Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021932.1 Corchorus olitorius cultivar O-4 contig21965, 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: 27140
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:5613 original size:30 final size:30
Alignment explanation
Indices: 5578--5666 Score: 106
Period size: 32 Copynumber: 2.9 Consensus size: 30
5568 TTTATTAATT
*
5578 TCCAAAATCTTCTTTAGGATTTCTTTATTC
1 TCCAAAATCTTCTTTAGGATTTCCTTATTC
* * *
5608 TCCAAAATCTTCTTTTGGGAATTACCTTATTT
1 TCCAAAATCTTC-TTTAGG-ATTTCCTTATTC
* *
5640 TCCAAAATCTTCTTTTGGATTTGCTTA
1 TCCAAAATCTTCTTTAGGATTTCCTTA
5667 AGAATATGTT
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
30 19 0.38
31 10 0.20
32 21 0.42
ACGTcount: A:0.24, C:0.19, G:0.09, T:0.48
Consensus pattern (30 bp):
TCCAAAATCTTCTTTAGGATTTCCTTATTC
Found at i:5644 original size:32 final size:31
Alignment explanation
Indices: 5576--5657 Score: 112
Period size: 32 Copynumber: 2.6 Consensus size: 31
5566 ATTTTATTAA
* * *
5576 TTTCCAAAATCTTC-TTTAGGATTTCTTTAT
1 TTTCCAAAATCTTCTTTTGGGATTACCTTAT
*
5606 TCTCCAAAATCTTCTTTTGGGAATTACCTTAT
1 TTTCCAAAATCTTCTTTTGGG-ATTACCTTAT
5638 TTTCCAAAATCTTCTTTTGG
1 TTTCCAAAATCTTCTTTTGG
5658 ATTTGCTTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
30 13 0.29
31 5 0.11
32 27 0.60
ACGTcount: A:0.23, C:0.20, G:0.09, T:0.49
Consensus pattern (31 bp):
TTTCCAAAATCTTCTTTTGGGATTACCTTAT
Found at i:12825 original size:48 final size:48
Alignment explanation
Indices: 12768--12872 Score: 185
Period size: 48 Copynumber: 2.2 Consensus size: 48
12758 TCTTATGTGT
12768 GTTTTTGTGTGCTTGTTCTTGGTGGGAAAAGATGGGAATTTGTGTATG
1 GTTTTTGTGTGCTTGTTCTTGGTGGGAAAAGATGGGAATTTGTGTATG
* *
12816 GTTTTTGTGTGTTTGTTCTTTGTGGGAAAAGATGGGAATTTGTGTATG
1 GTTTTTGTGTGCTTGTTCTTGGTGGGAAAAGATGGGAATTTGTGTATG
12864 G-TTTTGTGT
1 GTTTTTGTGT
12873 ATGTGTGGAG
Statistics
Matches: 55, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
47 8 0.15
48 47 0.85
ACGTcount: A:0.15, C:0.03, G:0.34, T:0.48
Consensus pattern (48 bp):
GTTTTTGTGTGCTTGTTCTTGGTGGGAAAAGATGGGAATTTGTGTATG
Found at i:13469 original size:44 final size:44
Alignment explanation
Indices: 13406--13496 Score: 157
Period size: 44 Copynumber: 2.1 Consensus size: 44
13396 TGTGCATTGT
*
13406 TGTATTACTATCTGTTGACTTTGATCTTGT-ATGATTCAATCTAA
1 TGTATTACTATCTGTTGACTTTGATCTTGTGA-GAGTCAATCTAA
13450 TGTATTACTATCTGTTGACTTTGATCTTGTGAGAGTCAATCTAA
1 TGTATTACTATCTGTTGACTTTGATCTTGTGAGAGTCAATCTAA
13494 TGT
1 TGT
13497 GTGTTGATGT
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
44 44 0.98
45 1 0.02
ACGTcount: A:0.24, C:0.13, G:0.16, T:0.46
Consensus pattern (44 bp):
TGTATTACTATCTGTTGACTTTGATCTTGTGAGAGTCAATCTAA
Found at i:15640 original size:26 final size:26
Alignment explanation
Indices: 15611--15689 Score: 88
Period size: 26 Copynumber: 3.0 Consensus size: 26
15601 CGTCTCCTGA
*
15611 TCAACTTCTTTGAATTGTCTTCCAAT
1 TCAACTTCTTTGAATCGTCTTCCAAT
*** *
15637 TCAATCTTCAGGGAATCGTCTTTCGAA-
1 TCAA-CTTCTTTGAATCGTC-TTCCAAT
15664 TCAACTTCTTTGAATCGTCTTCCAAT
1 TCAACTTCTTTGAATCGTCTTCCAAT
15690 CCAATATAAA
Statistics
Matches: 41, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
25 5 0.12
26 16 0.39
27 15 0.37
