Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014681.1 Corchorus olitorius cultivar O-4 contig14714, 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: 62643
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:866 original size:6 final size:6
Alignment explanation
Indices: 850--897 Score: 53
Period size: 6 Copynumber: 7.7 Consensus size: 6
840 GAAAAACACA
*
850 AAAACAC AAAAAC -AAAAC AAAAAC AAAATAC GAAAAAT AAAAAC AAAA
1 AAAA-AC AAAAAC AAAAAC AAAAAC AAAA-AC -AAAAAC AAAAAC AAAA
898 CTAAAGGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
5 5 0.14
6 20 0.56
7 7 0.19
8 4 0.11
ACGTcount: A:0.79, C:0.15, G:0.02, T:0.04
Consensus pattern (6 bp):
AAAAAC
Found at i:885 original size:19 final size:19
Alignment explanation
Indices: 842--897 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 19
832 AAAATTAAGA
842 AAAACACAAAAACACAAAAAC
1 AAAA-ACAAAAACA-AAAAAC
*
863 -AAAACAAAAACAAAATAC
1 AAAAACAAAAACAAAAAAC
*
881 GAAAAATAAAAACAAAA
1 -AAAAACAAAAACAAAA
898 CTAAAGGAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
18 5 0.16
19 9 0.29
20 17 0.55
ACGTcount: A:0.79, C:0.16, G:0.02, T:0.04
Consensus pattern (19 bp):
AAAAACAAAAACAAAAAAC
Found at i:11223 original size:17 final size:17
Alignment explanation
Indices: 11190--11248 Score: 52
Period size: 17 Copynumber: 3.6 Consensus size: 17
11180 GTAAAATTAC
* *
11190 AATTATATACAATTATT
1 AATTATATATAAATATT
11207 AATTATATATAAATATTT
1 AATTATATATAAATA-TT
*
11225 AATT-T-TAT-TATATT
1 AATTATATATAAATATT
*
11239 ATTTATATAT
1 AATTATATAT
11249 TGTTTATTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
14 5 0.14
15 4 0.11
16 6 0.17
17 14 0.40
18 6 0.17
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (17 bp):
AATTATATATAAATATT
Found at i:11500 original size:20 final size:20
Alignment explanation
Indices: 11475--11518 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
11465 ATGAACATAG
11475 TATGATGGCGGTTAGGTAAA
1 TATGATGGCGGTTAGGTAAA
11495 TATGATGGCGGTTAGGTAAA
1 TATGATGGCGGTTAGGTAAA
11515 TATG
1 TATG
11519 CCCCCATCGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.30, C:0.05, G:0.34, T:0.32
Consensus pattern (20 bp):
TATGATGGCGGTTAGGTAAA
Found at i:13961 original size:22 final size:24
Alignment explanation
Indices: 13926--13979 Score: 60
Period size: 22 Copynumber: 2.3 Consensus size: 24
13916 ATAAATGTTG
* *
13926 CTGATAA-TCTTCT-CTTTTATCT
1 CTGATAATTCTTCTCCATTTATCA
13948 CTGATAATTC-TCTCCATTTATCA
1 CTGATAATTCTTCTCCATTTATCA
13971 CTTGATAAT
1 C-TGATAAT
13980 ATCTAGCCAG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 10 0.37
23 10 0.37
24 7 0.26
ACGTcount: A:0.24, C:0.22, G:0.06, T:0.48
Consensus pattern (24 bp):
CTGATAATTCTTCTCCATTTATCA
Found at i:19442 original size:28 final size:28
Alignment explanation
Indices: 19336--19606 Score: 224
