Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015676.1 Corchorus capsularis cultivar CVL-1 contig15697, 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: 51634
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:250 original size:85 final size:86
Alignment explanation
Indices: 79--250 Score: 192
Period size: 85 Copynumber: 2.0 Consensus size: 86
69 ATAATAAAGT
* **
79 TGAGAATATTTTCTAAATCTTGCCAAATTGTGGAAGATTTAGGAGATATTTTAAGAAACAAATAA
1 TGAGAATATTTTCTAAATCTTGCCAAATTGTGGAAGATTTAGAAGATATTAAAAGAAACAAATAA
** *
144 ATATTGAAGATCGAATGATAA
66 ATATTGAAGATAAAATAATAA
* * *
165 TGAGAATATTTTCT-AATCTTGCCAACTTGTGGGAGATTTAGAAGATA-TAAAAGGAAATATAAT
1 TGAGAATATTTTCTAAATCTTGCCAAATTGTGGAAGATTTAGAAGATATTAAAA-GAAACA-AAT
228 CAAA-ATT-AA-ATAAAAGTAATAA
64 -AAATATTGAAGATAAAA-TAATAA
250 T
1 T
251 AAAAAAATAA
Statistics
Matches: 73, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
84 7 0.10
85 43 0.59
86 20 0.27
87 3 0.04
ACGTcount: A:0.45, C:0.07, G:0.16, T:0.32
Consensus pattern (86 bp):
TGAGAATATTTTCTAAATCTTGCCAAATTGTGGAAGATTTAGAAGATATTAAAAGAAACAAATAA
ATATTGAAGATAAAATAATAA
Found at i:256 original size:14 final size:15
Alignment explanation
Indices: 231--269 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 15
221 ATATAATCAA
231 AATTAAATAAAAGTAAT
1 AATTAAA-AAAA-TAAT
248 AA-TAAAAAAATAAT
1 AATTAAAAAAATAAT
262 AATTAAAA
1 AATTAAAA
270 GATAATTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
14 6 0.29
15 9 0.43
16 4 0.19
17 2 0.10
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.26
Consensus pattern (15 bp):
AATTAAAAAAATAAT
Found at i:274 original size:14 final size:14
Alignment explanation
Indices: 238--275 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
228 CAAAATTAAA
238 TAAAAG-TAATAAT
1 TAAAAGATAATAAT
* *
251 AAAAAAATAATAAT
1 TAAAAGATAATAAT
265 TAAAAGATAAT
1 TAAAAGATAAT
276 TTTAGACTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.26
Consensus pattern (14 bp):
TAAAAGATAATAAT
Found at i:1826 original size:20 final size:19
Alignment explanation
Indices: 1786--1823 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1776 TCTGACAAAA
* *
1786 AAAATAGCCACGTGGCATT
1 AAAATAGCCACCTGGAATT
1805 AAAATAGCCACCTGGAATT
1 AAAATAGCCACCTGGAATT
1824 TAATTAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.39, C:0.21, G:0.18, T:0.21
Consensus pattern (19 bp):
AAAATAGCCACCTGGAATT
Found at i:2419 original size:1 final size:1
Alignment explanation
Indices: 2413--2441 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
2403 AGGGATTGTA
2413 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
2442 GCGTTTTGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:11461 original size:22 final size:22
Alignment explanation
Indices: 11416--11468 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
11406 TGATTCCATC
* *
11416 ATGAAATTTTAATAACTTTCCT
1 ATGAAATTTTAATAACTATACT
11438 ATGAAATTTTAATAA-TGATACT
1 ATGAAATTTTAATAACT-ATACT
*
11460 ATGGAATTT
1 ATGAAATTT
11469 CGAGAACATT
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:0.40, C:0.08, G:0.09, T:0.43
Consensus pattern (22 bp):
ATGAAATTTTAATAACTATACT
