Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015704.1 Corchorus olitorius cultivar O-4 contig15737, 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: 47890
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:4917 original size:44 final size:44
Alignment explanation
Indices: 4855--4941 Score: 165
Period size: 44 Copynumber: 2.0 Consensus size: 44
4845 TATTTTCTTA
*
4855 TTTTTTTAATATTTTTATCATTGAGTCGGTAATGAGTTAGCTCT
1 TTTTTTTAATATTTTTATCATTGAGGCGGTAATGAGTTAGCTCT
4899 TTTTTTTAATATTTTTATCATTGAGGCGGTAATGAGTTAGCTC
1 TTTTTTTAATATTTTTATCATTGAGGCGGTAATGAGTTAGCTC
4942 GTGACGCCAA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.23, C:0.09, G:0.17, T:0.51
Consensus pattern (44 bp):
TTTTTTTAATATTTTTATCATTGAGGCGGTAATGAGTTAGCTCT
Found at i:8058 original size:208 final size:208
Alignment explanation
Indices: 7694--8106 Score: 754
Period size: 208 Copynumber: 2.0 Consensus size: 208
7684 GAGAGATTTT
* * *
7694 TTTTTTTTTTAGAAATAAATGAATATCATTATAGAGAAAGATCAGGATTACAAATGTCAGGTGAC
1 TTTTTTTTTAAGAAATAAATGAATATCATTATAGAGAAAGATCAGGATTACAAACGCCAGGTGAC
*
7759 AAAGACCCGCACCGCACATGATCAGTTCGTAAACTCGTTAATCGATGTGCCAAGACATTAGCCTC
66 AAAGACCCGCACCGCACATGATCAGTTCGTAAACTCGTTAATCGATGTGCCAAGACATTAACCTC
*
7824 CCTATTTACATGAGTAAAATCACACTCATCAAACAACAAGGCTAAATCCCTAATCTCATAAATTA
131 CCTATTTACATGAGTAAAACCACACTCATCAAACAACAAGGCTAAATCCCTAATCTCATAAATTA
7889 AATCACCTCCATG
196 AATCACCTCCATG
* * *
7902 TTTTTTTTTAAGAAATAAATGAATATCATTATAGAGAAGGATCAGGATTACAAACGCCGGGTGGC
1 TTTTTTTTTAAGAAATAAATGAATATCATTATAGAGAAAGATCAGGATTACAAACGCCAGGTGAC
7967 AAAGACCCGCACCGCACATGATCAGTTCGTAAACTCGTTAATCGATGTGCCAAGACATTAACCTC
66 AAAGACCCGCACCGCACATGATCAGTTCGTAAACTCGTTAATCGATGTGCCAAGACATTAACCTC
8032 CCTATTTACATGAGTAAAACCACACTCATCAAACAACAAGGCTAAATCCCTAATCTCATAAATTA
131 CCTATTTACATGAGTAAAACCACACTCATCAAACAACAAGGCTAAATCCCTAATCTCATAAATTA
8097 AATCACCTCC
196 AATCACCTCC
8107 TTCCCACCAA
Statistics
Matches: 197, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
208 197 1.00
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (208 bp):
TTTTTTTTTAAGAAATAAATGAATATCATTATAGAGAAAGATCAGGATTACAAACGCCAGGTGAC
AAAGACCCGCACCGCACATGATCAGTTCGTAAACTCGTTAATCGATGTGCCAAGACATTAACCTC
CCTATTTACATGAGTAAAACCACACTCATCAAACAACAAGGCTAAATCCCTAATCTCATAAATTA
AATCACCTCCATG
Found at i:17800 original size:27 final size:27
Alignment explanation
Indices: 17754--17805 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
17744 TATCAGAAAA
*
17754 AGAACAAAAACAGCAGC-AAACCAATT
1 AGAACAAAAACAACAGCAAAACCAATT
*
17780 AGAAGCAACAACAACAGCAAAACCAA
1 AGAA-CAAAAACAACAGCAAAACCAA
17806 GCCGCATCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 4 0.18
27 11 0.50
28 7 0.32
ACGTcount: A:0.60, C:0.25, G:0.12, T:0.04
Consensus pattern (27 bp):
AGAACAAAAACAACAGCAAAACCAATT
Found at i:19626 original size:17 final size:17
Alignment explanation
Indices: 19604--19637 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
19594 CTATATCTAT
19604 AGTATATATTGAATCCA
1 AGTATATATTGAATCCA
19621 AGTATATATTGAATCCA
1 AGTATATATTGAATCCA
19638 CGATTGTACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (17 bp):
AGTATATATTGAATCCA
Found at i:20125 original size:11 final size:12
