Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012236.1 Corchorus capsularis cultivar CVL-1 contig12257, 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: 43732
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.33
Found at i:2215 original size:22 final size:22
Alignment explanation
Indices: 2181--2312 Score: 108
Period size: 22 Copynumber: 6.0 Consensus size: 22
2171 AACGTAAAAT
*
2181 ATTT-ATAACCACACTGTGAAA
1 ATTTGATAACCACACTATGAAA
*
2202 ATTTGATAATCACACTATGAAA
1 ATTTGATAACCACACTATGAAA
* * * * *
2224 TTTTGATAACCTCAGTGTGCAA
1 ATTTGATAACCACACTATGAAA
* *
2246 TTTTGATAATCACACTAT-AAA
1 ATTTGATAACCACACTATGAAA
*
2267 A-TTGGTAACCCCACACTATGAAA
1 ATTTGATAA--CCACACTATGAAA
* *
2290 ATTTTGATAGCCACACCATGAAA
1 A-TTTGATAACCACACTATGAAA
2313 TTTCAATAAC
Statistics
Matches: 86, Mismatches: 19, Indels: 10
0.75 0.17 0.09
Matches are distributed among these distances:
20 6 0.07
21 6 0.07
22 53 0.62
23 16 0.19
25 5 0.06
ACGTcount: A:0.39, C:0.19, G:0.11, T:0.30
Consensus pattern (22 bp):
ATTTGATAACCACACTATGAAA
Found at i:2251 original size:44 final size:43
Alignment explanation
Indices: 2175--2269 Score: 127
Period size: 44 Copynumber: 2.2 Consensus size: 43
2165 TGCTCCAACG
2175 TAAAATATTTATAACCACACTGTGAAAATTTGATAATCACACTA
1 TAAAAT-TTTATAACCACACTGTGAAAATTTGATAATCACACTA
* * * * *
2219 TGAAATTTTGATAACCTCAGTGTGCAATTTTGATAATCACACTA
1 TAAAATTTT-ATAACCACACTGTGAAAATTTGATAATCACACTA
2263 TAAAATT
1 TAAAATT
2270 GGTAACCCCA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
43 3 0.07
44 41 0.93
ACGTcount: A:0.41, C:0.15, G:0.09, T:0.35
Consensus pattern (43 bp):
TAAAATTTTATAACCACACTGTGAAAATTTGATAATCACACTA
Found at i:2413 original size:22 final size:22
Alignment explanation
Indices: 2388--2430 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
2378 AAAATTTCCA
*
2388 TAATCTCGCTATGGAATTTTGT
1 TAATCTCCCTATGGAATTTTGT
*
2410 TAATCTCCCTATGTAATTTTG
1 TAATCTCCCTATGGAATTTTG
2431 ATAAACACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.23, C:0.16, G:0.14, T:0.47
Consensus pattern (22 bp):
TAATCTCCCTATGGAATTTTGT
Found at i:3038 original size:2 final size:2
Alignment explanation
Indices: 3031--3056 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3021 GGTAAATTAT
3031 AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC
3057 TATGTGGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:4898 original size:11 final size:11
Alignment explanation
Indices: 4884--4921 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
4874 ATTCATAACA
4884 AATTTATAATT
1 AATTTATAATT
4895 AATTTATAATT
1 AATTTATAATT
4906 -ATTTGATAATT
1 AATTT-ATAATT
*
4917 TATTT
1 AATTT
4922 TATATAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:6330 original size:4 final size:4
Alignment explanation
Indices: 6316--6349 Score: 50
Period size: 4 Copynumber: 8.0 Consensus size: 4
6306 GGAATGTGAG
6316 TTTA GTTTA TTTA TTTA TTTAA TTTA TTTA TTTA
1 TTTA -TTTA TTTA TTTA TTT-A TTTA TTTA TTTA
6350 ATTTCTTAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 20 0.71
5 8 0.29
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (4 bp):
TTTA
Found at i:6340 original size:13 final size:13
Alignment explanation
