTGATTAATATCA
* * *
1204764 ATAGTTGAATTAATATGATTAATATCA
1 ATATTTGAATGAATGTGATTAATATCA
1204791 ATATTTGAATGAATGTGATTAATATCA
1 ATATTTGAATGAATGTGATTAATATCA
1204818 ATATTTGAATGAATGTGATTAATATCA
1 ATATTTGAATGAATGTGATTAATATCA
* *
1204845 ATATTTGAATTAATATGAT
1 ATATTTGAATGAATGTGAT
1204864 GGATATTTGT
Statistics
Matches: 87, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 87 1.00
ACGTcount: A:0.41, C:0.02, G:0.14, T:0.43
Consensus pattern (27 bp):
ATATTTGAATGAATGTGATTAATATCA
Found at i:1204960 original size:27 final size:27
Alignment explanation
Indices: 1204889--1204954 Score: 114
Period size: 27 Copynumber: 2.4 Consensus size: 27
1204879 TTATATTTTT
1204889 AATGAATGTGATTAATATCAATAGTTG
1 AATGAATGTGATTAATATCAATAGTTG
* *
1204916 AATTAATGTGATTAATATCAATATTTG
1 AATGAATGTGATTAATATCAATAGTTG
1204943 AATGAATGTGAT
1 AATGAATGTGAT
1204955 GGATATTAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.41, C:0.03, G:0.17, T:0.39
Consensus pattern (27 bp):
AATGAATGTGATTAATATCAATAGTTG
Found at i:1206930 original size:111 final size:111
Alignment explanation
Indices: 1206806--1207220 Score: 715
Period size: 111 Copynumber: 3.7 Consensus size: 111
1206796 GCCACTAATA
* *
1206806 AAAGTTATCGATCGATTTTGTTAAATGCATAACGGTTCATTATCGGCATAAAAGGTGACACTCAT
1 AAAGTTATCGATCGATTTTGTTTAATGCATAACGGTGCATTATCGGCATAAAAGGTGACACTCAT
*
1206871 GATATTCATAAAAGGTGAATTACAATTTCGACATACTTCGTGTATG
66 GGTATTCATAAAAGGTGAATTACAATTTCGACATACTTCGTGTATG
*
1206917 AAAGTTATCGATCGATTTTGTTTAATGCATAACGGTGCATTATCGGCATAAAAGGTGCCACTCAT
1 AAAGTTATCGATCGATTTTGTTTAATGCATAACGGTGCATTATCGGCATAAAAGGTGACACTCAT
*
1206982 GGTATTCATAAAAGGTGAATTACAATTTCGACATACTTCGTATATG
66 GGTATTCATAAAAGGTGAATTACAATTTCGACATACTTCGTGTATG
* * *
1207028 AAAATTATCGATCGATTTTGTTTAATGCATAACGGTGCATTATCGGCATAAAATGTGCCACTCAT
1 AAAGTTATCGATCGATTTTGTTTAATGCATAACGGTGCATTATCGGCATAAAAGGTGACACTCAT
* * *
1207093 GGTATTCATAAAAAGTGAATTACCATTTTGACATACTTCGTGTATG
66 GGTATTCATAAAAGGTGAATTACAATTTCGACATACTTCGTGTATG
1207139 AAAGTTATCGATCGATTTTGTTTAATGCATAACGGTGCATTATCGGCATAAAAGGT-ACCACTCA
1 AAAGTTATCGATCGATTTTGTTTAATGCATAACGGTGCATTATCGGCATAAAAGGTGA-CACTCA
1207203 TGGTATTCATAAAAGGTG
65 TGGTATTCATAAAAGGTG
1207221 TGTAACATCC
Statistics
Matches: 288, Mismatches: 15, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
111 288 1.00
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Consensus pattern (111 bp):
AAAGTTATCGATCGATTTTGTTTAATGCATAACGGTGCATTATCGGCATAAAAGGTGACACTCAT
GGTATTCATAAAAGGTGAATTACAATTTCGACATACTTCGTGTATG
Found at i:1214387 original size:23 final size:23
Alignment explanation
Indices: 1214325--1214389 Score: 78
Period size: 23 Copynumber: 2.8 Consensus size: 23
1214315 CAGCTCCTAT
*
1214325 AATTGCACCGAAGTG-CAGCGTAG
1 AATTGCACCGAAGTGCCA-TGTAG
* *
1214348 AAATGCACCGTAGTGCCATGTAG
1 AATTGCACCGAAGTGCCATGTAG
*
1214371 GATTGCACCGAAGTGCCAT
1 AATTGCACCGAAGTGCCAT
1214390 ATAAAATGTC
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
23 33 0.94
24 2 0.06
ACGTcount: A:0.29, C:0.23, G:0.28, T:0.20
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCATGTAG
Found at i:1214650 original size:13 final size:13
Alignment explanation
Indices: 1214632--1214680 Score: 53
Period size: 13 Copynumber: 3.5 Consensus size: 13
1214622 ATGCATATAA
1214632 TCTCATGTCACAT
1 TCTCATGTCACAT
1214645 TCTCATATGGTCACAT
1 TCTC--AT-GTCACAT
*
1214661 AGCTCATGTCACAT
1 -TCTCATGTCACAT
1214675 TCTCAT
1 TCTCAT
1214681 ATGGTCACAT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
13 9 0.30
14 7 0.23
15 4 0.13
16 7 0.23
17 3 0.10
ACGTcount: A:0.24, C:0.29, G:0.10, T:0.37
Consensus pattern (13 bp):
TCTCATGTCACAT
Found at i:1214659 original size:16 final size:16
Alignment explanation
Indices: 1214638--1214690 Score: 67
Period size: 16 Copynumber: 3.4 Consensus size: 16
1214628 ATAATCTCAT
1214638 GTCACATTCTCATATG
1 GTCACATTCTCATATG
*
1214654 GTCACATAGCTC--AT-
1 GTCACAT-TCTCATATG
1214668 GTCACATTCTCATATG
1 GTCACATTCTCATATG
1214684 GTCACAT
1 GTCACAT
1214691 AGATCATATC
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
13 3 0.10
14 7 0.23
15 4 0.13
16 14 0.45
17 3 0.10
ACGTcount: A:0.26, C:0.26, G:0.13, T:0.34
Consensus pattern (16 bp):
GTCACATTCTCATATG
Found at i:1214668 original size:30 final size:30
Alignment explanation
Indices: 1214633--1214702 Score: 122
Period size: 30 Copynumber: 2.3 Consensus size: 30
1214623 TGCATATAAT
1214633 CTCATGTCACATTCTCATATGGTCACATAG
1 CTCATGTCACATTCTCATATGGTCACATAG
1214663 CTCATGTCACATTCTCATATGGTCACATAG
1 CTCATGTCACATTCTCATATGGTCACATAG
* *
1214693 ATCATATCAC
1 CTCATGTCAC
1214703 GTGGTTGTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.29, C:0.27, G:0.11, T:0.33
Consensus pattern (30 bp):
CTCATGTCACATTCTCATATGGTCACATAG
Found at i:1214699 original size:17 final size:17
Alignment explanation
Indices: 1214646--1214699 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 17
1214636 ATGTCACATT
1214646 CTCATATGGTCACATAG
1 CTCATATGGTCACATAG
*
1214663 CTC--AT-GTCACAT-T
1 CTCATATGGTCACATAG
1214676 CTCATATGGTCACATAG
1 CTCATATGGTCACATAG
*
1214693 ATCATAT
1 CTCATAT
1214700 CACGTGGTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
13 3 0.10
14 7 0.23
15 4 0.13
16 7 0.23
17 9 0.30
ACGTcount: A:0.30, C:0.24, G:0.13, T:0.33
Consensus pattern (17 bp):
CTCATATGGTCACATAG
Found at i:1216191 original size:39 final size:39
Alignment explanation
Indices: 1216147--1216221 Score: 150
Period size: 39 Copynumber: 1.9 Consensus size: 39
1216137 ATGCATCGAG
