Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013404.1 Corchorus olitorius cultivar O-4 contig13437, 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: 55615
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:595 original size:91 final size:91
Alignment explanation
Indices: 265--572 Score: 553
Period size: 91 Copynumber: 3.4 Consensus size: 91
255 AAATAATTCC
* *
265 TTTACCCCATTTTTTGCTTAAAGATAGCGGCGTTTCGAAATTAAAACGCTGCCAATTAAATAATT
1 TTTACCCCATTTTTTGCTTAAAGATAGCGGCGTTTCGGAATTAAAACGCCGCCAATTAAATAATT
* *
330 CCTTGAATATAAATTCGGGAAAATTT
66 CCTTGAATTTAAATGCGGGAAAATTT
* *
356 TTTACCCCATTTTTTGCTTATAGATAGCGGCGTTTCGGAATTAAAACGTCGCCAATTAAATAATT
1 TTTACCCCATTTTTTGCTTAAAGATAGCGGCGTTTCGGAATTAAAACGCCGCCAATTAAATAATT
421 CCTTGAATTTAAATGCGGGAAAATTT
66 CCTTGAATTTAAATGCGGGAAAATTT
*
447 TTTACCCCATTTTTTGATTAAAGATAGCGGCGTTTCGGAATTAAAACGCCGCCAATTAAATAATT
1 TTTACCCCATTTTTTGCTTAAAGATAGCGGCGTTTCGGAATTAAAACGCCGCCAATTAAATAATT
512 CCTTGAATTTAAATGCGGGAAAATTT
66 CCTTGAATTTAAATGCGGGAAAATTT
538 TTTACCCCATTTTTTGCTTAAAGATAGCGGCGTTT
1 TTTACCCCATTTTTTGCTTAAAGATAGCGGCGTTT
573 GTGGATAGAA
Statistics
Matches: 207, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
91 207 1.00
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (91 bp):
TTTACCCCATTTTTTGCTTAAAGATAGCGGCGTTTCGGAATTAAAACGCCGCCAATTAAATAATT
CCTTGAATTTAAATGCGGGAAAATTT
Found at i:724 original size:122 final size:123
Alignment explanation
Indices: 471--743 Score: 458
Period size: 122 Copynumber: 2.2 Consensus size: 123
461 TGATTAAAGA
* **
471 TAGCGGCGTTTCGGAATTAAAACGCCGCCAATTAAATAATTCCTTGAATTTAAATGCGGGAAAAT
1 TAGCGGCGTTTCAGAATTAAAACGCCGCCAATTAAATAATTCCTTGAACATAAATGCGGGAAAAT
*
536 TTTTTACCCCATTTTTTGCTTAAAGATAGCGGCGTTTGTGGATAGAAACGCCGCTAAT
66 TTTTTACACCATTTTTTGCTTAAAGATAGCGGCGTTTGTGGATAGAAACGCCGCTAAT
* *
594 TAGTGGCGTTTCAAAATTAAAACGCCGCCAATTAAATAATTCCTTGAACATAAATGCGGG-AAAT
1 TAGCGGCGTTTCAGAATTAAAACGCCGCCAATTAAATAATTCCTTGAACATAAATGCGGGAAAAT
*
658 TTTTTACACCATTTTTTGCTTAAAGATAGCGGTGTTTGTGGATAGAAACGCCGCTAAT
66 TTTTTACACCATTTTTTGCTTAAAGATAGCGGCGTTTGTGGATAGAAACGCCGCTAAT
* *
716 TAGCGGCGTTTCAGAGTTATAACGCCGC
1 TAGCGGCGTTTCAGAATTAAAACGCCGC
744 TATCTTCAAT
Statistics
Matches: 139, Mismatches: 11, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
122 84 0.60
123 55 0.40
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Consensus pattern (123 bp):
TAGCGGCGTTTCAGAATTAAAACGCCGCCAATTAAATAATTCCTTGAACATAAATGCGGGAAAAT
TTTTTACACCATTTTTTGCTTAAAGATAGCGGCGTTTGTGGATAGAAACGCCGCTAAT
Found at i:3983 original size:376 final size:373
Alignment explanation
Indices: 3100--4001 Score: 1574
Period size: 373 Copynumber: 2.4 Consensus size: 373
3090 GTTATATTTC
* * *
3100 CAATTATCAAT-TTTTGTTTTCCTTGTGTGAATTTAAACTAATTAATTAGAAAAAAGAAGATAAC
1 CAATCATCAATATTTTCTTTTACTTGTGTGAATTTAAACTAATTAATTAGAAAAAAGAAGATAAC
* * *
3164 CATTCTCTCTATGGATTCGACCCCGACTTACCCTAGCTAATATAGTTAGAATTTGTGGGGATATT
66 CATTCTCTCTGTGGATTCGACCCCTACTTACCCTAGCTACTATAGTTAGAATTTGTGGGGATATT
