Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168048.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_3, 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: 33276047
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 139000 characters in sequence are not A, C, G, or T
File 119 of 190
Found at i:18656047 original size:20 final size:21
Alignment explanation
Indices: 18656011--18656053 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
18656001 TTCAAACCTT
*
18656011 AAACCTCAAACCTCAAATCCA
1 AAACCTCAAACCCCAAATCCA
18656032 AAACCT-AAACCCCAAATCCA
1 AAACCTCAAACCCCAAATCCA
18656052 AA
1 AA
18656054 CGCTAAATCC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.51, C:0.37, G:0.00, T:0.12
Consensus pattern (21 bp):
AAACCTCAAACCCCAAATCCA
Found at i:18656061 original size:13 final size:13
Alignment explanation
Indices: 18656038--18656072 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
18656028 TCCAAAACCT
*
18656038 AAACCCCAAATCC
1 AAACCCTAAATCC
*
18656051 AAACGCTAAATCC
1 AAACCCTAAATCC
18656064 AAACCCTAA
1 AAACCCTAA
18656073 CCCCAAATCC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.49, C:0.37, G:0.03, T:0.11
Consensus pattern (13 bp):
AAACCCTAAATCC
Found at i:18656065 original size:19 final size:18
Alignment explanation
Indices: 18656024--18656110 Score: 59
Period size: 19 Copynumber: 4.6 Consensus size: 18
18656014 CCTCAAACCT
*
18656024 CAAATCCAAAACCTAAACCC
1 CAAATCC-AAACCTAAA-TC
18656044 CAAATCCAAACGCTAAATC
1 CAAATCCAAAC-CTAAATC
* * *
18656063 CAAACCCTAACCCCAAATC
1 CAAATCC-AAACCTAAATC
*
18656082 CTAA-CCTTAAACCTAAATC
1 CAAATCC--AAACCTAAATC
*
18656101 TAAATCCAAA
1 CAAATCCAAA
18656111 AGCCTAAAAA
Statistics
Matches: 54, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
18 5 0.09
19 32 0.59
20 17 0.31
ACGTcount: A:0.47, C:0.36, G:0.01, T:0.16
Consensus pattern (18 bp):
CAAATCCAAACCTAAATC
Found at i:18656295 original size:27 final size:26
Alignment explanation
Indices: 18656243--18656297 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 26
18656233 ATTTTATTCA
*
18656243 TATTATATTGCCATGCATTTATCATTT
1 TATTATATT-CCATGCATTCATCATTT
18656270 TATTATATT-CATGCATCTCATGCATTT
1 TATTATATTCCATGCAT-TCAT-CATTT
18656297 T
1 T
18656298 TTGGAAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
25 7 0.28
26 3 0.12
27 15 0.60
ACGTcount: A:0.25, C:0.16, G:0.07, T:0.51
Consensus pattern (26 bp):
TATTATATTCCATGCATTCATCATTT
Found at i:18657097 original size:7 final size:7
Alignment explanation
Indices: 18657067--18657230 Score: 57
Period size: 7 Copynumber: 24.7 Consensus size: 7
18657057 CCCCCAAATC
18657067 TAAACCT
1 TAAACCT
*
18657074 CAAA-CT
1 TAAACCT
18657080 TAAATCC-
1 TAAA-CCT
18657087 -AAACCT
1 TAAACCT
*
18657093 TAAACCC
1 TAAACCT
*
18657100 CAAACC-
1 TAAACCT
*
18657106 CAAACCT
1 TAAACCT
18657113 TAAA-CT
1 TAAACCT
* *
18657119 CCAAACCC
1 -TAAACCT
18657127 TAAATCC-
1 TAAA-CCT
*
18657134 -AAACCC
1 TAAACCT
18657140 TAAACC-
1 TAAACCT
18657146 TAAACCT
1 TAAACCT
*
18657153 TAATCC-
1 TAAACCT
*
18657159 CAAACCT
1 TAAACCT
* *
18657166 CAAACCC
1 TAAACCT
*
18657173 TAAACCC
1 TAAACCT
*
18657180 TAAACCC
1 TAAACCT
*
18657187 TAAATC-
1 TAAACCT
18657193 TAAACC-
1 TAAACCT
18657199 TAAATCC-
1 TAAA-CCT
18657206 T-AACCT
1 TAAACCT
*
18657212 TAAACCC
1 TAAACCT
*
18657219 TAACCCT
1 TAAACCT
18657226 TAAAC
1 TAAAC
18657231 TTGACCATAC
Statistics
Matches: 123, Mismatches: 19, Indels: 30
0.72 0.11 0.17
Matches are distributed among these distances:
5 6 0.05
6 41 0.33
7 72 0.59
8 4 0.03
ACGTcount: A:0.44, C:0.37, G:0.00, T:0.19
Consensus pattern (7 bp):
TAAACCT
Found at i:18657110 original size:20 final size:20
Alignment explanation
Indices: 18657085--18657218 Score: 107
Period size: 20 Copynumber: 6.8 Consensus size: 20
18657075 AAACTTAAAT
18657085 CCAAACCTTAAACCCCAAAC
1 CCAAACCTTAAACCCCAAAC
*
18657105 CCAAACCTTAAACTCCAAAC
1 CCAAACCTTAAACCCCAAAC
*
18657125 CCTAAATCC--AAACCCTAAAC
1 CC-AAA-CCTTAAACCCCAAAC
* *
18657145 CTAAACCTT-AATCCCAAAC
1 CCAAACCTTAAACCCCAAAC
* *
18657164 CTCAAACCCTAAACCCTAAAC
1 C-CAAACCTTAAACCCCAAAC
* * *
18657185 CCTAAATC-TAAA-CCTAAAT
1 CC-AAACCTTAAACCCCAAAC
*
18657204 CCTAACCTTAAACCC
1 CCAAACCTTAAACCC
18657219 TAACCCTTAA
Statistics
Matches: 91, Mismatches: 14, Indels: 18
0.74 0.11 0.15
Matches are distributed among these distances:
18 5 0.05
19 24 0.26
20 44 0.48
21 16 0.18
22 2 0.02
ACGTcount: A:0.43, C:0.40, G:0.00, T:0.17
Consensus pattern (20 bp):
CCAAACCTTAAACCCCAAAC
Found at i:18657134 original size:13 final size:13
Alignment explanation
Indices: 18657094--18657225 Score: 75
Period size: 13 Copynumber: 10.5 Consensus size: 13
18657084 TCCAAACCTT
* *
18657094 AAACCCCAAACCC
1 AAACCCTAAATCC
*
18657107 AAACCTTAAACTCC
1 AAACCCTAAA-TCC
18657121 AAACCCTAAATCC
1 AAACCCTAAATCC
18657134 AAACCCTAAA-CC
1 AAACCCTAAATCC
*
18657146 TAAA-CCTTAATCCC
1 -AAACCCTAAAT-CC
18657160 AAA-CC----T-C
1 AAACCCTAAATCC
*
18657167 AAACCCTAAACCC
1 AAACCCTAAATCC
*
18657180 TAAACCCTAAATCT
1 -AAACCCTAAATCC
18657194 AAA-CCTAAATCC
1 AAACCCTAAATCC
* * *
18657206 TAACCTTAAACCC
1 AAACCCTAAATCC
*
18657219 TAACCCT
1 AAACCCT
18657226 TAAACTTGAC
Statistics
Matches: 94, Mismatches: 13, Indels: 24
0.72 0.10 0.18
Matches are distributed among these distances:
7 4 0.04
8 2 0.02
9 1 0.01
12 17 0.18
13 46 0.49
14 24 0.26
ACGTcount: A:0.43, C:0.39, G:0.00, T:0.17
Consensus pattern (13 bp):
AAACCCTAAATCC
Found at i:18657138 original size:40 final size:40
Alignment explanation
Indices: 18657086--18657221 Score: 129
Period size: 40 Copynumber: 3.4 Consensus size: 40
18657076 AACTTAAATC
* *
18657086 CAAACCTTAAACCCCAAACCCAAACCTTAAACTCCAAACC-
1 CAAACCCTAAACCCTAAACCCAAACCTTAAAC-CCAAACCT
* * *
18657126 CTAAATCC-AAACCCTAAACCTAAACCTTAATCCCAAACCT
1 C-AAACCCTAAACCCTAAACCCAAACCTTAAACCCAAACCT
* *
18657166 CAAACCCTAAACCCTAAACCCTAAATC-TAAACCTAAATCCT
1 CAAACCCTAAACCCTAAACCC-AAACCTTAAACCCAAA-CCT
*
18657207 --AACCTTAAACCCTAA
1 CAAACCCTAAACCCTAA
18657222 CCCTTAAACT
Statistics
Matches: 80, Mismatches: 11, Indels: 11
0.78 0.11 0.11
Matches are distributed among these distances:
39 26 0.32
40 43 0.54
41 11 0.14
ACGTcount: A:0.44, C:0.38, G:0.00, T:0.18
Consensus pattern (40 bp):
CAAACCCTAAACCCTAAACCCAAACCTTAAACCCAAACCT
Found at i:18657211 original size:46 final size:47
Alignment explanation
Indices: 18657120--18657230 Score: 147
Period size: 46 Copynumber: 2.4 Consensus size: 47
18657110 CCTTAAACTC
* *
18657120 CAAACCCTAAATCC-AAACCCTAAACCTAAACCTTAATCCCAAACCT
1 CAAACCCTAAACCCTAAACCCTAAACCTAAACCTAAATCCCAAACCT
* *
18657166 CAAACCCTAAACCCTAAACCCTAAATCTAAACCTAAAT-CCTAACCT
1 CAAACCCTAAACCCTAAACCCTAAACCTAAACCTAAATCCCAAACCT
*
18657212 TAAACCCT-AACCCTTAAAC
1 CAAACCCTAAACCC-TAAAC
18657231 TTGACCATAC
Statistics
Matches: 58, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
45 5 0.09
46 32 0.55
47 21 0.36
ACGTcount: A:0.43, C:0.38, G:0.00, T:0.19
Consensus pattern (47 bp):
CAAACCCTAAACCCTAAACCCTAAACCTAAACCTAAATCCCAAACCT
Found at i:18657217 original size:53 final size:50
Alignment explanation
Indices: 18657108--18657230 Score: 123
Period size: 47 Copynumber: 2.5 Consensus size: 50
18657098 CCCAAACCCA
* *
18657108 AACCTTAAA-CTCCAAACCCTAAATCCAAACCCTAAACCTAAACCTTAATC
1 AACCTTAAACCT-CAAACCCTAAACCCAAACCCTAAACCTAAACCTAAATC
*
18657158 --CC--AAACCTCAAACCCTAAACCCTAAACCCTAAATCTAAACCTAAATCC
1 AACCTTAAACCTCAAACCCTAAACCC-AAACCCTAAACCTAAACCTAAAT-C
*
18657206 TAACCTTAAACC-CTAACCCTTAAAC
1 -AACCTTAAACCTCAAACCC-TAAAC
18657231 TTGACCATAC
Statistics
Matches: 60, Mismatches: 4, Indels: 15
0.76 0.05 0.19
Matches are distributed among these distances:
46 16 0.27
47 23 0.38
48 3 0.05
51 2 0.03
52 6 0.10
53 10 0.17
ACGTcount: A:0.43, C:0.37, G:0.00, T:0.20
Consensus pattern (50 bp):
AACCTTAAACCTCAAACCCTAAACCCAAACCCTAAACCTAAACCTAAATC
Found at i:18657713 original size:16 final size:16
Alignment explanation
Indices: 18657687--18657737 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 16
18657677 AAAAAAAAAG
18657687 TTTTGTTTTAAATTTGA
1 TTTT-TTTTAAATTTGA
***
18657704 TTTTTTTTAAA-AAAA
1 TTTTTTTTAAATTTGA
*
18657719 TTTGTTTTAAATTTGA
1 TTTTTTTTAAATTTGA
18657735 TTT
1 TTT
18657738 ATTTCTTATT
Statistics
Matches: 26, Mismatches: 7, Indels: 3
0.72 0.19 0.08
Matches are distributed among these distances:
15 11 0.42
16 11 0.42
17 4 0.15
ACGTcount: A:0.29, C:0.00, G:0.08, T:0.63
Consensus pattern (16 bp):
TTTTTTTTAAATTTGA
Found at i:18658279 original size:9 final size:9
Alignment explanation
Indices: 18658263--18658310 Score: 62
Period size: 9 Copynumber: 5.3 Consensus size: 9
18658253 ATTTCTTAAG
18658263 AAAAAATGA
1 AAAAAATGA
*
18658272 AGAAAATG-
1 AAAAAATGA
*
18658280 GAAAAATGA
1 AAAAAATGA
18658289 AAAAAATGA
1 AAAAAATGA
18658298 AAAAAATGGA
1 AAAAAAT-GA
18658308 AAA
1 AAA
18658311 GTGAAAATGA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
8 6 0.18
9 22 0.67
10 5 0.15
ACGTcount: A:0.73, C:0.00, G:0.17, T:0.10
Consensus pattern (9 bp):
AAAAAATGA
Found at i:18658297 original size:26 final size:26
Alignment explanation
Indices: 18658263--18658317 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
18658253 ATTTCTTAAG
*
18658263 AAAAAATGAAGAAAATGGAAAAATGA
1 AAAAAATGAAAAAAATGGAAAAATGA
*
18658289 AAAAAATGAAAAAAATGGAAAAGTGA
1 AAAAAATGAAAAAAATGGAAAAATGA
18658315 AAA
1 AAA
18658318 TGAAAATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.71, C:0.00, G:0.18, T:0.11
Consensus pattern (26 bp):
AAAAAATGAAAAAAATGGAAAAATGA
Found at i:18658302 original size:17 final size:17
Alignment explanation
Indices: 18658262--18658302 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
18658252 GATTTCTTAA
*
18658262 GAAAAAATGAAGAAAAT
1 GAAAAAATGAAAAAAAT
*
18658279 GGAAAAATGAAAAAAAT
1 GAAAAAATGAAAAAAAT
18658296 GAAAAAA
1 GAAAAAA
18658303 ATGGAAAAGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.73, C:0.00, G:0.17, T:0.10
Consensus pattern (17 bp):
GAAAAAATGAAAAAAAT
Found at i:18658380 original size:25 final size:25
Alignment explanation
Indices: 18658346--18658470 Score: 151
Period size: 25 Copynumber: 5.0 Consensus size: 25
18658336 GTGTATTTTA
18658346 CATTTCATGCATATTTTAATTATGT
1 CATTTCATGCATATTTTAATTATGT
* * *
18658371 CATTTCATGCATATTGTAAATATGA
1 CATTTCATGCATATTTTAATTATGT
* * *
18658396 CATTTCTTGTATATTTTAAATATGT
1 CATTTCATGCATATTTTAATTATGT
* *
18658421 CACTTCATACATATTTTTAATTATGT
1 CATTTCATGCATA-TTTTAATTATGT
* *
18658447 CATTTTATGCATATTTAAATTATG
1 CATTTCATGCATATTTTAATTATG
18658471 ATATTTATTT
Statistics
Matches: 83, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
25 62 0.75
26 21 0.25
ACGTcount: A:0.31, C:0.11, G:0.08, T:0.50
Consensus pattern (25 bp):
CATTTCATGCATATTTTAATTATGT
Found at i:18667327 original size:30 final size:31
Alignment explanation
Indices: 18667293--18667351 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
18667283 AGAATTAAGC
18667293 CTAGTCTAGCTAGCAC-AAGGAAAATTAAAA
1 CTAGTCTAGCTAGCACTAAGGAAAATTAAAA
* * *
18667323 CTAGTTTAGCTAGTACTAATGAAAATTAA
1 CTAGTCTAGCTAGCACTAAGGAAAATTAA
18667352 TCTTAGTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 14 0.56
31 11 0.44
ACGTcount: A:0.44, C:0.14, G:0.15, T:0.27
Consensus pattern (31 bp):
CTAGTCTAGCTAGCACTAAGGAAAATTAAAA
Found at i:18667425 original size:31 final size:30
Alignment explanation
Indices: 18667283--18667615 Score: 188
Period size: 31 Copynumber: 10.9 Consensus size: 30
18667273 GAAAAAGATA
* * *
18667283 AGAATTAAGCCTAGTCTAGCTAGCACAAGG
1 AGAATTAAGCCTAGTTTAGCTGGCACAAAG
* ** * * *
18667313 AAAATTAAAACTAGTTTAGCTAGTACTAATG
1 AGAATTAAGCCTAGTTTAGCTGGCAC-AAAG
