Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014971.1 Corchorus olitorius cultivar O-4 contig15004, 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: 36805
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.31
Found at i:415 original size:30 final size:29
Alignment explanation
Indices: 379--444 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 29
369 AATTCTTGCT
*
379 TCTTGAAATAATTCTTCAAT-GATCTTCATA
1 TCTTGAAATAA-TCTTCAATAAATCTTCA-A
*
409 TCTTGAAATTATCTTCAATAAATCTTCAA
1 TCTTGAAATAATCTTCAATAAATCTTCAA
*
438 TCATGAA
1 TCTTGAA
445 CTTCGAATCT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 15 0.47
30 17 0.53
ACGTcount: A:0.36, C:0.17, G:0.06, T:0.41
Consensus pattern (29 bp):
TCTTGAAATAATCTTCAATAAATCTTCAA
Found at i:4434 original size:13 final size:13
Alignment explanation
Indices: 4416--4457 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
4406 GAACGTGATT
*
4416 AAATCTTAAACGA
1 AAATCTTAAAAGA
*
4429 AAATCTTAAAATA
1 AAATCTTAAAAGA
*
4442 AAAACTTAAAAGA
1 AAATCTTAAAAGA
4455 AAA
1 AAA
4458 ATTAGTAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.64, C:0.10, G:0.05, T:0.21
Consensus pattern (13 bp):
AAATCTTAAAAGA
Found at i:5498 original size:21 final size:20
Alignment explanation
Indices: 5474--5516 Score: 77
Period size: 21 Copynumber: 2.1 Consensus size: 20
5464 CCTTAGGCAA
5474 CTCCAATGAGCTTGAAATCTT
1 CTCCAATGAGCTTGAAA-CTT
5495 CTCCAATGAGCTTGAAACTT
1 CTCCAATGAGCTTGAAACTT
5515 CT
1 CT
5517 TTGTGAGTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.33
Consensus pattern (20 bp):
CTCCAATGAGCTTGAAACTT
Found at i:12330 original size:33 final size:33
Alignment explanation
Indices: 12293--12397 Score: 97
Period size: 33 Copynumber: 3.2 Consensus size: 33
12283 ATTAGCCTCC
* *
12293 AAAACAGAATTT-GTTTCATCATAAACAACACCT
1 AAAACAG-ATTTAGTGTCATCACAAACAACACCT
12326 AAAACAGATTTAGTGTCATCACAAACAACA-CT
1 AAAACAGATTTAGTGTCATCACAAACAACACCT
** * * ** *
12358 CAAATTAGGTTTAGTATCATTGCAAACAACATCT
1 -AAAACAGATTTAGTGTCATCACAAACAACACCT
12392 AAAACA
1 AAAACA
12398 CTCTTTGCAA
Statistics
Matches: 59, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
32 6 0.10
33 51 0.86
34 2 0.03
ACGTcount: A:0.46, C:0.20, G:0.09, T:0.26
Consensus pattern (33 bp):
AAAACAGATTTAGTGTCATCACAAACAACACCT
Found at i:15241 original size:21 final size:20
Alignment explanation
Indices: 15217--15259 Score: 77
Period size: 21 Copynumber: 2.1 Consensus size: 20
15207 CCTTAGGCAA
15217 CTCCAATGAGCTTGAAACCTT
1 CTCCAATGAGCTTGAAA-CTT
15238 CTCCAATGAGCTTGAAACTT
1 CTCCAATGAGCTTGAAACTT
15258 CT
1 CT
15260 TTGTGAGTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.30
Consensus pattern (20 bp):
CTCCAATGAGCTTGAAACTT
Found at i:16147 original size:25 final size:25
Alignment explanation
Indices: 16114--16162 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
16104 GCGGCAACTA
*
16114 AGGGTGTCGACACCCTC-TCAAAAG
1 AGGGTGTCGACACCCCCTTCAAAAG
*
16138 AGGGATGTCGATACCCCCTTCAAAA
1 AGGG-TGTCGACACCCCCTTCAAAA
16163 ACAATAGAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 4 0.19
25 11 0.52
26 6 0.29
ACGTcount: A:0.31, C:0.29, G:0.22, T:0.18
Consensus pattern (25 bp):
AGGGTGTCGACACCCCCTTCAAAAG
Found at i:21396 original size:26 final size:26
Alignment explanation
Indices: 21367--21428 Score: 88
Period size: 26 Copynumber: 2.4 Consensus size: 26
21357 CTGCCCTCCT
* *
21367 CGTCTCCCTCTTCCTTTCTCCGACAG
1 CGTCTCCCTCTTCCTTCCTCCGACAA
*
21393 CGTCTCCCTGTTCCTTCCTCCGACAA
1 CGTCTCCCTCTTCCTTCCTCCGACAA
*
21419 CCTCTCCCTC
1 CGTCTCCCTC
21429 ACCCTGCACG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.08, C:0.50, G:0.10, T:0.32
Consensus pattern (26 bp):
CGTCTCCCTCTTCCTTCCTCCGACAA
Found at i:25232 original size:2 final size:2
Alignment explanation
Indices: 25225--25256 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
25215 TATTGGAATA
25225 AT AT AT AT AT AT AT 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
25257 GAATTGAATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25621 original size:32 final size:33
Alignment explanation
Indices: 25580--25647 Score: 111
Period size: 34 Copynumber: 2.1 Consensus size: 33
25570 ATAAATATTC
25580 TAATTTTATGTCA-CTAGAAGCAATTTTTTATG
1 TAATTTTATGTCACCTAGAAGCAATTTTTTATG
*
25612 TAATTTTATGTCACTCTAGATGCAATTTTTTATG
1 TAATTTTATGTCAC-CTAGAAGCAATTTTTTATG
25646 TA
1 TA
25648 TATGGAAGTG
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
32 13 0.39
34 20 0.61
ACGTcount: A:0.29, C:0.10, G:0.12, T:0.49
Consensus pattern (33 bp):
TAATTTTATGTCACCTAGAAGCAATTTTTTATG
Found at i:26017 original size:3 final size:3
Alignment explanation
Indices: 26003--26068 Score: 82
Period size: 3 Copynumber: 21.7 Consensus size: 3
25993 AAATTTTATC
*
26003 AAT AAT ATAT AAT AAT AAT AAT AAT AAT AAT AAT AATT TAT CAA- AA-
1 AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT -AAT AAT
26049 AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AA
26069 ATATCTCTTA
Statistics
Matches: 57, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
2 4 0.07
3 47 0.82
4 6 0.11
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:28592 original size:2 final size:2
Alignment explanation
Indices: 28585--28622 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
28575 AAAAGCAGGT
* *
28585 TA TA TA TA CA CA TA TA -A 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 TA TA TA TA TA TA T
28623 TAATTAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:36630 original size:2 final size:2
Alignment explanation
Indices: 36623--36659 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
36613 CTAAAATCAA
36623 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
36660 CACACACACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.