Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020310.1 Corchorus olitorius cultivar O-4 contig20343, 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: 50174
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:2856 original size:17 final size:17
Alignment explanation
Indices: 2834--2866 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2824 AATTTTATTA
2834 TTTTATTGTTTATTTAT
1 TTTTATTGTTTATTTAT
*
2851 TTTTATTGTTTCTTTA
1 TTTTATTGTTTATTTA
2867 ATTCAAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.03, G:0.06, T:0.76
Consensus pattern (17 bp):
TTTTATTGTTTATTTAT
Found at i:3938 original size:26 final size:27
Alignment explanation
Indices: 3909--3963 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
3899 CATAATTTTT
3909 TATTGGATTA-AAGTT-ATTGGGTTAAG
1 TATTGGATTATAA-TTAATTGGGTTAAG
*
3935 TATTGGGTTATAATTAATTGGGTTAAG
1 TATTGGATTATAATTAATTGGGTTAAG
3962 TA
1 TA
3964 GAGGCCTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 11 0.42
27 15 0.58
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (27 bp):
TATTGGATTATAATTAATTGGGTTAAG
Found at i:7598 original size:38 final size:38
Alignment explanation
Indices: 7554--7633 Score: 115
Period size: 38 Copynumber: 2.1 Consensus size: 38
7544 TAGAAATTCT
*
7554 AATGAGATTCTAAACATAGACCTAAGCAAGTTTCCTTA
1 AATGAGATTCTAAACATAGACCTAAGCAAGTTTACTTA
* * * *
7592 AATGAGATTTTGAACGTAGACCTAAGCAGGTTTACTTA
1 AATGAGATTCTAAACATAGACCTAAGCAAGTTTACTTA
7630 AATG
1 AATG
7634 GCAACTCTAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (38 bp):
AATGAGATTCTAAACATAGACCTAAGCAAGTTTACTTA
Found at i:12154 original size:2 final size:2
Alignment explanation
Indices: 12147--12177 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
12137 CGATAGCAAG
12147 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
12178 GAGAGAGAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12408 original size:21 final size:20
Alignment explanation
Indices: 12369--12408 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
12359 AGAGTCTTTA
*
12369 GAAACTTTGATAAGCCTATG
1 GAAACTTTGAAAAGCCTATG
*
12389 GAAACTTTTGAAAAGGCTAT
1 GAAAC-TTTGAAAAGCCTAT
12409 TACATTTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (20 bp):
GAAACTTTGAAAAGCCTATG
Found at i:13063 original size:47 final size:47
Alignment explanation
Indices: 13009--13103 Score: 190
Period size: 47 Copynumber: 2.0 Consensus size: 47
12999 CAGCCCATAT
13009 AAATCATTAATTGGAATTAAAATCCCAATTAATAACTCCTATATCCA
1 AAATCATTAATTGGAATTAAAATCCCAATTAATAACTCCTATATCCA
13056 AAATCATTAATTGGAATTAAAATCCCAATTAATAACTCCTATATCCA
1 AAATCATTAATTGGAATTAAAATCCCAATTAATAACTCCTATATCCA
13103 A
1 A
13104 GGAAATATCC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.45, C:0.19, G:0.04, T:0.32
Consensus pattern (47 bp):
AAATCATTAATTGGAATTAAAATCCCAATTAATAACTCCTATATCCA
Found at i:14630 original size:34 final size:35
Alignment explanation
Indices: 14587--14667 Score: 114
Period size: 34 Copynumber: 2.4 Consensus size: 35
14577 AGTTTATGCG
*
14587 TTTCTGCGTTTTTAAT-CTAAAAAAAAAAATTTGT
1 TTTCTGCGTTTTTAATCCTAAAAAAAAAAATTTGA
* *
14621 TTTCTGCGTTTTT-TTCCTTAAAAAAAAAATTTGA
1 TTTCTGCGTTTTTAATCCTAAAAAAAAAAATTTGA
14655 TTT-TGCGTTTTTA
1 TTTCTGCGTTTTTA
14668 GTTTGTGTGT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
33 10 0.24
34 32 0.76
ACGTcount: A:0.31, C:0.10, G:0.10, T:0.49
Consensus pattern (35 bp):
TTTCTGCGTTTTTAATCCTAAAAAAAAAAATTTGA
Found at i:14730 original size:20 final size:22
Alignment explanation
Indices: 14693--14732 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
14683 ATTTTGAAAA
*
14693 AAAAAAAAGTTCTTTGCGTTAT
1 AAAAAAAAGTTCTCTGCGTTAT
14715 AAAAAAAA-TT-TCTGCGTT
1 AAAAAAAAGTTCTCTGCGTT
14733 TTCAGAAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 2 0.12
22 8 0.47
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.35
Consensus pattern (22 bp):
