Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013457.1 Corchorus olitorius cultivar O-4 contig13490, 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: 83568
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:9735 original size:18 final size:18
Alignment explanation
Indices: 9714--9749 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
9704 AATTATATAA
*
9714 ATAAATATAAATATAATG
1 ATAAATAAAAATATAATG
*
9732 ATAAATAAAAATCTAATG
1 ATAAATAAAAATATAATG
9750 CTTTTTTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.61, C:0.03, G:0.06, T:0.31
Consensus pattern (18 bp):
ATAAATAAAAATATAATG
Found at i:10855 original size:16 final size:16
Alignment explanation
Indices: 10834--10886 Score: 67
Period size: 16 Copynumber: 3.5 Consensus size: 16
10824 AAGATCTTAA
10834 CTAAACTTATGCAAGT
1 CTAAACTTATGCAAGT
* *
10850 CTAAACTTCT-TAA--
1 CTAAACTTATGCAAGT
10863 CTAAACTTATGCAAGT
1 CTAAACTTATGCAAGT
10879 CTAAACTT
1 CTAAACTT
10887 CCAACTGGCC
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
13 9 0.30
14 2 0.07
15 2 0.07
16 17 0.57
ACGTcount: A:0.38, C:0.21, G:0.08, T:0.34
Consensus pattern (16 bp):
CTAAACTTATGCAAGT
Found at i:10870 original size:29 final size:29
Alignment explanation
Indices: 10828--10887 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
10818 ATAATTAAGA
10828 TCTTAACTAAACTTATGCAAGTCTAAACT
1 TCTTAACTAAACTTATGCAAGTCTAAACT
10857 TCTTAACTAAACTTATGCAAGTCTAAACT
1 TCTTAACTAAACTTATGCAAGTCTAAACT
10886 TC
1 TC
10888 CAACTGGCCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.37, C:0.22, G:0.07, T:0.35
Consensus pattern (29 bp):
TCTTAACTAAACTTATGCAAGTCTAAACT
Found at i:11578 original size:41 final size:41
Alignment explanation
Indices: 11516--11597 Score: 137
Period size: 41 Copynumber: 2.0 Consensus size: 41
11506 ATTGTTTGGG
11516 AGTAACTGATTGTCTTCATTGTCCTGTGTAAAGGTTTCTTT
1 AGTAACTGATTGTCTTCATTGTCCTGTGTAAAGGTTTCTTT
* * *
11557 AGTACCTGATTGTTTTGATTGTCCTGTGTAAAGGTTTCTTT
1 AGTAACTGATTGTCTTCATTGTCCTGTGTAAAGGTTTCTTT
11598 CCGAACAAAG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.18, C:0.13, G:0.21, T:0.48
Consensus pattern (41 bp):
AGTAACTGATTGTCTTCATTGTCCTGTGTAAAGGTTTCTTT
Found at i:13578 original size:7 final size:7
Alignment explanation
Indices: 13566--13599 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
13556 TCAACATCCA
13566 TCTGCAT
1 TCTGCAT
13573 TCTGCAT
1 TCTGCAT
13580 TCTGCAT
1 TCTGCAT
13587 TCTGCAT
1 TCTGCAT
13594 TCTGCA
1 TCTGCA
13600 GCAGGCTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.15, C:0.29, G:0.15, T:0.41
Consensus pattern (7 bp):
TCTGCAT
Found at i:15391 original size:23 final size:22
Alignment explanation
Indices: 15347--15400 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
15337 TTTACACCAA
*
15347 AAAAAGAAAAAATACATTTCCCT
1 AAAAA-AAAAAATACATGTCCCT
15370 CAAAAAAAAAAATAC-TAGTCCCT
1 -AAAAAAAAAAATACAT-GTCCCT
*
15393 ATAAAAAA
1 AAAAAAAA
15401 CAAGAAAATG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 8 0.30
23 14 0.52
24 5 0.19
ACGTcount: A:0.61, C:0.17, G:0.04, T:0.19
Consensus pattern (22 bp):
AAAAAAAAAAATACATGTCCCT
Found at i:18430 original size:2 final size:2
Alignment explanation
Indices: 18423--18526 Score: 199
Period size: 2 Copynumber: 51.5 Consensus size: 2
18413 CTAGTTAACT
18423 TC TC TC TC TC TC TC TC TC TC TC GTC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC -TC TC TC TC TC TC TC TC TC TC
18466 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
18508 TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC T
18527 TTATTATCTT
Statistics
Matches: 101, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
2 99 0.98
3 2 0.02
ACGTcount: A:0.00, C:0.49, G:0.01, T:0.50
Consensus pattern (2 bp):
TC
Found at i:21550 original size:3 final size:3
Alignment explanation
Indices: 21518--21567 Score: 50
Period size: 3 Copynumber: 16.7 Consensus size: 3
21508 AATAAGAGAG
* *
21518 TAA TAA TAC TAG TAA TTAA TAA GT-A TAA TAA TAA TAA TAA TAA T-A
1 TAA TAA TAA TAA TAA -TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA
21563 TAA TA
1 TAA TA
21568 TCTCATTTTC
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
