Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011313.1 Corchorus capsularis cultivar CVL-1 contig11334, 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: 74504
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:26 original size:2 final size:2
Alignment explanation
Indices: 14--44 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
4 TTATTTGTTG
14 AT AT A- 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
45 TACGTATAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6043 original size:45 final size:45
Alignment explanation
Indices: 5979--6116 Score: 251
Period size: 45 Copynumber: 3.1 Consensus size: 45
5969 CACTAAATTG
5979 TTTCTTTGTATTATGTAACTCAATATTTGATGGAACTCCTTCATT
1 TTTCTTTGTATTATGTAACTCAATATTTGATGGAACTCCTTCATT
*
6024 TTTCTTTGTATTATGTAACTCAATATTTGATGGAACTTCTTCATT
1 TTTCTTTGTATTATGTAACTCAATATTTGATGGAACTCCTTCATT
6069 TTTCTTTGTATTATGTAACTCAATA-TTGATGGAACTCCTTCATAT
1 TTTCTTTGTATTATGTAACTCAATATTTGATGGAACTCCTTCAT-T
6114 TTT
1 TTT
6117 TTTAATGTGC
Statistics
Matches: 90, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
44 17 0.19
45 73 0.81
ACGTcount: A:0.25, C:0.14, G:0.11, T:0.50
Consensus pattern (45 bp):
TTTCTTTGTATTATGTAACTCAATATTTGATGGAACTCCTTCATT
Found at i:7446 original size:10 final size:10
Alignment explanation
Indices: 7431--7472 Score: 50
Period size: 11 Copynumber: 4.1 Consensus size: 10
7421 TATAGTCGTT
7431 AAAATTAAAA
1 AAAATTAAAA
*
7441 AAAATT-ATA
1 AAAATTAAAA
7450 AAAATTATAAA
1 AAAATTA-AAA
7461 AAAATTTAAAA
1 AAAA-TTAAAA
7472 A
1 A
7473 GTAAAAAACT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
9 8 0.30
10 6 0.22
11 10 0.37
12 3 0.11
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (10 bp):
AAAATTAAAA
Found at i:7455 original size:19 final size:18
Alignment explanation
Indices: 7431--7480 Score: 73
Period size: 19 Copynumber: 2.7 Consensus size: 18
7421 TATAGTCGTT
7431 AAAATTAAAAAAAATTATA
1 AAAATTAAAAAAAATT-TA
7450 AAAATTATAAAAAAATTTA
1 AAAATTA-AAAAAAATTTA
*
7469 AAAAGTAAAAAA
1 AAAATTAAAAAA
7481 CTGGATTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 5 0.17
19 15 0.52
20 9 0.31
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (18 bp):
AAAATTAAAAAAAATTTA
Found at i:13978 original size:31 final size:32
Alignment explanation
Indices: 13916--13982 Score: 91
Period size: 32 Copynumber: 2.1 Consensus size: 32
13906 GGTATTGCTG
* * *
13916 ACGTGGTAATGCCATGTCGGACCAAAAATGCC
1 ACGTGGCAATGCCACGTCGGAACAAAAATGCC
*
13948 ACGTGGCAATGCCACGTTGGAAC-AAAATGCC
1 ACGTGGCAATGCCACGTCGGAACAAAAATGCC
13979 ACGT
1 ACGT
13983 CAGCAATATT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
31 12 0.39
32 19 0.61
