Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013191.1 Corchorus capsularis cultivar CVL-1 contig13212, 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: 36294
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.30
Found at i:201 original size:33 final size:32
Alignment explanation
Indices: 105--209 Score: 113
Period size: 33 Copynumber: 3.2 Consensus size: 32
95 TGCTAAAGAG
*
105 TGTTTTAGATGTTGTTTGCGATGATACT-AATCC
1 TGTTTTAG-TGTTGTTTGCGATGAAACTAAAT-C
* * *
138 TGATTTGAGTGTTGTTTGCAATGACACTAAATC
1 TG-TTTTAGTGTTGTTTGCGATGAAACTAAATC
* *
171 TGTTTTAAGTGTTGTTTGTGATGAAACTAAATT
1 TGTTTT-AGTGTTGTTTGCGATGAAACTAAATC
204 TGTTTT
1 TGTTTT
210 GGATGCTAAT
Statistics
Matches: 61, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
32 3 0.05
33 50 0.82
34 8 0.13
ACGTcount: A:0.24, C:0.09, G:0.21, T:0.47
Consensus pattern (32 bp):
TGTTTTAGTGTTGTTTGCGATGAAACTAAATC
Found at i:276 original size:33 final size:33
Alignment explanation
Indices: 239--343 Score: 165
Period size: 33 Copynumber: 3.2 Consensus size: 33
229 AACAAATCTA
* *
239 TTTTGATTAATCATAGCATTGCAAATAATTCTG
1 TTTTGGTTGATCATAGCATTGCAAATAATTCTG
*
272 TTTTGGTTGATCATAGCATTGCAAATAATTCTA
1 TTTTGGTTGATCATAGCATTGCAAATAATTCTG
* *
305 TTTTGGTTGATCATAACATTGAAAATAATTCTG
1 TTTTGGTTGATCATAGCATTGCAAATAATTCTG
338 TTTTGG
1 TTTTGG
344 GTGAAAAGAA
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 66 1.00
ACGTcount: A:0.30, C:0.10, G:0.15, T:0.44
Consensus pattern (33 bp):
TTTTGGTTGATCATAGCATTGCAAATAATTCTG
Found at i:896 original size:21 final size:21
Alignment explanation
Indices: 853--896 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
843 AGATGCCATT
**
853 AAGATGCCATTTGATCCTCTG
1 AAGATGCCATTTGATCCAATG
*
874 AAGATGCCATTTGGTCCAATG
1 AAGATGCCATTTGATCCAATG
895 AA
1 AA
897 AAGAGCAAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (21 bp):
AAGATGCCATTTGATCCAATG
Found at i:1714 original size:12 final size:12
Alignment explanation
Indices: 1695--1726 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
1685 TCGCATGCGA
1695 TGGCCGGTCATG
1 TGGCCGGTCATG
*
1707 TGGTCGGTCATG
1 TGGCCGGTCATG
1719 TGGCCGGT
1 TGGCCGGT
1727 GTTGCGCGGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.06, C:0.22, G:0.44, T:0.28
Consensus pattern (12 bp):
TGGCCGGTCATG
Found at i:7616 original size:32 final size:33
Alignment explanation
Indices: 7546--7633 Score: 97
Period size: 32 Copynumber: 2.7 Consensus size: 33
7536 TTTCAATGCT
* * * **
7546 ATCAACCAAATCAGGATTATTTGCAATGCTATA
1 ATCAACCAAAACAGAATTGTTTTTAATGCTATA
* *
7579 ATCAACCAAAACATAA-TGTTTTTAATGCTATG
1 ATCAACCAAAACAGAATTGTTTTTAATGCTATA
*
7611 TTCAACCAAAACAGAATTGTTTT
1 ATCAACCAAAACAGAATTGTTTT
7634 CATCACAATT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
32 26 0.58
33 19 0.42
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.33
Consensus pattern (33 bp):
ATCAACCAAAACAGAATTGTTTTTAATGCTATA
Found at i:7696 original size:33 final size:33
Alignment explanation
Indices: 7671--7779 Score: 157
Period size: 33 Copynumber: 3.3 Consensus size: 33
7661 TAGTTTTATT
7671 GCAAACAACACTCAAATTAGGTTTAGTATCATC
