Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019517.1 Corchorus olitorius cultivar O-4 contig19550, 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: 45229
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33
Found at i:7168 original size:39 final size:39
Alignment explanation
Indices: 7125--7200 Score: 125
Period size: 39 Copynumber: 1.9 Consensus size: 39
7115 CTAAGAGTTA
**
7125 ATTACTAAGAATGGATTATTCAATCAGGATTGGAATGCC
1 ATTACTAAGAATGGACCATTCAATCAGGATTGGAATGCC
*
7164 ATTACTAAGAATGGACCATTTAATCAGGATTGGAATG
1 ATTACTAAGAATGGACCATTCAATCAGGATTGGAATG
7201 TGTTGAGTTC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.30
Consensus pattern (39 bp):
ATTACTAAGAATGGACCATTCAATCAGGATTGGAATGCC
Found at i:18195 original size:13 final size:13
Alignment explanation
Indices: 18179--18235 Score: 53
Period size: 13 Copynumber: 4.4 Consensus size: 13
18169 ACCAGGAGAG
*
18179 AGAAAGAAGAAAG
1 AGAAAGAAGAAAA
*
18192 AGAAAAAAG-AAA
1 AGAAAGAAGAAAA
* *
18204 TGAAAGAGGAAAA
1 AGAAAGAAGAAAA
*
18217 AAAAAGGAAGAAAA
1 AGAAA-GAAGAAAA
18231 AGAAA
1 AGAAA
18236 CAAATAGATA
Statistics
Matches: 33, Mismatches: 9, Indels: 3
0.73 0.20 0.07
Matches are distributed among these distances:
12 8 0.24
13 14 0.42
14 11 0.33
ACGTcount: A:0.74, C:0.00, G:0.25, T:0.02
Consensus pattern (13 bp):
AGAAAGAAGAAAA
Found at i:21164 original size:105 final size:106
Alignment explanation
Indices: 20944--21224 Score: 451
Period size: 106 Copynumber: 2.7 Consensus size: 106
20934 TTCTAACCTT
*
20944 TAAAATAAAATTTTAATTT-GGGCTAAACTTAGTG-AATTAGTTATATATTTTATTTCTAAAACC
1 TAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAACC
* *
21007 CTATAACAATAAATTAATAATTATGGAATTTATCCTTAAAA
66 CTATAACAATAAATTAATAATTATGAAATTTACCCTTAAAA
*
21048 TGAAAATAAAATTTTAATTTGGGGC-ATACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAAC
1 T-AAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAAC
* *
21112 CCTATAACAATAAATTATTAATTTTGAAATTTACCCTTAAAA
65 CCTATAACAATAAATTAATAATTATGAAATTTACCCTTAAAA
* * *
21154 TAAAATAAAATTTTAATTTGGAGCTAAACTTAATGAAATTAGTTTTATATTTTATTTCTAAAACT
1 TAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAACC
21219 CTATAA
66 CTATAA
21225 TAAAAACCTT
Statistics
Matches: 163, Mismatches: 10, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
104 1 0.01
105 49 0.30
106 113 0.69
ACGTcount: A:0.42, C:0.09, G:0.08, T:0.42
Consensus pattern (106 bp):
TAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAACC
CTATAACAATAAATTAATAATTATGAAATTTACCCTTAAAA
Found at i:21258 original size:105 final size:102
Alignment explanation
Indices: 20944--21258 Score: 399
Period size: 106 Copynumber: 3.0 Consensus size: 102
20934 TTCTAACCTT
*
20944 TAAAATAAAATTTTAATTTGGGCTAAACTTAGTG-AATTAGTTATATATTTTATTTCTAAAACCC
1 TAAAATAAAATTTTAATTTGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAACCC
21008 TATAACAATAAA-TTAATAATTATGGAATTTA-TCCTTAAAA
66 TATAACAATAAATTTAAT--TTAT--AATTTACT-CTTAAAA
*
21048 TGAAAATAAAATTTTAATTTGGGGC-ATACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAAC
1 T-AAAATAAAATTTTAATTT-GGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAAC
*
21112 CCTATAACAATAAATTATTAATTT-TGAAATTTACCCTTAAAA
64 CCTATAACAATAAA-T-TTAATTTAT--AATTTACTCTTAAAA
* *
21154 TAAAATAAAATTTTAATTTGGAGCTAAACTTAATGAAATTAGTTTTATATTTTATTTCTAAAACT
1 TAAAATAAAATTTTAATTTGG-GCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAACC
*
21219 CTATAATAA-AAACCTTTAATTTCATAATTTACTCTTAAAA
65 CTATAACAATAAA--TTTAATTT-ATAATTTACTCTTAAAA
21259 ATCAAAATTT
Statistics
Matches: 189, Mismatches: 10, Indels: 23
0.85 0.05 0.10
Matches are distributed among these distances:
104 3 0.02
105 71 0.38
106 107 0.57
107 3 0.02
109 5 0.03
ACGTcount: A:0.42, C:0.09, G:0.07, T:0.42
Consensus pattern (102 bp):
TAAAATAAAATTTTAATTTGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAACCC
TATAACAATAAATTTAATTTATAATTTACTCTTAAAA
Found at i:24672 original size:2 final size:2
Alignment explanation
Indices: 24665--24690 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
24655 AACTAAACAG
24665 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
24691 CACACACCAA
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):
TA
Found at i:25931 original size:18 final size:20
Alignment explanation
Indices: 25878--25933 Score: 62
Period size: 23 Copynumber: 2.7 Consensus size: 20
25868 GATGGGCTTT
25878 ACTTCCTCAGGAAGGTGATTTCA
1 ACTT-CTCAGGAAGGTGA--TCA