ACGTcount: A:0.31, C:0.25, G:0.25, T:0.18
Consensus pattern (32 bp):
ACGTGGCAATGCCACGTCGGAACAAAAATGCC
Found at i:24506 original size:27 final size:27
Alignment explanation
Indices: 24476--24531 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
24466 AGTTTAATTA
24476 GAAAGAGATCGTATGG-TTCTCTCTAAC
1 GAAAGAGATCGT-TGGTTTCTCTCTAAC
24503 GAAAGAGATCGTTGGTTTCTCTCTAAC
1 GAAAGAGATCGTTGGTTTCTCTCTAAC
24530 GA
1 GA
24532 GCCCAAGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 3 0.11
27 25 0.89
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.30
Consensus pattern (27 bp):
GAAAGAGATCGTTGGTTTCTCTCTAAC
Found at i:24524 original size:71 final size:71
Alignment explanation
Indices: 24442--24575 Score: 214
Period size: 71 Copynumber: 1.9 Consensus size: 71
24432 CTATGATATT
* * * * *
24442 GTTGGGTTCTCTCTATCGAGTCCAAGTTTAATTAGAAAGAGATCGTATGGTTCTCTCTAACGAAA
1 GTTGGGTTCTCTCTAACGAGCCCAAGTTTAATTAGAAAAAGATCATAGGGTTCTCTCTAACGAAA
24507 GAGATC
66 GAGATC
*
24513 GTTGGTTTCTCTCTAACGAGCCCAAGTTTAATTAGAAAAAGATCATAGGGTTCTCTCTAACGA
1 GTTGGGTTCTCTCTAACGAGCCCAAGTTTAATTAGAAAAAGATCATAGGGTTCTCTCTAACGA
24576 GCCCTGGTTT
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
71 57 1.00
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (71 bp):
GTTGGGTTCTCTCTAACGAGCCCAAGTTTAATTAGAAAAAGATCATAGGGTTCTCTCTAACGAAA
GAGATC
Found at i:28340 original size:13 final size:13
Alignment explanation
Indices: 28322--28365 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
28312 TCATGCACCC
*
28322 AAAATCTTTTAAT
1 AAAATCATTTAAT
28335 AAAATCATTT-AT
1 AAAATCATTTAAT
*
28347 AAAAATAATTTAAT
1 -AAAATCATTTAAT
28361 AAAAT
1 AAAAT
28366 AGTTCCTCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 2 0.07
13 23 0.85
14 2 0.07
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.39
Consensus pattern (13 bp):
AAAATCATTTAAT
Found at i:28614 original size:28 final size:28
Alignment explanation
Indices: 28558--28614 Score: 64
Period size: 28 Copynumber: 2.0 Consensus size: 28
28548 CCAAAGTAAC
* *
28558 AAACAAAAATATCAAAAACAGTCATATA
1 AAACAAAAAAATCAAAAACAGTCACATA
28586 AAACAAAATAAATCACAAAA-AG-CACATA
1 AAACAAAA-AAATCA-AAAACAGTCACATA
28614 A
1 A
28615 CCCAGACCCT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
28 14 0.56
29 7 0.28
30 4 0.16
ACGTcount: A:0.67, C:0.16, G:0.04, T:0.14
Consensus pattern (28 bp):
AAACAAAAAAATCAAAAACAGTCACATA
Found at i:29066 original size:6 final size:6
Alignment explanation
Indices: 29057--29084 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
29047 ATAATATACT
29057 ATATTA ATATTA ATATTA ATATTA ATAT
1 ATATTA ATATTA ATATTA ATATTA ATAT
29085 AAGTTTTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
