Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010573.1 Corchorus capsularis cultivar CVL-1 contig10594, 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: 52918
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:10975 original size:21 final size:21
Alignment explanation
Indices: 10942--10988 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
10932 CGGCGAGGAC
*
10942 ACGGGTTTCGCCGCCGTGGTA
1 ACGGGTTTCGCCGCCGGGGTA
*
10963 ACGGAGTTT-GCCGTCGGGGTA
1 ACGG-GTTTCGCCGCCGGGGTA
10984 ACGGG
1 ACGGG
10989 GGAGGATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 1 0.04
21 18 0.78
22 4 0.17
ACGTcount: A:0.13, C:0.23, G:0.43, T:0.21
Consensus pattern (21 bp):
ACGGGTTTCGCCGCCGGGGTA
Found at i:11519 original size:2 final size:2
Alignment explanation
Indices: 11512--11549 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
11502 TGGTTTGTAG
*
11512 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
11550 CACCACTATT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:12467 original size:5 final size:5
Alignment explanation
Indices: 12457--12484 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
12447 ATATTAAGCC
12457 ATAAT ATAAT ATAAT ATAAT ATAAT ATA
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATA
12485 GTTGGTAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
ATAAT
Found at i:20732 original size:21 final size:21
Alignment explanation
Indices: 20706--20751 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
20696 TTTGTGGCAG
20706 TTTTTTCTAAAT-GAGTAGTTT
1 TTTTTTCTAAATAG-GTAGTTT
*
20727 TTTTTTTTAAATAGGTAGTTT
1 TTTTTTCTAAATAGGTAGTTT
20748 TTTT
1 TTTT
20752 AAATGATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 22 0.96
22 1 0.04
ACGTcount: A:0.22, C:0.02, G:0.13, T:0.63
Consensus pattern (21 bp):
TTTTTTCTAAATAGGTAGTTT
Found at i:24741 original size:28 final size:30
Alignment explanation
Indices: 24710--24774 Score: 105
Period size: 31 Copynumber: 2.2 Consensus size: 30
24700 TTTCTTTTTC
24710 TTTTTC-CTTCTTGTTCTTCTTTAAAGGTTT
1 TTTTTCTCTTCTTGTTCTTCTTTAAAGG-TT
*
24740 TTTTTCTTTTCTTGTTCTTCTTTAAAGGTT
1 TTTTTCTCTTCTTGTTCTTCTTTAAAGGTT
24770 TTTTT
1 TTTTT
24775 TAAGATTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
30 13 0.39
31 20 0.61
ACGTcount: A:0.09, C:0.14, G:0.09, T:0.68
Consensus pattern (30 bp):
TTTTTCTCTTCTTGTTCTTCTTTAAAGGTT
Found at i:24752 original size:31 final size:31
Alignment explanation
Indices: 24717--24775 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
24707 TTCTTTTTCC
24717 TTCTTGTTCTTCTTTAAAGGTTTTTTTTCTT
1 TTCTTGTTCTTCTTTAAAGGTTTTTTTTCTT
24748 TTCTTGTTCTTCTTTAAAGGTTTTTTTT
1 TTCTTGTTCTTCTTTAAAGGTTTTTTTT
24776 AAGATTTTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.10, C:0.12, G:0.10, T:0.68
Consensus pattern (31 bp):
TTCTTGTTCTTCTTTAAAGGTTTTTTTTCTT
Found at i:29371 original size:31 final size:31
Alignment explanation
Indices: 29328--29386 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