Indices: 6324--6353 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
6314 AGTTTAGTTT
6324 ATTTATTTATTTA
1 ATTTATTTATTTA
6337 ATTTATTTATTTA
1 ATTTATTTATTTA
6350 ATTT
1 ATTT
6354 CTTAGTTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
ATTTATTTATTTA
Found at i:6341 original size:17 final size:17
Alignment explanation
Indices: 6316--6349 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
6306 GGAATGTGAG
*
6316 TTTAGTTTATTTATTTA
1 TTTAATTTATTTATTTA
6333 TTTAATTTATTTATTTA
1 TTTAATTTATTTATTTA
6350 ATTTCTTAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (17 bp):
TTTAATTTATTTATTTA
Found at i:7487 original size:77 final size:78
Alignment explanation
Indices: 7346--7585 Score: 419
Period size: 78 Copynumber: 3.1 Consensus size: 78
7336 TTTTTTTAAT
7346 TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
1 TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
7411 GTTTTTAGTTGAG
66 GTTTTTAGTTGAG
*
7424 TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATA-TAGATTTAATTATATAAATATAGA
1 TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
7488 GTTTTTAGTTGAG
66 GTTTTTAGTTGAG
* * * *
7501 TAAAATAGTAAAATGGTAAAAATAAAATAGTTATAAAGATATTATATTTAATTAAATAAAAATAG
1 TAAAATAGTAAAATGGT-AAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAG
7566 AGTTTTTAGTTGAG
65 AGTTTTTAGTTGAG
7580 TAAAAT
1 TAAAAT
7586 TATAAAAATC
Statistics
Matches: 154, Mismatches: 6, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
77 53 0.34
78 61 0.40
79 40 0.26
ACGTcount: A:0.49, C:0.00, G:0.14, T:0.37
Consensus pattern (78 bp):
TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
GTTTTTAGTTGAG
Found at i:7634 original size:93 final size:93
Alignment explanation
Indices: 7527--7714 Score: 349
Period size: 93 Copynumber: 2.0 Consensus size: 93
7517 TAAAAATAAA
7527 ATAGTTATAAAGATATTATATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAATTATAAA
1 ATAGTTATAAAGATATTATATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAATTATAAA
* *
7592 AATCTAAACAATGGCAATTTAGAAATAT
66 AACCTAAACAATGACAATTTAGAAATAT
7620 ATAGTTATAAAGATATTATATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAATTATAAA
1 ATAGTTATAAAGATATTATATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAATTATAAA
*
7685 AACCTAAACAATGACAATTTAGTAATAT
66 AACCTAAACAATGACAATTTAGAAATAT
7713 AT
1 AT
7715 TTGACAAATA
Statistics
Matches: 92, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
93 92 1.00
ACGTcount: A:0.49, C:0.04, G:0.10, T:0.37
Consensus pattern (93 bp):
ATAGTTATAAAGATATTATATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAATTATAAA
AACCTAAACAATGACAATTTAGAAATAT
Found at i:15830 original size:11 final size:11
Alignment explanation
Indices: 15787--15824 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
15777 TTCCTATATA
*
15787 AAATAAATTAT
1 AAATTAATTAT
15798 CAAA-TAATTAT
1 -AAATTAATTAT
15809 AAATTAATTAT
1 AAATTAATTAT
15820 AAATT
1 AAATT
15825 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:16505 original size:127 final size:127
Alignment explanation
Indices: 16210--16907 Score: 892
Period size: 127 Copynumber: 5.5 Consensus size: 127
16200 GTTCTAGTTG
* * * * * *
16210 TTATTATAATACTAAGAAATTTCTTCTATATTTAT-ATCCCATTTTAATTATCACACTTTAATTG