Period size: 28 Copynumber: 8.8 Consensus size: 28
19326 CAATCTTAGG
*
19336 ATGACAACTTCCGGTGTCAATAATTTCCTCAGC
1 ATGACAACTTCTGGTGTCAATAATTT--T---C
*
19369 ATGACAACTTCTGGTGTCAAGATAATAATTTGAT
1 ATGACAACTTCTGGTGTC-A-ATAAT--TTT--C
*
19403 ATGACAATTTCTGGTGTCAATAATTTTC
1 ATGACAACTTCTGGTGTCAATAATTTTC
*
19431 ATGACAACTTCTGGTGTCAAGATAATGATTTGAT
1 ATGACAACTTCTGGTGTC-A-ATAAT--TTT--C
19465 ATGACAACTTCTGGTGTCAATAATTTTC
1 ATGACAACTTCTGGTGTCAATAATTTTC
19493 ATGACAACTTCTGGTGTCAAGATAATAATATAAT-
1 ATGACAACTTCTGGTGTC-A-ATAAT--T-T--TC
19527 ATGACAACTTCTGGTGTCAATAA-TTTC
1 ATGACAACTTCTGGTGTCAATAATTTTC
19554 TATGACAACTTCTGGTGTCAAGATAATTTAAT-
1 -ATGACAACTTCTGGTGTC-A-ATAATTT--TC
19586 ATGACAACTTCTGGTGTCAAT
1 ATGACAACTTCTGGTGTCAAT
19607 TAAATTTAAA
Statistics
Matches: 205, Mismatches: 9, Indels: 52
0.77 0.03 0.20
Matches are distributed among these distances:
26 1 0.00
28 54 0.26
29 6 0.03
30 21 0.10
31 20 0.10
32 18 0.09
33 22 0.11
34 54 0.26
35 7 0.03
37 2 0.01
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (28 bp):
ATGACAACTTCTGGTGTCAATAATTTTC
Found at i:19450 original size:62 final size:62
Alignment explanation
Indices: 19336--19606 Score: 406
Period size: 62 Copynumber: 4.3 Consensus size: 62
19326 CAATCTTAGG
* *
19336 ATGACAACTTCCGGTGTCAATAATTTCCTCAGCATGACAACTTCTGGTGTCAAGATAATAATTTG
1 ATGACAACTTCTGGTGTCAATAATTT--T---CATGACAACTTCTGGTGTCAAGATAATAATTTA
19401 AT
61 AT
* * *
19403 ATGACAATTTCTGGTGTCAATAATTTTCATGACAACTTCTGGTGTCAAGATAATGATTTGAT
1 ATGACAACTTCTGGTGTCAATAATTTTCATGACAACTTCTGGTGTCAAGATAATAATTTAAT
*
19465 ATGACAACTTCTGGTGTCAATAATTTTCATGACAACTTCTGGTGTCAAGATAATAATATAAT
1 ATGACAACTTCTGGTGTCAATAATTTTCATGACAACTTCTGGTGTCAAGATAATAATTTAAT
19527 ATGACAACTTCTGGTGTCAATAA-TTTCTATGACAACTTCTGGTGTCAAG---ATAATTTAAT
1 ATGACAACTTCTGGTGTCAATAATTTTC-ATGACAACTTCTGGTGTCAAGATAATAATTTAAT
19586 ATGACAACTTCTGGTGTCAAT
1 ATGACAACTTCTGGTGTCAAT
19607 TAAATTTAAA
Statistics
Matches: 195, Mismatches: 8, Indels: 10
0.92 0.04 0.05
Matches are distributed among these distances:
59 30 0.15
61 4 0.02
62 136 0.70
65 1 0.01
67 24 0.12
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (62 bp):
ATGACAACTTCTGGTGTCAATAATTTTCATGACAACTTCTGGTGTCAAGATAATAATTTAAT
Found at i:20001 original size:22 final size:24
Alignment explanation
Indices: 19966--20019 Score: 60
Period size: 22 Copynumber: 2.3 Consensus size: 24
19956 ATAAATGTTG
* *
19966 CTGATAA-TCTTCT-CTTTTATCT
1 CTGATAATTCTTCTCCATTTATCA
19988 CTGATAATTC-TCTCCATTTATCA
1 CTGATAATTCTTCTCCATTTATCA
20011 CTTGATAAT
1 C-TGATAAT
20020 ATCTAGTCAG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 10 0.37
23 10 0.37
24 7 0.26
ACGTcount: A:0.24, C:0.22, G:0.06, T:0.48
Consensus pattern (24 bp):
CTGATAATTCTTCTCCATTTATCA
Found at i:21922 original size:124 final size:124
Alignment explanation
