Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015382.1 Corchorus olitorius cultivar O-4 contig15415, 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: 51195
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:65 original size:2 final size:2
Alignment explanation
Indices: 58--123 Score: 80
Period size: 2 Copynumber: 32.5 Consensus size: 2
48 ACCTAGCTAG
* *
58 TA TA TA TA TA TA CA CTA TA CTA CA 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 TA TA TA
*
102 TA TA TA T- TA TA TA TA TA CA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
124 TATTTGAAAC
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
1 1 0.02
2 51 0.93
3 3 0.05
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:10062 original size:20 final size:20
Alignment explanation
Indices: 10037--10074 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
10027 GTTCAGTTTT
*
10037 CTGAGATAGAGAGAGAGAAA
1 CTGAGAAAGAGAGAGAGAAA
10057 CTGAGAAAGAGAGAGAGA
1 CTGAGAAAGAGAGAGAGA
10075 GTGAGGTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.05, G:0.37, T:0.08
Consensus pattern (20 bp):
CTGAGAAAGAGAGAGAGAAA
Found at i:10876 original size:114 final size:114
Alignment explanation
Indices: 10747--10975 Score: 431
Period size: 114 Copynumber: 2.0 Consensus size: 114
10737 CTCTAATGAG
*
10747 TAGTTTTATTTAAAATGGGTAGTTTTTATTTTGTTTTGAATTTTTATAAACTGAGTTTGTGTCCG
1 TAGTTTTATTTAAAATAGGTAGTTTTTATTTTGTTTTGAATTTTTATAAACTGAGTTTGTGTCCG
*
10812 AGTCAACTCGTGACACAAACTCAGGACTTGGCTTTATAATTAGTATAGA
66 AGTCAACTCGTGACACAAACTCAGGACTTGACTTTATAATTAGTATAGA
10861 TAGTTTTATTTAAAATAGGTAGTTTTTATTTTGTTTTGAATTTTTATAAACTGAGTTTGTGTCCG
1 TAGTTTTATTTAAAATAGGTAGTTTTTATTTTGTTTTGAATTTTTATAAACTGAGTTTGTGTCCG
*
10926 AGTCTACTCGTGACACAAACTCAGGACTTGACTTTATAATTAGTATAGA
66 AGTCAACTCGTGACACAAACTCAGGACTTGACTTTATAATTAGTATAGA
10975 T
1 T
10976 TATATATATA
Statistics
Matches: 112, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
114 112 1.00
ACGTcount: A:0.28, C:0.10, G:0.17, T:0.44
Consensus pattern (114 bp):
TAGTTTTATTTAAAATAGGTAGTTTTTATTTTGTTTTGAATTTTTATAAACTGAGTTTGTGTCCG
AGTCAACTCGTGACACAAACTCAGGACTTGACTTTATAATTAGTATAGA
Found at i:16427 original size:117 final size:117
Alignment explanation
Indices: 16217--16451 Score: 461
Period size: 117 Copynumber: 2.0 Consensus size: 117
16207 TACAAGTTTA
16217 TGCATGTTGGAATATGTTTTTGCTGACTTTTCTTCTTGTTACATTTATATTAAAGCATTATAATG
1 TGCATGTTGGAATATGTTTTTGCTGACTTTTCTTCTTGTTACATTTATATTAAAGCATTATAATG
16282 GGGTGTTATGCATTTGATTCAGGATGACTTAGGGTACCTGTACCTTGATTTG
66 GGGTGTTATGCATTTGATTCAGGATGACTTAGGGTACCTGTACCTTGATTTG
16334 TGCATGTTGGAATATGTTTTTGCTGACTTTTCTTCTTGTTACATTTATATTAAAGCATTATAATG
1 TGCATGTTGGAATATGTTTTTGCTGACTTTTCTTCTTGTTACATTTATATTAAAGCATTATAATG
*
16399 GGGTGTTATGCATTTGATTCAGGGTGACTTAGGGTACCTGTACCTTGATTTG
66 GGGTGTTATGCATTTGATTCAGGATGACTTAGGGTACCTGTACCTTGATTTG
16451 T
1 T
16452 ACTCGAGGAA
Statistics
Matches: 117, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
117 117 1.00
ACGTcount: A:0.22, C:0.12, G:0.22, T:0.45
Consensus pattern (117 bp):
TGCATGTTGGAATATGTTTTTGCTGACTTTTCTTCTTGTTACATTTATATTAAAGCATTATAATG
GGGTGTTATGCATTTGATTCAGGATGACTTAGGGTACCTGTACCTTGATTTG
Found at i:32518 original size:29 final size:31
Alignment explanation
Indices: 32465--32528 Score: 105
Period size: 29 Copynumber: 2.1 Consensus size: 31
32455 GCTATCGATC
*
32465 TTAACTATTTATATATCTAATCTTATTCGAA
1 TTAACTATTTATATATCTAATCTTATTCAAA
32496 TTAACTATTTATA-A-CTAATCTTATTCAAA
1 TTAACTATTTATATATCTAATCTTATTCAAA
32525 TTAA
1 TTAA
32529 GTCGGTTAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 18 0.56
30 1 0.03
31 13 0.41
ACGTcount: A:0.39, C:0.12, G:0.02, T:0.47
Consensus pattern (31 bp):
TTAACTATTTATATATCTAATCTTATTCAAA
Found at i:33646 original size:13 final size:13
Alignment explanation
Indices: 33625--33655 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
33615 AAATGGAAAA
*
33625 TTCAGAAGTGCTT
1 TTCAAAAGTGCTT
33638 TTCAAAAGTGCTT
1 TTCAAAAGTGCTT
33651 TTCAA
1 TTCAA
33656 TTATTTTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.39
Consensus pattern (13 bp):
TTCAAAAGTGCTT
Found at i:44204 original size:10 final size:10
Alignment explanation
Indices: 44189--44217 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
44179 CCATATTAAC
44189 AATTTTATTT
1 AATTTTATTT
44199 AATTTTATTT
1 AATTTTATTT
44209 -ATTTTATTT
1 AATTTTATTT
44218 CCTTTTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.47
10 10 0.53
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (10 bp):
AATTTTATTT
Found at i:49632 original size:19 final size:20
Alignment explanation
Indices: 49590--49633 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
49580 ATCATCTTTA
49590 AAAAATTTAATGAAACATAG
1 AAAAATTTAATGAAACATAG
* *
49610 AAAATTTTAATGAAA-ATAT
1 AAAAATTTAATGAAACATAG
49629 AAAAA
1 AAAAA
49634 AAACCTCTAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.64, C:0.02, G:0.07, T:0.27
Consensus pattern (20 bp):
AAAAATTTAATGAAACATAG
Done.