Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014819.1 Corchorus olitorius cultivar O-4 contig14852, 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: 41581
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:229 original size:29 final size:29
Alignment explanation
Indices: 180--238 Score: 68
Period size: 29 Copynumber: 2.0 Consensus size: 29
170 GTCTGTAAAA
* *
180 GGGTTAATTTGGCTAAGATTGATAGTTCAG
1 GGGTTAATTTGGCTAAAATTGA-AATTCAG
210 GGGTT-ATTTGG-TCAAAATTGAAATTCAG
1 GGGTTAATTTGGCT-AAAATTGAAATTCAG
238 G
1 G
239 AGTTCGCAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
28 8 0.31
29 13 0.50
30 5 0.19
ACGTcount: A:0.29, C:0.07, G:0.29, T:0.36
Consensus pattern (29 bp):
GGGTTAATTTGGCTAAAATTGAAATTCAG
Found at i:791 original size:22 final size:21
Alignment explanation
Indices: 766--819 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 21
756 GAAGTTCGTG
766 TTTGAAGACTTATTGAAGATAA
1 TTTGAAGA-TTATTGAAGATAA
*
788 TTTGAAGA-T-TTGAAGATCA
1 TTTGAAGATTATTGAAGATAA
807 -TTGAAGAATTATT
1 TTTGAAG-ATTATT
820 TCAAGAAGCA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 6 0.21
19 10 0.36
20 2 0.07
21 2 0.07
22 8 0.29
ACGTcount: A:0.39, C:0.04, G:0.19, T:0.39
Consensus pattern (21 bp):
TTTGAAGATTATTGAAGATAA
Found at i:4606 original size:37 final size:37
Alignment explanation
Indices: 4565--4726 Score: 186
Period size: 37 Copynumber: 4.4 Consensus size: 37
4555 TCTTCATCAT
*
4565 AGAGCTCTCCTTACCGCGGTAGCACCCTCTTTACCGC
1 AGAGCTCTCCTTACTGCGGTAGCACCCTCTTTACCGC
* * * *
4602 AGAGCTC-CTCTTACTGCGATAGTAACCTCTTTACCGT
1 AGAGCTCTC-CTTACTGCGGTAGCACCCTCTTTACCGC
* ** *
4639 AGAGCT-TCTTTACTGCGGCGGCTCCCAT-TTTCACCGC
1 AGAGCTCTCCTTACTGCGGTAGCACCC-TCTTT-ACCGC
*
4676 AGAGCTCTCCTTACTGCGGTAGAACCCTCTTTACCGC
1 AGAGCTCTCCTTACTGCGGTAGCACCCTCTTTACCGC
4713 AGAGCTCTCCTTAC
1 AGAGCTCTCCTTAC
4727 AAAGCACTAC
Statistics
Matches: 101, Mismatches: 18, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
36 15 0.15
37 68 0.67
38 18 0.18
ACGTcount: A:0.18, C:0.35, G:0.19, T:0.28
Consensus pattern (37 bp):
AGAGCTCTCCTTACTGCGGTAGCACCCTCTTTACCGC
Found at i:5792 original size:23 final size:24
Alignment explanation
Indices: 5760--5811 Score: 88
Period size: 23 Copynumber: 2.2 Consensus size: 24
5750 TTTCTCCGTA
5760 TTTTTAGGACTCCTTTGTGAGAG-
1 TTTTTAGGACTCCTTTGTGAGAGC
*
5783 TTTTTGGGACTCCTTTGTGAGAGC
1 TTTTTAGGACTCCTTTGTGAGAGC
5807 TTTTT
1 TTTTT
5812 CTATTGTCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
23 22 0.81
24 5 0.19
ACGTcount: A:0.13, C:0.13, G:0.25, T:0.48
Consensus pattern (24 bp):
TTTTTAGGACTCCTTTGTGAGAGC
Found at i:7620 original size:20 final size:20
Alignment explanation
Indices: 7595--7633 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
7585 GATGCTGCTC
*
7595 CTTGGAAATTTACGGGGTTG