Indices: 21700--21947 Score: 460
Period size: 124 Copynumber: 2.0 Consensus size: 124
21690 CATAACTCTG
* *
21700 CCTTAATAAATCCAAATTAAGTCATTCTTGTACCCAAATTGTAGGGTTTTGAGTCCTCTACAACT
1 CCTTAATAAATCCAAATTAAGTCATTCTTGTACCCAAATTGAAGGATTTTGAGTCCTCTACAACT
* *
21765 TTGTAGAAGGAACCGAGTTGAGATTTTATGTCTAAAATAGAGAAATGTGATCGTTTCTA
66 TTGTAGAAGGAACCGAGTTGAGATTTTAAGTCTAAAATAGAGAAATGTGATCATTTCTA
21824 CCTTAATAAATCCAAATTAAGTCATTCTTGTACCCAAATTGAAGGATTTTGAGTCCTCTACAACT
1 CCTTAATAAATCCAAATTAAGTCATTCTTGTACCCAAATTGAAGGATTTTGAGTCCTCTACAACT
21889 TTGTAGAAGGAACCGAGTTGAGATTTTAAGTCTAAAATAGAGAAATGTGATCATTTCTA
66 TTGTAGAAGGAACCGAGTTGAGATTTTAAGTCTAAAATAGAGAAATGTGATCATTTCTA
21948 TAACTGCACG
Statistics
Matches: 120, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
124 120 1.00
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Consensus pattern (124 bp):
CCTTAATAAATCCAAATTAAGTCATTCTTGTACCCAAATTGAAGGATTTTGAGTCCTCTACAACT
TTGTAGAAGGAACCGAGTTGAGATTTTAAGTCTAAAATAGAGAAATGTGATCATTTCTA
Found at i:30467 original size:18 final size:20
Alignment explanation
Indices: 30441--30483 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
30431 TTATTCTAAA
30441 ATTTCTTATTAT-TTTC-TTT
1 ATTTCTTATT-TCTTTCTTTT
30460 ATTT-TTATTTCTTTCTTTT
1 ATTTCTTATTTCTTTCTTTT
30479 ATTTC
1 ATTTC
30484 ACATTGGGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 1 0.05
18 9 0.43
19 11 0.52
ACGTcount: A:0.14, C:0.12, G:0.00, T:0.74
Consensus pattern (20 bp):
ATTTCTTATTTCTTTCTTTT
Found at i:30616 original size:24 final size:23
Alignment explanation
Indices: 30588--30647 Score: 77
Period size: 24 Copynumber: 2.6 Consensus size: 23
30578 GGCCCATGCG
*
30588 CCTGGCCTAGGCGCGCGGGCCAGC
1 CCTGGCCTAGGCGCGAGGGCC-GC
* *
30612 GCTGGCCTAGGCGCTAGGGCCGC
1 CCTGGCCTAGGCGCGAGGGCCGC
30635 CCTGGCCT-GGCGC
1 CCTGGCCTAGGCGC
30648 CTGGCCTAGC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
22 5 0.16
23 9 0.28
24 18 0.56
ACGTcount: A:0.07, C:0.40, G:0.42, T:0.12
Consensus pattern (23 bp):
CCTGGCCTAGGCGCGAGGGCCGC
Found at i:30625 original size:12 final size:12
Alignment explanation
Indices: 30555--30626 Score: 51
Period size: 12 Copynumber: 5.9 Consensus size: 12
30545 CCCAAGCTTA
30555 GCCTAGGCGCTGG
1 GCCTAGGCGCT-G
*
30568 GCC-AAGCGCTG
1 GCCTAGGCGCTG
* *
30579 GCCCATGCGCCTG
1 GCCTAGGCG-CTG
*
30592 GCCTAGGCGCGCGG
1 GCCTA-G-GCGCTG
30606 GCC-A-GCGCTG
1 GCCTAGGCGCTG
30616 GCCTAGGCGCT
1 GCCTAGGCGCT
30627 AGGGCCGCCC
Statistics
Matches: 47, Mismatches: 6, Indels: 13
0.71 0.09 0.20
Matches are distributed among these distances:
10 8 0.17
11 5 0.11
12 15 0.32
13 11 0.23
14 5 0.11
15 3 0.06
ACGTcount: A:0.10, C:0.38, G:0.40, T:0.12
Consensus pattern (12 bp):
GCCTAGGCGCTG
Found at i:40103 original size:17 final size:17
Alignment explanation
Indices: 40081--40115 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
