Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr7
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: 55462051
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2780933 characters in sequence are not A, C, G, or T
File 1 of 163
Found at i:407 original size:27 final size:25
Alignment explanation
Indices: 372--421 Score: 64
Period size: 27 Copynumber: 1.9 Consensus size: 25
362 GTATATATGA
*
372 TGTAATTTGGACTTTTGGACTGTTTGC
1 TGTAATTTGGA-TTTT-AACTGTTTGC
*
399 TGTACTTTGGATTTTAACTGTTT
1 TGTAATTTGGATTTTAACTGTTT
422 ACATGGACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 7 0.33
26 4 0.19
27 10 0.48
ACGTcount: A:0.16, C:0.10, G:0.22, T:0.52
Consensus pattern (25 bp):
TGTAATTTGGATTTTAACTGTTTGC
Found at i:4338 original size:71 final size:71
Alignment explanation
Indices: 4261--4399 Score: 215
Period size: 71 Copynumber: 2.0 Consensus size: 71
4251 ACCTAAGTGT
* * * * *
4261 CTAATAAATGTACTCTCATTGATACCACAATTCAAACATTTAGAATCTAACCCACTTACATCATT
1 CTAATAAATGCACCCTCATTGATACCACAATTCAAACATTTAGAATCCAAACCACATACATCATT
4326 TCCTGC
66 TCCTGC
* *
4332 CTAATAAATGCACCCTCATTGGTACCACAATTCAAACATTTAGAATCCAAATCACATACATCATT
1 CTAATAAATGCACCCTCATTGATACCACAATTCAAACATTTAGAATCCAAACCACATACATCATT
4397 TCC
66 TCC
4400 CAAAATACAA
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
71 61 1.00
ACGTcount: A:0.37, C:0.27, G:0.06, T:0.30
Consensus pattern (71 bp):
CTAATAAATGCACCCTCATTGATACCACAATTCAAACATTTAGAATCCAAACCACATACATCATT
TCCTGC
Found at i:5304 original size:25 final size:27
Alignment explanation
Indices: 5275--5333 Score: 70
Period size: 25 Copynumber: 2.3 Consensus size: 27
5265 CATATCTATC
5275 CATATAAAAATTT-CATATAA-C-ACTT
1 CATATAAAAATTTCCATATAATCGA-TT
**
5300 CATATAATTATTTCCATATAATCGATT
1 CATATAAAAATTTCCATATAATCGATT
5327 CATATAA
1 CATATAA
5334 TTATTTCTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
25 11 0.38
26 7 0.24
27 10 0.34
28 1 0.03
ACGTcount: A:0.44, C:0.15, G:0.02, T:0.39
Consensus pattern (27 bp):
CATATAAAAATTTCCATATAATCGATT
Found at i:5319 original size:14 final size:14
Alignment explanation
Indices: 5300--5340 Score: 50
Period size: 13 Copynumber: 3.0 Consensus size: 14
5290 TATAACACTT
5300 CATATAATTATTTC
1 CATATAATTATTTC
*
5314 CATATAATCGA-TT-
1 CATATAAT-TATTTC
5327 CATATAATTATTTC
1 CATATAATTATTTC
5341 TTTTATCTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 6
0.73 0.07 0.20
Matches are distributed among these distances:
12 1 0.05
13 10 0.45
14 10 0.45
15 1 0.05
ACGTcount: A:0.37, C:0.15, G:0.02, T:0.46
Consensus pattern (14 bp):
CATATAATTATTTC
Found at i:5383 original size:13 final size:13
Alignment explanation
Indices: 5365--5445 Score: 72
Period size: 13 Copynumber: 6.2 Consensus size: 13
5355 CTTTAACTGA
5365 TTCATATAACCAT
1 TTCATATAACCAT
* * *
5378 TACATATATCTAT
1 TTCATATAACCAT
*
5391 TTCTATATAACCAA
1 TTC-ATATAACCAT
* *
5405 TTCTTATAATCAT
1 TTCATATAACCAT
*
5418 TTCACATAACCAT
1 TTCATATAACCAT
* *
5431 TTCGTATAGCCAT
1 TTCATATAACCAT
5444 TT
1 TT
5446 AAAAGTGTTA
Statistics
Matches: 51, Mismatches: 16, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
13 41 0.80
14 10 0.20
ACGTcount: A:0.35, C:0.21, G:0.02, T:0.42
Consensus pattern (13 bp):
TTCATATAACCAT
Found at i:6629 original size:19 final size:19
Alignment explanation
Indices: 6577--6629 Score: 51
Period size: 19 Copynumber: 2.9 Consensus size: 19
6567 CAAGATGACT
6577 TACAACAATTTCAAAAA-C
1 TACAACAATTTCAAAAATC
* *
6595 -ATAA-AATTT-ATGAAATC
1 TACAACAATTTCA-AAAATC
6612 TACAACAATTTCAAAAAT
1 TACAACAATTTCAAAAAT
6630 GGAGTTTTGG
Statistics
Matches: 26, Mismatches: 4, Indels: 9
0.67 0.10 0.23
Matches are distributed among these distances:
15 1 0.04
16 8 0.31
17 4 0.15
18 3 0.12
19 9 0.35
20 1 0.04
ACGTcount: A:0.55, C:0.15, G:0.02, T:0.28
Consensus pattern (19 bp):
TACAACAATTTCAAAAATC
Found at i:8098 original size:17 final size:19
Alignment explanation
Indices: 8066--8100 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
8056 GTCGATTAGG
8066 TTAATTTAGATTTAATAAT
1 TTAATTTAGATTTAATAAT
8085 TTAA-TTAG-TTTAATAA
1 TTAATTTAGATTTAATAA
8101 ATCTATTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 4 0.25
19 4 0.25
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (19 bp):
TTAATTTAGATTTAATAAT
Found at i:9027 original size:154 final size:147
Alignment explanation
Indices: 8751--9032 Score: 440
Period size: 154 Copynumber: 1.9 Consensus size: 147
8741 TGACTAAAGC
8751 TATTGTTTTTGAAGTCAATTACCCTTAAAGTGGTAGGCAGAGCACTACTTTACACTGCAAAAGCG
1 TATTGTTTTTGAAGTCAATTACCCTTAAAGTGGTAGGCAGAGCACTACTTTACACTGCAAAAGCG
8816 TGTGGGACATCCACATTGAAAACAATTGTACGACTTCTCCAGCAAATTCAAAGTCTAGTCCTTAG
66 TGTGGGACATCCACATTGAAAACAATTGTACGACTTCTCCAGCAAATTCAAAGTCTAGTCCTTAG
8881 GATTTGGGAACCAATTA
131 GATTTGGGAACCAATTA
* *
8898 TATTGTTTTTTAAGTCAATTACCCTTTAAAG-GTGTAGGCAGAGCACTACTTTATACTGCAAAAG
1 TATTGTTTTTGAAGTCAATTACCC-TTAAAGTG-GTAGGCAGAGCACTACTTTACACTGCAAAAG
* * *
8962 CGTGTTGGAGTTGGACATTCACATTGAAAATAATTGTACGACTTCTCCAGCAAATTCGAAGTCTA
64 CGTG-T---G--GGACATCCACATTGAAAACAATTGTACGACTTCTCCAGCAAATTCAAAGTCTA
9027 GTCCTT
123 GTCCTT
9033 GGGAACCAAT
Statistics
Matches: 122, Mismatches: 5, Indels: 9
0.90 0.04 0.07
Matches are distributed among these distances:
147 24 0.20
148 40 0.33
149 1 0.01
152 1 0.01
154 56 0.46
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.32
Consensus pattern (147 bp):
TATTGTTTTTGAAGTCAATTACCCTTAAAGTGGTAGGCAGAGCACTACTTTACACTGCAAAAGCG
TGTGGGACATCCACATTGAAAACAATTGTACGACTTCTCCAGCAAATTCAAAGTCTAGTCCTTAG
GATTTGGGAACCAATTA
Found at i:9870 original size:16 final size:15
Alignment explanation
Indices: 9849--9880 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
9839 GTTCAAATAT
9849 ATAATAATTATAAAAA
1 ATAATAA-TATAAAAA
9865 ATAATAATATAAAAA
1 ATAATAATATAAAAA
9880 A
1 A
9881 CTTGACATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (15 bp):
ATAATAATATAAAAA
Found at i:10041 original size:18 final size:19
Alignment explanation
Indices: 10015--10050 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
10005 TTAATGTTAA
*
10015 ATAATTTTA-ATATTTTTT
1 ATAAATTTATATATTTTTT
10033 ATAAATTTATATATTTTT
1 ATAAATTTATATATTTTT
10051 AAATATTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
ATAAATTTATATATTTTTT
Found at i:10051 original size:18 final size:18
Alignment explanation
Indices: 10015--10068 Score: 53
Period size: 18 Copynumber: 3.1 Consensus size: 18
10005 TTAATGTTAA
*
10015 ATAATTTTA-ATATTTTTT
1 ATAAATTTATATA-TTTTT
10033 ATAAATTTATATATTTTT
1 ATAAATTTATATATTTTT
10051 A-AATATTT-T-TATTTTT
1 ATAA-ATTTATATATTTTT
10067 AT
1 AT
10069 TAATGCTTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
16 8 0.25
17 3 0.09
18 18 0.56
19 3 0.09
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
ATAAATTTATATATTTTT
Found at i:16540 original size:213 final size:212
Alignment explanation
Indices: 16151--16563 Score: 729
Period size: 213 Copynumber: 1.9 Consensus size: 212
16141 NNNNNNNNNN
16151 AGCAACCTTTAAGATAGAATCTCTCGAGAGATTTCAATTTGCAAAAGCTGCCAGGAAGGCAAACA
1 AGCAACCTTTAAGATAGAATCTCTCGAGAGATTTCAATTTGCAAAAGCTGCCAGGAAGGCAAACA
16216 AGGTTTTCACAGTTGTTCATATGCAAATTCTCAAGACCAATAAGATTGCCAATTGAGGATGGTAA
66 AGGTTTTCACAGTTGTTCATATGCAAATTCTCAAGACCAATAAGATTGCCAATTGAGGATGGTAA
* * * * * *
16281 TTCCTTCAAAGCCGTTCCACTGAAATCAAGTTCATACAACCTCTCCATGGTGTCCATGATTTCTG
131 TTCCTTCAAAGCCATTCCACTGAAAACAAGTGCATACAAACTCTCCATGGTGCCCACGATTTCT-
16346 GGAAAATCTCCAATCTCA
195 GGAAAATCTCCAATCTCA
16364 AGCAACCTTTAAGATAGAATCTCTCGAGAGATTTCAATTTGCAAAAGCTGCCAGGAAGGCAAACA
1 AGCAACCTTTAAGATAGAATCTCTCGAGAGATTTCAATTTGCAAAAGCTGCCAGGAAGGCAAACA
16429 AGGTTTTCACAGTTGTTCATATGCAAATTCTCAAGACCAATAAGATTGCCAATTGAGGATGGTAA
66 AGGTTTTCACAGTTGTTCATATGCAAATTCTCAAGACCAATAAGATTGCCAATTGAGGATGGTAA
* *
16494 TTCCTTCAAAGCCATTCCACTTAAAACAAGATGCCT-CAAACTCTCCATGGTGCCCACGATTTCT
131 TTCCTTCAAAGCCATTCCACTGAAAACAAG-TGCATACAAACTCTCCATGGTGCCCACGATTTCT
16558 GGAAAA
195 GGAAAA
16564 CTACACAGAT
Statistics
Matches: 191, Mismatches: 8, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
212 6 0.03
213 182 0.95
214 3 0.02
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (212 bp):
AGCAACCTTTAAGATAGAATCTCTCGAGAGATTTCAATTTGCAAAAGCTGCCAGGAAGGCAAACA
AGGTTTTCACAGTTGTTCATATGCAAATTCTCAAGACCAATAAGATTGCCAATTGAGGATGGTAA
TTCCTTCAAAGCCATTCCACTGAAAACAAGTGCATACAAACTCTCCATGGTGCCCACGATTTCTG
GAAAATCTCCAATCTCA
Found at i:36930 original size:20 final size:19
Alignment explanation
Indices: 36903--36962 Score: 68
Period size: 19 Copynumber: 3.1 Consensus size: 19
36893 AGCAATTAAT
36903 TTTAAAAATTATAAAAATTA
1 TTTAAAAA-TATAAAAATTA
*
36923 TTTGAAAAA-ATTAAAATTA
1 TTT-AAAAATATAAAAATTA
*
36942 TTTAAAAAGTATACAAATTA
1 TTTAAAAA-TATAAAAATTA
36962 T
1 T
36963 AAAAAAAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
18 5 0.15
19 12 0.35
20 12 0.35
21 5 0.15
ACGTcount: A:0.57, C:0.02, G:0.03, T:0.38
Consensus pattern (19 bp):
TTTAAAAATATAAAAATTA
Found at i:39717 original size:6 final size:6
Alignment explanation
Indices: 39706--39733 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
39696 GGATATCTCT
39706 CTTCCC CTTCCC CTTCCC CTTCCC CTTC
1 CTTCCC CTTCCC CTTCCC CTTCCC CTTC
39734 GCCTAAGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.64, G:0.00, T:0.36
Consensus pattern (6 bp):
CTTCCC
Found at i:41105 original size:22 final size:22
Alignment explanation
Indices: 41061--41105 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
41051 AAATAAGTAA
* * *
41061 TAAAATATTTAATAGATAAATT
1 TAAAATATATAATACACAAATT
*
41083 TAAAATATATAATACACATATT
1 TAAAATATATAATACACAAATT
41105 T
1 T
41106 TATTTTGTTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.40
