Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008312.1 Corchorus capsularis cultivar CVL-1 contig08333, 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: 47405
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:4274 original size:44 final size:43
Alignment explanation
Indices: 4226--4353 Score: 157
Period size: 44 Copynumber: 2.9 Consensus size: 43
4216 TTCATAGCAA
* * *
4226 AGTTTATTAAAATTTCATAGTTAGGTTATCAAAATTTCTTATGG
1 AGTTTATCAAAATTTAATAGTTA-GTTATCAAAATTTCATATGG
* * * *
4270 AGTTTATCACAATTTTATAGGTAATTATCAAAATTTCATATGG
1 AGTTTATCAAAATTTAATAGTTAGTTATCAAAATTTCATATGG
* *
4313 TGGTTATCAAAATTTAATAAGTTAGTTATCAAAATTTCATA
1 AGTTTATCAAAATTTAAT-AGTTAGTTATCAAAATTTCATA
4354 AAATTATTCA
Statistics
Matches: 71, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
43 32 0.45
44 39 0.55
ACGTcount: A:0.38, C:0.08, G:0.12, T:0.43
Consensus pattern (43 bp):
AGTTTATCAAAATTTAATAGTTAGTTATCAAAATTTCATATGG
Found at i:4305 original size:43 final size:44
Alignment explanation
Indices: 4251--4353 Score: 136
Period size: 43 Copynumber: 2.4 Consensus size: 44
4241 CATAGTTAGG
* * * *
4251 TTATCAAAATTTCTTATGGAGTTTATCACAATTTTAT-AGGTAA
1 TTATCAAAATTTCATATGGAGGTTATCAAAATTTAATAAGGTAA
* * *
4294 TTATCAAAATTTCATATGGTGGTTATCAAAATTTAATAAGTTAG
1 TTATCAAAATTTCATATGGAGGTTATCAAAATTTAATAAGGTAA
4338 TTATCAAAATTTCATA
1 TTATCAAAATTTCATA
4354 AAATTATTCA
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
43 32 0.62
44 20 0.38
ACGTcount: A:0.38, C:0.09, G:0.11, T:0.43
Consensus pattern (44 bp):
TTATCAAAATTTCATATGGAGGTTATCAAAATTTAATAAGGTAA
Found at i:4354 original size:22 final size:22
Alignment explanation
Indices: 4229--4354 Score: 114
Period size: 22 Copynumber: 5.8 Consensus size: 22
4219 ATAGCAAAGT
* *
4229 TTATTAAAATTTCAT-AGTTAGG
1 TTATCAAAATTTCATAAGGTA-G
* *
4251 TTATCAAAATTTCTTATGG-AG
1 TTATCAAAATTTCATAAGGTAG
* * *
4272 TTTATCACAATTTTAT-AGGTAA
1 -TTATCAAAATTTCATAAGGTAG
* *
4294 TTATCAAAATTTCATATGGTGG
1 TTATCAAAATTTCATAAGGTAG
* *
4316 TTATCAAAATTTAATAAGTTAG
1 TTATCAAAATTTCATAAGGTAG
4338 TTATCAAAATTTCATAA
1 TTATCAAAATTTCATAA
4355 AATTATTCAA
Statistics
Matches: 81, Mismatches: 19, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
21 16 0.20
22 64 0.79
23 1 0.01
ACGTcount: A:0.38, C:0.08, G:0.11, T:0.43
Consensus pattern (22 bp):
TTATCAAAATTTCATAAGGTAG
Found at i:4653 original size:21 final size:21
Alignment explanation
Indices: 4590--4653 Score: 87
Period size: 21 Copynumber: 3.1 Consensus size: 21
4580 TTGACACTGT
4590 TTAGGTACTGTACAGATGAGA
1 TTAGGTACTGTACAGATGAGA
* * *
4611 TTA--TACTATACAGATCAAA
1 TTAGGTACTGTACAGATGAGA
4630 TTAGGTACTGTACAGATGAGA
1 TTAGGTACTGTACAGATGAGA
4651 TTA
1 TTA
4654 TTAGAGCAAC
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
19 16 0.46
21 19 0.54
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.31
Consensus pattern (21 bp):
TTAGGTACTGTACAGATGAGA
Found at i:4927 original size:2 final size:2
