Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012272.1 Corchorus olitorius cultivar O-4 contig12305, 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: 108156
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:4534 original size:21 final size:21
Alignment explanation
Indices: 4508--4548 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
4498 TTAGAAACCC
4508 TAGTACCACTTAAATCCAATT
1 TAGTACCACTTAAATCCAATT
**
4529 TAGTACCACTTGTATCCAAT
1 TAGTACCACTTAAATCCAAT
4549 AGGGCTTCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.34, C:0.24, G:0.07, T:0.34
Consensus pattern (21 bp):
TAGTACCACTTAAATCCAATT
Found at i:7133 original size:11 final size:10
Alignment explanation
Indices: 7117--7164 Score: 55
Period size: 11 Copynumber: 4.8 Consensus size: 10
7107 AAAGTTCGTG
7117 ATTGAAGATTA
1 ATTGAAGA-TA
7128 ATTGAAGATA
1 ATTGAAGATA
7138 ACTTGAAG--A
1 A-TTGAAGATA
*
7147 ATTGAAGATC
1 ATTGAAGATA
7157 ATTGAAGA
1 ATTGAAGA
7165 ATTATTTCAA
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
8 6 0.18
9 2 0.06
10 11 0.33
11 14 0.42
ACGTcount: A:0.46, C:0.04, G:0.21, T:0.29
Consensus pattern (10 bp):
ATTGAAGATA
Found at i:7163 original size:18 final size:19
Alignment explanation
Indices: 7127--7167 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
7117 ATTGAAGATT
7127 AATTGAAGATAACTTGAAG
1 AATTGAAGATAACTTGAAG
*
7146 AATTGAAGATCA-TTGAAG
1 AATTGAAGATAACTTGAAG
7164 AATT
1 AATT
7168 ATTTCAAGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 10 0.48
19 11 0.52
ACGTcount: A:0.46, C:0.05, G:0.20, T:0.29
Consensus pattern (19 bp):
AATTGAAGATAACTTGAAG
Found at i:10597 original size:82 final size:81
Alignment explanation
Indices: 10454--10615 Score: 225
Period size: 82 Copynumber: 2.0 Consensus size: 81
10444 AAATATTTTT
* *
10454 TGTTTCAACCTTCAAAAGGTCGAACTCAACCTGGACAGGGTCGAACCAGCCTGTACAGAAGCTTC
1 TGTTTCAACCTTCAAAAGGTCGAACTCAACCTGAAAAGGGTCGAACCAGCCTGTACAGAAGCTTC
10519 AAATCTGAAAAATTTCC
66 AAATCTG-AAAATTTCC
** * ** ***
10536 TGTTTCAACCTTCAGCATGTCGAACTCAACCTGAAAAGGGTCGAACCAGTTTGTTTGGAAGCTTC
1 TGTTTCAACCTTCAAAAGGTCGAACTCAACCTGAAAAGGGTCGAACCAGCCTGTACAGAAGCTTC
10601 AAATCTGAAAATTTC
66 AAATCTGAAAATTTC
10616 TTCAATTCAA
Statistics
Matches: 70, Mismatches: 10, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
81 8 0.11
82 62 0.89
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (81 bp):
TGTTTCAACCTTCAAAAGGTCGAACTCAACCTGAAAAGGGTCGAACCAGCCTGTACAGAAGCTTC
AAATCTGAAAATTTCC
Found at i:10766 original size:22 final size:21
Alignment explanation
Indices: 10718--10771 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 21
10708 CACAAATCAA
*
10718 AAACCCTAATTTCAAACCTTT
1 AAACCCTAATTTCAAACCTTG
*
10739 AGAACCCTAATTTGAAACCCTTG
1 A-AACCCTAATTTCAAA-CCTTG
10762 AAACCC-AATT
1 AAACCCTAATT
10772 GAATTTCGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 5 0.17
22 19 0.66
23 5 0.17
ACGTcount: A:0.39, C:0.28, G:0.06, T:0.28
Consensus pattern (21 bp):
AAACCCTAATTTCAAACCTTG
Found at i:16270 original size:20 final size:20
Alignment explanation
Indices: 16231--16273 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
16221 TGTTTCGAAG
16231 AATGAAAAATGGACAAAGAAC
1 AATGAAAAATGGA-AAAGAAC
16252 AATGCAAAAATGG-AAAGAAC
1 AATG-AAAAATGGAAAAGAAC
16272 AA
1 AA
16274 AGAGAATTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 9 0.43
21 4 0.19
22 8 0.38
ACGTcount: A:0.63, C:0.09, G:0.19, T:0.09
Consensus pattern (20 bp):
