Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013643.1 Corchorus olitorius cultivar O-4 contig13676, 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: 35525
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Found at i:4235 original size:17 final size:17
Alignment explanation
Indices: 4188--4241 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 17
4178 ATAAATAATT
4188 AAAGTTTGTACCAAAAA
1 AAAGTTTGTACCAAAAA
* *** *
4205 AAAATGAATGCCAAAAA
1 AAAGTTTGTACCAAAAA
4222 AAAGTTTGTACCAAAAA
1 AAAGTTTGTACCAAAAA
4239 AAA
1 AAA
4242 TAGTTAAGTT
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.59, C:0.11, G:0.11, T:0.19
Consensus pattern (17 bp):
AAAGTTTGTACCAAAAA
Found at i:4893 original size:5 final size:5
Alignment explanation
Indices: 4883--4908 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
4873 AAAAAAATTA
4883 TAAAT TAAAT TAAAT TAAAT TAAAT T
1 TAAAT TAAAT TAAAT TAAAT TAAAT T
4909 GTTTAAAGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
TAAAT
Found at i:6322 original size:6 final size:7
Alignment explanation
Indices: 6306--6331 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
6296 TTTTTTTCTC
6306 TTTTAAT
1 TTTTAAT
6313 TTTTAAT
1 TTTTAAT
6320 TTTTAAT
1 TTTTAAT
6327 TTTTA
1 TTTTA
6332 CTTTATTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (7 bp):
TTTTAAT
Found at i:15708 original size:12 final size:12
Alignment explanation
Indices: 15675--15709 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
15665 CTTCTGCAAG
*
15675 GTAGTAGTAGTA
1 GTAGTAATAGTA
15687 GTAGTAATAGTA
1 GTAGTAATAGTA
*
15699 GTAGTGATAGT
1 GTAGTAATAGT
15710 TTTGGCAGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.34, C:0.00, G:0.31, T:0.34
Consensus pattern (12 bp):
GTAGTAATAGTA
Found at i:30149 original size:31 final size:31
Alignment explanation
Indices: 30057--30151 Score: 156
Period size: 31 Copynumber: 3.1 Consensus size: 31
30047 AAGTGACTAA
*
30057 TTTGTCCCAAAA-AAAAACATAAGGAATTTT
1 TTTGTCCCAAAAGAAAAACATAAGGGATTTT
30087 TTTGTCCCAAAAGAAAAACATAAGGGATTTT
1 TTTGTCCCAAAAGAAAAACATAAGGGATTTT
* *
30118 TTTGTCCCAAAAGAAAAACATTAGGGTTTTT
1 TTTGTCCCAAAAGAAAAACATAAGGGATTTT
30149 TTT
1 TTT
30152 TAGTATTTAG
Statistics
Matches: 61, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
30 12 0.20
31 49 0.80
ACGTcount: A:0.40, C:0.13, G:0.14, T:0.34
Consensus pattern (31 bp):
TTTGTCCCAAAAGAAAAACATAAGGGATTTT
Found at i:30603 original size:29 final size:28
Alignment explanation
