Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017773.1 Corchorus olitorius cultivar O-4 contig17806, 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: 45207
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:1010 original size:17 final size:18
Alignment explanation
Indices: 988--1038 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
978 CTGCCACGTC
*
988 ATATTTTTTATAAAGA-A-
1 ATATTTTTTA-AAAAATAT
1005 ATATTTTTTAAAAAATAT
1 ATATTTTTTAAAAAATAT
1023 ATATTTTTTAAAAAAT
1 ATATTTTTTAAAAAAT
1039 TGGGTGAGGG
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
16 4 0.13
17 11 0.35
18 16 0.52
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (18 bp):
ATATTTTTTAAAAAATAT
Found at i:1704 original size:11 final size:12
Alignment explanation
Indices: 1673--1709 Score: 58
Period size: 11 Copynumber: 3.1 Consensus size: 12
1663 GTTCTTCTCC
1673 ATCAAGCAAAGCA
1 ATCAA-CAAAGCA
1686 ATCAACAAAGCA
1 ATCAACAAAGCA
1698 A-CAACAAAGCA
1 ATCAACAAAGCA
1709 A
1 A
1710 AGTTCTTCTC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 11 0.46
12 8 0.33
13 5 0.21
ACGTcount: A:0.59, C:0.24, G:0.11, T:0.05
Consensus pattern (12 bp):
ATCAACAAAGCA
Found at i:1956 original size:42 final size:42
Alignment explanation
Indices: 1896--1988 Score: 141
Period size: 42 Copynumber: 2.2 Consensus size: 42
1886 TCAAATCTAG
* * *
1896 CAAATCCGGCAACGAGGAATAACAAGCCTTCGGCCATTTCTCT
1 CAAATCC-ACAACGAGGAATAACAAGCCTTCGACCATTCCTCT
*
1939 CAAATCCACAACGAGGAATAACAAGTCTTCGACCATTCCTCT
1 CAAATCCACAACGAGGAATAACAAGCCTTCGACCATTCCTCT
1981 CAAATCCA
1 CAAATCCA
1989 TTTCATCGAG
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
42 39 0.85
43 7 0.15
ACGTcount: A:0.34, C:0.31, G:0.14, T:0.20
Consensus pattern (42 bp):
CAAATCCACAACGAGGAATAACAAGCCTTCGACCATTCCTCT
Found at i:4885 original size:10 final size:10
Alignment explanation
Indices: 4872--4906 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
4862 AAAGTTTCAA
4872 AAAAAAAAAG
1 AAAAAAAAAG
4882 AAAAAAAAAG
1 AAAAAAAAAG
**
4892 AAAAATGAAG
1 AAAAAAAAAG
4902 AAAAA
1 AAAAA
4907 CGAACTACGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.86, C:0.00, G:0.11, T:0.03
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:5129 original size:46 final size:46
Alignment explanation
Indices: 5016--5210 Score: 282
Period size: 46 Copynumber: 4.2 Consensus size: 46
5006 ACACTCATGG
* * * *
5016 CCCGCCAGGAGGCCGGTGCAGAGGTAGAGGGTGATAAAGAAAAATCAAC
1 CCCGCCAAGACGCCGATGCAGAGGTAGAGGGCGAT--A-AAAAATCAAC
*
5065 CCCGCCAAGAGGCCGATGCAGAGGTAGAGGGCGATAAAAAATCAAC
1 CCCGCCAAGACGCCGATGCAGAGGTAGAGGGCGATAAAAAATCAAC
* *
5111 CCCGACAAGACGCTGATGCAGAGGTAGAGGGCGATAAAAAATCAAC
1 CCCGCCAAGACGCCGATGCAGAGGTAGAGGGCGATAAAAAATCAAC