Found at i:11625 original size:22 final size:22
Alignment explanation
Indices: 11493--11956 Score: 200
Period size: 22 Copynumber: 21.5 Consensus size: 22
11483 TTAATTTTTT
* * *
11493 TAACCTTCTTATGAAATTTTGT
1 TAACCTCCATATGAAATTTTGA
* *
11515 TAACCTCCCTAAGAAATTTTGA
1 TAACCTCCATATGAAATTTTGA
* * **
11537 AAATCTTAATATGAAATTTTGA
1 TAACCTCCATATGAAATTTTGA
*
11559 TAACTTCCCA-ATGAAATTTTGA
1 TAACCT-CCATATGAAATTTTGA
** * *
11581 TAACCAACACTATGAGATGTTGA
1 TAACCTCCA-TATGAAATTTTGA
* *
11604 TAACCTCCATATGATATATTGA
1 TAACCTCCATATGAAATTTTGA
* ** * *
11626 T-AGCTACGTTATGAAAATTTAA
1 TAACCT-CCATATGAAATTTTGA
*
11648 AAACCT-CATATG-AATTGTT-A
1 TAACCTCCATATGAAATT-TTGA
*
11668 GTAA--TCACACTCTGAAATTTTGA
1 -TAACCTC-CA-TATGAAATTTTGA
*
11691 TAA--TCACACTATGAAATTGTGA
1 TAACCTC-CA-TATGAAATTTTGA
*
11713 TAACCGCGC-TATGAAATTTTGA
1 TAACCTC-CATATGAAATTTTGA
* *
11735 TAAACCTCCCTATAAAATTTTGA
1 T-AACCTCCATATGAAATTTTGA
* * * *
11758 TAACTTTCTTATGAAATCTTGA
1 TAACCTCCATATGAAATTTTGA
*
11780 TAA----C-TA-CAAATTTTGA
1 TAACCTCCATATGAAATTTTGA
* **
11796 TAACCTCCCTATGATTTTTTGA
1 TAACCTCCATATGAAATTTTGA
*
11818 TAACCT-CATTATGAAATTTTGT
1 TAACCTCCA-TATGAAATTTTGA
* *
11840 TAATCTCCCTATGAAATTTTGA
1 TAACCTCCATATGAAATTTTGA
* * *
11862 TCTACATAC-TATGAAATTTTGA
1 T-AACCTCCATATGAAATTTTGA
*
11884 TAACC-CTCTTATGAAATTTTGA
1 TAACCTC-CATATGAAATTTTGA
* **
11906 -AAACTAAACTATGAAATTTTGA
1 TAACCTCCA-TATGAAATTTTGA
* *
11928 TATCCTCCCTA--AAATTTTGA
1 TAACCTCCATATGAAATTTTGA
*
11948 TTA-CTCCAT
1 TAACCTCCAT
11957 GATAAAAGTT
Statistics
Matches: 331, Mismatches: 81, Indels: 63
0.70 0.17 0.13
Matches are distributed among these distances:
16 11 0.03
17 2 0.01
18 1 0.00
19 6 0.02
20 15 0.05
21 24 0.07
22 219 0.66
23 51 0.15
24 2 0.01
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (22 bp):
TAACCTCCATATGAAATTTTGA
Found at i:12079 original size:22 final size:22
Alignment explanation
Indices: 12054--12178 Score: 96
Period size: 22 Copynumber: 5.7 Consensus size: 22
12044 AATCACATTT
12054 TGAAAATTTGATAACCTCTTTA
1 TGAAAATTTGATAACCTCTTTA
*
12076 TGAAATTTTGATAACCTCTTTA
1 TGAAAATTTGATAACCTCTTTA
* * * *
12098 T-AAAATTTTGTTGACCCCTCTA
1 TGAAAA-TTTGATAACCTCTTTA
* * *
12120 TG-AAATTCTGATAATCACATTA
1 TGAAAATT-TGATAACCTCTTTA
* *
12142 TGTAATTTTGATAACCTCTCTT-
1 TGAAAATTTGATAACCTCT-TTA
12164 TG-AAATTTCGATAAC
1 TGAAAATTT-GATAAC
12179 AACACTATGA
Statistics
Matches: 80, Mismatches: 17, Indels: 12
0.73 0.16 0.11
Matches are distributed among these distances:
21 10 0.12
22 64 0.80
23 6 0.08
ACGTcount: A:0.33, C:0.16, G:0.10, T:0.42
Consensus pattern (22 bp):
TGAAAATTTGATAACCTCTTTA
Found at i:12080 original size:44 final size:44
Alignment explanation
Indices: 12030--12222 Score: 148
Period size: 44 Copynumber: 4.4 Consensus size: 44
12020 GAAATACCAC
12030 TATGAAATTTTTG-TAATCACATTTTGAAAATTTGATAACCTCTT
1 TATGAAA-TTTTGATAATCACATTTTGAAAATTTGATAACCTCTT
* * * * * *
12074 TATGAAATTTTGATAACCTC-TTTAT-AAAATTTTGTTGACCCCTC
1 TATGAAATTTTGATAATCACATTT-TGAAAA-TTTGATAACCTCTT
* * * *
12118 TATGAAATTCTGATAATCACATTATGTAATTTTGATAACCTCTCT
1 TATGAAATTTTGATAATCACATTTTGAAAATTTGATAACCTCT-T
