Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011212.1 Corchorus capsularis cultivar CVL-1 contig11233, 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: 113581
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:3768 original size:2 final size:2
Alignment explanation
Indices: 3761--3817 Score: 57
Period size: 2 Copynumber: 29.5 Consensus size: 2
3751 GGTTTTAGGT
* * *
3761 TA TA TA TA TCA GA TA TA AA TA AA TA TA -A TA TA TA TA TA TA TA
1 TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3803 TA TA T- TA TA -A TA TA T
1 TA TA TA TA TA TA TA TA T
3818 GGGTCAGTCG
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
1 3 0.07
2 41 0.91
3 1 0.02
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (2 bp):
TA
Found at i:5042 original size:15 final size:16
Alignment explanation
Indices: 5022--5054 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
5012 TCAAAATATC
5022 GGGTC-ATTTGGGTTT
1 GGGTCAATTTGGGTTT
*
5037 GGGTCAATTTTGGTTT
1 GGGTCAATTTGGGTTT
5053 GG
1 GG
5055 TTTATTTTCG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.09, C:0.06, G:0.39, T:0.45
Consensus pattern (16 bp):
GGGTCAATTTGGGTTT
Found at i:6157 original size:324 final size:323
Alignment explanation
Indices: 5568--6351 Score: 1356
Period size: 324 Copynumber: 2.4 Consensus size: 323
5558 ATGAGGAGCG
* * * *
5568 AGAGAACTAATTTTTTTCGTCTTTTCCCACTTGGCCGATTACTTAAATGTCATAACTTTTGATTC
1 AGAGAACTTATTTTTTTCGTCTTTTCCTACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTC
* * *
5633 TTGAGGTGATTAAATAACTAGA-CTTTTTGGTCATTTCTCATTTGACTTT-AATAGAGTAGTGGA
66 TTGAGGGGATTAAATAA-TA-ATCTTTTTGGTCATTTCTCAATGGA-TTTGAATAGAGTAGTGGA
*
5696 ATTACTAAAAGATCCCTACCCCAAATTAATGATAAACTGGGTGGAATTACTATAAGATCCCTACC
128 ATTACTAAAAAATCCCTACCCCAAATTAATGATAAACTGGGTGGAATTACTATAAGATCCCTACC
5761 CCAGATTAATGATGAGCTGGAGAAGTAATCTTTTCCGTCTTTACCTACCTGGCAGATTACTTAAA
193 CCAGATTAATGATGAGCTGGAGAAGTAATCTTTTCCGTCTTTACCTACCTGGCAGATTACTTAAA
*
5826 TGTCCTAAACTTTAATAGAGTAGTGGAATTACTAAAAGATCCCTAACAAGACTTGCTTTTGGAGT
258 TGTCCTAAACTTTAATAGAGTAGTGGAATTACTAAAAGATCCCCAACAAGACTTGCTTTTGGAGT
5891 T
323 T
5892 AGAGAACTTATTTTTTTCGTCTTTTCCTACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTC
1 AGAGAACTTATTTTTTTCGTCTTTTCCTACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTC
*
5957 TTGAGGGGATTAAATAAGTAATCTTTCTGGTCATTTCTCAATGGATTTGAATAGAGTAGTGGAAT
66 TTGAGGGGATTAAATAA-TAATCTTTTTGGTCATTTCTCAATGGATTTGAATAGAGTAGTGGAAT
6022 TACTAAAAAATCCCTACCCCAAATTAATGATAAACTGGGTGGAATTACTATAAGATCCCTACCCC
130 TACTAAAAAATCCCTACCCCAAATTAATGATAAACTGGGTGGAATTACTATAAGATCCCTACCCC
* *
6087 AGATTAATGATGAGCTGGAGAAGTAATCTTTTTCGTCTTTACCTACCTGGCAGATTTCTTAAATG
195 AGATTAATGATGAGCTGGAGAAGTAATCTTTTCCGTCTTTACCTACCTGGCAGATTACTTAAATG
6152 TCCTAAACTTTAATAGAGTAGTGGAATTACTAAAAGATCCCCAACAAGACTTGCTTTTGGAGTT
260 TCCTAAACTTTAATAGAGTAGTGGAATTACTAAAAGATCCCCAACAAGACTTGCTTTTGGAGTT
* * * *
6216 GGAGAACTTATTTTTTCCGTCTTTTTCTACTTGACAGATTACTTAAATGTCCTAACTTTTGATTC
1 AGAGAACTTATTTTTTTCGTCTTTTCCTACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTC
*
6281 TTGAGGGGATTAAATAATAATCTTTTTGGTCATTTCTGAATGGATTTGAATAGAGTAGTGGAATT
66 TTGAGGGGATTAAATAATAATCTTTTTGGTCATTTCTCAATGGATTTGAATAGAGTAGTGGAATT
*
6346 ATTAAA
131 ACTAAA
6352 TGATGCCCTT
Statistics
Matches: 438, Mismatches: 20, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
323 55 0.13
324 383 0.87
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.36
Consensus pattern (323 bp):
AGAGAACTTATTTTTTTCGTCTTTTCCTACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTC
TTGAGGGGATTAAATAATAATCTTTTTGGTCATTTCTCAATGGATTTGAATAGAGTAGTGGAATT
ACTAAAAAATCCCTACCCCAAATTAATGATAAACTGGGTGGAATTACTATAAGATCCCTACCCCA
GATTAATGATGAGCTGGAGAAGTAATCTTTTCCGTCTTTACCTACCTGGCAGATTACTTAAATGT
CCTAAACTTTAATAGAGTAGTGGAATTACTAAAAGATCCCCAACAAGACTTGCTTTTGGAGTT
Found at i:7317 original size:2 final size:2
Alignment explanation
Indices: 7312--7336 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
7302 TGTGTGTGTG
7312 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 T
7337 TTCGTCTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:15994 original size:6 final size:6
Alignment explanation
Indices: 15954--16005 Score: 50
Period size: 6 Copynumber: 8.7 Consensus size: 6
15944 GCAAGGGGAG
* * * * * *
15954 GAGGAA GAGGTG GAGGAA GAGGAA GAGATA GAGGTA GAGGTG GAGGTA
1 GAGGTA GAGGTA GAGGTA GAGGTA GAGGTA GAGGTA GAGGTA GAGGTA
16002 GAGG
1 GAGG
16006 ATTTGGTATG
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.37, C:0.00, G:0.54, T:0.10
Consensus pattern (6 bp):
GAGGTA
Found at i:17801 original size:58 final size:57
Alignment explanation
Indices: 17706--17818 Score: 172
Period size: 58 Copynumber: 2.0 Consensus size: 57
17696 TCACACTTCA
*
17706 TAGGGGAAACAATATTTGATGAGCTTGTCAATTGTCAGTGGTTATTCATTCACCTTTG
1 TAGGGGAAACAATATTTGATGAGCTTGTCAATGGTCAGT-GTTATTCATTCACCTTTG
* * **
17764 TAGGGGAAACAATATTTGATGTGGTTGTCGCTGGTCAGTGTTATTCATTCACCTT
1 TAGGGGAAACAATATTTGATGAGCTTGTCAATGGTCAGTGTTATTCATTCACCTT
17819 ATGGTAGATC
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
57 16 0.32
58 34 0.68
ACGTcount: A:0.24, C:0.14, G:0.24, T:0.38
Consensus pattern (57 bp):
TAGGGGAAACAATATTTGATGAGCTTGTCAATGGTCAGTGTTATTCATTCACCTTTG
Found at i:17943 original size:2 final size:2
Alignment explanation
Indices: 17936--17966 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
17926 TTAAGCTCAA
17936 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
17967 TATATATATA
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:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:35984 original size:23 final size:23
Alignment explanation
Indices: 35954--35999 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
35944 TGTTTGTTTG
*
35954 TAGAGACCGAGTGAGAGTGCTCA
1 TAGAGACCGAGCGAGAGTGCTCA
35977 TAGAGACCGAGCGAGAGTGCTCA
1 TAGAGACCGAGCGAGAGTGCTCA
36000 AGATTGTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.30, C:0.20, G:0.35, T:0.15
Consensus pattern (23 bp):
TAGAGACCGAGCGAGAGTGCTCA
Found at i:40296 original size:50 final size:48
Alignment explanation
Indices: 40222--40316 Score: 145
Period size: 50 Copynumber: 1.9 Consensus size: 48
40212 GACAACTCCG
40222 AGCTTTCCCAAGCTCAAACAAGTGCTCCCCGCACTAATCACAAACCTA
1 AGCTTTCCCAAGCTCAAACAAGTGCTCCCCGCACTAATCACAAACCTA
* * *
40270 AGCTTTCCCCAAGCTTAGAACAAGTGCTCCCCGCACTGATTACAAAC
1 AGCTTT-CCCAAGCTCA-AACAAGTGCTCCCCGCACTAATCACAAAC
40317 AAATAGATAG
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
48 6 0.14
49 9 0.21
50 27 0.64
ACGTcount: A:0.32, C:0.36, G:0.13, T:0.20
Consensus pattern (48 bp):
AGCTTTCCCAAGCTCAAACAAGTGCTCCCCGCACTAATCACAAACCTA
Found at i:42509 original size:18 final size:18
Alignment explanation
Indices: 42486--42527 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
42476 CTGCAGCAAT
* *
42486 TTCTTCATCAGATTTTTC
1 TTCTTCAGCAGATTCTTC
*
42504 TTCTTCAGCAGCTTCTTC