25901 ACTTCTTCAGGAAGGTGA-CA
1 ACTTC-TCAGGAAGGTGATCA
25921 ACTTC-CAGGAAGG
1 ACTTCTCAGGAAGG
25934 AGAGGTGAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
18 8 0.25
20 7 0.22
22 1 0.03
23 16 0.50
ACGTcount: A:0.29, C:0.21, G:0.25, T:0.25
Consensus pattern (20 bp):
ACTTCTCAGGAAGGTGATCA
Found at i:33447 original size:67 final size:68
Alignment explanation
Indices: 33193--33570 Score: 414
Period size: 68 Copynumber: 5.6 Consensus size: 68
33183 AGTAAAGTTC
*
33193 TATTTTCTATTTCAAAAAATACCCATT-CGGTCGAAGGGTCATTTTCGTCTTCTTGCATTTAAGT
1 TATTTTCTATTTCCAAAAATACCC-TTCCGGTCGAAGGGTCATTTTCGTCTTCTTGCATTTAAGT
33257 TTAG
65 TTAG
* * * * *
33261 CATTTTCTATTTCCAAAAATACCCTTTCGGTGGAATGGTCATTTTCGTCTTTTTGCATTTAAGTT
1 TATTTTCTATTTCCAAAAATACCCTTCCGGTCGAAGGGTCATTTTCGTCTTCTTGCATTTAAGTT
33326 TAG
66 TAG
* * *
33329 TGTTTTCTATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTCTTACATTTAAGTT
1 TATTTTCTATTTCCAAAAATACCCTTCCGGTCGAAGGGTCATTTTCGTCTTCTTGCATTTAAGTT
33394 TAG
66 TAG
* * * * * *
33397 TATTTTC-GTTTCCAGAAATACCCTTCCGCTCGAAGGGTCAGTTTCATCTTCTTGC-GTTAAGGT
1 TATTTTCTATTTCCAAAAATACCCTTCCGGTCGAAGGGTCATTTTCGTCTTCTTGCATTTAA-GT
33460 TTAG
65 TTAG
* * * * * *
33464 T-TTTTC--TTTCCAAAAATATCCTTCCGGTCGAAGGGCCAGTTTCATCAGGATATTGCATTTAA
1 TATTTTCTATTTCCAAAAATACCCTTCCGGTCGAAGGGTCATTTTCGTC---TTCTTGCATTTAA
*
33526 GTCTAG
63 GTTTAG
* * *
33532 ---TCTCTCTTTCCAAAGAATACCCTTTCGGTCGAAGGGTCA
1 TATTTTCTATTTCCAAA-AATACCCTTCCGGTCGAAGGGTCA
33571 ATTCTGTCAT
Statistics
Matches: 269, Mismatches: 32, Indels: 17
0.85 0.10 0.05
Matches are distributed among these distances:
65 36 0.13
66 12 0.04
67 50 0.19
68 146 0.54
69 25 0.09
ACGTcount: A:0.23, C:0.20, G:0.16, T:0.40
Consensus pattern (68 bp):
TATTTTCTATTTCCAAAAATACCCTTCCGGTCGAAGGGTCATTTTCGTCTTCTTGCATTTAAGTT
TAG
Found at i:33523 original size:135 final size:133
Alignment explanation
Indices: 33195--33646 Score: 375
Period size: 135 Copynumber: 3.4 Consensus size: 133
33185 TAAAGTTCTA
* * * * * *
33195 TTTTCTATTTCAAAAAATACCCATT-CGGTCGAAGGGTCATTTTCGTCTTCTTGCATTTAAGTTT
1 TTTTC-ATTTCCAAAAATACCC-TTCCGGTCGAAGGGCCAGTTTCATCATATTGCATTTAAGTTT
* * * * * * *
33259 AGCATTTTCTATTTCCAAAAATACCCTTTCGGTGGAATGGTCATTTTCGTCTTTTTGCATTTAAG
64 AGTATTTTC--TTTCCAAAAATACCCTTTCGGTCGAAGGGTCAGTTTCATCTTCTTGCAGTTAAG
33324 TTTAGTG
127 TTTAGTG
* * * * * * *
33331 TTTTCTATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTCTTACATTTAAGTTTA
1 TTTTC-ATTTCCAAAAATACCCTTCCGGTCGAAGGGCCAGTTTCATCATATTGCATTTAAGTTTA
* * *
33396 GTATTTTCGTTTCCAGAAATACCCTTCCGCTCGAAGGGTCAGTTTCATCTTCTTGC-GTTAAGGT
65 GTATTTTC-TTTCCAAAAATACCCTTTCGGTCGAAGGGTCAGTTTCATCTTCTTGCAGTTAA-GT
33460 TTAGT-
128 TTAGTG
* *
33465 TTTTC-TTTCCAAAAATATCCTTCCGGTCGAAGGGCCAGTTTCATCAGGATATTGCATTTAAGTC
1 TTTTCATTTCCAAAAATACCCTTCCGGTCGAAGGGCCAGTTTCATC---ATATTGCATTTAAGTT
* * * * *
33529 TAGT-CTCTCTTTCCAAAGAATACCCTTTCGGTCGAAGGGTCA-ATTCTGTCATTCTT-AAGCTT
63 TAGTATTTTCTTTCCAAA-AATACCCTTTCGGTCGAAGGGTCAGTTTC-ATC-TTCTTGCAG-TT
* *
33591 GAGTTTA--C
124 AAGTTTAGTG
* * * *
33599 TTTTAATTTCCAAAAATACCCTTTCGGT-GAAAAGGTCAGTTTCATCAT
1 TTTTCATTTCCAAAAATACCCTTCCGGTCG-AAGGGCCAGTTTCATCAT
33647 TTTCACACTT
Statistics
Matches: 267, Mismatches: 36, Indels: 30
0.80 0.11 0.09
Matches are distributed among these distances:
132 37 0.14
133 10 0.04
134 41 0.15
135 109 0.41
136 70 0.26
ACGTcount: A:0.23, C:0.20, G:0.16, T:0.40
Consensus pattern (133 bp):
TTTTCATTTCCAAAAATACCCTTCCGGTCGAAGGGCCAGTTTCATCATATTGCATTTAAGTTTAG
TATTTTCTTTCCAAAAATACCCTTTCGGTCGAAGGGTCAGTTTCATCTTCTTGCAGTTAAGTTTA
GTG
Found at i:33647 original size:66 final size:65
Alignment explanation
Indices: 33538--33698 Score: 159
Period size: 66 Copynumber: 2.4 Consensus size: 65
33528 CTAGTCTCTC
* * *
33538 TTTCCAAAGAATACCCTTTCGGTCG-AAGGGTCAATTCTGTCATTCTT-A-AGCTTGAGTTTACT
1 TTTCCAAA-AATACCCTTTCGGT-GAAAAGGTCAATTCTATCATT-TTCACA-CTTCAGTTTA-T
*
33600 TTTAA
61 TCTAA
* *
33605 TTTCCAAAAATACCCTTTCGGTGAAAAGGTCAGTT-TCATCATTTTCACACTTCCGTTTATTCTA
1 TTTCCAAAAATACCCTTTCGGTGAAAAGGTCAATTCT-ATCATTTTCACACTTCAGTTTATTCTA
*
33669 C
65 A
* *
33670 TTTCCAAAAATGCCCTTTCGGTCAAAAGG
1 TTTCCAAAAATACCCTTTCGGTGAAAAGG
33699 GCAAGCTTTA
Statistics
Matches: 81, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
65 35 0.43
66 37 0.46
67 9 0.11
ACGTcount: A:0.27, C:0.22, G:0.14, T:0.37
Consensus pattern (65 bp):
TTTCCAAAAATACCCTTTCGGTGAAAAGGTCAATTCTATCATTTTCACACTTCAGTTTATTCTAA
Found at i:38314 original size:16 final size:15