Alignment explanation
Indices: 4920--4953 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
4910 ATATAATGAG
4920 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4954 TAAAGGGTCC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6013 original size:151 final size:152
Alignment explanation
Indices: 5721--6014 Score: 482
Period size: 151 Copynumber: 1.9 Consensus size: 152
5711 TGTATTAATG
*
5721 ACATTTTGCCCGCAAAAGTTTTGAACCTATATATAAATAATCATAAACATCTCATTTATTCATAA
1 ACATTTTGCCCGCAAAAGTTTTGAACCTATATATAAACAATCATAAACATCTCATTTATTCATAA
* *
5786 ATTTTTCAACTAATAATATAGGGAGTGCATGCGCAACCATTCATAATTTTTACAACTAATTACAA
66 ATTTTTCAACTAATAATATAGGGAGTGCATGCACAACCATTCATAACTTTTACAACTAATTACAA
*
5851 TCTATAGAGAAAACAATCATAA
131 TCTAGAGAGAAAACAATCATAA
* * **
5873 ACATTTTGCCC-CCAAATTTTTGCGCCTATATATAAACAATCATAAACATCTCATTTATTCATAA
1 ACATTTTGCCCGCAAAAGTTTTGAACCTATATATAAACAATCATAAACATCTCATTTATTCATAA
* * *
5937 CTTTTTCAACTAATAATATAGGGAGTGCCTGCACAACCATTCATAACTTTTACAACTAATTATAA
66 ATTTTTCAACTAATAATATAGGGAGTGCATGCACAACCATTCATAACTTTTACAACTAATTACAA
6002 TCTAGAGAGAAAA
131 TCTAGAGAGAAAA
6015 TTTGGTTCGT
Statistics
Matches: 131, Mismatches: 11, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
151 120 0.92
152 11 0.08
ACGTcount: A:0.40, C:0.19, G:0.09, T:0.33
Consensus pattern (152 bp):
ACATTTTGCCCGCAAAAGTTTTGAACCTATATATAAACAATCATAAACATCTCATTTATTCATAA
ATTTTTCAACTAATAATATAGGGAGTGCATGCACAACCATTCATAACTTTTACAACTAATTACAA
TCTAGAGAGAAAACAATCATAA
Found at i:11901 original size:18 final size:18
Alignment explanation
Indices: 11880--11931 Score: 68
Period size: 19 Copynumber: 2.8 Consensus size: 18
11870 AACAATGTCT
11880 CAGCACTGAACACAGCCC
1 CAGCACTGAACACAGCCC
* *
11898 CAGCACTTAAACACAGTCC
1 CAGCAC-TGAACACAGCCC
*
11917 CAGCACCGAACACAG
1 CAGCACTGAACACAG
11932 ATTCTATTCC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
18 13 0.45
19 16 0.55
ACGTcount: A:0.37, C:0.40, G:0.15, T:0.08
Consensus pattern (18 bp):
CAGCACTGAACACAGCCC
Found at i:12096 original size:16 final size:16
Alignment explanation
Indices: 12077--12188 Score: 86
Period size: 16 Copynumber: 7.0 Consensus size: 16
12067 AACCCGCCTG
12077 AACCTGAACCCGAAAA
1 AACCTGAACCCGAAAA
*
12093 AACCCGAACCCG-AAA
1 AACCTGAACCCGAAAA
** *
12108 AAGTTCAAACCCGAAAA
1 AACCT-GAACCCGAAAA
* * *
12125 AGCTTAAACCCGAAAA
1 AACCTGAACCCGAAAA
12141 AACCTGAACCCG-AAA
1 AACCTGAACCCGAAAA
* *
12156 AAGCTCAAACCCGAAAAA
1 AACCT-GAACCCG-AAAA
*
12174 AACC-GAATCCGAAAA
1 AACCTGAACCCGAAAA
12189 TTTATGAAAA
Statistics
Matches: 76, Mismatches: 15, Indels: 11
0.75 0.15 0.11
Matches are distributed among these distances:
15 16 0.21
16 48 0.63
17 6 0.08
18 6 0.08
ACGTcount: A:0.51, C:0.29, G:0.12, T:0.07
Consensus pattern (16 bp):
AACCTGAACCCGAAAA
Found at i:12186 original size:32 final size:32
Alignment explanation
Indices: 12077--12188 Score: 120
Period size: 32 Copynumber: 3.5 Consensus size: 32
12067 AACCCGCCTG
* * *
12077 AACCTGAACCCGAAAAAACCCGAACCCG-AAA
