Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012292.1 Corchorus olitorius cultivar O-4 contig12325, 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: 35995
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:7745 original size:50 final size:50
Alignment explanation
Indices: 7686--8227 Score: 888
Period size: 50 Copynumber: 10.8 Consensus size: 50
7676 GTAAGGCTTG
* * * *
7686 GATAGTTGACTCGTACGGAAACGAGTTTGGCTTGTGGAAAGGCCCATGTT
1 GATAATTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTT
*
7736 GATAATTGACTCGTATGGAAACGAGTTTGGCTTGTCGAAAAGCCTATGTT
1 GATAATTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTT
*
7786 GATAATTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCATGTT
1 GATAATTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTT
* *
7836 GATAATTGACTCGTATGGAAACGAATTTGGCTTGTGGAGAAGCCTATGTT
1 GATAATTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTT
7886 GATAATTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTT
1 GATAATTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTT
* *
7936 GATAATTGACTCGTATGGAAACGAGTTCGGCTTGTGGAGAAGCCTATGTT
1 GATAATTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTT
** *
7986 GATAATTGACTCGTATGGAAACGAGTTCAGCTTGTGGAAAAGCCAATGTT
1 GATAATTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTT
*
8036 GATAATTGACTCGTATGGAAACGAGTTCGGCTTGTGGAAAAGCCTATGTT
1 GATAATTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTT
*
8086 GATAATTGACTCGTATGGAAATGAGTTTGGCTTGTGGAAAAGCCTATGTT
1 GATAATTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTT
*
8136 GATAATTGACTCGTATGGAAACGA-TTTCGGCTTATGGAAAAGCCTATGTT
1 GATAATTGACTCGTATGGAAACGAGTTT-GGCTTGTGGAAAAGCCTATGTT
* * * *
8186 GATAATTGATTTGTATGGAAACGAGTTCGGCTTATGGAAAAG
1 GATAATTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAG
8228 TCAAAGCATT
Statistics
Matches: 464, Mismatches: 26, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
49 3 0.01
50 459 0.99
51 2 0.00
ACGTcount: A:0.28, C:0.13, G:0.28, T:0.31
Consensus pattern (50 bp):
GATAATTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTT
Found at i:9050 original size:50 final size:50
Alignment explanation
Indices: 8901--9050 Score: 228
Period size: 50 Copynumber: 3.0 Consensus size: 50
8891 CTTAAATGCC
* * **
8901 CTTTGAAAAACGAATTTTGATCTTGGACTCACAAATGGAATGCAATCCTA
1 CTTTGAAAAGCGAATTTTGATCTTGGACTCACAAATGGAAAGCAATTTTA
*
8951 CTTTGAAAAGCGAATTTTGATCTTGGACTTACAAATGGAAAGCAATTTTA
1 CTTTGAAAAGCGAATTTTGATCTTGGACTCACAAATGGAAAGCAATTTTA
* * *
9001 CTTTGAAAAGCGAATTTTGATCTTGAACTCATAAATGGAAAGCAGTTTTA
1 CTTTGAAAAGCGAATTTTGATCTTGGACTCACAAATGGAAAGCAATTTTA
9051 TTGTAAAACT
Statistics
Matches: 91, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 91 1.00
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (50 bp):
CTTTGAAAAGCGAATTTTGATCTTGGACTCACAAATGGAAAGCAATTTTA
Found at i:9648 original size:16 final size:15
Alignment explanation
Indices: 9627--9666 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 15
9617 TCCATTCTCT
9627 TTTGATTTTGATTTG
1 TTTGATTTTGATTTG
*
9642 ATTTGATTTTTATTTG
1 -TTTGATTTTGATTTG
9658 -TTGATTTTG
1 TTTGATTTTG
9667 TTTTTTTCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 8 0.36
16 14 0.64
ACGTcount: A:0.15, C:0.00, G:0.17, T:0.68
Consensus pattern (15 bp):
TTTGATTTTGATTTG
Found at i:32727 original size:22 final size:22
Alignment explanation
Indices: 32702--32773 Score: 62
Period size: 22 Copynumber: 3.3 Consensus size: 22
32692 GATCTTCATG
32702 TCTTCAAATTGACTCCAATTGA
1 TCTTCAAATTGACTCCAATTGA
* *
32724 TCTTC-AA-T--CTCGAACTTCA
1 TCTTCAAATTGACTCCAA-TTGA
32743 CGTCTTCAAATTGACTCCAATTGA
1 --TCTTCAAATTGACTCCAATTGA
*
32767 TATTCAA
1 TCTTCAA
32774 TCTCGAACTT
Statistics
Matches: 38, Mismatches: 5, Indels: 14
0.67 0.09 0.25
Matches are distributed among these distances:
18 5 0.13
19 3 0.08
20 1 0.03
21 7 0.18
22 13 0.34
23 1 0.03
24 3 0.08
25 5 0.13
ACGTcount: A:0.31, C:0.25, G:0.08, T:0.36
Consensus pattern (22 bp):
TCTTCAAATTGACTCCAATTGA
Found at i:32748 original size:43 final size:43
Alignment explanation
Indices: 32695--32796 Score: 186
Period size: 43 Copynumber: 2.4 Consensus size: 43
32685 CATCAATGAT
* *
32695 CTTCATGTCTTCAAATTGACTCCAATTGATCTTCAATCTCGAA
1 CTTCACGTCTTCAAATTGACTCCAATTGATATTCAATCTCGAA
32738 CTTCACGTCTTCAAATTGACTCCAATTGATATTCAATCTCGAA
1 CTTCACGTCTTCAAATTGACTCCAATTGATATTCAATCTCGAA
32781 CTTCACGTCTTCAAAT
1 CTTCACGTCTTCAAAT
32797 CTTCACTCAT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
43 57 1.00
ACGTcount: A:0.28, C:0.26, G:0.09, T:0.36
Consensus pattern (43 bp):
CTTCACGTCTTCAAATTGACTCCAATTGATATTCAATCTCGAA
Found at i:32798 original size:22 final size:21
Alignment explanation
Indices: 32724--32794 Score: 58
Period size: 21 Copynumber: 3.3 Consensus size: 21
32714 CTCCAATTGA
32724 TCTTCAATCTCGAACTTCACG
1 TCTTCAATCTCGAACTTCACG
* *
32745 TCTTCAAAT-T-G-ACTCCAATTG
1 TCTTC-AATCTCGAACTTC-A-CG
*
32766 ATATTCAATCTCGAACTTCACG
1 -TCTTCAATCTCGAACTTCACG
32788 TCTTCAA
1 TCTTCAA
32795 ATCTTCACTC
Statistics
Matches: 37, Mismatches: 6, Indels: 14
0.65 0.11 0.25
Matches are distributed among these distances:
19 4 0.11
20 2 0.05
21 16 0.43
22 9 0.24
23 2 0.05
24 4 0.11
ACGTcount: A:0.28, C:0.28, G:0.08, T:0.35
Consensus pattern (21 bp):
TCTTCAATCTCGAACTTCACG
Found at i:35476 original size:16 final size:16
Alignment explanation
Indices: 35457--35491 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
35447 TCCTCCCATT
35457 TTCAATTACCCCTCAA
1 TTCAATTACCCCTCAA
*
35473 TTCAATTACCCCTTAA
1 TTCAATTACCCCTCAA
35489 TTC
1 TTC
35492 CACCGAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.29, C:0.34, G:0.00, T:0.37
Consensus pattern (16 bp):
TTCAATTACCCCTCAA
Done.