Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024079.1 Corchorus olitorius cultivar O-4 contig24112, 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: 38872
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:4504 original size:19 final size:18
Alignment explanation
Indices: 4471--4506 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
4461 TTGAAATAAT
4471 TCTTCAAAAATCTTCAAG
1 TCTTCAAAAATCTTCAAG
*
4489 TCTTCAAATTATCTTCAA
1 TCTTCAAA-AATCTTCAA
4507 ATGGTTTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.36, C:0.22, G:0.03, T:0.39
Consensus pattern (18 bp):
TCTTCAAAAATCTTCAAG
Found at i:13448 original size:2 final size:2
Alignment explanation
Indices: 13441--13466 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
13431 GGGCTTTTGC
13441 CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA
13467 GTATATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:13473 original size:2 final size:2
Alignment explanation
Indices: 13468--13501 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
13458 ACACACACAG
13468 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
13502 AGTTAGGAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:13660 original size:41 final size:42
Alignment explanation
Indices: 13554--13797 Score: 300
Period size: 43 Copynumber: 5.8 Consensus size: 42
13544 TCAAGAGAAA
13554 TGCCTCTGTGTTATAAATGTGTTTGAGGACTTT-GAGATAGAGG
1 TGCCTCTGTGTTATAAATGTGTTTGAGGACTTTAGA-ATAGA-G
* * *
13597 TACC-CATGTGTTATAAATGTGTTTGGGGACTTTAGTATAGA-
1 TGCCTC-TGTGTTATAAATGTGTTTGAGGACTTTAGAATAGAG
* *
13638 TGCCTCTGTGTTATAAATGTGTTTGAGGACTTTGGAATAGAAT
1 TGCCTCTGTGTTATAAATGTGTTTGAGGACTTTAGAATAG-AG
* *
13681 TGCCTCTGTGTTATAATTGTGTTTGGGGACTTT-GATATAGA-
1 TGCCTCTGTGTTATAAATGTGTTTGAGGACTTTAGA-ATAGAG
* *
13722 TGTCTCTGTGTTATAAATGTGTTTGAGGACTTTGGAATAGAGG
1 TGCCTCTGTGTTATAAATGTGTTTGAGGACTTTAGAATAGA-G
* *
13765 TGCCCCTGTGTTATAAATGTGTTTGGGGACTTT
1 TGCCTCTGTGTTATAAATGTGTTTGAGGACTTT
13798 TAGTTTTTGG
Statistics
Matches: 177, Mismatches: 15, Indels: 18
0.84 0.07 0.09
Matches are distributed among these distances:
41 69 0.39
42 8 0.05
43 99 0.56
44 1 0.01
ACGTcount: A:0.23, C:0.10, G:0.27, T:0.40
Consensus pattern (42 bp):
TGCCTCTGTGTTATAAATGTGTTTGAGGACTTTAGAATAGAG
Found at i:13694 original size:84 final size:83
Alignment explanation
Indices: 13553--13797 Score: 386
Period size: 84 Copynumber: 2.9 Consensus size: 83
13543 ATCAAGAGAA
*
13553 ATGCCTCTGTGTTATAAATGTGTTTGAGGACTTT-GAGATAGAGGTACCCATGTGTTATAAATGT
1 ATGCCTCTGTGTTATAAATGTGTTTGAGGACTTTGGA-ATAGAGGTGCCC-TGTGTTATAAATGT
13617 GTTTGGGGACTTT-AGTATAG
64 GTTTGGGGACTTTGA-TATAG
** *
13637 ATGCCTCTGTGTTATAAATGTGTTTGAGGACTTTGGAATAGAATTGCCTCTGTGTTATAATTGTG
1 ATGCCTCTGTGTTATAAATGTGTTTGAGGACTTTGGAATAGAGGTGCC-CTGTGTTATAAATGTG
13702 TTTGGGGACTTTGATATAG
65 TTTGGGGACTTTGATATAG
*
13721 ATGTCTCTGTGTTATAAATGTGTTTGAGGACTTTGGAATAGAGGTGCCCCTGTGTTATAAATGTG
1 ATGCCTCTGTGTTATAAATGTGTTTGAGGACTTTGGAATAGAGGTG-CCCTGTGTTATAAATGTG
