Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 113035596
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: 113035596
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 271 characters in sequence are not A, C, G, or T
File 145 of 378
Found at i:41495244 original size:2 final size:2
Alignment explanation
Indices: 41495237--41495274 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
41495227 GAAATATGTG
41495237 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
41495275 GAGTTAGTCG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41495434 original size:45 final size:44
Alignment explanation
Indices: 41495373--41495592 Score: 214
Period size: 45 Copynumber: 5.0 Consensus size: 44
41495363 TAGGATTCCG
*
41495373 ATATGTGATTTCGTGTAAGACCATGTCTGGGACATTGGCATTGAT
1 ATATGTGATTTCGTGTAAGACCATGTCTGGGACATTGGCATCG-T
* *
41495418 ATATGTGATTTCGTGTAAGACCACGTCTGGGACATTGACATCGGT
1 ATATGTGATTTCGTGTAAGACCATGTCTGGGACATTGGCATC-GT
* * * * *
41495463 ATATATGGTTACGTGTAAGACCATGTATGGGACATCGGCATCGT
1 ATATGTGATTTCGTGTAAGACCATGTCTGGGACATTGGCATCGT
* * * *
41495507 AT-T-TGA-TTCATGTAAGACCCTGTCTGGGATAGTGGCATCG-
1 ATATGTGATTTCGTGTAAGACCATGTCTGGGACATTGGCATCGT
* ** * * * * *
41495547 ATATGAGATAGCATGTAAGAACACGTTTGGGACATTGGCATTGT
1 ATATGTGATTTCGTGTAAGACCATGTCTGGGACATTGGCATCGT
41495591 AT
1 AT
41495593 GGTATATGTG
Statistics
Matches: 142, Mismatches: 28, Indels: 11
0.78 0.15 0.06
Matches are distributed among these distances:
40 2 0.01
41 28 0.20
42 4 0.03
43 26 0.18
44 6 0.04
45 75 0.53
46 1 0.01
ACGTcount: A:0.26, C:0.15, G:0.27, T:0.32
Consensus pattern (44 bp):
ATATGTGATTTCGTGTAAGACCATGTCTGGGACATTGGCATCGT
Found at i:41500941 original size:60 final size:60
Alignment explanation
Indices: 41500848--41500967 Score: 240
Period size: 60 Copynumber: 2.0 Consensus size: 60
41500838 ACAATGATCC
41500848 ACCATTAGTCACATACGTGGTAAATCCAAAACCGAAGTATTAAAATCACTCTAACTTATT
1 ACCATTAGTCACATACGTGGTAAATCCAAAACCGAAGTATTAAAATCACTCTAACTTATT
41500908 ACCATTAGTCACATACGTGGTAAATCCAAAACCGAAGTATTAAAATCACTCTAACTTATT
1 ACCATTAGTCACATACGTGGTAAATCCAAAACCGAAGTATTAAAATCACTCTAACTTATT
41500968 CATTGCTACT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.40, C:0.22, G:0.10, T:0.28
Consensus pattern (60 bp):
ACCATTAGTCACATACGTGGTAAATCCAAAACCGAAGTATTAAAATCACTCTAACTTATT
Found at i:41504554 original size:18 final size:18
Alignment explanation
Indices: 41504524--41504558 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
41504514 TCTGACCTTG
41504524 TCTCATAAAAATTCAAATA
1 TCTCATAAAAATT-AAATA
41504543 TCTCAT-AAAATTAAAT
1 TCTCATAAAAATTAAAT
41504559 TCTTTTGCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 6 0.38
19 6 0.38
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.34
Consensus pattern (18 bp):
TCTCATAAAAATTAAATA
Found at i:41506105 original size:42 final size:42
Alignment explanation
Indices: 41506033--41506140 Score: 103
Period size: 42 Copynumber: 2.6 Consensus size: 42
41506023 TCGTATTAAT
** * * *
41506033 GCCATATCCTGGATATGGTCTTACATGAAAT-ATCATA-TCGAC
1 GCCATATCCCAGACATGGTCTTATACGAAATCA-CATACT-GAC
* * *
41506075 GCCATTTCCCTGACATGGTCTTATACGAAATCACATACTGAT
1 GCCATATCCCAGACATGGTCTTATACGAAATCACATACTGAC
*
41506117 GCCATATCCCAGATATGGTCTTAT
1 GCCATATCCCAGACATGGTCTTAT
41506141 TCGGAATCTC
Statistics
Matches: 54, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
42 52 0.96
43 2 0.04
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (42 bp):
GCCATATCCCAGACATGGTCTTATACGAAATCACATACTGAC
Found at i:41514334 original size:40 final size:39
Alignment explanation
Indices: 41514289--41514496 Score: 202
Period size: 40 Copynumber: 5.2 Consensus size: 39
41514279 CGGAATACAA
*
41514289 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* * *
41514329 CCGGATAGAACGACTTGCACAAATGCCTTCGGGTATTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* * *
41514369 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* *** *
41514409 CCGGATGTGGTCACTAGCAC-AATGGCCTTCGGGTCTTAAC
1 CCGGATATAACCACT-GCACAAAT-GCCTTCGGGTCTTAGC
** * * *
41514449 CCGGATATAATTACTAGCATAAATGTCTTCGGGACTTAGC
1 CCGGATATAACCACT-GCACAAATGCCTTCGGGTCTTAGC
41514489 CCGGATAT
1 CCGGATAT
41514497 CATTCAATTG
Statistics
Matches: 141, Mismatches: 24, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
39 4 0.03
40 134 0.95
41 3 0.02
ACGTcount: A:0.25, C:0.26, G:0.24, T:0.25
Consensus pattern (39 bp):
CCGGATATAACCACTGCACAAATGCCTTCGGGTCTTAGC
Found at i:41514429 original size:80 final size:80
Alignment explanation
Indices: 41514289--41514495 Score: 238
Period size: 80 Copynumber: 2.6 Consensus size: 80
41514279 CGGAATACAA
* * *
41514289 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTTGCACAAAT-
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTAGCAC-AATG
*
41514353 GCCTTCGGGTATTAGC
65 GCCTTCGGGTATTAAC
* * **
41514369 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATGTGGTC-ACTAGCACAATG
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGAT-AGAACGACTAGCACAATG
*
41514433 GCCTTCGGGTCTTAAC
65 GCCTTCGGGTATTAAC
** * ** * *
41514449 CCGGATATAATTACTAGCATAAATGTCTTCGGGACTTAGCCCGGATA
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATA
41514496 TCATTCAATT
Statistics
Matches: 107, Mismatches: 18, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
79 3 0.03
80 102 0.95
81 2 0.02
ACGTcount: A:0.25, C:0.26, G:0.24, T:0.25
Consensus pattern (80 bp):
CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTAGCACAATGG
CCTTCGGGTATTAAC
Found at i:41518026 original size:40 final size:40
Alignment explanation
Indices: 41517927--41518102 Score: 288
Period size: 40 Copynumber: 4.5 Consensus size: 40
41517917 AAACCAAGTA
* * *
41517927 CCTTCGGGATTTAG-CCGGATATAGCT-ACTCGCTCAACTG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
41517966 CCTTC-GGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
41518005 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
41518045 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
41518085 CCTTC-GGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
41518103 TTATCATCCG
Statistics
Matches: 131, Mismatches: 3, Indels: 6
0.94 0.02 0.04
Matches are distributed among these distances:
38 8 0.06
39 44 0.34
40 79 0.60
ACGTcount: A:0.24, C:0.29, G:0.23, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:41518075 original size:80 final size:79
Alignment explanation
Indices: 41517927--41518102 Score: 286
Period size: 79 Copynumber: 2.2 Consensus size: 79
41517917 AAACCAAGTA
* * *
41517927 CCTTCGGGATTTAG-CCGGATATAGCTACTCGCTCAACTGCCTTCGGACTTAGCCCGGATATAGT
1 CCTTCGGGACTTAGCCCGGATATAGCTACTCGCACAAATGCCTTCGGACTTAGCCCGGATATAGT
41517991 AACTCGCACAAATG
66 AACTCGCACAAATG
41518005 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATA
1 CCTTCGGGACTTAGCCCGGATATAGCT-ACTCGCACAAATGCCTTC-GGACTTAGCCCGGATATA
41518069 GTAACTCGCACAAATG
64 GTAACTCGCACAAATG
41518085 CCTTC-GGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
41518103 TTATCATCCG
Statistics
Matches: 92, Mismatches: 3, Indels: 5
0.92 0.03 0.05
Matches are distributed among these distances:
78 14 0.15
79 39 0.42
80 39 0.42
ACGTcount: A:0.24, C:0.29, G:0.23, T:0.24
Consensus pattern (79 bp):
CCTTCGGGACTTAGCCCGGATATAGCTACTCGCACAAATGCCTTCGGACTTAGCCCGGATATAGT
AACTCGCACAAATG
Found at i:41525889 original size:40 final size:40
Alignment explanation
Indices: 41525819--41525956 Score: 226
Period size: 40 Copynumber: 3.5 Consensus size: 40
41525809 AAACCAAGTA
* * *
41525819 CCTTCGGGATTTAG-CCGGATATAGCT-ACTCGCTCAACTG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
41525858 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
41525898 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
41525938 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
41525957 TTATCATGAA
Statistics
Matches: 94, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
39 14 0.15
40 80 0.85
ACGTcount: A:0.23, C:0.29, G:0.24, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:41530924 original size:79 final size:81
Alignment explanation
Indices: 41530823--41531007 Score: 218
Period size: 79 Copynumber: 2.3 Consensus size: 81
41530813 ACGACTCACT
** * *
41530823 CAAATGCCTTCGGGACGAAGCCCGG-TTATAGTGACTCGCACGAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCACGAATGCCTTC-GGATCCTAACCC
* *
41530886 GGGTTTAGTAACTT-GCA
64 GGATATAGTAACTTAGCA
* * **
41530903 CAAATACCTTCGGG-CTTAGCCCGGATTTATTAACTCGCACGAATGCCTTCGGATCCTAGTCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACGAATGCCTTCGGATCCTAACCCGG
*
41530967 ATATAGTCACTTAGCA
66 ATATAGTAACTTAGCA
41530983 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
41531008 CATCATTCGA
Statistics
Matches: 89, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
78 3 0.03
79 53 0.60
80 33 0.37
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.24
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACGAATGCCTTCGGATCCTAACCCGG
ATATAGTAACTTAGCA
Found at i:41530937 original size:39 final size:40
Alignment explanation
Indices: 41530823--41531007 Score: 180
Period size: 40 Copynumber: 4.7 Consensus size: 40
41530813 ACGACTCACT
** * *
41530823 CAAATGCCTTCGGGACGAAGCCCGG-TTATAGTGACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTTGCA
* * *
41530863 CGAATGCCTTCGGGACTTAACCCGGGTTTAGTAACTTGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTTGCA
* * *
41530903 CAAATACCTTCGGG-CTTAGCCCGGATTTATTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTTGCA
* * * * *
41530942 CGAATGCCTTC-GGATCCTAGTCCGGATATAGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAACTT-GCA
41530983 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
41531008 CATCATTCGA
Statistics
Matches: 117, Mismatches: 23, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
38 2 0.02
39 30 0.26
40 74 0.63
41 11 0.09
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTTGCA
Found at i:41534260 original size:28 final size:28
Alignment explanation
Indices: 41534214--41534282 Score: 113
Period size: 28 Copynumber: 2.5 Consensus size: 28
41534204 TTTAAAACCC
* *
41534214 TAGGGGT-ATATCGGTAATTTTGCTTTT
1 TAGGGGTAATTTCGGTAATTTTGCTCTT
41534241 TAGGGGTAATTTCGGTAATTTTGCTCTT
1 TAGGGGTAATTTCGGTAATTTTGCTCTT
41534269 TAGGGGTAATTTCG
1 TAGGGGTAATTTCG
41534283 TGATCTACGC
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
27 7 0.18
28 32 0.82
ACGTcount: A:0.19, C:0.09, G:0.28, T:0.45
Consensus pattern (28 bp):
TAGGGGTAATTTCGGTAATTTTGCTCTT
Found at i:41534987 original size:54 final size:54
Alignment explanation
Indices: 41534920--41535070 Score: 248
Period size: 54 Copynumber: 2.8 Consensus size: 54
41534910 TACCCTACAA
* *
41534920 GGGTATTTCGGTAATTTTATAAACAAAGGGTATTTTAGTAATTTTACAAACCAG
1 GGGTATTTTGGTAATTTTATAAACCAAGGGTATTTTAGTAATTTTACAAACCAG
* *
41534974 GGGTATTTTGGTAATTTTGTAAACCAAGGGTATTTTAGTAATTTTACAAACTAG
1 GGGTATTTTGGTAATTTTATAAACCAAGGGTATTTTAGTAATTTTACAAACCAG
* *
41535028 GGGTATTTTGGTGATTTTATAAACCAAGGGTATTTTGGTAATT
1 GGGTATTTTGGTAATTTTATAAACCAAGGGTATTTTAGTAATT
41535071 CTGTAAATTG
Statistics
Matches: 90, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 90 1.00
ACGTcount: A:0.31, C:0.07, G:0.21, T:0.40
Consensus pattern (54 bp):
GGGTATTTTGGTAATTTTATAAACCAAGGGTATTTTAGTAATTTTACAAACCAG
Found at i:41535008 original size:81 final size:81
Alignment explanation
Indices: 41534917--41535077 Score: 232
Period size: 81 Copynumber: 2.0 Consensus size: 81
41534907 TTCTACCCTA
* * *
41534917 CAAGGGTATTTCGGTAATTTTATAAACAAAGGGTATTTTAGTAATTTTACAAACCAGGGGTATTT
1 CAAGGGTATTTCAGTAATTTTACAAACAAAGGGTATTTTAGTAATTTTACAAACCAAGGGTATTT
*
41534982 TGGTAATTTTGTAAAC
66 TGGTAATTCTGTAAAC
* * * * * *
41534998 CAAGGGTATTTTAGTAATTTTACAAACTAGGGGTATTTTGGTGATTTTATAAACCAAGGGTATTT
