Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021954.1 Corchorus olitorius cultivar O-4 contig21987, 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: 38692
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:223 original size:126 final size:123
Alignment explanation
Indices: 76--314 Score: 338
Period size: 126 Copynumber: 1.9 Consensus size: 123
66 ATTCCCTAAA
*
76 AAAATGGTAAAGATAAAATAGTTATAAAAATATT-GAATTTAATTAAATAAAAATAGAAATTTTG
1 AAAATGGTAAAAATAAAATAGTTATAAAAATATTAG-ATTTAATTAAATAAAAATA-AAATTTT-
* *
140 GTAA-AATAAAACTGTAAAAGTTTAAATAATGTCATTTAAGAAATATATTTAATTAAAATAGT
63 -TAATAATAAAACTGTAAAAGTTTAAA-AATGACATTTAAAAAATATATTTAATTAAAATAGT
* *
202 AAAATGGTAAAAATAAAATAGTTATAAAAATATTAGATTTGATTAAATAAAAATAAAGTTTTTAA
1 AAAATGGTAAAAATAAAATAGTTATAAAAATATTAGATTTAATTAAATAAAAATAAAATTTTTAA
* *
267 TTGAGTAAAATTGTAAAAGTTTAAAAATGACATTTAAAAAATATATTT
66 -T-AATAAAACTGTAAAAGTTTAAAAATGACATTTAAAAAATATATTT
315 GAAAAATCAG
Statistics
Matches: 102, Mismatches: 7, Indels: 9
0.86 0.06 0.08
Matches are distributed among these distances:
123 3 0.03
125 27 0.26
126 71 0.70
127 1 0.01
ACGTcount: A:0.54, C:0.01, G:0.10, T:0.35
Consensus pattern (123 bp):
AAAATGGTAAAAATAAAATAGTTATAAAAATATTAGATTTAATTAAATAAAAATAAAATTTTTAA
TAATAAAACTGTAAAAGTTTAAAAATGACATTTAAAAAATATATTTAATTAAAATAGT
Found at i:875 original size:7 final size:7
Alignment explanation
Indices: 863--890 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
853 GAAGTTGAAG
863 GAAAAAA
1 GAAAAAA
870 GAAAAAA
1 GAAAAAA
877 GAAAAAA
1 GAAAAAA
884 GAAAAAA
1 GAAAAAA
891 ATCAATTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (7 bp):
GAAAAAA
Found at i:999 original size:31 final size:31
Alignment explanation
Indices: 933--1027 Score: 140
Period size: 31 Copynumber: 3.1 Consensus size: 31
923 ACTAAATACT
* *
933 AAAAAAATTCTCTTAT-ATTTTCTTTTGGGAC
1 AAAAAAA-TCCCTTATGTTTTTCTTTTGGGAC
*
964 -AAAAAATCCCTTATGTTTTTCTATTGGGAC
1 AAAAAAATCCCTTATGTTTTTCTTTTGGGAC
994 AAAAAAATCCCTTATGTTTTTCTTTTGGGAC
1 AAAAAAATCCCTTATGTTTTTCTTTTGGGAC
1025 AAA
1 AAA
1028 TCAGTCCCTT
Statistics
Matches: 58, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
29 7 0.12
30 19 0.33
31 32 0.55
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.41
Consensus pattern (31 bp):
AAAAAAATCCCTTATGTTTTTCTTTTGGGAC
Found at i:2648 original size:23 final size:23
Alignment explanation
Indices: 2618--2662 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
2608 GGAGTCCAAG
2618 TCCAATTAATAATTATGATGCAA
1 TCCAATTAATAATTATGATGCAA
*
2641 TCCAATTAGTAATTATGATGCA
1 TCCAATTAATAATTATGATGCA
2663 GTAATGATGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.40, C:0.13, G:0.11, T:0.36
Consensus pattern (23 bp):
TCCAATTAATAATTATGATGCAA
Found at i:4590 original size:22 final size:22
Alignment explanation
Indices: 4561--4858 Score: 173
Period size: 22 Copynumber: 13.5 Consensus size: 22
4551 GAAGAGGTAC
4561 TTATCAAAATTTCATATGGAGG
1 TTATCAAAATTTCATATGGAGG
* * * *
4583 ATATCAAAATCTT-ATAAGAAGAT
1 TTATCAAAAT-TTCATATGGAG-G
*
4606 TTATCAAAATTTAATA-GTGAGG
1 TTATCAAAATTTCATATG-GAGG
* * *
4628 TCATCAAAATTTTATAAGGAGG
1 TTATCAAAATTTCATATGGAGG
* * *
4650 TTATCAGAATTTTATA-GTATGG
1 TTATCAAAATTTCATATGGA-GG