* * * * *
12163 T-TGAAATTTCGATAA-CAACACTATGAAATTTTGATAATCT-TAT
1 TATGAAATTTTGATAATC-ACATTTTGAAAATTTGATAACCTCT-T
12206 TAT-AAATTTTGATAATC
1 TATGAAATTTTGATAATC
12223 TGATCTCTAT
Statistics
Matches: 117, Mismatches: 23, Indels: 18
0.74 0.15 0.11
Matches are distributed among these distances:
43 27 0.23
44 85 0.73
45 5 0.04
ACGTcount: A:0.35, C:0.13, G:0.09, T:0.43
Consensus pattern (44 bp):
TATGAAATTTTGATAATCACATTTTGAAAATTTGATAACCTCTT
Found at i:12143 original size:66 final size:66
Alignment explanation
Indices: 12073--12220 Score: 174
Period size: 66 Copynumber: 2.3 Consensus size: 66
12063 GATAACCTCT
* * * ** *
12073 TTATGAAATTTTGATAACCTCT-TTATAAAATTTTGTTGACCCCTCTATGAAATTCTGATAATCA
1 TTATGAAATTTTGATAACCTCTCTT-TAAAATTTCGATAACAACACTATGAAATTCTGATAATCA
12137 CA
65 CA
* * * **
12139 TTATGTAATTTTGATAACCTCTCTTTGAAATTTCGATAACAACACTATGAAATTTTGATAATCTT
1 TTATGAAATTTTGATAACCTCTCTTTAAAATTTCGATAACAACACTATGAAATTCTGATAATCAC
12204 A
66 A
12205 TTAT-AAATTTTGATAA
1 TTATGAAATTTTGATAA
12221 TCTGATCTCT
Statistics
Matches: 69, Mismatches: 12, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
65 11 0.16
66 56 0.81
67 2 0.03
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.43
Consensus pattern (66 bp):
TTATGAAATTTTGATAACCTCTCTTTAAAATTTCGATAACAACACTATGAAATTCTGATAATCAC
A
Found at i:12192 original size:88 final size:88
Alignment explanation
Indices: 12029--12195 Score: 212
Period size: 88 Copynumber: 1.9 Consensus size: 88
12019 AGAAATACCA
* * * **
12029 CTATGAAATTTTTGTAATCACATTTTGAAAATTTGATAACCTCTTTATGAAATTTTGATAACCTC
1 CTATGAAATTTCTGTAATCACATTATGAAAATTTGATAACCTCTTTATGAAATTTCGATAACAAC
**
12094 TTTATAAAATTTTGTTGACCCCT
66 ACTATAAAATTTTGTTGACCCCT
* *
12117 CTATGAAA-TTCTGATAATCACATTATGTAATTTTGATAACCTCTCTT-TGAAATTTCGATAACA
1 CTATGAAATTTCTG-TAATCACATTATGAAAATTTGATAACCTCT-TTATGAAATTTCGATAACA
*
12180 ACACTATGAAATTTTG
64 ACACTATAAAATTTTG
12196 ATAATCTTAT
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
87 4 0.06
88 61 0.91
89 2 0.03
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.42
Consensus pattern (88 bp):
CTATGAAATTTCTGTAATCACATTATGAAAATTTGATAACCTCTTTATGAAATTTCGATAACAAC
ACTATAAAATTTTGTTGACCCCT
Found at i:12237 original size:25 final size:23
Alignment explanation
Indices: 12116--12247 Score: 87
Period size: 22 Copynumber: 5.9 Consensus size: 23
12106 TGTTGACCCC
* **
12116 TCTATGAAATTCTGATAATCACA
1 TCTATGAAATTTTGATAATCTTA
* * *
12139 T-TATGTAATTTTGATAA-CCTC
1 TCTATGAAATTTTGATAATCTTA
* * *
12160 TCTTTGAAATTTCGATAA-C-AA
1 TCTATGAAATTTTGATAATCTTA
*
12181 CACTATGAAATTTTGATAATCTTA
1 -TCTATGAAATTTTGATAATCTTA
*
12205 T-TAT-AAATTTTGATAATCTGATC
1 TCTATGAAATTTTGATAATCT--TA
*
12228 TCTATGAAATTTCGATAATC
1 TCTATGAAATTTTGATAATC
12248 ACTCAATAAG
Statistics
Matches: 84, Mismatches: 17, Indels: 14
0.73 0.15 0.12
Matches are distributed among these distances:
21 17 0.20
22 46 0.55
23 4 0.05
24 4 0.05
25 13 0.15
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.42
Consensus pattern (23 bp):
TCTATGAAATTTTGATAATCTTA
Found at i:12335 original size:22 final size:21
Alignment explanation
Indices: 12306--12416 Score: 66
