Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020201.1 Corchorus olitorius cultivar O-4 contig20234, 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: 33912
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--27 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
28 TAAAATAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:309 original size:37 final size:37
Alignment explanation
Indices: 255--325 Score: 106
Period size: 37 Copynumber: 1.9 Consensus size: 37
245 ATATAATTAT
** * *
255 TCATAAAGTTATGTCTATTTGGAAAGACATGTATTGA
1 TCATAAAGTTAAATCTATATGAAAAGACATGTATTGA
292 TCATAAAGTTAAATCTATATGAAAAGACATGTAT
1 TCATAAAGTTAAATCTATATGAAAAGACATGTAT
326 GTTGATCAAG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.41, C:0.08, G:0.15, T:0.35
Consensus pattern (37 bp):
TCATAAAGTTAAATCTATATGAAAAGACATGTATTGA
Found at i:2753 original size:35 final size:35
Alignment explanation
Indices: 2714--2782 Score: 138
Period size: 35 Copynumber: 2.0 Consensus size: 35
2704 TATAAAAGGT
2714 ATCTTTATGATATAATTATTCATAAAGTTATGTCA
1 ATCTTTATGATATAATTATTCATAAAGTTATGTCA
2749 ATCTTTATGATATAATTATTCATAAAGTTATGTC
1 ATCTTTATGATATAATTATTCATAAAGTTATGTC
2783 TATTTGGAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.36, C:0.09, G:0.09, T:0.46
Consensus pattern (35 bp):
ATCTTTATGATATAATTATTCATAAAGTTATGTCA
Found at i:3825 original size:40 final size:40
Alignment explanation
Indices: 3770--3847 Score: 156
Period size: 40 Copynumber: 1.9 Consensus size: 40
3760 CAACTCCTTC
3770 CTATTTTTTGTCGGCCCGCTTTTGTAACTAATAACCCAAT
1 CTATTTTTTGTCGGCCCGCTTTTGTAACTAATAACCCAAT
3810 CTATTTTTTGTCGGCCCGCTTTTGTAACTAATAACCCA
1 CTATTTTTTGTCGGCCCGCTTTTGTAACTAATAACCCA
3848 GCCTTAATAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.22, C:0.26, G:0.13, T:0.40
Consensus pattern (40 bp):
CTATTTTTTGTCGGCCCGCTTTTGTAACTAATAACCCAAT
Found at i:6572 original size:15 final size:15
Alignment explanation
Indices: 6554--6612 Score: 79
Period size: 15 Copynumber: 4.1 Consensus size: 15
6544 CTTACTTCTC
6554 ATTATTACTATTACT
1 ATTATTACTATTACT
*
6569 ATTATTTCTATTAC-
1 ATTATTACTATTACT
6583 --TATTACTATTACT
1 ATTATTACTATTACT
*
6596 ATTATTACTACTACT
1 ATTATTACTATTACT
6611 AT
1 AT
6613 ATAAAAGCAC
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
12 11 0.29
15 27 0.71
ACGTcount: A:0.32, C:0.15, G:0.00, T:0.53
Consensus pattern (15 bp):
ATTATTACTATTACT
Found at i:6574 original size:9 final size:9
Alignment explanation
Indices: 6562--6605 Score: 52
Period size: 9 Copynumber: 4.9 Consensus size: 9
6552 TCATTATTAC
6562 TATTACTAT
1 TATTACTAT
*
6571 TATTTCTAT
1 TATTACTAT
* * *
6580 TACTATTAC
1 TATTACTAT
6589 TATTACTAT
1 TATTACTAT
6598 TATTACTA
1 TATTACTA
6606 CTACTATATA
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.32, C:0.14, G:0.00, T:0.55
Consensus pattern (9 bp):
TATTACTAT
Found at i:6581 original size:21 final size:21
Alignment explanation
Indices: 6556--6612 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
6546 TACTTCTCAT
*
6556 TATTACTATTACTATTATTTC
1 TATTACTATTACTATTATTAC
* *
6577 TATTACTATTACTATTACTAT
1 TATTACTATTACTATTATTAC
*
6598 TATTACTACTACTAT
1 TATTACTATTACTAT
6613 ATAAAAGCAC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.32, C:0.16, G:0.00, T:0.53
Consensus pattern (21 bp):
TATTACTATTACTATTATTAC
Found at i:6611 original size:6 final size:6
Alignment explanation
Indices: 6556--6599 Score: 67
Period size: 6 Copynumber: 7.8 Consensus size: 6
