Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011287.1 Corchorus olitorius cultivar O-4 contig11320, 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: 53427
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:22184 original size:65 final size:65
Alignment explanation
Indices: 22078--22199 Score: 156
Period size: 65 Copynumber: 1.9 Consensus size: 65
22068 CATAGGAAAG
* * * ** * *
22078 TTTATTAAAATTTCATTGTTAGGTTATCAAAGTTTTTTAGGGAATTTATCACAATTTTATAGGTA
1 TTTATCAAAATTTCATTGATAGGTTATCAAAATTTAATAGGGAAGTTATCAAAATTTTATAGGTA
*
22143 TTTATCAAAATTTCATATGATA-GTTATCAAAATTTAATAGGGTAGTTATCAAAATTT
1 TTTATCAAAATTTCAT-TGATAGGTTATCAAAATTTAATAGGGAAGTTATCAAAATTT
22200 CATAAAAATA
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
65 44 0.92
66 4 0.08
ACGTcount: A:0.36, C:0.07, G:0.12, T:0.45
Consensus pattern (65 bp):
TTTATCAAAATTTCATTGATAGGTTATCAAAATTTAATAGGGAAGTTATCAAAATTTTATAGGTA
Found at i:22188 original size:22 final size:22
Alignment explanation
Indices: 22100--22199 Score: 103
Period size: 22 Copynumber: 4.6 Consensus size: 22
22090 TCATTGTTAG
* * *
22100 GTTATCAAAGTTTTTTAGGGAA
1 GTTATCAAAATTTTATAGGGTA
* *
22122 TTTATCACAATTTTATA-GGTA
1 GTTATCAAAATTTTATAGGGTA
* * * *
22143 TTTATCAAAATTTCATATGATA
1 GTTATCAAAATTTTATAGGGTA
*
22165 GTTATCAAAATTTAATAGGGTA
1 GTTATCAAAATTTTATAGGGTA
22187 GTTATCAAAATTT
1 GTTATCAAAATTT
22200 CATAAAAATA
Statistics
Matches: 65, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
21 18 0.28
22 47 0.72
ACGTcount: A:0.37, C:0.07, G:0.13, T:0.43
Consensus pattern (22 bp):
GTTATCAAAATTTTATAGGGTA
Found at i:30078 original size:57 final size:57
Alignment explanation
Indices: 29985--30103 Score: 195
Period size: 57 Copynumber: 2.1 Consensus size: 57
29975 TAACCATTAG
*
29985 TAGCAGTTAGGCCTAATGAATTTGTGGAAGAAAATTGATTTGGGCCTGGATTTGGAC
1 TAGCAGTTAGGCCCAATGAATTTGTGGAAGAAAATTGATTTGGGCCTGGATTTGGAC
*
30042 TAGCAGCTT-GGCCCAATGAATTTGTGGAAGACAATTGATTTGGGCCTGGATTTGGAC
1 TAGCAG-TTAGGCCCAATGAATTTGTGGAAGAAAATTGATTTGGGCCTGGATTTGGAC
*
30099 CAGCA
1 TAGCA
30104 ACAAGTCGGG
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
57 56 0.97
58 2 0.03
ACGTcount: A:0.27, C:0.14, G:0.29, T:0.29
Consensus pattern (57 bp):
TAGCAGTTAGGCCCAATGAATTTGTGGAAGAAAATTGATTTGGGCCTGGATTTGGAC
Found at i:33230 original size:434 final size:435
Alignment explanation
Indices: 32455--33342 Score: 1196
Period size: 434 Copynumber: 2.0 Consensus size: 435
32445 AAAAAAATTG
* * *
32455 AAGCGTTAAATCGAGTAAAATAGAATTTGTAAAGGACTAAGTAGTATAAAGTAGAAAAGTATATG
1 AAGCGTTAAATCGATTAAAATAGAATTAGTAAAGGACTAAGTAGTATAAAATAGAAAAG-ATA-G
* * * *
32520 TGAGGGTCATTTGATAAATAATCCAAATAAGAAAATGTTTGTTTATAGAGATCTTCAAACATAAA
64 TGAGGGTCATTTCATAAATAAT-CAAATAAAAAAACGTTTGTTGATAGAGATCTTCAAACATAAA
* * * * *
32585 ACTTCCCTTTTGAACCCTTCATGAAACTTGTAGATCAAATTTAGCTTTCGGGTACTTCATGAAAG
128 AATTCCCTTTTGAACACTTAATGAAACTCGTAGATCAAATTTAGCTTTCGGATACTTCATGAAAG
* * * * *
32650 TCGTAGATCACGTAATAAGCTTTTAACCGACACTTAAATAACTTTAATCGGACATGTGGATCTAA
193 TCGTAGATCACGCAATAACCTTTTAACCGACACTTAAATAACATTAATCAGACATGTGGATCGAA
* * * *
32715 AATTATATGGTATTAAATAGACCGGCAATCAAAACCACTAAATTTGGGAAGTATTTTTCTTTGAA