Indices: 30571--30633 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
30561 TATAAGGATA
*
30571 TTAGATTTAATTAAATAAAAATAGAGTTT
1 TTAG-TTTAATTAAACAAAAATAGAGTTT
** **
30600 TTAGTTTTTTTACCCAAAAATAGAGTTT
1 TTAGTTTAATTAAACAAAAATAGAGTTT
30628 TTAGTT
1 TTAGTT
30634 GAGTAAAACT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 25 0.86
29 4 0.14
ACGTcount: A:0.38, C:0.05, G:0.11, T:0.46
Consensus pattern (28 bp):
TTAGTTTAATTAAACAAAAATAGAGTTT
Found at i:33715 original size:20 final size:20
Alignment explanation
Indices: 33678--33716 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
33668 TACTATTATT
33678 TTTTGAATTTAATATTTTAC
1 TTTTGAATTTAATATTTTAC
*
33698 TTTT-AATTTCAATTTTTTA
1 TTTTGAATTT-AATATTTTA
33717 AATGTCAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.64
Consensus pattern (20 bp):
TTTTGAATTTAATATTTTAC
Found at i:33939 original size:22 final size:21
Alignment explanation
Indices: 33914--34101 Score: 133
Period size: 22 Copynumber: 8.5 Consensus size: 21
33904 TAATTATTAT
*
33914 AATTTCATGAGGAGGCTATCAA
1 AATTTCAT-AGGAGGTTATCAA
* * *
33936 AATTCCATAGTGTGGTTACCAA
1 AATTTCATAG-GAGGTTATCAA
* *
33958 AATTTGATATGGAAGTTATCAA
1 AATTTCATA-GGAGGTTATCAA
*
33980 AATTTCATGGGAAGGTTATCAA
1 AATTTCATAGG-AGGTTATCAA
* *
34002 AATTTCATAGTGTGGTTACCAA
1 AATTTCATAG-GAGGTTATCAA
*
34024 AATTTCATAGGATCAGGTTATTAA
1 AATTTCATAGG---AGGTTATCAA
* **
34048 AATTTCTTAGGAAGGTTATTGA
1 AATTTCATAGG-AGGTTATCAA
* * *
34070 AACTTCATAGTGTGGTTATCAC
1 AATTTCATAG-GAGGTTATCAA
*
34092 AATTTTATAG
1 AATTTCATAG
34102 AAAAGTTATC
Statistics
Matches: 129, Mismatches: 29, Indels: 16
0.74 0.17 0.09
Matches are distributed among these distances:
21 5 0.04
22 104 0.81
23 3 0.02
24 17 0.13
ACGTcount: A:0.35, C:0.11, G:0.19, T:0.36
Consensus pattern (21 bp):
AATTTCATAGGAGGTTATCAA
Found at i:34065 original size:46 final size:44
Alignment explanation
Indices: 33914--34864 Score: 159
Period size: 44 Copynumber: 22.2 Consensus size: 44
33904 TAATTATTAT
* * * * *
33914 AATTTCATGAGG-AGGCTATCAAAATTCCATAGTG-TGGTTACCAA
1 AATTTCAT-AGGAAGGTTACCAAAATTTCATAG-GAAGGTTATCAA
* * *
33958 AATTTGATATGGAA-GTTATCAAAATTTCATGGGAAGGTTATCAA
1 AATTTCATA-GGAAGGTTACCAAAATTTCATAGGAAGGTTATCAA
* *
34002 AATTTCATAGTG-TGGTTACCAAAATTTCATAGGATCAGGTTATTAA
1 AATTTCATAG-GAAGGTTACCAAAATTTCATAGGA--AGGTTATCAA
* *** * * *
34048 AATTTCTTAGGAAGGTTATTGAAACTTCATAGTG-TGGTTATCAC
1 AATTTCATAGGAAGGTTACCAAAATTTCATAG-GAAGGTTATCAA
* * * * *
34092 AATTTTATAGAAAAGTT------A--TCAAAGG--GATTATCAA
