Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008521.1 Hibiscus syriacus cultivar Beakdansim tig00111388_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: 1601068
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 7
Found at i:1271808 original size:37 final size:36
Alignment explanation
Indices: 1271736--1271813 Score: 88
Period size: 37 Copynumber: 2.2 Consensus size: 36
1271726 ATTATTATTA
*
1271736 TTAT-TATTTTACTTATATATATATGCTTTTACTTTT
1 TTATATATTTTACTCATATATATATGCTTTTAC-TTT
* * *
1271772 TTATATATTTTACTCATTTATTTAT-CTATTTTCTTT
1 TTATATATTTTACTCATATATATATGCT-TTTACTTT
1271808 TTATAT
1 TTATAT
1271814 TTATCCTATA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
36 15 0.42
37 21 0.58
ACGTcount: A:0.24, C:0.09, G:0.01, T:0.65
Consensus pattern (36 bp):
TTATATATTTTACTCATATATATATGCTTTTACTTT
Found at i:1273411 original size:21 final size:21
Alignment explanation
Indices: 1273387--1273427 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1273377 AGTAAAAATT
*
1273387 TATCTAAAATATTATTATTTC
1 TATCTAAAATATTAATATTTC
1273408 TATCTAAAATATTAATATTT
1 TATCTAAAATATTAATATTT
1273428 TTTAACATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.51
Consensus pattern (21 bp):
TATCTAAAATATTAATATTTC
Found at i:1273773 original size:2 final size:2
Alignment explanation
Indices: 1273766--1273845 Score: 160
Period size: 2 Copynumber: 40.0 Consensus size: 2
1273756 ATTGTAGACG
1273766 AT AT AT AT AT 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 AT AT
1273808 AT AT AT 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
1273846 GGATTATGAT
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 78 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1274001 original size:14 final size:14
Alignment explanation
Indices: 1273975--1274015 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 14
1273965 ATTTTGAGAT
* *
1273975 TAAATTATAAAAAG
1 TAAAATATAAAAAC
1273989 TAAAAGTATAAAAAC
1 TAAAA-TATAAAAAC
1274004 TAAAATATAAAA
1 TAAAATATAAAA
1274016 TTTTAGCAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.68, C:0.02, G:0.05, T:0.24
Consensus pattern (14 bp):
TAAAATATAAAAAC
Found at i:1274347 original size:28 final size:28
Alignment explanation
Indices: 1274316--1274415 Score: 110
Period size: 28 Copynumber: 3.5 Consensus size: 28
1274306 GTTAAACGTT
1274316 AATTTTAAAATTATAGATAATAGCTTAA
1 AATTTTAAAATTATAGATAATAGCTTAA
* * * *
1274344 AATTTTAAAATTAAAGATCATAATGATGAAA
1 AATTTTAAAATTATAGATAAT-A-GCT-TAA
* * *
1274375 AAATTTAAAATTATAGACAATAACTTAA
1 AATTTTAAAATTATAGATAATAGCTTAA
1274403 AATTTTAAAATTA
1 AATTTTAAAATTA
1274416 AAGTTCAAAA
Statistics
Matches: 57, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
28 33 0.58
29 2 0.04
30 3 0.05
31 19 0.33
ACGTcount: A:0.54, C:0.04, G:0.06, T:0.36
Consensus pattern (28 bp):
AATTTTAAAATTATAGATAATAGCTTAA
Found at i:1275613 original size:2 final size:2
Alignment explanation
Indices: 1275606--1275652 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1275596 CAGCGTTTCA
1275606 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1275648 TC TC T
1 TC TC T
1275653 TTATTAAACA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1279228 original size:23 final size:24
Alignment explanation
Indices: 1279195--1279291 Score: 81
Period size: 23 Copynumber: 4.1 Consensus size: 24
1279185 TTACGTTCAC
*
1279195 TATGTTTATTTA-TTGTGTTCGTT
1 TATGTTCATTTACTTGTGTTCGTT
* * *
1279218 TACGTTCATTTA-TTATGTTCGCT
1 TATGTTCATTTACTTGTGTTCGTT
* * ***
1279241 TATGTTCGTTTACATCCATTCGTT
1 TATGTTCATTTACTTGTGTTCGTT
* *
1279265 TATGTTCATTCATTTGTGTTCGTT
1 TATGTTCATTTACTTGTGTTCGTT
1279289 TAT
1 TAT
1279292 CATTTAAATG
Statistics
Matches: 55, Mismatches: 18, Indels: 1
0.74 0.24 0.01
Matches are distributed among these distances:
23 29 0.53
24 26 0.47
ACGTcount: A:0.15, C:0.13, G:0.14, T:0.57
Consensus pattern (24 bp):
TATGTTCATTTACTTGTGTTCGTT
Found at i:1282592 original size:26 final size:26
Alignment explanation
Indices: 1282544--1282597 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
1282534 ACCAAAGTGT
* *
1282544 TAATACACATAAGGTCATTCCCATCA
1 TAATACACATAAGGTCATGCCCACCA
**
1282570 TAATACACATAAGGTTGTGCCCACCA
1 TAATACACATAAGGTCATGCCCACCA
1282596 TA
1 TA
1282598 TGCACTAAGT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.37, C:0.26, G:0.11, T:0.26
Consensus pattern (26 bp):
TAATACACATAAGGTCATGCCCACCA
Found at i:1288042 original size:2 final size:2
Alignment explanation
Indices: 1288035--1288064 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1288025 TAACCCATCC
1288035 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
1288065 GAACTTGTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1291373 original size:29 final size:29
Alignment explanation
Indices: 1291332--1291401 Score: 97
Period size: 29 Copynumber: 2.4 Consensus size: 29
1291322 ATATTTTTAT
*
1291332 ACAAAAACAAAATATATTTAATAAATTAAGA
1 ACAAAAA-TAAATATATTTAATAAATTAA-A
*
1291363 A-AAAAATAAATATATTTAATAAGTTAAA
1 ACAAAAATAAATATATTTAATAAATTAAA
1291391 ACAAAAATAAA
1 ACAAAAATAAA
1291402 GAGATAATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
28 2 0.06
29 28 0.78
30 5 0.14
31 1 0.03
ACGTcount: A:0.67, C:0.04, G:0.03, T:0.26
Consensus pattern (29 bp):
ACAAAAATAAATATATTTAATAAATTAAA
Found at i:1291670 original size:11 final size:11
Alignment explanation
Indices: 1291654--1291682 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
1291644 ATAAGTATAT
1291654 TAAATTTAAAA
1 TAAATTTAAAA
1291665 TAAA-TTAAAA
1 TAAATTTAAAA
1291675 TAAATTTA
1 TAAATTTA
1291683 GTCTTTCAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:1292854 original size:13 final size:13
Alignment explanation
Indices: 1292836--1292865 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
1292826 TAATTATACC
1292836 TATGGTAACTTAA
1 TATGGTAACTTAA
1292849 TATGGTAACTTAA
1 TATGGTAACTTAA
1292862 TATG
1 TATG
1292866 AATGCCATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.37, C:0.07, G:0.17, T:0.40
Consensus pattern (13 bp):
TATGGTAACTTAA
Found at i:1294394 original size:2 final size:2
Alignment explanation
Indices: 1294387--1294441 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
1294377 AGATTATGTG
1294387 TA TA TA TA TA TA TA TA TA 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
1294429 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
1294442 CTAACATGTG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1296274 original size:46 final size:46
Alignment explanation
Indices: 1296184--1296293 Score: 152
Period size: 46 Copynumber: 2.4 Consensus size: 46
1296174 GTCCTTTTTG
* * **
1296184 GATTTTCAACTTGAATCCTTATTTGGTTTCAAGACGTCGATTTTCCA
1 GATTTTCATCTTGAATCCTCATTTGGTTTCAAGACCCCGATTTT-CA
1296231 -ATTTTCATCTTGAATCCTCATTTGGTTTCAAGACACCCG-TTTTCA
1 GATTTTCATCTTGAATCCTCATTTGGTTTCAAGAC-CCCGATTTTCA
1296276 GATTTTCATCTTGAATCC
1 GATTTTCATCTTGAATCC
1296294 CCTTTTATTC
Statistics
Matches: 57, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
45 2 0.04
46 53 0.93
47 2 0.04
ACGTcount: A:0.23, C:0.22, G:0.13, T:0.43
Consensus pattern (46 bp):
GATTTTCATCTTGAATCCTCATTTGGTTTCAAGACCCCGATTTTCA
Found at i:1296336 original size:9 final size:9
Alignment explanation
Indices: 1296305--1296350 Score: 53
Period size: 8 Copynumber: 5.3 Consensus size: 9
1296295 CTTTTATTCT
*
1296305 TTTTTTTCTC
1 TTTTTTTC-A
1296315 TTTTTTTCA
1 TTTTTTTCA
1296324 -TTTTTTCA
1 TTTTTTTCA
1296332 -TTTTTT-A
1 TTTTTTTCA
1296339 TTTTTTTCA
1 TTTTTTTCA
1296348 TTT
1 TTT
1296351 CATTTTTTCT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
7 1 0.03
8 20 0.61
9 4 0.12
10 8 0.24
ACGTcount: A:0.09, C:0.11, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTTTTTCA
Found at i:1296359 original size:8 final size:8
Alignment explanation
Indices: 1296316--1296350 Score: 54
Period size: 8 Copynumber: 4.4 Consensus size: 8
1296306 TTTTTTCTCT
1296316 TTTTTTCA
1 TTTTTTCA
1296324 TTTTTTCA
1 TTTTTTCA
1296332 TTTTTT-A
1 TTTTTTCA
1296339 TTTTTTTCA
1 -TTTTTTCA
1296348 TTT
1 TTT
1296351 CATTTTTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
7 1 0.04
8 23 0.92
9 1 0.04
ACGTcount: A:0.11, C:0.09, G:0.00, T:0.80
Consensus pattern (8 bp):
TTTTTTCA
Found at i:1309959 original size:31 final size:31
Alignment explanation
Indices: 1309920--1310078 Score: 293
Period size: 31 Copynumber: 5.2 Consensus size: 31
1309910 GAAAGTATAG
* *
1309920 CTCT-TATTTGATTTGTATTTTATCTTCTCT
1 CTCTATATTTGATTTGTATTCTCTCTTCTCT
1309950 CTCTATATTTGATTTGTATTCTCTCTTCTCT
1 CTCTATATTTGATTTGTATTCTCTCTTCTCT
1309981 CTCTATATTTGATTTGTATTCTCTCTTCTCT
1 CTCTATATTTGATTTGTATTCTCTCTTCTCT
1310012 CTCTATATTTGATTTGTATTCTCTCTTCTCT
1 CTCTATATTTGATTTGTATTCTCTCTTCTCT
1310043 CTCTATATTTGATTTGTATTCTCTCTTCTCT
1 CTCTATATTTGATTTGTATTCTCTCTTCTCT
1310074 CTCTA
1 CTCTA
1310079 AAATTTCTCT
Statistics
Matches: 126, Mismatches: 2, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
30 4 0.03
31 122 0.97
ACGTcount: A:0.13, C:0.22, G:0.06, T:0.58
Consensus pattern (31 bp):
CTCTATATTTGATTTGTATTCTCTCTTCTCT
Found at i:1310925 original size:13 final size:13
Alignment explanation
Indices: 1310909--1310934 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1310899 ATTGGTGTTT
1310909 ATTTTGTTAAAAC
1 ATTTTGTTAAAAC
1310922 ATTTTGTTAAAAC
1 ATTTTGTTAAAAC
1310935 TCCTTTCCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (13 bp):
ATTTTGTTAAAAC
Found at i:1324753 original size:2 final size:2
Alignment explanation
Indices: 1324746--1324798 Score: 61
Period size: 2 Copynumber: 26.5 Consensus size: 2
1324736 GTATGTGTAT
* * * *