1 TTATTATACTAATAACAAATTTCTTCTCTATTTATAATTCCATTTTAATTATCACACTTTTATTG
16274 ----ATA---CATATGAAACAAATTATTAAACCAATAATAATAATTGACTATATTA-TTAT-TTA
66 ATACATATGTCATATGAAACAAATTATTAAACC------AATAATTGACTATATTATTTATATTA
16330 -TA
125 TTA
* * *
16332 TTATTATAATACTAAGAAATTTCTTCTCTATTTATAATTCCATTTTAATTATCACACTTTTATTG
1 TTATTATACTAATAACAAATTTCTTCTCTATTTATAATTCCATTTTAATTATCACACTTTTATTG
16397 ATACATATGTCATATGAAACAAATTATTAAACCAATAATTGACTATATTATTTATATTATTA
66 ATACATATGTCATATGAAACAAATTATTAAACCAATAATTGACTATATTATTTATATTATTA
16459 TTATTATACTAATAACAAATTTCTTCTCTATTTATAATTCCATTTTAATTATCACACTTTTATTG
1 TTATTATACTAATAACAAATTTCTTCTCTATTTATAATTCCATTTTAATTATCACACTTTTATTG
16524 ATACATATGTCATATGAAACAAATTATTAAACCAATAATTGACTATATTATTTATATTATTA
66 ATACATATGTCATATGAAACAAATTATTAAACCAATAATTGACTATATTATTTATATTATTA
16586 TTATTATACTAATAACAAATTTCTTCTCTATTTATAATTCCATTTTAATTATCACACTTTTATTG
1 TTATTATACTAATAACAAATTTCTTCTCTATTTATAATTCCATTTTAATTATCACACTTTTATTG
* *
16651 ATACATATGTCATATGAAACAAATTATTAAACTAATAATTGACTTTATTATTTATATTATTA
66 ATACATATGTCATATGAAACAAATTATTAAACCAATAATTGACTATATTATTTATATTATTA
* ** * *
16713 TTATTATACTAATAATAACAAATTTCTTCTCTATTTACAATTAAATTTTAATTAT-ATATCATAC
1 TTATTATAC---TAATAACAAATTTCTTCTCTATTTATAATTCCATTTTAATTATCACA-C-T-T
* * * *
16777 TT-TGGTTA-ATA---CATATGAAACAAATTACTAAACCAATATAATTGACCATATTATTTATAT
60 TTATTGATACATATGTCATATGAAACAAATTATTAAACC-A-ATAATTGACTATATTATTTATAT
16837 ATATTATA
123 -TA-T-TA
*
16845 TTATTATTA-TAATACTAACAAATTTCTTCTCTATTTACAATTCCATTTTAATTATCACACTTT
1 TTATTA-TACT-A-A-TAACAAATTTCTTCTCTATTTATAATTCCATTTTAATTATCACACTTT
16908 GGTTGATGCT
Statistics
Matches: 526, Mismatches: 23, Indels: 46
0.88 0.04 0.08
Matches are distributed among these distances:
122 34 0.06
123 27 0.05
124 17 0.03
125 4 0.01
126 3 0.01
127 284 0.54
128 1 0.00
129 24 0.05
130 71 0.13
131 8 0.02
132 49 0.09
133 4 0.01
ACGTcount: A:0.39, C:0.12, G:0.03, T:0.45
Consensus pattern (127 bp):
TTATTATACTAATAACAAATTTCTTCTCTATTTATAATTCCATTTTAATTATCACACTTTTATTG
ATACATATGTCATATGAAACAAATTATTAAACCAATAATTGACTATATTATTTATATTATTA
Found at i:18125 original size:7 final size:8
Alignment explanation
Indices: 18112--18153 Score: 50
Period size: 8 Copynumber: 5.4 Consensus size: 8
18102 ATAAAAGAAA
18112 ATATACAT
1 ATATACAT
18120 -TATACAT
1 ATATACAT
*
18127 ATATATAT
1 ATATACAT
*
18135 ATATATAT
1 ATATACAT
*
18143 ATATATAT
1 ATATACAT
18151 ATA
1 ATA
18154 CTCTATTCTA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
7 7 0.22
8 25 0.78
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (8 bp):
ATATACAT
Found at i:18132 original size:2 final size:2
Alignment explanation
Indices: 18120--18153 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
18110 AAATATACAT
*
18120 TA TA CA 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 TA TA
18154 CTCTATTCTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:25526 original size:7 final size:7
Alignment explanation
Indices: 25514--25543 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
25504 CAGTACTTCT
25514 GGGTCTG
1 GGGTCTG
25521 GGGTCTG
1 GGGTCTG
25528 GGGTCTG
1 GGGTCTG
25535 GGGTCTG
1 GGGTCTG
25542 GG
1 GG
25544 AAGTGCCATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.00, C:0.13, G:0.60, T:0.27
Consensus pattern (7 bp):
