Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018031.1 Corchorus olitorius cultivar O-4 contig18064, 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: 48365
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:4546 original size:19 final size:19
Alignment explanation
Indices: 4504--4547 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
4494 GTTATTAGTT
*
4504 AAGAGAGTGAGTATGAAGA
1 AAGAGAGTGAGTAGGAAGA
* * *
4523 GAGAGAGTGAGTGGGGAGA
1 AAGAGAGTGAGTAGGAAGA
4542 AAGAGA
1 AAGAGA
4548 ATAGGGGCAA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.43, C:0.00, G:0.45, T:0.11
Consensus pattern (19 bp):
AAGAGAGTGAGTAGGAAGA
Found at i:5364 original size:24 final size:24
Alignment explanation
Indices: 5336--5396 Score: 122
Period size: 24 Copynumber: 2.5 Consensus size: 24
5326 TTTTAACCAA
5336 TTTATGTTGATTGTTTGTGGATTT
1 TTTATGTTGATTGTTTGTGGATTT
5360 TTTATGTTGATTGTTTGTGGATTT
1 TTTATGTTGATTGTTTGTGGATTT
5384 TTTATGTTGATTG
1 TTTATGTTGATTG
5397 CTTGAGTTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.13, C:0.00, G:0.25, T:0.62
Consensus pattern (24 bp):
TTTATGTTGATTGTTTGTGGATTT
Found at i:5429 original size:24 final size:26
Alignment explanation
Indices: 5336--5430 Score: 96
Period size: 24 Copynumber: 3.7 Consensus size: 26
5326 TTTTAACCAA
5336 TTTATGTTGA--TTGTTTGTGGATTT
1 TTTATGTTGATTTTGTTTGTGGATTT
5360 TTTATGTTGA--TTGTTTGTGGATTT
1 TTTATGTTGATTTTGTTTGTGGATTT
5384 TTTATGTTGATTGCTTGAGTTT-T-G-TTGT
1 TTTATGTTGATT--TT--GTTTGTGGATT-T
5412 TTTATGTTGATTTTGTTTG
1 TTTATGTTGATTTTGTTTG
5431 GTTTTGATGG
Statistics
Matches: 63, Mismatches: 0, Indels: 15
0.81 0.00 0.19
Matches are distributed among these distances:
24 38 0.60
26 2 0.03
27 2 0.03
28 16 0.25
29 1 0.02
30 4 0.06
ACGTcount: A:0.12, C:0.01, G:0.24, T:0.63
Consensus pattern (26 bp):
TTTATGTTGATTTTGTTTGTGGATTT
Found at i:19674 original size:47 final size:48
Alignment explanation
Indices: 19618--19754 Score: 135
Period size: 43 Copynumber: 3.0 Consensus size: 48
19608 AGGGAAATTA
* *
19618 AGTAAAAGCAGTCAATAATTAGTTTAATTCTGGGTAATTAAACTAAAG
1 AGTAAGAGCAGTCAATAATTAGTTTAATTCTGGGTAATTAAACTAAAT
*
19666 GGTAA-AGCAG---A-AATTAGTTTAATTCTGGGTAATTAAACTAAAT
1 AGTAAGAGCAGTCAATAATTAGTTTAATTCTGGGTAATTAAACTAAAT
* * * * * *
19709 AGAAAAAGAAG--AAGAGGTCAGTTTAATTCTGGGTAATTAAACTAAA
1 AGTAAGAGCAGTCAATA-ATTAGTTTAATTCTGGGTAATTAAACTAAA
19755 AAAGAGTAAA
Statistics
Matches: 78, Mismatches: 7, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
43 34 0.44
44 5 0.06
45 1 0.01
46 1 0.01
47 33 0.42
48 4 0.05