6546 TACTTCTCAT
6556 TATTAC TATTAC TATTA- T-TT-C TATTAC TATTAC TATTAC TATTA
1 TATTAC TATTAC TATTAC TATTAC TATTAC TATTAC TATTAC TATTA
6600 TTACTACTAC
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
4 3 0.09
5 3 0.09
6 29 0.83
ACGTcount: A:0.32, C:0.14, G:0.00, T:0.55
Consensus pattern (6 bp):
TATTAC
Found at i:8873 original size:22 final size:22
Alignment explanation
Indices: 8848--9057 Score: 103
Period size: 22 Copynumber: 9.6 Consensus size: 22
8838 AAGGCTATCT
* *
8848 AAATTTAATAGTGTTGTTACCA
1 AAATTTCATAGTGTAGTTACCA
* *
8870 AAATTTCGTA-TGAAGGTTACCA
1 AAATTTCATAGTGTA-GTTACCA
* *
8892 AAACTTCATAGTGTAGTTATCA
1 AAATTTCATAGTGTAGTTACCA
* *
8914 AAATTTCACA-TAGAAGTTACCA
1 AAATTTCATAGT-GTAGTTACCA
* ** *
8936 ATATTTCATA--AAAGGTTATCA
1 AAATTTCATAGTGTA-GTTACCA
* * *
8957 AAATTTCTTAG-GGAGATTAACA
1 AAATTTCATAGTGTAG-TTACCA
** *
8979 AAATTTCATACG-AAAGTTATCA
1 AAATTTCATA-GTGTAGTTACCA
* *
9001 AAATTTTATAGTGTAGTTATCA
1 AAATTTCATAGTGTAGTTACCA
* *
9023 AAATTTCAT--TAGAAGGTTAACA
1 AAATTTCATAGT-GTA-GTTACCA
9045 AAATTTCATAGTG
1 AAATTTCATAGTG
9058 AGGAAATTTA
Statistics
Matches: 145, Mismatches: 31, Indels: 23
0.73 0.16 0.12
Matches are distributed among these distances:
20 3 0.02
21 21 0.14
22 113 0.78
23 7 0.05
24 1 0.01
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.35
Consensus pattern (22 bp):
AAATTTCATAGTGTAGTTACCA
Found at i:8983 original size:65 final size:66
Alignment explanation
Indices: 8863--8986 Score: 153
Period size: 65 Copynumber: 1.9 Consensus size: 66
8853 TAATAGTGTT
* * * *
8863 GTTACCAAAATTTCGTATGAAGGTTACCAAAACTTCATAGTGTAGTTATCAAAATTTCACATAGA
1 GTTACCAAAATTTCATATAAAGGTTACCAAAACTTCATAGTGGAGTTAACAAAATTTCACATAGA
8928 A
66 A
* * * *
8929 GTTACCAATATTTCATA-AAAGGTTATCAAAATTTCTTAG-GGAGATTAACAAAATTTCA
1 GTTACCAAAATTTCATATAAAGGTTACCAAAACTTCATAGTGGAG-TTAACAAAATTTCA
8987 TACGAAAGTT
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
64 3 0.06
65 31 0.63
66 15 0.31
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.33
Consensus pattern (66 bp):
GTTACCAAAATTTCATATAAAGGTTACCAAAACTTCATAGTGGAGTTAACAAAATTTCACATAGA
A
Found at i:9006 original size:44 final size:44
Alignment explanation
Indices: 8906--9057 Score: 138
Period size: 44 Copynumber: 3.5 Consensus size: 44
8896 TTCATAGTGT
* * * *
8906 AGTTATCAAAATTTC-ACA-TAGAAGTTACCAATATTTCATA-AA
1 AGTTATCAAAATTTCTATAGT-GGAGTTAACAAAATTTCATAGAA
8948 AGGTTATCAAAATTTCT-TAG-GGAGATTAACAAAATTTCATACGAA
1 A-GTTATCAAAATTTCTATAGTGGAG-TTAACAAAATTTCATA-GAA
* *
8993 AGTTATCAAAATTT-TATAGTGTAGTTATCAAAATTTCATTAGAA
1 AGTTATCAAAATTTCTATAGTGGAGTTAACAAAATTTCA-TAGAA
* *
9037 GGTTAACAAAATTTC-ATAGTG
1 AGTTATCAAAATTTCTATAGTG
9058 AGGAAATTTA
Statistics
Matches: 92, Mismatches: 8, Indels: 18
0.78 0.07 0.15
Matches are distributed among these distances:
42 4 0.04
43 30 0.33
44 50 0.54
45 8 0.09
ACGTcount: A:0.42, C:0.11, G:0.12, T:0.35
Consensus pattern (44 bp):
AGTTATCAAAATTTCTATAGTGGAGTTAACAAAATTTCATAGAA
Found at i:10274 original size:38 final size:38
Alignment explanation
Indices: 10223--10298 Score: 125
Period size: 38 Copynumber: 2.0 Consensus size: 38
10213 TTGACAAATG
* *
10223 ATATAATGAATGGTTTTAAATTTTTTGGTAAATATATA
1 ATATAATAAATGGTTTTAAATTTTTTGATAAATATATA
*
10261 ATATAATAAATGGTTTTAAGTTTTTTGATAAATATATA
1 ATATAATAAATGGTTTTAAATTTTTTGATAAATATATA
10299 CCTTTTTCAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (38 bp):
ATATAATAAATGGTTTTAAATTTTTTGATAAATATATA
