Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014587.1 Corchorus olitorius cultivar O-4 contig14620, 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: 39848
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1221 original size:18 final size:19
Alignment explanation
Indices: 1198--1239 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
1188 GCCATACTCG
1198 ATTATTACT-TTTTTAATT
1 ATTATTACTCTTTTTAATT
1216 ATTATTACTCTTTTTAATT
1 ATTATTACTCTTTTTAATT
*
1235 TTTAT
1 ATTAT
1240 CATCCAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 9 0.41
19 13 0.59
ACGTcount: A:0.26, C:0.07, G:0.00, T:0.67
Consensus pattern (19 bp):
ATTATTACTCTTTTTAATT
Found at i:5734 original size:21 final size:21
Alignment explanation
Indices: 5710--5792 Score: 73
Period size: 22 Copynumber: 3.8 Consensus size: 21
5700 TATCTTAGAT
5710 ATAAT-ATATATTATTAAATAA
1 ATAATAATATATT-TTAAATAA
5731 ATAATAAATATATTTTAAAT-A
1 ATAAT-AATATATTTTAAATAA
**
5752 ATAAATAATA-AGTTCAAAATAA
1 AT-AATAATATA-TTTTAAATAA
5774 ATAAATAATATATATTTAA
1 AT-AATAATATAT-TTTAA
5793 TTACTAAACG
Statistics
Matches: 51, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
20 1 0.02
21 18 0.35
22 21 0.41
23 11 0.22
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (21 bp):
ATAATAATATATTTTAAATAA
Found at i:10566 original size:10 final size:9
Alignment explanation
Indices: 10549--10603 Score: 53
Period size: 8 Copynumber: 6.1 Consensus size: 9
10539 GTACACAATA
10549 ATATATGAT
1 ATATATGAT
10558 ATGATATGAT
1 AT-ATATGAT
*
10568 AAGTAGATGAT
1 -A-TATATGAT
10579 ATATAT-AT
1 ATATATGAT
10587 ATATAT-AT
1 ATATATGAT
10595 ATATA-GAT
1 ATATATGAT
10603 A
1 A
10604 ATAACAACAC
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
8 18 0.45
9 6 0.15
10 8 0.20
11 7 0.17
12 1 0.03
ACGTcount: A:0.47, C:0.00, G:0.13, T:0.40
Consensus pattern (9 bp):
ATATATGAT
Found at i:11594 original size:8 final size:8
Alignment explanation
Indices: 11581--11605 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
11571 GTACTTTTTT
11581 TCCCTCTC
1 TCCCTCTC
11589 TCCCTCTC
1 TCCCTCTC
11597 TCCCTCTC
1 TCCCTCTC
11605 T
1 T
11606 GTCTCTGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.00, C:0.60, G:0.00, T:0.40
Consensus pattern (8 bp):
TCCCTCTC
Found at i:13426 original size:6 final size:6
Alignment explanation
Indices: 13411--13498 Score: 131
Period size: 6 Copynumber: 14.7 Consensus size: 6
13401 CGGTCATCAC
* *
13411 CATGGC CATGAT CATGGT CATGGT CATGGT CATGGT CATGGT CATGGT
1 CATGGT CATGGT CATGGT CATGGT CATGGT CATGGT CATGGT CATGGT
* * *
13459 CATGGT CATGGT CATGGT CATGGC CATGGC CATGGC CATG
1 CATGGT CATGGT CATGGT CATGGT CATGGT CATGGT CATG
13499 AACATCATCA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 78 1.00
ACGTcount: A:0.18, C:0.22, G:0.32, T:0.28
Consensus pattern (6 bp):
CATGGT
Found at i:25054 original size:30 final size:30
Alignment explanation
Indices: 25020--25081 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
25010 GTTAATAAGC
25020 CATTAAAATTTGAAGGTATAAGAGAAAAGT
1 CATTAAAATTTGAAGGTATAAGAGAAAAGT
* * *
25050 CATTAAATTTTGAGGGTATAAGAGGAAAGT
1 CATTAAAATTTGAAGGTATAAGAGAAAAGT
25080 CA
1 CA
25082 AGATAAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.45, C:0.05, G:0.23, T:0.27
Consensus pattern (30 bp):
CATTAAAATTTGAAGGTATAAGAGAAAAGT
Found at i:25596 original size:67 final size:68
Alignment explanation
Indices: 25474--25613 Score: 264
Period size: 67 Copynumber: 2.1 Consensus size: 68
25464 GTGTTCTAAA
25474 TTCTGATCTGCCCATAATATATACACATACACAGAAAGGGAAAGTTGAGAAGATGATTTGGGATA
1 TTCTGATCTGCCCATAATATATACACATA-ACAGAAAGGGAAAGTTGAGAAGATGATTTGGGATA
25539 ATAG
65 ATAG
25543 TTCTGATCTGCCCATAATATATACACAT-ACAGAAAGGGAAAGTTGAGAAGATGATTTGGGATAA
1 TTCTGATCTGCCCATAATATATACACATAACAGAAAGGGAAAGTTGAGAAGATGATTTGGGATAA
25607 TAG
66 TAG
25610 TTCT
1 TTCT
25614 CCTTTGTATG
Statistics
Matches: 71, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
67 43 0.61
69 28 0.39
ACGTcount: A:0.38, C:0.13, G:0.21, T:0.28
Consensus pattern (68 bp):
TTCTGATCTGCCCATAATATATACACATAACAGAAAGGGAAAGTTGAGAAGATGATTTGGGATAA
TAG
Found at i:29239 original size:3 final size:3
Alignment explanation
Indices: 29231--29255 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
29221 CCAGTTGCAA
29231 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
29256 TGTGGATAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:32406 original size:2 final size:2
Alignment explanation
Indices: 32399--32430 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
32389 AGTGGGCTTG
32399 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
32431 CTTGGAGATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:36471 original size:2 final size:2
Alignment explanation
Indices: 36464--36491 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
36454 GGTCCCTACG
36464 TA TA TA TA 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
36492 AACTTAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:39182 original size:2 final size:2
Alignment explanation
Indices: 39160--39203 Score: 56
Period size: 2 Copynumber: 23.0 Consensus size: 2
39150 AGACTTTGTG
* *
39160 TA TA AA TA TA TA -A T- TA CA TA 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
39200 TA TA
1 TA TA
39204 GATCCATCAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
1 2 0.06
2 34 0.94
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Done.