Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01004921.1 Corchorus capsularis cultivar CVL-1 contig04939, 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: 11905
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35
Found at i:2520 original size:18 final size:18
Alignment explanation
Indices: 2499--2545 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
2489 AGAGGTTTTG
2499 GCAGAGGTAATTTTGATC
1 GCAGAGGTAATTTTGATC
* *
2517 GCAGAGGCAACTTTGATC
1 GCAGAGGTAATTTTGATC
* *
2535 GAAAAGGTAAT
1 GCAGAGGTAAT
2546 ACTAATCAAA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.34, C:0.13, G:0.28, T:0.26
Consensus pattern (18 bp):
GCAGAGGTAATTTTGATC
Found at i:5382 original size:2 final size:2
Alignment explanation
Indices: 5358--5443 Score: 59
Period size: 2 Copynumber: 48.0 Consensus size: 2
5348 AACCGACGAA
5358 AT AT A- AT A- AT AT AT -T AT AT -T 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 AT AT AT AT AT
* * *
5396 -T TT AT AT -T AT AT TT A- AT -T AGT TT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT
5434 -T AT A- AT AT AT
1 AT AT AT AT AT AT
5444 CAGAAATATA
Statistics
Matches: 67, Mismatches: 5, Indels: 24
0.70 0.05 0.25
Matches are distributed among these distances:
1 11 0.16
2 55 0.82
3 1 0.01
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.53
Consensus pattern (2 bp):
AT
Found at i:5393 original size:24 final size:23
Alignment explanation
Indices: 5358--5437 Score: 73
Period size: 26 Copynumber: 3.6 Consensus size: 23
5348 AACCGACGAA
5358 ATATAATAATATA-TTATATTAT
1 ATATAATAATATATTTATATTAT
5380 ATATATATATATATATTTTATATTAT
1 ATATA-ATA-ATATA-TTTATATTAT
5406 AT-T--TAAT-TAGTTTATA-TAT
1 ATATAATAATATA-TTTATATTAT
*
5425 ATATAATATTATA
1 ATATAATAATATA
5438 ATATATCAGA
Statistics
Matches: 48, Mismatches: 2, Indels: 15
0.74 0.03 0.23
Matches are distributed among these distances:
19 5 0.10
20 9 0.19
21 2 0.04
22 10 0.21
23 5 0.10
24 5 0.10
25 1 0.02
26 11 0.23
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (23 bp):
ATATAATAATATATTTATATTAT
Found at i:5402 original size:31 final size:33
Alignment explanation
Indices: 5358--5443 Score: 92
Period size: 31 Copynumber: 2.8 Consensus size: 33
5348 AACCGACGAA
*
5358 ATATA-ATAATATATTATATTATATA-TA-TAT
1 ATATATATATTATATTATATTATATATTAGTAT
* *
5388 ATATATATTTTATATTATATT-TA-ATTAGTTT
1 ATATATATATTATATTATATTATATATTAGTAT
* *
5419 ATATATATATAATATTATAATATAT
1 ATATATATATTATATTATATTATAT
5444 CAGAAATATA
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
29 1 0.02
30 9 0.20
31 33 0.73
32 2 0.04
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.53
Consensus pattern (33 bp):
ATATATATATTATATTATATTATATATTAGTAT
Found at i:9136 original size:13 final size:14
Alignment explanation
Indices: 9103--9143 Score: 59
Period size: 13 Copynumber: 3.1 Consensus size: 14
9093 AAAAAAAAAT
*
9103 TATATA-TATAATA
1 TATATATTATATTA
9116 TATATATTATATTA
1 TATATATTATATTA
9130 -ATATATTATATTA
1 TATATATTATATTA
9143 T
1 T
9144 GTTATATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 19 0.76
14 6 0.24
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
TATATATTATATTA
Found at i:9140 original size:5 final size:5
Alignment explanation
Indices: 9101--9150 Score: 52
Period size: 5 Copynumber: 10.4 Consensus size: 5
9091 TCAAAAAAAA
* *
9101 ATTAT A-TAT ATAAT ATATAT ATTAT ATTA- A-TAT ATTAT ATTAT GTTAT
1 ATTAT ATTAT ATTAT AT-TAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
9149 AT
1 AT
9151 AAAAGAAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
3 2 0.05
4 6 0.16
5 25 0.68
6 4 0.11
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (5 bp):
ATTAT
Found at i:9472 original size:6 final size:6
Alignment explanation
Indices: 9461--9510 Score: 57
Period size: 6 Copynumber: 7.8 Consensus size: 6
9451 ATATTTTGTA
9461 TATATC TATATC TATATC TATCTATC TATCTATC TATATC TATA-C TATAT
1 TATATC TATATC TATATC TA--TATC TA--TATC TATATC TATATC TATAT
9511 ATAAAAGTAC
Statistics
Matches: 41, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
5 5 0.12
6 22 0.54
8 14 0.34
ACGTcount: A:0.32, C:0.18, G:0.00, T:0.50
Consensus pattern (6 bp):
TATATC
Found at i:9478 original size:12 final size:12
Alignment explanation
Indices: 9461--9510 Score: 57
Period size: 14 Copynumber: 3.9 Consensus size: 12
9451 ATATTTTGTA
9461 TATATCTATATC
1 TATATCTATATC
9473 TATATCTATCTATC
1 TATATCTA--TATC
9487 TATCTATCTATATC
1 TA--TATCTATATC
9501 TATA-CTATAT
1 TATATCTATAT
9511 ATAAAAGTAC
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
11 6 0.18
12 10 0.29
14 12 0.35
16 6 0.18
ACGTcount: A:0.32, C:0.18, G:0.00, T:0.50
Consensus pattern (12 bp):
TATATCTATATC
Done.