1 CTTGGAAATTTACCGGGTTG
7615 CTTGGAAATTTACCGGGTT
1 CTTGGAAATTTACCGGGTT
7634 TTATGGCAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.21, C:0.13, G:0.31, T:0.36
Consensus pattern (20 bp):
CTTGGAAATTTACCGGGTTG
Found at i:12804 original size:110 final size:107
Alignment explanation
Indices: 12594--12801 Score: 247
Period size: 110 Copynumber: 1.9 Consensus size: 107
12584 AGGATATTAC
* * * *
12594 TTATTTTTCATAAGGTTTAGCCCCAAATTAATTAAAGGAAAGAAATTAGGGTTATGCCTATTTTG
1 TTATTTTTCATAAGGTTTAGCCCCAAATTAATAAAAGAAAAGAAATTAGGGTAATGCCTATTTTA
* ** *
12659 AAATATTTATAGGATTAGGGTTTTAGATTTTTTATTAAAAGGAAA
66 AAATATTTACAAAACTAGGGTTTTAGA---TTTATTAAAAGGAAA
* *
12704 TTATTTTTCATCAGGTTTAGCCCCAAATTAATAAAAGAAAAGAAATTACATGGTAAAT-CCTATT
1 TTATTTTTCATAAGGTTTAGCCCCAAATTAATAAAAGAAAAGAAATT--AGGGT-AATGCCTATT
12768 TTAAAATATATTTACAAAACTAGGGTTTTAGATT
63 TT-AAA-ATATTTACAAAACTAGGGTTTTAGATT
12802 ATTTATTAAA
Statistics
Matches: 83, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
110 44 0.53
111 2 0.02
112 12 0.14
113 4 0.05
114 21 0.25
ACGTcount: A:0.38, C:0.09, G:0.14, T:0.38
Consensus pattern (107 bp):
TTATTTTTCATAAGGTTTAGCCCCAAATTAATAAAAGAAAAGAAATTAGGGTAATGCCTATTTTA
AAATATTTACAAAACTAGGGTTTTAGATTTATTAAAAGGAAA
Found at i:19984 original size:22 final size:22
Alignment explanation
Indices: 19942--19984 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
19932 TCTCAATTTC
*
19942 TTTTCTTCTATTTTTCTCTAAA
1 TTTTCTTCTATTTTGCTCTAAA
19964 TTTTCTTCTAGTTTTGC-CTAA
1 TTTTCTTCTA-TTTTGCTCTAA
19985 GGGTGTCGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.16, C:0.19, G:0.05, T:0.60
Consensus pattern (22 bp):
TTTTCTTCTATTTTGCTCTAAA
Found at i:20122 original size:17 final size:17
Alignment explanation
Indices: 20100--20135 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
20090 GATTTGGGAA
20100 TCCATGAGTAGCTAAAT
1 TCCATGAGTAGCTAAAT
*
20117 TCCATGAGTAGCTACAT
1 TCCATGAGTAGCTAAAT
20134 TC
1 TC
20136 TTAATACTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.31
Consensus pattern (17 bp):
TCCATGAGTAGCTAAAT
Found at i:22005 original size:25 final size:25
Alignment explanation
Indices: 21971--22019 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
21961 CCAAACAATC
21971 TTGAGCACTCTCGCTCGGTCTCTAT
1 TTGAGCACTCTCGCTCGGTCTCTAT
*
21996 TTGAGCACTCTCGCTCGGTTTCTA
1 TTGAGCACTCTCGCTCGGTCTCTA
22020 CAAACAATCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.12, C:0.31, G:0.20, T:0.37
Consensus pattern (25 bp):
TTGAGCACTCTCGCTCGGTCTCTAT
Found at i:23027 original size:21 final size:21
Alignment explanation
Indices: 23002--23042 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
22992 TATTCTTTTA
*
23002 AATTTATTATTCTTTTTTATC
1 AATTTATTATTATTTTTTATC
*
23023 AATTTTTTATTATTTTTTAT
1 AATTTATTATTATTTTTTAT