Alignment explanation
Indices: 38290--38323 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
38280 ATATTCTTTT
*
38290 AAAAAGATTTTTCAA
1 AAAAAGATTTCTCAA
38305 AAAAATGATTTCTCAA
1 AAAAA-GATTTCTCAA
38321 AAA
1 AAA
38324 TGTTTTCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.56, C:0.09, G:0.06, T:0.29
Consensus pattern (15 bp):
AAAAAGATTTCTCAA
Found at i:38334 original size:12 final size:14
Alignment explanation
Indices: 38305--38336 Score: 50
Period size: 12 Copynumber: 2.4 Consensus size: 14
38295 GATTTTTCAA
38305 AAAAATGATTTCTC
1 AAAAATGATTTCTC
38319 AAAAATG-TTT-TC
1 AAAAATGATTTCTC
38331 AAAAAT
1 AAAAAT
38337 TTGTTTTCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 8 0.44
13 3 0.17
14 7 0.39
ACGTcount: A:0.50, C:0.09, G:0.06, T:0.34
Consensus pattern (14 bp):
AAAAATGATTTCTC
Found at i:38645 original size:1 final size:1
Alignment explanation
Indices: 38634--38686 Score: 52
Period size: 1 Copynumber: 53.0 Consensus size: 1
38624 AATAAAGATG
* * * * * *
38634 AAAAAACAAAAAAAAAAAGAAAAAAAAGAAAGAAAAAAAAAGAAAAGAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
38687 TTTAAAAGTG
Statistics
Matches: 40, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 40 1.00
ACGTcount: A:0.89, C:0.02, G:0.09, T:0.00
Consensus pattern (1 bp):
A
Found at i:38657 original size:13 final size:13
Alignment explanation
Indices: 38641--38686 Score: 65
Period size: 14 Copynumber: 3.4 Consensus size: 13
38631 ATGAAAAAAC
38641 AAAAAAAAAAAGA
1 AAAAAAAAAAAGA
*
38654 AAAAAAAGAAAGAA
1 AAAAAAAAAAAG-A
38668 AAAAAAAGAAAAGA
1 AAAAAAA-AAAAGA
38682 AAAAA
1 AAAAA
38687 TTTAAAAGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
13 11 0.38
14 14 0.48
15 4 0.14
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAGA
Found at i:38658 original size:14 final size:14
Alignment explanation
Indices: 38641--38686 Score: 67
Period size: 13 Copynumber: 3.3 Consensus size: 14
38631 ATGAAAAAAC
38641 AAAAAAAAAAAG-A
1 AAAAAAAAAAAGAA
*
38654 AAAAAAAGAAAGAA
1 AAAAAAAAAAAGAA
38668 AAAAAAAGAAAAGAA
1 AAAAAAA-AAAAGAA
38683 AAAA
1 AAAA
38687 TTTAAAAGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
13 11 0.38
14 8 0.28
15 10 0.34
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAGAA
Found at i:38672 original size:28 final size:28
Alignment explanation
Indices: 38633--38686 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
38623 CAATAAAGAT
38633 GAAAAAACAAAAAAAAAAAGAAAAAAAA
1 GAAAAAACAAAAAAAAAAAGAAAAAAAA
*
38661 GAAAGAAA-AAAAAAGAAAAGAAAAAA
1 GAAA-AAACAAAAAAAAAAAGAAAAAA
38687 TTTAAAAGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 21 0.88
29 3 0.12
ACGTcount: A:0.87, C:0.02, G:0.11, T:0.00
Consensus pattern (28 bp):
GAAAAAACAAAAAAAAAAAGAAAAAAAA
Found at i:40009 original size:8 final size:8
Alignment explanation
Indices: 39996--40323 Score: 65
Period size: 8 Copynumber: 43.1 Consensus size: 8
39986 ACCTTTTTTT
39996 TTCAATTC
1 TTCAATTC
*
40004 TTCAATGC
1 TTCAATTC
40012 TTCAATATC
1 TTCAAT-TC
40021 -T---TTC
1 TTCAATTC
*
40025 TTCGATTC
1 TTCAATTC
*
40033 TTCTAACTC
1 TTC-AATTC
40042 TTCAATTC
1 TTCAATTC
* *
40050 TTCAGTAC
1 TTCAATTC
40058 TTCAATTTAC
1 TTCAA-TT-C
*
40068 TTCAGCA-TG
1 TTCA--ATTC
* *
40077 GT-ATATTA
1 TTCA-ATTC
*
40085 TTCAATTT
1 TTCAATTC
* *
40093 TTCAACTA
1 TTCAATTC
*
40101 TTCAGATCC
1 TTCA-ATTC
*
40110 TTCAATTA
1 TTCAATTC
* *
40118 TCCAAATTA
1 TTC-AATTC
*
40127 TTCAATTA
1 TTCAATTC
40135 TTCAA-T-
1 TTCAATTC
*
40141 TTCCATTC
1 TTCAATTC
40149 TTCAATGT-
1 TTCAAT-TC
40157 TTCAA-T-
1 TTCAATTC
40163 TTCAATTC
1 TTCAATTC
*
40171 TTCAATTA
1 TTCAATTC
* *
40179 TTTAA--A
1 TTCAATTC
40185 TTCAATGT-
1 TTCAAT-TC
40193 TTCAA-T-
1 TTCAATTC
40199 TTCAA-T-
1 TTCAATTC
40205 TTCAA-TC
1 TTCAATTC
40212 ATTCAATGT-
1 -TTCAAT-TC
40221 TTCAA-T-
1 TTCAATTC
*
40227 TTCGATTC
1 TTCAATTC
*
40235 TTCAATGC
1 TTCAATTC
*
40243 CTCAA-T-
1 TTCAATTC
*
40249 TTCAAATC
1 TTCAATTC
40257 TTC-ATTGC
1 TTCAATT-C
40265 TTCAA-T-
1 TTCAATTC
40271 TTCAATTC
1 TTCAATTC
40279 TTCAATAT-
1 TTCAAT-TC
40287 TTCAA-T-
1 TTCAATTC
40293 TTCAATTC
1 TTCAATTC
40301 TTCAA-T-
1 TTCAATTC
40307 TTCAATAT-
1 TTCAAT-TC
40315 TTCAATTC
1 TTCAATTC
40323 T
1 T
40324 CCAAATTCAA
Statistics
Matches: 244, Mismatches: 36, Indels: 80
0.68 0.10 0.22
Matches are distributed among these distances:
4 2 0.01
5 2 0.01
6 53 0.22
7 12 0.05
8 142 0.58
9 25 0.10
10 7 0.03
12 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.04, T:0.47
