Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024437.1 Corchorus olitorius cultivar O-4 contig24470, 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: 7085
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30
Found at i:536 original size:211 final size:211
Alignment explanation
Indices: 1--695 Score: 1344
Period size: 211 Copynumber: 3.3 Consensus size: 211
1 CCTCTCATGAGGAACCCAAAAAGAGAACAAACAATAAACGGGTTTAATTCCCGACAATCCTA-TT
1 CCTCTCATGAGGAACCCAAAAAGAGAACAAACAATAAACGGGTTTAATTCCCGACAATCCTATTT
65 TTTAAATTGGGAAAGTTACCCACCAAG-TTTAGTTTTCAATTTAGGGAAAGTTCCCGCCATATTC
66 TTTAAATTGGGAAAGTT-CCCACCAAGTTTTAGTTTTCAATTTAGGGAAAGTTCCCGCCATATTC
*
129 AG-TTTAGTCTTAGAATGGGAAAGTTCCCATCAAAAGCATCTTTCAAATCAAATTGTTTAATTGG
130 AGTTTTAGTCTTAAAATGGGAAAGTTCCCATCAAAAGCATCTTTCAAATCAAATTGTTTAATTGG
193 TAAGTTTTAAAGAAAAT
195 TAAGTTTTAAAGAAAAT
210 CCTCTCATGAGGAACCC-AAAAGAGAACAAACAATAAACGGGTTTAATTCCCGACAATCCTATTT
1 CCTCTCATGAGGAACCCAAAAAGAGAACAAACAATAAACGGGTTTAATTCCCGACAATCCTATTT
274 TTTAAATTGGGAAAGTTCCCACCAAGTTTTAGTTTTCAATTTAGGGAAAGTTCCCGCCATATTCA
66 TTTAAATTGGGAAAGTTCCCACCAAGTTTTAGTTTTCAATTTAGGGAAAGTTCCCGCCATATTCA
339 GTTTTAGTCTTAAAATGGGAAAGTTCCCATCAAAAGCATCTTTCAAATCAAATTGTTTAATTGGT
131 GTTTTAGTCTTAAAATGGGAAAGTTCCCATCAAAAGCATCTTTCAAATCAAATTGTTTAATTGGT
404 AAGTTTTAAAGAAAAT
196 AAGTTTTAAAGAAAAT
420 CCTCTCATGAGGAACCCAAAAAGAGAACAAACAATAAACGGGTTTAATTCCCGACAATCCTATTT
1 CCTCTCATGAGGAACCCAAAAAGAGAACAAACAATAAACGGGTTTAATTCCCGACAATCCTATTT
485 TTTAAATTGGGAAAGTTCCCACCAAGTTTTAGTTTTCAATTTAGGGAAAGTTCCCGCCATATTCA
66 TTTAAATTGGGAAAGTTCCCACCAAGTTTTAGTTTTCAATTTAGGGAAAGTTCCCGCCATATTCA
550 GTTTTAGTCTTAAAATGGGAAAGTTCCCATCAAAAGCATCTTTCAAATCAAATTGTTTAATTGGT
131 GTTTTAGTCTTAAAATGGGAAAGTTCCCATCAAAAGCATCTTTCAAATCAAATTGTTTAATTGGT
615 AAGTTTTAAAGAAAAT
196 AAGTTTTAAAGAAAAT
631 CCTCTCATGAGGAACCCAAAAAGAGAACAAACAATAAACGGGTTTAATTCCCGACAATCCTATTT
1 CCTCTCATGAGGAACCCAAAAAGAGAACAAACAATAAACGGGTTTAATTCCCGACAATCCTATTT
696 CAAAATTTAA
Statistics
Matches: 481, Mismatches: 1, Indels: 6
0.99 0.00 0.01
Matches are distributed among these distances:
208 53 0.11
209 75 0.16
210 95 0.20
211 258 0.54
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.30
Consensus pattern (211 bp):
CCTCTCATGAGGAACCCAAAAAGAGAACAAACAATAAACGGGTTTAATTCCCGACAATCCTATTT
TTTAAATTGGGAAAGTTCCCACCAAGTTTTAGTTTTCAATTTAGGGAAAGTTCCCGCCATATTCA
GTTTTAGTCTTAAAATGGGAAAGTTCCCATCAAAAGCATCTTTCAAATCAAATTGTTTAATTGGT
AAGTTTTAAAGAAAAT
Found at i:2120 original size:21 final size:23
Alignment explanation
