Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015295.1 Corchorus olitorius cultivar O-4 contig15328, 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: 25761
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Found at i:5249 original size:65 final size:66
Alignment explanation
Indices: 5144--5269 Score: 236
Period size: 65 Copynumber: 1.9 Consensus size: 66
5134 ACACCCCCAC
*
5144 TAACCTATTGATTCCACATCATATTTTGTATTTATCTTATCTTATCTTATCCTATTAACCTATTA
1 TAACCTATTGATTCCACATCATACTTTGTATTTATCTTATCTTATCTTATCCTATTAACCTATTA
5209 T
66 T
5210 TAACCTATTG-TTCCACATCATACTTTGTATTTATCTTATCTTATCTTATCCTATTAACCT
1 TAACCTATTGATTCCACATCATACTTTGTATTTATCTTATCTTATCTTATCCTATTAACCT
5270 TTTAATTCCA
Statistics
Matches: 59, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
65 49 0.83
66 10 0.17
ACGTcount: A:0.26, C:0.21, G:0.03, T:0.49
Consensus pattern (66 bp):
TAACCTATTGATTCCACATCATACTTTGTATTTATCTTATCTTATCTTATCCTATTAACCTATTA
T
Found at i:5279 original size:55 final size:54
Alignment explanation
Indices: 5207--5313 Score: 160
Period size: 55 Copynumber: 2.0 Consensus size: 54
5197 ATTAACCTAT
* *
5207 TATTAACCTATTGTTCCACATCATACTTTGTATTTATCTTATCTTATCTTATCC
1 TATTAACCTATTATTCCACATCATACTTTATATTTATCTTATCTTATCTTATCC
* **
5261 TATTAACCTTTTAATTCCATGTCATACTTTATATTTATCTTATCTTATCTTAT
1 TATTAACCTATT-ATTCCACATCATACTTTATATTTATCTTATCTTATCTTAT
5314 TTTATCTTAT
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
54 11 0.23
55 36 0.77
ACGTcount: A:0.25, C:0.20, G:0.03, T:0.52
Consensus pattern (54 bp):
TATTAACCTATTATTCCACATCATACTTTATATTTATCTTATCTTATCTTATCC
Found at i:6535 original size:13 final size:14
Alignment explanation
Indices: 6519--6547 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
6509 TTATGGTTAA
6519 CTTTTATTT-ATTT
1 CTTTTATTTAATTT
6532 CTTTTATTTAATTT
1 CTTTTATTTAATTT
6546 CT
1 CT
6548 AAAATCCTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.17, C:0.10, G:0.00, T:0.72
Consensus pattern (14 bp):
CTTTTATTTAATTT
Found at i:7023 original size:13 final size:14
Alignment explanation
Indices: 7007--7035 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
6997 TTATGGTTAA
7007 CTTTTATT-AATTT
1 CTTTTATTAAATTT
7020 CTTTTATTAAATTT
1 CTTTTATTAAATTT
7034 CT
1 CT
7036 AGAATCCGAT
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:0.24, C:0.10, G:0.00, T:0.66
Consensus pattern (14 bp):
CTTTTATTAAATTT
