Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011689.1 Corchorus capsularis cultivar CVL-1 contig11710, 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: 28473
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:1081 original size:6 final size:6
Alignment explanation
Indices: 1064--1107 Score: 81
Period size: 6 Copynumber: 7.5 Consensus size: 6
1054 GTACTTTTAT
1064 ATATAG -TATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATA
1 ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATA
1108 GATAGATAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
5 5 0.14
6 32 0.86
ACGTcount: A:0.50, C:0.00, G:0.16, T:0.34
Consensus pattern (6 bp):
ATATAG
Found at i:1116 original size:18 final size:17
Alignment explanation
Indices: 1064--1119 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 17
1054 GTACTTTTAT
1064 ATATAGTATAGAT-ATAG
1 ATATAG-ATAGATAATAG
1081 ATATAGATATAGAT-ATAG
1 ATATAG--ATAGATAATAG
1099 ATATAGATAGATAGATAG
1 ATATAGATAGATA-ATAG
1117 ATA
1 ATA
1120 GATAATATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.17
17 6 0.17
18 24 0.67
ACGTcount: A:0.50, C:0.00, G:0.18, T:0.32
Consensus pattern (17 bp):
ATATAGATAGATAATAG
Found at i:1965 original size:2 final size:2
Alignment explanation
Indices: 1958--1987 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1948 ATTTACATAC
1958 AT AT 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
1988 GAGTGTGAGA
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):
AT
Found at i:7394 original size:32 final size:31
Alignment explanation
Indices: 7358--7417 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 31
7348 CAAAATAGGT
7358 CCGAACTCGA-ATCAACCTGACCCAAATTTAAC
1 CCGAAC-CGATATCAACCTGA-CCAAATTTAAC
* *
7390 CCGAACCGATTTCAATCTGACCAAATTT
1 CCGAACCGATATCAACCTGACCAAATTT
7418 GACCTGACTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
31 11 0.44
32 14 0.56
ACGTcount: A:0.35, C:0.32, G:0.10, T:0.23
Consensus pattern (31 bp):
CCGAACCGATATCAACCTGACCAAATTTAAC
Found at i:14114 original size:99 final size:100
Alignment explanation
Indices: 13933--14118 Score: 284
Period size: 99 Copynumber: 1.9 Consensus size: 100
13923 TTATGGACAT
*
13933 TTTTGACAAGTTAATCAATTGAGGGTGGACATCTAGGACCAAATAAGGGTAGACACCATGTAAAA
1 TTTTGACAAGTTAATCAATTGAGGGTGGACATCTAGAACCAAATAAGGGTAGACACCATGTAAAA
* * *
13998 TTACATACCAAATATTAAGAAATAAGAAATGGGCA
66 TTACACACAAAAAATTAAGAAATAAGAAATGGGCA
* * * * *
14033 TTTTGACGAGTTAATCCATTGAGGGTGGGCATCTA-AACCAAATCAGGGTAGGCACCATGTAAAA
1 TTTTGACAAGTTAATCAATTGAGGGTGGACATCTAGAACCAAATAAGGGTAGACACCATGTAAAA
14097 TTACACACAAAAAATTAAGAAA
66 TTACACACAAAAAATTAAGAAA
14119 ATTGAAGGTT
Statistics
Matches: 77, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
99 45 0.58
100 32 0.42
ACGTcount: A:0.42, C:0.15, G:0.20, T:0.24
Consensus pattern (100 bp):
TTTTGACAAGTTAATCAATTGAGGGTGGACATCTAGAACCAAATAAGGGTAGACACCATGTAAAA
TTACACACAAAAAATTAAGAAATAAGAAATGGGCA
Found at i:16433 original size:35 final size:35
Alignment explanation
Indices: 16380--16458 Score: 108
Period size: 35 Copynumber: 2.3 Consensus size: 35
16370 TTTTGAAATG
*
16380 CCTCTA-TTTTTTCTTTAAAA-TAGGTTTCGGAAAC
1 CCTCTATTTTTTTCCTTAAAATTAGGTTTC-GAAAC
* *
16414 CCTCTTTTTTTTTCCTTAAAATTAGGTTTCGAAAT
1 CCTCTATTTTTTTCCTTAAAATTAGGTTTCGAAAC
16449 CCTCTATTTT
1 CCTCTATTTT
16459 GGTTCAAATT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
34 5 0.13
35 26 0.67
36 8 0.21
ACGTcount: A:0.23, C:0.19, G:0.09, T:0.49
Consensus pattern (35 bp):
CCTCTATTTTTTTCCTTAAAATTAGGTTTCGAAAC
Found at i:19575 original size:6 final size:6
Alignment explanation
Indices: 19557--19590 Score: 59
Period size: 6 Copynumber: 5.5 Consensus size: 6
19547 ATTAATTTGC
19557 TTTAGA TTTTAGA TTTAGA TTTAGA TTTAGA TTT
1 TTTAGA -TTTAGA TTTAGA TTTAGA TTTAGA TTT
19591 GCTTTGCTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 21 0.78
7 6 0.22
ACGTcount: A:0.29, C:0.00, G:0.15, T:0.56
Consensus pattern (6 bp):
TTTAGA
Found at i:21344 original size:18 final size:19
Alignment explanation
Indices: 21307--21344 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
21297 GTCCATCACG
* *
21307 ATCTTCATGGTCTCCTTGT
1 ATCTTCATGGCCTCCATGT
21326 ATCTTCAT-GCCTCCATGT
1 ATCTTCATGGCCTCCATGT
21344 A
1 A
21345 GCCCATGCAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.16, C:0.29, G:0.13, T:0.42
Consensus pattern (19 bp):
ATCTTCATGGCCTCCATGT
Found at i:23120 original size:33 final size:32
Alignment explanation
Indices: 23083--23189 Score: 142
Period size: 33 Copynumber: 3.2 Consensus size: 32
23073 CGCCAAGCGA
* *
23083 TGGCCGGTTGTGGCCGGACATGTCCATGTCGCG
1 TGGCCGG-TGTGGCCGGGCATCTCCATGTCGCG
*
23116 TGGCCGGTGATGGCCGGGCATCTCCATGTCGCA
1 TGGCCGGTG-TGGCCGGGCATCTCCATGTCGCG
* *
23149 TGGCCGGTGTTGCGCGGGCATCTCCAAGTCGCG
1 TGGCCGGTGTGGC-CGGGCATCTCCATGTCGCG
23182 TGGCCGGT
1 TGGCCGGT
23190 TCTCCAAGTC
Statistics
Matches: 66, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
32 5 0.08
33 61 0.92
ACGTcount: A:0.09, C:0.29, G:0.39, T:0.22
Consensus pattern (32 bp):
TGGCCGGTGTGGCCGGGCATCTCCATGTCGCG
Found at i:23195 original size:21 final size:21
Alignment explanation
Indices: 23169--23210 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
23159 TGCGCGGGCA
*
23169 TCTCCAAGTCGCGTGGCCGGT
1 TCTCCAAGTCGCATGGCCGGT
23190 TCTCCAAGTCGCATGGCCGGT
1 TCTCCAAGTCGCATGGCCGGT
23211 CACTTGTGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.12, C:0.33, G:0.31, T:0.24
Consensus pattern (21 bp):
TCTCCAAGTCGCATGGCCGGT
Done.