Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012082.1 Corchorus olitorius cultivar O-4 contig12115, 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: 46110
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:192 original size:21 final size:21
Alignment explanation
Indices: 168--208 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
158 GCGTTCCTGA
*
168 GGGTACCCAGGGCTGGGTAGG
1 GGGTACCCAGGGCCGGGTAGG
*
189 GGGTACCCCGGGCCGGGTAG
1 GGGTACCCAGGGCCGGGTAG
209 CCTCAGAACT
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:0.12, C:0.24, G:0.51, T:0.12
Consensus pattern (21 bp):
GGGTACCCAGGGCCGGGTAGG
Found at i:1481 original size:25 final size:26
Alignment explanation
Indices: 1430--1482 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
1420 TTACTATACT
*
1430 AAAAACTCAATTTTCAATTGCCGTTAA
1 AAAAACTCAATTTTCAATTG-CATTAA
* *
1457 AAAAAGTCAATTTTTAATTG-ATTAA
1 AAAAACTCAATTTTCAATTGCATTAA
1482 A
1 A
1483 TTAAATCTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 5 0.22
27 18 0.78
ACGTcount: A:0.45, C:0.11, G:0.08, T:0.36
Consensus pattern (26 bp):
AAAAACTCAATTTTCAATTGCATTAA
Found at i:1772 original size:22 final size:22
Alignment explanation
Indices: 1744--1800 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 22
1734 AGTGTGGTTA
1744 ATTATCAAAATTTCATAATGAG
1 ATTATCAAAATTTCATAATGAG
* * * *
1766 ATTATCACAATCTCATAGTGTG
1 ATTATCAAAATTTCATAATGAG
* *
1788 TTTACCAAAATTT
1 ATTATCAAAATTT
1801 TATGGGTAGG
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.39, C:0.14, G:0.09, T:0.39
Consensus pattern (22 bp):
ATTATCAAAATTTCATAATGAG
Found at i:2536 original size:22 final size:22
Alignment explanation
Indices: 2508--2724 Score: 140
Period size: 22 Copynumber: 9.9 Consensus size: 22
2498 ATCGAAGAGG
2508 TTATCAAAATTTCATAGTGAGA
1 TTATCAAAATTTCATAGTGAGA
*
2530 TTATCAAAATTTCA-A-TGAAA
1 TTATCAAAATTTCATAGTGAGA
* * * *
2550 GGTACCAAAATTTTATAGGGAGA
1 -TTATCAAAATTTCATAGTGAGA
* *
2573 TTATAAAAATTTCATAG-GAAA
1 TTATCAAAATTTCATAGTGAGA
* * * *
2594 GTTATCGAAATTTCATTGTGTGG
1 -TTATCAAAATTTCATAGTGAGA
** *
2617 TTATCAAAATTTCATA-ACAAA
1 TTATCAAAATTTCATAGTGAGA
* *
2638 GTTATCAAAA-ATCATAGGGA-A
1 -TTATCAAAATTTCATAGTGAGA
* * *
2659 GTTATCAAAATTTCAGAATGAGG
1 -TTATCAAAATTTCATAGTGAGA
* * *
2682 TTATTAAATTTTCATAGAGAGA
1 TTATCAAAATTTCATAGTGAGA
*
2704 TTATCGAAATTTCCATAGTGA
1 TTATCAAAATTT-CATAGTGA
2725 AGTTATTGAA
Statistics
Matches: 143, Mismatches: 42, Indels: 19
0.70 0.21 0.09
Matches are distributed among these distances:
20 4 0.03
21 31 0.22
22 97 0.68
23 11 0.08
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.34
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGAGA
Found at i:2626 original size:44 final size:44
Alignment explanation
Indices: 2507--2716 Score: 194
Period size: 44 Copynumber: 4.8 Consensus size: 44
2497 TATCGAAGAG
*
2507 GTTATCAAAATTTCATAGTGAGATTATCAAAATTTCA-ATGAAA
1 GTTATCAAAATTTCATAGTGAGATTATCAAAATTTCATAAGAAA
* * * * * *
2550 GGTACCAAAATTTTATAGGGAGATTATAAAAATTTCATAGGAAA
