Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013426.1 Corchorus olitorius cultivar O-4 contig13459, 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: 51268
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:6004 original size:2 final size:2
Alignment explanation
Indices: 5997--6031 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
5987 AAGAAAGAAA
5997 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
6032 AGATTTTCAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:7686 original size:4 final size:4
Alignment explanation
Indices: 7679--7710 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
7669 CCCCCCAAAA
7679 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
7711 GTTTAGATTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:11041 original size:18 final size:18
Alignment explanation
Indices: 11020--11077 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 18
11010 GATAGTTTTC
11020 TTTTTTAAATGGGTAGTT
1 TTTTTTAAATGGGTAGTT
* ** *
11038 TTTTTTAATTGATTTGTT
1 TTTTTTAAATGGGTAGTT
* *
11056 TTCTTTGAAATGGGCAGTT
1 TT-TTTTAAATGGGTAGTT
11075 TTT
1 TTT
11078 ATTTTTGATC
Statistics
Matches: 29, Mismatches: 10, Indels: 2
0.71 0.24 0.05
Matches are distributed among these distances:
18 17 0.59
19 12 0.41
ACGTcount: A:0.19, C:0.03, G:0.19, T:0.59
Consensus pattern (18 bp):
TTTTTTAAATGGGTAGTT
Found at i:11392 original size:16 final size:17
Alignment explanation
Indices: 11359--11393 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
11349 GGACTTGGAT
11359 TTATAATTAGTATATAGA
1 TTATAATTAG-ATATAGA
11377 TTATAATTAG-TATAGA
1 TTATAATTAGATATAGA
11393 T
1 T
11394 AATTTCAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
18 10 0.59
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.46
Consensus pattern (17 bp):
TTATAATTAGATATAGA
Found at i:14596 original size:23 final size:23
Alignment explanation
Indices: 14566--14613 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
14556 AAGTTAGTTC
14566 ATCTACCAATAAATAATATGAAT
1 ATCTACCAATAAATAATATGAAT
14589 ATCTACCAATAAATAATATGAAT
1 ATCTACCAATAAATAATATGAAT
14612 AT
1 AT
14614 GTATGAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.52, C:0.12, G:0.04, T:0.31
Consensus pattern (23 bp):
ATCTACCAATAAATAATATGAAT
Found at i:15809 original size:30 final size:30
Alignment explanation
Indices: 15719--15811 Score: 123
Period size: 30 Copynumber: 3.1 Consensus size: 30
15709 TGTGGTAATT
* *
15719 TCCAAGACGTTCGTCGTTCTTTTGACAATG
1 TCCAAGACGTTCGTCGTTCTTTTGCCAAGG
* * * *
15749 CCCAGGAAGTTCGTCGTTCATTTGCCAAGG
1 TCCAAGACGTTCGTCGTTCTTTTGCCAAGG
*
15779 TCCACGACGTTCGTCGTTCTTTTGCCAAGG
1 TCCAAGACGTTCGTCGTTCTTTTGCCAAGG
15809 TCC
1 TCC
15812 GGATGAACGC
Statistics
Matches: 53, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 53 1.00
ACGTcount: A:0.17, C:0.28, G:0.23, T:0.32