1216147 CACCTATGATTTAATTGAACATCGAATGCATTTCATGCA
1 CACCTATGATTTAATTGAACATCGAATGCATTTCATGCA
1216186 CACCTATGATTTAATTGAACATCGAATGCATTTCAT
1 CACCTATGATTTAATTGAACATCGAATGCATTTCAT
1216222 ATAATTCCTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.35
Consensus pattern (39 bp):
CACCTATGATTTAATTGAACATCGAATGCATTTCATGCA
Found at i:1217013 original size:348 final size:348
Alignment explanation
Indices: 1216371--1217067 Score: 1319
Period size: 348 Copynumber: 2.0 Consensus size: 348
1216361 TTAGTAAAAG
*
1216371 ATAATAAGTGATTAAATAAAAGTAATTAAAGTAAAAATAAGAAGATGAAGATTGTGAATAAATAC
1 ATAATAAGTGATTAAATAAAACTAATTAAAGTAAAAATAAGAAGATGAAGATTGTGAATAAATAC
1216436 GGTAAAAGTAGCCTCAAGCTTCGCTTTGATTCAATTTCCTTTAGATCATCGAATAAGATTTCTCT
66 GGTAAAAGTAGCCTCAAGCTTCGCTTTGATTCAATTTCCTTTAGATCATCGAATAAGATTTCTCT
1216501 TCGGATTCACGTCGGTTACTTTGTCTACAAGGGCTATCCTTGTGACTCTATCTTGTATACCGAAT
131 TCGGATTCACGTCGGTTACTTTGTCTACAAGGGCTATCCTTGTGACTCTATCTTGTATA-CGAAT
1216566 ACCCAAGGCAATCTTGATTCCGGCTTCGGTAGTTGATTCTAACAACATCTATTGTCGTAGATCAA
195 ACCCAAGGCAATCTTGATTCCGGCTTCGGTAGTTGATTCTAACAACATCTATTGTCGTAGATCAA
1216631 ATACCGTTTAAGTTCGTGGCGACCGACTCGGATTGTTGTTTCTAT-ACCGT-AATTCCGATCTCA
260 ATACCGTTTAAGTTCGTGGCGACCGACTCGGATTGTTGTTTCTATAACCGTCAATTCCGATCTCA
1216694 ATTCCCTCTTGGCGAAGCTATCTC
325 ATTCCCTCTTGGCGAAGCTATCTC
1216718 ATAATAAAGTGATTAAATAAAACTAATTAAAGTAAAAATAAGAAGATGAAGATTGTGAATAAATA
1 ATAAT-AAGTGATTAAATAAAACTAATTAAAGTAAAAATAAGAAGATGAAGATTGTGAATAAATA
1216783 CGGTAAAAGTAGCCTCAAGCTTCGCTTTGATTCAATTTCCTTTAGATCATCGAATAAGATTTTCT
65 CGGTAAAAGTAGCCTCAAGCTTCGCTTTGATTCAATTTCCTTTAGATCATCGAATAAGA-TTTCT
1216848 CTTCAGGATTCACGTCGGTTACTTTGTCTACAAGGGCTATCCTTGTGACTCTATCTTGTATA-GA
129 CTTC-GGATTCACGTCGGTTACTTTGTCTACAAGGGCTATCCTTGTGACTCTATCTTGTATACGA
*
1216912 ATACCCAAGGCAATCTTGATTTCGGCTTCGGTAGTTGATTCTAACAACATCTATTGTCGTAGATC
193 ATACCCAAGGCAATCTTGATTCCGGCTTCGGTAGTTGATTCTAACAACATCTATTGTCGTAGATC
1216977 AAATACCGTTTAAGTTCGTGGCGACCGACTCGGATTGTTGTTTCTATAACCGTCAATTCCGATCT
258 AAATACCGTTTAAGTTCGTGGCGACCGACTCGGATTGTTGTTTCTATAACCGTCAATTCCGATCT
1217042 CAATTCCCTCTTGGCGAAGCTATCTC
323 CAATTCCCTCTTGGCGAAGCTATCTC
1217068 GCCAAGTGTG
Statistics
Matches: 343, Mismatches: 2, Indels: 7
0.97 0.01 0.02
Matches are distributed among these distances:
347 5 0.01
348 230 0.67
349 14 0.04
350 94 0.27
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (348 bp):
ATAATAAGTGATTAAATAAAACTAATTAAAGTAAAAATAAGAAGATGAAGATTGTGAATAAATAC
GGTAAAAGTAGCCTCAAGCTTCGCTTTGATTCAATTTCCTTTAGATCATCGAATAAGATTTCTCT
TCGGATTCACGTCGGTTACTTTGTCTACAAGGGCTATCCTTGTGACTCTATCTTGTATACGAATA
CCCAAGGCAATCTTGATTCCGGCTTCGGTAGTTGATTCTAACAACATCTATTGTCGTAGATCAAA
TACCGTTTAAGTTCGTGGCGACCGACTCGGATTGTTGTTTCTATAACCGTCAATTCCGATCTCAA
TTCCCTCTTGGCGAAGCTATCTC
Found at i:1219399 original size:15 final size:15
Alignment explanation
Indices: 1219363--1219392 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1219353 ATGCTTAATC
1219363 GAAAAAAAAATAAAA
1 GAAAAAAAAATAAAA
1219378 GAAAAAAAAATAAAA
1 GAAAAAAAAATAAAA
1219393 ATAAAAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.87, C:0.00, G:0.07, T:0.07
Consensus pattern (15 bp):
GAAAAAAAAATAAAA
Found at i:1229487 original size:16 final size:15
Alignment explanation
Indices: 1229454--1229483 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1229444 TTCTCAATTT
*
1229454 TTAAAAAAAATCGAA
1 TTAAAAAAAATCAAA
1229469 TTAAAAAAAATCAAA
1 TTAAAAAAAATCAAA
1229484 ATTAGTGATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.70, C:0.07, G:0.03, T:0.20
Consensus pattern (15 bp):
TTAAAAAAAATCAAA
Found at i:1231734 original size:64 final size:63
Alignment explanation
Indices: 1231618--1231824 Score: 201
Period size: 64 Copynumber: 3.3 Consensus size: 63
1231608 ATTCAAGGTG
* * * *
1231618 ATGCACCGATGCA-TCAAACCATGCATCGATGCACCTATGAT-TTAATTGAACATCGAATGCATT
1 ATGCACCGATGCACTC--TCCATGCATCGATGCACC-AGGATATT-TTTCAACATCGAATGCATT
1231681 TC
62 TC
1231683 ATGCACCGATGCACTCTCCATGCATCGATGCACTC-GGA-ATATTTTCAAACATCGAATGCATTT
1 ATGCACCGATGCACTCTCCATGCATCGATGCAC-CAGGATAT-TTTTC-AACATCGAATGCATTT
*
1231746 G
63 C
* *** * * *
1231747 ATGCATCGATGCACAAGCCATGCATTGATGCACCAGGCTATTTTTCAACATCGAATGCACTTC
1 ATGCACCGATGCACTCTCCATGCATCGATGCACCAGGATATTTTTCAACATCGAATGCATTTC
1231810 ATG--CCGATGCACTCT
1 ATGCACCGATGCACTCT
1231825 TAGTACACCG
Statistics
Matches: 118, Mismatches: 17, Indels: 18
0.77 0.11 0.12
Matches are distributed among these distances:
61 8 0.07
63 24 0.20
64 68 0.58
65 16 0.14
66 2 0.02
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.28
Consensus pattern (63 bp):
ATGCACCGATGCACTCTCCATGCATCGATGCACCAGGATATTTTTCAACATCGAATGCATTTC
Found at i:1233846 original size:166 final size:167
Alignment explanation
Indices: 1233639--1233973 Score: 615
Period size: 170 Copynumber: 2.0 Consensus size: 167
1233629 TTACAAATCT
1233639 ACACTACTTAAAGAAAATCGTCCTCGAATTTCACTGAACAAATCAATAAG-ACATATCTTCTTAT
1 ACACTACTTAAAGAAAATCGTCCTCGAATTTCACTGAACAAATCAATAAGAACATATCTTCTTAT
1233703 GTTCTCATGCTACCTCCTTTACTTAATC-TTCATTCCTTT-GTTCTTCAACTATC-TTTTCCTTT
66 GTTCTCATGCTACCTCCTTTACTTAATCTTTCATTCCTTTAGTTCTTCAACTATCTTTTTCCTTT
1233765 ATAAATTTATCTAATGTTACTTACCATATAAACAGTA
131 ATAAATTTATCTAATGTTACTTACCATATAAACAGTA
1233802 ACACTACTTTAAAGAAAATTCGTCCTCGAATTTTCACTGAACAAATCAATAAGAACATATCTTCT
1 ACACTAC-TTAAAGAAAA-TCGTCCTCGAA-TTTCACTGAACAAATCAATAAGAACATATCTTCT
1233867 TATGTTCTCATGCTACCTCCTTTACTTAATCTTTCATTCCTTTAGTTCTTCAACTATCTTTTTCC
63 TATGTTCTCATGCTACCTCCTTTACTTAATCTTTCATTCCTTTAGTTCTTCAACTATCTTTTTCC
