Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012585.1 Corchorus capsularis cultivar CVL-1 contig12606, 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: 44598
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Found at i:16228 original size:6 final size:6
Alignment explanation
Indices: 16217--16249 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
16207 ATTAATCTGC
*
16217 TTTAGA TTTAGA TTTAGG TTTAGA TTTAGA TTT
1 TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTT
16250 GCTTTGCTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.27, C:0.00, G:0.18, T:0.55
Consensus pattern (6 bp):
TTTAGA
Found at i:16605 original size:26 final size:27
Alignment explanation
Indices: 16564--16620 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
16554 AAAAAAAAAG
*
16564 TTTGCGTCGATAAAAAAAAATTTTGTT
1 TTTGCGTCGATAAAAAAAAATTTCGTT
*
16591 TTTGCGTTGATAAAAAAAAATTTCGTT
1 TTTGCGTCGATAAAAAAAAATTTCGTT
16618 TTT
1 TTT
16621 CCGATTTTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.35, C:0.07, G:0.14, T:0.44
Consensus pattern (27 bp):
TTTGCGTCGATAAAAAAAAATTTCGTT
Found at i:19671 original size:6 final size:6
Alignment explanation
Indices: 19660--19692 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
19650 ATTAATCTGC
*
19660 TTTAGA TTTAGA TTTAGG TTTAGA TTTAGA TTT
1 TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTT
19693 GCTTTGCTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.27, C:0.00, G:0.18, T:0.55
Consensus pattern (6 bp):
TTTAGA
Found at i:29823 original size:68 final size:68
Alignment explanation
Indices: 29714--29928 Score: 324
Period size: 68 Copynumber: 3.2 Consensus size: 68
29704 ATGATTCAAT
* * *
29714 GGAGACGATCGTCTTATTGAAATTTACGATTC-AAGAATCGTTTTAGGTTTATATAAAACGGTCT
1 GGAGACGAACATCTTATTGAAATTTACGATTCAAAG-ATCGTTTTAAGTTTATATAAAACGGTCT
*
29778 CGAC
65 CGAA
29782 GGAGACGAACATCTTATTGAAATTTACGATTCAAAGATCGTTTTAAGTTTATATAAAACGGTCTC
1 GGAGACGAACATCTTATTGAAATTTACGATTCAAAGATCGTTTTAAGTTTATATAAAACGGTCTC
29847 GAA
66 GAA
* * * *
29850 GGAGACGAACGTCTTATTGAAATTTACGATTCAAGGACCGTTTTAAGTTTATATAAAATGGTCTC
1 GGAGACGAACATCTTATTGAAATTTACGATTCAAAGATCGTTTTAAGTTTATATAAAACGGTCTC
*
29915 AAA
66 GAA
*
29918 GGAGATGAACA
1 GGAGACGAACA
29929 CATTAACGTT
Statistics
Matches: 135, Mismatches: 11, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
68 132 0.98
69 3 0.02
ACGTcount: A:0.35, C:0.13, G:0.20, T:0.32
Consensus pattern (68 bp):
GGAGACGAACATCTTATTGAAATTTACGATTCAAAGATCGTTTTAAGTTTATATAAAACGGTCTC
GAA
Found at i:37306 original size:2 final size:2
Alignment explanation
Indices: 37293--37334 Score: 50
Period size: 2 Copynumber: 20.5 Consensus size: 2
37283 TTGGAAGTTG
*
37293 AT AT AGT AT AT AT AT AT AT AT AT AT AA ACT -T AT AT AT AT AT A
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT A
37335 GAAAATAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
1 1 0.03
2 32 0.91
3 2 0.06
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (2 bp):
AT
Found at i:44305 original size:21 final size:21
Alignment explanation
Indices: 44279--44319 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
44269 AAAAAAATGG
44279 AAAAATAATGGTCTGCAAAGA
1 AAAAATAATGGTCTGCAAAGA
44300 AAAAATAATGGTCTGCAAAG
1 AAAAATAATGGTCTGCAAAG
44320 TTATCATGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.51, C:0.10, G:0.20, T:0.20
Consensus pattern (21 bp):
AAAAATAATGGTCTGCAAAGA
Found at i:44466 original size:92 final size:92
Alignment explanation
Indices: 44309--44550 Score: 421
Period size: 92 Copynumber: 2.6 Consensus size: 92
44299 AAAAAATAAT
* * *
44309 GGTCTGCAAAGTTATCATGAAGAATCTCTGTAGATATTGTCTCCAATAATGCAAAGCTGACTCAT
1 GGTCTGCAAAGTTATCATGAAGAATCTCTGCAGAAATTGTCTCCAATAATGCAAAACTGACTCAT
44374 TGGATGAAGAGAAAGCCAAATTATGAA
66 TGGATGAAGAGAAAGCCAAATTATGAA
44401 GGTCTGCAAAGTTATCATGAAGAATCTCTGCAGAAATTGTCTCCAATAATGCAAAACTGACTCAT
1 GGTCTGCAAAGTTATCATGAAGAATCTCTGCAGAAATTGTCTCCAATAATGCAAAACTGACTCAT
44466 TGGATGAAGAGAAAGCCAAATTATGAA
66 TGGATGAAGAGAAAGCCAAATTATGAA
*
44493 GGTCTGCAAAGTTATCATGAAGAAATCTACTACAGAAAATTGTCTCCAATAATGCAAA
1 GGTCTGCAAAGTTATCATGAAG-AATCT-CTGCAG-AAATTGTCTCCAATAATGCAAA
44551 TAGTATAAAG
Statistics
Matches: 143, Mismatches: 4, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
92 111 0.78
93 5 0.03
94 5 0.03
95 22 0.15
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.26
Consensus pattern (92 bp):
GGTCTGCAAAGTTATCATGAAGAATCTCTGCAGAAATTGTCTCCAATAATGCAAAACTGACTCAT
TGGATGAAGAGAAAGCCAAATTATGAA
Done.