Indices: 2076--2121 Score: 60
Period size: 21 Copynumber: 2.0 Consensus size: 23
2066 TTTTTTCTTA
*
2076 TATGACGCAGAAACAAAATTTTTT
1 TATGACGCAG-AACAAAATCTTTT
2100 TATGACGCAG-A-AAAATCTTTT
1 TATGACGCAGAACAAAATCTTTT
2121 T
1 T
2122 TTTTTCTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 10 0.48
22 1 0.05
24 10 0.48
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (23 bp):
TATGACGCAGAACAAAATCTTTT
Found at i:2165 original size:27 final size:28
Alignment explanation
Indices: 2135--2187 Score: 83
Period size: 27 Copynumber: 1.9 Consensus size: 28
2125 TTCTTCTTGA
2135 CGCAAAACAC-AAAACT-TTTTTTTTTAT
1 CGCAAAA-ACGAAAACTCTTTTTTTTTAT
2162 CGCAAAAACGAAAACTCTTTTTTTTT
1 CGCAAAAACGAAAACTCTTTTTTTTT
2188 TTAGATTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 2 0.08
27 13 0.54
28 9 0.38
ACGTcount: A:0.36, C:0.19, G:0.06, T:0.40
Consensus pattern (28 bp):
CGCAAAAACGAAAACTCTTTTTTTTTAT
Found at i:2501 original size:15 final size:16
Alignment explanation
Indices: 2477--2516 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
2467 AGAGGTTGAA
*
2477 AGAAAGCAATTAAAC-
1 AGAAAACAATTAAACT
*
2492 AGAAAACAATTATACT
1 AGAAAACAATTAAACT
2508 AGAAAACAA
1 AGAAAACAA
2517 AGCAAAGTAA
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:0.62, C:0.12, G:0.10, T:0.15
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Found at i:5743 original size:29 final size:29
Alignment explanation
Indices: 5706--5887 Score: 247
Period size: 29 Copynumber: 5.9 Consensus size: 29
5696 TTAAAATGAC
*
5706 GGGAACTTTCCCTAAATTGAAAACTTGAT
1 GGGATCTTTCCCTAAATTGAAAACTTGAT
5735 GGGATCTTTCCCTAAATTGAAAACTTGAT
1 GGGATCTTTCCCTAAATTGAAAACTTGAT
*
5764 GGGATCTTTCCCTAAATTGAAAACTTAAT
1 GGGATCTTTCCCTAAATTGAAAACTTGAT
5793 GGGATCTTTCCCTAAATTGAAAATCTTGAAGAGACT
1 GGGATCTTTCCCTAAATTGAAAA-CTT-----GA-T
5829 GATGGAATCTTTCCCTAAATTTGAAAACTTGAT
1 G--GG-ATCTTTCCCTAAA-TTGAAAACTTGAT
5862 GGGATCTTTCCCTAAATTGAAAACTT
1 GGGATCTTTCCCTAAATTGAAAACTT
5888 CAAAACTACT
Statistics
Matches: 139, Mismatches: 3, Indels: 22
0.85 0.02 0.13
Matches are distributed among these distances:
29 89 0.64
30 16 0.12
31 2 0.01
33 2 0.01
34 2 0.01
35 1 0.01
36 2 0.01
38 2 0.01
39 16 0.12
40 7 0.05
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (29 bp):
GGGATCTTTCCCTAAATTGAAAACTTGAT
Found at i:5839 original size:39 final size:36
Alignment explanation
Indices: 5791--5927 Score: 135
Period size: 40 Copynumber: 3.8 Consensus size: 36
5781 TGAAAACTTA
5791 ATGGGATCTTTCCCTAAATTGAAAATCTTGAAGAGACTG
