Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015820.1 Corchorus olitorius cultivar O-4 contig15853, 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: 15471
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Found at i:123 original size:24 final size:24
Alignment explanation
Indices: 53--124 Score: 62
Period size: 21 Copynumber: 3.0 Consensus size: 24
43 GTATAGATTT
*
53 AGATAATTAATTTAATGTACCCAAAATA
1 AGATAATTAATTT-ATG-A--CAAAAAA
81 AGATAATT--TTCTAT-A-AAAAAA
1 AGATAATTAATT-TATGACAAAAAA
102 AGATAATTAATTTATGACAAAAA
1 AGATAATTAATTTATGACAAAAA
125 TATTTAATGA
Statistics
Matches: 38, Mismatches: 1, Indels: 14
0.72 0.02 0.26
Matches are distributed among these distances:
21 13 0.34
22 3 0.08
23 3 0.08
24 6 0.16
26 4 0.11
27 1 0.03
28 8 0.21
ACGTcount: A:0.54, C:0.07, G:0.07, T:0.32
Consensus pattern (24 bp):
AGATAATTAATTTATGACAAAAAA
Found at i:2791 original size:15 final size:16
Alignment explanation
Indices: 2762--2793 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2752 GTATAGATTA
*
2762 ATTTTTTTTTAAAAAT
1 ATTTTATTTTAAAAAT
2778 ATTTTATTTTAAAAAT
1 ATTTTATTTTAAAAAT
2794 CAGAAAGTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
ATTTTATTTTAAAAAT
Found at i:4640 original size:32 final size:32
Alignment explanation
Indices: 4604--4678 Score: 141
Period size: 32 Copynumber: 2.3 Consensus size: 32
4594 TATCAATGAT
4604 AATCAAGTTTTATTGTGCATCATCTCTCATCA
1 AATCAAGTTTTATTGTGCATCATCTCTCATCA
4636 AATCAAGTTTTATTGTGCATCATCTCTCATCA
1 AATCAAGTTTTATTGTGCATCATCTCTCATCA
*
4668 AATCAACTTTT
1 AATCAAGTTTT
4679 TTTTTGTTTA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.29, C:0.21, G:0.08, T:0.41
Consensus pattern (32 bp):
AATCAAGTTTTATTGTGCATCATCTCTCATCA
Found at i:8669 original size:31 final size:30
Alignment explanation
Indices: 8623--8710 Score: 95
Period size: 31 Copynumber: 2.8 Consensus size: 30
8613 GATAAGAGTT
* * *
8623 CAATATTTGCGAAAATGCTCAAATCATGGTC
1 CAAT-TTTGCAAAAATGCTCAAATAAAGGTC
*
8654 CAATGTTTGCAAAAATGCTCAAATAAAGGTT
1 CAAT-TTTGCAAAAATGCTCAAATAAAGGTC
* *
8685 CAATATTGCGAAAATTGCTCAAATAA
1 CAATTTTGC-AAAAATGCTCAAATAA
8711 GTCCCTGACA
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
30 4 0.08
31 45 0.92
ACGTcount: A:0.41, C:0.16, G:0.15, T:0.28
Consensus pattern (30 bp):
CAATTTTGCAAAAATGCTCAAATAAAGGTC
Found at i:8830 original size:29 final size:29
Alignment explanation
Indices: 8793--8865 Score: 121
Period size: 29 Copynumber: 2.6 Consensus size: 29
8783 ACGTTGGGCT
*
8793 CTTA-TTGAGCTTTTTTTTTCTTTAGGCC
1 CTTATTTGAGCATTTTTTTTCTTTAGGCC
8821 CTTATTTGAGCATTTTTTTTCTTTAGGCC
1 CTTATTTGAGCATTTTTTTTCTTTAGGCC
*
8850 CTTATTTTAGCATTTT
1 CTTATTTGAGCATTTT
8866 CGCAAATATT
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
28 4 0.10
29 38 0.90
ACGTcount: A:0.14, C:0.16, G:0.12, T:0.58
Consensus pattern (29 bp):
CTTATTTGAGCATTTTTTTTCTTTAGGCC
Found at i:9399 original size:16 final size:17
Alignment explanation
