Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021923.1 Corchorus olitorius cultivar O-4 contig21956, 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: 44199
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:1373 original size:58 final size:58
Alignment explanation
Indices: 1277--1389 Score: 156
Period size: 58 Copynumber: 1.9 Consensus size: 58
1267 ATTAATCAAA
* * *
1277 TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAAGACGTTTTCGGACCAAGACT
1 TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAAGACATTTTAGAACCAAGACT
* * *
1335 TATCGAGTGACATGTTTTTTTATTAGATGCCT-AAAAAAGACATTTTAGAACCAAG
1 TATCAAGTGACATG-TTCTTTATTAGATGCATAAAAAAAGACATTTTAGAACCAAG
1390 GCATGATGCT
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
58 33 0.69
59 15 0.31
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (58 bp):
TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAAGACATTTTAGAACCAAGACT
Found at i:2668 original size:36 final size:36
Alignment explanation
Indices: 2621--2691 Score: 115
Period size: 36 Copynumber: 2.0 Consensus size: 36
2611 TTCAATAACC
* *
2621 TTACATCTTTTGTGATTTTGGTTATCATATTTCTTA
1 TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
*
2657 TTACATTTTTTGTAATTTTGATTATCATATTTCTT
1 TTACATCTTTTGTAATTTTGATTATCATATTTCTT
2692 CAAAATCTCA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.21, C:0.10, G:0.08, T:0.61
Consensus pattern (36 bp):
TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
Found at i:3582 original size:204 final size:201
Alignment explanation
Indices: 3204--3613 Score: 757
Period size: 204 Copynumber: 2.0 Consensus size: 201
3194 GCTTAATAAC
3204 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
1 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
*
3269 GATACAACACATTATTATTATATATAAAACTATACCAAAAAAAAGTAGTTGAACATTAGTGGTTG
66 GATACAACACATTACTATTATATATAAAACTATACCAAAAAAAAGTAGTTGAACATTAGTGGTTG
*
3334 ATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATC
131 ATTTATTAAATTAAATTAGATCAATATCAAACAAAATTTCAAAATTATAAAAGATATT-AAGATC
3399 CGATTTA
195 CGATTTA
*
3406 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTTTAGTGAATAA
1 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
*
3471 GATACAACACATTACTATTATATATATAGAACTATACCAAAAAAAATTAGTTGAACATTAGTGGT
66 GATACAACACATTACTATTATATATA-A-AACTATACCAAAAAAAAGTAGTTGAACATTAGTGGT
3536 TGATTTATTAAATTAAATTAGATCAATATCAAACAAAATTTCAAAATTATAAAAGATATTAAGAT
129 TGATTTATTAAATTAAATTAGATCAATATCAAACAAAATTTCAAAATTATAAAAGATATTAAGAT
3601 CCGATTTA
194 CCGATTTA
3609 TTTAT
1 TTTAT
3614 TATTAAGGAA
Statistics
Matches: 202, Mismatches: 4, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
