Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020120.1 Corchorus olitorius cultivar O-4 contig20153, 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: 19521
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:3915 original size:30 final size:30
Alignment explanation
Indices: 3852--3913 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 30
3842 TATTCTGTCA
3852 TTATTTTTTATTTAGGTTAGTATTAGGCTT
1 TTATTTTTTATTTAGGTTAGTATTAGGCTT
*
3882 TTATTTTCTTATTTTA-GTTAGTATTGGGCTT
1 TTATTTT-TTA-TTTAGGTTAGTATTAGGCTT
3913 T
1 T
3914 ATGGGCTGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 7 0.24
31 18 0.62
32 4 0.14
ACGTcount: A:0.18, C:0.05, G:0.16, T:0.61
Consensus pattern (30 bp):
TTATTTTTTATTTAGGTTAGTATTAGGCTT
Found at i:6673 original size:12 final size:12
Alignment explanation
Indices: 6656--6691 Score: 72
Period size: 12 Copynumber: 3.0 Consensus size: 12
6646 AATGAAGAAC
6656 TTTCAGAGAAAA
1 TTTCAGAGAAAA
6668 TTTCAGAGAAAA
1 TTTCAGAGAAAA
6680 TTTCAGAGAAAA
1 TTTCAGAGAAAA
6692 AGCATTTCGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.50, C:0.08, G:0.17, T:0.25
Consensus pattern (12 bp):
TTTCAGAGAAAA
Found at i:7384 original size:743 final size:743
Alignment explanation
Indices: 5959--7422 Score: 2856
Period size: 743 Copynumber: 2.0 Consensus size: 743
5949 GTTCAACCGA
*
5959 TTGAACCGGTCGATCCGGTCCGATTTTTTATTCATGGCAAGAAACCACCTATACTTCTTAACATA
1 TTGAACCGGCCGATCCGGTCCGATTTTTTATTCATGGCAAGAAACCACCTATACTTCTTAACATA
6024 ACCAAATAAGCCCATTAACATCGATTTACATCGAATTAGACCTCAAAATGACTATAATTAATTGC
66 ACCAAATAAGCCCATTAACATCGATTTACATCGAATTAGACCTCAAAATGACTATAATTAATTGC
6089 ATTATTATTACATGGTCCGATATGATTTTATATAGTACCATGTAAAATTTGAATTTCTAGTCATA
131 ATTATTATTACATGGTCCGATATGATTTTATATAGTACCATGTAAAATTTGAATTTCTAGTCATA
6154 TCACAGCCAAAGATCTAATTGAGTGTTAAACTATGATTGAACATTTGGATCAACTGAATTTAATA
196 TCACAGCCAAAGATCTAATTGAGTGTTAAACTATGATTGAACATTTGGATCAACTGAATTTAATA
6219 TTTTCTATATATCCTTAAAAAAAGTTAGATGGCTTTTCCAAACTAGGATCCTATTGCACCAAATT
261 TTTTCTATATATCCTTAAAAAAAGTTAGATGGCTTTTCCAAACTAGGATCCTATTGCACCAAATT
6284 TTTCTTGTGTGCCTAAAAGGGTCTTTGACGTTAGATCTCTTTGAGAAAAGAGAAAGGTTCGAGGC
326 TTTCTTGTGTGCCTAAAAGGGTCTTTGACGTTAGATCTCTTTGAGAAAAGAGAAAGGTTCGAGGC
6349 GTGCCGGTTATTTTTGTAGAAGAATAACAAAAATTGTTTGTAAAACTTGAAAGTAAAAGATCATT
391 GTGCCGGTTATTTTTGTAGAAGAATAACAAAAATTGTTTGTAAAACTTGAAAGTAAAAGATCATT
* *
6414 TGGAGAGATCAGATGAATTGAGGGTTTTGGATCAAAGTCACAGCAAATCATTTAAATCATTGATC
456 TGGAGAGATCAGATGAATTGAGGGTTTTGGATCAAAGTCACACCAAACCATTTAAATCATTGATC
*
6479 CCAGATTGCTTGCGAACAAAAGTGATAAAAAGTTTTTCAAAAAACAGGAAAGAAAATAACAAAAA
521 CCAGATTGCTTGCGAACAAAAGTGATAAAAAGTTTTTCAAAAAACAGAAAAGAAAATAACAAAAA
*
6544 GATTGTTATTTGATTTCATTGCAACGGATTACAAAGGAAAAATCTTGAGTAGAGAAGATTGAAAT
586 GATTGTTATTTGATTTCATTGCAACGGATTACAAAGGAAAAATATTGAGTAGAGAAGATTGAAAT
6609 ATGAAAAATATCAAGAACAAGTAAGAACTTGATGAACAATGAAGAACTTTCAGAGAAAATTTCAG
651 ATGAAAAATATCAAGAACAAGTAAGAACTTGATGAACAATGAAGAACTTTCAGAGAAAATTTCAG
6674 AGAAAATTTCAGAGAAAAAGCATTTCGG