Consensus pattern (30 bp):
TCCAAGACGTTCGTCGTTCTTTTGCCAAGG
Found at i:18839 original size:3 final size:3
Alignment explanation
Indices: 18831--18873 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
18821 ATTTCTACTA
*
18831 TAT TAT TAT TAT TAT TAT TAT TTT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
18874 TATGATTTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TAT
Found at i:20112 original size:22 final size:23
Alignment explanation
Indices: 20062--20215 Score: 99
Period size: 22 Copynumber: 7.0 Consensus size: 23
20052 AAAATCATAG
* *
20062 GAAGTTTA-CAAATTTTCAT-AG
1 GAAGTTTATCAAAATTTCATAAT
*
20083 GAAGGTTTATTAAAATTTCATAAT
1 GAA-GTTTATCAAAATTTCATAAT
* *
20107 -TAGTTTATCAAAGTTTCAT-AT
1 GAAGTTTATCAAAATTTCATAAT
* *
20128 GAAGTTTATCACAATTTCAT-AG
1 GAAGTTTATCAAAATTTCATAAT
* *
20150 GTAA-ATTATCAAAATTTCATAGT
1 G-AAGTTTATCAAAATTTCATAAT
* * * **
20173 G-TGATTATCAAAATTTAATAGG
1 GAAGTTTATCAAAATTTCATAAT
*
20195 GTAG-TTATCAAAATTTCATAA
1 GAAGTTTATCAAAATTTCATAA
20216 AAATATTCAA
Statistics
Matches: 105, Mismatches: 20, Indels: 15
0.75 0.14 0.11
Matches are distributed among these distances:
21 5 0.05
22 85 0.81
23 14 0.13
24 1 0.01
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.40
Consensus pattern (23 bp):
GAAGTTTATCAAAATTTCATAAT
Found at i:20112 original size:44 final size:44
Alignment explanation
Indices: 20064--20214 Score: 119
Period size: 44 Copynumber: 3.4 Consensus size: 44
20054 AATCATAGGA
* *
20064 AGTTTA-CAAATTTTCATAGGAAGGTTTATTAAAATTTCATAATT
1 AGTTTATCAAAGTTTCATAGGAA-GTTTATCAAAATTTCATAATT
* * **
20108 AGTTTATCAAAGTTTCATATGAAGTTTATCACAATTTCATAGGT
1 AGTTTATCAAAGTTTCATAGGAAGTTTATCAAAATTTCATAATT
** * * * * **
20152 AAATTATCAAAATTTCATAGTG-TGATTATCAAAATTTAATAGGGT
1 AGTTTATCAAAGTTTCATAG-GAAGTTTATCAAAATTTCATA-ATT
*
20197 AG-TTATCAAAATTTCATA
1 AGTTTATCAAAGTTTCATA
20215 AAAATATTCA
Statistics
Matches: 89, Mismatches: 15, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
44 70 0.79
45 19 0.21
ACGTcount: A:0.39, C:0.09, G:0.12, T:0.40
Consensus pattern (44 bp):
AGTTTATCAAAGTTTCATAGGAAGTTTATCAAAATTTCATAATT
Found at i:20181 original size:66 final size:65
Alignment explanation
Indices: 20056--20194 Score: 149
Period size: 66 Copynumber: 2.1 Consensus size: 65
20046 TTATAAAAAA
* * *
20056 TCATAGGAAGTTTACAAATTTTCATAGGAAGGTTTATTAAAATTTCATAATTAGTTTATCAAAGT
1 TCATAGGAAGTTTACAAATTTTCATAGGAA-GATTATCAAAATTTCATAATTAGATTATCAAAGT
20121 T
65 T
* *
20122 TCATATGAAGTTTATCACAA-TTTCATAGGTAA-ATTATCAAAATTTCATAGTGT-GATTATCAA
1 TCATAGGAAGTTTA-CA-AATTTTCATAGG-AAGATTATCAAAATTTCATAAT-TAGATTATCAA
*
20184 AATT
62 AGTT
*
20188 TAATAGG
1 TCATAGG
20195 GTAGTTATCA
Statistics
Matches: 61, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
66 45 0.74
67 12 0.20
68 4 0.07
ACGTcount: A:0.39, C:0.09, G:0.13, T:0.40
Consensus pattern (65 bp):