Found at i:10931 original size:22 final size:21
Alignment explanation
Indices: 10902--11095 Score: 151
Period size: 22 Copynumber: 8.8 Consensus size: 21
10892 TGAATATTTT
*
10902 TATGAAATTTTAATAACTACC
1 TATGAAATTTTGATAACTACC
* *
10923 ATATTAAATTTTGATAACCACCC
1 -TATGAAATTTTGATAACTA-CC
*
10946 TATGAAATTTTGATAATTACC
1 TATGAAATTTTGATAACTACC
*
10967 TATGAAATTGTGATAAACT-CC
1 TATGAAATTTTGAT-AACTACC
* *
10988 ATATGAAACTTTGATAACCTAAC
1 -TATGAAATTTTGATAA-CTACC
* *
11011 TATGAAATTTTAATAAACCTTCC
1 TATGAAATTTTGAT-AA-CTACC
*
11034 TAT-AACATTTTGATAACCTAAC
1 TATGAA-ATTTTGATAA-CTACC
* *
11056 TATGAAATTTTAATAAATCTTCC
1 TATGAAATTTTGAT-AA-CTACC
11079 TAT-AACATTTTGATAAC
1 TATGAA-ATTTTGATAAC
11096 ATCCCGGTAA
Statistics
Matches: 139, Mismatches: 23, Indels: 21
0.76 0.13 0.11
Matches are distributed among these distances:
21 20 0.14
22 83 0.60
23 36 0.26
ACGTcount: A:0.40, C:0.15, G:0.07, T:0.38
Consensus pattern (21 bp):
TATGAAATTTTGATAACTACC
Found at i:11006 original size:65 final size:65
Alignment explanation
Indices: 10902--11026 Score: 164
Period size: 65 Copynumber: 1.9 Consensus size: 65
10892 TGAATATTTT
* * * * *
10902 TATGAAATTTTAATAACTACCATATTAAATTTTGATAACC-ACCCTATGAAATTTTGATAATTAC
1 TATGAAATTGTAATAACTACCATATGAAACTTTGATAACCTA-ACTATGAAATTTTAATAATTAC
10966 C
65 C
*
10967 TATGAAATTGTGATAAACT-CCATATGAAACTTTGATAACCTAACTATGAAATTTTAATAA
1 TATGAAATTGTAAT-AACTACCATATGAAACTTTGATAACCTAACTATGAAATTTTAATAA
11027 ACCTTCCTAT
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
65 47 0.90
66 5 0.10
ACGTcount: A:0.42, C:0.14, G:0.08, T:0.37
Consensus pattern (65 bp):
TATGAAATTGTAATAACTACCATATGAAACTTTGATAACCTAACTATGAAATTTTAATAATTACC
Found at i:11027 original size:44 final size:42
Alignment explanation
Indices: 10902--11095 Score: 178
Period size: 45 Copynumber: 4.4 Consensus size: 42
10892 TGAATATTTT
* * * *
10902 TATGAAATTTTAATAACTACCATATTAAATTTTGATAACCAC-CC
1 TATGAAATTTTGATAACTAAC-TATGAAATTTTAATAA--ACTCC
* * * *
10946 TATGAAATTTTGATAATTACCTATGAAATTGTGATAAACTCC
1 TATGAAATTTTGATAACTAACTATGAAATTTTAATAAACTCC
*
10988 ATATGAAACTTTGATAACCTAACTATGAAATTTTAATAAACCTTCC
1 -TATGAAATTTTGATAA-CTAACTATGAAATTTTAATAAA-C-TCC
11034 TAT-AACATTTTGATAACCTAACTATGAAATTTTAATAAATCTTCC
1 TATGAA-ATTTTGATAA-CTAACTATGAAATTTTAATAAA-C-TCC
11079 TAT-AACATTTTGATAAC
1 TATGAA-ATTTTGATAAC
11096 ATCCCGGTAA
Statistics
Matches: 133, Mismatches: 11, Indels: 12
0.85 0.07 0.08
Matches are distributed among these distances:
41 2 0.02
42 2 0.02
43 29 0.22
44 40 0.30
45 57 0.43
46 3 0.02
ACGTcount: A:0.40, C:0.15, G:0.07, T:0.38
Consensus pattern (42 bp):
TATGAAATTTTGATAACTAACTATGAAATTTTAATAAACTCC
Found at i:11057 original size:45 final size:45
Alignment explanation
Indices: 10997--11095 Score: 189
Period size: 45 Copynumber: 2.2 Consensus size: 45
10987 CATATGAAAC
10997 TTTGATAACCTAACTATGAAATTTTAATAAACCTTCCTATAACAT
1 TTTGATAACCTAACTATGAAATTTTAATAAACCTTCCTATAACAT
*
11042 TTTGATAACCTAACTATGAAATTTTAATAAATCTTCCTATAACAT
1 TTTGATAACCTAACTATGAAATTTTAATAAACCTTCCTATAACAT
11087 TTTGATAAC
1 TTTGATAAC
11096 ATCCCGGTAA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 53 1.00
ACGTcount: A:0.39, C:0.16, G:0.05, T:0.39
Consensus pattern (45 bp):
TTTGATAACCTAACTATGAAATTTTAATAAACCTTCCTATAACAT
Found at i:11668 original size:31 final size:31
Alignment explanation
Indices: 11627--11689 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
11617 TTTTGTAAAA
*
11627 CTTTTGAATCGACTATTATACCCTTATTTTT