Consensus pattern (22 bp):
TAAAATATATAATACACAAATT
Found at i:51346 original size:20 final size:22
Alignment explanation
Indices: 51321--51380 Score: 79
Period size: 24 Copynumber: 2.7 Consensus size: 22
51311 CACATGACTG
51321 TAACTAACCCTACTGCAGCCTAAC
1 TAACTAACCCTACTGCAGCC--AC
*
51345 TAACTAACCCTACTACAG-C-C
1 TAACTAACCCTACTGCAGCCAC
51365 TAACTAACCCTACTGC
1 TAACTAACCCTACTGC
51381 TAATTACACG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 16 0.47
23 1 0.03
24 17 0.50
ACGTcount: A:0.33, C:0.38, G:0.07, T:0.22
Consensus pattern (22 bp):
TAACTAACCCTACTGCAGCCAC
Found at i:51353 original size:24 final size:24
Alignment explanation
Indices: 51321--51372 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
51311 CACATGACTG
*
51321 TAACTAACCCTACTGCAGCCTAAC
1 TAACTAACCCTACTACAGCCTAAC
51345 TAACTAACCCTACTACAGCCTAAC
1 TAACTAACCCTACTACAGCCTAAC
51369 TAAC
1 TAAC
51373 CCTACTGCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.37, C:0.37, G:0.06, T:0.21
Consensus pattern (24 bp):
TAACTAACCCTACTACAGCCTAAC
Found at i:51971 original size:25 final size:25
Alignment explanation
Indices: 51943--52049 Score: 160
Period size: 25 Copynumber: 4.3 Consensus size: 25
51933 GTTTATATAT
* *
51943 TTATGTATTATGTAAATTATGTAAC
1 TTATGTATTATGTAAGTTATGTAAG
*
51968 TTATGTATTATGTAAGTTATGAAAG
1 TTATGTATTATGTAAGTTATGTAAG
* *
51993 TTGTGTATTACGTAAGTTATGTAAG
1 TTATGTATTATGTAAGTTATGTAAG
*
52018 TTGTGTATTATGTAAGTTATGTAAG
1 TTATGTATTATGTAAGTTATGTAAG
52043 TTATGTA
1 TTATGTA
52050 AGCTATAAAT
Statistics
Matches: 74, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 74 1.00
ACGTcount: A:0.32, C:0.02, G:0.20, T:0.47
Consensus pattern (25 bp):
TTATGTATTATGTAAGTTATGTAAG
Found at i:51977 original size:16 final size:17
Alignment explanation
Indices: 51959--52051 Score: 86
Period size: 16 Copynumber: 5.5 Consensus size: 17
51949 ATTATGTAAA
*
51959 TTATGTAACTTATGTA-
1 TTATGTAAGTTATGTAG
*
51975 TTATGTAAGTTATGAAAG
1 TTATGTAAGTTATG-TAG
* *
51993 TTGTGT-A-TTACGTAAG
1 TTATGTAAGTTATGT-AG
*
52009 TTATGTAAGTTGTGTA-
1 TTATGTAAGTTATGTAG
52025 TTATGTAAGTTATGTAAG
1 TTATGTAAGTTATGT-AG
52043 TTATGTAAG
1 TTATGTAAG
52052 CTATAAATTT
Statistics
Matches: 61, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
16 38 0.62
17 5 0.08
18 18 0.30
ACGTcount: A:0.31, C:0.02, G:0.22, T:0.45
Consensus pattern (17 bp):
TTATGTAAGTTATGTAG
Found at i:52051 original size:9 final size:9
Alignment explanation
Indices: 51950--52051 Score: 108
Period size: 9 Copynumber: 12.0 Consensus size: 9
51940 TATTTATGTA
*
51950 TTATGTAAA
1 TTATGTAAG
*
51959 TTATGTAAC
1 TTATGTAAG
51968 TTATGT-A-
1 TTATGTAAG
51975 TTATGTAAG
1 TTATGTAAG
*
51984 TTATGAAAG
1 TTATGTAAG
*
51993 TTGTGT-A-
1 TTATGTAAG
*
52000 TTACGTAAG
1 TTATGTAAG
52009 TTATGTAAG
1 TTATGTAAG
*
52018 TTGTGT-A-
1 TTATGTAAG
52025 TTATGTAAG
1 TTATGTAAG
52034 TTATGTAAG
1 TTATGTAAG
52043 TTATGTAAG
1 TTATGTAAG
52052 CTATAAATTT
Statistics
Matches: 78, Mismatches: 9, Indels: 12
0.79 0.09 0.12
Matches are distributed among these distances:
7 15 0.19
8 6 0.08
9 57 0.73
ACGTcount: A:0.32, C:0.02, G:0.21, T:0.45
Consensus pattern (9 bp):
TTATGTAAG
Found at i:57663 original size:9 final size:9
Alignment explanation
Indices: 57650--57965 Score: 323
Period size: 9 Copynumber: 37.4 Consensus size: 9
57640 TATTTATGTA
*
57650 TTATGTAAA
1 TTATGTAAG
*
57659 TTATGTAAC
1 TTATGTAAG
57668 TTATGTAA-
1 TTATGTAAG
57676 -TATGTAAG
1 TTATGTAAG
57684 TTATGTAAG
1 TTATGTAAG
*
57693 TTGTGT-A-
1 TTATGTAAG
57700 TTATGTAAG
1 TTATGTAAG
*
57709 TTATGTGAG
1 TTATGTAAG
57718 TTATGTAAG
1 TTATGTAAG
*
57727 CTATGT-A-
1 TTATGTAAG
57734 TTATGTAAG
1 TTATGTAAG
57743 TTATGTAAG
1 TTATGTAAG
*
57752 TTCTGT-A-
1 TTATGTAAG
57759 TTATGTAAG
1 TTATGTAAG
57768 TTATGTAAG
1 TTATGTAAG
**
57777 TTATGTGCG
1 TTATGTAAG
**
57786 TTATGTGCG
1 TTATGTAAG
*
57795 TTATATAAG
1 TTATGTAAG
*
57804 TTACGT-A-
1 TTATGTAAG
57811 TTATGTAAG
1 TTATGTAAG
57820 TTATGTAAG
1 TTATGTAAG
* *
57829 CTGTGT-A-
1 TTATGTAAG
57836 TTATGTAAG
1 TTATGTAAG
57845 TTATGTAAG
1 TTATGTAAG
*
57854 TTCTGT-A-
1 TTATGTAAG
57861 TTATGTAAG
1 TTATGTAAG
57870 TTATGTAAG
1 TTATGTAAG
57879 TTATGTAAG
1 TTATGTAAG
57888 TTATGT-A-
1 TTATGTAAG
57895 TTATGTAAG
1 TTATGTAAG
57904 TTATGTAAG
1 TTATGTAAG
*
57913 TTATATAAG
1 TTATGTAAG
57922 TTATGT-A-
1 TTATGTAAG
57929 TTATGT-A-
1 TTATGTAAG
* *
57936 TTATTTATG
1 TTATGTAAG
57945 -TATGTAAG
1 TTATGTAAG
57953 TTATGTAAG
1 TTATGTAAG
57962 TTAT
1 TTAT
57966 AAATTTTAAA
Statistics
Matches: 259, Mismatches: 29, Indels: 38
0.79 0.09 0.12
Matches are distributed among these distances:
7 54 0.21
8 21 0.08
9 184 0.71
ACGTcount: A:0.30, C:0.03, G:0.20, T:0.47
Consensus pattern (9 bp):
TTATGTAAG
Found at i:57671 original size:25 final size:27
Alignment explanation
Indices: 57643--57965 Score: 278
Period size: 25 Copynumber: 12.8 Consensus size: 27
57633 GTTTATATAT
*
57643 TTATGT-A-TTATGTAAATTATGTAAC
1 TTATGTAAGTTATGTAAATTATGTAAG
*
57668 TTATGTAA--TATGTAAGTTATGTAAG
1 TTATGTAAGTTATGTAAATTATGTAAG
* * *
57693 TTGTGT-A-TTATGTAAGTTATGTGAG
1 TTATGTAAGTTATGTAAATTATGTAAG
*
57718 TTATGTAAGCTATGT--ATTATGTAAG
1 TTATGTAAGTTATGTAAATTATGTAAG
*
57743 TTATGTAAGTTCTGT--ATTATGTAAG
1 TTATGTAAGTTATGTAAATTATGTAAG
*** **
57768 TTATGTAAGTTATGTGCGTTATGTGCG
1 TTATGTAAGTTATGTAAATTATGTAAG
* *
57795 TTATATAAGTTACGT--ATTATGTAAG
1 TTATGTAAGTTATGTAAATTATGTAAG
* *
57820 TTATGTAAGCTGTGT--ATTATGTAAG
1 TTATGTAAGTTATGTAAATTATGTAAG
*
57845 TTATGTAAGTTCTGT--ATTATGTAAG
1 TTATGTAAGTTATGTAAATTATGTAAG
*
57870 TTATGTAAGTTATGTAAGTTATGT-A-
1 TTATGTAAGTTATGTAAATTATGTAAG
* *
57895 TTATGTAAGTTATGTAAGTTATATAAG
1 TTATGTAAGTTATGTAAATTATGTAAG
* *
57922 TTATGT-A-TTATGT--ATTATTTATG
1 TTATGTAAGTTATGTAAATTATGTAAG
*
57945 -TATGTAAGTTATGTAAGTTAT
1 TTATGTAAGTTATGTAAATTAT
57966 AAATTTTAAA
Statistics
Matches: 252, Mismatches: 32, Indels: 27
0.81 0.10 0.09
Matches are distributed among these distances:
22 5 0.02
23 8 0.03
24 7 0.03
25 186 0.74
26 9 0.04
27 37 0.15
ACGTcount: A:0.30, C:0.02, G:0.20, T:0.47
Consensus pattern (27 bp):
TTATGTAAGTTATGTAAATTATGTAAG
Found at i:57689 original size:34 final size:34
Alignment explanation
Indices: 57650--57965 Score: 237
Period size: 34 Copynumber: 9.4 Consensus size: 34
57640 TATTTATGTA
57650 TTATGTAAATTATGTAACTTATGTAA-TATGTAAG
1 TTATGTAAATTATGTAA-TTATGTAAGTATGTAAG
* * *
57684 TTATGTAAGTTGTGT-ATTATGTAAGTTATGTGAG
1 TTATGTAAATTATGTAATTATGTAAG-TATGTAAG
**
57718 TTATGTAAGCTATGT-ATTATGTAAGTTATGTAAG
1 TTATGTAAATTATGTAATTATGTAAG-TATGTAAG
* **
57752 TTCTGT--ATTATGTAAGTTATGTAAGTTATGTGCG
1 TTATGTAAATTATGTAA-TTATGTAAG-TATGTAAG
*** * * *
57786 TTATGTGCGTTATATAAGTTACGT-ATTATGTAAG
1 TTATGTAAATTATGTAA-TTATGTAAGTATGTAAG
** *
57820 TTATGTAAGCTGTGT-ATTATGTAAGTTATGTAAG
1 TTATGTAAATTATGTAATTATGTAAG-TATGTAAG
*
57854 TTCTGT--ATTATGTAAGTTATGTAAGTTATGTAAG
1 TTATGTAAATTATGTAA-TTATGTAAG-TATGTAAG
*
57888 TTATGT--ATTATGTAAGTTATGTAAGTTATATAAG
1 TTATGTAAATTATGTAA-TTATGTAAG-TATGTAAG
* *
57922 TTATGT--ATTATGT-ATTATTTATGTATGTAAG
1 TTATGTAAATTATGTAATTATGTAAGTATGTAAG
*
57953 TTATGTAAGTTAT
1 TTATGTAAATTAT
57966 AAATTTTAAA
Statistics
Matches: 235, Mismatches: 35, Indels: 25
0.80 0.12 0.08
Matches are distributed among these distances:
31 13 0.06
32 29 0.12
33 10 0.04
34 169 0.72
35 1 0.00
36 13 0.06
ACGTcount: A:0.30, C:0.03, G:0.20, T:0.47
Consensus pattern (34 bp):
TTATGTAAATTATGTAATTATGTAAGTATGTAAG
Found at i:60081 original size:17 final size:19
Alignment explanation
Indices: 60059--60093 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
60049 TCTTAATAAT
60059 ATTTT-AATTTT-TTTAAC
1 ATTTTAAATTTTATTTAAC
60076 ATTTTAAATTTTATTTAA
1 ATTTTAAATTTTATTTAA
60094 TACTTTTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 6 0.38
19 5 0.31
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (19 bp):
ATTTTAAATTTTATTTAAC
Found at i:60082 original size:28 final size:29
Alignment explanation
Indices: 60046--60141 Score: 83
Period size: 30 Copynumber: 3.3 Consensus size: 29
60036 ATTTCGATAT
*
60046 CATTCTTAATAATATTTTAAT-TTTTTTAA
1 CATT-TTAATAATATTTTAATATTTTATAA
* *
60075 CATTTTAA-ATTTTATTTAATACTTTTATAA
1 CATTTTAATAATAT-TTTAATA-TTTTATAA
60105 -ATTTTAATAATATTTTACATA-TTTATAAA
1 CATTTTAATAATATTTTA-ATATTTTAT-AA
*
60134 AATTTTAA
1 CATTTTAA
60142 AAATTAAAAT
Statistics
Matches: 55, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
27 3 0.05
28 15 0.27
29 17 0.31
30 20 0.36
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (29 bp):
CATTTTAATAATATTTTAATATTTTATAA
Found at i:60194 original size:30 final size:30
Alignment explanation
Indices: 60136--60194 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
60126 TTTATAAAAA
* *
60136 TTTTAAAAATTAAAATTTTAAAAGAATTAT
1 TTTTAAAAATTAAAACTTTAAAAAAATTAT
*
60166 TTTTAAAAATT-AAGCTTTAAAATAAATTA
1 TTTTAAAAATTAAAACTTTAAAA-AAATTA
60195 ACCCTGGACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 9 0.36
30 16 0.64
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.42
Consensus pattern (30 bp):
TTTTAAAAATTAAAACTTTAAAAAAATTAT
Found at i:63934 original size:81 final size:82
Alignment explanation
Indices: 63775--63937 Score: 319
Period size: 81 Copynumber: 2.0 Consensus size: 82
63765 AACATAAACT
63775 GTAAACTCTATTTTTAATTATTTATTAGTTTAAGTATAAATAAAGTAACAAAATTACATATATAA
1 GTAAACTCTATTTTTAATTATTTATTAGTTTAAGTATAAATAAAGTAACAAAATTACATATATAA
63840 TATAATAAAATATTTCA
66 TATAATAAAATATTTCA
63857 GTAAACTCTA-TTTTAATTATTTATTAGTTTAAGTATAAATAAAGTAACAAAATTACATATATAA
1 GTAAACTCTATTTTTAATTATTTATTAGTTTAAGTATAAATAAAGTAACAAAATTACATATATAA
63921 TATAATAAAATATTTCA
66 TATAATAAAATATTTCA
63938 AGGAGTTTAT
Statistics
