Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015160.1 Kokia drynarioides strain JFW-HI SEQ_130204, 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: 450540
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Warning! 486 characters in sequence are not A, C, G, or T
Found at i:9694 original size:27 final size:30
Alignment explanation
Indices: 9655--9711 Score: 84
Period size: 27 Copynumber: 2.0 Consensus size: 30
9645 AAAGTTAAAA
*
9655 AAAACTTATAAAAGATT-AAAATA-AGTTT
1 AAAACTTATAAAAAATTCAAAATATAGTTT
9683 AAAA-TTATAAAAAATTCAAAATATAGTTT
1 AAAACTTATAAAAAATTCAAAATATAGTTT
9712 TAAGAAGCCT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 11 0.42
28 10 0.38
29 5 0.19
ACGTcount: A:0.58, C:0.04, G:0.05, T:0.33
Consensus pattern (30 bp):
AAAACTTATAAAAAATTCAAAATATAGTTT
Found at i:10739 original size:1 final size:1
Alignment explanation
Indices: 10694--10719 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
10684 TGTATTTCAC
10694 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
10720 NNNNNNNNNN
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:22770 original size:16 final size:17
Alignment explanation
Indices: 22746--22779 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
22736 GAAGGGATTA
22746 AGAAAAAAAA-ACCTTG
1 AGAAAAAAAAGACCTTG
*
22762 AGAATAAAAAGACCTTG
1 AGAAAAAAAAGACCTTG
22779 A
1 A
22780 CATCGTGTCA
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:0.59, C:0.12, G:0.15, T:0.15
Consensus pattern (17 bp):
AGAAAAAAAAGACCTTG
Found at i:22776 original size:17 final size:16
Alignment explanation
Indices: 22746--22779 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
22736 GAAGGGATTA
22746 AGAAAAAAAAACCTTG
1 AGAAAAAAAAACCTTG
*
22762 AGAATAAAAAGACCTTG
1 AGAA-AAAAAAACCTTG
22779 A
1 A
22780 CATCGTGTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.59, C:0.12, G:0.15, T:0.15
Consensus pattern (16 bp):
AGAAAAAAAAACCTTG
Found at i:26840 original size:16 final size:16
Alignment explanation
Indices: 26828--26859 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
26818 TAATTTTATT
26828 AATTTAAAATTTTAAA
1 AATTTAAAATTTTAAA
26844 AATTT-AAA-TTTAAA
1 AATTTAAAATTTTAAA
26858 AA
1 AA
26860 AAAAAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 3 0.19
16 5 0.31
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
AATTTAAAATTTTAAA
Found at i:26854 original size:15 final size:15
Alignment explanation
Indices: 26813--26859 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
26803 GTTAAAATAT
* **
26813 AATTTTAATTTTATT
1 AATTTAAATTTTAAA
26828 AATTTAAAATTTTAAA
1 AATTT-AAATTTTAAA
26844 AATTTAAA-TTTAAA
1 AATTTAAATTTTAAA
26858 AA
1 AA
26860 AAAAAAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 8 0.29
15 8 0.29
16 12 0.43
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
AATTTAAATTTTAAA
Found at i:26861 original size:16 final size:16
Alignment explanation
Indices: 26828--26860 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
26818 TAATTTTATT
*
26828 AATTTAAAATTTTAAA
1 AATTTAAAATTTAAAA
26844 AATTT-AAATTTAAAA
1 AATTTAAAATTTAAAA
26859 AA
1 AA
26861 AAAAAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
AATTTAAAATTTAAAA
Found at i:30056 original size:57 final size:56
Alignment explanation
Indices: 29963--30071 Score: 164
Period size: 57 Copynumber: 1.9 Consensus size: 56
29953 TATCTGTAAT
*
29963 TAGAGTTGCTCATGAGTCGAGTTGAATCGACCCAAATTAGAGAAAATTACATTCAAA
1 TAGAGTTGCTCATGAGTCGAGTTGAATCGACCCAAATTA-AAAAAATTACATTCAAA
* * **
30020 TAGAGTTGTTCATGAGTCGAGTTGGATCGATTCAAATTAAAAAAATTACATT
1 TAGAGTTGCTCATGAGTCGAGTTGAATCGACCCAAATTAAAAAAATTACATT
30072 GAAAAACTTA
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
56 12 0.26
57 35 0.74
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (56 bp):
TAGAGTTGCTCATGAGTCGAGTTGAATCGACCCAAATTAAAAAAATTACATTCAAA
Found at i:32313 original size:154 final size:151
Alignment explanation
Indices: 32029--32334 Score: 479
Period size: 152 Copynumber: 2.0 Consensus size: 151
32019 ATTCATCGAA
* *
32029 ATTCACAATCAATCTTATGATGAGTGAATACCACCAGGTTCTAGCTATCTCCTTGAGTGTGGTTG
1 ATTCACAATCAATCCTATGATGAGTGAATACCACCAGATTCTAGCTATCTCCTTGAGTGTGGTTG
* *
32094 CTCGGAAGAAATTAGAATTTTTTTCGAATGAGTCGAAATTAAATTGTGATTTTTACGATAATAAA
66 CACGGAAGAAATTAGAATTTTTTTCGAAGGAGTCGAAATTAAATTGTGATTTTTACGATAAT-AA
32159 AATATAATTTCATCATTTGTAT
130 AATATAATTTCATCATTTGTAT
*
32181 ATTCACAATCAATCCTATGATGAGTGAATACCATCAGATTCTAGCTATCTCCTTGAGTGTGTGGT
1 ATTCACAATCAATCCTATGATGAGTGAATACCACCAGATTCTAGCTATCTCCTTGA--GTGTGGT
* *** *
32246 TGCACGGGAGAAATTAG-ATTTTTTTTTTAGGAAGTCGAAATTAAATTGTGATTTTTACGATAGT
64 TGCACGGAAGAAATTAGAATTTTTTTCGAAGG-AGTCGAAATTAAATTGTGATTTTTACGATAAT
32310 AAAATATAATTTCATCATTTGTAT
128 AAAATATAATTTCATCATTTGTAT
32334 A
1 A
32335 GTTTATTTTT
Statistics
Matches: 141, Mismatches: 10, Indels: 5
0.90 0.06 0.03
Matches are distributed among these distances:
152 53 0.38
153 35 0.25
154 53 0.38
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38
Consensus pattern (151 bp):
ATTCACAATCAATCCTATGATGAGTGAATACCACCAGATTCTAGCTATCTCCTTGAGTGTGGTTG
CACGGAAGAAATTAGAATTTTTTTCGAAGGAGTCGAAATTAAATTGTGATTTTTACGATAATAAA
ATATAATTTCATCATTTGTAT
Found at i:42279 original size:19 final size:19
Alignment explanation
Indices: 42242--42280 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
42232 ATTTAAATTC
*
42242 AAATTCAATCCATCTATTT
1 AAATTCAATACATCTATTT
42261 AAATTCAAATACATC-ATTT
1 AAATTC-AATACATCTATTT
42280 A
1 A
42281 CCAAGTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.44, C:0.18, G:0.00, T:0.38
Consensus pattern (19 bp):
AAATTCAATACATCTATTT
Found at i:45354 original size:28 final size:28
Alignment explanation
Indices: 45296--45364 Score: 68
Period size: 28 Copynumber: 2.5 Consensus size: 28
45286 TTTTAATTAA
**
45296 TTATTATTTTGAATAATTTATATATGGT
1 TTATTATTTTGAATAATTTATATAAAGT
* *
45324 TTATTATTTT-AATTATTTATATTAAATT
1 TTATTATTTTGAATAATTTATA-TAAAGT
* *
45352 TTAATATTATGAA
1 TTATTATTTTGAA
45365 CCAAGTTTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
27 10 0.30
28 21 0.64
29 2 0.06
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (28 bp):
TTATTATTTTGAATAATTTATATAAAGT
Found at i:48256 original size:58 final size:58
Alignment explanation
Indices: 48166--48282 Score: 216
Period size: 58 Copynumber: 2.0 Consensus size: 58
48156 ATTAACTTAG
*
48166 TGTGGTTTTAAGGTCTTAATATAGAAGATGCTTCACGCCACTAGTAGTGGCACATAGT
1 TGTGGTTTCAAGGTCTTAATATAGAAGATGCTTCACGCCACTAGTAGTGGCACATAGT
*
48224 TGTGGTTTCAAGGTCTTAATATTGAAGATGCTTCACGCCACTAGTAGTGGCACATAGT
1 TGTGGTTTCAAGGTCTTAATATAGAAGATGCTTCACGCCACTAGTAGTGGCACATAGT
48282 T
1 T
48283 TACACCTAAT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
58 57 1.00
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.33
Consensus pattern (58 bp):
TGTGGTTTCAAGGTCTTAATATAGAAGATGCTTCACGCCACTAGTAGTGGCACATAGT
Found at i:54654 original size:35 final size:35
Alignment explanation
Indices: 54608--54685 Score: 156
Period size: 35 Copynumber: 2.2 Consensus size: 35
54598 TTTTCTCAGC
54608 AATCCAACAATAAAGTAAAGAAAGGGTACCTTGGG
1 AATCCAACAATAAAGTAAAGAAAGGGTACCTTGGG
54643 AATCCAACAATAAAGTAAAGAAAGGGTACCTTGGG
1 AATCCAACAATAAAGTAAAGAAAGGGTACCTTGGG
54678 AATCCAAC
1 AATCCAAC
54686 TGCCAATCGT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.46, C:0.17, G:0.21, T:0.17
Consensus pattern (35 bp):
AATCCAACAATAAAGTAAAGAAAGGGTACCTTGGG
Found at i:54801 original size:6 final size:6
Alignment explanation
Indices: 54784--54838 Score: 101
Period size: 6 Copynumber: 9.2 Consensus size: 6
54774 TTTTATTTTG
*
54784 GCTGTT GATGTT GCTGTT GCTGTT GCTGTT GCTGTT GCTGTT GCTGTT
1 GCTGTT GCTGTT GCTGTT GCTGTT GCTGTT GCTGTT GCTGTT GCTGTT
54832 GCTGTT G
1 GCTGTT G
54839 TTATTATTCT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.02, C:0.15, G:0.35, T:0.49
Consensus pattern (6 bp):
GCTGTT
Found at i:63275 original size:21 final size:21
Alignment explanation
Indices: 63249--63289 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
63239 TTGGAAGAAA
63249 TTGGGAGCTGGGAATTGGAAG
1 TTGGGAGCTGGGAATTGGAAG