1 AACCTGAACCCGAAAAAGCTCAAACCCGAAAA
** * *
12108 AAGTTCAAACCCGAAAAAGCTTAAACCCGAAAA
1 AACCT-GAACCCGAAAAAGCTCAAACCCGAAAA
12141 AACCTGAACCCGAAAAAGCTCAAACCCGAAAAA
1 AACCTGAACCCGAAAAAGCTCAAACCCG-AAAA
*
12174 AACC-GAATCCGAAAA
1 AACCTGAACCCGAAAA
12189 TTTATGAAAA
Statistics
Matches: 66, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
31 3 0.05
32 49 0.74
33 14 0.21
ACGTcount: A:0.51, C:0.29, G:0.12, T:0.07
Consensus pattern (32 bp):
AACCTGAACCCGAAAAAGCTCAAACCCGAAAA
Found at i:12186 original size:48 final size:47
Alignment explanation
Indices: 12077--12188 Score: 143
Period size: 48 Copynumber: 2.3 Consensus size: 47
12067 AACCCGCCTG
*
12077 AACCTGAACCCGAAAAAACCCGAACCCGAAAAAGTTCAAACCCGAAAA
1 AACC-GAACCCGAAAAAACCCGAACCCGAAAAAGCTCAAACCCGAAAA
* ** *
12125 AGCTTAAACCCGAAAAAACCTGAACCCGAAAAAGCTCAAACCCGAAAAA
1 AAC-CGAACCCGAAAAAACCCGAACCCGAAAAAGCTCAAACCCG-AAAA
*
12174 AACCGAATCCGAAAA
1 AACCGAACCCGAAAA
12189 TTTATGAAAA
Statistics
Matches: 53, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
48 47 0.89
49 6 0.11
ACGTcount: A:0.51, C:0.29, G:0.12, T:0.07
Consensus pattern (47 bp):
AACCGAACCCGAAAAAACCCGAACCCGAAAAAGCTCAAACCCGAAAA
Found at i:12366 original size:15 final size:16
Alignment explanation
Indices: 12343--12404 Score: 67
Period size: 15 Copynumber: 3.9 Consensus size: 16
12333 CTGAACCCGA
*
12343 ACCCGAATT-AACCTG
1 ACCCAAATTCAACCTG
12358 ACCCAAATTCAACAC-G
1 ACCCAAATTCAAC-CTG
*
12374 AACCCGAATT-AACCTG
1 -ACCCAAATTCAACCTG
12390 ACCCAAATTCAACCT
1 ACCCAAATTCAACCT
12405 TCAATGTGTG
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
15 17 0.44
16 13 0.33
17 9 0.23
ACGTcount: A:0.39, C:0.35, G:0.08, T:0.18
Consensus pattern (16 bp):
ACCCAAATTCAACCTG
Found at i:12376 original size:32 final size:32
Alignment explanation
Indices: 12326--12402 Score: 127
Period size: 32 Copynumber: 2.4 Consensus size: 32
12316 TCTGGCCAAA
* * *
12326 ACCCAAACTGAACCCGAACCCGAATTAACCTG
1 ACCCAAATTCAACACGAACCCGAATTAACCTG
12358 ACCCAAATTCAACACGAACCCGAATTAACCTG
1 ACCCAAATTCAACACGAACCCGAATTAACCTG
12390 ACCCAAATTCAAC
1 ACCCAAATTCAAC
12403 CTTCAATGTG
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.40, C:0.36, G:0.09, T:0.14
Consensus pattern (32 bp):
ACCCAAATTCAACACGAACCCGAATTAACCTG
Found at i:13355 original size:25 final size:25
Alignment explanation
Indices: 13327--13376 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
13317 TAAGCCTATA
* *
13327 GGAATTTATTTAATAAATTCATTTT
1 GGAATTTAATCAATAAATTCATTTT
13352 GGAATTTAATCAATAAATTCATTTT
1 GGAATTTAATCAATAAATTCATTTT
13377 TTACCATGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.38, C:0.06, G:0.08, T:0.48
Consensus pattern (25 bp):
GGAATTTAATCAATAAATTCATTTT
Found at i:18520 original size:25 final size:25
Alignment explanation
Indices: 18492--18541 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
18482 TAAGCCTATA
* *
18492 GGAATTTATTTAATAAATTCATTTT
1 GGAATTTAATCAATAAATTCATTTT