ACGTcount: A:0.45, C:0.07, G:0.19, T:0.29
Consensus pattern (48 bp):
AGTAAGAGCAGTCAATAATTAGTTTAATTCTGGGTAATTAAACTAAAT
Found at i:19687 original size:43 final size:44
Alignment explanation
Indices: 19634--20170 Score: 253
Period size: 47 Copynumber: 11.0 Consensus size: 44
19624 AGCAGTCAAT
* ** *
19634 AATTAGTTTAATTCTGGGTAATTAAACTAAA-GGGTAAAGCAGA
1 AATTAGTTTAATTCTGGGTAATTAAACTAAATAGAAAAAGAAGA
19677 AATTAGTTTAATTCTGGGTAATTAAACTAAATAGAAAAAGAAGA
1 AATTAGTTTAATTCTGGGTAATTAAACTAAATAGAAAAAGAAGA
* *
19721 AGAGGTCAGTTTAATTCTGGGTAATTAAACTAAAAAAGAGTAAAAGAAGAAGTAAAGCA
1 A-A--TTAGTTTAATTCTGGGTAATTAAACT----AA-A-T---AGAAAAAG--AAG-A
* * *
19780 GAAGTTAGTTTAATTCTGGGCAATTAAACTAAATAGTAAGAGAAGA
1 -AA-TTAGTTTAATTCTGGGTAATTAAACTAAATAGAAAAAGAAGA
* * *** *
19826 AGTAAAAATAATTCTGGGTAATTAAACTAAATAGTAAAAGCAGGAGTAAACAGT
1 AATTAGTTTAATTCTGGGTAATTAAACTAAATAG--AAA--A--AG---A-AGA
*
19880 AATTAGTTTAATTCTGGGTAATTAAACTAAA-AGAAGGAGCAA-ACAGT
1 AATTAGTTTAATTCTGGGTAATTAAACTAAATAGAA--A--AAGA-AGA
*
19927 AATTAGTTTAATTCTGGGTAATTAAACTAAATAGTAAAAGTAGGAGTAAACA
1 AATTAGTTTAATTCTGGGTAATTAAACTAAATAG--AAA--A--AG--AAGA
* *
19979 TTAATTAGTTTAATTCTGGGTAATTATACTAAA-AGAAGGAGCAA-ACAGT
1 --AATTAGTTTAATTCTGGGTAATTAAACTAAATAGAA--A--AAGA-AGA
*
20028 AATTAGTTTAATTCTGGGTAATTAAACTAAATAGTAAAAGTAGGAGTAAACA
1 AATTAGTTTAATTCTGGGTAATTAAACTAAATAG--AAA--A--AG--AAGA
* *
20080 TTAATTAGTTTAATTCTGGGTAATTATACTAAA-AGAAGGAGCAA-ACAGT
1 --AATTAGTTTAATTCTGGGTAATTAAACTAAATAGAA--A--AAGA-AGA
20129 AATTAGTTTAATTCTGGGTAATTAAACTAAATA-ATAAAAGAA
1 AATTAGTTTAATTCTGGGTAATTAAACTAAATAGA-AAAAGAA
20171 AGAGTAAGCA
Statistics
Matches: 395, Mismatches: 41, Indels: 115
0.72 0.07 0.21
Matches are distributed among these distances:
43 31 0.08
44 39 0.10
45 3 0.01
46 4 0.01
47 125 0.32
48 14 0.04
49 7 0.02
50 8 0.02
51 11 0.03
52 4 0.01
53 21 0.05
54 90 0.23
56 7 0.02
58 28 0.07
59 2 0.01
60 1 0.00
ACGTcount: A:0.46, C:0.07, G:0.18, T:0.29
Consensus pattern (44 bp):
AATTAGTTTAATTCTGGGTAATTAAACTAAATAGAAAAAGAAGA
Found at i:19874 original size:44 final size:44
Alignment explanation
Indices: 19790--19875 Score: 136
Period size: 44 Copynumber: 2.0 Consensus size: 44
19780 GAAGTTAGTT
*
19790 TAATTCTGGGCAATTAAACTAAATAGTAAGAGAAGAAGTAAAAA
1 TAATTCTGGGCAATTAAACTAAATAGTAAAAGAAGAAGTAAAAA
* * *
19834 TAATTCTGGGTAATTAAACTAAATAGTAAAAGCAGGAGTAAA
1 TAATTCTGGGCAATTAAACTAAATAGTAAAAGAAGAAGTAAA
19876 CAGTAATTAG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.50, C:0.07, G:0.19, T:0.24
Consensus pattern (44 bp):
TAATTCTGGGCAATTAAACTAAATAGTAAAAGAAGAAGTAAAAA
