Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012671.1 Corchorus olitorius cultivar O-4 contig12704, 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: 122325
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:4311 original size:15 final size:15
Alignment explanation
Indices: 4291--4321 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
4281 AGAAATTACA
4291 AAAAAAAAAAATAAT
1 AAAAAAAAAAATAAT
*
4306 AAAAAAGAAAATAAT
1 AAAAAAAAAAATAAT
4321 A
1 A
4322 CAACAAACAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.84, C:0.00, G:0.03, T:0.13
Consensus pattern (15 bp):
AAAAAAAAAAATAAT
Found at i:21733 original size:181 final size:181
Alignment explanation
Indices: 21429--21766 Score: 622
Period size: 181 Copynumber: 1.9 Consensus size: 181
21419 ATTGGGAATA
21429 AGGAATCGCAATGACCCAACTCTAGCTAATTCGCCCTCTGTTTCCTCTTCTACCTGATGAACATC
1 AGGAATCGCAATGACCCAACTCTAGCTAATTCGCCCTCTGTTTCCTCTTCTACCTGATGAACATC
* *
21494 CAGGATCTATTGCTTTGATGCTTGTAGGGCACTCATAACTCCCCTATGTGGGCACTCTTTAACTT
66 CAAGATCTATTGCTTTGATGCTTGTAGGGCACTCAAAACTCCCCTATGTGGGCACTCTTTAACTT
21559 TATGCGGTCCATTGCATAAGAAGCAAGTTCAATTTGGAATGTAGTGAAGTG
131 TATGCGGTCCATTGCATAAGAAGCAAGTTCAATTTGGAATGTAGTGAAGTG
*
21610 AGGAATCGCAATGACCCAACTCTAGCTAATTCGCTCTCTGTTTCCTCTTCTACCTGATGAACATC
1 AGGAATCGCAATGACCCAACTCTAGCTAATTCGCCCTCTGTTTCCTCTTCTACCTGATGAACATC
*
21675 CAAGATCTGTTGCTTTGATGCTTGTAGGGCACTCAAAACTCCCCTATGTGGGCACTCTTTAACTT
66 CAAGATCTATTGCTTTGATGCTTGTAGGGCACTCAAAACTCCCCTATGTGGGCACTCTTTAACTT
**
21740 TATGCGGTCTGTTGCATAAGAAGCAAG
131 TATGCGGTCCATTGCATAAGAAGCAAG
21767 CCAACAATTG
Statistics
Matches: 151, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
181 151 1.00
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.31
Consensus pattern (181 bp):
AGGAATCGCAATGACCCAACTCTAGCTAATTCGCCCTCTGTTTCCTCTTCTACCTGATGAACATC
CAAGATCTATTGCTTTGATGCTTGTAGGGCACTCAAAACTCCCCTATGTGGGCACTCTTTAACTT
TATGCGGTCCATTGCATAAGAAGCAAGTTCAATTTGGAATGTAGTGAAGTG
Found at i:26638 original size:8 final size:8
Alignment explanation
Indices: 26627--26652 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
26617 GGAAATAGGG
26627 AAGGAGAA
1 AAGGAGAA
26635 AAGGAGAA
1 AAGGAGAA
26643 AAGGAGAA
1 AAGGAGAA
26651 AA
1 AA
26653 AAAAGAACCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (8 bp):
AAGGAGAA
Found at i:28750 original size:51 final size:50
Alignment explanation
Indices: 28649--28750 Score: 118
Period size: 51 Copynumber: 2.0 Consensus size: 50
28639 GTTCATCAAA
* **
28649 TTTTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCTTTTAGTGT
1 TTTTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCGTACAGTGT
* *
28699 TTTTCTCTTGTTTCA-ATCTTGTCTCCGGACATACAAACACT-GTACACGTGT
1 TTTTC-CTTGTTT-AGATCTTGTCTCAGGACAAACAAACACTCGTACA-GTGT
28750 T
1 T
28751 CTTCATTCAG
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
50 7 0.16
51 36 0.82
52 1 0.02
ACGTcount: A:0.23, C:0.23, G:0.14, T:0.41
Consensus pattern (50 bp):
TTTTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCGTACAGTGT
Found at i:38080 original size:27 final size:26
Alignment explanation
Indices: 38047--38147 Score: 139
Period size: 27 Copynumber: 3.7 Consensus size: 26
38037 CGAGTATGCA
38047 AAATGACCAAAATGCCCCTGGATGTGC