* *
5157 CCCGCCAAGACGCCGATGCAGAGGTATAGGGCGATAAAAAATCAAT
1 CCCGCCAAGACGCCGATGCAGAGGTAGAGGGCGATAAAAAATCAAC
5203 CCCGCCAA
1 CCCGCCAA
5211 AAGCCAAACA
Statistics
Matches: 136, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
46 103 0.76
47 1 0.01
49 32 0.24
ACGTcount: A:0.36, C:0.24, G:0.29, T:0.10
Consensus pattern (46 bp):
CCCGCCAAGACGCCGATGCAGAGGTAGAGGGCGATAAAAAATCAAC
Found at i:5356 original size:66 final size:67
Alignment explanation
Indices: 5266--5416 Score: 232
Period size: 68 Copynumber: 2.3 Consensus size: 67
5256 ACATCCTGCC
* * * * *
5266 ATTCCATGAAGTCGGAGACGAAAGGTGGAGGATGAT-CAAAACTCAAAAGAGTGACCATCCCGTC
1 ATTCCATGAAGTCGAAGACAAAAGGTGAAGGATGATACAAAACTCAAAAGAGTGACAATCCCATC
5330 AA
66 AA
*
5332 ATTCCATGAAGTCGAAGACAAAAGGTGAAGGATGATGATAAAACTCAAAAGAGTGACAATCCCAT
1 ATTCCATGAAGTCGAAGACAAAAGGTGAAGGATGAT-ACAAAACTCAAAAGAGTGACAATCCCAT
5397 CAA
65 CAA
5400 ATTCCATGAAGTCGAAG
1 ATTCCATGAAGTCGAAG
5417 GCAGGTAGAG
Statistics
Matches: 77, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
66 33 0.43
68 44 0.57
ACGTcount: A:0.41, C:0.18, G:0.23, T:0.18
Consensus pattern (67 bp):
ATTCCATGAAGTCGAAGACAAAAGGTGAAGGATGATACAAAACTCAAAAGAGTGACAATCCCATC
AA
Found at i:8582 original size:44 final size:44
Alignment explanation
Indices: 8519--8613 Score: 172
Period size: 44 Copynumber: 2.1 Consensus size: 44
8509 TTCCAAGCCA
*
8519 CAGCAATCTCTCCAAATTCAAGGCAAGGCAAAGTTCTTCTCCAT
1 CAGCAATCTCTCCAAATTCAAGGCAAGACAAAGTTCTTCTCCAT
8563 CAGCAATCTCTCCAAATTCAAGGCAAGACAAAGTTCTTCTCCAT
1 CAGCAATCTCTCCAAATTCAAGGCAAGACAAAGTTCTTCTCCAT
8607 CAAGCAA
1 C-AGCAA
8614 ATTAATCAAC
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
44 44 0.90
45 5 0.10
ACGTcount: A:0.35, C:0.29, G:0.13, T:0.23
Consensus pattern (44 bp):
CAGCAATCTCTCCAAATTCAAGGCAAGACAAAGTTCTTCTCCAT
Found at i:8878 original size:42 final size:42
Alignment explanation
Indices: 8818--8910 Score: 141
Period size: 42 Copynumber: 2.2 Consensus size: 42
8808 TCAAATCTAG
* *
8818 CAAATCCGACAACGAGGAATAACAAGCCTTCGGCCATTTCTCT
1 CAAATCC-ACAACGAGGAATAACAAGCCTTCGACCATTCCTCT
* *
8861 CAAATCCACAACGAGGAATAATAAGTCTTCGACCATTCCTCT
1 CAAATCCACAACGAGGAATAACAAGCCTTCGACCATTCCTCT
8903 CAAATCCA
1 CAAATCCA
8911 TTTCATCGAG
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
42 39 0.85
43 7 0.15
ACGTcount: A:0.35, C:0.30, G:0.13, T:0.22
Consensus pattern (42 bp):
CAAATCCACAACGAGGAATAACAAGCCTTCGACCATTCCTCT
Found at i:10539 original size:43 final size:43
Alignment explanation
Indices: 10478--10560 Score: 148
Period size: 43 Copynumber: 1.9 Consensus size: 43
10468 TTTTTCTTTT
* *
10478 AAATGTTTGAAGTTTATTTAGGGATAAGTAAATCGAAAGAAAA
1 AAATGTTTGAAGTTTATTTAGGGATAAATAAATCAAAAGAAAA