1324746 AC AC AC AC AC AC AT AC AC AC AC AT AT AC AT AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
*
1324788 AT AC AC AC AC A
1 AC AC AC AC AC A
1324799 TATATATAGC
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.40, G:0.00, T:0.09
Consensus pattern (2 bp):
AC
Found at i:1324765 original size:10 final size:10
Alignment explanation
Indices: 1324750--1324800 Score: 75
Period size: 10 Copynumber: 5.1 Consensus size: 10
1324740 GTGTATACAC
1324750 ACACACACAT
1 ACACACACAT
1324760 ACACACACAT
1 ACACACACAT
* * *
1324770 ATACATACAC
1 ACACACACAT
1324780 ACACACACAT
1 ACACACACAT
1324790 ACACACACAT
1 ACACACACAT
1324800 A
1 A
1324801 TATATAGCAC
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 35 1.00
ACGTcount: A:0.51, C:0.37, G:0.00, T:0.12
Consensus pattern (10 bp):
ACACACACAT
Found at i:1324780 original size:30 final size:30
Alignment explanation
Indices: 1324744--1324811 Score: 118
Period size: 30 Copynumber: 2.2 Consensus size: 30
1324734 GTGTATGTGT
1324744 ATACACACACACACATACACACACATATAC
1 ATACACACACACACATACACACACATATAC
*
1324774 ATACACACACACACATACACACACATATAT
1 ATACACACACACACATACACACACATATAC
1324804 ATAGCACA
1 ATA-CACA
1324812 TATATAGCTA
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
30 32 0.89
31 4 0.11
ACGTcount: A:0.50, C:0.34, G:0.01, T:0.15
Consensus pattern (30 bp):
ATACACACACACACATACACACACATATAC
Found at i:1331146 original size:21 final size:21
Alignment explanation
Indices: 1331113--1331152 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1331103 AATTTGAAAT
1331113 AAAAAATTAAACTC-AAACTC
1 AAAAAATTAAACTCGAAACTC
*
1331133 AAAAAATTTTAACTCGAAAC
1 AAAAAA-TTAAACTCGAAAC
1331153 ATTCTCCAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 7 0.41
22 4 0.24
ACGTcount: A:0.57, C:0.17, G:0.03, T:0.23
Consensus pattern (21 bp):
AAAAAATTAAACTCGAAACTC
Found at i:1331872 original size:42 final size:40
Alignment explanation
Indices: 1331826--1331950 Score: 121
Period size: 42 Copynumber: 3.0 Consensus size: 40
1331816 TTTATTCTGT
*
1331826 ATTATTA-AATTATATTATTTAATTATTGAAAATATAA-AA
1 ATTATTATAAATATATTATTTAATTATT-AAAATATAATAA
*
1331865 TTTATTATAAAATATATTATTTTAACATT-TTAAAATATAATAA
1 ATTATTAT-AAATATATTA-TTT-A-ATTATTAAAATATAATAA
*
1331908 ATAATTATAAATATATTATTATAATTATTTTAAAATATTAATA
1 ATTATTATAAATATATTATT-TAATTA--TTAAAATA-TAATA
1331951 TACTCAGATC
Statistics
Matches: 71, Mismatches: 4, Indels: 17
0.77 0.04 0.18
Matches are distributed among these distances:
39 6 0.08
40 3 0.04
41 12 0.17
42 23 0.32
43 19 0.27
44 8 0.11
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (40 bp):
ATTATTATAAATATATTATTTAATTATTAAAATATAATAA
Found at i:1331931 original size:24 final size:23
Alignment explanation
Indices: 1331904--1331952 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
1331894 TTAAAATATA
*
1331904 ATAAATAATTATAAATATATTATT
1 ATAAATAATTATAAA-ATATTAAT
* *
1331928 AT-AATTATTTTAAAATATTAAT
1 ATAAATAATTATAAAATATTAAT
1331950 ATA
1 ATA
1331953 CTCAGATCAG
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
22 9 0.43
23 10 0.48
24 2 0.10
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
ATAAATAATTATAAAATATTAAT
Found at i:1340791 original size:15 final size:15
Alignment explanation
Indices: 1340771--1340805 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
1340761 AGACATTACT
*
1340771 CGCCCCGCATCCGCC
1 CGCCCCACATCCGCC
1340786 CGCCCCACATCCGCC
1 CGCCCCACATCCGCC
1340801 CGCCC
1 CGCCC
1340806 AGCTAAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.09, C:0.69, G:0.17, T:0.06
Consensus pattern (15 bp):
CGCCCCACATCCGCC
Found at i:1343520 original size:21 final size:21
Alignment explanation
Indices: 1343496--1343537 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1343486 AGTTTATTTT
1343496 TAAACTTTATTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
*
1343517 TAAACTTTGTTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
1343538 AACTTGAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.14, G:0.07, T:0.48
Consensus pattern (21 bp):
TAAACTTTATTTCAATTATCG
Found at i:1343585 original size:33 final size:32
Alignment explanation
Indices: 1343530--1343634 Score: 158
Period size: 33 Copynumber: 3.2 Consensus size: 32
1343520 ACTTTGTTTC
1343530 AATTATCGAACTT-GAAGTTTTTAAGTATTTG
1 AATTATCGAACTTGGAAGTTTTTAAGTATTTG
1343561 AATGTATCGAACTTGGAAGTTTTTAAGTATTTG
1 AAT-TATCGAACTTGGAAGTTTTTAAGTATTTG
* * *
1343594 AATTTATCAAACTTGGAAGTATTTAAGTATTTC
1 AA-TTATCGAACTTGGAAGTTTTTAAGTATTTG
1343627 AATTATCG
1 AATTATCG
1343635 TAAACTTTGT
Statistics
Matches: 67, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
31 3 0.04
32 15 0.22
33 48 0.72
34 1 0.01
ACGTcount: A:0.33, C:0.08, G:0.16, T:0.43
Consensus pattern (32 bp):
AATTATCGAACTTGGAAGTTTTTAAGTATTTG
Found at i:1343847 original size:15 final size:17
Alignment explanation
Indices: 1343821--1343852 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1343811 TTCTATGGGA
1343821 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
1343837 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
1343853 CGGATTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (17 bp):
AAAAACCGGATCCGGAT
Found at i:1345884 original size:22 final size:22
Alignment explanation
Indices: 1345843--1345883 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1345833 TGAAAAATAT
1345843 CAAGCAAAGCCGGTGCCCCCAC
1 CAAGCAAAGCCGGTGCCCCCAC
*
1345865 CAAGC-AAGCTGGTGCCCCC
1 CAAGCAAAGCCGGTGCCCCC
1345884 CTTTGACTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.24, C:0.44, G:0.24, T:0.07
Consensus pattern (22 bp):
CAAGCAAAGCCGGTGCCCCCAC
Found at i:1349887 original size:16 final size:17
Alignment explanation
Indices: 1349859--1349891 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
1349849 ATCGCCGACA
1349859 AAATTTCACTATTCACG
1 AAATTTCACTATTCACG
1349876 AAATTT-ACTATTCACG
1 AAATTTCACTATTCACG
1349892 TGAATAGTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.36, C:0.21, G:0.06, T:0.36
Consensus pattern (17 bp):
AAATTTCACTATTCACG
Found at i:1352417 original size:2 final size:2
Alignment explanation
Indices: 1352405--1352434 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1352395 ATTTTGAAGA
*
1352405 AT AT AT TT 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
1352435 TGTAATTTAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:1354024 original size:44 final size:43
Alignment explanation
Indices: 1353941--1354093 Score: 138
Period size: 43 Copynumber: 3.6 Consensus size: 43
1353931 TATATAGGAG
1353941 AAAA-TGAGATT-AAAAAAATTAGG-GACTTCAATTATAAAGTTA
1 AAAAGTGAGATTGAAAAAAA-TAGGAGAC-TCAATTATAAAGTTA
*
1353983 TAAAGTGAGATTGAAAAAAATAGGAG-CTACAATTATAAAAG-TA
1 AAAAGTGAGATTGAAAAAAATAGGAGACT-CAATTAT-AAAGTTA
* * * * * *
1354026 AAAAATGAAATTGAAAAAATTAAGAGTCTCAGTTATAAA-TATA
1 AAAAGTGAGATTGAAAAAAATAGGAGACTCAATTATAAAGT-TA
* *
1354069 AAAAGTGAGACTGAAAAAATTAGGA
1 AAAAGTGAGATTGAAAAAAATAGGA
1354094 ATTAAAAACA
Statistics
Matches: 92, Mismatches: 11, Indels: 15
0.78 0.09 0.13
Matches are distributed among these distances:
42 7 0.08
43 71 0.77
44 14 0.15
ACGTcount: A:0.54, C:0.05, G:0.16, T:0.25
Consensus pattern (43 bp):
AAAAGTGAGATTGAAAAAAATAGGAGACTCAATTATAAAGTTA
Found at i:1358470 original size:19 final size:19
Alignment explanation
Indices: 1358438--1358501 Score: 73
Period size: 17 Copynumber: 3.5 Consensus size: 19
1358428 TTCATTGAAA
1358438 AACCGAAAAA-TCGAACCG
1 AACCGAAAAACTCGAACCG
1358456 AACCGAAAAACTCGAACCG
1 AACCGAAAAACTCGAACCG
* *
1358475 TTA---AAAAACCCGAACCG
1 -AACCGAAAAACTCGAACCG
1358492 AACCGAAAAA
1 AACCGAAAAA
1358502 ACCGGTTTCG
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
16 1 0.03
17 13 0.34
18 10 0.26
19 13 0.34
20 1 0.03
ACGTcount: A:0.52, C:0.28, G:0.14, T:0.06
Consensus pattern (19 bp):
AACCGAAAAACTCGAACCG
Found at i:1364616 original size:64 final size:63
Alignment explanation
Indices: 1364534--1364690 Score: 167
Period size: 64 Copynumber: 2.5 Consensus size: 63
1364524 TTCAGTGTGT
* * * *
1364534 ATCGATGCACAGGAAGTGCATCGATGCACCC-CTTAAAAATGGAAATATCGAA-TGCAATTAGTG
1 ATCGATGCATAGGGAGTGCATCGATGCACCCGC-TAAAAATGAAAACATCGAAGTGC--TTAGTG
1364597 C
63 C
* * * * *
1364598 ATCGATGCATAGGGAGTGCATCGATACACCCGCTAAAGATTAAAACATCGAAGGTGCTTTGTGT
1 ATCGATGCATAGGGAGTGCATCGATGCACCCGCTAAAAATGAAAACATCGAA-GTGCTTAGTGC
1364662 ATCGATGCAT-GGGTAGTGCATCGATGCAC
1 ATCGATGCATAGGG-AGTGCATCGATGCAC
1364691 ATGTTAAGGG
Statistics
Matches: 79, Mismatches: 10, Indels: 8
0.81 0.10 0.08
Matches are distributed among these distances:
63 3 0.04
64 72 0.91
65 1 0.01
66 3 0.04
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.24
Consensus pattern (63 bp):
ATCGATGCATAGGGAGTGCATCGATGCACCCGCTAAAAATGAAAACATCGAAGTGCTTAGTGC
Found at i:1365803 original size:2 final size:2
Alignment explanation
Indices: 1365796--1365829 Score: 52
Period size: 2 Copynumber: 17.0 Consensus size: 2
1365786 AGGTAAAATG
1365796 AT AT AT AT AT AT AT AT AT AT AT A- ACT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
1365830 GACTATGAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 1 0.03
2 28 0.93
3 1 0.03
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1365834 original size:12 final size:11
Alignment explanation
Indices: 1365796--1365835 Score: 50
Period size: 10 Copynumber: 3.8 Consensus size: 11
1365786 AGGTAAAATG
1365796 ATATA-TATAT
1 ATATACTATAT
1365806 ATATA-TATAT
1 ATATACTATAT
1365816 ATA-ACTATAT
1 ATATACTATAT
1365826 ATATGACTAT
1 ATAT-ACTAT
1365836 GAGTTGGAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
9 1 0.04
10 21 0.78
12 5 0.19
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (11 bp):