1 TTCTTCAGCAGATTCTTC
42522 TTCTTC
1 TTCTTC
42528 CTCGTTCTCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.12, C:0.29, G:0.07, T:0.52
Consensus pattern (18 bp):
TTCTTCAGCAGATTCTTC
Found at i:49851 original size:21 final size:21
Alignment explanation
Indices: 49827--49866 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
49817 GTTGAACTTC
49827 TTCATTTCTGAATCTGTCTTT
1 TTCATTTCTGAATCTGTCTTT
*
49848 TTCATTTCTGTATCTGTCT
1 TTCATTTCTGAATCTGTCT
49867 CGTCCATGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.12, C:0.20, G:0.10, T:0.57
Consensus pattern (21 bp):
TTCATTTCTGAATCTGTCTTT
Found at i:51247 original size:26 final size:27
Alignment explanation
Indices: 51206--51256 Score: 86
Period size: 26 Copynumber: 1.9 Consensus size: 27
51196 CCAAGCCGTT
51206 ACAACAACCAAGCTTTCCCCAAGCTTG
1 ACAACAACCAAGCTTTCCCCAAGCTTG
*
51233 ACAAC-ACCGAGCTTTCCCCAAGCT
1 ACAACAACCAAGCTTTCCCCAAGCT
51257 CAAACAAGTG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 18 0.78
27 5 0.22
ACGTcount: A:0.31, C:0.39, G:0.12, T:0.18
Consensus pattern (27 bp):
ACAACAACCAAGCTTTCCCCAAGCTTG
Found at i:51263 original size:27 final size:27
Alignment explanation
Indices: 51206--51263 Score: 73
Period size: 26 Copynumber: 2.1 Consensus size: 27
51196 CCAAGCCGTT
**
51206 ACAACAACCAAGCTTTCCCCAAGCTTG
1 ACAACAACCAAGCTTTCCCCAAGCTAA
*
51233 ACAAC-ACCGAGCTTTCCCCAAGCTCAA
1 ACAACAACCAAGCTTTCCCCAAGCT-AA
51260 ACAA
1 ACAA
51264 GTGCTCCCCG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 18 0.67
27 9 0.33
ACGTcount: A:0.36, C:0.38, G:0.10, T:0.16
Consensus pattern (27 bp):
ACAACAACCAAGCTTTCCCCAAGCTAA
Found at i:51327 original size:50 final size:50
Alignment explanation
Indices: 51242--51387 Score: 240
Period size: 50 Copynumber: 2.9 Consensus size: 50
51232 GACAACACCG
* * *
51242 AGCTTTCCCCAAGCTCA-AACAAGTGCTCCCCGCACTAATCACAAACCTA
1 AGCTTTCCCCAAGCTTAGAACAAGTGCTCCCCGCACTGATTACAAACCTA
* *
51291 AGCTTTCCCCAAGCTTAGAATAAGTGCTCCCTGCACTGATTACAAACCTA
1 AGCTTTCCCCAAGCTTAGAACAAGTGCTCCCCGCACTGATTACAAACCTA
51341 AGCTTTCCCCAAGCTTAGAACAAGTGCTCCCCGCACTGATTACAAAC
1 AGCTTTCCCCAAGCTTAGAACAAGTGCTCCCCGCACTGATTACAAAC
51388 AAAGAGATAG
Statistics
Matches: 89, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
49 16 0.18
50 73 0.82
ACGTcount: A:0.31, C:0.34, G:0.13, T:0.22
Consensus pattern (50 bp):
AGCTTTCCCCAAGCTTAGAACAAGTGCTCCCCGCACTGATTACAAACCTA
Found at i:52445 original size:18 final size:18
Alignment explanation
Indices: 52419--52453 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
52409 CACCTTTTTC
52419 AAATATACCAAACCAAGG
1 AAATATACCAAACCAAGG
*
52437 AAATTTACCAAACCAAG
1 AAATATACCAAACCAAG
52454 AAGCTTGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.23, G:0.09, T:0.14
Consensus pattern (18 bp):
AAATATACCAAACCAAGG
Found at i:53007 original size:33 final size:33
Alignment explanation
Indices: 52970--53076 Score: 135
Period size: 33 Copynumber: 3.2 Consensus size: 33
52960 AGCACTAGCG
* *
52970 ACCGGCCATGCGACTTGGAGAAGTCCGGCCAAC
1 ACCGGCCACGCGACTTGGAGATGTCCGGCCAAC
* * *
53003 ACCGGCCACGTGACTCGGAGATGCCCGGCCAAC
1 ACCGGCCACGCGACTTGGAGATGTCCGGCCAAC
* *
53036 ACCGGCCACGCGACATGGACATGTCCGGCC-AC
1 ACCGGCCACGCGACTTGGAGATGTCCGGCCAAC
53068 AACCGGCCA
1 -ACCGGCCA
53077 TCGCTAGGCG
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
32 2 0.03
33 61 0.97
ACGTcount: A:0.23, C:0.38, G:0.29, T:0.09
Consensus pattern (33 bp):
ACCGGCCACGCGACTTGGAGATGTCCGGCCAAC
Found at i:54061 original size:8 final size:8
Alignment explanation
Indices: 54048--54081 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
54038 CACCTTCTTG
54048 AAAAATTC
1 AAAAATTC
54056 AAAAATTC
1 AAAAATTC
*
54064 AGAAACTTC
1 A-AAAATTC
54073 AAAAATTC
1 AAAAATTC
54081 A
1 A
54082 TAGCCAATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.59, C:0.15, G:0.03, T:0.24
Consensus pattern (8 bp):
AAAAATTC
Found at i:54172 original size:9 final size:9
Alignment explanation
Indices: 54154--54187 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
54144 AGTTATATCG
*
54154 AAAAATATA
1 AAAAAAATA
54163 AAAAAAATA
1 AAAAAAATA
54172 AAATAAAATA
1 AAA-AAAATA
54182 AAAAAA
1 AAAAAA
54188 TTTCGACCAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 14 0.61
10 9 0.39
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (9 bp):
AAAAAAATA
Found at i:59611 original size:33 final size:33
Alignment explanation
Indices: 59521--59623 Score: 93
Period size: 33 Copynumber: 3.1 Consensus size: 33
59511 CTAGCGACCA
* * * * *
59521 GCCATGCGACTTGGAGAAGTCCGACCAACACCG
1 GCCACGCGACTCGGACATGTCCGGCCAACACCG
* * *
59554 GCCACGTGACTCGGAGATGCCCGGCCAACACCG
1 GCCACGCGACTCGGACATGTCCGGCCAACACCG
*
59587 GCCGCGCGACAT-GGACATGTCCGGCC-ACAACCG
1 GCCACGCGAC-TCGGACATGTCCGGCCAAC-ACCG
59620 GCCA
1 GCCA
59624 TCGCTAGGCG
Statistics
Matches: 57, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
32 2 0.04
33 54 0.95
34 1 0.02
ACGTcount: A:0.23, C:0.38, G:0.29, T:0.10
Consensus pattern (33 bp):
GCCACGCGACTCGGACATGTCCGGCCAACACCG
Found at i:61366 original size:15 final size:14
Alignment explanation
Indices: 61315--61407 Score: 58
Period size: 11 Copynumber: 7.1 Consensus size: 14
61305 TTATGATTAG
*
61315 TTTTAATTAGTTAA
1 TTTTAATTAGTTTA
** *
61329 TTAAAATTA-CTTA
1 TTTTAATTAGTTTA
*
61342 GTTT-ATTAGTTTA
1 TTTTAATTAGTTTA
61355 TGTTTAATTAG--TA
1 T-TTTAATTAGTTTA
*
61368 -TCTAATTAGTTTA
1 TTTTAATTAGTTTA
61381 TTATTAATTAG--TA
1 TT-TTAATTAGTTTA
61394 -TTTAATTAGTTTA
1 TTTTAATTAGTTTA
61407 T
1 T
61408 GATTAAAATG
Statistics
Matches: 58, Mismatches: 11, Indels: 20
0.65 0.12 0.22
Matches are distributed among these distances:
11 16 0.28
12 5 0.09
13 14 0.24
14 11 0.19
15 12 0.21
ACGTcount: A:0.33, C:0.02, G:0.09, T:0.56
Consensus pattern (14 bp):
TTTTAATTAGTTTA
Found at i:61375 original size:26 final size:26
Alignment explanation
Indices: 61346--61413 Score: 102
Period size: 26 Copynumber: 2.6 Consensus size: 26
61336 TACTTAGTTT
61346 ATTAGTTTATGTTTAATTAGTATCTA
1 ATTAGTTTATGTTTAATTAGTATCTA
*
61372 ATTAGTTTAT-TATTAATTAGTATTTA
1 ATTAGTTTATGT-TTAATTAGTATCTA
*
61398 ATTAGTTTATGATTAA
1 ATTAGTTTATGTTTAA
61414 AATGAAGGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
25 1 0.03
26 37 0.97
ACGTcount: A:0.34, C:0.01, G:0.10, T:0.54
Consensus pattern (26 bp):
ATTAGTTTATGTTTAATTAGTATCTA
Found at i:61461 original size:24 final size:25
Alignment explanation
Indices: 61422--61481 Score: 79
Period size: 25 Copynumber: 2.5 Consensus size: 25
61412 AAAATGAAGG
*
61422 AAAATGAA-TTTGAAG-ATTTGTTA
1 AAAATGAAGTTTGAAGAAGTTGTTA
61445 AAAATGAAGTTTGAAGAAGTTGTTA
1 AAAATGAAGTTTGAAGAAGTTGTTA
* *
61470 GAAATTAAGTTT
1 AAAATGAAGTTT
61482 AGGGTTTGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
23 8 0.25
24 7 0.22
25 17 0.53
ACGTcount: A:0.43, C:0.00, G:0.20, T:0.37
Consensus pattern (25 bp):
AAAATGAAGTTTGAAGAAGTTGTTA
Found at i:63541 original size:22 final size:23
