Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012351.1 Corchorus olitorius cultivar O-4 contig12384, 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: 42835
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:2221 original size:31 final size:32
Alignment explanation
Indices: 2186--2249 Score: 121
Period size: 31 Copynumber: 2.0 Consensus size: 32
2176 TTTTAGAATC
2186 TAAGCTCTCAACAATAACCTTTA-TTTTTCTT
1 TAAGCTCTCAACAATAACCTTTATTTTTTCTT
2217 TAAGCTCTCAACAATAACCTTTATTTTTTCTT
1 TAAGCTCTCAACAATAACCTTTATTTTTTCTT
2249 T
1 T
2250 GTATTGTTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 23 0.72
32 9 0.28
ACGTcount: A:0.28, C:0.22, G:0.03, T:0.47
Consensus pattern (32 bp):
TAAGCTCTCAACAATAACCTTTATTTTTTCTT
Found at i:16815 original size:21 final size:21
Alignment explanation
Indices: 16791--16835 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
16781 GGTGTCCACA
* *
16791 TGGTTTCCTTGAGCACCCATG
1 TGGTTTCCTTGAGAACCCAGG
*
16812 TGGTTTGCTTGAGAACCCAGG
1 TGGTTTCCTTGAGAACCCAGG
16833 TGG
1 TGG
16836 GCAGTGTCAC
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:0.16, C:0.22, G:0.31, T:0.31
Consensus pattern (21 bp):
TGGTTTCCTTGAGAACCCAGG
Found at i:16905 original size:75 final size:76
Alignment explanation
Indices: 16769--16919 Score: 184
Period size: 75 Copynumber: 2.0 Consensus size: 76
16759 ACAAGGACCC
* *
16769 CGACTCCACCTAGGTGTCCACATGGTTTCCTTGAGCACCCATGTGGTTTGCTTGAGAACCCAGGT
1 CGACTCCACCTAGGTGTCCACATGGTTTCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
16834 GGGCAGTGTCA
66 GGGCAGTGTCA
* * **
16845 CGACTCCAGCTAGGTG-CCACATGGTTT-GTCTGAAG-ACCCATGT-GTTTCGCCTGATCACCCA
1 CGACTCCACCTAGGTGTCCACATGGTTTCCT-TG-AGCACCCATGTGGTTT-GCCTGAGAACCCA
*
16906 GATGGGCTGTGTCA
63 GATGGGCAGTGTCA
16920 TAGCTCATCA
Statistics
Matches: 65, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
74 5 0.08
75 43 0.66
76 17 0.26
ACGTcount: A:0.19, C:0.28, G:0.27, T:0.26
Consensus pattern (76 bp):
CGACTCCACCTAGGTGTCCACATGGTTTCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
GGGCAGTGTCA
Found at i:19702 original size:16 final size:16
Alignment explanation
Indices: 19683--19713 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
19673 TTGCATTGTT
19683 TTGCTTTGATTGATTA
1 TTGCTTTGATTGATTA
19699 TTGCTTTGATTGATT
1 TTGCTTTGATTGATT
19714 GCCTATTCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.16, C:0.06, G:0.19, T:0.58
Consensus pattern (16 bp):
TTGCTTTGATTGATTA
Found at i:23953 original size:26 final size:26
Alignment explanation
Indices: 23924--23981 Score: 89
Period size: 26 Copynumber: 2.2 Consensus size: 26
23914 ATTAATCAAT
*
23924 ATGCAATGCAAGATATGATATGCTAA
1 ATGCAATGCAAGATATGACATGCTAA
* *
23950 ATGCAATGTAATATATGACATGCTAA
1 ATGCAATGCAAGATATGACATGCTAA
23976 ATGCAA
1 ATGCAA
23982 CATTAAAGCT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.43, C:0.12, G:0.17, T:0.28
Consensus pattern (26 bp):
ATGCAATGCAAGATATGACATGCTAA
Found at i:26346 original size:11 final size:14
Alignment explanation
Indices: 26309--26341 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
26299 CTTCTAAAGC
26309 AGAAGGAACATGGA
1 AGAAGGAACATGGA
26323 AGAAGGAACATGGA
1 AGAAGGAACATGGA
26337 AGAAG
1 AGAAG
26342 AATGGTCTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.52, C:0.06, G:0.36, T:0.06
Consensus pattern (14 bp):
AGAAGGAACATGGA
Found at i:27124 original size:25 final size:25