10521 AAATGTTTGAAGTTTATTTAGGGATAAATAAATCAAAAGA
1 AAATGTTTGAAGTTTATTTAGGGATAAATAAATCAAAAGA
10561 GACAGAAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.47, C:0.02, G:0.19, T:0.31
Consensus pattern (43 bp):
AAATGTTTGAAGTTTATTTAGGGATAAATAAATCAAAAGAAAA
Found at i:15069 original size:26 final size:26
Alignment explanation
Indices: 15037--15099 Score: 117
Period size: 26 Copynumber: 2.4 Consensus size: 26
15027 ATCAGTAATT
15037 ATGATGTAGTAGTGCAAATAATTCTA
1 ATGATGTAGTAGTGCAAATAATTCTA
*
15063 ATGATGTAGTAGTGCAAATAATTCTG
1 ATGATGTAGTAGTGCAAATAATTCTA
15089 ATGATGTAGTA
1 ATGATGTAGTA
15100 ATTTCAAGAC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.37, C:0.06, G:0.22, T:0.35
Consensus pattern (26 bp):
ATGATGTAGTAGTGCAAATAATTCTA
Found at i:25156 original size:11 final size:12
Alignment explanation
Indices: 25134--25184 Score: 50
Period size: 13 Copynumber: 4.2 Consensus size: 12
25124 CCCGTTGAGG
*
25134 AAATGTTTTATA
1 AAATGCTTTATA
*
25146 ACA-GCTTTATA
1 AAATGCTTTATA
25157 TAAATGCTTTATA
1 -AAATGCTTTATA
*
25170 AAATGTTTTAATA
1 AAATGCTTT-ATA
25183 AA
1 AA
25185 TGTTTTGGGT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
11 7 0.22
12 12 0.38
13 13 0.41
ACGTcount: A:0.43, C:0.06, G:0.08, T:0.43
Consensus pattern (12 bp):
AAATGCTTTATA
Found at i:25179 original size:12 final size:13
Alignment explanation
Indices: 25134--25190 Score: 59
Period size: 12 Copynumber: 4.7 Consensus size: 13
25124 CCCGTTGAGG
25134 AAATGTTTTATA-
1 AAATGTTTTATAT
* *
25146 ACA-GCTTTATAT
1 AAATGTTTTATAT
*
25158 AAATGCTTTATA-
1 AAATGTTTTATAT
25170 AAATGTTTTA-AT
1 AAATGTTTTATAT
25182 AAATGTTTT
1 AAATGTTTT
25191 GGGTGCATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
11 8 0.21
12 22 0.58
13 8 0.21
ACGTcount: A:0.39, C:0.05, G:0.09, T:0.47
Consensus pattern (13 bp):
AAATGTTTTATAT
Found at i:33583 original size:13 final size:13
Alignment explanation
Indices: 33565--33592 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
33555 CTTGAATTGC
33565 AAAGGTGTGTCGA
1 AAAGGTGTGTCGA
33578 AAAGGTGTGTCGA
1 AAAGGTGTGTCGA
33591 AA
1 AA
33593 CCAAATTGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.07, G:0.36, T:0.21
Consensus pattern (13 bp):
AAAGGTGTGTCGA
Found at i:37508 original size:21 final size:22
Alignment explanation
Indices: 37483--37529 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
37473 GCAATTTAGG
*
37483 TTTAGATTTAA-ATTTCTTGTT
1 TTTAGATTTAAGATTTATTGTT
*
37504 TTTAGATTTAAGATTTATTTTT
1 TTTAGATTTAAGATTTATTGTT
37526 TTTA
1 TTTA
37530 TGCATCTTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 11 0.48
22 12 0.52
ACGTcount: A:0.26, C:0.02, G:0.09, T:0.64
Consensus pattern (22 bp):