ATATACTATAT
Found at i:1366399 original size:23 final size:23
Alignment explanation
Indices: 1366339--1366392 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
1366329 ACATTTTATA
1366339 TGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
* *
1366362 TAGTACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
1366385 TGGCACTT
1 TGGCACTT
1366393 TGCTGCATTT
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:0.19, C:0.24, G:0.24, T:0.33
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:1366695 original size:32 final size:32
Alignment explanation
Indices: 1366654--1366743 Score: 162
Period size: 32 Copynumber: 2.8 Consensus size: 32
1366644 CTAAGTAAGC
*
1366654 AACACACCATAACAAACTAATAACAAGCTAAT
1 AACAAACCATAACAAACTAATAACAAGCTAAT
*
1366686 AACAAACCATAACAAACTAATAACAAGCTGAT
1 AACAAACCATAACAAACTAATAACAAGCTAAT
1366718 AACAAACCATAACAAACTAATAACAA
1 AACAAACCATAACAAACTAATAACAA
1366744 ATACTAACTA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 56 1.00
ACGTcount: A:0.59, C:0.23, G:0.03, T:0.14
Consensus pattern (32 bp):
AACAAACCATAACAAACTAATAACAAGCTAAT
Found at i:1366697 original size:21 final size:22
Alignment explanation
Indices: 1366662--1366744 Score: 107
Period size: 21 Copynumber: 3.9 Consensus size: 22
1366652 GCAACACACC
*
1366662 ATAACAAACTAATAACAAGCTA
1 ATAACAAACTAATAACAAACTA
*
1366684 ATAACAAAC-CATAACAAACTA
1 ATAACAAACTAATAACAAACTA
* * *
1366705 ATAACAAGCTGATAACAAAC-C
1 ATAACAAACTAATAACAAACTA
1366726 ATAACAAACTAATAACAAA
1 ATAACAAACTAATAACAAA
1366745 TACTAACTAA
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
21 35 0.66
22 18 0.34
ACGTcount: A:0.60, C:0.20, G:0.04, T:0.16
Consensus pattern (22 bp):
ATAACAAACTAATAACAAACTA
Found at i:1366751 original size:10 final size:11
Alignment explanation
Indices: 1366662--1366744 Score: 107
Period size: 11 Copynumber: 7.7 Consensus size: 11
1366652 GCAACACACC
1366662 ATAACAAACTA
1 ATAACAAACTA
*
1366673 ATAACAAGCTA
1 ATAACAAACTA
*
1366684 ATAACAAAC-C
1 ATAACAAACTA
1366694 ATAACAAACTA
1 ATAACAAACTA
* *
1366705 ATAACAAGCTG
1 ATAACAAACTA
*
1366716 ATAACAAAC-C
1 ATAACAAACTA
1366726 ATAACAAACTA
1 ATAACAAACTA
1366737 ATAACAAA
1 ATAACAAA
1366745 TACTAACTAA
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
10 18 0.30
11 43 0.70
ACGTcount: A:0.60, C:0.20, G:0.04, T:0.16
Consensus pattern (11 bp):
ATAACAAACTA
Found at i:1366889 original size:36 final size:36
Alignment explanation
Indices: 1366849--1367314 Score: 506
Period size: 36 Copynumber: 12.9 Consensus size: 36
1366839 CGATACATCT
*
1366849 TTCCGTTCGACTTGAATCGGAAGTGGCGATGCTTCC
1 TTCCGTTCGACTTGAATCGGAAGTGCCGATGCTTCC
* * *
1366885 TTCCGTTTTGATTTGAATCGGAAGTGTCGATGCTTCC
1 TTCCG-TTCGACTTGAATCGGAAGTGCCGATGCTTCC
* * * ** * * * *
1366922 TTCCATTCAATTTGAATATGAAATGCTGATGCCTCA
1 TTCCGTTCGACTTGAATCGGAAGTGCCGATGCTTCC
* * * *
1366958 TTCCGTTCGATTTGAATCGAAAGTGCTGATGCCTCC
1 TTCCGTTCGACTTGAATCGGAAGTGCCGATGCTTCC
** *
1366994 TTCCGTTCGACTTGAATCGGAAGTGTTGATGCCTCC
1 TTCCGTTCGACTTGAATCGGAAGTGCCGATGCTTCC
* *
1367030 TTCCATTCGACTTGAATCGGAAGTGCCGATGCCTT-A
1 TTCCGTTCGACTTGAATCGGAAGTGCCGATG-CTTCC
* * *
1367066 TTCTGTTCAACTTGAATCGGAAGTGTCGATGCCTT-C
1 TTCCGTTCGACTTGAATCGGAAGTGCCGATG-CTTCC
* * * *
1367102 TTCCGTTCGACTTGAATCGGAAGTGTCAATCCCTCC
1 TTCCGTTCGACTTGAATCGGAAGTGCCGATGCTTCC
* * * *
1367138 TTTCGTTCGAATTGAATCAGAAGTGCCAATGCCTT-C
1 TTCCGTTCGACTTGAATCGGAAGTGCCGATG-CTTCC
* * * *
1367174 TTCCATTTGACTTGAATCGAAAGTGCCGATGCCTCC
1 TTCCGTTCGACTTGAATCGGAAGTGCCGATGCTTCC
* *
1367210 TTCCGTTCGACTTGAATCGGAAGTGCCGATGCCTCA
1 TTCCGTTCGACTTGAATCGGAAGTGCCGATGCTTCC
*
1367246 TTCCGTTCGACTTGAATCGGAAGTGCTGATGCTTCC
1 TTCCGTTCGACTTGAATCGGAAGTGCCGATGCTTCC
*
1367282 TTCCATTCGACTTGAATCGGAAGTGCCGATGCT
1 TTCCGTTCGACTTGAATCGGAAGTGCCGATGCT
1367315 AACTTTACCA
Statistics
Matches: 364, Mismatches: 61, Indels: 10
0.84 0.14 0.02
Matches are distributed among these distances:
35 4 0.01
36 324 0.89
37 36 0.10
ACGTcount: A:0.20, C:0.24, G:0.22, T:0.33
Consensus pattern (36 bp):
TTCCGTTCGACTTGAATCGGAAGTGCCGATGCTTCC
Found at i:1367061 original size:108 final size:108
Alignment explanation
Indices: 1366849--1367313 Score: 572
Period size: 108 Copynumber: 4.3 Consensus size: 108
1366839 CGATACATCT
* * * *
1366849 TTCCGTTCGACTTGAATCGGAAGTGGCGATGCTTCCTTCCGTTTTGATTTGAATCGGAAGTGTCG
1 TTCCGTTCGACTTGAATCGGAAGTGCCGATGCCTCCTTCCG-TTCGACTTGAATCGGAAGTGTCG
* * * ** * *
1366914 ATGCTTCCTTCCATTCAATTTGAATATGAAATGCTGATGCCTCA
65 ATGCCTCCTTCCATTCGACTTGAATCGGAAGTGCCGATGCCTCA
* * * *
1366958 TTCCGTTCGATTTGAATCGAAAGTGCTGATGCCTCCTTCCGTTCGACTTGAATCGGAAGTGTTGA
1 TTCCGTTCGACTTGAATCGGAAGTGCCGATGCCTCCTTCCGTTCGACTTGAATCGGAAGTGTCGA
*
1367023 TGCCTCCTTCCATTCGACTTGAATCGGAAGTGCCGATGCCTTA
66 TGCCTCCTTCCATTCGACTTGAATCGGAAGTGCCGATGCCTCA
* * * * *
1367066 TTCTGTTCAACTTGAATCGGAAGTGTCGATGCCTTCTTCCGTTCGACTTGAATCGGAAGTGTCAA
1 TTCCGTTCGACTTGAATCGGAAGTGCCGATGCCTCCTTCCGTTCGACTTGAATCGGAAGTGTCGA
* * * * * *
1367131 TCCCTCCTTTCGTTCGAATTGAATCAGAAGTGCCAATGCCTTC-
66 TGCCTCCTTCCATTCGACTTGAATCGGAAGTGCCGATGCC-TCA
* * * *
1367174 TTCCATTTGACTTGAATCGAAAGTGCCGATGCCTCCTTCCGTTCGACTTGAATCGGAAGTGCCGA
1 TTCCGTTCGACTTGAATCGGAAGTGCCGATGCCTCCTTCCGTTCGACTTGAATCGGAAGTGTCGA
* * * * *
1367239 TGCCTCATTCCGTTCGACTTGAATCGGAAGTGCTGATGCTTCC
66 TGCCTCCTTCCATTCGACTTGAATCGGAAGTGCCGATGCCTCA
*
1367282 TTCCATTCGACTTGAATCGGAAGTGCCGATGC
1 TTCCGTTCGACTTGAATCGGAAGTGCCGATGC
1367314 TAACTTTACC
Statistics
Matches: 303, Mismatches: 51, Indels: 5
0.84 0.14 0.01
Matches are distributed among these distances:
107 2 0.01
108 264 0.87
109 37 0.12
ACGTcount: A:0.20, C:0.25, G:0.22, T:0.33
Consensus pattern (108 bp):
TTCCGTTCGACTTGAATCGGAAGTGCCGATGCCTCCTTCCGTTCGACTTGAATCGGAAGTGTCGA
TGCCTCCTTCCATTCGACTTGAATCGGAAGTGCCGATGCCTCA
Found at i:1367516 original size:21 final size:20
Alignment explanation
Indices: 1367488--1367526 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
1367478 CCTGCTGGGA
1367488 TTTCAG-TTCTATAGAACCTT
1 TTTCAGTTTCT-TAGAACCTT
1367508 TTTCTAGTTTCTTAGAACC
1 TTTC-AGTTTCTTAGAACC
1367527 AGTAGAGTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 4 0.24
21 9 0.53
22 4 0.24
ACGTcount: A:0.23, C:0.21, G:0.10, T:0.46
Consensus pattern (20 bp):
TTTCAGTTTCTTAGAACCTT
Found at i:1368441 original size:10 final size:11
Alignment explanation
Indices: 1368362--1368434 Score: 103
Period size: 11 Copynumber: 6.7 Consensus size: 11
1368352 GCAACACACC
1368362 ATAACAAACTA
1 ATAACAAACTA
*
1368373 ATAACAAGCTA
1 ATAACAAACTA
1368384 ATAACAAACTA
1 ATAACAAACTA
* *
1368395 ATAACAAGCTG
1 ATAACAAACTA
*
1368406 ATAACAAAC-C
1 ATAACAAACTA
1368416 ATAACAAACTA
1 ATAACAAACTA
1368427 ATAACAAA
1 ATAACAAA
1368435 TACTAACTAA
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
10 9 0.17
11 45 0.83
ACGTcount: A:0.60, C:0.19, G:0.04, T:0.16
Consensus pattern (11 bp):
ATAACAAACTA
Found at i:1372656 original size:16 final size:16
Alignment explanation
Indices: 1372637--1372668 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1372627 AGGTAAAATG
1372637 ATATATATATAACTAT
1 ATATATATATAACTAT
*
1372653 ATATATATATGACTAT
1 ATATATATATAACTAT
1372669 GAGTTGAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (16 bp):
ATATATATATAACTAT
Found at i:1373566 original size:23 final size:23
Alignment explanation
Indices: 1373498--1373560 Score: 101
Period size: 23 Copynumber: 2.8 Consensus size: 23
1373488 ACATTTTATA
1373498 TGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
*
1373521 CGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
*
1373544 TGGCACTTTGGTG-AATT
1 TGGCACTTCGGTGCAATT
1373561 TATACGAGCT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
22 4 0.11
23 33 0.89
ACGTcount: A:0.17, C:0.24, G:0.27, T:0.32
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:1377666 original size:23 final size:23
Alignment explanation
Indices: 1377622--1377666 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
1377612 ATTTCTACAC
* *
1377622 GGCACTTCGGTGGAATTCTATGT
1 GGCACTTCGGTGCAATTATATGT
* *
1377645 GGCACTTTGGTGCATTTATATG
1 GGCACTTCGGTGCAATTATATG
1377667 AGTTGTGGTG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.18, C:0.16, G:0.29, T:0.38
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTATATGT
Found at i:1377946 original size:12 final size:12
Alignment explanation
Indices: 1377929--1377986 Score: 53
Period size: 12 Copynumber: 4.8 Consensus size: 12
1377919 ATATATTACA
1377929 TGATAATGATAT
1 TGATAATGATAT
* *
1377941 TGATAATAATAG
1 TGATAATGATAT
* * *
1377953 AGATCATGATAA
1 TGATAATGATAT
**
1377965 TGATGTTGATAT
1 TGATAATGATAT
1377977 TGATAATGAT
1 TGATAATGAT
1377987 GGTATATGTG
Statistics
Matches: 34, Mismatches: 12, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
12 34 1.00
ACGTcount: A:0.41, C:0.02, G:0.19, T:0.38
Consensus pattern (12 bp):
TGATAATGATAT
Found at i:1381684 original size:14 final size:15
Alignment explanation
Indices: 1381665--1381696 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1381655 CCGTAGACCC
1381665 CTACATCC-GAAGGA
1 CTACATCCTGAAGGA
1381679 CTACATCCTGAAGGA
1 CTACATCCTGAAGGA
1381694 CTA
1 CTA
1381697 TTATACCCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.34, C:0.28, G:0.19, T:0.19
Consensus pattern (15 bp):
CTACATCCTGAAGGA
Found at i:1381845 original size:23 final size:26
Alignment explanation
Indices: 1381808--1381860 Score: 85
Period size: 23 Copynumber: 2.2 Consensus size: 26
1381798 TTCTCTTGTG
1381808 ATCATGTATCTCATATCAC-T-TCAT
1 ATCATGTATCTCATATCACATGTCAT
1381832 ATCATGT-TCTCATATCACATGTCAT
1 ATCATGTATCTCATATCACATGTCAT
1381857 ATCA
1 ATCA
1381861 CATATATGTC