* *
63270 TTGGGAGTTGGGAGTTGGAA
1 TTGGGAGCTGGGAATTGGAA
63290 ACCTAATTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.22, C:0.02, G:0.49, T:0.27
Consensus pattern (21 bp):
TTGGGAGCTGGGAATTGGAAG
Found at i:63285 original size:14 final size:14
Alignment explanation
Indices: 63247--63287 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
63237 GGTTGGAAGA
*
63247 AATTGGGAGCTGGG
1 AATTGGGAGTTGGG
*
63261 AATTGGAAGTTGGG
1 AATTGGGAGTTGGG
*
63275 AGTTGGGAGTTGG
1 AATTGGGAGTTGG
63288 AAACCTAATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.22, C:0.02, G:0.49, T:0.27
Consensus pattern (14 bp):
AATTGGGAGTTGGG
Found at i:66327 original size:24 final size:24
Alignment explanation
Indices: 66299--66352 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
66289 CAAATAATTA
*
66299 AAATT-TTATCATTATATTAGTTTT
1 AAATTATTAT-ATTATATTAATTTT
*
66323 AAATTATTATTTTATATTAATTTT
1 AAATTATTATATTATATTAATTTT
*
66347 GAATTA
1 AAATTA
66353 GTAAGTTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 22 0.85
25 4 0.15
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (24 bp):
AAATTATTATATTATATTAATTTT
Found at i:73968 original size:27 final size:26
Alignment explanation
Indices: 73921--73987 Score: 73
Period size: 26 Copynumber: 2.5 Consensus size: 26
73911 AGAATTATTT
*
73921 AAAATATGAAAAAAGTTATAAACATTA
1 AAAATAT-AAAAAAGTTATAAACAGTA
*
73948 CAAAATCATAAAAAA-TTATAAATAGTA
1 -AAAAT-ATAAAAAAGTTATAAACAGTA
73975 AAAATTATAAAAA
1 AAAA-TATAAAAA
73988 TTTAAATAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
26 11 0.31
27 11 0.31
28 11 0.31
29 2 0.06
ACGTcount: A:0.66, C:0.04, G:0.04, T:0.25
Consensus pattern (26 bp):
AAAATATAAAAAAGTTATAAACAGTA
Found at i:73986 original size:25 final size:26
Alignment explanation
Indices: 73921--74021 Score: 84
Period size: 25 Copynumber: 3.8 Consensus size: 26
73911 AGAATTATTT
* *
73921 AAAAT-ATGAAAAAAGTTATAAACATTA
1 AAAATCAT-AAAAAA-TTATAAATAGTA
73948 CAAAATCATAAAAAATTATAAATAGTA
1 -AAAATCATAAAAAATTATAAATAGTA
*
73975 AAAATTAT-AAAAATT-TAAATAAGTA
1 AAAATCATAAAAAATTATAAAT-AGTA
*
74000 AAAATACA-ATAAAATATATAAA
1 AAAAT-CATAAAAAAT-TATAAA
74022 AAAAAAATTA
Statistics
Matches: 62, Mismatches: 5, Indels: 12
0.78 0.06 0.15
Matches are distributed among these distances:
24 5 0.08
25 16 0.26
26 13 0.21
27 11 0.18
28 15 0.24
29 2 0.03
ACGTcount: A:0.65, C:0.04, G:0.04, T:0.27
Consensus pattern (26 bp):
AAAATCATAAAAAATTATAAATAGTA
Found at i:74034 original size:20 final size:20
Alignment explanation
Indices: 73983--74034 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 20
73973 TAAAAATTAT
*
73983 AAAAATTTAAATAAGTAAAA
1 AAAAAATTAAATAAGTAAAA
* * *
74003 ATACAATAAAATATA-TAAAA
1 AAAAAATTAAATA-AGTAAAA
74023 AAAAAATTAAAT
1 AAAAAATTAAAT
74035 CAAAAAATGC
Statistics
Matches: 24, Mismatches: 7, Indels: 2
0.73 0.21 0.06
Matches are distributed among these distances:
20 23 0.96
21 1 0.04
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.25
Consensus pattern (20 bp):
AAAAAATTAAATAAGTAAAA
Found at i:80428 original size:4 final size:4
Alignment explanation
Indices: 80421--80445 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
80411 TTCGTCTAAT
80421 ATTA ATTA ATTA ATTA ATTA ATTA A
1 ATTA ATTA ATTA ATTA ATTA ATTA A
80446 AAAATATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
ATTA
Found at i:82182 original size:17 final size:18
Alignment explanation
Indices: 82125--82184 Score: 68
Period size: 18 Copynumber: 3.4 Consensus size: 18
82115 TCAGATATGT
*
82125 GAGCTCATTGAAAGCTAC
1 GAGCTCATTGAAAGTTAC
* * * *
82143 GAGCCCATTCAAAATTGC
1 GAGCTCATTGAAAGTTAC
82161 GAGCTCA-TGAAAGTTAC
1 GAGCTCATTGAAAGTTAC
82178 GAGCTCA
1 GAGCTCA
82185 ACCAAGCTGT
Statistics
Matches: 33, Mismatches: 9, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
17 14 0.42
18 19 0.58
ACGTcount: A:0.33, C:0.23, G:0.22, T:0.22
Consensus pattern (18 bp):
GAGCTCATTGAAAGTTAC
Found at i:100383 original size:21 final size:20
Alignment explanation
Indices: 100336--100383 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
100326 TACTGATTTG
*
100336 ATATTTCGTTATTTTTCTCT
1 ATATTTTGTTATTTTTCTCT
* *
100356 TTGTTTTGTTATTTTTCTACT
1 ATATTTTGTTATTTTTCT-CT
100377 ATATTTT
1 ATATTTT
100384 AATTTGATTT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
20 15 0.68
21 7 0.32
ACGTcount: A:0.15, C:0.10, G:0.06, T:0.69
Consensus pattern (20 bp):
ATATTTTGTTATTTTTCTCT
Found at i:102033 original size:16 final size:17
Alignment explanation
Indices: 102012--102057 Score: 60
Period size: 16 Copynumber: 2.8 Consensus size: 17
102002 TTTTAAAATT
102012 TATTTATTTATTTTA-A
1 TATTTATTTATTTTATA
* *
102028 TATTTAATAATTTTATA
1 TATTTATTTATTTTATA
102045 TATTT-TTTATTTT
1 TATTTATTTATTTT
102058 TTATTGAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
16 19 0.76
17 6 0.24
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
TATTTATTTATTTTATA
Found at i:102040 original size:20 final size:20
Alignment explanation
Indices: 102002--102040 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
101992 TCATATGATT
* *
102002 TTTTAAAATTTATTTATTTA
1 TTTTAAAATTTAATAATTTA
*
102022 TTTTAATATTTAATAATTT
1 TTTTAAAATTTAATAATTT
102041 TATATATTTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTTAAAATTTAATAATTTA
Found at i:107008 original size:173 final size:173
Alignment explanation
Indices: 106719--107066 Score: 687
Period size: 173 Copynumber: 2.0 Consensus size: 173
106709 CCTGCTTGAT
106719 TGATTATGCATGCCAACATCTGTAAGCATCGATAATAACCCAACAATGGTTTTTGATTGATTACA
1 TGATTATGCATGCCAACATCTGTAAGCATCGATAATAACCCAACAATGGTTTTTGATTGATTACA
106784 TTAAAAATGAGTAAAGTGCAAGGCCAAAAAGATCCTATTTCCTCAATTTGCTAAACTTAACAATT
66 TTAAAAATGAGTAAAGTGCAAGGCCAAAAAGATCCTATTTCCTCAATTTGCTAAACTTAACAATT
106849 CCACATAGGCACACATCTATGAGGAAAAAAAGATGCTACAACA
131 CCACATAGGCACACATCTATGAGGAAAAAAAGATGCTACAACA
*
106892 TGATTATGCATGCCAACATCTGTAAGCATCGATGATAACCCAACAATGGTTTTTGATTGATTACA
1 TGATTATGCATGCCAACATCTGTAAGCATCGATAATAACCCAACAATGGTTTTTGATTGATTACA
106957 TTAAAAATGAGTAAAGTGCAAGGCCAAAAAGATCCTATTTCCTCAATTTGCTAAACTTAACAATT
66 TTAAAAATGAGTAAAGTGCAAGGCCAAAAAGATCCTATTTCCTCAATTTGCTAAACTTAACAATT
107022 CCACATAGGCACACATCTATGAGGAAAAAAAGATGCTACAACA
131 CCACATAGGCACACATCTATGAGGAAAAAAAGATGCTACAACA
107065 TG
1 TG
107067 GTAAACAGGA
Statistics
Matches: 174, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
173 174 1.00
ACGTcount: A:0.39, C:0.19, G:0.15, T:0.27
Consensus pattern (173 bp):
TGATTATGCATGCCAACATCTGTAAGCATCGATAATAACCCAACAATGGTTTTTGATTGATTACA
TTAAAAATGAGTAAAGTGCAAGGCCAAAAAGATCCTATTTCCTCAATTTGCTAAACTTAACAATT
CCACATAGGCACACATCTATGAGGAAAAAAAGATGCTACAACA
Found at i:111517 original size:2 final size:2
Alignment explanation
Indices: 111510--111540 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
111500 GAAAAATGAC
*
111510 AG AG AG AG AG AG AG AG AG AG AG AG AG GG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
111541 TGAATTATTT
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:0.52, T:0.00
Consensus pattern (2 bp):
AG
Found at i:118767 original size:10 final size:10
Alignment explanation
Indices: 118699--118769 Score: 54
Period size: 10 Copynumber: 6.9 Consensus size: 10
118689 TGAAAAATTT
118699 TAAAAAGTATA
1 TAAAAA-TATA
*
118710 TAAAGATATA
1 TAAAAATATA
* * *
118720 TAAATATTTT
1 TAAAAATATA
*
118730 TAAAGATATAA
1 TAAAAATAT-A
*
118741 TAATAAATTTA
1 TAA-AAATATA
118752 -AAAAATATA
1 TAAAAATATA
118761 TAAAAATAT
1 TAAAAATAT
118770 GTTGACAATA
Statistics
Matches: 47, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
9 6 0.13
10 28 0.60
11 9 0.19
12 4 0.09
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (10 bp):
TAAAAATATA
Found at i:118768 original size:23 final size:23
Alignment explanation
Indices: 118735--118819 Score: 64
Period size: 23 Copynumber: 3.6 Consensus size: 23
118725 ATTTTTAAAG
*
118735 ATATAATAATAAATTTAAAAAAT
1 ATATAAAAATAAATTTAAAAAAT
** *
118758 ATATAAAAATATGTTGACAATAAAT
1 ATATAAAAATAAATTTA-AA-AAAT
* **
118783 A-ATAATATATAAATTTTTAAAAT
1 ATATAA-AAATAAATTTAAAAAAT
*
118806 ATGTAAAAATAAAT