AATGAAAAATGGAAAAGAAC
Found at i:20079 original size:1 final size:1
Alignment explanation
Indices: 20075--20101 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
20065 TGAAGGGGGG
20075 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
20102 GTAGTACCTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:27472 original size:16 final size:15
Alignment explanation
Indices: 27451--27481 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
27441 CTCTGATTAA
27451 GCAAGTAGCTGCAAAT
1 GCAAGTAGCT-CAAAT
27467 GCAAGTAGCTCAAAT
1 GCAAGTAGCTCAAAT
27482 TGAGCTGCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.39, C:0.19, G:0.23, T:0.19
Consensus pattern (15 bp):
GCAAGTAGCTCAAAT
Found at i:33549 original size:13 final size:12
Alignment explanation
Indices: 33526--33550 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
33516 ATATATAATA
33526 TCCAATTTTTTT
1 TCCAATTTTTTT
33538 TCCAATTTTTTT
1 TCCAATTTTTTT
33550 T
1 T
33551 ATTTTATATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.68
Consensus pattern (12 bp):
TCCAATTTTTTT
Found at i:35185 original size:76 final size:76
Alignment explanation
Indices: 35098--35250 Score: 270
Period size: 76 Copynumber: 2.0 Consensus size: 76
35088 ACAGTTATGG
** * *
35098 TTAAATGATCTTTTAGAAATTAAATTTTAGGAAAAACATGATATATGGAGCATAGCATTCAAGAC
1 TTAAATGATCTTTTAGAAAGGAAATTGTAGGAAAAACATGATATATGGAGCATAGCATTCAAAAC
35163 ATGGATCAAAA
66 ATGGATCAAAA
35174 TTAAATGATCTTTTAGAAAGGAAATTGTAGGAAAAACATGATATATGGAGCATAGCATTCAAAAC
1 TTAAATGATCTTTTAGAAAGGAAATTGTAGGAAAAACATGATATATGGAGCATAGCATTCAAAAC
35239 ATGGATCAAAA
66 ATGGATCAAAA
35250 T
1 T
35251 CATTAATCAT
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
76 73 1.00
ACGTcount: A:0.45, C:0.09, G:0.17, T:0.29
Consensus pattern (76 bp):
TTAAATGATCTTTTAGAAAGGAAATTGTAGGAAAAACATGATATATGGAGCATAGCATTCAAAAC
ATGGATCAAAA
Found at i:48883 original size:2 final size:2
Alignment explanation
Indices: 48876--48913 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
48866 TAATCCCATT
48876 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
48914 AAGTATTATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:48981 original size:43 final size:44
Alignment explanation
Indices: 48904--48991 Score: 169
Period size: 43 Copynumber: 2.0 Consensus size: 44
48894 TATATATATA
48904 TATATATATAAAGTATTATTCTCTGTTGTATTTCTTGAGAGCCT
1 TATATATATAAAGTATTATTCTCTGTTGTATTTCTTGAGAGCCT
48948 TATATATATAAAGTATT-TTCTCTGTTGTATTTCTTGAGAGCCT
1 TATATATATAAAGTATTATTCTCTGTTGTATTTCTTGAGAGCCT
48991 T
1 T
48992 GAGGCAGCCT
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
43 27 0.61
44 17 0.39
ACGTcount: A:0.26, C:0.11, G:0.14, T:0.49
Consensus pattern (44 bp):
TATATATATAAAGTATTATTCTCTGTTGTATTTCTTGAGAGCCT
Found at i:49860 original size:163 final size:163
Alignment explanation
Indices: 49590--49913 Score: 603
Period size: 163 Copynumber: 2.0 Consensus size: 163
49580 GCCTTAAGAA
* *
49590 ATGCAATTATTTTCTCCAATTGGCATAGACTTTAATTTTTGTGATATTAGATAAAAAATAGGTTA
1 ATGCAATTATTTTCTCCAATTGGCATAGACTTTAATTTCTGTGATACTAGATAAAAAATAGGTTA
*
49655 ATCATTTAGGTATTGTATGTTCTTAAACAGTAGACATTATATAAATAAGCTTTACAATTTAGATG
66 ATCATTTAGGTATTGTATGTTCTTAAACAGTAGACATTATATAAACAAGCTTTACAATTTAGATG
49720 ATATAATATGTTTCAAGCAAATCCAGTTTTCAC
131 ATATAATATGTTTCAAGCAAATCCAGTTTTCAC
*
49753 ATGCAATTATTTTCTCCAATTGGCGTAGACTTTAATTTCTGTGATACTAGATAAAAAATAGGTTA
1 ATGCAATTATTTTCTCCAATTGGCATAGACTTTAATTTCTGTGATACTAGATAAAAAATAGGTTA
