Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014238.1 Corchorus capsularis cultivar CVL-1 contig14259, 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: 46269
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:1062 original size:26 final size:26
Alignment explanation
Indices: 1011--1062 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
1001 TGAAATTTTT
* **
1011 AGGTTGAAGGTTTGAGAGAATTTGAA
1 AGGTTGAAAGTTTGAGAGAAAATGAA
1037 AGGTTAGAAAGTTTGA-AGAAAATGAA
1 AGGTT-GAAAGTTTGAGAGAAAATGAA
1063 GTAAATGGCG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 13 0.59
27 9 0.41
ACGTcount: A:0.42, C:0.00, G:0.31, T:0.27
Consensus pattern (26 bp):
AGGTTGAAAGTTTGAGAGAAAATGAA
Found at i:1200 original size:2 final size:2
Alignment explanation
Indices: 1193--1222 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1183 ACTTATTTAC
1193 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1223 TGCATTAGGG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:8561 original size:3 final size:3
Alignment explanation
Indices: 8553--8590 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
8543 TGGATTGAAC
8553 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
8591 TGTTGATCGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:8684 original size:14 final size:14
Alignment explanation
Indices: 8665--8692 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
8655 GGTATGTGTC
8665 ATTAATATTATGTA
1 ATTAATATTATGTA
8679 ATTAATATTATGTA
1 ATTAATATTATGTA
8693 TTTTTATGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
ATTAATATTATGTA
Found at i:9444 original size:23 final size:23
Alignment explanation
Indices: 9414--9460 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
9404 ACACCCTACA
9414 ATAAGAGATAAGAAAAACGTTAT
1 ATAAGAGATAAGAAAAACGTTAT
9437 ATAAGAGATAAGAAAAACGTTAT
1 ATAAGAGATAAGAAAAACGTTAT
9460 A
1 A
9461 CAATTAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.57, C:0.04, G:0.17, T:0.21
Consensus pattern (23 bp):
ATAAGAGATAAGAAAAACGTTAT
Found at i:11865 original size:23 final size:23
Alignment explanation
Indices: 11838--11885 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
11828 AAAATCAAAG
11838 TAATTAAAAGTAATAA-TT-ATTAA
1 TAATTAAAA-T-ATAATTTAATTAA
11861 TAATTAAAATATAATTTAATTAA
1 TAATTAAAATATAATTTAATTAA
11884 TA
1 TA
11886 TGGACTTACT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 4 0.17
22 3 0.13
23 16 0.70
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATTAAAATATAATTTAATTAA
Found at i:13794 original size:21 final size:21
Alignment explanation
Indices: 13751--13795 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
13741 TAAATCAATA
*
13751 TTTGCTAAACACCGCCCATTT
1 TTTGCTAAACACCGCCCACTT
* *
13772 TTTGCTAAATACCGCCCCCTT
1 TTTGCTAAACACCGCCCACTT
13793 TTT
1 TTT
13796 TACACTTTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.20, C:0.33, G:0.09, T:0.38
Consensus pattern (21 bp):
TTTGCTAAACACCGCCCACTT
Found at i:15203 original size:25 final size:26
Alignment explanation
Indices: 15179--15226 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
15169 TTAATGTTTA
15179 AATT-TTATTTT-TATTAAAAAATTT
1 AATTATTATTTTATATTAAAAAATTT
*
15203 AATTATTATTTTATTTTAAAAAAT
1 AATTATTATTTTATATTAAAAAAT
15227 AAATATGGGC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 4 0.19
25 7 0.33
26 10 0.48
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (26 bp):
AATTATTATTTTATATTAAAAAATTT
Found at i:15214 original size:24 final size:25
Alignment explanation
Indices: 15179--15226 Score: 64
Period size: 24 Copynumber: 1.9 Consensus size: 25
15169 TTAATGTTTA
15179 AATTTTATTTTTA-TTAAAAAATTT
1 AATTTTATTTTTATTTAAAAAATTT
15203 AATTATTA-TTTTATTTTAAAAAAT
1 AATT-TTATTTTTA-TTTAAAAAAT
15227 AAATATGGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 9 0.43
25 3 0.14
26 9 0.43
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
AATTTTATTTTTATTTAAAAAATTT
Found at i:16299 original size:31 final size:31
Alignment explanation