1 GTTATCAAAATTTCATAGTGAGATTATCAAAATTTCATAAGAAA
* * * * *
2594 GTTATCGAAATTTCATTGTGTGGTTATCAAAATTTCATAACAAA
1 GTTATCAAAATTTCATAGTGAGATTATCAAAATTTCATAAGAAA
* * * *
2638 GTTATCAAAA-ATCATAGGGA-AGTTATCAAAATTTCAGAATG-AG
1 GTTATCAAAATTTCATAGTGAGA-TTATCAAAATTTCATAA-GAAA
* * * *
2681 GTTATTAAATTTTCATAGAGAGATTATCGAAATTTC
1 GTTATCAAAATTTCATAGTGAGATTATCAAAATTTC
2717 CATAGTGAAG
Statistics
Matches: 131, Mismatches: 31, Indels: 9
0.77 0.18 0.05
Matches are distributed among these distances:
43 63 0.48
44 67 0.51
45 1 0.01
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.34
Consensus pattern (44 bp):
GTTATCAAAATTTCATAGTGAGATTATCAAAATTTCATAAGAAA
Found at i:2708 original size:65 final size:66
Alignment explanation
Indices: 2503--2730 Score: 168
Period size: 65 Copynumber: 3.5 Consensus size: 66
2493 ATCTTATCGA
* * * *
2503 AGAGGTTATCAAAATTTCATAGTGAGA-TTATCAAAATTTC--AATGAAAGG-TACCAAAATTTT
1 AGAGATTATCAAAAATTCATAG-GAAAGTTATCAAAATTTCAGAATG--AGGTTATC-AAATTTT
2564 -ATAG
62 CATAG
* * *** * *
2568 GGAGATTAT-AAAAATTTCATAGGAAAGTTATCGAAATTTCATTGTGTGGTTATCAAAATTTCAT
1 AGAGATTATCAAAAA-TTCATAGGAAAGTTATCAAAATTTCAGAATGAGGTTATCAAATTTTCAT
2632 A-
65 AG
* * * *
2633 ACAAAGTTATCAAAAA-TCATAGGGAAGTTATCAAAATTTCAGAATGAGGTTATTAAATTTTCAT
1 AGAGA-TTATCAAAAATTCATAGGAAAGTTATCAAAATTTCAGAATGAGGTTATCAAATTTTCAT
2697 AG
65 AG
* *
2699 AGAGATTATCGAAATTTCCATAGTG-AAGTTAT
1 AGAGATTATCAAAAATT-CATAG-GAAAGTTAT
2731 TGAAACTTTG
Statistics
Matches: 126, Mismatches: 25, Indels: 22
0.73 0.14 0.13
Matches are distributed among these distances:
64 7 0.06
65 85 0.67
66 14 0.11
67 19 0.15
68 1 0.01
ACGTcount: A:0.41, C:0.09, G:0.16, T:0.34
Consensus pattern (66 bp):
AGAGATTATCAAAAATTCATAGGAAAGTTATCAAAATTTCAGAATGAGGTTATCAAATTTTCATA
G
Found at i:2708 original size:87 final size:85
Alignment explanation
Indices: 2504--2716 Score: 205
Period size: 87 Copynumber: 2.4 Consensus size: 85
2494 TCTTATCGAA
** * *
2504 GAGGTTATCAAAATTTCATAGTGAGATTATCAAAATTTCAATGAAAGGTACCAAAATTTTATAGG
1 GAGGTTATC-AAATTTCATAGTGAGATTATCAAAATTTCAAACAAAGGTACCAAAATATCATAGG
*
2569 GAGATTATAAAAATTTCATAG
65 GAGATTATAAAAATTTCAAAG
* * * * * *
2590 GAAAGTTATCGAAATTTCATTGTGTGGTTATCAAAATTTCATAACAAAGTTATCAAAA-ATCATA
1 G-AGGTTATC-AAATTTCATAGTGAGATTATCAAAATTTCA-AACAAAGGTACCAAAATATCATA
* *
2654 GGGA-AGTTATCAAAATTTCAGAAT
63 GGGAGA-TTATAAAAATTTCA-AAG
* * *
2678 GAGGTTATTAAATTTTCATAGAGAGATTATCGAAATTTC
1 GAGGTTATCAAA-TTTCATAGTGAGATTATCAAAATTTC
2717 CATAGTGAAG
Statistics
Matches: 101, Mismatches: 21, Indels: 9
0.77 0.16 0.07
Matches are distributed among these distances:
86 5 0.05
87 82 0.81
88 14 0.14
ACGTcount: A:0.41, C:0.09, G:0.16, T:0.34
Consensus pattern (85 bp):
GAGGTTATCAAATTTCATAGTGAGATTATCAAAATTTCAAACAAAGGTACCAAAATATCATAGGG
AGATTATAAAAATTTCAAAG
Found at i:2766 original size:21 final size:21
Alignment explanation
Indices: 2741--2780 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
2731 TGAAACTTTG
2741 TAATGTGGTTATCAAAATTCA
1 TAATGTGGTTATCAAAATTCA
2762 TAATGTGGTTATCAAAATT