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
23 11 0.41
24 8 0.30
25 8 0.30
ACGTcount: A:0.30, C:0.25, G:0.06, T:0.40
Consensus pattern (26 bp):
ATCATGTATCTCATATCACATGTCAT
Found at i:1382269 original size:64 final size:63
Alignment explanation
Indices: 1382176--1382336 Score: 202
Period size: 64 Copynumber: 2.5 Consensus size: 63
1382166 TAATGAAGGT
* **
1382176 ATGCATCGATGCACT-CCTATGCATCGATGCACCAATTGCATTCGATG-TTTCATTATTAATGGG
1 ATGCATCGATGCACTACCTATGCATCGATGCACCAATTGCATTCAATGTTTTCATT-TTAA-AAG
** *
1382239 ATGCATCGATGCACTACCTATGCATCGATGCATGAATTGCATTCAATGTTTTTATTTTAAAAG
1 ATGCATCGATGCACTACCTATGCATCGATGCACCAATTGCATTCAATGTTTTCATTTTAAAAG
*
1382302 AGTGCATCGATGCACTA-CTAATGCATCGATACACC
1 A-TGCATCGATGCACTACCT-ATGCATCGATGCACC
1382337 TTCAAACAAT
Statistics
Matches: 85, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
63 19 0.22
64 60 0.71
65 6 0.07
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (63 bp):
ATGCATCGATGCACTACCTATGCATCGATGCACCAATTGCATTCAATGTTTTCATTTTAAAAG
Found at i:1388587 original size:23 final size:26
Alignment explanation
Indices: 1388553--1388605 Score: 85
Period size: 23 Copynumber: 2.2 Consensus size: 26
1388543 TTCTCTTGTG
1388553 ATCATGTATCTCATATCAC-T-TCAT
1 ATCATGTATCTCATATCACATGTCAT
1388577 ATCATGT-TCTCATATCACATGTCAT
1 ATCATGTATCTCATATCACATGTCAT
1388602 ATCA
1 ATCA
1388606 CATATCATCA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
23 11 0.41
24 8 0.30
25 8 0.30
ACGTcount: A:0.30, C:0.25, G:0.06, T:0.40
Consensus pattern (26 bp):
ATCATGTATCTCATATCACATGTCAT
Found at i:1389067 original size:60 final size:60
Alignment explanation
Indices: 1388921--1389094 Score: 165
Period size: 63 Copynumber: 2.8 Consensus size: 60
1388911 TAATGAAGGT
* * * ** * *
1388921 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAAGGTATTCGATGTATTATTATTGTGGG
1 ATGCATCGATGCACTACTTATGCATC-GAGCA-CAATTGCATTCGATGT-TTATTATTATGGG
*
1388984 ATGCATCGATGCACTCCTTATGCATCGA-C-CAATTGCATTCGATGTTTCATTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGAGCACAATTGCATTCGATGTTT-ATTATT-ATGGG
* *
1389044 ATGGCATCGATTCA-TACTTATGCATCGATGCATGAATTGCATTCGATGTTT
1 AT-GCATCGATGCACTACTTATGCATCGA-GCA-CAATTGCATTCGATGTTT
1389095 TATTTAAAAA
Statistics
Matches: 93, Mismatches: 11, Indels: 13
0.79 0.09 0.11
Matches are distributed among these distances:
58 2 0.02
59 18 0.19
60 19 0.20
61 11 0.12
62 2 0.02
63 24 0.26
64 17 0.18
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (60 bp):
ATGCATCGATGCACTACTTATGCATCGAGCACAATTGCATTCGATGTTTATTATTATGGG
Found at i:1390719 original size:15 final size:15
Alignment explanation
Indices: 1390699--1390730 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1390689 TAAGACATTA
*
1390699 CCCGCCCCGCATCCG
1 CCCGCCCAGCATCCG
1390714 CCCGCCCAGCATCCG
1 CCCGCCCAGCATCCG
1390729 CC
1 CC
1390731 GTCCAGCTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.09, C:0.66, G:0.19, T:0.06
Consensus pattern (15 bp):
CCCGCCCAGCATCCG
Found at i:1390901 original size:24 final size:24
Alignment explanation
Indices: 1390850--1390901 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
1390840 TAGGGATATT
* *
1390850 TAGTCTTTAATCTGATCTCTTCTT
1 TAGTCTTTAATCTGATCTCTTATG
*
1390874 TAGTCTTTAATCTGGTC-CTTATCG
1 TAGTCTTTAATCTGATCTCTTAT-G
1390898 TAGT
1 TAGT
1390902 TGACTACTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 4 0.17
24 20 0.83
ACGTcount: A:0.17, C:0.19, G:0.13, T:0.50
Consensus pattern (24 bp):
TAGTCTTTAATCTGATCTCTTATG
Found at i:1404410 original size:24 final size:25
Alignment explanation
Indices: 1404377--1404425 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
1404367 TATGTTTTCT
*
1404377 AAAATGAAGTCTTTAATTT-AATTTA
1 AAAATGAAGT-TTAAATTTAAATTTA
1404402 AAAAT-AAGTTTAAATTTAAATTTA
1 AAAATGAAGTTTAAATTTAAATTTA
1404426 TTATTACATC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 7 0.32
24 10 0.45
25 5 0.23
ACGTcount: A:0.49, C:0.02, G:0.06, T:0.43
Consensus pattern (25 bp):
AAAATGAAGTTTAAATTTAAATTTA
Found at i:1404965 original size:35 final size:29
Alignment explanation
Indices: 1404884--1405132 Score: 145
Period size: 30 Copynumber: 8.4 Consensus size: 29
1404874 TCAACTTATT
* *
1404884 AAATATATTATAATTTTATTTTAACTTAA
1 AAATATATTTTAATCTTATTTTAACTTAA
1404913 AAATATATTTTAATCTTATTTTAACTTAAA
1 AAATATATTTTAATCTTATTTTAACTT-AA
* * * * *
1404943 AAATATACTTTATTCCTATCTTAATTTTTAA
1 AAATATATTTTAATCTTATTTTAA--CTTAA
* * *
1404974 AAATATATTTTTAATTAAATTCACATATTAAAATTAA
1 AAATATA-TTTTAA-T--CTT---AT-TTTAACTTAA
**
1405011 AAATATATTTT-ATCTTAACTT-A-TT--
1 AAATATATTTTAATCTTATTTTAACTTAA
* *
1405035 AAATATATTTTATTCTTATTTTAAATTCAA
1 AAATATATTTTAATCTTATTTTAACTT-AA
* * *
1405065 AATTTTATTTTAATCTTATTTTAGCTT--
1 AAATATATTTTAATCTTATTTTAACTTAA
* * *
1405092 AAA-ATATTTTATTTTTATTTTAACTTATG
1 AAATATATTTTAATCTTATTTTAACTTA-A
1405121 AAATATATTTTA
1 AAATATATTTTA
1405133 CTTTTATAGT
Statistics
Matches: 168, Mismatches: 31, Indels: 41
0.70 0.13 0.17
Matches are distributed among these distances:
24 11 0.07
25 7 0.04
26 22 0.13
27 5 0.03
28 1 0.01
29 29 0.17
30 52 0.31
31 9 0.05
32 8 0.05
33 1 0.01
34 1 0.01
35 2 0.01
36 4 0.02
37 11 0.07
38 2 0.01
39 3 0.02
ACGTcount: A:0.40, C:0.06, G:0.01, T:0.53
Consensus pattern (29 bp):
AAATATATTTTAATCTTATTTTAACTTAA
Found at i:1405028 original size:24 final size:26
Alignment explanation
Indices: 1405001--1405052 Score: 65
Period size: 24 Copynumber: 2.1 Consensus size: 26
1404991 AATTCACATA
1405001 TTAAAATTA-AAAATATATTTTA-TC
1 TTAAAATTATAAAATATATTTTATTC
* *
1405025 TT-AACTTATTAAATATATTTTATTC
1 TTAAAATTATAAAATATATTTTATTC
1405050 TTA
1 TTA
1405053 TTTTAAATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
23 5 0.22
24 14 0.61
25 4 0.17
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (26 bp):
TTAAAATTATAAAATATATTTTATTC
Found at i:1405130 original size:56 final size:54
Alignment explanation
Indices: 1405004--1405132 Score: 138
Period size: 56 Copynumber: 2.4 Consensus size: 54
1404994 TCACATATTA
*
1405004 AAATTAAAAATATATTTT-ATCTTAACTTATTAAATATATTTTATTCTTATTTT
1 AAATTCAAAATATATTTTAATCTTAACTTATTAAATATATTTTATTCTTATTTT
* ** *
1405057 AAATTCAAAATTTTATTTTAATCTTATTTTAGCTTAAA-ATATTTTATTTTTATTTT
1 AAATTCAAAA-TATATTTTAATCTTAACTTA--TTAAATATATTTTATTCTTATTTT
*
1405113 AACTT-ATGAAATATATTTTA
1 AAATTCA--AAATATATTTTA
1405133 CTTTTATAGT
Statistics
Matches: 63, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
53 9 0.14
54 7 0.11
55 10 0.16
56 29 0.46
57 8 0.13
ACGTcount: A:0.38, C:0.05, G:0.02, T:0.55
Consensus pattern (54 bp):
AAATTCAAAATATATTTTAATCTTAACTTATTAAATATATTTTATTCTTATTTT
Found at i:1405199 original size:30 final size:30
Alignment explanation
Indices: 1405163--1405247 Score: 107
Period size: 30 Copynumber: 2.8 Consensus size: 30
1405153 AGATTTTTAA
* * *
1405163 AAGTTAATAGAAGAATAAGATATATCTTTT
1 AAGTTAAAATAAGAATAAAATATATCTTTT
* *
1405193 AAGTTAAAATAAGATTAAAATATATTTTTT
1 AAGTTAAAATAAGAATAAAATATATCTTTT
* *
1405223 AAATTAAAATAAAAATAAAATATAT
1 AAGTTAAAATAAGAATAAAATATAT
1405248 TTAATGAGTT
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 47 1.00
ACGTcount: A:0.55, C:0.01, G:0.07, T:0.36
Consensus pattern (30 bp):
AAGTTAAAATAAGAATAAAATATATCTTTT
Found at i:1405248 original size:30 final size:30
Alignment explanation
Indices: 1405176--1405290 Score: 113
Period size: 30 Copynumber: 3.8 Consensus size: 30
1405166 TTAATAGAAG
* * * *
1405176 AATAAGATATATCTTTTAAGTTAAAATAAG
1 AATAAAATATATTTTTTAAATTAAAATAAA
*
1405206 ATTAAAATATATTTTTTAAATTAAAATAAA
1 AATAAAATATATTTTTTAAATTAAAATAAA
** * * *
1405236 AATAAAATATATTTAATGAGTTAAGATAAA
1 AATAAAATATATTTTTTAAATTAAAATAAA
**
1405266 AATAGTATATATTTTTTAATATTAA
1 AATAAAATATATTTTTTAA-ATTAA
1405291 GATAGGAATA
Statistics
Matches: 67, Mismatches: 17, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
30 63 0.94
31 4 0.06
ACGTcount: A:0.52, C:0.01, G:0.06, T:0.41
Consensus pattern (30 bp):
AATAAAATATATTTTTTAAATTAAAATAAA
Found at i:1428216 original size:50 final size:50
Alignment explanation
Indices: 1428127--1428221 Score: 129
Period size: 49 Copynumber: 1.9 Consensus size: 50
1428117 CATTAATCAA
* * * *
1428127 GAAGGAGGTTTTTAATGAGGCCTTCAAATCTTATCAAAAAAAATAATTAT
1 GAAGGAGGGTTTTAACGAGGCCTCCAAATCTTATAAAAAAAAATAATTAT
*
1428177 GAAGG-GGGTTTTAACGAGGCCTCCAATTCTTATAAAAAAACAATA
1 GAAGGAGGGTTTTAACGAGGCCTCCAAATCTTATAAAAAAA-AATA
1428222 TGGCTAAAGA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
49 30 0.77
50 9 0.23
ACGTcount: A:0.41, C:0.13, G:0.18, T:0.28
Consensus pattern (50 bp):
GAAGGAGGGTTTTAACGAGGCCTCCAAATCTTATAAAAAAAAATAATTAT
Found at i:1433854 original size:18 final size:18
Alignment explanation
Indices: 1433821--1433856 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1433811 AAGCAAAAGG
**
1433821 AAATCAAAATTGCAATCA
1 AAATCAAAATCCCAATCA
1433839 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
1433857 CAACCGGCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.56, C:0.22, G:0.03, T:0.19
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:1435599 original size:21 final size:21
Alignment explanation
Indices: 1435574--1435655 Score: 112
Period size: 21 Copynumber: 3.9 Consensus size: 21
1435564 TGAACGGTGG
*
1435574 GAGGCCTCTTAAATGATGAGA
1 GAGGCCTCTTAAACGATGAGA
1435595 GAGGCCTCTTAAACGATGAGA
1 GAGGCCTCTTAAACGATGAGA
*
1435616 GAGGCCTCTTGAACGAT-AGGA
1 GAGGCCTCTTAAACGATGA-GA
* *
1435637 GGGGCCTCTTGAACGATGA
1 GAGGCCTCTTAAACGATGA
1435656 CAGATGAATC
Statistics
Matches: 56, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
20 1 0.02
21 54 0.96
22 1 0.02
ACGTcount: A:0.29, C:0.18, G:0.32, T:0.21
Consensus pattern (21 bp):