* * * *
18667344 AAAATTAATCTTAGTTTAGCTGGCATAAAG
1 AGAATTAAGCCTAGTTTAGCTGGCACAAAG
* ** *
18667374 AATAATTAAGCCTAAATTAGCTGGAACCAAAG
1 -AGAATTAAGCCTAGTTTAGCTGGCA-CAAAG
* ***
18667406 AGAATTAAGCTTAGTTTAGCTAGTG-TTGAAG
1 AGAATTAAGCCTAGTTTAGCT-G-GCACAAAG
* * *
18667437 AAAATTAAGCC-AGTTTAGCTTGCACTAAG
1 AGAATTAAGCCTAGTTTAGCTGGCACAAAG
*
18667466 A-AGATTAAGCCTAGTTTAGCTGGCACTAAG
1 AGA-ATTAAGCCTAGTTTAGCTGGCACAAAG
* * *
18667496 AAAAATTAAGCTTAGGTTAG-TGGGCACCAAAG
1 -AGAATTAAGCCTAGTTTAGCT-GGCA-CAAAG
* * *
18667528 AGAATTAAGCCAAGTTTAGCTTGCACCAAGG
1 AGAATTAAGCCTAGTTTAGCTGGCA-CAAAG
* * ** *
18667559 AGAATTAAGCCTAGTGTAACTAACACCAAG
1 AGAATTAAGCCTAGTTTAGCTGGCACAAAG
* * *
18667589 AACAATTAAGCCTAGATTAGTTGGCAC
1 -AGAATTAAGCCTAGTTTAGCTGGCAC
18667616 CATACATAGA
Statistics
Matches: 232, Mismatches: 57, Indels: 27
0.73 0.18 0.09
Matches are distributed among these distances:
28 2 0.01
29 12 0.05
30 54 0.23
31 152 0.66
32 11 0.05
33 1 0.00
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.26
Consensus pattern (30 bp):
AGAATTAAGCCTAGTTTAGCTGGCACAAAG
Found at i:18667505 original size:122 final size:123
Alignment explanation
Indices: 18667325--18667548 Score: 301
Period size: 122 Copynumber: 1.8 Consensus size: 123
18667315 AATTAAAACT
* * * *
18667325 AGTTTAGCTAGTACTAATGAAAATTAATCTTAGTTTAGCTGGCATAAAGAATAATTAAGCCTAAA
1 AGTTTAGCTAGCACTAATGAAAATTAAGCCTAGTTTAGCTGGCATAAAGAAAAATTAAGCCTAAA
**
18667390 TTAGCT-GGAACCAAAGAGAATTAAGCTTAGTTTAGCTAGTGTTGAAGAAAATTAAGCC
66 TTAG-TGGGAACCAAAGAGAATTAAGCCAAGTTTAGCTAGTGTTGAAGAAAATTAAGCC
* * * *
18667448 AGTTTAGCTTGCACTAA-GAAGATTAAGCCTAGTTTAGCTGGCACT-AAGAAAAATTAAGCTTAG
1 AGTTTAGCTAGCACTAATGAAAATTAAGCCTAGTTTAGCTGGCA-TAAAGAAAAATTAAGCCTAA
* *
18667511 GTTAGTGGGCACCAAAGAGAATTAAGCCAAGTTTAGCT
65 ATTAGTGGGAACCAAAGAGAATTAAGCCAAGTTTAGCT
18667549 TGCACCAAGG
Statistics
Matches: 87, Mismatches: 12, Indels: 5
0.84 0.12 0.05
Matches are distributed among these distances:
121 1 0.01
122 70 0.80
123 16 0.18
ACGTcount: A:0.38, C:0.13, G:0.21, T:0.29
Consensus pattern (123 bp):
AGTTTAGCTAGCACTAATGAAAATTAAGCCTAGTTTAGCTGGCATAAAGAAAAATTAAGCCTAAA
TTAGTGGGAACCAAAGAGAATTAAGCCAAGTTTAGCTAGTGTTGAAGAAAATTAAGCC
Found at i:18667534 original size:153 final size:154
Alignment explanation
Indices: 18667285--18667573 Score: 347
Period size: 153 Copynumber: 1.9 Consensus size: 154
18667275 AAAAGATAAG
*
18667285 AATTAAGCCTAGTCTAGCTAGCACAAGGAAAATTAAAACTAGTTTAGCTAGTACTAATGAAAATT
1 AATTAAGCCTAGTCTAGCTAGCACAAGGAAAATTAAAACTAGTTTAGCTAGCACTAATGAAAATT
* * * *
18667350 AATCTTAGTTTAGCTGGCATAAAGAATAATTAAGCCTAA-ATTAGCTGGAACCAAAGAGAATTAA
66 AAGCTTAGGTTAGCTGGCACAAAGAAGAATTAAGCC-AAGATTAGCTGGAACCAAAGAGAATTAA
*
18667414 GCTTAGTTTAGCTAGTGTTGAAGAA
130 GCCTAGTTTAGCTAGTGTTGAAGAA
* * * ** *
18667439 AATTAAGCC-AGTTTAGCTTGCACTAA-GAAGATTAAGCCTAGTTTAGCTGGCACTAA-GAAAAA
1 AATTAAGCCTAGTCTAGCTAGCAC-AAGGAAAATTAAAACTAGTTTAGCTAGCACTAATG-AAAA
* * * *
18667501 TTAAGCTTAGGTTAG-TGGGCACCAAAG-AGAATTAAGCCAAGTTTAGCTTGCACCAAGGAGAAT
64 TTAAGCTTAGGTTAGCT-GGCA-CAAAGAAGAATTAAGCCAAGATTAGCTGGAACCAAAGAGAAT
18667564 TAAGCCTAGT
127 TAAGCCTAGT
18667574 GTAACTAACA
Statistics
Matches: 114, Mismatches: 16, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
152 4 0.04
153 95 0.83
154 15 0.13
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (154 bp):
AATTAAGCCTAGTCTAGCTAGCACAAGGAAAATTAAAACTAGTTTAGCTAGCACTAATGAAAATT
AAGCTTAGGTTAGCTGGCACAAAGAAGAATTAAGCCAAGATTAGCTGGAACCAAAGAGAATTAAG
CCTAGTTTAGCTAGTGTTGAAGAA
Found at i:18667596 original size:93 final size:91
Alignment explanation
Indices: 18667434--18667617 Score: 242
Period size: 93 Copynumber: 2.0 Consensus size: 91
18667424 GCTAGTGTTG
* * * ** *
18667434 AAGAAAATTAAGCCAGTTTAGCTTGCACTAAGAAGATTAAGCCTAGTTTAGCTGGCACTAAGAAA
1 AAGAAAATTAAGCCAGTTTAGCTTGCACCAAGAAGATTAAGCCTAGTGTAACTAACACCAAGAAA
* *
18667499 AATTAAGCTTAGGTTAGTGGGCACCA
66 AATTAAGCCTAGATTAGTGGGCACCA
* *
18667525 AAGAGAATTAAGCCAAGTTTAGCTTGCACCAAGGAGAATTAAGCCTAGTGTAACTAACACCAAGA
1 AAGAAAATTAAGCC-AGTTTAGCTTGCACCAAGAAG-ATTAAGCCTAGTGTAACTAACACCAAGA
* *
18667590 ACAATTAAGCCTAGATTAGTTGGCACCA
64 AAAATTAAGCCTAGATTAGTGGGCACCA
18667618 TACATAGATT
Statistics
Matches: 79, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
91 13 0.16
92 19 0.24
93 47 0.59
ACGTcount: A:0.39, C:0.17, G:0.21, T:0.23
Consensus pattern (91 bp):
AAGAAAATTAAGCCAGTTTAGCTTGCACCAAGAAGATTAAGCCTAGTGTAACTAACACCAAGAAA
AATTAAGCCTAGATTAGTGGGCACCA
Found at i:18667727 original size:80 final size:80
Alignment explanation
Indices: 18667594--18667757 Score: 292
Period size: 80 Copynumber: 2.0 Consensus size: 80
18667584 CCAAGAACAA
* * * *
18667594 TTAAGCCTAGATTAGTTGGCACCATACATAGATTTTTTAAAGTTTAATCTATTTTATAAAAGCCT
1 TTAAGACTAGATTAATTGGCACCATACATAGATCTTTTAAAGTTTAATCTATTTTATAAAAGCCC
18667659 TTTTTGGATAGATTT
66 TTTTTGGATAGATTT
18667674 TTAAGACTAGATTAATTGGCACCATACATAGATCTTTTAAAGTTTAATCTATTTTATAAAAGCCC
1 TTAAGACTAGATTAATTGGCACCATACATAGATCTTTTAAAGTTTAATCTATTTTATAAAAGCCC
18667739 TTTTTGGATAGATTT
66 TTTTTGGATAGATTT
18667754 TTAA
1 TTAA
18667758 AGTTTAATGC
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
80 80 1.00
ACGTcount: A:0.33, C:0.12, G:0.13, T:0.43
Consensus pattern (80 bp):
TTAAGACTAGATTAATTGGCACCATACATAGATCTTTTAAAGTTTAATCTATTTTATAAAAGCCC
TTTTTGGATAGATTT
Found at i:18667784 original size:46 final size:46
Alignment explanation
Indices: 18667701--18668138 Score: 302
Period size: 46 Copynumber: 9.3 Consensus size: 46
18667691 GGCACCATAC
* ** *
18667701 ATAGATCTTTTAAAGTTTAAT--CTATTTTATAAAAGCCCTTTTTGG
1 ATAGAT-TTTTAAAGTTTGATGCCTATTTTATAGGAGCCCTTTTTAG
*
18667746 ATAGATTTTTAAAGTTTAATGCCTATTTTATAGGAGCCCTTTTCTTA-
1 ATAGATTTTTAAAGTTTGATGCCTATTTTATAGGAGCCC-TTT-TTAG
* * * *
18667793 ATAGATTTTTTAAGTTTAATGCCTA-TTTATAGGAGCTCTTTCTAG
1 ATAGATTTTTAAAGTTTGATGCCTATTTTATAGGAGCCCTTTTTAG
* * *
18667838 ATAGATTTTTGAAGTTTGATGCCTATTTTATATGAGCCCTTTCTAG
1 ATAGATTTTTAAAGTTTGATGCCTATTTTATAGGAGCCCTTTTTAG
* *
18667884 ATAGATTTTTCAAAATTTGATACCTA-TTTATAGGAG-CCTTTTCTAG
1 ATAGATTTTT-AAAGTTTGATGCCTATTTTATAGGAGCCCTTTT-TAG
* * * * * *
18667930 ATAAATTTTTAAAGTTTGATTCATATTTTATAAGAG--CTATTTCAT
1 ATAGATTTTTAAAGTTTGATGCCTATTTTATAGGAGCCCT-TTTTAG
* * * **
18667975 ATAGATTTTTTAAAGTTTGTTACCTATATTCATAGGAGCCCTTTCCAG
1 ATAGA-TTTTTAAAGTTTGATGCCTAT-TTTATAGGAGCCCTTTTTAG
* * * * * * * *
18668023 ACAAGTTTTTTAAAAAG-TTCATTGCCTATGTTCATAGAAGCCATTTCTAA
1 A-TAGATTTTT--AAAGTTTGA-TGCCTAT-TTTATAGGAGCCCTTTTTAG
* * * *
18668073 ATAGATTTTCTTTAAAGTTTGTTGCCTATGTTAATAAGAG-CCTTTTTCAA
1 ATAGA--TT-TTTAAAGTTTGATGCCTAT-TTTATAGGAGCCCTTTTT-AG
*
18668123 ATTGATTTTTAAAGTT
1 ATAGATTTTTAAAGTT
18668139 ACCTGCCTAT
Statistics
Matches: 320, Mismatches: 50, Indels: 44
0.77 0.12 0.11
Matches are distributed among these distances:
44 16 0.05
45 56 0.17
46 106 0.33
47 56 0.17
48 14 0.04
49 13 0.04
50 52 0.16
51 4 0.01
52 3 0.01
ACGTcount: A:0.29, C:0.12, G:0.13, T:0.45
Consensus pattern (46 bp):
ATAGATTTTTAAAGTTTGATGCCTATTTTATAGGAGCCCTTTTTAG
Found at i:18667853 original size:45 final size:46
Alignment explanation
Indices: 18667701--18668081 Score: 324
Period size: 46 Copynumber: 8.2 Consensus size: 46
18667691 GGCACCATAC
** * *
18667701 ATAGATCTTTTAAAGTTTAAT--CTATTTTATAAAAGCCCTTTTTGG
1 ATAGAT-TTTTAAAGTTTAATGCCTATTTTATAGGAGCCCTTTCTAG
18667746 ATAGATTTTTAAAGTTTAATGCCTATTTTATAGGAGCCCTTTTCTTA-
1 ATAGATTTTTAAAGTTTAATGCCTATTTTATAGGAGCCC-TTTC-TAG
* *
18667793 ATAGATTTTTTAAGTTTAATGCCTA-TTTATAGGAGCTCTTTCTAG
1 ATAGATTTTTAAAGTTTAATGCCTATTTTATAGGAGCCCTTTCTAG
* * *
18667838 ATAGATTTTTGAAGTTTGATGCCTATTTTATATGAGCCCTTTCTAG
1 ATAGATTTTTAAAGTTTAATGCCTATTTTATAGGAGCCCTTTCTAG
* * * *
18667884 ATAGATTTTTCAAAATTTGATACCTA-TTTATAGGAGCCTTTTCTAG
1 ATAGATTTTT-AAAGTTTAATGCCTATTTTATAGGAGCCCTTTCTAG
* * * * * ** *
18667930 ATAAATTTTTAAAGTTTGATTCATATTTTATAAGAGCTATTTC-AT
1 ATAGATTTTTAAAGTTTAATGCCTATTTTATAGGAGCCCTTTCTAG
** * * *
18667975 ATAGATTTTTTAAAGTTTGTTACCTATATTCATAGGAGCCCTTTCCAG
1 ATAGA-TTTTTAAAGTTTAATGCCTAT-TTTATAGGAGCCCTTTCTAG
* * * * * * * *
18668023 ACAAGTTTTTTAAAAAGTTCATTGCCTATGTTCATAGAAGCCATTTCTAA
1 A-TAGATTTTT--AAAGTTTAATGCCTAT-TTTATAGGAGCCCTTTCTAG
18668073 ATAGATTTT
1 ATAGATTTT
18668082 CTTTAAAGTT
Statistics
Matches: 278, Mismatches: 44, Indels: 24
0.80 0.13 0.07
Matches are distributed among these distances:
44 16 0.06
45 50 0.18
46 114 0.41
47 52 0.19
48 8 0.03
49 8 0.03
50 30 0.11
ACGTcount: A:0.30, C:0.12, G:0.13, T:0.45
Consensus pattern (46 bp):
ATAGATTTTTAAAGTTTAATGCCTATTTTATAGGAGCCCTTTCTAG
Found at i:18668868 original size:142 final size:140
Alignment explanation
Indices: 18668621--18669007 Score: 331
Period size: 144 Copynumber: 2.7 Consensus size: 140
18668611 GTATTTCAAA
** * * * *
18668621 AAGTGTAAAATTACCAAAACACCC-TTAGGGGTATTTTCATAATTTAGCTTTCTCAAAGTCATAT
1 AAGTGTAAAATTATAAAAATACCCGTTAGGGGTATTTTCGTAATTTA-CCTTCT-AAAGTCAAAT
* ** * * *
18668685 TTTTGTGAAAACTTCTAGATCAT-AAATGAGT-ATTTTATGAT-ATTTTTATACAC-T-AAAGAC
64 TTTTGTGAAATCTTC-AGATCATGATTTTA-TAATATT-TGATAATTTTTA-AAACTTCAAA-AC
18668745 CTAGATCGCACCTT-GG
124 CTAGATCGCACCTTAGG
* * *
18668761 TAGGTGTAAAGTTATAAAAATGCCCGTTAGGGGTATTTTCGTAATTTGACCTCTCTAAAGTCAAA
1 -AAGTGTAAAATTATAAAAATACCCGTTAGGGGTATTTTCGTAATTT-ACCT-TCTAAAGTCAAA
*
18668826 ATTTTGTGAAAGTCTTCAGATCATGATTTTATAATATTTGATAATTTTTAAAACTTTCAAAACCT
63 TTTTTGTGAAA-TCTTCAGATCATGATTTTATAATATTTGATAATTTTTAAAAC-TTCAAAACCT
* * *
18668891 TGATTGTACCTTAGG
126 AGATCGCACCTTAGG
* * * * * * **
18668906 AAGTGTAAAATTATCAAAATACTCTTTAGGGGTAATTTCGTAATTTAACCTTCCTGAGGTC-GTT
1 AAGTGTAAAATTATAAAAATACCCGTTAGGGGTATTTTCGTAATTT-ACCTT-CTAAAGTCAAAT
*
18668970 TTTTGTGAAACTTTTCAGATCATGATTTTATAATATTT
64 TTTTGTGAAA-TCTTCAGATCATGATTTTATAATATTT
18669008 AAAGATTTTT
Statistics
Matches: 200, Mismatches: 34, Indels: 22
0.78 0.13 0.09
Matches are distributed among these distances:
141 18 0.09
142 55 0.28
143 59 0.29
144 63 0.31
145 5 0.03
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.39
Consensus pattern (140 bp):
AAGTGTAAAATTATAAAAATACCCGTTAGGGGTATTTTCGTAATTTACCTTCTAAAGTCAAATTT
TTGTGAAATCTTCAGATCATGATTTTATAATATTTGATAATTTTTAAAACTTCAAAACCTAGATC
GCACCTTAGG
Found at i:18671397 original size:16 final size:18
Alignment explanation
Indices: 18671373--18671411 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
18671363 TTCTTATTTT
18671373 AAAAA-AAAAG-A-AGAA
1 AAAAAGAAAAGAATAGAA
18671388 AAAAAGAAAAGAATAGAA
1 AAAAAGAAAAGAATAGAA
18671406 AAAAAG
1 AAAAAG
18671412 GAATTAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.24
16 5 0.24
17 1 0.05
18 10 0.48
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (18 bp):
AAAAAGAAAAGAATAGAA
Found at i:18672427 original size:33 final size:33
Alignment explanation
Indices: 18672390--18672463 Score: 114
Period size: 33 Copynumber: 2.2 Consensus size: 33
18672380 AAAAGGGAAG
*
18672390 AGATTTAAGCC-AAGTTTAGCTTGCACTAAGATA
1 AGATTTAAGCCTAA-TTTAGCTAGCACTAAGATA
*
18672423 AGATTTAAGCCTAATTTAGCTAGCACTAAGATG
1 AGATTTAAGCCTAATTTAGCTAGCACTAAGATA
18672456 AGATTTAA
1 AGATTTAA
18672464 ACTAGATTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
33 36 0.95
34 2 0.05
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.31
Consensus pattern (33 bp):
AGATTTAAGCCTAATTTAGCTAGCACTAAGATA
Found at i:18680659 original size:135 final size:135
Alignment explanation
Indices: 18680417--18680675 Score: 331
Period size: 135 Copynumber: 1.9 Consensus size: 135
18680407 AAAAAAAAAG
* * * ** * **
18680417 GTTTTCTTTTGTAATAAATGGTGAAAAGAGTCTCGAAAGAGTTGTTGATCACTTTTAAAAATGAA
1 GTTTTCTTTTGTAATAAAAGGTGAAAAGAGTCCCAAAAGAGTTGTCAATCACTATTAAAAACAAA
* * * * *