Matches: 81, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
81 71 0.88
82 10 0.12
ACGTcount: A:0.48, C:0.06, G:0.05, T:0.41
Consensus pattern (82 bp):
GTAAACTCTATTTTTAATTATTTATTAGTTTAAGTATAAATAAAGTAACAAAATTACATATATAA
TATAATAAAATATTTCA
Found at i:66052 original size:2 final size:2
Alignment explanation
Indices: 66047--66077 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
66037 TTTTTCAATT
*
66047 TA TA TA TA TA TA TA GA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
66078 TTGCATTTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:71426 original size:6 final size:6
Alignment explanation
Indices: 71412--71475 Score: 119
Period size: 6 Copynumber: 10.7 Consensus size: 6
71402 CTTTTGGGTT
*
71412 ATTTCG ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG
1 ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG
71460 ATTTTG ATTTTG ATTT
1 ATTTTG ATTTTG ATTT
71476 AGGGTTATTT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 57 1.00
ACGTcount: A:0.17, C:0.02, G:0.16, T:0.66
Consensus pattern (6 bp):
ATTTTG
Found at i:74093 original size:21 final size:21
Alignment explanation
Indices: 74067--74110 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
74057 TTTATATAAG
74067 ATTAAT-AGTAAATT-TAGAATA
1 ATTAATGA-TAAATTATA-AATA
74088 ATTAATGATAAATTATAAATA
1 ATTAATGATAAATTATAAATA
74109 AT
1 AT
74111 AACACATGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
21 18 0.86
22 3 0.14
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.39
Consensus pattern (21 bp):
ATTAATGATAAATTATAAATA
Found at i:75087 original size:16 final size:17
Alignment explanation
Indices: 75066--75099 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
75056 AGCCAGAGAT
75066 AAAATAAAAT-AAAATA
1 AAAATAAAATCAAAATA
*
75082 AAAATACAATCAAAATA
1 AAAATAAAATCAAAATA
75099 A
1 A
75100 TAAAATTCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.18
Consensus pattern (17 bp):
AAAATAAAATCAAAATA
Found at i:76228 original size:16 final size:17
Alignment explanation
Indices: 76207--76240 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
76197 AGCCAGAGAT
76207 AAAATAAAAT-AAAATA
1 AAAATAAAATCAAAATA
*
76223 AAAATACAATCAAAATA
1 AAAATAAAATCAAAATA
76240 A
1 A
76241 TAAAATTCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.18
Consensus pattern (17 bp):
AAAATAAAATCAAAATA
Found at i:79001 original size:25 final size:24
Alignment explanation
Indices: 78953--79015 Score: 63
Period size: 25 Copynumber: 2.6 Consensus size: 24
78943 TGATCCCCAT
*
78953 ATTTTTTTTGTTTTAAGTAATTTA
1 ATTTTTTTTCTTTTAAGTAATTTA
* **
78977 ATTTTTTTTTCTTTTATGTTCTTTA
1 A-TTTTTTTTCTTTTAAGTAATTTA
**
79002 AACTTTTTTCTTTT
1 ATTTTTTTTCTTTT
79016 TCTTTTTTCC
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
24 12 0.38
25 20 0.62
ACGTcount: A:0.17, C:0.06, G:0.05, T:0.71
Consensus pattern (24 bp):
ATTTTTTTTCTTTTAAGTAATTTA
Found at i:79305 original size:11 final size:11
Alignment explanation
Indices: 79291--79319 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
79281 AAAAACAAAG
79291 AAAGAAAGTTA
1 AAAGAAAGTTA
79302 AAAGAAAGTTA
1 AAAGAAAGTTA
79313 AAAGAAA
1 AAAGAAA
79320 AACGAGCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.69, C:0.00, G:0.17, T:0.14
Consensus pattern (11 bp):
AAAGAAAGTTA
Found at i:81147 original size:25 final size:25
Alignment explanation
Indices: 81113--81183 Score: 142
Period size: 25 Copynumber: 2.8 Consensus size: 25
81103 TATTTTGATA
81113 TTATTTGATGTAATAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAGT
81138 TTATTTGATGTAATAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAGT
81163 TTATTTGATGTAATAAAATAG
1 TTATTTGATGTAATAAAATAG
81184 NNNNNNNNNN
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 46 1.00
ACGTcount: A:0.44, C:0.00, G:0.15, T:0.41
Consensus pattern (25 bp):
TTATTTGATGTAATAAAATAGAAGT
Found at i:90376 original size:1 final size:1
Alignment explanation
Indices: 90334--90369 Score: 63
Period size: 1 Copynumber: 36.0 Consensus size: 1
90324 GGATGTTCCC
*
90334 TTTTTTTTTTTTTTTTTTTTTTTTTTTTGTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
90370 AGTTTTTAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.03, T:0.97
Consensus pattern (1 bp):
T
Found at i:90542 original size:104 final size:104
Alignment explanation
Indices: 90370--90564 Score: 390
Period size: 104 Copynumber: 1.9 Consensus size: 104
90360 TTGTTTTTTT
90370 AGTTTTTAGATGTGGAATAATTACATGCCTTTTCTTTCACAACCACCTCAGAGGTAGCATCATCT
1 AGTTTTTAGATGTGGAATAATTACATGCCTTTTCTTTCACAACCACCTCAGAGGTAGCATCATCT
90435 GGAACTGAAGGCCAAACTGCCGGCTTTTCTGGTTTTATG
66 GGAACTGAAGGCCAAACTGCCGGCTTTTCTGGTTTTATG
90474 AGTTTTTAGATGTGGAATAATTACATGCCTTTTCTTTCACAACCACCTCAGAGGTAGCATCATCT
1 AGTTTTTAGATGTGGAATAATTACATGCCTTTTCTTTCACAACCACCTCAGAGGTAGCATCATCT
90539 GGAACTGAAGGCCAAACTGCCGGCTT
66 GGAACTGAAGGCCAAACTGCCGGCTT
90565 GGGCCAAGGC
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
104 91 1.00
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.32
Consensus pattern (104 bp):
AGTTTTTAGATGTGGAATAATTACATGCCTTTTCTTTCACAACCACCTCAGAGGTAGCATCATCT
GGAACTGAAGGCCAAACTGCCGGCTTTTCTGGTTTTATG
Found at i:93333 original size:33 final size:33
Alignment explanation
Indices: 93291--93356 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
93281 AAAATTTAGA
93291 AAAAAAAAAAAAAAAAAACCGTTCTATTTTTCT
1 AAAAAAAAAAAAAAAAAACCGTTCTATTTTTCT
*
93324 AAAAAAAAAAAAAAAGAACCGTTCTATTTTTCT
1 AAAAAAAAAAAAAAAAAACCGTTCTATTTTTCT
93357 CATTGTGTGG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.56, C:0.12, G:0.05, T:0.27
Consensus pattern (33 bp):
AAAAAAAAAAAAAAAAAACCGTTCTATTTTTCT
Found at i:102943 original size:5 final size:5
Alignment explanation
Indices: 102933--102962 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
102923 TATCATATGT
*
102933 CTGCA CTGCA CTGCA GTGCA CTGCA CTGCA
1 CTGCA CTGCA CTGCA CTGCA CTGCA CTGCA
102963 TGTTTTGTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.20, C:0.37, G:0.23, T:0.20
Consensus pattern (5 bp):
CTGCA
Found at i:102954 original size:15 final size:15
Alignment explanation
Indices: 102934--102962 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
102924 ATCATATGTC
102934 TGCACTGCACTGCAG
1 TGCACTGCACTGCAG
102949 TGCACTGCACTGCA
1 TGCACTGCACTGCA
102963 TGTTTTGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.34, G:0.24, T:0.21
Consensus pattern (15 bp):
TGCACTGCACTGCAG
Found at i:104121 original size:282 final size:283
Alignment explanation
Indices: 103606--104170 Score: 1123
Period size: 282 Copynumber: 2.0 Consensus size: 283
103596 AAAGTTAAAA
103606 TTGCACTGGGTCCCCTACAAATGATAAAATTTTATTTTAATCTTTTAAAAATTATAAATATAGAG
1 TTGCACTGGGTCCCCTACAAATGATAAAATTTTATTTTAATCTTTTAAAAATTATAAATATAGAG
103671 GTTATTAAATTGATGAAATTATATTTTTATTATTATAAAAATAGTACGGATTGGTTGTAATAGAC
66 GTTATTAAATTGATGAAATTATATTTTTATTATTATAAAAATAGTACGGATTGGTTGTAATAGAC
103736 AAAAAAACAGTTGAGTCAAGATTTTAATATTTTCTTTTATGATTTTTAATGATTTATTTAATTGA
131 AAAAAAACAGTTGAGTCAAGATTTTAATATTTTCTTTTATGATTTTTAATGATTTATTTAATTGA
103801 ACTTGACAAGTCGATTGAAATAGTGAACCAGGAACTTGATTGGTTTAACCGTTGACTTAACCTAA
196 ACTTGACAAGTCGATTGAAATAGTGAACCAGGAACTTGATTGGTTTAACCGTTGACTTAACCTAA
103866 AAACCTTGAAATTGGTTGAAATT
261 AAACCTTGAAATTGGTTGAAATT
103889 TTGCACTGGG-CCCCTACAAATGATAAAATTTTATTTTAATCTTTTAAAAATTATAAATATAGAG
1 TTGCACTGGGTCCCCTACAAATGATAAAATTTTATTTTAATCTTTTAAAAATTATAAATATAGAG
103953 GTTATTAAATTGATGAAATTATATTTTTATTATTATAAAAATAGTACGGATTGGTTGTAATAGAC
66 GTTATTAAATTGATGAAATTATATTTTTATTATTATAAAAATAGTACGGATTGGTTGTAATAGAC
104018 AAAAAAACAGTTGAGTCAAGATTTTAATATTTTCTTTTATGATTTTTAATGATTTATTTAATTGA
131 AAAAAAACAGTTGAGTCAAGATTTTAATATTTTCTTTTATGATTTTTAATGATTTATTTAATTGA
104083 ACTTGACAAGTCGATTGAAATAGTGAACCAGGAACTTGATTGGTTTAACCGTTGACTTAACCTAA
196 ACTTGACAAGTCGATTGAAATAGTGAACCAGGAACTTGATTGGTTTAACCGTTGACTTAACCTAA
104148 AAACCTTGAAATTGGTTGAAATT
261 AAACCTTGAAATTGGTTGAAATT
104171 GTGTATGGCG
Statistics
Matches: 282, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
282 272 0.96
283 10 0.04
ACGTcount: A:0.37, C:0.09, G:0.15, T:0.39
Consensus pattern (283 bp):
TTGCACTGGGTCCCCTACAAATGATAAAATTTTATTTTAATCTTTTAAAAATTATAAATATAGAG
GTTATTAAATTGATGAAATTATATTTTTATTATTATAAAAATAGTACGGATTGGTTGTAATAGAC
AAAAAAACAGTTGAGTCAAGATTTTAATATTTTCTTTTATGATTTTTAATGATTTATTTAATTGA
ACTTGACAAGTCGATTGAAATAGTGAACCAGGAACTTGATTGGTTTAACCGTTGACTTAACCTAA
AAACCTTGAAATTGGTTGAAATT
Found at i:110183 original size:106 final size:106
Alignment explanation
Indices: 109993--110204 Score: 406
Period size: 106 Copynumber: 2.0 Consensus size: 106
109983 TTTCTATATG
*
109993 GAATGGACATTGTTATCAGTTAATCCTAGCTGCTTGATGAATCTTTCTTCTTCTTTGACTTCTCT
1 GAATGGACATTGTTATCAGTTAATCCCAGCTGCTTGATGAATCTTTCTTCTTCTTTGACTTCTCT
*
110058 TAATCTGTTTGGGTGTCGTATGCAATGGAACTTCTCTTAAT
66 TAATCTGTTTGGGTATCGTATGCAATGGAACTTCTCTTAAT
110099 GAATGGACATTGTTATCAGTTAATCCCAGCTGCTTGATGAATCTTTCTTCTTCTTTGACTTCTCT
1 GAATGGACATTGTTATCAGTTAATCCCAGCTGCTTGATGAATCTTTCTTCTTCTTTGACTTCTCT
110164 TAATCTGTTTGGGTATCGTATGCAATGGAACTTCTCTTAAT
66 TAATCTGTTTGGGTATCGTATGCAATGGAACTTCTCTTAAT
110205 CTACCTCGAA
Statistics
Matches: 104, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
106 104 1.00
ACGTcount: A:0.21, C:0.18, G:0.17, T:0.43
Consensus pattern (106 bp):
GAATGGACATTGTTATCAGTTAATCCCAGCTGCTTGATGAATCTTTCTTCTTCTTTGACTTCTCT
TAATCTGTTTGGGTATCGTATGCAATGGAACTTCTCTTAAT
Found at i:112655 original size:22 final size:22
Alignment explanation
Indices: 112627--112669 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
112617 ATCCTTAAAC
112627 TTTGAAAGTAATTTAATGAAAA
1 TTTGAAAGTAATTTAATGAAAA
112649 TTTGAAAGTAATTTAATGAAA
1 TTTGAAAGTAATTTAATGAAA