1 CAAGGGTATTTCAGTAATTTTACAAACAAAGGGTATTTTAGTAATTTTACAAACCAAGGGTATTT
41535063 TGGTAATTCTGTAAA
66 TGGTAATTCTGTAAA
41535078 TTGAAGGTAA
Statistics
Matches: 70, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
81 70 1.00
ACGTcount: A:0.32, C:0.08, G:0.20, T:0.39
Consensus pattern (81 bp):
CAAGGGTATTTCAGTAATTTTACAAACAAAGGGTATTTTAGTAATTTTACAAACCAAGGGTATTT
TGGTAATTCTGTAAAC
Found at i:41535077 original size:27 final size:27
Alignment explanation
Indices: 41534917--41535070 Score: 209
Period size: 27 Copynumber: 5.7 Consensus size: 27
41534907 TTCTACCCTA
*
41534917 CAAGGGTATTTCGGTAATTTTATAAAC
1 CAAGGGTATTTTGGTAATTTTATAAAC
* * *
41534944 AAAGGGTATTTTAGTAATTTTACAAAC
1 CAAGGGTATTTTGGTAATTTTATAAAC
* *
41534971 CAGGGGTATTTTGGTAATTTTGTAAAC
1 CAAGGGTATTTTGGTAATTTTATAAAC
* *
41534998 CAAGGGTATTTTAGTAATTTTACAAAC
1 CAAGGGTATTTTGGTAATTTTATAAAC
* * *
41535025 TAGGGGTATTTTGGTGATTTTATAAAC
1 CAAGGGTATTTTGGTAATTTTATAAAC
41535052 CAAGGGTATTTTGGTAATT
1 CAAGGGTATTTTGGTAATT
41535071 CTGTAAATTG
Statistics
Matches: 106, Mismatches: 21, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 106 1.00
ACGTcount: A:0.32, C:0.08, G:0.21, T:0.40
Consensus pattern (27 bp):
CAAGGGTATTTTGGTAATTTTATAAAC
Found at i:41535096 original size:81 final size:81
Alignment explanation
Indices: 41534928--41535097 Score: 189
Period size: 81 Copynumber: 2.1 Consensus size: 81
41534918 AAGGGTATTT
* * *
41534928 CGGTAATTTTATAAACAAAGGGTATTTTAGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTG
1 CGGTAATTTTACAAACAAAGGGTATTTTAGTAATTTTACAAACCAAGGGTATTTTGGTAATTCTG
***
41534993 TAAACCAAGGGTATTT
66 TAAACCAAGGGTAAAA
** * * * * *
41535009 TAGTAATTTTACAAACTAGGGGTATTTTGGTGATTTTATAAACCAAGGGTATTTTGGTAATTCTG
1 CGGTAATTTTACAAACAAAGGGTATTTTAGTAATTTTACAAACCAAGGGTATTTTGGTAATTCTG
**
41535074 TAAATTGAA-GGTAAAA
66 TAAA-CCAAGGGTAAAA
41535090 CGGTAATT
1 CGGTAATT
41535098 CTGTAAACTG
Statistics
Matches: 71, Mismatches: 17, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
81 69 0.97
82 2 0.03
ACGTcount: A:0.34, C:0.08, G:0.21, T:0.38
Consensus pattern (81 bp):
CGGTAATTTTACAAACAAAGGGTATTTTAGTAATTTTACAAACCAAGGGTATTTTGGTAATTCTG
TAAACCAAGGGTAAAA
Found at i:41535327 original size:27 final size:28
Alignment explanation
Indices: 41535065--41535305 Score: 295
Period size: 27 Copynumber: 8.9 Consensus size: 28
41535055 GGGTATTTTG
* * *
41535065 GTAATTCTGTAAA-TTGAAGGTAAAACG
1 GTAATTCTGTAAACTCGAGGGTAAAACA
*
41535092 GTAATTCTGTAAACT-GAGGGTAAAACG
1 GTAATTCTGTAAACTCGAGGGTAAAACA
* *
41535119 GTAATTCTATAAA-TCGAGGGTAAAATA
1 GTAATTCTGTAAACTCGAGGGTAAAACA
41535146 GTAATTCTGTAAACT-GA-GGTGAAAACA
1 GTAATTCTGTAAACTCGAGGGT-AAAACA
* *
41535173 GTAATTCTGTAAA-TCGAGGATAAAATA
1 GTAATTCTGTAAACTCGAGGGTAAAACA
*
41535200 GTAATTCTGTAAACT-GAGGGTAAAACG
1 GTAATTCTGTAAACTCGAGGGTAAAACA
41535227 GTAATTCTGTAAA-TCGAGGGTAAAACA
1 GTAATTCTGTAAACTCGAGGGTAAAACA
**
41535254 GTAATTCTGTAAACT-GAGGGTAAAATG
1 GTAATTCTGTAAACTCGAGGGTAAAACA
*
41535281 GTAATTCTATAAA-TCGAGGGTAAAA
1 GTAATTCTGTAAACTCGAGGGTAAAA
41535306 TGGTAATTTT
Statistics
Matches: 189, Mismatches: 15, Indels: 20
0.84 0.07 0.09
Matches are distributed among these distances:
26 7 0.04
27 176 0.93
28 6 0.03
ACGTcount: A:0.41, C:0.09, G:0.22, T:0.28
Consensus pattern (28 bp):
GTAATTCTGTAAACTCGAGGGTAAAACA
Found at i:41535327 original size:54 final size:54
Alignment explanation
Indices: 41535064--41535313 Score: 385
Period size: 54 Copynumber: 4.6 Consensus size: 54
41535054 AGGGTATTTT
* * **
41535064 GGTAATTCTGTAAATTGAAGGTAAAACGGTAATTCTGTAAACTGAGGGTAAAAC
1 GGTAATTCTGTAAATCGAGGGTAAAATAGTAATTCTGTAAACTGAGGGTAAAAC
*
41535118 GGTAATTCTATAAATCGAGGGTAAAATAGTAATTCTGTAAACTGA-GGTGAAAAC
1 GGTAATTCTGTAAATCGAGGGTAAAATAGTAATTCTGTAAACTGAGGGT-AAAAC
* *
41535172 AGTAATTCTGTAAATCGAGGATAAAATAGTAATTCTGTAAACTGAGGGTAAAAC
1 GGTAATTCTGTAAATCGAGGGTAAAATAGTAATTCTGTAAACTGAGGGTAAAAC
* *
41535226 GGTAATTCTGTAAATCGAGGGTAAAACAGTAATTCTGTAAACTGAGGGTAAAAT
1 GGTAATTCTGTAAATCGAGGGTAAAATAGTAATTCTGTAAACTGAGGGTAAAAC
* *
41535280 GGTAATTCTATAAATCGAGGGTAAAATGGTAATT
1 GGTAATTCTGTAAATCGAGGGTAAAATAGTAATT
41535314 TTACAAGTCG
Statistics
Matches: 179, Mismatches: 15, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
53 3 0.02
54 173 0.97
55 3 0.02
ACGTcount: A:0.40, C:0.09, G:0.23, T:0.28
Consensus pattern (54 bp):
GGTAATTCTGTAAATCGAGGGTAAAATAGTAATTCTGTAAACTGAGGGTAAAAC
Found at i:41535327 original size:81 final size:81
Alignment explanation
Indices: 41535063--41535313 Score: 357
Period size: 81 Copynumber: 3.1 Consensus size: 81
41535053 AAGGGTATTT
* * * *
41535063 TGGTAATTCTGTAAATTGAAGGTAAAACGGTAATTCTGTAAACTGAGGGTAAAACGGTAATTCTA
1 TGGTAATTCTGTAAATCGAGGGTAAAACAGTAATTCTGTAAACTGAGGGTAAAATGGTAATTCTA
41535128 TAAATCGAGGGTAAAA
66 TAAATCGAGGGTAAAA
* * *
41535144 TAGTAATTCTGTAAA-CTGA-GGTGAAAACAGTAATTCTGTAAA-TCGAGGATAAAATAGTAATT
1 TGGTAATTCTGTAAATC-GAGGGT-AAAACAGTAATTCTGTAAACT-GAGGGTAAAATGGTAATT
*
41535206 CTGTAAA-CTGAGGGTAAAA
63 CTATAAATC-GAGGGTAAAA
*
41535225 CGGTAATTCTGTAAATCGAGGGTAAAACAGTAATTCTGTAAACTGAGGGTAAAATGGTAATTCTA
1 TGGTAATTCTGTAAATCGAGGGTAAAACAGTAATTCTGTAAACTGAGGGTAAAATGGTAATTCTA
41535290 TAAATCGAGGGTAAAA
66 TAAATCGAGGGTAAAA
41535306 TGGTAATT
1 TGGTAATT
41535314 TTACAAGTCG
Statistics
Matches: 149, Mismatches: 13, Indels: 16
0.84 0.07 0.09
Matches are distributed among these distances:
80 5 0.03
81 138 0.93
82 6 0.04
ACGTcount: A:0.40, C:0.09, G:0.23, T:0.29
Consensus pattern (81 bp):
TGGTAATTCTGTAAATCGAGGGTAAAACAGTAATTCTGTAAACTGAGGGTAAAATGGTAATTCTA
TAAATCGAGGGTAAAA
Found at i:41547047 original size:50 final size:49
Alignment explanation
Indices: 41546926--41547101 Score: 201
Period size: 50 Copynumber: 3.5 Consensus size: 49
41546916 TGAGGTCGCA
* * *
41546926 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACTC-GATAACTTCGATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTA-TCAGATAA-TT-GGTCACG
*
41546977 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGATTAGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATAATT-GGTCACG
* * * ** *
41547027 TGTGTAGTGCTAAGTGCAGGCTACTACATGTACCAGATAATTGGTTGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATAATTGGTCACG
* *
41547076 TGTGTAGTACTATGTACAGGCTACTA
1 TGTGTAGTACTAAGTGCAGGCTACTA
41547102 TGCGTACCAG
Statistics
Matches: 109, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
49 27 0.25
50 48 0.44
51 34 0.31
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.31
Consensus pattern (49 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATAATTGGTCACG
Found at i:41552756 original size:27 final size:27
Alignment explanation
Indices: 41552688--41552758 Score: 72
Period size: 27 Copynumber: 2.6 Consensus size: 27
41552678 CGACTTGTAA
* *
41552688 AATTACCAAAGTACTCC-CGATTTACAG
1 AATTACCAAAATAC-CCTCAATTTACAG
****
41552715 AATTACCGTTTTACCCTCAATTTACAG
1 AATTACCAAAATACCCTCAATTTACAG
41552742 AATTACCAAAATACCCT
1 AATTACCAAAATACCCT
41552759 TGGTTTATAA
Statistics
Matches: 34, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
26 2 0.06
27 32 0.94
ACGTcount: A:0.37, C:0.27, G:0.07, T:0.30
Consensus pattern (27 bp):
AATTACCAAAATACCCTCAATTTACAG
Found at i:41552765 original size:27 final size:27
Alignment explanation
Indices: 41552742--41552865 Score: 169
Period size: 27 Copynumber: 4.6 Consensus size: 27
41552732 CAATTTACAG
41552742 AATTACCAAAATACCCTTGGTTTATAA
1 AATTACCAAAATACCCTTGGTTTATAA
* * *
41552769 AATCACCAAAATACCCCTGGTTTGTAA
1 AATTACCAAAATACCCTTGGTTTATAA
* *
41552796 AATTACTAAAATACCCTTTGTTTATAA
1 AATTACCAAAATACCCTTGGTTTATAA
*
41552823 AATTACCAAAATACCCATGGTTTGA-AA
1 AATTACCAAAATACCCTTGGTTT-ATAA
*
41552850 AATTACTAAAATACCC
1 AATTACCAAAATACCC
41552866 CTGTAGGGTA
Statistics
Matches: 84, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
27 83 0.99
28 1 0.01
ACGTcount: A:0.42, C:0.20, G:0.07, T:0.31
Consensus pattern (27 bp):
AATTACCAAAATACCCTTGGTTTATAA
Found at i:41552784 original size:54 final size:53
Alignment explanation
Indices: 41552726--41552865 Score: 138
Period size: 54 Copynumber: 2.6 Consensus size: 53
41552716 ATTACCGTTT
41552726 TACCCTCAATT-TACAGAATTACCAAAATACCCTTGGTTTATAAAATCACCAAAA
1 TACCCTCAATTGTA-A-AATTACCAAAATACCCTTGGTTTATAAAATCACCAAAA
*** * * *
41552780 TACCCCTGGTTTGTAAAATTACTAAAATACCCTTTGTTTATAAAATTACCAAAA
1 TA-CCCTCAATTGTAAAATTACCAAAATACCCTTGGTTTATAAAATCACCAAAA
*** * *
41552834 TACCCATGGTTTGAAAAATTACTAAAATACCC
1 TACCC-TCAATTGTAAAATTACCAAAATACCC
41552866 CTGTAGGGTA
Statistics
Matches: 76, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
53 3 0.04
54 64 0.84
55 7 0.09
56 2 0.03
ACGTcount: A:0.41, C:0.21, G:0.07, T:0.31
Consensus pattern (53 bp):
TACCCTCAATTGTAAAATTACCAAAATACCCTTGGTTTATAAAATCACCAAAA
Found at i:41552877 original size:81 final size:81
Alignment explanation
Indices: 41552742--41552894 Score: 220
Period size: 81 Copynumber: 1.9 Consensus size: 81
41552732 CAATTTACAG
* **
41552742 AATTACCAAAATACCCTTGGTTTATAAAATCACCAAAATACCCCTGGTTTGTAAAATTACTAAAA
1 AATTACCAAAATACCCATGGTTTATAAAATCACCAAAATACCCCTGGTGGGTAAAATTACTAAAA
41552807 TACCCTTTGTTTATAA
66 TACCCTTTGTTTATAA
* * *
41552823 AATTACCAAAATACCCATGGTTTGA-AAAATTACTAAAATACCCCT-GTAGGGTAAAATTACTGA
1 AATTACCAAAATACCCATGGTTT-ATAAAATCACCAAAATACCCCTGGT-GGGTAAAATTACTAA
41552886 AATACCCTT
64 AATACCCTT
41552895 GTGGGGTAAA
Statistics
Matches: 64, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
80 2 0.03
81 61 0.95
82 1 0.02
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.31
Consensus pattern (81 bp):
AATTACCAAAATACCCATGGTTTATAAAATCACCAAAATACCCCTGGTGGGTAAAATTACTAAAA
TACCCTTTGTTTATAA
Found at i:41552878 original size:27 final size:27
Alignment explanation
Indices: 41552848--41552909 Score: 97
Period size: 27 Copynumber: 2.3 Consensus size: 27
41552838 CATGGTTTGA
41552848 AAAATTACTAAAATACCCCTGTAGGGT
1 AAAATTACTAAAATACCCCTGTAGGGT
* * *
41552875 AAAATTACTGAAATACCCTTGTGGGGT
1 AAAATTACTAAAATACCCCTGTAGGGT
41552902 AAAATTAC
1 AAAATTAC
41552910 CATTTTGCCC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.27
Consensus pattern (27 bp):
AAAATTACTAAAATACCCCTGTAGGGT
Found at i:41552878 original size:54 final size:54
Alignment explanation
Indices: 41552742--41552892 Score: 162
Period size: 54 Copynumber: 2.8 Consensus size: 54
41552732 CAATTTACAG
* ** * * *
41552742 AATTACCAAAATACCCT-TGGTTTATAAAATCACCAAAATACCCCTGGTTTGTAA
1 AATTACTAAAATACCCTCT-GTGGATAAAATTACCAAAATACCCATGGTTTGAAA
* **
41552796 AATTACTAAAATACCCTTTGTTTATAAAATTACCAAAATACCCATGGTTTGAAA
1 AATTACTAAAATACCCTCTGTGGATAAAATTACCAAAATACCCATGGTTTGAAA
* **
41552850 AATTACTAAAATACCC-CTGTAGGGTAAAATTACTGAAATACCC
1 AATTACTAAAATACCCTCTGT-GGATAAAATTACCAAAATACCC
41552893 TTGTGGGGTA
Statistics
Matches: 85, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
53 3 0.04
54 81 0.95
55 1 0.01
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.30
Consensus pattern (54 bp):
AATTACTAAAATACCCTCTGTGGATAAAATTACCAAAATACCCATGGTTTGAAA
Found at i:41554200 original size:9 final size:9
Alignment explanation
Indices: 41554186--41554210 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
41554176 TTAATTTGGG
41554186 TTTTTTTAT
1 TTTTTTTAT
41554195 TTTTTTTAT
1 TTTTTTTAT
41554204 TTTTTTT
1 TTTTTTT
41554211 TATTATGCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (9 bp):
TTTTTTTAT
Found at i:41554201 original size:10 final size:10
Alignment explanation
Indices: 41554186--41554214 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
41554176 TTAATTTGGG
41554186 TTTTTTTA-T
1 TTTTTTTATT
41554195 TTTTTTTATT
1 TTTTTTTATT
41554205 TTTTTTTATT
1 TTTTTTTATT
41554215 ATGCTTAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 8 0.42
10 11 0.58
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (10 bp):
TTTTTTTATT
Found at i:41556134 original size:40 final size:40
