Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007285.1 Corchorus capsularis cultivar CVL-1 contig07306, 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: 19595
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Found at i:1759 original size:19 final size:18
Alignment explanation
Indices: 1735--1770 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
1725 TGAAGATTTC
1735 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
1754 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
1771 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:11059 original size:30 final size:30
Alignment explanation
Indices: 11025--11099 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 30
11015 AGATGATGGG
* * *
11025 ATCGCATATGACCGGCCATTGGATGGAGCC
1 ATCGCACAAGACCGGCCATTGCATGGAGCC
*
11055 ATCGCACAAGACCGGCCATTGCATGGAG-T
1 ATCGCACAAGACCGGCCATTGCATGGAGCC
*
11084 AGCCGCACAAGACCGG
1 A-TCGCACAAGACCGG
11100 GCACATGACT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
29 1 0.03
30 38 0.97
ACGTcount: A:0.27, C:0.29, G:0.29, T:0.15
Consensus pattern (30 bp):
ATCGCACAAGACCGGCCATTGCATGGAGCC
Found at i:12371 original size:474 final size:474
Alignment explanation
Indices: 11484--12425 Score: 1884
Period size: 474 Copynumber: 2.0 Consensus size: 474
11474 ATTATGTAAT
11484 GTTATTTACTTTTCCTAGTAGGACAAGGAATAGGCAATTTCCTTGATCCTTCCTTTATGTTTATG
1 GTTATTTACTTTTCCTAGTAGGACAAGGAATAGGCAATTTCCTTGATCCTTCCTTTATGTTTATG
11549 CCGCCCTTAAGGCTTTAGCATTAGGGAGAGGTGCGTCCCCTACTACTATATAAAGGGACCATCCC
66 CCGCCCTTAAGGCTTTAGCATTAGGGAGAGGTGCGTCCCCTACTACTATATAAAGGGACCATCCC
11614 CCTTGTAAACACAAGTTAAGTTTTCAATAAAGATTTGAGGTTTATTCACCCAATTGATTATCTTA
131 CCTTGTAAACACAAGTTAAGTTTTCAATAAAGATTTGAGGTTTATTCACCCAATTGATTATCTTA
11679 GCTTCATTGTTCTAGTTTGAGCAAACTTAGGGTTCTTCAATCTTGTAGAGTCCTACTAAACAATT
196 GCTTCATTGTTCTAGTTTGAGCAAACTTAGGGTTCTTCAATCTTGTAGAGTCCTACTAAACAATT
11744 AGGTTGTGATTGCTTAATTGTTTGTAAATCTTGTGATCTTAAGAGTTCAATTGCAGGTCTAATTG
261 AGGTTGTGATTGCTTAATTGTTTGTAAATCTTGTGATCTTAAGAGTTCAATTGCAGGTCTAATTG
11809 AATACTTAGGGCGACGAACGAAGAGGTTAATCTTTGTGAAGATTGTTCAATCGATTCATCAAGGA
326 AATACTTAGGGCGACGAACGAAGAGGTTAATCTTTGTGAAGATTGTTCAATCGATTCATCAAGGA
11874 GTGGAGGAACTTCAAGTCGACTTTGGTGGCTATTCAAAGGGTAGATTTGAATCTAACACAACTAG
391 GTGGAGGAACTTCAAGTCGACTTTGGTGGCTATTCAAAGGGTAGATTTGAATCTAACACAACTAG
11939 ATTCGATATCAAACTTAGG
456 ATTCGATATCAAACTTAGG
11958 GTTATTTACTTTTCCTAGTAGGACAAGGAATAGGCAATTTCCTTGATCCTTCCTTTATGTTTATG
1 GTTATTTACTTTTCCTAGTAGGACAAGGAATAGGCAATTTCCTTGATCCTTCCTTTATGTTTATG
12023 CCGCCCTTAAGGCTTTAGCATTAGGGAGAGGTGCGTCCCCTACTACTATATAAAGGGACCATCCC
66 CCGCCCTTAAGGCTTTAGCATTAGGGAGAGGTGCGTCCCCTACTACTATATAAAGGGACCATCCC
12088 CCTTGTAAACACAAGTTAAGTTTTCAATAAAGATTTGAGGTTTATTCACCCAATTGATTATCTTA
131 CCTTGTAAACACAAGTTAAGTTTTCAATAAAGATTTGAGGTTTATTCACCCAATTGATTATCTTA
12153 GCTTCATTGTTCTAGTTTGAGCAAACTTAGGGTTCTTCAATCTTGTAGAGTCCTACTAAACAATT
196 GCTTCATTGTTCTAGTTTGAGCAAACTTAGGGTTCTTCAATCTTGTAGAGTCCTACTAAACAATT
12218 AGGTTGTGATTGCTTAATTGTTTGTAAATCTTGTGATCTTAAGAGTTCAATTGCAGGTCTAATTG
261 AGGTTGTGATTGCTTAATTGTTTGTAAATCTTGTGATCTTAAGAGTTCAATTGCAGGTCTAATTG
12283 AATACTTAGGGCGACGAACGAAGAGGTTAATCTTTGTGAAGATTGTTCAATCGATTCATCAAGGA
326 AATACTTAGGGCGACGAACGAAGAGGTTAATCTTTGTGAAGATTGTTCAATCGATTCATCAAGGA
12348 GTGGAGGAACTTCAAGTCGACTTTGGTGGCTATTCAAAGGGTAGATTTGAATCTAACACAACTAG
391 GTGGAGGAACTTCAAGTCGACTTTGGTGGCTATTCAAAGGGTAGATTTGAATCTAACACAACTAG
12413 ATTCGATATCAAA
456 ATTCGATATCAAA
12426 GATGGTGTAG
Statistics
Matches: 468, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
474 468 1.00
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (474 bp):
GTTATTTACTTTTCCTAGTAGGACAAGGAATAGGCAATTTCCTTGATCCTTCCTTTATGTTTATG
CCGCCCTTAAGGCTTTAGCATTAGGGAGAGGTGCGTCCCCTACTACTATATAAAGGGACCATCCC
CCTTGTAAACACAAGTTAAGTTTTCAATAAAGATTTGAGGTTTATTCACCCAATTGATTATCTTA
GCTTCATTGTTCTAGTTTGAGCAAACTTAGGGTTCTTCAATCTTGTAGAGTCCTACTAAACAATT
AGGTTGTGATTGCTTAATTGTTTGTAAATCTTGTGATCTTAAGAGTTCAATTGCAGGTCTAATTG
AATACTTAGGGCGACGAACGAAGAGGTTAATCTTTGTGAAGATTGTTCAATCGATTCATCAAGGA
GTGGAGGAACTTCAAGTCGACTTTGGTGGCTATTCAAAGGGTAGATTTGAATCTAACACAACTAG
ATTCGATATCAAACTTAGG
Found at i:12970 original size:19 final size:18
Alignment explanation
Indices: 12946--12981 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
12936 TGAAGATTTC
12946 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
12965 TTGAAGATTATTGAAGA
1 TTGAAGATAATTGAAGA
12982 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.00, G:0.22, T:0.36
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Done.