TCATAGGAAGTTTACAAATTTTCATAGGAAGATTATCAAAATTTCATAATTAGATTATCAAAGTT
Found at i:22061 original size:16 final size:16
Alignment explanation
Indices: 22033--22065 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
22023 GGCCATTGTG
22033 ATATAGATAATCAAGT
1 ATATAGATAATCAAGT
22049 ATATATGAT-ATCAAGT
1 ATATA-GATAATCAAGT
22065 A
1 A
22066 GGATTAGCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.81
17 3 0.19
ACGTcount: A:0.48, C:0.06, G:0.12, T:0.33
Consensus pattern (16 bp):
ATATAGATAATCAAGT
Found at i:30759 original size:22 final size:22
Alignment explanation
Indices: 30731--30776 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
30721 CATATACATC
30731 TTCATTATAATTAAAAGAATTA
1 TTCATTATAATTAAAAGAATTA
30753 TTCATTATAATTAAAAGAATTA
1 TTCATTATAATTAAAAGAATTA
30775 TT
1 TT
30777 GGTTTACATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.43
Consensus pattern (22 bp):
TTCATTATAATTAAAAGAATTA
Found at i:30829 original size:21 final size:21
Alignment explanation
Indices: 30803--30848 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
30793 AATTACAAAC
30803 ATTGTTAATTGAACTGAAAAG
1 ATTGTTAATTGAACTGAAAAG
30824 ATTGTTAATTGAACTGAAAAG
1 ATTGTTAATTGAACTGAAAAG
30845 ATTG
1 ATTG
30849 AGAACAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.41, C:0.04, G:0.20, T:0.35
Consensus pattern (21 bp):
ATTGTTAATTGAACTGAAAAG
Found at i:32191 original size:439 final size:437
Alignment explanation
Indices: 31282--32236 Score: 1310
Period size: 439 Copynumber: 2.2 Consensus size: 437
31272 TCAAGGAGTT
* * * *
31282 AAATCGTCCAACCTATAATTGTAAAGGATTCAATAGCATGAAA-CATAAAAGTATGAGGGTCATT
1 AAATCGTCCAACCCATAATTGTAAAGGATTAAATAGCAT-AAAGCATAAAAGTATAAGGATCATT
* * *
31346 AGATAAATAATCCAGCAAAAAAAAATAGTTTATGAATACAAAACATAAAAATTCCCTCTTGAATC
65 TGATAAATAATCCAGCAAAAAAAAATAGTTTATGAAGACAAAACATAAAAATTCCCTCTTGAACC
* * *
31411 CTCCACGAAACTCATTAATCAAATTCAACTTTCATGCCCTTAAAGAAAGTCGTAGATCACACAAT
130 CTCCACGAAACTCATTAACCAAATTCAACTTTCAGGCCCTTAAAGAAAGTCATAGATCACACAAT
* *
31476 AACCTTTTAACCAACACTTGAACAACTTCAATCGGACAAGTGGACCGAAAATTATACGATATTAA
195 AACCTTTTAACCAACACTTGAACAACCTCAATCGGACAAGTGGACCGAAAATTATACAATATTAA
* * *
31541 ATAGACCGGCAATCGAAACCACAAAATTTAAGAAATATTTTTTAGAATCAAAACATTAAAATTGA
260 ATAGACCGACAATCGAAACCACAAAATTTAAGAAACATTTTTTAGAATCAAAACATGAAAATTGA
** * * *
31606 CTTCTGAGTTTTTCATGAAAGTTGTAGATCATGAGATTATCTTTTAATAGACACTTGAATCACCT
325 CTTCTGAGTCCTTCATGAAAGTTGTAGATAATGAAATTACCTTTTAATAGACACTTGAATCACCT
* **
31671 TGACCGGACAAATAGAACAAAAAATACAAAAATAAAAGGTGATGCGTC
390 TGACCGGACAAATAAAACAAAAAATACAAAAATAAAAGGTGAAACGTC
* * *
31719 AAATCGTCCAATCCATAATTATAAAGGATTAAATAGCATAAAGCATAAAAGTATAAGGATAATTT
1 AAATCGTCCAACCCATAATTGTAAAGGATTAAATAGCATAAAGCATAAAAGTATAAGGATCATTT
* * * * *
31784 GATAAATAATCCAGCAAAAAATATATTTGTTTATGGAGACCAAACATAAAAATTTCCTCTTGAAC
66 GATAAATAATCCAGCAAAAAA-A-AATAGTTTATGAAGACAAAACATAAAAATTCCCTCTTGAAC
