Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01004931.1 Corchorus capsularis cultivar CVL-1 contig04949, 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: 5086
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Found at i:556 original size:109 final size:109
Alignment explanation
Indices: 400--694 Score: 423
Period size: 109 Copynumber: 2.7 Consensus size: 109
390 TAAATTAAAA
**
400 TGGTAAAAATAAAAAAAATATATAAA-ATATT-GAATTTAATTAAATGAAAATAGAGTTTTTAGT
1 TGGTAAAAAT-AAAGTAAT-TATAAAGATATTAG-ATTTAATTAAATGAAAATAGAGTTTTTAGT
*
463 AGAATAAAATTGTATATTAGAAAAAATTTTAATATATCCAAATTTTT
63 AGAATAAAATTGTATATTAGAAAAAATTTTAATATATCCAAATTTTG
*
510 TGGTAAAAATAAAGTAATTATAAAGATATTAGATTCAATTAAATGAAAATAGAGTTTTTAGTAGA
1 TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGA
*
575 ATAAAATTGTATATTAGAAAAAATTTTAGTATATCCAAATTTTG
66 ATAAAATTGTATATTAGAAAAAATTTTAATATATCCAAATTTTG
* * *
619 TGGTAAAAGTAAAGTAATTATAAAGATATTAGATTTAATTTAATTGAATAAAAATAGAGTTTCTA
1 TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAA-TT-A---AATGAAAATAGAGTTTTTA
*
684 GTAAAATAAAA
61 GTAGAATAAAA
695 CTATAATAGT
Statistics
Matches: 168, Mismatches: 10, Indels: 10
0.89 0.05 0.05
Matches are distributed among these distances:
108 6 0.04
109 121 0.72
110 13 0.08
111 1 0.01
114 27 0.16
ACGTcount: A:0.50, C:0.02, G:0.12, T:0.36
Consensus pattern (109 bp):
TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGA
ATAAAATTGTATATTAGAAAAAATTTTAATATATCCAAATTTTG
Found at i:2110 original size:74 final size:74
Alignment explanation
Indices: 2016--2172 Score: 255
Period size: 74 Copynumber: 2.1 Consensus size: 74
2006 AAACAATTAA
* * *
2016 GAAATGTGTAATTACGAAAAAGGGTAGAAGGAAAAGGAAT-GGGAGAAAGTCATAGAGGGGCTTT
1 GAAAAGTGTAATTACAAAAAAGGGTAGAAGGAAAAGGAATAGGG-GAAACTCATAGAGGGGCTTT
2080 TTAGTCATCC-
65 TTAGTCA-CCT
2090 GAAAAGTGTAATTACAAAAAAGGGTAGAAGGAAAAGGAATAGGGGAAACTCATAGAGGGGCTTTT
1 GAAAAGTGTAATTACAAAAAAGGGTAGAAGGAAAAGGAATAGGGGAAACTCATAGAGGGGCTTTT
2155 TAGTCACCT
66 TAGTCACCT
2164 GAAAAGTGT
1 GAAAAGTGT
2173 GAAAAGACCA
Statistics
Matches: 78, Mismatches: 3, Indels: 4
0.92 0.04 0.05
Matches are distributed among these distances:
73 2 0.03
74 73 0.94
75 3 0.04
ACGTcount: A:0.41, C:0.08, G:0.30, T:0.21
Consensus pattern (74 bp):
GAAAAGTGTAATTACAAAAAAGGGTAGAAGGAAAAGGAATAGGGGAAACTCATAGAGGGGCTTTT
TAGTCACCT
Found at i:3567 original size:31 final size:30
Alignment explanation
Indices: 3531--3597 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
3521 TACCCCAAAA
3531 AATCCCCCATGTTTTGCTTTTGGGACAAAATT
1 AATCCCCCATGTTTT-CTTTTGGGAC-AAATT
** *
3563 -ATCCCTTATGTTTTTTTTTGGGACAAATT
1 AATCCCCCATGTTTTCTTTTGGGACAAATT
3592 AATCCC
1 AATCCC
3598 TTACGTTTCA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
29 5 0.16
30 14 0.45
31 12 0.39
ACGTcount: A:0.24, C:0.21, G:0.13, T:0.42
Consensus pattern (30 bp):
AATCCCCCATGTTTTCTTTTGGGACAAATT
Found at i:3591 original size:29 final size:32
Alignment explanation
Indices: 3539--3605 Score: 95
Period size: 30 Copynumber: 2.2 Consensus size: 32
3529 AAAATCCCCC
3539 ATGTTTTGCTTTTGGGACAAAATT-ATCCCTT
1 ATGTTTTGCTTTTGGGACAAAATTAATCCCTT
*
3570 ATGTTTT-TTTTTGGGAC-AAATTAATCCCTT
1 ATGTTTTGCTTTTGGGACAAAATTAATCCCTT
*
3600 ACGTTT
1 ATGTTT
3606 CAAAAATGAG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
29 5 0.15
30 21 0.64
31 7 0.21
ACGTcount: A:0.22, C:0.15, G:0.15, T:0.48
Consensus pattern (32 bp):
ATGTTTTGCTTTTGGGACAAAATTAATCCCTT
Found at i:3806 original size:31 final size:29
Alignment explanation
Indices: 3749--3852 Score: 140
Period size: 28 Copynumber: 3.6 Consensus size: 29
3739 AAGGGGCTAA
3749 TTTG-CCCAAAAAAAACATAAGGGATTTT
1 TTTGTCCCAAAAAAAACATAAGGGATTTT
*
3777 TTTGTCCCAAAAGAAATACATAAGAGATTTT
1 TTTGTCCCAAAA-AAA-ACATAAGGGATTTT
*
3808 TTTGTCCC-AAAAAAACATAAGGGATTAT
1 TTTGTCCCAAAAAAAACATAAGGGATTTT
*
3836 TTTATCCCAAAAGAAAA
1 TTTGTCCCAAAA-AAAA
3853 ACTATAATTT
Statistics
Matches: 67, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
28 23 0.34
29 13 0.19
30 10 0.15
31 21 0.31
ACGTcount: A:0.44, C:0.14, G:0.12, T:0.29
Consensus pattern (29 bp):
TTTGTCCCAAAAAAAACATAAGGGATTTT
Found at i:3853 original size:31 final size:31
Alignment explanation
Indices: 3759--3859 Score: 136
Period size: 31 Copynumber: 3.3 Consensus size: 31
3749 TTTGCCCAAA
3759 AAAAACATAAGGGATTTTTTTGTCCCAAAAG
1 AAAAACATAAGGGATTTTTTTGTCCCAAAAG
* *
3790 AAATACATAAGAGATTTTTTTGTCCC--AA-
1 AAAAACATAAGGGATTTTTTTGTCCCAAAAG
* *
3818 AAAAACATAAGGGATTATTTTATCCCAAAAG
1 AAAAACATAAGGGATTTTTTTGTCCCAAAAG
3849 AAAAACTATAA
1 AAAAAC-ATAA
3860 TTTAATTTTT
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
28 22 0.37
29 2 0.03
30 2 0.03
31 30 0.50
32 4 0.07
ACGTcount: A:0.47, C:0.13, G:0.12, T:0.29
Consensus pattern (31 bp):
AAAAACATAAGGGATTTTTTTGTCCCAAAAG
Done.