Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015795.1 Corchorus olitorius cultivar O-4 contig15828, 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: 41386
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.32
Found at i:4118 original size:15 final size:15
Alignment explanation
Indices: 4100--4135 Score: 63
Period size: 15 Copynumber: 2.3 Consensus size: 15
4090 TTTCTTCGTT
4100 TTTTTATTTTTTTAA
1 TTTTTATTTTTTTAA
4115 TTTTTATTTTTTTAA
1 TTTTTATTTTTTTAA
4130 TCTTTT
1 T-TTTT
4136 GTGAGTGTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 16 0.80
16 4 0.20
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.81
Consensus pattern (15 bp):
TTTTTATTTTTTTAA
Found at i:11257 original size:20 final size:20
Alignment explanation
Indices: 11216--11257 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
11206 ATCAAAGGTT
*
11216 AAAAAAAATAGTAAATACAAA
1 AAAAAAAATAGTAAA-AAAAA
*
11237 AAAAAAATTA-TAAAAAAAA
1 AAAAAAAATAGTAAAAAAAA
11256 AA
1 AA
11258 TCCAAAGTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 6 0.32
20 4 0.21
21 9 0.47
ACGTcount: A:0.81, C:0.02, G:0.02, T:0.14
Consensus pattern (20 bp):
AAAAAAAATAGTAAAAAAAA
Found at i:17591 original size:27 final size:27
Alignment explanation
Indices: 17560--17615 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
17550 ATATAAATGA
17560 TTTTTATT-GATATACTTTTTCTATTAC
1 TTTTTATTAGATA-ACTTTTTCTATTAC
*
17587 TTTTTTTTAGATAACTTTTTCTATTAC
1 TTTTTATTAGATAACTTTTTCTATTAC
17614 TT
1 TT
17616 AAGATATGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 23 0.85
28 4 0.15
ACGTcount: A:0.21, C:0.11, G:0.04, T:0.64
Consensus pattern (27 bp):
TTTTTATTAGATAACTTTTTCTATTAC
Found at i:21325 original size:2 final size:2
Alignment explanation
Indices: 21318--21359 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
21308 ACATGGATAC
* *
21318 AT AT AT AT AT AT AT AT GT AT AT AT AT AT GT 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
21360 CATTAACCTT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
AT
Found at i:22296 original size:22 final size:22
Alignment explanation
Indices: 22268--22312 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
22258 CCCGTTATTG
*
22268 CTCAAAAAGGCCCCTGAACTTA
1 CTCAAAAAGGCCCCTGAAATTA
22290 CTCAAAAAGGCCCCTGAAATTA
1 CTCAAAAAGGCCCCTGAAATTA
22312 C
1 C
22313 AACATGTCCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.38, C:0.31, G:0.13, T:0.18
Consensus pattern (22 bp):
CTCAAAAAGGCCCCTGAAATTA
Found at i:23751 original size:29 final size:30
Alignment explanation
Indices: 23686--23755 Score: 99
Period size: 29 Copynumber: 2.4 Consensus size: 30
23676 CATCAGAAAA
**
23686 GGGCTTATTTGGTCTTTATTAAGAGTTCAT
1 GGGCTTATTTGGTCTCAATTAAGAGTTCAT
23716 GGGCTTATTTGG-CTGCAATTAA-AGTTCAT
1 GGGCTTATTTGGTCT-CAATTAAGAGTTCAT
23745 GGGCTTATTTG
1 GGGCTTATTTG
23756 ACCGTTTTGT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
29 20 0.54
30 17 0.46
ACGTcount: A:0.20, C:0.11, G:0.26, T:0.43
Consensus pattern (30 bp):
GGGCTTATTTGGTCTCAATTAAGAGTTCAT
Found at i:30624 original size:2 final size:2
Alignment explanation
Indices: 30617--30684 Score: 86
Period size: 2 Copynumber: 34.5 Consensus size: 2
30607 GATTCTTATC
* * *
30617 TA TA TA TA TA TA TA TA TA TA TA TA TA TGA T- TC T- TA TC TA AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA
30658 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
30685 TAACATCAAA
Statistics
Matches: 59, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
1 2 0.03
2 55 0.93
3 2 0.03
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.50
Consensus pattern (2 bp):
TA
Found at i:30655 original size:37 final size:37
Alignment explanation
Indices: 30605--30680 Score: 143
Period size: 37 Copynumber: 2.1 Consensus size: 37
30595 AGAAATGAAA
*
30605 ATGATTCTTATCTATATATATATATATATATATATAT
1 ATGATTCTTATCTAAATATATATATATATATATATAT
30642 ATGATTCTTATCTAAATATATATATATATATATATAT
1 ATGATTCTTATCTAAATATATATATATATATATATAT
30679 AT
1 AT
30681 ATATTAACAT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.42, C:0.05, G:0.03, T:0.50
Consensus pattern (37 bp):
ATGATTCTTATCTAAATATATATATATATATATATAT
Found at i:31332 original size:16 final size:17
Alignment explanation
Indices: 31311--31344 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
31301 GTATGTATAA
*
31311 ATTATAT-TTAATAAAT
1 ATTATATATTAACAAAT
31327 ATTATATATTAACAAAT
1 ATTATATATTAACAAAT
31344 A
1 A
31345 AAAATAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
ATTATATATTAACAAAT
Found at i:35093 original size:18 final size:18
Alignment explanation
Indices: 35070--35108 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
35060 TATCTTTCAT
35070 GAACAATATGAAAAAAAG
1 GAACAATATGAAAAAAAG
35088 GAACAATATGAAAAAAAG
1 GAACAATATGAAAAAAAG
35106 GAA
1 GAA
35109 AAAAAAAATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.67, C:0.05, G:0.18, T:0.10
Consensus pattern (18 bp):
GAACAATATGAAAAAAAG
Done.