1 ATATAAAAATAAAT
118820 ATATTTTTTG
Statistics
Matches: 46, Mismatches: 12, Indels: 8
0.70 0.18 0.12
Matches are distributed among these distances:
23 25 0.54
24 10 0.22
25 11 0.24
ACGTcount: A:0.60, C:0.01, G:0.04, T:0.35
Consensus pattern (23 bp):
ATATAAAAATAAATTTAAAAAAT
Found at i:118822 original size:29 final size:30
Alignment explanation
Indices: 118777--118857 Score: 76
Period size: 29 Copynumber: 2.7 Consensus size: 30
118767 TATGTTGACA
*
118777 ATAAATAATAATATATAAATTTTT-AAAATAT
1 ATAAA-AATAA-ATATAAATTTTTGAAAAAAT
* *
118808 GTAAAAATAAATAT-ATTTTTTGAAAAAAT
1 ATAAAAATAAATATAAATTTTTGAAAAAAT
* * *
118837 ATAATAGTAAATTTAAATTTT
1 ATAAAAATAAATATAAATTTT
118858 ATATTATTAC
Statistics
Matches: 40, Mismatches: 8, Indels: 5
0.75 0.15 0.09
Matches are distributed among these distances:
28 6 0.15
29 20 0.50
30 10 0.25
31 4 0.10
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (30 bp):
ATAAAAATAAATATAAATTTTTGAAAAAAT
Found at i:123419 original size:17 final size:17
Alignment explanation
Indices: 123388--123421 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
123378 ATTATATCAA
*
123388 ATAAATTTAGTTTTGTT
1 ATAAATTTAGGTTTGTT
*
123405 ATAAATTTGGGTTTGTT
1 ATAAATTTAGGTTTGTT
123422 TAAGTATTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.26, C:0.00, G:0.18, T:0.56
Consensus pattern (17 bp):
ATAAATTTAGGTTTGTT
Found at i:132701 original size:20 final size:20
Alignment explanation
Indices: 132676--132730 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
132666 ATGTATTGAT
*
132676 GTATTGATATCT-TATTAAA
1 GTATTGATATCTGGATTAAA
*
132695 GGTATTGATAT-TGGATTCAA
1 -GTATTGATATCTGGATTAAA
132715 GTATTGATATCTGGAT
1 GTATTGATATCTGGAT
132731 ATCGATACTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 11 0.35
20 20 0.65
ACGTcount: A:0.31, C:0.05, G:0.20, T:0.44
Consensus pattern (20 bp):
GTATTGATATCTGGATTAAA
Found at i:141313 original size:188 final size:192
Alignment explanation
Indices: 141026--141377 Score: 455
Period size: 188 Copynumber: 1.9 Consensus size: 192
141016 GCTTTAGTTT
* * * *
141026 GGGACCCCATTGATCCCTTGAAATCATTAAAAGACACATCACTGCATCTTCACTAAATTAAGGTT
1 GGGACCCCACTGATCCCTTGAAAGCATTAAAAGACACATCACAGCATCTTCACTAAATTAAGGAT
* *
141091 CAAGAGGAAGTGCTTCAGATTGGTTTGGTTTTGGACTCC-ACTAATCCTTTGAAAACATTAAAAG
66 CAAGAGGAAGTGCTTCAGATTGGTTTGGTTTTGGAC-CCAACTAATCCTTTGAAAACACTAAAAA
* *
141155 ATACATCACAACATCTTCACTAGATAAAGGTTCATAAGGTAGTGCTTCAGTTCGGTCTTGTTA
130 ACACATCACAACATCTTCACTAGATAAAGATTCATAAGGTAGTGCTTCAGTTCGGTCTTGTTA
* * * *
141218 GGGACTCCACTGATCCCTTGAAAGCA-TAAAAGGCGCATCGCAGCATCTTCACTAAA-T-A-GAT
1 GGGACCCCACTGATCCCTTGAAAGCATTAAAAGACACATCACAGCATCTTCACTAAATTAAGGAT
* * * * **
141279 CATGAGGAAGTGCTTCA-ACTTGGTTTTGTTTTGGACCCAATTGATCCTTTGAAAGTACTAAAAA
66 CAAGAGGAAGTGCTTCAGA-TTGGTTTGGTTTTGGACCCAACTAATCCTTTGAAAACACTAAAAA
** *
141343 ACACATTTCAACATTTTCACTAGATAAAGATTCAT
130 ACACATCACAACATCTTCACTAGATAAAGATTCAT
141378 GAGAAAGAGC
Statistics
Matches: 137, Mismatches: 21, Indels: 8
0.83 0.13 0.05
Matches are distributed among these distances:
187 3 0.02
188 83 0.61
189 1 0.01
190 1 0.01
191 26 0.19
192 23 0.17
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.30
Consensus pattern (192 bp):
GGGACCCCACTGATCCCTTGAAAGCATTAAAAGACACATCACAGCATCTTCACTAAATTAAGGAT
CAAGAGGAAGTGCTTCAGATTGGTTTGGTTTTGGACCCAACTAATCCTTTGAAAACACTAAAAAA
CACATCACAACATCTTCACTAGATAAAGATTCATAAGGTAGTGCTTCAGTTCGGTCTTGTTA
Found at i:141324 original size:92 final size:93
Alignment explanation
Indices: 141022--141348 Score: 309
Period size: 96 Copynumber: 3.5 Consensus size: 93
141012 AAGTGCTTTA
* * * *
141022 GTTTGGGACCCCATTGATCCCTTGAAATCATTAAAAGACACATCACTGCATCTTCACTAAATTAA
1 GTTTGGGACTCCACTGATCCCTTGAAAGCATTAAAAGACACATCACAGCATCTTCACTAAA-T-A
* *
141087 GGTTCAAGAGGAAGTGCTTCAGATTGGTTTG
64 GGTTCATGAGGAAGTGCTTCA-ATTGGTTTT
* * * * * * *
141118 GTTTTGGACTCCACTAATCCTTTGAAAACATTAAAAGATACATCACAACATCTTCACTAGATAAA
1 GTTTGGGACTCCACTGATCCCTTGAAAGCATTAAAAGACACATCACAGCATCTTCACTA-A-ATA
* * * *
141183 GGTTCATAAGGTAGTGCTTCAGTTCGGTCTT
64 GGTTCATGAGGAAGTGCTTCAATT-GGTTTT
* * * *
141214 GTTAGGGACTCCACTGATCCCTTGAAAGCA-TAAAAGGCGCATCGCAGCATCTTCACTAAATA-G
1 GTTTGGGACTCCACTGATCCCTTGAAAGCATTAAAAGACACATCACAGCATCTTCACTAAATAGG
*
141277 ATCATGAGGAAGTGCTTCAACTTGGTTTT
66 TTCATGAGGAAGTGCTTCAA-TTGGTTTT
* * * * * *
141306 GTTTTGGAC-CCAATTGATCCTTTGAAAGTACTAAAAAACACAT
1 GTTTGGGACTCC-ACTGATCCCTTGAAAGCATTAAAAGACACAT
141349 TTCAACATTT
Statistics
Matches: 185, Mismatches: 40, Indels: 15
0.77 0.17 0.06
Matches are distributed among these distances:
91 2 0.01
92 44 0.24
93 13 0.07
94 1 0.01
95 25 0.14
96 98 0.53
97 1 0.01
98 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.30
Consensus pattern (93 bp):
GTTTGGGACTCCACTGATCCCTTGAAAGCATTAAAAGACACATCACAGCATCTTCACTAAATAGG
TTCATGAGGAAGTGCTTCAATTGGTTTT
Found at i:141519 original size:15 final size:15
Alignment explanation
Indices: 141495--141529 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
141485 TGCCTCGCTA
141495 GAAA-GTTCATGTTT
1 GAAAGGTTCATGTTT
141509 GAAAGGTTCATGTTT
1 GAAAGGTTCATGTTT
*
141524 GGAAGG
1 GAAAGG
141530 ACAACTAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 4 0.21
15 15 0.79
ACGTcount: A:0.29, C:0.06, G:0.31, T:0.34
Consensus pattern (15 bp):
GAAAGGTTCATGTTT
Found at i:142039 original size:42 final size:42
Alignment explanation
Indices: 141959--142040 Score: 119
Period size: 42 Copynumber: 2.0 Consensus size: 42
141949 AATCTAGTGA
* ** **
141959 AGATGTTATAATGTGTCTTTAATACTTTCAGGTTATCAGCGG
1 AGATGTTACAATGCATCTTTAATACTTTCAGGAGATCAGCGG
142001 AGATGTTACAATGCATCTTTAATACTTTCAGGAGATCAGC
1 AGATGTTACAATGCATCTTTAATACTTTCAGGAGATCAGC
142041 AGATTCCAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.37
Consensus pattern (42 bp):
AGATGTTACAATGCATCTTTAATACTTTCAGGAGATCAGCGG
Found at i:144767 original size:52 final size:52
Alignment explanation
Indices: 144701--144803 Score: 134
Period size: 52 Copynumber: 2.0 Consensus size: 52
144691 GATGGGTCGA
* * * *
144701 AGGTTCCTTGAGTTTAAGTAGGTTCGAGGATACTTGAGTTTGAGCTGGTTGG
1 AGGTCCCTTGAGTTTAAGTAGGTCCAAGGACACTTGAGTTTGAGCTGGTTGG
* * * *
144753 AGGTCCCTTGAGTTTGAGTGGGTCCAAGGACCCTTGAGTTTGAGTTGGTTG
1 AGGTCCCTTGAGTTTAAGTAGGTCCAAGGACACTTGAGTTTGAGCTGGTTG
144804 AAGGACCATG
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
52 43 1.00
ACGTcount: A:0.17, C:0.13, G:0.35, T:0.35
Consensus pattern (52 bp):
AGGTCCCTTGAGTTTAAGTAGGTCCAAGGACACTTGAGTTTGAGCTGGTTGG
Found at i:144807 original size:26 final size:26
Alignment explanation
Indices: 144706--144810 Score: 104
Period size: 26 Copynumber: 4.0 Consensus size: 26
144696 GTCGAAGGTT
* * *
144706 CCTTGAGTTTAAGTAGGTTCG-AGGAT
1 CCTTGAGTTTGAGTTGGTT-GAAGGAC
* * * *
144732 ACTTGAGTTTGAGCTGGTTGGAGGTC
1 CCTTGAGTTTGAGTTGGTTGAAGGAC
* **
144758 CCTTGAGTTTGAGTGGGTCCAAGGAC
1 CCTTGAGTTTGAGTTGGTTGAAGGAC
144784 CCTTGAGTTTGAGTTGGTTGAAGGAC
1 CCTTGAGTTTGAGTTGGTTGAAGGAC
144810 C
1 C
144811 ATGAGCAGAT
Statistics
Matches: 62, Mismatches: 16, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
25 1 0.02
26 61 0.98
ACGTcount: A:0.19, C:0.14, G:0.34, T:0.32
Consensus pattern (26 bp):
CCTTGAGTTTGAGTTGGTTGAAGGAC
Found at i:145872 original size:3 final size:3
Alignment explanation
Indices: 145864--145906 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
145854 CCTAAAATTT
145864 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
145907 ATACAATATT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:154006 original size:55 final size:55
Alignment explanation
Indices: 153945--154054 Score: 220
Period size: 55 Copynumber: 2.0 Consensus size: 55
153935 ATGAGACTAG
153945 GGTTACTCGTACTAAAAGGAAAAAGTAGTTGGGGAATGGATCAAGATGCAGCTTT
1 GGTTACTCGTACTAAAAGGAAAAAGTAGTTGGGGAATGGATCAAGATGCAGCTTT
154000 GGTTACTCGTACTAAAAGGAAAAAGTAGTTGGGGAATGGATCAAGATGCAGCTTT
1 GGTTACTCGTACTAAAAGGAAAAAGTAGTTGGGGAATGGATCAAGATGCAGCTTT
154055 CTTTGTAGAG
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.35, C:0.11, G:0.29, T:0.25
Consensus pattern (55 bp):
GGTTACTCGTACTAAAAGGAAAAAGTAGTTGGGGAATGGATCAAGATGCAGCTTT
