Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008274.1 Corchorus capsularis cultivar CVL-1 contig08295, 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: 69034
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1097 original size:13 final size:13
Alignment explanation
Indices: 1079--1103 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1069 AATTATTGTT
1079 TGCTTTATTAATA
1 TGCTTTATTAATA
1092 TGCTTTATTAAT
1 TGCTTTATTAAT
1104 TTACTTTATA
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:0.28, C:0.08, G:0.08, T:0.56
Consensus pattern (13 bp):
TGCTTTATTAATA
Found at i:7569 original size:53 final size:53
Alignment explanation
Indices: 7508--7614 Score: 169
Period size: 53 Copynumber: 2.0 Consensus size: 53
7498 AAAAACTTAT
* * *
7508 AAAATAAAACAATCGTACACGAAGTGCGGTCGGGAAGTTCTAGTATAAATTAC
1 AAAATAAAACAACCGCACACGAAGTGCGGCCGGGAAGTTCTAGTATAAATTAC
* *
7561 AAAATAAAACAGCCGCACACGAAGTGTGGCCGGGAAGTTCTAGTATAAATTAC
1 AAAATAAAACAACCGCACACGAAGTGCGGCCGGGAAGTTCTAGTATAAATTAC
7614 A
1 A
7615 GTATTGATTG
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
53 49 1.00
ACGTcount: A:0.41, C:0.17, G:0.21, T:0.21
Consensus pattern (53 bp):
AAAATAAAACAACCGCACACGAAGTGCGGCCGGGAAGTTCTAGTATAAATTAC
Found at i:8508 original size:7 final size:7
Alignment explanation
Indices: 8498--8523 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
8488 AGCTGAAAGA
8498 GTGATGG
1 GTGATGG
8505 GTGATGG
1 GTGATGG
8512 GTGATGG
1 GTGATGG
8519 GTGAT
1 GTGAT
8524 TCTGGCGGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.00, G:0.54, T:0.31
Consensus pattern (7 bp):
GTGATGG
Found at i:21646 original size:90 final size:88
Alignment explanation
Indices: 21487--21672 Score: 293
Period size: 90 Copynumber: 2.1 Consensus size: 88
21477 CAATCAGGAA
*
21487 TCGGTACCCAGTTCGATATCGGTATACATACTATTGGATAGTCAACGTGCCACGTTGATCCGGTT
1 TCGGTACCCAGTTCGATATCGGTATACATACTATTGCATAGTCAACGTGCCACGTTGATCCGGTT
*
21552 CAACCGTAGTTGAACCGGCCGTT
66 CAACCGTAGTTGAACCGGCCATT
* * *
21575 TCGGTACCCAGTTCGGTATCGGTATACATACAATATTGCATAGTCAATGTGTCACGTTGA-CCTG
1 TCGGTACCCAGTTCGATATCGGTATACATAC--TATTGCATAGTCAACGTGCCACGTTGATCC-G
21639 GTTCAACCGTAGTTGAACCGGCCATT
63 GTTCAACCGTAGTTGAACCGGCCATT
21665 TCGGTACC
1 TCGGTACC
21673 AAACCCATTT
Statistics
Matches: 90, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
88 30 0.33
89 2 0.02
90 58 0.64
ACGTcount: A:0.23, C:0.25, G:0.23, T:0.29
Consensus pattern (88 bp):
TCGGTACCCAGTTCGATATCGGTATACATACTATTGCATAGTCAACGTGCCACGTTGATCCGGTT
CAACCGTAGTTGAACCGGCCATT
Found at i:33070 original size:20 final size:22
Alignment explanation
Indices: 33024--33070 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 22
33014 GAGAATTTCT
*
33024 ATTACACTAAAAAAAGATATCG
1 ATTACACCAAAAAAAGATATCG
33046 A-TACACCAAAAAAAGA-ATC-
1 ATTACACCAAAAAAAGATATCG
33065 ATTACA
1 ATTACA
33071 TATGTTGATT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 1 0.04
20 7 0.30
21 14 0.61
22 1 0.04
ACGTcount: A:0.57, C:0.17, G:0.06, T:0.19
Consensus pattern (22 bp):
ATTACACCAAAAAAAGATATCG
Found at i:38128 original size:2 final size:2
Alignment explanation
Indices: 38121--38154 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
38111 AATAGAGTAA
*
38121 AT AT AT AT AT AT AT AT AT AT AT AT -T AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
38155 AAATTAGTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39334 original size:19 final size:22
Alignment explanation
Indices: 39281--39323 Score: 77
Period size: 23 Copynumber: 1.9 Consensus size: 22
39271 TCACTGTAAA