1 GCAAACAACACTCAAATTAGGTTTAGTATCATC
** * * *
7704 GCAAACAACA-TCTAAAACAGATTTAGTGTCATT
1 GCAAACAACACTC-AAATTAGGTTTAGTATCATC
7737 GCAAACAACACTCAAATTAGGTTTAGTATCATC
1 GCAAACAACACTCAAATTAGGTTTAGTATCATC
7770 GCAAACAACA
1 GCAAACAACA
7780 TCTAAAAGAC
Statistics
Matches: 64, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
32 2 0.03
33 60 0.94
34 2 0.03
ACGTcount: A:0.42, C:0.21, G:0.12, T:0.25
Consensus pattern (33 bp):
GCAAACAACACTCAAATTAGGTTTAGTATCATC
Found at i:7703 original size:66 final size:66
Alignment explanation
Indices: 7646--7786 Score: 228
Period size: 66 Copynumber: 2.1 Consensus size: 66
7636 TCACAATTAG
* * *
7646 CATCCAAAACAGATTTAGTTTTATTGCAAACAACACTCAAATTAGGTTTAGTATCATCGCAAACA
1 CATCCAAAACAGATTTAGTGTCATTGCAAACAACACTCAAATTAGGTTTAGTATCATCACAAACA
7711 A
66 A
* *
7712 CATCTAAAACAGATTTAGTGTCATTGCAAACAACACTCAAATTAGGTTTAGTATCATCGCAAACA
1 CATCCAAAACAGATTTAGTGTCATTGCAAACAACACTCAAATTAGGTTTAGTATCATCACAAACA
7777 A
66 A
*
7778 CATCTAAAA
1 CATCCAAAA
7787 GACACTTTTC
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 72 1.00
ACGTcount: A:0.42, C:0.20, G:0.11, T:0.28
Consensus pattern (66 bp):
CATCCAAAACAGATTTAGTGTCATTGCAAACAACACTCAAATTAGGTTTAGTATCATCACAAACA
A
Found at i:13703 original size:30 final size:30
Alignment explanation
Indices: 13663--13727 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
13653 AAGGATCCAT
*
13663 TGGCCGGTTGT-GCGCGGATGGCCCAAGCGA
1 TGGCCAGTTGTGGC-CGGATGGCCCAAGCGA
* * *
13693 TGGCCAGTTGTGGCCGGTTGTCCCATGCGA
1 TGGCCAGTTGTGGCCGGATGGCCCAAGCGA
13723 TGGCC
1 TGGCC
13728 CATGTGATGG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 28 0.93
31 2 0.07
ACGTcount: A:0.11, C:0.28, G:0.40, T:0.22
Consensus pattern (30 bp):
TGGCCAGTTGTGGCCGGATGGCCCAAGCGA
Found at i:14305 original size:33 final size:33
Alignment explanation
Indices: 14262--14373 Score: 152
Period size: 33 Copynumber: 3.4 Consensus size: 33
14252 GCCACGCAAC
* * ** *
14262 ACCGGCCACATGACTTGGAGATGCCCGGCCACC
1 ACCGGTCACATGACTCGGCCATGCCCGGCCACA
*
14295 ATCGGTCACATGACTCGGCCATGCCCGGCCACA
1 ACCGGTCACATGACTCGGCCATGCCCGGCCACA
* *
14328 ACCGGCCACATGACTCCGCCATGCCCGGCCACA
1 ACCGGTCACATGACTCGGCCATGCCCGGCCACA
14361 ACCGGTCACATGA
1 ACCGGTCACATGA
14374 TCCTTTAACT
Statistics
Matches: 69, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 69 1.00
ACGTcount: A:0.22, C:0.41, G:0.24, T:0.12
Consensus pattern (33 bp):
ACCGGTCACATGACTCGGCCATGCCCGGCCACA
Found at i:17185 original size:33 final size:33
Alignment explanation
Indices: 17141--17225 Score: 118
Period size: 33 Copynumber: 2.6 Consensus size: 33
17131 TCTTTTCACC
*
17141 CAAAAA-AGAATTATTTTTAATGCTATAAACAA
1 CAAAAACAGAATTATTTTCAATGCTATAAACAA
* * *
17173 CAAAAACAGAATTATTTGCAATGCTATGATCAA
1 CAAAAACAGAATTATTTTCAATGCTATAAACAA
*
17206 CCAAAACAGAATTATTTTCA
1 CAAAAACAGAATTATTTTCA
17226 TCACAATTAG
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
32 6 0.13
33 40 0.87
ACGTcount: A:0.48, C:0.14, G:0.08, T:0.29
Consensus pattern (33 bp):
CAAAAACAGAATTATTTTCAATGCTATAAACAA
Found at i:17319 original size:33 final size:33