TTTAGATTTAAGATTTATTGTT
Found at i:37888 original size:31 final size:33
Alignment explanation
Indices: 37811--37890 Score: 137
Period size: 34 Copynumber: 2.5 Consensus size: 33
37801 GAATACTTGA
37811 TAGGTTTATTGTTTGAATAATTGAGTCATATGC
1 TAGGTTTATTGTTTGAATAATTGAGTCATATGC
37844 TAGTGTTTATTGTTTGAATAATTGAGTCATATGC
1 TAG-GTTTATTGTTTGAATAATTGAGTCATATGC
37878 TA-G-TTATTGTTTG
1 TAGGTTTATTGTTTG
37891 CATGAGAACC
Statistics
Matches: 46, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
31 10 0.22
32 1 0.02
33 3 0.07
34 32 0.70
ACGTcount: A:0.25, C:0.05, G:0.21, T:0.49
Consensus pattern (33 bp):
TAGGTTTATTGTTTGAATAATTGAGTCATATGC
Found at i:40828 original size:19 final size:23
Alignment explanation
Indices: 40804--40855 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 23
40794 TACAAATATG
40804 GTTGCCTAAA-G-T-TTAAATT-
1 GTTGCCTAAATGCTATTAAATTA
40823 GTTGCC-AAATGCTTATTAAATTA
1 GTTGCCTAAATGC-TATTAAATTA
40846 GTTGCCTAAA
1 GTTGCCTAAA
40856 CTCGTATTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
18 3 0.11
19 7 0.26
21 1 0.04
22 7 0.26
23 6 0.22
24 3 0.11
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.38
Consensus pattern (23 bp):
GTTGCCTAAATGCTATTAAATTA
Found at i:42483 original size:19 final size:19
Alignment explanation
Indices: 42455--42491 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
42445 TTGGAGGCTT
*
42455 TTATTAATTGTTTTCTTGA
1 TTATTAATTGCTTTCTTGA
*
42474 TTATTCATTGCTTTCTTG
1 TTATTAATTGCTTTCTTG
42492 TTAATTGTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.16, C:0.11, G:0.11, T:0.62
Consensus pattern (19 bp):
TTATTAATTGCTTTCTTGA
Found at i:42503 original size:15 final size:16
Alignment explanation
Indices: 42457--42505 Score: 55
Period size: 19 Copynumber: 2.9 Consensus size: 16
42447 GGAGGCTTTT
42457 ATTAATTGTTTTCTTG
1 ATTAATTGTTTTCTTG
*
42473 ATTATTCATTGCTTTCTTG
1 ATTA---ATTGTTTTCTTG
42492 -TTAATTGTTTTCTT
1 ATTAATTGTTTTCTT
42506 TAATTTTCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
15 10 0.36
16 4 0.14
18 3 0.11
19 11 0.39
ACGTcount: A:0.16, C:0.10, G:0.10, T:0.63
Consensus pattern (16 bp):
ATTAATTGTTTTCTTG
Found at i:44165 original size:26 final size:27
Alignment explanation
Indices: 44109--44180 Score: 74
Period size: 26 Copynumber: 2.7 Consensus size: 27
44099 AGGGTCATCC
**
44109 AGGGGCATTTTGATCATTTTTACACTA
1 AGGGGCATTTTGATCATTTGCACACTA
* * *
44136 A-GGGCATTTTGATCATTTGCATATTC
1 AGGGGCATTTTGATCATTTGCACACTA
* *
44162 AGGGGCATGTTGGTCATTT
1 AGGGGCATTTTGATCATTT
44181 TAAGTCCACC
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
26 21 0.57
27 16 0.43
ACGTcount: A:0.22, C:0.14, G:0.24, T:0.40
Consensus pattern (27 bp):
AGGGGCATTTTGATCATTTGCACACTA
Done.