ATATTA
Found at i:29187 original size:19 final size:19
Alignment explanation
Indices: 29148--29187 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
29138 TTCGGCCCTA
* * *
29148 CTTTTCTTTTTTCTTTTTT
1 CTTTTCCTTTTTCCTTCTT
29167 CTTTTCCTTTTTCCTTCTT
1 CTTTTCCTTTTTCCTTCTT
29186 CT
1 CT
29188 CCTTCCTCTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (19 bp):
CTTTTCCTTTTTCCTTCTT
Found at i:29754 original size:18 final size:18
Alignment explanation
Indices: 29731--29769 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
29721 TGTGTATATA
29731 TATATTAGC-ATGAAAATG
1 TATATT-GCTATGAAAATG
29749 TATATTGCTATGAAAATG
1 TATATTGCTATGAAAATG
29767 TAT
1 TAT
29770 TGCGTTTCAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 2 0.10
18 18 0.90
ACGTcount: A:0.41, C:0.05, G:0.15, T:0.38
Consensus pattern (18 bp):
TATATTGCTATGAAAATG
Found at i:31566 original size:19 final size:19
Alignment explanation
Indices: 31522--31572 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
31512 TAGTATTTAC
*
31522 ATATTTCCATATTTCTCTT
1 ATATTTCCTTATTTCTCTT
*
31541 TTATTTCCTTATTTCTCCTT
1 ATATTTCCTTATTTCT-CTT
31561 AT-TTTCCTTATT
1 ATATTTCCTTATT
31573 CTTTTTTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 24 0.86
20 4 0.14
ACGTcount: A:0.16, C:0.22, G:0.00, T:0.63
Consensus pattern (19 bp):
ATATTTCCTTATTTCTCTT
Found at i:31583 original size:18 final size:19
Alignment explanation
Indices: 31525--31582 Score: 66
Period size: 19 Copynumber: 3.2 Consensus size: 19
31515 TATTTACATA
* *
31525 TTTCCATATTTCTCTTTTA
1 TTTCCTTATTTCTCTTTTT
* *
31544 TTTCCTTATTTCTCCTTAT
1 TTTCCTTATTTCTCTTTTT
31563 TTTCCTTA-TTCT-TTTTT
1 TTTCCTTATTTCTCTTTTT
31580 TTT
1 TTT
31583 TTAATTTGGG
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
17 6 0.18
18 4 0.12
19 23 0.70
ACGTcount: A:0.10, C:0.21, G:0.00, T:0.69
Consensus pattern (19 bp):
TTTCCTTATTTCTCTTTTT
Found at i:32747 original size:27 final size:29
Alignment explanation
Indices: 32711--32764 Score: 85
Period size: 27 Copynumber: 1.9 Consensus size: 29
32701 AAAAAATGGC
*
32711 TTTTTTTTTCAGTT-CTTTCTT-TTCTTT
1 TTTTTTTTTCACTTACTTTCTTCTTCTTT
32738 TTTTTTTTTCACTTACTTTCTTCTTCT
1 TTTTTTTTTCACTTACTTTCTTCTTCT
32765 CCTTCTTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 13 0.54
28 7 0.29
29 4 0.17
ACGTcount: A:0.06, C:0.19, G:0.02, T:0.74
Consensus pattern (29 bp):
TTTTTTTTTCACTTACTTTCTTCTTCTTT
Found at i:41541 original size:27 final size:27
Alignment explanation
Indices: 41482--41541 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
41472 AAAGTTGTAT
*
41482 ATAAAATGTAATAACAAAATTTCTACA
1 ATAAAATGTAATAACAAAATTACTACA