Indices: 9362--9399 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 17
9352 TTCTATTAAT
9362 TATT-TTTAGATTATAA
1 TATTATTTAGATTATAA
9378 TA-TATTTA-ATTATAA
1 TATTATTTAGATTATAA
9393 TATTATT
1 TATTATT
9400 ATTTATAGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (17 bp):
TATTATTTAGATTATAA
Found at i:10634 original size:334 final size:329
Alignment explanation
Indices: 9728--11050 Score: 1272
Period size: 334 Copynumber: 4.0 Consensus size: 329
9718 ATACTTTACA
*
9728 TCATCTAATCAAATCTCAGCAACATTGGATTTAAGAAATTT-TTTTACGAA-CATCTGAATCTTG
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAG-AATTTGTTTTAC-AAGCATCTGAATCTTG
* * * * * *
9791 TTTCGATTTAATTAGAAATTAATTTAGAATAAAATAAGAAATACGATATTAAGAGCGTAAAAAGC
64 TTTCGATTTAATTAGAAATTAATTCAGAA-AAAATATGAAAAACAATATTAAAAGCGTGAAAAGC
* * *
9856 CCTCCAATATTTTTGGCATTGAATTATATATTTTTAAGAGTATTTTAGCCAAAAATTGAGGAGAA
128 CCTCCAATCTTTTTGGCATTAAATTATATATTTTTATGAGTATTTTAGCCAAAAATTGAGGA-AA
** * * *
9921 ACCTTTT-GTGTCAATTTTTACAAAATTTTAGCC-GAA---A--T-C-AACCATCACGG--TTTC
192 AAATTTTCGGGTCAATTTTTACAAAATTTTAGCCAAAATCGATGTACTAACCATCACGGTTTTTG
* * * * ** * * * *
9975 GC------GC-TCCGGGGACCCGGCTCAATTTTGTTTGATTTTTGGCTCCGAGACTACTTGAAAT
257 GCTAAAAAGCGTTCTGGGCCCCGACTCAATTTTGCATGATTTTTGACGCCAAGACTCCTTGAAAT
10033 ATCTATAT
322 ATCTATAT
* * *
10041 TCATCTAATTAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACAAGCATCTGAATCTTGG
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAGAATTTG-TTTTACAAGCATCTGAATCTTGT
** * * * * *
10106 TTCGATTTAATTAGAAATTAATTTGGAAAAAAATAGGAAAAACGATATTATAAA-TGTCAAAAAC
65 TTCGATTTAATTAGAAATTAATTCAG-AAAAAATATGAAAAACAATATTA-AAAGCGTGAAAAGC
* * * * * *
10170 CCTTCAATCTTTTTGGCGTTGAATTATATATCTTATATGAGTAATTTAGCCAAAAGTTGAGGAAA
128 CCTCCAATCTTTTTGGCATTAAATTATATAT-TTTTATGAGTATTTTAGCCAAAAATTGAGGAAA
* * *** * * * * *
10235 TATTTTTCTAATCAATTTTTACAATATTTTAG-CAGCAATCG-TGTAATAATCATCACAGTTTTT
192 AAATTTTCGGGTCAATTTTTACAAAATTTTAGCCA-AAATCGATGTACTAACCATCAC-GGTTTT
* *
10298 TGGCTAAAAAAGCGTTCTGGGACCCCGACTCAATTTTGCATGATTTTTTACGCCAAGACTTCTTG
255 TGGCT-AAAAAGCGTTCTGGG-CCCCGACTCAATTTTGCATGATTTTTGACGCCAAGACTCCTTG
* *
10363 AGATATCCATAT
318 AAATATCTATAT
*
10375 TCATCTAATCAAAT-TCCAGCCACATTGGATCTAAGAATTTGTTTTGACAAGCATCTGAATCTTG
1 TCATCTAATCAAATCT-CAGCCACATTGGATTTAAGAATTTGTTTT-ACAAGCATCTGAATCTTG
*
10439 TTTCGATTTAATTAGAAATTAATTCA-AAAAAATATGAAAAACAATATTAAAAGCGTGAAAAGTC
64 TTTCGATTTAATTAGAAATTAATTCAGAAAAAATATGAAAAACAATATTAAAAGCGTGAAAAGCC
* * * * *
10503 CTCCAATCTTTTTGGCGTTAAATTATATATATTTTATGAGTATTTTATCCAGAAATAGGGGAAAA
129 CTCCAATCTTTTTGGCATTAAATTATATAT-TTTTATGAGTATTTTAGCCAAAAATTGAGGAAAA
* * *
10568 AATTTTCGGGTCATTTTTTTGCAAAGTTTTAGCCAAAATCGTATGTACTAACCATCACGGTTTTT
193 AATTTTCGGGTCA-ATTTTTACAAAATTTTAGCCAAAATCG-ATGTACTAACCATCACGGTTTTT
* * * **
10633 GGCTAAAAATGCGTT-TCGAGGCCCCGACTCAGTTTTGCATGGTTTTTGGCGCTGAGACTCCTTG
256 GGCTAAAAA-GCGTTCT-G-GGCCCCGACTCAATTTTGCATGATTTTTGACGCCAAGACTCCTTG
*
10697 AAATATTTATAT
318 AAATATCTATAT