18680482 CTCATCAAATAACTTTACACATTTTTCAAATTAGCTAATTTCACTCATCAAACATAACCCCTTAA
66 CCCATCAAATAACTTCACACACTTTTCAAATCAACTAATTTCACTCATCAAACATAACCCCTTAA
18680547 GAGGT
131 GAGGT
* *
18680552 GTTTTCTTTTGTAATAAAAGGTGAAGAGAGTCCCAAAAGAGTTAG-CAATCACTATTAGAAACAA
1 GTTTTCTTTTGTAATAAAAGGTGAAAAGAGTCCCAAAAGAGTT-GTCAATCACTATTAAAAACAA
* * * *
18680616 ACCCATCAAATATCTTCACACACTTTTCAAATCAATTGATTTCACTCATCAATCATAACC
65 ACCCATCAAATAACTTCACACACTTTTCAAATCAACTAATTTCACTCATCAAACATAACC
18680676 TTAAAGAGGC
Statistics
Matches: 104, Mismatches: 19, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
135 103 0.99
136 1 0.01
ACGTcount: A:0.37, C:0.19, G:0.12, T:0.32
Consensus pattern (135 bp):
GTTTTCTTTTGTAATAAAAGGTGAAAAGAGTCCCAAAAGAGTTGTCAATCACTATTAAAAACAAA
CCCATCAAATAACTTCACACACTTTTCAAATCAACTAATTTCACTCATCAAACATAACCCCTTAA
GAGGT
Found at i:18681230 original size:17 final size:18
Alignment explanation
Indices: 18681197--18681230 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
18681187 AAGAAAAAAA
18681197 AAAAGGAAAAAATGAAAT
1 AAAAGGAAAAAATGAAAT
*
18681215 AAAATGAAAAAA-GAAA
1 AAAAGGAAAAAATGAAA
18681231 ATTTTTTTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.76, C:0.00, G:0.15, T:0.09
Consensus pattern (18 bp):
AAAAGGAAAAAATGAAAT
Found at i:18681232 original size:18 final size:19
Alignment explanation
Indices: 18681192--18681232 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
18681182 CTAAAAAGAA
*
18681192 AAAAAAAAAGGAAAAAATG
1 AAAATAAAAGGAAAAAATG
*
18681211 -AAATAAAATGAAAAAA-G
1 AAAATAAAAGGAAAAAATG
18681228 AAAAT
1 AAAAT
18681233 TTTTTTGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
17 1 0.05
18 18 0.95
ACGTcount: A:0.78, C:0.00, G:0.12, T:0.10
Consensus pattern (19 bp):
AAAATAAAAGGAAAAAATG
Found at i:18681741 original size:28 final size:26
Alignment explanation
Indices: 18681710--18681795 Score: 88
Period size: 27 Copynumber: 3.2 Consensus size: 26
18681700 AGAAAAGGGA
18681710 AGAAAATAAAAGAAAGAACAAAAAAATG
1 AGAAAATAAAAGAAAGAA-AAAAAAA-G
*
18681738 AGAAAGA-AAAAGAAA-AAAAAAGAAG
1 AGAAA-ATAAAAGAAAGAAAAAAAAAG
*
18681763 -GAAAAATAGAAGAAAAGAAAAAAAAAG
1 AG-AAAATAAAAG-AAAGAAAAAAAAAG
18681790 AGAAAA
1 AGAAAA
18681796 ATGAACAATT
Statistics
Matches: 49, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
24 2 0.04
25 8 0.16
26 9 0.18
27 15 0.31
28 14 0.29
29 1 0.02
ACGTcount: A:0.78, C:0.01, G:0.17, T:0.03
Consensus pattern (26 bp):
AGAAAATAAAAGAAAGAAAAAAAAAG
Found at i:18681757 original size:10 final size:10
Alignment explanation
Indices: 18681691--18681796 Score: 63
Period size: 10 Copynumber: 10.7 Consensus size: 10
18681681 TCAACTCAAG
18681691 GAAAAAAAAA
1 GAAAAAAAAA
***
18681701 GAAAAGGGAA
1 GAAAAAAAAA
*
18681711 GAAAATAAAA
1 GAAAAAAAAA
* *
18681721 G-AAAGAACA
1 GAAAAAAAAA
**
18681730 -AAAAAATGA
1 GAAAAAAAAA
*
18681739 GAAAGAAAAA
1 GAAAAAAAAA
18681749 GAAAAAAAAA
1 GAAAAAAAAA
**
18681759 GAAGGAAAAA
1 GAAAAAAAAA
* * *
18681769 TAGAAGAAAA
1 GAAAAAAAAA
18681779 GAAAAAAAAA
1 GAAAAAAAAA
18681789 GAGAAAAA
1 GA-AAAAA
18681797 TGAACAATTG
Statistics
Matches: 68, Mismatches: 25, Indels: 5
0.69 0.26 0.05
Matches are distributed among these distances:
9 11 0.16
10 52 0.76
11 5 0.07
ACGTcount: A:0.77, C:0.01, G:0.19, T:0.03
Consensus pattern (10 bp):
GAAAAAAAAA
Found at i:18681760 original size:34 final size:30
Alignment explanation
Indices: 18681708--18681796 Score: 90
Period size: 30 Copynumber: 2.9 Consensus size: 30
18681698 AAAGAAAAGG
* *
18681708 GAAGAAAA-TAAAAGAAAGAACAAAAAAATGA
1 GAAGAAAAGAAAAAAAAAGAA-AAAAAAAT-A
**
18681739 GAAAGAAAAAGAAAAAAAAAGAAGGAAAAATA
1 G-AAG-AAAAGAAAAAAAAAGAAAAAAAAATA
*
18681771 GAAGAAAAGAAAAAAAAAGAGAAAAA
1 GAAGAAAAGAAAAAAAAAGAAAAAAA
18681797 TGAACAATTG
Statistics
Matches: 48, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
30 19 0.40
31 4 0.08
32 5 0.10
33 10 0.21
34 10 0.21
ACGTcount: A:0.78, C:0.01, G:0.18, T:0.03
Consensus pattern (30 bp):
GAAGAAAAGAAAAAAAAAGAAAAAAAAATA
Found at i:18681761 original size:20 final size:20
Alignment explanation
Indices: 18681691--18681796 Score: 74
Period size: 20 Copynumber: 5.3 Consensus size: 20
18681681 TCAACTCAAG
**
18681691 GAAAAAAAAAGAAA-AGGGAA
1 GAAAAAAAAAGAAAGA-AAAA
* *
18681711 GAAAATAAAAGAAAG-AACA
1 GAAAAAAAAAGAAAGAAAAA
**
18681730 -AAAAAATGAGAAAGAAAAA
1 GAAAAAAAAAGAAAGAAAAA
*
18681749 GAAAAAAAAAGAAGGAAAAA
1 GAAAAAAAAAGAAAGAAAAA
* * * *
18681769 TAGAAGAAAAGAAAAAAAAA
1 GAAAAAAAAAGAAAGAAAAA
18681789 GAGAAAAA
1 GA-AAAAA
18681797 TGAACAATTG
Statistics
Matches: 63, Mismatches: 19, Indels: 7
0.71 0.21 0.08
Matches are distributed among these distances:
18 11 0.17
19 4 0.06
20 45 0.71
21 3 0.05
ACGTcount: A:0.77, C:0.01, G:0.19, T:0.03
Consensus pattern (20 bp):
GAAAAAAAAAGAAAGAAAAA
Found at i:18681766 original size:24 final size:23
Alignment explanation
Indices: 18681717--18681784 Score: 59
Period size: 24 Copynumber: 2.8 Consensus size: 23
18681707 GGAAGAAAAT
*
18681717 AAAAGAAAGAACAAAAAAATGAGA
1 AAAATAAAGAA-AAAAAAATGAGA
18681741 AAGAA-AAAGAAAAAAAAA-GAAGGA
1 AA-AATAAAGAAAAAAAAATG-A-GA
18681765 AAAATAGAAGAAAAGAAAAA
1 AAAATA-AAGAAAA-AAAAA
18681785 AAAAGAGAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
22 1 0.03
23 10 0.26
24 13 0.34
25 9 0.24
26 5 0.13
ACGTcount: A:0.78, C:0.01, G:0.18, T:0.03
Consensus pattern (23 bp):
AAAATAAAGAAAAAAAAATGAGA
Found at i:18683633 original size:35 final size:35
Alignment explanation
Indices: 18683587--18683704 Score: 107
Period size: 35 Copynumber: 3.3 Consensus size: 35
18683577 TAAGTTTGAA
18683587 TTTCATTAAAACTTTCTCGATGATGAAATCTAACT
1 TTTCATTAAAACTTTCTCGATGATGAAATCTAACT
* * *
18683622 TTTCATTAAAACATTCTTGATGGTGAAAT-TCAACCT
1 TTTCATTAAAACTTTCTCGATGATGAAATCT-AA-CT
* * * *
18683658 TTT-TTTAAAACTCTTTCCCGAAGATGAAA-CTTGACT
1 TTTCATTAAAA--CTTTCTCGATGATGAAATC-TAACT
18683694 TTTCATTAAAA
1 TTTCATTAAAA
18683705 TTCTCCTGGT
Statistics
Matches: 65, Mismatches: 11, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
34 1 0.02
35 34 0.52
36 10 0.15
37 19 0.29
38 1 0.02
ACGTcount: A:0.34, C:0.17, G:0.09, T:0.40
Consensus pattern (35 bp):
TTTCATTAAAACTTTCTCGATGATGAAATCTAACT
Found at i:18684602 original size:48 final size:49
Alignment explanation
Indices: 18684500--18684657 Score: 160
Period size: 48 Copynumber: 3.2 Consensus size: 49
18684490 GACTTTCAAA
* * * * *
18684500 CCTTTTAAAAAAGAGATTTTTAAAATTTATTGCCTAT-TTTCATAGGAGC
1 CCTTTTCAAAATGAGATTTTT-AAGTTTGTTGCCTATCTTTCATAAGAGC
*
18684549 CCTTTTCAAAATGAGATTTTTAAGTTTGTTGCCTATCTTT-ATAAGAGG
1 CCTTTTCAAAATGAGATTTTTAAGTTTGTTGCCTATCTTTCATAAGAGC
* * * *
18684597 CCTTTTCAAAATTAGATTTTCAAAGTTTTGTTACCTATC-TTCATATGAGC
1 CCTTTTCAAAATGAGATTTT-TAAG-TTTGTTGCCTATCTTTCATAAGAGC
* *
18684647 CATTTTAAAAA
1 CCTTTTCAAAA
18684658 AAAAAAAAGC
Statistics
Matches: 92, Mismatches: 13, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
48 38 0.41
49 27 0.29
50 27 0.29
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.42
Consensus pattern (49 bp):
CCTTTTCAAAATGAGATTTTTAAGTTTGTTGCCTATCTTTCATAAGAGC
Found at i:18687040 original size:29 final size:28
Alignment explanation
Indices: 18686995--18687054 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 28
18686985 ATGAAATCCC
18686995 AAATTTGAAACCTTAAACCCTAAAACCCT
1 AAATTTGAAACCTTAAACCCT-AAACCCT
18687024 AAATTTGAAA-CTCTAAACCCTAAACCCT
1 AAATTTGAAACCT-TAAACCCTAAACCCT
18687052 AAA
1 AAA
18687055 ACCAATCCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
28 12 0.40
29 18 0.60
ACGTcount: A:0.47, C:0.27, G:0.03, T:0.23
Consensus pattern (28 bp):
AAATTTGAAACCTTAAACCCTAAACCCT
Found at i:18691334 original size:15 final size:15
Alignment explanation
Indices: 18691311--18691340 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
18691301 AAATTCTAAT
18691311 CATTGTAAGAAAATA
1 CATTGTAAGAAAATA
*
18691326 CATTTTAAGAAAATA
1 CATTGTAAGAAAATA
18691341 AGTTATTGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.53, C:0.07, G:0.10, T:0.30
Consensus pattern (15 bp):
CATTGTAAGAAAATA
Found at i:18691698 original size:48 final size:47
Alignment explanation
Indices: 18691637--18691728 Score: 123
Period size: 48 Copynumber: 1.9 Consensus size: 47
18691627 ATAAGCCTTA
* **
18691637 TTTTTAAAAGTTGTGTGCCTTTGTGTTGAA-TGAACCTTTAATTTCTT
1 TTTTTAAAAGTTGTGCGCCTTCATGTTGAAGT-AACCTTTAATTTCTT
*
18691684 TTTTTAAGAAGTTGTGCGCCTTCATGTTGAAGTAGCCTTTAATTT
1 TTTTTAA-AAGTTGTGCGCCTTCATGTTGAAGTAACCTTTAATTT
18691729 TTAAAGTTAC
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
47 7 0.18
48 31 0.79
49 1 0.03
ACGTcount: A:0.22, C:0.12, G:0.18, T:0.48
Consensus pattern (47 bp):
TTTTTAAAAGTTGTGCGCCTTCATGTTGAAGTAACCTTTAATTTCTT
Found at i:18693312 original size:57 final size:57
Alignment explanation
Indices: 18693190--18693315 Score: 173
Period size: 57 Copynumber: 2.2 Consensus size: 57
18693180 TTATGAATTC
* * * *
18693190 TACCAAATTATTGAAGAATTTCATAGTAAAATTTCATAAAAAATAAATTTTTAATCT
1 TACCAAACTATTAAAGAATTTCATAATAAAATTTCATAAAAAATAAATTTTTAATCA
** *
18693247 TATTAAACTATTAAAGAATTTCATAATAAAATTTCATAAAAAAT-AATTTTTCGATCA
1 TACCAAACTATTAAAGAATTTCATAATAAAATTTCATAAAAAATAAATTTTT-AATCA
18693304 TACCAAACTATT
1 TACCAAACTATT
18693316 GGAGGACTTA
Statistics
Matches: 59, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
56 7 0.12
57 52 0.88
ACGTcount: A:0.48, C:0.10, G:0.04, T:0.38
Consensus pattern (57 bp):
TACCAAACTATTAAAGAATTTCATAATAAAATTTCATAAAAAATAAATTTTTAATCA
Found at i:18698281 original size:25 final size:26
Alignment explanation
Indices: 18698253--18698305 Score: 67
Period size: 25 Copynumber: 2.1 Consensus size: 26
18698243 TAAAAATTTC
*
18698253 AATTTAAAG-TAATGAGTAA-AATAAT
1 AATTTAAAGATAAT-AATAATAATAAT
18698278 AA-TTAAAGATAATAATAATAATAAT
1 AATTTAAAGATAATAATAATAATAAT
18698303 AAT
1 AAT
18698306 AAGTAAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
24 10 0.42
25 14 0.58
ACGTcount: A:0.60, C:0.00, G:0.08, T:0.32
Consensus pattern (26 bp):
AATTTAAAGATAATAATAATAATAAT
Found at i:18698331 original size:28 final size:27
Alignment explanation
Indices: 18698270--18698393 Score: 84
Period size: 28 Copynumber: 4.6 Consensus size: 27
18698260 AGTAATGAGT
* *
18698270 AAAATAATAATTAAAGATAATAATAATA
1 AAAATAATAAGTAAAAATAA-AATAATA
*
18698298 ATAATAATAAGTAAAAATAAAA-AATCTA
1 AAAATAATAAGTAAAAATAAAATAA--TA
*
18698326 AAAATAA-AAG-GAAAATAAAATAGA-A
1 AAAATAATAAGTAAAAATAAAATA-ATA
18698351 AAAATAA-AA-T-AAAATAAAATCAA-A
1 AAAATAATAAGTAAAAATAAAAT-AATA
*
18698375 ACAAAAAATAAGATAAAAA
1 A-AAATAATAAG-TAAAAA
18698394 AAGAAAAACC
Statistics
Matches: 79, Mismatches: 6, Indels: 21
0.75 0.06 0.20
Matches are distributed among these distances:
24 13 0.16
25 16 0.20
26 13 0.16
27 6 0.08
28 27 0.34
29 4 0.05
ACGTcount: A:0.73, C:0.02, G:0.05, T:0.19
Consensus pattern (27 bp):
AAAATAATAAGTAAAAATAAAATAATA
Found at i:18698382 original size:23 final size:24
Alignment explanation
Indices: 18698325--18698401 Score: 77
Period size: 24 Copynumber: 3.2 Consensus size: 24
18698315 TAAAAAATCT
*
18698325 AAAAATAAAAGGAAAATAAAATAGA
1 AAAAATAAAA-TAAAATAAAATAGA
18698350 AAAAATAAAATAAAATAAAATCA-A
1 AAAAATAAAATAAAATAAAAT-AGA
* * *
18698374 AACAA-AAAATAAGATAAAAAAAGA
1 AAAAATAAAATAAAAT-AAAATAGA
18698398 AAAA
1 AAAA
18698402 CCTGTGATCG
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
23 10 0.23
24 23 0.52
25 11 0.25
ACGTcount: A:0.79, C:0.03, G:0.06, T:0.12
Consensus pattern (24 bp):
AAAAATAAAATAAAATAAAATAGA
Found at i:18699807 original size:84 final size:84
Alignment explanation
Indices: 18699484--18699814 Score: 276
Period size: 84 Copynumber: 3.9 Consensus size: 84
18699474 ACCCGAAGGT