* *
41509 AAAAAATGTAATAACAGAATTAACTA-A
1 ATAAAATGTAATAACAAAATT-ACTACA
41536 ATAAAA
1 ATAAAA
41542 GAAAATTTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 25 0.89
28 3 0.11
ACGTcount: A:0.62, C:0.08, G:0.05, T:0.25
Consensus pattern (27 bp):
ATAAAATGTAATAACAAAATTACTACA
Found at i:45387 original size:16 final size:16
Alignment explanation
Indices: 45367--45490 Score: 171
Period size: 16 Copynumber: 7.8 Consensus size: 16
45357 GCGGGCTGGG
45367 CGGGTTTCGGGTCA-T
1 CGGGTTTCGGGTCATT
* *
45382 CTGGG-TTCGGGTTATA
1 C-GGGTTTCGGGTCATT
45398 CGGGTTTCGGGTCATT
1 CGGGTTTCGGGTCATT
* *
45414 CGGGTCTCGGGTCATA
1 CGGGTTTCGGGTCATT
45430 CGGGTTTCGGGTCATT
1 CGGGTTTCGGGTCATT
*
45446 CGGGTCTCGGGTCATT
1 CGGGTTTCGGGTCATT
45462 CGGGTTTCGGGTCATT
1 CGGGTTTCGGGTCATT
*
45478 CGGGTCTCGGGTC
1 CGGGTTTCGGGTC
45491 TACCGGGTCT
Statistics
Matches: 95, Mismatches: 11, Indels: 5
0.86 0.10 0.05
Matches are distributed among these distances:
15 12 0.13
16 83 0.87
ACGTcount: A:0.07, C:0.21, G:0.39, T:0.33
Consensus pattern (16 bp):
CGGGTTTCGGGTCATT
Found at i:45431 original size:32 final size:32
Alignment explanation
Indices: 45367--45505 Score: 212
Period size: 32 Copynumber: 4.4 Consensus size: 32
45357 GCGGGCTGGG
*
45367 CGGGTTTCGGGTCA-TCTGGGT-TCGGGTTATA
1 CGGGTTTCGGGTCATTC-GGGTCTCGGGTCATA
45398 CGGGTTTCGGGTCATTCGGGTCTCGGGTCATA
1 CGGGTTTCGGGTCATTCGGGTCTCGGGTCATA
*
45430 CGGGTTTCGGGTCATTCGGGTCTCGGGTCATT
1 CGGGTTTCGGGTCATTCGGGTCTCGGGTCATA
45462 CGGGTTTCGGGTCATTCGGGTCTCGGGTC-TA
1 CGGGTTTCGGGTCATTCGGGTCTCGGGTCATA
*
45493 CCGGGTCTCGGGT
1 -CGGGTTTCGGGT
45506 TGGGCGGGTT
Statistics
Matches: 101, Mismatches: 4, Indels: 5
0.92 0.04 0.05
Matches are distributed among these distances:
31 19 0.19
32 82 0.81
ACGTcount: A:0.07, C:0.22, G:0.39, T:0.32
Consensus pattern (32 bp):
CGGGTTTCGGGTCATTCGGGTCTCGGGTCATA
Found at i:45497 original size:16 final size:16
Alignment explanation
Indices: 45367--45505 Score: 167
Period size: 16 Copynumber: 8.8 Consensus size: 16
45357 GCGGGCTGGG
*
45367 CGGGTTTCGGGTCA-T
1 CGGGTCTCGGGTCATT
* *
45382 CTGGGT-TCGGGTTATA
1 C-GGGTCTCGGGTCATT
*
45398 CGGGTTTCGGGTCATT
1 CGGGTCTCGGGTCATT
*
45414 CGGGTCTCGGGTCATA
1 CGGGTCTCGGGTCATT
*
45430 CGGGTTTCGGGTCATT
1 CGGGTCTCGGGTCATT
45446 CGGGTCTCGGGTCATT
1 CGGGTCTCGGGTCATT
*
45462 CGGGTTTCGGGTCATT
1 CGGGTCTCGGGTCATT
*
45478 CGGGTCTCGGGTC-TAC
1 CGGGTCTCGGGTCAT-T
45494 CGGGTCTCGGGT
1 CGGGTCTCGGGT
45506 TGGGCGGGTT
Statistics
Matches: 108, Mismatches: 12, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
15 13 0.12
16 95 0.88
ACGTcount: A:0.07, C:0.22, G:0.39, T:0.32
Consensus pattern (16 bp):
CGGGTCTCGGGTCATT