2 3 0.08
3 33 0.82
4 4 0.10
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:21632 original size:34 final size:35
Alignment explanation
Indices: 21589--21672 Score: 143
Period size: 35 Copynumber: 2.4 Consensus size: 35
21579 TCCTAATCAG
21589 TTAGTTAGAAGTTGTG-TTTTTTTTTTTAAAAATA
1 TTAGTTAGAAGTTGTGTTTTTTTTTTTTAAAAATA
* *
21623 TTAGTTAGAAGTTGTGTTTTTTTTTTTTTAAATTA
1 TTAGTTAGAAGTTGTGTTTTTTTTTTTTAAAAATA
21658 TTAGTTAGAAGTTGT
1 TTAGTTAGAAGTTGT
21673 TAATGTTGGT
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
34 16 0.34
35 31 0.66
ACGTcount: A:0.26, C:0.00, G:0.17, T:0.57
Consensus pattern (35 bp):
TTAGTTAGAAGTTGTGTTTTTTTTTTTTAAAAATA
Found at i:25212 original size:7 final size:7
Alignment explanation
Indices: 25200--25245 Score: 83
Period size: 7 Copynumber: 6.6 Consensus size: 7
25190 GACTTCTTGC
25200 TTGGGAA
1 TTGGGAA
25207 TTGGGAA
1 TTGGGAA
*
25214 TTGAGAA
1 TTGGGAA
25221 TTGGGAA
1 TTGGGAA
25228 TTGGGAA
1 TTGGGAA
25235 TTGGGAA
1 TTGGGAA
25242 TTGG
1 TTGG
25246 AATGATGCTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
7 37 1.00
ACGTcount: A:0.28, C:0.00, G:0.41, T:0.30
Consensus pattern (7 bp):
TTGGGAA
Found at i:31398 original size:11 final size:11
Alignment explanation
Indices: 31374--31413 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
31364 TCATTTTCGT
*
31374 TTTTTATTTT-
1 TTTTTGTTTTG
31384 TTTTTGTTTTG
1 TTTTTGTTTTG
*
31395 TTTTCGTTTTG
1 TTTTTGTTTTG
31406 TTTTTGTT
1 TTTTTGTT
31414 GCGCTGTCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
10 9 0.35
11 17 0.65
ACGTcount: A:0.03, C:0.03, G:0.12, T:0.82
Consensus pattern (11 bp):
TTTTTGTTTTG
Found at i:34668 original size:33 final size:36
Alignment explanation
Indices: 34624--34698 Score: 102
Period size: 36 Copynumber: 2.2 Consensus size: 36
34614 TTTTAAAAAA
*
34624 TTTTTTCAAAAAAAAG-AAAA-GAAG-AAAATGATT
1 TTTTTTCAAAAAAAAGAAAAATAAAGAAAAATGATT
* *
34657 TTTTTTGAAAAAACAGAAAAATAAAGAAAAATGATT
1 TTTTTTCAAAAAAAAGAAAAATAAAGAAAAATGATT
34693 TTTTTT
1 TTTTTT
34699 TTAATTTTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
33 14 0.39
34 4 0.11
35 3 0.08
36 15 0.42
ACGTcount: A:0.53, C:0.03, G:0.11, T:0.33
Consensus pattern (36 bp):
TTTTTTCAAAAAAAAGAAAAATAAAGAAAAATGATT
Found at i:41603 original size:2 final size:2
Alignment explanation
Indices: 41596--41624 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
41586 AAATTTAGGG
41596 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
41625 ATTTCTTCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:52271 original size:15 final size:15
Alignment explanation
Indices: 52253--52287 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
52243 ATGAATACAG
52253 TGATGAT-GATGACGA
1 TGATGATGGA-GACGA
52268 TGATGATGGAGACGA
1 TGATGATGGAGACGA
52283 TGATG
1 TGATG
52288 GATTGAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 17 0.89
16 2 0.11
ACGTcount: A:0.31, C:0.06, G:0.37, T:0.26
Consensus pattern (15 bp):
TGATGATGGAGACGA
Found at i:68052 original size:12 final size:14
Alignment explanation
Indices: 68020--68058 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 14
68010 ATTAATTAGC
68020 CTGCAACTGCAACAA
1 CTGCAACTGCAAC-A
68035 CTGCAACTGCAAC-
1 CTGCAACTGCAACA
68048 C-GCAACTGCAA
1 CTGCAACTGCAA
68059 GAGAGGAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 10 0.42
13 1 0.04
15 13 0.54
ACGTcount: A:0.36, C:0.36, G:0.15, T:0.13
Consensus pattern (14 bp):
CTGCAACTGCAACA
Found at i:81713 original size:5 final size:5
Alignment explanation
Indices: 81705--81731 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
81695 AGTAGAGTAA
81705 ATTAC ATTAC ATTAC ATTAC ATTAC AT
1 ATTAC ATTAC ATTAC ATTAC ATTAC AT
81732 AATAATAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.41, C:0.19, G:0.00, T:0.41
Consensus pattern (5 bp):
ATTAC
Found at i:83155 original size:13 final size:13
Alignment explanation
Indices: 83137--83161 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
83127 ATATAATCCT
83137 ATAATTTTTCATA
1 ATAATTTTTCATA
83150 ATAATTTTTCAT
1 ATAATTTTTCAT
83162 TTTGGATTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (13 bp):
ATAATTTTTCATA
Done.