1 AAATGACCAAAATGCCCCT-GATGTGC
* *
38074 AAGTGACCAAAATGCCCCTTAATGTGC
1 AAATGACCAAAATGCCCC-TGATGTGC
38101 AAATGACCAAAATGCCCCCTGAGTGTGC
1 AAATGACCAAAATG-CCCCTGA-TGTGC
*
38129 AAATGACCAAAATACCCCT
1 AAATGACCAAAATGCCCCT
38148 AGGTGACCCT
Statistics
Matches: 66, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
27 43 0.65
28 23 0.35
ACGTcount: A:0.36, C:0.28, G:0.18, T:0.19
Consensus pattern (26 bp):
AAATGACCAAAATGCCCCTGATGTGC
Found at i:40766 original size:53 final size:53
Alignment explanation
Indices: 40704--40809 Score: 185
Period size: 53 Copynumber: 2.0 Consensus size: 53
40694 ATAAATACTA
* *
40704 AGGGAGACAAAAAAAAATGACATGACATGAAATCTAAACTCTAACCATGACAT
1 AGGGAGACAAAAAAAAATAACATGACATGAAATCTAAACCCTAACCATGACAT
*
40757 AGGGAGACAAAAAAAAATAACATGACATGATATCTAAACCCTAACCATGACAT
1 AGGGAGACAAAAAAAAATAACATGACATGAAATCTAAACCCTAACCATGACAT
40810 GACAAACCTT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 50 1.00
ACGTcount: A:0.51, C:0.18, G:0.14, T:0.17
Consensus pattern (53 bp):
AGGGAGACAAAAAAAAATAACATGACATGAAATCTAAACCCTAACCATGACAT
Found at i:41976 original size:32 final size:32
Alignment explanation
Indices: 41916--41976 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
41906 CGTGGCATTT
41916 TTTATTTATAAATATTTTTTATTCTTTTTATA
1 TTTATTTATAAATATTTTTTATTCTTTTTATA
*
41948 TTTATTT-TTAATATTTATTTAATT-TTTTT
1 TTTATTTATAAATATTT-TTT-ATTCTTTTT
41977 GGCCAAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
31 8 0.31
32 15 0.58
33 3 0.12
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (32 bp):
TTTATTTATAAATATTTTTTATTCTTTTTATA
Found at i:42059 original size:66 final size:65
Alignment explanation
Indices: 41938--42067 Score: 210
Period size: 65 Copynumber: 2.0 Consensus size: 65
41928 TATTTTTTAT
*
41938 TCTTTTTATATTTATTTTTAATATTTATTTAATTTTTTTGGCCAAAAAATATTTTTTGAAATTCA
1 TCTTTTTATATTTATTTTTAATAATTATTTAATTTTTTTGGCCAAAAAATATTTTTTGAAATTCA
*
42003 TCTTTTTATATTTATTTTTTAATACATT-TTTCATTTTTTTGG-CAAAAAATATTTTTTGAAATT
1 TCTTTTTATATTTA-TTTTTAATA-ATTATTTAATTTTTTTGGCCAAAAAATATTTTTTGAAATT
42066 CA
64 CA
42068 CGTTTATATT
Statistics
Matches: 61, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
65 37 0.61
66 22 0.36
67 2 0.03
ACGTcount: A:0.30, C:0.07, G:0.05, T:0.58
Consensus pattern (65 bp):
TCTTTTTATATTTATTTTTAATAATTATTTAATTTTTTTGGCCAAAAAATATTTTTTGAAATTCA
Found at i:42982 original size:530 final size:530
Alignment explanation
Indices: 42140--43198 Score: 2030
Period size: 530 Copynumber: 2.0 Consensus size: 530
42130 ATTACTTCTT
42140 CCGAATATTTTCTCTCTACTTTTCAAAAAAGGGAAATGACATTGATTAAAATAATTGTTTCCAAC
1 CCGAATATTTTCTCTCTACTTTTCAAAAAAGGGAAATGACATTGATTAAAATAATTGTTTCCAAC
* * * *
42205 ATCATTACATGAACAAGCTCCCAAAACCGTGTTAAAGTCTAAACTGTGCAGAATAATTAATATTA
66 ATCATCACATGAACAAGCTCCCAAAACCCTGCTAAAGTCTAAACTATGCAGAATAATTAATATTA
42270 AATAATGTCAACTACCAAATCTTCAAAAAAGGGAGCCATAATAACCCTAAACCATCTAATATTCC
131 AATAATGTCAACTACCAAATCTTCAAAAAAGGGAGCCATAATAACCCTAAACCATCTAATATTCC
42335 AAAATAAACATCCATCATTCAACCACCTATAAGGCTATAACAATTACATTTTCAAAATAACAATT
196 AAAATAAACATCCATCATTCAACCACCTATAAGGCTATAACAATTACATTTTCAAAATAACAATT
42400 TCTGCTTTCCTTTAAAAGTTTCAGTTGTTGTTCCACTTGCCGTTCCACTATGCTGACTTCCACGT
