Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021252.1 Corchorus olitorius cultivar O-4 contig21285, 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: 44960
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:1405 original size:24 final size:23
Alignment explanation
Indices: 1361--1409 Score: 55
Period size: 24 Copynumber: 2.1 Consensus size: 23
1351 ACTGGGCTGC
1361 AAAAGTCTATTGCATCCAAAAGTT
1 AAAAGTCTATTGCATCCAAAA-TT
**
1385 AAAA-TCTAATTGCATTTAAAATT
1 AAAAGTCT-ATTGCATCCAAAATT
1408 AA
1 AA
1410 TTTAAATTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
23 7 0.32
24 15 0.68
ACGTcount: A:0.47, C:0.12, G:0.08, T:0.33
Consensus pattern (23 bp):
AAAAGTCTATTGCATCCAAAATT
Found at i:15794 original size:21 final size:21
Alignment explanation
Indices: 15770--15814 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
15760 GTAAGTGATG
*
15770 AAGT-AGTGGAATTGATGATTA
1 AAGTGAGT-GAATTGATGAATA
*
15791 AAGTGAGTGAATTTATGAATA
1 AAGTGAGTGAATTGATGAATA
15812 AAG
1 AAG
15815 GTAATAGAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 18 0.86
22 3 0.14
ACGTcount: A:0.42, C:0.00, G:0.27, T:0.31
Consensus pattern (21 bp):
AAGTGAGTGAATTGATGAATA
Found at i:23713 original size:16 final size:14
Alignment explanation
Indices: 23682--23717 Score: 54
Period size: 16 Copynumber: 2.4 Consensus size: 14
23672 AGTGAAGGAG
23682 GAAAAAGAAGAAAA
1 GAAAAAGAAGAAAA
23696 GAAAAAGAGAGAAAAA
1 GAAAAAGA-AG-AAAA
23712 GAAAAA
1 GAAAAA
23718 AAGGAAAGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 8 0.40
15 2 0.10
16 10 0.50
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (14 bp):
GAAAAAGAAGAAAA
Found at i:26118 original size:15 final size:16
Alignment explanation
Indices: 26096--26146 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
26086 ACCAGCAGAC
26096 CCGAAACCCGAATGA-
1 CCGAAACCCGAATGAG
26111 CCTG-AACCC-AGATGAG
1 CC-GAAACCCGA-ATGAG
*
26127 CCGAAACCCGAATGAT
1 CCGAAACCCGAATGAG
26143 CCGA
1 CCGA
26147 GTAAATTACC
Statistics
Matches: 30, Mismatches: 1, Indels: 9
0.75 0.03 0.22
Matches are distributed among these distances:
14 1 0.03
15 12 0.40
16 16 0.53
17 1 0.03
ACGTcount: A:0.35, C:0.33, G:0.22, T:0.10
Consensus pattern (16 bp):
CCGAAACCCGAATGAG
Found at i:26817 original size:131 final size:131
Alignment explanation
Indices: 26651--26913 Score: 422
Period size: 131 Copynumber: 2.0 Consensus size: 131
26641 GTTTAAGAAA
* * *
26651 TATATTTTAAAAATTCTAATATATCTAAGTTTTTTAATTAAATTAGTAAAATGGTAAAAATAAAA
1 TATATTTTAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAACAAAA
*
26716 TAGGTATAAGGATATTAGATTTAATTAAATATAAA-AGAGTTTTTAGTTGAGTAAAACTATAAAA
66 TAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAA
26780 G
131 G
*
26781 TATA-TTTAAGAAATTTCTCATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAACAA
1 TATATTTTAA-AAA-TTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAACAA
** *
26845 AATATTTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAATTATAA
64 AATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAA
26910 AAG
129 AAG
26913 T
1 T
26914 TTTAACAATG
Statistics
Matches: 122, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
129 5 0.04
130 7 0.06
131 80 0.66
132 30 0.25
ACGTcount: A:0.48, C:0.02, G:0.11, T:0.39
Consensus pattern (131 bp):
TATATTTTAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAACAAAA
TAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAA
G
Found at i:28522 original size:31 final size:32
Alignment explanation
Indices: 28487--28633 Score: 198
Period size: 34 Copynumber: 4.6 Consensus size: 32
28477 TTAAATTTAA
28487 TTGACACCAGAAGTTGTCATATTAA-ATTATC
1 TTGACACCAGAAGTTGTCATATTAATATTATC
28518 TTGACACCAGAAGTTGTCATATTATATTATTATC
1 TTGACACCAGAAGTTGTCATATTA-A-TATTATC
28552 TTGACACCAGAAGTTGTCATGA--AA-ATT-T-