* *
3229 TTGTGGTTTGCTAATAACCAATCATAAAGAAAGGCAACACCAAAAGGGACATGAAGATCAATTGA
131 TTGTGGTTTGCTAATGACCGATCATAAAGAAAGGCAACACCAAAAGGGACATGAAGATCAATTGA
* *
3294 AATCTAAACCTTTTTGATCGAATTAGGGAAGAAGGAAGAAACCTTCAACCTCTTATTGGCCTATA
196 AATCTAAACCTTTTTGATCGAATTAAGGAAGAAGGAAGAAACCTTCAACCTCTTATTGGCCTACA
* * *
3359 CGTATCACTAGTGAAACCTTGATCAATCAGAATGCACTTCAAACAACCTTAGTAATAAAGATTAT
261 CGTATCACTAATGAAACCTTGATCAATCAAAATGCACTTCAAACAACCTTAGTAAGAAAGATTAT
3424 GGAGTAAGAAGAAAAGAAGCTAAGGCAAGCTTCTGACAATCAAGCATT
326 GGAGTAAGAAGAAAAGAAGCTAAGGCAAGCTTCTGACAATCAAGCATT
3472 CAATCATCAATATTTTCTTTTACTTGTGTGAATTTAAACTAATTAATTAGAAAAAAGAAGATAAC
1 CAATCATCAATATTTTCTTTTACTTGTGTGAATTTAAACTAATTAATTAGAAAAAAGAAGATAAC
* *
3537 CATTCTTTCTGTGGATTCGACCCCTACTTACTCTAGCTACTATAGTTAGAATTTGTGGGGATATT
66 CATTCTCTCTGTGGATTCGACCCCTACTTACCCTAGCTACTATAGTTAGAATTTGTGGGGATATT
3602 TTGTGGTTTGCTAATGACCGATCATAAAGAAAGGCAACACCAAAAGGGACATGAAGATCAATTGA
131 TTGTGGTTTGCTAATGACCGATCATAAAGAAAGGCAACACCAAAAGGGACATGAAGATCAATTGA
3667 AATCTAAAAACCTTTTTGATCGAATTAAGGAAGAAGGAAGAAAACCTTCAACCTCTTATTGGCCT
196 AATCT--AAACCTTTTTGATCGAATTAAGGAAGAAGGAAG-AAACCTTCAACCTCTTATTGGCCT
3732 ACACGTATCACTAATGAAACCTTGATCAATCAAAATGCACTTCAAACAACCTTAGTAAGAAAGAT
258 ACACGTATCACTAATGAAACCTTGATCAATCAAAATGCACTTCAAACAACCTTAGTAAGAAAGAT
*
3797 TATGGAGTAAGAAGAAAAGGAGCTAAGGCAAGCTTCTGACAATCAAGCATT
323 TATGGAGTAAGAAGAAAAGAAGCTAAGGCAAGCTTCTGACAATCAAGCATT
*
3848 CAATCATCAATATTTT-TTTTACTTGTGTGAATTTAAACTAACTAATTAGAAAAAAGAAGATAAC
1 CAATCATCAATATTTTCTTTTACTTGTGTGAATTTAAACTAATTAATTAGAAAAAAGAAGATAAC
* *
3912 CATTCTCTCTGTGGATTCGACCCCTACTTTCCCTAGCTACTATAGTTAGAATTTGTGGGGATTAG
66 CATTCTCTCTGTGGATTCGACCCCTACTTACCCTAGCTACTATAGTTAGAATTTGTGGGGA-TAT
*
3977 TTTGTGGTTTGCTAACGACCGATCA
130 TTTGTGGTTTGCTAATGACCGATCA
4002 CAATTTTGGC
Statistics
Matches: 503, Mismatches: 22, Indels: 6
0.95 0.04 0.01
Matches are distributed among these distances:
372 10 0.02
373 179 0.36
375 137 0.27
376 177 0.35
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Consensus pattern (373 bp):
CAATCATCAATATTTTCTTTTACTTGTGTGAATTTAAACTAATTAATTAGAAAAAAGAAGATAAC
CATTCTCTCTGTGGATTCGACCCCTACTTACCCTAGCTACTATAGTTAGAATTTGTGGGGATATT
TTGTGGTTTGCTAATGACCGATCATAAAGAAAGGCAACACCAAAAGGGACATGAAGATCAATTGA
AATCTAAACCTTTTTGATCGAATTAAGGAAGAAGGAAGAAACCTTCAACCTCTTATTGGCCTACA
CGTATCACTAATGAAACCTTGATCAATCAAAATGCACTTCAAACAACCTTAGTAAGAAAGATTAT
GGAGTAAGAAGAAAAGAAGCTAAGGCAAGCTTCTGACAATCAAGCATT
Found at i:8634 original size:9 final size:9
Alignment explanation
Indices: 8617--8648 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
8607 GATTGAAGAC
*
8617 GAAGCCCTT
1 GAAGACCTT
8626 GAAGACCTT
1 GAAGACCTT
8635 GAAGACCTT
1 GAAGACCTT
8644 GAAGA
1 GAAGA
8649 TATGGAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.34, C:0.22, G:0.25, T:0.19
Consensus pattern (9 bp):
GAAGACCTT
Found at i:10881 original size:15 final size:15
Alignment explanation