716 AGAAAATTTCAGAGAAAAAGCATTTCGG
*
6702 TTGAACCGGCCGATCCGGTCCGATTTTTTATTCATTGCAAGAAACCACCTATACTTCTTAACATA
1 TTGAACCGGCCGATCCGGTCCGATTTTTTATTCATGGCAAGAAACCACCTATACTTCTTAACATA
6767 ACCAAATAAGCCCATTAACATCGATTTACATCGAATTAGACCTCAAAATGACTATAATTAATTGC
66 ACCAAATAAGCCCATTAACATCGATTTACATCGAATTAGACCTCAAAATGACTATAATTAATTGC
6832 ATTATTATTACATGGTCCGATATGATTTTATATAGTACCATGTAAAATTTGAATTTCTAGTCATA
131 ATTATTATTACATGGTCCGATATGATTTTATATAGTACCATGTAAAATTTGAATTTCTAGTCATA
6897 TCACAGCCAAAGATCTAATTGAGTGTTAAACTATGATTGAACATTTGGATCAACTGAATTTAATA
196 TCACAGCCAAAGATCTAATTGAGTGTTAAACTATGATTGAACATTTGGATCAACTGAATTTAATA
6962 TTTTCTATATATCCTTAAAAAAAGTTAGATGGCTTTTCCAAACTAGGATCCTATTGCACCAAATT
261 TTTTCTATATATCCTTAAAAAAAGTTAGATGGCTTTTCCAAACTAGGATCCTATTGCACCAAATT
*
7027 TTTTTTGTGTGCCTAAAAGGGTCTTTGACGTTAGATCTCTTTGAGAAAAGAGAAAGGTTCGAGGC
326 TTTCTTGTGTGCCTAAAAGGGTCTTTGACGTTAGATCTCTTTGAGAAAAGAGAAAGGTTCGAGGC
7092 GTGCCGGTTATTTTTGTAGAAGAATAACAAAAATTGTTTGTAAAACTTGAAAGTAAAAGATCATT
391 GTGCCGGTTATTTTTGTAGAAGAATAACAAAAATTGTTTGTAAAACTTGAAAGTAAAAGATCATT
7157 TGGAGAGATCAGATGAATTGAGGGTTTTGGATCAAAGTCACACCAAACCATTTAAATCATTGATC
456 TGGAGAGATCAGATGAATTGAGGGTTTTGGATCAAAGTCACACCAAACCATTTAAATCATTGATC
*
7222 CCAGATTGCTTGCGAACAAAAGTGATTAAAAGTTTTTCAAAAAACAGAAAAGAAAATAACAAAAA
521 CCAGATTGCTTGCGAACAAAAGTGATAAAAAGTTTTTCAAAAAACAGAAAAGAAAATAACAAAAA
7287 GATTGTTATTTGATTTCATTGCAACGGATTACAAAGGAAAAATATTGAGTAGAGAAGATTGAAAT
586 GATTGTTATTTGATTTCATTGCAACGGATTACAAAGGAAAAATATTGAGTAGAGAAGATTGAAAT
7352 ATGAAAAATATCAAGAACAAGTAAGAACTTGATGAACAATGAAGAACTTTCAGAGAAAATTTCAG
651 ATGAAAAATATCAAGAACAAGTAAGAACTTGATGAACAATGAAGAACTTTCAGAGAAAATTTCAG
7417 AGAAAA
716 AGAAAA
7423 AGCATTGGGC
Statistics
Matches: 713, Mismatches: 8, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
743 713 1.00
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.31
Consensus pattern (743 bp):
TTGAACCGGCCGATCCGGTCCGATTTTTTATTCATGGCAAGAAACCACCTATACTTCTTAACATA
ACCAAATAAGCCCATTAACATCGATTTACATCGAATTAGACCTCAAAATGACTATAATTAATTGC
ATTATTATTACATGGTCCGATATGATTTTATATAGTACCATGTAAAATTTGAATTTCTAGTCATA
TCACAGCCAAAGATCTAATTGAGTGTTAAACTATGATTGAACATTTGGATCAACTGAATTTAATA
TTTTCTATATATCCTTAAAAAAAGTTAGATGGCTTTTCCAAACTAGGATCCTATTGCACCAAATT
TTTCTTGTGTGCCTAAAAGGGTCTTTGACGTTAGATCTCTTTGAGAAAAGAGAAAGGTTCGAGGC
GTGCCGGTTATTTTTGTAGAAGAATAACAAAAATTGTTTGTAAAACTTGAAAGTAAAAGATCATT
TGGAGAGATCAGATGAATTGAGGGTTTTGGATCAAAGTCACACCAAACCATTTAAATCATTGATC
CCAGATTGCTTGCGAACAAAAGTGATAAAAAGTTTTTCAAAAAACAGAAAAGAAAATAACAAAAA
GATTGTTATTTGATTTCATTGCAACGGATTACAAAGGAAAAATATTGAGTAGAGAAGATTGAAAT
ATGAAAAATATCAAGAACAAGTAAGAACTTGATGAACAATGAAGAACTTTCAGAGAAAATTTCAG
AGAAAATTTCAGAGAAAAAGCATTTCGG
Found at i:17365 original size:16 final size:16
Alignment explanation
Indices: 17344--17375 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
17334 AAAAGGAGAT
17344 TAATATAATGAATTTA
1 TAATATAATGAATTTA
*
17360 TAATATAATGACTTTA
1 TAATATAATGAATTTA
17376 ATACCAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (16 bp):
TAATATAATGAATTTA
Done.