Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022821.1 Corchorus olitorius cultivar O-4 contig22854, 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: 10454
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.30
Found at i:2946 original size:19 final size:18
Alignment explanation
Indices: 2913--2948 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
2903 TTGAAATTAT
2913 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
2931 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
2949 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:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAA
Found at i:5377 original size:33 final size:33
Alignment explanation
Indices: 5332--5444 Score: 147
Period size: 33 Copynumber: 3.4 Consensus size: 33
5322 CCACGGTCAT
* * *
5332 GTCGCGATCCGGTCGCGACTAACCCACAGGCTA
1 GTCGTGATCCGGTCGCGACTAACCCACGGGCTG
* * *
5365 GTCGTGAACCGGTCGTGACTAGCCCACGGGCTG
1 GTCGTGATCCGGTCGCGACTAACCCACGGGCTG
*
5398 GTCGCGATCCGGTCGCGAC-AAGCCCACGGGCTG
1 GTCGTGATCCGGTCGCGACTAA-CCCACGGGCTG
5431 GTCGTGATCCGGTC
1 GTCGTGATCCGGTC
5445 TCGGTTGAGC
Statistics
Matches: 68, Mismatches: 11, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
32 1 0.01
33 67 0.99
ACGTcount: A:0.16, C:0.34, G:0.34, T:0.17
Consensus pattern (33 bp):
GTCGTGATCCGGTCGCGACTAACCCACGGGCTG
Found at i:5402 original size:66 final size:66
Alignment explanation
Indices: 5318--5444 Score: 186
Period size: 66 Copynumber: 1.9 Consensus size: 66
5308 GGCTTGCGAT
*
5318 TAGCCCACGGTCATGTCGCGATCCGGTCGCGACTAA-CCCACAGGCTAGTCGTGAACCGGTCGTG
1 TAGCCCACGGGCATGTCGCGATCCGGTCGCGAC-AAGCCCACAGGCTAGTCGTGAACCGGTCGTG
5382 AC
65 AC
* * *
5384 TAGCCCACGGGC-TGGTCGCGATCCGGTCGCGACAAGCCCACGGGCTGGTCGTGATCCGGTC
1 TAGCCCACGGGCAT-GTCGCGATCCGGTCGCGACAAGCCCACAGGCTAGTCGTGAACCGGTC
5445 TCGGTTGAGC
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
65 3 0.05
66 52 0.95
ACGTcount: A:0.17, C:0.34, G:0.32, T:0.17
Consensus pattern (66 bp):
TAGCCCACGGGCATGTCGCGATCCGGTCGCGACAAGCCCACAGGCTAGTCGTGAACCGGTCGTGA
C
Found at i:5469 original size:66 final size:66
Alignment explanation
Indices: 5318--5478 Score: 168
Period size: 66 Copynumber: 2.4 Consensus size: 66
5308 GGCTTGCGAT
*
5318 TAGCCCACGGTCATG-TCGCGATCCGGTCGCGACTAACCCACAGGCTAGTCGTGAACCGGTCGTG
1 TAGCCCACGGAC-TGATCGCGATCCGGTCGCGACTAACCCACAGGCTAGTCGTGAACCGGTCGTG
5382 AC
65 AC
* * * * *
5384 TAGCCCACGGGCTGGTCGCGATCCGGTCGCGAC-AAGCCCACGGGCTGGTCGTGATCCGGTC-TC
1 TAGCCCACGGACTGATCGCGATCCGGTCGCGACTAA-CCCACAGGCTAGTCGTGAACCGGTCGT-
**
5447 GGT
64 GAC
* *
5450 TGAG-CCGCGGACTGATCGCGAACCGGTCG
1 T-AGCCCACGGACTGATCGCGATCCGGTCG
5479 TGACCGATCC
Statistics
Matches: 81, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
65 5 0.06
66 74 0.91
67 2 0.02
ACGTcount: A:0.16, C:0.33, G:0.34, T:0.17
Consensus pattern (66 bp):
TAGCCCACGGACTGATCGCGATCCGGTCGCGACTAACCCACAGGCTAGTCGTGAACCGGTCGTGA
C
Found at i:5556 original size:20 final size:20
Alignment explanation
Indices: 5521--5561 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
5511 ATTTTAATCA
5521 AATTTATTTTTAATATTTATT
1 AATTTATTTTTAATA-TTATT
*
5542 AATTTGTTTTT-ATATTATT
1 AATTTATTTTTAATATTATT
5561 A
1 A
5562 GCCGAATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 6 0.32
20 3 0.16
21 10 0.53
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (20 bp):
AATTTATTTTTAATATTATT
Found at i:9033 original size:24 final size:24
Alignment explanation
Indices: 9006--9080 Score: 98
Period size: 24 Copynumber: 3.1 Consensus size: 24
8996 AATTTTATGA
9006 AAAAATAGAGA-AGATATTTTAAAG
1 AAAAATAGAGAGA-ATATTTTAAAG
*
9030 AAAAATAGAGAGAATATTTTAATG
1 AAAAATAGAGAGAATATTTTAAAG
* *
9054 AAAATTTAGAGAGAATATTTGAAAG
1 AAAA-ATAGAGAGAATATTTTAAAG
9079 AA
1 AA
9081 TTATAATTAT
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
24 25 0.56
25 20 0.44
ACGTcount: A:0.56, C:0.00, G:0.17, T:0.27
Consensus pattern (24 bp):
AAAAATAGAGAGAATATTTTAAAG
Found at i:9069 original size:25 final size:24
Alignment explanation
Indices: 8997--9073 Score: 95
Period size: 24 Copynumber: 3.2 Consensus size: 24
8987 GACCTCACCA
8997 ATTTT-ATGAAAAAATAGAGA-AGAT
1 ATTTTAATG-AAAAATAGAGAGA-AT
*
9021 ATTTTAAAGAAAAATAGAGAGAAT
1 ATTTTAATGAAAAATAGAGAGAAT
*
9045 ATTTTAATGAAAATTTAGAGAGAAT
1 ATTTTAATGAAAA-ATAGAGAGAAT
9070 ATTT
1 ATTT
9074 GAAAGAATTA
Statistics
Matches: 47, Mismatches: 3, Indels: 5
0.85 0.05 0.09
Matches are distributed among these distances:
24 30 0.64
25 17 0.36
ACGTcount: A:0.52, C:0.00, G:0.16, T:0.32
Consensus pattern (24 bp):
ATTTTAATGAAAAATAGAGAGAAT
Found at i:9337 original size:15 final size:15
Alignment explanation
Indices: 9317--9348 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
9307 TATTAATTAG
9317 AAGAAATTAAAATAC
1 AAGAAATTAAAATAC
9332 AAGAAATTAAAATAC
1 AAGAAATTAAAATAC
9347 AA
1 AA
9349 ATTATTCGGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.69, C:0.06, G:0.06, T:0.19
Consensus pattern (15 bp):
AAGAAATTAAAATAC
Done.