Alignment explanation
Indices: 63505--63577 Score: 82
Period size: 23 Copynumber: 3.2 Consensus size: 23
63495 CATGTGAAAA
63505 ACAAGAGCTGTGAAAAAACAAAG
1 ACAAGAGCTGTGAAAAAACAAAG
*
63528 ACAAG-GCCT-TGAAAAACAGGAAAG
1 ACAAGAG-CTGTGAAAAA-A-CAAAG
63552 -CAAGAGCTGTG-AAAAACAAAG
1 ACAAGAGCTGTGAAAAAACAAAG
63573 ACAAG
1 ACAAG
63578 CTCTTGGAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 13
0.74 0.04 0.23
Matches are distributed among these distances:
21 4 0.10
22 13 0.31
23 18 0.43
24 7 0.17
ACGTcount: A:0.53, C:0.15, G:0.23, T:0.08
Consensus pattern (23 bp):
ACAAGAGCTGTGAAAAAACAAAG
Found at i:64444 original size:21 final size:21
Alignment explanation
Indices: 64415--64469 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
64405 ATGAAATGTT
* *
64415 TTTGTGGTTTGATTATCAA-A
1 TTTGGGGTTTGACTATCAACA
*
64435 CTTTGGGGTTTGACTATCATCA
1 -TTTGGGGTTTGACTATCAACA
64457 TTTGGGGTTTGAC
1 TTTGGGGTTTGAC
64470 CATGTATGTA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
21 29 0.97
22 1 0.03
ACGTcount: A:0.18, C:0.11, G:0.25, T:0.45
Consensus pattern (21 bp):
TTTGGGGTTTGACTATCAACA
Found at i:64521 original size:21 final size:21
Alignment explanation
Indices: 64492--64546 Score: 76
Period size: 21 Copynumber: 2.6 Consensus size: 21
64482 ATGAAATGTT
*
64492 TTTGTGGTTTGACTATCAA-A
1 TTTGGGGTTTGACTATCAACA
*
64512 CTTTGGGGTTTGACTATCATCA
1 -TTTGGGGTTTGACTATCAACA
64534 TTTGGGGTTTGAC
1 TTTGGGGTTTGAC
64547 CATGTATCTA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
21 30 0.97
22 1 0.03
ACGTcount: A:0.18, C:0.13, G:0.25, T:0.44
Consensus pattern (21 bp):
TTTGGGGTTTGACTATCAACA
Found at i:64659 original size:76 final size:77
Alignment explanation
Indices: 64375--64677 Score: 450
Period size: 77 Copynumber: 3.9 Consensus size: 77
64365 TTATTAAAAT
* * *
64375 ATCATTTTGGGGTTTGATCATACATGTACAATGAAATGTTTTTGTGGTTTGATTATCAAACTTTG
1 ATCA-TTTGGGGTTTGACCATATATGTACAATGAAATGTTTTTGTGGTTTGACTATCAAACTTTG
64440 GGGTTTGACTATC
65 GGGTTTGACTATC
*
64453 ATCATTTGGGGTTTGACCATGTATGTACAATGAAATGTTTTTGTGGTTTGACTATCAAACTTTGG
1 ATCATTTGGGGTTTGACCATATATGTACAATGAAATGTTTTTGTGGTTTGACTATCAAACTTTGG
64518 GGTTTGACTATC
66 GGTTTGACTATC
* * ** * * *
64530 ATCATTTGGGGTTTGACCATGTATCTACAATGAAATGTTTTT-TTATTTAACTATCAAATTTTGA
1 ATCATTTGGGGTTTGACCATATATGTACAATGAAATGTTTTTGTGGTTTGACTATCAAACTTTGG
64594 GGTTTGACTATC
66 GGTTTGACTATC
* *
64606 ATCATTT-GGGTTTGACCATATATGTACAATGAAATGTTCTTGTGGTTTGACTATC-ATCATTTG
1 ATCATTTGGGGTTTGACCATATATGTACAATGAAATGTTTTTGTGGTTTGACTATCAAAC-TTTG
64669 GGGTTTGAC
65 GGGTTTGAC
64678 CACGTATGTA
Statistics
Matches: 204, Mismatches: 19, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
75 32 0.16
76 58 0.28
77 110 0.54
78 4 0.02
ACGTcount: A:0.25, C:0.12, G:0.21, T:0.43
Consensus pattern (77 bp):
ATCATTTGGGGTTTGACCATATATGTACAATGAAATGTTTTTGTGGTTTGACTATCAAACTTTGG
GGTTTGACTATC
Found at i:64693 original size:56 final size:56
Alignment explanation
Indices: 64594--64733 Score: 212
Period size: 56 Copynumber: 2.5 Consensus size: 56
64584 CAAATTTTGA
*
64594 GGTTTGACTATCATCATTT-GGGTTTGACCATATATGTACAATGAAATGTTCTTGT
1 GGTTTGACTATCATCATTTGGGGTTTGACCACATATGTACAATGAAATGTTCTTGT
* *
64649 GGTTTGACTATCATCATTTGGGGTTTGACCACGTATGTATAATGAAATGTTCTTGT
1 GGTTTGACTATCATCATTTGGGGTTTGACCACATATGTACAATGAAATGTTCTTGT
* *
64705 GGTTTGACTATTA-AACTTTGGGGTTTGAC
1 GGTTTGACTATCATCA-TTTGGGGTTTGAC
64734 TATCATTATT
Statistics
Matches: 78, Mismatches: 5, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
55 20 0.26
56 58 0.74
ACGTcount: A:0.24, C:0.12, G:0.23, T:0.41
Consensus pattern (56 bp):
GGTTTGACTATCATCATTTGGGGTTTGACCACATATGTACAATGAAATGTTCTTGT
Found at i:64731 original size:21 final size:21
Alignment explanation
Indices: 64705--64754 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
64695 ATGTTCTTGT
*
64705 GGTTTGACTATTA-AACTTTGG
1 GGTTTGACTATCATAA-TTTGG
*
64726 GGTTTGACTATCATTATTTGG
1 GGTTTGACTATCATAATTTGG
64747 GGTTTGAC
1 GGTTTGAC
64755 CATGCATGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 25 0.96
22 1 0.04
ACGTcount: A:0.20, C:0.10, G:0.26, T:0.44
Consensus pattern (21 bp):
GGTTTGACTATCATAATTTGG
Found at i:64739 original size:77 final size:77
Alignment explanation
Indices: 64649--64810 Score: 270
Period size: 77 Copynumber: 2.1 Consensus size: 77
64639 ATGTTCTTGT
* *
64649 GGTTTGACTATCATCATTTGGGGTTTGACCACGTATGTATAATGAAATGTTCTTGTGGTTTGACT
1 GGTTTGACTATCATCATTTGGGGTTTGACCACGCATGTACAATGAAATGTTCTTGTGGTTTGACT
*
64714 ATTAAACTTTGG
66 ATCAAACTTTGG
* * *
64726 GGTTTGACTATCATTATTTGGGGTTTGACCATGCATGTACAATGAAATGTTTTTGTGGTTTGACT
1 GGTTTGACTATCATCATTTGGGGTTTGACCACGCATGTACAATGAAATGTTCTTGTGGTTTGACT
64791 ATCAAACTTTGG
66 ATCAAACTTTGG
64803 GGTTTGAC
1 GGTTTGAC
64811 CATGTATATA
Statistics
Matches: 79, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
77 79 1.00
ACGTcount: A:0.23, C:0.12, G:0.24, T:0.41
Consensus pattern (77 bp):
GGTTTGACTATCATCATTTGGGGTTTGACCACGCATGTACAATGAAATGTTCTTGTGGTTTGACT
ATCAAACTTTGG
Found at i:64786 original size:56 final size:56
Alignment explanation
Indices: 64721--64862 Score: 223
Period size: 56 Copynumber: 2.5 Consensus size: 56
64711 ACTATTAAAC
* * *
64721 TTTGGGGTTTGACTATCATTA-TTTGGGGTTTGACCATGCATGTACAATGAAATGTT
1 TTTGTGGTTTGACTATCA-AACTTTGGGGTTTGACCATGCATATACAATGAAATGTT
*
64777 TTTGTGGTTTGACTATCAAACTTTGGGGTTTGACCATGTATATACAATGAAATGTT
1 TTTGTGGTTTGACTATCAAACTTTGGGGTTTGACCATGCATATACAATGAAATGTT
*
64833 CTTGTGGTTTGACTATCAAACTTTGGGGTT
1 TTTGTGGTTTGACTATCAAACTTTGGGGTT
64863 GACTATCATC
Statistics
Matches: 80, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
55 1 0.01
56 79 0.99
ACGTcount: A:0.23, C:0.11, G:0.24, T:0.42
Consensus pattern (56 bp):
TTTGTGGTTTGACTATCAAACTTTGGGGTTTGACCATGCATATACAATGAAATGTT
Found at i:64790 original size:133 final size:132
Alignment explanation
Indices: 64513--64942 Score: 607
Period size: 132 Copynumber: 3.3 Consensus size: 132
64503 ACTATCAAAC
* * * * **
64513 TTTGGGGTTTGACTATC-ATCATTTGGGGTTTGACCATGTATCTACAATGAAATGTT-TTTTTAT
1 TTTGTGGTTTGACTATCAAAC-TTTGGGGTTTGACCATGTATATACAATGAAATGTTCTTGTGGT
* * * *
64576 TTAACTATCAAATTTTGAGGTTTGACTATCATCATTTGGGTTTGACCATATATGTACAATGAAAT
65 TTGACTATCAAACTTTGGGGTTTGACTATCATCATTTGGGTTTGACCATACATGTACAATGAAAT
64641 GTT
130 GTT
* * * * *
64644 CTTGTGGTTTGACTATC-ATCATTTGGGGTTTGACCACGTATGTATAATGAAATGTTCTTGTGGT
1 TTTGTGGTTTGACTATCAAAC-TTTGGGGTTTGACCATGTATATACAATGAAATGTTCTTGTGGT
* * *
64708 TTGACTATTAAACTTTGGGGTTTGACTATCATTATTTGGGGTTTGACCATGCATGTACAATGAAA
65 TTGACTATCAAACTTTGGGGTTTGACTATCATCATTT-GGGTTTGACCATACATGTACAATGAAA
64773 TGTT
129 TGTT
64777 TTTGTGGTTTGACTATCAAACTTTGGGGTTTGACCATGTATATACAATGAAATGTTCTTGTGGTT
1 TTTGTGGTTTGACTATCAAACTTTGGGGTTTGACCATGTATATACAATGAAATGTTCTTGTGGTT
* *
64842 TGACTATCAAACTTTGGGG-TTGACTATCATCCTTTCGGGTTTGACCATTCATGTACAATGAAAT
66 TGACTATCAAACTTTGGGGTTTGACTATCATCATTT-GGGTTTGACCATACATGTACAATGAAAT
64906 GTT
130 GTT
*