Found at i:7264 original size:489 final size:488
Alignment explanation
Indices: 6254--7703 Score: 2171
Period size: 489 Copynumber: 3.0 Consensus size: 488
6244 GTGTCCTACC
* * **
6254 AAACCGTTTGTTTAATTGT-AACAAGTTTTGGTGGAATTAATAACTTCACTTATAAAATTAATAT
1 AAACCGTTTGTTTAATTATGAATAAGTTTTGGTGGAATTAATAACTTCACTTATGGAATTAATAT
* *
6318 ATTAATATATCTAAATTAAAATATTAATTATTCCAATTGAGATGATGATGACCGTAGAAATTGAT
66 ATTAATTTATCTAAATTAAAATATTAATTATTCCAATTGAGATGATGATGACCATAGAAATTGAT
* * * * *
6383 TGATATTGAGAATGTAGTATTGTACGTTGAAATTCTAAGAAAGAATTAAAACTAATAATGATTTA
131 TGATATTGGGAATGTAGTATTGTACGTTGAAGTTCTAAAAAAGAATTAAAAATAATAATGA-TTC
** * *
6448 AATCCAAA-CCAGATTAGTCAGAGCA-TTCAATAATGATATTTGGGGCTAAATTCTTATTAAATT
195 GGT-CAAATTCGGATTAGTCAGAG-ATTTCAATAATGATATTTGGGGCTAAATT-TTATTAAATT
* *
6511 ATGGTTAACTTTTATTTATTTCTTTTATTTAATTTCTAAAATCCTATAACAATATGA-TTAAATT
257 ATGGTTAACTTTTATTAATTTCTTTTATTAAATTTCTAAAATCCTATAACAATATGATTTAAATT
* *
6575 TTAAGATTTACCCTTAAAATCAATAAATATTATAATTCAAGGCTAAACAATAATTATTACATGGG
322 TTAAGATTTACCCTTAAAATCAATAAATATTATAATTCAAGGATAAACAATAATTATTACAGGGG
* *
6640 CATTATTGTCTTACAACAATTAGGAGACACACTTTGTGCTTTTAGCAAAACCTCGAAAATAACAA
387 CATTATTGTCTTACAACAATTAGGAGACATACTTTGTGCTTTTAGCAAAA-CTCCAAAATAACAA
* ** * *
6705 TTGGTTCTTCACGGGTGCCCCTGGGAAACTTGTTAGCC
451 TTGGCTCTTCACGGGTGCCCCTGGGAAACCCGTTAACA
* * *
6743 AAACAGTTTGTTTAATTATG-ATAAGATTTGGTGGAATTAATAACTTCACTTATGGAATTAGTAT
1 AAACCGTTTGTTTAATTATGAATAAGTTTTGGTGGAATTAATAACTTCACTTATGGAATTAATAT
* *
6807 ATTAATTTATCTAAATTAAAATATTAATTATTCCAATTAAGATGATGATGGCCATAGAAATTGAT
66 ATTAATTTATCTAAATTAAAATATTAATTATTCCAATTGAGATGATGATGACCATAGAAATTGAT
* *
6872 TGATATTGGGAATGTGGTATTGTACGTTGAAGTTTTAAAAAAGAATTAAAAATAATAATGATTCG
131 TGATATTGGGAATGTAGTATTGTACGTTGAAGTTCTAAAAAAGAATTAAAAATAATAATGATTCG
* *
6937 TGTCAAATTCGGATTAGTCAGAGATTTCAATAATGATATTTAGGCCTAAATTTTATTAAATTATG
196 -GTCAAATTCGGATTAGTCAGAGATTTCAATAATGATATTTGGGGCTAAATTTTATTAAATTATG
* *
7002 GTTAACTTTTATTAATTTCTTTTATTAAATTTCTAGAATCCGATAACAATA-GATTTAAATTTTA
260 GTTAACTTTTATTAATTTCTTTTATTAAATTTCTAAAATCCTATAACAATATGATTTAAATTTTA
* *
7066 AGATTTACTCTTAAAATCAATAAATATTATAATTCAAGGATAAACAATAATTATTATAGGGGCAT
325 AGATTTACCCTTAAAATCAATAAATATTATAATTCAAGGATAAACAATAATTATTACAGGGGCAT
* * *
7131 TATTGCCTTACAACAATTAAGAGACATACTTTGTG-TTTTAGCACAAACTCCAAAATAATAATTG
390 TATTGTCTTACAACAATTAGGAGACATACTTTGTGCTTTTAGCA-AAACTCCAAAATAACAATTG
* * *
