Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022092.1 Corchorus olitorius cultivar O-4 contig22125, 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: 32387
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Found at i:216 original size:15 final size:14
Alignment explanation
Indices: 196--225 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
186 ATCTCTTTAA
196 TTTTCCTTGCATTAT
1 TTTTCCTTG-ATTAT
211 TTTTCCTTGATTAT
1 TTTTCCTTGATTAT
225 T
1 T
226 GCTTTGATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.13, C:0.17, G:0.07, T:0.63
Consensus pattern (14 bp):
TTTTCCTTGATTAT
Found at i:3131 original size:15 final size:15
Alignment explanation
Indices: 3101--3142 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
3091 TTACTTTGCT
3101 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
3117 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
*
3132 TTGCTTTCTGT
1 TTGTTTTCTGT
3143 CAATCTCTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.12, C:0.10, G:0.14, T:0.64
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:3518 original size:24 final size:26
Alignment explanation
Indices: 3489--3543 Score: 78
Period size: 25 Copynumber: 2.2 Consensus size: 26
3479 TTGTTTTGTG
3489 TTTTGCGTC-GAAAAAAAAAA-TAGT
1 TTTTGCGTCAGAAAAAAAAAATTAGT
* *
3513 TTTTGCGTCATAAAAAAAAAATTTGT
1 TTTTGCGTCAGAAAAAAAAAATTAGT
3539 TTTTG
1 TTTTG
3544 TGTCTGCATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
24 9 0.33
25 10 0.37
26 8 0.30
ACGTcount: A:0.40, C:0.07, G:0.15, T:0.38
Consensus pattern (26 bp):
TTTTGCGTCAGAAAAAAAAAATTAGT
Found at i:8564 original size:11 final size:11
Alignment explanation
Indices: 8548--8573 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
8538 CTAGCCCTAA
8548 AAAACTAGAAG
1 AAAACTAGAAG
8559 AAAACTAGAAG
1 AAAACTAGAAG
8570 AAAA
1 AAAA
8574 GAAATTATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.69, C:0.08, G:0.15, T:0.08
Consensus pattern (11 bp):
AAAACTAGAAG
Found at i:9194 original size:19 final size:18
Alignment explanation
Indices: 9161--9196 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
9151 TTGAAATAGA
9161 TCTTCAAAAATCTTCAAG
1 TCTTCAAAAATCTTCAAG
*
9179 TCTTCAAATTATCTTCAA
1 TCTTCAAA-AATCTTCAA
9197 ATGGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.36, C:0.22, G:0.03, T:0.39
Consensus pattern (18 bp):
TCTTCAAAAATCTTCAAG
Found at i:10964 original size:16 final size:15
Alignment explanation
Indices: 10943--10989 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
10933 AGGAATAGGC
10943 AATCAATCAAAGCAA
1 AATCAATCAAAGCAA
*
10958 TAATCAATCAGAGCAA
1 -AATCAATCAAAGCAA
10974 AA-CAATGCAAAG-AA
1 AATCAAT-CAAAGCAA
10988 AA
1 AA
10990 AGTAAATGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 8 0.29
15 6 0.21
16 14 0.50
ACGTcount: A:0.60, C:0.17, G:0.11, T:0.13
Consensus pattern (15 bp):
AATCAATCAAAGCAA
Found at i:13352 original size:32 final size:31
Alignment explanation
Indices: 13311--13403 Score: 84
Period size: 32 Copynumber: 3.0 Consensus size: 31
13301 GAAAATATAT
*
13311 ATTTTTTTTTGAAAACGCAAAAACAAGAAAAG
1 ATTTTTTTTTGAAAACGCAAAAACAA-AAAAA
* *
13343 ATTTTTTTTTTAAATA---AAAACGCAAAAAAA
1 ATTTTTTTTTGAAA-ACGCAAAA-ACAAAAAAA
