Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01004957.1 Corchorus capsularis cultivar CVL-1 contig04975, 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: 5538
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Found at i:111 original size:2 final size:2
Alignment explanation
Indices: 98--128 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
88 GTTAAAAATA
98 AT AT AT AGT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT
129 GACATTAGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:461 original size:2 final size:2
Alignment explanation
Indices: 454--478 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
444 AGGAGGCAAG
454 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
479 AGAGGGAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1837 original size:6 final size:6
Alignment explanation
Indices: 1826--1855 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
1816 GGATTTTAAA
1826 AAAATT AAAATT AAAAATT AAAATT AAAAT
1 AAAATT AAAATT -AAAATT AAAATT AAAAT
1856 AAATTATATC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (6 bp):
AAAATT
Found at i:1843 original size:13 final size:13
Alignment explanation
Indices: 1825--1854 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
1815 TGGATTTTAA
1825 AAAAATTAAAATT
1 AAAAATTAAAATT
1838 AAAAATTAAAATT
1 AAAAATTAAAATT
1851 AAAA
1 AAAA
1855 TAAATTATAT
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:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (13 bp):
AAAAATTAAAATT
Found at i:2106 original size:138 final size:130
Alignment explanation
Indices: 1866--2133 Score: 446
Period size: 138 Copynumber: 2.0 Consensus size: 130
1856 AAATTATATC
1866 TTCTTATATTCTTGAGAAGAACAAAATTTAAGGCAAACTCTTTTTTTTTTGCCAGAAAATTTCAT
1 TTCTTATATTCTTGAGAAGAACAAAATTTAAGGCAAACTCTTTTTTTTTTGCCAGAAAATTTCAT
*
1931 AGCTTTAGTAATTGAAATTCCAACTGAAAATACTACCAACTAATAGGCCAAGTTTAATCAAACAA
66 AGCTTTAGTAATTGAAATTCCAACTGAAAATACTACCAACTAACAGGCCAAGTTTAATCAAACAA
1996 TTCTTATATTCTTGAGAAGAACAAAATTTAAGGCAAACTCTTTTTCTTTTCTTTTTTTGCCAGAA
1 TTCTTATATTCTTGAGAAGAACAAAATTTAAGGCAAA--C----TC-TTT-TTTTTTTGCCAGAA
*
2061 AATTTCATGGCTTTAGTAATTGAAATTCCAACTGAAAATACTACCAACTAACAGGCCAAGTTTAA
58 AATTTCATAGCTTTAGTAATTGAAATTCCAACTGAAAATACTACCAACTAACAGGCCAAGTTTAA
2126 TCAAACAA
123 TCAAACAA
2134 CAAATTCACA
Statistics
Matches: 128, Mismatches: 2, Indels: 8
0.93 0.01 0.06
Matches are distributed among these distances:
130 37 0.29
132 1 0.01
136 2 0.02
137 3 0.02
138 85 0.66
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.35
Consensus pattern (130 bp):
TTCTTATATTCTTGAGAAGAACAAAATTTAAGGCAAACTCTTTTTTTTTTGCCAGAAAATTTCAT
AGCTTTAGTAATTGAAATTCCAACTGAAAATACTACCAACTAACAGGCCAAGTTTAATCAAACAA
Found at i:2943 original size:19 final size:19
Alignment explanation
Indices: 2919--2957 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
2909 TTCTGCCCAA
*
2919 CAACAGCAGCAACAGCAAC
1 CAACAGCAGCAACAACAAC
2938 CAACAGCAGCAACAACAAC
1 CAACAGCAGCAACAACAAC
2957 C
1 C
2958 CACGTCTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.49, C:0.38, G:0.13, T:0.00
Consensus pattern (19 bp):
CAACAGCAGCAACAACAAC
Found at i:3626 original size:28 final size:30
Alignment explanation
Indices: 3563--3638 Score: 111
Period size: 28 Copynumber: 2.6 Consensus size: 30
3553 GCTTAATACC
*
3563 CAAATTAGCCCCTTAACTATCCATTTTGGGA
1 CAAATTGGCCCCTTAACTAT-CATTTTGGGA
*
3594 CAAATTGGCCCCTTAACT-T-TTTTTGGGA
1 CAAATTGGCCCCTTAACTATCATTTTGGGA
3622 CAAATTGGCCCCTTAAC
1 CAAATTGGCCCCTTAAC
3639 CTTTAAAAAC
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
28 25 0.58
30 1 0.02
31 17 0.40
ACGTcount: A:0.26, C:0.26, G:0.14, T:0.33
Consensus pattern (30 bp):
CAAATTGGCCCCTTAACTATCATTTTGGGA
Found at i:4412 original size:31 final size:29
Alignment explanation
Indices: 4333--4390 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
4323 TCTCATTTTT
*
4333 AAAAGTTAAGGGGCCAATTTATCCTAAAA
1 AAAAGTTAAGGGGCCAATTTATCCCAAAA
4362 AAAAGTTAAGGGGCCAATTTATCCCAAAA
1 AAAAGTTAAGGGGCCAATTTATCCCAAAA
4391 TGGATAGTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.45, C:0.16, G:0.17, T:0.22
Consensus pattern (29 bp):
AAAAGTTAAGGGGCCAATTTATCCCAAAA
Done.