7195 ACTCATCACGGGTGCCTCTGGGAAACCCGTTAACA
454 GCTCTTCACGGGTGCCCCTGGGAAACCCGTTAACA
* *
7230 AAACCTTTTGTTTAATTCTGATATAAGTTTTGGTGGAATTAATAACTTCACTTATGGAATTAATA
1 AAACCGTTTGTTTAATTATGA-ATAAGTTTTGGTGGAATTAATAACTTCACTTATGGAATTAATA
* * * * *
7295 TATCAATTTATCTAAATTAAAATATTAATTATTCCAATTGAGCTGATAATGATCATAGAATTTGA
65 TATTAATTTATCTAAATTAAAATATTAATTATTCCAATTGAGATGATGATGACCATAGAAATTGA
7360 TTGATATTGGGAATGTAGTATTGTACGTTGAAGTTCTAAAAAAGAATTAAAAATAATAATGATTC
130 TTGATATTGGGAATGTAGTATTGTACGTTGAAGTTCTAAAAAAGAATTAAAAATAATAATGATTC
* * *
7425 AGGTCAAATTCGGATTAGTCAGAGCTTTCAATAATGATATTGGGGGCTAAATTATATTAAATTAT
195 -GGTCAAATTCGGATTAGTCAGAGATTTCAATAATGATATTTGGGGCTAAATTTTATTAAATTAT
* *
7490 GGTTAA-TTTTATTAATTTATTTTATTTAATTTTCTAAAATCCTATAACAATATG-TTTAAATTT
259 GGTTAACTTTTATTAATTTCTTTTA-TTAAATTTCTAAAATCCTATAACAATATGATTTAAATTT
* * * *
7553 TAAGATTTACCCTTAAAATCAATAAATATTATAATTCAAAGTTAAACAATAATTATTACGGGGGT
323 TAAGATTTACCCTTAAAATCAATAAATATTATAATTCAAGGATAAACAATAATTATTACAGGGGC
* *
7618 ATTATTGTCTTACAGCAATTAGGAGACATACTTTGTGCTTTTAGCAAAACTTCAAAATAACAATT
388 ATTATTGTCTTACAACAATTAGGAGACATACTTTGTGCTTTTAGCAAAACTCCAAAATAACAATT
*
7683 GGCTCTTCACAGGTGCCCCTG
453 GGCTCTTCACGGGTGCCCCTG
7704 CTGCACCCGA
Statistics
Matches: 866, Mismatches: 83, Indels: 24
0.89 0.09 0.02
Matches are distributed among these distances:
487 69 0.08
488 190 0.22
489 597 0.69
490 10 0.01
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.38
Consensus pattern (488 bp):
AAACCGTTTGTTTAATTATGAATAAGTTTTGGTGGAATTAATAACTTCACTTATGGAATTAATAT
ATTAATTTATCTAAATTAAAATATTAATTATTCCAATTGAGATGATGATGACCATAGAAATTGAT
TGATATTGGGAATGTAGTATTGTACGTTGAAGTTCTAAAAAAGAATTAAAAATAATAATGATTCG
GTCAAATTCGGATTAGTCAGAGATTTCAATAATGATATTTGGGGCTAAATTTTATTAAATTATGG
TTAACTTTTATTAATTTCTTTTATTAAATTTCTAAAATCCTATAACAATATGATTTAAATTTTAA
GATTTACCCTTAAAATCAATAAATATTATAATTCAAGGATAAACAATAATTATTACAGGGGCATT
ATTGTCTTACAACAATTAGGAGACATACTTTGTGCTTTTAGCAAAACTCCAAAATAACAATTGGC
TCTTCACGGGTGCCCCTGGGAAACCCGTTAACA
Found at i:16306 original size:12 final size:12
Alignment explanation
Indices: 16289--16313 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
16279 TGTAAAAAAA
16289 TTTCAATAAATT
1 TTTCAATAAATT
16301 TTTCAATAAATT
1 TTTCAATAAATT
16313 T
1 T
16314 GTATGTCATT
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:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (12 bp):
TTTCAATAAATT