Alignment explanation
Indices: 17240--17309 Score: 113
Period size: 33 Copynumber: 2.1 Consensus size: 33
17230 AATTAGCATC
17240 CAAAACAGATTTAGTATCATCACAAACAACACT
1 CAAAACAGATTTAGTATCATCACAAACAACACT
* * *
17273 TAAAACAGATTTAGTGTCATTACAAACAACACT
1 CAAAACAGATTTAGTATCATCACAAACAACACT
17306 CAAA
1 CAAA
17310 TTAGGTTTAG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.49, C:0.21, G:0.07, T:0.23
Consensus pattern (33 bp):
CAAAACAGATTTAGTATCATCACAAACAACACT
Found at i:25035 original size:33 final size:33
Alignment explanation
Indices: 24998--25106 Score: 173
Period size: 33 Copynumber: 3.3 Consensus size: 33
24988 TTCTTTTCAC
* * *
24998 CCAAAACATAATTATTTTCAATGTTATGATCAA
1 CCAAAACAGAATTATTTGCAATGCTATGATCAA
* *
25031 CCAAAATAGAATTCTTTGCAATGCTATGATCAA
1 CCAAAACAGAATTATTTGCAATGCTATGATCAA
25064 CCAAAACAGAATTATTTGCAATGCTATGATCAA
1 CCAAAACAGAATTATTTGCAATGCTATGATCAA
25097 CCAAAACAGA
1 CCAAAACAGA
25107 TTTGTTTTCA
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 69 1.00
ACGTcount: A:0.43, C:0.18, G:0.10, T:0.28
Consensus pattern (33 bp):
CCAAAACAGAATTATTTGCAATGCTATGATCAA
Found at i:25134 original size:66 final size:66
Alignment explanation
Indices: 24998--25139 Score: 160
Period size: 66 Copynumber: 2.2 Consensus size: 66
24988 TTCTTTTCAC
* * * * * * *
24998 CCAAAACATAATTATTTTCAATGTTATGATCAACCAAAATAGAATTCTTTGCAATGCTATGATCA
1 CCAAAACAGAATTATTTGCAATGCTATGATCAACCAAAACAGAATTCTTTGCAATACAATGAGCA
25063 A
66 A
* * * *
25064 CCAAAACAGAATTATTTGCAATGCTATGATCAACCAAAACAGATTTGTTTTC-ATCACAATTAGC
1 CCAAAACAGAATTATTTGCAATGCTATGATCAACCAAAACAGAATTCTTTGCAAT-ACAATGAGC
*
25128 AT
65 AA
25130 CCAAAACAGA
1 CCAAAACAGA
25140 TTTAGTATCA
Statistics
Matches: 63, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
65 2 0.03
66 61 0.97
ACGTcount: A:0.42, C:0.19, G:0.10, T:0.30
Consensus pattern (66 bp):
CCAAAACAGAATTATTTGCAATGCTATGATCAACCAAAACAGAATTCTTTGCAATACAATGAGCA
A
Found at i:25169 original size:33 final size:33
Alignment explanation
Indices: 25132--25236 Score: 140
Period size: 33 Copynumber: 3.2 Consensus size: 33
25122 ATTAGCATCC
*
25132 AAAACAGATTTAGTATCATCACAAACAACACTT
1 AAAACAGATTTAGTATCATCGCAAACAACACTT
* * *
25165 AAAACAGATTTAGTGTCATTGCAAACAACACTC
1 AAAACAGATTTAGTATCATCGCAAACAACACTT
* *
25198 AAAATAGGTTTAGTATCATCGCAAACAACA-TCT
1 AAAACAGATTTAGTATCATCGCAAACAACACT-T
25231 AAAACA
1 AAAACA
25237 CTCTTTGCAA
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
32 1 0.02
33 60 0.98
ACGTcount: A:0.47, C:0.20, G:0.10, T:0.24
Consensus pattern (33 bp):
AAAACAGATTTAGTATCATCGCAAACAACACTT
Found at i:28304 original size:33 final size:33
Alignment explanation
Indices: 28267--28345 Score: 104
Period size: 33 Copynumber: 2.4 Consensus size: 33
28257 GGCGCGAGTG
*
28267 ACCGGCCATGCGACTTGGAGAAGCCCGGCCAAC
1 ACCGGCCATGCGACTCGGAGAAGCCCGGCCAAC
* * *
28300 ACCGGCCATGCGACTCGGAGATGGCCGGCCATC
1 ACCGGCCATGCGACTCGGAGAAGCCCGGCCAAC
* *
28333 ACTGGCCACGCGA
1 ACCGGCCATGCGA
28346 AATGGACATG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.22, C:0.37, G:0.32, T:0.10
Consensus pattern (33 bp):
ACCGGCCATGCGACTCGGAGAAGCCCGGCCAAC