1 AATTTCATAGGAAGGTTACCAAAATTTCATAGGAAGGTTATCAA
* * *
34126 AATGTT-ATAGCG-AGGTTA-TAAGAATTTCATAGTG-TGGTTAACAA
1 AAT-TTCATAG-GAAGGTTACCAA-AATTTCATAG-GAAGGTTATCAA
* * * * * *
34170 AATTTCATAAGG-AGATTACTAATATATCATGGGGAGGTTATCAA
1 AATTTCAT-AGGAAGGTTACCAAAATTTCATAGGAAGGTTATCAA
* * * **
34214 AATTTCATAGTG-TGGTTATCAAAATTTCATATGAATATTAT-AA
1 AATTTCATAG-GAAGGTTACCAAAATTTCATAGGAAGGTTATCAA
* * *
34257 AAGTCTCAATTTCATGAGAA--CTACCAAAATTTGATA-GAAGGTTATC-A
1 AA-TTTC-A--T-A-G-GAAGGTTACCAAAATTTCATAGGAAGGTTATCAA
* * * *
34304 AATCTCATA--AAGTGATTATCGAAATTTCATAGAGATCGGATTATCAA
1 AATTTCATAGGAAG-G-TTACCAAAATTTCATAG-GA-AGG-TTATCAA
* * **
34351 AATTT-ATAGGAAGATTATCAAAATTTCATAGTG-TTGTTATCAA
1 AATTTCATAGGAAGGTTACCAAAATTTCATAG-GAAGGTTATCAA
* * * * *
34394 AATTTCAAAGCG-AGGTTATCAAAATTACATA--ATGTTATTATCAA
1 AATTTCATAG-GAAGGTTACCAAAATTTCATAGGAAG--GTTATCAA
* * * *
34438 AATTTCATA-GAGGGGTCAACAAAATTTTATA-GAGAGGTTATCAA
1 AATTTCATAGGA-AGGTTACCAAAATTTCATAGGA-AGGTTATCAA
* * * *
34482 AATTTCATA-AAGAGGTTATCAAATTTTCA-A--AATGTGATTACCAA
1 AATTTCATAGGA-AGGTTACCAAAATTTCATAGGAA-G-G-TTATCAA
* *
34526 AATTTCATA-G-TGG-T------ATTTC-TAGGGAGGTTATCAA
1 AATTTCATAGGAAGGTTACCAAAATTTCATAGGAAGGTTATCAA
* * * *
34560 AATTTCATAGTATGATTACC-AAA--T--TAGGAAGGTTATTAA
1 AATTTCATAGGAAGGTTACCAAAATTTCATAGGAAGGTTATCAA
* * * * * * *
34599 ACTTTTATTATGAA-GTAATCAAAATTTC--AGGGAGGATATCAA
1 AATTTCA-TAGGAAGGTTACCAAAATTTCATAGGAAGGTTATCAA
* * ** *
34641 AATTTCATATGAAGGTTATCAAAATTTCATAGTTTA-GTTTTCAA
1 AATTTCATAGGAAGGTTACCAAAATTTCATAG-GAAGGTTATCAA
* * * * *
34685 AATTTCATAAG-AGAGTTATCAAAATTTCATA-GTATGTAGATCAA
1 AATTTCATAGGAAG-GTTACCAAAATTTCATAGGAAGGT-TATCAA
* * * * *
34729 AATCTCATCGGGAA-ATTAACAAAATTTCATAATG-AGGTTATCAA
1 AATTTCAT-AGGAAGGTTACCAAAATTTCAT-AGGAAGGTTATCAA
** ** *
34773 AAAATCATAGGAAAATTATCAAAATTT-AT----A-GTTATCAA
1 AATTTCATAGGAAGGTTACCAAAATTTCATAGGAAGGTTATCAA
* * * *
34811 GATTTCATAAGG-AGGTTATCAAAATTTTATAGGGAGGTTTATCAA
1 AATTTCAT-AGGAAGGTTACCAAAATTTCATAGGAAGG-TTATCAA
34856 AATTTCATA
1 AATTTCATA
34865 ACGAGGTTAT
Statistics
Matches: 678, Mismatches: 136, Indels: 186
0.68 0.14 0.19
Matches are distributed among these distances:
34 33 0.05
35 9 0.01
36 8 0.01
37 2 0.00
38 29 0.04
39 27 0.04
40 8 0.01
41 8 0.01
42 57 0.08
43 39 0.06
44 324 0.48
45 33 0.05
46 65 0.10
47 17 0.03
48 17 0.03
49 2 0.00
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (44 bp):
AATTTCATAGGAAGGTTACCAAAATTTCATAGGAAGGTTATCAA
Found at i:34077 original size:68 final size:65
Alignment explanation