* * * * * * * * *
18699484 CTTAAAGATTACGCTCAAAGGTCTTACAAATCTCAACTCTGATATAGATTCCGCTAGAAATATTT
1 CTTAGAGATTACGCTCGAAGGTCTTACAAATCTTAACTCTAAAATAGATTCAGCTCGAAAAACTT
* * * *
18699549 ACAAATCTTACCTGGAGGA
66 ACGAATCTTGCCTGAATGA
* * * ** * *
18699568 CCTAGAAATTACGCTTGAAGGTCTTACAAATCTCGA-TCTTAAAATAGATTTAGCTCGAAAGACT
1 CTTAGAGATTACGCTCGAAGGTCTTACAAATCTTAACTC-TAAAATAGATTCAGCTCGAAAAACT
*
18699632 TACAAATCTTGCCT-AATGGA
65 TACGAATCTTGCCTGAAT-GA
* * * * * * *
18699652 CTTCA-AAATTATGC-CTAGAGGTCTTTCAAATCTTGACTCTAAAATAGATTTAGCTC-AGAAGA
1 CTT-AGAGATTACGCTCGA-AGGTCTTACAAATCTTAACTCTAAAATAGATTCAGCTCGA-AAAA
18699714 CTTACGAATCTTGCCTGAATGA
63 CTTACGAATCTTGCCTGAATGA
* * * *
18699736 CTTAGAGATTAAGCTCGAAGGTCTTACAAATTTTAACTTTAAAATAGATTCAACTCGAAAAACTT
1 CTTAGAGATTACGCTCGAAGGTCTTACAAATCTTAACTCTAAAATAGATTCAGCTCGAAAAACTT
* *
18699801 ATGAATCTTACCTG
66 ACGAATCTTGCCTG
18699815 GAGAACTTGG
Statistics
Matches: 202, Mismatches: 35, Indels: 20
0.79 0.14 0.08
Matches are distributed among these distances:
83 6 0.03
84 187 0.93
85 9 0.04
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.31
Consensus pattern (84 bp):
CTTAGAGATTACGCTCGAAGGTCTTACAAATCTTAACTCTAAAATAGATTCAGCTCGAAAAACTT
ACGAATCTTGCCTGAATGA
Found at i:18699828 original size:84 final size:81
Alignment explanation
Indices: 18699552--18699888 Score: 215
Period size: 84 Copynumber: 4.1 Consensus size: 81
18699542 AATATTTACA
* * * * * * *
18699552 AATCTTACCTGGAGGACCTAGAAATTACGCTTGAAGGTCTTACAAATCT-CGATCTTAAAATAGA
1 AATCTTACCTGAATGACTTAGAGATTAAGCCTGAAGGTCTTACAAATTTAC--TC-TAAAATAGA
* * * **
18699616 TTTAGCTCGAAAGACTTACA
63 TTCAACTC-AAAAACTTATG
* * * *
18699636 AATCTTGCCT-AATGGACTTCA-AAATTATGCCT-AGAGGTCTTTCAAATCTTGACTCTAAAATA
1 AATCTTACCTGAAT-GACTT-AGAGATTAAGCCTGA-AGGTCTTACAAAT-TT-ACTCTAAAATA
* * * *
18699698 GATTTAGCTCAGAAGACTTACG
61 GATTCAACTCA-AAAACTTATG
* *
18699720 AATCTTGCCTGAATGACTTAGAGATTAAG-CTCGAAGGTCTTACAAATTTTAACTTTAAAATAGA
1 AATCTTACCTGAATGACTTAGAGATTAAGCCT-GAAGGTCTTACAAA-TTT-ACTCTAAAATAGA
18699784 TTCAACTCGAAAAACTTATG
63 TTCAACTC-AAAAACTTATG
* * * * *
18699804 AATCTTACCTGGA-GAACTTGGAGATTATGCCTGAAAGTTTTACAAA--T-CTCTAAAATAGATT
1 AATCTTACCTGAATG-ACTTAGAGATTAAGCCTGAAGGTCTTACAAATTTACTCTAAAATAGATT
*
18699865 CAACTCAAAAGACGTATG
65 CAACTCAAAA-ACTTATG
18699883 AATCTT
1 AATCTT
18699889 GCTCGGAGAT
Statistics
Matches: 211, Mismatches: 26, Indels: 37
0.77 0.09 0.14
Matches are distributed among these distances:
78 4 0.02
79 31 0.15
81 1 0.00
83 7 0.03
84 155 0.73
85 12 0.06
87 1 0.00
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (81 bp):
AATCTTACCTGAATGACTTAGAGATTAAGCCTGAAGGTCTTACAAATTTACTCTAAAATAGATTC
AACTCAAAAACTTATG
Found at i:18711927 original size:22 final size:24
Alignment explanation
Indices: 18711901--18711958 Score: 68
Period size: 23 Copynumber: 2.5 Consensus size: 24
18711891 AAAAAATGGA
* *
18711901 TTTTTCAAAATAA-TTAT-TTGTTT
1 TTTTTCAAAA-AATTTATAATGTAT
18711924 TTTTTCAAAAAATTTATAATG-AT
1 TTTTTCAAAAAATTTATAATGTAT
18711947 TTTTTCAAAAAA
1 TTTTTCAAAAAA
18711959 AAAATATAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
22 2 0.06
23 27 0.87
24 2 0.06
ACGTcount: A:0.40, C:0.05, G:0.03, T:0.52
Consensus pattern (24 bp):
TTTTTCAAAAAATTTATAATGTAT
Found at i:18712063 original size:17 final size:15
Alignment explanation
Indices: 18712033--18712085 Score: 56
Period size: 16 Copynumber: 3.5 Consensus size: 15
18712023 TTTGGCAAGA
18712033 AGAAAAAATAAAAAT
1 AGAAAAAATAAAAAT
18712048 AGAATAAAATAGAAAAT
1 AGAA-AAAATA-AAAAT
* *
18712065 AGAGAAGA-AAAAA-
1 AGAAAAAATAAAAAT
18712078 AGAAAAAA
1 AGAAAAAA
18712086 ATGAAAAGTA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
13 6 0.19
14 4 0.12
15 5 0.16
16 9 0.28
17 8 0.25
ACGTcount: A:0.77, C:0.00, G:0.13, T:0.09
Consensus pattern (15 bp):
AGAAAAAATAAAAAT
Found at i:18712076 original size:30 final size:29
Alignment explanation
Indices: 18712042--18712105 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 29
18712032 AAGAAAAAAT
* *
18712042 AAAAATAGAATAAAATAGAAAA-TAGAGAAG
1 AAAAAAAGAAAAAAAT-GAAAAGTA-AGAAG
18712072 AAAAAAAGAAAAAAATGAAAAGTAAGAAG
1 AAAAAAAGAAAAAAATGAAAAGTAAGAAG
18712101 AAAAA
1 AAAAA
18712106 CTTATAGTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
29 15 0.48
30 16 0.52
ACGTcount: A:0.75, C:0.00, G:0.16, T:0.09
Consensus pattern (29 bp):
AAAAAAAGAAAAAAATGAAAAGTAAGAAG
Found at i:18712235 original size:18 final size:17
Alignment explanation
Indices: 18712191--18712264 Score: 60
Period size: 18 Copynumber: 4.1 Consensus size: 17
18712181 GAATATAAAT
18712191 TTATTTTTAAAAAA-AA
1 TTATTTTTAAAAAATAA
* *
18712207 GTTAATATTAAAAAATCAA
1 -TTATTTTTAAAAAAT-AA
* *
18712226 TTATTTTTAATAAGTAAA
1 TTATTTTTAAAAAAT-AA
18712244 TTATTTTTCAAAAAAGTAA
1 TTATTTTT-AAAAAA-TAA
18712263 TT
1 TT
18712265 TTTATCAAAA
Statistics
Matches: 44, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
17 12 0.27
18 21 0.48
19 10 0.23
20 1 0.02
ACGTcount: A:0.50, C:0.03, G:0.04, T:0.43
Consensus pattern (17 bp):
TTATTTTTAAAAAATAA
Found at i:18712274 original size:18 final size:20
Alignment explanation
Indices: 18712237--18712274 Score: 53
Period size: 18 Copynumber: 2.0 Consensus size: 20
18712227 TATTTTTAAT
*
18712237 AAGTAAATTATTTTTCAAAA
1 AAGTAAATTATTTATCAAAA
18712257 AAGT-AATT-TTTATCAAAA
1 AAGTAAATTATTTATCAAAA
18712275 CTATATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 9 0.53
19 4 0.24
20 4 0.24
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.39
Consensus pattern (20 bp):
AAGTAAATTATTTATCAAAA
Found at i:18712337 original size:21 final size:20
Alignment explanation
Indices: 18712295--18712349 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
18712285 TATTTATTAA
*
18712295 AAAAAAGAGAGAAAGAAAGG
1 AAAAAAGAGAGAAAAAAAGG
18712315 AAAAAAGA-ACGAAAAAAAGG
1 AAAAAAGAGA-GAAAAAAAGG
*
18712335 GAAAAAG-GA-AAAAAA
1 AAAAAAGAGAGAAAAAA
18712350 TAGTTTGAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
18 6 0.19
19 1 0.03
20 24 0.77
ACGTcount: A:0.75, C:0.02, G:0.24, T:0.00
Consensus pattern (20 bp):
AAAAAAGAGAGAAAAAAAGG
Found at i:18715878 original size:13 final size:13
Alignment explanation
Indices: 18715857--18715950 Score: 54
Period size: 13 Copynumber: 7.1 Consensus size: 13
18715847 ACATTTTTAT
18715857 TTTATTTATATATA
1 TTTA-TTATATATA
18715871 TTTA-T-TAT-TA
1 TTTATTATATATA
18715881 -TTATTATATATA
1 TTTATTATATATA
* *
18715893 TTTCTTATGTATTTA
1 TTTATTA--TATATA
* *
18715908 CTATTATTATTTTTA
1 -T-TTATTATATATA
18715923 TTTATTAT-TACTA
1 TTTATTATATA-TA
18715936 TTTATTAATATATA
1 TTTATT-ATATATA
18715950 T
1 T
18715951 ATCCTTATTA
Statistics
Matches: 64, Mismatches: 5, Indels: 22
0.70 0.05 0.24
Matches are distributed among these distances:
9 3 0.05
10 3 0.05
11 6 0.09
12 4 0.06
13 20 0.31
14 10 0.16
15 12 0.19
16 1 0.02
17 5 0.08
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (13 bp):
TTTATTATATATA
Found at i:18715990 original size:43 final size:44
Alignment explanation
Indices: 18715911--18715991 Score: 107
Period size: 43 Copynumber: 1.9 Consensus size: 44
18715901 GTATTTACTA
*
18715911 TTATTATTTTTATTTATTATTACTATTTATTAATATATATATCC
1 TTATTATTTTTATTTATTATTAATATTTATTAATATATATATCC
*
18715955 TTATTATTTTT-TTT-TCTGTTAATATTTA-T-ATATATAT
1 TTATTATTTTTATTTAT-TATTAATATTTATTAATATATAT
18715992 TTATCTGATT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
41 8 0.24
42 2 0.06
43 13 0.38
44 11 0.32
ACGTcount: A:0.30, C:0.05, G:0.01, T:0.64
Consensus pattern (44 bp):
TTATTATTTTTATTTATTATTAATATTTATTAATATATATATCC
Found at i:18715998 original size:26 final size:26
Alignment explanation
Indices: 18715969--18716029 Score: 74
Period size: 26 Copynumber: 2.3 Consensus size: 26
18715959 TATTTTTTTT
18715969 TCTGTTAATAT-TTAT-ATATATATTTA
1 TCTGTTAATATATTATAAT-TA-ATTTA
18715995 TCTGATT-ATATATTATAATTAATTTA
1 TCTG-TTAATATATTATAATTAATTTA
18716021 TCTGTTAAT
1 TCTGTTAAT
18716030 TTTTTGGTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
25 2 0.06
26 19 0.61
27 8 0.26
28 2 0.06
ACGTcount: A:0.34, C:0.05, G:0.05, T:0.56
Consensus pattern (26 bp):
TCTGTTAATATATTATAATTAATTTA
Found at i:18716070 original size:14 final size:15
Alignment explanation
Indices: 18716043--18716090 Score: 55
Period size: 14 Copynumber: 3.3 Consensus size: 15
18716033 TTGGTTTATC
*
18716043 TTAT-TATTTATTTA
1 TTATATATTTTTTTA
18716057 TTA-ATATTTTTTTA
1 TTATATATTTTTTTA
*
18716071 TTATTTGATTTTTTTA
1 TTATAT-ATTTTTTTA
18716087 TTAT
1 TTAT
18716091 TTTTCTAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
14 15 0.52
15 1 0.03
16 13 0.45
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (15 bp):
TTATATATTTTTTTA
Found at i:18716083 original size:16 final size:16
Alignment explanation
Indices: 18716062--18716092 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
18716052 ATTTATTAAT
18716062 ATTTTTTTATTATTTG
1 ATTTTTTTATTATTTG
18716078 ATTTTTTTATTATTT
1 ATTTTTTTATTATTT
18716093 TTCTAATTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.77
Consensus pattern (16 bp):
ATTTTTTTATTATTTG
Found at i:18716984 original size:21 final size:21
Alignment explanation
Indices: 18716960--18717032 Score: 85
Period size: 21 Copynumber: 3.3 Consensus size: 21
18716950 TTTATTTTTA
18716960 TCTTTATTTTTATTTTACTTT
1 TCTTTATTTTTATTTTACTTT
18716981 TCTTTATTTTTATTTTCACTCTCT
1 TCTTTATTTTTATTTT-ACT-T-T
*
18717005 TTTTTATTTTATTATTTTA-TTT
1 TCTTTA-TTT-TTATTTTACTTT
18717027 TCTTTA
1 TCTTTA
18717033 AATAAAATTC
Statistics
Matches: 45, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
21 16 0.36
22 9 0.20
23 2 0.04
24 7 0.16
25 4 0.09
26 7 0.16
ACGTcount: A:0.15, C:0.11, G:0.00, T:0.74
Consensus pattern (21 bp):
TCTTTATTTTTATTTTACTTT
Found at i:18716994 original size:39 final size:37
Alignment explanation
Indices: 18716946--18717027 Score: 103
Period size: 39 Copynumber: 2.2 Consensus size: 37
18716936 ATTTGTTTAA
* * *
18716946 TATTTTTATTTTTA-TCTTTATTTTTATTTTACTTTTCTT
1 TATTTTTATTTTCACTCTCT-TTTTTATTTTA-TTAT-TT
18716985 TATTTTTATTTTCACTCTCTTTTTTATTTTATTATTT
1 TATTTTTATTTTCACTCTCTTTTTTATTTTATTATTT
18717022 TATTTT
1 TATTTT
18717028 CTTTAAATAA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
37 8 0.21
38 3 0.08
39 24 0.62
40 4 0.10
ACGTcount: A:0.16, C:0.09, G:0.00, T:0.76
Consensus pattern (37 bp):
TATTTTTATTTTCACTCTCTTTTTTATTTTATTATTT
Found at i:18717014 original size:6 final size:6
Alignment explanation
Indices: 18716946--18716996 Score: 57
Period size: 6 Copynumber: 8.0 Consensus size: 6
18716936 ATTTGTTTAA
* *
18716946 TATTTT TATTTT TATCTT TATTTT TATTTT ACTTTTCTT TATTTT TATTTT
1 TATTTT TATTTT TATTTT TATTTT TATTTT --TATT-TT TATTTT TATTTT
18716997 CACTCTCTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
6 30 0.79
7 3 0.08
8 3 0.08
9 2 0.05
ACGTcount: A:0.16, C:0.06, G:0.00, T:0.78
Consensus pattern (6 bp):
TATTTT
Found at i:18717180 original size:119 final size:119
Alignment explanation
Indices: 18717054--18717322 Score: 459
Period size: 119 Copynumber: 2.3 Consensus size: 119
18717044 AAAAAAAATA
*
18717054 TTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAAAGTTTCTAAAAAATATTTTTG
1 TTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAAAGTTTCCAAAAAATATTTTTG
* * *
18717119 GGAAAAAGTTGAAAGTATCAATTTTCCTTAAGAATAAATTTTCAAAAAA-GGTTT
66 GGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAACAAA-TTTCAAAAAAGGGGTT
* *
18717173 TTTTTGAGGAAAAATTGAAAGTATCAATTTTCCTTGAAATTAAAAGTTTCCAAAAAATATTTTTG
1 TTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAAAGTTTCCAAAAAATATTTTTG
*
18717238 GGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAACAAATTTCAAAAAAGGGGTT
66 GGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAACAAATTTCAAAAAAGGGGTT
18717292 TTTTTGAGGAAAAGTTGAAAGTATCAATTTT
1 TTTTTGAGGAAAAGTTGAAAGTATCAATTTT
18717323 TCCCTGTACA
Statistics
Matches: 141, Mismatches: 8, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
118 10 0.07
119 131 0.93
ACGTcount: A:0.41, C:0.07, G:0.15, T:0.36
Consensus pattern (119 bp):
TTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAAAGTTTCCAAAAAATATTTTTG
GGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAACAAATTTCAAAAAAGGGGTT
Found at i:18717205 original size:60 final size:57
Alignment explanation
Indices: 18717046--18717322 Score: 319
Period size: 59 Copynumber: 4.7 Consensus size: 57
18717036 AAAATTCAAA
* * *
18717046 AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAAAGTTTC
1 AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCT-TAAAATAAAATTTTC
18717104 TAAAAAATATTTTTG-GGAAAAAGTTGAAAGTATCAATTTTCCTTAAGAAT-AAATTTTC
1 -AAAAAATATTTTTGAGG-AAAAGTTGAAAGTATCAATTTTCCTTAA-AATAAAATTTTC
* * * *
18717162 AAAAAAGGTTTTTTTTGAGGAAAAATTGAAAGTATCAATTTTCCTTGAAATTAAAAGTTTCC
1 AAAAAA---TATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTT-AAAATAAAA-TTTTC
*
18717224 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAA-ACAAA-TTTC
1 AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAATA-AAATTTTC
*
18717280 AAAAAAGGGGTTTTTTTGAGGAAAAGTTGAAAGTATCAATTTT
1 AAAAAA----TATTTTTGAGGAAAAGTTGAAAGTATCAATTTT
18717323 TCCCTGTACA
Statistics
Matches: 190, Mismatches: 14, Indels: 27
0.82 0.06 0.12
Matches are distributed among these distances:
56 9 0.05
57 7 0.04
58 17 0.09
59 75 0.39
60 65 0.34
61 7 0.04
62 10 0.05
ACGTcount: A:0.42, C:0.07, G:0.15, T:0.36
Consensus pattern (57 bp):
AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAATAAAATTTTC
Found at i:18727511 original size:9 final size:8
Alignment explanation
Indices: 18727490--18727536 Score: 78
Period size: 8 Copynumber: 5.9 Consensus size: 8
18727480 TATGCTTAAA
18727490 GAAAAAAT
1 GAAAAAAT
18727498 GAAAAAAT
1 GAAAAAAT
18727506 GAAAAAAAT
1 G-AAAAAAT
18727515 GAAAAAAT
1 GAAAAAAT
18727523 GAAAAAA-
1 GAAAAAAT
18727530 GAAAAAA
1 GAAAAAA
18727537 AGAGTGAATG
Statistics
Matches: 38, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
7 7 0.18
8 23 0.61
9 8 0.21
ACGTcount: A:0.79, C:0.00, G:0.13, T:0.09
Consensus pattern (8 bp):
GAAAAAAT
Found at i:18727518 original size:25 final size:24
Alignment explanation
Indices: 18727490--18727537 Score: 87
Period size: 25 Copynumber: 2.0 Consensus size: 24
18727480 TATGCTTAAA
18727490 GAAAAAATGAAAAAATGAAAAAAAT
1 GAAAAAATGAAAAAA-GAAAAAAAT
18727515 GAAAAAATGAAAAAAGAAAAAAA
1 GAAAAAATGAAAAAAGAAAAAAA
18727538 GAGTGAATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 8 0.35
25 15 0.65
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.08
Consensus pattern (24 bp):
GAAAAAATGAAAAAAGAAAAAAAT
Found at i:18727537 original size:8 final size:8
Alignment explanation
Indices: 18727487--18727539 Score: 63
Period size: 8 Copynumber: 6.6 Consensus size: 8
18727477 TACTATGCTT
18727487 AAAGAAAA
1 AAAGAAAA
*
18727495 AATGAAAA
1 AAAGAAAA
*
18727503 AATGAAAA
1 AAAGAAAA
18727511 AAATGAAAA
1 AAA-GAAAA
*
18727520 AATG-AAA
1 AAAGAAAA
18727527 AAAGAAAA
1 AAAGAAAA
18727535 AAAGA
1 AAAGA
18727540 GTGAATGAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
7 6 0.15
8 26 0.67
9 7 0.18
ACGTcount: A:0.79, C:0.00, G:0.13, T:0.08
Consensus pattern (8 bp):
AAAGAAAA
Found at i:18727537 original size:17 final size:17
Alignment explanation
Indices: 18727491--18727529 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
18727481 ATGCTTAAAG
18727491 AAAAAATGAAAAAATGA
1 AAAAAATGAAAAAATGA
18727508 AAAAAATGAAAAAATGA
1 AAAAAATGAAAAAATGA
18727525 AAAAA
1 AAAAA
18727530 GAAAAAAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.79, C:0.00, G:0.10, T:0.10
Consensus pattern (17 bp):
AAAAAATGAAAAAATGA
Found at i:18728593 original size:41 final size:41
Alignment explanation
Indices: 18728535--18728874 Score: 451
Period size: 41 Copynumber: 8.3 Consensus size: 41
18728525 ATGATTGTCA
*
18728535 AGGAGTAATTATA-TTTCCAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATT-TACTTTCCAAAGTCGTGGTGCCTCTGTTTAG
*
18728576 AGGAGCAATTTACTTTCCAAAGTTGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAG
**
18728617 AGGAGCAATTTACTTTTTAAAGTTTCGT--TGCCTCTGTTTAG
1 AGGAGCAATTTACTTTCCAAAG--TCGTGGTGCCTCTGTTTAG
* *
18728658 AGGAGCAATTTATTTTCCAAAGTTTCAT--TGCCTCTGTTTAG
1 AGGAGCAATTTACTTTCCAAAG--TCGTGGTGCCTCTGTTTAG
* *
18728699 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTTTGTTTAG
1 AGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAG
*
18728740 AGGAGCAATTTATTTTCCAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAG
* * *
18728781 AGGAGCAATTTATTTTTCAAAGTCGTGGTTGCCTCTATTTAG
1 AGGAGCAATTTACTTTCCAAAGTCGTGG-TGCCTCTGTTTAG
*
18728823 AGGAGCAATTTACTTTTCAAAGT-GATGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTCCAAAGTCG-TGGTGCCTCTGTTTAG
18728864 AGGAGC-ATTTA
1 AGGAGCAATTTA
18728875 TTTTTGAAGT
Statistics
Matches: 272, Mismatches: 20, Indels: 15
0.89 0.07 0.05
Matches are distributed among these distances:
39 3 0.01
40 7 0.03
41 222 0.82
42 37 0.14
43 3 0.01
ACGTcount: A:0.24, C:0.15, G:0.23, T:0.39
Consensus pattern (41 bp):
AGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAG
Found at i:18729123 original size:46 final size:44
Alignment explanation
Indices: 18728986--18729182 Score: 202
Period size: 45 Copynumber: 4.4 Consensus size: 44
18728976 ATAAATAAAA
* * * *
18728986 AGCCTCTGATTAGAGGAGCTTTGTTTATCTTTCCAAAATTTGTTG
1 AGCCTCTGATTAGAGGAGCATTGTTTATTTTTCC-AAAGTCGTTG
* * *
18729031 AGCCTCTGATTAAATGAGCCA---TTTATTTTTCCAAAGTCGTCG
1 AGCCTCTGATTAGAGGAG-CATTGTTTATTTTTCCAAAGTCGTTG
* *
18729073 AGCCTCTGATTAGAGGAGCATTGTTTATTCATTTTCAAAGTCGTTA
1 AGCCTCTGATTAGAGGAGCATTGTTTATT--TTTCCAAAGTCGTTG
* * * *
18729119 AGCCTTTGATTAGAGGAGTATTGTTTATGTTTTTCAAAATCGTTG
1 AGCCTCTGATTAGAGGAGCATTGTTTAT-TTTTCCAAAGTCGTTG
*
18729164 AGCCTCTGCTTAGAGGAGC
1 AGCCTCTGATTAGAGGAGC
18729183 CTTGATCAAA
Statistics
Matches: 126, Mismatches: 19, Indels: 14
0.79 0.12 0.09
Matches are distributed among these distances:
41 2 0.02
42 23 0.18
43 10 0.08
44 6 0.05
45 45 0.36
46 39 0.31
47 1 0.01
ACGTcount: A:0.24, C:0.16, G:0.21, T:0.39
Consensus pattern (44 bp):
AGCCTCTGATTAGAGGAGCATTGTTTATTTTTCCAAAGTCGTTG
Found at i:18729471 original size:22 final size:20
Alignment explanation
Indices: 18729430--18729476 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
18729420 ATTATATATA
18729430 TATTTTTCTTATGTATTTAC
1 TATTTTTCTTATGTATTTAC
* *
18729450 TATTTTTTTTATTTATTATTAC
1 TATTTTTCTTATGTA-T-TTAC
18729472 TATTT
1 TATTT
18729477 ATTAATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 13 0.57
21 1 0.04
22 9 0.39
ACGTcount: A:0.21, C:0.06, G:0.02, T:0.70
Consensus pattern (20 bp):
TATTTTTCTTATGTATTTAC
Found at i:18729535 original size:26 final size:26
Alignment explanation
Indices: 18729506--18729566 Score: 65
Period size: 26 Copynumber: 2.3 Consensus size: 26
18729496 ATTATTTTTT
18729506 TCTGTTAATAT-TTAT-ATATATATTTA
1 TCTGTTAATATATTATAAT-TA-ATTTA
18729532 TCTGATT-ATATATTATAATTAATTTA
1 TCTG-TTAATATATTATAATTAATTTA
*
18729558 TCTATTAAT
1 TCTGTTAAT
18729567 TTTTTGGTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
25 2 0.07
26 18 0.60
27 8 0.27
28 2 0.07
ACGTcount: A:0.36, C:0.05, G:0.03, T:0.56
Consensus pattern (26 bp):
TCTGTTAATATATTATAATTAATTTA
Found at i:18729618 original size:9 final size:9
Alignment explanation
Indices: 18729604--18729647 Score: 54
Period size: 10 Copynumber: 4.8 Consensus size: 9
18729594 TTAATATATA
18729604 TTTTTTTA-
1 TTTTTTTAT
18729612 TTTTTTTAT
1 TTTTTTTAT
*
18729621 TTTTAATTAT
1 TTTT-TTTAT
18729631 TTTTTTTAT
1 TTTTTTTAT
18729640 TTCTTTTT
1 TT-TTTTT
18729648 TTCGACTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
8 8 0.26
9 10 0.32
10 13 0.42
ACGTcount: A:0.14, C:0.02, G:0.00, T:0.84
Consensus pattern (9 bp):
TTTTTTTAT
Found at i:18729623 original size:8 final size:8
Alignment explanation
Indices: 18729602--18729646 Score: 54
Period size: 8 Copynumber: 5.1 Consensus size: 8
18729592 TATTAATATA
18729602 TATTTTTT
1 TATTTTTT
18729610 TATTTTTT
1 TATTTTTT
18729618 TATTTTTAAT
1 TATTTTT--T
18729628 TATTTTTTT
1 TA-TTTTTT
18729637 TATTTCTTT
1 TATTT-TTT
18729646 T
1 T
18729647 TTTCGACTGA
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
8 18 0.55
9 7 0.21
10 3 0.09
11 5 0.15
ACGTcount: A:0.16, C:0.02, G:0.00, T:0.82
Consensus pattern (8 bp):
TATTTTTT
Found at i:18729649 original size:26 final size:29
Alignment explanation
Indices: 18729586--18729649 Score: 89
Period size: 27 Copynumber: 2.3 Consensus size: 29
18729576 TATCTGATTA
*
18729586 TTTATTTATTAATATATATTTTTTTATTTT
1 TTTATTT-TTAATATATATTTTTTTATTTC
18729616 TTTATTTTTAAT-TAT-TTTTTTTATTTC
1 TTTATTTTTAATATATATTTTTTTATTTC
18729643 TTT-TTTT
1 TTTATTTT
18729650 CGACTGAAGA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
26 4 0.12
27 14 0.42
28 3 0.09
29 5 0.15
30 7 0.21
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (29 bp):
TTTATTTTTAATATATATTTTTTTATTTC
Found at i:18730539 original size:12 final size:12
Alignment explanation
Indices: 18730522--18730562 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
18730512 TTTAATATTT
18730522 TTTATTTTTATC
1 TTTATTTTTATC
18730534 TTTATTTTTAT-
1 TTTATTTTTATC
*
18730545 TTTA-CTTT-TC
1 TTTATTTTTATC
18730555 TTTATTTT
1 TTTATTTT
18730563 GGTTTTCACT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
9 1 0.04
10 7 0.28
11 6 0.24
12 11 0.44
ACGTcount: A:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (12 bp):
TTTATTTTTATC
Found at i:18730773 original size:58 final size:59
Alignment explanation
Indices: 18730617--18730771 Score: 244
Period size: 58 Copynumber: 2.7 Consensus size: 59
18730607 TAAAATTCAA
*
18730617 AAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTCAAAATTAAAAGTTTC
1 AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTCAAAATTAAAAGTTTC
* * *
18730676 -CAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCTTCGAAATTAAAA-TTTC
1 AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTCAAAATTAAAAGTTTC
*
18730733 AAAAAAATA-TCTTGGGGAAAAGTTGAAAGTATCAATTTT
1 AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTT
18730772 TCCTTGTACA
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
57 33 0.37
58 56 0.63
ACGTcount: A:0.44, C:0.08, G:0.14, T:0.34
Consensus pattern (59 bp):
AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTCAAAATTAAAAGTTTC
Found at i:18733455 original size:3 final size:3
Alignment explanation
Indices: 18733433--18733542 Score: 55
Period size: 3 Copynumber: 34.7 Consensus size: 3
18733423 TTTTACATTT
* *
18733433 TTA TT- TTA TTTA TATA TTA TTA TTA TTA TTA TATA TATA TTT TTC TTA
1 TTA TTA TTA -TTA T-TA TTA TTA TTA TTA TTA T-TA T-TA TTA TTA TTA
* * *
18733481 TGTA TTTA CTA TTA TT- TT- TTA TTTA TTA TTA CTA TTTA TTA ATA TATA
1 T-TA -TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA -TTA TTA TTA T-TA
**
18733529 TCC TTA TTA TTA TT
1 TTA TTA TTA TTA TT
18733543 TTTTTCTGTT
Statistics
Matches: 84, Mismatches: 13, Indels: 20
0.72 0.11 0.17
Matches are distributed among these distances:
2 6 0.07
3 52 0.62
4 25 0.30
5 1 0.01
ACGTcount: A:0.30, C:0.05, G:0.01, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:18733458 original size:17 final size:17
Alignment explanation
Indices: 18733452--18733520 Score: 66
Period size: 17 Copynumber: 4.1 Consensus size: 17