Found at i:16724 original size:22 final size:22
Alignment explanation
Indices: 16625--16817 Score: 90
Period size: 22 Copynumber: 8.7 Consensus size: 22
16615 CCCACCCTAA
*
16625 ATGAAATTTTGATAACCATACT
1 ATGAAATTTTGATAACCATTCT
16647 AT-AAATTTTGATAACC-TTCGT
1 ATGAAATTTTGATAACCATTC-T
* * *
16668 ATAAAATTTTGTTAACGACACTCT
1 ATGAAATTTTGATAAC--CATTCT
* * * *
16692 AAGAAAATTTGATAACCTTTTT
1 ATGAAATTTTGATAACCATTCT
* * *
16714 ATGAAATTTTGGTAACGC-CTAT
1 ATGAAATTTTGATAAC-CATTCT
* * * **
16736 ATAAAATGTTGATAACTACACT
1 ATGAAATTTTGATAACCATTCT
** *
16758 ATGACGTTTTGATAACC-TCCAT
1 ATGAAATTTTGATAACCATTC-T
* **
16780 ATGAAATTTT-AGTAACAACACT
1 ATGAAATTTTGA-TAACCATTCT
*
16802 ATGAAAATTTGATAAC
1 ATGAAATTTTGATAAC
16818 TTTCCTATGT
Statistics
Matches: 126, Mismatches: 34, Indels: 22
0.69 0.19 0.12
Matches are distributed among these distances:
20 2 0.02
21 19 0.15
22 86 0.68
23 3 0.02
24 14 0.11
25 2 0.02
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.36
Consensus pattern (22 bp):
ATGAAATTTTGATAACCATTCT
Found at i:18213 original size:119 final size:118
Alignment explanation
Indices: 17971--18322 Score: 598
Period size: 119 Copynumber: 3.0 Consensus size: 118
17961 TTTTAACACG
17971 TTTGGGATCTAAGAATTAAGGAGTAATTTATACTATTTTTATTGGAAGAGTTGGTTTGAAGTGGA
1 TTTGGGATCTAAGAATTAAGGAGTAATTTATACTATTTTTATTGGAAGAGTTGGTTTGAAGTGGA
*
18036 AAATTTAAGGACTTGAAATTCCTCAAAACAATATTCATGGTTGTGGTGGAGAG
66 AAATTTAAGGACTTGAAATTCCTCAAAACAATATTCATGGTTGTGGTGGAGAC
* *
18089 TTTGGGACCTAAGAATTAAGGAGTAATTTATACTATTTTTA-TGGAAGGGTTGGTTTGAAGTGGA
1 TTTGGGATCTAAGAATTAAGGAGTAATTTATACTATTTTTATTGGAAGAGTTGGTTTGAAGTGGA
* * *
18153 AAATTTAAAGACTTGAGAAATTTCTCAAAACAATATTCATGGTTGTGGTGGAGCC
66 AAATTTAAGGACTT--GAAATTCCTCAAAACAATATTCATGGTTGTGGTGGAGAC
*
18208 TTTGGGATCTAAGAATTAAGGAGTAATTTATACTATTTTTATTGGAAGAGTTGGTTTGAAATGGA
1 TTTGGGATCTAAGAATTAAGGAGTAATTTATACTATTTTTATTGGAAGAGTTGGTTTGAAGTGGA
* *
18273 AAAATGAAGGACTTGAAATTCCTCAAAACAATATTCATGGTTGTGGTGGA
66 AAATTTAAGGACTTGAAATTCCTCAAAACAATATTCATGGTTGTGGTGGA
18323 TGTTCTTCCA
Statistics
Matches: 218, Mismatches: 13, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
117 35 0.16
118 75 0.34
119 76 0.35
120 32 0.15
ACGTcount: A:0.34, C:0.07, G:0.24, T:0.35
Consensus pattern (118 bp):
TTTGGGATCTAAGAATTAAGGAGTAATTTATACTATTTTTATTGGAAGAGTTGGTTTGAAGTGGA
AAATTTAAGGACTTGAAATTCCTCAAAACAATATTCATGGTTGTGGTGGAGAC
Found at i:18642 original size:7 final size:6