64909 TTTGTGGTTTGACTACCAAACTTTGGGGTTTGAC
1 TTTGTGGTTTGACTATCAAACTTTGGGGTTTGAC
64943 TATCATTATT
Statistics
Matches: 270, Mismatches: 26, Indels: 5
0.90 0.09 0.02
Matches are distributed among these distances:
131 51 0.19
132 113 0.42
133 104 0.39
134 2 0.01
ACGTcount: A:0.24, C:0.13, G:0.21, T:0.42
Consensus pattern (132 bp):
TTTGTGGTTTGACTATCAAACTTTGGGGTTTGACCATGTATATACAATGAAATGTTCTTGTGGTT
TGACTATCAAACTTTGGGGTTTGACTATCATCATTTGGGTTTGACCATACATGTACAATGAAATG
TT
Found at i:64876 original size:20 final size:20
Alignment explanation
Indices: 64841--64882 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
64831 TTCTTGTGGT
*
64841 TTGACTATCAAACTTTGGGG
1 TTGACTATCAAACTTTCGGG
**
64861 TTGACTATCATCCTTTCGGG
1 TTGACTATCAAACTTTCGGG
64881 TT
1 TT
64883 TGACCATTCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.40
Consensus pattern (20 bp):
TTGACTATCAAACTTTCGGG
Found at i:64884 original size:76 final size:76
Alignment explanation
Indices: 64785--65088 Score: 389
Period size: 76 Copynumber: 4.0 Consensus size: 76
64775 TTTTTGTGGT
** * * *
64785 TTGACTATCAAACTTTGGGGTTTGACCATGT-ATATACAATGAAATGTTCTTGTGGTTTGACTAT
1 TTGACTATCATCCTTTCGGGTTTGACCAT-TCATGTACAATGAAATGTTTTTGTGGTTTGACTAT
64849 CAAACTTTGGGG
65 CAAACTTTGGGG
*
64861 TTGACTATCATCCTTTCGGGTTTGACCATTCATGTACAATGAAATGTTTTTGTGGTTTGACTACC
1 TTGACTATCATCCTTTCGGGTTTGACCATTCATGTACAATGAAATGTTTTTGTGGTTTGACTATC
64926 AAACTTTGGGG
66 AAACTTTGGGG
** * * *
64937 TTTGACTATCATTATTTGGGGTTTGACCATTCATGTACAATAAAATGATTTTTGTGATTTGACTA
1 -TTGACTATCATCCTTTCGGGTTTGACCATTCATGTACAATGAAATG-TTTTTGTGGTTTGACTA
**
65002 TCAAACTTTGAGAT
64 TCAAACTTTG-GGG
* *
65016 TTGACTATAATCC-TTCGGGATTTGACCATGCATGTACAAATGAAATGTTTTTGTGGTTTGACTA
1 TTGACTATCATCCTTTCGGG-TTTGACCATTCATGTAC-AATGAAATGTTTTTGTGGTTTGACTA
*
65080 T-AAAATTTG
64 TCAAACTTTG
65089 ATTATCAAAC
Statistics
Matches: 200, Mismatches: 22, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
75 1 0.00
76 68 0.34
77 54 0.27
78 68 0.34
79 9 0.05
ACGTcount: A:0.27, C:0.13, G:0.20, T:0.40
Consensus pattern (76 bp):
TTGACTATCATCCTTTCGGGTTTGACCATTCATGTACAATGAAATGTTTTTGTGGTTTGACTATC
AAACTTTGGGG
Found at i:64938 original size:21 final size:21
Alignment explanation
Indices: 64909--64963 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
64899 ATGAAATGTT
*
64909 TTTGTGGTTTGACTACCA-AA
1 TTTGGGGTTTGACTACCATAA
* *
64929 CTTTGGGGTTTGACTATCATTA
1 -TTTGGGGTTTGACTACCATAA
64951 TTTGGGGTTTGAC
1 TTTGGGGTTTGAC
64964 CATTCATGTA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
21 29 0.97
22 1 0.03
ACGTcount: A:0.18, C:0.13, G:0.25, T:0.44
Consensus pattern (21 bp):
TTTGGGGTTTGACTACCATAA
Found at i:65040 original size:78 final size:76
Alignment explanation
Indices: 64777--65089 Score: 380
Period size: 78 Copynumber: 4.1 Consensus size: 76
64767 ATGAAATGTT
* * * * * *
64777 TTTGTGGTTTGACTATCAAACTTTGGGGTTTGACCATGT-ATATACAATGAAATGTTCTTGTGGT
1 TTTGAGGTTTGACTATC-ATCCTTCGGGTTTGACCAT-TCATGTACAATGAAATGTTTTTGTGGT
64841 TTGACTATCAAAC
64 TTGACTATCAAAC
*
64854 TTTG-GGGTTGACTATCATCCTTTCGGGTTTGACCATTCATGTACAATGAAATGTTTTTGTGGTT
1 TTTGAGGTTTGACTATCATCC-TTCGGGTTTGACCATTCATGTACAATGAAATGTTTTTGTGGTT
*
64918 TGACTACCAAAC
65 TGACTATCAAAC
* ** * * *
64930 TTTGGGGTTTGACTATCATTATTTGGGGTTTGACCATTCATGTACAATAAAATGATTTTTGTGAT
1 TTTGAGGTTTGACTATCA-TCCTTCGGGTTTGACCATTCATGTACAATGAAATG-TTTTTGTGGT
64995 TTGACTATCAAAC
64 TTGACTATCAAAC
* * *
65008 TTTGAGATTTGACTATAATCCTTCGGGATTTGACCATGCATGTACAAATGAAATGTTTTTGTGGT
1 TTTGAGGTTTGACTATCATCCTTCGGG-TTTGACCATTCATGTAC-AATGAAATGTTTTTGTGGT
*
65073 TTGACTAT-AAAA
64 TTGACTATCAAAC
65085 TTTGA
1 TTTGA
65090 TTATCAAACT
Statistics
Matches: 205, Mismatches: 24, Indels: 14
0.84 0.10 0.06
Matches are distributed among these distances:
75 3 0.01
76 64 0.31
77 60 0.29
78 70 0.34
79 8 0.04
ACGTcount: A:0.26, C:0.13, G:0.20, T:0.41
Consensus pattern (76 bp):
TTTGAGGTTTGACTATCATCCTTCGGGTTTGACCATTCATGTACAATGAAATGTTTTTGTGGTTT
GACTATCAAAC
Found at i:69354 original size:45 final size:46
Alignment explanation
Indices: 69267--69363 Score: 178
Period size: 46 Copynumber: 2.1 Consensus size: 46
69257 CTACATTAGT
69267 GAAGATATCTTACCTTTGCCAAAAAAAAAAAAAAAAGAAAAAAGAA
1 GAAGATATCTTACCTTTGCCAAAAAAAAAAAAAAAAGAAAAAAGAA
*
69313 GAAGATATCTTACCTTTGCCAAAAAAAAAAAAAATAG-AAAAAGAA
1 GAAGATATCTTACCTTTGCCAAAAAAAAAAAAAAAAGAAAAAAGAA
69358 GAAGAT
1 GAAGAT
69364 TATATTAAAT
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
45 14 0.28
46 36 0.72
ACGTcount: A:0.61, C:0.10, G:0.12, T:0.16
Consensus pattern (46 bp):
GAAGATATCTTACCTTTGCCAAAAAAAAAAAAAAAAGAAAAAAGAA
Found at i:69536 original size:13 final size:13
Alignment explanation
Indices: 69518--69543 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
69508 TTTGGAATTC
69518 TAAATAATATTTA
1 TAAATAATATTTA
69531 TAAATAATATTTA
1 TAAATAATATTTA
69544 GAATTATAAT
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:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
TAAATAATATTTA
Found at i:74629 original size:158 final size:154
Alignment explanation
Indices: 74339--74652 Score: 574
Period size: 158 Copynumber: 2.0 Consensus size: 154
74329 GCATATCTGC
74339 ATCTACTCGAGTGGGAACATGGCCTATTACCGGATTCAACGCTGCCATCGTTGGAGTAGTTGAAG
1 ATCTACTCGAGTGGGAACATGGCCTATTACCGGATTCAACGCTGCCATCGTTGGAGTAGTTGAAG
*
74404 TAAACATGTCCTGATAGTAATTACACATAATTTCCTCGACATCCTTAACCTCTGTCCTCCACACA
66 TAAACATGTCCTGATAGTAATTACACACAATTTCCTCGACATCCTTAACCTCTGTCCTCCACACA
74469 CCATTAAAATCTTCAATACCCAAA
131 CCATTAAAATCTTCAATACCCAAA
*
74493 ATCTACTCGAGTGGGAACATGGCTTATTACCGGATTCAACGCTGCCATCGTTGGAGTAGTTGAAG
1 ATCTACTCGAGTGGGAACATGGCCTATTACCGGATTCAACGCTGCCATCGTTGGAGTAGTTGAAG
74558 TAATTAAACATGTCCTGATAGTAATTACACACAATTTCCTCGACATCCTTAACCTCTGTCCTCCA
66 ----TAAACATGTCCTGATAGTAATTACACACAATTTCCTCGACATCCTTAACCTCTGTCCTCCA
74623 CACACCATTAAAATCTTCAATACCCAAA
127 CACACCATTAAAATCTTCAATACCCAAA
74651 AT
1 AT
74653 GAAATTCTTT
Statistics
Matches: 154, Mismatches: 2, Indels: 4
0.96 0.01 0.03
Matches are distributed among these distances:
154 64 0.42
158 90 0.58
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (154 bp):
ATCTACTCGAGTGGGAACATGGCCTATTACCGGATTCAACGCTGCCATCGTTGGAGTAGTTGAAG
TAAACATGTCCTGATAGTAATTACACACAATTTCCTCGACATCCTTAACCTCTGTCCTCCACACA
CCATTAAAATCTTCAATACCCAAA
Found at i:78180 original size:30 final size:30
Alignment explanation
Indices: 78145--78201 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
78135 TCAACTAATT
78145 AATCAATCAAAAGTAATTAATATATTTGTC
1 AATCAATCAAAAGTAATTAATATATTTGTC
*
78175 AATCAATCTAAAGTAATTAATATATTT
1 AATCAATCAAAAGTAATTAATATATTT
78202 CCTTTTTTCC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.47, C:0.09, G:0.05, T:0.39
Consensus pattern (30 bp):
AATCAATCAAAAGTAATTAATATATTTGTC
Found at i:78417 original size:43 final size:43
Alignment explanation
Indices: 78370--78501 Score: 104
Period size: 43 Copynumber: 3.2 Consensus size: 43