* * **
4672 TTTTCAAAATTTCATTTGGATA
1 TTATCAAAATTTCATATGGAGG
* * *
4694 TTACCGAAATTTCATATTGAGG
1 TTATCAAAATTTCATATGGAGG
* * *
4716 TTA-AAAAATTTCACATAGAGG
1 TTATCAAAATTTCATATGGAGG
* *
4737 TTATCGAAATTTCAT-TGTATGG
1 TTATCAAAATTTCATATGGA-GG
*
4759 TTATCAAAATTTCATA-GAGATG
1 TTATCAAAATTTCATATG-GAGG
* *
4781 TTATCGAAATTTCATA-GTGAGA
1 TTATCAAAATTTCATATG-GAGG
* *
4803 TTATCAAAATTTTCATAT-AAAG
1 TTATCAAAA-TTTCATATGGAGG
* *
4825 TTATCGAAATTTCATA-GTATGG
1 TTATCAAAATTTCATATGGA-GG
*
4847 TTATTAAAATTT
1 TTATCAAAATTT
4859 TATAGAGATA
Statistics
Matches: 210, Mismatches: 51, Indels: 30
0.72 0.18 0.10
Matches are distributed among these distances:
21 29 0.14
22 154 0.73
23 27 0.13
ACGTcount: A:0.38, C:0.08, G:0.14, T:0.39
Consensus pattern (22 bp):
TTATCAAAATTTCATATGGAGG
Found at i:4683 original size:44 final size:45
Alignment explanation
Indices: 4561--4667 Score: 121
Period size: 45 Copynumber: 2.4 Consensus size: 45
4551 GAAGAGGTAC
* * *
4561 TTATCAAAATTTCATA-TGGAGGAT-ATCAAAATCTTATAAGAAGAT
1 TTATCAAAATTTAATAGT-GAGG-TCATCAAAATTTTATAAGAAGAG
*
4606 TTATCAAAATTTAATAGTGAGGTCATCAAAATTTTATAAGGAG-G
1 TTATCAAAATTTAATAGTGAGGTCATCAAAATTTTATAAGAAGAG
* *
4650 TTATCAGAATTTTATAGT
1 TTATCAAAATTTAATAGT
4668 ATGGTTTTCA
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
44 17 0.31
45 36 0.67
46 1 0.02
ACGTcount: A:0.41, C:0.07, G:0.15, T:0.36
Consensus pattern (45 bp):
TTATCAAAATTTAATAGTGAGGTCATCAAAATTTTATAAGAAGAG
Found at i:4726 original size:21 final size:21
Alignment explanation
Indices: 4700--4739 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
4690 GATATTACCG
* *
4700 AAATTTCATATTGAGGTTAAA
1 AAATTTCACATAGAGGTTAAA
4721 AAATTTCACATAGAGGTTA
1 AAATTTCACATAGAGGTTA
4740 TCGAAATTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.42, C:0.07, G:0.15, T:0.35
Consensus pattern (21 bp):
AAATTTCACATAGAGGTTAAA
Found at i:4748 original size:87 final size:88
Alignment explanation
Indices: 4646--4870 Score: 271
Period size: 87 Copynumber: 2.6 Consensus size: 88
4636 ATTTTATAAG
* *
4646 GAGGTTATC-AGAATTTTATAGTATGGTTTTCAAAATTTCATTTG-GATATTACCGAAATTTCAT
1 GAGGTTATCGA-AATTTCATAGTATGGTTTTCAAAATTTCA-TAGAGATATTACCGAAATTTCAT
* *
4709 ATTGAGGTTA-AAAAATTTCACATA
64 AGTGAGATTACAAAAATTTCACATA
* * * *
4733 GAGGTTATCGAAATTTCATTGTATGGTTATCAAAATTTCATAGAGATGTTATCGAAATTTCATAG
1 GAGGTTATCGAAATTTCATAGTATGGTTTTCAAAATTTCATAGAGATATTACCGAAATTTCATAG
* *
4798 TGAGATTATCAAAATTTTCATATA
66 TGAGATTA-CAAAAATTTCACATA
* *
4822 -AAGTTATCGAAATTTCATAGTATGGTTATT-AAAATTTTATAGAGATATT
1 GAGGTTATCGAAATTTCATAGTATGGTT-TTCAAAATTTCATAGAGATATT
4871 TAATTTAAAC
Statistics
Matches: 118, Mismatches: 15, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
86 2 0.02
87 60 0.51
88 43 0.36
89 13 0.11
ACGTcount: A:0.36, C:0.08, G:0.15, T:0.40
Consensus pattern (88 bp):
GAGGTTATCGAAATTTCATAGTATGGTTTTCAAAATTTCATAGAGATATTACCGAAATTTCATAG
TGAGATTACAAAAATTTCACATA
Found at i:4784 original size:44 final size:43
Alignment explanation
Indices: 4561--4867 Score: 223
Period size: 44 Copynumber: 7.0 Consensus size: 43
4551 GAAGAGGTAC
* * *
4561 TTATCAAAATTTCATATGGAGGATATCAAAATCTT-ATAAGAAGAT-
1 TTATCGAAATTTCATA-GTAGGTTATCAAAAT-TTCAT-AG-AGATG