1233932 TTTATAAATTTATCTAATGTTACTTACCATATAAACAGTA
128 TTTATAAATTTATCTAATGTTACTTACCATATAAACAGTA
1233972 AC
1 AC
1233974 CCATAACCTC
Statistics
Matches: 165, Mismatches: 0, Indels: 7
0.96 0.00 0.04
Matches are distributed among these distances:
163 7 0.04
164 10 0.06
165 11 0.07
166 22 0.13
167 42 0.25
168 11 0.07
169 14 0.08
170 48 0.29
ACGTcount: A:0.31, C:0.22, G:0.06, T:0.40
Consensus pattern (167 bp):
ACACTACTTAAAGAAAATCGTCCTCGAATTTCACTGAACAAATCAATAAGAACATATCTTCTTAT
GTTCTCATGCTACCTCCTTTACTTAATCTTTCATTCCTTTAGTTCTTCAACTATCTTTTTCCTTT
ATAAATTTATCTAATGTTACTTACCATATAAACAGTA
Found at i:1234336 original size:11 final size:12
Alignment explanation
Indices: 1234303--1234343 Score: 50
Period size: 11 Copynumber: 3.5 Consensus size: 12
1234293 TTTAACTCAA
1234303 TTCCTTTCATTC
1 TTCCTTTCATTC
*
1234315 TT-ATTTCATTC
1 TTCCTTTCATTC
1234326 TTCCTTT-ATTC
1 TTCCTTTCATTC
1234337 ATTCCTT
1 -TTCCTT
1234344 ATACACAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
11 14 0.56
12 11 0.44
ACGTcount: A:0.12, C:0.27, G:0.00, T:0.61
Consensus pattern (12 bp):
TTCCTTTCATTC
Found at i:1236329 original size:23 final size:21
Alignment explanation
Indices: 1236280--1236331 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
1236270 ATCATTTTTT
*
1236280 TGTCACATATTCACATATTCA
1 TGTCACATATGCACATATTCA
* *
1236301 TTTCACATATGCATATAATCTCA
1 TGTCACATATGCACAT-AT-TCA
1236324 TGTCACAT
1 TGTCACAT
1236332 TCTCATATGG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 13 0.52
22 2 0.08
23 10 0.40
ACGTcount: A:0.33, C:0.23, G:0.06, T:0.38
Consensus pattern (21 bp):
TGTCACATATGCACATATTCA
Found at i:1236337 original size:13 final size:13
Alignment explanation
Indices: 1236319--1236367 Score: 53
Period size: 13 Copynumber: 3.5 Consensus size: 13
1236309 ATGCATATAA
1236319 TCTCATGTCACAT
1 TCTCATGTCACAT
1236332 TCTCATATGGTCACAT
1 TCTC--AT-GTCACAT
*
1236348 AGCTCATGTCACAT
1 -TCTCATGTCACAT
1236362 TCTCAT
1 TCTCAT
1236368 ATGGTCACAT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
13 9 0.30
14 7 0.23
15 4 0.13
16 7 0.23
17 3 0.10
ACGTcount: A:0.24, C:0.29, G:0.10, T:0.37
Consensus pattern (13 bp):
TCTCATGTCACAT
Found at i:1236346 original size:16 final size:16
Alignment explanation
Indices: 1236325--1236377 Score: 67
Period size: 16 Copynumber: 3.4 Consensus size: 16
1236315 ATAATCTCAT
1236325 GTCACATTCTCATATG
1 GTCACATTCTCATATG
*
1236341 GTCACATAGCTC--AT-
1 GTCACAT-TCTCATATG
1236355 GTCACATTCTCATATG
1 GTCACATTCTCATATG
1236371 GTCACAT
1 GTCACAT
1236378 AGATCATATC
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
13 3 0.10
14 7 0.23
15 4 0.13
16 14 0.45
17 3 0.10
ACGTcount: A:0.26, C:0.26, G:0.13, T:0.34
Consensus pattern (16 bp):
GTCACATTCTCATATG
Found at i:1236355 original size:30 final size:30
Alignment explanation
Indices: 1236320--1236389 Score: 122
Period size: 30 Copynumber: 2.3 Consensus size: 30
1236310 TGCATATAAT
1236320 CTCATGTCACATTCTCATATGGTCACATAG
1 CTCATGTCACATTCTCATATGGTCACATAG
1236350 CTCATGTCACATTCTCATATGGTCACATAG
1 CTCATGTCACATTCTCATATGGTCACATAG
* *
1236380 ATCATATCAC
1 CTCATGTCAC
1236390 GTGGTTGTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.29, C:0.27, G:0.11, T:0.33
Consensus pattern (30 bp):
CTCATGTCACATTCTCATATGGTCACATAG
Found at i:1236386 original size:17 final size:17
Alignment explanation
Indices: 1236333--1236386 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 17
1236323 ATGTCACATT
1236333 CTCATATGGTCACATAG
1 CTCATATGGTCACATAG
*
1236350 CTC--AT-GTCACAT-T
1 CTCATATGGTCACATAG
1236363 CTCATATGGTCACATAG
1 CTCATATGGTCACATAG
*
1236380 ATCATAT
1 CTCATAT
1236387 CACGTGGTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
13 3 0.10
14 7 0.23
15 4 0.13
16 7 0.23
17 9 0.30
ACGTcount: A:0.30, C:0.24, G:0.13, T:0.33
Consensus pattern (17 bp):
CTCATATGGTCACATAG
Found at i:1238938 original size:2 final size:2
Alignment explanation
Indices: 1238931--1238956 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1238921 AGTAACATTG
1238931 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1238957 GATAGTAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1242520 original size:100 final size:100
Alignment explanation
Indices: 1242334--1242521 Score: 231
Period size: 100 Copynumber: 1.9 Consensus size: 100
1242324 ATTAAAAAAA
* * * *
1242334 TAAACTAAACTTACCAAATCACTCAATACGATTTAATATGTAAAATCAAAATAGATATTTCAATA
1 TAAACTAAACTTACCAAATCACTCAATACAACTTAATATGTAAAATCAAAAAAAATATTTCAATA
* *** *
1242399 ATTTATATTGCTCAATAAAAAATAAAAATATAATT
66 ATTTAAATTGAAAAAAAAAAAATAAAAATATAATT
1242434 TAAACTAAACTTACCAAA-CTACTCAAATACAACTTAATATGTAAAAT-AAAAAAAATAGTTT-A
1 TAAACTAAACTTACCAAATC-ACTC-AATACAACTTAATATGTAAAATCAAAAAAAATA-TTTCA
1242496 ATAATTTAAATT-AAAAAAACAAAAAT
63 ATAATTTAAATTGAAAAAAA-AAAAAT
1242522 TAGACTAAAA
Statistics
Matches: 75, Mismatches: 9, Indels: 8
0.82 0.10 0.09
Matches are distributed among these distances:
99 4 0.05
100 48 0.64
101 23 0.31
ACGTcount: A:0.55, C:0.12, G:0.03, T:0.30
Consensus pattern (100 bp):
TAAACTAAACTTACCAAATCACTCAATACAACTTAATATGTAAAATCAAAAAAAATATTTCAATA
ATTTAAATTGAAAAAAAAAAAATAAAAATATAATT
Found at i:1243331 original size:21 final size:20
Alignment explanation
Indices: 1243305--1243343 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
1243295 GATAAAAATT
1243305 TATTTTTATTAAATATTTTGG
1 TATTTTTATTAAAT-TTTTGG
*
1243326 TATTTTTATTTAATTTTT
1 TATTTTTATTAAATTTTT
1243344 AAATAATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (20 bp):