78360 CGAAAGTGAA
78370 TAATTATTGATAGAATATTGATCTAGTTAATTAATATGCAAAT
1 TAATTATTGATAGAATATTGATCTAGTTAATTAATATGCAAAT
* * * *
78413 TAATTA-TAATTAGTTTAA-ATTTGA-CCA-AT-A-GAA-A-GTC-AA-
1 TAATTATTGA-TAG---AATA-TTGATCTAGTTAATTAATATG-CAAAT
78452 TAATTATTGATAGAATATTGATCTAGTTAATTAATATGCAAAT
1 TAATTATTGATAGAATATTGATCTAGTTAATTAATATGCAAAT
78495 TAATTAT
1 TAATTAT
78502 AATTGCTTTA
Statistics
Matches: 65, Mismatches: 8, Indels: 32
0.62 0.08 0.30
Matches are distributed among these distances:
36 6 0.09
37 3 0.05
38 1 0.02
39 10 0.15
40 7 0.11
41 4 0.06
42 7 0.11
43 17 0.26
44 1 0.02
45 3 0.05
46 6 0.09
ACGTcount: A:0.43, C:0.05, G:0.11, T:0.41
Consensus pattern (43 bp):
TAATTATTGATAGAATATTGATCTAGTTAATTAATATGCAAAT
Found at i:78464 original size:82 final size:82
Alignment explanation
Indices: 78361--78528 Score: 311
Period size: 82 Copynumber: 2.0 Consensus size: 82
78351 TACAATTATC
*
78361 GAAAGTGAATAATTATTGATAGAATATTGATCTAGTTAATTAATATGCAAATTAATTATAATTAG
1 GAAAGTCAATAATTATTGATAGAATATTGATCTAGTTAATTAATATGCAAATTAATTATAATT-G
78426 -TTTAAATTTGACCAATA
65 CTTTAAATTTGACCAATA
78443 GAAAGTCAATAATTATTGATAGAATATTGATCTAGTTAATTAATATGCAAATTAATTATAATTGC
1 GAAAGTCAATAATTATTGATAGAATATTGATCTAGTTAATTAATATGCAAATTAATTATAATTGC
78508 TTTAAATTTGACCAATA
66 TTTAAATTTGACCAATA
78525 GAAA
1 GAAA
78529 AGTTCTTTTC
Statistics
Matches: 84, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
81 1 0.01
82 83 0.99
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.38
Consensus pattern (82 bp):
GAAAGTCAATAATTATTGATAGAATATTGATCTAGTTAATTAATATGCAAATTAATTATAATTGC
TTTAAATTTGACCAATA
Found at i:81481 original size:30 final size:30
Alignment explanation
Indices: 81447--81504 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
81437 CAACTAATTA
81447 ATCAATCAAAAGTAATTAATATATTTCCCT
1 ATCAATCAAAAGTAATTAATATATTTCCCT
*
81477 ATCAATCTAAAGTAATTAATATATTTCC
1 ATCAATCAAAAGTAATTAATATATTTCC
81505 TTTTGTCCAA
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:0.43, C:0.16, G:0.03, T:0.38
Consensus pattern (30 bp):
ATCAATCAAAAGTAATTAATATATTTCCCT
Found at i:81824 original size:21 final size:21
Alignment explanation
Indices: 81798--81839 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
81788 CAAACTAAGA
81798 AAAACACCAGGAAAGATCACC
1 AAAACACCAGGAAAGATCACC
81819 AAAACACCAGGAAAGATCACC
1 AAAACACCAGGAAAGATCACC
81840 CGTGACAGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.52, C:0.29, G:0.14, T:0.05
Consensus pattern (21 bp):
AAAACACCAGGAAAGATCACC
Found at i:83225 original size:21 final size:21
Alignment explanation
Indices: 83201--83242 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
83191 AGATCGGGAG
83201 AAAGAAGAAAA-AGAAAGAAAA
1 AAAGAAGAAAAGA-AAAGAAAA
83222 AAAGAAGAAAAGAAAAGAAAA
1 AAAGAAGAAAAGAAAAGAAAA
83243 GAAAAAAACC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 19 0.95
22 1 0.05
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (21 bp):
AAAGAAGAAAAGAAAAGAAAA
Found at i:83236 original size:5 final size:5
Alignment explanation
Indices: 83209--83247 Score: 53
Period size: 5 Copynumber: 7.8 Consensus size: 5
83199 AGAAAGAAGA
*
83209 AAAAG -AAAG AAAAA AAGAAG AAAAG AAAAG AAAAG AAAA
1 AAAAG AAAAG AAAAG AA-AAG AAAAG AAAAG AAAAG AAAA
83248 AAACCCTAGC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
4 4 0.13
5 22 0.73
6 4 0.13
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:85246 original size:26 final size:26
Alignment explanation
Indices: 85217--85268 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
85207 AATTGGCTTA
85217 AGACTTGACGGGTTGGGCCGCACGGG
1 AGACTTGACGGGTTGGGCCGCACGGG
85243 AGACTTGACGGGTTGGGCCGCACGGG
1 AGACTTGACGGGTTGGGCCGCACGGG
85269 GGAGAGATGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.15, C:0.23, G:0.46, T:0.15
Consensus pattern (26 bp):
AGACTTGACGGGTTGGGCCGCACGGG
Found at i:87041 original size:14 final size:14
Alignment explanation
Indices: 87022--87049 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
87012 ACAGTAACCA
87022 ATCAGCTGATAATT
1 ATCAGCTGATAATT
87036 ATCAGCTGATAATT
1 ATCAGCTGATAATT
87050 TGGTTACTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (14 bp):
ATCAGCTGATAATT
Found at i:91703 original size:1 final size:1
Alignment explanation
Indices: 91699--91729 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
91689 CTTTTTTAGT
91699 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
91730 CTGGATGATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:95326 original size:12 final size:13
Alignment explanation
Indices: 95309--95337 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
95299 CACGGTGGCA
95309 GGTGG-TGTTTAT
1 GGTGGTTGTTTAT
95321 GGTGGTTGTTTAT
1 GGTGGTTGTTTAT
95334 GGTG
1 GGTG
95338 TTGCTAGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.31
13 11 0.69
ACGTcount: A:0.07, C:0.00, G:0.45, T:0.48
Consensus pattern (13 bp):
GGTGGTTGTTTAT
Found at i:96612 original size:32 final size:34
Alignment explanation
Indices: 96545--96613 Score: 106
Period size: 34 Copynumber: 2.1 Consensus size: 34
96535 TTACCTCTTG
96545 ATTAATGATTACCATTTTTACTTTTCTAAACCTA
1 ATTAATGATTACCATTTTTACTTTTCTAAACCTA
* *
96579 ATTACTGATTACCCTTTTT-CTTTT-TAAACCTA
1 ATTAATGATTACCATTTTTACTTTTCTAAACCTA
96611 ATT
1 ATT
96614 TCTTAATCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 11 0.33
33 5 0.15
34 17 0.52
ACGTcount: A:0.29, C:0.19, G:0.03, T:0.49
Consensus pattern (34 bp):
ATTAATGATTACCATTTTTACTTTTCTAAACCTA
Found at i:96676 original size:27 final size:28
Alignment explanation
Indices: 96645--96703 Score: 102
Period size: 27 Copynumber: 2.1 Consensus size: 28
96635 GGTGTCATTT
96645 TTACTCTTTTCTTACTCT-TTTTACTGA
1 TTACTCTTTTCTTACTCTCTTTTACTGA
*
96672 TTACTCTTTTCTTACTCTCTTTTATTGA
1 TTACTCTTTTCTTACTCTCTTTTACTGA
96700 TTAC
1 TTAC
96704 CACTTTTTAC
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 18 0.60
28 12 0.40
ACGTcount: A:0.15, C:0.22, G:0.03, T:0.59
Consensus pattern (28 bp):
TTACTCTTTTCTTACTCTCTTTTACTGA
Found at i:96693 original size:13 final size:13
Alignment explanation
Indices: 96648--96694 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
96638 GTCATTTTTA
96648 CTCTTTTCTTACT
1 CTCTTTTCTTACT
* *
96661 CT-TTTTACTGATT
1 CTCTTTT-CTTACT
96674 ACTCTTTTCTTACT
1 -CTCTTTTCTTACT
96688 CTCTTTT
1 CTCTTTT
96695 ATTGATTACC
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
12 4 0.15
13 13 0.48
14 6 0.22
15 4 0.15
ACGTcount: A:0.11, C:0.26, G:0.02, T:0.62
Consensus pattern (13 bp):
CTCTTTTCTTACT
Found at i:96713 original size:27 final size:27
Alignment explanation
Indices: 96645--96717 Score: 87
Period size: 27 Copynumber: 2.7 Consensus size: 27
96635 GGTGTCATTT
*
96645 TTACTCTTTTCTTACTCTTTTTACTGA
1 TTACTCCTTTCTTACTCTTTTTACTGA
* *
96672 TTACTCTTTTCTTACTCTCTTTTATTGA
1 TTACTCCTTTCTTACTCT-TTTTACTGA
96700 TTAC-CACTTT-TTACTCTT
1 TTACTC-CTTTCTTACTCTT
96718 CATTTTTTTC