202 89 0.44
203 19 0.09
204 94 0.47
ACGTcount: A:0.44, C:0.09, G:0.11, T:0.37
Consensus pattern (201 bp):
TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
GATACAACACATTACTATTATATATAAAACTATACCAAAAAAAAGTAGTTGAACATTAGTGGTTG
ATTTATTAAATTAAATTAGATCAATATCAAACAAAATTTCAAAATTATAAAAGATATTAAGATCC
GATTTA
Found at i:3777 original size:39 final size:39
Alignment explanation
Indices: 3723--3811 Score: 126
Period size: 39 Copynumber: 2.3 Consensus size: 39
3713 ATATCTAAGA
* *
3723 ATTTAATTAATGTAAGTATTTCAGTTATTATA-GTATTAC
1 ATTTAATTAATGTAAGCATTT-AGTTATTATATATATTAC
3762 ATTTAATTAATGTAAGCATTTAGTTATTATATATATTAC
1 ATTTAATTAATGTAAGCATTTAGTTATTATATATATTAC
*
3801 ATATGAATTAA
1 AT-TTAATTAA
3812 AAATTAATTG
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
38 10 0.22
39 28 0.62
40 7 0.16
ACGTcount: A:0.39, C:0.04, G:0.09, T:0.47
Consensus pattern (39 bp):
ATTTAATTAATGTAAGCATTTAGTTATTATATATATTAC
Found at i:7881 original size:4 final size:4
Alignment explanation
Indices: 7872--7898 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
7862 ACTCAATCTA
7872 ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATA
7899 TATTTATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.22, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:10687 original size:29 final size:28
Alignment explanation
Indices: 10633--10687 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
10623 CTACTTTCAC
* *
10633 AAAAAAATCAATTTCGTCCATCTACTAA
1 AAAAAAATCAATTTAGTCCATATACTAA
*
10661 AAAAACAATCAATTTAGTCCCTATACT
1 AAAAA-AATCAATTTAGTCCATATACT
10688 TTGCACTTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 5 0.22
29 18 0.78
ACGTcount: A:0.45, C:0.22, G:0.04, T:0.29
Consensus pattern (28 bp):
AAAAAAATCAATTTAGTCCATATACTAA
Found at i:12421 original size:27 final size:27
Alignment explanation
Indices: 12391--12476 Score: 75
Period size: 27 Copynumber: 3.2 Consensus size: 27
12381 ATCATCATCA
**
12391 TCATCATCATCTTCTTCTTCTTCTTCT
1 TCATCATCAAGTTCTTCTTCTTCTTCT
* * ** *
12418 TCATCGTCAGGTAGATT-TTTTTCTTCT
1 TCATCATCAAGT-TCTTCTTCTTCTTCT
* *
12445 TCATCTTCAAGTTCTTCTTCTTCCTCT
1 TCATCATCAAGTTCTTCTTCTTCTTCT
12472 TCATC
1 TCATC
12477 TACTGTTTCT
Statistics
Matches: 45, Mismatches: 12, Indels: 4
0.74 0.20 0.07
Matches are distributed among these distances:
26 2 0.04
27 41 0.91
28 2 0.04
ACGTcount: A:0.13, C:0.29, G:0.06, T:0.52
Consensus pattern (27 bp):
TCATCATCAAGTTCTTCTTCTTCTTCT
Found at i:12477 original size:27 final size:27
Alignment explanation
Indices: 12402--12477 Score: 82
Period size: 27 Copynumber: 2.8 Consensus size: 27
12392 CATCATCATC
* *
12402 TTCTTCTTCTTCTTCTTCATCGTCAGG
1 TTCTTCTTCTTCTTCTTCATCTTCAAG