TATTTTTATTAAATTTTTGG
Found at i:1243924 original size:163 final size:165
Alignment explanation
Indices: 1243752--1244080 Score: 635
Period size: 163 Copynumber: 2.0 Consensus size: 165
1243742 AATTACACGA
1243752 AAATTTAATTAAACTTACCAAGCCACTCGAATACAGTTTAATATGTAAATTCAAAATAACAATCT
1 AAATTTAATTAAACTTACCAAGCCACTCGAATACAGTTTAATATGTAAATTCAAAATAACAATCT
*
1243817 TATTAATTATATTTCAAATAAAAAATTAAATAGAAACAATAAAATTTACACTAAA-TT-TCAAAT
66 TATTAATTATATTTCAAATAAAAAATTAAATAAAAACAATAAAATTTACACTAAATTTATCAAAT
1243880 CGCTTACGATAGCTCTCGAATTCTTCCTTCCTTCG
131 CGCTTACGATAGCTCTCGAATTCTTCCTTCCTTCG
1243915 AAATTTAATTAAACTTACCAAGCCACTCGAATACAGTTTAATATGTAAATTCAAAATAACAATCT
1 AAATTTAATTAAACTTACCAAGCCACTCGAATACAGTTTAATATGTAAATTCAAAATAACAATCT
1243980 TATTAATTATATTTCAAATAAAAAATTAAATAAAAACAATAAAATTTACACTAAATTTATCAAAT
66 TATTAATTATATTTCAAATAAAAAATTAAATAAAAACAATAAAATTTACACTAAATTTATCAAAT
1244045 CGCTTACGATAGCTCTCGAATTCTTCCTTCCTTCG
131 CGCTTACGATAGCTCTCGAATTCTTCCTTCCTTCG
1244080 A
1 A
1244081 TCGAACTCTC
Statistics
Matches: 163, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
163 119 0.73
164 2 0.01
165 42 0.26
ACGTcount: A:0.43, C:0.17, G:0.06, T:0.34
Consensus pattern (165 bp):
AAATTTAATTAAACTTACCAAGCCACTCGAATACAGTTTAATATGTAAATTCAAAATAACAATCT
TATTAATTATATTTCAAATAAAAAATTAAATAAAAACAATAAAATTTACACTAAATTTATCAAAT
CGCTTACGATAGCTCTCGAATTCTTCCTTCCTTCG
Found at i:1245037 original size:41 final size:42
Alignment explanation
Indices: 1244981--1245063 Score: 150
Period size: 41 Copynumber: 2.0 Consensus size: 42
1244971 TTCCCAAAAT
*
1244981 TTTAATATAGTTTTTCAAATTTCCTTTGA-TTTTTAACTAAA
1 TTTAATATAGCTTTTCAAATTTCCTTTGATTTTTTAACTAAA
1245022 TTTAATATAGCTTTTCAAATTTCCTTTGATTTTTTAACTAAA
1 TTTAATATAGCTTTTCAAATTTCCTTTGATTTTTTAACTAAA
1245064 GCATCTTCCA
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
41 28 0.70
42 12 0.30
ACGTcount: A:0.31, C:0.11, G:0.05, T:0.53
Consensus pattern (42 bp):
TTTAATATAGCTTTTCAAATTTCCTTTGATTTTTTAACTAAA
Found at i:1250663 original size:18 final size:18
Alignment explanation
Indices: 1250640--1250674 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1250630 GGTCGTACAA
*
1250640 TTTTCTTCTTCTCTTTCT
1 TTTTCTGCTTCTCTTTCT
*
1250658 TTTTCTGCTTCTTTTTC
1 TTTTCTGCTTCTCTTTC
1250675 ATCCCTTGTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.00, C:0.26, G:0.03, T:0.71
Consensus pattern (18 bp):
TTTTCTGCTTCTCTTTCT
Found at i:1252565 original size:2 final size:2
Alignment explanation
Indices: 1252558--1252586 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1252548 ATTAATATTT
1252558 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1252587 CAAAATAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1252814 original size:2 final size:2
Alignment explanation
Indices: 1252807--1252837 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1252797 TTATTTTAAC
1252807 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1252838 CCACTTACAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1253707 original size:3 final size:3
Alignment explanation
Indices: 1253699--1253796 Score: 196
Period size: 3 Copynumber: 32.7 Consensus size: 3
1253689 GTTACACCAC
1253699 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1253747 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1253795 AT
1 AT
1253797 ATTCAAGAAC
Statistics
Matches: 95, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 95 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1254959 original size:14 final size:14
Alignment explanation
Indices: 1254940--1254966 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1254930 CGTTCGTGAA
1254940 CGTTTGGTTATGTT
1 CGTTTGGTTATGTT
1254954 CGTTTGGTTATGT
1 CGTTTGGTTATGT
1254967 CCGCTTATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.07, G:0.30, T:0.56
Consensus pattern (14 bp):
CGTTTGGTTATGTT
Found at i:1254974 original size:24 final size:24
Alignment explanation
Indices: 1254947--1255002 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
1254937 GAACGTTTGG
* *
1254947 TTATGTTCGTTTGGTTATGTCCGC
1 TTATGTTCGTTCGATTATGTCCGC
* *
1254971 TTATGTTCGTTCGATTATGTTCGT
1 TTATGTTCGTTCGATTATGTCCGC
1254995 TTATGTTC
1 TTATGTTC
1255003 ATTCATTTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.11, C:0.14, G:0.21, T:0.54
Consensus pattern (24 bp):
TTATGTTCGTTCGATTATGTCCGC
Found at i:1255012 original size:24 final size:24
Alignment explanation
Indices: 1254947--1255015 Score: 68
Period size: 24 Copynumber: 2.9 Consensus size: 24
1254937 GAACGTTTGG
* * * *
1254947 TTATGTTCGTTTGGTTATGTCCGC
1 TTATGTTCATTCGATTATGTTCGC
* *
1254971 TTATGTTCGTTCGATTATGTTCGT
1 TTATGTTCATTCGATTATGTTCGC
1254995 TTATGTTCATTC-ATTTATGTT
1 TTATGTTCATTCGA-TTATGTT
1255016 TAACCCAATC
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
23 1 0.03
24 38 0.97
ACGTcount: A:0.13, C:0.13, G:0.19, T:0.55
Consensus pattern (24 bp):
TTATGTTCATTCGATTATGTTCGC
Found at i:1255772 original size:16 final size:16
Alignment explanation
Indices: 1255753--1255819 Score: 111
Period size: 16 Copynumber: 4.3 Consensus size: 16
1255743 TTTATGTTTG
1255753 TTTATGTTCGTGTTCA
1 TTTATGTTCGTGTTCA
*
1255769 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
1255785 TTTATGTTCGTGTTCA
1 TTTATGTTCGTGTTCA
1255801 TTTATGTTCGT-TT-A
1 TTTATGTTCGTGTTCA
1255815 TTTAT
1 TTTAT
1255820 TAAATGAACG
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
14 6 0.12
15 2 0.04
16 41 0.84
ACGTcount: A:0.12, C:0.10, G:0.18, T:0.60