29318 AGTTTTTAGA
* *
29328 AACTTTTGAAATACCTATTGTACCCTTATTT
1 AACTTTTAAAATACCTATTATACCCTTATTT
*
29359 AACTTTTAAAATACCTATTATATCCTTA
1 AACTTTTAAAATACCTATTATACCCTTA
29387 CTTATCTAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.34, C:0.19, G:0.03, T:0.44
Consensus pattern (31 bp):
AACTTTTAAAATACCTATTATACCCTTATTT
Found at i:30259 original size:105 final size:110
Alignment explanation
Indices: 30137--30353 Score: 320
Period size: 111 Copynumber: 2.0 Consensus size: 110
30127 ATAATGTAAA
* *
30137 AATTAATTAACAATATCCTT-ATCAATTTTTTTGTTTT-TTATTT-CGAATAT-CTCAGCTTTAT
1 AATTAATTAACAATATCCTTAATCAATTTTTTTGTTTTCTTATTTCCGAATATCCT-AGCCTTAA
* * *
30198 AAT-T-TATAATGTAAAGTCGGATTATTTTGTTCAAGAATTAATAT
65 AATATATATAATGTAAAGTCAGATTATTTCGTTAAAGAATTAATAT
*
30242 AATTAATTAACAATATCCTTAAATCAATTTTTTTGTTTTCTTTTTTCCGAATATCCTAGCCTTAA
1 AATTAATTAACAATATCCTT-AATCAATTTTTTTGTTTTCTTATTTCCGAATATCCTAGCCTTAA
30307 AATATATATAATGTAAAGTCAGATTATTTCGTTAAAGAATTAATAT
65 AATATATATAATGTAAAGTCAGATTATTTCGTTAAAGAATTAATAT
30353 A
1 A
30354 TCCGATTAAT
Statistics
Matches: 99, Mismatches: 6, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
105 20 0.20
107 17 0.17
108 5 0.05
109 16 0.16
110 3 0.03
111 38 0.38
ACGTcount: A:0.35, C:0.11, G:0.08, T:0.46
Consensus pattern (110 bp):
AATTAATTAACAATATCCTTAATCAATTTTTTTGTTTTCTTATTTCCGAATATCCTAGCCTTAAA
ATATATATAATGTAAAGTCAGATTATTTCGTTAAAGAATTAATAT
Found at i:44940 original size:6 final size:6
Alignment explanation
Indices: 44929--44965 Score: 65
Period size: 6 Copynumber: 6.2 Consensus size: 6
44919 CTTTGAAATC
*
44929 CTTCAT CTTCAT CTTCAT CTTCAT CTCCAT CTTCAT C
1 CTTCAT CTTCAT CTTCAT CTTCAT CTTCAT CTTCAT C
44966 CTCAGAGGCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.16, C:0.38, G:0.00, T:0.46
Consensus pattern (6 bp):
CTTCAT
Found at i:48327 original size:85 final size:85
Alignment explanation
Indices: 48184--48353 Score: 286
Period size: 85 Copynumber: 2.0 Consensus size: 85
48174 TGATGTCAAG
* *
48184 GACATACAGATAACATAGACCACCATATTATCAATGAAGAAACTAAAAACTAATGAAAGGAATGA
1 GACATACAGAGAACATAGACCACCATAATATCAATGAAGAAACTAAAAACTAATGAAAGGAATGA
*
48249 CTCTGATCAAGGGAACCAAC
66 CTCTGATCAAGGAAACCAAC
* * *
48269 GACATATAGAGAACATAGACCACCATAATATCGATGAAGAAACTAAAAAGTAATGAAAGGAATGA
1 GACATACAGAGAACATAGACCACCATAATATCAATGAAGAAACTAAAAACTAATGAAAGGAATGA
48334 CTCTGATCAAGGAAACCAAC
66 CTCTGATCAAGGAAACCAAC
48354 TTTGAAGAAG
Statistics
Matches: 79, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
85 79 1.00
ACGTcount: A:0.49, C:0.18, G:0.16, T:0.17
Consensus pattern (85 bp):
GACATACAGAGAACATAGACCACCATAATATCAATGAAGAAACTAAAAACTAATGAAAGGAATGA
CTCTGATCAAGGAAACCAAC
Found at i:50697 original size:1 final size:1
Alignment explanation
Indices: 50693--50728 Score: 72
Period size: 1 Copynumber: 36.0 Consensus size: 1
50683 AATGTAACGC
50693 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
50729 CCTTATAAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Done.