* * * * *
10709 TCATCTAAT-AATATCTTAGCCACATTGCATTCAAGGATTTGTTTCTACGAGCATCTTG-ATCTT
1 TCATCTAATCAA-ATCTCAGCCACATTGGATTTAAGAATTTGTTT-TACAAGCATC-TGAATCTT
*
10772 GTTTCGATTTAATTAGAAATTAATTCAGAAAAAATAT-AAAAAAATTATATTAAAAGCGTGAAAA
63 GTTTCGATTTAATTAGAAATTAATTCAGAAAAAATATGAAAAACA--ATATTAAAAGCGTGAAAA
* * * *
10836 GCCCTTCAATCTTTTTGGCATTAAATTATATATTTTTTATGAGCATTAT-GACTAAAAATTGAGG
126 GCCCTCCAATCTTTTTGGCATTAAATTATATA-TTTTTATGAGTATTTTAG-CCAAAAATTGAGG
* * * * *
10900 -AAATATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCAAAATCG-TGTAATATAATCATTACGG
189 AAAAAAT-TTTCGGGTCAATTTTTACAAAATTTTAGCCAAAATCGATGT-A-CTAACCATCACGG
* * * * * ** * *
10963 TTTTTGACTTAAAACGAGTTCCGGGGCCCGGTTCAATTTTGAATGATTTTT-AGCGCCAAGCCTC
251 TTTTTGGC-TAAAAAGCGTTCTGGGCCCCGACTCAATTTTGCATGATTTTTGA-CGCCAAGACTC
11027 CTTGAAATATCTATAT
314 CTTGAAATATCTATAT
11043 TCATCTAA
1 TCATCTAA
11051 CCGAATCCCA
Statistics
Matches: 831, Mismatches: 126, Indels: 85
0.80 0.12 0.08
Matches are distributed among these distances:
312 4 0.00
313 35 0.04
314 105 0.13
315 51 0.06
316 2 0.00
320 1 0.00
322 8 0.01
323 1 0.00
325 5 0.01
331 3 0.00
332 93 0.11
333 40 0.05
334 318 0.38
335 80 0.10
336 84 0.10
337 1 0.00
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (329 bp):
TCATCTAATCAAATCTCAGCCACATTGGATTTAAGAATTTGTTTTACAAGCATCTGAATCTTGTT
TCGATTTAATTAGAAATTAATTCAGAAAAAATATGAAAAACAATATTAAAAGCGTGAAAAGCCCT
CCAATCTTTTTGGCATTAAATTATATATTTTTATGAGTATTTTAGCCAAAAATTGAGGAAAAAAT
TTTCGGGTCAATTTTTACAAAATTTTAGCCAAAATCGATGTACTAACCATCACGGTTTTTGGCTA
AAAAGCGTTCTGGGCCCCGACTCAATTTTGCATGATTTTTGACGCCAAGACTCCTTGAAATATCT
ATAT
Found at i:12748 original size:42 final size:43
Alignment explanation
Indices: 12697--12790 Score: 138
Period size: 45 Copynumber: 2.2 Consensus size: 43
12687 AGTACATTAT
*
12697 CTAA-ATTCTA-CTCCATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG
*
12738 CTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAT
1 CTAATATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAG
12783 CTAATATT
1 CTAATATT
12791 AATTGTTGCT
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
41 4 0.09
42 6 0.13
45 37 0.79
ACGTcount: A:0.38, C:0.22, G:0.04, T:0.35
Consensus pattern (43 bp):
CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG
Found at i:13620 original size:13 final size:13
Alignment explanation
Indices: 13602--13723 Score: 50
Period size: 13 Copynumber: 9.9 Consensus size: 13
13592 AGAAATATAT
13602 AATATATATAATA
1 AATATATATAATA
*
13615 AATATAGAT-ATA
1 AATATATATAATA
* *
13627 CATAT-TGT-ATA
1 AATATATATAATA
* *
13638 GATATATAAAATA
1 AATATATATAATA
*
13651 TATA-ATAATAATA
1 AATATAT-ATAATA
13664 TAATAT-TATAAT-
1 -AATATATATAATA
* *
13676 ATTATA-ATATTA
1 AATATATATAATA
13688 TAATAT-TATAAT-
1 -AATATATATAATA
*
13700 ATTATATAATAAT-
1 AATATAT-ATAATA
13713 AATA-ATATAAT
1 AATATATATAAT
13724 TCAATACCAA
Statistics
Matches: 82, Mismatches: 16, Indels: 24
0.67 0.13 0.20
Matches are distributed among these distances:
11 25 0.30
12 13 0.16
13 40 0.49
14 4 0.05
ACGTcount: A:0.55, C:0.01, G:0.02, T:0.42
Consensus pattern (13 bp):
AATATATATAATA
Found at i:13631 original size:6 final size:5
Alignment explanation
Indices: 13598--13716 Score: 70
Period size: 5 Copynumber: 23.6 Consensus size: 5
13588 CCATAGAAAT
* *
13598 ATATA ATAT- ATATA ATA-A ATATA GATATA CATATT GTATA GATAT-
1 ATATA ATATA ATATA ATATA ATATA -ATATA -ATATA ATATA -ATATA
* * *
13643 ATA-A A-AT- ATATA ATAATA ATATA ATATT ATAATA TTATA ATATT ATAATA
1 ATATA ATATA ATATA AT-ATA ATATA ATATA AT-ATA ATATA ATATA AT-ATA
* *
13693 TTATA ATATT ATATA ATAATA ATA
1 ATATA ATATA ATATA AT-ATA ATA
13717 ATATAATTCA
Statistics
Matches: 87, Mismatches: 15, Indels: 24
0.69 0.12 0.19
Matches are distributed among these distances:
3 2 0.02
4 14 0.16
5 43 0.49
6 28 0.32
ACGTcount: A:0.55, C:0.01, G:0.03, T:0.42
Consensus pattern (5 bp):
ATATA
Found at i:13668 original size:8 final size:8
Alignment explanation
Indices: 13598--13723 Score: 79
Period size: 8 Copynumber: 15.9 Consensus size: 8
13588 CCATAGAAAT
13598 ATATAATA
1 ATATAATA
13606 TATATAATA
1 -ATATAATA
13615 A-AT-ATA
1 ATATAATA
13621 GATATACATA
1 -ATATA-ATA
*
13631 TTGTATAGAT-
1 --ATATA-ATA
13641 ATATAA-A
1 ATATAATA
13648 ATAT-AT-
1 ATATAATA
13654 A-ATAATA
1 ATATAATA
13661 ATATAATA
1 ATATAATA
*
13669 TTATAATA
1 ATATAATA
*
13677 TTATAATA
1 ATATAATA
*
13685 TTATAATA
1 ATATAATA
*
13693 TTATAATA
1 ATATAATA
*
13701 TTAT-ATA
1 ATATAATA
13708 ATAATAATA
1 AT-ATAATA
13717 ATATAAT
1 ATATAAT
13724 TCAATACCAA
Statistics
Matches: 99, Mismatches: 6, Indels: 25
0.76 0.05 0.19
Matches are distributed among these distances:
5 2 0.02
6 7 0.07
7 13 0.13
8 55 0.56
9 13 0.13
10 3 0.03
11 6 0.06
ACGTcount: A:0.55, C:0.01, G:0.02, T:0.42
Consensus pattern (8 bp):
ATATAATA
Found at i:13674 original size:16 final size:16
Alignment explanation
Indices: 13650--13723 Score: 96
Period size: 16 Copynumber: 4.6 Consensus size: 16
13640 TATATAAAAT
*
13650 ATATAATAATAATATA
1 ATATTATAATAATATA
*
13666 ATATTATAATATTATA
1 ATATTATAATAATATA
*
13682 ATATTATAATATTATA
1 ATATTATAATAATATA
13698 ATATTAT-ATAATAATA
1 ATATTATAATAAT-ATA
*
13714 ATAATATAAT
1 ATATTATAAT
13724 TCAATACCAA
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
15 4 0.08
16 46 0.88
17 2 0.04
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
ATATTATAATAATATA
Found at i:13682 original size:24 final size:24
Alignment explanation
Indices: 13650--13723 Score: 105
Period size: 24 Copynumber: 3.1 Consensus size: 24
13640 TATATAAAAT
*
13650 ATATAATAATAATATAATATTATA
1 ATATTATAATAATATAATATTATA
*
13674 ATATTATAATATTATAATATTATA
1 ATATTATAATAATATAATATTATA
*
13698 ATATTAT-ATAATAATAATAATATA
1 ATATTATAATAAT-ATAATATTATA
13722 AT
1 AT
13724 TCAATACCAA
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
23 4 0.09
24 41 0.91
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (24 bp):
ATATTATAATAATATAATATTATA
Done.