Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012486.1 Corchorus olitorius cultivar O-4 contig12519, 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: 26930
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.35
Found at i:81 original size:5 final size:5
Alignment explanation
Indices: 68--97 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
58 ATAAGACATT
*
68 CAAAT CAAAA CAAAA CAAAA CAAAA CAAAA
1 CAAAA CAAAA CAAAA CAAAA CAAAA CAAAA
98 ATTTAGTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.77, C:0.20, G:0.00, T:0.03
Consensus pattern (5 bp):
CAAAA
Found at i:715 original size:13 final size:13
Alignment explanation
Indices: 683--708 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
673 CTCTCTAACC
683 TCATAAATCATAT
1 TCATAAATCATAT
696 TCATAAATCATAT
1 TCATAAATCATAT
709 ATTTAAACCC
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:0.46, C:0.15, G:0.00, T:0.38
Consensus pattern (13 bp):
TCATAAATCATAT
Found at i:848 original size:19 final size:20
Alignment explanation
Indices: 819--864 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
809 TGAGTAGTTT
*
819 TAAAGTAAAAATGTAAT-TTA
1 TAAA-TAAAAATATAATATTA
839 TAAATAAAAATATAATATTA
1 TAAATAAAAATATAATATTA
859 -AAATAA
1 TAAATAA
865 TTAATAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (20 bp):
TAAATAAAAATATAATATTA
Found at i:4544 original size:21 final size:20
Alignment explanation
Indices: 4520--4558 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
4510 AAAAATGGCC
*
4520 AAAAAGAAGAATAAAAATTGA
1 AAAAAGAA-AAAAAAAATTGA
4541 AAAAAGAAAAAAAAAATT
1 AAAAAGAAAAAAAAAATT
4559 CATTTTTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.77, C:0.00, G:0.10, T:0.13
Consensus pattern (20 bp):
AAAAAGAAAAAAAAAATTGA
Found at i:5304 original size:45 final size:45
Alignment explanation
Indices: 5254--5348 Score: 163
Period size: 45 Copynumber: 2.1 Consensus size: 45
5244 ATGTCACCAA
5254 CTTTTGATAGATTTCTATTTTACTAACTATAACTACACAAAAATG
1 CTTTTGATAGATTTCTATTTTACTAACTATAACTACACAAAAATG
* *
5299 CTTTTGATAGATTTCTATTTTACTCATTATAACTACACAAAAATG
1 CTTTTGATAGATTTCTATTTTACTAACTATAACTACACAAAAATG
*
5344 TTTTT
1 CTTTT
5349 TGAGAGAGGC
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.35, C:0.15, G:0.06, T:0.44
Consensus pattern (45 bp):
CTTTTGATAGATTTCTATTTTACTAACTATAACTACACAAAAATG
Found at i:6995 original size:25 final size:23
Alignment explanation
Indices: 6966--7011 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
6956 TTGGCATCGC
*
6966 TTTCGTTTTTTGTTTTTTGTTTTCG
1 TTTCG-TTTCTGTTTTTT-TTTTCG
6991 TTTCGTTTCTGTTTTTTTTTT
1 TTTCGTTTCTGTTTTTTTTTT
7012 GTTACACTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 4 0.20
24 11 0.55
25 5 0.25
ACGTcount: A:0.00, C:0.09, G:0.13, T:0.78
Consensus pattern (23 bp):
TTTCGTTTCTGTTTTTTTTTTCG
Found at i:7521 original size:17 final size:17
Alignment explanation
Indices: 7495--7528 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
7485 TTGAAAATAG
*
7495 CTAATTCAAACTAAAAA
1 CTAATGCAAACTAAAAA