Alignment explanation
Indices: 27096--27146 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
27086 TTCCTCCCTC
*
27096 CTCTACCTGATCCTTCTTGGAATGA
1 CTCTACCCGATCCTTCTTGGAATGA
*
27121 CTCTACCCGATCCTTCTTGGACTGA
1 CTCTACCCGATCCTTCTTGGAATGA
27146 C
1 C
27147 ACGAACCGGG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.18, C:0.33, G:0.16, T:0.33
Consensus pattern (25 bp):
CTCTACCCGATCCTTCTTGGAATGA
Found at i:28496 original size:3 final size:3
Alignment explanation
Indices: 28488--28513 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
28478 GGGAGGCGCG
28488 GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GA
28514 CTTTAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:30552 original size:19 final size:18
Alignment explanation
Indices: 30519--30554 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
30509 TCGAGATAAT
30519 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
30537 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
30555 TAAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:31817 original size:22 final size:22
Alignment explanation
Indices: 31789--31834 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
31779 AAAATTGGGG
31789 AAAATAAGATTAATCCAAAAAC
1 AAAATAAGATTAATCCAAAAAC
31811 AAAATAAGATTAATCCAAAAAC
1 AAAATAAGATTAATCCAAAAAC
31833 AA
1 AA
31835 TCAAATTCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.65, C:0.13, G:0.04, T:0.17
Consensus pattern (22 bp):
AAAATAAGATTAATCCAAAAAC
Found at i:35950 original size:19 final size:18
Alignment explanation
Indices: 35917--35952 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
35907 TCGAGATATT
35917 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
35935 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
35953 TAAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:36288 original size:51 final size:52
Alignment explanation
Indices: 36207--36556 Score: 301
Period size: 50 Copynumber: 6.9 Consensus size: 52
36197 CCCAAAATTT
* *
36207 AAGGTTTGGTTAGTTTTGAAATAAATAAATGAAATCTTTAA-TCCAAAAAGA-TA
1 AAGGTTTGGTTAATTTTGAAAT-AA-AAATGAAATCTTTAAGT-TAAAAAGATTA
* * * * *
36260 AAGGTTTGGTTAGTTTTGAAATAAAAATGAGACCTTTAA-TAAAAAAAATT-
1 AAGGTTTGGTTAATTTTGAAATAAAAATGAAATCTTTAAGTTAAAAAGATTA
* *
36310 AAGGTTTGGTTAATTTTGGAA-AAAAATGAAATCTTTAAGTTAAAAAGATTG
1 AAGGTTTGGTTAATTTTGAAATAAAAATGAAATCTTTAAGTTAAAAAGATTA
** * * * *
36361 AATTTTTGATGAA-TTTGGAATAAAAATTAAATCTTTAAGTTAAAAAGATTA
1 AAGGTTTGGTTAATTTTGAAATAAAAATGAAATCTTTAAGTTAAAAAGATTA
* * * * * *
36412 AA--TTTTGATAAATTTGAAATAAAAATGAAATCTTTGAGTTAAAAAGACTG
1 AAGGTTTGGTTAATTTTGAAATAAAAATGAAATCTTTAAGTTAAAAAGATTA
** * * * *
36462 AATTTTTGG-TAA-TTTGTAATAAAGATGAAATCTTTAAGTTAAAAAAATTG
1 AAGGTTTGGTTAATTTTGAAATAAAAATGAAATCTTTAAGTTAAAAAGATTA
* * * * *
36512 AA--TTTTGATAAATTTGGAATAAAAATGAAATCTTTGAGTTAAAAA
1 AAGGTTTGGTTAATTTTGAAATAAAAATGAAATCTTTAAGTTAAAAA
36557 AAAGATTGAA
Statistics
Matches: 253, Mismatches: 35, Indels: 21
0.82 0.11 0.07
Matches are distributed among these distances:
48 4 0.02
49 23 0.09
50 141 0.56
51 57 0.23
52 6 0.02
53 22 0.09
ACGTcount: A:0.46, C:0.03, G:0.15, T:0.36
Consensus pattern (52 bp):
AAGGTTTGGTTAATTTTGAAATAAAAATGAAATCTTTAAGTTAAAAAGATTA
Found at i:36355 original size:100 final size:101
Alignment explanation
Indices: 36221--36631 Score: 361
Period size: 100 Copynumber: 4.0 Consensus size: 101