** *
12429 TAGATT-TTTTTCTTCTTCATCTTCAAG
1 T-TCTTCTTCTTCTTCTTCATCTTCAAG
*
12456 TTCTTCTTCTTCCTCTTCATCT
1 TTCTTCTTCTTCTTCTTCATCT
12478 ACTGTTTCTT
Statistics
Matches: 38, Mismatches: 9, Indels: 4
0.75 0.18 0.08
Matches are distributed among these distances:
26 2 0.05
27 34 0.89
28 2 0.05
ACGTcount: A:0.11, C:0.28, G:0.07, T:0.55
Consensus pattern (27 bp):
TTCTTCTTCTTCTTCTTCATCTTCAAG
Found at i:14274 original size:16 final size:17
Alignment explanation
Indices: 14253--14290 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
14243 GAGAAAAATT
*
14253 GAGAGGGAATTG-GAGA
1 GAGAGGGAATTGAAAGA
*
14269 GAGAGGGATTTGAAAGA
1 GAGAGGGAATTGAAAGA
14286 GAGAG
1 GAGAG
14291 AGTGTTTTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.39, C:0.00, G:0.47, T:0.13
Consensus pattern (17 bp):
GAGAGGGAATTGAAAGA
Found at i:16619 original size:553 final size:553
Alignment explanation
Indices: 15573--16679 Score: 2169
Period size: 553 Copynumber: 2.0 Consensus size: 553
15563 TTTGTAACAG
*
15573 AAACTTTGACAGTCTTTCATACCAAGCTCTAGGAGCTTGTTTGAGACCATACAAAACTTTGTGCA
1 AAACTTTAACAGTCTTTCATACCAAGCTCTAGGAGCTTGTTTGAGACCATACAAAACTTTGTGCA
15638 ATCTGAAAACATCATTTGGTCTTTGAAATCTTCAAAATCAGGAGGTTGTTTAACATACACTTCCT
66 ATCTGAAAACATCATTTGGTCTTTGAAATCTTCAAAATCAGGAGGTTGTTTAACATACACTTCCT
*
15703 CTTGAATGTAACCATTCTGGAAAGCACTTTTCACATCTATTTGAAACAGTTTAAAGTCCATATGA
131 CTTGAATGTAACCATTCAGGAAAGCACTTTTCACATCTATTTGAAACAGTTTAAAGTCCATATGA
15768 CAAGCAAATGCAAGTAAAAGACGAATAGCCTCTAACCTGGCAACATGAGCAAAGGTTTCATCATA
196 CAAGCAAATGCAAGTAAAAGACGAATAGCCTCTAACCTGGCAACATGAGCAAAGGTTTCATCATA
15833 ATCAATGCCTTCTTCCTGGTTATAGCCTTTGGCTACCAGTCGGGTCTTGTTTCTTACCACTCTAC
261 ATCAATGCCTTCTTCCTGGTTATAGCCTTTGGCTACCAGTCGGGTCTTGTTTCTTACCACTCTAC
15898 CAGTTTCATTTATTTTGTTTCTGAAAACCCATTTAGTGCCAACAATCGGGTGATCATCAGGTCTT
326 CAGTTTCATTTATTTTGTTTCTGAAAACCCATTTAGTGCCAACAATCGGGTGATCATCAGGTCTT
*
15963 GGCACTAAAGTCTAGACTTTGCTTCATTCAAACTGGTTGAGCTCTTCTTGCATTGTTGTCATCCA
391 GGCACTAAAGTCTAGACTTTGCTTCATTCAAACTAGTTGAGCTCTTCTTGCATTGTTGTCATCCA
16028 ACTTTCTTCTTTTTCTGCTTCTTCAAATGTTTTTGGTTCCACTTGTGAAATGAATGCAGCAAATT
456 ACTTTCTTCTTTTTCTGCTTCTTCAAATGTTTTTGGTTCCACTTGTGAAATGAATGCAGCAAATT
16093 CACAAGTCTCTTTAAGTCCACTTCTTGTTCTCA
521 CACAAGTCTCTTTAAGTCCACTTCTTGTTCTCA
16126 AAACTTTAACAGTCTTTCATACCAAGCTCTAGGAGCTTGTTTGAGACCATACAAAACTTTGTGCA
1 AAACTTTAACAGTCTTTCATACCAAGCTCTAGGAGCTTGTTTGAGACCATACAAAACTTTGTGCA
16191 ATCTGAAAACATCATTTGGTCTTTGAAATCTTCAAAATCAGGAGGTTGTTTAACATACACTTCCT
66 ATCTGAAAACATCATTTGGTCTTTGAAATCTTCAAAATCAGGAGGTTGTTTAACATACACTTCCT
16256 CTTGAATGTAACCATTCAGGAAAGCACTTTTCACATCTATTTGAAACAGTTTAAAGTCCATATGA