GGGTCTG
Found at i:28239 original size:433 final size:431
Alignment explanation
Indices: 27358--28302 Score: 1152
Period size: 432 Copynumber: 2.2 Consensus size: 431
27348 ATAACCTTTT
* *
27358 AAAGTTGTAGATCATGAAATTATCTTTTAATAGACATTTGAATTATCTTAATCGGACAAATAGAA
1 AAAGTTGTAGATCATGAAATTATCTTTTAATAGACATCTGAATCATCTTAATCGGACAAATAGAA
* *
27423 AAGAATAATAAAGTTGAACCTTTAAATCGATTAAGATAGAATTAGTAAAGGACTAAGTAGTATAA
66 AA-AA-AATAAAGCTGAACATTTAAA-C-ATTAAGATAGAATTAGTAAAGGACTAAGTAGTATAA
* * * * * * *
27488 AATAGAAAAATGTGAGGGTCATTTGATAAATAATCCAAATAAGAAAATGTTTGTTGGTGGAGATC
127 AATAAAAAAATATGAGGATCATTCGATAAATAATCCAAATAAGAAAATGTTTGTTGATGAAAATC
* *
27553 TTGAAACATAAAAATTTATTTTTGAGCCCTTCATGAAACTCGTAGATCAAATTTAGTTTTCGGAC
192 TTGAAACATAAAAATTTAGTTTTGAGCCCTTCATGAAACTCGTAGATCAAATTTAGCTTTCGGAC
* * * * *
27618 CCTTCACAAAAGTCATAGATCATGCAATAACCTTTTAACCGAAACTTTAATAATTTTAATTGGAC
257 CCTTCACAAAAGTCATAGATCATGCAATAAACTTTTAACCGAAACTTAAATAACTTTAACTAGAC
*** * * * ** * * *
27683 ATGTAGATTAAAAATTATTTGGTATTAAATAGACTGGTAAGCGAAACCACAAAATTTTAAAAGTA
322 ACACAGATTAAAAATTATATGATATTAAATAGACCGACAAGCAAAACCACAAAATTTAAAAAGCA
*
27748 TTTTTTAGAATTGAAACATAAAAATTGACTTTTGACTTCTTCATG
387 TTTTTTAGAATTGAAACATAAAAATTGACTTTTGACTTCTTCACG
*
27793 AAAGTTGTAGATCATGAAATTATCTTTTAATAGACATCTGAATCATCTTAATCAGACAAATAG-A
1 AAAGTTGTAGATCATGAAATTATCTTTTAATAGACATCTGAATCATCTTAATCGGACAAATAGAA
* * *
27857 AAAAAATAAAGCTGAA-ATGTT-AA-ATTAAGGTAGAATTAGTAAAGGACTAAGTAGTATGAAGT
66 AAAAAATAAAGCTGAACAT-TTAAACATTAAGATAGAATTAGTAAAGGACTAAGTAGTATAAAAT
* *
27919 AAAAAAATATGATGATCATTCGATAAATAATTCAAATAAGAAAATGTTTGTTGATGAAAATTAAT
130 AAAAAAATATGAGGATCATTCGATAAATAATCCAAATAAGAAAATGTTTGTTGATG--AA--AAT
* * * *
27984 CTTGAAACATGAAAATTCT-GTTTTGAGTCCTTTTATGAAACTCGTATATCAAATTTAGCTTTCG
191 CTTGAAACATAAAAATT-TAGTTTTGAG-CCCTTCATGAAACTCGTAGATCAAATTTAGCTTTCG
** ** * **
28048 GGTCC-TCATGAAAGTCGTAGATCATGCAATAAACTTTTAACCGGCA-TCTAAATAACTTTAACT
254 GACCCTTCACAAAAGTCATAGATCATGCAATAAACTTTTAACCGAAACT-TAAATAACTTTAACT
* * * *
28111 AGACACACAGATTGAAAATTATATGATATTAAATAGACCGACAATCAAAATCACTAAATTTAAGA
318 AGACACACAGATTAAAAATTATATGATATTAAATAGACCGACAAGCAAAACCACAAAATTTAA-A
* * *
28176 AAGCATTTTTTTGAATTGAAACATTAAAATTGGCTTTTGA-TTCCTTCACG
382 AAGCATTTTTTAGAATTGAAACATAAAAATTGACTTTTGACTT-CTTCACG
* * * * *
28226 AAAGTTGTAGATCATGAGATTACCTTTTAATAGACA-CATGAATCACCTTAATTGGACAAACAGA
1 AAAGTTGTAGATCATGAAATTATCTTTTAATAGACATC-TGAATCATCTTAATCGGACAAATAGA
28290 ACAAAAAATAAAG
65 A-AAAAAATAAAG
28303 AAAATAAAAC
Statistics
Matches: 437, Mismatches: 60, Indels: 26
0.84 0.11 0.05
Matches are distributed among these distances:
428 85 0.19
430 1 0.00
431 4 0.01
432 136 0.31
433 136 0.31
434 4 0.01
435 71 0.16
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.32
Consensus pattern (431 bp):
AAAGTTGTAGATCATGAAATTATCTTTTAATAGACATCTGAATCATCTTAATCGGACAAATAGAA
AAAAAATAAAGCTGAACATTTAAACATTAAGATAGAATTAGTAAAGGACTAAGTAGTATAAAATA
AAAAAATATGAGGATCATTCGATAAATAATCCAAATAAGAAAATGTTTGTTGATGAAAATCTTGA
AACATAAAAATTTAGTTTTGAGCCCTTCATGAAACTCGTAGATCAAATTTAGCTTTCGGACCCTT
CACAAAAGTCATAGATCATGCAATAAACTTTTAACCGAAACTTAAATAACTTTAACTAGACACAC
AGATTAAAAATTATATGATATTAAATAGACCGACAAGCAAAACCACAAAATTTAAAAAGCATTTT
TTAGAATTGAAACATAAAAATTGACTTTTGACTTCTTCACG
Done.