Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021681.1 Corchorus olitorius cultivar O-4 contig21714, 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: 11552
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--36 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
37 AAAGAGTTCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:589 original size:9 final size:9
Alignment explanation
Indices: 575--610 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
565 ATAGTAGTAA
575 TAATAATAG
1 TAATAATAG
584 TAATAATAG
1 TAATAATAG
593 ---TAATAG
1 TAATAATAG
599 TAATAATAG
1 TAATAATAG
608 TAA
1 TAA
611 AGATTGTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
6 6 0.25
9 18 0.75
ACGTcount: A:0.56, C:0.00, G:0.11, T:0.33
Consensus pattern (9 bp):
TAATAATAG
Found at i:607 original size:15 final size:15
Alignment explanation
Indices: 565--610 Score: 74
Period size: 15 Copynumber: 3.1 Consensus size: 15
555 TTTTATATAT
* *
565 ATAGTAGTAATAATA
1 ATAGTAATAATAGTA
580 ATAGTAATAATAGTA
1 ATAGTAATAATAGTA
595 ATAGTAATAATAGTA
1 ATAGTAATAATAGTA
610 A
1 A
611 AGATTGTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.54, C:0.00, G:0.13, T:0.33
Consensus pattern (15 bp):
ATAGTAATAATAGTA
Found at i:793 original size:21 final size:21
Alignment explanation
Indices: 764--808 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
754 TTGACACTGT
764 TTAGATACTGTACAGATTAAA
1 TTAGATACTGTACAGATTAAA
* * *
785 TTAGGTACTGTATAGATTAGA
1 TTAGATACTGTACAGATTAAA
806 TTA
1 TTA
809 TTAGAGCAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.07, G:0.18, T:0.38
Consensus pattern (21 bp):
TTAGATACTGTACAGATTAAA
Found at i:1204 original size:29 final size:30
Alignment explanation
Indices: 1171--1230 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
1161 TAAACCGTAT
1171 TGTTCAGAATTT-TTTTTTCAGTTAACTAG
1 TGTTCAGAATTTCTTTTTTCAGTTAACTAG
* *
1200 TGTTCAGATTTTCTTTTTTCAGTTAATTAG
1 TGTTCAGAATTTCTTTTTTCAGTTAACTAG
1230 T
1 T
1231 ATTTCTTTCC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
29 11 0.39
30 17 0.61
ACGTcount: A:0.22, C:0.10, G:0.13, T:0.55
Consensus pattern (30 bp):
TGTTCAGAATTTCTTTTTTCAGTTAACTAG
Found at i:5025 original size:2 final size:2
Alignment explanation
Indices: 5018--5058 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
5008 GTAATCAAAC
5018 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5059 CACGCTACAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:11473 original size:233 final size:233
Alignment explanation
Indices: 11066--11552 Score: 974
Period size: 233 Copynumber: 2.1 Consensus size: 233
11056 GATTCACTCA
11066 AATTCTTCCTTGTTTCCTTTTTTTGTTTCGACATACCTTTTTTTAGAAAGAAACTGGAATAAACC
1 AATTCTTCCTTGTTTCCTTTTTTTGTTTCGACATACCTTTTTTTAGAAAGAAACTGGAATAAACC
11131 GCAAGGGAAGTTGATAAGAAAACTCTGTCCAACACTAGAAGCAGGTGTTGAAGAAAAATGAAGAG
66 GCAAGGGAAGTTGATAAGAAAACTCTGTCCAACACTAGAAGCAGGTGTTGAAGAAAAATGAAGAG
11196 AAAAAAGAAACATTTCAAGTACAGCAGCACTGCCTTTGGACATGAATTGGCTCTGTATTTGATTT
131 AAAAAAGAAACATTTCAAGTACAGCAGCACTGCCTTTGGACATGAATTGGCTCTGTATTTGATTT
11261 AAAACTAGATTCTTGCTTGCGCAACTTGTTTTACATAT
196 AAAACTAGATTCTTGCTTGCGCAACTTGTTTTACATAT
11299 AATTCTTCCTTGTTTCCTTTTTTTGTTTCGACATACCTTTTTTTAGAAAGAAACTGGAATAAACC
1 AATTCTTCCTTGTTTCCTTTTTTTGTTTCGACATACCTTTTTTTAGAAAGAAACTGGAATAAACC
11364 GCAAGGGAAGTTGATAAGAAAACTCTGTCCAACACTAGAAGCAGGTGTTGAAGAAAAATGAAGAG
66 GCAAGGGAAGTTGATAAGAAAACTCTGTCCAACACTAGAAGCAGGTGTTGAAGAAAAATGAAGAG
11429 AAAAAAGAAACATTTCAAGTACAGCAGCACTGCCTTTGGACATGAATTGGCTCTGTATTTGATTT
131 AAAAAAGAAACATTTCAAGTACAGCAGCACTGCCTTTGGACATGAATTGGCTCTGTATTTGATTT
11494 AAAACTAGATTCTTGCTTGCGCAACTTGTTTTACATAT
196 AAAACTAGATTCTTGCTTGCGCAACTTGTTTTACATAT
11532 AATTCTTCCTTGTTTCCTTTT
1 AATTCTTCCTTGTTTCCTTTT
Statistics
Matches: 254, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
233 254 1.00
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Consensus pattern (233 bp):
AATTCTTCCTTGTTTCCTTTTTTTGTTTCGACATACCTTTTTTTAGAAAGAAACTGGAATAAACC
GCAAGGGAAGTTGATAAGAAAACTCTGTCCAACACTAGAAGCAGGTGTTGAAGAAAAATGAAGAG
AAAAAAGAAACATTTCAAGTACAGCAGCACTGCCTTTGGACATGAATTGGCTCTGTATTTGATTT
AAAACTAGATTCTTGCTTGCGCAACTTGTTTTACATAT
Done.