Alignment explanation
Indices: 18632--18705 Score: 65
Period size: 5 Copynumber: 13.3 Consensus size: 6
18622 TTTGTGATTT
*
18632 TATATA GTATATA -ATATA TAAATA TATA-A TATA-A TATATA -ATATA
1 TATATA -TATATA TATATA TATATA TATATA TATATA TATATA TATATA
18677 -ATATA TA-ATA TA-ATA TATACTA TA-ATA TA
1 TATATA TATATA TATATA TATA-TA TATATA TA
18706 ATGACTAATA
Statistics
Matches: 60, Mismatches: 2, Indels: 12
0.81 0.03 0.16
Matches are distributed among these distances:
5 39 0.65
6 11 0.18
7 10 0.17
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (6 bp):
TATATA
Found at i:18667 original size:12 final size:12
Alignment explanation
Indices: 18633--18705 Score: 101
Period size: 12 Copynumber: 5.8 Consensus size: 12
18623 TTGTGATTTT
*
18633 ATATAGTATATAA
1 ATATAATATAT-A
18646 TATATAAATATATA
1 -ATAT-AATATATA
18660 ATATAATATATA
1 ATATAATATATA
18672 ATATAATATATA
1 ATATAATATATA
18684 ATATAATATATA
1 ATATAATATATA
*
18696 CTATAATATA
1 ATATAATATA
18706 ATGACTAATA
Statistics
Matches: 56, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
12 41 0.73
13 4 0.07
14 5 0.09
15 6 0.11
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.41
Consensus pattern (12 bp):
ATATAATATATA
Found at i:24523 original size:35 final size:35
Alignment explanation
Indices: 24477--25200 Score: 822
Period size: 35 Copynumber: 20.3 Consensus size: 35
24467 ATCAATGTGA
* *
24477 AGATCAACTCTGATCATTAAAAACTTCTTGAAACG
1 AGATCAACTCTGATCATAAAAAACTTCTTGAAATG
* *
24512 AGATCAACTCTGATCATCAAAAACTTCTTGAAAGG
1 AGATCAACTCTGATCATAAAAAACTTCTTGAAATG
*
24547 AGATCAACTCTGATCATAAAAAAAAAAAAACTTCTTGGAATG
1 AGATCAACTCTGATCAT-------AAAAAACTTCTTGAAATG
*
24589 AGATCAACTCTGATCATAAAAAAATATCTTGAAATG
1 AGATCAACTCTGATCATAAAAAACT-TCTTGAAATG
* * *
24625 AGATCAACTCTAATCA-ACGAAAACTTCTTGAATTG
1 AGATCAACTCTGATCATA-AAAAACTTCTTGAAATG
* * *
24660 ACATCAACTCTGATCATAAGAAACTTCTTGAAACG
1 AGATCAACTCTGATCATAAAAAACTTCTTGAAATG
* * *
24695 AGATCAACTCAGATCA-ACAAAAACTACTTGAAACG
1 AGATCAACTCTGATCATA-AAAAACTTCTTGAAATG
* *
24730 AGATCAACTCTGATCA-ACGAAAATTTCTTGAAATG
1 AGATCAACTCTGATCATA-AAAAACTTCTTGAAATG
* * * *
24765 AGATCAACTCTAATCA-ACGAAAATTTCTTGAAAGG
1 AGATCAACTCTGATCATA-AAAAACTTCTTGAAATG
*
24800 AGATCAACTCTGAT-A-AAGGAAAACTTCTTGAAAGG
1 AGATCAACTCTGATCATAA--AAAACTTCTTGAAATG
*
24835 AGATCAACTCTGATCATAAAAAACTTCTTGAAAGG
1 AGATCAACTCTGATCATAAAAAACTTCTTGAAATG