131 CTTGAATGTAACCATTCAGGAAAGCACTTTTCACATCTATTTGAAACAGTTTAAAGTCCATATGA
*
16321 CAAGCAAATGCAAGTAAAAGACGAATAGCCTTTAACCTGGCAACATGAGCAAAGGTTTCATCATA
196 CAAGCAAATGCAAGTAAAAGACGAATAGCCTCTAACCTGGCAACATGAGCAAAGGTTTCATCATA
16386 ATCAATGCCTTCTTCCTGGTTATAGCCTTTGGCTACCAGTCGGGTCTTGTTTCTTACCACTCTAC
261 ATCAATGCCTTCTTCCTGGTTATAGCCTTTGGCTACCAGTCGGGTCTTGTTTCTTACCACTCTAC
16451 CAGTTTCATTTATTTTGTTTCTGAAAACCCATTTAGTGCCAACAATCGGGTGATCATCAGGTCTT
326 CAGTTTCATTTATTTTGTTTCTGAAAACCCATTTAGTGCCAACAATCGGGTGATCATCAGGTCTT
16516 GGCACTAAAGTCTAGACTTTGCTTCATTCAAACTAGTTGAGCTCTTCTTGCATTGTTGTCATCCA
391 GGCACTAAAGTCTAGACTTTGCTTCATTCAAACTAGTTGAGCTCTTCTTGCATTGTTGTCATCCA
16581 ACTTTCTTCTTTTTCTGCTTCTTCAAATGTTTTTGGTTCCACTTGTGAAATGAATGCAGCAAATT
456 ACTTTCTTCTTTTTCTGCTTCTTCAAATGTTTTTGGTTCCACTTGTGAAATGAATGCAGCAAATT
*
16646 CACAAGTCTCTTTAAGTCCATTTCTTGTTCTCA
521 CACAAGTCTCTTTAAGTCCACTTCTTGTTCTCA
16679 A
1 A
16680 TCCTTCTCTA
Statistics
Matches: 549, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
553 549 1.00
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.35
Consensus pattern (553 bp):
AAACTTTAACAGTCTTTCATACCAAGCTCTAGGAGCTTGTTTGAGACCATACAAAACTTTGTGCA
ATCTGAAAACATCATTTGGTCTTTGAAATCTTCAAAATCAGGAGGTTGTTTAACATACACTTCCT
CTTGAATGTAACCATTCAGGAAAGCACTTTTCACATCTATTTGAAACAGTTTAAAGTCCATATGA
CAAGCAAATGCAAGTAAAAGACGAATAGCCTCTAACCTGGCAACATGAGCAAAGGTTTCATCATA
ATCAATGCCTTCTTCCTGGTTATAGCCTTTGGCTACCAGTCGGGTCTTGTTTCTTACCACTCTAC
CAGTTTCATTTATTTTGTTTCTGAAAACCCATTTAGTGCCAACAATCGGGTGATCATCAGGTCTT
GGCACTAAAGTCTAGACTTTGCTTCATTCAAACTAGTTGAGCTCTTCTTGCATTGTTGTCATCCA
ACTTTCTTCTTTTTCTGCTTCTTCAAATGTTTTTGGTTCCACTTGTGAAATGAATGCAGCAAATT
CACAAGTCTCTTTAAGTCCACTTCTTGTTCTCA
Found at i:19012 original size:21 final size:21
Alignment explanation
Indices: 18987--19046 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
18977 TGTGATCATA
18987 ATTTCTGTATCTTTCTCTATC
1 ATTTCTGTATCTTTCTCTATC
* * * *
19008 ATTTCTGAATCTGTCTTTTTC
1 ATTTCTGTATCTTTCTCTATC
19029 ATTTCTGTAT-TTGTCTCT
1 ATTTCTGTATCTT-TCTCT
19047 TCTATAGCCT
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
20 1 0.03
21 30 0.97
ACGTcount: A:0.13, C:0.20, G:0.08, T:0.58
Consensus pattern (21 bp):
ATTTCTGTATCTTTCTCTATC
Found at i:25765 original size:10 final size:10
Alignment explanation
Indices: 25750--25795 Score: 74
Period size: 10 Copynumber: 4.6 Consensus size: 10
25740 ATACCTCGAT
25750 ATATCCGTAA
1 ATATCCGTAA
*
25760 ATATCCATAA
1 ATATCCGTAA
25770 ATATCCGTAA
1 ATATCCGTAA
*
25780 ATATCCGTAT
1 ATATCCGTAA
25790 ATATCC
1 ATATCC
25796 ATATTAAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 33 1.00
ACGTcount: A:0.39, C:0.22, G:0.07, T:0.33
Consensus pattern (10 bp):
ATATCCGTAA