Alignment explanation
Indices: 41556054--41556272 Score: 354
Period size: 40 Copynumber: 5.5 Consensus size: 40
41556044 TTCGGATGAC
*
41556054 ATCCGGGCTAAGTCCCGAAGGCA-TGGTGCTAGTGACTAT
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAT
* *
41556093 ATCCGGGCTAAGTCCTGAAGGCAGTTGTGCTAGTGACTAT
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAT
*
41556133 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACTAT
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAT
41556173 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAT
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAT
*
41556213 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTG-CTAT
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGACTAT
*
41556253 ATCC-GGCTAAATCCCGAAGG
1 ATCCGGGCTAAGTCCCGAAGG
41556273 TACTTGGGTT
Statistics
Matches: 170, Mismatches: 8, Indels: 4
0.93 0.04 0.02
Matches are distributed among these distances:
39 37 0.22
40 131 0.77
41 2 0.01
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (40 bp):
ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAT
Found at i:41558506 original size:40 final size:40
Alignment explanation
Indices: 41558451--41558660 Score: 305
Period size: 40 Copynumber: 5.2 Consensus size: 40
41558441 AACATTGGAA
41558451 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
41558491 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
41558531 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * *
41558571 ATATATCCGGGCTAAGACCCGAAGGCCTTTGTGCAAG-TC
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * * * *
41558610 ACCAAATCCGGGTTATGACCCGAAGGCAATCGTGCGAGTCG
1 A-TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
*
41558651 CTATATCCGG
1 ATATATCCGG
41558661 TTAAATCCCG
Statistics
Matches: 151, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
39 2 0.01
40 149 0.99
ACGTcount: A:0.25, C:0.24, G:0.29, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
Found at i:41566641 original size:40 final size:40
Alignment explanation
Indices: 41566586--41566795 Score: 305
Period size: 40 Copynumber: 5.2 Consensus size: 40
41566576 AACATTGGAA
41566586 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
41566626 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
41566666 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * *
41566706 ATATATCCGGGCTAAGACCCGAAGGCCTTTGTGCAAG-TC
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * * * *
41566745 ACCAAATCCGGGTTATGACCCGAAGGCAATCGTGCGAGTCG
1 A-TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
*
41566786 CTATATCCGG
1 ATATATCCGG
41566796 TTAAATCCCG
Statistics
Matches: 151, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
39 2 0.01
40 149 0.99
ACGTcount: A:0.25, C:0.24, G:0.29, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
Found at i:41571840 original size:23 final size:26
Alignment explanation
Indices: 41571790--41571842 Score: 67
Period size: 23 Copynumber: 2.2 Consensus size: 26
41571780 ATGCAAATTA
*
41571790 CATGAGAGATATTGGCATGGGAATAT
1 CATGAGAGATATTGGCATGGGAAAAT
*
41571816 CATGAGA-AT-TT-GCATGGTAAAAT
1 CATGAGAGATATTGGCATGGGAAAAT
41571839 CATG
1 CATG
41571843 GGTATGAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 14 0.56
24 2 0.08
25 2 0.08
26 7 0.28
ACGTcount: A:0.36, C:0.09, G:0.26, T:0.28
Consensus pattern (26 bp):
CATGAGAGATATTGGCATGGGAAAAT
Found at i:41574083 original size:16 final size:16
Alignment explanation
Indices: 41574062--41574093 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
41574052 TTGGATAGCT
41574062 GGCCTATCTGAGTTTC
1 GGCCTATCTGAGTTTC
41574078 GGCCTATCTGAGTTTC
1 GGCCTATCTGAGTTTC
41574094 AAGTCCTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.25, G:0.25, T:0.38
Consensus pattern (16 bp):
GGCCTATCTGAGTTTC
Found at i:41581400 original size:43 final size:43
Alignment explanation
Indices: 41581351--41581477 Score: 159
Period size: 43 Copynumber: 3.0 Consensus size: 43
41581341 GGTTATCAAG
*
41581351 ATGTGATTTCATGTAAGACCATGTCTGGGACATTGGCATTGTAT
1 ATGTGATTACATGTAAGACCATGTCTGGGACA-TGGCATTGTAT
* * *
41581395 -TGTGATTACGTGTAAGACCCTGTCTGGGACAGTGGCA-TCTAT
1 ATGTGATTACATGTAAGACCATGTCTGGGACA-TGGCATTGTAT
* * *
41581437 ATGTGATAACATGTAAGACCATATCTGGGATATGGCATTGT
1 ATGTGATTACATGTAAGACCATGTCTGGGACATGGCATTGT
41581478 TTGAGCTTTA
Statistics
Matches: 70, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
42 9 0.13
43 61 0.87
ACGTcount: A:0.26, C:0.15, G:0.26, T:0.33
Consensus pattern (43 bp):
ATGTGATTACATGTAAGACCATGTCTGGGACATGGCATTGTAT
Found at i:41583941 original size:27 final size:28
Alignment explanation
Indices: 41583907--41583976 Score: 97
Period size: 27 Copynumber: 2.5 Consensus size: 28
41583897 ATAGTGAGTC
*
41583907 CGCACACTCAGTGCTATATAAT-CAACT
1 CGCACACTTAGTGCTATATAATCCAACT
* * *
41583934 CGCGCACTTAGTGATATATGATCCAACT
1 CGCACACTTAGTGCTATATAATCCAACT
41583962 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
41583977 GTACAAATTT
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
27 18 0.50
28 18 0.50
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCCAACT
Found at i:41587820 original size:44 final size:44
Alignment explanation
Indices: 41587769--41587877 Score: 191
Period size: 44 Copynumber: 2.5 Consensus size: 44
41587759 TGGCTGAGTA
*
41587769 AATGGCACTATGTGTGCGATACCAATATAAGTTTAGTTTCAGGT
1 AATGGCACTATGTGTGCGATACCAATATAAGTTTAGTTTAAGGT
41587813 AATGGCACTATGTGTGCGATACCAATATAAGTTTAGTTTAAGGT
1 AATGGCACTATGTGTGCGATACCAATATAAGTTTAGTTTAAGGT
* *
41587857 AATGGCACTAAGTGTGTGATA
1 AATGGCACTATGTGTGCGATA
41587878 TAATTATAGC
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 62 1.00
ACGTcount: A:0.31, C:0.12, G:0.24, T:0.33
Consensus pattern (44 bp):
AATGGCACTATGTGTGCGATACCAATATAAGTTTAGTTTAAGGT
Found at i:41597715 original size:46 final size:46
Alignment explanation
Indices: 41597643--41597817 Score: 172
Period size: 46 Copynumber: 3.8 Consensus size: 46
41597633 TGTAACCCGC
*
41597643 CCATAAGTGAACTCGGACTCACCTCAACGAGCTCGGGCGTTCACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCACAT
* * * *
41597689 CCATAAGTGAACTCGGACTCAACTCAACGAGCTAGGGTG-CCTACTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTC-ACAT
* *** * * * * * *
41597735 ACATCTCTCGAACTCGGACTCAACACAACGAGTTCAGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCACAT
* *
41597782 CCATAAGTGAACTCAGACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG
41597818 ATGCCCAAAT
Statistics
Matches: 100, Mismatches: 26, Indels: 6
0.76 0.20 0.05
Matches are distributed among these distances:
45 1 0.01
46 68 0.68
47 30 0.30
48 1 0.01
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCACAT
Found at i:41612484 original size:27 final size:27
Alignment explanation
Indices: 41612453--41612597 Score: 141
Period size: 27 Copynumber: 5.4 Consensus size: 27
41612443 GGATAAGTTA
*
41612453 TAGAATTACCAAAATACCCCTGTAAGG
1 TAGAATTACCGAAATACCCCTGTAAGG
*
41612480 TAGAATTACCGAAATACCCCTAT-AGG
1 TAGAATTACCGAAATACCCCTGTAAGG
* *
41612506 ATAGAATTACCGAAATACCCTTGTAGGG
1 -TAGAATTACCGAAATACCCCTGTAAGG
* *
41612534 TAGAAATATCGAAATACCCCTGT-AGG
1 TAGAATTACCGAAATACCCCTGTAAGG
* * * * **
41612560 ATAAAATTACTGAGATACCCTTGTGGGG
1 -TAGAATTACCGAAATACCCCTGTAAGG
*
41612588 TAAAATTACC
1 TAGAATTACC
41612598 ATTTTGCCCC
Statistics
Matches: 97, Mismatches: 17, Indels: 8
0.80 0.14 0.07
Matches are distributed among these distances:
26 5 0.05
27 88 0.91
28 4 0.04
ACGTcount: A:0.38, C:0.19, G:0.18, T:0.25
Consensus pattern (27 bp):
TAGAATTACCGAAATACCCCTGTAAGG
Found at i:41612536 original size:54 final size:54
Alignment explanation
Indices: 41612452--41612597 Score: 193
Period size: 54 Copynumber: 2.7 Consensus size: 54
41612442 TGGATAAGTT
* * *
41612452 ATAGAATTACCAAAATACCCCTGTAAGGTAGAATTACCGAAATACCCCTATAGG
1 ATAGAATTACCGAAATACCCTTGTAGGGTAGAATTACCGAAATACCCCTATAGG
* * *
41612506 ATAGAATTACCGAAATACCCTTGTAGGGTAGAAATATCGAAATACCCCTGTAGG
1 ATAGAATTACCGAAATACCCTTGTAGGGTAGAATTACCGAAATACCCCTATAGG
* * * * *
41612560 ATAAAATTACTGAGATACCCTTGTGGGGTAAAATTACC
1 ATAGAATTACCGAAATACCCTTGTAGGGTAGAATTACC
41612598 ATTTTGCCCC
Statistics
Matches: 79, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
54 79 1.00
ACGTcount: A:0.38, C:0.19, G:0.18, T:0.25
Consensus pattern (54 bp):
ATAGAATTACCGAAATACCCTTGTAGGGTAGAATTACCGAAATACCCCTATAGG
Found at i:41617500 original size:27 final size:27
Alignment explanation
Indices: 41617470--41617559 Score: 94
Period size: 27 Copynumber: 3.3 Consensus size: 27
41617460 TGGATAAGTT
41617470 GTAGAATTACCGAAATACCATTGTAAG
1 GTAGAATTACCGAAATACCATTGTAAG
* *
41617497 GTAGATTTAGCGAAATACCATTGT-AG
1 GTAGAATTACCGAAATACCATTGTAAG
* * * *
41617523 TGTATAAATACCGAAATAACC-CTGTAGG
1 -GTAGAATTACCGAAAT-ACCATTGTAAG
41617551 GTAGAATTA
1 GTAGAATTA
41617560 TTAAGATACC
Statistics
Matches: 50, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
26 2 0.04
27 44 0.88
28 4 0.08
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.28
Consensus pattern (27 bp):
GTAGAATTACCGAAATACCATTGTAAG
Found at i:41622016 original size:43 final size:44
Alignment explanation
Indices: 41621879--41622097 Score: 295
Period size: 45 Copynumber: 5.0 Consensus size: 44
41621869 ATATCGCACA
* *
41621879 ATACTATTCGGGCCTCTGAGCATAGCAGGCTATAATG-CGGATGAG
1 ATACTATTCGGGCTTC-GAGCCTAGCAGGCTATAATGCCGG-TGAG
*
41621924 ATACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAG
1 ATACTATTCGGG-CTTCGAGCCTAGCAGGCTATAATGCCGGTGAG
*
41621969 ATACTATTCGGGCTTCGAGCCTAGCAGGCGA-AATGCCGGTGAG
1 ATACTATTCGGGCTTCGAGCCTAGCAGGCTATAATGCCGGTGAG
* *
41622012 ATACTATTCGGGCTTTCGAGCCTAGCAGGCTATAATGCTGGTGAA
1 ATACTATTCGGGC-TTCGAGCCTAGCAGGCTATAATGCCGGTGAG
*
41622057 ATGA-TA-TCGGGCTTCGAGCCTAGCAGGCGA-AATGCCGGTGA
1 AT-ACTATTCGGGCTTCGAGCCTAGCAGGCTATAATGCCGGTGA
41622098 ATGAATTTGG
Statistics
Matches: 159, Mismatches: 10, Indels: 13
0.87 0.05 0.07
Matches are distributed among these distances:
42 10 0.06
43 42 0.26
44 40 0.25
45 61 0.38
46 6 0.04
ACGTcount: A:0.24, C:0.21, G:0.30, T:0.24
Consensus pattern (44 bp):
ATACTATTCGGGCTTCGAGCCTAGCAGGCTATAATGCCGGTGAG
Found at i:41622033 original size:88 final size:88
Alignment explanation
Indices: 41621878--41622097 Score: 322
Period size: 88 Copynumber: 2.5 Consensus size: 88
41621868 AATATCGCAC
* * *
41621878 AATACTATTCGGGCCTCTGAGCATAGCAGGCTATAATG-CGGATGAGATACTATTCGGGCCTTTG
1 AATACTATTCGGGCTTC-GAGCCTAGCAGGCGA-AATGCCGG-TGAGATACTATTCGGGCCTTTG
41621942 AGCCTAGCAGGCTATAATGCCGGTGA
63 AGCCTAGCAGGCTATAATGCCGGTGA
*
41621968 GATACTATTCGGGCTTCGAGCCTAGCAGGCGAAATGCCGGTGAGATACTATTCGGG-CTTTCGAG
1 AATACTATTCGGGCTTCGAGCCTAGCAGGCGAAATGCCGGTGAGATACTATTCGGGCCTTT-GAG
*
41622032 CCTAGCAGGCTATAATGCTGGTGA
65 CCTAGCAGGCTATAATGCCGGTGA
41622056 AATGA-TA-TCGGGCTTCGAGCCTAGCAGGCGAAATGCCGGTGA
1 AAT-ACTATTCGGGCTTCGAGCCTAGCAGGCGAAATGCCGGTGA
41622098 ATGAATTTGG
Statistics
Matches: 121, Mismatches: 6, Indels: 9
0.89 0.04 0.07
Matches are distributed among these distances:
87 39 0.32
88 50 0.41
89 17 0.14
90 15 0.12
ACGTcount: A:0.25, C:0.21, G:0.30, T:0.24
Consensus pattern (88 bp):
AATACTATTCGGGCTTCGAGCCTAGCAGGCGAAATGCCGGTGAGATACTATTCGGGCCTTTGAGC
CTAGCAGGCTATAATGCCGGTGA
Found at i:41624598 original size:22 final size:23
Alignment explanation
Indices: 41624553--41624598 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
41624543 AACCTCGGAG
* *
41624553 GGATTTATTACGTGCGAAGGATC
1 GGATTTATAACGTGCGAAGCATC
*
41624576 GGATTTGTAACGT-CGAAGCATC
1 GGATTTATAACGTGCGAAGCATC
41624598 G
1 G
41624599 AAACATGACA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.26, C:0.15, G:0.30, T:0.28
Consensus pattern (23 bp):
GGATTTATAACGTGCGAAGCATC
Found at i:41637034 original size:40 final size:40
Alignment explanation