Found at i:162318 original size:21 final size:20
Alignment explanation
Indices: 162290--162331 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
162280 TTTTCAAGGG
*
162290 GTTTTTTT-TCATTTTTAATA
1 GTTTTTTTATCA-GTTTAATA
162310 GTTTCTTTTATCAGTTTAATA
1 GTTT-TTTTATCAGTTTAATA
162331 G
1 G
162332 ATTTAAAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 4 0.21
21 12 0.63
22 3 0.16
ACGTcount: A:0.21, C:0.07, G:0.10, T:0.62
Consensus pattern (20 bp):
GTTTTTTTATCAGTTTAATA
Found at i:169145 original size:3 final size:3
Alignment explanation
Indices: 169137--169164 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
169127 CCTTAATCAA
169137 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
169165 ATGTATATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:186970 original size:76 final size:76
Alignment explanation
Indices: 186844--186993 Score: 282
Period size: 76 Copynumber: 2.0 Consensus size: 76
186834 TGGATACTTG
* *
186844 CATATTAATTTGTGAAAAATAATTAACCCTCCCTTCAGATATTGCCTTTTTACTATATATAATAT
1 CATATTAATTTGTGAAAAACAATTAACCCTCCCTCCAGATATTGCCTTTTTACTATATATAATAT
186909 TGGGAATATCA
66 TGGGAATATCA
186920 CATATTAATTTGTGAAAAACAATTAACCCTCCCTCCAGATATTGCCTTTTTACTATATATAATAT
1 CATATTAATTTGTGAAAAACAATTAACCCTCCCTCCAGATATTGCCTTTTTACTATATATAATAT
186985 TGGGAATAT
66 TGGGAATAT
186994 AACTCGAAGT
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
76 72 1.00
ACGTcount: A:0.35, C:0.17, G:0.09, T:0.39
Consensus pattern (76 bp):
CATATTAATTTGTGAAAAACAATTAACCCTCCCTCCAGATATTGCCTTTTTACTATATATAATAT
TGGGAATATCA
Found at i:192165 original size:18 final size:19
Alignment explanation
Indices: 192130--192181 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 19
192120 ATAATAAGAT
192130 TAAAA-ATTTTC-A-AATA
1 TAAAATATTTTCAATAATA
*
192146 TAAAATATTTATCAATTATA
1 TAAAATATTT-TCAATAATA
*
192166 TAAAATATTTTTAATA
1 TAAAATATTTTCAATA
192182 TGCTTCGCAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
16 5 0.17
17 4 0.14
18 2 0.07
19 5 0.17
20 13 0.45
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (19 bp):
TAAAATATTTTCAATAATA
Found at i:193211 original size:19 final size:18
Alignment explanation
Indices: 193160--193227 Score: 61
Period size: 17 Copynumber: 3.8 Consensus size: 18
193150 ACTTATTTTT
*
193160 ATTTTT-TATACTTTTGA
1 ATTTTTATATATTTTTGA
* *
193177 ATTTTTAAAATGTTTTTGA
1 ATTTTT-ATATATTTTTGA
*
193196 ATTGTTTATATA-TTTTCA
1 ATT-TTTATATATTTTTGA
193214 ATTTTTATA-ATTTT
1 ATTTTTATATATTTT
193228 ATAAAATATA
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
16 1 0.02
17 15 0.37
18 8 0.20
19 14 0.34
20 3 0.07
ACGTcount: A:0.28, C:0.03, G:0.06, T:0.63
Consensus pattern (18 bp):
ATTTTTATATATTTTTGA
Found at i:193222 original size:17 final size:17
Alignment explanation
Indices: 193190--193227 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
193180 TTTAAAATGT
*
193190 TTTTGAATTGTTTATATA
1 TTTTCAATTGTTTATA-A
193208 TTTTCAATT-TTTATAA
1 TTTTCAATTGTTTATAA
193224 TTTT
1 TTTT
193228 ATAAAATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 5 0.26
17 6 0.32
18 8 0.42
ACGTcount: A:0.26, C:0.03, G:0.05, T:0.66
Consensus pattern (17 bp):
TTTTCAATTGTTTATAA
Found at i:198462 original size:12 final size:12
Alignment explanation
Indices: 198445--198476 Score: 55
Period size: 12 Copynumber: 2.6 Consensus size: 12
198435 ATAAGTTGTA
198445 TTTTTTGTTTTT
1 TTTTTTGTTTTT
198457 TTTTTTGTTTTT
1 TTTTTTGTTTTT
198469 TGTTTTTG
1 T-TTTTTG
198477 CTATATATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 13 0.68
13 6 0.32
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (12 bp):
TTTTTTGTTTTT
Found at i:199309 original size:12 final size:12
Alignment explanation
Indices: 199292--199317 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
199282 AGAAATTGCT
199292 TTATTATTATTG
1 TTATTATTATTG
199304 TTATTATTATTG
1 TTATTATTATTG
199316 TT
1 TT
199318 TCTAAGGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.08, T:0.69
Consensus pattern (12 bp):
TTATTATTATTG
Found at i:211414 original size:12 final size:12
Alignment explanation
Indices: 211399--211425 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
211389 ATATTTTAAA
211399 TTTTTTATAATT
1 TTTTTTATAATT
211411 TTTTTTATAATT
1 TTTTTTATAATT
211423 TTT
1 TTT
211426 AAATTATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (12 bp):
TTTTTTATAATT
Found at i:215267 original size:28 final size:28
Alignment explanation
Indices: 215227--215292 Score: 80
Period size: 28 Copynumber: 2.4 Consensus size: 28
215217 TTAAATGTAT
*
215227 AAAAAACATTAAAATATGAAATACAGAG
1 AAAAAACATTAAAACATGAAATACAGAG
* * **
215255 AAAAGACATTAAAACATTAAATGTAGAG
1 AAAAAACATTAAAACATGAAATACAGAG
215283 AAAAAA-ATTA
1 AAAAAACATTA
215293 TTGTCTGGAT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
27 4 0.12
28 28 0.88
ACGTcount: A:0.64, C:0.06, G:0.11, T:0.20
Consensus pattern (28 bp):
AAAAAACATTAAAACATGAAATACAGAG
Found at i:215487 original size:17 final size:14
Alignment explanation
Indices: 215463--215505 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
215453 TTATTCTCAC
215463 TTATTTTTGTAATTA
1 TTATTTTTGTAA-TA
*
215478 TTTAATTTTTTTAATA
1 -TT-ATTTTTGTAATA
215494 TTATTTTTGTAA
1 TTATTTTTGTAA
215506 AAATACTCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
14 9 0.38
15 2 0.08
16 4 0.17
17 9 0.38
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (14 bp):
TTATTTTTGTAATA
Found at i:229600 original size:21 final size:21
Alignment explanation
Indices: 229581--229628 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
229571 AACACATTAG
*
229581 TAAAATTGATAAAAATATTAAA
1 TAAAATTCA-AAAAATATTAAA
*
229603 TAAAATTCAAAAAATA-AAAA
1 TAAAATTCAAAAAATATTAAA
229623 TAAAAT
1 TAAAAT
229629 AAAAACCAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 9 0.38
21 7 0.29
22 8 0.33
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (21 bp):
TAAAATTCAAAAAATATTAAA
Found at i:230058 original size:21 final size:22
Alignment explanation
Indices: 230010--230062 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
230000 TTTGATTCTG
*
230010 GATTTAATTTTTAAATAACTTT
1 GATTTTATTTTTAAATAACTTT
*
230032 TATTTTATTTTTAAA-AA-TTT
1 GATTTTATTTTTAAATAACTTT
230052 GAGTTTTATTT
1 GA-TTTTATTT
230063 AATATTTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 4 0.15
21 10 0.37
22 13 0.48
ACGTcount: A:0.32, C:0.02, G:0.06, T:0.60
Consensus pattern (22 bp):
GATTTTATTTTTAAATAACTTT
Found at i:230079 original size:21 final size:21
Alignment explanation
Indices: 230055--230102 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
230045 AAAATTTGAG
*
230055 TTTTATTTAATAT-TTTATAAA
1 TTTTATATAATATGTTTA-AAA
*
230076 TTTTA-ATAATGTGTTTAAAA
1 TTTTATATAATATGTTTAAAA
230096 TTTTATA
1 TTTTATA
230103 ATTTAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 13 0.57
21 10 0.43
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (21 bp):
TTTTATATAATATGTTTAAAA
Found at i:231802 original size:43 final size:44
Alignment explanation
Indices: 231749--231833 Score: 127
Period size: 43 Copynumber: 2.0 Consensus size: 44
231739 CACGTAACAC
* * * *
231749 CTATTGATGGAAATTGAATCTTT-CATACATATAGAATTATAAT
1 CTATTAATGGAAATAGAATCTTTAAATACATATAGAAATATAAT
231792 CTATTAATGGAAATAGAATCTTTAAATACATATAGAAATATA
1 CTATTAATGGAAATAGAATCTTTAAATACATATAGAAATATA
231834 TTTGTTTGCA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
43 21 0.57
44 16 0.43
ACGTcount: A:0.45, C:0.08, G:0.11, T:0.36
Consensus pattern (44 bp):
CTATTAATGGAAATAGAATCTTTAAATACATATAGAAATATAAT
Found at i:236561 original size:2 final size:2
Alignment explanation
Indices: 236554--236581 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
236544 ATGTAAGAAC
236554 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
236582 GGAGGGAGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:237057 original size:20 final size:21
Alignment explanation
Indices: 237022--237062 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
237012 ATACAATTAA
*
237022 CTTTATGAGTTTTAACATTGG
1 CTTTATGAGTTATAACATTGG