36211 TTTGGTTAGT
* * ** *
36221 TTTGAAATAAATAAATGAAATCTTTAA-TCCAAAAAGA-TAAAGGTTTGGTTAGTTTTGAAATAA
1 TTTGAAAT-AA-AAATGAAATCTTTAAGT-TAAAAAGACTGAATTTTTGGTTA-ATTTGAAATAA
* * * * *
36284 AAATGAGACCTTTAA-TAAAAAAAATTAAGGTTTGGTTAAT
62 AAATGAAATCTTTAAGTTAAAAAAATTAA-GTTTGGATAAA
* * * * *
36324 TTTGGAA-AAAAATGAAATCTTTAAGTTAAAAAGATTGAATTTTTGATGAATTTGGAATAAAAAT
1 TTTGAAATAAAAATGAAATCTTTAAGTTAAAAAGACTGAATTTTTGGTTAATTTGAAATAAAAAT
* * * *
36388 TAAATCTTTAAGTTAAAAAGATTAAATTTTGATAAA
66 GAAATCTTTAAGTTAAAAAAATTAAGTTTGGATAAA
* * *
36424 TTTGAAATAAAAATGAAATCTTTGAGTTAAAAAGACTGAATTTTTGG-TAATTTGTAATAAAGAT
1 TTTGAAATAAAAATGAAATCTTTAAGTTAAAAAGACTGAATTTTTGGTTAATTTGAAATAAAAAT
*
36488 GAAATCTTTAAGTTAAAAAAATTGAA-TTTTGATAAA
66 GAAATCTTTAAGTTAAAAAAATT-AAGTTTGGATAAA
* * * * * * *
36524 TTTGGAATAAAAATGAAATCTTTGAGTTAAAAAAAAGATTGAATTCTT-GATAGATTGGGAATAA
1 TTTGAAATAAAAATGAAATCTTTAAGTT---AAAAAGACTGAATTTTTGGTTA-ATTTGAAATAA
* * * *
36588 ATATGAAATCTTTAAGTTAACAAGATTAACTTT-GATAAAA
62 AAATGAAATCTTTAAGTTAAAAAAATTAAGTTTGGAT-AAA
36628 TTTG
1 TTTG
36632 GAATGAAATG
Statistics
Matches: 261, Mismatches: 35, Indels: 23
0.82 0.11 0.07
Matches are distributed among these distances:
100 128 0.49
101 61 0.23
102 1 0.00
103 28 0.11
104 43 0.16
ACGTcount: A:0.46, C:0.04, G:0.14, T:0.36
Consensus pattern (101 bp):
TTTGAAATAAAAATGAAATCTTTAAGTTAAAAAGACTGAATTTTTGGTTAATTTGAAATAAAAAT
GAAATCTTTAAGTTAAAAAAATTAAGTTTGGATAAA
Found at i:37174 original size:26 final size:27
Alignment explanation
Indices: 37119--37189 Score: 72
Period size: 26 Copynumber: 2.7 Consensus size: 27
37109 GTCACATAGG
**
37119 GGGGCATTTTGGTCATTTTTACACTAA
1 GGGGCATTTTGGTCATTTGCACACTAA
* * *
37146 -GGGCATTTTGGTCATTTGCATATTCA
1 GGGGCATTTTGGTCATTTGCACACTAA
**
37172 GGGGCACGTTGGTCATTT
1 GGGGCATTTTGGTCATTT
37190 TAAGTCCTCT
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
26 21 0.58
27 15 0.42
ACGTcount: A:0.18, C:0.15, G:0.27, T:0.39
Consensus pattern (27 bp):
GGGGCATTTTGGTCATTTGCACACTAA
Found at i:38721 original size:21 final size:21
Alignment explanation
Indices: 38695--38737 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
38685 TCTCTCACCC
38695 CTTACATTTGATAAATGAACA
1 CTTACATTTGATAAATGAACA
38716 CTTACATTTGATAAATGAACA
1 CTTACATTTGATAAATGAACA
38737 C
1 C
38738 CCACATAGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.42, C:0.16, G:0.09, T:0.33
Consensus pattern (21 bp):
CTTACATTTGATAAATGAACA
Found at i:38743 original size:21 final size:21
Alignment explanation
Indices: 38698--38743 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
38688 CTCACCCCTT
**
38698 ACATTTGATAAATGAACACTT
1 ACATTTGATAAATGAACACCC
38719 ACATTTGATAAATGAACACCC
1 ACATTTGATAAATGAACACCC
38740 ACAT
1 ACAT
38744 AGGATTCATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.43, C:0.20, G:0.09, T:0.28
Consensus pattern (21 bp):
ACATTTGATAAATGAACACCC
Found at i:41333 original size:16 final size:15
Alignment explanation
Indices: 41295--41336 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
41285 AAAGAGGTTG
41295 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
*
41310 ACAGAAAATAATTAA
1 ACAGAAAACAATTAA
41325 ACTAGAAAACAA
1 AC-AGAAAACAA
41337 AACAAAGTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 16 0.67
16 8 0.33
ACGTcount: A:0.67, C:0.12, G:0.07, T:0.14
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Done.