28 5 0.12
ACGTcount: A:0.24, C:0.24, G:0.11, T:0.41
Consensus pattern (26 bp):
TCAACTTCTTTGAATCGTCTTCCAAT
Found at i:15734 original size:23 final size:23
Alignment explanation
Indices: 15708--15788 Score: 65
Period size: 23 Copynumber: 3.3 Consensus size: 23
15698 AAAAGGGACC
15708 GTCTTCCACTTATCCTTTGAACT
1 GTCTTCCACTTATCCTTTGAACT
* * * *
15731 GTCTTCCAATTCAAT-CTTAAAAGGACC
1 GTCTTCCACTT--ATCCTT---TGAACT
*
15758 GTCTTCCGCTTATCCTTTGAACT
1 GTCTTCCACTTATCCTTTGAACT
15781 GTCTTCCA
1 GTCTTCCA
15789 ATTCAATCTT
Statistics
Matches: 42, Mismatches: 10, Indels: 12
0.66 0.16 0.19
Matches are distributed among these distances:
23 20 0.48
24 3 0.07
25 4 0.10
26 3 0.07
27 12 0.29
ACGTcount: A:0.21, C:0.30, G:0.11, T:0.38
Consensus pattern (23 bp):
GTCTTCCACTTATCCTTTGAACT
Found at i:15776 original size:50 final size:50
Alignment explanation
Indices: 15671--15893 Score: 349
Period size: 50 Copynumber: 4.4 Consensus size: 50
15661 GAATCAACTT
* * * *
15671 CTTTGAA-TCGTCTTCCAATCCAATATAAAAAGGGACCGTCTTCCACTTATC
1 CTTTGAACT-GTCTTCCAATTCAATCTTAAAA-GGACCGTCTTCCGCTTATC
15722 CTTTGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
1 CTTTGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
15772 CTTTGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
1 CTTTGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
* * *
15822 CTTTGAACCGTCTTCCAATTCGATCTTAGAAAGGACCGTCTTCTGCTTATC
1 CTTTGAACTGTCTTCCAATTCAATCTTA-AAAGGACCGTCTTCCGCTTATC
15873 CTTTGAACTGTCTTCCAATTC
1 CTTTGAACTGTCTTCCAATTC
15894 GCTCCCGGAT
Statistics
Matches: 162, Mismatches: 8, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
50 94 0.58
51 67 0.41
52 1 0.01
ACGTcount: A:0.24, C:0.28, G:0.13, T:0.35
Consensus pattern (50 bp):
CTTTGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
Found at i:15870 original size:101 final size:101
Alignment explanation
Indices: 15671--15893 Score: 351
Period size: 101 Copynumber: 2.2 Consensus size: 101
15661 GAATCAACTT
* *
15671 CTTTGAA-TCGTCTTCCAATCCAATATAAAAAGGGACCGTCTTCCACTTATCCTTTGAACTGTCT
1 CTTTGAACT-GTCTTCCAATTCAATATAAAAAGGGACCGTCTTCCACTTATCCTTTGAACCGTCT
15735 TCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
65 TCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
* * *
15772 CTTTGAACTGTCTTCCAATTCAATCTTAAAA-GGACCGTCTTCCGCTTATCCTTTGAACCGTCTT
1 CTTTGAACTGTCTTCCAATTCAATATAAAAAGGGACCGTCTTCCACTTATCCTTTGAACCGTCTT
* *
15836 CCAATTCGATCTTAGAAAGGACCGTCTTCTGCTTATC
66 CCAATTCAATCTTA-AAAGGACCGTCTTCCGCTTATC
15873 CTTTGAACTGTCTTCCAATTC
1 CTTTGAACTGTCTTCCAATTC
15894 GCTCCCGGAT
Statistics
Matches: 113, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
100 44 0.39
101 68 0.60
102 1 0.01
ACGTcount: A:0.24, C:0.28, G:0.13, T:0.35
Consensus pattern (101 bp):
CTTTGAACTGTCTTCCAATTCAATATAAAAAGGGACCGTCTTCCACTTATCCTTTGAACCGTCTT
CCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
Found at i:16587 original size:2 final size:2
Alignment explanation
Indices: 16580--16619 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
16570 AAGGAATTTA
16580 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16620 GAGTGCCAAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17790 original size:25 final size:26