112670 TTCAAGCTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.49, C:0.00, G:0.14, T:0.37
Consensus pattern (22 bp):
TTTGAAAGTAATTTAATGAAAA
Found at i:118420 original size:18 final size:20
Alignment explanation
Indices: 118399--118443 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
118389 GAGAAATCAT
*
118399 TATGAGATGAT-AA-TGAGA
1 TATGAAATGATGAATTGAGA
118417 TATGAAATGATGAATTGAGA
1 TATGAAATGATGAATTGAGA
118437 TATGAAA
1 TATGAAA
118444 CTTGAATGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 10 0.42
19 2 0.08
20 12 0.50
ACGTcount: A:0.47, C:0.00, G:0.24, T:0.29
Consensus pattern (20 bp):
TATGAAATGATGAATTGAGA
Found at i:119272 original size:13 final size:13
Alignment explanation
Indices: 119254--119278 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
119244 GAGCGTGTGT
119254 CACACATGGGCAA
1 CACACATGGGCAA
119267 CACACATGGGCA
1 CACACATGGGCA
119279 TGTGTCACAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.32, G:0.24, T:0.08
Consensus pattern (13 bp):
CACACATGGGCAA
Found at i:119285 original size:30 final size:30
Alignment explanation
Indices: 119249--119312 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
119239 CACACGAGCG
* *
119249 TGTGTCACACATGGGCAACACACATGGGCA
1 TGTGTCACACACGGGCAACACACATAGGCA
*
119279 TGTGTCACACACGGGCAACACACATAGGCG
1 TGTGTCACACACGGGCAACACACATAGGCA
119309 TGTG
1 TGTG
119313 ACCCAAGTCA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.28, C:0.27, G:0.28, T:0.17
Consensus pattern (30 bp):
TGTGTCACACACGGGCAACACACATAGGCA
Found at i:119846 original size:49 final size:49
Alignment explanation
Indices: 119774--119875 Score: 159
Period size: 49 Copynumber: 2.1 Consensus size: 49
119764 TCAAGAAGGG
* *
119774 ATAAATAGTGATAAGAGTGTAGACAGTGGAAGACTAAGTTTAGCAATGT
1 ATAAATAGTGATAAGAGTGTAGACAGTGAAAGACCAAGTTTAGCAATGT
* * *
119823 ATAAATAGTGATAAGAGTTTAGACAGTGAAATACCAAGTTTAGCATTGT
1 ATAAATAGTGATAAGAGTGTAGACAGTGAAAGACCAAGTTTAGCAATGT
119872 ATAA
1 ATAA
119876 CATGAATCAT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.42, C:0.07, G:0.23, T:0.28
Consensus pattern (49 bp):
ATAAATAGTGATAAGAGTGTAGACAGTGAAAGACCAAGTTTAGCAATGT
Found at i:121422 original size:44 final size:44
Alignment explanation
Indices: 121369--121527 Score: 193
Period size: 44 Copynumber: 3.6 Consensus size: 44
121359 TGAGTAATCA
*
121369 TGTAAGACCACGTCTGGGATGTTGGAATCGATTTGATATTTACG
1 TGTAAGACCACGTCTGGGATGTTGGCATCGATTTGATATTTACG
*
121413 TGTAAGACCACGTCTGGGACGTTGGCATCGATTTGATATTTACG
1 TGTAAGACCACGTCTGGGATGTTGGCATCGATTTGATATTTACG
* * * *
121457 TGTAAGACC-CTGTTTGGGACAG-TGGCATCAATGTT--TGA-TTACA
1 TGTAAGACCAC-GTCTGGGA-TGTTGGCATCGAT-TTGAT-ATTTACG
121500 TGTAAGACCACGTCTGGGATGTTGGCAT
1 TGTAAGACCACGTCTGGGATGTTGGCAT
121528 TGTACGAGCT
Statistics
Matches: 101, Mismatches: 8, Indels: 13
0.83 0.07 0.11
Matches are distributed among these distances:
42 1 0.01
43 28 0.28
44 69 0.68
45 3 0.03
ACGTcount: A:0.24, C:0.16, G:0.28, T:0.32
Consensus pattern (44 bp):
TGTAAGACCACGTCTGGGATGTTGGCATCGATTTGATATTTACG
Found at i:129072 original size:18 final size:21
Alignment explanation
Indices: 129030--129074 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
129020 AAAAAGTAGG
*
129030 TTATATATTATTTTTCTAATA
1 TTATATATTATTTATCTAATA
129051 TTATATATT-TTTAT-TAAT-
1 TTATATATTATTTATCTAATA
129069 TTATAT
1 TTATAT
129075 TTAAATAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 6 0.26
19 4 0.17
20 4 0.17
21 9 0.39
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (21 bp):
TTATATATTATTTATCTAATA
Found at i:129920 original size:29 final size:30
Alignment explanation
Indices: 129876--129937 Score: 99
Period size: 29 Copynumber: 2.1 Consensus size: 30
129866 ACTTATTTTA
129876 TTGTTAAATTTGTTATTATTTTAAAGACAT
1 TTGTTAAATTTGTTATTATTTTAAAGACAT
* *
129906 TTGTT-AATTTTTTATTATTTTAGAGACAT
1 TTGTTAAATTTGTTATTATTTTAAAGACAT
129935 TTG
1 TTG
129938 CTTGTTAAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 25 0.83
30 5 0.17
ACGTcount: A:0.29, C:0.03, G:0.11, T:0.56
Consensus pattern (30 bp):
TTGTTAAATTTGTTATTATTTTAAAGACAT
Found at i:130759 original size:13 final size:12
Alignment explanation
Indices: 130721--130752 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
130711 CTGCCCGTAT
130721 TAATTTTTTATA
1 TAATTTTTTATA
*
130733 TTATTTTTTATA
1 TAATTTTTTATA
130745 TAATTTTT
1 TAATTTTT
130753 AAATATATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (12 bp):
TAATTTTTTATA
Found at i:131015 original size:30 final size:30
Alignment explanation
Indices: 130970--131031 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
130960 CTTAATAAGT
*
130970 AAATACCTCTAAAATAATAACAGAATTAAC
1 AAATACCTCTAAAATAATAACAAAATTAAC
* *
131000 AAATGCCTTTAAAATAATAACAAAATTAAC
1 AAATACCTCTAAAATAATAACAAAATTAAC
131030 AA
1 AA
131032 TAAAGTAAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.58, C:0.15, G:0.03, T:0.24
Consensus pattern (30 bp):
AAATACCTCTAAAATAATAACAAAATTAAC
Found at i:132472 original size:147 final size:147
Alignment explanation
Indices: 132205--132498 Score: 588
Period size: 147 Copynumber: 2.0 Consensus size: 147
132195 TTTAAGCTCA
132205 TCCAACTAAACACACCACATAGGACCTCGAAAGGCCCATCCAACCCTACACACAATGTATGTGGA
1 TCCAACTAAACACACCACATAGGACCTCGAAAGGCCCATCCAACCCTACACACAATGTATGTGGA
132270 CTAAGCCACTCAGATAATAATACGTAGCAAGGCTGGTGTATGTGCAGTACAGTGCATTATTGTGG
66 CTAAGCCACTCAGATAATAATACGTAGCAAGGCTGGTGTATGTGCAGTACAGTGCATTATTGTGG
132335 TAAACCACTGTATCGAT
131 TAAACCACTGTATCGAT
132352 TCCAACTAAACACACCACATAGGACCTCGAAAGGCCCATCCAACCCTACACACAATGTATGTGGA
1 TCCAACTAAACACACCACATAGGACCTCGAAAGGCCCATCCAACCCTACACACAATGTATGTGGA
132417 CTAAGCCACTCAGATAATAATACGTAGCAAGGCTGGTGTATGTGCAGTACAGTGCATTATTGTGG
66 CTAAGCCACTCAGATAATAATACGTAGCAAGGCTGGTGTATGTGCAGTACAGTGCATTATTGTGG
132482 TAAACCACTGTATCGAT
131 TAAACCACTGTATCGAT
132499 AAGTTGTAGT
Statistics
Matches: 147, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
147 147 1.00
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.22
Consensus pattern (147 bp):
TCCAACTAAACACACCACATAGGACCTCGAAAGGCCCATCCAACCCTACACACAATGTATGTGGA
CTAAGCCACTCAGATAATAATACGTAGCAAGGCTGGTGTATGTGCAGTACAGTGCATTATTGTGG
TAAACCACTGTATCGAT
Found at i:132835 original size:17 final size:17
Alignment explanation
Indices: 132813--132847 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
132803 TAATCAGATA
*
132813 AAAAACAAACACAGTAC
1 AAAAACAAACACAATAC
*
132830 AAAAACAGACACAATAC
1 AAAAACAAACACAATAC
132847 A
1 A
132848 TAGAATCATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.66, C:0.23, G:0.06, T:0.06
Consensus pattern (17 bp):
AAAAACAAACACAATAC
Found at i:132863 original size:25 final size:25
Alignment explanation
Indices: 132792--132886 Score: 91
Period size: 25 Copynumber: 3.7 Consensus size: 25
132782 GGGTCAGAAC
*
132792 ACATAGAATCATAATCAGATAAAAA
1 ACATAGAATCATAATCAGACAAAAA
* * * * * *
132817 ACAAACACAGTACAAAAACAGACACAAT
1 ACATAGA-A-T-CATAATCAGACAAAAA
*
132845 ACATAGAATCATAATCAGATAAAAA
1 ACATAGAATCATAATCAGACAAAAA
132870 ACATAGAATCATAATCA
1 ACATAGAATCATAATCA
132887 TAATCAGATA
Statistics
Matches: 53, Mismatches: 14, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
25 33 0.62
26 2 0.04
27 2 0.04
28 16 0.30
ACGTcount: A:0.59, C:0.17, G:0.07, T:0.17
Consensus pattern (25 bp):
ACATAGAATCATAATCAGACAAAAA
Found at i:133728 original size:18 final size:16
Alignment explanation
Indices: 133699--133732 Score: 50
Period size: 18 Copynumber: 2.0 Consensus size: 16
133689 AAATCAAAGG
133699 AAATTGAAAAAGAAGA
1 AAATTGAAAAAGAAGA
133715 AAATGTGAAGAAAGAAGA
1 AAAT-TGAA-AAAGAAGA
133733 GAAGAACCTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 4 0.25
18 8 0.50
ACGTcount: A:0.65, C:0.00, G:0.24, T:0.12
Consensus pattern (16 bp):
AAATTGAAAAAGAAGA
Found at i:140727 original size:2 final size:2
Alignment explanation
Indices: 140720--140745 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
140710 AAGCACCTCC
140720 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
140746 TAACCCTTTA
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:141818 original size:21 final size:22
Alignment explanation
Indices: 141789--141851 Score: 94
Period size: 21 Copynumber: 3.0 Consensus size: 22
141779 GGACTTTGTT
* *
141789 CTGAGTATGATTCGTAAACAC-
1 CTGACTATGTTTCGTAAACACA
141810 CTGACTATGTTTCGTAAAC-CA
1 CTGACTATGTTTCGTAAACACA
141831 CTGACTATGTTTCGTAAACAC
1 CTGACTATGTTTCGTAAACAC
141852 TTGGAGAATC
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 1 0.03
21 36 0.95
22 1 0.03
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.32
Consensus pattern (22 bp):
CTGACTATGTTTCGTAAACACA
Found at i:146405 original size:16 final size:16
Alignment explanation
Indices: 146386--146419 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
146376 CAATAAATCG
146386 AAAATAA-TCTAAATTT
1 AAAATAATTC-AAATTT
146402 AAAATAATTCAAATTT
1 AAAATAATTCAAATTT
146418 AA
1 AA
146420 TTAAAAACCC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 15 0.88
17 2 0.12
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (16 bp):
AAAATAATTCAAATTT
Found at i:147198 original size:21 final size:21
Alignment explanation
Indices: 147172--147222 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
147162 AACACATAAC
* *
147172 CCCAAAACTTTAAACTTTAAA
1 CCCAAAACCTTAAACCTTAAA
* *
147193 CCCAAACCCTTAAACCTTGAA
1 CCCAAAACCTTAAACCTTAAA
*
147214 CTCAAAACC
1 CCCAAAACC
147223 CAAAACCCAA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.43, C:0.33, G:0.02, T:0.22
Consensus pattern (21 bp):
CCCAAAACCTTAAACCTTAAA
Found at i:147201 original size:28 final size:28
Alignment explanation
Indices: 147155--147247 Score: 71