Indices: 33879--34114 Score: 224
Period size: 66 Copynumber: 3.5 Consensus size: 65
33869 TCTTGTCTCT
* * * * * * *
33879 GTGTGGTTATCAAGATTTCATAAGATAATTATTATAATTTCATGAGG-AGGCTATCAAAA-TTCC
1 GTGTGGTTACCAAAATTTCATAGGA-AGTTATCAAAATTTCAT-AGGAAGGTTATCAAAACTT-C
33942 ATA
63 ATA
* * *
33945 GTGTGGTTACCAAAATTTGATATGGAAGTTATCAAAATTTCATGGGAAGGTTATCAAAATTTCAT
1 GTGTGGTTACCAAAATTTCATA-GGAAGTTATCAAAATTTCATAGGAAGGTTATCAAAACTTCAT
34010 A
65 A
* * **
34011 GTGTGGTTACCAAAATTTCATAGGATCAGGTTATTAAAATTTCTTAGGAAGGTTATTGAAACTTC
1 GTGTGGTTACCAAAATTTCATAGGA--A-GTTATCAAAATTTCATAGGAAGGTTATCAAAACTTC
34076 ATA
63 ATA
* * * *
34079 GTGTGGTTATCACAATTTTATAGAAAAGTTATCAAA
1 GTGTGGTTACCAAAATTTCATAG-GAAGTTATCAAA
34115 GGGATTATCA
Statistics
Matches: 142, Mismatches: 21, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
65 5 0.04
66 77 0.54
67 6 0.04
68 53 0.37
69 1 0.01
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.36
Consensus pattern (65 bp):
GTGTGGTTACCAAAATTTCATAGGAAGTTATCAAAATTTCATAGGAAGGTTATCAAAACTTCATA
Found at i:34157 original size:22 final size:21
Alignment explanation
Indices: 34119--34507 Score: 85
Period size: 22 Copynumber: 17.5 Consensus size: 21
34109 ATCAAAGGGA
*
34119 TTATCAAAATGTT-ATAGCGAGG
1 TTAT-AAAAT-TTCATAGTGAGG
*
34141 TTATAAGAATTTCATAGTGTGG
1 TTATAA-AATTTCATAGTGAGG
* *
34163 TTAACAAAATTTCATAAG-GAGA
1 TT-ATAAAATTTCAT-AGTGAGG
* * * *
34185 TTACTAATATATCATGGGGAGG
1 TTA-TAAAATTTCATAGTGAGG
*
34207 TTATCAAAATTTCATAGTGTGG
1 TTAT-AAAATTTCATAGTGAGG
**
34229 TTATCAAAATTTCATA-TGAATA
1 TTAT-AAAATTTCATAGTG-AGG
* *
34251 TTATAAAAGTCTCAATTTCA-TGAGAA
1 TTATAAAA-TTTC-A--T-AGTGAG-G
* * * *
34277 CTACCAAAATTTGATAG-AAGG
1 TTA-TAAAATTTCATAGTGAGG
* *
34298 TTATCAAATCTCATAAAGTGA--
1 TTATAAAATTTCAT--AGTGAGG
* *
34319 TTATCGAAATTTCATAGAGATCGG
1 TTAT-AAAATTTCATAGTGA--GG
*
34343 ATTATCAAAATTT-ATAG-GAAGA
1 -TTAT-AAAATTTCATAGTG-AGG
**
34365 TTATCAAAATTTCATAGTGTTG
1 TTAT-AAAATTTCATAGTGAGG
* *
34387 TTATCAAAATTTCAAAGCGAGG
1 TTAT-AAAATTTCATAGTGAGG
* * ***
34409 TTATCAAAATTACATAATGTTA
1 TTAT-AAAATTTCATAGTGAGG
* *
34431 TTATCAAAATTTCATAGAGGGG
1 TTAT-AAAATTTCATAGTGAGG
* * * *
34453 TCAACAAAATTTTATAGAGAGG
1 T-TATAAAATTTCATAGTGAGG
**
34475 TTATCAAAATTTCATAAAGAGG
1 TTAT-AAAATTTCATAGTGAGG
*
34497 TTATCAAATTT
1 TTATAAAATTT
34508 TCAAAATGTG
Statistics
Matches: 271, Mismatches: 66, Indels: 61
0.68 0.17 0.15
Matches are distributed among these distances:
20 11 0.04
21 38 0.14
22 180 0.66
23 11 0.04
24 5 0.02
25 14 0.05
26 8 0.03