Alignment explanation
Indices: 17761--17814 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
17751 ACAAAATCTT
*
17761 TTTACC-ATTTGATT-TTTTCTAAAAA
1 TTTACCAATTTGATTAATTTC-AAAAA
*
17786 TTTACCAATTTTATTAATTTCAAAAA
1 TTTACCAATTTGATTAATTTCAAAAA
17812 TTT
1 TTT
17815 TCTTTCGGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 6 0.24
26 15 0.60
27 4 0.16
ACGTcount: A:0.35, C:0.11, G:0.02, T:0.52
Consensus pattern (26 bp):
TTTACCAATTTGATTAATTTCAAAAA
Found at i:18664 original size:41 final size:41
Alignment explanation
Indices: 18600--18695 Score: 131
Period size: 41 Copynumber: 2.3 Consensus size: 41
18590 AGAAAAATAA
* *
18600 GGACCAAATTG-AGCCAAACAGTAATTAGAATCCTAAATCAG
1 GGACCAAATTGTA-TCAAACAGTAAATAGAATCCTAAATCAG
* * *
18641 GGACTAAATTGTATCAAATAGTAAATAGAATCCTAAATTAG
1 GGACCAAATTGTATCAAACAGTAAATAGAATCCTAAATCAG
18682 GGACCAAATTGTAT
1 GGACCAAATTGTAT
18696 TTAATTAGGT
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
41 47 0.98
42 1 0.02
ACGTcount: A:0.44, C:0.15, G:0.17, T:0.25
Consensus pattern (41 bp):
GGACCAAATTGTATCAAACAGTAAATAGAATCCTAAATCAG
Found at i:18813 original size:41 final size:41
Alignment explanation
Indices: 18762--18904 Score: 171
Period size: 41 Copynumber: 3.5 Consensus size: 41
18752 AAAAATTCTG
* * * *
18762 AATCCGGGACAAAATTGAATCAATAAATAAATATTA-CTCTA
1 AATCAGGGACAAAATTGAATTAATGAATAAATATCAGC-CTA
*
18803 GATCAGGGACAAAATTGAATTAATGAATAAATATCAGCCTA
1 AATCAGGGACAAAATTGAATTAATGAATAAATATCAGCCTA
* **
18844 AATTAGGGACCCAATTGAATTAATGAATAAATATCAGCCTA
1 AATCAGGGACAAAATTGAATTAATGAATAAATATCAGCCTA
* **
18885 AATTAGGGACCCAATTGAAT
1 AATCAGGGACAAAATTGAAT
18905 GAAATCACAC
Statistics
Matches: 92, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
41 91 0.99
42 1 0.01
ACGTcount: A:0.45, C:0.14, G:0.15, T:0.26
Consensus pattern (41 bp):
AATCAGGGACAAAATTGAATTAATGAATAAATATCAGCCTA
Found at i:21247 original size:27 final size:27
Alignment explanation
Indices: 21184--21244 Score: 86
Period size: 27 Copynumber: 2.2 Consensus size: 27
21174 GTGAACTTAC
*
21184 AATGACCAAAATGCCCCTAAATGTGCA
1 AATGACCAAAATGCCCCTAAATGTCCA
* *
21211 AATGACCAAAATGCCCCTAGATGATCCT
1 AATGACCAAAATGCCCCTAAATG-TCCA
21239 AATGAC
1 AATGAC
21245 AAATAAGAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 22 0.73
28 8 0.27
ACGTcount: A:0.39, C:0.26, G:0.15, T:0.20
Consensus pattern (27 bp):
AATGACCAAAATGCCCCTAAATGTCCA
Found at i:21621 original size:51 final size:51
Alignment explanation
Indices: 21493--21701 Score: 339
Period size: 51 Copynumber: 4.1 Consensus size: 51
21483 CAGTCTAATA
21493 TTAAAAGGACCGTCTTCCGCTTATCCTTTAAACTGTCTACCAATTCAATC-
1 TTAAAAGGACCGTCTTCCGCTTATCCTTTAAACTGTCTACCAATTCAATCT
* *
21543 TTGAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCT
1 TTAAAAGGACCGTCTTCCGCTTATCCTTTAAACTGTCTACCAATTCAATCT
* * *
21594 TTAAAAGGATCGTCTTCCGTTTATCCTTTAAATTGTCTACCAATTCAATCT
1 TTAAAAGGACCGTCTTCCGCTTATCCTTTAAACTGTCTACCAATTCAATCT
* * *
21645 TTAAAAGGACTGTCTTTCGCTTATCCTTTGAACTGTCTACCAATTCAATCT
1 TTAAAAGGACCGTCTTCCGCTTATCCTTTAAACTGTCTACCAATTCAATCT
21696 TTAAAA
1 TTAAAA
21702 AAGGTAATGC
Statistics
Matches: 145, Mismatches: 13, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