Consensus pattern (8 bp):
TTCAATTC
Found at i:40160 original size:22 final size:22
Alignment explanation
Indices: 40122--40323 Score: 195
Period size: 22 Copynumber: 9.3 Consensus size: 22
40112 CAATTATCCA
*
40122 AATTATTCAAT-TATTCAATTTC
1 AATTCTTCAATGT-TTCAATTTC
*
40144 CATTCTTCAATGTTTCAATTTC
1 AATTCTTCAATGTTTCAATTTC
* *
40166 AATTCTTCAAT-TATTTAAATTC
1 AATTCTTCAATGT-TTCAATTTC
40188 AATGT-TTCAA--TTTCAATTTC
1 AAT-TCTTCAATGTTTCAATTTC
40208 AA-TCATTCAATGTTTCAATTTC
1 AATTC-TTCAATGTTTCAATTTC
* **
40230 GATTCTTCAATGCCTCAATTTC
1 AATTCTTCAATGTTTCAATTTC
* * *
40252 AAATCTTCATTGCTTCAATTTC
1 AATTCTTCAATGTTTCAATTTC
*
40274 AATTCTTCAATATTTCAATTTC
1 AATTCTTCAATGTTTCAATTTC
40296 AATTCTTCAA--TTTCAATATTTC
1 AATTCTTCAATGTTTC-A-ATTTC
40318 AATTCT
1 AATTCT
40324 CCAAATTCAA
Statistics
Matches: 152, Mismatches: 18, Indels: 20
0.80 0.09 0.11
Matches are distributed among these distances:
18 1 0.01
20 18 0.12
21 3 0.02
22 126 0.83
23 4 0.03
ACGTcount: A:0.30, C:0.19, G:0.03, T:0.48
Consensus pattern (22 bp):
AATTCTTCAATGTTTCAATTTC
Found at i:40166 original size:14 final size:13
Alignment explanation
Indices: 40127--40566 Score: 103
Period size: 14 Copynumber: 30.2 Consensus size: 13
40117 ATCCAAATTA
40127 TTCAATTATTCAAT
1 TTCAATT-TTCAAT
*
40141 TTCCATTCTTCAATGT
1 TTCAATT-TTCAA--T
40157 TTCAA-TTTCAATT
1 TTCAATTTTCAA-T
* *
40170 CTTCAATTATTTAAA
1 -TTCAATT-TTCAAT
40185 TTCAATGTTTCAAT
1 TTCAAT-TTTCAAT
40199 TTCAA-TTTCAAT
1 TTCAATTTTCAAT
40211 CATTCAATGTTTCAAT
1 --TTCAAT-TTTCAAT
*
40227 TTCGATTCTTCAAT
1 TTCAATT-TTCAAT
*
40241 GCCTCAA-TTTCAAAT
1 --TTCAATTTTC-AAT
40256 CTTC-ATTGCTTCAAT
1 -TTCAATT--TTCAAT
40271 TTCAATTCTTCAATAT
1 TTCAATT-TTC-A-AT
40287 TTCAA-TTTCAATT
1 TTCAATTTTCAA-T
40300 CTTCAA-TTTCAATAT
1 -TTCAATTTTC-A-AT
* *
40315 TTCAATTCTCCAAA
1 TTCAATT-TTCAAT
*
40329 TTCAATCCTTCAAAT
1 TTCAAT-TTTC-AAT
*
40344 GTCTCAA-TTTCCAT
1 -T-TCAATTTTCAAT
40358 TCTCCAATGTTTCAAT
1 T-T-CAAT-TTTCAAT
40374 TTCAAATATTTCAACT
1 TTC-AAT-TTTCAA-T
* *
40390 CCTCAA-ATTCAATT
1 -TTCAATTTTCAA-T
40404 CTTCAATGTTTCAAT
1 -TTCAAT-TTTCAAT
40419 TTCAATATTTCAAT
1 TTCAAT-TTTCAAT
*
40433 GCTTCAA-ATTCAATT
1 --TTCAATTTTCAA-T
40448 CTTCAATGTTTCAAT
1 -TTCAAT-TTTCAAT
* *
40463 TTCAGTATTTCAACGC
1 TTCAAT-TTTCAA--T
*
40479 TCCAA-TTTCAAT
1 TTCAATTTTCAAT
*
40491 TCCTCAA-ATTCAATT
1 T--TCAATTTTCAA-T
40506 CTTCAATGTTTCAAT
1 -TTCAAT-TTTCAAT
40521 TTCAATATTTCAAT
1 TTCAAT-TTTCAAT
*
40535 GCTTCAA-ATTCAATT
1 --TTCAATTTTCAA-T
40550 CTTCAATGTTTCAAT
1 -TTCAAT-TTTCAAT
40565 TT
1 TT
40567 TAGTATTTCA
Statistics
Matches: 329, Mismatches: 41, Indels: 112
0.68 0.09 0.23
Matches are distributed among these distances:
12 9 0.03
13 8 0.02
14 188 0.57
15 41 0.12
16 77 0.23
17 6 0.02
ACGTcount: A:0.30, C:0.21, G:0.04, T:0.45
Consensus pattern (13 bp):
TTCAATTTTCAAT
Found at i:40169 original size:36 final size:36
Alignment explanation
Indices: 40127--40334 Score: 98
Period size: 36 Copynumber: 5.8 Consensus size: 36
40117 ATCCAAATTA
**
40127 TTCAATTATTCAATT-TCCATTCTTCAATGTTTCAAT
1 TTCAATTATTCAATTATCCA-AATTCAATGTTTCAAT
* **
40163 TTCAATTCTTCAATTATTTAAATTCAATGTTTCAAT
1 TTCAATTATTCAATTATCCAAATTCAATGTTTCAAT
40199 TTCAA-T-TTC-A--AT-C--ATTCAATGTTTCAAT
1 TTCAATTATTCAATTATCCAAATTCAATGTTTCAAT
* * * * *
40227 TTCGATTCTTCAATGCCTCAATTTCAAATCTTCATTGCTTCAAT
1 TTCAATTATTCAAT---T--A-TCCAAA--TTCAATGTTTCAAT
* * *
40271 TTCAATTCTTCAA-TATTTCAATTTCAAT-TCTTCAAT
1 TTCAATTATTCAATTA-TCCAAATTCAATGT-TTCAAT
*
40307 TTCAA-TATTTCAATTCTCCAAATTCAAT
1 TTCAATTA-TTCAATTATCCAAATTCAAT
40335 CCTTCAAATG
Statistics
Matches: 135, Mismatches: 17, Indels: 40
0.70 0.09 0.21
Matches are distributed among these distances:
28 19 0.14
29 1 0.01
30 3 0.02
31 3 0.02
33 1 0.01
34 3 0.02
35 2 0.01
36 64 0.47
37 3 0.02
38 8 0.06
39 1 0.01
40 2 0.01
42 1 0.01
44 24 0.18
ACGTcount: A:0.30, C:0.20, G:0.03, T:0.47
Consensus pattern (36 bp):
TTCAATTATTCAATTATCCAAATTCAATGTTTCAAT
Found at i:40177 original size:44 final size:44
Alignment explanation
Indices: 40122--40566 Score: 302
Period size: 44 Copynumber: 10.5 Consensus size: 44
40112 CAATTATCCA
* * *
40122 AATTATTCAATTATTCAATTTCCATTCTTCAATGTTTCAATTTC
1 AATTCTTCAATTCTTCAATTTCAATTCTTCAATGTTTCAATTTC
* * *
40166 AATTCTTCAATTATTTAAATTCAATGT-TTCAA--TTTCAATTTC
1 AATTCTTCAATTCTTCAATTTCAAT-TCTTCAATGTTTCAATTTC
* **
40208 AA-TCATTCAATGT-TTCAATTTCGATTCTTCAATGCCTCAATTTC