261 TCTGCTTTCCTTTAAAAGTTTCAGTTGTTGTTCCACTTGCCGTTCCACTATGCTGACTTCCACGT
* *
42465 AGAGAGAGACCAGGCACATGTTCAGTTGTCATGGCACCCTTGGAGAAAAAAATACATATTTGTTA
326 AGAGAAAGACCAGGCACATGTTAAGTTGTCATGGCACCCTTGGAG-AAAAAATACATATTTGTTA
42530 GGAAAATTCTAAGTTTTTTTGTACCACAAAAATTAAACAAGATATTGAAAACAAATTACCTCGTT
390 GGAAAATTCTAAGTTTTTTTGTACCACAAAAATTAAACAAGATATTGAAAACAAATTACCTCGTT
42595 AATCTTCAAGGCAACTTGTCTCTTTCTAAACTTGTTTTCTGCAGCACGCCTGAGATTACTAGCAG
455 AATCTTCAAGGCAACTTGTCTCTTTCTAAACTTGTTTTCTGCAGCACGCCTGAGATTACTAGCAG
42660 TCAGTGGTCTC
520 TCAGTGGTCTC
42671 CCGAATATTTTCTCTCTACTTTTCAAAAAAGGGAAATGACATTGATTAAAATAATTGTTTCCAAC
1 CCGAATATTTTCTCTCTACTTTTCAAAAAAGGGAAATGACATTGATTAAAATAATTGTTTCCAAC
*
42736 ATCATCACATGAACAGGCTCCCAAAACCCTGCTAAAGTCTAAACTATGCAGAATAATTAATATTA
66 ATCATCACATGAACAAGCTCCCAAAACCCTGCTAAAGTCTAAACTATGCAGAATAATTAATATTA
42801 AATAATGTCAACTACC-AATCTTCAAAAAAGGGAGCCATAATAACCCTAAACCATCTAATATTCC
131 AATAATGTCAACTACCAAATCTTCAAAAAAGGGAGCCATAATAACCCTAAACCATCTAATATTCC
*
42865 AAAATAAACATCCATTATTCAACCACCTATAAGGCTATAACAATTACATTTTCAAAATAACAATT
196 AAAATAAACATCCATCATTCAACCACCTATAAGGCTATAACAATTACATTTTCAAAATAACAATT
42930 TCTGCTTTCCTTTAAAAGTTTCAGTTGTTGTTCCACTTGCCGTTCCACTATGCTGACTTCCACGT
261 TCTGCTTTCCTTTAAAAGTTTCAGTTGTTGTTCCACTTGCCGTTCCACTATGCTGACTTCCACGT
42995 AGAGAAAGACCAGGCACATGTTAAGTTGTCATGGCACCCTTGGAGAAAAAATACATATTTGTTAG
326 AGAGAAAGACCAGGCACATGTTAAGTTGTCATGGCACCCTTGGAGAAAAAATACATATTTGTTAG
43060 GAAAATTCTAAGTTTTTTTGTACCACAAAAATTAAACAAGATATTGAAAACAAATTACCTCGTTA
391 GAAAATTCTAAGTTTTTTTGTACCACAAAAATTAAACAAGATATTGAAAACAAATTACCTCGTTA
43125 ATCTTCAAGGCAACTTGTCTCTTTCTAAACTTGTTTTCTGCAGCACGCCTGAGATTACTAGCAGT
456 ATCTTCAAGGCAACTTGTCTCTTTCTAAACTTGTTTTCTGCAGCACGCCTGAGATTACTAGCAGT
43190 CAGTGGTCT
521 CAGTGGTCT
43199 TTGGTTAGAA
Statistics
Matches: 520, Mismatches: 8, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
529 159 0.31
530 220 0.42
531 141 0.27
ACGTcount: A:0.36, C:0.21, G:0.13, T:0.31
Consensus pattern (530 bp):
CCGAATATTTTCTCTCTACTTTTCAAAAAAGGGAAATGACATTGATTAAAATAATTGTTTCCAAC
ATCATCACATGAACAAGCTCCCAAAACCCTGCTAAAGTCTAAACTATGCAGAATAATTAATATTA
AATAATGTCAACTACCAAATCTTCAAAAAAGGGAGCCATAATAACCCTAAACCATCTAATATTCC
AAAATAAACATCCATCATTCAACCACCTATAAGGCTATAACAATTACATTTTCAAAATAACAATT
TCTGCTTTCCTTTAAAAGTTTCAGTTGTTGTTCCACTTGCCGTTCCACTATGCTGACTTCCACGT
AGAGAAAGACCAGGCACATGTTAAGTTGTCATGGCACCCTTGGAGAAAAAATACATATTTGTTAG
GAAAATTCTAAGTTTTTTTGTACCACAAAAATTAAACAAGATATTGAAAACAAATTACCTCGTTA
ATCTTCAAGGCAACTTGTCTCTTTCTAAACTTGTTTTCTGCAGCACGCCTGAGATTACTAGCAGT
CAGTGGTCTC
Found at i:47179 original size:31 final size:29
Alignment explanation
Indices: 47140--47212 Score: 101
Period size: 29 Copynumber: 2.4 Consensus size: 29
47130 TTGAAATATT
*
47140 ACCAAATTGAGCCGATTTGGAAAGGTTTGGC
1 ACCAAATTGAGCAGATTT--AAAGGTTTGGC
**
47171 ACTGAATTGAGCAGATTTAAAGGTTTGGC
1 ACCAAATTGAGCAGATTTAAAGGTTTGGC
47200 ACCAAATTGAGCA
1 ACCAAATTGAGCA
47213 TCTGGCCAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 22 0.59
31 15 0.41
ACGTcount: A:0.33, C:0.15, G:0.26, T:0.26
Consensus pattern (29 bp):
ACCAAATTGAGCAGATTTAAAGGTTTGGC
Found at i:47201 original size:29 final size:30
Alignment explanation
Indices: 47140--47243 Score: 106
Period size: 31 Copynumber: 3.4 Consensus size: 30
47130 TTGAAATATT