Period size: 22 Copynumber: 5.1 Consensus size: 21
12296 AAATTGAGAC
12306 TTTT-ATAACCTTCATATGAAA
1 TTTTGATAACC-TCATATGAAA
* *
12327 TTTTGATAACCACACTATAAAA
1 TTTTGATAACCTCA-TATGAAA
* **
12349 TTTTAATAACCTCCCCATGAAA
1 TTTTGATAACCT-CATATGAAA
*
12371 TATT-AGTAACCTTC-TAATGAAA
1 TTTTGA-TAACC-TCAT-ATGAAA
* *
12393 TTTTGTTAACCACACTATGAAA
1 TTTTGATAACCTCA-TATGAAA
12415 TT
1 TT
12417 CTTTTAATTT
Statistics
Matches: 69, Mismatches: 12, Indels: 17
0.70 0.12 0.17
Matches are distributed among these distances:
21 8 0.12
22 58 0.84
23 3 0.04
ACGTcount: A:0.39, C:0.18, G:0.06, T:0.37
Consensus pattern (21 bp):
TTTTGATAACCTCATATGAAA
Found at i:12565 original size:22 final size:22
Alignment explanation
Indices: 12537--12599 Score: 108
Period size: 22 Copynumber: 2.9 Consensus size: 22
12527 TAACATGATC
12537 CTATGAAATTTTGGTAACCACA
1 CTATGAAATTTTGGTAACCACA
12559 CTATGAAATTTTGGTAACCACA
1 CTATGAAATTTTGGTAACCACA
* *
12581 CTATGGAATTTTGATAACC
1 CTATGAAATTTTGGTAACC
12600 TCCTCATAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.33
Consensus pattern (22 bp):
CTATGAAATTTTGGTAACCACA
Found at i:12612 original size:22 final size:22
Alignment explanation
Indices: 12587--12644 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
12577 CACACTATGG
12587 AATTTTGATAACC-TCCTCATAA
1 AATTTTGATAACCAT-CTCATAA
* * * *
12609 AATTATAATAACCATCTTATGA
1 AATTTTGATAACCATCTCATAA
12631 AATTTTGATAACCA
1 AATTTTGATAACCA
12645 CATAGAGACA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
22 28 0.97
23 1 0.03
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (22 bp):
AATTTTGATAACCATCTCATAA
Found at i:12612 original size:44 final size:44
Alignment explanation
Indices: 12489--12646 Score: 124
Period size: 44 Copynumber: 3.5 Consensus size: 44
12479 AATCAATTAC
** * * *
12489 CCTATGAAATTTCAATAACCA-ACCTAAAAAAATTTTAATAACATGAT
1 CCTATGAAATTTTGATAACCACA-CT-ATAAAATTATAATAAC--CAT
* * * **
12536 CCTATGAAATTTTGGTAACCACACTATGAAATTTTGGTAACCA-
1 CCTATGAAATTTTGATAACCACACTATAAAATTATAATAACCAT
* *
12579 CACTATGGAATTTTGATAACCTC-CTCATAAAATTATAATAACCAT
1 C-CTATGAAATTTTGATAACCACACT-ATAAAATTATAATAACCAT
*
12624 CTTATGAAATTTTGATAACCACA
1 CCTATGAAATTTTGATAACCACA
12647 TAGAGACAAG
Statistics
Matches: 88, Mismatches: 18, Indels: 12
0.75 0.15 0.10
Matches are distributed among these distances:
43 3 0.03
44 51 0.58
45 1 0.01
46 12 0.14
47 20 0.23
48 1 0.01
ACGTcount: A:0.41, C:0.18, G:0.08, T:0.32
Consensus pattern (44 bp):
CCTATGAAATTTTGATAACCACACTATAAAATTATAATAACCAT
Found at i:12840 original size:19 final size:20
Alignment explanation
Indices: 12809--12846 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
12799 TATTGACATT
12809 TAAAAATTGAAATT-AAAAG
1 TAAAAATTGAAATTCAAAAG
12828 TAAAATATT-AAATTCAAAA
1 TAAAA-ATTGAAATTCAAAA
12847 AATAATAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (20 bp):
TAAAAATTGAAATTCAAAAG
Found at i:12977 original size:25 final size:26
Alignment explanation
Indices: 12920--12969 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
12910 GTCTAAATTG
* *
12920 AAAATTTTAATTAATTTTTAAATAAT
1 AAAATTTTAACTAAATTTTAAATAAT