1 AATTC-TTCAAT-TCTTCAATTTCAATTCTTCAATGTTTCAATTTC
* *
40252 AAATCTTC-ATTGCTTCAATTTCAATTCTTCAATATTTCAATTTC
1 AATTCTTCAATT-CTTCAATTTCAATTCTTCAATGTTTCAATTTC
* *
40296 AATTCTTCAA-T-TTCAA--T--A-T-TTCAAT-TCTCCAAATTC
1 AATTCTTCAATTCTTCAATTTCAATTCTTCAATGT-TTCAATTTC
* * *
40332 AATCCTTCAAATGTC-TCAATTTCCATTCTCCAATGTTTCAATTTC
1 AATTCTTC-AAT-TCTTCAATTTCAATTCTTCAATGTTTCAATTTC
* * *
40377 AAATAT-TTCAACTCCTCAAATTCAATTCTTCAATGTTTCAATTTC
1 -AAT-TCTTCAATTCTTCAATTTCAATTCTTCAATGTTTCAATTTC
* *
40422 AATAT-TTCAATGCTTCAAATTCAATTCTTCAATGTTTCAATTTC
1 AAT-TCTTCAATTCTTCAATTTCAATTCTTCAATGTTTCAATTTC
* ** * *
40466 AGTAT-TTCAACGCTCCAATTTCAATTC--C------TCAAATTC
1 AAT-TCTTCAATTCTTCAATTTCAATTCTTCAATGTTTCAATTTC
* *
40502 AATTCTTCAATGT-TTCAATTTCAATAT-TTCAATGCTTCAAATTC
1 AATTCTTCAAT-TCTTCAATTTCAAT-TCTTCAATGTTTCAATTTC
40546 AATTCTTCAATGT-TTCAATTT
1 AATTCTTCAAT-TCTTCAATTT
40567 TAGTATTTCA
Statistics
Matches: 328, Mismatches: 37, Indels: 72
0.75 0.08 0.16
Matches are distributed among these distances:
35 2 0.01
36 45 0.14
37 4 0.01
38 2 0.01
39 5 0.02
40 1 0.00
41 4 0.01
42 39 0.12
43 4 0.01
44 170 0.52
45 45 0.14
46 7 0.02
ACGTcount: A:0.31, C:0.21, G:0.04, T:0.45
Consensus pattern (44 bp):
AATTCTTCAATTCTTCAATTTCAATTCTTCAATGTTTCAATTTC
Found at i:40332 original size:22 final size:22
Alignment explanation
Indices: 40139--40490 Score: 147
Period size: 22 Copynumber: 16.0 Consensus size: 22
40129 CAATTATTCA
*
40139 ATTTCCATTCTTCAATGTTTC-A-
1 ATTTCAATTCTTCAA--TTTCAAT
*
40161 ATTTCAATTCTTCAATTATTTAA-
1 ATTTCAATTCTTCAA-T-TTCAAT
40184 A-TTCAATGT-TTCAATTTC-A-
1 ATTTCAAT-TCTTCAATTTCAAT
40203 ATTTCAA-TCATTCAATGTTTC-A-
1 ATTTCAATTC-TTCAA--TTTCAAT
* *
40225 ATTTCGATTCTTCAATGCCTC-A-
1 ATTTCAATTCTTCAAT--TTCAAT
* *
40247 ATTTCAAATCTTCATTGCTTC-A-
1 ATTTCAATTCTTCAAT--TTCAAT
40269 ATTTCAATTCTTCAATATTTC-A-
1 ATTTCAATTCTTC-A-ATTTCAAT
40291 ATTTCAATTCTTCAATTTCAAT
1 ATTTCAATTCTTCAATTTCAAT
* *
40313 ATTTCAATTCTCCAAATTCAAT
1 ATTTCAATTCTTCAATTTCAAT
** *
40335 CCTTCAAATGTC-TCAATTTCCAT
1 ATTTC-AAT-TCTTCAATTTCAAT
*
40358 -TCTCCAATGT-TTCAATTTCAAAT
1 AT-TTCAAT-TCTTCAATTTC-AAT
* * *
40381 ATTTCAACTCCTCAAATTCAAT
1 ATTTCAATTCTTCAATTTCAAT
40403 -TCTTCAATGT-TTCAATTTCAAT
1 AT-TTCAAT-TCTTCAATTTCAAT
* *
40425 ATTTCAATGCTTCAAATTCAAT
1 ATTTCAATTCTTCAATTTCAAT
*
40447 -TCTTCAATGT-TTCAATTTCAGT
1 AT-TTCAAT-TCTTCAATTTCAAT
** *
40469 ATTTCAACGCTCCAATTTCAAT
1 ATTTCAATTCTTCAATTTCAAT
40491 TCCTCAAATT
Statistics
Matches: 262, Mismatches: 38, Indels: 60
0.73 0.11 0.17
Matches are distributed among these distances:
18 1 0.00
19 2 0.01
20 18 0.07
21 6 0.02
22 196 0.75
23 35 0.13
24 4 0.02
ACGTcount: A:0.30, C:0.21, G:0.04, T:0.45
Consensus pattern (22 bp):
ATTTCAATTCTTCAATTTCAAT
Found at i:40340 original size:36 final size:36
Alignment explanation
Indices: 40157--40341 Score: 102
Period size: 36 Copynumber: 5.1 Consensus size: 36
40147 TCTTCAATGT
* **
40157 TTCAATTTCAATTCTTCAATTATT-TAAATTCAATGT
1 TTCAATTTCAATTCTTCAA-TATTCCAAATTCAATCC
*
40193 TTCAATTTCAA-T-TTCAATCATT-CAATGTTTCAAT--
1 TTCAATTTCAATTCTTCAAT-ATTCCAA--ATTCAATCC
* * * * *
40227 TTCGATTCTTCAATGCCTCAAT-TT-CAAATCTTCATTGC
1 TTC-AAT-TTCAATTCTTCAATATTCCAAA--TTCAATCC
* * *
40265 TTCAATTTCAATTCTTCAATATTTCAATTTCAATTC
1 TTCAATTTCAATTCTTCAATATTCCAAATTCAATCC
40301 TTCAATTTCAATAT-TTCAAT-TCTCCAAATTCAATCC
1 TTCAATTTCAAT-TCTTCAATAT-TCCAAATTCAATCC
40337 TTCAA
1 TTCAA
40342 ATGTCTCAAT
Statistics
Matches: 118, Mismatches: 16, Indels: 30
0.72 0.10 0.18
Matches are distributed among these distances:
33 1 0.01
34 13 0.11
35 4 0.03
36 84 0.71
37 5 0.04
38 11 0.09
ACGTcount: A:0.31, C:0.21, G:0.03, T:0.46
Consensus pattern (36 bp):
TTCAATTTCAATTCTTCAATATTCCAAATTCAATCC
Found at i:40408 original size:8 final size:7
Alignment explanation
Indices: 40397--40567 Score: 68
Period size: 8 Copynumber: 23.3 Consensus size: 7
40387 ACTCCTCAAA
40397 TTCAATT
1 TTCAATT
40404 CTTCAATGT
1 -TTCAAT-T
40413 TTCAA-T
1 TTCAATT
40419 TTCAATAT
1 TTCAAT-T
*
40427 TTCAATGC
1 TTCAAT-T
*
40435 TTCAA-A
1 TTCAATT
40441 TTCAATT
1 TTCAATT
40448 CTTCAATGT
1 -TTCAAT-T
40457 TTCAA-T
1 TTCAATT
*
40463 TTCAGTAT
1 TTCAAT-T
**
40471 TTCAACGC
1 TTCAA-TT
*
40479 TCCAA-T
1 TTCAATT
40485 TTCAATT
1 TTCAATT
* *
40492 CCTCAA-A
1 -TTCAATT
40499 TTCAATT
1 TTCAATT
40506 CTTCAATGT
1 -TTCAAT-T
40515 TTCAA-T
1 TTCAATT
40521 TTCAATAT
1 TTCAAT-T
*
40529 TTCAATGC
1 TTCAAT-T
*
40537 TTCAA-A
1 TTCAATT
40543 TTCAATT
1 TTCAATT
40550 CTTCAATGT