GAGGCCTCTTAAACGATGAGA
Found at i:1436014 original size:63 final size:63
Alignment explanation
Indices: 1435947--1436090 Score: 155
Period size: 63 Copynumber: 2.3 Consensus size: 63
1435937 CGTAGAACGG
* * *
1435947 CTACCTCATCACGTAAAG-TAGATACCTCACCACATAAAGCACCATTGTCATCGCGTAAAGCAT
1 CTACCTCATCACGTAAAGATAG-TACCTCACCACACAAAGCACCATTGTCATCACGTAAAGCAC
* * * * * * * *
1436010 CTACCTCACCACGTAAAGATCGTACCTCATCACGCCATGCACCATTGTCGTCACGTAAAGTAC
1 CTACCTCATCACGTAAAGATAGTACCTCACCACACAAAGCACCATTGTCATCACGTAAAGCAC
* *
1436073 CGACCTCATCACGCAAAG
1 CTACCTCATCACGTAAAG
1436091 CATTGACCTC
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
63 64 0.97
64 2 0.03
ACGTcount: A:0.32, C:0.33, G:0.14, T:0.21
Consensus pattern (63 bp):
CTACCTCATCACGTAAAGATAGTACCTCACCACACAAAGCACCATTGTCATCACGTAAAGCAC
Found at i:1436024 original size:21 final size:21
Alignment explanation
Indices: 1435947--1436109 Score: 73
Period size: 21 Copynumber: 7.8 Consensus size: 21
1435937 CGTAGAACGG
* *
1435947 CTACCTCATCACGTAAAGTAG
1 CTACCTCATCACGTAAAGCAT
* * *
1435968 ATACCTCACCACATAAAGCA-
1 CTACCTCATCACGTAAAGCAT
* ** *
1435988 CCATTGTCATCGCGTAAAGCAT
1 CTA-CCTCATCACGTAAAGCAT
*
1436010 CTACCTCACCACGTAAAG-AT
1 CTACCTCATCACGTAAAGCAT
** *
1436030 CGTACCTCATCACGCCATGCA-
1 C-TACCTCATCACGTAAAGCAT
* ** * * *
1436051 CCATTGTCGTCACGTAAAGTAC
1 CTA-CCTCATCACGTAAAGCAT
* *
1436073 CGACCTCATCACGCAAAGCAT
1 CTACCTCATCACGTAAAGCAT
1436094 -TGACCTCATCACGTAA
1 CT-ACCTCATCACGTAA
1436110 CTCCTCTAAC
Statistics
Matches: 98, Mismatches: 37, Indels: 14
0.66 0.25 0.09
Matches are distributed among these distances:
20 5 0.05
21 88 0.90
22 5 0.05
ACGTcount: A:0.32, C:0.33, G:0.13, T:0.21
Consensus pattern (21 bp):
CTACCTCATCACGTAAAGCAT
Found at i:1436100 original size:63 final size:63
Alignment explanation
Indices: 1435985--1436106 Score: 156
Period size: 63 Copynumber: 1.9 Consensus size: 63
1435975 ACCACATAAA
* * * *
1435985 GCACCATTGTCATCGCGTAAAGCATCTACCTCACCACGTAAAGATCGTACCTCATCACGCCAT
1 GCACCATTGTCATCACGTAAAGCACCGACCTCACCACGCAAAGATCGTACCTCATCACGCCAT
* * * *
1436048 GCACCATTGTCGTCACGTAAAGTACCGACCTCATCACGCAAAGCATTG-ACCTCATCACG
1 GCACCATTGTCATCACGTAAAGCACCGACCTCACCACGCAAAG-ATCGTACCTCATCACG
1436107 TAACTCCTCT
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
63 47 0.94
64 3 0.06
ACGTcount: A:0.29, C:0.34, G:0.16, T:0.21
Consensus pattern (63 bp):
GCACCATTGTCATCACGTAAAGCACCGACCTCACCACGCAAAGATCGTACCTCATCACGCCAT
Found at i:1438361 original size:20 final size:20
Alignment explanation
Indices: 1438336--1438373 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1438326 CTTTGTGAAA
1438336 TTGACTTATGTGTTGCGAAT
1 TTGACTTATGTGTTGCGAAT
*
1438356 TTGACTTCTGTGTTGCGA
1 TTGACTTATGTGTTGCGA
1438374 TTTACAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.16, C:0.13, G:0.26, T:0.45
Consensus pattern (20 bp):
TTGACTTATGTGTTGCGAAT
Found at i:1438390 original size:20 final size:20
Alignment explanation
Indices: 1438367--1438433 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
1438357 TGACTTCTGT
*
1438367 GTTGCGATTTACAAATTCGC
1 GTTGCGATTTACATATTCGC
* *
1438387 GTTGCGATTTATATATTCAC
1 GTTGCGATTTACATATTCGC
*
1438407 GTTGTGATTTACATATTCGC
1 GTTGCGATTTACATATTCGC
1438427 GTTGCGA
1 GTTGCGA
1438434 ATTTCAAAAC
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.22, C:0.16, G:0.21, T:0.40
Consensus pattern (20 bp):
GTTGCGATTTACATATTCGC
Found at i:1446497 original size:21 final size:21
Alignment explanation
Indices: 1446473--1446526 Score: 56
Period size: 23 Copynumber: 2.5 Consensus size: 21
1446463 TATACATTTC
1446473 TATAAAAATATA-TAAAATCAT
1 TATAAAAATATATTAAAAT-AT
* *
1446494 TATAAAATAATATATTATAATGT
1 TAT-AAA-AATATATTAAAATAT
1446517 TATAAAAATA
1 TATAAAAATA
1446527 ATCTATACAT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
21 7 0.25
22 6 0.21
23 10 0.36
24 5 0.18
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (21 bp):
TATAAAAATATATTAAAATAT
Found at i:1446533 original size:21 final size:21
Alignment explanation
Indices: 1446455--1446533 Score: 54
Period size: 21 Copynumber: 3.6 Consensus size: 21
1446445 TAAAAAAATT
*
1446455 AAATAATCTATACATTTCTATAA
1 AAATAATCTATA-ATAT-TATAA
* *
1446478 AAAT-ATATAAAATCATTATAAA
1 AAATAATCTATAAT-ATTAT-AA
*
1446500 ATAATATAT-TATAATGTTATAA
1 A-AATA-ATCTATAATATTATAA
1446522 AAATAATCTATA
1 AAATAATCTATA
1446534 CATTTAGTTA
Statistics
Matches: 45, Mismatches: 5, Indels: 14
0.70 0.08 0.22
Matches are distributed among these distances:
20 2 0.04
21 13 0.29
22 12 0.27
23 11 0.24
24 5 0.11
25 2 0.04
ACGTcount: A:0.54, C:0.06, G:0.01, T:0.38
Consensus pattern (21 bp):
AAATAATCTATAATATTATAA
Found at i:1447301 original size:39 final size:39
Alignment explanation
Indices: 1447197--1447302 Score: 110
Period size: 39 Copynumber: 2.7 Consensus size: 39
1447187 TATAATCATC
*
1447197 AAATTATTTCAC-TCTAACATTATAAAATCCTAATTTCTT
1 AAATTATTTCACAT-TAACATTATAAATTCCTAATTTCTT
* * *
1447236 AAATT-TTGACACCA-TAACATTCTAAATTCTTAATTTCTT
1 AAATTATT-TCA-CATTAACATTATAAATTCCTAATTTCTT
* *
1447275 AAATTATTTCACATTAACGTTTTAAATT
1 AAATTATTTCACATTAACATTATAAATT
1447303 ATTTTAACTT
Statistics
Matches: 55, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
38 4 0.07
39 48 0.87
40 3 0.05
ACGTcount: A:0.38, C:0.16, G:0.02, T:0.44
Consensus pattern (39 bp):
AAATTATTTCACATTAACATTATAAATTCCTAATTTCTT
Found at i:1447540 original size:21 final size:22
Alignment explanation
Indices: 1447516--1447574 Score: 75
Period size: 21 Copynumber: 2.6 Consensus size: 22
1447506 TAATTTTATA
*
1447516 TATATTAACTTAAAATGT-TTT
1 TATATTAACTTAAAATATATTT
1447537 TATATTAACTTATTAAATATATTT
1 TATATTAACTTA--AAATATATTT
1447561 TACTATTAACTTAA
1 TA-TATTAACTTAA
1447575 TTTAAAAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
21 12 0.36
23 6 0.18
24 5 0.15
25 10 0.30
ACGTcount: A:0.41, C:0.07, G:0.02, T:0.51
Consensus pattern (22 bp):
TATATTAACTTAAAATATATTT
Found at i:1447561 original size:25 final size:27
Alignment explanation
Indices: 1447520--1447588 Score: 74
Period size: 25 Copynumber: 2.6 Consensus size: 27
1447510 TTTATATATA
* *
1447520 TTAACTTAAAATGTTTTTA-TATTAAC
1 TTAATTTAAAATATTTTTACTATTAAC
1447546 TT-A-TT-AAATATATTTTACTATTAAC
1 TTAATTTAAAATAT-TTTTACTATTAAC
1447571 TTAATTTAAAAATATTTT
1 TTAATTT-AAAATATTTT
1447589 ATTTTCATTT
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
23 5 0.14
24 7 0.19
25 10 0.28
26 3 0.08
27 2 0.06
28 3 0.08
29 6 0.17
ACGTcount: A:0.41, C:0.06, G:0.01, T:0.52
Consensus pattern (27 bp):
TTAATTTAAAATATTTTTACTATTAAC
Found at i:1447586 original size:27 final size:24
Alignment explanation
Indices: 1447534--1447590 Score: 78
Period size: 27 Copynumber: 2.2 Consensus size: 24
1447524 CTTAAAATGT
*
1447534 TTTTATATTAACTTATTAAATATA
1 TTTTATATTAACTTATTAAAAATA
1447558 TTTTACTATTAACTTAATTTAAAAATA
1 TTTTA-TATTAACTT-A-TTAAAAATA
1447585 TTTTAT
1 TTTTAT
1447591 TTTCATTTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
24 5 0.17
25 9 0.31
26 2 0.07
27 13 0.45
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.54
Consensus pattern (24 bp):
TTTTATATTAACTTATTAAAAATA
Found at i:1454235 original size:23 final size:23
Alignment explanation
Indices: 1454209--1454278 Score: 60
Period size: 23 Copynumber: 3.2 Consensus size: 23
1454199 TTGGAAGGTG
1454209 GTACACCATTGAATAGAGAAGCA
1 GTACACCATTGAATAGAGAAGCA
* * *
1454232 GT--ACCA--AAAGTTG-GAAGGA
1 GTACACCATTGAA-TAGAGAAGCA
1454251 GGTACACCATTGAATAGAGAAGCA
1 -GTACACCATTGAATAGAGAAGCA
1454275 GTAC
1 GTAC
1454279 CAATAGTTGG
Statistics
Matches: 34, Mismatches: 6, Indels: 14
0.63 0.11 0.26
Matches are distributed among these distances:
19 7 0.21
20 4 0.12
21 4 0.12
22 4 0.12
23 8 0.24
24 7 0.21
ACGTcount: A:0.41, C:0.16, G:0.26, T:0.17
Consensus pattern (23 bp):
GTACACCATTGAATAGAGAAGCA
Found at i:1454237 original size:21 final size:21
Alignment explanation
Indices: 1454213--1454280 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
1454203 AAGGTGGTAC
1454213 ACCATTGAATAGAGAAGCAGT
1 ACCATTGAATAGAGAAGCAGT
* * *
1454234 ACCA--AAAGTTG-GAAGGAGGT
1 ACCATTGAA-TAGAGAAGCA-GT
1454254 ACACCATTGAATAGAGAAGCAGT
1 --ACCATTGAATAGAGAAGCAGT
1454277 ACCA
1 ACCA
1454281 ATAGTTGGGG
Statistics
Matches: 34, Mismatches: 6, Indels: 14
0.63 0.11 0.26
Matches are distributed among these distances:
19 7 0.21
20 4 0.12
21 8 0.24
22 4 0.12
23 4 0.12
24 7 0.21
ACGTcount: A:0.43, C:0.16, G:0.25, T:0.16
Consensus pattern (21 bp):
ACCATTGAATAGAGAAGCAGT
Found at i:1454255 original size:43 final size:43
Alignment explanation
Indices: 1454194--1454288 Score: 172
Period size: 43 Copynumber: 2.2 Consensus size: 43
1454184 ATAGCGTGCA
*
1454194 AAAAGTTGGAAGGTGGTACACCATTGAATAGAGAAGCAGTACC
1 AAAAGTTGGAAGGAGGTACACCATTGAATAGAGAAGCAGTACC
1454237 AAAAGTTGGAAGGAGGTACACCATTGAATAGAGAAGCAGTACC
1 AAAAGTTGGAAGGAGGTACACCATTGAATAGAGAAGCAGTACC
*
1454280 AATAGTTGG
1 AAAAGTTGG
1454289 GGATGAGCAT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 50 1.00
ACGTcount: A:0.40, C:0.13, G:0.28, T:0.19
Consensus pattern (43 bp):
AAAAGTTGGAAGGAGGTACACCATTGAATAGAGAAGCAGTACC
Found at i:1455474 original size:4 final size:4
Alignment explanation
Indices: 1455465--1455496 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
1455455 AAGGAGAATA
1455465 GAAG GAAG GAAG GAAG GAAG GAAG GAAG GAAG
1 GAAG GAAG GAAG GAAG GAAG GAAG GAAG GAAG
1455497 AAAAGAAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (4 bp):
GAAG
Found at i:1455641 original size:20 final size:21
Alignment explanation
Indices: 1455599--1455658 Score: 63
Period size: 20 Copynumber: 2.9 Consensus size: 21
1455589 TTTAAATCAA
