Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013651.1 Corchorus capsularis cultivar CVL-1 contig13672, 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: 66089
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:14346 original size:2 final size:2
Alignment explanation
Indices: 14329--14367 Score: 55
Period size: 2 Copynumber: 20.0 Consensus size: 2
14319 TGACTTTTCT
14329 TA TA CTA TA T- TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
14368 ATAATAATAA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 2 0.06
2 30 0.88
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:14371 original size:8 final size:9
Alignment explanation
Indices: 14329--14373 Score: 51
Period size: 8 Copynumber: 5.2 Consensus size: 9
14319 TGACTTTTCT
*
14329 TATACTATAT
1 TATA-TATAA
14339 TATATAT-A
1 TATATATAA
14347 TATATAT-A
1 TATATATAA
14355 TATATATAA
1 TATATATAA
14364 TATA-ATAA
1 TATATATAA
14372 TA
1 TA
14374 ATAAGTAAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
8 21 0.64
9 8 0.24
10 4 0.12
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (9 bp):
TATATATAA
Found at i:15321 original size:26 final size:25
Alignment explanation
Indices: 15266--15321 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
15256 TATGATTATC
**
15266 TAATAAAACCCAATTCTTTTTTTGG
1 TAATAAAACCCAATTCTTTTTTTAA
*
15291 TAATAGAACCCAATT-TATTATTTTAA
1 TAATAAAACCCAATTCT-TT-TTTTAA
15317 TAATA
1 TAATA
15322 CCATTAATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
24 1 0.04
25 16 0.62
26 9 0.35
ACGTcount: A:0.39, C:0.12, G:0.05, T:0.43
Consensus pattern (25 bp):
TAATAAAACCCAATTCTTTTTTTAA
Found at i:33650 original size:3 final size:3
Alignment explanation
Indices: 33644--33682 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
33634 TGGTGGCCAC
33644 GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT
1 GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT
33683 CCATAAATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.00, C:0.00, G:0.67, T:0.33
Consensus pattern (3 bp):
GGT
Found at i:34257 original size:22 final size:22
Alignment explanation
Indices: 34211--34257 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
34201 TAGGGTTTAA
* *
34211 TGCCCAAATTTTTCACTGAATT
1 TGCCCAAATTCTTCACTGAACT
34233 TGCCCAAATTCTTCA-TGGAACT
1 TGCCCAAATTCTTCACT-GAACT
34255 TGC
1 TGC
34258 ATAAAAGGGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 21 0.95
ACGTcount: A:0.26, C:0.26, G:0.13, T:0.36
Consensus pattern (22 bp):
TGCCCAAATTCTTCACTGAACT
Found at i:34740 original size:3 final size:3
Alignment explanation
Indices: 34732--34783 Score: 68
Period size: 3 Copynumber: 16.7 Consensus size: 3
34722 ACCTTCAACT
* *
34732 CAC CAC CAC CAC CAC CAC CAC CAC CAC CAAC CAC CGC ACAT CAC CAC
1 CAC CAC CAC CAC CAC CAC CAC CAC CAC C-AC CAC CAC -CAC CAC CAC
34779 CAC CA
1 CAC CA
34784 AAGCAACCAC
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
3 39 0.91
4 4 0.09
ACGTcount: A:0.35, C:0.62, G:0.02, T:0.02
Consensus pattern (3 bp):
CAC
Found at i:36952 original size:17 final size:18
Alignment explanation
Indices: 36923--36957 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
36913 GAAACTGATT
36923 AATTTCAATTTTAAGTAA
1 AATTTCAATTTTAAGTAA
*
36941 AATTTC-ATTTTATGTAA
1 AATTTCAATTTTAAGTAA
36958 TAGCAATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.49
Consensus pattern (18 bp):
AATTTCAATTTTAAGTAA
Found at i:37088 original size:13 final size:13
Alignment explanation