Consensus pattern (16 bp):
TTTATGTTCGTGTTCA
Found at i:1255902 original size:16 final size:16
Alignment explanation
Indices: 1255881--1255913 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1255871 AAAAAAATTT
1255881 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
1255897 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
1255913 T
1 T
1255914 TTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:1256779 original size:16 final size:16
Alignment explanation
Indices: 1256758--1256791 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1256748 AGCCCATCTC
1256758 TCTTTCTTACTCTTAG
1 TCTTTCTTACTCTTAG
*
1256774 TCTTTCTTATTCTTAG
1 TCTTTCTTACTCTTAG
1256790 TC
1 TC
1256792 GAAACCATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.12, C:0.24, G:0.06, T:0.59
Consensus pattern (16 bp):
TCTTTCTTACTCTTAG
Found at i:1264727 original size:18 final size:21
Alignment explanation
Indices: 1264704--1264749 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
1264694 TTTTTTGTAC
1264704 TGATACTC-A-TG-AGAGTAT
1 TGATACTCAAGTGTAGAGTAT
1264722 TGATAC-CAAGTGTAGAGTAT
1 TGATACTCAAGTGTAGAGTAT
*
1264742 CGATACTC
1 TGATACTC
1264750 CCCATAGGGG
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
17 1 0.04
18 7 0.30
19 2 0.09
20 12 0.52
21 1 0.04
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.30
Consensus pattern (21 bp):
TGATACTCAAGTGTAGAGTAT
Found at i:1266573 original size:30 final size:30
Alignment explanation
Indices: 1266534--1266607 Score: 94
Period size: 30 Copynumber: 2.5 Consensus size: 30
1266524 TATTAAAATA
* * *
1266534 TGAACGTGTTCTATGTAAAAGTGCTTTATG
1 TGAAAGTGTTCTATGTAAAAATGCTCTATG
* *
1266564 TGAATGTGTTCTACGTAAAAATGCTCTATG
1 TGAAAGTGTTCTATGTAAAAATGCTCTATG
*
1266594 CGAAAGTGTTCTAT
1 TGAAAGTGTTCTAT
1266608 ATGGATGAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.28, C:0.12, G:0.22, T:0.38
Consensus pattern (30 bp):
TGAAAGTGTTCTATGTAAAAATGCTCTATG
Found at i:1266606 original size:15 final size:15
Alignment explanation
Indices: 1266539--1266607 Score: 59
Period size: 15 Copynumber: 4.6 Consensus size: 15
1266529 AAATATGAAC
1266539 GTGTTCTATGTAAAA
1 GTGTTCTATGTAAAA
* *
1266554 GTGCTT-TATGTGAAT
1 GTG-TTCTATGTAAAA
*
1266569 GTGTTCTACGTAAAA
1 GTGTTCTATGTAAAA
* * **
1266584 ATGCTCTATGCGAAA
1 GTGTTCTATGTAAAA
1266599 GTGTTCTAT
1 GTGTTCTAT
1266608 ATGGATGAAA
Statistics
Matches: 40, Mismatches: 12, Indels: 4
0.71 0.21 0.07
Matches are distributed among these distances:
14 2 0.05
15 36 0.90
16 2 0.05
ACGTcount: A:0.28, C:0.12, G:0.22, T:0.39
Consensus pattern (15 bp):
GTGTTCTATGTAAAA
Found at i:1266773 original size:24 final size:23
Alignment explanation
Indices: 1266715--1266776 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
1266705 GAGTCGAGGG
*
1266715 TTCTACGCGGTCCTTCGGGACAA
1 TTCTACGCGGTCCTTCGAGACAA
**
1266738 TTCTACATGGTCCTTCGAGACAAA
1 TTCTACGCGGTCCTTCGAGAC-AA
1266762 TTCTACGCGGTCCTT
1 TTCTACGCGGTCCTT
1266777 TAGGACATAT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
23 18 0.55
24 15 0.45
ACGTcount: A:0.19, C:0.29, G:0.21, T:0.31
Consensus pattern (23 bp):
TTCTACGCGGTCCTTCGAGACAA
Found at i:1266783 original size:24 final size:24
Alignment explanation
Indices: 1266715--1266783 Score: 70
Period size: 24 Copynumber: 2.9 Consensus size: 24
1266705 GAGTCGAGGG
**
1266715 TTCTACGCGGTCCTTCGGGAC-AA
1 TTCTACGCGGTCCTTTAGGACAAA
** *
1266738 TTCTACATGGTCC-TTCGAGACAAA
1 TTCTACGCGGTCCTTTAG-GACAAA
1266762 TTCTACGCGGTCCTTTAGGACA
1 TTCTACGCGGTCCTTTAGGACA
1266784 TATCTATGTG
Statistics
Matches: 36, Mismatches: 7, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
22 2 0.06
23 14 0.39
24 17 0.47
25 3 0.08
ACGTcount: A:0.22, C:0.28, G:0.22, T:0.29
Consensus pattern (24 bp):
TTCTACGCGGTCCTTTAGGACAAA
Found at i:1266829 original size:24 final size:23
Alignment explanation
Indices: 1266782--1266830 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 23
1266772 TCCTTTAGGA
* **
1266782 CATATCTATGTGGCACTTTGGTG
1 CATATCTACGTGGCACTTCAGTG
1266805 CATATTCTACGTGGCACTTCAGTG
1 CATA-TCTACGTGGCACTTCAGTG
1266829 CA
1 CA
1266831 AATTTTATGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 4 0.18
24 18 0.82
ACGTcount: A:0.20, C:0.22, G:0.22, T:0.35
Consensus pattern (23 bp):
CATATCTACGTGGCACTTCAGTG
Found at i:1272910 original size:20 final size:20
Alignment explanation
Indices: 1272866--1272910 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
1272856 AACAATATTG
*
1272866 ATACTGATTGAAGTAGTATCG
1 ATACTGATTGAAG-AGTATCA
1272887 ATACTGATGTGAAG-GTATCA
1 ATACTGAT-TGAAGAGTATCA
1272907 ATAC
1 ATAC
1272911 CAAGAGTAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 9 0.41
21 8 0.36
22 5 0.23
ACGTcount: A:0.36, C:0.11, G:0.22, T:0.31
Consensus pattern (20 bp):
ATACTGATTGAAGAGTATCA
Found at i:1273423 original size:15 final size:15
Alignment explanation
Indices: 1273400--1273476 Score: 91
Period size: 15 Copynumber: 5.1 Consensus size: 15
1273390 TATTAAAATA
* *
1273400 TGAATGTGTTCCATG
1 TGAAAGTGTTCTATG
*
1273415 TGAAAGTGTTTTATG
1 TGAAAGTGTTCTATG
* *
1273430 TGAATGTGTTCTACG
1 TGAAAGTGTTCTATG
* *
1273445 TGAAAATGCTCTATG
1 TGAAAGTGTTCTATG
1273460 TGAAAGTGTTCTATG
1 TGAAAGTGTTCTATG
1273475 TG
1 TG
1273477 GATAAAAGAC
Statistics
Matches: 50, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 50 1.00
ACGTcount: A:0.25, C:0.09, G:0.26, T:0.40
Consensus pattern (15 bp):
TGAAAGTGTTCTATG
Found at i:1273689 original size:24 final size:23