Found at i:26008 original size:18 final size:17
Alignment explanation
Indices: 25985--26022 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
25975 CCCAAATTAC
*
25985 TTATGGAAATTGGGGAAA
1 TTATGGAAATT-AGGAAA
26003 TTATGGAAATTAGGAAA
1 TTATGGAAATTAGGAAA
26020 TTA
1 TTA
26023 AATGAATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.42, C:0.00, G:0.26, T:0.32
Consensus pattern (17 bp):
TTATGGAAATTAGGAAA
Found at i:26020 original size:8 final size:9
Alignment explanation
Indices: 25985--26022 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
25975 CCCAAATTAC
25985 TTATGGAAA
1 TTATGGAAA
**
25994 TTGGGGAAA
1 TTATGGAAA
26003 TTATGGAAA
1 TTATGGAAA
26012 TTA-GGAAA
1 TTATGGAAA
26020 TTA
1 TTA
26023 AATGAATTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
8 8 0.32
9 17 0.68
ACGTcount: A:0.42, C:0.00, G:0.26, T:0.32
Consensus pattern (9 bp):
TTATGGAAA
Found at i:28409 original size:9 final size:9
Alignment explanation
Indices: 28395--28419 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
28385 TTTTCGCAGT
28395 AAAAATATA
1 AAAAATATA
28404 AAAAATATA
1 AAAAATATA
28413 AAAAATA
1 AAAAATA
28420 ATGTCTACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (9 bp):
AAAAATATA
Found at i:28630 original size:25 final size:24
Alignment explanation
Indices: 28581--28636 Score: 67
Period size: 25 Copynumber: 2.3 Consensus size: 24
28571 CATCGATACC
* *
28581 TCGATATATTCGTCTATATAACCA
1 TCGATATATCCGTCGATATAACCA
*
28605 TCGATATATCCGTTCGATATATCCA
1 TCGATATATCCG-TCGATATAACCA
*
28630 TGGATAT
1 TCGATAT
28637 CTGTATTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
24 11 0.41
25 16 0.59
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.38
Consensus pattern (24 bp):
TCGATATATCCGTCGATATAACCA
Found at i:28812 original size:27 final size:27
Alignment explanation
Indices: 28774--28833 Score: 111
Period size: 27 Copynumber: 2.2 Consensus size: 27
28764 GCCCTGCTTG
*
28774 TAATTATTAATTTCCTAAATAATTAAA
1 TAATTATTAATTTCCTAAAAAATTAAA
28801 TAATTATTAATTTCCTAAAAAATTAAA
1 TAATTATTAATTTCCTAAAAAATTAAA
28828 TAATTA
1 TAATTA
28834 ATCAATGATT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (27 bp):
TAATTATTAATTTCCTAAAAAATTAAA
Found at i:36474 original size:27 final size:27
Alignment explanation
Indices: 36444--36498 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
36434 CATCAAAAAT
*
36444 TGAACTTAATAGAGTAAATTAACTAAG
1 TGAACATAATAGAGTAAATTAACTAAG
36471 TGAACATAATAGAGTAAATTAACTAAG
1 TGAACATAATAGAGTAAATTAACTAAG
36498 T
1 T
36499 CGTCATTACA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.49, C:0.07, G:0.15, T:0.29
Consensus pattern (27 bp):
TGAACATAATAGAGTAAATTAACTAAG
Done.