AAAAAAAAGTTCTCTGCGTTAT
Found at i:27741 original size:36 final size:35
Alignment explanation
Indices: 27699--27794 Score: 133
Period size: 33 Copynumber: 2.8 Consensus size: 35
27689 ATCAATTTTA
* *
27699 TTATTTTCCAAAATCTTCTTTTGGATTTTTAAACTT
1 TTATTTTCCAAAATCTCCTTTTGGATTATT-AACTT
* *
27735 TTATTTTCCAAAATCTCCTTTCGGA--ATTACCTT
1 TTATTTTCCAAAATCTCCTTTTGGATTATTAACTT
27768 TTATTTTCCAAAATCTCCTTTTGGATT
1 TTATTTTCCAAAATCTCCTTTTGGATT
27795 CCTTAATTAA
Statistics
Matches: 53, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
33 28 0.53
34 2 0.04
36 23 0.43
ACGTcount: A:0.24, C:0.19, G:0.06, T:0.51
Consensus pattern (35 bp):
TTATTTTCCAAAATCTCCTTTTGGATTATTAACTT
Found at i:30119 original size:47 final size:47
Alignment explanation
Indices: 30027--30137 Score: 138
Period size: 47 Copynumber: 2.3 Consensus size: 47
30017 TAAACTCGTG
*
30027 TGGAAGCGAGAAAAAGACCAACTTTGTTCACTAAATCGTAGACTCGCA
1 TGGAAGCGAG-AAAAGACCAACTTTGTTCACTAAATCGCAGACTCGCA
*
30075 TGGAAGCGAGAAAAGACCAACTTT-TGTCACTAAAAT-GCCA-ACTCGCG
1 TGGAAGCGAGAAAAGACCAACTTTGT-TCACT-AAATCG-CAGACTCGCA
*
30122 TGGAAACGAGAAAAGA
1 TGGAAGCGAGAAAAGA
30138 TTACTTGGAT
Statistics
Matches: 57, Mismatches: 3, Indels: 7
0.85 0.04 0.10
Matches are distributed among these distances:
46 1 0.02
47 41 0.72
48 15 0.26
ACGTcount: A:0.40, C:0.20, G:0.23, T:0.18
Consensus pattern (47 bp):
TGGAAGCGAGAAAAGACCAACTTTGTTCACTAAATCGCAGACTCGCA
Found at i:30401 original size:69 final size:69
Alignment explanation
Indices: 30248--30895 Score: 898
Period size: 69 Copynumber: 9.3 Consensus size: 69
30238 CTCATTGAAC
* * * * * *
30248 TTGGCTTATGGAAAAG-CTCATGTTGCTTGAATGGAACCAATGCTTGAACTGAGTCGTATGGAAA
1 TTGGCTTGTGGAAAAGCCTC-TGCTGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAA
30312 CGAGT
65 CGAGT
* * *
30317 TTGGCTCGTGGAAAAGCCCCTGCTGCTTGGATGGAATCAAGGC-TAAACTGACTCGTATGGAAAC
1 TTGGCTTGTGGAAAAGCCTCTGCTGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAAC
30381 GAGT
66 GAGT
* * *
30385 TTGGCTTGTGGAAAAAGCCTCTGCTGCTCGGATGGAACCAAGG-ATAAACTGACTCGTGTGGAAA
1 TTGGCTTGTGG-AAAAGCCTCTGCTGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAA
30449 CGAGT
65 CGAGT
*
30454 TTGGCTTGTGGAAAAGCCTCTGCTGCTTGGATGGAACCAAGGC-TAAACTGACTCGTGTGGAAAC
1 TTGGCTTGTGGAAAAGCCTCTGCTGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAAC
30518 GAGT
66 GAGT
*
30522 TTGGCTTGTGGAAAAGCCTCTGCTGCTTGGATGGAACCAAGGC-TAAACTGACTCGTGTGGAAAC
1 TTGGCTTGTGGAAAAGCCTCTGCTGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAAC
30586 GAGT
66 GAGT
30590 TTGGCTTGTGGAAAAGCCTCTGCTGCTTGGATGGAACCAAGGCTTAGAACTGACTCGTATGGAAA
1 TTGGCTTGTGGAAAAGCCTCTGCTGCTTGGATGGAACCAAGGCTTA-AACTGACTCGTATGGAAA
*
30655 CGNGT
65 CGAGT
*
30660 TTAGGCTTGTGGAAAAGCC-CTGGACTGCTTGGATGGGAACCAAAGGCAAAATCTTGAACTGACT
1 TT-GGCTTGTGGAAAAGCCTCT-G-CTGCTTGGAT-GGAACC-AAGG------CTTAAACTGACT
30724 CGTATGGAAACGAGT
55 CGTATGGAAACGAGT
* * *
30739 TTGGCTTGTGGAAAAGCCTATG-TGGCTTGGATGGAACCAAGGCTTGAACTAACTCGTATGGAAA
1 TTGGCTTGTGGAAAAGCCTCTGCT-GCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAA
30803 CGAGT
65 CGAGT
* *
30808 TTGGCTTGTGGAAAAGCCTATG-TGGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAA
1 TTGGCTTGTGGAAAAGCCTCTGCT-GCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAA
30872 CGAGT
65 CGAGT
*
30877 TTGACTTGTGGAAAAGCCT
1 TTGGCTTGTGGAAAAGCCT
30896 ATGTTGATAA
Statistics
Matches: 537, Mismatches: 23, Indels: 38
0.90 0.04 0.06
Matches are distributed among these distances:
68 199 0.37
69 210 0.39
70 27 0.05
71 17 0.03
72 10 0.02
73 6 0.01
74 4 0.01
75 4 0.01
76 7 0.01
77 8 0.01
78 17 0.03
79 25 0.05
80 3 0.01
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.25
Consensus pattern (69 bp):
TTGGCTTGTGGAAAAGCCTCTGCTGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAAC
GAGT
Found at i:30911 original size:50 final size:50
Alignment explanation
Indices: 30857--31144 Score: 477