Indices: 16261--16325 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
16251 TTGGGTTATC
16261 AGTCTCCAGATCTTTAGATCTTGGATGTTTG
1 AGTCTCCAGATCTTTAGATCTTGGATGTTTG
*
16292 AGTCTCCAGATTTTTAGATCTTGGATGTTTG
1 AGTCTCCAGATCTTTAGATCTTGGATGTTTG
16323 AGT
1 AGT
16326 TAGTTCAGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.20, C:0.14, G:0.23, T:0.43
Consensus pattern (31 bp):
AGTCTCCAGATCTTTAGATCTTGGATGTTTG
Found at i:29573 original size:12 final size:12
Alignment explanation
Indices: 29557--29610 Score: 99
Period size: 12 Copynumber: 4.5 Consensus size: 12
29547 TGGCAGTCGA
29557 GGAGGCAAAGGC
1 GGAGGCAAAGGC
*
29569 AGAGGCAAAGGC
1 GGAGGCAAAGGC
29581 GGAGGCAAAGGC
1 GGAGGCAAAGGC
29593 GGAGGCAAAGGC
1 GGAGGCAAAGGC
29605 GGAGGC
1 GGAGGC
29611 GCAGGAGGTT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 40 1.00
ACGTcount: A:0.33, C:0.17, G:0.50, T:0.00
Consensus pattern (12 bp):
GGAGGCAAAGGC
Found at i:36776 original size:3 final size:3
Alignment explanation
Indices: 36768--36816 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
36758 ATAGTAGGTT
36768 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
36816 T
1 T
36817 TGTTATGGAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:37159 original size:3 final size:3
Alignment explanation
Indices: 37151--37192 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
37141 CATTAGTTTT
37151 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
37193 TTATTATTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:39832 original size:12 final size:12
Alignment explanation
Indices: 39810--39842 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
39800 ATTATTAATG
39810 ATTAT-TATTAT
1 ATTATATATTAT
39821 ATTATATATTAT
1 ATTATATATTAT
*
39833 TTTATATATT
1 ATTATATATT
39843 TTTATTATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 5 0.25
12 15 0.75
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
ATTATATATTAT
Found at i:41197 original size:15 final size:17
Alignment explanation
Indices: 41172--41204 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
41162 TAAAAAGTGA
41172 TTTAAATAAAA-TATTT
1 TTTAAATAAAATTATTT
41188 TTTAAA-AAAATTATTT
1 TTTAAATAAAATTATTT
41204 T
1 T
41205 CTTCTGAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TTTAAATAAAATTATTT
Found at i:41338 original size:31 final size:31
Alignment explanation
Indices: 41300--41375 Score: 109
Period size: 31 Copynumber: 2.5 Consensus size: 31
41290 CAAAACACGT
41300 AATTAAGGATATAACGATTTT-GATTTCAACC
1 AATTAAGGATATAACG-TTTTCGATTTCAACC
* * *
41331 AATTAAGGATATGATGTTTTCGATTTCAAGC
1 AATTAAGGATATAACGTTTTCGATTTCAACC
41362 AATTAAGGATATAA
1 AATTAAGGATATAA
41376 TCAATTAGAG
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
30 4 0.10
31 36 0.90
ACGTcount: A:0.39, C:0.09, G:0.16, T:0.36
Consensus pattern (31 bp):
AATTAAGGATATAACGTTTTCGATTTCAACC
Found at i:41578 original size:29 final size:31
Alignment explanation
Indices: 41505--41571 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
41495 TCTAACTGAC
41505 TATATCCTTAATTGCTCGTTTTTCGTAACAT
1 TATATCCTTAATTGCTCGTTTTTCGTAACAT
* *
41536 TATATCCTTAATTGCTTG-TTTT-GTAACGT
1 TATATCCTTAATTGCTCGTTTTTCGTAACAT
41565 TATATCC
1 TATATCC
41572 CAAATTGTGT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 13 0.38
30 4 0.12
31 17 0.50
ACGTcount: A:0.22, C:0.18, G:0.10, T:0.49
Consensus pattern (31 bp):
TATATCCTTAATTGCTCGTTTTTCGTAACAT
Found at i:41586 original size:29 final size:30
Alignment explanation
Indices: 41505--41588 Score: 82
Period size: 29 Copynumber: 2.8 Consensus size: 30
41495 TCTAACTGAC
** *
41505 TATATCCTTAATTGCTCGTTTTTCGTAACAT
1 TATATCCCAAATTGCT-GTTTTTTGTAACAT
** * *
41536 TATATCCTTAATTGCT-TGTTTTGTAACGT
1 TATATCCCAAATTGCTGTTTTTTGTAACAT
41565 TATATCCCAAATTG-TGTTTTTTGT
1 TATATCCCAAATTGCTGTTTTTTGT
41589 CAAACCTTAT
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
28 1 0.02
29 29 0.63
31 16 0.35
ACGTcount: A:0.21, C:0.15, G:0.12, T:0.51
Consensus pattern (30 bp):
TATATCCCAAATTGCTGTTTTTTGTAACAT
Done.