Alignment explanation
Indices: 20095--20127 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
20085 CTTATAATTA
*
20095 ATTTTAATTATT
1 ATTTTAATTTTT
20107 ATTTTAATTTTT
1 ATTTTAATTTTT
20119 A-TTTAATTT
1 ATTTTAATTT
20128 AAACACACTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 8 0.40
12 12 0.60
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (12 bp):
ATTTTAATTTTT
Found at i:27546 original size:296 final size:292
Alignment explanation
Indices: 26962--27840 Score: 1356
Period size: 292 Copynumber: 3.0 Consensus size: 292
26952 TTTAGTAACC
* *
26962 ATGGAAATTACTTAAAGACCAAATTGAGGATTAATGTGGTG-TCTCATTTTG-TTTTTTTTTTGT
1 ATGGAAATTACCTAAAGGCCAAATTGAGGATTAATGTGGTGCT-TC-TTTTGATTTTTTTTTTGT
* * * *
27025 CTTTTCTCAATTTTCGGGTGACTAAAAAGGCCCTTGATAAATTTCCT-CCTTACTTTTCCTCCTG
64 CTTTTCTCACTTTTCGGGTGACTAAAAAGGCCCTCGATGAATTTCCTCCCTTACTTTTCCTACTG
** * *
27089 CCCTTTTTTGTAATTTACTATTTTTGCATTTATGATTAAGTGTGTTTTAATTATGTATTAATTGT
129 CCCTTTTTTGTAATTTACTATTTTTATATTTATGATTAAGTGTGTTTTAATTATATATTGATTGT
*
27154 GTGTGGATATTAGGATTTACCGTTTCAACTCCTCTGCCGTAATTCCAAAGGATTGGTGCTATAAA
194 GTGTGGATATTAGGATTTACCGTTT-AACTCCTCTGCCGGAATTCCAAAGGATTGGTGCTATAAA
27219 TGTATCTACCCGAGTTCATTAATTTAACAATTGCT
258 TGTATCTACCCGAGTTCATTAATTTAACAATTGCT
*
27254 ATGGAAATTACCTAAATGGCCAAATTGATGATTAATGTGGTGCTTCCTTTTGACTTTTTTTTTTG
1 ATGGAAATTACCTAAA-GGCCAAATTGAGGATTAATGTGGTGCTT-CTTTTGA-TTTTTTTTTTG
27319 TCTTTTCTCACTTTTCGGGTGACTAAAAAGGCCCTCGATGAATTTCCTCCCTTACTTTTCCTACT
63 TCTTTTCTCACTTTTCGGGTGACTAAAAAGGCCCTCGATGAATTTCCTCCCTTACTTTTCCTACT
27384 GCCCTTTTTTGTAATTTACTATTTTTATATTTATGATTAAGTGTGTTTTAATTATATATTGATTG
128 GCCCTTTTTTGTAATTTACTATTTTTATATTTATGATTAAGTGTGTTTTAATTATATATTGATTG
* * *
27449 TGTGTGAATATTAGGATTTACCGGTTTAACTCCTCTGCCGGAATTCCTAAGGATTGGTACTATAA
193 TGTGTGGATATTAGGATTTACC-GTTTAACTCCTCTGCCGGAATTCCAAAGGATTGGTGCTATAA
*
27514 ATGTATCTACCCGAGTTCATTAATTTAACAATTGTT
257 ATGTATCTACCCGAGTTCATTAATTTAACAATTGCT
*
27550 ATGGAAATTACCTAAAAGGCCAAATTGAGGATTAATGTGGTGC-T-TTTGGATTTTTTTTTTGTC
1 ATGGAAATTACCT-AAAGGCCAAATTGAGGATTAATGTGGTGCTTCTTTTGATTTTTTTTTTGTC
* *
27613 TTTTCTCACTTTTCGGGTGACTAAAAAGGTCCTCGATGAATTTCCTCCCCTACTTTTCCTGA-TG
65 TTTTCTCACTTTTCGGGTGACTAAAAAGGCCCTCGATGAATTTCCTCCCTTACTTTTCCT-ACTG
* *
27677 CCCTTTTTTGTAATTTACTATTTTTTTATTTATGATTAAGTGTGTTTTAATTACATATTGATTGT
129 CCCTTTTTTGTAATTTACTATTTTTATATTTATGATTAAGTGTGTTTTAATTATATATTGATTGT
* * * * *
27742 GTGTGGATATTAAGATTTACTAGTTCAACTCCTCTGCCGGAATTCCAAAGGATTAGTGCTGTAAA
194 GTGTGGATATTAGGATTTAC-CGTTTAACTCCTCTGCCGGAATTCCAAAGGATTGGTGCTATAAA
* * * *
27807 TATGTTTACCCGAGTTTATTAATTTAACAATTGC
258 TGTATCTACCCGAGTTCATTAATTTAACAATTGC
27841 AATCAAGATT
Statistics
Matches: 542, Mismatches: 35, Indels: 20
0.91 0.06 0.03
Matches are distributed among these distances:
292 236 0.44
293 35 0.06
294 2 0.00
295 57 0.11
296 205 0.38
297 7 0.01
ACGTcount: A:0.25, C:0.16, G:0.16, T:0.44
Consensus pattern (292 bp):
ATGGAAATTACCTAAAGGCCAAATTGAGGATTAATGTGGTGCTTCTTTTGATTTTTTTTTTGTCT
TTTCTCACTTTTCGGGTGACTAAAAAGGCCCTCGATGAATTTCCTCCCTTACTTTTCCTACTGCC
CTTTTTTGTAATTTACTATTTTTATATTTATGATTAAGTGTGTTTTAATTATATATTGATTGTGT
GTGGATATTAGGATTTACCGTTTAACTCCTCTGCCGGAATTCCAAAGGATTGGTGCTATAAATGT
ATCTACCCGAGTTCATTAATTTAACAATTGCT