*
49818 ATCATTTAGGTATTGTATGTTTTTAAACAGTAGACATTATATAAACAAGCTTTACAATTTAGATG
66 ATCATTTAGGTATTGTATGTTCTTAAACAGTAGACATTATATAAACAAGCTTTACAATTTAGATG
49883 ATATAATATGTTTCAAGCAAATCCAGTTTTC
131 ATATAATATGTTTCAAGCAAATCCAGTTTTC
49914 CATTTATAGA
Statistics
Matches: 156, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
163 156 1.00
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.40
Consensus pattern (163 bp):
ATGCAATTATTTTCTCCAATTGGCATAGACTTTAATTTCTGTGATACTAGATAAAAAATAGGTTA
ATCATTTAGGTATTGTATGTTCTTAAACAGTAGACATTATATAAACAAGCTTTACAATTTAGATG
ATATAATATGTTTCAAGCAAATCCAGTTTTCAC
Found at i:52101 original size:31 final size:31
Alignment explanation
Indices: 52066--52202 Score: 125
Period size: 31 Copynumber: 4.5 Consensus size: 31
52056 GTCAAATAAT
* * * *
52066 CAATTTAGGATATAACGTTTGCTGTCACAAG
1 CAATTAAGGATATAACGTTTACTATAACAAG
*
52097 CAATTAAGGATATAACG-TTAC-AAAACAAG
1 CAATTAAGGATATAACGTTTACTATAACAAG
* * **
52126 CAATTAATGATATAACGTTTTCTATTTCAAG
1 CAATTAAGGATATAACGTTTACTATAACAAG
* * * **
52157 CAATTAAGGATATGACGTTTTCGATTTCAAG
1 CAATTAAGGATATAACGTTTACTATAACAAG
*
52188 CAATTATGGATATAA
1 CAATTAAGGATATAA
52203 TCAGTTAGGT
Statistics
Matches: 89, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
29 21 0.24
30 6 0.07
31 62 0.70
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.33
Consensus pattern (31 bp):
CAATTAAGGATATAACGTTTACTATAACAAG
Found at i:52366 original size:31 final size:29
Alignment explanation
Indices: 52331--52396 Score: 96
Period size: 31 Copynumber: 2.2 Consensus size: 29
52321 TCTAACGGAC
52331 TATATCCTTAATTGCTCACTTTTCGTAACGT
1 TATATCCTTAATTGCT-ACTTTT-GTAACGT
**
52362 TATATCCTTAATTGCTTGTTTTGTAACGT
1 TATATCCTTAATTGCTACTTTTGTAACGT
52391 TATATC
1 TATATC
52397 TCAAATTGCA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 13 0.39
30 4 0.12
31 16 0.48
ACGTcount: A:0.23, C:0.18, G:0.11, T:0.48
Consensus pattern (29 bp):
TATATCCTTAATTGCTACTTTTGTAACGT
Found at i:54850 original size:73 final size:75
Alignment explanation
Indices: 54724--54863 Score: 248
Period size: 73 Copynumber: 1.9 Consensus size: 75
54714 AGCATTCAAG
54724 TTAATAGTGGAAGTTAAGTTGGAAAGGCAGTAGTACTGAAGTGCATTTCATGTCTTAAGTTTTTA
1 TTAATAGTGGAAGTTAAGTTGGAAA-G-AGTAGTACTGAAGTGCATTTCATGTCTTAAGTTTTTA
54789 TATGGAGAATTT
64 TATGGAGAATTT
54801 TTAATAGTGGAAGTTAAGTTGG-AA-AGTAGTACTGAAGTGCATTTCATGTCTTAAGTTTTTATA
1 TTAATAGTGGAAGTTAAGTTGGAAAGAGTAGTACTGAAGTGCATTTCATGTCTTAAGTTTTTATA
54864 GTGATTTTTT
Statistics
Matches: 63, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
73 39 0.62
76 2 0.03
77 22 0.35
ACGTcount: A:0.31, C:0.06, G:0.24, T:0.39
Consensus pattern (75 bp):
TTAATAGTGGAAGTTAAGTTGGAAAGAGTAGTACTGAAGTGCATTTCATGTCTTAAGTTTTTATA
TGGAGAATTT
Found at i:57222 original size:28 final size:30
Alignment explanation
Indices: 57157--57227 Score: 103
Period size: 30 Copynumber: 2.4 Consensus size: 30
57147 TTGTGAACAT
57157 AAACCATTGACTTTATATCTGGCAAAAAAA
1 AAACCATTGACTTTATATCTGGCAAAAAAA
*
57187 AAACCATTGACTTTAT-T-TGGTGAAAAAAA
1 AAACCATTGACTTTATATCTGG-CAAAAAAA
57216 AAA-CATTGACTT
1 AAACCATTGACTT
57228 CAATTTTGCA
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 12 0.31
29 11 0.28
30 16 0.41
ACGTcount: A:0.45, C:0.14, G:0.11, T:0.30
Consensus pattern (30 bp):
AAACCATTGACTTTATATCTGGCAAAAAAA
Found at i:57335 original size:23 final size:23
Alignment explanation
Indices: 57308--57356 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