1 TTGACACCAGAAGTTGTCAT-ATTAATATTATC
*
28580 TTGACACCAGAAGTTGTCATATCAAATTATTATC
1 TTGACACCAGAAGTTGTCATAT-TAA-TATTATC
28614 TTGACACCAGAAGTTGTCAT
1 TTGACACCAGAAGTTGTCAT
28634 GCTGAGGAAA
Statistics
Matches: 105, Mismatches: 0, Indels: 19
0.85 0.00 0.15
Matches are distributed among these distances:
27 1 0.01
28 20 0.19
29 1 0.01
30 5 0.05
31 24 0.23
32 5 0.05
33 2 0.02
34 46 0.44
35 1 0.01
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.35
Consensus pattern (32 bp):
TTGACACCAGAAGTTGTCATATTAATATTATC
Found at i:28599 original size:62 final size:63
Alignment explanation
Indices: 28487--28666 Score: 247
Period size: 62 Copynumber: 2.8 Consensus size: 63
28477 TTAAATTTAA
* * *
28487 TTGACACCAGAAGTTGTCAT-ATTAAATTATCTTGACACCAGAAGTTGTCATATTATATTATTAT
1 TTGACACCAGAAGTTGTCATGA-GAAATT-T-TTGACACCAGAAGTTGTCATATCAAATTATTAT
28551 C
63 C
28552 TTGACACCAGAAGTTGTCATGA-AAATTTTTGACACCAGAAGTTGTCATATCAAATTATTATC
1 TTGACACCAGAAGTTGTCATGAGAAATTTTTGACACCAGAAGTTGTCATATCAAATTATTATC
*
28614 TTGACACCAGAAGTTGTCATGCTGAGGAAATTATTGACACCAGAAGTTGTCAT
1 TTGACACCAGAAGTTGTCA---TGA-GAAATTTTTGACACCAGAAGTTGTCAT
28667 CCTCAGATTG
Statistics
Matches: 106, Mismatches: 3, Indels: 10
0.89 0.03 0.08
Matches are distributed among these distances:
62 51 0.48
63 1 0.01
64 5 0.05
65 23 0.22
66 1 0.01
67 25 0.24
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (63 bp):
TTGACACCAGAAGTTGTCATGAGAAATTTTTGACACCAGAAGTTGTCATATCAAATTATTATC
Found at i:36552 original size:15 final size:16
Alignment explanation
Indices: 36519--36558 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
36509 TTACTTTGCT
36519 TTGTTTTCTAGTATAA
1 TTGTTTTCTAGTATAA
*
36535 TTGTTTTCT-GTTTAA
1 TTGTTTTCTAGTATAA
*
36550 TTGCTTTCT
1 TTGTTTTCT
36559 TTCAACCTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.15, C:0.10, G:0.12, T:0.62
Consensus pattern (16 bp):
TTGTTTTCTAGTATAA
Found at i:39563 original size:15 final size:16
Alignment explanation
Indices: 39530--39569 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
39520 TTACTTTGCT
39530 TTGTTTTCTAGTATAA
1 TTGTTTTCTAGTATAA
*
39546 TTGTTTTCT-GTTTAA
1 TTGTTTTCTAGTATAA
*
39561 TTGCTTTCT
1 TTGTTTTCT
39570 TTCAACCTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.15, C:0.10, G:0.12, T:0.62
Consensus pattern (16 bp):
TTGTTTTCTAGTATAA
Found at i:40245 original size:42 final size:42
Alignment explanation
Indices: 40195--40319 Score: 153
Period size: 42 Copynumber: 3.0 Consensus size: 42
40185 ATTATTTTTG
*
40195 TTGTTTAATTAAGGTGAAAGTAAATATATAATGAATTAAAAC
1 TTGTTTAATTAAGGTGAAAGTAAATATAGAATGAATTAAAAC
* * * **
40237 TTGTTTAATTAATGAGAAAGGAAATATAGAATGAATTAAATG
1 TTGTTTAATTAAGGTGAAAGTAAATATAGAATGAATTAAAAC
* * *
40279 TTGTATT-ACTAAGATAAAAGTAAATATAGAATGAATTAAAA
1 TTGT-TTAATTAAGGTGAAAGTAAATATAGAATGAATTAAAA
40320 GTTGATTTCA
Statistics
Matches: 69, Mismatches: 13, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
42 67 0.97
43 2 0.03
ACGTcount: A:0.50, C:0.02, G:0.15, T:0.34
Consensus pattern (42 bp):
TTGTTTAATTAAGGTGAAAGTAAATATAGAATGAATTAAAAC
Found at i:40777 original size:15 final size:15
Alignment explanation
Indices: 40757--40791 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
40747 GATCTTGGAT
*
40757 GTTTGAGTCAGTTTA
1 GTTTGAGTCAGTTGA
40772 GTTTGAGTCAGTTGA
1 GTTTGAGTCAGTTGA
40787 GTTTG
1 GTTTG
40792 TTGAGTTAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.17, C:0.06, G:0.31, T:0.46
Consensus pattern (15 bp):
GTTTGAGTCAGTTGA
Found at i:44527 original size:2 final size:2
Alignment explanation
Indices: 44520--44545 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
44510 GCATACATAC
44520 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
44546 TTGAAGGCTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.