Indices: 41636932--41637115 Score: 174
Period size: 40 Copynumber: 4.6 Consensus size: 40
41636922 AAATTGAATG
* * * * *
41636932 ATATCCGGGCTAAGCCCCGAAGACAATTATGCT-GAAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAG-TAGTT
* *
41636972 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
* *
41637012 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCAAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTAGTAGTT
* * * * * *
41637052 AAATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGTG
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
* * *
41637092 ATATCCGGGTTAAGTCCCGTAGGC
1 ATATCCGGGCTAAGACCCGAAGGC
41637116 CTTGGTGCGG
Statistics
Matches: 121, Mismatches: 20, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
39 3 0.02
40 115 0.95
41 3 0.02
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
Found at i:41645096 original size:39 final size:40
Alignment explanation
Indices: 41645038--41645138 Score: 132
Period size: 39 Copynumber: 2.5 Consensus size: 40
41645028 AAATTGAATG
* *
41645038 ATATCCGGGCTAAGCCCCGAAGACAATTATGCT-GAAATT
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
* * * * *
41645077 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAGCT
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
41645117 ATATCCGGGCTAAGACCCGAAG
1 ATATCCGGGCTAAGACCCGAAG
41645139 GCATTCGTGC
Statistics
Matches: 53, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
39 29 0.55
40 24 0.45
ACGTcount: A:0.31, C:0.23, G:0.25, T:0.22
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
Found at i:41645131 original size:40 final size:40
Alignment explanation
Indices: 41645038--41645220 Score: 181
Period size: 40 Copynumber: 4.6 Consensus size: 40
41645028 AAATTGAATG
* * * * *
41645038 ATATCCGGGCTAAGCCCCGAAGACAATTATGCT-GAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
* *
41645077 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
* *
41645117 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCAAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTAGTAGTT
* * * * * *
41645157 AAATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGTG
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
* * *
41645197 ATATCCGGGTTAAGTCCCGTAGGC
1 ATATCCGGGCTAAGACCCGAAGGC
41645221 CTTGGTGCGG
Statistics
Matches: 121, Mismatches: 20, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
39 32 0.26
40 87 0.72
41 2 0.02
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
Found at i:41646720 original size:39 final size:40
Alignment explanation
Indices: 41646666--41646771 Score: 155
Period size: 39 Copynumber: 2.7 Consensus size: 40
41646656 GGTGTTACAT
*
41646666 GAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAG-TCC
1 GAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGACCC
*
41646705 GAAGGCATTTGTGCTATTGA-TATATCCGGGCTAAGACCC
1 GAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGACCC
*
41646744 GAAGGCATTTGTGCGAGTTG-CTATATCC
1 GAAGGCATTTGTGCTAG-TGACTATATCC
41646772 AGCTAAATCC
Statistics
Matches: 60, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
38 15 0.25
39 36 0.60
40 9 0.15
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (40 bp):
GAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGACCC
Found at i:41646787 original size:39 final size:40
Alignment explanation
Indices: 41646665--41646787 Score: 148
Period size: 39 Copynumber: 3.1 Consensus size: 40
41646655 GGGTGTTACA
*
41646665 TGAAGGCATTTGTGCTAG-TGACTATATCCGGGCTAAGTCC
1 TGAAGGCATTTGTGCTAGTTG-CTATATCCGGGCTAAATCC
*
41646705 -GAAGGCATTTGTGCTA-TTGATATATCCGGGCTAAGA-CC
1 TGAAGGCATTTGTGCTAGTTGCTATATCCGGGCTAA-ATCC
* * *
41646743 CGAAGGCATTTGTGCGAGTTGCTATATCC-AGCTAAATCC
1 TGAAGGCATTTGTGCTAGTTGCTATATCCGGGCTAAATCC
41646782 TGAAGG
1 TGAAGG
41646788 TACTTGGCCA
Statistics
Matches: 72, Mismatches: 6, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
38 17 0.24
39 45 0.62
40 10 0.14
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.28
Consensus pattern (40 bp):
TGAAGGCATTTGTGCTAGTTGCTATATCCGGGCTAAATCC
Found at i:41647201 original size:39 final size:40
Alignment explanation
Indices: 41647143--41647243 Score: 132
Period size: 39 Copynumber: 2.5 Consensus size: 40
41647133 AAATTGAATG
* *
41647143 ATATCCGGGCTAAGCCCCGAAGACAATTATGCT-GAAATT
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
* * * * *
41647182 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAGCT
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
41647222 ATATCCGGGCTAAGACCCGAAG
1 ATATCCGGGCTAAGACCCGAAG
41647244 GCATTCGTGC
Statistics
Matches: 53, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
39 29 0.55
40 24 0.45
ACGTcount: A:0.31, C:0.23, G:0.25, T:0.22
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
Found at i:41647236 original size:40 final size:40
Alignment explanation
Indices: 41647143--41647325 Score: 181
Period size: 40 Copynumber: 4.6 Consensus size: 40
41647133 AAATTGAATG
* * * * *
41647143 ATATCCGGGCTAAGCCCCGAAGACAATTATGCT-GAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
* *
41647182 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
* *
41647222 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCAAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTAGTAGTT
* * * * * *
41647262 AAATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGTG
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
* * *
41647302 ATATCCGGGTTAAGTCCCGTAGGC
1 ATATCCGGGCTAAGACCCGAAGGC
41647326 CTTGGTGCGG
Statistics
Matches: 121, Mismatches: 20, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
39 32 0.26
40 87 0.72
41 2 0.02
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
Found at i:41657451 original size:40 final size:40
Alignment explanation
Indices: 41657349--41657532 Score: 174
Period size: 40 Copynumber: 4.6 Consensus size: 40
41657339 AAATTGAATG
* * * * *
41657349 ATATCCGGGCTAAGCCCCGAAGACAATTATGCT-GAAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAG-TAGTT
* *
41657389 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
* *
41657429 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCAAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTAGTAGTT
* * * * * *
41657469 AAATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGTG
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
* * *
41657509 ATATCCGGGTTAAGTCCCGTAGGC
1 ATATCCGGGCTAAGACCCGAAGGC
41657533 CTTGGTGCGG
Statistics
Matches: 121, Mismatches: 20, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
39 3 0.02
40 115 0.95
41 3 0.02
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
Found at i:41665559 original size:40 final size:40
Alignment explanation
Indices: 41665457--41665640 Score: 174
Period size: 40 Copynumber: 4.6 Consensus size: 40
41665447 AAATTGAATG
* * * * *
41665457 ATATCCGGGCTAAGCCCCGAAGACAATTATGCT-GAAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAG-TAGTT
* *
41665497 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
* *
41665537 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCAAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTAGTAGTT
* * * * * *
41665577 AAATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGTG
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
* * *
41665617 ATATCCGGGTTAAGTCCCGTAGGC
1 ATATCCGGGCTAAGACCCGAAGGC
41665641 CTTGGTGCGG
Statistics
Matches: 121, Mismatches: 20, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
39 3 0.02
40 115 0.95
41 3 0.02
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
Found at i:41667143 original size:40 final size:40
Alignment explanation
Indices: 41667088--41667195 Score: 173
Period size: 40 Copynumber: 2.7 Consensus size: 40
41667078 GGTGTTACAT
*
41667088 GAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTCCC
1 GAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGACCC
*
41667128 GAAGGCATTTGTGCTATTGACTATATCCGGGCTAAGACCC
1 GAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGACCC
*
41667168 GAAGGCATTTGTGCGAGTTG-CTATATCC
1 GAAGGCATTTGTGCTAG-TGACTATATCC
41667196 AGCTAAATCC
Statistics
Matches: 63, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
40 61 0.97
41 2 0.03
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (40 bp):
GAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGACCC
Found at i:41668188 original size:14 final size:14
Alignment explanation
Indices: 41668169--41668197 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
41668159 AATTCACTAT
41668169 AGAGACTGATTACA
1 AGAGACTGATTACA
41668183 AGAGACTGATTACA
1 AGAGACTGATTACA
41668197 A
1 A
41668198 ACCCCTTAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.14, G:0.21, T:0.21
Consensus pattern (14 bp):
AGAGACTGATTACA
Found at i:41672467 original size:46 final size:46
Alignment explanation
Indices: 41672399--41672667 Score: 192
Period size: 46 Copynumber: 5.8 Consensus size: 46
41672389 TGTAACCCGC
* *
41672399 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGTTCGCAT
* ** * *
41672445 CCATAAGTGAACTCGGAGTCAACTCAATAAGCTCAGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTC-G--GAC--GTTCGCAT
* * *
41672495 CTCA-CA---AACTCAGACTCAACTCAACGAGTTCGGACGTTCGCAT
1 C-CATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGTTCGCAT
* * * * *
41672538 CCATAAGTGAACTCGGACTCAACTCAATGAGCTCGGATGCCTAG-TT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACG-TTCGCAT
* * * * * * *
41672584 ACAACTCA-CGAACTTGGACTTAACTCAACGAGTTCGGACATTCGCAT
1 -CCA-TAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGTTCGCAT
* *
41672631 CCATAAGTGAACTCGGACTCAACTCAATGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
41672668 TGCCCAAATA
Statistics
Matches: 167, Mismatches: 40, Indels: 32
0.70 0.17 0.13
Matches are distributed among these distances:
42 5 0.03
43 5 0.03
44 2 0.01
45 2 0.01
46 88 0.53
47 51 0.31
48 2 0.01
49 2 0.01
50 5 0.03
51 5 0.03
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGTTCGCAT
Found at i:41672659 original size:93 final size:93
Alignment explanation
Indices: 41672406--41672671 Score: 424
Period size: 93 Copynumber: 2.9 Consensus size: 93
41672396 CGCCCATAAG
* * *
41672406 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGAGTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
* * *
41672471 ATAAGCTCAGATGCCTAGTTACATCTCA
66 ATGAGCTCGGATGCCTAGTTACAACTCA
* *
41672499 CAAACTCAGACTCAACTCAACGAGTTCGGACGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
41672564 ATGAGCTCGGATGCCTAGTTACAACTCA
66 ATGAGCTCGGATGCCTAGTTACAACTCA
* * *
41672592 CGAACTTGGACTTAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
*
41672657 ATGAGTTCGGATGCC
66 ATGAGCTCGGATGCC
41672672 CAAATATCCA
Statistics
Matches: 159, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 159 1.00
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
ATGAGCTCGGATGCCTAGTTACAACTCA
Found at i:41685021 original size:30 final size:29
Alignment explanation
Indices: 41684927--41685028 Score: 109
Period size: 28 Copynumber: 3.5 Consensus size: 29
41684917 TATAGTGAAT
* * *
41684927 CCGCACACTTAGTGCTATATATTTTCAGC
1 CCGCACACTTAGTGCTATAAATTTTAAAC
* *
41684956 TCGCACACTTAGTGCTATAGAA--TCAAAC
1 CCGCACACTTAGTGCTATA-AATTTTAAAC
* *
41684984 TCGCACACTTAGTGCTGTACAATTTTAAAC
1 CCGCACACTTAGTGCTATA-AATTTTAAAC
41685014 CCGCACACTTAGTGC
1 CCGCACACTTAGTGC
41685029 CAATCTTGTC
Statistics
Matches: 61, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
28 23 0.38
29 18 0.30
30 20 0.33
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.29
Consensus pattern (29 bp):
CCGCACACTTAGTGCTATAAATTTTAAAC
Found at i:41692503 original size:15 final size:15
Alignment explanation
Indices: 41692485--41692519 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