23043 AGTTGAGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (21 bp):
AATTTATTATTATTTTTTATC
Found at i:23106 original size:11 final size:11
Alignment explanation
Indices: 23090--23127 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
23080 TATTTTTAAA
23090 TTTTTATTTCT
1 TTTTTATTTCT
23101 TTTTTATTATCT
1 TTTTTATT-TCT
*
23113 TTATTATTTCT
1 TTTTTATTTCT
23124 TTTT
1 TTTT
23128 ATTGTTATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 14 0.58
12 10 0.42
ACGTcount: A:0.13, C:0.08, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTTTATTTCT
Found at i:28149 original size:64 final size:65
Alignment explanation
Indices: 28048--28186 Score: 262
Period size: 64 Copynumber: 2.2 Consensus size: 65
28038 TCAGTCTCCT
28048 AGTTTTTTTTTCTTTGGGTTTTTGTTTGTTGGTCTTCCTCCTTGACTAGTACGGTCAATGGGA-G
1 AGTTTTTTTTTCTTTGGGTTTTTGTTTGTTGGTCTTCCTCCTTGACTAGTACGGTCAATGGGAGG
28112 AGTTTTTTTTTCTTTGGGTTTTTGTTTGTTGGTCTTCCTCCTTGACTAGTACGGTCAATGGGAGG
1 AGTTTTTTTTTCTTTGGGTTTTTGTTTGTTGGTCTTCCTCCTTGACTAGTACGGTCAATGGGAGG
*
28177 AGGTTTTTTT
1 AGTTTTTTTT
28187 GAAGTAATCA
Statistics
Matches: 73, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
64 63 0.86
65 10 0.14
ACGTcount: A:0.11, C:0.13, G:0.25, T:0.51
Consensus pattern (65 bp):
AGTTTTTTTTTCTTTGGGTTTTTGTTTGTTGGTCTTCCTCCTTGACTAGTACGGTCAATGGGAGG
Found at i:30433 original size:2 final size:2
Alignment explanation
Indices: 30428--30455 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
30418 AAATAAAAAA
30428 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
30456 CTTCCCTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:30712 original size:147 final size:147
Alignment explanation
Indices: 30445--30729 Score: 570
Period size: 147 Copynumber: 1.9 Consensus size: 147
30435 GAGAGAGAGA
30445 GAGAGAGAGAGCTTCCCTATTAAGTAACAATTGCCATAACCCTAGGGCAAATTCTGCTTTCATGG
1 GAGAGAGAGAGCTTCCCTATTAAGTAACAATTGCCATAACCCTAGGGCAAATTCTGCTTTCATGG
30510 CTGCAGAAATGTTTCATGTCCATCAATCCATGCATTTTAGTAAAAGACTTATGGGATTTGAAGGA
66 CTGCAGAAATGTTTCATGTCCATCAATCCATGCATTTTAGTAAAAGACTTATGGGATTTGAAGGA
30575 AATGACTTATGGGATTT
131 AATGACTTATGGGATTT
30592 GAGAGAGAGAGCTTCCCTATTAAGTAACAATTGCCATAACCCTAGGGCAAATTCTGCTTTCATGG
1 GAGAGAGAGAGCTTCCCTATTAAGTAACAATTGCCATAACCCTAGGGCAAATTCTGCTTTCATGG
30657 CTGCAGAAATGTTTCATGTCCATCAATCCATGCATTTTAGTAAAAGACTTATGGGATTTGAAGGA
66 CTGCAGAAATGTTTCATGTCCATCAATCCATGCATTTTAGTAAAAGACTTATGGGATTTGAAGGA
30722 AATGACTT
131 AATGACTT
30730 CCTCTTGCTT
Statistics
Matches: 138, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
147 138 1.00
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.30
Consensus pattern (147 bp):
GAGAGAGAGAGCTTCCCTATTAAGTAACAATTGCCATAACCCTAGGGCAAATTCTGCTTTCATGG
CTGCAGAAATGTTTCATGTCCATCAATCCATGCATTTTAGTAAAAGACTTATGGGATTTGAAGGA
AATGACTTATGGGATTT
Done.