1 -TTCAAT-T
40559 TTCAATT
1 TTCAATT
40566 TT
1 TT
40568 AGTATTTCAA
Statistics
Matches: 125, Mismatches: 19, Indels: 39
0.68 0.10 0.21
Matches are distributed among these distances:
6 35 0.28
7 4 0.03
8 82 0.66
9 4 0.03
ACGTcount: A:0.30, C:0.20, G:0.05, T:0.46
Consensus pattern (7 bp):
TTCAATT
Found at i:40474 original size:58 final size:57
Alignment explanation
Indices: 40405--40555 Score: 196
Period size: 58 Copynumber: 2.6 Consensus size: 57
40395 AATTCAATTC
* *
40405 TTCAATGTTTCAATTTCAATATTTCAATGCTTCAAATTCAATTCTTCAATGTTTCAAT
1 TTCAATATTTCAATTTCAA-ATTTCAATTCTTCAAATTCAATTCTTCAATGTTTCAAT
* ** * *
40463 TTCAGTATTTCAACGCTCCAATTTCAATTCCTCAAATTCAATTCTTCAATGTTTCAAT
1 TTCAATATTTCAA-TTTCAAATTTCAATTCTTCAAATTCAATTCTTCAATGTTTCAAT
40521 TTCAATATTTCAATGCTTCAAA-TTCAATTCTTCAA
1 TTCAATATTTCAAT--TTCAAATTTCAATTCTTCAA
40556 TGTTTCAATT
Statistics
Matches: 78, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
58 71 0.91
59 7 0.09
ACGTcount: A:0.31, C:0.21, G:0.05, T:0.44
Consensus pattern (57 bp):
TTCAATATTTCAATTTCAAATTTCAATTCTTCAAATTCAATTCTTCAATGTTTCAAT
Found at i:40557 original size:22 final size:22
Alignment explanation
Indices: 40485--40563 Score: 97
Period size: 22 Copynumber: 3.6 Consensus size: 22
40475 ACGCTCCAAT
* *
40485 TTCAATTCCTCAAATTCAATTC
1 TTCAATGCTTCAAATTCAATTC
* *
40507 TTCAATGTTTCAATTTCAATAT-
1 TTCAATGCTTCAAATTCAAT-TC
40529 TTCAATGCTTCAAATTCAATTC
1 TTCAATGCTTCAAATTCAATTC
*
40551 TTCAATGTTTCAA
1 TTCAATGCTTCAA
40564 TTTTAGTATT
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
21 1 0.02
22 46 0.96
23 1 0.02
ACGTcount: A:0.32, C:0.20, G:0.04, T:0.44
Consensus pattern (22 bp):
TTCAATGCTTCAAATTCAATTC
Found at i:40574 original size:44 final size:44
Alignment explanation
Indices: 40483--40887 Score: 172
Period size: 44 Copynumber: 9.2 Consensus size: 44
40473 CAACGCTCCA
* *
40483 ATTTCAATTCCTCAAATTCAATTCTTCAATGTTTCAATTTCAAT
1 ATTTCAATGCTTCAAATTCAATTCTTCAATGTTTCAATTTCAAT
* *
40527 ATTTCAATGCTTCAAATTCAATTCTTCAATGTTTCAATTTTAGT
1 ATTTCAATGCTTCAAATTCAATTCTTCAATGTTTCAATTTCAAT
* * * * * *
40571 ATTTCAACGCTCCAATTTCAATTCCTCAA--ATTCAATCCTTCCAT
1 ATTTCAATGCTTCAAATTCAATTCTTCAATGTTTCAAT--TTCAAT
* * *
40615 GTTTCAAT--TTCAATATGTC-ATTGCTTCAA--TTTCAGTATCACAGT
1 ATTTCAATGCTTCAA-AT-TCAATT-CTTCAATGTTTCAATTTCA-A-T
* * *
40659 GTTTCAATTCTTCAAATCTTCAA-T-TTCAAT-TCTTCAATTTCCAT
1 ATTTCAATGCTTCAAA--TTCAATTCTTCAATGT-TTCAATTTCAAT
* * * * *
40703 -TCTTCGATGCTTTAATTTCAATGC-TCCA-GTTTCAATTCTTCAA-
1 AT-TTCAATGCTTCAAATTCAATTCTTCAATGTTTCAA-T-TTCAAT
* * * *
40746 A-TACAAAG-TGTCAACGCTTCAA-T-TT-AAT-TCTTCAAATTCAGA-
1 ATTTCAATGCT-TCAA--ATTCAATTCTTCAATGT-TTCAATTTCA-AT
*
40788 ATGTCAATGCTTCAAATTCAATTCTTCAATGAATGCTTCAATTTCAAT
1 ATTTCAATGCTTCAAATTCAATTCTTCAATG--T--TTCAATTTCAAT
* * *
40836 GTTTCAATGCTGCAATTTCAATTCTTCAAT-TCTTCAATTTCAAT
1 ATTTCAATGCTTCAAATTCAATTCTTCAATGT-TTCAATTTCAAT
40880 -TCTTCAAT
1 AT-TTCAAT
40888 TATTTATTGT
Statistics
Matches: 274, Mismatches: 48, Indels: 78
0.69 0.12 0.19
Matches are distributed among these distances:
41 10 0.04
42 34 0.12
43 28 0.10
44 143 0.52
45 4 0.01
46 15 0.05
47 4 0.01
48 36 0.13
ACGTcount: A:0.30, C:0.21, G:0.06, T:0.43
Consensus pattern (44 bp):
ATTTCAATGCTTCAAATTCAATTCTTCAATGTTTCAATTTCAAT
Found at i:40576 original size:22 final size:22
Alignment explanation
Indices: 40494--40592 Score: 94
Period size: 22 Copynumber: 4.5 Consensus size: 22
40484 TTTCAATTCC
*
40494 TCAAATTCAAT-TCTTCAATGTT
1 TCAATTTCAATAT-TTCAATGTT
*
40516 TCAATTTCAATATTTCAATGCT
1 TCAATTTCAATATTTCAATGTT
*
40538 TCAAATTCAAT-TCTTCAATGTT
1 TCAATTTCAATAT-TTCAATGTT
* * * *
40560 TCAATTTTAGTATTTCAACGCT
1 TCAATTTCAATATTTCAATGTT
*
40582 CCAATTTCAAT
1 TCAATTTCAAT
40593 TCCTCAAATT
Statistics
Matches: 62, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
21 1 0.02
22 59 0.95
23 2 0.03
ACGTcount: A:0.31, C:0.19, G:0.05, T:0.44
Consensus pattern (22 bp):
TCAATTTCAATATTTCAATGTT
Found at i:40576 original size:58 final size:59
Alignment explanation
Indices: 40441--40630 Score: 174
Period size: 58 Copynumber: 3.3 Consensus size: 59
40431 ATGCTTCAAA
* * * * * * *
40441 TTCAATTCTTCAATGTTTCAATTTCAGTATTTCAACGCTCCAATTTCAATTCCTCAA--A
1 TTCAATT-TTCAATATTTCAATTTCAATATTTCAATGCTTCAAATTCAATTCTTCAATGT
*
40499 TTCAATTCTTCAATGTTTCAATTTCAATATTTCAATGCTTCAAATTCAATTCTTCAATGT
1 TTCAATT-TTCAATATTTCAATTTCAATATTTCAATGCTTCAAATTCAATTCTTCAATGT
* ** * * * * *
40559 TTCAATTTT-AGTATTTCAACGCTCCA-ATTTCAATTCCTCAAATTCAATCCTTCCATGT