40071 TCAAATTGTG
*
40081 TGTTTGGTGTTTACTGT
1 TGTTTGGTGTGTACTGT
40098 TGTTTGGTGTGTACTGT
1 TGTTTGGTGTGTACTGT
40115 T
1 T
40116 CTTGCTGCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.06, C:0.06, G:0.31, T:0.57
Consensus pattern (17 bp):
TGTTTGGTGTGTACTGT
Found at i:41075 original size:47 final size:47
Alignment explanation
Indices: 40999--41089 Score: 121
Period size: 47 Copynumber: 1.9 Consensus size: 47
40989 AAACAGAGAT
* * * *
40999 AATAATTCGGGAGAGAAGTTTTTTTTTTTTTTTTTTACATTGCCGAG
1 AATAATTCGGGAGAGAAGTTATTCTTTTTTCTTGTTACATTGCCGAG
*
41046 AATAATT-TGGAGAGAAGTTAATTCTTTTTTCTTGTTACATTGCC
1 AATAATTCGGGAGAGAAGTT-ATTCTTTTTTCTTGTTACATTGCC
41090 AAGCCACAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
46 11 0.29
47 27 0.71
ACGTcount: A:0.25, C:0.10, G:0.18, T:0.47
Consensus pattern (47 bp):
AATAATTCGGGAGAGAAGTTATTCTTTTTTCTTGTTACATTGCCGAG
Found at i:42424 original size:30 final size:29
Alignment explanation
Indices: 42353--42426 Score: 73
Period size: 30 Copynumber: 2.6 Consensus size: 29
42343 AAAAAGATTA
*
42353 AATTTTA--ATGTATACATATAAATTATT
1 AATTTTATTATGTATACATACAAATTATT
* *
42380 -GTTGTAATTAATGTATACATACAAATTATT
1 AATT-TTATT-ATGTATACATACAAATTATT
42410 CAATTTTATTATGTATA
1 -AATTTTATTATGTATA
42427 AATATAATTA
Statistics
Matches: 36, Mismatches: 5, Indels: 9
0.72 0.10 0.18
Matches are distributed among these distances:
26 2 0.06
27 2 0.06
30 26 0.72
31 4 0.11
32 2 0.06
ACGTcount: A:0.41, C:0.05, G:0.07, T:0.47
Consensus pattern (29 bp):
AATTTTATTATGTATACATACAAATTATT
Found at i:43198 original size:32 final size:32
Alignment explanation
Indices: 43123--43198 Score: 91
Period size: 32 Copynumber: 2.4 Consensus size: 32
43113 CTCGAGCTCG
* *
43123 AGCTTGACCCGAATCGAGTATCGAGCTATTCG
1 AGCTTGACTCGAATCGAGTATCGAGCTATTCA
* * *
43155 AG-TTCGGCTCGAATCGAGTATTGTGCTATTCA
1 AGCTT-GACTCGAATCGAGTATCGAGCTATTCA
43187 AGCTTGACTCGA
1 AGCTTGACTCGA
43199 TAAATTTGAT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
31 2 0.06
32 32 0.89
33 2 0.06
ACGTcount: A:0.24, C:0.22, G:0.25, T:0.29
Consensus pattern (32 bp):
AGCTTGACTCGAATCGAGTATCGAGCTATTCA
Found at i:46233 original size:59 final size:60
Alignment explanation
Indices: 46141--46287 Score: 215
Period size: 60 Copynumber: 2.5 Consensus size: 60
46131 TTTTGACTAA
* * *
46141 TTTGCACAAAACCCAATAGTACAGGGACCCATATGA-CCAAAATTTTGTACAGGGACTTG
1 TTTGCACAATACCTAATAGTACAGGGACCCATATGACCCAAAATTTTGTACAAGGACTTG
* * *
46200 TTTGCACAATACCTAACAGTACAAGGACCCATATGACCCGAAATTTTGTACAAGGACTTG
1 TTTGCACAATACCTAATAGTACAGGGACCCATATGACCCAAAATTTTGTACAAGGACTTG
* *
46260 TTTGCACAGTAACTAATAGTACAGGGAC
1 TTTGCACAATACCTAATAGTACAGGGAC
46288 ATGTAGGGTA
Statistics
Matches: 77, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
59 32 0.42
60 45 0.58