Period size: 50 Copynumber: 5.8 Consensus size: 50
30847 AGGCTTGAAC
*
30857 TGACTCGTATGGAAACGAGTTTGACTTGTGGAAAAGCCTATGTTGATAAT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
*
30907 TGACTCGTATGGAAACGAGCTTGGCTTGTGGAAAAGCCTATGTTGATAAT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
* *
30957 TGACTCGTATGGAAACAAGTTGGGCTTGTGGAAAAGCCTATGTTGATAAT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
* *
31007 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTCGATAAC
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
* * *
31057 CGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTCGATAAC
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
* *
31107 TGACTCGTATGGAAACGAGTTTGACTTATGGAAAAGCC
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCC
31145 AAAGCATTCG
Statistics
Matches: 225, Mismatches: 13, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
50 225 1.00
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (50 bp):
TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
Found at i:32449 original size:6 final size:6
Alignment explanation
Indices: 32438--32469 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
32428 ATCCATTCTC
32438 TTTTGA TTTTGA TTTTGA -TTTGA -TTTGA TTTT
1 TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTT
32470 TTTTATTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 10 0.40
6 15 0.60
ACGTcount: A:0.16, C:0.00, G:0.16, T:0.69
Consensus pattern (6 bp):
TTTTGA
Found at i:32491 original size:19 final size:19
Alignment explanation
Indices: 32469--32511 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
32459 GATTTGATTT
32469 TTTTTATTT-TTCTTTTCTC
1 TTTTTATTTATT-TTTTCTC
* *
32488 TTTTGATTTATTTTTTTTC
1 TTTTTATTTATTTTTTCTC
32507 TTTTT
1 TTTTT
32512 TTGAATTTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
19 18 0.90
20 2 0.10
ACGTcount: A:0.07, C:0.09, G:0.02, T:0.81
Consensus pattern (19 bp):
TTTTTATTTATTTTTTCTC
Found at i:36562 original size:9 final size:9
Alignment explanation
Indices: 36548--36574 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
36538 CAATAAACAT
36548 CAAAACAAA
1 CAAAACAAA
36557 CAAAACAAA
1 CAAAACAAA
36566 CAAAACAAA
1 CAAAACAAA
36575 GCAACCGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.78, C:0.22, G:0.00, T:0.00
Consensus pattern (9 bp):
CAAAACAAA
Found at i:37157 original size:36 final size:35
Alignment explanation
Indices: 37116--37211 Score: 117
Period size: 33 Copynumber: 2.8 Consensus size: 35
37106 ATCAATTTTA
* * *
37116 TTATTTTTCAAAATCTTCTTTTGGATTTTTAAACC-T
1 TTATTTTCCAAAATCTCCTTTTGGATTATT--ACCTT
*
37152 TTATTTTCCAAAATCTCCTTTCGGA--ATTACCTT
1 TTATTTTCCAAAATCTCCTTTTGGATTATTACCTT
37185 TTATTTTCCAAAATCTCCTTTTGGATT
1 TTATTTTCCAAAATCTCCTTTTGGATT
37212 CCTTAATAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
32 3 0.06
33 25 0.48
34 2 0.04
36 22 0.42
ACGTcount: A:0.24, C:0.19, G:0.06, T:0.51
Consensus pattern (35 bp):
TTATTTTCCAAAATCTCCTTTTGGATTATTACCTT
Found at i:39765 original size:26 final size:26
Alignment explanation
Indices: 39736--39787 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
39726 TTATGCCTAT
39736 TTAGCTCTGACCTTGCTTCTAGTTCC
1 TTAGCTCTGACCTTGCTTCTAGTTCC
*
39762 TTAGCTCTGACCTTGCTTCTTGTTCC
1 TTAGCTCTGACCTTGCTTCTAGTTCC
39788 ATATTTGCAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.10, C:0.31, G:0.15, T:0.44
Consensus pattern (26 bp):
TTAGCTCTGACCTTGCTTCTAGTTCC
Found at i:45975 original size:19 final size:18
Alignment explanation
Indices: 45942--45977 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
45932 TGGAAATAAT
45942 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
45960 TCTTCAGATTGTCTTCAA
1 TCTTCA-ATGGTCTTCAA
45978 TAAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.25, C:0.22, G:0.11, T:0.42
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAA
Done.