41692475 AGTTCCAGTG
41692485 TTTATTAATGAATGT
1 TTTATTAATGAATGT
*
41692500 TTTATTAATGACTGT
1 TTTATTAATGAATGT
41692515 TTTAT
1 TTTAT
41692520 GAAAAACAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.29, C:0.03, G:0.11, T:0.57
Consensus pattern (15 bp):
TTTATTAATGAATGT
Found at i:41696691 original size:79 final size:82
Alignment explanation
Indices: 41696580--41696763 Score: 227
Period size: 79 Copynumber: 2.3 Consensus size: 82
41696570 GCTACTCGTT
* * **
41696580 CAAATGCCTTCGGGACATAGCCC-GGTTATAGTAACTCGCGTAAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGGATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
41696643 GGATTTAGTAAC-TCGCA
65 GGATATAGTAACTTAGCA
* **
41696660 TAAATGCCTTCGGG-CTTAGCCCGGGAT-TAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGGATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
*
41696723 GATATAGTCACTTAGCA
66 GATATAGTAACTTAGCA
41696740 CAAA-GCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGG
41696764 ACATCATTCG
Statistics
Matches: 89, Mismatches: 11, Indels: 8
0.82 0.10 0.07
Matches are distributed among these distances:
78 3 0.03
79 53 0.60
80 33 0.37
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGGATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:41696764 original size:40 final size:40
Alignment explanation
Indices: 41696561--41696764 Score: 229
Period size: 40 Copynumber: 5.1 Consensus size: 40
41696551 CGGCATTTAA
** *
41696561 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* ** *
41696601 CCGGTTATAGTAACTCGCGTAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
41696641 CCGGATTTAGTAACTCGCATAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
41696680 CCGGGAT-TAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
1 CC-GGATATAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* *
41696720 CCGGATATAGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
41696760 CCGGA
1 CCGGA
41696765 CATCATTCGA
Statistics
Matches: 142, Mismatches: 15, Indels: 14
0.83 0.09 0.08
Matches are distributed among these distances:
38 2 0.01
39 34 0.24
40 95 0.67
41 11 0.08
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:41704718 original size:79 final size:80
Alignment explanation
Indices: 41704607--41704787 Score: 199
Period size: 79 Copynumber: 2.3 Consensus size: 80
41704597 GCTACTCGTT
* * * **
41704607 CAAACGCCTTCGGGACATAGCC-CGGTTATAGTAACTCGCGTAAATGCCTTCGGGA-CTTAACCC
1 CAAA-GCCTTCGGGACTTAGCCTGGGAT-TAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
41704670 GGATTTAGTAAC-TCGCA
63 GGATATAGTAACTTAGCA
* **
41704687 TAAATGCCTTCGGG-CTTAGCCTGGGATTAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGG
1 CAAA-GCCTTCGGGACTTAGCCTGGGATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGG
*
41704751 ATATAGTCACTTAGCA
65 ATATAGTAACTTAGCA
41704767 CAAAGCCTTCGGGACTTAGCC
1 CAAAGCCTTCGGGACTTAGCC
41704788 CGGACATCAT
Statistics
Matches: 84, Mismatches: 13, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
78 3 0.04
79 52 0.62
80 29 0.35
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (80 bp):
CAAAGCCTTCGGGACTTAGCCTGGGATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
TATAGTAACTTAGCA
Found at i:41704731 original size:39 final size:38
Alignment explanation
Indices: 41704607--41704787 Score: 170
Period size: 40 Copynumber: 4.6 Consensus size: 38
41704597 GCTACTCGTT
* * * *
41704607 CAAACGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCG
1 CAAATGCCTTCGGGACTTAG-CCGGAT-TAGTAACTCGCA
* *
41704647 TAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTT-AGCCGGA-TTAGTAACTCGCA
*
41704687 TAAATGCCTTCGGG-CTTAGCCTGGGATTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCC--GGATTAGTAACTCGCA
* *
41704726 CAAATGCCTTC-GGATCTTAGTCCGGATATAGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAG-CCGGAT-TAGTAAC-TCGCA
41704767 CAAA-GCCTTCGGGACTTAGCC
1 CAAATGCCTTCGGGACTTAGCC
41704788 CGGACATCAT
Statistics
Matches: 121, Mismatches: 10, Indels: 21
0.80 0.07 0.14
Matches are distributed among these distances:
38 5 0.04
39 32 0.26
40 69 0.57
41 15 0.12
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (38 bp):
CAAATGCCTTCGGGACTTAGCCGGATTAGTAACTCGCA
Found at i:41707370 original size:30 final size:30
Alignment explanation
Indices: 41707336--41707396 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
41707326 TCCTTAACTC
41707336 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
41707366 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
41707396 A
1 A
41707397 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:41712087 original size:25 final size:25
Alignment explanation
Indices: 41712052--41712099 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
41712042 TTATAATACG
*
41712052 AAAATGACCATTTTACCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
*
41712077 AAAATGCCCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
41712100 GTTTATATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.35, C:0.27, G:0.12, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:41712165 original size:20 final size:20
Alignment explanation
Indices: 41712140--41712186 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
41712130 TGATAAACAC
41712140 GATATGTATGATATGCACAT
1 GATATGTATGATATGCACAT
41712160 GATATGTATGATATGCACAT
1 GATATGTATGATATGCACAT
*
41712180 GAGATGT
1 GATATGT
41712187 TCATAAATGC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.34, C:0.09, G:0.23, T:0.34
Consensus pattern (20 bp):
GATATGTATGATATGCACAT
Found at i:41712258 original size:24 final size:24
Alignment explanation
Indices: 41712231--41712384 Score: 220
Period size: 24 Copynumber: 6.4 Consensus size: 24
41712221 GGAGGAAGTG
*
41712231 CAAAAGGGCTTATGCCCTAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
* *
41712255 CAAAAGGACTTATGCCCCAGTTAC
1 CAAAAGGGCTTATGCCCCAGTTAT
*
41712279 CAAAAGGGCTTATGCCCCAATTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
41712303 CAAAAGGGCTTATGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
*
41712327 -TAAAGGGCTTATGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
* *
41712350 TAAAAGGGCTTTTGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
*
41712374 TAAAAGAGGCT
1 CAAAAG-GGCT
41712385 AGGCCTCCAG
Statistics
Matches: 118, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
23 22 0.19
24 92 0.78
25 4 0.03
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.27
Consensus pattern (24 bp):
CAAAAGGGCTTATGCCCCAGTTAT
Found at i:41712355 original size:47 final size:47
Alignment explanation
Indices: 41712233--41712377 Score: 218
Period size: 47 Copynumber: 3.1 Consensus size: 47
41712223 AGGAAGTGCA
* * **
41712233 AAAGGGCTTATGCCCTAGTTATCAAAAGGACTTATGCCCCAGTTACCA
1 AAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTA-TT
*
41712281 AAAGGGCTTATGCCCCAATTATCAAAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATT
* *
41712328 AAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTTTGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATT
41712375 AAA
1 AAA
41712378 AGAGGCTAGG
Statistics
Matches: 89, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
47 47 0.53
48 42 0.47
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (47 bp):
AAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATT
Found at i:41712629 original size:31 final size:31
Alignment explanation
Indices: 41712591--41712654 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
41712581 CGTTTACAAT
41712591 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
** *
41712622 AAAGGCTTCGGCCCAGTGTTATGAATTATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
41712653 AA
1 AA
41712655 TATGAAAAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:41723552 original size:29 final size:28
Alignment explanation
Indices: 41723497--41723649 Score: 155
Period size: 29 Copynumber: 5.4 Consensus size: 28
41723487 GTGAGCATGA
*
41723497 ATATGAATGTGATTGGGCCTAACGGGCC
1 ATATGAATGTGATTGGGCCTAATGGGCC
*
41723525 ATATAAATGTGATTTGGGCCTAATGGGCC
1 ATATGAATGTGA-TTGGGCCTAATGGGCC
* * *
41723554 ATATGAATGTGAATTTGGCTTAGTGGGCC
1 ATATGAATGTG-ATTGGGCCTAATGGGCC
* * *
41723583 ATAAGAATATGAACTGGGCC-ATATGGGCC
1 ATATGAATGTG-ATTGGGCCTA-ATGGGCC
* * *
41723612 ATATGAATGAGATTGGGCCCAGTGGGCC
1 ATATGAATGTGATTGGGCCTAATGGGCC
*
41723640 ATATGCATGT
1 ATATGAATGT
41723650 ATCTAGGGGT
Statistics
Matches: 102, Mismatches: 19, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
28 33 0.32
29 68 0.67
30 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.30, T:0.27
Consensus pattern (28 bp):
ATATGAATGTGATTGGGCCTAATGGGCC
Found at i:41725798 original size:43 final size:42
Alignment explanation
Indices: 41725678--41725809 Score: 115
Period size: 43 Copynumber: 3.1 Consensus size: 42
41725668 TGTGAGCTAG
** * * *
41725678 TGTAAGACCATGTCTGGGACATGGCAACGGCATGAGGCATCG
1 TGTAAGACCATGTCTGGGACATGGCATTGGTATGAGACATCA
* ** **
41725720 TGTAAGACCGTAG-CTGGG-CTATTGGCATTAATATGAGATTTCCA
1 TGTAAGACCAT-GTCTGGGAC-A-TGGCATTGGTATGAGACAT-CA
*
41725764 TGTAAGACCATGTCTGGGACATGGCATTGGTATGATACATCA
1 TGTAAGACCATGTCTGGGACATGGCATTGGTATGAGACATCA
41725806 TGTA
1 TGTA
41725810 CGAGTTTTCC
Statistics
Matches: 68, Mismatches: 16, Indels: 12
0.71 0.17 0.12
Matches are distributed among these distances:
41 1 0.01
42 22 0.32
43 27 0.40
44 17 0.25
45 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.27
Consensus pattern (42 bp):
TGTAAGACCATGTCTGGGACATGGCATTGGTATGAGACATCA
Found at i:41728758 original size:20 final size:20
Alignment explanation
Indices: 41728733--41728770 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
41728723 ATAATTCAAG
41728733 TTTTACATTGCAACAAATAT
1 TTTTACATTGCAACAAATAT
41728753 TTTTACATTGCAACAAAT
1 TTTTACATTGCAACAAAT
41728771 GAATACACGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.39, C:0.16, G:0.05, T:0.39
Consensus pattern (20 bp):
TTTTACATTGCAACAAATAT
Found at i:41731693 original size:31 final size:31
Alignment explanation
Indices: 41731655--41731729 Score: 123
Period size: 31 Copynumber: 2.4 Consensus size: 31
41731645 GAAACAGGGT
41731655 CACACGCCCGTGTGGGTACGCCGTGTGGTCA
1 CACACGCCCGTGTGGGTACGCCGTGTGGTCA
* * *
41731686 CACACGCCTGTGCGGGTAGGCCGTGTGGTCA
1 CACACGCCCGTGTGGGTACGCCGTGTGGTCA
41731717 CACACGCCCGTGT
1 CACACGCCCGTGT
41731730 CCTCAGCCCG
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.13, C:0.33, G:0.35, T:0.19
Consensus pattern (31 bp):
CACACGCCCGTGTGGGTACGCCGTGTGGTCA
Found at i:41731741 original size:31 final size:30
Alignment explanation
Indices: 41731675--41731742 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 30
41731665 TGTGGGTACG
* * *
41731675 CCGTGTGGTCACACACGCCTGTGCGGGTAGG
1 CCGTGTGGTCACACACGCCCGTGC-GCTAGC
41731706 CCGTGTGGTCACACACGCCCGTGTC-CTCAGC
1 CCGTGTGGTCACACACGCCCGTG-CGCT-AGC
41731737 CCGTGT
1 CCGTGT
41731743 AACTCTCTGT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
30 1 0.03
31 30 0.94
32 1 0.03
ACGTcount: A:0.12, C:0.35, G:0.32, T:0.21
Consensus pattern (30 bp):
CCGTGTGGTCACACACGCCCGTGCGCTAGC
Found at i:41733517 original size:41 final size:40
Alignment explanation
Indices: 41733390--41733534 Score: 193
Period size: 40 Copynumber: 3.6 Consensus size: 40
41733380 CTCGCACAAG
* * * * *
41733390 GCCTTCGGGTCTTAGCACGGATATGGTCACTAGCATAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
41733430 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
* * *
41733470 GCCTTC-GGATCTTAGTCCGGATGTAGTCGCTTAGCACAAAA
1 GCCTTCGGGA-CTTAGCCCGGATATAGTCGC-TAGCACAAAT
41733511 GCCTTCGGGACTTAGCCCGGATAT
1 GCCTTCGGGACTTAGCCCGGATAT
41733535 CATTCGAGTA
Statistics
Matches: 92, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
39 3 0.03
40 59 0.64
41 27 0.29
42 3 0.03