1455599 TTAG-TTAATTTAGATTATTT
1 TTAGATTAATTTAGATTATTT
1455619 TTAGATTAATTT-G-TTATTAT
1 TTAGATTAATTTAGATTATT-T
*
1455639 TTAAATTAATGTTTAGATTA
1 TTAGATTAA--TTTAGATTA
1455659 ATTATTGTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
19 5 0.15
20 14 0.42
21 7 0.21
22 3 0.09
23 1 0.03
24 3 0.09
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (21 bp):
TTAGATTAATTTAGATTATTT
Found at i:1457555 original size:27 final size:26
Alignment explanation
Indices: 1457500--1457553 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
1457490 ATTGGGAGAA
* *
1457500 TATTTTATTTAAAAGTATTTTATTTT
1 TATTTTATTTAAAAATATTATATTTT
1457526 TATTTTCATTTAAAAATATATATATTTT
1 TATTTT-ATTTAAAAATAT-TATATTTT
1457554 ATGTTAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 6 0.25
27 11 0.46
28 7 0.29
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (26 bp):
TATTTTATTTAAAAATATTATATTTT
Found at i:1458053 original size:30 final size:30
Alignment explanation
Indices: 1458017--1458077 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
1458007 ATATATCAGG
* **
1458017 GGCGGATGCATTAAGTCTCATAGGGGTCAA
1 GGCGGATGCACTAAACCTCATAGGGGTCAA
1458047 GGCGGATGCACTAAACCTCATAGGGGTCAA
1 GGCGGATGCACTAAACCTCATAGGGGTCAA
1458077 G
1 G
1458078 TGCATCCCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.28, C:0.20, G:0.33, T:0.20
Consensus pattern (30 bp):
GGCGGATGCACTAAACCTCATAGGGGTCAA
Found at i:1463459 original size:18 final size:19
Alignment explanation
Indices: 1463436--1463480 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
1463426 GAAAACTTAA
* *
1463436 TTTTATATGTTTG-AATTT
1 TTTTATATGATGGCAATTT
*
1463454 TTTTATAAGATGGCAATTT
1 TTTTATATGATGGCAATTT
1463473 TTTTATAT
1 TTTTATAT
1463481 TGTACAATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 10 0.45
19 12 0.55
ACGTcount: A:0.27, C:0.02, G:0.11, T:0.60
Consensus pattern (19 bp):
TTTTATATGATGGCAATTT
Found at i:1466159 original size:17 final size:17
Alignment explanation
Indices: 1466137--1466171 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1466127 TGGAAAATTT
*
1466137 AAACTTTTATTAACATA
1 AAACTTGTATTAACATA
*
1466154 AAACTTGTATTTACATA
1 AAACTTGTATTAACATA
1466171 A
1 A
1466172 CTAGGTTCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.46, C:0.11, G:0.03, T:0.40
Consensus pattern (17 bp):
AAACTTGTATTAACATA
Found at i:1466691 original size:30 final size:30
Alignment explanation
Indices: 1466656--1466713 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
1466646 GAAGGACCTA
*
1466656 TCCATATGTTCCGAAGAACATAGGTAACTG
1 TCCATATGTCCCGAAGAACATAGGTAACTG
1466686 TCCATATGTCCCGAAGAACATAGGTAAC
1 TCCATATGTCCCGAAGAACATAGGTAAC
1466714 CCTCGACTCT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.24
Consensus pattern (30 bp):
TCCATATGTCCCGAAGAACATAGGTAACTG
Found at i:1467311 original size:24 final size:21
Alignment explanation
Indices: 1467279--1467350 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 21
1467269 CTTTATAATA
1467279 TATCGATACATTCCTTAACATGTG
1 TATCGATACATT-C-T-ACATGTG
1467303 TATCGATACA--CTACATGTG
1 TATCGATACATTCTACATGTG
1467322 TATCGATACA-T-TACATGTG
1 TATCGATACATTCTACATGTG
1467341 TATCGATACA
1 TATCGATACA
1467351 CTACCTATGT
Statistics
Matches: 47, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
19 35 0.74
20 1 0.02
21 1 0.02
24 10 0.21
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.35
Consensus pattern (21 bp):
TATCGATACATTCTACATGTG
Found at i:1467320 original size:19 final size:19
Alignment explanation
Indices: 1467296--1467364 Score: 111
Period size: 19 Copynumber: 3.6 Consensus size: 19
1467286 ACATTCCTTA
1467296 ACATGTGTATCGATACACT
1 ACATGTGTATCGATACACT
*
1467315 ACATGTGTATCGATACATT
1 ACATGTGTATCGATACACT
1467334 ACATGTGTATCGATACACT
1 ACATGTGTATCGATACACT
* *
1467353 ACCTATGTATCG
1 ACATGTGTATCG
1467365 GTATACAAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 46 1.00
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.33
Consensus pattern (19 bp):
ACATGTGTATCGATACACT
Found at i:1469979 original size:2 final size:2
Alignment explanation
Indices: 1469972--1470017 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
1469962 CAAACTTTTC
1469972 AT AT AT AT AT 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 AT AT
1470014 AT AT
1 AT AT
1470018 TCTTTACAGT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1471308 original size:64 final size:63
Alignment explanation
Indices: 1471219--1471379 Score: 180
Period size: 64 Copynumber: 2.5 Consensus size: 63
1471209 TTGTTTAAGG
* * * *
1471219 TGCATCGATGCACATGCAGTGCATCGATGCAT-TAATTTAAAAAGATAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGCAGTGCATCGATGCATCCAA-TTAAAAACA-AACATCGAATAGGATTTA
* * * *
1471283 TGCATCGATGCATAAGGAGTTCATCGATGCATCCCCATTAAATACAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGCAGTGCATCGATGCAT-CCAATTAAAAACAAACATCGAATAGGATTTA
** *
1471347 TGCATCGATGCATGGTGTAGTGCATCGATGCAT
1 TGCATCGATGCAT-AAGCAGTGCATCGATGCAT
1471380 ACCTTCATTA
Statistics
Matches: 82, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
64 59 0.72
65 22 0.27
66 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (63 bp):
TGCATCGATGCATAAGCAGTGCATCGATGCATCCAATTAAAAACAAACATCGAATAGGATTTA
Found at i:1472310 original size:30 final size:30
Alignment explanation
Indices: 1472274--1472366 Score: 134
Period size: 30 Copynumber: 3.1 Consensus size: 30
1472264 GTGGTCCTTA
1472274 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
1472304 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
* * * * *
1472334 TGGATAATTACC-AGGGTCTTTGTGACCTT
1 TGGACAGTTACCGAGGATCTTTATGACCTC
1472363 TGGA
1 TGGA
1472367 TAGGTCCTTC
Statistics
Matches: 58, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
29 18 0.31
30 40 0.69
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.32
Consensus pattern (30 bp):
TGGACAGTTACCGAGGATCTTTATGACCTC
Found at i:1475264 original size:30 final size:30
Alignment explanation
Indices: 1475229--1475286 Score: 100
Period size: 30 Copynumber: 1.9 Consensus size: 30
1475219 GAAGGACCTA
1475229 TCCATATGT-TCTGAAGAACATAGGTAACTG
1 TCCATATGTCTC-GAAGAACATAGGTAACTG
1475259 TCCATATGTCTCGAAGAACATAGGTAAC
1 TCCATATGTCTCGAAGAACATAGGTAAC
1475287 CCTCGACTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
30 25 0.93
31 2 0.07
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (30 bp):
TCCATATGTCTCGAAGAACATAGGTAACTG
Found at i:1476015 original size:30 final size:31
Alignment explanation
Indices: 1475976--1476048 Score: 91
Period size: 30 Copynumber: 2.5 Consensus size: 31
1475966 AATGGATTTA
* *
1475976 TTTA-GTGACCAAATTATAAA-TTTGGTAAAG
1 TTTAGGTGACCAAAGTATAAACTTT-GAAAAG
1476006 TTT-GGTGACCAAAGTATAAACTTTGAAAAG
1 TTTAGGTGACCAAAGTATAAACTTTGAAAAG
1476036 TTTAGG-GACCAAA
1 TTTAGGTGACCAAA
1476049 AATGTAATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
30 33 0.87
31 5 0.13
ACGTcount: A:0.40, C:0.10, G:0.19, T:0.32
Consensus pattern (31 bp):
TTTAGGTGACCAAAGTATAAACTTTGAAAAG
Found at i:1485287 original size:22 final size:22
Alignment explanation
Indices: 1485247--1485299 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
1485237 TGTATCGGTA
* *
1485247 CACTGTTCACAGTATTGTTTAT
1 CACTGTTCACAGTACTGTTCAT
1485269 CACTGTTCAC-GATACTGTTCAT
1 CACTGTTCACAG-TACTGTTCAT
*
1485291 CACTATTCA
1 CACTGTTCA
1485300 TAAAAAAATC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 1 0.04
22 26 0.96
ACGTcount: A:0.25, C:0.25, G:0.11, T:0.40
Consensus pattern (22 bp):
CACTGTTCACAGTACTGTTCAT
Found at i:1492803 original size:3 final size:3
Alignment explanation
Indices: 1492784--1492840 Score: 71
Period size: 3 Copynumber: 18.7 Consensus size: 3
1492774 TCGAAAAGAA
* *
1492784 TAT TAAT TAT ATAT TAT TAT TAA T-T TAT TAT TAT TAT AAT TAT TAT
1 TAT T-AT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1492830 TAT TAT TAT TA
1 TAT TAT TAT TA
1492841 AACATATTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
2 1 0.02
3 40 0.85
4 6 0.13
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:1494560 original size:29 final size:30
Alignment explanation
Indices: 1494511--1494681 Score: 170
Period size: 30 Copynumber: 5.8 Consensus size: 30
1494501 AAATTGTTGT
* * * * *
1494511 TTTTTTCTTTTTTAATCCCTTAAATTTCTA
1 TTTTTGCTATTTTAGTCCTTTAAGTTTCTA
1494541 TTTTTGCTATTTTAGTCCTTTAAGTTTCTA
1 TTTTTGCTATTTTAGTCCTTTAAGTTTCTA
* * *
1494571 TATTTGTTATTTT-GTCCTTTAAGTTTCTG
1 TTTTTGCTATTTTAGTCCTTTAAGTTTCTA
* *
1494600 TTTTTGCTA-TTTAGACCCTTAAGTTT-TGA
1 TTTTTGCTATTTTAGTCCTTTAAGTTTCT-A
* *
1494629 TTTTTACTATTTTA-TCCCTTTAAGTTTTTA
1 TTTTTGCTATTTTAGT-CCTTTAAGTTTCTA
* *
1494659 TTTTTGCCATTTTGGTCCTTTAA
1 TTTTTGCTATTTTAGTCCTTTAA
1494682 CTTTATGTAT
Statistics
Matches: 116, Mismatches: 19, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
28 4 0.03
29 41 0.35
30 69 0.59
31 2 0.02
ACGTcount: A:0.18, C:0.14, G:0.09, T:0.60
Consensus pattern (30 bp):
TTTTTGCTATTTTAGTCCTTTAAGTTTCTA
Found at i:1494605 original size:59 final size:60
Alignment explanation
Indices: 1494520--1494699 Score: 190
Period size: 59 Copynumber: 3.0 Consensus size: 60
1494510 TTTTTTTCTT
* **
1494520 TTTTAATCCC-TTAAATTTCTATTTTTGCTATTTTAGTCCTTTAAGTTTCT-ATATTTGTTA
1 TTTT-ATCCCTTTAAGTTTCTATTTTTGCTATTTTAGTCCTTTAAGTTT-TGATATTTACTA
* * * * *
1494580 TTTTGT-CCTTTAAGTTTCTGTTTTTGCTA-TTTAGACCCTTAAGTTTTGATTTTTACTA
1 TTTTATCCCTTTAAGTTTCTATTTTTGCTATTTTAGTCCTTTAAGTTTTGATATTTACTA
* * * *
1494638 TTTTATCCCTTTAAGTTTTTATTTTTGCCATTTTGGTCCTTTAACTTTATG-TATTTACTA
1 TTTTATCCCTTTAAGTTTCTATTTTTGCTATTTTAGTCCTTTAAGTTT-TGATATTTACTA
1494698 TT
1 TT
1494700 CAACCCTTTA
Statistics
Matches: 98, Mismatches: 17, Indels: 10