Found at i:19892 original size:54 final size:53
Alignment explanation
Indices: 19834--20283 Score: 542
Period size: 54 Copynumber: 8.8 Consensus size: 53
19824 GAAGTAAAAA
19834 TAATTCTGGGTAATTAAACTAAATAGTAAAAGCAGGAGTAAACAGTAATTAGTT
1 TAATTCTGGGTAATTAAACTAAATAGTAAAAG-AGGAGTAAACAGTAATTAGTT
*
19888 TAATTCTGGGTAATTAAACTAAA-AG----A-AGGAGCAAACAGTAATTAGTT
1 TAATTCTGGGTAATTAAACTAAATAGTAAAAGAGGAGTAAACAGTAATTAGTT
*
19935 TAATTCTGGGTAATTAAACTAAATAGTAAAAGTAGGAGTAAACATTAATTAGTT
1 TAATTCTGGGTAATTAAACTAAATAGTAAAAG-AGGAGTAAACAGTAATTAGTT
* *
19989 TAATTCTGGGTAATTATACTAAA-AG----A-AGGAGCAAACAGTAATTAGTT
1 TAATTCTGGGTAATTAAACTAAATAGTAAAAGAGGAGTAAACAGTAATTAGTT
*
20036 TAATTCTGGGTAATTAAACTAAATAGTAAAAGTAGGAGTAAACATTAATTAGTT
1 TAATTCTGGGTAATTAAACTAAATAGTAAAAG-AGGAGTAAACAGTAATTAGTT
* *
20090 TAATTCTGGGTAATTATACTAAA-AG----A-AGGAGCAAACAGTAATTAGTT
1 TAATTCTGGGTAATTAAACTAAATAGTAAAAGAGGAGTAAACAGTAATTAGTT
* * * *
20137 TAATTCTGGGTAATTAAACTAAATAATAAAAGAAAGAGTAAGCAGTAATGAGTT
1 TAATTCTGGGTAATTAAACTAAATAGTAAAAG-AGGAGTAAACAGTAATTAGTT
* * * *
20191 TAATTCTGGGTAATTAAGCTAAAAAGTAAAAGAAAGAGTAAGCAGTAATTAGTT
1 TAATTCTGGGTAATTAAACTAAATAGTAAAAG-AGGAGTAAACAGTAATTAGTT
* * * * *
20245 TAGTTCAGAGTAATTAAACTAAAAAGTAAAA-AGCAGTAA
1 TAATTCTGGGTAATTAAACTAAATAGTAAAAGAGGAGTAA
20284 TAAGTAAAAT
Statistics
Matches: 347, Mismatches: 28, Indels: 44
0.83 0.07 0.11
Matches are distributed among these distances:
47 125 0.36
48 5 0.01
49 3 0.01
52 9 0.03
53 6 0.02
54 199 0.57
ACGTcount: A:0.46, C:0.07, G:0.18, T:0.29
Consensus pattern (53 bp):
TAATTCTGGGTAATTAAACTAAATAGTAAAAGAGGAGTAAACAGTAATTAGTT
Found at i:19972 original size:101 final size:101
Alignment explanation
Indices: 19663--20275 Score: 726
Period size: 101 Copynumber: 6.0 Consensus size: 101
19653 AATTAAACTA
* **
19663 AAGG-GTAAAGCAGAAATTAGTTTAATTCTGGGTAATTAAACTAAATAGAAAAAG-AAGA-AG-A
1 AAGGAGTAAA-CAGTAATTAGTTTAATTCTGGGTAATTAAACTAAA-AGAAGGAGCAA-ACAGTA
* * *
19724 GGTCAGTTTAATTCTGGGTAATTAAACTAAAAAAGAGTAAAAG
63 -ATTAGTTTAATTCTGGGTAATTAAACT---AAATAGTAAAAG
* *
19767 AAGAAGTAAAGCAG-AAGTTAGTTTAATTCTGGGCAATTAAACTAAATAGTAA-GAG-AAGA-AG
1 AAGGAGTAAA-CAGTAA-TTAGTTTAATTCTGGGTAATTAAACTAAA-AG-AAGGAGCAA-ACAG
**
19828 TAA--A-AATAATTCTGGGTAATTAAACTAAATAGTAAAAG
61 TAATTAGTTTAATTCTGGGTAATTAAACTAAATAGTAAAAG
*
19866 CAGGAGTAAACAGTAATTAGTTTAATTCTGGGTAATTAAACTAAAAGAAGGAGCAAACAGTAATT
1 AAGGAGTAAACAGTAATTAGTTTAATTCTGGGTAATTAAACTAAAAGAAGGAGCAAACAGTAATT
19931 AGTTTAATTCTGGGTAATTAAACTAAATAGTAAAAG
66 AGTTTAATTCTGGGTAATTAAACTAAATAGTAAAAG
* * *