1 CTTTTAAATCGACTATTATACCCTTATTTTT
11658 CTTTTAAATCGACTATTATACCCTTATTTTT
1 CTTTTAAATCGACTATTATACCCTTATTTTT
11689 C
1 C
11690 GAATATATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.24, C:0.21, G:0.05, T:0.51
Consensus pattern (31 bp):
CTTTTAAATCGACTATTATACCCTTATTTTT
Found at i:12167 original size:83 final size:84
Alignment explanation
Indices: 12077--12234 Score: 246
Period size: 83 Copynumber: 1.9 Consensus size: 84
12067 AGATTTTTTG
**
12077 ATCTCTTTATAACTATTTTATTTTTACCATTTTACTATTTTAATT-AAAAAAATAGATATATTAG
1 ATCTCTTTATAACTATTTTATTTTTACCATTAAACTATTTTAATTGAAAAAAATAGATATATTAG
12141 AATTTTTTAATTAAACCTA
66 AATTTTTTAATTAAACCTA
* * ** *
12160 ATCTCTTTATAACTATTTTATTTTTACTATTAAACTATTTTAATTGCAAAACTTAGATATATTAT
1 ATCTCTTTATAACTATTTTATTTTTACCATTAAACTATTTTAATTGAAAAAAATAGATATATTAG
12225 AATTTTTTAA
66 AATTTTTTAA
12235 ATATATATTT
Statistics
Matches: 67, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
83 42 0.63
84 25 0.37
ACGTcount: A:0.37, C:0.09, G:0.03, T:0.51
Consensus pattern (84 bp):
ATCTCTTTATAACTATTTTATTTTTACCATTAAACTATTTTAATTGAAAAAAATAGATATATTAG
AATTTTTTAATTAAACCTA
Found at i:15438 original size:164 final size:158
Alignment explanation
Indices: 15125--15539 Score: 507
Period size: 160 Copynumber: 2.5 Consensus size: 158
15115 TTGATCCCTT
* * * *
15125 TGGAGTGTGCTTCCAATGTAAAACTTGGAGAAGTAGAATCCATATTCCAAATCTGAAAATTGGAG
1 TGGAGTGTGCATACAATGTAAAACTTGGAGAAGCAGAATCCATATTCCAAATCTGAAAATTGGAC
*
15190 ACATTTCCAGATATTATAACATAAACAAGACATTAATTCGTATTCGTATATAATAAAAACATTGT
66 ACATTGCCAGATA-TATAACATAAACAAGAC---AA----TATTCG-ATATAATAAAAACATTGT
15255 ACAAATTGCATTAAATTGACAAGGCCTATATATTACCTTTA
122 ACAAATTGCATTAAATTGACAAGGCC----TATTACCTTTA
*
15296 TGGAGTGTGCGA-ACAATGTAAAACTTGAAGAAGCAGATTAATCCATATTAATCCAAATCTGAAA
1 TGGAGTGTGC-ATACAATGTAAAACTTGGAGAAGCAG---AATCCATA-T--TCCAAATCTGAAA
*
15360 ATTGGACACATTGCCAGATATATAACATAAACAAGAC-A-ATTC-ATAT-ATAAGAACATTGTAC
59 ATTGGACACATTGCCAGATATATAACATAAACAAGACAATATTCGATATAATAAAAACATTGTAC
*
15421 AAATTGCATTGAATTGACAAGGCCTATTACCTTTA
124 AAATTGCATTAAATTGACAAGGCCTATTACCTTTA
* *
15456 TGGAGTGTGCATCCAATGTAAAACTGGGAGAAGCAGAATCCATATTCCAAATCTGAAAATTGGAC
1 TGGAGTGTGCATACAATGTAAAACTTGGAGAAGCAGAATCCATATTCCAAATCTGAAAATTGGAC
15521 ACATATTGCCAGATATATA
66 AC--ATTGCCAGATATATA
15540 TATCTTATCT
Statistics
Matches: 223, Mismatches: 11, Indels: 35
0.83 0.04 0.13
Matches are distributed among these distances:
154 22 0.10
156 16 0.07
157 8 0.04
159 1 0.00
160 42 0.19
164 37 0.17
165 4 0.02
167 4 0.02
171 31 0.14
172 1 0.00
174 8 0.04
175 1 0.00
176 17 0.08
177 31 0.14
ACGTcount: A:0.40, C:0.15, G:0.16, T:0.29
Consensus pattern (158 bp):
TGGAGTGTGCATACAATGTAAAACTTGGAGAAGCAGAATCCATATTCCAAATCTGAAAATTGGAC
ACATTGCCAGATATATAACATAAACAAGACAATATTCGATATAATAAAAACATTGTACAAATTGC
ATTAAATTGACAAGGCCTATTACCTTTA
Found at i:15778 original size:17 final size:19
Alignment explanation
Indices: 15756--15790 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
15746 TTTGAAATAT
15756 TTTATTT-A-TAATTTATA
1 TTTATTTAATTAATTTATA
15773 TTTATTTAATTAATTTAT
1 TTTATTTAATTAATTTAT
15791 CTGTGGCTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 1 0.06
19 8 0.50
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (19 bp):
TTTATTTAATTAATTTATA
Found at i:18214 original size:22 final size:21
Alignment explanation
Indices: 18188--18333 Score: 82
Period size: 22 Copynumber: 6.6 Consensus size: 21
18178 ACAATCAAAC
18188 CAAAATTATATAGGAAGGTTAT