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
26 1 0.02
27 26 0.62
28 15 0.36
ACGTcount: A:0.15, C:0.23, G:0.03, T:0.59
Consensus pattern (27 bp):
TTACTCCTTTCTTACTCTTTTTACTGA
Found at i:96789 original size:20 final size:20
Alignment explanation
Indices: 96764--96802 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
96754 TACAGATCAC
*
96764 CTTTTACTCTTATTGATTAT
1 CTTTTACTCTTACTGATTAT
96784 CTTTTACTCTTACTGATTA
1 CTTTTACTCTTACTGATTA
96803 CCCTTTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.21, C:0.18, G:0.05, T:0.56
Consensus pattern (20 bp):
CTTTTACTCTTACTGATTAT
Found at i:96910 original size:20 final size:20
Alignment explanation
Indices: 96885--96944 Score: 53
Period size: 20 Copynumber: 3.3 Consensus size: 20
96875 CTGATTACTT
96885 TTTACTCTTTAACATTCTTC
1 TTTACTCTTTAACATTCTTC
96905 TTTA--C--TAATCA--C-TC
1 TTTACTCTTTAA-CATTCTTC
*
96919 TTTACTCTTTACCATTCTTC
1 TTTACTCTTTAACATTCTTC
96939 TTTACT
1 TTTACT
96945 GATTACCCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 16
0.65 0.02 0.33
Matches are distributed among these distances:
14 6 0.19
15 1 0.03
16 4 0.13
17 4 0.13
18 3 0.10
19 1 0.03
20 12 0.39
ACGTcount: A:0.20, C:0.27, G:0.00, T:0.53
Consensus pattern (20 bp):
TTTACTCTTTAACATTCTTC
Found at i:96923 original size:34 final size:33
Alignment explanation
Indices: 96840--96963 Score: 139
Period size: 34 Copynumber: 3.7 Consensus size: 33
96830 TTACTTTTTT
96840 TTTACTATTACTCTTTTACTCTTTACCA-T-TT-
1 TTTACTATTACTC-TTTACTCTTTACCATTCTTC
* *
96871 TTTACTGATTACTTTTTACTCTTTAACATTCTTC
1 TTTACT-ATTACTCTTTACTCTTTACCATTCTTC
*
96905 TTTACTAATCACTCTTTACTCTTTACCATTCTTC
1 TTTACT-ATTACTCTTTACTCTTTACCATTCTTC
*
96939 TTTACTGATTACCCTTTTACT-TTTA
1 TTTACT-ATTACTC-TTTACTCTTTA
96964 ACTGGTTACC
Statistics
Matches: 79, Mismatches: 9, Indels: 7
0.83 0.09 0.07
Matches are distributed among these distances:
31 19 0.24
32 7 0.09
33 2 0.03
34 45 0.57
35 6 0.08
ACGTcount: A:0.20, C:0.23, G:0.02, T:0.55
Consensus pattern (33 bp):
TTTACTATTACTCTTTACTCTTTACCATTCTTC
Found at i:96972 original size:22 final size:22
Alignment explanation
Indices: 96942--97039 Score: 114
Period size: 22 Copynumber: 4.5 Consensus size: 22
96932 ATTCTTCTTT
96942 ACTGATTACCCTTTT-ACTTTTA
1 ACTGATTA-CCTTTTAACTTTTA
*
96964 ACTGGTTACCTTTTAACTTTCT-
1 ACTGATTACCTTTTAACTTT-TA
96986 ACTGATTACCATTTT-ACTTTTA
1 ACTGATTACC-TTTTAACTTTTA
*
97008 ACTGGTTACCTTTTAACTTTCT-
1 ACTGATTACCTTTTAACTTT-TA
97030 ACTGATTACC
1 ACTGATTACC
97040 ATTACTTTTT
Statistics
Matches: 66, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
21 11 0.17
22 49 0.74
23 6 0.09
ACGTcount: A:0.22, C:0.22, G:0.07, T:0.48
Consensus pattern (22 bp):
ACTGATTACCTTTTAACTTTTA
Found at i:96991 original size:44 final size:44
Alignment explanation
Indices: 96941--97042 Score: 195
Period size: 44 Copynumber: 2.3 Consensus size: 44
96931 CATTCTTCTT
*
96941 TACTGATTACCCTTTTACTTTTAACTGGTTACCTTTTAACTTTC
1 TACTGATTACCATTTTACTTTTAACTGGTTACCTTTTAACTTTC
96985 TACTGATTACCATTTTACTTTTAACTGGTTACCTTTTAACTTTC
1 TACTGATTACCATTTTACTTTTAACTGGTTACCTTTTAACTTTC
97029 TACTGATTACCATT
1 TACTGATTACCATT
97043 ACTTTTTACT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 57 1.00
ACGTcount: A:0.23, C:0.22, G:0.07, T:0.49
Consensus pattern (44 bp):
TACTGATTACCATTTTACTTTTAACTGGTTACCTTTTAACTTTC
Found at i:97082 original size:22 final size:22
Alignment explanation
Indices: 97057--97204 Score: 79
Period size: 22 Copynumber: 6.8 Consensus size: 22
97047 TTTACTATTA
*
97057 CTCTTCACTGATTACCACTTTG
1 CTCTTTACTGATTACCACTTTG
* * *
97079 CTCTTTACTAATTACTATTTTG
1 CTCTTTACTGATTACCACTTTG
* * *
97101 CCCTTTACTGATTATCC-TTTTA
1 CTCTTTACTGATTA-CCACTTTG
* * * *
97123 CTATTTACTGATTACTATTTTA
1 CTCTTTACTGATTACCACTTTG
* * *
97145 TTC-TTATTGATTACCA-TTCTA
1 CTCTTTACTGATTACCACTT-TG
* *
97166 CTTTTTACTGATTACCA-TGTG
1 CTCTTTACTGATTACCACTTTG
* *
97187 ACTCTTTTCTAATTACCA
1 -CTCTTTACTGATTACCA
97205 TTTTACCCCT
Statistics
Matches: 98, Mismatches: 23, Indels: 10
0.75 0.18 0.08
Matches are distributed among these distances:
20 2 0.02
21 16 0.16
22 79 0.81
23 1 0.01
ACGTcount: A:0.22, C:0.22, G:0.06, T:0.49
Consensus pattern (22 bp):
CTCTTTACTGATTACCACTTTG
Found at i:97205 original size:22 final size:22
Alignment explanation
Indices: 97154--97318 Score: 126
Period size: 22 Copynumber: 7.6 Consensus size: 22
97144 ATTCTTATTG
*
97154 ATTACCATTCT-ACT-TTTTACTG
1 ATTACCATT-TGACTCTTTT-CTA
*
97176 ATTACCATGTGACTCTTTTCTA
1 ATTACCATTTGACTCTTTTCTA
* * *
97198 ATTACCATTTTACCCCTTTCTA
1 ATTACCATTTGACTCTTTTCTA
* **
97220 ATTACTATTTGA--CTTTAATA
1 ATTACCATTTGACTCTTTTCTA
** *
97240 ATTACCATTCCAGT-TTTTGCTA
1 ATTACCATTTGACTCTTTT-CTA
*
97262 ATTACCATATGACTCTTTTCTA
1 ATTACCATTTGACTCTTTTCTA
* *
97284 ATTACCATTTTAC-CCTTTCTA
1 ATTACCATTTGACTCTTTTCTA
*
97305 ATTACTATTTGACT
1 ATTACCATTTGACT
97319 TTAATAATTA
Statistics
Matches: 111, Mismatches: 25, Indels: 14
0.74 0.17 0.09
Matches are distributed among these distances:
20 14 0.13
21 22 0.20
22 67 0.60
23 8 0.07
ACGTcount: A:0.25, C:0.22, G:0.05, T:0.47
Consensus pattern (22 bp):
ATTACCATTTGACTCTTTTCTA
Found at i:97267 original size:86 final size:85
Alignment explanation
Indices: 97154--97328 Score: 296
Period size: 86 Copynumber: 2.0 Consensus size: 85
97144 ATTCTTATTG
* * *
97154 ATTACCATTCTACTTTTTACTGATTACCATGTGACTCTTTTCTAATTACCATTTTACCCCTTTCT
1 ATTACCATTCCACTTTTTACTAATTACCATATGACTCTTTTCTAATTACCATTTTA-CCCTTTCT
97219 AATTACTATTTGACTTTAATA
65 AATTACTATTTGACTTTAATA
* *
97240 ATTACCATTCCAGTTTTTGCTAATTACCATATGACTCTTTTCTAATTACCATTTTACCCTTTCTA
1 ATTACCATTCCACTTTTTACTAATTACCATATGACTCTTTTCTAATTACCATTTTACCCTTTCTA
97305 ATTACTATTTGACTTTAATA
66 ATTACTATTTGACTTTAATA
97325 ATTA
1 ATTA
97329 TCTTTTACTT
Statistics
Matches: 84, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
85 33 0.39
86 51 0.61
ACGTcount: A:0.27, C:0.21, G:0.05, T:0.47
Consensus pattern (85 bp):
ATTACCATTCCACTTTTTACTAATTACCATATGACTCTTTTCTAATTACCATTTTACCCTTTCTA
ATTACTATTTGACTTTAATA
Found at i:97385 original size:21 final size:20
Alignment explanation
Indices: 97328--97405 Score: 102
Period size: 20 Copynumber: 3.9 Consensus size: 20
97318 TTTAATAATT
*
97328 ATCTTTTACTTTTACTGGTC
1 ATCTTTTACTTTTACTGATC
* *
97348 ATCTTTTACTCTTACTGATT
1 ATCTTTTACTTTTACTGATC
*
97368 TTCTTTTACTTTTTACTGATC
1 ATCTTTTAC-TTTTACTGATC
*
97389 ATCTTTTACTCTTACTG
1 ATCTTTTACTTTTACTG
97406 CTTATTAATT
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
20 32 0.65
21 17 0.35
ACGTcount: A:0.17, C:0.21, G:0.06, T:0.56
Consensus pattern (20 bp):
ATCTTTTACTTTTACTGATC
Found at i:97391 original size:41 final size:40
Alignment explanation
Indices: 97329--97405 Score: 136
Period size: 41 Copynumber: 1.9 Consensus size: 40
97319 TTAATAATTA
*
97329 TCTTTTACTTTTACTGGTCATCTTTTACTCTTACTGATTT
1 TCTTTTACTTTTACTGATCATCTTTTACTCTTACTGATTT
97369 TCTTTTACTTTTTACTGATCATCTTTTACTCTTACTG