237043 CTTTAT-AGTTATAACATTGG
1 CTTTATGAGTTATAACATTGG
237063 ATAAGAGGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.27, C:0.10, G:0.17, T:0.46
Consensus pattern (21 bp):
CTTTATGAGTTATAACATTGG
Found at i:242093 original size:29 final size:30
Alignment explanation
Indices: 242031--242086 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
242021 ACTTTATAAG
* *
242031 AATTAGATTAAATTAAAATTTCATATAAAA
1 AATTAGATAAAATCAAAATTTCATATAAAA
*
242061 AATTATATAAAATCAAAATTT-ATATA
1 AATTAGATAAAATCAAAATTTCATATA
242087 TATAATTGCA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
29 5 0.22
30 18 0.78
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.38
Consensus pattern (30 bp):
AATTAGATAAAATCAAAATTTCATATAAAA
Found at i:246140 original size:23 final size:22
Alignment explanation
Indices: 246100--246142 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
246090 TTTATTTTCA
246100 TTAGTTTTTATTTAAAAAATCT
1 TTAGTTTTTATTTAAAAAATCT
* *
246122 TTAGATTTTTTTTTTAAAAAT
1 TTAG-TTTTTATTTAAAAAAT
246143 TTATAAGTAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.35, C:0.02, G:0.05, T:0.58
Consensus pattern (22 bp):
TTAGTTTTTATTTAAAAAATCT
Found at i:247195 original size:15 final size:16
Alignment explanation
Indices: 247175--247208 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
247165 ATTTAAAAAG
*
247175 TAAAAAAAAAAAAATT
1 TAAAAATAAAAAAATT
*
247191 TAAAAATAAAGAAATT
1 TAAAAATAAAAAAATT
247207 TA
1 TA
247209 TTTTATAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (16 bp):
TAAAAATAAAAAAATT
Found at i:254629 original size:6 final size:6
Alignment explanation
Indices: 254618--254660 Score: 50
Period size: 6 Copynumber: 6.8 Consensus size: 6
254608 TAGTTTGAAA
* *
254618 TATATG TATATG TATATG TATATG CATATATG CATATA TATAT
1 TATATG TATATG TATATG TATATG --TATATG TATATG TATAT
254661 AATGACTAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
6 26 0.81
8 6 0.19
ACGTcount: A:0.37, C:0.05, G:0.12, T:0.47
Consensus pattern (6 bp):
TATATG
Found at i:257845 original size:2 final size:2
Alignment explanation
Indices: 257829--257867 Score: 55
Period size: 2 Copynumber: 20.0 Consensus size: 2
257819 AAAAACTAGT
257829 TA TA T- TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA GTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
257868 CCATAAAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 2 0.06
2 30 0.88
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:258840 original size:25 final size:25
Alignment explanation
Indices: 258811--258862 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
258801 AAAATTAAAC
258811 ATATTTAA-AATGATTATTAATTATT
1 ATATTTAATAAT-ATTATTAATTATT
**
258836 ATATTTAATAATATTATTGCTTATT
1 ATATTTAATAATATTATTAATTATT
258861 AT
1 AT
258863 GTTTTTCATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 21 0.88
26 3 0.12
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (25 bp):
ATATTTAATAATATTATTAATTATT
Found at i:265175 original size:73 final size:73
Alignment explanation
Indices: 265088--265234 Score: 294
Period size: 73 Copynumber: 2.0 Consensus size: 73
265078 CATGTAAAAC
265088 AAAAGAAAACTACTTCTCATCATCTGCCATACCAAAATTTCATGGCGCCTACTCTTGGCCTCACA
1 AAAAGAAAACTACTTCTCATCATCTGCCATACCAAAATTTCATGGCGCCTACTCTTGGCCTCACA
265153 GACTTCTT
66 GACTTCTT
265161 AAAAGAAAACTACTTCTCATCATCTGCCATACCAAAATTTCATGGCGCCTACTCTTGGCCTCACA
1 AAAAGAAAACTACTTCTCATCATCTGCCATACCAAAATTTCATGGCGCCTACTCTTGGCCTCACA
265226 GACTTCTT
66 GACTTCTT
265234 A
1 A
265235 GTCCTGATAA
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 74 1.00
ACGTcount: A:0.31, C:0.30, G:0.11, T:0.29
Consensus pattern (73 bp):
AAAAGAAAACTACTTCTCATCATCTGCCATACCAAAATTTCATGGCGCCTACTCTTGGCCTCACA
GACTTCTT
Found at i:266175 original size:22 final size:23
Alignment explanation
Indices: 266125--266175 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
266115 TGTCTGTCTT
** *
266125 TTTTTTTAATTATTTATTATTTA
1 TTTTTTTAAAAATTTATAATTTA
266148 -TTTTTTAAAAATTTA-AATTTA
1 TTTTTTTAAAAATTTATAATTTA
266169 TTTTTTT
1 TTTTTTT
266176 TGGTGTAGCC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 5 0.21
22 19 0.79
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (23 bp):
TTTTTTTAAAAATTTATAATTTA
Found at i:266250 original size:101 final size:100
Alignment explanation
Indices: 266123--266303 Score: 272
Period size: 101 Copynumber: 1.8 Consensus size: 100
266113 AATGTCTGTC
* * * *
266123 TTTTTTTTTAATTATTTATTATTTATTTTTTAAAAATTTAAATTTATTTTTTTTGGTGTAGCCAT
1 TTTTTTTTTAAGTATTTATTATTTATTTCTTAAAAATTTAAATTTA-TTTTTTTGATGAAGCCAT
266188 CTTAAATGGTGCCACCACAAGGAGTCAGTTTTTTTT
65 CTTAAATGGTGCCACCACAAGGAGTCAGTTTTTTTT
* * ** *
266224 TTTTTTTTTTAGTATTTATTATTTATTTCTTAAAAATTTTAATTTATTTTTTTGATGAAGTTATT
1 TTTTTTTTTAAGTATTTATTATTTATTTCTTAAAAATTTAAATTTATTTTTTTGATGAAGCCATC
266289 TTAAATGGTGCCACC
66 TTAAATGGTGCCACC
266304 CAATTGATTT
Statistics
Matches: 71, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
100 29 0.41
101 42 0.59
ACGTcount: A:0.26, C:0.08, G:0.10, T:0.56
Consensus pattern (100 bp):
TTTTTTTTTAAGTATTTATTATTTATTTCTTAAAAATTTAAATTTATTTTTTTGATGAAGCCATC
TTAAATGGTGCCACCACAAGGAGTCAGTTTTTTTT
Found at i:266841 original size:3 final size:3
Alignment explanation
Indices: 266835--266877 Score: 77
Period size: 3 Copynumber: 14.0 Consensus size: 3
266825 TTTTTATTTG
266835 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TTAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA
266878 AAATGAAGAT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 36 0.92
4 3 0.08
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:267731 original size:2 final size:2
Alignment explanation
Indices: 267726--267753 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
267716 TTTTTTTTTA
267726 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
267754 TTTAATATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:281512 original size:2 final size:2
Alignment explanation
Indices: 281505--281546 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
281495 CTAACCCTTG
281505 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
281547 GATTATCAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:284817 original size:13 final size:13
Alignment explanation
Indices: 284785--284822 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
284775 TTTTTAAAGC
*
284785 TACTTTTCTAAAT
1 TACTTTTCTAAAA
*
284798 TAATTTTCTAAAA
1 TACTTTTCTAAAA
284811 TACTTTT-TAAAA
1 TACTTTTCTAAAA
284823 CATTTCTCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
12 5 0.23
13 17 0.77
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.50
Consensus pattern (13 bp):
TACTTTTCTAAAA
Found at i:287245 original size:21 final size:22
Alignment explanation
Indices: 287202--287250 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 22
287192 TTTATATTGT
* * *
287202 TGTTTTGGTGTTTTTTTTTTAC
1 TGTTTTGGTGATTGTTTTATAC
287224 TGTTTTGGT-ATTGTTTTATAC
1 TGTTTTGGTGATTGTTTTATAC
287245 TGTTTT
1 TGTTTT
287251 AGTTGTTGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 15 0.62
22 9 0.38
ACGTcount: A:0.08, C:0.04, G:0.18, T:0.69
Consensus pattern (22 bp):
TGTTTTGGTGATTGTTTTATAC
Found at i:287274 original size:12 final size:12
Alignment explanation
Indices: 287259--287310 Score: 52
Period size: 12 Copynumber: 4.4 Consensus size: 12
287249 TTAGTTGTTG
*
287259 TTTTGGTGCTAT
1 TTTTGGTACTAT
**
287271 TTTTTTTACTA-
1 TTTTGGTACTAT
287282 TTTTGGTACTAT
1 TTTTGGTACTAT
* *
287294 TTTTGCTATTAT
1 TTTTGGTACTAT
287306 TTTTG
1 TTTTG
287311 TTGCTGTTTT
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
11 9 0.28
12 23 0.72
ACGTcount: A:0.13, C:0.08, G:0.13, T:0.65
Consensus pattern (12 bp):
TTTTGGTACTAT
Found at i:287306 original size:23 final size:23
Alignment explanation
Indices: 287259--287308 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
287249 TTAGTTGTTG
* **
287259 TTTTGGTGCTATTTTTTTTACTA
1 TTTTGGTACTATTTTTGCTACTA
*
287282 TTTTGGTACTATTTTTGCTATTA
1 TTTTGGTACTATTTTTGCTACTA
287305 TTTT
1 TTTT
