Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015180.1 Corchorus olitorius cultivar O-4 contig15213, 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: 46667
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Found at i:4583 original size:33 final size:33
Alignment explanation
Indices: 4541--4707 Score: 325
Period size: 33 Copynumber: 5.1 Consensus size: 33
4531 ATTACGAGAA
4541 AAAGAAGAGCAAGCAAGAAGAGAAAGAGGCAGC
1 AAAGAAGAGCAAGCAAGAAGAGAAAGAGGCAGC
*
4574 AAAGAAGAGCAAGCAAGAAGAGGAAGAGGCAGC
1 AAAGAAGAGCAAGCAAGAAGAGAAAGAGGCAGC
4607 AAAGAAGAGCAAGCAAGAAGAGAAAGAGGCAGC
1 AAAGAAGAGCAAGCAAGAAGAGAAAGAGGCAGC
4640 AAAGAAGAGCAAGCAAGAAGAGAAAGAGGCAGC
1 AAAGAAGAGCAAGCAAGAAGAGAAAGAGGCAGC
4673 AAAGAAGAGCAAGCAAGAAGAGAAAGAGGCAGC
1 AAAGAAGAGCAAGCAAGAAGAGAAAGAGGCAGC
4706 AA
1 AA
4708 GGAAAGAAAA
Statistics
Matches: 132, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
33 132 1.00
ACGTcount: A:0.54, C:0.12, G:0.34, T:0.00
Consensus pattern (33 bp):
AAAGAAGAGCAAGCAAGAAGAGAAAGAGGCAGC
Found at i:4732 original size:99 final size:99
Alignment explanation
Indices: 4541--4732 Score: 305
Period size: 99 Copynumber: 1.9 Consensus size: 99
4531 ATTACGAGAA
*
4541 AAAGAAGAGCAAGCAAGAAGAGAAAGAGGCAGCAAAGAAGAGCAAGCAAGAAGAGGAAGAGGCAG
1 AAAGAAGAGCAAGCAAGAAGAGAAAGAGGCAGCAAAGAAGAGCAAGCAAGAAGAGAAAGAGGCAG
* ** * *
4606 CAAAGAAGAGCAAGCAAGAAGAGAAAGAGGCAGC
66 CAAAGAAGAGAAAAAAAGAAAAAAAAGAGGCAGC
4640 AAAGAAGAGCAAGCAAGAAGAGAAAGAGGCAGCAAAGAAGAGCAAGCAAGAAGAGAAAGAGGCAG
1 AAAGAAGAGCAAGCAAGAAGAGAAAGAGGCAGCAAAGAAGAGCAAGCAAGAAGAGAAAGAGGCAG
*
4705 CAAGGAA-AGAAAAAAAGGAAAAAAAAGA
66 CAAAGAAGAGAAAAAAA-GAAAAAAAAGA
4733 AAAAGAAATA
Statistics
Matches: 85, Mismatches: 7, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
98 6 0.07
99 79 0.93
ACGTcount: A:0.57, C:0.10, G:0.32, T:0.00
Consensus pattern (99 bp):
AAAGAAGAGCAAGCAAGAAGAGAAAGAGGCAGCAAAGAAGAGCAAGCAAGAAGAGAAAGAGGCAG
CAAAGAAGAGAAAAAAAGAAAAAAAAGAGGCAGC
Found at i:23873 original size:15 final size:15
Alignment explanation
Indices: 23853--23894 Score: 75
Period size: 15 Copynumber: 2.8 Consensus size: 15
23843 AGAAATAGCA
23853 CACCATCAGGACGCT
1 CACCATCAGGACGCT
23868 CACCATCAGGACGCT
1 CACCATCAGGACGCT
*
23883 TACCATCAGGAC
1 CACCATCAGGAC
23895 AACTTATATC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.29, C:0.38, G:0.19, T:0.14
Consensus pattern (15 bp):
CACCATCAGGACGCT
Found at i:25578 original size:31 final size:32
Alignment explanation
Indices: 25540--25618 Score: 133
Period size: 33 Copynumber: 2.5 Consensus size: 32
25530 ATCAATCAGT
25540 TATAAAACAAACAGA-TCAATCAATCTTCTCA
1 TATAAAACAAACAGACTCAATCAATCTTCTCA
*
25571 TATAAAACAAACCGATCTCAATCAATCTTCTCA
1 TATAAAACAAACAGA-CTCAATCAATCTTCTCA
25604 TATAAAACAAACAGA
1 TATAAAACAAACAGA
25619 ACGTGAAGTT
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
31 14 0.32
33 30 0.68
ACGTcount: A:0.49, C:0.23, G:0.04, T:0.24
Consensus pattern (32 bp):
TATAAAACAAACAGACTCAATCAATCTTCTCA
Found at i:27113 original size:45 final size:45
Alignment explanation
Indices: 27062--27151 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
27052 TATTCATTTT
27062 TAAGTATGTCCCATCTATTTTCATTTTTTCCATTTATCATATTAA