Found at i:45514 original size:48 final size:48
Alignment explanation
Indices: 45365--45520 Score: 151
Period size: 48 Copynumber: 3.3 Consensus size: 48
45355 GGGCGGGCTG
*
45365 GGCGGGTTTCGGGTCA-TCTGGGTTCGGGT-TATACGGGTTTCGGGTCA
1 GGCGGGTTTCGGGTCATTC-GGGTTCGGGTCTATACGGGTCTCGGGTCA
** * * *
45412 TTCGGGTCTCGGGTCATACGGGTTTCGGGTC-ATTCGGGTCTCGGGTCA
1 GGCGGGTTTCGGGTCATTCGGG-TTCGGGTCTATACGGGTCTCGGGTCA
** * **
45460 TTCGGGTTTCGGGTCATTCGGGTCTCGGGTCTA-CCGGGTCTCGGGTTG
1 GGCGGGTTTCGGGTCATTCGGGT-TCGGGTCTATACGGGTCTCGGGTCA
45508 GGCGGG-TTCGGGT
1 GGCGGGTTTCGGGT
45521 TTTGACTTCG
Statistics
Matches: 91, Mismatches: 13, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
47 24 0.26
48 66 0.73
49 1 0.01
ACGTcount: A:0.06, C:0.21, G:0.42, T:0.31
Consensus pattern (48 bp):
GGCGGGTTTCGGGTCATTCGGGTTCGGGTCTATACGGGTCTCGGGTCA
Found at i:45994 original size:21 final size:21
Alignment explanation
Indices: 45953--46000 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
45943 TATCCAATTT
*
45953 ATAATAGGTAAAATCATAACA
1 ATAATAGGTAAAATCACAACA
* * *
45974 GTAATTGGTAAAATTACAACA
1 ATAATAGGTAAAATCACAACA
45995 ATAATA
1 ATAATA
46001 TAAATTGTAT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.54, C:0.08, G:0.10, T:0.27
Consensus pattern (21 bp):
ATAATAGGTAAAATCACAACA
Found at i:46128 original size:16 final size:16
Alignment explanation
Indices: 46107--46217 Score: 127
Period size: 16 Copynumber: 6.9 Consensus size: 16
46097 GGTTAATGTC
*
46107 TCGGGTTATTCGGGTT
1 TCGGGTCATTCGGGTT
* *
46123 TCGGGTCATACGGGTC
1 TCGGGTCATTCGGGTT
46139 TCGGGTCATTCGGGTT
1 TCGGGTCATTCGGGTT
46155 TCGGGTCA-TCTGGGTT
1 TCGGGTCATTC-GGGTT
* *
46171 ACGGGTCATTCGGGTC
1 TCGGGTCATTCGGGTT
46187 TCGGGTCA-TCTGGGTT
1 TCGGGTCATTC-GGGTT
* *
46203 GCGGGTTATTCGGGT
1 TCGGGTCATTCGGGT
46218 CACAGGTTCG
Statistics
Matches: 80, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
15 4 0.05
16 72 0.90
17 4 0.05
ACGTcount: A:0.08, C:0.19, G:0.39, T:0.34
Consensus pattern (16 bp):
TCGGGTCATTCGGGTT
Found at i:46141 original size:32 final size:32
Alignment explanation
Indices: 46108--46217 Score: 152
Period size: 32 Copynumber: 3.4 Consensus size: 32
46098 GTTAATGTCT
*
46108 CGGGTTATTCGGGTTTCGGGTCATAC-GGGTCT-
1 CGGGTCATTCGGGTTTCGGGTCAT-CTGGGT-TA
46140 CGGGTCATTCGGGTTTCGGGTCATCTGGGTTA
1 CGGGTCATTCGGGTTTCGGGTCATCTGGGTTA
* *
46172 CGGGTCATTCGGGTCTCGGGTCATCTGGGTTG
1 CGGGTCATTCGGGTTTCGGGTCATCTGGGTTA
*
46204 CGGGTTATTCGGGT
1 CGGGTCATTCGGGT
46218 CACAGGTTCG
Statistics
Matches: 72, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
31 2 0.03
32 70 0.97
ACGTcount: A:0.08, C:0.19, G:0.39, T:0.34
Consensus pattern (32 bp):
CGGGTCATTCGGGTTTCGGGTCATCTGGGTTA