0.78 0.14 0.08
Matches are distributed among these distances:
57 1 0.01
58 29 0.30
59 39 0.40
60 27 0.28
61 2 0.02
ACGTcount: A:0.19, C:0.14, G:0.09, T:0.58
Consensus pattern (60 bp):
TTTTATCCCTTTAAGTTTCTATTTTTGCTATTTTAGTCCTTTAAGTTTTGATATTTACTA
Found at i:1496022 original size:14 final size:13
Alignment explanation
Indices: 1496003--1496055 Score: 54
Period size: 14 Copynumber: 4.0 Consensus size: 13
1495993 TTAGTTTACT
1496003 ATAACTTTTGAAAA
1 ATAACTTTT-AAAA
1496017 ATAACTTTT-AAA
1 ATAACTTTTAAAA
* *
1496029 ATTATTTTTAGAAA
1 ATAACTTTTA-AAA
*
1496043 AGAACTTTTAAAA
1 ATAACTTTTAAAA
1496056 GTGTTATACA
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
12 10 0.31
13 3 0.09
14 19 0.59
ACGTcount: A:0.49, C:0.06, G:0.06, T:0.40
Consensus pattern (13 bp):
ATAACTTTTAAAA
Found at i:1502031 original size:3 final size:3
Alignment explanation
Indices: 1502023--1502064 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
1502013 TTATTTTGAA
1502023 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
1502065 TATGCAATTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1510309 original size:3 final size:3
Alignment explanation
Indices: 1510301--1510371 Score: 88
Period size: 3 Copynumber: 23.0 Consensus size: 3
1510291 CCATTTTTAT
* * *
1510301 TTA TTA TTA TTA TTA TTA TAA TTA TTA TAA TTA TAA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
1510349 TAA TATA TATA TTA TTA TTA TTA
1 TTA T-TA T-TA TTA TTA TTA TTA
1510372 AAAAAATAAT
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
3 53 0.90
4 6 0.10
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:1511877 original size:23 final size:22
Alignment explanation
Indices: 1511831--1511875 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1511821 ATATTATAAA
1511831 AAATTATAATTTAATTTTATTT
1 AAATTATAATTTAATTTTATTT
*
1511853 AAATTATTATATTAATATTTATT
1 AAATTATAAT-TTAAT-TTTATT
1511876 AATATCGAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 9 0.45
23 5 0.25
24 6 0.30
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
AAATTATAATTTAATTTTATTT
Found at i:1512518 original size:14 final size:15
Alignment explanation
Indices: 1512499--1512560 Score: 63
Period size: 16 Copynumber: 4.0 Consensus size: 15
1512489 TTTTCATAGC
1512499 ATTTATATTT-TTTT
1 ATTTATATTTATTTT
1512513 ATTTATATTTCATTTT
1 ATTTATATTT-ATTTT
* **
1512529 ATTTACAAGTATTTT
1 ATTTATATTTATTTT
1512544 ATTTCATTATTTATTTT
1 ATTT-A-TATTTATTTT
1512561 TTCTGTCAGA
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
14 10 0.26
15 9 0.24
16 12 0.32
17 7 0.18
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.68
Consensus pattern (15 bp):
ATTTATATTTATTTT
Found at i:1512530 original size:16 final size:14
Alignment explanation
Indices: 1512499--1512533 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
1512489 TTTTCATAGC
1512499 ATTTATATTTTTTT
1 ATTTATATTTTTTT
1512513 ATTTATATTTCATTTT
1 ATTTATATTT--TTTT
1512529 ATTTA
1 ATTTA
1512534 CAAGTATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 10 0.53
16 9 0.47
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (14 bp):
ATTTATATTTTTTT
Found at i:1515824 original size:15 final size:15
Alignment explanation
Indices: 1515804--1515834 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1515794 TCAATACCTC
1515804 TTTGCATACATACAT
1 TTTGCATACATACAT
*
1515819 TTTGCATACATTCAT
1 TTTGCATACATACAT
1515834 T
1 T
1515835 ATTCATTTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.19, G:0.06, T:0.45
Consensus pattern (15 bp):
TTTGCATACATACAT
Found at i:1523166 original size:6 final size:6
Alignment explanation
Indices: 1523143--1523218 Score: 66
Period size: 6 Copynumber: 12.5 Consensus size: 6
1523133 ATTCTTGAAG
* * *
1523143 AAAGAAA AAAGAA CAAGAA AAAGAA AAA-AA AAGGAAA AAAGAG AAAGAA
1 AAAG-AA AAAGAA AAAGAA AAAGAA AAAGAA AAAG-AA AAAGAA AAAGAA
* *
1523192 AAA-AA AGAGAA AAGAAAA AAAGAA AAA
1 AAAGAA AAAGAA AA-AGAA AAAGAA AAA
1523219 AAGGGGGTCA
Statistics
Matches: 55, Mismatches: 10, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
5 8 0.15
6 33 0.60
7 14 0.25
ACGTcount: A:0.82, C:0.01, G:0.17, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:1523168 original size:23 final size:21
Alignment explanation
Indices: 1523140--1523221 Score: 85
Period size: 22 Copynumber: 3.6 Consensus size: 21
1523130 ATTATTCTTG
1523140 AAGAAAGAAAAAAGAACAAGAAA
1 AAGAAA-AAAAAAGAA-AAGAAA
*
1523163 AAGAAAAAAAAAGGAAAAAAGAGA
1 AAGAAAAAAAAA-G--AAAAGAAA
1523187 AAGAAAAAAAAGAGAAAAGAAA
1 AAGAAAAAAAA-AGAAAAGAAA
1523209 AA-AAGAAAAAAAG
1 AAGAA-AAAAAAAG
1523222 GGGGTCAAGA
Statistics
Matches: 52, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
21 4 0.08
22 21 0.40
23 7 0.13
24 17 0.33
25 3 0.06
ACGTcount: A:0.80, C:0.01, G:0.18, T:0.00
Consensus pattern (21 bp):
AAGAAAAAAAAAGAAAAGAAA
Found at i:1523182 original size:30 final size:29
Alignment explanation
Indices: 1523146--1523217 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 29
1523136 CTTGAAGAAA
1523146 GAAAAAAGAACAAGAAAAAGAAA-AAAAAAG
1 GAAAAAAGAA-AAGAAAAA-AAAGAAAAAAG
*
1523176 GAAAAAAGAGAAAGAAAAAAAAGAGAAAAG
1 GAAAAAAGA-AAAGAAAAAAAAGAAAAAAG
*
1523206 AAAAAAAGAAAA
1 GAAAAAAGAAAA
1523218 AAAGGGGGTC
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
29 6 0.16
30 31 0.82
31 1 0.03
ACGTcount: A:0.81, C:0.01, G:0.18, T:0.00
Consensus pattern (29 bp):
GAAAAAAGAAAAGAAAAAAAAGAAAAAAG
Found at i:1523184 original size:24 final size:24
Alignment explanation
Indices: 1523140--1523220 Score: 89
Period size: 24 Copynumber: 3.4 Consensus size: 24
1523130 ATTATTCTTG
*
1523140 AAGAAAGAAAAAA-G-AACAAGAAA
1 AAGAAA-AAAAAAGGAAAAAAGAAA
*
1523163 AAGAAAAAAAAAGGAAAAAAGAGA
1 AAGAAAAAAAAAGGAAAAAAGAAA
1523187 AAG-AAAAAAAAGAGAAAAGAA-AAA
1 AAGAAAAAAAAAG-GAAAA-AAGAAA
1523211 AAGAAAAAAA
1 AAGAAAAAAA
1523221 GGGGGTCAAG
Statistics
Matches: 50, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
22 6 0.12
23 16 0.32
24 20 0.40
25 8 0.16
ACGTcount: A:0.81, C:0.01, G:0.17, T:0.00
Consensus pattern (24 bp):
AAGAAAAAAAAAGGAAAAAAGAAA
Found at i:1523197 original size:15 final size:15
Alignment explanation
Indices: 1523147--1523212 Score: 64
Period size: 16 Copynumber: 4.3 Consensus size: 15
1523137 TTGAAGAAAG
1523147 AAAAAAGA-ACAAGAA
1 AAAAAAGAGA-AAGAA
* * *
1523162 AAAGAAAAAAAAAG-G
1 AAA-AAAGAGAAAGAA
1523177 AAAAAAGAGAAAGAA
1 AAAAAAGAGAAAGAA
1523192 AAAAAAGAGAAAAGAA
1 AAAAAAGAG-AAAGAA
1523208 AAAAA
1 AAAAA
1523213 GAAAAAAAGG
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
14 8 0.19
15 15 0.36
16 18 0.43
17 1 0.02
ACGTcount: A:0.82, C:0.02, G:0.17, T:0.00
Consensus pattern (15 bp):
AAAAAAGAGAAAGAA
Found at i:1523219 original size:15 final size:15
Alignment explanation
Indices: 1523143--1523219 Score: 70
Period size: 15 Copynumber: 5.2 Consensus size: 15
1523133 ATTCTTGAAG
1523143 AAAG-AAAAAAG-AA
1 AAAGAAAAAAAGAAA
* *
1523156 CAAGAAAAAGAAAAAA
1 AAAGAAAAA-AAGAAA
* *
1523172 AAAGGAAAAAAG-AG
1 AAAGAAAAAAAGAAA
*
1523186 AAAGAAAAAAAAGAGA
1 AAAG-AAAAAAAGAAA
1523202 AAAGAAAAAAAGAAA
1 AAAGAAAAAAAGAAA
1523217 AAA
1 AAA
1523220 AGGGGGTCAA
Statistics
Matches: 49, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
13 3 0.06
14 9 0.18
15 24 0.49
16 13 0.27
ACGTcount: A:0.82, C:0.01, G:0.17, T:0.00
Consensus pattern (15 bp):
AAAGAAAAAAAGAAA
Found at i:1524364 original size:93 final size:93
Alignment explanation
Indices: 1524203--1524493 Score: 555
Period size: 93 Copynumber: 3.1 Consensus size: 93
1524193 AACAAGTGCC
1524203 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCA
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCA
1524268 AAAACCCATCATTGGATTTGAAAGATGA
66 AAAACCCATCATTGGATTTGAAAGATGA
*
1524296 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCTA
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCA
1524361 AAAACCCATCATTGGATTTGAAAGATGA
66 AAAACCCATCATTGGATTTGAAAGATGA
*
1524389 ATGTGCTCATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCA
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCA
*
1524454 AAAACCAATCATTGGATTTGAAAGATGA
66 AAAACCCATCATTGGATTTGAAAGATGA
1524482 ATGTGCTCATAG
1 ATGTGCTCATAG
1524494 TAGAAATAAG
Statistics
Matches: 194, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
93 194 1.00
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.35
Consensus pattern (93 bp):
ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCA
AAAACCCATCATTGGATTTGAAAGATGA
Found at i:1524599 original size:115 final size:115
Alignment explanation
Indices: 1524397--1524711 Score: 517
Period size: 115 Copynumber: 2.7 Consensus size: 115
1524387 GAATGTGCTC
1524397 ATAGCATCTTT-TGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCAAAAACCA
1 ATAGCAT-TTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCAAAAACCA
1524461 ATCATTGGATTTGAAAGATGAATGTGCTCATAGTAGAAATAAGAAGACCCA
65 ATCATTGGATTTGAAAGATGAATGTGCTCATAGTAGAAATAAGAAGACCCA
* *
1524512 ATAGCATTTTCTGGAAGTGTTCTTTGAGTTATCTGATCTAGTTTGATATGAACCCCAAAAACCAA
1 ATAGCATTTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCAAAAACCAA
*
1524577 TCATTGGATTTGAAAGATGAATGTGCTCATAGTAGAGATAAGAAGACCCA
66 TCATTGGATTTGAAAGATGAATGTGCTCATAGTAGAAATAAGAAGACCCA
* * * * *
1524627 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTCGGTAGGAACCAC-AGAACCAA
1 ATAGCATTTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCAAAAACCAA
* *
1524691 TCATTGGAATTAAAAGATGAA
66 TCATTGGATTTGAAAGATGAA
1524712 CTGCATGATC
Statistics
Matches: 187, Mismatches: 12, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
114 29 0.16
115 158 0.84
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31