ACGTcount: A:0.23, C:0.26, G:0.26, T:0.26
Consensus pattern (40 bp):
GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
Found at i:41760974 original size:16 final size:17
Alignment explanation
Indices: 41760943--41760977 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
41760933 ACGAGCCAGA
41760943 ATGGGCTAAATGGGCCC
1 ATGGGCTAAATGGGCCC
*
41760960 ATGGGCT-ATTGGGCCC
1 ATGGGCTAAATGGGCCC
41760976 AT
1 AT
41760978 AATAGGCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.20, C:0.23, G:0.34, T:0.23
Consensus pattern (17 bp):
ATGGGCTAAATGGGCCC
Found at i:41761089 original size:29 final size:28
Alignment explanation
Indices: 41761034--41761186 Score: 155
Period size: 29 Copynumber: 5.4 Consensus size: 28
41761024 GTGAGCATGA
*
41761034 ATATGAATGTGATTGGGCCTAACGGGCC
1 ATATGAATGTGATTGGGCCTAATGGGCC
*
41761062 ATATAAATGTGATTTGGGCCTAATGGGCC
1 ATATGAATGTGA-TTGGGCCTAATGGGCC
* * *
41761091 ATATGAATGTGAATTTGGCTTAGTGGGCC
1 ATATGAATGTG-ATTGGGCCTAATGGGCC
* * *
41761120 ATAAGAATATGAACTGGGCC-ATATGGGCC
1 ATATGAATGTG-ATTGGGCCTA-ATGGGCC
* * *
41761149 ATATGAATGAGATTGGGCCCAGTGGGCC
1 ATATGAATGTGATTGGGCCTAATGGGCC
*
41761177 ATATGCATGT
1 ATATGAATGT
41761187 ATCTAGGGGT
Statistics
Matches: 102, Mismatches: 19, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
28 33 0.32
29 68 0.67
30 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.30, T:0.27
Consensus pattern (28 bp):
ATATGAATGTGATTGGGCCTAATGGGCC
Found at i:41763319 original size:43 final size:42
Alignment explanation
Indices: 41763199--41763330 Score: 115
Period size: 43 Copynumber: 3.1 Consensus size: 42
41763189 TGTGAGCTAG
** * * *
41763199 TGTAAGACCATGTCTGGGACATGGCAACGGCATGAGGCATCG
1 TGTAAGACCATGTCTGGGACATGGCATTGGTATGAGACATCA
* ** **
41763241 TGTAAGACCGTAG-CTGGG-CTATTGGCATTAATATGAGATTTCCA
1 TGTAAGACCAT-GTCTGGGAC-A-TGGCATTGGTATGAGACAT-CA
*
41763285 TGTAAGACCATGTCTGGGACATGGCATTGGTATGATACATCA
1 TGTAAGACCATGTCTGGGACATGGCATTGGTATGAGACATCA
41763327 TGTA
1 TGTA
41763331 TGAGTTTTCC
Statistics
Matches: 68, Mismatches: 16, Indels: 12
0.71 0.17 0.12
Matches are distributed among these distances:
41 1 0.01
42 22 0.32
43 27 0.40
44 17 0.25
45 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.27
Consensus pattern (42 bp):
TGTAAGACCATGTCTGGGACATGGCATTGGTATGAGACATCA
Found at i:41765703 original size:37 final size:40
Alignment explanation
Indices: 41765607--41765758 Score: 125
Period size: 40 Copynumber: 3.9 Consensus size: 40
41765597 TCGAATGATG
* * * * * *
41765607 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTAACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTCGTGC-GAGTCACAAAAC
* * * *
41765647 CCGGACTAGGAT-CCGAAGGCATTCGTGCGAGTTA-AAAAT
1 CCGGGCTAAG-TCCCGAAGGCATTCGTGCGAGTCACAAAAC
* * *
41765686 CC-GGCTAAG-CCCGAAGGCATTTGTGCAAGTCACTAAAC
1 CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTCACAAAAC
*
41765724 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTCAC
1 CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTCAC
41765759 TATAACGGGC
Statistics
Matches: 89, Mismatches: 17, Indels: 12
0.75 0.14 0.10
Matches are distributed among these distances:
37 19 0.21
38 10 0.11
39 11 0.12
40 42 0.47
41 7 0.08
ACGTcount: A:0.26, C:0.25, G:0.27, T:0.22
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTCACAAAAC
Found at i:41765740 original size:77 final size:78
Alignment explanation
Indices: 41765610--41765755 Score: 199
Period size: 77 Copynumber: 1.9 Consensus size: 78
41765600 AATGATGCCG
* * *
41765610 GGCTAAGTCCCGAAGGCTTTGTGCTAAGTAACTATATCCGGACTAGGATCCGAAGGCATTCGTGC
1 GGCTAAGTCCCGAAGGCTTTGTGCTAAGTAACTAAACCCGGACTAAGATCCGAAGGCATTCGTGC
41765675 GAGTTAAAAATCC
66 GAGTTAAAAATCC
* **
41765688 GGCTAAG-CCCGAAGGCATTTGTGC-AAGTCACTAAACCCGGGTTAAG-TCCCGAAGGCATTCGT
1 GGCTAAGTCCCGAAGGC-TTTGTGCTAAGTAACTAAACCCGGACTAAGAT-CCGAAGGCATTCGT
41765750 GCGAGT
64 GCGAGT
41765756 CACTATAACG
Statistics
Matches: 60, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
76 1 0.02
77 45 0.75
78 14 0.23
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (78 bp):
GGCTAAGTCCCGAAGGCTTTGTGCTAAGTAACTAAACCCGGACTAAGATCCGAAGGCATTCGTGC
GAGTTAAAAATCC
Found at i:41765792 original size:38 final size:39
Alignment explanation
Indices: 41765607--41765794 Score: 122
Period size: 40 Copynumber: 4.8 Consensus size: 39
41765597 TCGAATGATG
* * * *
41765607 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTAACTATAT
1 CCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTCACTA-AA
** * * * *
41765647 CCGGACTAGGAT-CCGAAGGCATTCGTGCGAGTTA-AAAA
1 CCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTCACTAAA
* *
41765685 TCC-GGCTAAG-CCCGAAGGCATTTGTGCAAGTCACTAAA
1 -CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTCACTAAA
*
41765723 CCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTCACTATAA
1 -CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTCACTA-AA
* *
41765764 -CGGGCTT-CGT-CCGAAGGCATTTGAGCGAGTC
1 CCGGG-TTAAGTCCCGAAGGCATTTGTGCGAGTC
41765795 TATATCCGGT
Statistics
Matches: 119, Mismatches: 20, Indels: 20
0.75 0.13 0.13
Matches are distributed among these distances:
37 19 0.16
38 30 0.25
39 15 0.13
40 46 0.39
41 9 0.08
ACGTcount: A:0.26, C:0.24, G:0.28, T:0.22
Consensus pattern (39 bp):
CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTCACTAAA
Found at i:41767429 original size:10 final size:10
Alignment explanation
Indices: 41767414--41767439 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
41767404 ATCATCGAGA
41767414 TCAAACCATT
1 TCAAACCATT
41767424 TCAAACCATT
1 TCAAACCATT
41767434 TCAAAC
1 TCAAAC
41767440 AAAAAAAAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.42, C:0.31, G:0.00, T:0.27
Consensus pattern (10 bp):
TCAAACCATT
Found at i:41768567 original size:21 final size:22
Alignment explanation
Indices: 41768538--41768578 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
41768528 ACTCTAAATT
41768538 TAAATCCCTAAACCTGAGACTC
1 TAAATCCCTAAACCTGAGACTC
*
41768560 TAAA-CCCTAAACCTTAGAC
1 TAAATCCCTAAACCTGAGAC
41768579 CACAAACACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.39, C:0.32, G:0.07, T:0.22
Consensus pattern (22 bp):
TAAATCCCTAAACCTGAGACTC
Found at i:41769719 original size:12 final size:12
Alignment explanation
Indices: 41769704--41769729 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
41769694 TTTTTTTGAT
41769704 AAAACGCCGCTA
1 AAAACGCCGCTA
41769716 AAAACGCCGCTA
1 AAAACGCCGCTA
41769728 AA
1 AA
41769730 GCCCTATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.31, G:0.15, T:0.08
Consensus pattern (12 bp):
AAAACGCCGCTA
Found at i:41771455 original size:31 final size:31
Alignment explanation
Indices: 41771417--41771491 Score: 132
Period size: 31 Copynumber: 2.4 Consensus size: 31
41771407 GAAACAGGGT
41771417 CACACGCCCGTGTGGGTAGGCCGTGTGGTCA
1 CACACGCCCGTGTGGGTAGGCCGTGTGGTCA
* *
41771448 CACACGCCTGTGCGGGTAGGCCGTGTGGTCA
1 CACACGCCCGTGTGGGTAGGCCGTGTGGTCA
41771479 CACACGCCCGTGT
1 CACACGCCCGTGT
41771492 CCTCAGCCCG
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.13, C:0.32, G:0.36, T:0.19
Consensus pattern (31 bp):
CACACGCCCGTGTGGGTAGGCCGTGTGGTCA
Found at i:41771503 original size:31 final size:30
Alignment explanation
Indices: 41771417--41771504 Score: 79
Period size: 31 Copynumber: 2.8 Consensus size: 30
41771407 GAAACAGGGT
* * *
41771417 CACACGCCCGTGTGGGTAGGCCGTGTGGTCA
1 CACACGCCCGTG-CGCTAGCCCGTGTGGTCA
* * *
41771448 CACACGCCTGTGCGGGTAGGCCGTGTGGTCA
1 CACACGCCCGTGC-GCTAGCCCGTGTGGTCA
41771479 CACACGCCCGTGTC-CTCAGCCCGTGT
1 CACACGCCCGTG-CGCT-AGCCCGTGT
41771505 AACTCTCTGT
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
30 1 0.02
31 47 0.96
32 1 0.02
ACGTcount: A:0.12, C:0.34, G:0.34, T:0.19
Consensus pattern (30 bp):
CACACGCCCGTGCGCTAGCCCGTGTGGTCA
Found at i:41773977 original size:46 final size:44
Alignment explanation
Indices: 41773870--41773994 Score: 164
Period size: 44 Copynumber: 2.8 Consensus size: 44
41773860 ATATTCGTGC
* * *
41773870 CGATGCATGTCCCAGACATGTCTTACACTAGCACATCTCGTAGT
1 CGATGCATGTCCCAGACATGTCTTACACTGGCTCATCTCGTAAT
*
41773914 CGATGCATGTCCCAGACATGCCTTACACTGGCTC-TCGTC-TCAAT
1 CGATGCATGTCCCAGACATGTCTTACACTGGCTCATC-TCGT-AAT
41773958 GCTGATGCATGTCCCAGACATGTCTTACACTGGCTCA
1 -C-GATGCATGTCCCAGACATGTCTTACACTGGCTCA
41773995 CATAATAGCA
Statistics
Matches: 71, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
43 3 0.04
44 35 0.49
45 1 0.01
46 32 0.45
ACGTcount: A:0.22, C:0.31, G:0.19, T:0.27
Consensus pattern (44 bp):
CGATGCATGTCCCAGACATGTCTTACACTGGCTCATCTCGTAAT
Found at i:41777284 original size:40 final size:40
Alignment explanation
Indices: 41777176--41777429 Score: 190
Period size: 41 Copynumber: 6.3 Consensus size: 40
41777166 GTGGCGTTTT
* * * * *
41777176 TAGCGGCGTTTTATCAAAAAATGCCTC-AAAAATTATA-CAT
1 TAGCGGCGTTTTA-CCAAAAACGCCGCTAAAAA-TAGAGCAA
* *
41777216 TAGCGGCGTTTTA-TAAAAACGCCGCTAAAAATAGAGAAA
1 TAGCGGCGTTTTACCAAAAACGCCGCTAAAAATAGAGCAA
* * *
41777255 TAGTGGCGTTTTACCAAAAACGCCGCTAAAAACCAGGGCAA
1 TAGCGGCGTTTTACCAAAAACGCCGCTAAAAA-TAGAGCAA
*
41777296 TAGCGGCGTTTTACCAAAAACGCCGCTAAAACCTAGAGCAA
1 TAGCGGCGTTTTACCAAAAACGCCGCTAAAA-ATAGAGCAA
**** * * *
41777337 TAGCGGCGTTTTTGGTAAAACGCCACTAAAAACCAGAACAA
1 TAGCGGCGTTTTACCAAAAACGCCGCTAAAAA-TAGAGCAA
* * **** * * *
41777378 TGGTGGCGTTTTTGGTAAAACGCTGCTAAAAACCAAAGCAA
1 TAGCGGCGTTTTACCAAAAACGCCGCTAAAAA-TAGAGCAA
41777419 TAGCGGCGTTT
1 TAGCGGCGTTT
41777430 ATGGTCAAAA
Statistics
Matches: 177, Mismatches: 31, Indels: 11
0.81 0.14 0.05
Matches are distributed among these distances:
38 12 0.07
39 18 0.10
40 30 0.17
41 117 0.66
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.22
Consensus pattern (40 bp):
TAGCGGCGTTTTACCAAAAACGCCGCTAAAAATAGAGCAA
Found at i:41777310 original size:41 final size:41
Alignment explanation
Indices: 41777216--41777429 Score: 227
Period size: 41 Copynumber: 5.3 Consensus size: 41
41777206 AATTATACAT
* * *
41777216 TAGCGGCGTTTTA-TAAAAACGCCGCTAAAAA-TAGAGAAA
1 TAGCGGCGTTTTACCAAAAACGCCGCTAAAAACCAGAGCAA
* *
41777255 TAGTGGCGTTTTACCAAAAACGCCGCTAAAAACCAGGGCAA
1 TAGCGGCGTTTTACCAAAAACGCCGCTAAAAACCAGAGCAA
41777296 TAGCGGCGTTTTACCAAAAACGCCGCT-AAAACCTAGAGCAA
1 TAGCGGCGTTTTACCAAAAACGCCGCTAAAAACC-AGAGCAA
**** * *
41777337 TAGCGGCGTTTTTGGTAAAACGCCACTAAAAACCAGAACAA
1 TAGCGGCGTTTTACCAAAAACGCCGCTAAAAACCAGAGCAA
* * **** * *
41777378 TGGTGGCGTTTTTGGTAAAACGCTGCTAAAAACCAAAGCAA
1 TAGCGGCGTTTTACCAAAAACGCCGCTAAAAACCAGAGCAA
41777419 TAGCGGCGTTT
1 TAGCGGCGTTT
41777430 ATGGTCAAAA
Statistics
Matches: 150, Mismatches: 21, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
39 12 0.08
40 23 0.15
41 109 0.73
42 6 0.04
ACGTcount: A:0.36, C:0.21, G:0.22, T:0.21
Consensus pattern (41 bp):
TAGCGGCGTTTTACCAAAAACGCCGCTAAAAACCAGAGCAA
Found at i:41777722 original size:15 final size:15
Alignment explanation
Indices: 41777676--41777735 Score: 61
Period size: 15 Copynumber: 4.1 Consensus size: 15
41777666 TTTATCTTGG
*
41777676 GGTTTAGGGTTTAAT
1 GGTTTAAGGTTTAAT
* *
41777691 -ATTTAAGG-TCAAT
1 GGTTTAAGGTTTAAT
* *
41777704 GGTTTAGGGTTTTAT
1 GGTTTAAGGTTTAAT
41777719 GGTTTAAGGTTTAAT
1 GGTTTAAGGTTTAAT
41777734 GG
1 GG
41777736 CCATGGGTAT
Statistics
Matches: 34, Mismatches: 9, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
13 4 0.12
14 12 0.35
15 18 0.53
ACGTcount: A:0.23, C:0.02, G:0.30, T:0.45
Consensus pattern (15 bp):
GGTTTAAGGTTTAAT
Found at i:41778410 original size:27 final size:26
Alignment explanation
Indices: 41778380--41778444 Score: 62
Period size: 28 Copynumber: 2.4 Consensus size: 26
41778370 AAATATTAGT
41778380 TAAATTTTAAAA-ACTTATTTATTTAAA
1 TAAATTTTAAAATAC-TA-TTATTTAAA
**
41778407 TAAAAAATTAAAATACTATTATTTAAA
1 T-AAATTTTAAAATACTATTATTTAAA
41778434 -ATAATTTTAAA