13786 TTTGGGGACTTT
65 TTTGGGGACTTT
13798 TAGTTTTTGG
Statistics
Matches: 149, Mismatches: 8, Indels: 8
0.90 0.05 0.05
Matches are distributed among these distances:
84 143 0.96
85 6 0.04
ACGTcount: A:0.23, C:0.10, G:0.27, T:0.40
Consensus pattern (83 bp):
ATGCCTCTGTGTTATAAATGTGTTTGAGGACTTTGGAATAGAGGTGCCCTGTGTTATAAATGTGT
TTGGGGACTTTGATATAG
Found at i:16098 original size:14 final size:14
Alignment explanation
Indices: 16076--16109 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
16066 TTTAACCAAG
* *
16076 GCTTATCAAAATTT
1 GCTTCTCAAAAATT
16090 GCTTCTCAAAAATT
1 GCTTCTCAAAAATT
16104 GCTTCT
1 GCTTCT
16110 ATGCGATTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.29, C:0.21, G:0.09, T:0.41
Consensus pattern (14 bp):
GCTTCTCAAAAATT
Found at i:25261 original size:21 final size:21
Alignment explanation
Indices: 25211--25255 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
25201 GTGACACCGC
*
25211 CCACCTGGGTCCTCAAGCAAA
1 CCACATGGGTCCTCAAGCAAA
* *
25232 CCACATGGGTGCTCAAGGAAA
1 CCACATGGGTCCTCAAGCAAA
25253 CCA
1 CCA
25256 TGTGGGCGCC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.33, G:0.22, T:0.13
Consensus pattern (21 bp):
CCACATGGGTCCTCAAGCAAA
Found at i:26833 original size:4 final size:4
Alignment explanation
Indices: 26824--26848 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
26814 TTACTTGATG
26824 AGAA AGAA AGAA AGAA AGAA AGAA A
1 AGAA AGAA AGAA AGAA AGAA AGAA A
26849 AAAATACCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:28692 original size:61 final size:61
Alignment explanation
Indices: 28597--28722 Score: 252
Period size: 61 Copynumber: 2.1 Consensus size: 61
28587 TGTAAGAGAT
28597 CTTTGGGAGCTTGATGCTATGAAATCTGTAAATGCAGCCATGGTATTTTTCATCACAAGGA
1 CTTTGGGAGCTTGATGCTATGAAATCTGTAAATGCAGCCATGGTATTTTTCATCACAAGGA
28658 CTTTGGGAGCTTGATGCTATGAAATCTGTAAATGCAGCCATGGTATTTTTCATCACAAGGA
1 CTTTGGGAGCTTGATGCTATGAAATCTGTAAATGCAGCCATGGTATTTTTCATCACAAGGA
28719 CTTT
1 CTTT
28723 ATTCCCATTC
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 65 1.00
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.34
Consensus pattern (61 bp):
CTTTGGGAGCTTGATGCTATGAAATCTGTAAATGCAGCCATGGTATTTTTCATCACAAGGA
Found at i:31492 original size:178 final size:178
Alignment explanation
Indices: 31228--31565 Score: 527
Period size: 178 Copynumber: 1.9 Consensus size: 178
31218 CCGATTAAGG
*
31228 TGATTTAAGTGTCTATTAAAAGATTGTTCCATAATCTACAACTTTCATGAAGGACTCGAAAACTA
1 TGATTCAAGTGTCTATTAAAAGATTGTTCCATAATCTACAACTTTCATGAAGGACTCGAAAACTA
* *
31293 AATTTAATGTTTCAAGTATAAAAAATGCTTCCAAAAAATTTGTTGTTTCGGTTAACGGGAATAGA
66 AATTTAATGTTTCAAGTATAAAAAATGCTTCCAAAAAATTAGTTGTTTCGGTTAACGGAAATAGA
*
31358 CGGTCCACTTAATATTATATAACTTT-TGCTCCAGATGTCTGATTGAGA
131 CGGTCCACTTAATATTACATAA-TTTGTGCTCCAGATGTCTGATTGAGA
* * * *
31406 TGATTCAAGTGTCTCTTAAAAGGTTGTTCCATGATTTACAACTTTCATGAAGGACTCGAAAACTA
1 TGATTCAAGTGTCTATTAAAAGATTGTTCCATAATCTACAACTTTCATGAAGGACTCGAAAACTA