1 CAAAATT-TATAGGAAGGTTAT
*
18210 CAAAATTTCATA-CAGAGGTTA-
1 CAAAATTT-ATAGGA-AGGTTAT
* *
18231 CTAAAATTTCATAGGGAGGTTAA
1 C-AAAATTT-ATAGGAAGGTTAT
*
18254 CAAAATTTTATATGAAGGTTAT
1 CAAAA-TTTATAGGAAGGTTAT
* * * *
18276 CGAAATTTTATATTG-TGGTTGT
1 C-AAAATTTATA-GGAAGGTTAT
* * *
18298 CAAAATTTCATAAGAATGTTAA
1 CAAAATTT-ATAGGAAGGTTAT
18320 CAAAATTTCATAGG
1 CAAAATTT-ATAGG
18334 GACTGAAGTT
Statistics
Matches: 98, Mismatches: 16, Indels: 20
0.73 0.12 0.15
Matches are distributed among these distances:
21 10 0.10
22 79 0.81
23 9 0.09
ACGTcount: A:0.40, C:0.08, G:0.16, T:0.35
Consensus pattern (21 bp):
CAAAATTTATAGGAAGGTTAT
Found at i:18271 original size:66 final size:66
Alignment explanation
Indices: 18188--18333 Score: 168
Period size: 66 Copynumber: 2.2 Consensus size: 66
18178 ACAATCAAAC
* * *
18188 CAAAATTATATAGGAAGGTTATCAAAATTTCATACAGAGGTTACT-AAAATTTCATAGGGAGGTT
1 CAAAATTTTATAGGAAGGTTATCAAAATTTCATACAGAGGTT-CTCAAAATTTCATAAGAAGGTT
18252 AA
65 AA
* * * ** * * *
18254 CAAAATTTTATATGAAGGTTATCGAAATTTTATATTGTGGTTGTCAAAATTTCATAAGAATGTTA
1 CAAAATTTTATAGGAAGGTTATCAAAATTTCATACAGAGGTTCTCAAAATTTCATAAGAAGGTTA
18319 A
66 A
*
18320 CAAAATTTCATAGG
1 CAAAATTTTATAGG
18334 GACTGAAGTT
Statistics
Matches: 66, Mismatches: 13, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
65 1 0.02
66 65 0.98
ACGTcount: A:0.40, C:0.08, G:0.16, T:0.35
Consensus pattern (66 bp):
CAAAATTTTATAGGAAGGTTATCAAAATTTCATACAGAGGTTCTCAAAATTTCATAAGAAGGTTA
A
Found at i:18273 original size:44 final size:43
Alignment explanation
Indices: 18189--18353 Score: 120
Period size: 44 Copynumber: 3.7 Consensus size: 43
18179 CAATCAAACC
* *
18189 AAAATTAT-ATAGGAAGGTTATCAAAATTTCATACAGAGGTTACT
1 AAAATT-TCATAGGGAGGTTATCAAAATTTCATAGA-AGGTTACT
* *
18233 AAAATTTCATAGGGAGGTTAACAAAATTTTATATGAAGGTTA-T
1 AAAATTTCATAGGGAGGTTATCAAAATTTCATA-GAAGGTTACT
* * ** * * *
18276 CGAAATTTTATATTGTGGTTGTCAAAATTTCATAAGAATGTTAAC-
1 -AAAATTTCATAGGGAGGTTATCAAAATTTCAT-AGAAGGTT-ACT
18321 AAAATTTCATAGGGACTGAAGTTATCAAAATTT
1 AAAATTTCATAGGGA--G--GTTATCAAAATTT
18354 GTGCTTATCG
Statistics
Matches: 92, Mismatches: 19, Indels: 16
0.72 0.15 0.13
Matches are distributed among these distances:
43 2 0.02
44 74 0.80
45 3 0.03
46 1 0.01
48 12 0.13
ACGTcount: A:0.41, C:0.08, G:0.16, T:0.35
Consensus pattern (43 bp):
AAAATTTCATAGGGAGGTTATCAAAATTTCATAGAAGGTTACT
Found at i:18443 original size:22 final size:22
Alignment explanation
Indices: 18358--18641 Score: 82
Period size: 22 Copynumber: 12.7 Consensus size: 22
18348 AAATTTGTGC
* *
18358 TTATCGAAATTTCCTATG-GAGG
1 TTATCAAAATTTCATA-GAGAGG
* *
18380 TTAACAAAATTTTATATG-GAGG
1 TTATCAAAATTTCATA-GAGAGG
* *
18402 TTAT-GAAA-TT-ATATGAAGAGA
1 TTATCAAAATTTCATA-G-AGAGG
*
18423 TTATCAAAATTTCATAGAGAGA
1 TTATCAAAATTTCATAGAGAGG
* * *
18445 ATATCACAGTTTCATTCTCATAGGGAGG
1 TTATCA-A----AATT-TCATAGAGAGG
* * * *
18473 TTATCGAAATTTCATGGTGTGG
1 TTATCAAAATTTCATAGAGAGG
* *
18495 TTATCAAAATTTTA-AGAGGAGA
1 TTATCAAAATTTCATAGA-GAGG
* *
18517 TTATCAAAATTTTCACAGTA-TGG
1 TTATCAAAA-TTTCATAG-AGAGG
* * * * * *
18540 TT-TC-CAATTTTACAGTGTGA
1 TTATCAAAATTTCATAGAGAGG
* **
18560 TTATCAAAATTTCACACTGAGG
1 TTATCAAAATTTCATAGAGAGG
* *
18582 TTATCAAAATTTCATAGTGTGG
1 TTATCAAAATTTCATAGAGAGG
* * * *
18604 TTATCAAATTTTCATTGGGTGG
1 TTATCAAAATTTCATAGAGAGG
*
18626 TTATCGAAATTTCATA
1 TTATCAAAATTTCATA
18642 ATAAGGTTAT
Statistics
Matches: 199, Mismatches: 45, Indels: 36
0.71 0.16 0.13
Matches are distributed among these distances:
19 5 0.03
20 13 0.07
21 15 0.08
22 129 0.65
23 14 0.07
24 5 0.03
25 1 0.01
27 4 0.02
28 13 0.07
ACGTcount: A:0.34, C:0.11, G:0.18, T:0.37
Consensus pattern (22 bp):
TTATCAAAATTTCATAGAGAGG
Found at i:18658 original size:109 final size:110
Alignment explanation
Indices: 18469--18669 Score: 239
Period size: 109 Copynumber: 1.8 Consensus size: 110
18459 TTCTCATAGG
* *
18469 GAGGTTATCGAAATTTCATGGTGTGGTTATCAAAATTTTAAGAGGAGATTATCAAAATTTTCACA
1 GAGGTTATCAAAATTTCATAGTGTGGTTATCAAAATTTTAAGAGGAGATTATCAAAATTTTCACA
* * * *
18534 GTATGGTTTCCAATTTT-ACAGTGTGATTATCAAAATTTCACACT
66 ATAAGGTTTCAAATTTTCACAATGTGATTATCAAAATTTCACACT
* * * *
18578 GAGGTTATCAAAATTTCATAGTGTGGTTATC-AAATTTTCATTG-GGTGGTTATCGAAA-TTTCA
1 GAGGTTATCAAAATTTCATAGTGTGGTTATCAAAATTTT-A-AGAGGAGATTATCAAAATTTTCA
* *
18640 TAATAAGGTTATTAAATTTTCACAATGTGA
64 CAATAAGGTT-TCAAATTTTCACAATGTGA
18670 ATAAATTGAA
Statistics
Matches: 76, Mismatches: 12, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
108 19 0.25
109 48 0.63
110 9 0.12
ACGTcount: A:0.33, C:0.10, G:0.18, T:0.39
Consensus pattern (110 bp):
GAGGTTATCAAAATTTCATAGTGTGGTTATCAAAATTTTAAGAGGAGATTATCAAAATTTTCACA
ATAAGGTTTCAAATTTTCACAATGTGATTATCAAAATTTCACACT
Found at i:28133 original size:39 final size:40
Alignment explanation
Indices: 28077--28157 Score: 137
Period size: 39 Copynumber: 2.0 Consensus size: 40
28067 TTTAATTCCT
28077 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
* *
28117 ATGTAATA-CTATAATAACTGAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
28156 AT
1 AT
28158 TCTTAGGTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 31 0.79
40 8 0.21
ACGTcount: A:0.51, C:0.09, G:0.04, T:0.37
Consensus pattern (40 bp):
ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
Found at i:28182 original size:24 final size:25
Alignment explanation
Indices: 28148--28194 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
28138 AATACTTACA
28148 TTAATTAAA-TTCTTAGGTATTTTT
1 TTAATTAAATTTCTTAGGTATTTTT
*
28172 TTAATTCAATTTCTTAGGTATTT
1 TTAATTAAATTTCTTAGGTATTT
28195 GTGTAAACGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.28, C:0.06, G:0.09, T:0.57
Consensus pattern (25 bp):
TTAATTAAATTTCTTAGGTATTTTT
Found at i:28512 original size:205 final size:202
Alignment explanation
Indices: 28271--28676 Score: 740
Period size: 205 Copynumber: 2.0 Consensus size: 202
28261 TTAATAATAA
*
28271 ATAAATCGGATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTAATTT
1 ATAAATCGGATCTTAATATCTTTTATAATCTTGAAATTTTGTTTGACATTGATCTAATTTAATTT
* *
28336 AATAAATCAACCACTAATGTTCAACTAATTTTTTTTTGGTATAGTTCTATATATATAATAGTAAT
66 AATAAATCAACCACTAATGTTCAACTAAATTTTTTTTGGTATAG-T-TATATATATAATAATAAT
*
28401 GTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATTCAT
129 GTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTAAAAAAATTAATAACATTCAT
*
28466 CATTGATAT
194 CATCGATAT
28475 ATAAATCGGATCTTTAATATCTTTTATAATCTTGAAATTTTGTTTGACATTGATCTAATTTAATT
1 ATAAATCGGATC-TTAATATCTTTTATAATCTTGAAATTTTGTTTGACATTGATCTAATTTAATT
28540 TAATAAATCAACCACTAATGTTCAACTAAATTTTTTTTGGTATAGTTATATATATAATAATAATG
65 TAATAAATCAACCACTAATGTTCAACTAAATTTTTTTTGGTATAGTTATATATATAATAATAATG
28605 TGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTAAAAAAATTAATAACATTCATC
130 TGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTAAAAAAATTAATAACATTCATC
28670 ATCGATA
195 ATCGATA
28677 AAGTTATTAA
Statistics
Matches: 196, Mismatches: 5, Indels: 3
0.96 0.02 0.01