Alignment explanation
Indices: 1273581--1273689 Score: 80
Period size: 23 Copynumber: 4.7 Consensus size: 23
1273571 GAGTCGAGGG
* *
1273581 TTCTACGTGGTCCTTTGGGACA-A
1 TTCTACGTGGTACTTCGGG-CATA
*
1273604 TTCTACGTGGT-CTTTCAGGGCAAA
1 TTCTACGTGGTAC-TTC-GGGCATA
* *
1273628 TTCTACGTAGTCCTTCGGGACATA
1 TTCTACGTGGTACTTCGGG-CATA
* **
1273652 -TCTATGTGACACTTCGGTGCATA
1 TTCTACGTGGTACTTCGG-GCATA
1273675 TTCTACGTGGTACTT
1 TTCTACGTGGTACTT
1273690 TGGTGCAATT
Statistics
Matches: 68, Mismatches: 11, Indels: 13
0.74 0.12 0.14
Matches are distributed among these distances:
22 1 0.01
23 34 0.50
24 32 0.47
25 1 0.01
ACGTcount: A:0.19, C:0.22, G:0.23, T:0.36
Consensus pattern (23 bp):
TTCTACGTGGTACTTCGGGCATA
Found at i:1278686 original size:16 final size:16
Alignment explanation
Indices: 1278648--1278686 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
1278638 GATACAAGGG
1278648 AAAAATAAAATAAATA
1 AAAAATAAAATAAATA
*
1278664 AATAATAAAGATAAA-A
1 AAAAATAAA-ATAAATA
1278680 AAAAATA
1 AAAAATA
1278687 GTAAAATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 15 0.75
17 5 0.25
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (16 bp):
AAAAATAAAATAAATA
Found at i:1279247 original size:60 final size:58
Alignment explanation
Indices: 1279145--1279256 Score: 156
Period size: 60 Copynumber: 1.9 Consensus size: 58
1279135 ATATTAAAGA
*
1279145 AATATATATATATATATATATAATAATAATAAATATAGTAAAAAAATAAATGAAATATTT
1 AATATATATATATATACATATAATAATAATAAATATAGT--AAAAATAAATGAAATATTT
*
1279205 AATATATATATATATACATATAATAATAACATGAATA-A-TAAAAATAAATGAA
1 AATATATATATATATACATATAATAAT-A-ATAAATATAGTAAAAATAAATGAA
1279257 TAAAATATAC
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
58 13 0.27
60 27 0.56
61 2 0.04
62 6 0.12
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.34
Consensus pattern (58 bp):
AATATATATATATATACATATAATAATAATAAATATAGTAAAAATAAATGAAATATTT
Found at i:1279257 original size:17 final size:18
Alignment explanation
Indices: 1279224--1279259 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1279214 ATATATACAT
*
1279224 ATAATAATAACATGAATA
1 ATAAAAATAACATGAATA
1279242 ATAAAAATAA-ATGAATA
1 ATAAAAATAACATGAATA
1279259 A
1 A
1279260 AATATACATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.67, C:0.03, G:0.06, T:0.25
Consensus pattern (18 bp):
ATAAAAATAACATGAATA
Found at i:1280566 original size:105 final size:105
Alignment explanation
Indices: 1280262--1280892 Score: 932
Period size: 105 Copynumber: 6.0 Consensus size: 105
1280252 GCATTGTTCC
* * ** *
1280262 GAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTG-GAACAGGGAAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAG-ATTGGGAAGTTG-TTGTTGACA
* * * * *
1280326 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
64 AGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1280368 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGA-A-T--GAAATT-TTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
*
1280428 CAGCGGTCCCTTCGTCGTGGAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
1280468 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
*
1280533 TAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1280573 GAGTCCAATATCATTCGTTGTGAAGTTGAAATTGGCTCTGAGATTTGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
1280638 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
1280678 AAGTCCAATATCCTTTGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTTACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
*
1280743 CAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1280783 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTG-TTGTTGACAA
* * * * *
1280848 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
65 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
1280889 GAGT
1 GAGT
1280893 GTCACGATAT
Statistics
Matches: 484, Mismatches: 34, Indels: 14
0.91 0.06 0.03
Matches are distributed among these distances:
100 85 0.18
101 1 0.00
102 7 0.01
104 5 0.01
105 301 0.62
106 85 0.18
ACGTcount: A:0.22, C:0.17, G:0.27, T:0.34
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:1281139 original size:36 final size:36
Alignment explanation
Indices: 1281092--1281167 Score: 116
Period size: 36 Copynumber: 2.1 Consensus size: 36
1281082 TGTTTGGAGA
* * *
1281092 GAAACTGTCTCAAGGGAGACAAAATTCGTTTCAAGG
1 GAAACTATCTCAAGCGAGACAAAATTCATTTCAAGG
*
1281128 GAAACTATCTCAAGCGAGATAAAATTCATTTCAAGG
1 GAAACTATCTCAAGCGAGACAAAATTCATTTCAAGG
1281164 GAAA
1 GAAA
1281168 TGTTTTCAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.41, C:0.16, G:0.21, T:0.22
Consensus pattern (36 bp):
GAAACTATCTCAAGCGAGACAAAATTCATTTCAAGG
Found at i:1281357 original size:39 final size:39
Alignment explanation
Indices: 1281284--1281362 Score: 95
Period size: 39 Copynumber: 2.0 Consensus size: 39
1281274 TCAATGTTTA
* ** *
1281284 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTC
1 TGTTTCAAGAGAAACTATCTCAAGCAAGACAAAATCTTC
* * *
1281323 TGTTTCGAGGGAAACTATCTCAAGCAAGATAAAATCTTC
1 TGTTTCAAGAGAAACTATCTCAAGCAAGACAAAATCTTC
1281362 T
1 T
1281363 TAAAAACAGC
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.29
Consensus pattern (39 bp):
TGTTTCAAGAGAAACTATCTCAAGCAAGACAAAATCTTC
Found at i:1281357 original size:102 final size:103
Alignment explanation
Indices: 1281070--1281358 Score: 464
Period size: 101 Copynumber: 2.8 Consensus size: 103
1281060 GTTAAATTGC
* ** *
1281070 TTTCAAAGTTTATGTTTGGAGAGAAACTGTCTCAAGGGAGACAAAA--TTC-GTTTCAAGGGAAA
