Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023700.1 Corchorus olitorius cultivar O-4 contig23733, 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: 69119
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:610 original size:15 final size:15
Alignment explanation
Indices: 580--621 Score: 75
Period size: 15 Copynumber: 2.7 Consensus size: 15
570 TTACTTTGTT
580 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
596 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
611 TTGTTTTCTGT
1 TTGTTTTCTGT
622 CAACCTCTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 17 0.65
16 9 0.35
ACGTcount: A:0.12, C:0.07, G:0.14, T:0.67
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:1108 original size:36 final size:35
Alignment explanation
Indices: 1045--1125 Score: 92
Period size: 36 Copynumber: 2.3 Consensus size: 35
1035 TTTGTGTCAT
* * *
1045 AAAAAAAAATTGTTTTGTGTTTTTGCGTTTTTCTAA
1 AAAAAAAAATTATTTTGTGTTTATGCG-TTTTCAAA
*
1081 AAAAAAAAATTATTTTCT-TGTTATGCGTTTTCAAA
1 AAAAAAAAATTATTTTGTGT-TTATGCGTTTTCAAA
1116 AAGAAAAAAA
1 AA-AAAAAAA
1126 ATTTTCCTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
35 10 0.26
36 29 0.74
ACGTcount: A:0.42, C:0.06, G:0.11, T:0.41
Consensus pattern (35 bp):
AAAAAAAAATTATTTTGTGTTTATGCGTTTTCAAA
Found at i:5816 original size:10 final size:10
Alignment explanation
Indices: 5801--5826 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
5791 ACCGCCAATT
5801 TCGGTTTCGG
1 TCGGTTTCGG
5811 TCGGTTTCGG
1 TCGGTTTCGG
5821 TCGGTT
1 TCGGTT
5827 ATATTTGGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.00, C:0.19, G:0.38, T:0.42
Consensus pattern (10 bp):
TCGGTTTCGG
Found at i:11637 original size:15 final size:16
Alignment explanation
Indices: 11607--11644 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
11597 TTACTTTGTT
*
11607 TTGTTTTCTAGTTTAA
1 TTGTTTTATAGTTTAA
11623 TTGTTTTAT-GTTTAA
1 TTGTTTTATAGTTTAA
11638 TTGTTTT
1 TTGTTTT
11645 CTGTCAACCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.16, C:0.03, G:0.13, T:0.68
Consensus pattern (16 bp):
TTGTTTTATAGTTTAA
Found at i:12570 original size:18 final size:18
Alignment explanation
Indices: 12547--12581 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
12537 TACACTTTAA
12547 ATCATTAGGAAA-AATTAT
1 ATCATTA-GAAAGAATTAT
12565 ATCATTAGAAAGAATTA
1 ATCATTAGAAAGAATTA
12582 ATTGAGACCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.51, C:0.06, G:0.11, T:0.31
Consensus pattern (18 bp):
ATCATTAGAAAGAATTAT
Found at i:12859 original size:36 final size:35
Alignment explanation
Indices: 12790--12881 Score: 139
Period size: 36 Copynumber: 2.6 Consensus size: 35
12780 ATAAACTATA
* *
12790 AAAACAACTAAACATGACAATAGTATTACACAATT
1 AAAACAACTAAACATGAGAATAGTAATACACAATT
*
12825 AAAACAACTAAACATGAGAATACGTAATAGACAATT
1 AAAACAACTAAACATGAGAATA-GTAATACACAATT
*
12861 AAAATAACTAAACATGAGAAT
1 AAAACAACTAAACATGAGAAT
12882 GCTAGTTTTA
Statistics
Matches: 52, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
35 21 0.40
36 31 0.60
ACGTcount: A:0.57, C:0.14, G:0.09, T:0.21
Consensus pattern (35 bp):
AAAACAACTAAACATGAGAATAGTAATACACAATT
Found at i:12899 original size:25 final size:25