Indices: 37070--37094 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
37060 TTCAATGTTT
37070 TAAATATTATTTA
1 TAAATATTATTTA
37083 TAAATATTATTT
1 TAAATATTATTT
37095 GGAATTCCAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TAAATATTATTTA
Found at i:41513 original size:24 final size:26
Alignment explanation
Indices: 41466--41513 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
41456 TTGATCCAAC
* *
41466 AAAAAAAAGATGGTCTATTATCAAAA
1 AAAAAAAAGATGGTCAACTATCAAAA
41492 AAAAAAAAGATGGT-AACT-TCAA
1 AAAAAAAAGATGGTCAACTATCAA
41514 GTGAGAGTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 4 0.20
25 2 0.10
26 14 0.70
ACGTcount: A:0.58, C:0.08, G:0.12, T:0.21
Consensus pattern (26 bp):
AAAAAAAAGATGGTCAACTATCAAAA
Found at i:42759 original size:31 final size:30
Alignment explanation
Indices: 42710--42768 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
42700 ATATTAGAGC
* * *
42710 ACAAAATTATCCATTAACCTACTCCAAATTG
1 ACAAAATCACCCACTAACCTAC-CCAAATTG
42741 ACAAAATCACCCACTAACCTACCCAAAT
1 ACAAAATCACCCACTAACCTACCCAAAT
42769 GGGCAATAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 6 0.24
31 19 0.76
ACGTcount: A:0.44, C:0.32, G:0.02, T:0.22
Consensus pattern (30 bp):
ACAAAATCACCCACTAACCTACCCAAATTG
Found at i:46610 original size:10 final size:10
Alignment explanation
Indices: 46595--46625 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
46585 GAAATTGGCC
46595 AGCCAGAATT
1 AGCCAGAATT
46605 AGCCAGAATT
1 AGCCAGAATT
*
46615 AACCAGAATT
1 AGCCAGAATT
46625 A
1 A
46626 TCCAATACCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.45, C:0.19, G:0.16, T:0.19
Consensus pattern (10 bp):
AGCCAGAATT
Found at i:54677 original size:34 final size:34
Alignment explanation
Indices: 54634--54754 Score: 233
Period size: 34 Copynumber: 3.6 Consensus size: 34
54624 TTTTAAACGA
*
54634 AGTTTGTGTTGATTGTCTTGCTAATTTGAATACT
1 AGTTTGTGTTGGTTGTCTTGCTAATTTGAATACT
54668 AGTTTGTGTTGGTTGTCTTGCTAATTTGAATACT
1 AGTTTGTGTTGGTTGTCTTGCTAATTTGAATACT
54702 AGTTTGTGTTGGTTGTCTTGCTAATTTGAATACT
1 AGTTTGTGTTGGTTGTCTTGCTAATTTGAATACT
54736 AGTTTGTGTTGGTTGTCTT
1 AGTTTGTGTTGGTTGTCTT
54755 CCTTTTAAAC
Statistics
Matches: 86, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
34 86 1.00
ACGTcount: A:0.17, C:0.08, G:0.24, T:0.51
Consensus pattern (34 bp):
AGTTTGTGTTGGTTGTCTTGCTAATTTGAATACT
Found at i:57277 original size:31 final size:30
Alignment explanation
Indices: 57236--57432 Score: 163
Period size: 31 Copynumber: 6.5 Consensus size: 30
57226 AGGGGCTAAT
57236 TGCTCAAATAAGGGCCTAACGTTTGTCAAAA
1 TGCTCAAATAAGGGCCTAACGTTT-TCAAAA
* * * **
57267 TGTTCAAATAAGGGTCTGATC-TTTT-AATT
1 TGCTCAAATAAGGGCCT-AACGTTTTCAAAA
* *
57296 TGGC-CAAATAAGGGCCTAACATTATCGAAAA
1 T-GCTCAAATAAGGGCCTAACGTTTTC-AAAA
* **
57327 TGCTCAAATAAGGGCCT-A-GTCTTTTAATT
1 TGCTCAAATAAGGGCCTAACGT-TTTCAAAA
* *
57356 TGGC-CAAATAAGGGCCTAATGTTATTGAAAA
1 T-GCTCAAATAAGGGCCTAACGTT-TTCAAAA
*
57387 TGCTCAAATAAGGGCCTAACGTTATCGAAAA
1 TGCTCAAATAAGGGCCTAACGTTTTC-AAAA
57418 TGCTCAAATAAGGGC
1 TGCTCAAATAAGGGC
57433 TTGGTTTCAG
Statistics
Matches: 131, Mismatches: 22, Indels: 26
0.73 0.12 0.15
Matches are distributed among these distances:
28 2 0.02
29 35 0.27
30 14 0.11
31 78 0.60
32 2 0.02
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (30 bp):
TGCTCAAATAAGGGCCTAACGTTTTCAAAA
Found at i:57334 original size:60 final size:60
Alignment explanation
Indices: 57240--57404 Score: 235
Period size: 60 Copynumber: 2.8 Consensus size: 60
57230 GCTAATTGCT
* * * *