287309 TGTTGCTGTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.14, C:0.08, G:0.12, T:0.66
Consensus pattern (23 bp):
TTTTGGTACTATTTTTGCTACTA
Found at i:288655 original size:26 final size:27
Alignment explanation
Indices: 288598--288663 Score: 107
Period size: 26 Copynumber: 2.5 Consensus size: 27
288588 GAGGAACACG
*
288598 AAGTGGCGGCACCAATGGAGGGTTATT
1 AAGTGGCGGCACCAAGGGAGGGTTATT
*
288625 AAGTGGCGGCACCAAGGGA-TGTTATT
1 AAGTGGCGGCACCAAGGGAGGGTTATT
288651 AAGTGGCGGCACC
1 AAGTGGCGGCACC
288664 CCATTGTGCC
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
26 19 0.51
27 18 0.49
ACGTcount: A:0.26, C:0.18, G:0.36, T:0.20
Consensus pattern (27 bp):
AAGTGGCGGCACCAAGGGAGGGTTATT
Found at i:288841 original size:16 final size:16
Alignment explanation
Indices: 288800--288845 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
288790 CAAATAAACG
288800 AGAAA-GAAAGAAAGA
1 AGAAAGGAAAGAAAGA
*
288815 AGGAGAGGAAAGAAAGA
1 A-GAAAGGAAAGAAAGA
288832 AGAAAGGAAAGAAA
1 AGAAAGGAAAGAAA
288846 TGTAATGTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
15 1 0.04
16 15 0.56
17 11 0.41
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (16 bp):
AGAAAGGAAAGAAAGA
Found at i:290587 original size:8 final size:9
Alignment explanation
Indices: 290567--290597 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
290557 TTTTATTTTT
290567 AAATATATAA
1 AAATA-ATAA
290577 AAATAATAA
1 AAATAATAA
290586 AAATAATAA
1 AAATAATAA
290595 AAA
1 AAA
290598 AACACGTGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 16 0.76
10 5 0.24
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (9 bp):
AAATAATAA
Found at i:293066 original size:1 final size:1
Alignment explanation
Indices: 293020--293046 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
293010 AAAATAATTG
293020 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
293047 NNNNNNNNNN
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:303037 original size:142 final size:142
Alignment explanation
Indices: 302781--303064 Score: 552
Period size: 142 Copynumber: 2.0 Consensus size: 142
302771 AAAAAAAAGT
302781 CTAAATTGATTAGAATAATAAAAACAAAAGACAAATTGATTTAAAATTTAAGATTACGCACATAA
1 CTAAATTGATTAGAATAATAAAAACAAAAGACAAATTGATTTAAAATTTAAGATTACGCACATAA
302846 TAAGAGATTATTTAAAGAATGAGTTGTATTGAAATAAACATTATATTATGAAATGATCGTAATGT
66 TAAGAGATTATTTAAAGAATGAGTTGTATTGAAATAAACATTATATTATGAAATGATCGTAATGT
302911 GAAATTACAACA
131 GAAATTACAACA
302923 CTAAATTGATTAGAATAATAAAAACAAAAGACAAATTGATTTAAAATTTAAGATTACGCACATAA
1 CTAAATTGATTAGAATAATAAAAACAAAAGACAAATTGATTTAAAATTTAAGATTACGCACATAA
302988 TATA-AGATTATTTAAAGAATGAGTTGTATTGAAATAAACATTATATTATGAAATGATCGTAATG
66 TA-AGAGATTATTTAAAGAATGAGTTGTATTGAAATAAACATTATATTATGAAATGATCGTAATG
303052 TGAAATTACAACA
130 TGAAATTACAACA
303065 TAATCGAAAT
Statistics
Matches: 141, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
142 140 0.99
143 1 0.01
ACGTcount: A:0.49, C:0.07, G:0.12, T:0.31
Consensus pattern (142 bp):
CTAAATTGATTAGAATAATAAAAACAAAAGACAAATTGATTTAAAATTTAAGATTACGCACATAA
TAAGAGATTATTTAAAGAATGAGTTGTATTGAAATAAACATTATATTATGAAATGATCGTAATGT
GAAATTACAACA
Found at i:306891 original size:23 final size:23
Alignment explanation
Indices: 306848--306891 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
306838 GAAATTAAAT
* *
306848 TATAATTTTTATAATAATAAAAA
1 TATAATTTTTAAAAGAATAAAAA
*
306871 TATAATTTTTAAAAGATTAAA
1 TATAATTTTTAAAAGAATAAA
306892 TTAAAATTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (23 bp):
TATAATTTTTAAAAGAATAAAAA
Found at i:307207 original size:2 final size:2
Alignment explanation
Indices: 307197--307261 Score: 87
Period size: 2 Copynumber: 32.0 Consensus size: 2
307187 TTTTAAAAAT
* *
307197 TA TA AA TA TA TA -A CTA TA AA 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 TA TA TA TA TA TA TA TA
307239 TA TA TA TA TA TA TA TA TA CTA TA
1 TA TA TA TA TA TA TA TA TA -TA TA
307262 ATTTAATTTT
Statistics
Matches: 56, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
1 1 0.02
2 52 0.93
3 3 0.05
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:315137 original size:27 final size:27
Alignment explanation
Indices: 315107--315214 Score: 128
Period size: 27 Copynumber: 4.0 Consensus size: 27
315097 CCTTCAGGTG
315107 CGTCAAAAAGGCTATTCTTTCATAGTT
1 CGTCAAAAAGGCTATTCTTTCATAGTT
*
315134 CGTCACAAAGGCTATTCTTTCATAGTT
1 CGTCAAAAAGGCTATTCTTTCATAGTT
* * *
315161 TGCCACAAAA-GCTATTCTTTCATAATT
1 CGTCA-AAAAGGCTATTCTTTCATAGTT
* ** *
315188 CTTCACGAAGGCTATTCTTTCGTAGTT
1 CGTCAAAAAGGCTATTCTTTCATAGTT
315215 TGCCATATCG
Statistics
Matches: 67, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
26 2 0.03
27 62 0.93
28 3 0.04
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.38
Consensus pattern (27 bp):
CGTCAAAAAGGCTATTCTTTCATAGTT
Found at i:315199 original size:54 final size:55
Alignment explanation
Indices: 315112--315219 Score: 173
Period size: 54 Copynumber: 2.0 Consensus size: 55
315102 AGGTGCGTCA
*
315112 AAAAGGCTATTCTTTCATAGTTCGTCACAAAGGCTATTCTTTCATAGTTTGCCAC
1 AAAAGGCTATTCTTTCATAATTCGTCACAAAGGCTATTCTTTCATAGTTTGCCAC
* * *
315167 AAAA-GCTATTCTTTCATAATTCTTCACGAAGGCTATTCTTTCGTAGTTTGCCA
1 AAAAGGCTATTCTTTCATAATTCGTCACAAAGGCTATTCTTTCATAGTTTGCCA
315220 TATCGTCCTG
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
54 45 0.92
55 4 0.08
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.38
Consensus pattern (55 bp):
AAAAGGCTATTCTTTCATAATTCGTCACAAAGGCTATTCTTTCATAGTTTGCCAC
Found at i:323358 original size:29 final size:30
Alignment explanation
Indices: 323321--323380 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 30
323311 CATAAGTAAA
323321 TTTAGAATTTAA-TATT-TATATTTTT-ATT
1 TTTAGAATTTAATTATTCTAT-TTTTTGATT
323349 TTTAGTAATTTAATTATTCTATTTTTTGATT
1 TTTAG-AATTTAATTATTCTATTTTTTGATT
323380 T
1 T
323381 CAAAATTCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
28 5 0.18
29 7 0.25
30 9 0.32
31 7 0.25
ACGTcount: A:0.28, C:0.02, G:0.05, T:0.65
Consensus pattern (30 bp):
TTTAGAATTTAATTATTCTATTTTTTGATT
Found at i:324258 original size:13 final size:12
Alignment explanation
Indices: 324240--324273 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
324230 ATATACACCA
324240 TTTTGTTTTTTGT
1 TTTTGTTTTTT-T
324253 TTTTGTTTTTTT
1 TTTTGTTTTTTT
324265 TTTT-TTTTT
1 TTTTGTTTTT
324274 GTATAAGAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 5 0.24
12 5 0.24
13 11 0.52
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (12 bp):
TTTTGTTTTTTT
Found at i:328059 original size:23 final size:24
Alignment explanation
Indices: 328011--328073 Score: 67
Period size: 24 Copynumber: 2.6 Consensus size: 24
328001 AAAAAGTTTT
* *
328011 AAAAGTTAATAAAAATATTCACAA
1 AAAAATTAATAAAAATAGTCACAA
328035 AAAAATTAATAAAAATAAGT-A-AA
1 AAAAATTAATAAAAAT-AGTCACAA
*
328058 AAAATTTAATTAAAAA
1 AAAAATTAA-TAAAAA
328074 AAAAAAGGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
23 10 0.29
24 22 0.65
25 2 0.06
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.25
Consensus pattern (24 bp):
AAAAATTAATAAAAATAGTCACAA
Found at i:328414 original size:14 final size:15
Alignment explanation
Indices: 328391--328419 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
328381 ATTTTGATTT
328391 AATAATATAAATAAA
1 AATAATATAAATAAA
328406 AATAA-ATAAATAAA
1 AATAATATAAATAAA
328420 TAAATACATC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (15 bp):
AATAATATAAATAAA
Found at i:328585 original size:30 final size:31
Alignment explanation
Indices: 328535--328594 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
328525 GAATTGAATC
*
328535 AAATCAAAATTTTATGTATAAAATTACATAA
1 AAATCAAAATTTTATATATAAAATTACATAA
*
328566 AAATCAAAA-TTTATATATAAAATTGCATA
1 AAATCAAAATTTTATATATAAAATTACATA
328595 TTAATTGATA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 18 0.67
31 9 0.33
ACGTcount: A:0.55, C:0.07, G:0.03, T:0.35
Consensus pattern (31 bp):
AAATCAAAATTTTATATATAAAATTACATAA
Found at i:328693 original size:3 final size:3
Alignment explanation
Indices: 328678--328713 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
328668 ATAACTATTA
*
