Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010680.1 Corchorus capsularis cultivar CVL-1 contig10701, 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: 27495
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:5186 original size:38 final size:37
Alignment explanation
Indices: 5137--5212 Score: 116
Period size: 38 Copynumber: 2.0 Consensus size: 37
5127 TAAAAAAATT
* *
5137 AAAAAGCAAAAACAGAAAATAAAAATATATTTTTTTTA
1 AAAAAGCAAAAACAGAAAAGAAAAAT-TAATTTTTTTA
*
5175 AAAAAGGAAAAACAGAAAAGAAAAATTAATTTTTTTA
1 AAAAAGCAAAAACAGAAAAGAAAAATTAATTTTTTTA
5212 A
1 A
5213 TATCGATGCA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
37 11 0.31
38 24 0.69
ACGTcount: A:0.62, C:0.04, G:0.08, T:0.26
Consensus pattern (37 bp):
AAAAAGCAAAAACAGAAAAGAAAAATTAATTTTTTTA
Found at i:5272 original size:27 final size:24
Alignment explanation
Indices: 5229--5282 Score: 63
Period size: 27 Copynumber: 2.1 Consensus size: 24
5219 TGCAAACCCT
*
5229 AAATTTTTTTTTTAAAAATCGCAA
1 AAATTTTTTTTTTAAAAAACGCAA
*
5253 AAATCTTTTTTTTTAGAAAAAACGGAA
1 AAAT-TTTTTTTTT--AAAAAACGCAA
5280 AAA
1 AAA
5283 AGGAAAAACT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 4 0.16
25 9 0.36
27 12 0.48
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.39
Consensus pattern (24 bp):
AAATTTTTTTTTTAAAAAACGCAA
Found at i:5298 original size:34 final size:33
Alignment explanation
Indices: 5250--5326 Score: 102
Period size: 34 Copynumber: 2.3 Consensus size: 33
5240 TTAAAAATCG
5250 CAAAAATCT-TTTTTTTTAGAAAAAACGGAAAAAA
1 CAAAAA-CTATTTTTTTTA-AAAAAACGGAAAAAA
* *
5284 GGAAAAACTATTTTTTTTATAAAAACGGAAAAAA
1 -CAAAAACTATTTTTTTTAAAAAAACGGAAAAAA
5318 CAAAAACTA
1 CAAAAACTA
5327 ATTCTTGGAT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
33 8 0.21
34 16 0.42
35 14 0.37
ACGTcount: A:0.55, C:0.09, G:0.09, T:0.27
Consensus pattern (33 bp):
CAAAAACTATTTTTTTTAAAAAAACGGAAAAAA
Found at i:5624 original size:6 final size:6
Alignment explanation
Indices: 5604--5640 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
5594 AAAACAAAGC
5604 AAAT-T AAAT-T AAATCT AAATCT AAATCT AAATCT AAA
1 AAATCT AAATCT AAATCT AAATCT AAATCT AAATCT AAA
5641 GCAAATTAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 9 0.29
6 22 0.71
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (6 bp):
AAATCT
Found at i:15891 original size:151 final size:150
Alignment explanation
Indices: 15621--15893 Score: 370
Period size: 151 Copynumber: 1.8 Consensus size: 150
15611 TTATTTTTCG
* * * *
15621 AATATATTTCATAAATGACATTGTTTAAACTGTTATAGTTTTACTCAATTAAAAACTCTTTTTTT
1 AATATATTTCATAAATGACATTGTTTAAACTGTTACAGTTTTACTCAACTAAAAACTCTATATTT
*
15686 ATTTAATTAAATCTAATATCTTTATAACTATTTTATATTACCATTTTACTATTTTAATTAAAACT
66 ATTTAATTAAATCTAATATCTTTATAAATATTTTATATTACCATTTTAC-ATTTTAATTAAAACT
15751 TGATATATTAGAATTTTTTTA
130 TGATATATTAGAATTTTTTTA
* * * * * * *
15772 AATATATTTCTTAAATGATATTGTTTAAACTTTTACAGTTTTATTCTACTGAAAATTCTATATTT
1 AATATATTTCATAAATGACATTGTTTAAACTGTTACAGTTTTACTCAACTAAAAACTCTATATTT
* *
15837 ATTTAATTAAAT-TCAATATTTTTATAAATATTTTATTTTTACCATTTTTA-ATTTTAA
66 ATTTAATTAAATCT-AATATCTTTATAAATATTTTA-TATTACCA-TTTTACATTTTAA
15894 AAAATTGGAG
Statistics
Matches: 105, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
150 1 0.01
151 92 0.88
152 7 0.07
153 5 0.05
ACGTcount: A:0.36, C:0.08, G:0.04, T:0.52
Consensus pattern (150 bp):
AATATATTTCATAAATGACATTGTTTAAACTGTTACAGTTTTACTCAACTAAAAACTCTATATTT
ATTTAATTAAATCTAATATCTTTATAAATATTTTATATTACCATTTTACATTTTAATTAAAACTT
GATATATTAGAATTTTTTTA
Found at i:17444 original size:14 final size:13