1 TTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGGAAA
*
1281132 CTATCTCAAGCGAGATAAAATTCATTTCAAGGGAAATGT
66 CTATCTCAAGCAAGATAAAA-TCATTTCAAGGGAAATGT
1281171 TTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGA-GGAAA
1 TTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGGAAA
*
1281235 CTATCTCAAG-AGAGAAAAAATCATTTCAAGGGAAATG-
66 CTATCTCAAGCA-AGATAAAATCATTTCAAGGGAAATGT
1281272 TTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGGAAA
1 TTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGGAAA
1281337 CTATCTCAAGCAAGATAAAATC
66 CTATCTCAAGCAAGATAAAATC
1281359 TTCTTAAAAA
Statistics
Matches: 175, Mismatches: 7, Indels: 11
0.91 0.04 0.06
Matches are distributed among these distances:
101 102 0.58
102 41 0.23
103 26 0.15
104 6 0.03
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (103 bp):
TTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGGAAA
CTATCTCAAGCAAGATAAAATCATTTCAAGGGAAATGT
Found at i:1281488 original size:70 final size:71
Alignment explanation
Indices: 1281364--1281535 Score: 195
Period size: 70 Copynumber: 2.4 Consensus size: 71
1281354 AAATCTTCTT
** * * *
1281364 AAAAACAGCCTTGAGTGAAATGAAATGCCTTTTTTCGAGTGAAAACGGTCTCAAGCGAGACAAAT
1 AAAAACAATCTTGAGTGAAAT--AAT--CTTCTTTCGAGTAAAAACAGTCTCAAGCGAGACAAAT
*
1281429 TTGTTTTAAG
62 ATGTTTTAAG
* *
1281439 AAAAACAATCTTGAGTGAAATAATCTTCTTTCGAG-AAAAACAGTCTCAAGTGAGACAAGTATGT
1 AAAAACAATCTTGAGTGAAATAATCTTCTTTCGAGTAAAAACAGTCTCAAGCGAGACAAATATGT
1281503 TTTAAG
66 TTTAAG
*
1281509 AAAAACAAAT-TTGAGTGATAATCATCT
1 AAAAAC-AATCTTGAGTGA-AATAATCT
1281536 GCATTAAAAG
Statistics
Matches: 86, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
70 44 0.51
71 20 0.23
73 3 0.03
75 19 0.22
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.28
Consensus pattern (71 bp):
AAAAACAATCTTGAGTGAAATAATCTTCTTTCGAGTAAAAACAGTCTCAAGCGAGACAAATATGT
TTTAAG
Found at i:1281511 original size:35 final size:34
Alignment explanation
Indices: 1281405--1281515 Score: 89
Period size: 35 Copynumber: 3.2 Consensus size: 34
1281395 TTTTCGAGTG
* * *
1281405 AAAACGGTCTCAAGCGAGACAAATTTGTTTTAAGA
1 AAAACAGTCTCAAGTGAGAC-AATATGTTTTAAGA
* ** * * * *
1281440 AAAACAATCTTGAGTGAAATAATCT-TCTTTCGAGA
1 AAAACAGTCTCAAGTGAGACAATATGT-TTT-AAGA
1281475 AAAACAGTCTCAAGTGAGACAAGTATGTTTTAAGA
1 AAAACAGTCTCAAGTGAGACAA-TATGTTTTAAGA
1281510 AAAACA
1 AAAACA
1281516 AATTTGAGTG
Statistics
Matches: 56, Mismatches: 16, Indels: 8
0.70 0.20 0.10
Matches are distributed among these distances:
33 1 0.02
34 7 0.12
35 42 0.75
36 5 0.09
37 1 0.02
ACGTcount: A:0.43, C:0.14, G:0.17, T:0.26
Consensus pattern (34 bp):
AAAACAGTCTCAAGTGAGACAATATGTTTTAAGA
Found at i:1283011 original size:181 final size:182
Alignment explanation
Indices: 1282652--1283182 Score: 878
Period size: 181 Copynumber: 2.9 Consensus size: 182
1282642 ATCAGGTTTA
* * * *
1282652 ACTGAAGGGTTC-ATCATCACAAAGTCTTTGACCTGACAAAAGTAGTGGAGTAAACACCGAATTG
1 ACTGAAGGGTTCTCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATTG
* **
1282716 CCAAGTGTCCGAGCAATGTCAT-GATTTGAATGTAATCTATTCATAAAGCCAGGGCTTTCGAGTT
66 CCAAGTGTCCGAGCAGTGTCATAG-TTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
1282780 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
130 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
1282833 ACTGAAGGGTTCGTCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
1 ACTGAAGGGTTC-TCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
1282898 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCA-GGCTTTCGAGTT
65 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
*
1282962 TCCTCTATAA-CTATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
130 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
*
1283014 ACTGAAGGGTTTCATCTCATCACAAAGTC-TTGGCCTGAC-AAAGCAGTGGAGCAAACATCG-AT
1 ACTGAAGGG-TTC-TCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAAT
*
1283076 TGCCAAGTGTCTGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGT
64 TGCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGT
*
1283141 TTCCTATATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
129 TTCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
1283183 CGGATTTAAT
Statistics
Matches: 331, Mismatches: 13, Indels: 12
0.93 0.04 0.03
Matches are distributed among these distances:
179 54 0.16
180 41 0.12
181 101 0.31
182 40 0.12
183 94 0.28
184 1 0.00
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (182 bp):
ACTGAAGGGTTCTCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATTG
CCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTTT
CCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
Found at i:1283591 original size:198 final size:199
Alignment explanation
Indices: 1283253--1283653 Score: 786
Period size: 198 Copynumber: 2.0 Consensus size: 199
1283243 TCAAGGGATC
*
1283253 TCATCTTTAGAGTTCAATTTCCAAACAACTGACCTAAACTAGATTTGCTTACTCGACTATTCCCT
1 TCATCTTTAGAGTTCAATTTCCAAACAACTGACCTAAACTAGATTTGCTTACTCGACTATTCCAT
1283318 CTGTGAAGATCATTATCATCCCTGAACATCATAAACAAGTGTATAAACCAATTAGTTTTGCAATC
66 CTGTGAAGATCATTATCATCCCTGAACATCATAAACAAGTGTATAAACCAATTAGTTTTGCAATC
1283383 TCATGTGCTAGTTGCCCTATTCTGTTCGCTCTTAATAC-TGTCTGAATACCAAACCTTGGATGGA
131 TCATGTGCTAGTTGCCCTATTCTGTTCGCTCTTAATACGTGTCTGAATACCAAACCTTGGATGGA
1283447 CTCT
196 CTCT
1283451 TCATCTTTAGAGTTCAATTTCCAAACAACTGACCTAAACTAGATTTGCTTACTCGACTATTCCAT
1 TCATCTTTAGAGTTCAATTTCCAAACAACTGACCTAAACTAGATTTGCTTACTCGACTATTCCAT