Consensus pattern (115 bp):
ATAGCATTTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCAAAAACCAA
TCATTGGATTTGAAAGATGAATGTGCTCATAGTAGAAATAAGAAGACCCA
Found at i:1525699 original size:112 final size:113
Alignment explanation
Indices: 1525425--1525900 Score: 531
Period size: 112 Copynumber: 4.2 Consensus size: 113
1525415 CAGCTTTTCC
* * *
1525425 AGAACAAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCACTCAGTGGAAC
1 AGAA-AAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCATTCAATGGATC
** * * * *
1525490 AGTAGTACCAGTTAGAGTTCATAATAAGAAGAACTCACCTAAAGAAGGA
65 AACATTACCAGTTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* *
1525539 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATTCATCATTCAATGGATCA
1 AGAAAAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCATTCAATGGATCA
* * *
1525604 ACATTACCAGTTCGAGTTCAT-ATGAGAAGAACTCATATGAAGAAGGC
66 ACATTACCAGTTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* * * * ** *
1525651 ATAAAAAGTTCATAAGGAGAAGAACTTGTTCAACCTTTTGTTTAAATTCATCATTTGATGGATTA
1 AGAAAAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCATTCAATGGATCA
* *
1525716 ACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGA
66 ACATTACCAGTTAGAGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGA
* * * * *
1525767 AGAAGAAA-TTCATAATGAGAAGAATTTGTTCAAATTTTTACTCAAA-TCTATCACTT-GATGGA
1 AGAA-AAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTC-ATCA-TTCAATGGA
* *
1525829 TCAACTTTTCCAG--AGAGGTTCATAATGAGAAGAACTCATCT---GAA-GA
63 TCAACATTACCAGTTAGA-GTTCATAATGAGAAGAACTCATCTGAAGAAGGA
*
1525875 AGAAAAAGTTCATAATGAGAACAACT
1 AGAAAAAGTTCATAATGAGAAGAACT
1525901 CATCTGAAGG
Statistics
Matches: 312, Mismatches: 41, Indels: 24
0.83 0.11 0.06
Matches are distributed among these distances:
107 3 0.01
108 22 0.07
109 3 0.01
112 101 0.32
113 84 0.27
114 7 0.02
115 20 0.06
116 67 0.21
117 5 0.02
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (113 bp):
AGAAAAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCATTCAATGGATCA
ACATTACCAGTTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
Found at i:1525875 original size:228 final size:220
Alignment explanation
Indices: 1525425--1525900 Score: 555
Period size: 228 Copynumber: 2.1 Consensus size: 220
1525415 CAGCTTTTCC
*
1525425 AGAACAAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCACTCAGTGGAAC
1 AGAA-AAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCACTCAGTGGAAC
** * *
1525490 AGTAGTACCAGTTAGAGTTCATAATAAGAAGAACTCACCTAAAGAAGGAAGAAGAAGTTCATAAT
65 AACAGTACCAGGTAGAGTTCATAATAAGAAGAACTCACCTAAAGAAGGAAGAAGAAATTCATAAT
* * ** *
1525555 GAGAAGAACTTGTTCAACTTTTTGCTTGAATTCATCATTCAATGGATCAACATTACCAGTTCGAG
130 GAGAAGAACTTGTTCAAATTTTTACTCAAATTCATCATTCAATGGATCAACATTACCAG-TAGAG
1525620 TTCATATGAGAAGAACTCATATGAAGA
194 TTCATATGAGAAGAACTCATATGAAGA
* * **
1525647 AGGCATAAAAAGTTCATAAGGAGAAGAACTTGTTCAACCTTTTGTTTAAATTCATCA-TTTGATG
1 A-G---AAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCACTCAG-TG
** * * * * *
1525711 GATTAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAAT
61 GAACAACAGTACCAGGTAGAGTTCATAATAAGAAGAA--C-TCACCTAAAGAAGGAAGAAGAAAT
* * * *
1525776 TCATAATGAGAAGAATTTGTTCAAATTTTTACTCAAA-TCTATCACTT-GATGGATCAACTTTTC
123 TCATAATGAGAAGAACTTGTTCAAATTTTTACTCAAATTC-ATCA-TTCAATGGATCAACATTAC
*
1525839 CAG-AGAGGTTCATAATGAGAAGAACTCATCTGAAGA
186 CAGTAGA-GTTCAT-ATGAGAAGAACTCATATGAAGA
*
1525875 AGAAAAAGTTCATAATGAGAACAACT
1 AGAAAAAGTTCATAATGAGAAGAACT
1525901 CATCTGAAGG
Statistics
Matches: 214, Mismatches: 28, Indels: 22
0.81 0.11 0.08
Matches are distributed among these distances:
222 1 0.00
223 1 0.00
224 24 0.11
225 77 0.36
226 4 0.02
227 10 0.05
228 95 0.44
229 2 0.01
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (220 bp):
AGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCACTCAGTGGAACA
ACAGTACCAGGTAGAGTTCATAATAAGAAGAACTCACCTAAAGAAGGAAGAAGAAATTCATAATG
AGAAGAACTTGTTCAAATTTTTACTCAAATTCATCATTCAATGGATCAACATTACCAGTAGAGTT
CATATGAGAAGAACTCATATGAAGA
Found at i:1525893 original size:36 final size:38
Alignment explanation
Indices: 1525846--1525936 Score: 132
Period size: 36 Copynumber: 2.4 Consensus size: 38
1525836 TTCCAGAGAG
1525846 GTTCATAATGAGAAGAACTCATCTG-A-AGAAGAAAAA
1 GTTCATAATGAGAAGAACTCATCTGAAGAGAAGAAAAA
*
1525882 GTTCATAATGAGAACAACTCATCTGAAGGAGAAGAAAAA
1 GTTCATAATGAGAAGAACTCATCTGAA-GAGAAGAAAAA
* *
1525921 GTTTACAATGAGAAGA
1 GTTCATAATGAGAAGA
1525937 GCTTATTTCA
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
36 24 0.50
37 1 0.02
39 23 0.48
ACGTcount: A:0.48, C:0.11, G:0.21, T:0.20
Consensus pattern (38 bp):
GTTCATAATGAGAAGAACTCATCTGAAGAGAAGAAAAA
Found at i:1526202 original size:112 final size:108
Alignment explanation
Indices: 1525996--1526294 Score: 354
Period size: 112 Copynumber: 2.7 Consensus size: 108
1525986 CATCAGCTTT
*
1525996 CCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGCAGAAAAAGTTCATAAGGAGAAGA
1 CCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG-A---AGAAAAA-TTCATAATGAGAAGA
* * * * *
1526061 ACTTGTTCAACCTTTTGTTTAAATTCATCATTTGATGGATTAACATTG
61 ACTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAACATTG
*
1526109 CCAG-GTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGAAGAAATTCATAATGAGAAGA
1 CCAGAG-AAAGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGAA-AAATTCATAATGAGAAGA
* * * *
1526173 ATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTT
61 ACTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAACATTG
* * *
1526221 CCAGAGAAAGTTCATAATGAGAAGAACTCATCT-AA-AA-AAAAGTTCATAATGAGAAGAGCTTA
1 CCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAAATTCATAATGAGAAGAACTTG
1526283 TTCAACCTTTTG
66 TTCAACCTTTTG
1526295 AATGACTCTA
Statistics
Matches: 164, Mismatches: 16, Indels: 20
0.82 0.08 0.10
Matches are distributed among these distances:
105 31 0.19
106 2 0.01
107 2 0.01
108 2 0.01
109 6 0.04
110 1 0.01
112 81 0.49
113 27 0.16
115 2 0.01
116 10 0.06
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.28
Consensus pattern (108 bp):
CCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAAATTCATAATGAGAAGAACTTG
TTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAACATTG
Found at i:1526533 original size:3 final size:3
Alignment explanation
Indices: 1526525--1526586 Score: 52
Period size: 3 Copynumber: 20.0 Consensus size: 3
1526515 CCATTTTTAT
* * * * * *
1526525 TTA TTA TTA TTA TTA TAA TTA TTA TTA TAA TAA TAA TAA TAA TTA TATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
1526574 TATA TTA TTA TTA
1 T-TA TTA TTA TTA
1526587 AAAAATAATA
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
3 47 0.87
4 7 0.13
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (3 bp):
TTA
Found at i:1527616 original size:20 final size:20
Alignment explanation
Indices: 1527593--1527640 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
1527583 GATTTAATCC
1527593 TTTAATTTTAA-TAAATATAT
1 TTTAATTTTAAGTAAATAT-T
** *
1527613 TTTAATCCTAAGTATATATT
1 TTTAATTTTAAGTAAATATT
1527633 TTTAATTT
1 TTTAATTT
1527641 ATTTATATGA
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
20 16 0.73
21 6 0.27
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (20 bp):
TTTAATTTTAAGTAAATATT
Found at i:1528100 original size:23 final size:22
Alignment explanation
Indices: 1528054--1528098 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1528044 ATATTATAAA
1528054 AAATTATAATTTAATTTTATTT
1 AAATTATAATTTAATTTTATTT
*
1528076 AAATTATTATATTAATATTTATT
1 AAATTATAAT-TTAAT-TTTATT
1528099 AATATCGAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 9 0.45
23 5 0.25
24 6 0.30
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
AAATTATAATTTAATTTTATTT
Found at i:1531248 original size:141 final size:143
Alignment explanation
Indices: 1530944--1531249 Score: 474
Period size: 141 Copynumber: 2.1 Consensus size: 143
1530934 GAGTCGAGGG
* *
1530944 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACATAT
1 TCTACGCGG-CCTTCGGG--ATA--TATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
*
1531009 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATCATTA
61 ACTTGATCCCTAATATATG-ATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATCATTA
*
1531074 TATGGCACTACGGTGCAAT
125 TATGGCACTACGGCGCAAT
*
1531093 TCTACGCGTCCTTCGGGATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACATACTT-
1 TCTACGCGGCCTTCGGGATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACATACTTG
*
1531157 ATCCCTAATATATG-TATGATTCTTAAGGAATAATATGTGGTCCTTATGGACAT-TTTATATGGC
66 ATCCCTAATATATGATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATCATTATATGGC
1531220 ACTACGGCGCAAT
131 ACTACGGCGCAAT
1531233 TCTACGCGGCACTTCGG
1 TCTACGCGGC-CTTCGG
1531250 TGCAATTTAT
Statistics
Matches: 149, Mismatches: 7, Indels: 10
0.90 0.04 0.06
Matches are distributed among these distances:
140 30 0.20
141 45 0.30
143 13 0.09
144 42 0.28
146 3 0.02
148 8 0.05
149 8 0.05
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (143 bp):
TCTACGCGGCCTTCGGGATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACATACTTG
ATCCCTAATATATGATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATCATTATATGGC
ACTACGGCGCAAT
Found at i:1549381 original size:18 final size:18
Alignment explanation
Indices: 1549358--1549392 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1549348 TTGTTTATTA
1549358 TTTTATAAATTTTAATAT
1 TTTTATAAATTTTAATAT
**
1549376 TTTTATTTATTTTAATA
1 TTTTATAAATTTTAATA
1549393 AATTTTTATT
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:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
TTTTATAAATTTTAATAT
Done.