1 TAAGTATGTCCCATCTATTTTCATTTTTTCCATTTATCATATTAA
27107 TAAGTATGTCCCATCTATTTTCATTTTTTCCATTTATCATATTAA
1 TAAGTATGTCCCATCTATTTTCATTTTTTCCATTTATCATATTAA
27152 CAATATTAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.27, C:0.18, G:0.04, T:0.51
Consensus pattern (45 bp):
TAAGTATGTCCCATCTATTTTCATTTTTTCCATTTATCATATTAA
Found at i:27208 original size:12 final size:12
Alignment explanation
Indices: 27191--27216 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
27181 GTTTTTCTCC
27191 ATGAACATGCTT
1 ATGAACATGCTT
27203 ATGAACATGCTT
1 ATGAACATGCTT
27215 AT
1 AT
27217 TGGTCCATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (12 bp):
ATGAACATGCTT
Found at i:28633 original size:12 final size:12
Alignment explanation
Indices: 28616--28646 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
28606 ATCTTCTTCA
28616 TCCTCTCATCTT
1 TCCTCTCATCTT
*
28628 TCCTCTGATCTT
1 TCCTCTCATCTT
28640 TCCTCTC
1 TCCTCTC
28647 TTCAAGTTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.06, C:0.42, G:0.03, T:0.48
Consensus pattern (12 bp):
TCCTCTCATCTT
Found at i:30898 original size:37 final size:37
Alignment explanation
Indices: 30857--30930 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
30847 CTGAAAAAAG
30857 AAGCTAAAAGACGGTGAGAGAAATTAGGGTTTGGAAA
1 AAGCTAAAAGACGGTGAGAGAAATTAGGGTTTGGAAA
30894 AAGCTAAAAGACGGTGAGAGAAATTAGGGTTTGGAAA
1 AAGCTAAAAGACGGTGAGAGAAATTAGGGTTTGGAAA
30931 CTATTAGAGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.43, C:0.05, G:0.32, T:0.19
Consensus pattern (37 bp):
AAGCTAAAAGACGGTGAGAGAAATTAGGGTTTGGAAA
Found at i:32285 original size:37 final size:37
Alignment explanation
Indices: 32244--32316 Score: 128
Period size: 37 Copynumber: 2.0 Consensus size: 37
32234 ATTTGAAAAA
*
32244 AAAAACCTAAAAGACGGTGAGAGAAATTAGGGTTTGC
1 AAAAACCTAAAAGACAGTGAGAGAAATTAGGGTTTGC
*
32281 AAAAAGCTAAAAGACAGTGAGAGAAATTAGGGTTTG
1 AAAAACCTAAAAGACAGTGAGAGAAATTAGGGTTTG
32317 GAAACTATCA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.45, C:0.08, G:0.27, T:0.19
Consensus pattern (37 bp):
AAAAACCTAAAAGACAGTGAGAGAAATTAGGGTTTGC
Found at i:33767 original size:38 final size:39
Alignment explanation
Indices: 33715--33794 Score: 144
Period size: 38 Copynumber: 2.1 Consensus size: 39
33705 TGAAAAAAAA
*
33715 AAAAGAAGCTAAAAGACGGTTAGAGAAATTAGGGTTTGG
1 AAAAGAAGCTAAAAGACGGTGAGAGAAATTAGGGTTTGG
33754 AAAA-AAGCTAAAAGACGGTGAGAGAAATTAGGGTTTGG
1 AAAAGAAGCTAAAAGACGGTGAGAGAAATTAGGGTTTGG
33792 AAA
1 AAA
33795 CTATTAGAGT
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
38 36 0.90
39 4 0.10
ACGTcount: A:0.46, C:0.05, G:0.30, T:0.19
Consensus pattern (39 bp):
AAAAGAAGCTAAAAGACGGTGAGAGAAATTAGGGTTTGG
Found at i:34286 original size:37 final size:37
Alignment explanation
Indices: 34238--34314 Score: 154
Period size: 37 Copynumber: 2.1 Consensus size: 37
34228 ATGTATGCGC
34238 TTTTAACTCTTCCTTGAGGTCACTTATTGAGGGCCCT
1 TTTTAACTCTTCCTTGAGGTCACTTATTGAGGGCCCT
34275 TTTTAACTCTTCCTTGAGGTCACTTATTGAGGGCCCT
1 TTTTAACTCTTCCTTGAGGTCACTTATTGAGGGCCCT
34312 TTT
1 TTT
34315 AACAAAGATG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.16, C:0.23, G:0.18, T:0.43