*
47140 ACCAAATTGAGCCGATTTGGAAAGGTTTGGC
1 ACCAAATTGAGCAGATTT-GAAAGGTTTGGC
**
47171 ACTGAATTGAGCAGATTT-AAAGGTTTGGC
1 ACCAAATTGAGCAGATTTGAAAGGTTTGGC
* *
47200 ACCAAATTGAGC--ATCTGGCCAAAGGTTTGGT
1 ACCAAATTGAGCAGAT-TTG--AAAGGTTTGGC
47231 ACCAAATTGAGCA
1 ACCAAATTGAGCA
47244 TTTAGCCTAT
Statistics
Matches: 61, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
27 2 0.03
28 1 0.02
29 21 0.34
31 37 0.61
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.26
Consensus pattern (30 bp):
ACCAAATTGAGCAGATTTGAAAGGTTTGGC
Found at i:50458 original size:56 final size:56
Alignment explanation
Indices: 50396--50508 Score: 208
Period size: 56 Copynumber: 2.0 Consensus size: 56
50386 TCTTGAATGC
* *
50396 TCAATCCTTAATTATGCTATTTGGATGCAGTTTTAATCTATTTGTCCAGTTTGACT
1 TCAATCCTTAAATACGCTATTTGGATGCAGTTTTAATCTATTTGTCCAGTTTGACT
50452 TCAATCCTTAAATACGCTATTTGGATGCAGTTTTAATCTATTTGTCCAGTTTGACT
1 TCAATCCTTAAATACGCTATTTGGATGCAGTTTTAATCTATTTGTCCAGTTTGACT
50508 T
1 T
50509 TAACAAAAAC
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 55 1.00
ACGTcount: A:0.24, C:0.17, G:0.14, T:0.45
Consensus pattern (56 bp):
TCAATCCTTAAATACGCTATTTGGATGCAGTTTTAATCTATTTGTCCAGTTTGACT
Found at i:60730 original size:42 final size:42
Alignment explanation
Indices: 60671--60801 Score: 201
Period size: 42 Copynumber: 3.1 Consensus size: 42
60661 CAAAATCGGC
* *
60671 TTTGGCTCCTAAGAGAGATACTGTCTCTGATTGAGATCCTGA
1 TTTGGATCCCAAGAGAGATACTGTCTCTGATTGAGATCCTGA
* *
60713 TTTGGATCCCAAGAGAGATACCGTCTCTGATCGAGATCCTGA
1 TTTGGATCCCAAGAGAGATACTGTCTCTGATTGAGATCCTGA
*
60755 TTTGGTTCCCAAGAGAGATA-TCGTCTCTGATTGAGATCCTGA
1 TTTGGATCCCAAGAGAGATACT-GTCTCTGATTGAGATCCTGA
60797 TTTGG
1 TTTGG
60802 CTTCATCGTT
Statistics
Matches: 81, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
42 81 1.00
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (42 bp):
TTTGGATCCCAAGAGAGATACTGTCTCTGATTGAGATCCTGA
Found at i:62557 original size:13 final size:13
Alignment explanation
Indices: 62539--62564 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
62529 AGCCAAAGAA
62539 GTTTATAACTTTG
1 GTTTATAACTTTG
62552 GTTTATAACTTTG
1 GTTTATAACTTTG
62565 AGTAATCTCA
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:0.23, C:0.08, G:0.15, T:0.54
Consensus pattern (13 bp):
GTTTATAACTTTG
Found at i:63503 original size:10 final size:10
Alignment explanation
Indices: 63488--63518 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
63478 ACTCCAAGAT
63488 CTTTCCTTAA
1 CTTTCCTTAA
63498 CTTTCCTTAA
1 CTTTCCTTAA
63508 CTTTTCCTTAA
1 C-TTTCCTTAA
63519 GTTTTCATAG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 11 0.55
11 9 0.45
ACGTcount: A:0.19, C:0.29, G:0.00, T:0.52
Consensus pattern (10 bp):
CTTTCCTTAA
Found at i:63515 original size:11 final size:11
Alignment explanation
Indices: 63489--63524 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
63479 CTCCAAGATC
63489 TTTCCTTAAC-
1 TTTCCTTAACT
63499 TTTCCTTAACT
1 TTTCCTTAACT
*
63510 TTTCCTTAAGT
1 TTTCCTTAACT
63521 TTTC
1 TTTC
63525 ATAGAATGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 10 0.42
11 14 0.58
ACGTcount: A:0.17, C:0.25, G:0.03, T:0.56
Consensus pattern (11 bp):
TTTCCTTAACT
Found at i:67783 original size:23 final size:23