Period size: 28 Copynumber: 3.3 Consensus size: 28
147145 GTGAACCCCG
* * *
147155 AACTCATAACACATAACCCCAAAACTTTA
1 AACTCAAAACCCA-AACCCCAAAACCTTA
** ** *
147184 AACTTTAAACCCAAACCCTTAAACCTTG
1 AACTCAAAACCCAAACCCCAAAACCTTA
* *
147212 AACTCAAAACCCAAAACCC-AAACCCTA
1 AACTCAAAACCCAAACCCCAAAACCTTA
147239 AACCTCAAA
1 AA-CTCAAA
147248 TCTCAAATCC
Statistics
Matches: 49, Mismatches: 14, Indels: 3
0.74 0.21 0.05
Matches are distributed among these distances:
27 8 0.16
28 32 0.65
29 9 0.18
ACGTcount: A:0.47, C:0.34, G:0.01, T:0.17
Consensus pattern (28 bp):
AACTCAAAACCCAAACCCCAAAACCTTA
Found at i:148293 original size:7 final size:7
Alignment explanation
Indices: 148283--148308 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
148273 ATTTTTTTAA
148283 TTTAAAT
1 TTTAAAT
148290 TTTAAAT
1 TTTAAAT
148297 TTTAAAT
1 TTTAAAT
148304 TTTAA
1 TTTAA
148309 TTATTAATAT
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:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (7 bp):
TTTAAAT
Found at i:148767 original size:25 final size:25
Alignment explanation
Indices: 148739--148838 Score: 119
Period size: 25 Copynumber: 4.0 Consensus size: 25
148729 AGAACCAAAT
* *
148739 AGAACAGAGCAGAACAGGACAGAGC
1 AGAACATATCAGAACAGGACAGAGC
* *
148764 AGAACATATTAGAACAGGACAGGGC
1 AGAACATATCAGAACAGGACAGAGC
* *
148789 AGAACATATCAGAACAGGACAAACC
1 AGAACATATCAGAACAGGACAGAGC
* * *
148814 AGAATATAACAGAATAGGACAGAGC
1 AGAACATATCAGAACAGGACAGAGC
148839 TACAAAGAGG
Statistics
Matches: 62, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 62 1.00
ACGTcount: A:0.49, C:0.18, G:0.25, T:0.08
Consensus pattern (25 bp):
AGAACATATCAGAACAGGACAGAGC
Found at i:151483 original size:19 final size:20
Alignment explanation
Indices: 151451--151495 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
151441 CCCAACATCA
151451 ATTTAAATAAAAAA-ATATT
1 ATTTAAATAAAAAATATATT
**
151470 ATTTAAATTTAAAATATATT
1 ATTTAAATAAAAAATATATT
*
151490 TTTTAA
1 ATTTAA
151496 TATAGGCTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
ATTTAAATAAAAAATATATT
Found at i:151710 original size:107 final size:107
Alignment explanation
Indices: 151514--151719 Score: 333
Period size: 107 Copynumber: 1.9 Consensus size: 107
151504 TGGACTTAAA
* *
151514 AAAATTTTGGTTGAATAAAATTCTATCACTAAACAAAATCTAACTCAAAACTTTTATAATTCTAA
1 AAAATTTTGATTGAATAAAATTCTATCACTAAACAAAATCTAACTCAAAACTTTTAAAATTCTAA
*
151579 TTAACTTAGACCTATCAATTGAAAAAAAATTGAATGAAAATTT
66 TTAACTTAGACCTACCAATTG-AAAAAAATTGAATGAAAATTT
* * *
151622 AAAA-TTTGATTGAATAAAATTCTTTGACTAAACAAAATCTGACTCAAAACTTTTAAAATTCTAA
1 AAAATTTTGATTGAATAAAATTCTATCACTAAACAAAATCTAACTCAAAACTTTTAAAATTCTAA
*
151686 TTAACTTAGACCTGCCAATTGAAAAAAATTGAAT
66 TTAACTTAGACCTACCAATTGAAAAAAATTGAAT
151720 TAAATTTTTG
Statistics
Matches: 91, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
106 13 0.14
107 74 0.81
108 4 0.04
ACGTcount: A:0.47, C:0.13, G:0.07, T:0.33
Consensus pattern (107 bp):
AAAATTTTGATTGAATAAAATTCTATCACTAAACAAAATCTAACTCAAAACTTTTAAAATTCTAA
TTAACTTAGACCTACCAATTGAAAAAAATTGAATGAAAATTT
Found at i:151916 original size:17 final size:17
Alignment explanation
Indices: 151894--151929 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
151884 TTTCAGTATC
151894 AACGATCAATATCAGTG
1 AACGATCAATATCAGTG
*
151911 AACGATCACTATCAGTG
1 AACGATCAATATCAGTG
151928 AA
1 AA
151930 TAGAATGAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.42, C:0.19, G:0.17, T:0.22
Consensus pattern (17 bp):
AACGATCAATATCAGTG
Found at i:153545 original size:20 final size:21
Alignment explanation
Indices: 153509--153548 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
153499 AAATGCCTAT
153509 GAAAAGATGGCTTGGATTTAA
1 GAAAAGATGGCTTGGATTTAA
*
153530 GAAAAGTTGG-TTGGATTTA
1 GAAAAGATGGCTTGGATTTA
153549 TCAATGATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.35, C:0.03, G:0.30, T:0.33
Consensus pattern (21 bp):
GAAAAGATGGCTTGGATTTAA
Found at i:153795 original size:22 final size:22
Alignment explanation
Indices: 153746--153795 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
153736 AAAATATGTG
*
153746 TTATATATTATATACTTATACT
1 TTATATATTATATACTAATACT
* *
153768 TAATATATTATATACCTAAT-TT
1 TTATATATTATATA-CTAATACT
153790 TTATAT
1 TTATAT
153796 TTCATATTCT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 19 0.83
23 4 0.17
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (22 bp):
TTATATATTATATACTAATACT
Found at i:157958 original size:13 final size:13
Alignment explanation
Indices: 157940--157965 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
157930 TGTATAAATT
157940 GATTTTTAAATAA
1 GATTTTTAAATAA
157953 GATTTTTAAATAA
1 GATTTTTAAATAA
157966 CGATAAAGTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (13 bp):
GATTTTTAAATAA
Found at i:158733 original size:6 final size:6
Alignment explanation
Indices: 158714--158748 Score: 52
Period size: 6 Copynumber: 5.5 Consensus size: 6
158704 AAAGGATCTC
158714 AAAAGCA AACAAGA AAAAGA AAAAGA AAAAGA AAA
1 AAAAG-A AA-AAGA AAAAGA AAAAGA AAAAGA AAA
158749 CAAAACAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
6 19 0.70
7 5 0.19
8 3 0.11
ACGTcount: A:0.80, C:0.06, G:0.14, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:159316 original size:13 final size:14
Alignment explanation
Indices: 159286--159319 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
159276 TATTTTGTAA
*
159286 TTGGGCTCGGGTTG
1 TTGGGCTAGGGTTG
159300 TTGGGCTAGGG-TG
1 TTGGGCTAGGGTTG
159313 TTGGGCT
1 TTGGGCT
159320 TATTTTGTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.47
14 10 0.53
ACGTcount: A:0.03, C:0.12, G:0.50, T:0.35
Consensus pattern (14 bp):
TTGGGCTAGGGTTG
Found at i:159316 original size:44 final size:44
Alignment explanation
Indices: 159253--159344 Score: 175
Period size: 44 Copynumber: 2.1 Consensus size: 44
159243 TTGACTTGGT
159253 TTGTTGGGCAAGGGTGTTGGGCTTATTTTGTAATTGGGCTCGGG
1 TTGTTGGGCAAGGGTGTTGGGCTTATTTTGTAATTGGGCTCGGG
*
159297 TTGTTGGGCTAGGGTGTTGGGCTTATTTTGTAATTGGGCTCGGG
1 TTGTTGGGCAAGGGTGTTGGGCTTATTTTGTAATTGGGCTCGGG
159341 TTGT
1 TTGT
159345 AATGGGTAGT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 47 1.00
ACGTcount: A:0.10, C:0.09, G:0.40, T:0.41
Consensus pattern (44 bp):
TTGTTGGGCAAGGGTGTTGGGCTTATTTTGTAATTGGGCTCGGG
Found at i:160251 original size:132 final size:132
Alignment explanation
Indices: 160025--160553 Score: 801
Period size: 132 Copynumber: 4.0 Consensus size: 132
160015 ATAAGACTAA
* * * *
160025 TGGCTTCAATCTGCTTCCTTACTACTTTGGGAAGATAAGATTCACCGTCTAT-AATCTGCTCCAC
1 TGGCTTAAATCTGCTTCCCTACTACCTTGGGAAGATAAGATTCACCGTCT-TCGATCTGCTCCAC
* *
160089 TACTGCTTAGGGAGACAAGATCTGCAATCTTCAACCTACTCCATTGCGGCTCAAGGAGATAGGAC
65 TACTGCTTAGGGAGACAAGATCTGCAATCTTCAACCTACTCCACTGCTGCTCAAGGAGATAGGAC
160154 TGG
130 TGG
*
160157 TGGCTTAAATCTGCTTCCCTACTACCTTGGAAAGATAAGATTCACCGTCTTCGATCTGCTCCACT
1 TGGCTTAAATCTGCTTCCCTACTACCTTGGGAAGATAAGATTCACCGTCTTCGATCTGCTCCACT
* * * * * * *
160222 ACTACTCATGGAGACAAGATCTGCGATCTTCAACCTACTCCACTACTGCTCAGGGAGATAGGAAT
66 ACTGCTTAGGGAGACAAGATCTGCAATCTTCAACCTACTCCACTGCTGCTCAAGGAGATAGGACT
160287 GG
131 GG
* * *
160289 TGGCTTAAATTTGCTTCCCTACTACCTTGGGAAGATAAGATTCACCGTCTTTGATCTGCTTCACT
1 TGGCTTAAATCTGCTTCCCTACTACCTTGGGAAGATAAGATTCACCGTCTTCGATCTGCTCCACT
*
160354 ACTGCTTAGGGAGACAAGATCTGCAATCTTCAACCTACTCCACTGCTGCTCAGGGAGATAGGACT
66 ACTGCTTAGGGAGACAAGATCTGCAATCTTCAACCTACTCCACTGCTGCTCAAGGAGATAGGACT
160419 GG
131 GG
* * * * *
160421 TGGCTTAAATCTACTTCCCTACTACATTGGGAAGATAAGATTCGCTGTCTTCGATCTGCGCCACT
1 TGGCTTAAATCTGCTTCCCTACTACCTTGGGAAGATAAGATTCACCGTCTTCGATCTGCTCCACT
* *
160486 ACTGCTTAGGGAGACAGGATCTACAATCTTCAACCTACTCCACTGCTGCTC-AGAGAGATAGGAC
66 ACTGCTTAGGGAGACAAGATCTGCAATCTTCAACCTACTCCACTGCTGCTCAAG-GAGATAGGAC
160550 TGG
130 TGG
160553 T
1 T
160554 CATGGTGTGA
Statistics
Matches: 360, Mismatches: 35, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
131 2 0.01
132 358 0.99
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28
Consensus pattern (132 bp):
TGGCTTAAATCTGCTTCCCTACTACCTTGGGAAGATAAGATTCACCGTCTTCGATCTGCTCCACT
ACTGCTTAGGGAGACAAGATCTGCAATCTTCAACCTACTCCACTGCTGCTCAAGGAGATAGGACT
GG
Found at i:160403 original size:44 final size:44
Alignment explanation
Indices: 160350--160535 Score: 119
Period size: 44 Copynumber: 4.2 Consensus size: 44
160340 TGATCTGCTT
160350 CACTACTGCTTAGGGAGACAAGATCTGCAATCTTCAACCTACTC
1 CACTACTGCTTAGGGAGACAAGATCTGCAATCTTCAACCTACTC
* * * * **** * *
160394 CACTGCTGCTCAGGGAGATAGGA-CTGGTGGCTTAAATCTACTTC
1 CACTACTGCTTAGGGAGACAAGATCTGCAATCTTCAACCTAC-TC
* * ** * * * *
160438 C-CTACTACATT-GGGAAGATAAGAT-TCGCTGTCTTCGATCTGCGC
1 CACTACTGC-TTAGGG-AGACAAGATCT-GCAATCTTCAACCTACTC
* *
160482 CACTACTGCTTAGGGAGACAGGATCTACAATCTTCAACCTACTC
1 CACTACTGCTTAGGGAGACAAGATCTGCAATCTTCAACCTACTC
*
160526 CACTGCTGCT
1 CACTACTGCT
160536 CAGAGAGATA
Statistics
Matches: 103, Mismatches: 31, Indels: 16
0.69 0.21 0.11
Matches are distributed among these distances:
43 20 0.19
44 62 0.60
45 21 0.20
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.27
Consensus pattern (44 bp):
CACTACTGCTTAGGGAGACAAGATCTGCAATCTTCAACCTACTC
Found at i:167846 original size:63 final size:63
Alignment explanation
Indices: 167773--167899 Score: 254
Period size: 63 Copynumber: 2.0 Consensus size: 63
167763 CAAAACTTAC
167773 AATAATTCAAATTTAATAAAAATAAAACCCAAAATTAACTTTGTTGATACAGAAATACAACAA
1 AATAATTCAAATTTAATAAAAATAAAACCCAAAATTAACTTTGTTGATACAGAAATACAACAA
167836 AATAATTCAAATTTAATAAAAATAAAACCCAAAATTAACTTTGTTGATACAGAAATACAACAA
1 AATAATTCAAATTTAATAAAAATAAAACCCAAAATTAACTTTGTTGATACAGAAATACAACAA
167899 A
1 A
167900 GAGAAGATAT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 64 1.00
