Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007913.1 Corchorus capsularis cultivar CVL-1 contig07934, 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: 75454
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:973 original size:102 final size:103
Alignment explanation
Indices: 776--1043 Score: 398
Period size: 103 Copynumber: 2.6 Consensus size: 103
766 TGGATAAAAT
* * * * ** **
776 AATGGTCTGCAAAAGTTATCCCTATCATGGAGGAATCTCTACAAAAATTGTCTCCAA--TTATGT
1 AATGGTCTGC-AAAGTTATCCCAATTATGAAGGAATCTCTGCAAAAATTGTCTCCAAGGCAAAAT
*
839 CAATAATGCAAGGCAAACTCATTGGATGAAGATAAAGC-
65 CAATAATGCAAGGCAAACTCATTAGATGAAGATAAAGCA
*
877 AATGGTCTGCAAAGTTATCCCAATTATGAAGGAATCTCTGCAAAAATTGTCTTCAAGGCAAAATC
1 AATGGTCTGCAAAGTTATCCCAATTATGAAGGAATCTCTGCAAAAATTGTCTCCAAGGCAAAATC
942 AATAATGCAAGGCAAACTCATTAGATGAAGATAAAGCA
66 AATAATGCAAGGCAAACTCATTAGATGAAGATAAAGCA
* *
980 AATGGTCTTCAAAGTTATTCCAATTATGAAGGAATCTCTGCAAAAATTGTCTCCAAGGCAAAAT
1 AATGGTCTGCAAAGTTATCCCAATTATGAAGGAATCTCTGCAAAAATTGTCTCCAAGGCAAAAT
1044 TATGTCAATA
Statistics
Matches: 151, Mismatches: 13, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
100 41 0.27
101 10 0.07
102 39 0.26
103 61 0.40
ACGTcount: A:0.39, C:0.17, G:0.17, T:0.26
Consensus pattern (103 bp):
AATGGTCTGCAAAGTTATCCCAATTATGAAGGAATCTCTGCAAAAATTGTCTCCAAGGCAAAATC
AATAATGCAAGGCAAACTCATTAGATGAAGATAAAGCA
Found at i:1355 original size:2 final size:2
Alignment explanation
Indices: 1348--1374 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1338 GTCTGGTATC
1348 AT 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 AT A
1375 AAGCTATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:27420 original size:6 final size:6
Alignment explanation
Indices: 27409--27434 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
27399 AATTTGCCAA
27409 AAATTT AAATTT AAATTT AAATTT AA
1 AAATTT AAATTT AAATTT AAATTT AA
27435 GTCGTAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (6 bp):
AAATTT
Found at i:28648 original size:22 final size:22
Alignment explanation
Indices: 28623--28676 Score: 54
Period size: 27 Copynumber: 2.2 Consensus size: 22
28613 GCCCTTAGCC
28623 ACGGCAGAGCCGCCCCACTAGG
1 ACGGCAGAGCCGCCCCACTAGG
*
28645 ACGGCTTGGCGGAGCCGCCCCACTAGG
1 A---C--GGCAGAGCCGCCCCACTAGG
28672 ACGGC
1 ACGGC
28677 TTAGTCACGG
Statistics
Matches: 26, Mismatches: 1, Indels: 10
0.70 0.03 0.27
Matches are distributed among these distances:
22 4 0.15
24 1 0.04
25 1 0.04
27 20 0.77
ACGTcount: A:0.19, C:0.39, G:0.35, T:0.07
Consensus pattern (22 bp):
ACGGCAGAGCCGCCCCACTAGG
Found at i:28694 original size:33 final size:33
Alignment explanation
Indices: 28616--28709 Score: 119
Period size: 33 Copynumber: 3.0 Consensus size: 33
28606 CACTTTTGCC
* *
28616 CTTAGCCACGGCAGAGCCGCCCCACTAGGACGG
1 CTTAGTCACGGCGGAGCCGCCCCACTAGGACGG
28649 C-T--T---GGCGGAGCCGCCCCACTAGGACGG
1 CTTAGTCACGGCGGAGCCGCCCCACTAGGACGG
*
28676 CTTAGTCACGGCGGAGCCGCCCCACTAGGGCGG
1 CTTAGTCACGGCGGAGCCGCCCCACTAGGACGG
28709 C
1 C
28710 AAGGTTATTT
Statistics
Matches: 52, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
27 24 0.46
28 1 0.02
30 1 0.02
32 1 0.02
33 25 0.48
ACGTcount: A:0.17, C:0.38, G:0.34, T:0.11
Consensus pattern (33 bp):
CTTAGTCACGGCGGAGCCGCCCCACTAGGACGG
Found at i:31685 original size:2 final size:2
Alignment explanation
Indices: 31661--31736 Score: 53
Period size: 2 Copynumber: 42.0 Consensus size: 2
31651 TAATAAATAA
*
31661 AT AT AT -T AT AT -T A- AT -T AT TT 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 AT AT AT AT