19967 TAGGAGTAAACATTAATTAGTTTAATTCTGGGTAATTATACTAAAAGAAGGAGCAAACAGTAATT
1 AAGGAGTAAACAGTAATTAGTTTAATTCTGGGTAATTAAACTAAAAGAAGGAGCAAACAGTAATT
20032 AGTTTAATTCTGGGTAATTAAACTAAATAGTAAAAG
66 AGTTTAATTCTGGGTAATTAAACTAAATAGTAAAAG
* * *
20068 TAGGAGTAAACATTAATTAGTTTAATTCTGGGTAATTATACTAAAAGAAGGAGCAAACAGTAATT
1 AAGGAGTAAACAGTAATTAGTTTAATTCTGGGTAATTAAACTAAAAGAAGGAGCAAACAGTAATT
*
20133 AGTTTAATTCTGGGTAATTAAACTAAATAATAAAAG
66 AGTTTAATTCTGGGTAATTAAACTAAATAGTAAAAG
* * * * * *
20169 AAAGAGTAAGCAGTAATGAGTTTAATTCTGGGTAATTAAGCTAAAAAGTAAAAGAAAGAGTAAGC
1 AAGGAGTAAACAGTAATTAGTTTAATTCTGGGTAATTAAACT-AAAAG---AAG---GAGCAAAC
* * * *
20234 AGTAATTAGTTTAGTTCAGAGTAATTAAACTAAAAAGTAAAA
59 AGTAATTAGTTTAATTCTGGGTAATTAAACTAAATAGTAAAA
20276 AGCAGTAATA
Statistics
Matches: 461, Mismatches: 30, Indels: 32
0.88 0.06 0.06
Matches are distributed among these distances:
96 2 0.00
97 6 0.01
98 38 0.08
99 21 0.05
100 1 0.00
101 265 0.57
102 25 0.05
103 1 0.00
104 5 0.01
105 51 0.11
106 3 0.01
108 43 0.09
ACGTcount: A:0.46, C:0.07, G:0.19, T:0.28
Consensus pattern (101 bp):
AAGGAGTAAACAGTAATTAGTTTAATTCTGGGTAATTAAACTAAAAGAAGGAGCAAACAGTAATT
AGTTTAATTCTGGGTAATTAAACTAAATAGTAAAAG
Found at i:20312 original size:108 final size:107
Alignment explanation
Indices: 20109--20312 Score: 234
Period size: 108 Copynumber: 1.9 Consensus size: 107
20099 GTAATTATAC
* * *
20109 TAAAAGAAGGAGCAAACAGTAATTAGTTTAATTCTGGGTAATTAAACTAAATAATAAAAGAAAGA
1 TAAAAGAAAGAGCAAACAGTAATTAGTTTAATTCAGAGTAATTAAACTAAATAAT-AAAGAAAGA
* * * *
20174 GTAAGCAGTAATGAGTTTAATTCTGGGTAATTAAGCTAAAAAG
65 GTAAGAAGTAATGAGCTTAATTCAGAGTAATTAAGCTAAAAAG
* * *
20217 TAAAAGAAAGAGTAAGCAGTAATTAGTTTAGTTCAGAGTAATTAAACTAAA-AAGT-AA-AAAGC
1 TAAAAGAAAGAGCAAACAGTAATTAGTTTAATTCAGAGTAATTAAACTAAATAA-TAAAGAAAG-
* *
20279 AGTAATAAGTAAAATGGGCTTAATTCAGAGTAAT
64 AGTAAGAAGT--AATGAGCTTAATTCAGAGTAAT
20313 CCATAGTGAG
Statistics
Matches: 80, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
105 4 0.05
106 10 0.12
107 2 0.03
108 64 0.80
ACGTcount: A:0.48, C:0.06, G:0.19, T:0.26
Consensus pattern (107 bp):
TAAAAGAAAGAGCAAACAGTAATTAGTTTAATTCAGAGTAATTAAACTAAATAATAAAGAAAGAG
TAAGAAGTAATGAGCTTAATTCAGAGTAATTAAGCTAAAAAG
Found at i:20916 original size:2 final size:2
Alignment explanation
Indices: 20909--20934 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
20899 TGCAATACAA
20909 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
20935 TACGTTATCA
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:33445 original size:21 final size:21
Alignment explanation
Indices: 33421--33462 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