ACGTcount: A:0.56, C:0.13, G:0.05, T:0.27
Consensus pattern (63 bp):
AATAATTCAAATTTAATAAAAATAAAACCCAAAATTAACTTTGTTGATACAGAAATACAACAA
Found at i:168852 original size:21 final size:21
Alignment explanation
Indices: 168826--168881 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
168816 AATAGCAGTG
*
168826 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGATACTGTA
* * *
168847 GCGGTGACAATGGATACTGTA
1 GCGGTGAGATTAGATACTGTA
*
168868 GCAGTGAGATTAGA
1 GCGGTGAGATTAGA
168882 AACAATGGTG
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.29, C:0.11, G:0.34, T:0.27
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTGTA
Found at i:169571 original size:20 final size:21
Alignment explanation
Indices: 169535--169578 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
169525 TAAAAGAAAA
*
169535 AAAAATAGATTTATAAATTCT
1 AAAAATAAATTTATAAATTCT
*
169556 AAAAATAAATTT-TAAATTTT
1 AAAAATAAATTTATAAATTCT
169576 AAA
1 AAA
169579 TTTAAAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (21 bp):
AAAAATAAATTTATAAATTCT
Found at i:170113 original size:65 final size:65
Alignment explanation
Indices: 170037--170168 Score: 246
Period size: 65 Copynumber: 2.0 Consensus size: 65
170027 TCAATTTCAT
170037 TTCAAAGTCAAATGCTAATTTTCAAAAATTTCTATTTTATAAATTATTTTTATAATTTTTATTTA
1 TTCAAAGTCAAATGCTAATTTTCAAAAATTTCTATTTTATAAATTATTTTTATAATTTTTATTTA
* *
170102 TTCAAAGTCAAATGCTAATTTTCTAAAATTTCTATTTTGTAAATTATTTTTATAATTTTTATTTA
1 TTCAAAGTCAAATGCTAATTTTCAAAAATTTCTATTTTATAAATTATTTTTATAATTTTTATTTA
170167 TT
1 TT
170169 ATTAAACTTT
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
65 65 1.00
ACGTcount: A:0.35, C:0.08, G:0.04, T:0.54
Consensus pattern (65 bp):
TTCAAAGTCAAATGCTAATTTTCAAAAATTTCTATTTTATAAATTATTTTTATAATTTTTATTTA
Found at i:179585 original size:23 final size:23
Alignment explanation
Indices: 179559--179602 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
179549 GAATAAATTG
179559 ATGATTTAATTCATTAACAAAGC
1 ATGATTTAATTCATTAACAAAGC
179582 ATGATTTAATTCATTAACAAA
1 ATGATTTAATTCATTAACAAA
179603 ACATCCATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.45, C:0.11, G:0.07, T:0.36
Consensus pattern (23 bp):
ATGATTTAATTCATTAACAAAGC
Found at i:187146 original size:3 final size:3
Alignment explanation
Indices: 187138--187175 Score: 67
Period size: 3 Copynumber: 12.3 Consensus size: 3
187128 AAAATGAGTA
187138 AAT AAT AAT AAT AAT AAT AAT CAAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT A
187176 CAAGATTAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:187240 original size:17 final size:17
Alignment explanation
Indices: 187220--187252 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
187210 ATAAAATAGA
187220 AATACAATAAC-AATAAT
1 AATACAA-AACTAATAAT
187237 AATACAAAACTAATAA
1 AATACAAAACTAATAA
187253 CAAAATATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.67, C:0.12, G:0.00, T:0.21
Consensus pattern (17 bp):
AATACAAAACTAATAAT
Found at i:190532 original size:31 final size:31
Alignment explanation
Indices: 190494--190583 Score: 153
Period size: 32 Copynumber: 2.9 Consensus size: 31
190484 AGGCAAATTA
190494 CAAGAGTAATTGAATCCTAATAAAACTATTT
1 CAAGAGTAATTGAATCCTAATAAAACTATTT
*
190525 CAAGAGTAATTGAATCCTAATAAAAACTCTTT
1 CAAGAGTAATTGAATCCTAAT-AAAACTATTT
*
190557 AAAGAGTAATTGAATCCTAATAAAACT
1 CAAGAGTAATTGAATCCTAATAAAACT
190584 CTTTAAAATT
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
31 27 0.48
32 29 0.52
ACGTcount: A:0.47, C:0.13, G:0.10, T:0.30
Consensus pattern (31 bp):
CAAGAGTAATTGAATCCTAATAAAACTATTT
Found at i:190585 original size:31 final size:31
Alignment explanation
Indices: 190495--190590 Score: 165
Period size: 31 Copynumber: 3.1 Consensus size: 31
190485 GGCAAATTAC
* *
190495 AAGAGTAATTGAATCCTAATAAAACTATTTC
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
190526 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAAT-AAAACTCTTTA
190558 AAGAGTAATTGAATCCTAATAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
190589 AA
1 AA
190591 ATTATCTAAG
Statistics
Matches: 62, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
31 33 0.53
32 29 0.47
ACGTcount: A:0.47, C:0.12, G:0.09, T:0.31
Consensus pattern (31 bp):
AAGAGTAATTGAATCCTAATAAAACTCTTTA
Found at i:192838 original size:20 final size:20
Alignment explanation
Indices: 192813--192852 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
192803 AAATTAAGCC
*
192813 TAAAAA-ATTATATTTATTTT
1 TAAAAATATT-TATTAATTTT
192833 TAAAAATATTTATTAATTTT
1 TAAAAATATTTATTAATTTT
192853 AATATTGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TAAAAATATTTATTAATTTT
Found at i:193114 original size:23 final size:25
Alignment explanation
Indices: 193088--193138 Score: 63
Period size: 23 Copynumber: 2.1 Consensus size: 25
193078 TGTTTTTTAT
193088 TTTAAAAAATAATG-AG-T-AATATA
1 TTTAAAAAAT-ATGTAGTTCAATATA
*
193111 TTTATAAAATATGTAGTTCAATATA
1 TTTAAAAAATATGTAGTTCAATATA
193136 TTT
1 TTT
193139 TAAATTAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
22 3 0.12
23 11 0.46
24 1 0.04
25 9 0.38
ACGTcount: A:0.47, C:0.02, G:0.08, T:0.43
Consensus pattern (25 bp):
TTTAAAAAATATGTAGTTCAATATA
Found at i:199422 original size:21 final size:22
Alignment explanation
Indices: 199398--199445 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
199388 CCATTGCTTG
*
199398 TGGCTATACAA-TTGTTTGCAA
1 TGGCTATACAATTTATTTGCAA
* *
199419 TGGCTATATAATTTATTTGCAG
1 TGGCTATACAATTTATTTGCAA
199441 TGGCT
1 TGGCT
199446 CCATCTGCTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 10 0.43
22 13 0.57
ACGTcount: A:0.25, C:0.12, G:0.21, T:0.42
Consensus pattern (22 bp):
TGGCTATACAATTTATTTGCAA
Found at i:208329 original size:16 final size:16
Alignment explanation
Indices: 208301--208348 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
208291 AATCAAAAAC
208301 AATCAAAACTTAAAATA
1 AATCAAAA-TTAAAATA
* *
208318 ATTCAAATTTAATAA-A
1 AATCAAAATTAA-AATA
208334 AATCAAAATTAAAAT
1 AATCAAAATTAAAAT
208349 TAACTTTGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
15 2 0.08
16 15 0.60
17 8 0.32
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.29
Consensus pattern (16 bp):
AATCAAAATTAAAATA
Found at i:213191 original size:93 final size:94
Alignment explanation
Indices: 213085--213272 Score: 369
Period size: 93 Copynumber: 2.0 Consensus size: 94
213075 TTATTTTTAA
213085 AATTTTTATTTATTATTAAACTTTTTTAGAATTTAGAAATTTATTTTTATTTTTAATAGATATAG
1 AATTTTTATTTATTATTAAACTTTTTTAGAATTTAGAAATTTATTTTTATTTTTAATAGATATAG
213150 ATGTCATGTAACACTTAA-TTCTAATTGG
66 ATGTCATGTAACACTTAATTTCTAATTGG
213178 AATTTTTATTTATTATTAAACTTTTTTAGAATTTAGAAATTTATTTTTATTTTTAATAGATATAG
1 AATTTTTATTTATTATTAAACTTTTTTAGAATTTAGAAATTTATTTTTATTTTTAATAGATATAG
213243 ATGTCATGTAACACTTAATTTCTAATTGG
66 ATGTCATGTAACACTTAATTTCTAATTGG
213272 A
1 A
213273 TTAAAGTGCC
Statistics
Matches: 94, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
93 83 0.88
94 11 0.12
ACGTcount: A:0.35, C:0.05, G:0.09, T:0.52
Consensus pattern (94 bp):
AATTTTTATTTATTATTAAACTTTTTTAGAATTTAGAAATTTATTTTTATTTTTAATAGATATAG
ATGTCATGTAACACTTAATTTCTAATTGG
Found at i:231973 original size:15 final size:15
Alignment explanation
Indices: 231941--231985 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
231931 TAATTCTTTG
*
231941 ATTTATATTCATATAT
1 ATTTATA-TCATACAT
*
231957 ATTTATATCATCCAT
1 ATTTATATCATACAT
231972 ATTTAT-TCATACAT
1 ATTTATATCATACAT
231986 TCAAAGTTGG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
14 7 0.27
15 12 0.46
16 7 0.27
ACGTcount: A:0.36, C:0.13, G:0.00, T:0.51
Consensus pattern (15 bp):
ATTTATATCATACAT
Found at i:232143 original size:657 final size:657
Alignment explanation
Indices: 231183--232470 Score: 2294
Period size: 657 Copynumber: 2.0 Consensus size: 657
231173 CGAAATATCA
*
231183 TTAAAGACAGTATCCAACACGTCTCAAGTTATTCAACTTTTATTTTTTATTCTTTAAATTGAATA
1 TTAAAGACAGTATCCAACACGTCTCAAGTTATTCAACTTGTATTTTTTATTCTTTAAATTGAATA
*
231248 TTTACAAGAATACATACCAACACTTTTAATTCTTTGATTTCTATTCATATATATTTATATCATCC
66 TTTACAAGAATACATACCAACACTTTTAATTCTTTGATTTATATTCATATATATTTATATCATCC
** *
231313 ATATTTATTCATACATTCAAAGTTGGGAAAGCAGTTGTGATTTTGTGAGCTTGGAGTCTTAATTT
131 ATATTTATTCATACATTCAAAGTTGGGAAAGCAGTTGTGATTTCATGAGCTTGGAGTATTAATTT
231378 AATCCCAACAAAACCTTAACAAATCATCAGCAAATGAGATTCAGCTACAATCGATTGGATGATCA
196 AATCCCAACAAAACCTTAACAAATCATCAGCAAATGAGATTCAGCTACAATCGATTGGATGATCA
* *
231443 AAGAATAAAAATTGTTTCTATAGTTATACATCGTATTGTGAAGATTCGAGAATCCTAAAGGAATA
261 AAGAATAAAAATTGTTTCTATAGTTACACATCGTATCGTGAAGATTCGAGAATCCTAAAGGAATA
231508 ATTGATAAGGGATTAGATTGGAAAGGGATTAATAGAGGATATGGGTAACATGGAAGCAAACTTTG
326 ATTGATAAGGGATTAGATTGGAAAGGGATTAATAGAGGATATGGGTAACATGGAAGCAAACTTTG
231573 ACAACTGTCAGACAATACTAAGAACATTAGTTGATAATTGATTGTTAGAAAATGTAGGAAATGGA
391 ACAACTGTCAGACAATACTAAGAACATTAGTTGATAATTGATTGTTAGAAAATGTAGGAAATGGA
231638 AGAGTGAAAATGCATGATTTTGTAATAGATATGGCTAAACTAATCACCAATGA-GTTATATGAAT
456 AGAGTGAAAATGCATGATTTTGTAATAGATATGGCTAAACTAATCACCAATGAGGTT-TATGAAT
** *
231702 CATGAATTAACATTGCAACTTTAACCTATGTATAATTTAGCTCCAACATTTATATTTTTTTATTA
520 CATGAATTAACATTGCAACTTTAACCTATGTATAATCAAGCTCCAACATTTATAATTTTTTATTA
*
231767 ACTAAAATGATACAATAAATCAAAAACAATCAAAACTTAAATTAATTAAAATTAACTTTGTATTT
585 ACTAAAATGATACAATAAATCAAAAACAATCAAAACTTAAAATAATTAAAATTAACTTTGTATTT
231832 TTTATTCT
650 TTTATTCT
*
231840 TTAAAGACAGTATCCAACACGTCTCTAGTTATTCAACTTGTATTTTTTATTCTTTAAATTGAATA
1 TTAAAGACAGTATCCAACACGTCTCAAGTTATTCAACTTGTATTTTTTATTCTTTAAATTGAATA
231905 TTTACAAGAATACATACCAACACTTTTAATTCTTTGATTTATATTCATATATATTTATATCATCC
66 TTTACAAGAATACATACCAACACTTTTAATTCTTTGATTTATATTCATATATATTTATATCATCC
* *