18733442 TTATATATTA
*
18733452 TTATTATTATTATATAT
1 TTATTATTATTATTTAT
* * * *
18733469 ATATTTTTCTTATGTAT
1 TTATTATTATTATTTAT
* *
18733486 TTACTATTATTTTTTAT
1 TTATTATTATTATTTAT
*
18733503 TTATTATTACTATTTAT
1 TTATTATTATTATTTAT
18733520 T
1 T
18733521 AATATATATC
Statistics
Matches: 39, Mismatches: 13, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
17 39 1.00
ACGTcount: A:0.28, C:0.04, G:0.01, T:0.67
Consensus pattern (17 bp):
TTATTATTATTATTTAT
Found at i:18733469 original size:23 final size:23
Alignment explanation
Indices: 18733433--18733521 Score: 66
Period size: 23 Copynumber: 4.0 Consensus size: 23
18733423 TTTTACATTT
*
18733433 TTATT-TTATTTATATATTATTA
1 TTATTATTATATATATATTATTA
* *
18733455 TTATTATTATATATATATTTTTC
1 TTATTATTATATATATATTATTA
18733478 TTATGTATT-TACTAT-TATT-TT-
1 TTAT-TATTATA-TATATATTATTA
18733499 TTATTTATTAT-TACTAT-TTATTA
1 TTA-TTATTATATA-TATATTATTA
18733522 ATATATATCC
Statistics
Matches: 55, Mismatches: 3, Indels: 17
0.73 0.04 0.23
Matches are distributed among these distances:
20 2 0.04
21 10 0.18
22 12 0.22
23 24 0.44
24 7 0.13
ACGTcount: A:0.29, C:0.03, G:0.01, T:0.66
Consensus pattern (23 bp):
TTATTATTATATATATATTATTA
Found at i:18733505 original size:61 final size:61
Alignment explanation
Indices: 18733410--18733529 Score: 156
Period size: 61 Copynumber: 2.0 Consensus size: 61
18733400 GAGTAAGCTC
* * * *
18733410 ATTTTTTTTTGTATTTTACATTTTTATTTTATTTATATATTATTA-TTATTATTATATATAT
1 ATTTTTTTATGTATTTTACATTATTATTTTATTTAT-TATTACTATTTATTAATATATATAT
18733471 ATTTTTCTTATGTA-TTTACTATTATT-TTTTATTTATTATTACTATTTATTAATATATAT
1 ATTTTT-TTATGTATTTTAC-ATTATTATTTTATTTATTATTACTATTTATTAATATATAT
18733530 CCTTATTATT
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
60 7 0.13
61 34 0.65
62 11 0.21
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.67
Consensus pattern (61 bp):
ATTTTTTTATGTATTTTACATTATTATTTTATTTATTATTACTATTTATTAATATATATAT
Found at i:18733576 original size:26 final size:26
Alignment explanation
Indices: 18733547--18733607 Score: 65
Period size: 26 Copynumber: 2.3 Consensus size: 26
18733537 ATTATTTTTT
18733547 TCTGTTAATAT-TTAT-ATATATATTTA
1 TCTGTTAATATATTATAAT-TA-ATTTA
18733573 TCTGATT-ATATATTATAATTAATTTA
1 TCTG-TTAATATATTATAATTAATTTA
*
18733599 TCTATTAAT
1 TCTGTTAAT
18733608 TTTTTGGTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
25 2 0.07
26 18 0.60
27 8 0.27
28 2 0.07
ACGTcount: A:0.36, C:0.05, G:0.03, T:0.56
Consensus pattern (26 bp):
TCTGTTAATATATTATAATTAATTTA
Found at i:18733674 original size:26 final size:29
Alignment explanation
Indices: 18733635--18733691 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 29
18733625 TATTTATTTA
*
18733635 TTAATATATATTTTTTTATTT-TTTTATT
1 TTAATATATATTTTTTGATTTCTTTTATT
*
18733663 TTAAT-TAT-TTTTTTGATTTCTTTTTTT
1 TTAATATATATTTTTTGATTTCTTTTATT
18733690 TT
1 TT
18733692 GGCTGAAGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 10 0.38
27 11 0.42
28 5 0.19
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.77
Consensus pattern (29 bp):
TTAATATATATTTTTTGATTTCTTTTATT
Found at i:18734574 original size:6 final size:6
Alignment explanation
Indices: 18734563--18734632 Score: 72
Period size: 6 Copynumber: 11.7 Consensus size: 6
18734553 TGTTTAATAT
* * * *
18734563 TTTTTA TTTTTA TCTTTA TTTTTA -TTTTA TTTTTA TTTTCA CTTTCA
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
18734610 TTTTTA -TTTTA TTATTTTA TTTT
1 TTTTTA TTTTTA -T-TTTTA TTTT
18734633 CTTTAAATAA
Statistics
Matches: 54, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
5 10 0.19
6 38 0.70
7 1 0.02
8 5 0.09
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.77
Consensus pattern (6 bp):
TTTTTA
Found at i:18734599 original size:29 final size:30
Alignment explanation
Indices: 18734560--18734633 Score: 107
Period size: 29 Copynumber: 2.5 Consensus size: 30
18734550 ATTTGTTTAA
*
18734560 TATTTTTTATTTTTATCTTT-ATTTTTATTT
1 TATTTTTTATTTTCA-CTTTCATTTTTATTT
18734590 TA-TTTTTATTTTCACTTTCATTTTTATTT
1 TATTTTTTATTTTCACTTTCATTTTTATTT
18734619 TATTATTTTATTTTC
1 TATT-TTTTATTTTC
18734634 TTTAAATAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
28 4 0.10
29 23 0.57
30 3 0.08
31 10 0.25
ACGTcount: A:0.18, C:0.07, G:0.00, T:0.76
Consensus pattern (30 bp):
TATTTTTTATTTTCACTTTCATTTTTATTT
Found at i:18734722 original size:58 final size:57
Alignment explanation
Indices: 18734652--18734866 Score: 247
Period size: 58 Copynumber: 3.7 Consensus size: 57
18734642 AAATTCAAAA
18734652 AAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAAAGTTTTC
1 AAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAAA-TTTTC
* * * *
18734710 AAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCT-TAAA-AACAAATTATC
1 AAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTCGAAATTA-AAATTTTC
* * *
18734766 AAAAAAGGGTTTTTTTTTTAGGAAAAGTTGAAAGTATCAATTTTCTTCGAAATTAAAA-TTTC
1 -AAAAA-----TATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAAATTTTC
* *
18734828 AAAAAAATATTTTGGGGAAAAGTTGAAAGTATCAATTTT
1 AAAAATAT-TTTTGAGGAAAAGTTGAAAGTATCAATTTT
18734867 TCCTTGTACA
Statistics
Matches: 132, Mismatches: 15, Indels: 21
0.79 0.09 0.12
Matches are distributed among these distances:
56 6 0.05
57 39 0.30
58 40 0.30
61 5 0.04
62 35 0.27
63 6 0.05
64 1 0.01
ACGTcount: A:0.42, C:0.07, G:0.14, T:0.36
Consensus pattern (57 bp):
AAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAAATTTTC
Found at i:18737622 original size:18 final size:19
Alignment explanation
Indices: 18737590--18737627 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
18737580 AGTTCGAAAC
18737590 ATTTTTTAATCATTT-TTT
1 ATTTTTTAATCATTTGTTT
* *
18737608 ATTTTTTGATGATTTGTTT
1 ATTTTTTAATCATTTGTTT
18737627 A
1 A
18737628 CAAAAGCTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.21, C:0.03, G:0.08, T:0.68
Consensus pattern (19 bp):
ATTTTTTAATCATTTGTTT
Found at i:18738407 original size:12 final size:12
Alignment explanation
Indices: 18738376--18738414 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
18738366 ATATATATAC
* *
18738376 ATATAAACAAAA
1 ATATAAATAATA
18738388 ATATAAATAATA
1 ATATAAATAATA
18738400 ATATAAATAATA
1 ATATAAATAATA
18738412 ATA
1 ATA
18738415 AATAACAATG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (12 bp):
ATATAAATAATA
Found at i:18741101 original size:6 final size:6
Alignment explanation
Indices: 18741090--18741179 Score: 74
Period size: 6 Copynumber: 14.2 Consensus size: 6
18741080 GAAAAGAATG
* * * * *
18741090 AAGAAA AAGAAA GAGAGA AAGCAAA AAAAAA AAGAAA AAAAAA GAAGAGA
1 AAGAAA AAGAAA AAGAAA AAG-AAA AAGAAA AAGAAA AAGAAA -AAGAAA
18741140 AAGAAA AAGTAAA AAGAAA AGAGGAAAA AAGAAA AA-AAA A
1 AAGAAA AAG-AAA AAGAAA A-A-G-AAA AAGAAA AAGAAA A
18741180 GGTTAGATTT
Statistics
Matches: 68, Mismatches: 10, Indels: 13
0.75 0.11 0.14
Matches are distributed among these distances:
5 4 0.06
6 42 0.62
7 16 0.24
8 2 0.03
9 4 0.06
ACGTcount: A:0.79, C:0.01, G:0.19, T:0.01
Consensus pattern (6 bp):
AAGAAA
Found at i:18741125 original size:31 final size:32
Alignment explanation
Indices: 18741081--18741159 Score: 99
Period size: 32 Copynumber: 2.5 Consensus size: 32
18741071 AAAAGTTCAG
** *
18741081 AAAAGAATGAAGAAAAAGAAAG-AGAGAAAGCA
1 AAAAGAAAAAAGAAAAAAAAAGAAGAGAAAG-A
18741113 AAAA-AAAAAAGAAAAAAAAAGAAGAGAAAGA
1 AAAAGAAAAAAGAAAAAAAAAGAAGAGAAAGA
*
18741144 AAAAGTAAAAAGAAAA
1 AAAAGAAAAAAGAAAA
18741160 GAGGAAAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
31 19 0.46
32 22 0.54
ACGTcount: A:0.77, C:0.01, G:0.19, T:0.03
Consensus pattern (32 bp):
AAAAGAAAAAAGAAAAAAAAAGAAGAGAAAGA
Found at i:18741143 original size:44 final size:46
Alignment explanation
Indices: 18741089--18741180 Score: 118
Period size: 44 Copynumber: 2.0 Consensus size: 46
18741079 AGAAAAGAAT
* *
18741089 GAAGAAAAAGAAAGAG-AGAAAGCAAAA-A-AAAAAAGAAAAAAAAA
1 GAAGAAAAAGAAAAAGTAAAAAG-AAAAGAGAAAAAAGAAAAAAAAA
*
18741133 GAAGAGAAAGAAAAAGTAAAAAGAAAAGAGGAAAAAAGAAAAAAAAA
1 GAAGAAAAAGAAAAAGTAAAAAGAAAAGA-GAAAAAAGAAAAAAAAA
18741180 G
1 G
18741181 GTTAGATTTA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
44 18 0.44
45 6 0.15
47 17 0.41
ACGTcount: A:0.77, C:0.01, G:0.21, T:0.01
Consensus pattern (46 bp):
GAAGAAAAAGAAAAAGTAAAAAGAAAAGAGAAAAAAGAAAAAAAAA
Found at i:18741153 original size:24 final size:21
Alignment explanation
Indices: 18741116--18741179 Score: 65
Period size: 25 Copynumber: 2.8 Consensus size: 21
18741106 GAAAGCAAAA
18741116 AAAAAAAGAAAAAAAAAGAAGAG
1 AAAAAAAG-AAAAAAAA-AAGAG
*
18741139 AAAGAAAAAGTAAAAAGAAAAGAG
1 -AA-AAAAAG-AAAAAAAAAAGAG
*
18741163 GAAAAAAGAAAAAAAAA
1 AAAAAAAGAAAAAAAAA
18741180 GGTTAGATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
21 8 0.23
22 6 0.17
23 1 0.03
24 7 0.20
25 13 0.37
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (21 bp):
AAAAAAAGAAAAAAAAAAGAG
Found at i:18744368 original size:11 final size:12
Alignment explanation
Indices: 18744348--18744392 Score: 67
Period size: 11 Copynumber: 3.9 Consensus size: 12
18744338 GAATTCCCTT
*
18744348 AAAAAGGAAAGG
1 AAAAAGAAAAGG
18744360 AAAAAGAAAAGG
1 AAAAAGAAAAGG
18744372 -AAAAGAAAAGG
1 AAAAAGAAAAGG
18744383 AAAAA-AAAAG
1 AAAAAGAAAAG
18744393 AGTTTTTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
11 16 0.52
12 15 0.48
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (12 bp):
AAAAAGAAAAGG
Found at i:18744369 original size:17 final size:17
Alignment explanation
Indices: 18744349--18744386 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
18744339 AATTCCCTTA
*
18744349 AAAAGGAAAGGAAAAAG
1 AAAAGGAAAAGAAAAAG
*
18744366 AAAAGGAAAAGAAAAGG
1 AAAAGGAAAAGAAAAAG
18744383 AAAA
1 AAAA
18744387 AAAAAGAGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (17 bp):
AAAAGGAAAAGAAAAAG
Found at i:18745593 original size:26 final size:24
Alignment explanation
Indices: 18745552--18745609 Score: 62
Period size: 26 Copynumber: 2.3 Consensus size: 24
18745542 AATTGAAGAA
18745552 AATGAAAAAAAAAAAAAGCAAAGG
1 AATGAAAAAAAAAAAAAGCAAAGG
* * *
18745576 AATGAGAAAATAAGAAAAAGGAAAGAA
1 AATGA-AAAA-AAAAAAAAGCAAAG-G
18745603 AATGAAA
1 AATGAAA
18745610 GAAATGAGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
24 5 0.18
25 4 0.14
26 14 0.50
27 5 0.18
ACGTcount: A:0.72, C:0.02, G:0.19, T:0.07
Consensus pattern (24 bp):
AATGAAAAAAAAAAAAAGCAAAGG
Found at i:18745602 original size:19 final size:19
Alignment explanation
Indices: 18745562--18745663 Score: 66
Period size: 20 Copynumber: 5.2 Consensus size: 19
18745552 AATGAAAAAA
*
18745562 AAAAAAAG-CAAAGGAATGAG
1 AAAAAAAGAAAAAGGAA--AG
*
18745582 AAAATAAGAAAAAGGAAAG
1 AAAAAAAGAAAAAGGAAAG
*
18745601 AAAATGAAAG-AAATGAGAAA-
1 AAAA--AAAGAAAAAG-GAAAG
* *
18745621 AAAAAAACAAAAGAAGAAAG
1 AAAAAAAGAAAA-AGGAAAG
*
18745641 AAAAAAAGGAAAAAGAAAAG
1 AAAAAAA-GAAAAAGGAAAG
18745661 AAA
1 AAA
18745664 TGCATGGTTC
Statistics
Matches: 64, Mismatches: 10, Indels: 16
0.71 0.11 0.18
Matches are distributed among these distances:
18 3 0.05
19 13 0.20
20 30 0.47
21 18 0.28
ACGTcount: A:0.75, C:0.02, G:0.20, T:0.04
Consensus pattern (19 bp):
AAAAAAAGAAAAAGGAAAG
Found at i:18745638 original size:36 final size:36
Alignment explanation
Indices: 18745556--18745639 Score: 86
Period size: 36 Copynumber: 2.4 Consensus size: 36
18745546 GAAGAAAATG
* * *
18745556 AAAAAA-AAA-AAAA-GCAAAGGAATGAGAAAATAAG
1 AAAAAAGAAAGAAAATG-AAAGAAATGAGAAAAAAAA
*
18745590 AAAAAGGAAAGAAAATGAAAGAAATGAGAAAAAAAA
1 AAAAAAGAAAGAAAATGAAAGAAATGAGAAAAAAAA
18745626 AACAAAAG-AAGAAA
1 AA-AAAAGAAAGAAA
18745640 GAAAAAAAGG
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