Alignment explanation
Indices: 12865--12912 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
12855 ACAATTAAAA
*
12865 TAACTAAACATGAGAATGCTAGTTT
1 TAACTAAACATGAGAATACTAGTTT
12890 TAACTAAACATGAGAATACTAGT
1 TAACTAAACATGAGAATACTAGT
12913 AGACAATTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.44, C:0.12, G:0.15, T:0.29
Consensus pattern (25 bp):
TAACTAAACATGAGAATACTAGTTT
Found at i:14512 original size:51 final size:51
Alignment explanation
Indices: 14436--14545 Score: 177
Period size: 51 Copynumber: 2.2 Consensus size: 51
14426 TGAATGACAT
*
14436 TATATTCTTCTGCTTTTTTTTTGTCATACAATGACAAT-ATATTCAAACGAA
1 TATATTCTTCTGCTCTTTTTTTGTCATACAATGACAATGA-ATTCAAACGAA
* *
14487 TATATTCTTCTTCTCTTTTTTTGTCATACAATGACATTGAATTCAAACGAA
1 TATATTCTTCTGCTCTTTTTTTGTCATACAATGACAATGAATTCAAACGAA
14538 TATATTCT
1 TATATTCT
14546 AAAGGAAAGG
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
51 54 0.98
52 1 0.02
ACGTcount: A:0.30, C:0.16, G:0.07, T:0.46
Consensus pattern (51 bp):
TATATTCTTCTGCTCTTTTTTTGTCATACAATGACAATGAATTCAAACGAA
Found at i:17731 original size:41 final size:42
Alignment explanation
Indices: 17679--17758 Score: 153
Period size: 41 Copynumber: 1.9 Consensus size: 42
17669 TAATTTTTTG
17679 TTTTAGTTTAGTATTCTGTTGGAAATTTGGAACTTTGTTTCA
1 TTTTAGTTTAGTATTCTGTTGGAAATTTGGAACTTTGTTTCA
17721 TTTT-GTTTAGTATTCTGTTGGAAATTTGGAACTTTGTT
1 TTTTAGTTTAGTATTCTGTTGGAAATTTGGAACTTTGTT
17759 GATTTTGATT
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
41 34 0.89
42 4 0.11
ACGTcount: A:0.20, C:0.06, G:0.20, T:0.54
Consensus pattern (42 bp):
TTTTAGTTTAGTATTCTGTTGGAAATTTGGAACTTTGTTTCA
Found at i:17771 original size:46 final size:42
Alignment explanation
Indices: 17674--17765 Score: 138
Period size: 41 Copynumber: 2.3 Consensus size: 42
17664 GTTGTTAATT
17674 TTTTG-TTTTAGTTTAGTATTCTGTTGGAAATTTGGAACTTTG
1 TTTTGATTTT-GTTTAGTATTCTGTTGGAAATTTGGAACTTTG
*
17716 -TTTCATTTTGTTTAGTATTCTGTTGGAAATTTGGAACTTTG
1 TTTTGATTTTGTTTAGTATTCTGTTGGAAATTTGGAACTTTG
17757 --TTGATTTTG
1 TTTTGATTTTG
17766 ATTTTGGCTT
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
40 8 0.17
41 35 0.74
42 4 0.09
ACGTcount: A:0.18, C:0.05, G:0.21, T:0.55
Consensus pattern (42 bp):
TTTTGATTTTGTTTAGTATTCTGTTGGAAATTTGGAACTTTG
Found at i:19079 original size:2 final size:2
Alignment explanation
Indices: 19072--19130 Score: 76
Period size: 2 Copynumber: 32.5 Consensus size: 2
19062 ATAATATGTG
19072 TA TA TA TA TA TA TA TA -A TA TA -A TA TA TA -A TA TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19110 TA TA -A TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
19131 TTTTCTTATA
Statistics
Matches: 51, Mismatches: 0, Indels: 12
0.81 0.00 0.19
Matches are distributed among these distances:
1 6 0.12
2 45 0.88
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:19098 original size:7 final size:7
Alignment explanation
Indices: 19072--19130 Score: 86
Period size: 7 Copynumber: 8.4 Consensus size: 7
19062 ATAATATGTG
19072 TATAT-A
1 TATATAA
19078 TATATATA
1 TATATA-A
19086 TAATATAA
1 T-ATATAA
19094 TATATAA
1 TATATAA
19101 TATATAA
1 TATATAA
19108 TATATAA
1 TATATAA
19115 TATAT-A