57240 CAAATAAGGGCCTAACGTTTGTC-AAAATGTTCAAATAAGGGTCT-GATCTTTTAATTTGGC
1 CAAATAAGGGCCTAAC-ATTATCGAAAATGCTCAAATAAGGGCCTAG-TCTTTTAATTTGGC
57300 CAAATAAGGGCCTAACATTATCGAAAATGCTCAAATAAGGGCCTAGTCTTTTAATTTGGC
1 CAAATAAGGGCCTAACATTATCGAAAATGCTCAAATAAGGGCCTAGTCTTTTAATTTGGC
** *
57360 CAAATAAGGGCCTAATGTTATTGAAAATGCTCAAATAAGGGCCTA
1 CAAATAAGGGCCTAACATTATCGAAAATGCTCAAATAAGGGCCTA
57405 ACGTTATCGA
Statistics
Matches: 96, Mismatches: 7, Indels: 4
0.90 0.07 0.04
Matches are distributed among these distances:
59 4 0.04
60 91 0.95
61 1 0.01
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.29
Consensus pattern (60 bp):
CAAATAAGGGCCTAACATTATCGAAAATGCTCAAATAAGGGCCTAGTCTTTTAATTTGGC
Found at i:57373 original size:29 final size:29
Alignment explanation
Indices: 57271--57373 Score: 95
Period size: 29 Copynumber: 3.5 Consensus size: 29
57261 TCAAAATGTT
*
57271 CAAATAAGGGTCT-GATCTTTTAATTTGGC
1 CAAATAAGGGCCTAG-TCTTTTAATTTGGC
* * **
57300 CAAATAAGGGCCTA-ACATTATCGAAAAT-GC
1 CAAATAAGGGCCTAGTC-TT-T-TAATTTGGC
57330 TCAAATAAGGGCCTAGTCTTTTAATTTGGC
1 -CAAATAAGGGCCTAGTCTTTTAATTTGGC
57360 CAAATAAGGGCCTA
1 CAAATAAGGGCCTA
57374 ATGTTATTGA
Statistics
Matches: 58, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
28 1 0.02
29 31 0.53
30 6 0.10
31 19 0.33
32 1 0.02
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.29
Consensus pattern (29 bp):
CAAATAAGGGCCTAGTCTTTTAATTTGGC
Found at i:57496 original size:31 final size:31
Alignment explanation
Indices: 57461--57626 Score: 108
Period size: 31 Copynumber: 5.5 Consensus size: 31
57451 ACATATGAGA
*
57461 TAGGCCCTTATTTGAGCATTTTGGCAAATAT
1 TAGGCCCTTATTTGAGCATTTTGGCAAACAT
** * *
57492 TAGGCCCTTATTTG-GCCAAATT--CAAAGAC
1 TAGGCCCTTATTTGAG-CATTTTGGCAAACAT
** * *
57521 CGGGCCCTTATTTGAACATTTTGGCAAACGT
1 TAGGCCCTTATTTGAGCATTTTGGCAAACAT
* * ** * *
57552 TAGGCCCTTATGTGACCAAATT--AAAAGAT
1 TAGGCCCTTATTTGAGCATTTTGGCAAACAT
* * * *
57581 CATGTCCTTATTTGAGCATTTTGGCAAACCT
1 TAGGCCCTTATTTGAGCATTTTGGCAAACAT
*
57612 TAGACCCTTATTTGA
1 TAGGCCCTTATTTGA
57627 ACAATTAGCC
Statistics
Matches: 94, Mismatches: 35, Indels: 12
0.67 0.25 0.09
Matches are distributed among these distances:
29 40 0.43
30 1 0.01
31 53 0.56
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (31 bp):
TAGGCCCTTATTTGAGCATTTTGGCAAACAT
Found at i:57530 original size:60 final size:60
Alignment explanation
Indices: 57462--57626 Score: 222
Period size: 60 Copynumber: 2.8 Consensus size: 60
57452 CATATGAGAT
* * *
57462 AGGCCCTTATTTGAGCATTTTGGCAAATATTAGGCCCTTATTTGGCCAAATTCAAAGACC
1 AGGCCCTTATTTGAGCATTTTGGCAAACATTAGGCCCTTATTTGACCAAATTAAAAGACC
* * * * *
57522 GGGCCCTTATTTGAACATTTTGGCAAACGTTAGGCCCTTATGTGACCAAATTAAAAGATC
1 AGGCCCTTATTTGAGCATTTTGGCAAACATTAGGCCCTTATTTGACCAAATTAAAAGACC
* * * *
57582 ATGTCCTTATTTGAGCATTTTGGCAAACCTTAGACCCTTATTTGA
1 AGGCCCTTATTTGAGCATTTTGGCAAACATTAGGCCCTTATTTGA
57627 ACAATTAGCC
Statistics
Matches: 90, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
60 90 1.00
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (60 bp):
AGGCCCTTATTTGAGCATTTTGGCAAACATTAGGCCCTTATTTGACCAAATTAAAAGACC
Found at i:65235 original size:14 final size:14
Alignment explanation
Indices: 65216--65250 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
65206 AGTTAGCGTC
65216 CATTTGGTTTGGGG
1 CATTTGGTTTGGGG
65230 CATTTGGTTTGGGG
1 CATTTGGTTTGGGG
*
65244 TATTTGG
1 CATTTGG
65251 GAGGGGTGGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.09, C:0.06, G:0.40, T:0.46
Consensus pattern (14 bp):
CATTTGGTTTGGGG
Done.