34 5 0.12
35 3 0.07
36 28 0.68
37 5 0.12
ACGTcount: A:0.75, C:0.02, G:0.18, T:0.05
Consensus pattern (36 bp):
AAAAAAGAAAGAAAATGAAAGAAATGAGAAAAAAAA
Found at i:18745661 original size:27 final size:28
Alignment explanation
Indices: 18745590--18745662 Score: 75
Period size: 27 Copynumber: 2.7 Consensus size: 28
18745580 AGAAAATAAG
*
18745590 AAAAAGG--AAAGAAAATGAAAGAAATGAG
1 AAAAAGGAAAAAGAAAA-G-AAGAAATGAA
*
18745618 AAAAA--AAAAACAAAAGAAGAAA-GAA
1 AAAAAGGAAAAAGAAAAGAAGAAATGAA
18745643 AAAAAGGAAAAAGAAAAGAA
1 AAAAAGGAAAAAGAAAAGAA
18745663 ATGCATGGTT
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
25 7 0.18
26 6 0.16
27 13 0.34
28 12 0.32
ACGTcount: A:0.77, C:0.01, G:0.19, T:0.03
Consensus pattern (28 bp):
AAAAAGGAAAAAGAAAAGAAGAAATGAA
Found at i:18746454 original size:21 final size:20
Alignment explanation
Indices: 18746415--18746454 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
18746405 CTTCAAGTCA
**
18746415 TGAAACCTTTTTGGATGAAT
1 TGAAACCTTGATGGATGAAT
18746435 TGAAACCTTGATGTGATGAA
1 TGAAACCTTGATG-GATGAA
18746455 CTGTTCAACC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.35
Consensus pattern (20 bp):
TGAAACCTTGATGGATGAAT
Found at i:18746621 original size:113 final size:114
Alignment explanation
Indices: 18746417--18746646 Score: 399
Period size: 113 Copynumber: 2.0 Consensus size: 114
18746407 TCAAGTCATG
* *
18746417 AAACCTTTTTGGATGAATTGAAACCTTGATGTGATGAACTGTTCAACCTATTTGAAAAGAAAATG
1 AAACCTTTTTGGATGAATTGAAACCTTGATGTGATGAACTGTTCAACCCATCTGAAAAGAAAATG
* *
18746482 GTCTTCTCTTTCATTTCTAATAGAGAACACCAATTTCCAAAAGACTCCT
66 GTCTGCTCTTTCATTCCTAATAGAGAACACCAATTTCCAAAAGACTCCT
*
18746531 AAACC-TTTTGGATGAATTGAAACCTTGATGTGATGAACTGTTTAACCCATCTGAAAAGAAAATG
1 AAACCTTTTTGGATGAATTGAAACCTTGATGTGATGAACTGTTCAACCCATCTGAAAAGAAAATG
*
18746595 GTCTGCTCTTTCATTCCTAATAGAGAACACCAATTTTCAAAAGACTCCT
66 GTCTGCTCTTTCATTCCTAATAGAGAACACCAATTTCCAAAAGACTCCT
18746644 AAA
1 AAA
18746647 GTCACATTTG
Statistics
Matches: 110, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
113 105 0.95
114 5 0.05
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.32
Consensus pattern (114 bp):
AAACCTTTTTGGATGAATTGAAACCTTGATGTGATGAACTGTTCAACCCATCTGAAAAGAAAATG
GTCTGCTCTTTCATTCCTAATAGAGAACACCAATTTCCAAAAGACTCCT
Found at i:18747850 original size:14 final size:13
Alignment explanation
Indices: 18747822--18747867 Score: 56
Period size: 14 Copynumber: 3.4 Consensus size: 13
18747812 AAAGAGTGTG
*
18747822 AAGAAAGAGAAAA
1 AAGAAAGAAAAAA
18747835 AAGAAAGGAAAAAA
1 AAGAAA-GAAAAAA
*
18747849 AAGAAAAAAAATAA
1 AAGAAAGAAAA-AA
18747863 AAGAA
1 AAGAA
18747868 GAGACAAAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
13 10 0.34
14 19 0.66
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.02
Consensus pattern (13 bp):
AAGAAAGAAAAAA
Found at i:18748119 original size:31 final size:31
Alignment explanation
Indices: 18748078--18748736 Score: 209
Period size: 33 Copynumber: 20.4 Consensus size: 31
18748068 AAAAAAATGA
* *
18748078 AGATTCAAGCCCAGTTTAGCTGGCACTGATG
1 AGATTTAAGCCCAGTTTAGTTGGCACTGATG
* * * * *
18748109 AGAATTAAGCCTAGTTTAATTGGCACCTAAAAG
1 AGATTTAAGCCCAGTTTAGTTGGCA-CT-GATG
* * ** * *
18748142 AGATTTAAGCCTAATTTAGTTCACACCTAAGTA
1 AGATTTAAGCCCAGTTTAGTTGGCA-CTGA-TG
* * ** *
18748175 AGATTTAAGTCTAGTTTACCTGGCACCTGAATA
1 AGATTTAAGCCCAGTTTAGTTGGCA-CTG-ATG
* **
18748208 AGATTTTAAACTTAGTTTAGTTGGCACTAAGATG
1 AGA-TTTAAGCCCAGTTTAGTTGGCACT--GATG
* *
18748242 AGATTTAAGCCCAGTTTAATTGGCACCTAAATG
1 AGATTTAAGCCCAGTTTAGTTGGCA-CT-GATG
* * * * *
18748275 AGATTTAAGCCTAATCTAGCTGGCACTAATG
1 AGATTTAAGCCCAGTTTAGTTGGCACTGATG
* * * * *
18748306 AGAATTAAGCCCAATCTGGTTGGCACCTAAATG
1 AGATTTAAGCCCAGTTTAGTTGGCA-CT-GATG
** * * *
18748339 AGATTTAAGTACAATTTAGCTGGCACTTATG
1 AGATTTAAGCCCAGTTTAGTTGGCACTGATG
* * * *
18748370 AAAATTTAAGCCTAGTTTAGTTAGCACTCAT-
1 -AGATTTAAGCCCAGTTTAGTTGGCACTGATG
*
18748401 ATGAATATTAAGCCCTA-TTTAGTTGGCACTAAGAAG
1 A-G-AT-TTAAGCCC-AGTTTAGTTGGCACT--GATG
18748437 AGATTTTAAGCCCAGATTT-GTTGGCACAT-ATG
1 AGA-TTTAAGCCCAG-TTTAGTTGGCAC-TGATG
* * * **
18748469 AGATTTAAACCTAGTTTAATTGGCACAAATG
1 AGATTTAAGCCCAGTTTAGTTGGCACTGATG
* * * * * *
18748500 TGATTTAAGCCCAATCTGGCTAGCACAT-ATG
1 AGATTTAAGCCCAGTTTAGTTGGCAC-TGATG
* * * * *
18748531 ATATTTAAGCCTAGTTTAGCTAGCACCTAGA-A
1 AGATTTAAGCCCAGTTTAGTTGGCA-CT-GATG
* * * * * *
18748563 AGATTTAAGCCCAATTCAGCTAGCACCCAGATA
1 AGATTTAAGCCCAGTTTAGTTGGCA--CTGATG
* * ** * * *
18748596 AGATTTAAGTCTAACTTAGCTAGTA-TCGAT-
1 AGATTTAAGCCCAGTTTAGTTGGCACT-GATG
** ** *
18748626 ATGATTTAAGCTTAGTTTAACTGGCACAGATG
1 A-GATTTAAGCCCAGTTTAGTTGGCACTGATG
**
18748658 AGATTTAAGCCCAGTTTAAATGGCACATAGATG
1 AGATTTAAGCCCAGTTTAGTTGGCAC-T-GATG
* * *
18748691 AGAATTAAACCCAGTTTAGTTGGCATCTAAGTG
1 AGATTTAAGCCCAGTTTAGTTGGCA-CTGA-TG
*
18748724 AGATTTAAACCCA
1 AGATTTAAGCCCA
18748737 ATCCTAGATT
Statistics
Matches: 478, Mismatches: 112, Indels: 74
0.72 0.17 0.11
Matches are distributed among these distances:
30 5 0.01
31 152 0.32
32 65 0.14
33 203 0.42
34 44 0.09
35 8 0.02
36 1 0.00
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.31
Consensus pattern (31 bp):
AGATTTAAGCCCAGTTTAGTTGGCACTGATG
Found at i:18748298 original size:100 final size:100
Alignment explanation
Indices: 18748120--18748300 Score: 229
Period size: 100 Copynumber: 1.8 Consensus size: 100
18748110 GAATTAAGCC
* * * *
18748120 TAGTTTAATTGGCACCTAAAAGAGATTTAAGCCTAATTTAGTTCACACCTAAGTAAGATTTAAGT
1 TAGTTTAATTGGCACCTAAAAGAGATTTAAGCCCAATTTAATTCACACCTAAATAAGATTTAAGC
* *
18748185 CTAGTTTACCTGGCACCTGAATAAGATTTTAAACT
66 CTAATCTACCTGGCACCTGAATAAGATTTTAAACT
* * * ** *
18748220 TAGTTTAGTTGGCA-CTAAGATGAGATTTAAGCCCAGTTTAATTGGCACCTAAATGAGATTTAAG
1 TAGTTTAATTGGCACCTAA-AAGAGATTTAAGCCCAATTTAATTCACACCTAAATAAGATTTAAG
*
18748284 CCTAATCTAGCTGGCAC
65 CCTAATCTACCTGGCAC
18748301 TAATGAGAAT
Statistics
Matches: 67, Mismatches: 13, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
99 4 0.06
100 63 0.94
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Consensus pattern (100 bp):
TAGTTTAATTGGCACCTAAAAGAGATTTAAGCCCAATTTAATTCACACCTAAATAAGATTTAAGC
CTAATCTACCTGGCACCTGAATAAGATTTTAAACT
Found at i:18748329 original size:64 final size:64
Alignment explanation
Indices: 18748072--18748512 Score: 286
Period size: 64 Copynumber: 6.8 Consensus size: 64
18748062 ATTTAAAAAA
* * * * *
18748072 AAATGAAGATTCAAGCCCAGTTTAGCTGGCACTGATGAGAATTAAGCCTAGTTTAATTGGCACCT
1 AAATG-AGATTTAAGCCTAATTTAGCTGGCACTAATGAGAATTAAGCCCAGTTTAATTGGCACCT
* * ** * * * * **
18748137 AAAAGAGATTTAAGCCTAATTTAGTTCACACCTAAGTAAGATTTAAGTCTAGTTTACCTGGCACC
1 AAATGAGATTTAAGCCTAATTTAGCTGGCA-CTAA-TGAGAATTAAGCCCAGTTTAATTGGCACC
18748202 T
64 T
* * * * * * *
18748203 GAATAAGATTTTAAACTTAGTTTAGTTGGCACTAAGATGAGATTTAAGCCCAGTTTAATTGGCAC
1 AAATGAGA-TTTAAGCCTAATTTAGCTGGCACT-A-ATGAGAATTAAGCCCAGTTTAATTGGCAC
18748268 CT
63 CT
* * * **
18748270 AAATGAGATTTAAGCCTAATCTAGCTGGCACTAATGAGAATTAAGCCCAATCTGGTTGGCACCT
1 AAATGAGATTTAAGCCTAATTTAGCTGGCACTAATGAGAATTAAGCCCAGTTTAATTGGCACCT
* * * * * *
18748334 AAATGAGATTTAAGTAC-AATTTAGCTGGCACTTATGAAAATTTAAGCCTAGTTTAGTTAGCA-C
1 AAATGAGATTTAAG-CCTAATTTAGCTGGCACTAATGAGAA-TTAAGCCCAGTTTAATTGGCACC
18748397 T
64 T
* * *
18748398 CATATGA-ATATTAAGCCCT-ATTTAGTTGGCACTAA-GAAGAGATTTTAAGCCCAGATTT-GTT
1 -AAATGAGAT-TTAAG-CCTAATTTAGCTGGCACTAATG-AGA-A--TTAAGCCCAG-TTTAATT
18748459 GGCA-C-
58 GGCACCT
* * * ** * * *
18748464 ATATGAGATTTAAACCTAGTTTAATTGGCACAAATGTGATTTAAGCCCA
1 AAATGAGATTTAAGCCTAATTTAGCTGGCACTAATGAGAATTAAGCCCA
18748513 ATCTGGCTAG
Statistics
Matches: 298, Mismatches: 61, Indels: 37
0.75 0.15 0.09
Matches are distributed among these distances:
62 9 0.03
64 87 0.29
65 77 0.26
66 55 0.18
67 66 0.22
68 4 0.01
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (64 bp):
AAATGAGATTTAAGCCTAATTTAGCTGGCACTAATGAGAATTAAGCCCAGTTTAATTGGCACCT
Found at i:18748584 original size:32 final size:33
Alignment explanation
Indices: 18748533--18748604 Score: 101
Period size: 32 Copynumber: 2.2 Consensus size: 33
18748523 CACATATGAT
* * * *
18748533 ATTTAAGCCTAGTTTAGCTAGCACCTAGA-AAG
1 ATTTAAGCCCAATTCAGCTAGCACCCAGATAAG
18748565 ATTTAAGCCCAATTCAGCTAGCACCCAGATAAG
1 ATTTAAGCCCAATTCAGCTAGCACCCAGATAAG
18748598 ATTTAAG
1 ATTTAAG
18748605 TCTAACTTAG
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
32 25 0.71
33 10 0.29
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.26
Consensus pattern (33 bp):
ATTTAAGCCCAATTCAGCTAGCACCCAGATAAG
Found at i:18748837 original size:46 final size:46
Alignment explanation
Indices: 18748745--18749301 Score: 337
Period size: 46 Copynumber: 12.5 Consensus size: 46
18748735 CAATCCTAGA
* * * * **
18748745 TTAACTTTATTTTCAAAAGTTATTGAGCCTTTAT-CAAAAGGTGCTT
1 TTAAATTTATTTTCAAAAGTTGTTAAGCCTTT-TCCTAAAGAAGCTT
* *
18748791 TTAAATTTACTTACAAAAGTTGTTAAGCCTTTTCCTAAAGAAGCTT
1 TTAAATTTATTTTCAAAAGTTGTTAAGCCTTTTCCTAAAGAAGCTT
* * * * * *
18748837 TTAAATTTAGTATAAAAAATTGTTGAGACTTTTCCT-AAGAGAGCTT
1 TTAAATTTATTTTCAAAAGTTGTTAAGCCTTTTCCTAAAGA-AGCTT
* * * *
18748883 TTAGATTTATTTTTAAAAGTTATTAAGCCTTTACCTAAA-AGAGCTT
1 TTAAATTTATTTTCAAAAGTTGTTAAGCCTTTTCCTAAAGA-AGCTT
* *
18748929 TTAGATTTATTTTCAAAAGTTGTTGAG-C-TTT--T--AG-A---T
1 TTAAATTTATTTTCAAAAGTTGTTAAGCCTTTTCCTAAAGAAGCTT
*** * * *
18748965 TT--ATTT-TTAAAA---GTTATTGAGCCTTTACCTAAATG-AGCTT
1 TTAAATTTATTTTCAAAAGTTGTTAAGCCTTTTCCTAAA-GAAGCTT
* *
18749005 TTAGATTTATTTTCAAAAGTTGTT--GCGCTTTTACCTAAA-AGAGTTT
1 TTAAATTTATTTTCAAAAGTTGTTAAGC-CTTTT-CCTAAAGA-AGCTT
** * * * *
18749051 TTAAATTTGCTCTCAAAAGTTATTGAGCCTTTTCCTAAAGTAGCTT
1 TTAAATTTATTTTCAAAAGTTGTTAAGCCTTTTCCTAAAGAAGCTT
* * ** *
18749097 TTAAATTT-TTTTCAAAAGTTGTTGAGCCATTTCCTAAAGGGGTTT
1 TTAAATTTATTTTCAAAAGTTGTTAAGCCTTTTCCTAAAGAAGCTT
*
18749142 TTAAATTTATTTTCAAAAGTTGTTCAA-CCTTTTCC-AAA-AAGAGTT
1 TTAAATTTATTTTCAAAAGTTGTT-AAGCCTTTTCCTAAAGAAG-CTT
* * * * *
18749187 TTAAATTTATTATCAAAAGTTATTGAA-CCTTTTTCTAAAGGAGATT
1 TTAAATTTATTTTCAAAAGTTGTT-AAGCCTTTTCCTAAAGAAGCTT
* *** *
18749233 TTCAA-TTATTTTTCAAAAGTTGTTGAA-CCTTTGATTAAAGGAGCTT
1 TTAAATTTA-TTTTCAAAAGTTGTT-AAGCCTTTTCCTAAAGAAGCTT
*
18749279 TTAAATTTATTTTCAAAAATTGT
1 TTAAATTTATTTTCAAAAGTTGT
18749302 ATTGCTTTTA
Statistics
Matches: 404, Mismatches: 73, Indels: 68
0.74 0.13 0.12
Matches are distributed among these distances:
30 8 0.02
31 1 0.00
32 2 0.00
33 3 0.01
34 5 0.01
36 4 0.01
37 2 0.00
39 1 0.00
40 4 0.01
42 5 0.01
43 3 0.01
44 5 0.01
45 87 0.22
46 259 0.64
47 13 0.03
48 2 0.00
ACGTcount: A:0.32, C:0.11, G:0.13, T:0.44
Consensus pattern (46 bp):
TTAAATTTATTTTCAAAAGTTGTTAAGCCTTTTCCTAAAGAAGCTT
Found at i:18748957 original size:30 final size:30
Alignment explanation
Indices: 18748923--18748991 Score: 111
Period size: 30 Copynumber: 2.3 Consensus size: 30
18748913 TTACCTAAAA
*
18748923 GAGCTTTTAGATTTATTTTCAAAAGTTGTT
1 GAGCTTTTAGATTTATTTTCAAAAGTTATT
*
18748953 GAGCTTTTAGATTTATTTTTAAAAGTTATT
1 GAGCTTTTAGATTTATTTTCAAAAGTTATT
*
18748983 GAGCCTTTA
1 GAGCTTTTA
18748992 CCTAAATGAG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.28, C:0.07, G:0.16, T:0.49
Consensus pattern (30 bp):
GAGCTTTTAGATTTATTTTCAAAAGTTATT
Found at i:18748996 original size:122 final size:122
Alignment explanation
Indices: 18748832--18749083 Score: 308
Period size: 122 Copynumber: 2.1 Consensus size: 122
18748822 TTCCTAAAGA
* *
18748832 AGCTTTTAAATTTAGTATAAAAAATTGTTGAGACTTTTCCTAAGA-GAGCTTTTAGATTTATTTT
1 AGCTTTTAAATTTAGTATAAAAAATTATTGAGACTTTACCTAA-ATGAGCTTTTAGATTTATTTT
* * * * *
18748896 TAAAAGTTATTAAGCCTTTACCTAAAAGAGCTTTTAGATTTATTTTCAAAAGTTGTTG
65 CAAAAGTTATTAAGCCTTTACCTAAAAGAGCTTTTAAATTTACTCTCAAAAGTTATTG