1 TATATAA
19121 TATATAA
1 TATATAA
19128 TAT
1 TAT
19131 TTTTCTTATA
Statistics
Matches: 49, Mismatches: 0, Indels: 7
0.88 0.00 0.12
Matches are distributed among these distances:
6 11 0.22
7 29 0.59
8 4 0.08
9 5 0.10
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (7 bp):
TATATAA
Found at i:29445 original size:44 final size:44
Alignment explanation
Indices: 29395--29482 Score: 167
Period size: 44 Copynumber: 2.0 Consensus size: 44
29385 CTACAATTTC
*
29395 TTCAATGAAGAAAATGGAAAAAGGCTCTGTTTTGGAACATTACA
1 TTCAATGAAGAAAATGGAAAAAGGCTCTGCTTTGGAACATTACA
29439 TTCAATGAAGAAAATGGAAAAAGGCTCTGCTTTGGAACATTACA
1 TTCAATGAAGAAAATGGAAAAAGGCTCTGCTTTGGAACATTACA
29483 GGCAAGATTA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.41, C:0.12, G:0.20, T:0.26
Consensus pattern (44 bp):
TTCAATGAAGAAAATGGAAAAAGGCTCTGCTTTGGAACATTACA
Found at i:29510 original size:17 final size:17
Alignment explanation
Indices: 29488--29522 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
29478 TTACAGGCAA
29488 GATTACAAGTTGAAAAG
1 GATTACAAGTTGAAAAG
29505 GATTACAAGTTGAAAAG
1 GATTACAAGTTGAAAAG
29522 G
1 G
29523 CACCTTAGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.46, C:0.06, G:0.26, T:0.23
Consensus pattern (17 bp):
GATTACAAGTTGAAAAG
Found at i:37177 original size:13 final size:12
Alignment explanation
Indices: 37159--37191 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
37149 TAGGCTTTTC
*
37159 TTTTTTTCTTAT
1 TTTTTTTCCTAT
37171 TTTTTTTCCTAT
1 TTTTTTTCCTAT
37183 TTTTTTTCC
1 TTTTTTTCC
37192 CTTTCTTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.06, C:0.15, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTTTTTCCTAT
Found at i:37713 original size:252 final size:252
Alignment explanation
Indices: 37269--37772 Score: 884
Period size: 252 Copynumber: 2.0 Consensus size: 252
37259 CTTTTTAGCA
* * **
37269 GGTAAAAGTACCCGGGAGGTCCCTGTATTATACGAAATGTTGATTTTGGTCTTTGTACTTTTTTT
1 GGTAAAAGTACCCGAGAGGTCCCTGTACTATACGAAATGTTGATTTTGGTCCCTGTACTTTTTTT
* * **
37334 TCTACAAATTCGTCCCTCTATTATCAGAATCTATCACCCGAGGTCCCTCACGTTAGTGTGCCGTG
66 TCTACAAATTCGTCCCTCTACTATCAGAACCTATCACCCGAGGTCCCTCACGTTAGCATGCCGTG
* * * *
37399 ACAGACCCGTCAAATATGCTGACGTGGCACTAGCACCGTCTTTTTTGCTGACGTGGCAGGTGACA
131 ACAGACCCATCAAATATGCTGACATGACACTAACACCGTCTTTTTTGCTGACGTGGCAGGTGACA
37464 CGTGGAATAAAAATTAAATA-TTTTTTAATATATTTTATTTTATTGAAATTTATTTT
196 CGTGGAATAAAAATTAAATATTTTTTTAATATATTTTATTTTATTGAAATTTATTTT
37520 GGTAAAAGTACCCGAGAGGTCCCTGTACTATACGAAATGTTGATTTTGGTCCCTGTACTTTTTTT
1 GGTAAAAGTACCCGAGAGGTCCCTGTACTATACGAAATGTTGATTTTGGTCCCTGTAC-TTTTTT
37585 TTCTACAAATTCGTCCCTCTACTATCAGAACCTATCACCCGAGGTCCCTCACGTTAGCATGCCGT
65 TTCTACAAATTCGTCCCTCTACTATCAGAACCTATCACCCGAGGTCCCTCACGTTAGCATGCCGT
37650 GACAGACCCATCAAATATGCTGACATGACACTAACACCGTCTTTTTTGCTGACGTGGCAGGTGAC
130 GACAGACCCATCAAATATGCTGACATGACACTAACACCGTCTTTTTTGCTGACGTGGCAGGTGAC
37715 ACGTGGAATAAAAATTAAATATTTTTTTAATATATTTTATTTTATTGAAATTTATTTT
195 ACGTGGAATAAAAATTAAATATTTTTTTAATATATTTTATTTTATTGAAATTTATTTT
37773 TTAAAAAAAT
Statistics
Matches: 239, Mismatches: 12, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
251 54 0.23
252 149 0.62