Alignment explanation
Indices: 67753--67800 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
67743 GGGGTGTTTG
67753 AACTTGAA-CTTC-ACTCGAAACTC
1 AACTTGAAGC-TCAACTCG-AACTC
67776 AACTTGAAGCTCAACTCGAACTC
1 AACTTGAAGCTCAACTCGAACTC
67799 AA
1 AA
67801 TCAAATATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.38, C:0.29, G:0.10, T:0.23
Consensus pattern (23 bp):
AACTTGAAGCTCAACTCGAACTC
Found at i:79386 original size:20 final size:20
Alignment explanation
Indices: 79358--79395 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
79348 GGTTGGTGGT
* *
79358 TATCTTGGGATATTACCGGG
1 TATCCTGGGAGATTACCGGG
79378 TATCCTGGGAGATTACCG
1 TATCCTGGGAGATTACCG
79396 TCGAATGGCC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.18, G:0.29, T:0.32
Consensus pattern (20 bp):
TATCCTGGGAGATTACCGGG
Found at i:79862 original size:21 final size:21
Alignment explanation
Indices: 79833--79888 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
79823 ATTTTTAATG
*
79833 TTGATTGTTTGTGGATTTATC
1 TTGAATGTTTGTGGATTTATC
* * *
79854 TTGAATGTTTGTAGATTTTTT
1 TTGAATGTTTGTGGATTTATC
*
79875 TTGAATGTATGTGG
1 TTGAATGTTTGTGG
79889 GTTTTTTATG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.18, C:0.02, G:0.25, T:0.55
Consensus pattern (21 bp):
TTGAATGTTTGTGGATTTATC
Found at i:79893 original size:21 final size:21
Alignment explanation
Indices: 79854--79895 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
79844 TGGATTTATC
*
79854 TTGAATGTTTGTAGATTTTTT
1 TTGAATGTATGTAGATTTTTT
* *
79875 TTGAATGTATGTGGGTTTTTT
1 TTGAATGTATGTAGATTTTTT
79896 ATGTTGATTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.00, G:0.24, T:0.60
Consensus pattern (21 bp):
TTGAATGTATGTAGATTTTTT
Found at i:80057 original size:10 final size:10
Alignment explanation
Indices: 80042--80066 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
80032 TGGCTGTCAG
80042 TTTTGATGGC
1 TTTTGATGGC
80052 TTTTGATGGC
1 TTTTGATGGC
80062 TTTTG
1 TTTTG
80067 GATTTATGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.08, C:0.08, G:0.28, T:0.56
Consensus pattern (10 bp):
TTTTGATGGC
Found at i:81781 original size:25 final size:24
Alignment explanation
Indices: 81753--81810 Score: 57
Period size: 25 Copynumber: 2.4 Consensus size: 24
81743 TCTCCCAAAT
81753 TCCCCTTTTCGGATCC-CTCGCTTTC
1 TCCCCTTTTCGGATCCTC-CG-TTTC
** *
81778 TCCCGATTTAGGATCCTCCGTTTC
1 TCCCCTTTTCGGATCCTCCGTTTC
81802 T-CCCTTTTC
1 TCCCCTTTTC
81811 TTCGCCGGCG
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
23 5 0.19
24 5 0.19
25 15 0.58
26 1 0.04
ACGTcount: A:0.07, C:0.40, G:0.12, T:0.41
Consensus pattern (24 bp):
TCCCCTTTTCGGATCCTCCGTTTC
Found at i:89280 original size:3 final size:3
Alignment explanation
Indices: 89272--89340 Score: 95
Period size: 3 Copynumber: 23.3 Consensus size: 3
89262 TATATGCTAT
* * * *
89272 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TAA TAA TAA T-A AGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
89319 TGA TGA TGA TGA TGA TGA TGA T
1 TGA TGA TGA TGA TGA TGA TGA T
89341 AATAATAATA
Statistics
Matches: 62, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
2 1 0.02
3 61 0.98
ACGTcount: A:0.39, C:0.00, G:0.28, T:0.33
Consensus pattern (3 bp):
