Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015292.1 Corchorus capsularis cultivar CVL-1 contig15313, 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: 33921
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:243 original size:23 final size:21
Alignment explanation
Indices: 217--261 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 21
207 TAAAAAATAT
217 ATTTTGAAAAATTTAAGTTTTAA
1 ATTTTGAAAAATTT-A-TTTTAA
**
240 ATTTTTCAAAATTTATTTTAA
1 ATTTTGAAAAATTTATTTTAA
261 A
1 A
262 AATCATATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 7 0.35
22 1 0.05
23 12 0.60
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.51
Consensus pattern (21 bp):
ATTTTGAAAAATTTATTTTAA
Found at i:11051 original size:6 final size:6
Alignment explanation
Indices: 11040--11069 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
11030 GGGGGTATAC
*
11040 TCCCCG TCCCCG TCCCCG TCCCCA TCCCCG
1 TCCCCG TCCCCG TCCCCG TCCCCG TCCCCG
11070 GCAGGGAATT
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:0.03, C:0.67, G:0.13, T:0.17
Consensus pattern (6 bp):
TCCCCG
Found at i:11468 original size:26 final size:26
Alignment explanation
Indices: 11408--11461 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
11398 TATAGTGATT
11408 TAGTGATTTTATTTAACATATATATA
1 TAGTGATTTTATTTAACATATATATA
11434 TAGTGATTTTATTTAACATATATATA
1 TAGTGATTTTATTTAACATATATATA
11460 TA
1 TA
11462 TATATTTATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.39, C:0.04, G:0.07, T:0.50
Consensus pattern (26 bp):
TAGTGATTTTATTTAACATATATATA
Found at i:23188 original size:6 final size:6
Alignment explanation
Indices: 23177--23203 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
23167 TCTCCGTTTG
23177 TTTTCT TTTTCT TTTTCT TTTTCT TTT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTT
23204 GGTCAGACGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTCT
Found at i:23583 original size:12 final size:13
Alignment explanation
Indices: 23566--23604 Score: 53
Period size: 12 Copynumber: 3.0 Consensus size: 13
23556 GAATTATTAT
23566 TAATATAT-AGTA
1 TAATATATAAGTA
23578 TAATATATAAGTA
1 TAATATATAAGTA
*
23591 TATTATTATAAGTA
1 TAATA-TATAAGTA
23605 CTATATAACA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 8 0.33
13 8 0.33
14 8 0.33
ACGTcount: A:0.49, C:0.00, G:0.08, T:0.44
Consensus pattern (13 bp):
TAATATATAAGTA
Found at i:23832 original size:31 final size:31
Alignment explanation
Indices: 23755--23824 Score: 131
Period size: 31 Copynumber: 2.3 Consensus size: 31
23745 TCGGCTAAAT
23755 GCTCAATTTGGTCCTAAACCTTTGAGCGAGC
1 GCTCAATTTGGTCCTAAACCTTTGAGCGAGC
23786 GCTCAATTTGGTCCTAAACCTTTGAGCGAGC
1 GCTCAATTTGGTCCTAAACCTTTGAGCGAGC
*
23817 TCTCAATT
1 GCTCAATT
23825 CAGTCCTATT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.23, C:0.26, G:0.20, T:0.31
Consensus pattern (31 bp):
GCTCAATTTGGTCCTAAACCTTTGAGCGAGC
Found at i:27399 original size:31 final size:31
Alignment explanation
Indices: 27361--27459 Score: 114
Period size: 31 Copynumber: 3.3 Consensus size: 31
27351 AATAGGACTG
* *
27361 AATTGAGCGACCGCTCAAAGATTTAGAACCA
1 AATTGAGCGACCGCTCAAAGGTTTAGGACCA
* * *
27392 AATTGAGC-A-GGTTTAAAGGTTTAGGACCA
1 AATTGAGCGACCGCTCAAAGGTTTAGGACCA
*
27421 AATTGAGCG-CTCGCTCAAAGGGTTAGGACCA
1 AATTGAGCGAC-CGCTCAAAGGTTTAGGACCA
27452 AATTGAGC
1 AATTGAGC
27460 ATTTAGCCCT
Statistics
Matches: 56, Mismatches: 9, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
29 23 0.41
30 1 0.02
31 32 0.57
ACGTcount: A:0.34, C:0.18, G:0.25, T:0.22
Consensus pattern (31 bp):
AATTGAGCGACCGCTCAAAGGTTTAGGACCA
Found at i:27557 original size:70 final size:70
Alignment explanation
Indices: 27444--27581 Score: 276
Period size: 70 Copynumber: 2.0 Consensus size: 70
27434 CTCAAAGGGT
27444 TAGGACCAAATTGAGCATTTAGCCCTCCATCTTCCTTGGAAAGTTACTCTATTGGCCTTTGTTAG
1 TAGGACCAAATTGAGCATTTAGCCCTCCATCTTCCTTGGAAAGTTACTCTATTGGCCTTTGTTAG
27509 TGTAG
66 TGTAG
27514 TAGGACCAAATTGAGCATTTAGCCCTCCATCTTCCTTGGAAAGTTACTCTATTGGCCTTTGTTAG
1 TAGGACCAAATTGAGCATTTAGCCCTCCATCTTCCTTGGAAAGTTACTCTATTGGCCTTTGTTAG
27579 TGT
66 TGT
27582 TACTACCTTA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 68 1.00
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.36
Consensus pattern (70 bp):
TAGGACCAAATTGAGCATTTAGCCCTCCATCTTCCTTGGAAAGTTACTCTATTGGCCTTTGTTAG
TGTAG
Found at i:27730 original size:54 final size:54
Alignment explanation
Indices: 27648--27757 Score: 220
Period size: 54 Copynumber: 2.0 Consensus size: 54
27638 GCGGCGAAGA
27648 ATAGAATGAAGTTGGATTTAAGCTTTATTTCTGGGTGTTTTGTTATTAAGTTTC
1 ATAGAATGAAGTTGGATTTAAGCTTTATTTCTGGGTGTTTTGTTATTAAGTTTC
27702 ATAGAATGAAGTTGGATTTAAGCTTTATTTCTGGGTGTTTTGTTATTAAGTTTC
1 ATAGAATGAAGTTGGATTTAAGCTTTATTTCTGGGTGTTTTGTTATTAAGTTTC
27756 AT
1 AT
27758 GTCAAATAGG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 56 1.00
ACGTcount: A:0.25, C:0.05, G:0.22, T:0.48
Consensus pattern (54 bp):
ATAGAATGAAGTTGGATTTAAGCTTTATTTCTGGGTGTTTTGTTATTAAGTTTC
Done.