* * * *
31849 CCTCCACGAAACTCATTAACCAAATTCAGCTTTCAGGTCCTTGACGAAAGTCATAGATCACACAA
129 CCTCCACGAAACTCATTAACCAAATTCAACTTTCAGGCCCTTAAAGAAAGTCATAGATCACACAA
* * * * * *
31914 TAACCTTTTAACCGACACTTTAACAACCTCAATTGGACAAGTGGATCGAAAATTGTATAATATTA
194 TAACCTTTTAACCAACACTTGAACAACCTCAATCGGACAAGTGGACCGAAAATTATACAATATTA
* * * * *
31979 GATAGACTGACAATCGAGACCACAAAATTTAAGAAGCATTTTTTAGAATCGAAACATGAAAATTG
259 AATAGACCGACAATCGAAACCACAAAATTTAAGAAACATTTTTTAGAATCAAAACATGAAAATTG
*
32044 -GTT-TGCAGTCCTTCATGAAAGTTGTAGATAATGAAATTACCTTTTAATAGACACTTGAATCAC
324 ACTTCTG-AGTCCTTCATGAAAGTTGTAGATAATGAAATTACCTTTTAATAGACACTTGAATCAC
* * *
32107 CTTGATCGGACAAGTAAAACAAAAAATA-AAAGAATTAAA-GTCGAAACGTTC
388 CTTGACCGGACAAATAAAACAAAAAATACAAA-AATAAAAGGT-GAAACG-TC
* * * *
32158 -AATCGTCCAACCCAGAATTTGTGAGGGATTAAATAGCATAAAGCATAAAAGTATAGGGATCATT
1 AAATCGTCCAACCCATAA-TTGTAAAGGATTAAATAGCATAAAGCATAAAAGTATAAGGATCATT
32222 TGATAAATAATCCAG
65 TGATAAATAATCCAG
32237 TAGTAAAATG
Statistics
Matches: 453, Mismatches: 57, Indels: 14
0.86 0.11 0.03
Matches are distributed among these distances:
436 3 0.01
437 81 0.18
438 105 0.23
439 264 0.58
ACGTcount: A:0.43, C:0.17, G:0.14, T:0.27
Consensus pattern (437 bp):
AAATCGTCCAACCCATAATTGTAAAGGATTAAATAGCATAAAGCATAAAAGTATAAGGATCATTT
GATAAATAATCCAGCAAAAAAAAATAGTTTATGAAGACAAAACATAAAAATTCCCTCTTGAACCC
TCCACGAAACTCATTAACCAAATTCAACTTTCAGGCCCTTAAAGAAAGTCATAGATCACACAATA
ACCTTTTAACCAACACTTGAACAACCTCAATCGGACAAGTGGACCGAAAATTATACAATATTAAA
TAGACCGACAATCGAAACCACAAAATTTAAGAAACATTTTTTAGAATCAAAACATGAAAATTGAC
TTCTGAGTCCTTCATGAAAGTTGTAGATAATGAAATTACCTTTTAATAGACACTTGAATCACCTT
GACCGGACAAATAAAACAAAAAATACAAAAATAAAAGGTGAAACGTC
Found at i:34981 original size:21 final size:21
Alignment explanation
Indices: 34881--34990 Score: 139
Period size: 21 Copynumber: 5.2 Consensus size: 21
34871 GTTTAACGTG
* *
34881 TTGAATATCAAAATTTGGGGT
1 TTGACTATCAAACTTTGGGGT
34902 TTGACTATCAAACTTTGGGGT
1 TTGACTATCAAACTTTGGGGT
* *
34923 TTGACTTTCAAACTATGGGGT
1 TTGACTATCAAACTTTGGGGT
* *
34944 TTGATTATCAAAATTTGGGGT
1 TTGACTATCAAACTTTGGGGT
** *
34965 TTGACTATCATCCTTTGTGGT
1 TTGACTATCAAACTTTGGGGT
34986 TTGAC
1 TTGAC
34991 CATGTATGTA
Statistics
Matches: 76, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 76 1.00
ACGTcount: A:0.25, C:0.12, G:0.23, T:0.41
Consensus pattern (21 bp):
TTGACTATCAAACTTTGGGGT
Found at i:47066 original size:2 final size:2
Alignment explanation
Indices: 47059--47111 Score: 83
Period size: 2 Copynumber: 27.5 Consensus size: 2
47049 ATGGTTCTTT
*
47059 TC TC TC TC TC TC TC TC TC TC -C TC CC TC -C TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
47099 TC TC TC TC TC TC T
1 TC TC TC TC TC TC T
47112 AAATGTTGCT
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
1 2 0.04
2 45 0.96
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
TC
Done.