Alignment explanation
Indices: 17425--17471 Score: 55
Period size: 11 Copynumber: 3.8 Consensus size: 13
17415 CTCTATTCAA
*
17425 ATAATATGTAGTAT
1 ATAATATATA-TAT
17439 ATAATATATATAT
1 ATAATATATATAT
17452 AT-ATATATAT-T
1 ATAATATATATAT
17463 AT-ATATATA
1 ATAATATATA
17472 CTACATATGA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
11 10 0.31
12 8 0.25
13 5 0.16
14 9 0.28
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (13 bp):
ATAATATATATAT
Found at i:17447 original size:2 final size:2
Alignment explanation
Indices: 17436--17471 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
17426 TAATATGTAG
17436 TA TA TA -A TA TA TA TA TA TA TA TA TA T- TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17472 CTACATATGA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:17479 original size:11 final size:10
Alignment explanation
Indices: 17436--17471 Score: 58
Period size: 9 Copynumber: 3.8 Consensus size: 10
17426 TAATATGTAG
17436 TATATA-ATA
1 TATATATATA
17445 TATATATATA
1 TATATATATA
17455 TATATAT-TA
1 TATATATATA
17464 TATATATA
1 TATATATA
17472 CTACATATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 15 0.60
10 10 0.40
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (10 bp):
TATATATATA
Found at i:17771 original size:45 final size:45
Alignment explanation
Indices: 17720--17807 Score: 149
Period size: 45 Copynumber: 2.0 Consensus size: 45
17710 TAATATAGTA
* * *
17720 GTGGAATTACTAAATGATCCCTACCCTGGATTAATGATGAGCTGG
1 GTGGAATTACTAAAAGATCCCTACCCCGGATTAATAATGAGCTGG
17765 GTGGAATTACTAAAAGATCCCTACCCCGGATTAATAATGAGCT
1 GTGGAATTACTAAAAGATCCCTACCCCGGATTAATAATGAGCT
17808 CGAGAAGTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (45 bp):
GTGGAATTACTAAAAGATCCCTACCCCGGATTAATAATGAGCTGG
Found at i:19888 original size:6 final size:6
Alignment explanation
Indices: 19877--19913 Score: 67
Period size: 6 Copynumber: 6.3 Consensus size: 6
19867 ATAATTGCTA
19877 TAGATT TAGATT TAGATT TAGATT TAGATT TA-ATT TA
1 TAGATT TAGATT TAGATT TAGATT TAGATT TAGATT TA
19914 CTTTGCTTAG
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.16
6 26 0.84
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (6 bp):
TAGATT
Found at i:19953 original size:14 final size:14
Alignment explanation
Indices: 19934--19960 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
19924 TTTTTAGTTT
19934 AATTGATTTCTTTC
1 AATTGATTTCTTTC
19948 AATTGATTTCTTT
1 AATTGATTTCTTT
19961 TTAATCCCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.11, G:0.07, T:0.59
Consensus pattern (14 bp):
AATTGATTTCTTTC
Found at i:20428 original size:27 final size:26
Alignment explanation
Indices: 20398--20459 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 26
20388 ATTCCCCTTT
20398 TTAAAATATATTTCTAA-ATTGCCATTA
1 TTAAAATATATTT-TAATATT-CCATTA
*
20425 TTAAAAAATATTTTAATTATTCCATTA
1 TTAAAATATATTTTAA-TATTCCATTA
20452 TTAAAATA
1 TTAAAATA
20460 ATGAAAATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
26 3 0.10
27 25 0.81
28 3 0.10
ACGTcount: A:0.45, C:0.08, G:0.02, T:0.45
Consensus pattern (26 bp):
TTAAAATATATTTTAATATTCCATTA
Found at i:21020 original size:222 final size:222
Alignment explanation
Indices: 20634--21060 Score: 617
Period size: 222 Copynumber: 1.9 Consensus size: 222
20624 GGCAAAATTA
* * *
20634 GAGGTAAATATAAAAGTTTTAGATGTTGGAATCCTCTTTCCAACGGTACTTCATTTGCATTTTTC
1 GAGGTAAACATAAAAGTTTTAGATCTTGGAATCCTCTTTCCAACGGTACCTCATTTGCATTTTTC
* * *
20699 TGAGTTCTAGATCAAAAATTATGAAATTTCTTCTAAAACTATTCTTGTGAAGTCCTCCTTTGAAG
66 TGAGTTCTAGATAAAAAATTATGAAATTTCTTCTAAAACTACTCTTGTGAAGTACTCCTTTGAAG