* * *
31471 AATTTAGTG-TTCAAGGTATAAAAAATGCTTCCAAAGAATTAGTTGTTTTGGTTAACGGAAATAG
66 AATTTAATGTTTCAA-GTATAAAAAATGCTTCCAAAAAATTAGTTGTTTCGGTTAACGGAAATAG
**
31535 ACGGTCTGCTTAATATTACATAATTTGTGCT
130 ACGGTCCACTTAATATTACATAATTTGTGCT
31566 TATGGTGGAA
Statistics
Matches: 145, Mismatches: 13, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
177 8 0.06
178 137 0.94
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.36
Consensus pattern (178 bp):
TGATTCAAGTGTCTATTAAAAGATTGTTCCATAATCTACAACTTTCATGAAGGACTCGAAAACTA
AATTTAATGTTTCAAGTATAAAAAATGCTTCCAAAAAATTAGTTGTTTCGGTTAACGGAAATAGA
CGGTCCACTTAATATTACATAATTTGTGCTCCAGATGTCTGATTGAGA
Found at i:32933 original size:4 final size:4
Alignment explanation
Indices: 32924--32955 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
32914 TATGCAAAAC
32924 ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTA
1 ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTA
32956 CACTTTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
ATTA
Found at i:33614 original size:8 final size:8
Alignment explanation
Indices: 33601--33652 Score: 58
Period size: 8 Copynumber: 7.0 Consensus size: 8
33591 GCATTGCCAA
33601 ATGCCATT
1 ATGCCATT
*
33609 ATGCCA-A
1 ATGCCATT
33616 ATGCCATT
1 ATGCCATT
*
33624 ATGCCA-A
1 ATGCCATT
33631 ATGCCATT
1 ATGCCATT
33639 ATGCCA--
1 ATGCCATT
33645 ATGCCATT
1 ATGCCATT
33653 GCTCAGCAGC
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
6 6 0.17
7 12 0.33
8 18 0.50
ACGTcount: A:0.31, C:0.27, G:0.13, T:0.29
Consensus pattern (8 bp):
ATGCCATT
Found at i:33615 original size:15 final size:15
Alignment explanation
Indices: 33595--33652 Score: 109
Period size: 15 Copynumber: 3.9 Consensus size: 15
33585 GAGCTGGCAT
33595 TGCCAAATGCCATTA
1 TGCCAAATGCCATTA
33610 TGCCAAATGCCATTA
1 TGCCAAATGCCATTA
33625 TGCCAAATGCCATTA
1 TGCCAAATGCCATTA
33640 TGCC-AATGCCATT
1 TGCCAAATGCCATT
33653 GCTCAGCAGC
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
14 9 0.21
15 34 0.79
ACGTcount: A:0.31, C:0.28, G:0.14, T:0.28
Consensus pattern (15 bp):
TGCCAAATGCCATTA
Found at i:34651 original size:3 final size:3
Alignment explanation
Indices: 34643--34672 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
34633 CCTCACTTGT
34643 TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC
1 TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC
34673 GGTTGCCGCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.33, G:0.33, T:0.33
Consensus pattern (3 bp):
TGC
Found at i:37909 original size:20 final size:20
Alignment explanation
Indices: 37881--37925 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
37871 GTTCTGTTGT
*
37881 TTAATATCTAACGCAACGAC
1 TTAAGATCTAACGCAACGAC
37901 TTAAGATCTAACGCAACGAC
1 TTAAGATCTAACGCAACGAC
*
37921 CTAAG
1 TTAAG
37926 TGTCCGCTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.40, C:0.24, G:0.13, T:0.22
Consensus pattern (20 bp):
TTAAGATCTAACGCAACGAC
Done.