Found at i:30457 original size:31 final size:31
Alignment explanation
Indices: 30419--30482 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
30409 TAACTCAGAT
30419 ATTTTTTTCTACTCATAAACATGATATTTAA
1 ATTTTTTTCTACTCATAAACATGATATTTAA
30450 ATTTTTTTCTACTCATAAACATGATATTTAA
1 ATTTTTTTCTACTCATAAACATGATATTTAA
30481 AT
1 AT
30483 GAGTCACACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.36, C:0.12, G:0.03, T:0.48
Consensus pattern (31 bp):
ATTTTTTTCTACTCATAAACATGATATTTAA
Found at i:32780 original size:20 final size:20
Alignment explanation
Indices: 32755--32807 Score: 106
Period size: 20 Copynumber: 2.6 Consensus size: 20
32745 AAAAGAACAC
32755 AAAGTGGCACCAACAAATTA
1 AAAGTGGCACCAACAAATTA
32775 AAAGTGGCACCAACAAATTA
1 AAAGTGGCACCAACAAATTA
32795 AAAGTGGCACCAA
1 AAAGTGGCACCAA
32808 GTTTGGTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.49, C:0.21, G:0.17, T:0.13
Consensus pattern (20 bp):
AAAGTGGCACCAACAAATTA
Found at i:33549 original size:15 final size:15
Alignment explanation
Indices: 33526--33563 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
33516 CTTGAATGAA
*
33526 GAGAAAATCGAATAC-
1 GAGACAATCGAAT-CT
33541 GAGACAATCGAATCT
1 GAGACAATCGAATCT
33556 GAGACAAT
1 GAGACAAT
33564 TGAAGAAGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 1 0.05
15 20 0.95
ACGTcount: A:0.47, C:0.16, G:0.21, T:0.16
Consensus pattern (15 bp):
GAGACAATCGAATCT
Found at i:39659 original size:17 final size:18
Alignment explanation
Indices: 39626--39659 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
39616 TTTAAAAAAA
*
39626 GTATTTAATAATTAAATT
1 GTATTTAATAATAAAATT
39644 GTATTT-ATAATAAAAT
1 GTATTTAATAATAAAAT
39660 ATAAGAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (18 bp):
GTATTTAATAATAAAATT
Found at i:42950 original size:21 final size:21
Alignment explanation
Indices: 42890--42951 Score: 70
Period size: 26 Copynumber: 2.7 Consensus size: 21
42880 TGAGATGATA
42890 TAATATTCCATCAAACAATTG
1 TAATATTCCATCAAACAATTG
*
42911 TAATACACAATTTCATCAAACAATTG
1 TAAT-----ATTCCATCAAACAATTG
42937 TAATATTCCATCAAA
1 TAATATTCCATCAAA
42952 AAAGTGAAAC
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
21 14 0.41
26 20 0.59
ACGTcount: A:0.45, C:0.19, G:0.03, T:0.32
Consensus pattern (21 bp):
TAATATTCCATCAAACAATTG
Found at i:43514 original size:10 final size:11
Alignment explanation
Indices: 43499--43525 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
43489 ATTGTTAAGG
43499 TTTTTTTAAAT
1 TTTTTTTAAAT
43510 TTTTTTTAAAT
1 TTTTTTTAAAT
43521 TTTTT
1 TTTTT
43526 ATAACTAGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (11 bp):
TTTTTTTAAAT
Found at i:45048 original size:15 final size:14
Alignment explanation
Indices: 45029--45062 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
45019 ATTTAACAAA
45029 TTTAATTCAATTTT
1 TTTAATTCAATTTT
45043 TGTTAA-TCAATTTT
1 T-TTAATTCAATTTT
45057 TTTAAT
1 TTTAAT
45063 AAATAAGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
13 4 0.22
14 10 0.56
15 4 0.22
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.62
Consensus pattern (14 bp):
TTTAATTCAATTTT
Found at i:47246 original size:49 final size:47
Alignment explanation