1 TAATGTGGTTATCAAAATT
2781 GTGATCTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.38, C:0.07, G:0.15, T:0.40
Consensus pattern (21 bp):
TAATGTGGTTATCAAAATTCA
Found at i:14712 original size:10 final size:10
Alignment explanation
Indices: 14697--14721 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
14687 AACTATTCTC
14697 CATTTATAGT
1 CATTTATAGT
14707 CATTTATAGT
1 CATTTATAGT
14717 CATTT
1 CATTT
14722 TGGTTCTTGT
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:0.28, C:0.12, G:0.08, T:0.52
Consensus pattern (10 bp):
CATTTATAGT
Found at i:14861 original size:109 final size:109
Alignment explanation
Indices: 14727--14940 Score: 385
Period size: 109 Copynumber: 2.0 Consensus size: 109
14717 CATTTTGGTT
*
14727 CTTGTATTTTTCTTTAAATCCAATAGTTCATTGCACTTTGTATTGTTTGGTATGTGTGCTTATTT
1 CTTGTATTTTTCTTTAAATCCAATAGTTCATTGCACTTTGTATTGTTTGATATGTGTGCTTATTT
*
14792 AATATGTTCAATTGAATAAA-CAACACAATTAATAATAATAGGTG
66 AATAGGTTCAATTGAATAAATC-ACACAATTAATAATAATAGGTG
*
14836 CTTGTATTTTTCTTTAAATCCAATAGTTCATTGCATTTTGTATTGTTTGATATGTGTGCTTATTT
1 CTTGTATTTTTCTTTAAATCCAATAGTTCATTGCACTTTGTATTGTTTGATATGTGTGCTTATTT
14901 AATAGGTTCAATTGAATAAATCACACAATTAATAATAATA
66 AATAGGTTCAATTGAATAAATCACACAATTAATAATAATA
14941 TATATAATAG
Statistics
Matches: 101, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
109 100 0.99
110 1 0.01
ACGTcount: A:0.32, C:0.11, G:0.13, T:0.45
Consensus pattern (109 bp):
CTTGTATTTTTCTTTAAATCCAATAGTTCATTGCACTTTGTATTGTTTGATATGTGTGCTTATTT
AATAGGTTCAATTGAATAAATCACACAATTAATAATAATAGGTG
Found at i:18778 original size:36 final size:36
Alignment explanation
Indices: 18726--18794 Score: 120
Period size: 36 Copynumber: 1.9 Consensus size: 36
18716 GACCGTGAGG
18726 TCCTCGGTTCAAGTCTCACGGAATGTGAGTTTACGA
1 TCCTCGGTTCAAGTCTCACGGAATGTGAGTTTACGA
* *
18762 TCCTGGGTTCAAGTCTCACGGGATGTGAGTTTA
1 TCCTCGGTTCAAGTCTCACGGAATGTGAGTTTA
18795 GTTTGTAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.20, C:0.20, G:0.28, T:0.32
Consensus pattern (36 bp):
TCCTCGGTTCAAGTCTCACGGAATGTGAGTTTACGA
Found at i:20580 original size:40 final size:44
Alignment explanation
Indices: 20525--20609 Score: 142
Period size: 40 Copynumber: 2.0 Consensus size: 44
20515 CGTCGTTTTG
20525 ATTTTTATTTTTATTTAAA-T-TAT-TA-TATATATTATAAAGT
1 ATTTTTATTTTTATTTAAATTATATATATTATATATTATAAAGT
20565 ATTTTTATTTTTATTTAAATTATATATATTATATATTATAAAGT
1 ATTTTTATTTTTATTTAAATTATATATATTATATATTATAAAGT
20609 A
1 A
20610 ATATATGATA
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
40 19 0.46
41 1 0.02
42 3 0.07
43 2 0.05
44 16 0.39
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (44 bp):
ATTTTTATTTTTATTTAAATTATATATATTATATATTATAAAGT
Found at i:22119 original size:15 final size:15
Alignment explanation
Indices: 22099--22130 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
22089 CCTTCACCTA
22099 TCCTTAGTATTGCTG
1 TCCTTAGTATTGCTG
*
22114 TCCTTAGTATTGTTG
1 TCCTTAGTATTGCTG
22129 TC
1 TC
22131 ATTTACTAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.12, C:0.19, G:0.19, T:0.50