1 TTCAATTTTCAATATTTCAA-TTTCAATATTTCAATGCTTCAAATTCAATTCTTCAATGT
40617 TTCAA-TTTCAATAT
1 TTCAATTTTCAATAT
40631 GTCATTGCTT
Statistics
Matches: 112, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
57 3 0.03
58 97 0.87
59 5 0.04
60 7 0.06
ACGTcount: A:0.29, C:0.22, G:0.05, T:0.44
Consensus pattern (59 bp):
TTCAATTTTCAATATTTCAATTTCAATATTTCAATGCTTCAAATTCAATTCTTCAATGT
Found at i:40645 original size:58 final size:58
Alignment explanation
Indices: 40527--40648 Score: 154
Period size: 58 Copynumber: 2.1 Consensus size: 58
40517 CAATTTCAAT
* * * * *
40527 ATTTCAATGCTTCAAATTCAATTCTTCAATGTTTCAATTTTAGTATTTCAACGCTCCA
1 ATTTCAATGCCTCAAATTCAATCCTTCAATGTTTCAATTTCAATATGTCAACGCTCCA
* * ** *
40585 ATTTCAATTCCTCAAATTCAATCCTTCCATGTTTCAATTTCAATATGTCATTGCTTCA
1 ATTTCAATGCCTCAAATTCAATCCTTCAATGTTTCAATTTCAATATGTCAACGCTCCA
40643 ATTTCA
1 ATTTCA
40649 GTATCACAGT
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
58 54 1.00
ACGTcount: A:0.29, C:0.22, G:0.06, T:0.43
Consensus pattern (58 bp):
ATTTCAATGCCTCAAATTCAATCCTTCAATGTTTCAATTTCAATATGTCAACGCTCCA
Found at i:40664 original size:22 final size:22
Alignment explanation
Indices: 40614--40667 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
40604 AATCCTTCCA
** *
40614 TGTTTCAATTTCAATATGTCAT
1 TGTTTCAATTTCAATATCACAG
* *
40636 TGCTTCAATTTCAGTATCACAG
1 TGTTTCAATTTCAATATCACAG
40658 TGTTTCAATT
1 TGTTTCAATT
40668 CTTCAAATCT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.26, C:0.17, G:0.11, T:0.46
Consensus pattern (22 bp):
TGTTTCAATTTCAATATCACAG
Found at i:40667 original size:102 final size:102
Alignment explanation
Indices: 40381--40648 Score: 473
Period size: 102 Copynumber: 2.6 Consensus size: 102
40371 AATTTCAAAT
*
40381 ATTTCAACTCCTCAAATTCAATTCTTCAATGTTTCAATTTCAATATTTCAATGCTTCAAATTCAA
1 ATTTCAATTCCTCAAATTCAATTCTTCAATGTTTCAATTTCAATATTTCAATGCTTCAAATTCAA
40446 TTCTTCAATGTTTCAATTTCAGTATTTCAACGCTCCA
66 TTCTTCAATGTTTCAATTTCAGTATTTCAACGCTCCA
40483 ATTTCAATTCCTCAAATTCAATTCTTCAATGTTTCAATTTCAATATTTCAATGCTTCAAATTCAA
1 ATTTCAATTCCTCAAATTCAATTCTTCAATGTTTCAATTTCAATATTTCAATGCTTCAAATTCAA
*
40548 TTCTTCAATGTTTCAATTTTAGTATTTCAACGCTCCA
66 TTCTTCAATGTTTCAATTTCAGTATTTCAACGCTCCA
* * * * *
40585 ATTTCAATTCCTCAAATTCAATCCTTCCATGTTTCAATTTCAATATGTCATTGCTTCAATTTCA
1 ATTTCAATTCCTCAAATTCAATTCTTCAATGTTTCAATTTCAATATTTCAATGCTTCAAATTCA
40649 GTATCACAGT
Statistics
Matches: 159, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
102 159 1.00
ACGTcount: A:0.30, C:0.22, G:0.05, T:0.43
Consensus pattern (102 bp):
ATTTCAATTCCTCAAATTCAATTCTTCAATGTTTCAATTTCAATATTTCAATGCTTCAAATTCAA
TTCTTCAATGTTTCAATTTCAGTATTTCAACGCTCCA
Found at i:40672 original size:8 final size:8
Alignment explanation
Indices: 40661--40697 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
40651 ATCACAGTGT
40661 TTCAATTC
1 TTCAATTC
*
40669 TTCAAATC
1 TTCAATTC
40677 TTCAA-T-
1 TTCAATTC
40683 TTCAATTC
1 TTCAATTC
40691 TTCAATT
1 TTCAATT
40698 TCCATTCTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
6 5 0.19
7 2 0.08
8 19 0.73
ACGTcount: A:0.30, C:0.22, G:0.00, T:0.49
Consensus pattern (8 bp):
TTCAATTC
Found at i:40692 original size:14 final size:14
Alignment explanation
Indices: 40669--40707 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
40659 GTTTCAATTC
*
40669 TTCAAATCTTCAAT
1 TTCAATTCTTCAAT
40683 TTCAATTCTTCAAT
1 TTCAATTCTTCAAT
*
40697 TTCCATTCTTC
1 TTCAATTCTTC
40708 GATGCTTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.49
Consensus pattern (14 bp):
TTCAATTCTTCAAT
Found at i:40777 original size:35 final size:36
Alignment explanation
Indices: 40733--40816 Score: 118
Period size: 35 Copynumber: 2.4 Consensus size: 36
40723 ATGCTCCAGT
40733 TTCAATTCTTCAAATACA-AAGTGTCAACGCTTC-AA
1 TTCAATTCTTCAAATACAGAA-TGTCAACGCTTCAAA
* * *
40768 TTTAATTCTTCAAATTCAGAATGTCAATGCTTCAAA
1 TTCAATTCTTCAAATACAGAATGTCAACGCTTCAAA
40804 TTCAATTCTTCAA
1 TTCAATTCTTCAA
40817 TGAATGCTTC
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
35 27 0.63
36 16 0.37
ACGTcount: A:0.36, C:0.20, G:0.07, T:0.37
Consensus pattern (36 bp):
TTCAATTCTTCAAATACAGAATGTCAACGCTTCAAA
Found at i:40808 original size:14 final size:14
Alignment explanation
Indices: 40791--40842 Score: 54
Period size: 14 Copynumber: 3.9 Consensus size: 14
40781 ATTCAGAATG
40791 TCAATGCTTCAAAT
1 TCAATGCTTCAAAT
*
40805 TCAATTCTTC-AA-
1 TCAATGCTTCAAAT
* *
40817 TGAATGCTTCAATT