* * * * *
4606 TTATCAAAATTTAATAGTGAGGTCATCAAAATTTTATA-AGGAGG
1 TTATCGAAATTTCATAGT-AGGTTATCAAAATTTCATAGA-GATG
* * * *
4650 TTATC-AGAATTTTATAGTATGGTTTTCAAAATTTCATTTG-GATA
1 TTATCGA-AATTTCATAGTA-GGTTATCAAAATTTCA-TAGAGATG
* * * * * *
4694 TTACCGAAATTTCATATTGAGGTTA-AAAAATTTCACATAGAGG
1 TTATCGAAATTTCATAGT-AGGTTATCAAAATTTCATAGAGATG
*
4737 TTATCGAAATTTCATTGTATGGTTATCAAAATTTCATAGAGATG
1 TTATCGAAATTTCATAGTA-GGTTATCAAAATTTCATAGAGATG
* * *
4781 TTATCGAAATTTCATAGTGAGATTATCAAAATTTTCATATA-AAG
1 TTATCGAAATTTCATAGT-AGGTTATCAAAA-TTTCATAGAGATG
* *
4825 TTATCGAAATTTCATAGTATGGTTATTAAAATTTTATAGAGAT
1 TTATCGAAATTTCATAGTA-GGTTATCAAAATTTCATAGAGAT
4868 ATTTAATTTA
Statistics
Matches: 207, Mismatches: 38, Indels: 35
0.74 0.14 0.12
Matches are distributed among these distances:
42 2 0.01
43 43 0.21
44 122 0.59
45 40 0.19
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.39
Consensus pattern (43 bp):
TTATCGAAATTTCATAGTAGGTTATCAAAATTTCATAGAGATG
Found at i:5728 original size:20 final size:19
Alignment explanation
Indices: 5703--5757 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 19
5693 AACTGAATGT
5703 AGAAGAAGACTATTTTGAG
1 AGAAGAAGACTATTTTGAG
*
5722 AAGAAGAAGACTGA--ATG-G
1 -AGAAGAAGACT-ATTTTGAG
5740 AGAAGAAGACTATTTTGA
1 AGAAGAAGACTATTTTGA
5758 ATGAGTGTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
16 1 0.03
17 11 0.38
18 3 0.10
19 2 0.07
20 11 0.38
21 1 0.03
ACGTcount: A:0.45, C:0.05, G:0.27, T:0.22
Consensus pattern (19 bp):
AGAAGAAGACTATTTTGAG
Found at i:15793 original size:14 final size:14
Alignment explanation
Indices: 15774--15803 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
15764 GTGGGGGCAC
15774 ATTTATAAGTATAT
1 ATTTATAAGTATAT
15788 ATTTATAAGTATAT
1 ATTTATAAGTATAT
15802 AT
1 AT
15804 AGTCATAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
ATTTATAAGTATAT
Found at i:16637 original size:27 final size:28
Alignment explanation
Indices: 16607--16668 Score: 74
Period size: 27 Copynumber: 2.2 Consensus size: 28
16597 GGGCAAAACT
* *
16607 GTAATTTT-ACTAGATCAGGGGCAA-ATG
1 GTAATTTTAAC-AGATCAAGGGCAACATA
*
16634 GTAATTTTAACAGATCAAGGGTAACATA
1 GTAATTTTAACAGATCAAGGGCAACATA
16662 GTAATTT
1 GTAATTT
16669 AACCCAAACA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
27 19 0.63
28 11 0.37
ACGTcount: A:0.37, C:0.10, G:0.21, T:0.32
Consensus pattern (28 bp):
GTAATTTTAACAGATCAAGGGCAACATA
Found at i:25233 original size:18 final size:17
Alignment explanation
Indices: 25203--25250 Score: 69
Period size: 18 Copynumber: 2.8 Consensus size: 17
25193 ATAAGGTTTA
*
25203 AAAAAAATTAATAAAGG
1 AAAAAAGTTAATAAAGG
*
25220 ATATAAAGTTAATAAAGG
1 A-AAAAAGTTAATAAAGG
25238 AAAAAAGTTAATA
1 AAAAAAGTTAATA
25251 GTTTTTTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
17 12 0.44
18 15 0.56
ACGTcount: A:0.65, C:0.00, G:0.12, T:0.23
Consensus pattern (17 bp):
AAAAAAGTTAATAAAGG
Found at i:26169 original size:12 final size:12
Alignment explanation
Indices: 26152--26184 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
26142 CCAAGCAAAA
26152 AACCAGAACTCC
1 AACCAGAACTCC
*
26164 AACCAGAATTCC
1 AACCAGAACTCC
26176 AACCAGAAC
1 AACCAGAAC