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.24
Consensus pattern (60 bp):
TTTGCACAATACCTAATAGTACAGGGACCCATATGACCCAAAATTTTGTACAAGGACTTG
Found at i:55599 original size:136 final size:136
Alignment explanation
Indices: 55355--55630 Score: 435
Period size: 136 Copynumber: 2.0 Consensus size: 136
55345 CAATCGGACG
* **
55355 GGTTGGACGGATTTTGGGTCATCTGTATCCAAGTCAAATGAGTCAGGTAATCTTCTCAGGTCATT
1 GGTTGGACGGATTTTGGGTCATCTGGATCCAAGTCAAATGAGTCACATAATCTTCTCAGGTCATT
* *
55420 CGGGTCTTGACTCATCTGGGTTCAAGTCATTGGATTCTCGGGTCTGTTAGATCTAGGGGCAGGCG
66 CGGGTCTTGACTCATCTGGGTTCAAGTCATTGGAGTCTCGGGTCTGCTAGATCTAGGGGCAGGCG
55485 GGTTCA
131 GGTTCA
* * *
55491 GGTTGGACGGATTTTGGGTCATCTGGGTCCAAGTCAAATGAGTCACATAATTTTCTCGGGTCATT
1 GGTTGGACGGATTTTGGGTCATCTGGATCCAAGTCAAATGAGTCACATAATCTTCTCAGGTCATT
* * * * *
55556 TGGGTCTTGGCTCATCTGGGTTCAAGTCATTGGGGTCTCGGGTCTGCTGGATCTAGGGTCAGGCG
66 CGGGTCTTGACTCATCTGGGTTCAAGTCATTGGAGTCTCGGGTCTGCTAGATCTAGGGGCAGGCG
55621 GGTTCA
131 GGTTCA
55627 GGTT
1 GGTT
55631 TTGGTCTCAG
Statistics
Matches: 127, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
136 127 1.00
ACGTcount: A:0.17, C:0.18, G:0.32, T:0.33
Consensus pattern (136 bp):
GGTTGGACGGATTTTGGGTCATCTGGATCCAAGTCAAATGAGTCACATAATCTTCTCAGGTCATT
CGGGTCTTGACTCATCTGGGTTCAAGTCATTGGAGTCTCGGGTCTGCTAGATCTAGGGGCAGGCG
GGTTCA
Found at i:55664 original size:16 final size:16
Alignment explanation
Indices: 55640--55674 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
55630 TTTGGTCTCA
55640 GGTTCTGGGTTATTCG
1 GGTTCTGGGTTATTCG
* *
55656 GGTTTTGGGTTTTTCG
1 GGTTCTGGGTTATTCG
55672 GGT
1 GGT
55675 CTAGGATCCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.03, C:0.09, G:0.40, T:0.49
Consensus pattern (16 bp):
GGTTCTGGGTTATTCG
Found at i:58934 original size:57 final size:57
Alignment explanation
Indices: 58865--58979 Score: 230
Period size: 57 Copynumber: 2.0 Consensus size: 57
58855 CTAACTAAGT
58865 AGCTTGGGTAAGCAGGGGTCAAATATCCCACAGAAAAGGATGAAATGAATATGGAAA
1 AGCTTGGGTAAGCAGGGGTCAAATATCCCACAGAAAAGGATGAAATGAATATGGAAA
58922 AGCTTGGGTAAGCAGGGGTCAAATATCCCACAGAAAAGGATGAAATGAATATGGAAA
1 AGCTTGGGTAAGCAGGGGTCAAATATCCCACAGAAAAGGATGAAATGAATATGGAAA
58979 A
1 A
58980 CAAAACACTT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 58 1.00
ACGTcount: A:0.43, C:0.12, G:0.28, T:0.17
Consensus pattern (57 bp):
AGCTTGGGTAAGCAGGGGTCAAATATCCCACAGAAAAGGATGAAATGAATATGGAAA
Found at i:62060 original size:19 final size:19
Alignment explanation
Indices: 62036--62074 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
62026 GGATGATTTT
62036 AAGGAAAAGAAAAGTATCA
1 AAGGAAAAGAAAAGTATCA
62055 AAGGAAAAGAAAAGTATCA
1 AAGGAAAAGAAAAGTATCA
62074 A
1 A
62075 TGTAAGAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.64, C:0.05, G:0.21, T:0.10
Consensus pattern (19 bp):
AAGGAAAAGAAAAGTATCA
Done.