258 AATTATATGATATTAAATAGACCGGCAATCAAAACCACTAAATTTCGGAAGCATTTTTCTTAGAA
** * ** *
32780 TTGAAATGTAAAAATTGGCTTTTGAGTTTTTCATGAAAGTTGGAGATCATGAAATTACCTTTTAA
323 TTGAAACATAAAAATTGGCTTTTAAGTCCTTCATGAAAGTTGGAAATCATGAAATTACCTTTTAA
* * *
32845 TCGACACATGAATCACCTTAATCGGACAAATAGAACAAAAAAATAAAGCTT
388 TAGACACATGAATCACCTTAATCGGAC-AA-AGAACAAAAAAA-AAACCTA
* *
32896 ACGCGTTAAATCGATTAAGATAGAATTAGTAAAGGACTAAGTAGTATAAAATAGAAAA-ATA-TG
1 AAGCGTTAAATCGATTAAAATAGAATTAGTAAAGGACTAAGTAGTATAAAATAGAAAAGATAGTG
* * *
32959 AGTGTCATTTCATAAATAAT-AAA-AAAAAAACGTTTGTTGATGGAGATCTTGAAACATAAAAAT
66 AGGGTCATTTCATAAATAATCAAATAAAAAAACGTTTGTTGATAGAGATCTTCAAACATAAAAAT
*
33022 TCCCTTTTGAACACTTAATGAAACTCGTAGATCAAATTTAGCTTTCGGATCCTTCATGAAAGTCG
131 TCCCTTTTGAACACTTAATGAAACTCGTAGATCAAATTTAGCTTTCGGATACTTCATGAAAGTCG
* * * *
33087 TAGATCATGCAATAACCTTTTAAGCGACACTTGAGA-AACATTAATCAGACATGTTGATCGAAAA
196 TAGATCACGCAATAACCTTTTAACCGACACTT-AAATAACATTAATCAGACATGTGGATCGAAAA
* * *
33151 TTATATGATATATTAAATAGATCGGCAATCAAAATCACTAAATTTCGGTAGCA-TTTT-TTAGAA
260 TTATATG--ATATTAAATAGACCGGCAATCAAAACCACTAAATTTCGGAAGCATTTTTCTTAGAA
* * *
33214 TTGAAACATGAAAATTGTCTTTTAAGTCCTTCATGAAAGTTGTAAATCATGAAATTACCTTTTAA
323 TTGAAACATAAAAATTGGCTTTTAAGTCCTTCATGAAAGTTGGAAATCATGAAATTACCTTTTAA
* * * *
33279 TATACACCTGAATCACTTTAATCGGACAAAGAATAAAAAAAAAACCTA
388 TAGACACATGAATCACCTTAATCGGACAAAGAACAAAAAAAAAACCTA
33327 AAGCGTTAAATCGATT
1 AAGCGTTAAATCGATT
33343 TGTAAAGGAC
Statistics
Matches: 393, Mismatches: 51, Indels: 16
0.85 0.11 0.03
Matches are distributed among these distances:
431 20 0.05
432 11 0.03
433 2 0.01
434 237 0.60
435 9 0.02
436 38 0.10
437 20 0.05
439 3 0.01
441 53 0.13
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.31
Consensus pattern (435 bp):
AAGCGTTAAATCGATTAAAATAGAATTAGTAAAGGACTAAGTAGTATAAAATAGAAAAGATAGTG
AGGGTCATTTCATAAATAATCAAATAAAAAAACGTTTGTTGATAGAGATCTTCAAACATAAAAAT
TCCCTTTTGAACACTTAATGAAACTCGTAGATCAAATTTAGCTTTCGGATACTTCATGAAAGTCG
TAGATCACGCAATAACCTTTTAACCGACACTTAAATAACATTAATCAGACATGTGGATCGAAAAT
TATATGATATTAAATAGACCGGCAATCAAAACCACTAAATTTCGGAAGCATTTTTCTTAGAATTG
AAACATAAAAATTGGCTTTTAAGTCCTTCATGAAAGTTGGAAATCATGAAATTACCTTTTAATAG
ACACATGAATCACCTTAATCGGACAAAGAACAAAAAAAAAACCTA
Found at i:33928 original size:178 final size:178
Alignment explanation
Indices: 33609--33934 Score: 433
Period size: 178 Copynumber: 1.8 Consensus size: 178
33599 TTGTTTTGTA
* * *
33609 TAATATTAAGTAAACCGTACATTCCCGCTAACTGAAACAACTAATTCTTCGTAAGCATTTTCTTA
1 TAATATTAAGTAAACCGTACATTCCCGCTAACCGAAACAACTAATTCTTCGGAAGCATTTTCTGA
* *
33674 TACTTTAAACATTAAATTTAGCTTTCAAGTCCTTCATAAAAGTTGAAGATTATGGAACAACATTT
66 TACTTGAAACATTAAATTTAGCTTTCAAGT-CTTCATAAAAGTTGAAGATCATGGAACAACATTT
*
33739 TAAAAGACACTTGAATCACCTCAATCAGACATCTAGAGCAAAATTTATG
130 TAAAAGACACTTAAATCACCTCAATCAGACATCTAGAGCAAAATTTATG
** * * *
33788 TAATATTAAGTGGACCGTATATTCCCGTTAACCGAAACAACTAATAT-TTTGGAAGCATTTT-TG
1 TAATATTAAGTAAACCGTACATTCCCGCTAACCGAAACAACTAAT-TCTTCGGAAGCATTTTCTG
* * * * *
33851 ATACTTGAAACATTAAATTTAGTTTTCGAGT-TTGAGTAGAAAGTTGTAGATCATGGAACAATAT
65 ATACTTGAAACATTAAATTTAGCTTTCAAGTCTTCA-TA-AAAGTTGAAGATCATGGAACAACAT
**
33915 TTTAGTAGACACTTAAATCA
128 TTTAAAAGACACTTAAATCA
33935 TCTTGATCGG
Statistics