1 TCAATGCTTCAAAT
*
40831 TCAATGTTTCAA
1 TCAATGCTTCAA
40843 TGCTGCAATT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
12 8 0.27
13 3 0.10
14 19 0.63
ACGTcount: A:0.33, C:0.19, G:0.08, T:0.40
Consensus pattern (14 bp):
TCAATGCTTCAAAT
Found at i:40815 original size:8 final size:8
Alignment explanation
Indices: 40804--40888 Score: 58
Period size: 8 Copynumber: 10.9 Consensus size: 8
40794 ATGCTTCAAA
40804 TTCAATTC
1 TTCAATTC
40812 TTCAATGAATGC
1 TTCAAT---T-C
40824 TTCAA-T-
1 TTCAATTC
40830 TTCAATGT-
1 TTCAAT-TC
*
40838 TTCAATGC
1 TTCAATTC
*
40846 TGCAATT-
1 TTCAATTC
40853 T-CAATTC
1 TTCAATTC
40860 TTCAATTC
1 TTCAATTC
40868 TTCAA-T-
1 TTCAATTC
40874 TTCAATTC
1 TTCAATTC
40882 TTCAATT
1 TTCAATT
40889 ATTTATTGTT
Statistics
Matches: 63, Mismatches: 3, Indels: 22
0.72 0.03 0.25
Matches are distributed among these distances:
6 15 0.24
7 4 0.06
8 37 0.59
11 1 0.02
12 6 0.10
ACGTcount: A:0.28, C:0.20, G:0.06, T:0.46
Consensus pattern (8 bp):
TTCAATTC
Found at i:40816 original size:22 final size:22
Alignment explanation
Indices: 40791--40887 Score: 115
Period size: 22 Copynumber: 4.2 Consensus size: 22
40781 ATTCAGAATG
*
40791 TCAATGCTTCAAATTCAATTCT
1 TCAATGCTTCAATTTCAATTCT
40813 TCAATGAATGCTTCAATTTCAATGT-T
1 TC----AATGCTTCAATTTCAAT-TCT
*
40839 TCAATGCTGCAATTTCAATTCT
1 TCAATGCTTCAATTTCAATTCT
*
40861 TCAATTCTTCAATTTCAATTCT
1 TCAATGCTTCAATTTCAATTCT
40883 TCAAT
1 TCAAT
40888 TATTTATTGT
Statistics
Matches: 65, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
21 1 0.02
22 44 0.68
26 19 0.29
27 1 0.02
ACGTcount: A:0.30, C:0.21, G:0.06, T:0.43
Consensus pattern (22 bp):
TCAATGCTTCAATTTCAATTCT
Found at i:40827 original size:26 final size:26
Alignment explanation
Indices: 40793--40844 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
40783 TCAGAATGTC
40793 AATGCTTCAAATTCAAT-TCTTCAATG
1 AATGCTTCAAATTCAATGT-TTCAATG
*
40819 AATGCTTCAATTTCAATGTTTCAATG
1 AATGCTTCAAATTCAATGTTTCAATG
40845 CTGCAATTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 23 0.96
27 1 0.04
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (26 bp):
AATGCTTCAAATTCAATGTTTCAATG
Found at i:40865 original size:14 final size:14
Alignment explanation
Indices: 40860--40888 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
40850 ATTTCAATTC
40860 TTCAATTCTTCAAT
1 TTCAATTCTTCAAT
40874 TTCAATTCTTCAAT
1 TTCAATTCTTCAAT
40888 T
1 T
40889 ATTTATTGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.21, G:0.00, T:0.52
Consensus pattern (14 bp):
TTCAATTCTTCAAT
Found at i:40953 original size:24 final size:24
Alignment explanation
Indices: 40926--40990 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 24
40916 TCCAGGGTGG
40926 TCTTTCTTCGTTCTTCAATTTATT
1 TCTTTCTTCGTTCTTCAATTTATT
**
40950 TC-TTC--AATTCTTCAA-TTATT
1 TCTTTCTTCGTTCTTCAATTTATT
* *
40970 TGTTGCTTCAGTTCTTCAATT
1 TCTTTCTTC-GTTCTTCAATT
40991 ATTCAAATGC
Statistics
Matches: 30, Mismatches: 6, Indels: 9
0.67 0.13 0.20
Matches are distributed among these distances:
20 6 0.20
21 10 0.33
23 3 0.10
24 10 0.33
25 1 0.03
ACGTcount: A:0.17, C:0.20, G:0.06, T:0.57
Consensus pattern (24 bp):
TCTTTCTTCGTTCTTCAATTTATT
Found at i:40991 original size:24 final size:22
Alignment explanation
Indices: 40928--40993 Score: 82
Period size: 24 Copynumber: 3.0 Consensus size: 22
40918 CAGGGTGGTC
*
40928 TTTCTTC-GTTCTTCAATT-TA
1 TTTCTTCAGTTCTTCAATTATT
*
40948 TTTCTTCAATTCTTCAATTATT
1 TTTCTTCAGTTCTTCAATTATT
40970 TGTTGCTTCAGTTCTTCAATTATT
1 T-TT-CTTCAGTTCTTCAATTATT
40994 CAAATGCTTC
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
20 7 0.18
21 10 0.26
22 2 0.05
23 2 0.05
24 18 0.46
ACGTcount: A:0.18, C:0.18, G:0.06, T:0.58
Consensus pattern (22 bp):
TTTCTTCAGTTCTTCAATTATT
Found at i:41593 original size:42 final size:43
Alignment explanation
Indices: 41542--41635 Score: 138
Period size: 45 Copynumber: 2.2 Consensus size: 43
41532 AGCGTTTTAA
* *
41542 CTAA-ATTCTA-CTCCATCTCTAGGTAATTCATCCAAATAAAG
1 CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG
41583 CTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAG
1 CTAATATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAG
41628 CTAATATT
1 CTAATATT
41636 AATTGTTGTT
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
41 4 0.09
42 6 0.13
45 37 0.79
ACGTcount: A:0.37, C:0.23, G:0.05, T:0.34
Consensus pattern (43 bp):
CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG
Done.