328678 CTT CTT CTA CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
328714 ATTATTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.03, C:0.33, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:331894 original size:21 final size:21
Alignment explanation
Indices: 331853--331900 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
331843 TGAACCTCAG
331853 GGTTCAAGATTCAAGAGTTAA
1 GGTTCAAGATTCAAGAGTTAA
* * *
331874 TGTTCAAGATTCAATATTTAA
1 GGTTCAAGATTCAAGAGTTAA
331895 GGTTCA
1 GGTTCA
331901 GAGTTTTAGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.35
Consensus pattern (21 bp):
GGTTCAAGATTCAAGAGTTAA
Found at i:332418 original size:17 final size:16
Alignment explanation
Indices: 332398--332444 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
332388 TCTTTATAAT
332398 TAATATATAAATTTTAA
1 TAATATATAAATTTT-A
332415 TAAT-TATTAAATTTTA
1 TAATATA-TAAATTTTA
* *
332431 TAAAATTTAAATTT
1 TAATATATAAATTT
332445 ATTGATAACA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 13 0.50
17 13 0.50
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TAATATATAAATTTTA
Found at i:332419 original size:21 final size:18
Alignment explanation
Indices: 332369--332430 Score: 56
Period size: 19 Copynumber: 3.3 Consensus size: 18
332359 ATATAAATAT
332369 TTTTAATAATGTAATTATA
1 TTTTAATAAT-TAATTATA
332388 TCTTT-ATAATTAATATATAAA
1 T-TTTAATAATTAAT-TAT--A
*
332409 TTTTAATAATT-ATTAAA
1 TTTTAATAATTAATTATA
332426 TTTTA
1 TTTTA
332431 TAAAATTTAA
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
17 6 0.16
18 4 0.11
19 11 0.30
20 8 0.22
21 8 0.22
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (18 bp):
TTTTAATAATTAATTATA
Found at i:332882 original size:17 final size:18
Alignment explanation
Indices: 332848--332880 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
332838 TATGTATCTC
332848 ATTTCTTTTATATATTTA
1 ATTTCTTTTATATATTTA
332866 ATTT-TTTTA-ATATTT
1 ATTTCTTTTATATATTT
332881 TATTATACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 5 0.33
18 4 0.27
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (18 bp):
ATTTCTTTTATATATTTA
Found at i:333300 original size:22 final size:22
Alignment explanation
Indices: 333274--333321 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
333264 ATACATAATG
*
333274 TAATA-ATATATTTTAAAACTAT
1 TAATACATATA-TATAAAACTAT
*
333296 TAATACATATATATATAACTAT
1 TAATACATATATATAAAACTAT
333318 TAAT
1 TAAT
333322 TGGTCCAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (22 bp):
TAATACATATATATAAAACTAT
Found at i:336319 original size:4 final size:4
Alignment explanation
Indices: 336310--336337 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
336300 CACCATGCAA
336310 AAAT AAAT AAAT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT
336338 CACCAGTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:341484 original size:2 final size:2
Alignment explanation
Indices: 341477--341509 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
341467 CAAGAAAGCA
341477 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
341510 ATTTGCTCCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:349185 original size:17 final size:17
Alignment explanation
Indices: 349158--349204 Score: 87
Period size: 17 Copynumber: 2.8 Consensus size: 17
349148 TCAGTCAACA
349158 GTTTG-ACTTGGTTTGG
1 GTTTGAACTTGGTTTGG
349174 GTTTGAACTTGGTTTGG
1 GTTTGAACTTGGTTTGG
349191 GTTTGAACTTGGTT
1 GTTTGAACTTGGTT
349205 CAATTTAGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
16 5 0.17
17 25 0.83
ACGTcount: A:0.11, C:0.06, G:0.34, T:0.49
Consensus pattern (17 bp):
GTTTGAACTTGGTTTGG
Found at i:371154 original size:16 final size:16
Alignment explanation
Indices: 371128--371165 Score: 67
Period size: 16 Copynumber: 2.3 Consensus size: 16
371118 TGCTTTGCCA
371128 TTGATTGATGCACTTTG
1 TTGA-TGATGCACTTTG
371145 TTGATGATGCACTTTG
1 TTGATGATGCACTTTG
371161 TTGAT
1 TTGAT
371166 AAGTTTTCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 17 0.81
17 4 0.19
ACGTcount: A:0.18, C:0.11, G:0.24, T:0.47
Consensus pattern (16 bp):
TTGATGATGCACTTTG
Found at i:381572 original size:20 final size:20
Alignment explanation
Indices: 381547--381586 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
381537 ATATTGTTGT
381547 ACAAACTTATTTCAGACTAA
1 ACAAACTTATTTCAGACTAA
381567 ACAAACTTATTTCAGACTAA
1 ACAAACTTATTTCAGACTAA
381587 CTTAGCATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.20, G:0.05, T:0.30
Consensus pattern (20 bp):
ACAAACTTATTTCAGACTAA
Found at i:384082 original size:242 final size:242
Alignment explanation
Indices: 383657--384136 Score: 890
Period size: 242 Copynumber: 2.0 Consensus size: 242
383647 AGAGCCGTAT
383657 CACTGGGAAATTAATTAACAGTTGTGTTTTCTTCCTTATTATGTAAGGTGAGTTGCAATTTTCAG
1 CACTGGGAAATTAATTAACAGTTGTGTTTTCTTCCTTATTATGTAAGGTGAGTTGCAATTTTCAG
*
383722 ATTAAGATGAAAATTATTTTTCAGAACCACTGAATAGCATCCAGCATCTGTAGCAGGTGATGTTG
66 ATTAAGATGAAAATTATTTTTCAGAACCACTGAATAGCATCCAGCATCTGCAGCAGGTGATGTTG
*
383787 TAATTCCTTGCCAGAAAGTAAATCAAAATCAGCACTAAAATCTCCATTAGAAAAATGATCTGATT
131 TAAGTCCTTGCCAGAAAGTAAATCAAAATCAGCACTAAAATCTCCATTAGAAAAATGATCTGATT
*
383852 CAACGCTAACAAAATTTAATTTTAAGATAAATGAAAAAAAGCTGAAC
196 CAACGATAACAAAATTTAATTTTAAGATAAATGAAAAAAAGCTGAAC
*
383899 CACTGGGAAATTAATTAACAGATT-TGTTTTCTTCTTTATTATGTAAGGTGAGTTGCAATTTTCA
1 CACTGGGAAATTAATTAACAG-TTGTGTTTTCTTCCTTATTATGTAAGGTGAGTTGCAATTTTCA
*
383963 GATTAAGATGAAAATTATTTTTCAGAACCACTGAATAGCATCCAGCATCTGCGGCAGGTGATGTT
65 GATTAAGATGAAAATTATTTTTCAGAACCACTGAATAGCATCCAGCATCTGCAGCAGGTGATGTT
*
384028 GTAAGTCCTTGCCAGGAAGTAAATCAAAATCAGCACTAAAATCTCCATTAGAAAAATGATCTGAT
130 GTAAGTCCTTGCCAGAAAGTAAATCAAAATCAGCACTAAAATCTCCATTAGAAAAATGATCTGAT
384093 TCAACGATAACAAAATTTAATTTTAAGATAAATGAAAAAAAGCT
195 TCAACGATAACAAAATTTAATTTTAAGATAAATGAAAAAAAGCT
384137 TCACTTCCAG
Statistics
Matches: 231, Mismatches: 6, Indels: 2
0.97 0.03 0.01
Matches are distributed among these distances:
242 229 0.99
243 2 0.01
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.31
Consensus pattern (242 bp):
CACTGGGAAATTAATTAACAGTTGTGTTTTCTTCCTTATTATGTAAGGTGAGTTGCAATTTTCAG
ATTAAGATGAAAATTATTTTTCAGAACCACTGAATAGCATCCAGCATCTGCAGCAGGTGATGTTG
TAAGTCCTTGCCAGAAAGTAAATCAAAATCAGCACTAAAATCTCCATTAGAAAAATGATCTGATT
CAACGATAACAAAATTTAATTTTAAGATAAATGAAAAAAAGCTGAAC
Found at i:386983 original size:41 final size:41
Alignment explanation
Indices: 386926--387021 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 41
386916 GTATTTTATT
386926 TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACC
1 TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACC
*
386967 TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTTCACC
1 TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACC
*
387008 TTGACAAGAATTCT
1 TTAACAAGAATTCT
387022 CTACGAACAA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.36, C:0.28, G:0.06, T:0.29
Consensus pattern (41 bp):
TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACC
Found at i:387033 original size:17 final size:17
Alignment explanation
Indices: 387011--387049 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
387001 CTTCACCTTG
* *
387011 ACAAGAATTCTCTACGA
1 ACAAGAACTCTCAACGA
*
387028 ACAAGAACTCTCAATGA
1 ACAAGAACTCTCAACGA
387045 ACAAG
1 ACAAG
387050 TTCTCCACCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.46, C:0.23, G:0.13, T:0.18
Consensus pattern (17 bp):
ACAAGAACTCTCAACGA
Found at i:400215 original size:16 final size:17
Alignment explanation
Indices: 400194--400225 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
400184 TTTTTAACGT
400194 TATTTTA-ATTTTTTAG
1 TATTTTATATTTTTTAG
400210 TATTTTATATTTTTTA
1 TATTTTATATTTTTTA
400226 AAGTTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (17 bp):
TATTTTATATTTTTTAG
Found at i:401347 original size:31 final size:31
Alignment explanation
Indices: 401298--401357 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
401288 AAAAGAGCCG
*
401298 AACCTTCTCGAAAGTGCTCAAATAAGGGCCA
1 AACCTTCTCGAAACTGCTCAAATAAGGGCCA
* *
401329 AACCTTTTTGAAACTGCTCAAATAAGGGC