231970 ATATTTATTCATACATTCAAAGTTGGGAGAGCTGTTGTGATTTCATGAGCTTGGAGTATTAATTT
131 ATATTTATTCATACATTCAAAGTTGGGAAAGCAGTTGTGATTTCATGAGCTTGGAGTATTAATTT
*
232035 AATCCCAACAAAACCTTAACAAATCATCAGCAAATGAGATTCAGTTACAA-CTGATTGGATGATC
196 AATCCCAACAAAACCTTAACAAATCATCAGCAAATGAGATTCAGCTACAATC-GATTGGATGATC
* *
232099 AAAGAATAAAAATTGTTTCTATAGTTACGCA-CTGTATCGTGAAGATTCGAGAATTCTAAAGGAA
260 AAAGAATAAAAATTGTTTCTATAGTTACACATC-GTATCGTGAAGATTCGAGAATCCTAAAGGAA
*
232163 TAATTGATAAGGGATTAGATTGGAAAGGGATTAATAGAGGATGTGGGTAACATGGAAGCAAACTT
324 TAATTGATAAGGGATTAGATTGGAAAGGGATTAATAGAGGATATGGGTAACATGGAAGCAAACTT
* * * * *
232228 TGCCAAGTGTCAGACTATCCTAAGAACATTAGTTGATAGTTGATTGTTAGAAAATGTAGGAAATG
389 TGACAACTGTCAGACAATACTAAGAACATTAGTTGATAATTGATTGTTAGAAAATGTAGGAAATG
*
232293 GAAGAGTTAAAATGCATGATTTTGTAATAGATATGGCTAAACTAATCACCAATGAGGTTTATGAA
454 GAAGAGTGAAAATGCATGATTTTGTAATAGATATGGCTAAACTAATCACCAATGAGGTTTATGAA
*
232358 TCATGAATTAATATTGCAACTTTAACCTATGTATAATCAAGCTCCAACATTTATAATTTTTTATT
519 TCATGAATTAACATTGCAACTTTAACCTATGTATAATCAAGCTCCAACATTTATAATTTTTTATT
*
232423 AACTAAAATGATGCAATAAATCAAAAACAATCAAAACTTAAAATAATT
584 AACTAAAATGATACAATAAATCAAAAACAATCAAAACTTAAAATAATT
232471 CGAATTTAAT
Statistics
Matches: 602, Mismatches: 26, Indels: 6
0.95 0.04 0.01
Matches are distributed among these distances:
656 2 0.00
657 597 0.99
658 3 0.00
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.34
Consensus pattern (657 bp):
TTAAAGACAGTATCCAACACGTCTCAAGTTATTCAACTTGTATTTTTTATTCTTTAAATTGAATA
TTTACAAGAATACATACCAACACTTTTAATTCTTTGATTTATATTCATATATATTTATATCATCC
ATATTTATTCATACATTCAAAGTTGGGAAAGCAGTTGTGATTTCATGAGCTTGGAGTATTAATTT
AATCCCAACAAAACCTTAACAAATCATCAGCAAATGAGATTCAGCTACAATCGATTGGATGATCA
AAGAATAAAAATTGTTTCTATAGTTACACATCGTATCGTGAAGATTCGAGAATCCTAAAGGAATA
ATTGATAAGGGATTAGATTGGAAAGGGATTAATAGAGGATATGGGTAACATGGAAGCAAACTTTG
ACAACTGTCAGACAATACTAAGAACATTAGTTGATAATTGATTGTTAGAAAATGTAGGAAATGGA
AGAGTGAAAATGCATGATTTTGTAATAGATATGGCTAAACTAATCACCAATGAGGTTTATGAATC
ATGAATTAACATTGCAACTTTAACCTATGTATAATCAAGCTCCAACATTTATAATTTTTTATTAA
CTAAAATGATACAATAAATCAAAAACAATCAAAACTTAAAATAATTAAAATTAACTTTGTATTTT
TTATTCT
Found at i:237184 original size:30 final size:28
Alignment explanation
Indices: 237141--237198 Score: 80
Period size: 30 Copynumber: 2.0 Consensus size: 28
237131 TTTTCTTCCC
237141 CTGTTTTCGTCTCTTTCTCTGTTTCTTTT
1 CTGTTTTCGTCTCTTTCTCTG-TTCTTTT
* *
237170 CTGTTCTTCTTCTCTTTTTCTGTTCTTTT
1 CTGTT-TTCGTCTCTTTCTCTGTTCTTTT
237199 ATTTCATTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 12 0.46
30 14 0.54
ACGTcount: A:0.00, C:0.24, G:0.09, T:0.67
Consensus pattern (28 bp):
CTGTTTTCGTCTCTTTCTCTGTTCTTTT
Found at i:238450 original size:24 final size:26
Alignment explanation
Indices: 238423--238481 Score: 79
Period size: 24 Copynumber: 2.3 Consensus size: 26
238413 TATTGTTTTT
238423 TATTTTAAAAAATAATG-AG-TA-ATA
1 TATTTTAAAAAAT-ATGTAGTTATATA
*
238447 TATTTTATAAAATATGTAGTTATATA
1 TATTTTAAAAAATATGTAGTTATATA
238473 TATTTTAAA
1 TATTTTAAA
238482 TTAATTTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
23 3 0.10
24 14 0.47
25 2 0.07
26 11 0.37
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.46
Consensus pattern (26 bp):
TATTTTAAAAAATATGTAGTTATATA
Found at i:240242 original size:41 final size:41
Alignment explanation
Indices: 240197--240274 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 41
240187 AAATAAAAAT
*
240197 TTAAAATAAATATTAAAACAAAAAACAAATTAAAAATGAGA
1 TTAAAACAAATATTAAAACAAAAAACAAATTAAAAATGAGA
* * * * *
240238 TTAAAACAATTCTTAAAACAATACACAAATTGAAAAT
1 TTAAAACAAATATTAAAACAAAAAACAAATTAAAAAT
240275 ATAATAAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 31 1.00
ACGTcount: A:0.63, C:0.09, G:0.04, T:0.24
Consensus pattern (41 bp):
TTAAAACAAATATTAAAACAAAAAACAAATTAAAAATGAGA
Found at i:244694 original size:16 final size:16
Alignment explanation
Indices: 244670--244704 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
244660 AAATTTGACG
* *
244670 AAAATATTAATAATAT
1 AAAAAATTAAAAATAT
244686 AAAAAATTAAAAATAT
1 AAAAAATTAAAAATAT
244702 AAA
1 AAA
244705 TTTATTTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAAAATTAAAAATAT
Found at i:244964 original size:23 final size:24
Alignment explanation
Indices: 244933--244990 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 24
244923 TTAAATTCGT
244933 ATTTGTATTATTTATAAATTT-AGA
1 ATTT-TATTATTTATAAATTTAAGA
**
244957 ATTTTATT-TTTATATTTTTAAGA
1 ATTTTATTATTTATAAATTTAAGA
*
244980 ATTTAATTATT
1 ATTTTATTATT
244991 CATTTATCAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
22 9 0.31
23 14 0.48
24 6 0.21
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.60
Consensus pattern (24 bp):
ATTTTATTATTTATAAATTTAAGA
Found at i:249510 original size:20 final size:20
Alignment explanation
Indices: 249436--249511 Score: 61
Period size: 20 Copynumber: 3.9 Consensus size: 20
249426 GACTGTATAG
*
249436 AATTTTATAATTTTTTTCTTC
1 AATTTTATAATTTTTTT-TAC
** * *
249457 --TTTTACGA-TTTTTATAA
1 AATTTTATAATTTTTTTTAC
249474 AATTTTATAATTTTTTTTAC
1 AATTTTATAATTTTTTTTAC
249494 AATTCTTAT-ATTTTTTTT
1 AATT-TTATAATTTTTTTT
249512 CTAGTTTTTT
Statistics
Matches: 42, Mismatches: 9, Indels: 9
0.70 0.15 0.15
Matches are distributed among these distances:
17 1 0.02
18 5 0.12
19 12 0.29
20 20 0.48
21 4 0.10
ACGTcount: A:0.26, C:0.07, G:0.01, T:0.66
Consensus pattern (20 bp):
AATTTTATAATTTTTTTTAC
Found at i:249567 original size:27 final size:28
Alignment explanation
Indices: 249517--249578 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 28
249507 TTTTTCTAGT
* *
249517 TTTTTAATAAAATTTAAATATTTTTATA
1 TTTTTATTAAAATTTAAATATTTTAATA
249545 TTTTTATTAAAATTTAAAT-TTTTAATA
1 TTTTTATTAAAATTTAAATATTTTAATA
249572 TTTTTAT
1 TTTTTAT
249579 CACATGTCAC
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 14 0.44
28 18 0.56
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (28 bp):
TTTTTATTAAAATTTAAATATTTTAATA
Found at i:253357 original size:124 final size:124
Alignment explanation
Indices: 253189--253479 Score: 494
Period size: 124 Copynumber: 2.3 Consensus size: 124
253179 TTATTTCGAG
* * *
253189 TTGACGTTTCTG-GACAAATAGTATAAAATCACGCCCTCGAGGATGCTAATTGGGAAGAAATTGT
1 TTGACGTTTCTGAG-CAAATAGTATAAAATCGCGCCCTCGTGGATGCTAATTGAGAAGAAATTGT
* *
253253 GAAATCGTGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAAGAAATAATTTTTT
65 GAAATCGTGCCCTCGTGGACGCGATTTCACTACAGTTAGTCATGTAAGAAATAATTTTTT
253313 TTGACGTTTCTGAGCAAATAGTATAAAATCGCGCCCTCGTGGATGCTAATTGAGAAGAAATTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCGCCCTCGTGGATGCTAATTGAGAAGAAATTGTG
*
253378 AAATCGTGCCCTCGTGGACGCGATTTCACTACAGTTAGTCATGTAAGAAATATTTTTTT
66 AAATCGTGCCCTCGTGGACGCGATTTCACTACAGTTAGTCATGTAAGAAATAATTTTTT
* *
253437 TTGACGTTTCTGAACAAATAGTATAAAATCGAGCCCTCGTGGA
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCGCCCTCGTGGA
253480 CGCGATTTTG
Statistics
Matches: 158, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
124 157 0.99
125 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Consensus pattern (124 bp):
TTGACGTTTCTGAGCAAATAGTATAAAATCGCGCCCTCGTGGATGCTAATTGAGAAGAAATTGTG
AAATCGTGCCCTCGTGGACGCGATTTCACTACAGTTAGTCATGTAAGAAATAATTTTTT
Found at i:256427 original size:56 final size:56
Alignment explanation
Indices: 256338--256462 Score: 189
Period size: 56 Copynumber: 2.2 Consensus size: 56
256328 TATGTAAAAC
* **
256338 TATGTAAAATTATTAAGCCCAATAACTTCTGTTAATGGTTAGTAA-ATTTATCAAAT
1 TATGTAAAATTATTAAGCCCAAAAAAGTCTGTTAATGGTTAGTAAGA-TTATCAAAT
*
256394 TATGTAAAATTATTAAGCCCAAAAAAGTGTGTTAATGGTTAGTAAGATTATCAAAT
1 TATGTAAAATTATTAAGCCCAAAAAAGTCTGTTAATGGTTAGTAAGATTATCAAAT
*
256450 TAGGTAAAATTAT
1 TATGTAAAATTAT
256463 GTTATGGTTT
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
56 62 0.98
57 1 0.02
ACGTcount: A:0.42, C:0.08, G:0.14, T:0.37
Consensus pattern (56 bp):
TATGTAAAATTATTAAGCCCAAAAAAGTCTGTTAATGGTTAGTAAGATTATCAAAT
Found at i:256489 original size:23 final size:23
Alignment explanation
Indices: 256463--256517 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
256453 GTAAAATTAT
*
256463 GTTATGGTTTTTAAATAAACTAG
1 GTTAAGGTTTTTAAATAAACTAG
* * *
256486 GTTAGGGTTTTTAATTAAATTAG
1 GTTAAGGTTTTTAAATAAACTAG
256509 GTTAAGGTT
1 GTTAAGGTT
256518 AGGGGTTTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.31, C:0.02, G:0.22, T:0.45
Consensus pattern (23 bp):
GTTAAGGTTTTTAAATAAACTAG
Found at i:256518 original size:29 final size:29
Alignment explanation
Indices: 256484--256812 Score: 543
Period size: 29 Copynumber: 11.4 Consensus size: 29
256474 TAAATAAACT
256484 AGGTTAGGGTTTTTAATTAAATTAGGTTA
1 AGGTTAGGGTTTTTAATTAAATTAGGTTA
*
256513 AGGTTAGGGGTTTTAATTAAATTAGGTTA
1 AGGTTAGGGTTTTTAATTAAATTAGGTTA
*
256542 GGGTTAGGGTTTTTAATTAAATTAGGTTA
1 AGGTTAGGGTTTTTAATTAAATTAGGTTA
*
256571 AGGTTAGGGGTTTTAATTAAATTAGGTTA
1 AGGTTAGGGTTTTTAATTAAATTAGGTTA
*
256600 GGGTTAGGGTTTTTAATTAAATTAGGTTA
1 AGGTTAGGGTTTTTAATTAAATTAGGTTA
*
256629 AGGTTAGGGGTTTTAATTAAATTAGGTTA
1 AGGTTAGGGTTTTTAATTAAATTAGGTTA
*
256658 GGGTTAGGGTTTTTAATTAAATTAGGTTA
1 AGGTTAGGGTTTTTAATTAAATTAGGTTA
256687 AGGTTAGGGTTTTTAATTAAATTAGGTTA
1 AGGTTAGGGTTTTTAATTAAATTAGGTTA
* *
256716 AAGTTAGGGGTTTTAATTAAATTAGGTTA
1 AGGTTAGGGTTTTTAATTAAATTAGGTTA
*
256745 GGGTTAGGGTTTTTAATTAAATTAGGTTA
1 AGGTTAGGGTTTTTAATTAAATTAGGTTA
* *
256774 GGGTTAAGG-TTTTAATTAAATTAGGTTA
1 AGGTTAGGGTTTTTAATTAAATTAGGTTA
*
256802 GGGTTAGGGTT
1 AGGTTAGGGTT
256813 AGGGTATGAA
Statistics
Matches: 280, Mismatches: 19, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
28 27 0.10
29 253 0.90
ACGTcount: A:0.29, C:0.00, G:0.27, T:0.43
Consensus pattern (29 bp):
AGGTTAGGGTTTTTAATTAAATTAGGTTA