39281 ACAATATTTAAACAAAATTATC
1 ACAATATTTAAACAAAATTATC
39303 ATCAATATTTAAACAAAATTA
1 A-CAATATTTAAACAAAATTA
39324 CCATATGTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 1 0.05
23 19 0.95
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
ACAATATTTAAACAAAATTATC
Found at i:41978 original size:4 final size:4
Alignment explanation
Indices: 41962--41991 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
41952 GCAGAGTACC
41962 AAAG AAA- AAAG AAAG AAAG AAAG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
41992 CAGAGCAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 22 0.88
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:42191 original size:15 final size:15
Alignment explanation
Indices: 42171--42201 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
42161 AGACTTTGAG
42171 AAGGAAAAGAAGAGA
1 AAGGAAAAGAAGAGA
*
42186 AAGGAAGAGAAGAGA
1 AAGGAAAAGAAGAGA
42201 A
1 A
42202 CAACTATGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (15 bp):
AAGGAAAAGAAGAGA
Found at i:47207 original size:31 final size:31
Alignment explanation
Indices: 47163--47314 Score: 173
Period size: 31 Copynumber: 4.9 Consensus size: 31
47153 CATGGCATGC
* *
47163 CACGTGTACCAAAAAGTGACATGTGACACG-
1 CACGTGTACAAAAAAGTGACATGTGGCACGT
* * *
47193 CTATGTATACCAAAAAGTGACATGTGGCACGT
1 C-ACGTGTACAAAAAAGTGACATGTGGCACGT
47225 CACGTGTACAAAAAAGTGACATGTGGCACGT
1 CACGTGTACAAAAAAGTGACATGTGGCACGT
* * *
47256 CACGTGTACAAAAAAGTGACACGTGGCATGC
1 CACGTGTACAAAAAAGTGACATGTGGCACGT
* * *
47287 CACATGTTTC-AAAAAGTGACACGTGGCA
1 CACGTG-TACAAAAAAGTGACATGTGGCA
47315 TGCCATGTGC
Statistics
Matches: 108, Mismatches: 11, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
30 1 0.01
31 104 0.96
32 3 0.03
ACGTcount: A:0.36, C:0.21, G:0.24, T:0.20
Consensus pattern (31 bp):
CACGTGTACAAAAAAGTGACATGTGGCACGT
Found at i:49249 original size:11 final size:11
Alignment explanation
Indices: 49225--49259 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
49215 TTGACAGGAC
49225 AACAAAAACAA
1 AACAAAAACAA
* *
49236 AACGAAAACGA
1 AACAAAAACAA
49247 AACAAAAACAA
1 AACAAAAACAA
49258 AA
1 AA
49260 AACAGAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.77, C:0.17, G:0.06, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:50561 original size:11 final size:11
Alignment explanation
Indices: 50545--50587 Score: 68
Period size: 11 Copynumber: 3.9 Consensus size: 11
50535 TATACTATAT
50545 CTAATTAATAG
1 CTAATTAATAG
*
50556 CTAATTAATAT
1 CTAATTAATAG
50567 CTAATTAATAG
1 CTAATTAATAG
*
50578 TTAATTAATA
1 CTAATTAATA
50588 ATGAATAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.42
Consensus pattern (11 bp):
CTAATTAATAG
Found at i:50566 original size:22 final size:22
Alignment explanation
Indices: 50541--50587 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
50531 CCATTATACT
50541 ATATCTAATTAATAGCTAATTA
1 ATATCTAATTAATAGCTAATTA
*
50563 ATATCTAATTAATAGTTAATTA
1 ATATCTAATTAATAGCTAATTA
50585 ATA
1 ATA
50588 ATGAATAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (22 bp):
ATATCTAATTAATAGCTAATTA
Found at i:67386 original size:32 final size:32
Alignment explanation
Indices: 67344--67407 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
67334 AAAAAAGTAA
* *
67344 TGTAAGACGTTATAAGCAGATCACATGGTTAG
1 TGTAAAACGTTATAAGCAGATCACATGATTAG
67376 TGTAAAACGTTATAAGCAGATCACATGATTAG
1 TGTAAAACGTTATAAGCAGATCACATGATTAG
67408 CAACTTACTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.38, C:0.12, G:0.22, T:0.28
Consensus pattern (32 bp):
TGTAAAACGTTATAAGCAGATCACATGATTAG
Done.