Consensus pattern (15 bp):
TCCTTAGTATTGCTG
Found at i:31193 original size:12 final size:12
Alignment explanation
Indices: 31176--31209 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
31166 GTTGTTGTTT
*
31176 CAGAAAAAAACA
1 CAGAAAAAAAAA
31188 CAGAAAAAAAAA
1 CAGAAAAAAAAA
*
31200 AAGAAAAAAA
1 CAGAAAAAAA
31210 TCCTCAGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.82, C:0.09, G:0.09, T:0.00
Consensus pattern (12 bp):
CAGAAAAAAAAA
Found at i:36491 original size:23 final size:23
Alignment explanation
Indices: 36460--36505 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
36450 TATGATAATT
*
36460 ATTAGTAATTTATTTTAAATTTA
1 ATTAGTAATTCATTTTAAATTTA
*
36483 ATTATTAATTCATTTTAAATTTA
1 ATTAGTAATTCATTTTAAATTTA
36506 GTAAAAAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (23 bp):
ATTAGTAATTCATTTTAAATTTA
Found at i:38220 original size:14 final size:15
Alignment explanation
Indices: 38203--38231 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
38193 TATCATTATA
38203 TTTATATAT-ATAAT
1 TTTATATATAATAAT
38217 TTTATATATAATAAT
1 TTTATATATAATAAT
38232 ATAATGTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TTTATATATAATAAT
Found at i:38960 original size:44 final size:44
Alignment explanation
Indices: 38911--38996 Score: 172
Period size: 44 Copynumber: 2.0 Consensus size: 44
38901 AAACAAGTAA
38911 GTTGAATCGCGTTAGATCTCCTCTAATCACAAGATTCGAATCTT
1 GTTGAATCGCGTTAGATCTCCTCTAATCACAAGATTCGAATCTT
38955 GTTGAATCGCGTTAGATCTCCTCTAATCACAAGATTCGAATC
1 GTTGAATCGCGTTAGATCTCCTCTAATCACAAGATTCGAATC
38997 CCCTCTAATC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Consensus pattern (44 bp):
GTTGAATCGCGTTAGATCTCCTCTAATCACAAGATTCGAATCTT
Found at i:39006 original size:24 final size:24
Alignment explanation
Indices: 38974--39021 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
38964 CGTTAGATCT
38974 CCTCTAATCACAAGATTCGAATCC
1 CCTCTAATCACAAGATTCGAATCC
38998 CCTCTAATCACAAGATTCGAATCC
1 CCTCTAATCACAAGATTCGAATCC
39022 GAGACTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.33, G:0.08, T:0.25
Consensus pattern (24 bp):
CCTCTAATCACAAGATTCGAATCC
Found at i:39503 original size:12 final size:12
Alignment explanation
Indices: 39486--39511 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
39476 CATCAATGTA
39486 AAATCAGAAGTT
1 AAATCAGAAGTT
39498 AAATCAGAAGTT
1 AAATCAGAAGTT
39510 AA
1 AA
39512 TTTAACGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.54, C:0.08, G:0.15, T:0.23
Consensus pattern (12 bp):
AAATCAGAAGTT
Found at i:45614 original size:16 final size:16
Alignment explanation
Indices: 45577--45614 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
45567 TTGATAGGGA
45577 GGAAAGAAATAGAATG
1 GGAAAGAAATAGAATG
*
45593 GAAAAGAAATAGTAA-G
1 GGAAAGAAATAG-AATG
45609 GGAAAG
1 GGAAAG
45615 GAATTAGGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
16 17 0.89
17 2 0.11
ACGTcount: A:0.58, C:0.00, G:0.32, T:0.11
Consensus pattern (16 bp):
GGAAAGAAATAGAATG
Done.