Found at i:259317 original size:38 final size:37
Alignment explanation
Indices: 259228--259300 Score: 112
Period size: 37 Copynumber: 2.0 Consensus size: 37
259218 GTCTCCAAAT
* *
259228 TCACATTTCAATTC-AATTTCACTTTTTCACTTTCAA
1 TCACAATTCAATTCAAAATTCACTTTTTCACTTTCAA
*
259264 TCACAATTCAATTCAAAATTCACTTTTTCATTTTCAA
1 TCACAATTCAATTCAAAATTCACTTTTTCACTTTCAA
259301 ATCAATATTC
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
36 13 0.39
37 20 0.61
ACGTcount: A:0.32, C:0.23, G:0.00, T:0.45
Consensus pattern (37 bp):
TCACAATTCAATTCAAAATTCACTTTTTCACTTTCAA
Found at i:261476 original size:11 final size:11
Alignment explanation
Indices: 261460--261538 Score: 92
Period size: 11 Copynumber: 7.2 Consensus size: 11
261450 TTTAAATAGG
261460 AATTTGAGAGA
1 AATTTGAGAGA
261471 AATTTGAGAGGA
1 AATTTGAGA-GA
261483 AA-TTGAGAGCA
1 AATTTGAGAG-A
261494 AATTT-AGAGA
1 AATTTGAGAGA
261504 AATTTGAGAGA
1 AATTTGAGAGA
**
261515 ATATTAAAGAGA
1 A-ATTTGAGAGA
261527 AA-TTGAGAGA
1 AATTTGAGAGA
261537 AA
1 AA
261539 GGATTTAGTT
Statistics
Matches: 59, Mismatches: 4, Indels: 11
0.80 0.05 0.15
Matches are distributed among these distances:
10 15 0.25
11 29 0.49
12 15 0.25
ACGTcount: A:0.49, C:0.01, G:0.25, T:0.24
Consensus pattern (11 bp):
AATTTGAGAGA
Found at i:261503 original size:33 final size:33
Alignment explanation
Indices: 261451--261538 Score: 99
Period size: 33 Copynumber: 2.6 Consensus size: 33
261441 TTAAGCTCTT
* *
261451 TTAAATAGGAATTTGAGAGAAATTTGAGAGGAA-A
1 TTAAAGAGAAATTT-AGAGAAATTTGAGA-GAATA
*
261485 TT-GAGAGCAAATTTAGAGAAATTTGAGAGAATA
1 TTAAAGAG-AAATTTAGAGAAATTTGAGAGAATA
*
261518 TTAAAGAGAAATTGAGAGAAA
1 TTAAAGAGAAATTTAGAGAAA
261539 GGATTTAGTT
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
32 3 0.07
33 32 0.70
34 11 0.24
ACGTcount: A:0.49, C:0.01, G:0.25, T:0.25
Consensus pattern (33 bp):
TTAAAGAGAAATTTAGAGAAATTTGAGAGAATA
Found at i:264915 original size:27 final size:28
Alignment explanation
Indices: 264858--264915 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 28
264848 CAGCCCAGCC
** * *
264858 TAATTTATTATTTAATAATTAAAATTTA
1 TAATTTATTATTTAATAAAAAAAACTAA
*
264886 TAATTTTTTA-TTAATAAAAAAAACTAA
1 TAATTTATTATTTAATAAAAAAAACTAA
264913 TAA
1 TAA
264916 GCGAAGGACA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
27 16 0.64
28 9 0.36
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (28 bp):
TAATTTATTATTTAATAAAAAAAACTAA
Found at i:265431 original size:10 final size:10
Alignment explanation
Indices: 265418--265492 Score: 59
Period size: 10 Copynumber: 7.9 Consensus size: 10
265408 ACATGTGACA
265418 AAAAATTATT
1 AAAAATTATT
**
265428 AAAAA--AAG
1 AAAAATTATT
265436 AAAAATTATT
1 AAAAATTATT
*
265446 AAAAGTT-TT
1 AAAAATTATT
265455 AAAAATTATT
1 AAAAATTATT
** *
265465 AAATTTTAAT
1 AAAAATTATT
*
265475 AAAAA-TATA
1 AAAAATTATT
265484 AAAAATTAT
1 AAAAATTAT
265493 AAATGTATCA
Statistics
Matches: 48, Mismatches: 13, Indels: 8
0.70 0.19 0.12
Matches are distributed among these distances:
8 6 0.12
9 15 0.31
10 27 0.56
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.35
Consensus pattern (10 bp):
AAAAATTATT
Found at i:265632 original size:21 final size:20
Alignment explanation
Indices: 265606--265651 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
265596 ACATGTGACA
265606 AAAATTGATAAAAAAATTAAT
1 AAAATTGAT-AAAAAATTAAT
* * *
265627 AAAATTTATAGAAAATTTAT
1 AAAATTGATAAAAAATTAAT
265647 AAAAT
1 AAAAT
265652 GCTTCTTTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (20 bp):
AAAATTGATAAAAAATTAAT
Found at i:265713 original size:21 final size:21
Alignment explanation
Indices: 265670--265713 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
265660 TAGTATGGTA
* *
265670 TTTTTATATATTTCTTTATAC
1 TTTTTATATATTTCTTAAAAC
265691 TTTTTATA-ATTTTCTTAAAAC
1 TTTTTATATA-TTTCTTAAAAC
265712 TT
1 TT
265714 AATAAAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 19 0.95
ACGTcount: A:0.27, C:0.09, G:0.00, T:0.64
Consensus pattern (21 bp):
TTTTTATATATTTCTTAAAAC
Found at i:266122 original size:7 final size:7
Alignment explanation
Indices: 266106--266150 Score: 54
Period size: 7 Copynumber: 6.3 Consensus size: 7
266096 CCTTAAGCCT
*
266106 AAAAATA
1 AAAAAGA
266113 AAAAAGA
1 AAAAAGA
266120 AAAAAGAA
1 AAAAAG-A
266128 AAAAAGA
1 AAAAAGA
*
266135 AATAAGA
1 AAAAAGA
*
266142 AATAAGA
1 AAAAAGA
266149 AA
1 AA
266151 TAAAAATTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
7 28 0.80
8 7 0.20
ACGTcount: A:0.82, C:0.00, G:0.11, T:0.07
Consensus pattern (7 bp):
AAAAAGA
Found at i:266130 original size:15 final size:15
Alignment explanation
Indices: 266112--266143 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
266102 GCCTAAAAAT
266112 AAAAAAGAAAAAAGA
1 AAAAAAGAAAAAAGA
*
266127 AAAAAAGAAATAAGA
1 AAAAAAGAAAAAAGA
266142 AA
1 AA
266144 TAAGAAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.84, C:0.00, G:0.12, T:0.03
Consensus pattern (15 bp):
AAAAAAGAAAAAAGA
Found at i:266132 original size:22 final size:22
Alignment explanation
Indices: 266106--266155 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
266096 CCTTAAGCCT
*
266106 AAAAATAAAAAAGAAAAAAGAA
1 AAAAAGAAAAAAGAAAAAAGAA
* *
266128 AAAAAGAAATAAGAAATAAGAA
1 AAAAAGAAAAAAGAAAAAAGAA
266150 ATAAAA
1 A-AAAA
266156 ATTATAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 20 0.83
23 4 0.17
ACGTcount: A:0.82, C:0.00, G:0.10, T:0.08
Consensus pattern (22 bp):
AAAAAGAAAAAAGAAAAAAGAA
Found at i:266151 original size:7 final size:7
Alignment explanation
Indices: 266116--266157 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
266106 AAAAATAAAA
*
266116 AAGAAAA
1 AAGAAAT
*
266123 AAGAAAAA
1 AAG-AAAT
266131 AAGAAAT
1 AAGAAAT
266138 AAGAAAT
1 AAGAAAT
266145 AAGAAAT
1 AAGAAAT
266152 AA-AAAT
1 AAGAAAT
266158 TATAAAAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
6 4 0.12
7 22 0.67
8 7 0.21
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.10
Consensus pattern (7 bp):
AAGAAAT
Found at i:272103 original size:7 final size:7
Alignment explanation
Indices: 272076--272110 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
272066 TAATGTTGTT
272076 TTTATTA
1 TTTATTA
*
272083 TTTCTTA
1 TTTATTA
*
272090 GTTATTA
1 TTTATTA
272097 TTTATTA
1 TTTATTA
272104 TTTATTA
1 TTTATTA
272111 ATAAAAAGAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.69
Consensus pattern (7 bp):
TTTATTA
Found at i:272804 original size:3 final size:3
Alignment explanation
Indices: 272796--272825 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
272786 AAGTGAAAAT
272796 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
272826 CCTCTCTTGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:276232 original size:17 final size:17
Alignment explanation
Indices: 276210--276242 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
276200 GGCCGGAATT
*
276210 AAATTATTTTATTTAAA
1 AAATTAATTTATTTAAA
276227 AAATTAATTTATTTAA
1 AAATTAATTTATTTAA
276243 TATCAAAATC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
AAATTAATTTATTTAAA
Found at i:276250 original size:22 final size:22
Alignment explanation
Indices: 276206--276250 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
276196 AATTGGCCGG
* *
276206 AATTAAATTATTTTATTTAAAA
1 AATTAAATTATTTAATATAAAA
* *
276228 AATTAATTTATTTAATATCAAA
1 AATTAAATTATTTAATATAAAA
276250 A
1 A
276251 TCGAGAGGTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (22 bp):
AATTAAATTATTTAATATAAAA
Found at i:277811 original size:30 final size:30
Alignment explanation
Indices: 277775--277834 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
277765 TGTGGCAATC
* *
277775 CACATACTTTTGTAAAAATTCAAACGAATT
1 CACATACTTTTATAAAAATTCAAAAGAATT
*
277805 CACATACTTTTATAAAAATTGAAAAGAATT
1 CACATACTTTTATAAAAATTCAAAAGAATT
277835 AATAAAAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.47, C:0.13, G:0.07, T:0.33
Consensus pattern (30 bp):
CACATACTTTTATAAAAATTCAAAAGAATT
Found at i:284437 original size:28 final size:29
Alignment explanation
Indices: 284379--284442 Score: 85
Period size: 28 Copynumber: 2.2 Consensus size: 29
284369 TCCACATTTT
* *
284379 AAATAAAAAAACACATTTTCGTTCAAAAA
1 AAATAAAAAAACACATTTTAGATCAAAAA
284408 AAAT-AAAAAACACATTTTAGATCATTAAAA
1 AAATAAAAAAACACATTTTAGATCA--AAAA
284438 AAATA
1 AAATA
284443 CCTTTTAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 18 0.60
29 4 0.13
30 8 0.27
ACGTcount: A:0.61, C:0.11, G:0.03, T:0.25
Consensus pattern (29 bp):
AAATAAAAAAACACATTTTAGATCAAAAA
Found at i:292789 original size:22 final size:22
Alignment explanation
Indices: 292750--292821 Score: 76
Period size: 23 Copynumber: 3.2 Consensus size: 22
292740 GGGGTTGAAA
292750 TTAAAT-TATATATATTTATTAT
1 TTAAATATATATAT-TTTATTAT
*
292772 TATAAATATATA-ATTTTATAAT
1 T-TAAATATATATATTTTATTAT
* *
292794 TTTAATAGTGTATATTTTATTAT
1 TTAAATA-TATATATTTTATTAT
292817 TTAAA
1 TTAAA
292822 AAAGATTGAA
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
21 5 0.12
22 12 0.29
23 20 0.49
24 4 0.10
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.56
Consensus pattern (22 bp):
TTAAATATATATATTTTATTAT
Found at i:297315 original size:26 final size:25
Alignment explanation
Indices: 297263--297324 Score: 70
Period size: 26 Copynumber: 2.4 Consensus size: 25
297253 TCTAAAATCA
*
297263 TAACAAAATTAACAATAAAACAATAG
1 TAACAAAA-TAACAACAAAACAATAG
* * *
297289 TTATAAAATAACAACAAAATAAGTAG
1 TAACAAAATAACAACAAAACAA-TAG
297315 TAACAAAATA
1 TAACAAAATA
297325 GTGAAAAAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
25 12 0.41
26 17 0.59
ACGTcount: A:0.65, C:0.10, G:0.05, T:0.21
Consensus pattern (25 bp):
TAACAAAATAACAACAAAACAATAG
Done.