Consensus pattern (37 bp):
TTTTAACTCTTCCTTGAGGTCACTTATTGAGGGCCCT
Found at i:35278 original size:38 final size:38
Alignment explanation
Indices: 35227--35305 Score: 140
Period size: 38 Copynumber: 2.1 Consensus size: 38
35217 GAAAAAAAAA
*
35227 AAAAAAGCTAAAAGACGGTTAGAGAAATTAAGGTTTGG
1 AAAAAAGCTAAAAGACGGTGAGAGAAATTAAGGTTTGG
*
35265 AAAAAAGCTAAAAGACGGTGAGAGAAATTAGGGTTTGG
1 AAAAAAGCTAAAAGACGGTGAGAGAAATTAAGGTTTGG
35303 AAA
1 AAA
35306 CTATTCGAGT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.48, C:0.05, G:0.28, T:0.19
Consensus pattern (38 bp):
AAAAAAGCTAAAAGACGGTGAGAGAAATTAAGGTTTGG
Found at i:36746 original size:36 final size:36
Alignment explanation
Indices: 36696--36770 Score: 141
Period size: 36 Copynumber: 2.1 Consensus size: 36
36686 TCTGAAAAAA
36696 AAAAGCTAAAAGACGGTGAGAGAAATTAGGGTTTGG
1 AAAAGCTAAAAGACGGTGAGAGAAATTAGGGTTTGG
*
36732 AAAAGCTAATAGACGGTGAGAGAAATTAGGGTTTGG
1 AAAAGCTAAAAGACGGTGAGAGAAATTAGGGTTTGG
36768 AAA
1 AAA
36771 CTATTAGAGT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.43, C:0.05, G:0.32, T:0.20
Consensus pattern (36 bp):
AAAAGCTAAAAGACGGTGAGAGAAATTAGGGTTTGG
Found at i:38561 original size:13 final size:13
Alignment explanation
Indices: 38543--38575 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
38533 ATAATTAATA
38543 AATATTTGATATT
1 AATATTTGATATT
38556 AATATTTGATATT
1 AATATTTGATATT
38569 AATATTT
1 AATATTT
38576 ATTTCCTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (13 bp):
AATATTTGATATT
Found at i:39047 original size:6 final size:6
Alignment explanation
Indices: 39036--39102 Score: 82
Period size: 6 Copynumber: 11.2 Consensus size: 6
39026 CTAAAATTCA
* ** *
39036 AGCTCG AGCTCG AGTTCG AGCTCG AATTCG ATAC-CG AGCTCG AGCTCG
1 AGCTCG AGCTCG AGCTCG AGCTCG AGCTCG A-GCTCG AGCTCG AGCTCG
39084 AGCTCG AGCTCG AGCTCG A
1 AGCTCG AGCTCG AGCTCG A
39103 CAGGTATATA
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
5 1 0.02
6 51 0.96
7 1 0.02
ACGTcount: A:0.21, C:0.30, G:0.30, T:0.19
Consensus pattern (6 bp):
AGCTCG
Found at i:40934 original size:41 final size:41
Alignment explanation
Indices: 40833--40936 Score: 156
Period size: 41 Copynumber: 2.5 Consensus size: 41
40823 GGATGTTTAC
*** *
40833 AAGTCATATTTTAGGCTTGAGCTTTTTTTGGCTGTAAAAAG
1 AAGTCATATTTTAGGCTTGTTTTTTTTTTGGCAGTAAAAAG
40874 AAGTCATATTTTAGGCTTGTTTTTTTTTTGGCAGTAAAGAA-
1 AAGTCATATTTTAGGCTTGTTTTTTTTTTGGCAGTAAA-AAG
40915 AAGTCATATTTTAGGCTTGTTT
1 AAGTCATATTTTAGGCTTGTTT
40937 AGTAGCCAAT
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
41 56 0.97
42 2 0.03
ACGTcount: A:0.26, C:0.09, G:0.20, T:0.45
Consensus pattern (41 bp):
AAGTCATATTTTAGGCTTGTTTTTTTTTTGGCAGTAAAAAG
Found at i:41655 original size:30 final size:30
Alignment explanation
Indices: 41580--41660 Score: 114
Period size: 28 Copynumber: 2.8 Consensus size: 30
41570 TCTACTAGCG
41580 TCGAAACGGGCTAAATTTATGATGTCACTC
1 TCGAAACGGGCTAAATTTATGATGTCACTC
41610 TCTG--A-GGGCTAAATTTATGATGTCACTC
1 TC-GAAACGGGCTAAATTTATGATGTCACTC
* *
41638 TCGAAACGGGCTGAATTTCTGAT
1 TCGAAACGGGCTAAATTTATGAT
41661 ATGTCAATCT
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
27 1 0.02
28 25 0.56