Matches are distributed among these distances:
203 88 0.45
204 13 0.07
205 95 0.48
ACGTcount: A:0.36, C:0.11, G:0.09, T:0.44
Consensus pattern (202 bp):
ATAAATCGGATCTTAATATCTTTTATAATCTTGAAATTTTGTTTGACATTGATCTAATTTAATTT
AATAAATCAACCACTAATGTTCAACTAAATTTTTTTTGGTATAGTTATATATATAATAATAATGT
GTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTAAAAAAATTAATAACATTCATCA
TCGATAT
Found at i:29239 original size:36 final size:36
Alignment explanation
Indices: 29192--29261 Score: 122
Period size: 36 Copynumber: 1.9 Consensus size: 36
29182 GAGATTTTGG
* *
29192 AGAAATATGATAATCAAAATTACAAAAAATGTAATA
1 AGAAATATGATAACCAAAATCACAAAAAATGTAATA
29228 AGAAATATGATAACCAAAATCACAAAAAATGTAA
1 AGAAATATGATAACCAAAATCACAAAAAATGTAA
29262 GGTTATTGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.61, C:0.09, G:0.09, T:0.21
Consensus pattern (36 bp):
AGAAATATGATAACCAAAATCACAAAAAATGTAATA
Found at i:32528 original size:14 final size:14
Alignment explanation
Indices: 32509--32543 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
32499 AAAATGCAAA
32509 TTTTGAATTTTGAC
1 TTTTGAATTTTGAC
*
32523 TTTTGACTTTTGAC
1 TTTTGAATTTTGAC
32537 TTTTGAA
1 TTTTGAA
32544 GAATGAAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.20, C:0.09, G:0.14, T:0.57
Consensus pattern (14 bp):
TTTTGAATTTTGAC
Found at i:32605 original size:7 final size:7
Alignment explanation
Indices: 32593--32817 Score: 324
Period size: 7 Copynumber: 32.1 Consensus size: 7
32583 AGAGCCATGA
32593 AATTTTG
1 AATTTTG
32600 AATTTTG
1 AATTTTG
32607 AATTTTG
1 AATTTTG
*
32614 AGTTTTG
1 AATTTTG
*
32621 AGTTTTG
1 AATTTTG
*
32628 AGTTTTG
1 AATTTTG
32635 AATTTTG
1 AATTTTG
*
32642 AGTTTTG
1 AATTTTG
*
32649 AGTTTTG
1 AATTTTG
*
32656 AGTTTTG
1 AATTTTG
*
32663 AGTTTTG
1 AATTTTG
*
32670 AGTTTTG
1 AATTTTG
*
32677 AGTTTTG
1 AATTTTG
32684 AATTTTG
1 AATTTTG
32691 AATTTTG
1 AATTTTG
32698 AATTTTG
1 AATTTTG
32705 AATTTTG
1 AATTTTG
32712 AATTTTG
1 AATTTTG
32719 AATTTTG
1 AATTTTG
32726 AATTTTG
1 AATTTTG
32733 AATTTTG
1 AATTTTG
32740 AATTTTG
1 AATTTTG
32747 AATTTTG
1 AATTTTG
32754 AATTTTG
1 AATTTTG
32761 AATTTTG
1 AATTTTG
32768 AATTTTG
1 AATTTTG
*
32775 AGTTTTG
1 AATTTTG
*
32782 AGTTTTG
1 AATTTTG
*
32789 AGTTTTG
1 AATTTTG
*
32796 AGTTTTG
1 AATTTTG
*
32803 AATTTTT
1 AATTTTG
32810 AATTTTG
1 AATTTTG
32817 A
1 A
32818 GCAATGAAAT
Statistics
Matches: 210, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 210 1.00
ACGTcount: A:0.23, C:0.00, G:0.20, T:0.57
Consensus pattern (7 bp):
AATTTTG
Found at i:32995 original size:33 final size:33
Alignment explanation
Indices: 32953--33030 Score: 120
Period size: 33 Copynumber: 2.4 Consensus size: 33
32943 AGAAATTGTG
* * *
32953 GATTTTGAACTTTGAGTTTTGATATGATATGCA
1 GATTTTGAACTTTGAATTTTGAAATGAAATGCA
32986 GATTTTGAACTTTGAATTTTGAAATGAAATGCA
1 GATTTTGAACTTTGAATTTTGAAATGAAATGCA
*
33019 AATTTTGAACTT
1 GATTTTGAACTT
33031 CTTAATTAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.32, C:0.06, G:0.18, T:0.44
Consensus pattern (33 bp):
GATTTTGAACTTTGAATTTTGAAATGAAATGCA
Found at i:33244 original size:54 final size:54
Alignment explanation
Indices: 33134--33400 Score: 322
Period size: 54 Copynumber: 4.8 Consensus size: 54
33124 TGATCATCGT
* * * * * *
33134 AAACTTCT-TGGAATGACCACACTGGATCAACTTTAAGATCAACTTAGATTTTTGA
1 AAACTTCTAT-GAAAGACCACACAGGGTCATC-TTAAGATCAACTTAGATCTCTGA
* *
33189 AAACTTCTACT-AAAGACCACACAGGGTCGTCTGAAGATCAACTTAGATCTCTGA
1 AAACTTCTA-TGAAAGACCACACAGGGTCATCTTAAGATCAACTTAGATCTCTGA