1 ATGGGATCTTTCCCTAAATTGAAAA-CTT-AA-AGACTG
*
5830 ATGGAATCTTTCCCTAAATTTGAAAAC-T------TG
1 ATGGGATCTTTCCCTAAA-TTGAAAACTTAAAGACTG
*
5860 ATGGGATCTTTCCCTAAATTGAAAACTTCAAAACTACTGG
1 ATGGGATCTTTCCCTAAATTGAAAACTT--AAA-GACT-G
5900 ATGGGATCTTTCCCTAAATTGAAAACTT
1 ATGGGATCTTTCCCTAAATTGAAAACTT
5928 TGAAAAAACT
Statistics
Matches: 84, Mismatches: 2, Indels: 23
0.77 0.02 0.21
Matches are distributed among these distances:
29 8 0.10
30 20 0.24
38 1 0.01
39 19 0.23
40 36 0.43
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.33
Consensus pattern (36 bp):
ATGGGATCTTTCCCTAAATTGAAAACTTAAAGACTG
Found at i:5862 original size:30 final size:29
Alignment explanation
Indices: 5828--5887 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 29
5818 TTGAAGAGAC
5828 TGATGGAATCTTTCCCTAAATTTGAAAACT
1 TGATGGAATCTTTCCCTAAA-TTGAAAACT
*
5858 TGATGGGATCTTTCCCTAAATTGAAAACT
1 TGATGGAATCTTTCCCTAAATTGAAAACT
5887 T
1 T
5888 CAAAACTACT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 10 0.34
30 19 0.66
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.37
Consensus pattern (29 bp):
TGATGGAATCTTTCCCTAAATTGAAAACT
Found at i:5870 original size:69 final size:68
Alignment explanation
Indices: 5760--5927 Score: 257
Period size: 69 Copynumber: 2.4 Consensus size: 68
5750 ATTGAAAACT
* *
5760 TGATGGGATCTTTCCCTAAATTGAAAACTTAATGGGATCTTTCCCTAAATTGAAAATCTTGAAGA
1 TGATGGGATCTTTCCCTAAATTGAAAACTTAATGGGATCTTTCCCTAAATTGAAAA-CTTCAAAA
5825 -GAC
65 CGAC
* *
5828 TGATGGAATCTTTCCCTAAATTTGAAAACTTGATGGGATCTTTCCCTAAATTGAAAACTTCAAAA
1 TGATGGGATCTTTCCCTAAA-TTGAAAACTTAATGGGATCTTTCCCTAAATTGAAAACTTCAAAA
*
5893 CTAC
65 CGAC
5897 TGGATGGGATCTTTCCCTAAATTGAAAACTT
1 T-GATGGGATCTTTCCCTAAATTGAAAACTT
5928 TGAAAAAACT
Statistics
Matches: 91, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
68 25 0.27
69 48 0.53
70 18 0.20
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Consensus pattern (68 bp):
TGATGGGATCTTTCCCTAAATTGAAAACTTAATGGGATCTTTCCCTAAATTGAAAACTTCAAAAC
GAC
Found at i:6662 original size:25 final size:24
Alignment explanation
Indices: 6626--6684 Score: 100
Period size: 25 Copynumber: 2.4 Consensus size: 24
6616 AAAAACCAAG
*
6626 GTCCAAACAAAATGTGACAATGAA
1 GTCCAAATAAAATGTGACAATGAA
6650 GTCCGAAATAAAATGTGACAATGAA
1 GTCC-AAATAAAATGTGACAATGAA
6675 GTCCAAATAA
1 GTCCAAATAA
6685 CTTCCCCAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
24 10 0.30
25 23 0.70
ACGTcount: A:0.49, C:0.15, G:0.17, T:0.19
Consensus pattern (24 bp):
GTCCAAATAAAATGTGACAATGAA
Done.