Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016359.1 Corchorus capsularis cultivar CVL-1 contig16380, 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: 41582
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:5133 original size:130 final size:128
Alignment explanation
Indices: 4935--5177 Score: 344
Period size: 130 Copynumber: 1.9 Consensus size: 128
4925 ACTTTCACTC
* *
4935 AACTAAAAATTCTACTTTTATTTAATTAAATCTAATATCCTTATAACTATTTAATTTTTACCATT
1 AACTAAAAACTCAACTTTTATTTAATTAAATCTAATATCCTTATAACTATTTAATTTTTACCATT
* *
5000 TTACT-TTTAATTAAAAAAACTTATATATATTAGAATTTTTTTAAATATACTTTATAGTTTTACA
66 TTACTATTTAATT--AAAAACTTAGATATATTAGAA-TTTTTAAAATATACTTTATAGTTTTACA
5064 T
128 T
* * * * * *
5065 AACTAAAAACTCAATTTTTATTTTATTAAATCTAATATTCTTATACCTATTTTATTTTTATCATT
1 AACTAAAAACTCAACTTTTATTTAATTAAATCTAATATCCTTATAACTATTTAATTTTTACCATT
*
5130 TTACTAATTTAATTAAAAATTTAGATATATTAGAATTTTTAAAATATA
66 TTACT-ATTTAATTAAAAACTTAGATATATTAGAATTTTTAAAATATA
5178 TTTCTTAAAT
Statistics
Matches: 100, Mismatches: 11, Indels: 5
0.86 0.09 0.04
Matches are distributed among these distances:
129 12 0.12
130 81 0.81
132 7 0.07
ACGTcount: A:0.40, C:0.09, G:0.02, T:0.49
Consensus pattern (128 bp):
AACTAAAAACTCAACTTTTATTTAATTAAATCTAATATCCTTATAACTATTTAATTTTTACCATT
TTACTATTTAATTAAAAACTTAGATATATTAGAATTTTTAAAATATACTTTATAGTTTTACAT
Found at i:8194 original size:27 final size:28
Alignment explanation
Indices: 8144--8199 Score: 80
Period size: 27 Copynumber: 2.0 Consensus size: 28
8134 TTTTTTAATC
*
8144 AGAAATCATTTTAAATTATCCTAAAAAA
1 AGAAATCATTTAAAATTATCCTAAAAAA
8172 AGAAATCA-TTAAAATT-TACCTAAAAAA
1 AGAAATCATTTAAAATTAT-CCTAAAAAA
8199 A
1 A
8200 TCATTTTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 1 0.04
27 17 0.65
28 8 0.31
ACGTcount: A:0.57, C:0.11, G:0.04, T:0.29
Consensus pattern (28 bp):
AGAAATCATTTAAAATTATCCTAAAAAA
Found at i:8204 original size:23 final size:25
Alignment explanation
Indices: 8169--8214 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
8159 TTATCCTAAA
8169 AAAAGAAATCA-TTAAAATTTACCT
1 AAAAGAAATCATTTAAAATTTACCT
*
8193 AAAA-AAATCATTTTAAATTTAC
1 AAAAGAAATCATTTAAAATTTAC
8215 ACCACCTGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.54, C:0.11, G:0.02, T:0.33
Consensus pattern (25 bp):
AAAAGAAATCATTTAAAATTTACCT
Found at i:13264 original size:30 final size:29
Alignment explanation
Indices: 13210--13267 Score: 80
Period size: 30 Copynumber: 2.0 Consensus size: 29
13200 ACTAGATGGT
* *
13210 TCACTGTATTTTAGGGTACCTAACTAATC
1 TCACTGTATTTCAGGGTACATAACTAATC
*
13239 TCACTGTCATTTCAGGGTATATAACTAAT
1 TCACTGT-ATTTCAGGGTACATAACTAAT
13268 ATTTATCAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 7 0.28
30 18 0.72
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (29 bp):
TCACTGTATTTCAGGGTACATAACTAATC
Found at i:30287 original size:2 final size:2
Alignment explanation
Indices: 30280--30321 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
30270 TAGGAAAAGA
30280 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
30322 GAAAAATCTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:35759 original size:25 final size:25
Alignment explanation
Indices: 35706--35759 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
35696 GTTCATGCAA
* * *
35706 TTTCTTTCCAATCATATCCCGCGAT
1 TTTCTTTCCAATCATATCACACAAT
35731 TTTCTTTCC-ATCATATCACACAAT
1 TTTCTTTCCAATCATATCACACAAT
35755 GTTTC
1 -TTTC
35760 ATCTATCATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 12 0.48
25 13 0.52
ACGTcount: A:0.22, C:0.30, G:0.06, T:0.43
Consensus pattern (25 bp):
TTTCTTTCCAATCATATCACACAAT
Found at i:36568 original size:2 final size:2
Alignment explanation
Indices: 36561--36593 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
36551 CAAAGCATTT
36561 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
36594 CCCATACTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Done.