Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006360.1 Corchorus capsularis cultivar CVL-1 contig06381, 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: 15575
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Found at i:1286 original size:2 final size:2
Alignment explanation
Indices: 1279--1327 Score: 59
Period size: 2 Copynumber: 26.0 Consensus size: 2
1269 CGACCCCGAA
* *
1279 AT AT AT AT AT AT -T AT GT GT AT AT AT AT AT AT AT AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1319 A- AT AT AT AT
1 AT AT AT AT AT
1328 GTTTTTTTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
1 3 0.07
2 39 0.93
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1425 original size:20 final size:20
Alignment explanation
Indices: 1400--1458 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
1390 AGATATGTTT
1400 TACTAATAAATAATAATATA
1 TACTAATAAATAATAATATA
*
1420 TACTAATAAAT-A-AATATT
1 TACTAATAAATAATAATATA
* *
1438 TACTAATTTACTAATAATATA
1 TACTAA-TAAATAATAATATA
1459 AATATATATT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
18 11 0.34
19 4 0.12
20 12 0.38
21 5 0.16
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (20 bp):
TACTAATAAATAATAATATA
Found at i:1666 original size:6 final size:6
Alignment explanation
Indices: 1650--1679 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
1640 CATTCCCCGC
*
1650 CGGGGA TGGGGA CGGGGA CGGGGA CGGGGA
1 CGGGGA CGGGGA CGGGGA CGGGGA CGGGGA
1680 TAGGGTTGTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.17, C:0.13, G:0.67, T:0.03
Consensus pattern (6 bp):
CGGGGA
Found at i:4603 original size:25 final size:25
Alignment explanation
Indices: 4571--4621 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
4561 TTTGATTCAC
4571 TCTAAATTTTGCTTCAATTTTGGGT
1 TCTAAATTTTGCTTCAATTTTGGGT
* *
4596 TCTAAATTTTGTTTCAATTTTTGGT
1 TCTAAATTTTGCTTCAATTTTGGGT
4621 T
1 T
4622 AAACAAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.20, C:0.10, G:0.14, T:0.57
Consensus pattern (25 bp):
TCTAAATTTTGCTTCAATTTTGGGT
Found at i:5872 original size:14 final size:14
Alignment explanation
Indices: 5845--5883 Score: 69
Period size: 14 Copynumber: 2.7 Consensus size: 14
5835 GGGCTGCTCA
5845 TTTTTCGGTGTCGGT
1 TTTTTCGGT-TCGGT
5860 TTTTTCGGTTCGGT
1 TTTTTCGGTTCGGT
5874 TTTTTCGGTT
1 TTTTTCGGTT
5884 TTTATTTTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 15 0.62
15 9 0.38
ACGTcount: A:0.00, C:0.13, G:0.28, T:0.59
Consensus pattern (14 bp):
TTTTTCGGTTCGGT
Found at i:6314 original size:18 final size:19
Alignment explanation
Indices: 6285--6320 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
6275 TTTGCACCAT
6285 TTCAAGTCGGTTCGGTCGG
1 TTCAAGTCGGTTCGGTCGG
6304 TTCAA-TCGGTTCGGTCG
1 TTCAAGTCGGTTCGGTCG
6321 ATTTTTGGCC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.11, C:0.22, G:0.33, T:0.33
Consensus pattern (19 bp):
TTCAAGTCGGTTCGGTCGG
Found at i:7931 original size:21 final size:19
Alignment explanation
Indices: 7907--7959 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 19
7897 GAATTATCTC
7907 TAATTAAGTTAGAGTTAGTAA
1 TAATTAA-TTAGAGTT-GTAA
* *
7928 TAATTAATTAGTAGTTTTCA
1 TAATTAATTAG-AGTTGTAA
7948 TAATTAATTAGA
1 TAATTAATTAGA
7960 AACAAAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 1 0.03
20 17 0.59
21 11 0.38
ACGTcount: A:0.42, C:0.02, G:0.13, T:0.43
Consensus pattern (19 bp):
TAATTAATTAGAGTTGTAA
Found at i:8830 original size:15 final size:15
Alignment explanation
Indices: 8806--8839 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
8796 TATATTCTTC
8806 AAAA-TTGTTTTAAA
1 AAAATTTGTTTTAAA
8820 AAAATTTGTTTTAAA
1 AAAATTTGTTTTAAA
8835 AAAAT
1 AAAAT
8840 GATTTTTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 4 0.21
15 15 0.79
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (15 bp):
AAAATTTGTTTTAAA
Found at i:11490 original size:3 final size:3
Alignment explanation
Indices: 11482--11515 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
11472 GATTTACTTT
11482 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
11516 ATTTATAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Done.