27 4 0.01
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (21 bp):
TTATAAAATTTCATAGTGAGG
Found at i:34509 original size:22 final size:22
Alignment explanation
Indices: 34281--34534 Score: 153
Period size: 22 Copynumber: 11.5 Consensus size: 22
34271 TGAGAACTAC
* *
34281 CAAAATTTGATAGA-AGGTTAT
1 CAAAATTTCATAAAGAGGTTAT
* * *
34302 C-AAATCTCATAAAGTGATTAT
1 CAAAATTTCATAAAGAGGTTAT
* *
34323 CGAAATTTCATAGAGATCGGATTAT
1 CAAAATTTCATAAAGA--GG-TTAT
34348 CAAAATTT-ATAGGAAGA--TTAT
1 CAAAATTTCATA--AAGAGGTTAT
** **
34369 CAAAATTTCATAGTGTTGTTAT
1 CAAAATTTCATAAAGAGGTTAT
*
34391 CAAAATTTCA-AAGCGAGGTTAT
1 CAAAATTTCATAA-AGAGGTTAT
* * ***
34413 CAAAATTACATAATGTTATTAT
1 CAAAATTTCATAAAGAGGTTAT
* * * *
34435 CAAAATTTCATAGAGGGGTCAA
1 CAAAATTTCATAAAGAGGTTAT
* *
34457 CAAAATTTTATAGAGAGGTTAT
1 CAAAATTTCATAAAGAGGTTAT
34479 CAAAATTTCATAAAGAGGTTAT
1 CAAAATTTCATAAAGAGGTTAT
* * * *
34501 CAAATTTTCA-AAATGTGATTAC
1 CAAAATTTCATAAA-GAGGTTAT
34523 CAAAATTTCATA
1 CAAAATTTCATA
34535 GTGGTATTTC
Statistics
Matches: 177, Mismatches: 42, Indels: 26
0.72 0.17 0.11
Matches are distributed among these distances:
20 10 0.06
21 23 0.13
22 123 0.69
23 3 0.02
24 4 0.02
25 11 0.06
26 3 0.02
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.34
Consensus pattern (22 bp):
CAAAATTTCATAAAGAGGTTAT
Found at i:34527 original size:66 final size:66
Alignment explanation
Indices: 34112--34904 Score: 250
Period size: 66 Copynumber: 12.3 Consensus size: 66
34102 AAAAGTTATC
* * ** * *
34112 AAAGGGATTATCAAAATGTT-ATAGCGAGGTTAT-AAGAATTTCATAGTGTGGTTAACAAAATTT
1 AAAGTGATTATCAAAAT-TTCATAGAGAGGTTATCAA-AATTTCATAAAGAGGTTATCAAAATTT
34175 CAT
64 CAT
* * * * * * ** *
34178 AAGGAGATTA-CTAATATATCATGGGGAGGTTATCAAAATTTCATAGTGTGGTTATCAAAATTTC
1 AAAGTGATTATC-AAAATTTCATAGAGAGGTTATCAAAATTTCATAAAGAGGTTATCAAAATTTC
34242 AT
65 AT
* ** * * *
34244 ATGAA-T-ATTAT-AAAAGTCTCAATTTCATGAGA-ACTACCAAAATTTGATAGA-AGGTTATC-
1 A--AAGTGATTATCAAAA-TTTC-A--T-A-GAGAGGTTATCAAAATTTCATAAAGAGGTTATCA
*
34303 AAATCTCAT
58 AAATTTCAT
*
34312 AAAGTGATTATCGAAATTTCATAGAGATCGGATTATCAAAATTT-ATAGGAAGA--TTATCAAAA
1 AAAGTGATTATCAAAATTTCATAGAGA--GG-TTATCAAAATTTCATA--AAGAGGTTATCAAAA
34374 TTTCAT
61 TTTCAT
** * * * * ***
34380 AGTGTTG-TTATCAAAATTTCAAAGCGAGGTTATCAAAATTACATAATGTTATTATCAAAATTTC
1 AAAG-TGATTATCAAAATTTCATAGAGAGGTTATCAAAATTTCATAAAGAGGTTATCAAAATTTC
34444 AT
65 AT
* * * * * * *
34446 AGAGGGGTCAACAAAATTTTATAGAGAGGTTATCAAAATTTCATAAAGAGGTTATCAAATTTTCA
1 AAAGTGATTATCAAAATTTCATAGAGAGGTTATCAAAATTTCATAAAGAGGTTATCAAAATTTCA