* *
13373 ATTTTTTTTAGAAAAACGCAAAAACACAAAA
1 ATTTTTTTTTG-AAAACGCAAAAACAAAAAA
13404 CAAAAAGTTT
Statistics
Matches: 48, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
30 18 0.38
31 6 0.12
32 19 0.40
33 5 0.10
ACGTcount: A:0.53, C:0.10, G:0.08, T:0.30
Consensus pattern (31 bp):
ATTTTTTTTTGAAAACGCAAAAACAAAAAAA
Found at i:13556 original size:32 final size:31
Alignment explanation
Indices: 13498--13564 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 31
13488 CACACAACAC
13498 AAAATTTTTTTTTAAATTAAAGACGCAAAGA
1 AAAATTTTTTTTTAAATTAAAGACGCAAAGA
*
13529 AAAATATTTTTTTTCAGAA-TAAA-ACGCAGAGA
1 AAAAT-TTTTTTTT-A-AATTAAAGACGCAAAGA
13561 AAAA
1 AAAA
13565 GAAAAACGCA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
31 5 0.16
32 20 0.62
33 5 0.16
34 2 0.06
ACGTcount: A:0.51, C:0.07, G:0.10, T:0.31
Consensus pattern (31 bp):
AAAATTTTTTTTTAAATTAAAGACGCAAAGA
Found at i:15291 original size:19 final size:18
Alignment explanation
Indices: 15258--15293 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
15248 TTGAAATAGA
15258 TCTTCAAAAATCTTCAAG
1 TCTTCAAAAATCTTCAAG
*
15276 TCTTCAAATTATCTTCAA
1 TCTTCAAA-AATCTTCAA
15294 ATGGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.36, C:0.22, G:0.03, T:0.39
Consensus pattern (18 bp):
TCTTCAAAAATCTTCAAG
Found at i:20571 original size:15 final size:15
Alignment explanation
Indices: 20548--20589 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
20538 CATGAATGAA
20548 GAGAAAATCGAATAC
1 GAGAAAATCGAATAC
* *
20563 GAGATAATCGAATAT
1 GAGAAAATCGAATAC
*
20578 GAGACAATCGAA
1 GAGAAAATCGAA
20590 GCAGTTTCCA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.50, C:0.12, G:0.21, T:0.17
Consensus pattern (15 bp):
GAGAAAATCGAATAC
Found at i:21664 original size:15 final size:15
Alignment explanation
Indices: 21641--21682 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
21631 CATGAATGAA
21641 GAGAAAATCGAATAC-
1 GAGAAAATCGAAT-CT
*
21656 GAGATAATCGAATCT
1 GAGAAAATCGAATCT
*
21671 GAGACAATCGAA
1 GAGAAAATCGAA
21683 GAAGTTTCCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 1 0.04
15 23 0.96
ACGTcount: A:0.48, C:0.14, G:0.21, T:0.17
Consensus pattern (15 bp):
GAGAAAATCGAATCT
Found at i:26601 original size:21 final size:21
Alignment explanation
Indices: 26536--26594 Score: 91
Period size: 21 Copynumber: 2.8 Consensus size: 21
26526 GTGACACTAC
* *
26536 CCACCTGGGTTCTCAAGCAAA
1 CCACATGGGTGCTCAAGCAAA
*
26557 CCACATGGGTGCTTAAGCAAA
1 CCACATGGGTGCTCAAGCAAA
26578 CCACATGGGTGCTCAAG
1 CCACATGGGTGCTCAAG
26595 GCAACCATGT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.29, C:0.29, G:0.24, T:0.19
Consensus pattern (21 bp):
CCACATGGGTGCTCAAGCAAA
Found at i:29386 original size:21 final size:21
Alignment explanation
Indices: 29347--29395 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
29337 TCAATGCTTT
**
29347 AGGAATGCAAGAGGGATTTCAA
1 AGGAA-GCAAGAGCCATTTCAA
*
29369 AGGAAGCAAGAGCCATTTCCA
1 AGGAAGCAAGAGCCATTTCAA
29390 A-GAAGC
1 AGGAAGC
29396 TACAATTCTC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 5 0.21
21 14 0.58
22 5 0.21
ACGTcount: A:0.41, C:0.16, G:0.29, T:0.14
Consensus pattern (21 bp):
AGGAAGCAAGAGCCATTTCAA
Done.