Found at i:46232 original size:48 final size:48
Alignment explanation
Indices: 46124--46241 Score: 118
Period size: 48 Copynumber: 2.5 Consensus size: 48
46114 ATTCGGGTTT
* *
46124 CGGGTCA-TACGGGTCTCGGGTCATTCGGGTTTCGGGTCATCTGGGTTA
1 CGGGTCAGT-CGGGTCTCGGGTCATTCGGGTTGCGGGTCATCTGGGTCA
* *
46172 CGGGTCATTCGGGTCTCGGGTCA-TCTGGGTTGCGGGTTAT-TCGGGTCA
1 CGGGTCAGTCGGGTCTCGGGTCATTC-GGGTTGCGGGTCATCT-GGGTCA
* *
46220 CAGGTTC-GTCGGGTCTCCGGTC
1 C-GGGTCAGTCGGGTCTCGGGTC
46242 GCGCGGGTTC
Statistics
Matches: 60, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
47 3 0.05
48 52 0.87
49 5 0.08
ACGTcount: A:0.08, C:0.23, G:0.38, T:0.31
Consensus pattern (48 bp):
CGGGTCAGTCGGGTCTCGGGTCATTCGGGTTGCGGGTCATCTGGGTCA
Found at i:46317 original size:18 final size:18
Alignment explanation
Indices: 46276--46321 Score: 78
Period size: 17 Copynumber: 2.7 Consensus size: 18
46266 TTCTGGTCAA
46276 ATCGGGTT-GGGCGGGTT
1 ATCGGGTTCGGGCGGGTT
46293 A-CGGGTTCGGGCGGGTT
1 ATCGGGTTCGGGCGGGTT
46310 ATCGGGTTCGGG
1 ATCGGGTTCGGG
46322 TCAAATTTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.22
17 11 0.41
18 10 0.37
ACGTcount: A:0.07, C:0.15, G:0.52, T:0.26
Consensus pattern (18 bp):
ATCGGGTTCGGGCGGGTT
Found at i:49914 original size:21 final size:21
Alignment explanation
Indices: 49885--49959 Score: 89
Period size: 21 Copynumber: 3.6 Consensus size: 21
49875 TGACCGGCCA
*
49885 CATGCCCGGCCATCACCATTG
1 CATGACCGGCCATCACCATTG
*
49906 CATGACCGGCCATCACCATCG
1 CATGACCGGCCATCACCATTG
*
49927 CATGCCCGGCCATCATCCA-TG
1 CATGACCGGCCATCA-CCATTG
**
49948 CACAACCGGCCA
1 CATGACCGGCCA
49960 CATGATCCTT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
21 43 0.93
22 3 0.07
ACGTcount: A:0.23, C:0.44, G:0.19, T:0.15
Consensus pattern (21 bp):
CATGACCGGCCATCACCATTG
Found at i:52529 original size:12 final size:12
Alignment explanation
Indices: 52512--52551 Score: 71
Period size: 12 Copynumber: 3.3 Consensus size: 12
52502 CAAGTGGCCG
52512 GATGGCCCGTGC
1 GATGGCCCGTGC
*
52524 GATGGCCCGTAC
1 GATGGCCCGTGC
52536 GATGGCCCGTGC
1 GATGGCCCGTGC
52548 GATG
1 GATG
52552 TCCGGTTGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.12, C:0.30, G:0.40, T:0.17
Consensus pattern (12 bp):
GATGGCCCGTGC
Found at i:58617 original size:14 final size:14
Alignment explanation
Indices: 58598--58638 Score: 82
Period size: 14 Copynumber: 2.9 Consensus size: 14
58588 TTCAAGAGAT
58598 AAAAGAGCCCTTAA
1 AAAAGAGCCCTTAA
58612 AAAAGAGCCCTTAA
1 AAAAGAGCCCTTAA
58626 AAAAGAGCCCTTA
1 AAAAGAGCCCTTA
58639 TAACTTGGAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.49, C:0.22, G:0.15, T:0.15
Consensus pattern (14 bp):
AAAAGAGCCCTTAA
Done.