1 TA-AATTTTAAA
41778445 GTTTTTCGGG
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
25 1 0.03
26 7 0.23
27 10 0.32
28 11 0.35
29 2 0.06
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (26 bp):
TAAATTTTAAAATACTATTATTTAAA
Found at i:41780203 original size:30 final size:30
Alignment explanation
Indices: 41780167--41780267 Score: 118
Period size: 28 Copynumber: 3.5 Consensus size: 30
41780157 GACAAGATTG
* * *
41780167 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGTTTAAAATTATATA
* *
41780197 GCACTAAGTGTGCGAGTTT--GATTCTATA
1 GCACTAAGTGTGCGAGTTTAAAATTATATA
* *
41780225 GCACTAAGTGTGCGAGCTGAAAA-TATATA
1 GCACTAAGTGTGCGAGTTTAAAATTATATA
41780254 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
41780268 GATTCACTAT
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
28 23 0.38
29 19 0.31
30 19 0.31
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
GCACTAAGTGTGCGAGTTTAAAATTATATA
Found at i:41780279 original size:29 final size:28
Alignment explanation
Indices: 41780196--41780271 Score: 75
Period size: 29 Copynumber: 2.7 Consensus size: 28
41780186 AAAATTGTAC
* *
41780196 AGCACTAAGTGTGCGAGTTTGAT-TCTAT
1 AGCACTAAGTGTGCG-GATTGATATATAT
* *
41780224 AGCACTAAGTGTGC-GAGCTGAAAATATAT
1 AGCACTAAGTGTGCGGA-TTG-ATATATAT
41780253 AGCACTAAGTGTGCGGATT
1 AGCACTAAGTGTGCGGATT
41780272 CACTATATGC
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
26 1 0.03
27 2 0.05
28 15 0.38
29 19 0.49
30 2 0.05
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.29
Consensus pattern (28 bp):
AGCACTAAGTGTGCGGATTGATATATAT
Found at i:41788088 original size:30 final size:30
Alignment explanation
Indices: 41788052--41788152 Score: 118
Period size: 28 Copynumber: 3.5 Consensus size: 30
41788042 GACAAGATTG
* * *
41788052 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGTTTAAAATTATATA
* *
41788082 GCACTAAGTGTGCGAGTTT--GATTCTATA
1 GCACTAAGTGTGCGAGTTTAAAATTATATA
* *
41788110 GCACTAAGTGTGCGAGCTGAAAA-TATATA
1 GCACTAAGTGTGCGAGTTTAAAATTATATA
41788139 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
41788153 GATTCACTAT
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
28 23 0.38
29 19 0.31
30 19 0.31
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
GCACTAAGTGTGCGAGTTTAAAATTATATA
Found at i:41788164 original size:29 final size:28
Alignment explanation
Indices: 41788081--41788156 Score: 75
Period size: 29 Copynumber: 2.7 Consensus size: 28
41788071 AAAATTGTAC
* *
41788081 AGCACTAAGTGTGCGAGTTTGAT-TCTAT
1 AGCACTAAGTGTGCG-GATTGATATATAT
* *
41788109 AGCACTAAGTGTGC-GAGCTGAAAATATAT
1 AGCACTAAGTGTGCGGA-TTG-ATATATAT
41788138 AGCACTAAGTGTGCGGATT
1 AGCACTAAGTGTGCGGATT
41788157 CACTATATGC
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
26 1 0.03
27 2 0.05
28 15 0.38
29 19 0.49
30 2 0.05
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.29
Consensus pattern (28 bp):
AGCACTAAGTGTGCGGATTGATATATAT
Found at i:41789706 original size:3 final size:3
Alignment explanation
Indices: 41789698--41789741 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
41789688 TATTTTAGTA
41789698 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
41789742 AAGAGAAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:41791393 original size:2 final size:2
Alignment explanation
Indices: 41791386--41791418 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
41791376 AATTGGTATT
*
41791386 TG TG TG TG TG TG TG TG TT TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
41791419 TTTCTTATGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.45, T:0.55
Consensus pattern (2 bp):
TG
Found at i:41798719 original size:48 final size:48
Alignment explanation
Indices: 41798648--41798885 Score: 412
Period size: 48 Copynumber: 5.0 Consensus size: 48
41798638 AGATAAATAT
* *
41798648 ATATATATGTGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
*
41798696 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATA--TATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
41798742 ATATGTATATG-GGTAAAGCCGAATGGCTAGT-TGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
41798788 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
*
41798836 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTAGGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
41798884 AT
1 AT
41798886 GTGTGTATAT
Statistics
Matches: 181, Mismatches: 5, Indels: 8
0.93 0.03 0.04
Matches are distributed among these distances:
44 7 0.04
45 19 0.10
46 34 0.19
47 20 0.11
48 101 0.56
ACGTcount: A:0.34, C:0.06, G:0.29, T:0.31
Consensus pattern (48 bp):
ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
Found at i:41798796 original size:92 final size:95
Alignment explanation
Indices: 41798648--41798885 Score: 410
Period size: 92 Copynumber: 2.5 Consensus size: 95
41798638 AGATAAATAT
* *
41798648 ATATATATGTGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATATGTGGTAA
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATATGTGGTAA
41798713 AGCCGAATGGCTAATGTGAAATA-TATGAG
66 AGCCGAATGGCTAATGTGAAATAGTATGAG
41798742 ATATGTATATG-GGTAAAGCCGAATGGCTAGT-TGAAATATGTATGAGATATGTATATGTGGTAA
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATATGTGGTAA
*
41798805 AGCCGAATGGCTAGTGTGAAATATGTATGAG
66 AGCCGAATGGCTAATGTGAAATA-GTATGAG
*
41798836 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTAGGAGAT
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGAT
41798886 GTGTGTATAT
Statistics
Matches: 136, Mismatches: 4, Indels: 6
0.93 0.03 0.04
Matches are distributed among these distances:
92 54 0.40
93 20 0.15
94 26 0.19
95 20 0.15
96 16 0.12
ACGTcount: A:0.34, C:0.06, G:0.29, T:0.31
Consensus pattern (95 bp):
ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATATGTGGTAA
AGCCGAATGGCTAATGTGAAATAGTATGAG
Found at i:41799076 original size:37 final size:37
Alignment explanation
Indices: 41799026--41799127 Score: 179
Period size: 36 Copynumber: 2.8 Consensus size: 37
41799016 GGAAATATAT
41799026 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
*
41799063 TCCGGGTAAGACCCGATGACTACGTGT-GAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
*
41799099 TCCGGGTAAGACCCGATAACTACGTGTGG
1 TCCGGGTAAGACCCGATGACTACGTGTGG
41799128 GGACTATTCG
Statistics
Matches: 62, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
36 34 0.55
37 28 0.45
ACGTcount: A:0.24, C:0.21, G:0.31, T:0.25
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
Found at i:41800591 original size:40 final size:40
Alignment explanation
Indices: 41800415--41800582 Score: 282
Period size: 40 Copynumber: 4.2 Consensus size: 40
41800405 TATATATATT
*
41800415 CGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATC
1 CGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTATC
* *
41800455 CGGGCTAAGTTCCAAAGAGCATTCATGCTAGTGATGTATC
1 CGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTATC
* *
41800495 CGGGCTAAGTTCCGAAGAGCATTTGTGCTAGTAATGTATC
1 CGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTATC
*
41800535 CGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATATATC
1 CGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTATC
41800575 CGGGCTAA
1 CGGGCTAA
41800583 ACCTCGAAGG
Statistics
Matches: 118, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 118 1.00
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (40 bp):
CGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTATC
Found at i:41800591 original size:80 final size:80
Alignment explanation
Indices: 41800408--41800602 Score: 261
Period size: 80 Copynumber: 2.5 Consensus size: 80
41800398 TGAAAGTTAT
* * *
41800408 ATATATTCGGGCTAAGTCC-CGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAAGTTCCAAAG
1 ATATATCCGGGCTAA-ACCTCGAAGAGCATTCGTGCTAGTAATGTATCCGGGCTAAGTTCCAAAG
41800472 AGCATTCATGCTAGTG
65 AGCATTCATGCTAGTG
* ** * *
41800488 ATGTATCCGGGCT-AAGTTCCGAAGAGCATTTGTGCTAGTAATGTATCCGGGCTAAGTTCCGAAG
1 ATATATCCGGGCTAAACCT-CGAAGAGCATTCGTGCTAGTAATGTATCCGGGCTAAGTTCCAAAG
*
41800552 AGCATTCGTGCTAGTG
65 AGCATTCATGCTAGTG
*
41800568 ATATATCCGGGCTAAACCTCGAAG-GCATTCATGCT
1 ATATATCCGGGCTAAACCTCGAAGAGCATTCGTGCT
41800603 GGAGTTATGA
Statistics
Matches: 98, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
79 10 0.10
80 85 0.87
81 3 0.03
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.28
Consensus pattern (80 bp):
ATATATCCGGGCTAAACCTCGAAGAGCATTCGTGCTAGTAATGTATCCGGGCTAAGTTCCAAAGA
GCATTCATGCTAGTG
Found at i:41800651 original size:28 final size:26
Alignment explanation
Indices: 41800609--41800770 Score: 108
Period size: 28 Copynumber: 5.7 Consensus size: 26
41800599 TGCTGGAGTT
* *
41800609 ATGAGGCACTGTGTGTGCAAGTTTTTCA
1 ATGA-GCACTATGTGTGCGAGTTTTT-A
* ***
41800637 ACTGAGCACTATGTGTGCCAGATCAGTA
1 A-TGAGCACTATGTGTGCGAG-TTTTTA
* *
41800665 GTTGAGGCACTATGTGTGCGAGTTCTTCA
1 -ATGA-GCACTATGTGTGCGAGTT-TTTA
**
41800694 ATCGAGCACTATGTGTGCGAGATTGGTA
1 AT-GAGCACTATGTGTGCGAG-TTTTTA
41800722 ATTGAGGCACTATGTGTGCGAGTTCTTTA
1 A-TGA-GCACTATGTGTGCGAGTT-TTTA
*
41800751 ATCGAGCGCTATGTGTGCGA
1 AT-GAGCACTATGTGTGCGA
41800771 AATCAGTCAG
Statistics
Matches: 105, Mismatches: 18, Indels: 22
0.72 0.12 0.15
Matches are distributed among these distances:
28 58 0.55
29 47 0.45
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.31
Consensus pattern (26 bp):
ATGAGCACTATGTGTGCGAGTTTTTA
Found at i:41800681 original size:29 final size:28
Alignment explanation
Indices: 41800642--41800770 Score: 118
Period size: 29 Copynumber: 4.5 Consensus size: 28
41800632 TTTCAACTGA
* *
41800642 GCACTATGTGTGCCAGATCAGTAGTTGAG
1 GCACTATGTGTGCGAGATC-GTAATTGAG
* * *
41800671 GCACTATGTGTGCGAGTTCTTCAATCGA-
1 GCACTATGTGTGCGAGATCGT-AATTGAG
*
41800699 GCACTATGTGTGCGAGATTGGTAATTGAG
1 GCACTATGTGTGCGAGA-TCGTAATTGAG
* * *
41800728 GCACTATGTGTGCGAGTTCTTTAATCGA-
1 GCACTATGTGTGCGAGATC-GTAATTGAG
*
41800756 GCGCTATGTGTGCGA
1 GCACTATGTGTGCGA
41800771 AATCAGTCAG
Statistics
Matches: 82, Mismatches: 14, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
28 37 0.45
29 45 0.55
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.31
Consensus pattern (28 bp):
GCACTATGTGTGCGAGATCGTAATTGAG
Found at i:41800701 original size:57 final size:57
Alignment explanation
Indices: 41800610--41800798 Score: 231
Period size: 57 Copynumber: 3.3 Consensus size: 57
41800600 GCTGGAGTTA
* * * *
41800610 TGAGGCACTGTGTGTGCAAGTTTTTCAA-CTGAGCACTATGTGTGCCAGATCAGTAGT
1 TGAGGCACTATGTGTGCGAGTTCTTCAATC-GAGCACTATGTGTGCGAGATCAGTAGT
** *
41800667 TGAGGCACTATGTGTGCGAGTTCTTCAATCGAGCACTATGTGTGCGAGATTGGTAAT
1 TGAGGCACTATGTGTGCGAGTTCTTCAATCGAGCACTATGTGTGCGAGATCAGTAGT
* * *
41800724 TGAGGCACTATGTGTGCGAGTTCTTTAATCGAGCGCTATGTGTGCGAAATCAGTCAG-
1 TGAGGCACTATGTGTGCGAGTTCTTCAATCGAGCACTATGTGTGCGAGATCAGT-AGT
* *
41800781 TG-GGCACTGTGTATGCGA
1 TGAGGCACTATGTGTGCGA
41800799 AGTGTGTTTC
Statistics
Matches: 115, Mismatches: 15, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
56 14 0.12
57 99 0.86
58 2 0.02
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.31
Consensus pattern (57 bp):
TGAGGCACTATGTGTGCGAGTTCTTCAATCGAGCACTATGTGTGCGAGATCAGTAGT
Found at i:41803346 original size:53 final size:53
Alignment explanation
Indices: 41803277--41803382 Score: 203
Period size: 53 Copynumber: 2.0 Consensus size: 53
41803267 ATGATATGTG
41803277 ATTGCCAAATGTGATTGTTAAGTGAATAATATTAGTTAAGTAATTAAGCAAAT
1 ATTGCCAAATGTGATTGTTAAGTGAATAATATTAGTTAAGTAATTAAGCAAAT
*
41803330 ATTGCCAAATGTGATTGTTAAGTGAATAATATTAGTTAAGTACTTAAGCAAAT
1 ATTGCCAAATGTGATTGTTAAGTGAATAATATTAGTTAAGTAATTAAGCAAAT
41803383 CTATTGTTTT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.41, C:0.07, G:0.17, T:0.36
Consensus pattern (53 bp):
ATTGCCAAATGTGATTGTTAAGTGAATAATATTAGTTAAGTAATTAAGCAAAT
Found at i:41804348 original size:48 final size:48