7512 CTAATGCAAACTAAAAA
1 CTAATGCAAACTAAAAA
7529 GTGTTTGCTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.59, C:0.18, G:0.03, T:0.21
Consensus pattern (17 bp):
CTAATGCAAACTAAAAA
Found at i:8615 original size:19 final size:18
Alignment explanation
Indices: 8591--8626 Score: 63
Period size: 18 Copynumber: 1.9 Consensus size: 18
8581 GGCCTAGCCC
8591 ATAAGAAATAAGAAAAAGA
1 ATAAGAAA-AAGAAAAAGA
8610 ATAAGAAAAAGAAAAAG
1 ATAAGAAAAAGAAAAAG
8627 GGCCTAGCCC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.75, C:0.00, G:0.17, T:0.08
Consensus pattern (18 bp):
ATAAGAAAAAGAAAAAGA
Found at i:8623 original size:6 final size:6
Alignment explanation
Indices: 8593--8626 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
8583 CCTAGCCCAT
*
8593 AAGAAA TAAGAAA AAGAAT AAGAAA AAGAAA AAG
1 AAGAAA -AAGAAA AAGAAA AAGAAA AAGAAA AAG
8627 GGCCTAGCCC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
6 19 0.76
7 6 0.24
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.06
Consensus pattern (6 bp):
AAGAAA
Found at i:8663 original size:9 final size:9
Alignment explanation
Indices: 8642--8691 Score: 50
Period size: 10 Copynumber: 5.4 Consensus size: 9
8632 AGCCCATAAC
8642 GAAGAAGAAA
1 GAAGAA-AAA
8652 GAAGAAAAA
1 GAAGAAAAA
8661 GAAGAAAGAA
1 GAAGAAA-AA
8671 -AAG-AAAA
1 GAAGAAAAA
*
8678 GAAAAGAAAA
1 GAAGA-AAAA
8688 GAAG
1 GAAG
8692 GAAATTTGGA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
7 2 0.06
8 4 0.12
9 13 0.38
10 15 0.44
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (9 bp):
GAAGAAAAA
Found at i:8664 original size:16 final size:17
Alignment explanation
Indices: 8643--8690 Score: 66
Period size: 16 Copynumber: 3.0 Consensus size: 17
8633 GCCCATAACG
*
8643 AAGAAGAAAGAAGA-AA
1 AAGAAGAAAGAAAAGAA
8659 AAGAAGAAAGAAAAGAA
1 AAGAAGAAAGAAAAGAA
8676 AAG-A-AAAGAAAAGAA
1 AAGAAGAAAGAAAAGAA
8691 GGAAATTTGG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
15 11 0.37
16 14 0.47
17 5 0.17
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (17 bp):
AAGAAGAAAGAAAAGAA
Found at i:8675 original size:5 final size:5
Alignment explanation
Indices: 8653--8690 Score: 53
Period size: 5 Copynumber: 8.0 Consensus size: 5
8643 AAGAAGAAAG
*
8653 AAGAA AA-AG AAG-A AAGAA AAGAA AAGAA AAGAA AAGAA
1 AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA
8691 GGAAATTTGG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
4 6 0.21
5 23 0.79
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:12265 original size:107 final size:102
Alignment explanation
Indices: 12028--12289 Score: 375
Period size: 107 Copynumber: 2.5 Consensus size: 102
12018 ATAAATTTTT
* * *
12028 AATTTTAATTT-GGGCTAAACTTGGTG-AATTAGTTATATATTTTATTTCTAAAACCTTATAACA
1 AATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAACCCTATAACA
* *
12091 ATATTATTAATTATGGAATTTACCCTTAAAATGAAAA
66 ATATTATTAATTATGAAATTTACCCTTAAAATCAAAA
** *
12128 AATAATAATTTGGGGCTAAACTTAGTGAAATTAGTTTTGTATTTTATTTCTAAAACCCTATAACA
1 AATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAACCCTATAACA
*
12193 ATAAATTATTAATTTTGAAATTTACCCTTAAAATAACAATAA
66 AT--ATTATTAATTATGAAATTTACCCTTAAAAT--CAA-AA
*
12235 AATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTCCTAAAA
1 AATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAA
12290 ATCTATTATA
Statistics
Matches: 142, Mismatches: 13, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
100 9 0.06
101 14 0.10
102 36 0.25
104 28 0.20
106 2 0.01
107 53 0.37
ACGTcount: A:0.39, C:0.09, G:0.10, T:0.42
Consensus pattern (102 bp):
AATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAACCCTATAACA
ATATTATTAATTATGAAATTTACCCTTAAAATCAAAA
Found at i:23054 original size:20 final size:20
Alignment explanation
Indices: 23010--23055 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
23000 TCAAGGAAAC
23010 AACCCGTTGAAACCCGGTGT
1 AACCCGTTGAAACCCGGTGT
*
23030 GACCCGTTGAAACCCGGAT-T
1 AACCCGTTGAAACCCGG-TGT
23050 AACCCG
1 AACCCG
23056 GTGATCCGGC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 22 0.96
21 1 0.04
ACGTcount: A:0.26, C:0.33, G:0.24, T:0.17
Consensus pattern (20 bp):
AACCCGTTGAAACCCGGTGT
Found at i:23663 original size:206 final size:206
Alignment explanation
Indices: 23319--23732 Score: 801
Period size: 206 Copynumber: 2.0 Consensus size: 206
23309 AAATAAATTC
*
23319 ATCATATATATATAATGATAACAATGTACACTACAAATATGGAAACTCTTTAAATGTTGAGGCCT
1 ATCATATATATATAATGATAACAATGTACACTACAAATATAGAAACTCTTTAAATGTTGAGGCCT
*
23384 CCAAATCTCGACATGTGTCTCTAATTAATTCTAATATTCATTATATTGATATATTGATTAGAAAA
66 CCAAATCTCGACACGTGTCTCTAATTAATTCTAATATTCATTATATTGATATATTGATTAGAAAA
23449 AAGCCTTTGGTATATTTTAAGAAAGAACAATAATTTCTCTTACAAATTTTTAAGATTTTAATTAA
131 AAGCCTTTGGTATATTTTAAGAAAGAACAATAATTTCTCTTACAAATTTTTAAGATTTTAATTAA
23514 AAAATAAAGAA
196 AAAATAAAGAA
*
23525 ATCATATATATATAATGATAACAATGTACACTACAAATATAGAAACTTTTTAAATGTTGAGGCCT
1 ATCATATATATATAATGATAACAATGTACACTACAAATATAGAAACTCTTTAAATGTTGAGGCCT
23590 CCAAATCTCGACACGTGTCTCTAATTAATTCTAATATTCATTATATTGATATATTGATTAGAAAA
66 CCAAATCTCGACACGTGTCTCTAATTAATTCTAATATTCATTATATTGATATATTGATTAGAAAA
23655 AAGCCTTTGGTATATTTTAAGAAAGAACAATAATTTCTCTTACAAATTTTTAAGATTTTAATTAA
131 AAGCCTTTGGTATATTTTAAGAAAGAACAATAATTTCTCTTACAAATTTTTAAGATTTTAATTAA
23720 AAAATAAAGAA
196 AAAATAAAGAA
23731 AT
1 AT
23733 TAATAATGAA
Statistics
Matches: 205, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
206 205 1.00
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.36
Consensus pattern (206 bp):
ATCATATATATATAATGATAACAATGTACACTACAAATATAGAAACTCTTTAAATGTTGAGGCCT
CCAAATCTCGACACGTGTCTCTAATTAATTCTAATATTCATTATATTGATATATTGATTAGAAAA
AAGCCTTTGGTATATTTTAAGAAAGAACAATAATTTCTCTTACAAATTTTTAAGATTTTAATTAA
AAAATAAAGAA
Found at i:25427 original size:12 final size:13
Alignment explanation
Indices: 25404--25432 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
25394 TAAGTTTGGT
25404 TTCTCTCTTCTTC
1 TTCTCTCTTCTTC
25417 TTCTC-CTTCTTC
1 TTCTCTCTTCTTC
25429 TTCT
1 TTCT
25433 TTCGTTTTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (13 bp):
TTCTCTCTTCTTC
Done.