57298 ACAAAATCAC
57308 TGACTTCATTACCAACAGGTGAG
1 TGACTTCATTACCAACAGGTGAG
57331 TGACTTCATTACCAACAGGTGAG
1 TGACTTCATTACCAACAGGTGAG
57354 TGA
1 TGA
57357 TTGGTTGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (23 bp):
TGACTTCATTACCAACAGGTGAG
Found at i:60697 original size:2 final size:2
Alignment explanation
Indices: 60685--60742 Score: 107
Period size: 2 Copynumber: 29.0 Consensus size: 2
60675 GATAGTGAGC
*
60685 GA GA AA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
60727 GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA
60743 TTCATGGTTT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
GA
Found at i:67165 original size:30 final size:30
Alignment explanation
Indices: 67131--67191 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
67121 GTGCGTTCCT
*
67131 TCGCTTTAGTTTTGGAATCCTTCTTCTGCC
1 TCGCTTTAGTTTTGGAATCCTTCCTCTGCC
67161 TCGCTTTAGTTTTGGAATCCTTCCTCTGCC
1 TCGCTTTAGTTTTGGAATCCTTCCTCTGCC
67191 T
1 T
67192 TTTTTTTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.10, C:0.28, G:0.16, T:0.46
Consensus pattern (30 bp):
TCGCTTTAGTTTTGGAATCCTTCCTCTGCC
Found at i:69941 original size:20 final size:20
Alignment explanation
Indices: 69909--69951 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
69899 TTTTCATGTA
* *
69909 ATGCTAAATCAAC-AATAAC
1 ATGCTAAACCAACTAAAAAC
69928 ATGCATAAACCAACTAAAAAC
1 ATGC-TAAACCAACTAAAAAC
69949 ATG
1 ATG
69952 GGTCTAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 4 0.20
20 8 0.40
21 8 0.40
ACGTcount: A:0.53, C:0.21, G:0.07, T:0.19
Consensus pattern (20 bp):
ATGCTAAACCAACTAAAAAC
Found at i:74651 original size:17 final size:17
Alignment explanation
Indices: 74629--74661 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
74619 TTCATATTCA
74629 TAGTGCTAGAACCTAGT
1 TAGTGCTAGAACCTAGT
74646 TAGTGCTAGAACCTAG
1 TAGTGCTAGAACCTAG
74662 CCTCCAAGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.27
Consensus pattern (17 bp):
TAGTGCTAGAACCTAGT
Found at i:80070 original size:15 final size:14
Alignment explanation
Indices: 80045--80074 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
80035 AATAAAAATA
80045 AATATTTTTATTTT
1 AATATTTTTATTTT
80059 AATATATTTTATTTT
1 AATAT-TTTTATTTT
80074 A
1 A
80075 TTGAAAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
AATATTTTTATTTT
Found at i:80717 original size:11 final size:11
Alignment explanation
Indices: 80701--80725 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
80691 CTTTGCAGAC
80701 ATTCATGTTTG
1 ATTCATGTTTG
80712 ATTCATGTTTG
1 ATTCATGTTTG
80723 ATT
1 ATT
80726 GTTTTGATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.20, C:0.08, G:0.16, T:0.56
Consensus pattern (11 bp):
ATTCATGTTTG
Found at i:86267 original size:16 final size:17
Alignment explanation
Indices: 86246--86289 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
86236 TCTTTTAATA
86246 ATAAAAAATTAAA-ATT
1 ATAAAAAATTAAATATT
86262 ATAAAAAATTAAATATT
1 ATAAAAAATTAAATATT
*
86279 TTAAAATAATT
1 ATAAAA-AATT
86290 TTAATTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 13 0.52
17 8 0.32
18 4 0.16
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
ATAAAAAATTAAATATT
Found at i:87610 original size:17 final size:16
Alignment explanation
Indices: 87588--87622 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
87578 AAATTTATGA
87588 TTTATTGATTTAAATAT
1 TTTATT-ATTTAAATAT
*
87605 TTTATTTTTTAAATAT
1 TTTATTATTTAAATAT