Found at i:29317 original size:8 final size:8
Alignment explanation
Indices: 29304--29337 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
29294 ACCCTTCTTG
29304 AAAAATTC
1 AAAAATTC
29312 AAAAATTC
1 AAAAATTC
*
29320 AGAAACTTC
1 A-AAAATTC
29329 AAAAATTC
1 AAAAATTC
29337 A
1 A
29338 TAGGTGATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.59, C:0.15, G:0.03, T:0.24
Consensus pattern (8 bp):
AAAAATTC
Found at i:31678 original size:33 final size:32
Alignment explanation
Indices: 31640--31716 Score: 91
Period size: 33 Copynumber: 2.3 Consensus size: 32
31630 TGCCCGCGAA
* *
31640 ACACCGGCCATGCAACATGGAGATGCCCGGCC
1 ACACCGGCCACGCAACATGGACATGCCCGGCC
* * *
31672 ATCACCGGCCACGCGATATGGCCATGCCCGGCC
1 A-CACCGGCCACGCAACATGGACATGCCCGGCC
31705 ACACCCGGCCAC
1 ACA-CCGGCCAC
31717 ATGACTCGGC
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
32 3 0.08
33 35 0.92
ACGTcount: A:0.22, C:0.43, G:0.26, T:0.09
Consensus pattern (32 bp):
ACACCGGCCACGCAACATGGACATGCCCGGCC
Found at i:32833 original size:33 final size:33
Alignment explanation
Indices: 32774--32870 Score: 115
Period size: 33 Copynumber: 2.9 Consensus size: 33
32764 TGGTCGGTTG
* *
32774 TGGCCGGACATGTCC-ATGTCGCGTGGCCGGTGA
1 TGGCCGGGCATCTCCGA-GTCGCGTGGCCGGTGA
* *
32807 TGGCTGGGCATCTCCGAGTCGCGTGGCCGGTGT
1 TGGCCGGGCATCTCCGAGTCGCGTGGCCGGTGA
* * *
32840 TGGCCGGGCTTCTCCTAGTCGCATGGCCGGT
1 TGGCCGGGCATCTCCGAGTCGCGTGGCCGGT
32871 CACTCGCGCC
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
33 54 0.98
34 1 0.02
ACGTcount: A:0.08, C:0.29, G:0.39, T:0.24
Consensus pattern (33 bp):
TGGCCGGGCATCTCCGAGTCGCGTGGCCGGTGA
Found at i:34765 original size:33 final size:31
Alignment explanation
Indices: 34656--34762 Score: 117
Period size: 33 Copynumber: 3.4 Consensus size: 31
34646 CTCGTCCCCT
*
34656 AAAACAGATTTATTTTCAATGCTA-TCAACC
1 AAAACAGAATTATTTTCAATGCTATTCAACC
* * *
34686 AAAACAGGATTATTTGCAATGATATAATCAACC
1 AAAACAGAATTATTTTCAATGCTAT--TCAACC
* *
34719 AAAACAGAATTGTTTTTAATGCTATGTTCAACC
1 AAAACAGAATTATTTTCAATGCTA--TTCAACC
34752 AAAACAGAATT
1 AAAACAGAATT
34763 GTTGATGCGC
Statistics
Matches: 63, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
30 20 0.32
33 42 0.67
35 1 0.02
ACGTcount: A:0.43, C:0.16, G:0.10, T:0.31
Consensus pattern (31 bp):
AAAACAGAATTATTTTCAATGCTATTCAACC
Found at i:34960 original size:33 final size:33
Alignment explanation
Indices: 34907--35029 Score: 124
Period size: 33 Copynumber: 3.7 Consensus size: 33
34897 CGCACAACAA
*
34907 CGGCCACAAGACCGGGCACGCGACATGGACATGTC
1 CGGCCAC-A-ACCGGCCACGCGACATGGACATGTC
*
34942 CGGCCATC-ACCGGCCACGCGACATGGGCATGTC
1 CGGCCA-CAACCGGCCACGCGACATGGACATGTC
* ** * *
34975 CGGCTACAACCGGCCAAACGAC-TCGGCCATGCC
1 CGGCCACAACCGGCCACGCGACAT-GGACATGTC
*
35008 CGGCCACAACCGGCCATGCGAC
1 CGGCCACAACCGGCCACGCGAC
35030 CCTTTGTCTA
Statistics
Matches: 75, Mismatches: 10, Indels: 8
0.81 0.11 0.09
Matches are distributed among these distances:
32 2 0.03
33 66 0.88
35 6 0.08
36 1 0.01
ACGTcount: A:0.23, C:0.40, G:0.28, T:0.09
Consensus pattern (33 bp):
CGGCCACAACCGGCCACGCGACATGGACATGTC
Done.