TGA
Found at i:89326 original size:32 final size:32
Alignment explanation
Indices: 89285--89348 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
89275 TGATGATGAT
89285 GATGATGATGATGATGATGATAATAATAATAA
1 GATGATGATGATGATGATGATAATAATAATAA
*
89317 GATGATGATGATGATGATGATGATAATAATAA
1 GATGATGATGATGATGATGATAATAATAATAA
89349 TAATAATAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.45, C:0.00, G:0.23, T:0.31
Consensus pattern (32 bp):
GATGATGATGATGATGATGATAATAATAATAA
Found at i:89328 original size:35 final size:35
Alignment explanation
Indices: 89282--89351 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
89272 TGATGATGAT
89282 GATGATGATGATGATGATGATGATAATAATAATAA
1 GATGATGATGATGATGATGATGATAATAATAATAA
89317 GATGATGATGATGATGATGATGATAATAATAATAA
1 GATGATGATGATGATGATGATGATAATAATAATAA
89352 TAATAATAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.46, C:0.00, G:0.23, T:0.31
Consensus pattern (35 bp):
GATGATGATGATGATGATGATGATAATAATAATAA
Found at i:89345 original size:3 final size:3
Alignment explanation
Indices: 89339--89363 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
89329 GATGATGATG
89339 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
89364 CCTCTACTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:92652 original size:8 final size:8
Alignment explanation
Indices: 92639--92666 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
92629 TTTGGCATCG
92639 TTTTCTGT
1 TTTTCTGT
92647 TTTTCTGT
1 TTTTCTGT
92655 TTTTCTGT
1 TTTTCTGT
92663 TTTT
1 TTTT
92667 GTTTCATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.00, C:0.11, G:0.11, T:0.79
Consensus pattern (8 bp):
TTTTCTGT
Found at i:96403 original size:90 final size:90
Alignment explanation
Indices: 96243--96431 Score: 234
Period size: 90 Copynumber: 2.1 Consensus size: 90
96233 GGGGATTGGA
* ** * *
96243 ATTCGGTGAGCTCGGTGCAGCACATTTTCAAATAGATCAGGGTGATTCGGTGAATCAAGTTAATG
1 ATTCGGTGAGCTCGGTGCAGCACATTTTCAAACAGATCAGGACGATTCAGTGAATCAACTTAATG
* * * *
96308 TGGTGCATTATTTCTTTAAGGTAGG
66 CGGTGCAGTATTTCTTCAAAGTAGG
* * * * *
96333 ATTCGGTGAGCTTGGTGCAGCACATTTTCAAACAGTTGAGGACGATTCAGTGAATTAACTTACTG
1 ATTCGGTGAGCTCGGTGCAGCACATTTTCAAACAGATCAGGACGATTCAGTGAATCAACTTAATG
**
96398 CGGTGCAGTATTTCTTCAAAGTTTG
66 CGGTGCAGTATTTCTTCAAAGTAGG
96423 ATTCGGTGA
1 ATTCGGTGA
96432 ATCAAGGTTT
Statistics
Matches: 83, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
90 83 1.00
ACGTcount: A:0.25, C:0.15, G:0.26, T:0.33
Consensus pattern (90 bp):
ATTCGGTGAGCTCGGTGCAGCACATTTTCAAACAGATCAGGACGATTCAGTGAATCAACTTAATG
CGGTGCAGTATTTCTTCAAAGTAGG
Found at i:99640 original size:214 final size:214
Alignment explanation
Indices: 99265--99803 Score: 979
Period size: 214 Copynumber: 2.5 Consensus size: 214
99255 ATCATAGGTC
*
99265 TGTTAAGCATCCAACCTAAAACCAATTGGCAATAGGTGGAGAGGCCCTTCATGTATATAAGACAC
1 TGTTAAGCATCCAACCTAAAACCAATTGGCAATAGGTGGAGAGGCCCTTCATGTATATAAGGCAC
* *
99330 CCAGTCATGTCGAACAAAACCAATGTGAGATATTACCACTTTAACACACCCCCTCACGTGTAGCC
66 CCAGTCATGTCGAACATAACCAATGTGGGATATTACCACTTTAACACACCCCCTCACGTGTAGCC
*
99395 CGGGACAACACCCAAAACAGAACGGGCCTACACGTGGACAACCGAGTCTAGGGCACAACAGGACA
131 CGGGACAACACCCAAAACAGAACGAGCCTACACGTGGACAACCGAGTCTAGGGCACAACAGGACA