253 36 0.15
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.36
Consensus pattern (252 bp):
GGTAAAAGTACCCGAGAGGTCCCTGTACTATACGAAATGTTGATTTTGGTCCCTGTACTTTTTTT
TCTACAAATTCGTCCCTCTACTATCAGAACCTATCACCCGAGGTCCCTCACGTTAGCATGCCGTG
ACAGACCCATCAAATATGCTGACATGACACTAACACCGTCTTTTTTGCTGACGTGGCAGGTGACA
CGTGGAATAAAAATTAAATATTTTTTTAATATATTTTATTTTATTGAAATTTATTTT
Found at i:38866 original size:13 final size:13
Alignment explanation
Indices: 38850--38893 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
38840 ATTTTTTTCT
38850 TTTTTTTTGGTTA
1 TTTTTTTTGGTTA
*
38863 TTTTTTTTGAGATA
1 TTTTTTTTG-GTTA
* *
38877 CTTTTTTTCGTTA
1 TTTTTTTTGGTTA
38890 TTTT
1 TTTT
38894 AAGAAGAGGT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 15 0.60
14 10 0.40
ACGTcount: A:0.11, C:0.05, G:0.11, T:0.73
Consensus pattern (13 bp):
TTTTTTTTGGTTA
Found at i:38950 original size:5 final size:5
Alignment explanation
Indices: 38903--38948 Score: 76
Period size: 5 Copynumber: 9.4 Consensus size: 5
38893 TAAGAAGAGG
*
38903 TTGTT TTGTT TTGTT TTGTT TTGTT TTGTT TTGTT TTATT TT-TT TT
1 TTGTT TTGTT TTGTT TTGTT TTGTT TTGTT TTGTT TTGTT TTGTT TT
38949 TTCAAAACTT
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
4 4 0.10
5 36 0.90
ACGTcount: A:0.02, C:0.00, G:0.15, T:0.83
Consensus pattern (5 bp):
TTGTT
Found at i:39641 original size:21 final size:21
Alignment explanation
Indices: 39602--39641 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
39592 TTATATCAAC
*
39602 TACTTTTTTTACTTGATTTAT
1 TACTTTTTTTACTTAATTTAT
39623 TACTTTTTTT-CTCTAATTT
1 TACTTTTTTTACT-TAATTT
39642 TTTTTATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.17, C:0.12, G:0.03, T:0.68
Consensus pattern (21 bp):
TACTTTTTTTACTTAATTTAT
Found at i:40274 original size:38 final size:38
Alignment explanation
Indices: 40223--40303 Score: 126
Period size: 38 Copynumber: 2.1 Consensus size: 38
40213 TATAAACAAA
* *
40223 TTAAGAGTTGACTGATTAAAACATTTAAATTTGTAAAT
1 TTAAGAGTCGACTGATTAAAACATTTAAATTTATAAAT
**
40261 TTAAGAGTCGACTGATTAAAATGTTTAAATTTATAAAT
1 TTAAGAGTCGACTGATTAAAACATTTAAATTTATAAAT
40299 TTAAG
1 TTAAG
40304 TAGGAGAGAG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.42, C:0.05, G:0.14, T:0.40
Consensus pattern (38 bp):
TTAAGAGTCGACTGATTAAAACATTTAAATTTATAAAT
Found at i:61101 original size:18 final size:18
Alignment explanation
Indices: 61074--61108 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
61064 TCGGGGGATT
61074 CTCCTCTTTCTGTTATGG
1 CTCCTCTTTCTGTTATGG
*
61092 CTCCTTTTTCTGTTATG
1 CTCCTCTTTCTGTTATG
61109 CCCAAAACTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.06, C:0.26, G:0.14, T:0.54
Consensus pattern (18 bp):
CTCCTCTTTCTGTTATGG
Found at i:66540 original size:24 final size:25
Alignment explanation
Indices: 66487--66539 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
66477 TTGGGCCATA
*
66487 AAAATTGTTTTTATCTAACCTGTAT
1 AAAATTGTTTTTATCTAACCTATAT
66512 AAAATTGTTTTTATCTAACCTATAT
1 AAAATTGTTTTTATCTAACCTATAT
66537 AAA
1 AAA
66540 TATGGCTCAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.38, C:0.11, G:0.06, T:0.45
Consensus pattern (25 bp):
AAAATTGTTTTTATCTAACCTATAT
Done.