Indices: 10848--10880 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
10838 TTTACTAACA
10848 TTTTAATTTTCTTTC
1 TTTTAATTTTCTTTC
*
10863 TTTTATTTTTCTTT-
1 TTTTAATTTTCTTTC
10877 TTTT
1 TTTT
10881 TTTAGGATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTTAATTTTCTTTC
Found at i:11933 original size:19 final size:18
Alignment explanation
Indices: 11909--11948 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
11899 TTGAAGATTT
*
11909 ATTGAAGATAATTTGAAGA
1 ATTGAAGACAA-TTGAAGA
*
11928 ATTGAAGACCATTGAAGA
1 ATTGAAGACAATTGAAGA
11946 ATT
1 ATT
11949 ATTTCAAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.45, C:0.05, G:0.20, T:0.30
Consensus pattern (18 bp):
ATTGAAGACAATTGAAGA
Found at i:17235 original size:18 final size:18
Alignment explanation
Indices: 17212--17248 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
17202 CTCCTCTTGC
*
17212 ATGAAAACACTTCTTTTT
1 ATGAAAACAATTCTTTTT
*
17230 ATGAAAACAATTTTTTTT
1 ATGAAAACAATTCTTTTT
17248 A
1 A
17249 AACTACCCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.38, C:0.11, G:0.05, T:0.46
Consensus pattern (18 bp):
ATGAAAACAATTCTTTTT
Found at i:24706 original size:21 final size:21
Alignment explanation
Indices: 24682--24722 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
24672 GGTGATGACA
**
24682 CGGGCATGCCCGGTGGTGGCT
1 CGGGCATAACCGGTGGTGGCT
*
24703 CGGGCTTAACCGGTGGTGGC
1 CGGGCATAACCGGTGGTGGC
24723 ACGGTGATGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.07, C:0.27, G:0.46, T:0.20
Consensus pattern (21 bp):
CGGGCATAACCGGTGGTGGCT
Found at i:28870 original size:18 final size:19
Alignment explanation
Indices: 28847--28883 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
28837 ACACCCTTGC
*
28847 CTAGAATTAGAAGA-AAAA
1 CTAGAACTAGAAGAGAAAA
28865 CTAGAACTAGAAGAGAAAA
1 CTAGAACTAGAAGAGAAAA
28884 AAGTAGAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.59, C:0.08, G:0.19, T:0.14
Consensus pattern (19 bp):
CTAGAACTAGAAGAGAAAA
Found at i:38124 original size:16 final size:16
Alignment explanation
Indices: 38103--38140 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
38093 TTGAAGTCAA
*
38103 CAACCATCAAGGAGTC
1 CAACCATCAAGAAGTC
*
38119 CAACCATCAATAAGTC
1 CAACCATCAAGAAGTC
38135 CAACCA
1 CAACCA
38141 CAGGGAGAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.42, C:0.34, G:0.11, T:0.13
Consensus pattern (16 bp):
CAACCATCAAGAAGTC
Found at i:38402 original size:21 final size:20
Alignment explanation
Indices: 38382--38433 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
38372 TCCATGCCAG
*
38382 GACCGGCCATGTCCGCACCA
1 GACCAGCCATGTCCGCACCA
* *
38402 GTCCATGCCATGTCCGCTCCAA
1 GACCA-GCCATGTCCGCACC-A
38424 GACCAGCCAT
1 GACCAGCCAT
38434 CACCGTGCCA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 3 0.12
21 18 0.69
22 5 0.19
ACGTcount: A:0.21, C:0.42, G:0.21, T:0.15
Consensus pattern (20 bp):
GACCAGCCATGTCCGCACCA
Found at i:38497 original size:11 final size:11
Alignment explanation