99460 GACCTGAGCTCTGATACCA
196 GACCTGAGCTCTGATACCA
*
99479 TGTTAAGCATCCAACCTAAAACCAATTGGCAATATGTGGAGAGGCCCTTCATGTATATAAGGCAC
1 TGTTAAGCATCCAACCTAAAACCAATTGGCAATAGGTGGAGAGGCCCTTCATGTATATAAGGCAC
99544 CCAGTCATGTCGAACATAACCAATGTGGGATATTACCACTTTAACACACCCCCTCACGTGTAGCC
66 CCAGTCATGTCGAACATAACCAATGTGGGATATTACCACTTTAACACACCCCCTCACGTGTAGCC
* * * *
99609 CGGGACAACACCCGAAATAGAACGAGCCTACACGTGGACAACCGAGTCTGGGGCGCAACAGGACA
131 CGGGACAACACCCAAAACAGAACGAGCCTACACGTGGACAACCGAGTCTAGGGCACAACAGGACA
99674 GACCTGAGCTCTGATACCA
196 GACCTGAGCTCTGATACCA
* *
99693 TGTTAAGCATCCAACCTAAAACCAATTGGCAATAGGTGGAGAGACACTTCATGTATATAAGGCAC
1 TGTTAAGCATCCAACCTAAAACCAATTGGCAATAGGTGGAGAGGCCCTTCATGTATATAAGGCAC
99758 CCAGTCATGTCGAACATAACCAATGTGGGATATTACCACTTTAACA
66 CCAGTCATGTCGAACATAACCAATGTGGGATATTACCACTTTAACA
99804 AGGTCCATGT
Statistics
Matches: 313, Mismatches: 12, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
214 313 1.00
ACGTcount: A:0.34, C:0.27, G:0.20, T:0.19
Consensus pattern (214 bp):
TGTTAAGCATCCAACCTAAAACCAATTGGCAATAGGTGGAGAGGCCCTTCATGTATATAAGGCAC
CCAGTCATGTCGAACATAACCAATGTGGGATATTACCACTTTAACACACCCCCTCACGTGTAGCC
CGGGACAACACCCAAAACAGAACGAGCCTACACGTGGACAACCGAGTCTAGGGCACAACAGGACA
GACCTGAGCTCTGATACCA
Found at i:103235 original size:2 final size:2
Alignment explanation
Indices: 103228--103254 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
103218 AGAAATCCAT
103228 TA 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 TA T
103255 GGTGAGAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:106267 original size:22 final size:22
Alignment explanation
Indices: 106242--106293 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
106232 AATTATTTCC
*
106242 TCTTGAAATAATTCTTCAAT-AG
1 TCTTCAAATAA-TCTTCAATGAG
*
106264 TCTTCAAATTATCTTCAATGAG
1 TCTTCAAATAATCTTCAATGAG
106286 TCTTCAAA
1 TCTTCAAA
106294 CACGAACTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 8 0.30
22 19 0.70
ACGTcount: A:0.35, C:0.17, G:0.08, T:0.40
Consensus pattern (22 bp):
TCTTCAAATAATCTTCAATGAG
Found at i:109837 original size:26 final size:26
Alignment explanation
Indices: 109800--109892 Score: 105
Period size: 28 Copynumber: 3.4 Consensus size: 26
109790 GAAGATATTT
109800 TTTTTCTTTTTGAAAACGCAAAAACAA
1 TTTTT-TTTTTGAAAACGCAAAAACAA
* **
109827 TTTTTTTTTTGAAAACGTAAAAACTCTT
1 TTTTTTTTTTGAAAACGCAAAAA--CAA
*
109855 TTTTTTTTTTCAAAAACGCAGAAAACAA
1 TTTTTTTTTT-GAAAACGCA-AAAACAA
109883 TTTTTTTTTT
1 TTTTTTTTTT
109893 AAATTTAAAA
Statistics
Matches: 55, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
26 17 0.31
27 5 0.09
28 22 0.40
29 7 0.13
30 4 0.07
ACGTcount: A:0.34, C:0.12, G:0.06, T:0.47
Consensus pattern (26 bp):
TTTTTTTTTTGAAAACGCAAAAACAA
Found at i:110208 original size:21 final size:22
Alignment explanation
Indices: 110186--110226 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
110176 TAATAATTGA
*
110186 AAAG-AAAGC-AATTAAATTAG
1 AAAGCAAAGCAAAATAAATTAG
110206 AAAGCAAAGCAAAATAAATTA
1 AAAGCAAAGCAAAATAAATTA
110227 AATCTAGATC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 5 0.28
22 9 0.50
ACGTcount: A:0.63, C:0.07, G:0.12, T:0.17
Consensus pattern (22 bp):
AAAGCAAAGCAAAATAAATTAG
Found at i:113405 original size:3 final size:3
