Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009370.1 Corchorus capsularis cultivar CVL-1 contig09391, 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: 10204
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:362 original size:7 final size:7
Alignment explanation
Indices: 350--383 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
340 TTATATTTGT
350 TTAATTA
1 TTAATTA
357 TTAATTA
1 TTAATTA
* *
364 TTACTAA
1 TTAATTA
371 TTAATTA
1 TTAATTA
378 TTAATT
1 TTAATT
384 TAAATTTTGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (7 bp):
TTAATTA
Found at i:1302 original size:9 final size:9
Alignment explanation
Indices: 1258--1301 Score: 61
Period size: 9 Copynumber: 4.9 Consensus size: 9
1248 TTACAAATAC
1258 AAATGTTAT
1 AAATGTTAT
*
1267 ACATGTTAT
1 AAATGTTAT
*
1276 AAATGTTCT
1 AAATGTTAT
*
1285 AAATGTTAA
1 AAATGTTAT
1294 AAATGTTA
1 AAATGTTA
1302 ACAGTAATAG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 30 1.00
ACGTcount: A:0.43, C:0.05, G:0.11, T:0.41
Consensus pattern (9 bp):
AAATGTTAT
Found at i:1983 original size:36 final size:37
Alignment explanation
Indices: 1917--1987 Score: 92
Period size: 36 Copynumber: 1.9 Consensus size: 37
1907 GCTCCCTCAC
* *
1917 AGCTGCTCTCTCCCTCAGAATTCGAGCCTCTCTCTGA
1 AGCTGCTCTCTCCCTCAGAACTCGAACCTCTCTCTGA
*
1954 AGCT-CTCTCTCCCTCTGAAGCTC-AACCTCTCTCT
1 AGCTGCTCTCTCCCTCAGAA-CTCGAACCTCTCTCT
1988 CCCTGCGGGC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
36 24 0.80
37 6 0.20
ACGTcount: A:0.15, C:0.41, G:0.13, T:0.31
Consensus pattern (37 bp):
AGCTGCTCTCTCCCTCAGAACTCGAACCTCTCTCTGA
Found at i:1987 original size:18 final size:17
Alignment explanation
Indices: 1943--1987 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
1933 AGAATTCGAG
*
1943 CCTCTCTCTGAAGCTCT
1 CCTCTCTCTGAAGCTCA
*
1960 CTCTCCCTCTGAAGCTCAA
1 C-CTCTCTCTGAAGCTC-A
1979 CCTCTCTCT
1 CCTCTCTCT
1988 CCCTGCGGGC
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
17 1 0.04
18 21 0.91
19 1 0.04
ACGTcount: A:0.13, C:0.44, G:0.09, T:0.33
Consensus pattern (17 bp):
CCTCTCTCTGAAGCTCA
Found at i:2143 original size:18 final size:18
Alignment explanation
Indices: 2120--2169 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
2110 ATTAATCGTA
2120 AATAAACTAATTAAAACT
1 AATAAACTAATTAAAACT
* ***
2138 AATAAAATAATTATCCCT
1 AATAAACTAATTAAAACT
*
2156 AATAAACTATTTAA
1 AATAAACTAATTAA
2170 CAATAATTAA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (18 bp):
AATAAACTAATTAAAACT
Found at i:2302 original size:21 final size:20
Alignment explanation
Indices: 2278--2338 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 20
2268 TAATTAATCT
*
2278 AAATTCAAATTAAGAATTTCA
1 AAATTCAAATTAATAATTT-A
*
2299 AAATTTAAATTAATAATAATTA
1 AAATTCAAATTAATAAT--TTA
2321 AAATTC-AATTAATAATTT
1 AAATTCAAATTAATAATTT
2339 TTTTTTAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
19 2 0.06
21 25 0.71
22 6 0.17
23 2 0.06
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.39
Consensus pattern (20 bp):
AAATTCAAATTAATAATTTA
Found at i:3918 original size:78 final size:78
Alignment explanation
Indices: 3802--3952 Score: 200
Period size: 78 Copynumber: 1.9 Consensus size: 78
3792 GTTTGCCTCA
*
3802 ATAATTCGATACTTAAATTAAAAAATTCATTAAAAAATCATTTTTAGCTT-AAATTTGAATTCGA
1 ATAATTCGATACTT-AATTAAAAAATT-ATTAAAAAATCATTTTTAG-TTCAAATTTGAACTCGA
*
3866 GCTCGAGCTCGGTTCG
63 ACTCGAGCTCGGTTCG
*
3882 ATAATTCGATACTT-GTTAAAAAATT-TGTAAACAAATCATTTTTAGTTCAAATTTGAACTCGAA
1 ATAATTCGATACTTAATTAAAAAATTAT-TAAA-AAATCATTTTTAGTTCAAATTTGAACTCGAA
*
3945 CTTGAGCT
64 CTCGAGCT
3953 TGAGCTCAAA
Statistics
Matches: 64, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
76 1 0.02
77 6 0.09
78 43 0.67
80 14 0.22
ACGTcount: A:0.38, C:0.13, G:0.12, T:0.37
Consensus pattern (78 bp):
ATAATTCGATACTTAATTAAAAAATTATTAAAAAATCATTTTTAGTTCAAATTTGAACTCGAACT
CGAGCTCGGTTCG
Found at i:4072 original size:74 final size:74
Alignment explanation
Indices: 3983--4145 Score: 290
Period size: 74 Copynumber: 2.2 Consensus size: 74
3973 AGTTTGAGAG
3983 CTCGAGCTTGAGCTCAACAAGTATATATAGGTATACCGAGTAGCTCGACGAGTATCGAATCAAGC
1 CTCGAGCTTGAGCTCAACAAGTATATATAGGTATACCGAGTAGCTCGACGAGTATCGAATCAAGC
4048 ATCCCTGAA
66 ATCCCTGAA
* * *
4057 CTTGAGCTTGAGCTCAATAGGTATATATAGGTATACCGAGTAGCTCGACGAGTATCGAATCAAGC
1 CTCGAGCTTGAGCTCAACAAGTATATATAGGTATACCGAGTAGCTCGACGAGTATCGAATCAAGC
4122 ATCCCTGAA
66 ATCCCTGAA
*
4131 CTCGAGCTCGAGCTC
1 CTCGAGCTTGAGCTC
4146 GGCTCAACAT
Statistics
Matches: 84, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
74 84 1.00
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.24
Consensus pattern (74 bp):
CTCGAGCTTGAGCTCAACAAGTATATATAGGTATACCGAGTAGCTCGACGAGTATCGAATCAAGC
ATCCCTGAA
Found at i:9888 original size:2 final size:2
Alignment explanation
Indices: 9881--9905 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
9871 GCAGTCTTGT
9881 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
9906 ATCTTCTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:9915 original size:3 final size:3
Alignment explanation
Indices: 9907--9931 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
9897 TCTCTCTCTA
9907 TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT T
9932 TTTTTTTTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Done.