* *
31699 -T AT AT AT GT AT AT -T AT AT TT A- AT -T AGT -T AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT
31737 TAGAAACCTG
Statistics
Matches: 58, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
1 9 0.16
2 48 0.83
3 1 0.02
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (2 bp):
AT
Found at i:32777 original size:2 final size:2
Alignment explanation
Indices: 32765--32796 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
32755 GGGACAAATA
*
32765 AT AT GT 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
32797 TTAACTAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:32922 original size:21 final size:22
Alignment explanation
Indices: 32896--32940 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
32886 AAGAAGGAGA
32896 TTGCTAAATACCGTCCCA-TTT
1 TTGCTAAATACCGTCCCACTTT
**
32917 TTGCTATTTACCGTCCCACTTT
1 TTGCTAAATACCGTCCCACTTT
32939 TT
1 TT
32941 ACACTTTTGC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.18, C:0.29, G:0.09, T:0.44
Consensus pattern (22 bp):
TTGCTAAATACCGTCCCACTTT
Found at i:33008 original size:33 final size:33
Alignment explanation
Indices: 32956--33019 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
32946 TTTGCCCTCA
*
32956 GCCACGGCGGAGCCTCCCCACTAGGACGGCTCT
1 GCCACGGCGGAGCCGCCCCACTAGGACGGCTCT
* *
32989 GCCACGGCGTAGCCGCCCCACTAGGGCGGCT
1 GCCACGGCGGAGCCGCCCCACTAGGACGGCT
33020 AGACTATTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.14, C:0.42, G:0.33, T:0.11
Consensus pattern (33 bp):
GCCACGGCGGAGCCGCCCCACTAGGACGGCTCT
Found at i:44226 original size:2 final size:2
Alignment explanation
Indices: 44219--44244 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
44209 AGACAAACTT
44219 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
44245 AATAGTTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:67302 original size:27 final size:27
Alignment explanation
Indices: 67248--67302 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
67238 TTCTCAATGT
**
67248 ATCTTCTTCTTCTGATTGTAATGTTGA
1 ATCTTCTTCTTCTGATTGTAATACTGA
*
67275 ATCTTCTT-TTCCTGTTTGTAATACTGA
1 ATCTTCTTCTT-CTGATTGTAATACTGA
67302 A
1 A
67303 CCTATTTGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 2 0.08
27 22 0.92
ACGTcount: A:0.20, C:0.16, G:0.13, T:0.51
Consensus pattern (27 bp):
ATCTTCTTCTTCTGATTGTAATACTGA
Found at i:70581 original size:23 final size:23
Alignment explanation
Indices: 70551--70619 Score: 120
Period size: 23 Copynumber: 3.0 Consensus size: 23
70541 CAAACAATCT
70551 TGAGCACTCTCGCTCGGTCTCTA
1 TGAGCACTCTCGCTCGGTCTCTA
*
70574 TGAGCACTCTCGCTCAGTCTCTA
1 TGAGCACTCTCGCTCGGTCTCTA
*
70597 TGAGCACTCTCGCTCGTTCTCTA
1 TGAGCACTCTCGCTCGGTCTCTA
70620 CAAATTAACA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.14, C:0.35, G:0.19, T:0.32
Consensus pattern (23 bp):
TGAGCACTCTCGCTCGGTCTCTA
Found at i:70973 original size:2 final size:2
Alignment explanation
Indices: 70966--70995 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
70956 CCTTAGCTTG
70966 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
70996 CACATAGTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:74173 original size:1 final size:1
Alignment explanation
Indices: 74167--74195 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
74157 ACTTAACTGG
74167 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
74196 ATCAAGACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Done.