Alignment explanation
Indices: 113397--113495 Score: 180
Period size: 3 Copynumber: 33.0 Consensus size: 3
113387 ACTAGTGTAT
* *
113397 ATA ATA ATA ATA ATA ACA ATA ATA ATA ATA ACA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
113445 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
113493 ATA
1 ATA
113496 TTTATTATTA
Statistics
Matches: 92, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 92 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:113973 original size:3 final size:3
Alignment explanation
Indices: 113965--114014 Score: 91
Period size: 3 Copynumber: 16.7 Consensus size: 3
113955 ATAATTAGTA
*
113965 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATA ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
114013 AT
1 AT
114015 AAAAATAATT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:115671 original size:13 final size:14
Alignment explanation
Indices: 115653--115681 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
115643 TGATATGCAC
115653 TTATTTAT-CTTAA
1 TTATTTATGCTTAA
115666 TTATTTATGCTTAA
1 TTATTTATGCTTAA
115680 TT
1 TT
115682 TGATAATTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.28, C:0.07, G:0.03, T:0.62
Consensus pattern (14 bp):
TTATTTATGCTTAA
Found at i:116701 original size:15 final size:16
Alignment explanation
Indices: 116676--116714 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
116666 GGAGGTTGAA
116676 AAAAGCAATTAAAC-AG
1 AAAA-CAATTAAACTAG
*
116692 AAAACAATTATACTAG
1 AAAACAATTAAACTAG
116708 AAAACAA
1 AAAACAA
116715 AGCAAAGTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.64, C:0.13, G:0.08, T:0.15
Consensus pattern (16 bp):
AAAACAATTAAACTAG
Found at i:121736 original size:27 final size:27
Alignment explanation
Indices: 121713--121771 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 27
121703 AAAGCAAGAA
*
121713 AAATTTTTTTTTTCGAAAACGCAAAACC
1 AAATTTTTTTTTTCAAAAACGCAAAA-C
* *
121741 GATTTTTTTTTTTCAAAAACGCAAACAC
1 AAATTTTTTTTTTCAAAAACGCAAA-AC
121769 AAA
1 AAA
121772 ACAAAATTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
28 24 0.96
29 1 0.04
ACGTcount: A:0.41, C:0.17, G:0.07, T:0.36
Consensus pattern (27 bp):
AAATTTTTTTTTTCAAAAACGCAAAAC
Found at i:121834 original size:28 final size:29
Alignment explanation
Indices: 121778--121843 Score: 82
Period size: 28 Copynumber: 2.2 Consensus size: 29
121768 CAAAACAAAA
121778 TTTTTTTTTTAAATTAAAAACGCAAAGAATT
1 TTTTTTTTTTAAA-TAAAAACGC-AAGAATT
121809 TTTTTTTTTTAGAA-AAAAACGC-AGAATT
1 TTTTTTTTTTA-AATAAAAACGCAAGAATT
*
121837 TGTTTTT
1 TTTTTTT
121844 AGAGAAAACA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
28 12 0.36
30 8 0.24
31 11 0.33
32 2 0.06
ACGTcount: A:0.36, C:0.06, G:0.09, T:0.48
Consensus pattern (29 bp):
TTTTTTTTTTAAATAAAAACGCAAGAATT
Found at i:122123 original size:15 final size:16
Alignment explanation
Indices: 122098--122136 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
122088 AGAGGTTGAA
122098 AAAAGCAATTAAAC-AG
1 AAAA-CAATTAAACTAG
*
122114 AAAACAATTATACTAG
1 AAAACAATTAAACTAG
122130 AAAACAA
1 AAAACAA
122137 AGCAAAGTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.64, C:0.13, G:0.08, T:0.15
Consensus pattern (16 bp):
AAAACAATTAAACTAG
Done.