26185 CAAATTCTCC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.36, G:0.09, T:0.09
Consensus pattern (12 bp):
AACCAGAACTCC
Found at i:27989 original size:40 final size:40
Alignment explanation
Indices: 27937--28013 Score: 127
Period size: 40 Copynumber: 1.9 Consensus size: 40
27927 TAAATGTTAA
*
27937 TTATAATAAATCCCATCCCTCTTAATTATCTAGAATTATG
1 TTATAATAAATCCCATCCCCCTTAATTATCTAGAATTATG
* *
27977 TTATAATAAATCCTATCCCCCTTAATTATCTATAATT
1 TTATAATAAATCCCATCCCCCTTAATTATCTAGAATT
28014 GTAACCTCTC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.35, C:0.21, G:0.03, T:0.42
Consensus pattern (40 bp):
TTATAATAAATCCCATCCCCCTTAATTATCTAGAATTATG
Found at i:28780 original size:16 final size:16
Alignment explanation
Indices: 28761--28807 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
28751 TCTCTCTTTC
28761 TTTCTCTTCAAAATTT
1 TTTCTCTTCAAAATTT
*
28777 TTTCTCTTTC-TAATTT
1 TTTCTC-TTCAAAATTT
*
28793 TTTTTCTCTCAAAAT
1 TTTCTCT-TCAAAAT
28808 ATCTATCAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
15 1 0.04
16 18 0.72
17 6 0.24
ACGTcount: A:0.21, C:0.19, G:0.00, T:0.60
Consensus pattern (16 bp):
TTTCTCTTCAAAATTT
Found at i:30816 original size:3 final size:3
Alignment explanation
Indices: 30808--30841 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
30798 CTTTAATCCC
*
30808 CCA CCA CCA CCA CCA CCA CCA CCA TCA CCA CCA C
1 CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA C
30842 GACCTCTCGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.32, C:0.65, G:0.00, T:0.03
Consensus pattern (3 bp):
CCA
Found at i:31767 original size:16 final size:16
Alignment explanation
Indices: 31746--31776 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
31736 TTTTTGCTGC
31746 TTTCTTTTTCTTTTCT
1 TTTCTTTTTCTTTTCT
*
31762 TTTCTTTTTTTTTTC
1 TTTCTTTTTCTTTTC
31777 CCAATTTTTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (16 bp):
TTTCTTTTTCTTTTCT
Found at i:37185 original size:17 final size:17
Alignment explanation
Indices: 37163--37199 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
37153 ACCTCCCTTG
37163 TCAACAAAAGAATAACA
1 TCAACAAAAGAATAACA
**
37180 TCAACAAAAGTCTAACA
1 TCAACAAAAGAATAACA
37197 TCA
1 TCA
37200 GTATTAAGCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.57, C:0.22, G:0.05, T:0.16
Consensus pattern (17 bp):
TCAACAAAAGAATAACA
Found at i:37920 original size:2 final size:2
Alignment explanation
Indices: 37913--37938 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
37903 ACACCAAGCA
37913 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
37939 GTAACACTAA
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:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38277 original size:30 final size:32
Alignment explanation
Indices: 38222--38282 Score: 90
Period size: 34 Copynumber: 1.9 Consensus size: 32
38212 CTTAATAAGA
38222 ATATAAGATAATCTAAACCAAAAAAACAGTCTGC
1 ATATAAGATAATCT-AA-CAAAAAAACAGTCTGC
38256 ATATAAGATAATCT-A-AAAAAAACAGTC
1 ATATAAGATAATCTAACAAAAAAACAGTC
38283 CATCAAACAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
30 12 0.44
32 1 0.04
34 14 0.52
ACGTcount: A:0.56, C:0.15, G:0.08, T:0.21
Consensus pattern (32 bp):
ATATAAGATAATCTAACAAAAAAACAGTCTGC
Done.