Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014546.1 Corchorus olitorius cultivar O-4 contig14579, 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: 22075
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Found at i:546 original size:47 final size:46
Alignment explanation
Indices: 477--580 Score: 172
Period size: 47 Copynumber: 2.2 Consensus size: 46
467 CCGATCAGAG
* * *
477 TCTAACTTAGAGTCCAAGTTAGATTAAAATTCATCCTAGAGTAGAA
1 TCTAAGTTAAAGTCCAAGTTAGATTAAAACTCATCCTAGAGTAGAA
523 TTCTAAGTTAAAGTCCAAGTTAGATTAAAACTCATCCTAGAGTAGAA
1 -TCTAAGTTAAAGTCCAAGTTAGATTAAAACTCATCCTAGAGTAGAA
570 TCTAAGTTAAA
1 TCTAAGTTAAA
581 ATAGGATCCT
Statistics
Matches: 54, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
46 11 0.20
47 43 0.80
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.31
Consensus pattern (46 bp):
TCTAAGTTAAAGTCCAAGTTAGATTAAAACTCATCCTAGAGTAGAA
Found at i:8683 original size:31 final size:30
Alignment explanation
Indices: 8613--8684 Score: 72
Period size: 31 Copynumber: 2.3 Consensus size: 30
8603 CAAAAAATGC
** *
8613 AATCTAGGATATAACGTTACGACTTGTGTCA
1 AATC-AGGATATAACGTTACGACACGGGTCA
* * *
8644 ATTTAGGATATAACGTTATCGAGACGGGTCA
1 AATCAGGATATAACGTTA-CGACACGGGTCA
8675 AATCAGGATA
1 AATCAGGATA
8685 AAATCAGACG
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
30 14 0.44
31 18 0.56
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (30 bp):
AATCAGGATATAACGTTACGACACGGGTCA
Found at i:10014 original size:36 final size:36
Alignment explanation
Indices: 9967--10040 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
9957 AATATCCTAT
9967 AGTTTGGAAAGCCATTTTTGCTAAGTTGAGAATTCC
1 AGTTTGGAAAGCCATTTTTGCTAAGTTGAGAATTCC
10003 AGTTTGGAAAGCCATTTTTGCTAAGTTGAGAATTCC
1 AGTTTGGAAAGCCATTTTTGCTAAGTTGAGAATTCC
10039 AG
1 AG
10041 CACAGTGGCT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.28, C:0.14, G:0.23, T:0.35
Consensus pattern (36 bp):
AGTTTGGAAAGCCATTTTTGCTAAGTTGAGAATTCC
Found at i:10347 original size:30 final size:31
Alignment explanation
Indices: 10288--10354 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
10278 AGGGTAATTT
*
10288 TATCCTAAATTGATACAACCCGATAACGTTA
1 TATCCTAAATTGACACAACCCGATAACGTTA
**
10319 TATCCTAAATTGACACAAGTCG-TAACGTTA
1 TATCCTAAATTGACACAACCCGATAACGTTA
10349 TATCCT
1 TATCCT
10355 GGATTGCATT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
30 14 0.42
31 19 0.58
ACGTcount: A:0.36, C:0.22, G:0.10, T:0.31
Consensus pattern (31 bp):
TATCCTAAATTGACACAACCCGATAACGTTA
Found at i:12842 original size:67 final size:67
Alignment explanation
Indices: 12694--13194 Score: 754
Period size: 67 Copynumber: 7.5 Consensus size: 67
12684 GCTCAAGAAT
* * * * * * *
12694 GACAGAATTGACCCTTCGACCGAAAGGGTATTCTTTGGAAA-G-AGAGACTAGACTTGAATGCAA
1 GACAAAATCGACCCTTTGACCGAAAGGGTATT-TTTGGAAATGAAAATACTAAACTTGGATGCAA
12757 AAA
65 AAA
** * *
12760 GATGAAACCGACCCTTTGACCGAAAGGGTATTTTTGGAAATGAAAATACTAAACTTGGATGAAAA
1 GACAAAATCGACCCTTTGACCGAAAGGGTATTTTTGGAAATGAAAATACTAAACTTGGATGCAAA
12825 AA
66 AA
*
12827 GACAAAATCGACCCTTTGACCGAAAGGGTATTTCTGGAAATGAAAATACTAAACTTGGATGCAAA
1 GACAAAATCGACCCTTTGACCGAAAGGGTATTTTTGGAAATGAAAATACTAAACTTGGATGCAAA
12892 AA
66 AA
* ***
12894 GACAAAATCGACCCTTTGATCGAAAGGGTATTTCAAGAAATGAAAATACTAAACTTGGATGCAAA
1 GACAAAATCGACCCTTTGACCGAAAGGGTATTTTTGGAAATGAAAATACTAAACTTGGATGCAAA
12959 AA
66 AA
* *
12961 GACAAAATCGACCCTTTGACCGAAAAGGTATTTCTGGAAATGAAAATACTAAACTTGGATGCAAA
1 GACAAAATCGACCCTTTGACCGAAAGGGTATTTTTGGAAATGAAAATACTAAACTTGGATGCAAA
*
13026 CA
66 AA
13028 GACAAAATCGACCCTTTGACCGAAAGGGTATTTTTGGAAATGAAAATACTAAACTTGGATGCAAA
1 GACAAAATCGACCCTTTGACCGAAAGGGTATTTTTGGAAATGAAAATACTAAACTTGGATGCAAA
13093 AA
66 AA
* * *
13095 GATAAAATCGACCTTTTGATCGAAAAGGGTATTTTTGGAAATGAAAATACTAAACTTGGATGCAA
1 GACAAAATCGACCCTTTGACCG-AAAGGGTATTTTTGGAAATGAAAATACTAAACTTGGATGCAA
13160 AAA
65 AAA
* *
13163 GACGAAATCGATCCTTTGACCGAAAGGGTATT
1 GACAAAATCGACCCTTTGACCGAAAGGGTATT
13195 ACTGGAAAGA
Statistics
Matches: 397, Mismatches: 35, Indels: 5
0.91 0.08 0.01
Matches are distributed among these distances:
65 8 0.02
66 27 0.07
67 300 0.76
68 62 0.16
ACGTcount: A:0.41, C:0.15, G:0.20, T:0.24
Consensus pattern (67 bp):
GACAAAATCGACCCTTTGACCGAAAGGGTATTTTTGGAAATGAAAATACTAAACTTGGATGCAAA
AA
Found at i:15354 original size:11 final size:11
Alignment explanation
Indices: 15338--15368 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
15328 GAAGTTCGTG
*
15338 TTTGAAGATCA
1 TTTGAAGATAA
15349 TTTGAAGATAA
1 TTTGAAGATAA
15360 TTTGAAGAT
1 TTTGAAGAT
15369 TTGAAGACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.39, C:0.03, G:0.19, T:0.39
Consensus pattern (11 bp):
TTTGAAGATAA
Found at i:21646 original size:18 final size:18
Alignment explanation
Indices: 21623--21668 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
21613 TGAAATTAAT
21623 TAATTATTAATTAAATAA
1 TAATTATTAATTAAATAA
** *
21641 TAATTATTTTTTGAATAA
1 TAATTATTAATTAAATAA
*
21659 TTATTATTAA
1 TAATTATTAA
21669 ATTTCTAGTG
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (18 bp):
TAATTATTAATTAAATAA
Done.