Indices: 47176--47291 Score: 144
Period size: 49 Copynumber: 2.4 Consensus size: 47
47166 CAAGCAATCC
* *
47176 TTTACTTTTACTGCACTTTTTCTCAATTTTTACA-ACAAAATTTAACT
1 TTTAATTTTACTGCACTTTTTCTCAATTTTTA-AGACAAAATTGAACT
* *
47223 TTTATTTTTACTTGCATCTTTTTCTCAATTTTTAAGACAAAATTGATCT
1 TTTAATTTTAC-TGCA-CTTTTTCTCAATTTTTAAGACAAAATTGAACT
*
47272 TTTAATTTTCATTGCACTTT
1 TTTAATTTT-ACTGCACTTT
47292 GTTAGGGGCC
Statistics
Matches: 60, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
47 10 0.17
48 9 0.15
49 40 0.67
50 1 0.02
ACGTcount: A:0.27, C:0.16, G:0.04, T:0.53
Consensus pattern (47 bp):
TTTAATTTTACTGCACTTTTTCTCAATTTTTAAGACAAAATTGAACT
Found at i:47724 original size:43 final size:43
Alignment explanation
Indices: 47479--47728 Score: 330
Period size: 43 Copynumber: 5.9 Consensus size: 43
47469 CCAATAACCA
* * *
47479 AAAGTCCCCAAACACATATATAACACAGGGGCGTTTCTATTCC
1 AAAGTCCCCAAACACATATATAACACAGAGGCATTTCTATTAC
*
47522 AAAAGTCCTCAAACACATATATAACACAGAGGCA--TCTA-TACC
1 -AAAGTCCCCAAACACATATATAACACAGAGGCATTTCTATTA-C
* * **
47564 CAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTAC
1 AAAGTCCCCAAACACATATATAACACAGAGGCATTTCTATTAC
* * *
47607 AAAGTCCTCAAACACATATATAACATAGAGGCATTTATA-T-C
1 AAAGTCCCCAAACACATATATAACACAGAGGCATTTCTATTAC
*
47648 AAAGTCCCCAAACACATATATAACACAGGGGCATTTCTATTAC
1 AAAGTCCCCAAACACATATATAACACAGAGGCATTTCTATTAC
*
47691 AAAGTCCTCAAACACATATATAACACAGAGGCATTTCT
1 AAAGTCCCCAAACACATATATAACACAGAGGCATTTCT
47729 CCTTATGGCA
Statistics
Matches: 180, Mismatches: 20, Indels: 13
0.85 0.09 0.06
Matches are distributed among these distances:
41 67 0.37
42 7 0.04
43 74 0.41
44 32 0.18
ACGTcount: A:0.41, C:0.26, G:0.11, T:0.22
Consensus pattern (43 bp):
AAAGTCCCCAAACACATATATAACACAGAGGCATTTCTATTAC
Found at i:47753 original size:84 final size:84
Alignment explanation
Indices: 47479--47726 Score: 415
Period size: 84 Copynumber: 2.9 Consensus size: 84
47469 CCAATAACCA
* *
47479 AAAGTCCCCAAACACATATATAACACAGGGGCGTTTCTATTCCAAAAGTCCTCAAACACATATAT
1 AAAGTCCCCAAACACATATATAACACAGGGGCATTTCTATTAC-AAAGTCCTCAAACACATATAT
*
47544 AACACAGAGGCATCTATACC
65 AACACAGAGGCATTTATACC
* **
47564 CAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCATTTCTATTACAAAGTCCTCAAACACATATATA
* *
47629 ACATAGAGGCATTTATATC
66 ACACAGAGGCATTTATACC
47648 AAAGTCCCCAAACACATATATAACACAGGGGCATTTCTATTACAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCATTTCTATTACAAAGTCCTCAAACACATATATA
47713 ACACAGAGGCATTT
66 ACACAGAGGCATTT
47727 CTCCTTATGG
Statistics
Matches: 151, Mismatches: 12, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
84 113 0.75
85 38 0.25
ACGTcount: A:0.41, C:0.25, G:0.11, T:0.22
Consensus pattern (84 bp):
AAAGTCCCCAAACACATATATAACACAGGGGCATTTCTATTACAAAGTCCTCAAACACATATATA
ACACAGAGGCATTTATACC
Found at i:47847 original size:2 final size:2
Alignment explanation
Indices: 47835--47887 Score: 90
Period size: 2 Copynumber: 26.5 Consensus size: 2
47825 ACCAAATTCC
47835 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
47876 TA TA CTA TA TA T
1 TA TA -TA TA TA T
47888 GTA
Statistics
Matches: 49, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 1 0.02
2 46 0.94
3 2 0.04
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.