*
18517 GGAATTTAATCAATAAATTCGTTTT
1 GGAATTTAATCAATAAATTCATTTT
18542 TTACCATGTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.36, C:0.06, G:0.10, T:0.48
Consensus pattern (25 bp):
GGAATTTAATCAATAAATTCATTTT
Found at i:21483 original size:23 final size:24
Alignment explanation
Indices: 21421--21483 Score: 85
Period size: 24 Copynumber: 2.7 Consensus size: 24
21411 AAGGAAAAAA
*
21421 AAAACTTGCACTAGAACAAGACTG
1 AAAACTTGCACTAGAGCAAGACTG
21445 AAAACTTGCACTAGAGCAAGACT-
1 AAAACTTGCACTAGAGCAAGACTG
*
21468 AAACCTCT-CACTAGAG
1 AAAACT-TGCACTAGAG
21484 AACGGTTCTA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
23 13 0.36
24 23 0.64
ACGTcount: A:0.43, C:0.24, G:0.16, T:0.17
Consensus pattern (24 bp):
AAAACTTGCACTAGAGCAAGACTG
Found at i:23959 original size:10 final size:10
Alignment explanation
Indices: 23944--23969 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
23934 AATTTAATAT
23944 GGATATTTAC
1 GGATATTTAC
23954 GGATATTTAC
1 GGATATTTAC
23964 GGATAT
1 GGATAT
23970 ATCGAGATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.31, C:0.08, G:0.23, T:0.38
Consensus pattern (10 bp):
GGATATTTAC
Found at i:24771 original size:22 final size:21
Alignment explanation
Indices: 24716--24776 Score: 63
Period size: 20 Copynumber: 2.9 Consensus size: 21
24706 TATATTTAAT
*
24716 TATTCATGATATATATAGAATA
1 TATTTATGATATATATA-AATA
* *
24738 TATGTA--AAATATATAAATTA
1 TATTTATGATATATATAAA-TA
24758 TATTTATGATATATATAAA
1 TATTTATGATATATATAAA
24777 AAATATATAA
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
19 2 0.06
20 15 0.48
22 14 0.45
ACGTcount: A:0.49, C:0.02, G:0.07, T:0.43
Consensus pattern (21 bp):
TATTTATGATATATATAAATA
Found at i:32668 original size:4 final size:4
Alignment explanation
Indices: 32659--32689 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
32649 AATGGACTCC
32659 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
32690 TTAAATCTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:39961 original size:109 final size:109
Alignment explanation
Indices: 39827--40040 Score: 392
Period size: 109 Copynumber: 2.0 Consensus size: 109
39817 ATTTATGATG
**
39827 ATAAAAATAAAAAGCTTTAAATGGTGACATTCTTTACTGTCACTCTGATACTTTCCCTTCTTGTT
1 ATAAAAATAAAAAGCTTTAAATGGTGACATTCTTTACTGTCACTCTGATACTTTCCCTTCTCCTT
39892 ATTTATTTATCTTCATCATACTTAATTTGATAATGGTATAATGA
66 ATTTATTTATCTTCATCATACTTAATTTGATAATGGTATAATGA
*
39936 ATAAAAATAAAAAGCTTTAAATGGTGACATTCTTTACTGTCACTCTGATACTTTCGCTTCTCCTT
1 ATAAAAATAAAAAGCTTTAAATGGTGACATTCTTTACTGTCACTCTGATACTTTCCCTTCTCCTT
*
40001 ATTTATTTATTTTCATCATACTTAATTTGATAATGGTATA
66 ATTTATTTATCTTCATCATACTTAATTTGATAATGGTATA
40041 TGGTTGCTGA
Statistics
Matches: 101, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
109 101 1.00
ACGTcount: A:0.32, C:0.15, G:0.10, T:0.43
Consensus pattern (109 bp):
ATAAAAATAAAAAGCTTTAAATGGTGACATTCTTTACTGTCACTCTGATACTTTCCCTTCTCCTT
ATTTATTTATCTTCATCATACTTAATTTGATAATGGTATAATGA
Done.