34511 -
66 T
* * **
34511 AAATGTGATTACCAAAATTTCAT--AGTGG---T----ATTTC-TAGGGAGGTTATCAAAATTTC
1 AAA-GTGATTATCAAAATTTCATAGAGAGGTTATCAAAATTTCATAAAGAGGTTATCAAAATTTC
34566 AT
65 AT
* * * * * * * * * *
34568 AGTA-TGATTA-CCAAA-TT-A-GGA-AGGTTATTAAACTTTTATTATGAAGTAATCAAAATTTC
1 A-AAGTGATTATCAAAATTTCATAGAGAGGTTATCAAAATTTCATAAAGAGGTTATCAAAATTTC
*
34627 AG
65 AT
** *** *
34629 GGAG-GA-TATCAAAATTTCATATGA-AGGTTATCAAAATTTCATAGTTTA-GTTTTCAAAATTT
1 AAAGTGATTATCAAAATTTCATA-GAGAGGTTATCAAAATTTCATA-AAGAGGTTATCAAAATTT
34690 CAT
64 CAT
* * * * * *** ** *
34693 -AAGAGAGTTATCAAAATTTCATAG-TATGTAGATCAAAATCTCATCGGGAAATTAACAAAATTT
1 AAAGTGA-TTATCAAAATTTCATAGAGAGGT-TATCAAAATTTCATAAAGAGGTTATCAAAATTT
34756 CAT
64 CAT
* * * ** ** *
34759 AATGAGGTTATCAAAAAATCATAG-GAAAATTATCAAAATTT-AT----A-GTTATCAAGATTTC
1 AAAGTGATTATCAAAATTTCATAGAG-AGGTTATCAAAATTTCATAAAGAGGTTATCAAAATTTC
34817 AT
65 AT
* * * * * * * * *
34819 AAGGAGGTTATCAAAATTTTATAGGGAGGTTTATCAAAATTTCATAACGAGGTTATTACAATTTT
1 AAAGTGATTATCAAAATTTCATAGAGAGG-TTATCAAAATTTCATAAAGAGGTTATCAAAATTTC
34884 AT
65 AT
**
34886 AGTGTGATTATCAAAATTT
1 AAAGTGATTATCAAAATTT
34905 TCAGAGTGTG
Statistics
Matches: 544, Mismatches: 119, Indels: 127
0.69 0.15 0.16
Matches are distributed among these distances:
53 3 0.01
54 3 0.01
55 4 0.01
56 26 0.05
57 6 0.01
58 1 0.00
59 2 0.00
60 44 0.08
61 34 0.06
62 3 0.01
63 6 0.01
64 39 0.07
65 29 0.05
66 214 0.39
67 53 0.10
68 46 0.08
69 14 0.03
70 14 0.03
71 3 0.01
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.35
Consensus pattern (66 bp):
AAAGTGATTATCAAAATTTCATAGAGAGGTTATCAAAATTTCATAAAGAGGTTATCAAAATTTCA
T
Found at i:34663 original size:22 final size:22
Alignment explanation
Indices: 34587--35191 Score: 132
Period size: 22 Copynumber: 27.8 Consensus size: 22
34577 ACCAAATTAG
* * *
34587 GAAGGTTATTAAACTTTTATTAT
1 GAAGGTTATCAAAATTTCA-TAT
* *
34610 GAA-GTAATCAAAATTTC--AG
1 GAAGGTTATCAAAATTTCATAT
* *
34629 GGAGGATATCAAAATTTCATAT
1 GAAGGTTATCAAAATTTCATAT
34651 GAAGGTTATCAAAATTTCATAGT
1 GAAGGTTATCAAAATTTCATA-T
** * *
34674 TTA-GTTTTCAAAATTTCATAA
1 GAAGGTTATCAAAATTTCATAT
34695 G-AGAGTTATCAAAATTTCATA-
1 GAAG-GTTATCAAAATTTCATAT
* * * * **
34716 GTATGTAGATCAAAATCTCATCGG
1 GAAGGT-TATCAAAATTTCAT-AT
* *
34740 GAA-ATTAACAAAATTTCATAAT
1 GAAGGTTATCAAAATTTCAT-AT
** *
34762 G-AGGTTATCAAAAAATCATAG
1 GAAGGTTATCAAAATTTCATAT
**
34783 GAAAATTATCAAAA-TT--TAT
1 GAAGGTTATCAAAATTTCATAT
* *
34802 --A-GTTATCAAGATTTCATAA
1 GAAGGTTATCAAAATTTCATAT