Indices: 38483--38519 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
38473 GCCACCACCG
38483 GCCACAGCCGA
1 GCCACAGCCGA
38494 GCCACCA-CCG-
1 GCCA-CAGCCGA
38504 GCCACAGCCGA
1 GCCACAGCCGA
38515 GCCAC
1 GCCAC
38520 CACCGGCCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
9 2 0.09
10 7 0.30
11 12 0.52
12 2 0.09
ACGTcount: A:0.24, C:0.51, G:0.24, T:0.00
Consensus pattern (11 bp):
GCCACAGCCGA
Found at i:38539 original size:21 final size:21
Alignment explanation
Indices: 38473--38528 Score: 112
Period size: 21 Copynumber: 2.7 Consensus size: 21
38463 CCAACACCGT
38473 GCCACCACCGGCCACAGCCGA
1 GCCACCACCGGCCACAGCCGA
38494 GCCACCACCGGCCACAGCCGA
1 GCCACCACCGGCCACAGCCGA
38515 GCCACCACCGGCCA
1 GCCACCACCGGCCA
38529 TGCCCGTGCC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.23, C:0.54, G:0.23, T:0.00
Consensus pattern (21 bp):
GCCACCACCGGCCACAGCCGA
Found at i:38787 original size:15 final size:15
Alignment explanation
Indices: 38767--38800 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
38757 CTAACCCTTA
38767 ATTTTTCTTTCTT-TT
1 ATTTTTCTTT-TTCTT
38782 ATTTTTCTTTTTCTT
1 ATTTTTCTTTTTCTT
38797 ATTT
1 ATTT
38801 GGATTTCATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 2 0.11
15 16 0.89
ACGTcount: A:0.09, C:0.12, G:0.00, T:0.79
Consensus pattern (15 bp):
ATTTTTCTTTTTCTT
Found at i:39775 original size:31 final size:31
Alignment explanation
Indices: 39734--39793 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
39724 GCCCTCTGAA
* *
39734 AAAAAAAAAAGAGTGTTAGTAACCTCAAAAT
1 AAAAAAAAAAGAGAGTTAGTAACCCCAAAAT
* *
39765 AAAAATAAAAGGGAGTTAGTAACCCCAAA
1 AAAAAAAAAAGAGAGTTAGTAACCCCAAA
39794 TCATGAACAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.57, C:0.12, G:0.15, T:0.17
Consensus pattern (31 bp):
AAAAAAAAAAGAGAGTTAGTAACCCCAAAAT
Found at i:47898 original size:28 final size:28
Alignment explanation
Indices: 47818--47901 Score: 88
Period size: 28 Copynumber: 3.1 Consensus size: 28
47808 GTATCGATCG
47818 TTACTATTAGTTAAGCATCCACATATAT
1 TTACTATTAGTTAAGCATCCACATATAT
* * *
47846 TTA-TGGTTA--TATA-CA-ACTCATATAT
1 TTACT-ATTAGTTA-AGCATCCACATATAT
47871 TTACTATTAGTTAAGCATCCACATATAT
1 TTACTATTAGTTAAGCATCCACATATAT
47899 TTA
1 TTA
47902 TGCTATTATT
Statistics
Matches: 43, Mismatches: 6, Indels: 14
0.68 0.10 0.22
Matches are distributed among these distances:
25 14 0.33
26 6 0.14
27 6 0.14
28 17 0.40
ACGTcount: A:0.36, C:0.15, G:0.07, T:0.42
Consensus pattern (28 bp):
TTACTATTAGTTAAGCATCCACATATAT
Found at i:53369 original size:31 final size:31
Alignment explanation
Indices: 53311--53369 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
53301 CAAATTGGTT
*
53311 AACTTTTGAAAGGTTTAGACTCAAATTGAGC
1 AACTTTTGAAAGGTTTACACTCAAATTGAGC
* *
53342 AACTTTTGAAAGGTTTACCCTCGAATTG
1 AACTTTTGAAAGGTTTACACTCAAATTG
53370 GTGGCTAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.34
Consensus pattern (31 bp):
AACTTTTGAAAGGTTTACACTCAAATTGAGC
Done.