29 2 0.04
30 16 0.36
31 1 0.02
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.32
Consensus pattern (30 bp):
TCGAAACGGGCTAAATTTATGATGTCACTC
Found at i:42128 original size:17 final size:17
Alignment explanation
Indices: 42106--42138 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
42096 GTACAGTAAA
42106 TACAAAATACAAAAATT
1 TACAAAATACAAAAATT
42123 TACAAAATACAAAAAT
1 TACAAAATACAAAAAT
42139 GTAGTTAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.67, C:0.12, G:0.00, T:0.21
Consensus pattern (17 bp):
TACAAAATACAAAAATT
Found at i:43101 original size:85 final size:85
Alignment explanation
Indices: 42958--43129 Score: 326
Period size: 85 Copynumber: 2.0 Consensus size: 85
42948 ATAAGTAACT
* *
42958 ATCATTATTACAATTCATTACTATTGCCATAAGAGAGATTAGATTCAAGGTTCAACATGAGAAAC
1 ATCATTATTACAATTCATTACTATTACCATAAGAGAGATTAGATCCAAGGTTCAACATGAGAAAC
43023 AAACCCTAACCCTATAGTTA
66 AAACCCTAACCCTATAGTTA
43043 ATCATTATTACAATTCATTACTATTACCATAAGAGAGATTAGATCCAAGGTTCAACATGAGAAAC
1 ATCATTATTACAATTCATTACTATTACCATAAGAGAGATTAGATCCAAGGTTCAACATGAGAAAC
43108 AAACCCTAACCCTATAGTTA
66 AAACCCTAACCCTATAGTTA
43128 AT
1 AT
43130 GAAGCTACCA
Statistics
Matches: 85, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
85 85 1.00
ACGTcount: A:0.41, C:0.19, G:0.11, T:0.29
Consensus pattern (85 bp):
ATCATTATTACAATTCATTACTATTACCATAAGAGAGATTAGATCCAAGGTTCAACATGAGAAAC
AAACCCTAACCCTATAGTTA
Found at i:43423 original size:96 final size:89
Alignment explanation
Indices: 43264--43443 Score: 270
Period size: 96 Copynumber: 1.9 Consensus size: 89
43254 AAGATAGACC
*
43264 AAAGGAAAAAAATCAAAACCCTAATTTTTGGGATCTGATGCTACACTGGCTCTATTCCTTCATAT
1 AAAGGAAAAAAATCAAAACCCTAATTTTTGGGATCTGATGCTACACTGGCCCTATTCCTTCATAT
43329 TCGGAAAATAAAAATAAAAACCAGAG
66 TCGGAAAA-AAAAA-AAAAACCAGAG
*
43355 AAAGGAAAAAAATCAAAACCGATTCCTAATTTTTGGGATCTGATGCTACACTGGCCCTATTTCTT
1 AAAGGAAAAAAATCAAAA-C----CCTAATTTTTGGGATCTGATGCTACACTGGCCCTATTCCTT
*
43420 CATATTTGGAAAAAAAAAAAAAAC
61 CATATTCGGAAAAAAAAAAAAAAC
43444 ACCAAAGATC
Statistics
Matches: 81, Mismatches: 3, Indels: 7
0.89 0.03 0.08
Matches are distributed among these distances:
91 18 0.22
92 1 0.01
94 6 0.07
95 5 0.06
96 51 0.63
ACGTcount: A:0.43, C:0.17, G:0.14, T:0.26
Consensus pattern (89 bp):
AAAGGAAAAAAATCAAAACCCTAATTTTTGGGATCTGATGCTACACTGGCCCTATTCCTTCATAT
TCGGAAAAAAAAAAAAAACCAGAG
Found at i:43622 original size:22 final size:22
Alignment explanation
Indices: 43594--43637 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
43584 TACCAATCAC
*
43594 CTTCAAACGGTCCTCCTTGGTA
1 CTTCAAACAGTCCTCCTTGGTA
43616 CTTCAAACAGTCCTCCTTGGTA
1 CTTCAAACAGTCCTCCTTGGTA
43638 TGATTTTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.32, G:0.16, T:0.32
Consensus pattern (22 bp):
CTTCAAACAGTCCTCCTTGGTA
Found at i:43861 original size:11 final size:11
Alignment explanation
Indices: 43845--43869 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
43835 AATTTTATAC
43845 CTTAGCAGCTT
1 CTTAGCAGCTT
43856 CTTAGCAGCTT
1 CTTAGCAGCTT
43867 CTT
1 CTT
43870 GTTAATGTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.28, G:0.16, T:0.40
Consensus pattern (11 bp):
CTTAGCAGCTT
Done.