* * * * * *
18748954 AGCTTTTAGATTTATTTTTAAAAGTTATTGAGCCTTTACCTAAATGAGCTTTTAGATTTATTTTC
1 AGCTTTTAAATTTAGTATAAAAAATTATTGAGACTTTACCTAAATGAGCTTTTAGATTTATTTTC
* ** * * *
18749019 AAAAGTTGTTGCGCTTTTACCTAAAAGAGTTTTTAAATTTGCTCTCAAAAGTTATTG
66 AAAAGTTATTAAGCCTTTACCTAAAAGAGCTTTTAAATTTACTCTCAAAAGTTATTG
18749076 AGCCTTTT
1 AG-CTTTT
18749084 CCTAAAGTAG
Statistics
Matches: 109, Mismatches: 19, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
121 1 0.01
122 103 0.94
123 5 0.05
ACGTcount: A:0.31, C:0.11, G:0.14, T:0.44
Consensus pattern (122 bp):
AGCTTTTAAATTTAGTATAAAAAATTATTGAGACTTTACCTAAATGAGCTTTTAGATTTATTTTC
AAAAGTTATTAAGCCTTTACCTAAAAGAGCTTTTAAATTTACTCTCAAAAGTTATTG
Found at i:18749003 original size:76 final size:76
Alignment explanation
Indices: 18748877--18749037 Score: 295
Period size: 76 Copynumber: 2.1 Consensus size: 76
18748867 TTTCCTAAGA
18748877 GAGCTTTTAGATTTATTTTTAAAAGTTATTAAGCCTTTACCTAAAAGAGCTTTTAGATTTATTTT
1 GAGCTTTTAGATTTATTTTTAAAAGTTATTAAGCCTTTACCTAAAAGAGCTTTTAGATTTATTTT
18748942 CAAAAGTTGTT
66 CAAAAGTTGTT
* *
18748953 GAGCTTTTAGATTTATTTTTAAAAGTTATTGAGCCTTTACCTAAATGAGCTTTTAGATTTATTTT
1 GAGCTTTTAGATTTATTTTTAAAAGTTATTAAGCCTTTACCTAAAAGAGCTTTTAGATTTATTTT
18749018 CAAAAGTTGTT
66 CAAAAGTTGTT
*
18749029 GCGCTTTTA
1 GAGCTTTTA
18749038 CCTAAAAGAG
Statistics
Matches: 82, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
76 82 1.00
ACGTcount: A:0.29, C:0.10, G:0.14, T:0.47
Consensus pattern (76 bp):
GAGCTTTTAGATTTATTTTTAAAAGTTATTAAGCCTTTACCTAAAAGAGCTTTTAGATTTATTTT
CAAAAGTTGTT
Found at i:18749074 original size:168 final size:167
Alignment explanation
Indices: 18748787--18749123 Score: 410
Period size: 168 Copynumber: 2.0 Consensus size: 167
18748777 ATCAAAAGGT
* *
18748787 GCTTTTAAATTTACTTACAAAAGTTGTTAAGCCTTTTCCTAAAGAAGCTTTTAAATTTAGTATAA
1 GCTTTTAAATTTACTTACAAAAGTTATTAAGCCTTTACCTAAAGAAGCTTTTAAATTTAGTATAA
* * * * *
18748852 AAAATTGTTGAGACTTTTCCTAAGAGAGCTTTTAGATTTATTTTTAAAAGTTATTAAGCCTTTAC
66 AAAATTGTTGAGACTTTTCCTAAAAGAGCTTTTAAATTTACTCTCAAAAGTTATTAAGCCTTTAC
*
18748917 CTAAAAG-AGCTTTTAGATTTATTTTCAAAAGTTGTTGA
131 CT-AAAGTAGCTTTTAAATTT-TTTTCAAAAGTTGTTGA
* * ** * * * * *
18748955 GCTTTTAGATTTATTTTTAAAAGTTATTGAGCCTTTACCTAAATG-AGCTTTTAGATTTATTTTC
1 GCTTTTAAATTTACTTACAAAAGTTATTAAGCCTTTACCTAAA-GAAGCTTTTAAATTTAGTATA
* * * * *
18749019 AAAAGTTGTTGCG-CTTTTACCTAAAAGAGTTTTTAAATTTGCTCTCAAAAGTTATTGAGCCTTT
65 AAAAATTGTTGAGACTTTT-CCTAAAAGAGCTTTTAAATTTACTCTCAAAAGTTATTAAGCCTTT
*
18749083 TCCTAAAGTAGCTTTTAAATTTTTTTCAAAAGTTGTTGA
129 ACCTAAAGTAGCTTTTAAATTTTTTTCAAAAGTTGTTGA
18749122 GC
1 GC
18749124 CATTTCCTAA
Statistics
Matches: 143, Mismatches: 23, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
167 28 0.20
168 114 0.80
169 1 0.01
ACGTcount: A:0.31, C:0.12, G:0.14, T:0.44
Consensus pattern (167 bp):
GCTTTTAAATTTACTTACAAAAGTTATTAAGCCTTTACCTAAAGAAGCTTTTAAATTTAGTATAA
AAAATTGTTGAGACTTTTCCTAAAAGAGCTTTTAAATTTACTCTCAAAAGTTATTAAGCCTTTAC
CTAAAGTAGCTTTTAAATTTTTTTCAAAAGTTGTTGA
Found at i:18749123 original size:137 final size:135
Alignment explanation
Indices: 18748953--18749301 Score: 425
Period size: 137 Copynumber: 2.5 Consensus size: 135
18748943 AAAAGTTGTT
* * * * *
18748953 GAGCTTTTAGATTTATTTTTAAAAGTTATTGAGCCTTTACCTAAATGAGCTTTTAGATTTATTTT
1 GAGCTTTTAAATTT-TTTTCAAAAGTTGTTGAGCCTTTACCTAAAGGAGCTTTTAAATTTATTTT
* * * * *
18749018 CAAAAGTTGTTGC-GCTTTTACCTAAAAGAGTTTTTAAATTTGCTCTCAAAAGTTATTGAGCCTT
65 CAAAAGTTGTT-CACCTTTT-CCAAAAAGAG-TTTTAAATTTACTATCAAAAGTTATTGAACCTT
18749082 TTCCTAAAG
127 TTCCTAAAG
* * *
18749091 TAGCTTTTAAATTTTTTTCAAAAGTTGTTGAGCCATTT-CCTAAAGGGGTTTTTAAATTTATTTT
1 GAGCTTTTAAATTTTTTTCAAAAGTTGTTGAGCC-TTTACCTAAAGGAGCTTTTAAATTTATTTT
*
18749155 CAAAAGTTGTTCAACCTTTTCCAAAAAGAGTTTTAAATTTATTATCAAAAGTTATTGAACCTTTT
65 CAAAAGTTGTTC-ACCTTTTCCAAAAAGAGTTTTAAATTTACTATCAAAAGTTATTGAACCTTTT
*
18749220 TCTAAAG
129 CCTAAAG
* * * *
18749227 GAGATTTTCAATTATTTTTCAAAAGTTGTTGAACCTTTGA-TTAAAGGAGCTTTTAAATTTATTT
1 GAGCTTTTAAATT-TTTTTCAAAAGTTGTTGAGCCTTT-ACCTAAAGGAGCTTTTAAATTTATTT
*
18749291 TCAAAAATTGT
64 TCAAAAGTTGT
18749302 ATTGCTTTTA
Statistics
Matches: 182, Mismatches: 23, Indels: 13
0.83 0.11 0.06
Matches are distributed among these distances:
136 51 0.28
137 111 0.61
138 20 0.11
ACGTcount: A:0.31, C:0.11, G:0.13, T:0.44
Consensus pattern (135 bp):
GAGCTTTTAAATTTTTTTCAAAAGTTGTTGAGCCTTTACCTAAAGGAGCTTTTAAATTTATTTTC
AAAAGTTGTTCACCTTTTCCAAAAAGAGTTTTAAATTTACTATCAAAAGTTATTGAACCTTTTCC
TAAAG
Found at i:18749147 original size:91 final size:91
Alignment explanation
Indices: 18748957--18749301 Score: 349
Period size: 91 Copynumber: 3.8 Consensus size: 91
18748947 GTTGTTGAGC
* * * * *
18748957 TTTTAGATTTATTTTTAAAAGTTATTGAGCCTTTACCTAAA-TGAGCTTTTAGATTTATTTTCAA
1 TTTTAAATTT-TTTTCAAAAGTTATTGAACCTTTTCCTAAAGT-AGCTTTTAAATTTATTTTCAA
* *
18749021 AAGTTGTTGCG-CTTTTACCTAAAAGAGT
64 AAGTTGTTGAGCCTTTT-CCTAAAGGAGT
* * *
18749049 TTTTAAATTTGCTCTCAAAAGTTATTGAGCCTTTTCCTAAAGTAGCTTTTAAATTT-TTTTCAAA
1 TTTTAAATTT-TTTTCAAAAGTTATTGAACCTTTTCCTAAAGTAGCTTTTAAATTTATTTTCAAA
* *
18749113 AGTTGTTGAGCCATTTCCTAAAGGGGT
65 AGTTGTTGAGCCTTTTCCTAAAGGAGT
* * * *
18749140 TTTTAAATTTATTTTCAAAAGTTGTTCAACCTTTTCCAAAAAG-AG-TTTTAAATTTATTATCAA
1 TTTTAAATTT-TTTTCAAAAGTTATTGAACCTTTTCC-TAAAGTAGCTTTTAAATTTATTTTCAA
* * * *
18749203 AAGTTATTGAACCTTTTTCTAAAGGAGA
64 AAGTTGTTGAGCCTTTTCCTAAAGGAGT
* * *** *
18749231 TTTTCAATTATTTTTCAAAAGTTGTTGAACCTTTGATTAAAGGAGCTTTTAAATTTATTTTCAAA
1 TTTTAAATT-TTTTTCAAAAGTTATTGAACCTTTTCCTAAAGTAGCTTTTAAATTTATTTTCAAA
*
18749296 AATTGT
65 AGTTGT
18749302 ATTGCTTTTA
Statistics
Matches: 212, Mismatches: 34, Indels: 14
0.82 0.13 0.05
Matches are distributed among these distances:
90 14 0.07
91 119 0.56
92 78 0.37
93 1 0.00
ACGTcount: A:0.31, C:0.11, G:0.13, T:0.45
Consensus pattern (91 bp):
TTTTAAATTTTTTTCAAAAGTTATTGAACCTTTTCCTAAAGTAGCTTTTAAATTTATTTTCAAAA
GTTGTTGAGCCTTTTCCTAAAGGAGT
Found at i:18752009 original size:22 final size:23
Alignment explanation
Indices: 18751975--18752018 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
18751965 TTTTTCGAAA
18751975 AAATAATAATAAAAAAAAAATTT
1 AAATAATAATAAAAAAAAAATTT
**
18751998 AAATAA-AATAAATTAAAAATT
1 AAATAATAATAAAAAAAAAATT
18752019 AAAAATGAGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (23 bp):
AAATAATAATAAAAAAAAAATTT
Found at i:18756206 original size:10 final size:10
Alignment explanation
Indices: 18756191--18756228 Score: 67
Period size: 10 Copynumber: 3.8 Consensus size: 10
18756181 AAGTTGAGTT
*
18756191 GTTAGTAATA
1 GTTAGTTATA
18756201 GTTAGTTATA
1 GTTAGTTATA
18756211 GTTAGTTATA
1 GTTAGTTATA
18756221 GTTAGTTA
1 GTTAGTTA
18756229 ATTCAATTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.32, C:0.00, G:0.21, T:0.47
Consensus pattern (10 bp):
GTTAGTTATA
Found at i:18759987 original size:14 final size:14
Alignment explanation
Indices: 18759953--18759990 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
18759943 GCTTTCATTT
*
18759953 GTTTAGATATAAGA
1 GTTTAGCTATAAGA
18759967 GTTTAGCTATAAGA
1 GTTTAGCTATAAGA
18759981 GTTTAGCTAT
1 GTTTAGCTAT
18759991 CAACTTTGGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.39
Consensus pattern (14 bp):
GTTTAGCTATAAGA
Found at i:18763425 original size:12 final size:12
Alignment explanation
Indices: 18763375--18763428 Score: 54
Period size: 13 Copynumber: 4.3 Consensus size: 12
18763365 GGGTTTTTAG
* *
18763375 GGTTTCACTTTA
1 GGTTTTACTTAA
18763387 GAGTTTTACTTAA
1 G-GTTTTACTTAA
* *
18763400 AGTTTTAGGTTAA
1 GGTTTTA-CTTAA
18763413 GGTTTTACTTAA
1 GGTTTTACTTAA
18763425 GGTT
1 GGTT
18763429 CTGAGTTAGG
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
12 15 0.44
13 19 0.56
ACGTcount: A:0.24, C:0.07, G:0.20, T:0.48
Consensus pattern (12 bp):
GGTTTTACTTAA
Found at i:18763436 original size:25 final size:24
Alignment explanation
Indices: 18763384--18763452 Score: 70
Period size: 25 Copynumber: 2.8 Consensus size: 24
18763374 GGGTTTCACT
* *
18763384 TTAGAGTTTTACTTAAAGTTTTAGG
1 TTAG-GTTTTACTTAAGGTTTGAGG
18763409 TTAAGGTTTTACTTAAGGTTCTGA-G
1 TT-AGGTTTTACTTAAGGTT-TGAGG
*
18763434 TTAGGTTTCACTT-AGGTTT
1 TTAGGTTTTACTTAAGGTTT
18763453 TCCACAAATT
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
22 1 0.03
23 5 0.13
24 10 0.26
25 19 0.49
26 4 0.10
ACGTcount: A:0.23, C:0.07, G:0.22, T:0.48
Consensus pattern (24 bp):
TTAGGTTTTACTTAAGGTTTGAGG
Found at i:18764005 original size:3 final size:3
Alignment explanation
Indices: 18763997--18764023 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
18763987 TAAATTTAAA
18763997 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
18764024 CCTAACTGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:18766876 original size:79 final size:79
Alignment explanation
Indices: 18766770--18766929 Score: 302
Period size: 79 Copynumber: 2.0 Consensus size: 79
18766760 GAAATATGAG
*
18766770 TAGAACTCATATTATAATTATTGTCTATATTATTTTCTGAAAATGATTATTTATATTCATGTTTC
1 TAGAACTCATATTATAATTATTGTCTATATTATTTTCTGAAAATGATTATTTAGATTCATGTTTC
18766835 ATGACTTGCATTGA
66 ATGACTTGCATTGA
*
18766849 TAGAACTCATATTATAATTATTGTCTATATTATTTTTTGAAAATGATTATTTAGATTCATGTTTC
1 TAGAACTCATATTATAATTATTGTCTATATTATTTTCTGAAAATGATTATTTAGATTCATGTTTC
18766914 ATGACTTGCATTGA
66 ATGACTTGCATTGA
18766928 TA
1 TA
18766930 TGGTGATCTA
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
79 79 1.00
ACGTcount: A:0.32, C:0.09, G:0.11, T:0.48
Consensus pattern (79 bp):
TAGAACTCATATTATAATTATTGTCTATATTATTTTCTGAAAATGATTATTTAGATTCATGTTTC
ATGACTTGCATTGA
Found at i:18769738 original size:25 final size:23
Alignment explanation
Indices: 18769693--18769741 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 23
18769683 CTATCCTCGT
* *
18769693 TTCTGTTTTTTTTTATTTTTTTC
1 TTCTCTTTTTTTTTATCTTTTTC
18769716 TTCTCTTTTTTCTTTATACTTTTTC
1 TTCTCTTTTTT-TTTAT-CTTTTTC
18769741 T
1 T
18769742 ACTATTGAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 10 0.45
24 5 0.23
25 7 0.32
ACGTcount: A:0.06, C:0.14, G:0.02, T:0.78
Consensus pattern (23 bp):
TTCTCTTTTTTTTTATCTTTTTC
Found at i:18770132 original size:8 final size:9
Alignment explanation
Indices: 18770112--18770150 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
18770102 TTTATATATA
18770112 TTTTAAAAT
1 TTTTAAAAT
*
18770121 TTTTAAACT
1 TTTTAAAAT
18770130 TTTTAAAA-
1 TTTTAAAAT
*
18770138 TTTTAAGAT
1 TTTTAAAAT
18770147 TTTT
1 TTTT
18770151 TATTTTTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
8 7 0.27
9 19 0.73
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.59
Consensus pattern (9 bp):
TTTTAAAAT
Found at i:18771909 original size:17 final size:18
Alignment explanation
Indices: 18771883--18771922 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
18771873 ATTAAGAGTA
18771883 TCTTAGATTTTTCTC-TT
1 TCTTAGATTTTTCTCTTT
*
18771900 TCTTATATTTTTCTCTTT
1 TCTTAGATTTTTCTCTTT
18771918 TCTTA
1 TCTTA
18771923 ATCAAGAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 14 0.67
18 7 0.33
ACGTcount: A:0.12, C:0.17, G:0.03, T:0.68
Consensus pattern (18 bp):
TCTTAGATTTTTCTCTTT
Found at i:18777891 original size:17 final size:18
Alignment explanation
Indices: 18777869--18777917 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 18
18777859 TGGAGTTTGG
* *
18777869 AAAAAGAATGACAAAA-T
1 AAAAAGAAAGAAAAAACT
18777886 AAAAAGAAAGAAAAAACT
1 AAAAAGAAAGAAAAAACT
18777904 AAAAA-AAA-AAAAAA
1 AAAAAGAAAGAAAAAA
18777918 AAGCCAATCT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 6 0.21
17 17 0.59
18 6 0.21
ACGTcount: A:0.82, C:0.04, G:0.08, T:0.06
Consensus pattern (18 bp):
AAAAAGAAAGAAAAAACT
Done.