12946 AAAATTTT-ACTAAATTTT-AATAAT
1 AAAATTTTAACTAAATTTTAAATAAT
12970 GGAAATTTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 6 0.27
25 8 0.36
26 8 0.36
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (26 bp):
AAAATTTTAACTAAATTTTAAATAAT
Found at i:15240 original size:2 final size:2
Alignment explanation
Indices: 15233--15269 Score: 65
Period size: 2 Copynumber: 18.0 Consensus size: 2
15223 TTCGTACTTT
15233 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
15270 GATAAGTCTA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 32 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:23370 original size:6 final size:6
Alignment explanation
Indices: 23359--23388 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
23349 ATTCTGCTTC
23359 AGATTT AGATTT AGATTT AGATTT AGATTT
1 AGATTT AGATTT AGATTT AGATTT AGATTT
23389 GCTTTGCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (6 bp):
AGATTT
Found at i:30684 original size:17 final size:18
Alignment explanation
Indices: 30650--30684 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
30640 TCAACCTAAG
30650 ACTAGAAAAAAAACTAGA
1 ACTAGAAAAAAAACTAGA
*
30668 ACTAGAAGAAAAA-TAGA
1 ACTAGAAAAAAAACTAGA
30685 TGAAGAGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.66, C:0.09, G:0.14, T:0.11
Consensus pattern (18 bp):
ACTAGAAAAAAAACTAGA
Found at i:37572 original size:17 final size:18
Alignment explanation
Indices: 37550--37586 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
37540 TATGACTAAA
37550 AAATAC-TAGAACCCAAC
1 AAATACGTAGAACCCAAC
37567 AAATACTGTAGAACCCAAC
1 AAATAC-GTAGAACCCAAC
37586 A
1 A
37587 CCAACAGGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.33
19 12 0.67
ACGTcount: A:0.51, C:0.27, G:0.08, T:0.14
Consensus pattern (18 bp):
AAATACGTAGAACCCAAC
Found at i:37661 original size:28 final size:28
Alignment explanation
Indices: 37630--37684 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
37620 CCCCATAACT
*
37630 ACAAACCCTAAAACCCAAGAACAAGCCA
1 ACAAACCCTAAAAACCAAGAACAAGCCA
37658 ACAAACCCTAAAAACCAAGAACAAGCC
1 ACAAACCCTAAAAACCAAGAACAAGCC
37685 TCCCCATCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.55, C:0.35, G:0.07, T:0.04
Consensus pattern (28 bp):
ACAAACCCTAAAAACCAAGAACAAGCCA
Found at i:42429 original size:23 final size:23
Alignment explanation
Indices: 42399--42444 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
42389 GTTCCAAGAG
42399 CAACTTATTATGCTCAGAATGAA
1 CAACTTATTATGCTCAGAATGAA
42422 CAACTTATTATGCTCAGAATGAA
1 CAACTTATTATGCTCAGAATGAA
42445 GTGAATGTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.39, C:0.17, G:0.13, T:0.30
Consensus pattern (23 bp):
CAACTTATTATGCTCAGAATGAA
Found at i:50278 original size:16 final size:16
Alignment explanation
Indices: 50254--50292 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
50244 GGTTTTACCC
*
50254 CAAATGAACCTCGACA
1 CAAACGAACCTCGACA
50270 CAAACGAACCTCGACA
1 CAAACGAACCTCGACA
50286 CAAACGA
1 CAAACGA
50293 TGTCCATGTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.46, C:0.33, G:0.13, T:0.08
Consensus pattern (16 bp):
CAAACGAACCTCGACA
Done.