50 48 0.33
51 97 0.67
ACGTcount: A:0.27, C:0.24, G:0.11, T:0.37
Consensus pattern (51 bp):
TTAAAAGGACCGTCTTCCGCTTATCCTTTAAACTGTCTACCAATTCAATCT
Found at i:22499 original size:50 final size:50
Alignment explanation
Indices: 22445--22636 Score: 251
Period size: 50 Copynumber: 3.8 Consensus size: 50
22435 CTTAAATGCC
* * * * * *
22445 CTTTGAAAAGCGAATTTTGATATTGGACTCACAACTGGAATGCAATCTTA
1 CTTTGAAAAGCGAATTTTGATCTTGAACTCTCAAATGGAAAGCAATTTTA
* * *
22495 CTTTGAAACGCGAATTTTAATCTTGAACTCTCAAATGAAAAGCAATTTTA
1 CTTTGAAAAGCGAATTTTGATCTTGAACTCTCAAATGGAAAGCAATTTTA
* *
22545 TTTTGAAAAGCGAATTTTGATCTTGAACTCTCAAGTGGAAAGCAATTTTA
1 CTTTGAAAAGCGAATTTTGATCTTGAACTCTCAAATGGAAAGCAATTTTA
* *
22595 TTTTGAAAAGCGAATTTTAATCTTGAACTCAT-AAATGGAAAG
1 CTTTGAAAAGCGAATTTTGATCTTGAACTC-TCAAATGGAAAG
22637 AAATCTTGTT
Statistics
Matches: 125, Mismatches: 16, Indels: 2
0.87 0.11 0.01
Matches are distributed among these distances:
50 124 0.99
51 1 0.01
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (50 bp):
CTTTGAAAAGCGAATTTTGATCTTGAACTCTCAAATGGAAAGCAATTTTA
Found at i:23280 original size:5 final size:6
Alignment explanation
Indices: 23242--23299 Score: 50
Period size: 6 Copynumber: 9.7 Consensus size: 6
23232 ATCAATTCTC
* *
23242 TTTTGA TTTTGA TTTTGA -TTTGA -TATGA TTTTTTA TTTTGA -TTTGA
1 TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA -TTTTGA TTTTGA TTTTGA
23288 GTTTTTGA TTTT
1 --TTTTGA TTTT
23300 TTTTTCTTTG
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
5 14 0.33
6 21 0.49
7 3 0.07
8 5 0.12
ACGTcount: A:0.17, C:0.00, G:0.16, T:0.67
Consensus pattern (6 bp):
TTTTGA
Found at i:23281 original size:18 final size:19
Alignment explanation
Indices: 23254--23299 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
23244 TTGATTTTGA
23254 TTTTGA-TTTGATATGA-T
1 TTTTGATTTTGATATGAGT
* *
23271 TTTTTATTTTGATTTGAGT
1 TTTTGATTTTGATATGAGT
23290 TTTTGATTTT
1 TTTTGATTTT
23300 TTTTTCTTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 5 0.21
18 9 0.38
19 10 0.42
ACGTcount: A:0.17, C:0.00, G:0.15, T:0.67
Consensus pattern (19 bp):
TTTTGATTTTGATATGAGT
Found at i:25327 original size:29 final size:28
Alignment explanation
Indices: 25262--25336 Score: 98
Period size: 29 Copynumber: 2.6 Consensus size: 28
25252 GAACTTACAC
25262 TGACCAAAATGCCCCTAAATGTGAAAAA
1 TGACCAAAATGCCCCTAAATGTGAAAAA
* * *
25290 TGACTAAAATGCCCCTAGATTCTTG-AAAA
1 TGACCAAAATGCCCCTA-AAT-GTGAAAAA
25319 TGACCAAAATGCCCCTAA
1 TGACCAAAATGCCCCTAA
25337 GTGATCCTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
28 17 0.41
29 22 0.54
30 2 0.05
ACGTcount: A:0.41, C:0.24, G:0.13, T:0.21
Consensus pattern (28 bp):
TGACCAAAATGCCCCTAAATGTGAAAAA
Found at i:25765 original size:28 final size:28
Alignment explanation
Indices: 25729--25789 Score: 113
Period size: 28 Copynumber: 2.2 Consensus size: 28
25719 CTTAGGTCTA
*
25729 TATTGGTGTATTATCATTTGATTAGTGT
1 TATTAGTGTATTATCATTTGATTAGTGT
25757 TATTAGTGTATTATCATTTGATTAGTGT
1 TATTAGTGTATTATCATTTGATTAGTGT
25785 TATTA
1 TATTA
25790 TTGGTACATT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.25, C:0.03, G:0.18, T:0.54
Consensus pattern (28 bp):
TATTAGTGTATTATCATTTGATTAGTGT
Done.