Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017217.1 Corchorus olitorius cultivar O-4 contig17250, 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: 19329
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.31
Found at i:1557 original size:22 final size:23
Alignment explanation
Indices: 1514--1557 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
1504 CAATTTGTAT
* * *
1514 GATTTAATTGAATTAAATTTAGG
1 GATTAAATTGAATGAAAGTTAGG
1537 GATTAAATTGAA-GAAAGTTAG
1 GATTAAATTGAATGAAAGTTAG
1558 AAAATTTACC
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.43, C:0.00, G:0.20, T:0.36
Consensus pattern (23 bp):
GATTAAATTGAATGAAAGTTAGG
Found at i:3484 original size:56 final size:55
Alignment explanation
Indices: 3351--3473 Score: 203
Period size: 56 Copynumber: 2.2 Consensus size: 55
3341 GCTAATTTAC
3351 CAATGATAGCATGCAAGAAATGTAAATATGCAAATTACAATTTTGTTTTTTCCAAATG
1 CAAT-ATAG-ATGCAAGAAATGTAAATATGCAAATTACAATTTTGTTTTTT-CAAATG
*
3409 CAATATAGTTGCAAGAAATGTAAATATGCAAATTACAATTTTGTTTTTT-AAATG
1 CAATATAGATGCAAGAAATGTAAATATGCAAATTACAATTTTGTTTTTTCAAATG
3463 CAATATAGATG
1 CAATATAGATG
3474 ATTAAGAAAT
Statistics
Matches: 63, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
54 15 0.24
56 40 0.63
57 4 0.06
58 4 0.06
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.36
Consensus pattern (55 bp):
CAATATAGATGCAAGAAATGTAAATATGCAAATTACAATTTTGTTTTTTCAAATG
Found at i:8166 original size:29 final size:30
Alignment explanation
Indices: 8119--8178 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
8109 GAAGTTCATG
* *
8119 TTTGAAGACTCATTGAAGACTTATTTGAAGA
1 TTTGAAGAC-CATTGAAGAATTATTTCAAGA
8150 TTTGAAGA-CATTGAAGAATTATTTCAAGA
1 TTTGAAGACCATTGAAGAATTATTTCAAGA
8179 GGAAAGAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 19 0.70
31 8 0.30
ACGTcount: A:0.38, C:0.08, G:0.18, T:0.35
Consensus pattern (30 bp):
TTTGAAGACCATTGAAGAATTATTTCAAGA
Found at i:9590 original size:15 final size:16
Alignment explanation
Indices: 9557--9596 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
9547 TTACTTTGTT
9557 TTGTTTTCTAGTATAA
1 TTGTTTTCTAGTATAA
*
9573 TTGTTTTCT-GTTTAA
1 TTGTTTTCTAGTATAA
*
9588 TTGCTTTCT
1 TTGTTTTCT
9597 TTCAACCTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.15, C:0.10, G:0.12, T:0.62
Consensus pattern (16 bp):
TTGTTTTCTAGTATAA
Found at i:12895 original size:21 final size:21
Alignment explanation
Indices: 12871--12913 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
12861 CCGAGCTGCG
*
12871 CCGAGACACCTGCCCGGCCAC
1 CCGAGACACCTACCCGGCCAC
* *
12892 CCGAGCCATCTACCCGGCCAC
1 CCGAGACACCTACCCGGCCAC
12913 C
1 C
12914 AGCGCTACCC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.19, C:0.53, G:0.21, T:0.07
Consensus pattern (21 bp):
CCGAGACACCTACCCGGCCAC
Found at i:13281 original size:21 final size:21
Alignment explanation
Indices: 13255--13309 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
13245 CGGCCATACA
*
13255 CCGTGCCACCACCGGTTAAGC
1 CCGTGCCACCACCGGCTAAGC
* * *
13276 CCGTGCTACTACCGGCTATGC
1 CCGTGCCACCACCGGCTAAGC
*
13297 CCGTGCCATCACC
1 CCGTGCCACCACC
13310 ATTCCAAGCC
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.16, C:0.44, G:0.22, T:0.18
Consensus pattern (21 bp):
CCGTGCCACCACCGGCTAAGC
Found at i:15194 original size:29 final size:30
Alignment explanation
Indices: 15147--15206 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
15137 GAAGTTCGTG
* *
15147 TTTGAAGACTCATTGAAGACTTATTTGAAGA
1 TTTGAAGAC-CATTGAAGAATTATTTCAAGA
15178 TTTGAAGA-CATTGAAGAATTATTTCAAGA
1 TTTGAAGACCATTGAAGAATTATTTCAAGA
15207 GGAAAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 19 0.70
31 8 0.30
ACGTcount: A:0.38, C:0.08, G:0.18, T:0.35
Consensus pattern (30 bp):
TTTGAAGACCATTGAAGAATTATTTCAAGA
Found at i:18016 original size:19 final size:18
Alignment explanation
Indices: 17983--18018 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
17973 TTGAAATTAT
*
17983 TCTTCAATGGTCTTCAAA
1 TCTTCAATAGTCTTCAAA
18001 TCTTCAAATAGTCTTCAA
1 TCTTC-AATAGTCTTCAA
18019 TAAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.31, C:0.22, G:0.08, T:0.39
Consensus pattern (18 bp):
TCTTCAATAGTCTTCAAA
Done.