33411 CGGCAACTCA
*
33421 TCCACCAACAAAACGAGACAC
1 TCCACCAACAAAACAAGACAC
* *
33442 TCCAGCAGCAAAACAAGACAC
1 TCCACCAACAAAACAAGACAC
33463 AAGAGTTAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.48, C:0.36, G:0.12, T:0.05
Consensus pattern (21 bp):
TCCACCAACAAAACAAGACAC
Found at i:34578 original size:2 final size:2
Alignment explanation
Indices: 34571--34598 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
34561 ATTTGTTGCA
34571 AT 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 AT
34599 TACCTTATCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42014 original size:31 final size:31
Alignment explanation
Indices: 41979--42053 Score: 105
Period size: 31 Copynumber: 2.4 Consensus size: 31
41969 GCCGTCGCAT
41979 GCAATTAAGGATATAACATTATCGACTTCAA
1 GCAATTAAGGATATAACATTATCGACTTCAA
* * * * *
42010 GCAATTGAGGTTATGACGTTATCGATTTCAA
1 GCAATTAAGGATATAACATTATCGACTTCAA
42041 GCAATTAAGGATA
1 GCAATTAAGGATA
42054 ATCAAACGAG
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (31 bp):
GCAATTAAGGATATAACATTATCGACTTCAA
Found at i:43976 original size:31 final size:31
Alignment explanation
Indices: 43941--44005 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
43931 TTATTAGTGA
*
43941 GGTCAATACTATAAAACTTTCATTTTAATGG
1 GGTCAATACAATAAAACTTTCATTTTAATGG
* *
43972 GGTCAATACAATAAATCTTTCATTTTAGTGG
1 GGTCAATACAATAAAACTTTCATTTTAATGG
44003 GGT
1 GGT
44006 TAATTAGTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.38
Consensus pattern (31 bp):
GGTCAATACAATAAAACTTTCATTTTAATGG
Found at i:45022 original size:31 final size:31
Alignment explanation
Indices: 44952--45026 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 31
44942 TTTTGCTTAT
* * *
44952 CCTTAGTTGCTCGAAATCAATAACATTAAAT
1 CCTTAATTGCTTGAAATCAATAACATTAAAC
* ** *
44983 CCTCAATTGCTTGAAATCAATAATGTTATAC
1 CCTTAATTGCTTGAAATCAATAACATTAAAC
45014 CCTTAATTGCTTG
1 CCTTAATTGCTTG
45027 TATTATAACT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.33, C:0.20, G:0.11, T:0.36
Consensus pattern (31 bp):
CCTTAATTGCTTGAAATCAATAACATTAAAC
Found at i:45597 original size:26 final size:26
Alignment explanation
Indices: 45548--45597 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
45538 TGTATCATCT
* *
45548 AAACCTATCAAATAATGTGGCAAAAA
1 AAACCTATCAAATAAAGTGACAAAAA
*
45574 AAACCTATCAAATAAAGTTACAAA
1 AAACCTATCAAATAAAGTGACAAA
45598 CTTTGTAGCT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.56, C:0.16, G:0.08, T:0.20
Consensus pattern (26 bp):
AAACCTATCAAATAAAGTGACAAAAA
Done.