1 TCTTTTAC-TTTTACTGATCATCTTTTACTCTTACTG
97406 CTTATTAATT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
40 8 0.23
41 27 0.77
ACGTcount: A:0.16, C:0.21, G:0.06, T:0.57
Consensus pattern (40 bp):
TCTTTTACTTTTACTGATCATCTTTTACTCTTACTGATTT
Found at i:97418 original size:41 final size:41
Alignment explanation
Indices: 97333--97418 Score: 113
Period size: 41 Copynumber: 2.1 Consensus size: 41
97323 TAATTATCTT
* **
97333 TTAC-TTTTACTGGTCATCTTTTACTCTTACTGATTTTCTT
1 TTACTTTTTACTGATCATCTTTTACTCTTACTGATTTTCAA
*
97373 TTACTTTTTACTGATCATCTTTTACTCTTACTGCTTATT-AA
1 TTACTTTTTACTGATCATCTTTTACTCTTACTGATT-TTCAA
97414 TTACT
1 TTACT
97419 AACTTATTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
40 4 0.10
41 34 0.85
42 2 0.05
ACGTcount: A:0.19, C:0.20, G:0.06, T:0.56
Consensus pattern (41 bp):
TTACTTTTTACTGATCATCTTTTACTCTTACTGATTTTCAA
Found at i:99555 original size:49 final size:49
Alignment explanation
Indices: 99481--99919 Score: 569
Period size: 49 Copynumber: 9.0 Consensus size: 49
99471 GGAAAAGGCA
* * * **
99481 TTTGGGAAATGGCAGGTAAGAATAAATACCTTCCGTCCGGGAAGGGCGT
1 TTTGGGAAATAGCAAGTAAAAATAAATGGCTTCCGTCCGGGAAGGGCGT
*
99530 TTTGGGAAATAGCAAGTAAAGATAAATGGCTTCCGTCCGGGAAGGGCGT
1 TTTGGGAAATAGCAAGTAAAAATAAATGGCTTCCGTCCGGGAAGGGCGT
* * * *
99579 TTTGGGGAGATAGCAAGCAAAAATAAATGGCTTCCGT-CTGGAAGGGCAT
1 TTT-GGGAAATAGCAAGTAAAAATAAATGGCTTCCGTCCGGGAAGGGCGT
** *
99628 TTTGGGAAATAGCAAGCGAAAATAAATGGCTTCCGTCTGGGAAGGGCGT
1 TTTGGGAAATAGCAAGTAAAAATAAATGGCTTCCGTCCGGGAAGGGCGT
* * *
99677 TTTGGGAAATAACAAGTAAAGATAAACGGCTTCCGTCCGGGAAGGGCGT
1 TTTGGGAAATAGCAAGTAAAAATAAATGGCTTCCGTCCGGGAAGGGCGT
* * * *
99726 TTTGGGGAGATAGCAAGCAAAAATAAATGGCTTCCGT-CTGGAAGGGCAT
1 TTT-GGGAAATAGCAAGTAAAAATAAATGGCTTCCGTCCGGGAAGGGCGT
** * *
99775 TTTGGGAAATAGCAAGCGAAAATAAATGGCTTCCGT-CTGGAAGGGCGC
1 TTTGGGAAATAGCAAGTAAAAATAAATGGCTTCCGTCCGGGAAGGGCGT
* * *
99823 TTTGGGAAATAGCAAGTAAAAATAAAATGGCTTCCGTCTGGGAATGGCGC
1 TTTGGGAAATAGCAAGTAAAAAT-AAATGGCTTCCGTCCGGGAAGGGCGT
* *
99873 TTTGGGAAATAGCAAGTAAAAATAAATGGCTTCCTTCTGGGAAGGGC
1 TTTGGGAAATAGCAAGTAAAAATAAATGGCTTCCGTCCGGGAAGGGC
99920 AAAAACGGAA
Statistics
Matches: 345, Mismatches: 40, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
48 93 0.27
49 162 0.47
50 90 0.26
ACGTcount: A:0.32, C:0.15, G:0.31, T:0.23
Consensus pattern (49 bp):
TTTGGGAAATAGCAAGTAAAAATAAATGGCTTCCGTCCGGGAAGGGCGT
Found at i:99748 original size:147 final size:147
Alignment explanation
Indices: 99477--99920 Score: 691
Period size: 147 Copynumber: 3.0 Consensus size: 147
99467 GCCCGGAAAA
* ** *
99477 GGCA-TTTGGGAAATGGC-AG-GTAAGAATAAATACCTTCCGTCCGGGAAGGGCGTTTTGGGAAA
1 GGCATTTTGGGAAATAGCAAGCG-AA-AATAAATGGCTTCCGTCTGGGAAGGGCGTTTTGGGAAA
99539 TAGCAAGTAAAGATAAATGGCTTCCGTCCGGGAAGGGCGTTTTGGGGAGATAGCAAGCAAAAATA
64 TAGCAAGTAAAGATAAATGGCTTCCGTCCGGGAAGGGCGTTTTGGGGAGATAGCAAGCAAAAATA
99604 AATGGCTTCCGTCTGGAAG
129 AATGGCTTCCGTCTGGAAG
99623 GGCATTTTGGGAAATAGCAAGCGAAAATAAATGGCTTCCGTCTGGGAAGGGCGTTTTGGGAAATA
1 GGCATTTTGGGAAATAGCAAGCGAAAATAAATGGCTTCCGTCTGGGAAGGGCGTTTTGGGAAATA
* *
99688 ACAAGTAAAGATAAACGGCTTCCGTCCGGGAAGGGCGTTTTGGGGAGATAGCAAGCAAAAATAAA
66 GCAAGTAAAGATAAATGGCTTCCGTCCGGGAAGGGCGTTTTGGGGAGATAGCAAGCAAAAATAAA
99753 TGGCTTCCGTCTGGAAG
131 TGGCTTCCGTCTGGAAG
*
99770 GGCATTTTGGGAAATAGCAAGCGAAAATAAATGGCTTCCGTCT-GGAAGGGCGCTTTGGGAAATA
1 GGCATTTTGGGAAATAGCAAGCGAAAATAAATGGCTTCCGTCTGGGAAGGGCGTTTTGGGAAATA
* * * * * *
99834 GCAAGTAAAAATAAAATGGCTTCCGTCTGGGAATGGCGCTTT-GGGAAATAGCAAGTAAAAATAA
66 GCAAGTAAAGAT-AAATGGCTTCCGTCCGGGAAGGGCGTTTTGGGGAGATAGCAAGCAAAAATAA
*
99898 ATGGCTTCCTTCTGGGAAG
130 ATGGCTTCCGTCT-GGAAG
99917 GGCA
1 GGCA
99921 AAAACGGAAA
Statistics
Matches: 277, Mismatches: 16, Indels: 9
0.92 0.05 0.03
Matches are distributed among these distances:
146 66 0.24
147 206 0.74
148 4 0.01
149 1 0.00
ACGTcount: A:0.32, C:0.15, G:0.31, T:0.22
Consensus pattern (147 bp):
GGCATTTTGGGAAATAGCAAGCGAAAATAAATGGCTTCCGTCTGGGAAGGGCGTTTTGGGAAATA
GCAAGTAAAGATAAATGGCTTCCGTCCGGGAAGGGCGTTTTGGGGAGATAGCAAGCAAAAATAAA
TGGCTTCCGTCTGGAAG
Found at i:100642 original size:50 final size:52
Alignment explanation
Indices: 100529--100642 Score: 130
Period size: 51 Copynumber: 2.2 Consensus size: 52
100519 TTATTAACAG
* *
100529 TTCAATCTTTTA-ACTCAAAGATCTCATTTTTATTCCAAAGATTAATCAAAA
1 TTCAATCTTTTAGACTCAAAGATCTCATTTTTATTACAAAGATTAATAAAAA
* * *
100580 TTCAACCTTTTAGTCT-AAAGA-CTTCATTTTTATTTACAAA-TTTAA-AAAAA
1 TTCAATCTTTTAGACTCAAAGATC-TCATTTTTA-TTACAAAGATTAATAAAAA
100630 TTCAATCTTTTAG
1 TTCAATCTTTTAG
100643 CTTAGGGATT
Statistics
Matches: 54, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
50 17 0.31
51 29 0.54
52 8 0.15
ACGTcount: A:0.38, C:0.16, G:0.04, T:0.42
Consensus pattern (52 bp):
TTCAATCTTTTAGACTCAAAGATCTCATTTTTATTACAAAGATTAATAAAAA
Found at i:100922 original size:51 final size:51
Alignment explanation
Indices: 100804--101076 Score: 345
Period size: 51 Copynumber: 5.3 Consensus size: 51
100794 TTATGGATTC
* *
100804 AATCTTTATTTACAAAAATTACTTAAAAG-TTCAATCTTTTAATT-AAAAATT
1 AATCTTTATTTAC--AAATTACTTAAAAGATTCAATCTTTCACTTAAAAAATT
*** * * *
100855 CAATAAATATTCACAAACTACTTAAAAGATTTAATCTTTCACTTAGAAAAA-T
1 -AATCTTTATTTACAAATTACTTAAAAGATTCAATCTTTCACTTA-AAAAATT
*
100907 AACCTTTATTTACAAATTACTTAAAAGATTCAATCTTTCACTTAAAAAATT
1 AATCTTTATTTACAAATTACTTAAAAGATTCAATCTTTCACTTAAAAAATT
100958 AATCTTTATTTACAAATTACTTAAAAGATTCAATCTTTCACTTAAAAAATT
1 AATCTTTATTTACAAATTACTTAAAAGATTCAATCTTTCACTTAAAAAATT
* * * * ** *
101009 AATCTTTATTTACAAATTACGTAAAAGATTCAATCTTTTAATCAAAAGCTC
1 AATCTTTATTTACAAATTACTTAAAAGATTCAATCTTTCACTTAAAAAATT
101060 AATCTTTATTTACAAAT
1 AATCTTTATTTACAAAT
101077 AAATTTCCAA
Statistics
Matches: 194, Mismatches: 23, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
50 18 0.09
51 161 0.83
52 10 0.05
53 5 0.03
ACGTcount: A:0.44, C:0.14, G:0.03, T:0.39
Consensus pattern (51 bp):
AATCTTTATTTACAAATTACTTAAAAGATTCAATCTTTCACTTAAAAAATT
Found at i:100963 original size:20 final size:21
Alignment explanation
Indices: 100925--100964 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
100915 TTTACAAATT
*
100925 ACTTAAAAGATTCAATCTTTC
1 ACTTAAAAAATTCAATCTTTC
100946 ACTTAAAAAATT-AATCTTT
1 ACTTAAAAAATTCAATCTTT
100965 ATTTACAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.42, C:0.15, G:0.03, T:0.40
Consensus pattern (21 bp):
ACTTAAAAAATTCAATCTTTC
Found at i:101014 original size:20 final size:21
Alignment explanation
Indices: 100976--101015 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
100966 TTTACAAATT
*
100976 ACTTAAAAGATTCAATCTTTC
1 ACTTAAAAAATTCAATCTTTC
100997 ACTTAAAAAATT-AATCTTT
1 ACTTAAAAAATTCAATCTTT
101016 ATTTACAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.42, C:0.15, G:0.03, T:0.40
Consensus pattern (21 bp):
ACTTAAAAAATTCAATCTTTC
Found at i:106518 original size:103 final size:103
Alignment explanation
Indices: 106336--106543 Score: 407