Matches: 126, Mismatches: 18, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
176 3 0.02
177 2 0.02
178 68 0.54
179 52 0.41
180 1 0.01
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.34
Consensus pattern (178 bp):
TAATATTAAGTAAACCGTACATTCCCGCTAACCGAAACAACTAATTCTTCGGAAGCATTTTCTGA
TACTTGAAACATTAAATTTAGCTTTCAAGTCTTCATAAAAGTTGAAGATCATGGAACAACATTTT
AAAAGACACTTAAATCACCTCAATCAGACATCTAGAGCAAAATTTATG
Found at i:37487 original size:7 final size:7
Alignment explanation
Indices: 37475--37515 Score: 59
Period size: 7 Copynumber: 6.0 Consensus size: 7
37465 ATGTGTCAGA
37475 ATTTTTT
1 ATTTTTT
37482 ATTTTTT
1 ATTTTTT
37489 A-TTTTT
1 ATTTTTT
37495 ATTTTTT
1 ATTTTTT
37502 -TATTTTT
1 AT-TTTTT
37509 ATTTTTT
1 ATTTTTT
37516 TAAATACAGG
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
6 7 0.23
7 23 0.74
8 1 0.03
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (7 bp):
ATTTTTT
Found at i:37516 original size:14 final size:14
Alignment explanation
Indices: 37477--37517 Score: 75
Period size: 14 Copynumber: 3.0 Consensus size: 14
37467 GTGTCAGAAT
37477 TTTTTA-TTTTTTA
1 TTTTTATTTTTTTA
37490 TTTTTATTTTTTTA
1 TTTTTATTTTTTTA
37504 TTTTTATTTTTTTA
1 TTTTTATTTTTTTA
37518 AATACAGGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 6 0.22
14 21 0.78
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (14 bp):
TTTTTATTTTTTTA
Found at i:50926 original size:31 final size:31
Alignment explanation
Indices: 50890--50958 Score: 84
Period size: 32 Copynumber: 2.2 Consensus size: 31
50880 CAAAAAGTGA
50890 TCAATTTAATCCATGTACTCACAAGATTGGG
1 TCAATTTAATCCATGTACTCACAAGATTGGG
* ** * *
50921 TCAATTTTAGTCTTTGTGCTCATAAGATTGGG
1 TCAA-TTTAATCCATGTACTCACAAGATTGGG
50953 TCAATT
1 TCAATT
50959 GAGTCCTTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
31 6 0.19
32 26 0.81
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.39
Consensus pattern (31 bp):
TCAATTTAATCCATGTACTCACAAGATTGGG
Found at i:51033 original size:31 final size:31
Alignment explanation
Indices: 50991--51087 Score: 135
Period size: 31 Copynumber: 3.2 Consensus size: 31
50981 GATTGGATGC
*
50991 AATTGACCCAATCTTGTGAGTACATGGACTA
1 AATTGATCCAATCTTGTGAGTACATGGACTA
51022 AATTGATCCAATCTTGTGAGTACATGGACTA
1 AATTGATCCAATCTTGTGAGTACATGGACTA
* * * *
51053 AATTGAT-C-ACCTTTTGAGTACAGGGACGA
1 AATTGATCCAATCTTGTGAGTACATGGACTA
51082 AATTGA
1 AATTGA
51088 ACATCTTTAA
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
29 23 0.38
30 1 0.02
31 37 0.61
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (31 bp):
AATTGATCCAATCTTGTGAGTACATGGACTA
Found at i:51095 original size:29 final size:29
Alignment explanation
Indices: 51001--51094 Score: 116
Period size: 29 Copynumber: 3.2 Consensus size: 29
50991 AATTGACCCA
*
51001 ATCTTGTGAGTACATGGACTAAATTGATCC
1 ATCTTGTGAGTACATGGACTAAATTGA-AC
*
51031 AATCTTGTGAGTACATGGACTAAATTGATC
1 -ATCTTGTGAGTACATGGACTAAATTGAAC
* * * *
51061 ACCTTTTGAGTACAGGGACGAAATTGAAC
1 ATCTTGTGAGTACATGGACTAAATTGAAC
51090 ATCTT
1 ATCTT
51095 TAAGCAGTTA
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
29 28 0.50
30 1 0.02
31 27 0.48
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (29 bp):
ATCTTGTGAGTACATGGACTAAATTGAAC
Done.