* * *
34821 GGAGGTTATCAAAATTTTATAG
1 GAAGGTTATCAAAATTTCATAT
* *
34843 GGAGGTTTATCAAAATTTCATAAC
1 GAAGG-TTATCAAAATTTCAT-AT
* * *
34867 G-AGGTTATTACAATTTTATAGT
1 GAAGGTTATCAAAATTTCATA-T
* * *
34889 G-TGATTATCAAAATTTTCAGAGT
1 GAAGGTTATCAAAA-TTTCATA-T
* *
34912 G-TGATTA-CTAACAA-TTCATAT
1 GAAGGTTATC-AA-AATTTCATAT
* * * *
34933 GGAGGCTT-TTAAATTTTCATAAC
1 GAAGG-TTATCAAAATTTCAT-AT
* * *
34956 G-TGGTTATCAATATATCATAT
1 GAAGGTTATCAAAATTTCATAT
* * *
34977 GGAGGTTATCAACATCTCATAGT
1 GAAGGTTATCAAAATTTCATA-T
**
35000 GTTGGTTATCAAAATTTCAT-T
1 GAAGGTTATCAAAATTTCATAT
*
35021 GGGAA-GTTATCAAAATTTCACAGT
1 --GAAGGTTATCAAAATTTCATA-T
* * *
35045 G-AGGTCT-TCAAAATTCCTTAG
1 GAAGGT-TATCAAAATTTCATAT
* * * *
35066 GCAGCTTAACAAAATTTCATAA
1 GAAGGTTATCAAAATTTCATAT
* * * *
35088 GAAGGTTA-AAAAAATTAATAA
1 GAAGGTTATCAAAATTTCATAT
* * * *
35109 AAAGGTTCTCGAAA-TTC-TGT
1 GAAGGTTATCAAAATTTCATAT
** * * *
35129 AGTATCGTTATTAAAATTTCGTAG
1 -G-AAGGTTATCAAAATTTCATAT
* *
35153 GAATGTTATCAAAATTTCATAG
1 GAAGGTTATCAAAATTTCATAT
* *
35175 GGAGATTATCAAAATTT
1 GAAGGTTATCAAAATTT
35192 TATAAGGAGG
Statistics
Matches: 423, Mismatches: 114, Indels: 91
0.67 0.18 0.14
Matches are distributed among these distances:
16 8 0.02
17 3 0.01
19 7 0.02
20 14 0.03
21 38 0.09
22 279 0.66
23 66 0.16
24 8 0.02
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (22 bp):
GAAGGTTATCAAAATTTCATAT
Found at i:34907 original size:45 final size:45
Alignment explanation
Indices: 34804--34904 Score: 132
Period size: 45 Copynumber: 2.3 Consensus size: 45
34794 AAATTTATAG
* * *
34804 TTATCAAGATTTCATAAGGAGGTTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTCATAACGAGGTTATCAAAATTTTATAGGGAGGA
* * * *
34849 TTATCAAAATTTCATAACGAGGTTATTACAATTTTATAGTG-TGA
1 TTATCAAAATTTCATAACGAGGTTATCAAAATTTTATAGGGAGGA
34893 TTATCAAAATTT
1 TTATCAAAATTT
34905 TCAGAGTGTG
Statistics
Matches: 49, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
44 13 0.27
45 36 0.73
ACGTcount: A:0.37, C:0.08, G:0.16, T:0.40
Consensus pattern (45 bp):
TTATCAAAATTTCATAACGAGGTTATCAAAATTTTATAGGGAGGA
Found at i:35200 original size:22 final size:22
Alignment explanation
Indices: 35158--35200 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
35148 CGTAGGAATG
*
35158 TTATCAAAATTTCATAGGGAGA
1 TTATCAAAATTTCATAAGGAGA
*
35180 TTATCAAAATTTTATAAGGAG
1 TTATCAAAATTTCATAAGGAG
35201 GTCATAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.42, C:0.07, G:0.16, T:0.35
Consensus pattern (22 bp):
TTATCAAAATTTCATAAGGAGA
Done.