*
33243 AAACTTCTATGAAAGACCACACTGGGTCATCTTAAGATCAACTTAGATCTCTGA
1 AAACTTCTATGAAAGACCACACAGGGTCATCTTAAGATCAACTTAGATCTCTGA
*
33297 AAACTTCTATGAAAGACCACACCGGCACTGGGTCATCTTAAGATCAACTTAAATCTCTGA
1 AAACTTCTATGAAAGACCACA----CA--GGGTCATCTTAAGATCAACTTAGATCTCTGA
* * *
33357 AAACTTCTATGAAAGACCACACTGGATCAACTTAAGATCAACTT
1 AAACTTCTATGAAAGACCACACAGGGTCATCTTAAGATCAACTT
33401 TCTAGAGAGA
Statistics
Matches: 187, Mismatches: 16, Indels: 19
0.84 0.07 0.09
Matches are distributed among these distances:
53 1 0.01
54 109 0.58
55 23 0.12
56 1 0.01
57 1 0.01
58 1 0.01
60 51 0.27
ACGTcount: A:0.36, C:0.22, G:0.15, T:0.27
Consensus pattern (54 bp):
AAACTTCTATGAAAGACCACACAGGGTCATCTTAAGATCAACTTAGATCTCTGA
Found at i:33371 original size:114 final size:108
Alignment explanation
Indices: 33134--33400 Score: 367
Period size: 114 Copynumber: 2.4 Consensus size: 108
33124 TGATCATCGT
* * *
33134 AAACTTCT-TGGAATGACCACACTGGATCAACTTTAAGATCAACTTAGATTTTTGAAAACTTCTA
1 AAACTTCTAT-GAAAGACCACACTGGATCAAC-TTAAGATCAACTTAGATCTCTGAAAACTTCTA
* *
33198 CTAAAGACCACACAGGGTCGTCTGAAGATCAACTTAGATCTCTGA
64 CTAAAGACCACACAGGGTCATCTGAAGATCAACTTAAATCTCTGA
* *
33243 AAACTTCTATGAAAGACCACACTGGGTCATCTTAAGATCAACTTAGATCTCTGAAAACTTCTA-T
1 AAACTTCTATGAAAGACCACACTGGATCAACTTAAGATCAACTTAGATCTCTGAAAACTTCTACT
*
33307 GAAAGACCACACCGGCACTGGGTCATCTTAAGATCAACTTAAATCTCTGA
66 -AAAGACCACA----CA--GGGTCATCTGAAGATCAACTTAAATCTCTGA
33357 AAACTTCTATGAAAGACCACACTGGATCAACTTAAGATCAACTT
1 AAACTTCTATGAAAGACCACACTGGATCAACTTAAGATCAACTT
33401 TCTAGAGAGA
Statistics
Matches: 140, Mismatches: 10, Indels: 11
0.87 0.06 0.07
Matches are distributed among these distances:
107 1 0.01
108 40 0.29
109 26 0.19
110 1 0.01
112 2 0.01
114 70 0.50
ACGTcount: A:0.36, C:0.22, G:0.15, T:0.27
Consensus pattern (108 bp):
AAACTTCTATGAAAGACCACACTGGATCAACTTAAGATCAACTTAGATCTCTGAAAACTTCTACT
AAAGACCACACAGGGTCATCTGAAGATCAACTTAAATCTCTGA
Found at i:33550 original size:37 final size:37
Alignment explanation
Indices: 33497--33912 Score: 379
Period size: 37 Copynumber: 11.2 Consensus size: 37
33487 AAACTGGGAT
* * *
33497 TTTGAAGAGATACCTAAACAGGTACCTTAAATAAGGA
1 TTTGATGAGACACCTAAACAGGGACCTTAAATAAGGA
* * * * ** * *
33534 TTTAATAAGAAACCTAAACAGGAAATTTGAACAA-GA
1 TTTGATGAGACACCTAAACAGGGACCTTAAATAAGGA
33570 TTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGA
1 -TTTGATGAGACACCTAAACAGGGACCTTAAATAAGGA
* * * * * * *
33608 TTTAATGAGAAACCAAAACAGGAATCTTGAACAA-GA
1 TTTGATGAGACACCTAAACAGGGACCTTAAATAAGGA
**
33644 TTTTGATGAGACACCTAAACAGGGACCTTAAACCA-GA
1 -TTTGATGAGACACCTAAACAGGGACCTTAAATAAGGA
*
33681 TTTCGATGAGACACCTAAAGAGGGACCTTAAATAAGGA
1 TTT-GATGAGACACCTAAACAGGGACCTTAAATAAGGA
* * *
33719 TTTGATAAGACACCTAAACAGGAACCTTAGATAAGGA
1 TTTGATGAGACACCTAAACAGGGACCTTAAATAAGGA
* *
33756 TTTAATCAGACACCTAAACAGGGACCTTAAATAAGGA
1 TTTGATGAGACACCTAAACAGGGACCTTAAATAAGGA
* * * * * * * * *
33793 TTTGATAAGAAAGCTAACCAGGAATCTTGAACAAGGT
1 TTTGATGAGACACCTAAACAGGGACCTTAAATAAGGA
*
33830 TTTGATGAGACACCTATACAGGGACCTTAAATAAGGA
1 TTTGATGAGACACCTAAACAGGGACCTTAAATAAGGA
** * ** * * *
33867 TTTGACAAGAAAACCTAAACAGTAATCTTGAATAAGGT
1 TTTGATGAG-ACACCTAAACAGGGACCTTAAATAAGGA
33905 TTTGATGA
1 TTTGATGA
Statistics
Matches: 300, Mismatches: 73, Indels: 11
0.78 0.19 0.03
Matches are distributed among these distances:
36 7 0.02
37 259 0.86
38 34 0.11
ACGTcount: A:0.43, C:0.15, G:0.19, T:0.23
Consensus pattern (37 bp):
TTTGATGAGACACCTAAACAGGGACCTTAAATAAGGA
Done.