87621 TT
1 TT
87623 CTTGATTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (16 bp):
TTTATTATTTAAATAT
Found at i:88834 original size:15 final size:15
Alignment explanation
Indices: 88804--88845 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
88794 TTACTCTGCT
88804 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
88820 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
*
88835 TTGCTTTCTGT
1 TTGTTTTCTGT
88846 CAATCTCTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.12, C:0.10, G:0.14, T:0.64
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:90983 original size:23 final size:23
Alignment explanation
Indices: 90955--90999 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
90945 TTGATATATT
90955 TTTGATATATC-CTTTACCCATTC
1 TTTGATA-ATCACTTTACCCATTC
*
90978 TTTGATAGTCACTTTACCCATT
1 TTTGATAATCACTTTACCCATT
91000 AGCCCCATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 2 0.10
23 18 0.90
ACGTcount: A:0.22, C:0.24, G:0.07, T:0.47
Consensus pattern (23 bp):
TTTGATAATCACTTTACCCATTC
Found at i:96228 original size:27 final size:25
Alignment explanation
Indices: 96184--96236 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 25
96174 ACCTTTATTG
96184 AGATATTTTTTTCGACATTTGATTTCA
1 AGATATTTTTTTCGACA-TTG-TTTCA
*
96211 AGAT-TTTTTTTTGAACATTGTTTCA
1 AGATATTTTTTTCG-ACATTGTTTCA
96236 A
1 A
96237 ATACATACTC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
25 6 0.25
26 11 0.46
27 7 0.29
ACGTcount: A:0.26, C:0.09, G:0.11, T:0.53
Consensus pattern (25 bp):
AGATATTTTTTTCGACATTGTTTCA
Found at i:100078 original size:11 final size:10
Alignment explanation
Indices: 100062--100108 Score: 53
Period size: 11 Copynumber: 4.7 Consensus size: 10
100052 AAGTTCGTGT
100062 TTGAAGACTCA
1 TTGAAGA-TCA
*
100073 TTGAAGATAA
1 TTGAAGATCA
100083 TTTGAAGAT--
1 -TTGAAGATCA
100092 TTGAAGATCA
1 TTGAAGATCA
100102 TTGAAGA
1 TTGAAGA
100109 ATTATTTCAA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
8 8 0.25
10 9 0.28
11 15 0.47
ACGTcount: A:0.40, C:0.06, G:0.21, T:0.32
Consensus pattern (10 bp):
TTGAAGATCA
Found at i:100097 original size:19 final size:18
Alignment explanation
Indices: 100073--100108 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
100063 TGAAGACTCA
100073 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
100092 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
100109 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:101649 original size:6 final size:6
Alignment explanation
Indices: 101638--101673 Score: 63
Period size: 6 Copynumber: 5.8 Consensus size: 6
101628 TTGTGAATTA
101638 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TATTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC T-TTTT
101674 GATTTGCACT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 25 0.86
7 4 0.14
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTTC
Found at i:105219 original size:18 final size:18
Alignment explanation
Indices: 105172--105224 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 18
105162 TTTTTTATTT
*
105172 TATTTAAATAAATAAAAAA
1 TATTAAAATAAA-AAAAAA
* *
105191 TAATAAAAATAAAAAGAAA
1 T-ATTAAAATAAAAAAAAA
105210 TATTAAAATAAAAAA
1 TATTAAAATAAAAAA
105225 TAAAAAATCA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
18 12 0.43
19 7 0.25
20 9 0.32
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.25
Consensus pattern (18 bp):
TATTAAAATAAAAAAAAA
Done.