Alignment explanation
Indices: 41804284--41804429 Score: 247
Period size: 48 Copynumber: 3.0 Consensus size: 48
41804274 CAAGATAAAT
* * *
41804284 ATATATATGTGTGGTAAAGCTGAATGGCTAGTGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
*
41804332 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
*
41804380 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTAGGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
41804428 AT
1 AT
41804430 GTGTGTATAT
Statistics
Matches: 92, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 92 1.00
ACGTcount: A:0.34, C:0.05, G:0.29, T:0.32
Consensus pattern (48 bp):
ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
Found at i:41804620 original size:37 final size:37
Alignment explanation
Indices: 41804570--41804672 Score: 179
Period size: 37 Copynumber: 2.8 Consensus size: 37
41804560 GGAAATATAT
41804570 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
*
41804607 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
* *
41804644 TCCGGGTAAGACCCGATAACTATGTGTGG
1 TCCGGGTAAGACCCGATGACTACGTGTGG
41804673 GGACTATTCG
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 63 1.00
ACGTcount: A:0.23, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
Found at i:41807112 original size:40 final size:40
Alignment explanation
Indices: 41807019--41807238 Score: 223
Period size: 40 Copynumber: 5.5 Consensus size: 40
41807009 ACCCAAGTAT
* * ** * *
41807019 CTTCAGGATTTAG-CCGGATATAACCACTCGCAC-AAGGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* * * *
41807057 CTGCGGGTCTTAGCCCGGATATGGTCACTAGCATAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* *
41807097 CTTCGGGACTTAGCCCGGATATAATCGCTAGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* *
41807137 CTTCGGGTCTTAGCCCGGATATAG-CAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGC
* * *
41807177 CTTC-GGATCTTAGTCCGGATATAGTCACTAGCATAAAAGC
1 CTTCGGGA-CTTAGCCCGGATATAGTCACTAGCACAAATGC
* *
41807217 CTTTGAGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATAT
41807239 CATTTGAATA
Statistics
Matches: 148, Mismatches: 28, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
38 9 0.06
39 18 0.12
40 118 0.80
41 3 0.02
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.25
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:41824989 original size:40 final size:40
Alignment explanation
Indices: 41824907--41825126 Score: 214
Period size: 40 Copynumber: 5.5 Consensus size: 40
41824897 ACCCAAGTAT
** * *
41824907 CTTCGGGAT-TTAG-CCGGATATAACCACTCGCAC-AAGGC
1 CTTCGGG-TCTTAGCCCGGATATAGTCACTAGCACAAATGC
* * *
41824945 CTTCGGGTCTTAGCCCGAATATGGTCACTAGCATAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
* * *
41824985 CTTCGGGACTTAGCCCGGATATAATCGCTAGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
* * *
41825025 CTTAGGGTCTTAGCTCGGATATAG-CAACTCGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGTC-ACTAGCACAAATGC
* * * * * *
41825065 CTTCAGATCTTAGTCCAGATATAGTCACTAGCATAAAAGC
1 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
*
41825105 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGTCTTAGCCCGGATAT
41825127 CATTCGAATA
Statistics
Matches: 144, Mismatches: 33, Indels: 8
0.78 0.18 0.04
Matches are distributed among these distances:
37 1 0.01
38 11 0.08
39 15 0.10
40 116 0.81
41 1 0.01
ACGTcount: A:0.27, C:0.26, G:0.22, T:0.25
Consensus pattern (40 bp):
CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:41828207 original size:46 final size:45
Alignment explanation
Indices: 41828148--41828278 Score: 160
Period size: 46 Copynumber: 2.8 Consensus size: 45
41828138 CTCGTAGTCA
41828148 ATGCATGTCCCAAACATGTCTTACACTGGCTCTCGTC-TCAA-T-GCCG
1 ATGCATGTCCCAAACATGTCTTACACTGGCT-T--TCAT-AAGTGGCCG
*
41828194 ATGCATGTCCCAAACATGTCTTACACTAGCATTTCATAATGTGGCCG
1 ATGCATGTCCCAAACATGTCTTACACTGGC-TTTCATAA-GTGGCCG
* *
41828241 ATGCATGTCCCAGACATGTCTTACACTGGCTTACATAA
1 ATGCATGTCCCAAACATGTCTTACACTGGCTTTCATAA
41828279 CAGCAGTGTC
Statistics
Matches: 76, Mismatches: 4, Indels: 10
0.84 0.04 0.11
Matches are distributed among these distances:
44 4 0.05
45 1 0.01
46 38 0.50
47 33 0.43
ACGTcount: A:0.26, C:0.28, G:0.17, T:0.29
Consensus pattern (45 bp):
ATGCATGTCCCAAACATGTCTTACACTGGCTTTCATAAGTGGCCG
Found at i:41828211 original size:90 final size:91
Alignment explanation
Indices: 41828099--41828271 Score: 233
Period size: 93 Copynumber: 1.9 Consensus size: 91
41828089 CACATATTCG
* * * *
41828099 TGCCGAAGCATGTCGCAGACATGTCTTACACTAGCA-CAT-CTCGTAGTCAATGCATGTCCCAAA
1 TGCCGAAGCATGTCCCAAACATGTCTTACACTAGCATCATAAT-GTAGCCAATGCATGTCCCAAA
41828162 CATGTCTTACACTGGCTCTCGTCTCAA
65 CATGTCTTACACTGGCTCTCGTCTCAA
* * * *
41828189 TGCCGATGCATGTCCCAAACATGTCTTACACTAGCATTTCATAATGTGGCCGATGCATGTCCCAG
1 TGCCGAAGCATGTCCCAAACATGTCTTACACTAGCA--TCATAATGTAGCCAATGCATGTCCCAA
41828254 ACATGTCTTACACTGGCT
64 ACATGTCTTACACTGGCT
41828272 TACATAACAG
Statistics
Matches: 71, Mismatches: 8, Indels: 5
0.85 0.10 0.06
Matches are distributed among these distances:
90 33 0.46
93 37 0.52
94 1 0.01
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.28
Consensus pattern (91 bp):
TGCCGAAGCATGTCCCAAACATGTCTTACACTAGCATCATAATGTAGCCAATGCATGTCCCAAAC
ATGTCTTACACTGGCTCTCGTCTCAA
Found at i:41838517 original size:49 final size:48
Alignment explanation
Indices: 41838445--41838618 Score: 167
Period size: 49 Copynumber: 3.6 Consensus size: 48
41838435 CATGCGTGTC
41838445 AGTGTAAAACCTATCTGGGACATGGCATCGGCCTCAAGATATGCAAGCT
1 AGTGTAAAACCTATCTGGGACATGGCATCGGCCTCAAGATATG-AAGCT
* * * * *
41838494 AGTGTAAGACCTGTCTGGGACATGGCATC-GACAC-AGATAAGTGAGAGCC
1 AGTGTAAAACCTATCTGGGACATGGCATCGGCCTCAAGAT-A-TGA-AGCT
* * *
41838543 AGTGTAAAAGCTATCTGGGACATGGCATCGGCCTTGATG-TATGTAAG-T
1 AGTGTAAAACCTATCTGGGACATGGCATCGGCC-TCAAGATATG-AAGCT
* *
41838591 CAGTGTAAGACCTGTCTGGGACATGGCA
1 -AGTGTAAAACCTATCTGGGACATGGCA
41838619 CCGACTTATA
Statistics
Matches: 101, Mismatches: 16, Indels: 16
0.76 0.12 0.12
Matches are distributed among these distances:
47 4 0.04
48 5 0.05
49 86 0.85
50 4 0.04
51 1 0.01
52 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.29, T:0.23
Consensus pattern (48 bp):
AGTGTAAAACCTATCTGGGACATGGCATCGGCCTCAAGATATGAAGCT
Found at i:41838613 original size:98 final size:96
Alignment explanation
Indices: 41838444--41838645 Score: 282
Period size: 98 Copynumber: 2.1 Consensus size: 96
41838434 ACATGCGTGT
41838444 CAGTGTAAAACCTATCTGGGACATGGCATCGGCCTCAAGATATGCAAGCTAGTGTAAGACCTGTC
1 CAGTGTAAAACCTATCTGGGACATGGCATCGGCCTCAAGATATGCAAGCTAGTGTAAGACCTGTC
*
41838509 TGGGACATGGCATCGACACAGATAAGTGAGAGC
66 TGGGACATGGCACCG--ACAGATAAGTGAGAGC
* * * *
41838542 CAGTGTAAAAGCTATCTGGGACATGGCATCGGCCTTGATG-TATGTAAG-TCAGTGTAAGACCTG
1 CAGTGTAAAACCTATCTGGGACATGGCATCGGCC-TCAAGATATGCAAGCT-AGTGTAAGACCTG
** *
41838605 TCTGGGACATGGCACCGACTTATATGTGAGAGC
64 TCTGGGACATGGCACCGACAGATAAGTGAGAGC
41838638 CAGTGTAA
1 CAGTGTAA
41838646 GACCATGTTT
Statistics
Matches: 94, Mismatches: 8, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
96 21 0.22
97 1 0.01
98 69 0.73
99 3 0.03
ACGTcount: A:0.29, C:0.20, G:0.28, T:0.23
Consensus pattern (96 bp):
CAGTGTAAAACCTATCTGGGACATGGCATCGGCCTCAAGATATGCAAGCTAGTGTAAGACCTGTC
TGGGACATGGCACCGACAGATAAGTGAGAGC
Found at i:41845753 original size:6 final size:6
Alignment explanation
Indices: 41845744--41845836 Score: 59
Period size: 6 Copynumber: 15.2 Consensus size: 6
41845734 TGTCTTTCAA
* * * *
41845744 AAAAAT AAAATAAT AAAAAT -GAAAT GAAAAT AAAAAT CAAAAGAA AAAAAA
1 AAAAAT -AAA-AAT AAAAAT AAAAAT AAAAAT AAAAAT -AAAA-AT AAAAAT
*
41845795 AGAAAAT -AAAAT -AAAAT AAAAAT AAGAAT AAATAA- AAAAAT A
1 A-AAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAA-AAT AAAAAT A
41845837 GGAGTCAATG
Statistics
Matches: 71, Mismatches: 7, Indels: 17
0.75 0.07 0.18
Matches are distributed among these distances:
5 16 0.23
6 31 0.44
7 20 0.28
8 4 0.06
ACGTcount: A:0.78, C:0.01, G:0.05, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:41845755 original size:5 final size:5
Alignment explanation
Indices: 41845745--41845831 Score: 70
Period size: 5 Copynumber: 16.8 Consensus size: 5
41845735 GTCTTTCAAA
* * * *
41845745 AAAAT AAAAT AATA- AAAAT GAAAT GAAAAT AAAAAT CAAAAG AAAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT -AAAAT -AAAAT -AAAAT AAAAT
*
41845792 AAAAG AAAAT AAAAT AAAAT AAAAAT AAGAAT -AAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT -AAAAT AA-AAT AAAAT AAAA
41845832 AAATAGGAGT
Statistics
Matches: 67, Mismatches: 10, Indels: 10
0.77 0.11 0.11
Matches are distributed among these distances:
4 6 0.09
5 40 0.60
6 21 0.31
ACGTcount: A:0.78, C:0.01, G:0.06, T:0.15
Consensus pattern (5 bp):
AAAAT
Found at i:41845775 original size:17 final size:17
Alignment explanation
Indices: 41845755--41845810 Score: 64
Period size: 17 Copynumber: 3.4 Consensus size: 17
41845745 AAAATAAAAT
41845755 AATAAAAATGAAATGAA
1 AATAAAAATGAAATGAA
* *
41845772 AATAAAAATCAAAAGAA
1 AATAAAAATGAAATGAA
41845789 AA-AAAAA-GAAAAT-AA
1 AATAAAAATG-AAATGAA
41845804 AATAAAA
1 AATAAAA
41845811 TAAAAATAAG
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
15 4 0.12
16 12 0.36
17 17 0.52
ACGTcount: A:0.79, C:0.02, G:0.07, T:0.12
Consensus pattern (17 bp):
AATAAAAATGAAATGAA
Found at i:41845834 original size:43 final size:43
Alignment explanation
Indices: 41845742--41845834 Score: 100
Period size: 43 Copynumber: 2.2 Consensus size: 43
41845732 TATGTCTTTC
* * * *
41845742 AAAAAAATAAAATAATAAAAATGAAATGAAAATAAAAATCAAA
1 AAAAAAAAAAAAAAATAAAAATAAAATAAAAATAAAAATCAAA
* *
41845785 AGAAAAAAAAAGAAAAT-AAAATAAAATAAAAATAAGAAT-AAA
1 A-AAAAAAAAAAAAAATAAAAATAAAATAAAAATAAAAATCAAA
*
41845827 TAAAAAAA
1 AAAAAAAA
41845835 TAGGAGTCAA
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
41 7 0.17
42 3 0.07
43 20 0.48
44 12 0.29
ACGTcount: A:0.80, C:0.01, G:0.05, T:0.14
Consensus pattern (43 bp):
AAAAAAAAAAAAAAATAAAAATAAAATAAAAATAAAAATCAAA
Found at i:41854692 original size:49 final size:49
Alignment explanation
Indices: 41854632--41854805 Score: 258
Period size: 49 Copynumber: 3.5 Consensus size: 49
41854622 TGAGGTCATG
* * *
41854632 TGTGCAGTACTAAGTGCAGGATACTACGTGTACCAGATTATTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCA
* ** * *
41854681 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGTTAGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT-GGTCGCA
*
41854731 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCA
41854780 TGTGTAGTACTAAGTGCAGGCTACTA
1 TGTGTAGTACTAAGTGCAGGCTACTA
41854806 TGCGTACTAG
Statistics
Matches: 111, Mismatches: 13, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
49 68 0.61
50 43 0.39
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.29
Consensus pattern (49 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCA
Found at i:41854795 original size:99 final size:99
Alignment explanation
Indices: 41854624--41854805 Score: 319
Period size: 99 Copynumber: 1.8 Consensus size: 99
41854614 ATATATTGTG
* *
41854624 AGGTCATGTGTGCAGTACTAAGTGCAGGATACTACGTGTACCAGATTATTGGTCGCATGTGTAGT
1 AGGTCACGTGTGCAGTACTAAGTGCAGGATACTACGTGTACCAGATAATTGGTCGCATGTGTAGT
41854689 ACTAAGTGCAGGCTACTACGTGTATCAGATGGTT
66 ACTAAGTGCAGGCTACTACGTGTATCAGATGGTT
* * *
41854723 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCATGTGTAGT
1 AGGTCACGTGTGCAGTACTAAGTGCAGGATACTACGTGTACCAGATAATTGGTCGCATGTGTAGT
41854788 ACTAAGTGCAGGCTACTA
66 ACTAAGTGCAGGCTACTA
41854806 TGCGTACTAG
Statistics
Matches: 78, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
99 78 1.00
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.29
Consensus pattern (99 bp):
AGGTCACGTGTGCAGTACTAAGTGCAGGATACTACGTGTACCAGATAATTGGTCGCATGTGTAGT
ACTAAGTGCAGGCTACTACGTGTATCAGATGGTT
Done.