Period size: 103 Copynumber: 2.0 Consensus size: 103
106326 TGGGATCAAT
106336 TGTCCTTAAGGGAACCATCTTGGAGGTGCTCTGGAGATGCTGAGGATTATGCGAAAATGAAGGAA
1 TGTCCTTAAGGGAACCATCTTGGAGGTGCTCTGGAGATGCTGAGGATTATGCGAAAATGAAGGAA
*
106401 GAAATGCAAGTTTATCAGTTTTGCATGGCACTCACTAA
66 GAAATGCAAATTTATCAGTTTTGCATGGCACTCACTAA
106439 TGTCCTTAAGGGAACCATCTTGGAGGTGCTCTGGAGATGCTGAGGATTATGCGAAAATGAAGGAA
1 TGTCCTTAAGGGAACCATCTTGGAGGTGCTCTGGAGATGCTGAGGATTATGCGAAAATGAAGGAA
106504 GAAATGCAAATTTATCAGTTTTGCATGGCACTCACTAA
66 GAAATGCAAATTTATCAGTTTTGCATGGCACTCACTAA
106542 TG
1 TG
106544 AGTTTGAATC
Statistics
Matches: 104, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
103 104 1.00
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.27
Consensus pattern (103 bp):
TGTCCTTAAGGGAACCATCTTGGAGGTGCTCTGGAGATGCTGAGGATTATGCGAAAATGAAGGAA
GAAATGCAAATTTATCAGTTTTGCATGGCACTCACTAA
Found at i:110895 original size:22 final size:22
Alignment explanation
Indices: 110827--110895 Score: 72
Period size: 22 Copynumber: 3.2 Consensus size: 22
110817 AGATTATGAA
110827 GATAACCACACTA--AAACTT-T
1 GATAACCACACTATGAAA-TTAT
*
110847 GATAACCACACTATGAAATTCT
1 GATAACCACACTATGAAATTAT
* **
110869 TATAACCTTACTATGAAATTAT
1 GATAACCACACTATGAAATTAT
110891 GATAA
1 GATAA
110896 GCTCTTTGAT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
20 13 0.32
21 2 0.05
22 26 0.63
ACGTcount: A:0.43, C:0.19, G:0.07, T:0.30
Consensus pattern (22 bp):
GATAACCACACTATGAAATTAT
Found at i:111060 original size:42 final size:43
Alignment explanation
Indices: 110979--111060 Score: 103
Period size: 42 Copynumber: 1.9 Consensus size: 43
110969 AACTTGATTT
* * * *
110979 TATAATAATTTGATAACCTTCTTATGAAATTCTGGTAACCACA
1 TATAATAATTTGATAACCTCCCTACGAAATTCTGATAACCACA
* *
111022 TATAA-AATTTGATAACCTCCCTACGAAATTTTTATAACC
1 TATAATAATTTGATAACCTCCCTACGAAATTCTGATAACC
111061 TCAAAATGAA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
42 28 0.85
43 5 0.15
ACGTcount: A:0.38, C:0.18, G:0.07, T:0.37
Consensus pattern (43 bp):
TATAATAATTTGATAACCTCCCTACGAAATTCTGATAACCACA
Found at i:111371 original size:18 final size:19
Alignment explanation
Indices: 111334--111374 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
111324 AAAGTCATTT
111334 TTTTAAATTTAATTTAGTA
1 TTTTAAATTTAATTTAGTA
* *
111353 TTTTAGATTT-ATTTGGTA
1 TTTTAAATTTAATTTAGTA
111371 TTTT
1 TTTT
111375 TAGTTTTTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.27, C:0.00, G:0.10, T:0.63
Consensus pattern (19 bp):
TTTTAAATTTAATTTAGTA
Found at i:111375 original size:19 final size:20
Alignment explanation
Indices: 111333--111377 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
111323 TAAAGTCATT
*
111333 TTTTTAAATTTAATTTAGTA
1 TTTTTAGATTTAATTTAGTA
*
111353 -TTTTAGATTT-ATTTGGTA
1 TTTTTAGATTTAATTTAGTA
111371 TTTTTAG
1 TTTTTAG
111378 TTTTTGATCT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.27, C:0.00, G:0.11, T:0.62
Consensus pattern (20 bp):
TTTTTAGATTTAATTTAGTA
Found at i:111965 original size:22 final size:23
Alignment explanation
Indices: 111940--111988 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
111930 AACCATATTG
* *
111940 TGAAAATAT-GATAAGCTCATTA
1 TGAAAATATCAATAACCTCATTA
*
111962 TG-AAATTTCAATAACCTCATTA
1 TGAAAATATCAATAACCTCATTA
111984 TGAAA
1 TGAAA
111989 TTTCTTTAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
21 5 0.23
22 15 0.68
23 2 0.09
ACGTcount: A:0.45, C:0.12, G:0.10, T:0.33
Consensus pattern (23 bp):
TGAAAATATCAATAACCTCATTA
Found at i:111989 original size:22 final size:22
Alignment explanation
Indices: 111950--112010 Score: 77
Period size: 22 Copynumber: 2.8 Consensus size: 22
111940 TGAAAATATG
*
111950 ATAAGCTCATTATGAAATTTCA
1 ATAACCTCATTATGAAATTTCA
*
111972 ATAACCTCATTATGAAATTTCT
1 ATAACCTCATTATGAAATTTCA
* **
111994 TTAACCTCCCTATGAAA
1 ATAACCTCATTATGAAA
112011 ATTTGATAAC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.38, C:0.20, G:0.07, T:0.36
Consensus pattern (22 bp):
ATAACCTCATTATGAAATTTCA
Found at i:112020 original size:22 final size:22
Alignment explanation
Indices: 111995--112420 Score: 92
Period size: 22 Copynumber: 19.3 Consensus size: 22
111985 GAAATTTCTT
111995 TAACCTCCCTATGAAAATTTGA
1 TAACCTCCCTATGAAAATTTGA
* * *
112017 TAACCACAC--TGAAATTTTGA
1 TAACCTCCCTATGAAAATTTGA
*
112037 TAATCTCCCTATG-AAA---GA
1 TAACCTCCCTATGAAAATTTGA
* * * *
112055 TAATCACACTAT-AAAA-TTGG
1 TAACCTCCCTATGAAAATTTGA
* ** *
112075 TAACCGCAATATGAAAATTTTTA
1 TAACCTCCCTATGAAAA-TTTGA
* * *
112098 TAACCACACAATG-AAATTTCGA
1 TAACCTCCCTATGAAAATTT-GA
* * *
112120 TAACCTCCTTATGAGAATGGAACTATAA
1 TAACCTCCCTAT--GAA---AA-TTTGA
* * * *
112148 TATCCTCTCTATGTAATTTTGA
1 TAACCTCCCTATGAAAATTTGA
* *
112170 TAATCTCTCC-AT-AAAATTTTCA
1 TAACCTC-CCTATGAAAA-TTTGA
* *
112192 TAACATCCCTAT-AAAATTTTA
1 TAACCTCCCTATGAAAATTTGA
* *
112213 TTAACCTCCCTAGGAAATTTTGA
1 -TAACCTCCCTATGAAAATTTGA
* *
112236 TAACCTCACTCCCTATGAAATTTTGT
1 TAA---C-CTCCCTATGAAAATTTGA
* * *
112262 TAACATTCTTAT-AAAATTTTGA
1 TAACCTCCCTATGAAAA-TTTGA
* * *
112284 TAACCACACTA-CAAAATTTCGA
1 TAACCTCCCTATGAAAATTT-GA
* * * * *
112306 TAACCTTCGTGTGAAAATTCGG
1 TAACCTCCCTATGAAAATTTGA
* *
112328 TAACCTCCCTAAGAAACTTTGA
1 TAACCTCCCTATGAAAATTTGA
*** *
112350 TAACCTTTTTATG-AAATTTGG
1 TAACCTCCCTATGAAAATTTGA
** * *
112371 TAACCTCTTTATTAAATTTTGA
1 TAACCTCCCTATGAAAATTTGA
* **
112393 TAA-CTACGCTATGAAGTTTTGA
1 TAACCT-CCCTATGAAAATTTGA
112415 TAACCT
1 TAACCT
112421 TCATAAATTA
Statistics
Matches: 286, Mismatches: 86, Indels: 63
0.66 0.20 0.14
Matches are distributed among these distances:
18 15 0.05
20 26 0.09
21 42 0.15
22 135 0.47
23 30 0.10
24 1 0.00
25 2 0.01
26 21 0.07
28 12 0.04
29 2 0.01
ACGTcount: A:0.36, C:0.19, G:0.09, T:0.35
Consensus pattern (22 bp):
TAACCTCCCTATGAAAATTTGA
Found at i:112257 original size:48 final size:48
Alignment explanation
Indices: 112197--112293 Score: 122
Period size: 48 Copynumber: 2.0 Consensus size: 48
112187 TTTCATAACA
* * *
112197 TCCCTATAAAATTTTATTAACCTCCCTAGGAAATTTTGATAACCTCAC
1 TCCCTATAAAATTTTATTAACATCCCTAGAAAATTTTGATAACCACAC
* * * * *
112245 TCCCTATGAAATTTTGTTAACATTCTTATAAAATTTTGATAACCACAC
1 TCCCTATAAAATTTTATTAACATCCCTAGAAAATTTTGATAACCACAC
112293 T
1 T
112294 ACAAAATTTC
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
48 41 1.00
ACGTcount: A:0.34, C:0.22, G:0.06, T:0.38
Consensus pattern (48 bp):
TCCCTATAAAATTTTATTAACATCCCTAGAAAATTTTGATAACCACAC
Found at i:112374 original size:21 final size:21
Alignment explanation
Indices: 112340--112396 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 21
112330 ACCTCCCTAA
*
112340 GAAACTTTGATAACCTTTTTAT
1 GAAA-TTTGATAACCTCTTTAT
*
112362 GAAATTTGGTAACCTCTTTAT
1 GAAATTTGATAACCTCTTTAT
*
112383 TAAATTTTGATAAC
1 GAAA-TTTGATAAC
112397 TACGCTATGA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 18 0.60
22 12 0.40
ACGTcount: A:0.33, C:0.12, G:0.11, T:0.44
Consensus pattern (21 bp):
GAAATTTGATAACCTCTTTAT
Done.