24870 AGATCAACTCTGATCATAAAAAACTTCTTTG-AATG
1 AGATCAACTCTGATCATAAAAAACTTC-TTGAAATG
* *
24905 AGATCAACTCTGATCATAAAAAAATTTTTTTGAAATG
1 AGATCAACTCTGATCAT-AAAAAA-CTTCTTGAAATG
* *
24942 AGATCAACTCTGATCA-ACGAAAACTTCTTGAAAGG
1 AGATCAACTCTGATCATA-AAAAACTTCTTGAAATG
* * *
24977 AGATCAACTCTAATCGTAAAAAACTTCTTGAAACG
1 AGATCAACTCTGATCATAAAAAACTTCTTGAAATG
* *
25012 AGATCAACTCTGATCA-ATGAAAACTTCTTGAAAGG
1 AGATCAACTCTGATCATA-AAAAACTTCTTGAAATG
25047 AGATCAACTCTGATCATAAAAAACTTCTTTG-AATG
1 AGATCAACTCTGATCATAAAAAACTTC-TTGAAATG
25082 AGATCAACTCTGATCATAAAAAAAAAAACTTCTTGAAATG
1 AGATCAACTCTGATCAT-----AAAAAACTTCTTGAAATG
* *
25122 AGATCAACTCTGATCA-ACGAAAACTTCTTGAAAGG
1 AGATCAACTCTGATCATA-AAAAACTTCTTGAAATG
*
25157 AGATCAACTCTGATCATAAAAAACTTCTTGAAACG
1 AGATCAACTCTGATCATAAAAAACTTCTTGAAATG
25192 AGATCAACT
1 AGATCAACT
25201 GTGAAGCCTA
Statistics
Matches: 605, Mismatches: 52, Indels: 64
0.84 0.07 0.09
Matches are distributed among these distances:
34 5 0.01
35 458 0.76
36 53 0.09
37 24 0.04
39 3 0.00
40 30 0.05
42 32 0.05
ACGTcount: A:0.43, C:0.18, G:0.13, T:0.26
Consensus pattern (35 bp):
AGATCAACTCTGATCATAAAAAACTTCTTGAAATG
Found at i:24748 original size:19 final size:19
Alignment explanation
Indices: 24691--24749 Score: 52
Period size: 19 Copynumber: 3.3 Consensus size: 19
24681 AACTTCTTGA
*
24691 AACGAGATCAACTCAGATC
1 AACGAGATCAACTCTGATC
* * * *
24710 AACAAAAACTACT-TGA--
1 AACGAGATCAACTCTGATC
24726 AACGAGATCAACTCTGATC
1 AACGAGATCAACTCTGATC
24745 AACGA
1 AACGA
24750 AAATTTCTTG
Statistics
Matches: 28, Mismatches: 9, Indels: 6
0.65 0.21 0.14
Matches are distributed among these distances:
16 9 0.32
17 3 0.11
18 2 0.07
19 14 0.50
ACGTcount: A:0.46, C:0.24, G:0.14, T:0.17
Consensus pattern (19 bp):
AACGAGATCAACTCTGATC
Found at i:24819 original size:19 final size:20
Alignment explanation
Indices: 24793--24848 Score: 61
Period size: 16 Copynumber: 3.0 Consensus size: 20
24783 GAAAATTTCT
24793 TGAAAGGAGATCAACTCTGA
1 TGAAAGGAGATCAACTCTGA
24813 T-AAAGGA-A--AACTTCT--
1 TGAAAGGAGATCAAC-TCTGA
24828 TGAAAGGAGATCAACTCTGA
1 TGAAAGGAGATCAACTCTGA
24848 T
1 T
24849 CATAAAAAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 14
0.67 0.00 0.33
Matches are distributed among these distances:
15 1 0.03
16 9 0.31
17 4 0.14
18 4 0.14
19 9 0.31
20 2 0.07
ACGTcount: A:0.41, C:0.14, G:0.21, T:0.23
Consensus pattern (20 bp):
TGAAAGGAGATCAACTCTGA
Done.