1283516 CTGTGAAGATCATTATCATCCCTGAACATCATAAACAAGTGTATAAACCAATTAGTTTTGCAATC
66 CTGTGAAGATCATTATCATCCCTGAACATCATAAACAAGTGTATAAACCAATTAGTTTTGCAATC
1283581 TCATGTGCTAGTTGCCCTATTCTGTTCGCTCTTAATACGTGTCTGAATACCAAACCTTGGATGGA
131 TCATGTGCTAGTTGCCCTATTCTGTTCGCTCTTAATACGTGTCTGAATACCAAACCTTGGATGGA
1283646 CTCT
196 CTCT
1283650 TCAT
1 TCAT
1283654 GAGAAGAGAA
Statistics
Matches: 201, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
198 167 0.83
199 34 0.17
ACGTcount: A:0.29, C:0.23, G:0.13, T:0.34
Consensus pattern (199 bp):
TCATCTTTAGAGTTCAATTTCCAAACAACTGACCTAAACTAGATTTGCTTACTCGACTATTCCAT
CTGTGAAGATCATTATCATCCCTGAACATCATAAACAAGTGTATAAACCAATTAGTTTTGCAATC
TCATGTGCTAGTTGCCCTATTCTGTTCGCTCTTAATACGTGTCTGAATACCAAACCTTGGATGGA
CTCT
Found at i:1285262 original size:18 final size:18
Alignment explanation
Indices: 1285204--1285265 Score: 72
Period size: 18 Copynumber: 3.3 Consensus size: 18
1285194 TTAAGGAGTA
1285204 GTCCTTCGGGACATAGTG
1 GTCCTTCGGGACATAGTG
*
1285222 GTCCTAC-GGACATATACAGTG
1 GTCCTTCGGGAC--AT--AGTG
1285243 GTCCTTCGGGACATAGTG
1 GTCCTTCGGGACATAGTG
1285261 GTCCT
1 GTCCT
1285266 ACGGACGAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
17 4 0.11
18 15 0.41
19 2 0.05
20 2 0.05
21 10 0.27
22 4 0.11
ACGTcount: A:0.19, C:0.24, G:0.29, T:0.27
Consensus pattern (18 bp):
GTCCTTCGGGACATAGTG
Found at i:1290117 original size:22 final size:18
Alignment explanation
Indices: 1290075--1290144 Score: 77
Period size: 18 Copynumber: 3.7 Consensus size: 18
1290065 TTAAGGAGTA
*
1290075 GTCCTTCGGGACATAGTG
1 GTCCTACGGGACATAGTG
1290093 GTCCTACGGGACATATACAGTG
1 GTCCTACGGGAC--AT--AGTG
* *
1290115 GTCCTTCGGGGCATAGTG
1 GTCCTACGGGACATAGTG
1290133 GTCCTACGGGAC
1 GTCCTACGGGAC
1290145 GAATACTGAA
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
18 25 0.58
20 4 0.09
22 14 0.33
ACGTcount: A:0.19, C:0.24, G:0.33, T:0.24
Consensus pattern (18 bp):
GTCCTACGGGACATAGTG
Found at i:1294073 original size:2 final size:2
Alignment explanation
Indices: 1294062--1294099 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1294052 AAAGGAAAAA
*
1294062 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1294100 CAAAGTATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1294318 original size:12 final size:13
Alignment explanation
Indices: 1294291--1294336 Score: 51
Period size: 12 Copynumber: 3.6 Consensus size: 13
1294281 AAAAAATAAT
*
1294291 AATATATAATAATG
1 AATATA-AAAAATG
1294305 AATA-AAAAAATG
1 AATATAAAAAATG
*
1294317 AAAATAAAAAAT-
1 AATATAAAAAATG
1294329 AATATAAA
1 AATATAAA
1294337 GTTATAAGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
12 16 0.57
13 8 0.29
14 4 0.14
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.24
Consensus pattern (13 bp):
AATATAAAAAATG
Found at i:1294559 original size:44 final size:44
Alignment explanation
Indices: 1294464--1294566 Score: 120
Period size: 44 Copynumber: 2.3 Consensus size: 44
1294454 AGATAATTAC
* * *
1294464 AATATATATATAGTAATATTAAACTTATAAGTAAAATATTAAAGA
1 AATATATATATA-TAATAATAAACATATAAGTAAAATAATAAAGA
**
1294509 AATATATATATATAATAATAAA-ATAT-AGTAAAAATAATAAATTT
1 AATATATATATATAATAATAAACATATAAGT-AAAATAATAAA-GA
1294553 AATATATATATATA
1 AATATATATATATA
1294567 TATACATATA
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
42 3 0.06
43 13 0.25
44 23 0.45
45 12 0.24
ACGTcount: A:0.58, C:0.01, G:0.04, T:0.37
Consensus pattern (44 bp):
AATATATATATATAATAATAAACATATAAGTAAAATAATAAAGA
Found at i:1294596 original size:17 final size:17
Alignment explanation
Indices: 1294574--1294615 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
1294564 ATATATACAT
*
1294574 ATAATAATAATACATGA
1 ATAATAATAATAAATGA
*
1294591 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
1294608 ATAA-AATA
1 ATAATAATA
1294616 TCCATATAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 3 0.14
17 19 0.86
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:1295018 original size:37 final size:37
Alignment explanation
Indices: 1294968--1295072 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
1294958 GTGCTTGTGG
* * * *
1294968 ATCCTATCTTTAGGAATTTAAATCTTAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
* * *
1295005 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAATTTT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
*
1295042 ATCCGATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
1295073 GACGAAAATG
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 59 1.00
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.42
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
Found at i:1303373 original size:23 final size:23
Alignment explanation
Indices: 1303346--1303399 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
1303336 AGCTCATATA
1303346 AATTGCACCAAAGTACCACGTAG
1 AATTGCACCAAAGTACCACGTAG
* * *
1303369 AATTGCACCATAGTGCCGCGTAG
1 AATTGCACCAAAGTACCACGTAG
*
1303392 AAATGCAC
1 AATTGCAC
1303400 TGAAGTGCCA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (23 bp):
AATTGCACCAAAGTACCACGTAG
Found at i:1305125 original size:21 final size:21
Alignment explanation
Indices: 1305095--1305141 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
1305085 GGGGAATCGG
*
1305095 TTCCCCTTGAATGGGTACCGA
1 TTCCCATTGAATGGGTACCGA
1305116 TTCCCATTGAATGGGTACCGA
1 TTCCCATTGAATGGGTACCGA
1305137 TTCCC
1 TTCCC
1305142 CTAGCCCAGG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.19, C:0.30, G:0.21, T:0.30
Consensus pattern (21 bp):
TTCCCATTGAATGGGTACCGA
Done.