* * * * *
20764 AGGGTTTAACATTGCTGCATCAGGGTAGAATCATTACTGCATCATAATTACTGATTGGAGTTGGA
131 AGGATTTAAAAATGCTGCATCAGGGTAGAATCATTACTGCATCATAATTACTGATTGGACTCGGA
20829 CTCCTTCTTTAGGAAGATCTAGGTCTC
196 CTCCTTCTTTAGGAAGATCTAGGTCTC
*
20856 GAGGTAAACATAAAA-TTTGTAGATCTTGGAATCTTCTTTCCAACGGTACCTCATTTGCATTTTT
1 GAGGTAAACATAAAAGTTT-TAGATCTTGGAATCCTCTTTCCAACGGTACCTCATTTGCATTTTT
* *
20920 CTGAGTTCT-GAATAAAAAATTATGAATTTTCTTCTAAAACTGCTCTTGTGAAGTACTCCTTTGA
65 CTGAGTTCTAG-ATAAAAAATTATGAAATTTCTTCTAAAACTACTCTTGTGAAGTACTCCTTTGA
* * * * * * *
20984 ATATGATTTAAAAATGCTGCATTATGGTTA-AATCATTATTGCATCTTAATTACTGATTTGACTC
129 AGAGGATTTAAAAATGCTGCATCA-GGGTAGAATCATTACTGCATCATAATTACTGATTGGACTC
21048 GGACTCCTTCTTT
193 GGACTCCTTCTTT
21061 GGGCTTCCAT
Statistics
Matches: 181, Mismatches: 21, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
221 4 0.02
222 173 0.96
223 4 0.02
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.39
Consensus pattern (222 bp):
GAGGTAAACATAAAAGTTTTAGATCTTGGAATCCTCTTTCCAACGGTACCTCATTTGCATTTTTC
TGAGTTCTAGATAAAAAATTATGAAATTTCTTCTAAAACTACTCTTGTGAAGTACTCCTTTGAAG
AGGATTTAAAAATGCTGCATCAGGGTAGAATCATTACTGCATCATAATTACTGATTGGACTCGGA
CTCCTTCTTTAGGAAGATCTAGGTCTC
Found at i:21730 original size:26 final size:27
Alignment explanation
Indices: 21679--21731 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 27
21669 ATTATTAAAA
21679 TATTTTATTTAGTAAAAAATTCAATTTT
1 TATTTTATTTAG-AAAAAATTCAATTTT
*
21707 TATTTTATTTA-ATAAAATTCAATTT
1 TATTTTATTTAGAAAAAATTCAATTT
21732 CTACAATACC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 13 0.54
28 11 0.46
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.55
Consensus pattern (27 bp):
TATTTTATTTAGAAAAAATTCAATTTT
Found at i:23767 original size:21 final size:20
Alignment explanation
Indices: 23730--23768 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
23720 TTTAGAAGCA
*
23730 ATTAATTAAAAGCATTAAAC
1 ATTAATTAAAAACATTAAAC
23750 ATTAATTAAAAACAATTAA
1 ATTAATTAAAAAC-ATTAA
23769 GGAAGGGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.59, C:0.08, G:0.03, T:0.31
Consensus pattern (20 bp):
ATTAATTAAAAACATTAAAC
Found at i:23866 original size:73 final size:74
Alignment explanation
Indices: 23775--23930 Score: 253
Period size: 74 Copynumber: 2.1 Consensus size: 74
23765 TTAAGGAAGG
* *
23775 GAAATGTGTAATTACG-AAAAGGGTAGAAGGAAAAGGAATGGGGGAAACTCATAAAGGGGCTTTT
1 GAAAAGTGTAATTACGAAAAAGGGTAGAAGGAAAAGGAATAGGGGAAACTCATAAAGGGGCTTTT
23839 TAGTCATCC-
66 TAGTCA-CCT
* *
23848 GAAAAGTGTAATTACGAAAAAGGGTAGAAGGAAAAGGAATAGGGGAAACTCATAGAGGGGTTTTT
1 GAAAAGTGTAATTACGAAAAAGGGTAGAAGGAAAAGGAATAGGGGAAACTCATAAAGGGGCTTTT
23913 TAGTCACCT
66 TAGTCACCT
23922 GAAAAGTGT
1 GAAAAGTGT
23931 GAAAAGACTA
Statistics
Matches: 77, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
73 17 0.22
74 60 0.78
ACGTcount: A:0.40, C:0.08, G:0.30, T:0.22
Consensus pattern (74 bp):
GAAAAGTGTAATTACGAAAAAGGGTAGAAGGAAAAGGAATAGGGGAAACTCATAAAGGGGCTTTT
TAGTCACCT
Found at i:25360 original size:2 final size:2
Alignment explanation
Indices: 25353--25379 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
25343 CTTACTCAAC
25353 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
25380 TTCTAACTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:26510 original size:2 final size:2
Alignment explanation
Indices: 26505--26534 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
26495 TCTCTCTCTC
26505 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
26535 GTGTGGCTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.