1 AACCTTCTCGAAACTGCTCAAATAAGGGC
401358 TTCTCAAATG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.23
Consensus pattern (31 bp):
AACCTTCTCGAAACTGCTCAAATAAGGGCCA
Found at i:405369 original size:2 final size:2
Alignment explanation
Indices: 405364--405394 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
405354 TAAAAAAAGG
405364 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
405395 TACAATATCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:406702 original size:6 final size:6
Alignment explanation
Indices: 406691--406715 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
406681 AAGTATGTGA
406691 TGAAAG TGAAAG TGAAAG TGAAAG T
1 TGAAAG TGAAAG TGAAAG TGAAAG T
406716 CTCTTCATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.32, T:0.20
Consensus pattern (6 bp):
TGAAAG
Found at i:412113 original size:30 final size:28
Alignment explanation
Indices: 412070--412176 Score: 73
Period size: 31 Copynumber: 3.8 Consensus size: 28
412060 AAATTTTAAA
*
412070 TTAATAATAATAAAATTATATCTTAATCCTT
1 TTAAAAAT-ATAAAATTATAT-TTAAT-CTT
*
412101 TTAAAAATATAAAAATT-TAATTTAATTTT
1 TTAAAAATAT-AAAATTAT-ATTTAATCTT
* *
412130 TTAAAAATTATAAAA--ATA--TAAACTA
1 TTAAAAA-TATAAAATTATATTTAATCTT
412155 TT-AAAATAATAAAATTATATTT
1 TTAAAAAT-ATAAAATTATATTT
412177 TTATTATTAT
Statistics
Matches: 62, Mismatches: 5, Indels: 21
0.70 0.06 0.24
Matches are distributed among these distances:
23 1 0.02
24 10 0.16
25 6 0.10
26 3 0.05
27 1 0.02
28 2 0.03
29 13 0.21
30 11 0.18
31 15 0.24
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (28 bp):
TTAAAAATATAAAATTATATTTAATCTT
Found at i:412201 original size:82 final size:82
Alignment explanation
Indices: 412028--412205 Score: 193
Period size: 82 Copynumber: 2.2 Consensus size: 82
412018 CCTAAAATAA
* * * * *
412028 AAAAATTTTATTTAAGTTTTTTATAATTTATAAAATTTTAAATTAATAATAATAAAATTATATCT
1 AAAAATTTAATTTAAGTTTTTTAAAAATTATAAAATATAAAATTAATAATAATAAAATTATATCT
* *
412093 TAATCCTTTTAAAAATAT
66 TAAT-CTATTAAAAACAT
412111 AAAAATTTAATTTAA-TTTTTTAAAAATTATAAAAATATAAACTATTAA-AATAATAAAATTATA
1 AAAAATTTAATTTAAGTTTTTTAAAAATTAT-AAAATATAAA--ATTAATAATAATAAAATTATA
* *
412174 TTTTTAT-TATTATAAAACAT
63 TCTTAATCTATTA-AAAACAT
*
412194 -ACAATTTAATTT
1 AAAAATTTAATTT
412206 CGATGTTAAA
Statistics
Matches: 81, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
82 28 0.35
83 28 0.35
84 20 0.25
85 5 0.06
ACGTcount: A:0.50, C:0.03, G:0.01, T:0.46
Consensus pattern (82 bp):
AAAAATTTAATTTAAGTTTTTTAAAAATTATAAAATATAAAATTAATAATAATAAAATTATATCT
TAATCTATTAAAAACAT
Found at i:419556 original size:24 final size:24
Alignment explanation
Indices: 419528--419584 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 24
419518 GACTAATAAG
* *
419528 AGTTTGACTCAAATAAATAAACAA
1 AGTTTAACTCAAACAAATAAACAA
* *
419552 AGTTTAATTGAAACAAATAAACAA
1 AGTTTAACTCAAACAAATAAACAA
*
419576 AATTTAACT
1 AGTTTAACT
419585 GAAAGATTAT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.54, C:0.11, G:0.07, T:0.28
Consensus pattern (24 bp):
AGTTTAACTCAAACAAATAAACAA
Found at i:419587 original size:24 final size:24
Alignment explanation
Indices: 419542--419588 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
419532 TGACTCAAAT
* *
419542 AAATAAACAAAGTTTAATTGAAAC
1 AAATAAACAAAATTTAACTGAAAC
419566 AAATAAACAAAATTTAACTGAAA
1 AAATAAACAAAATTTAACTGAAA
419589 GATTATTTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.62, C:0.09, G:0.06, T:0.23
Consensus pattern (24 bp):
AAATAAACAAAATTTAACTGAAAC
Found at i:437989 original size:21 final size:20
Alignment explanation
Indices: 437947--437986 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
437937 TACTTCAATT
*
437947 TTAAAATTTAAAAAATTAAA
1 TTAAAATTTAAAAAATAAAA
* *
437967 TTAAATTTTTAAAAATAAAA
1 TTAAAATTTAAAAAATAAAA
437987 ATTTAAGGAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
TTAAAATTTAAAAAATAAAA
Found at i:437998 original size:29 final size:28
Alignment explanation
Indices: 437945--438003 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 28
437935 TATACTTCAA
*
437945 TTTTAAAATTTAAAAAATTAAATTAAAT
1 TTTTAAAATATAAAAAATTAAATTAAAT
*
437973 TTTTAAAA-ATAAAAATTTAAGGATTAAAT
1 TTTTAAAATATAAAAAATTAA--ATTAAAT
438002 TT
1 TT
438004 ATATTTGTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 10 0.37
28 8 0.30
29 9 0.33
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.42
Consensus pattern (28 bp):
TTTTAAAATATAAAAAATTAAATTAAAT
Found at i:439621 original size:6 final size:6
Alignment explanation
Indices: 439610--439641 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
439600 ATCGCCTATC
439610 GTCACG GTCACG GTCACG GTCACG GTCACG GT
1 GTCACG GTCACG GTCACG GTCACG GTCACG GT
439642 TCAATAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.16, C:0.31, G:0.34, T:0.19
Consensus pattern (6 bp):
GTCACG
Found at i:439850 original size:14 final size:16
Alignment explanation
Indices: 439833--439864 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
439823 ATTTTCAAAA
439833 TTTT-AATTTT-TAAT
1 TTTTAAATTTTATAAT
439847 TTTTAAATTTTATAAT
1 TTTTAAATTTTATAAT
439863 TT
1 TT
439865 AAAACTAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.25
15 6 0.38
16 6 0.38
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
TTTTAAATTTTATAAT
Found at i:440257 original size:62 final size:65
Alignment explanation
Indices: 440150--440335 Score: 254
Period size: 62 Copynumber: 2.9 Consensus size: 65
440140 ACGTTAATGT
* *
440150 AAGATT-CCTGGAGCTAATAATCTTACGTTTACATCGTGTCAAGATTTCAAAATGTGGAG-TTC-
1 AAGATTACCTTGAGCTAATAATCTTACATTTACATCGTGTCAAGATTTCAAAATGTGGAGTTTCA
* * * *
440212 AA-ATTAGCTTGAGCTAATAATCTTACATTTACATCCTATCAAGATTTCAAAATGTAGAGTTTCA
1 AAGATTACCTTGAGCTAATAATCTTACATTTACATCGTGTCAAGATTTCAAAATGTGGAGTTTCA
* * * *
440276 AAGATTACCTTCAACTAATAATCTTACATCTACATAGTGTCAAGATTTCAAAATGTGGAG
1 AAGATTACCTTGAGCTAATAATCTTACATTTACATCGTGTCAAGATTTCAAAATGTGGAG
440336 ATAATTTCAT
Statistics
Matches: 106, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
61 3 0.03
62 49 0.46
63 3 0.03
64 2 0.02
65 49 0.46
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (65 bp):
AAGATTACCTTGAGCTAATAATCTTACATTTACATCGTGTCAAGATTTCAAAATGTGGAGTTTCA
Found at i:440319 original size:65 final size:62
Alignment explanation
Indices: 440163--440331 Score: 230
Period size: 65 Copynumber: 2.7 Consensus size: 62
440153 ATTCCTGGAG
* * * * *
440163 CTAATAATCTTACGTTTACATCGTGTCAAGATTTCAAAATGTGGAGTTCAAATTAGCTTGAG
1 CTAATAATCTTACATTTACATCGTGTCAAGATTTCAAAATGTAGAGTTCAAATTACCTTCAA
* *
440225 CTAATAATCTTACATTTACATCCTATCAAGATTTCAAAATGTAGAGTTTCAAAGATTACCTTCAA
1 CTAATAATCTTACATTTACATCGTGTCAAGATTTCAAAATGTAGAG-TTC-AA-ATTACCTTCAA
* *
440290 CTAATAATCTTACATCTACATAGTGTCAAGATTTCAAAATGT
1 CTAATAATCTTACATTTACATCGTGTCAAGATTTCAAAATGT
440332 GGAGATAATT
Statistics
Matches: 93, Mismatches: 11, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
62 42 0.45
63 3 0.03
64 2 0.02
65 46 0.49
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.36
Consensus pattern (62 bp):
CTAATAATCTTACATTTACATCGTGTCAAGATTTCAAAATGTAGAGTTCAAATTACCTTCAA
Found at i:446023 original size:30 final size:30
Alignment explanation
Indices: 445954--446030 Score: 86
Period size: 31 Copynumber: 2.6 Consensus size: 30
445944 AAAATGGAGT
* * *
445954 TTTAAGTTTATTAAAAATTGGAGAAAAAAT
1 TTTAAGTTTTTTAAAAGTTGGAGAAAAAAA
*
445984 TTATAAGTTTTTTAAAAGTT-GATAAAATAAA
1 TT-TAAGTTTTTTAAAAGTTGGAGAAAA-AAA
446015 TTTAAG-TTTTTAAAAG
1 TTTAAGTTTTTTAAAAG
446031 CTAAAAATAA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
29 10 0.24
30 12 0.29
31 19 0.46
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.42
Consensus pattern (30 bp):
TTTAAGTTTTTTAAAAGTTGGAGAAAAAAA
Found at i:447397 original size:6 final size:6
Alignment explanation
Indices: 447386--447412 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
447376 TTAAAATTGT
447386 CGTTGC CGTTGC CGTTGC CGTTGC CGT
1 CGTTGC CGTTGC CGTTGC CGTTGC CGT
447413 CATTTATATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.33, G:0.33, T:0.33
Consensus pattern (6 bp):
CGTTGC
Done.