Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A05
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: 100714657
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3970000 characters in sequence are not A, C, G, or T
File 170 of 318
Found at i:53723082 original size:25 final size:24
Alignment explanation
Indices: 53723049--53723272 Score: 95
Period size: 25 Copynumber: 9.5 Consensus size: 24
53723039 TATATACTGG
53723049 CATTATCACATATATACACTTTCA
1 CATTATCACATATATACACTTTCA
**** ***
53723073 CATTCATCACAT-CGGCCA-TTAGG
1 CATT-ATCACATATATACACTTTCA
53723096 CATTATCACATATATACACTTTCA
1 CATTATCACATATATACACTTTCA
**** ***
53723120 CATTCATCACAT-CGGCCA-TTAGG
1 CATT-ATCACATATATACACTTTCA
*
53723143 CCTTATCACATATATACACTTTCA
1 CATTATCACATATATACACTTTCA
*** ***
53723167 CATTCATCACATCGGT-CA-TTAGG
1 CATT-ATCACATATATACACTTTCA
53723190 CATTATCACATATATACACTTTCA
1 CATTATCACATATATACACTTTCA
**** ***
53723214 CATTCATCACAT-CGGCCA-TTAGG
1 CATT-ATCACATATATACACTTTCA
53723237 CATTATCACATATATACACTTTCA
1 CATTATCACATATATACACTTTCA
53723261 CATTCATCACAT
1 CATT-ATCACAT
53723273 CGGCCATTAG
Statistics
Matches: 131, Mismatches: 56, Indels: 25
0.62 0.26 0.12
Matches are distributed among these distances:
22 29 0.22
23 31 0.24
24 35 0.27
25 36 0.27
ACGTcount: A:0.32, C:0.28, G:0.07, T:0.33
Consensus pattern (24 bp):
CATTATCACATATATACACTTTCA
Found at i:53723200 original size:22 final size:23
Alignment explanation
Indices: 53723073--53723247 Score: 70
Period size: 22 Copynumber: 7.5 Consensus size: 23
53723063 TACACTTTCA
*
53723073 CATTCATCACATCGGCCATTAGG
1 CATTCATCACATCGGTCATTAGG
*** ***
53723096 CATT-ATCACATATATACACTTTCA
1 CATTCATCACATCGGT-CA-TTAGG
*
53723120 CATTCATCACATCGGCCATTAGG
1 CATTCATCACATCGGTCATTAGG
* *** ***
53723143 CCTT-ATCACATATATACACTTTCA
1 CATTCATCACATCGGT-CA-TTAGG
53723167 CATTCATCACATCGGTCATTAGG
1 CATTCATCACATCGGTCATTAGG
*** ***
53723190 CATT-ATCACATATATACACTTTCA
1 CATTCATCACATCGGT-CA-TTAGG
*
53723214 CATTCATCACATCGGCCATTAGG
1 CATTCATCACATCGGTCATTAGG
53723237 CATT-ATCACAT
1 CATTCATCACAT
53723248 ATATACACTT
Statistics
Matches: 101, Mismatches: 42, Indels: 19
0.62 0.26 0.12
Matches are distributed among these distances:
22 29 0.29
23 27 0.27
24 23 0.23
25 22 0.22
ACGTcount: A:0.31, C:0.28, G:0.09, T:0.32
Consensus pattern (23 bp):
CATTCATCACATCGGTCATTAGG
Found at i:53723332 original size:47 final size:47
Alignment explanation
Indices: 53722880--53723331 Score: 560
Period size: 47 Copynumber: 9.7 Consensus size: 47
53722870 GCCCTTCGGG
* * **
53722880 ACTTATCACATTCATCACATCGACTATTAGGCCCTATCACATATATATAC
1 ACTT-TCACATTCATCACATCGGCCATTAGGCATTATCAC--ATATATAC
*
53722930 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 ACTTTCACATTCATCACATCGGCCATTAGGCATTATCACATATATAC
* *** * ****
53722977 ACTTTCACATTCA-CATATATACACTTTCA--CATTCATCACAT-CGGCC
1 ACTTTCACATTCATCACATCGGC-CATT-AGGCATT-ATCACATATATAC
*** * **** *
53723023 A-TTAGGCCTT-ATCACAT-ATATACT-GGCATTATCACATATATAC
1 ACTTTCACATTCATCACATCGGCCATTAGGCATTATCACATATATAC
53723066 ACTTTCACATTCATCACATCGGCCATTAGGCATTATCACATATATAC
1 ACTTTCACATTCATCACATCGGCCATTAGGCATTATCACATATATAC
*
53723113 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 ACTTTCACATTCATCACATCGGCCATTAGGCATTATCACATATATAC
*
53723160 ACTTTCACATTCATCACATCGGTCATTAGGCATTATCACATATATAC
1 ACTTTCACATTCATCACATCGGCCATTAGGCATTATCACATATATAC
53723207 ACTTTCACATTCATCACATCGGCCATTAGGCATTATCACATATATAC
1 ACTTTCACATTCATCACATCGGCCATTAGGCATTATCACATATATAC
*
53723254 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 ACTTTCACATTCATCACATCGGCCATTAGGCATTATCACATATATAC
53723301 ACTTTCACATTCATCACATCGGCCATTAGGC
1 ACTTTCACATTCATCACATCGGCCATTAGGC
53723332 CATACTATCA
Statistics
Matches: 349, Mismatches: 42, Indels: 25
0.84 0.10 0.06
Matches are distributed among these distances:
42 7 0.02
43 7 0.02
44 6 0.02
45 16 0.05
46 12 0.03
47 264 0.76
48 1 0.00
49 32 0.09
50 4 0.01
ACGTcount: A:0.31, C:0.28, G:0.08, T:0.32
Consensus pattern (47 bp):
ACTTTCACATTCATCACATCGGCCATTAGGCATTATCACATATATAC
Found at i:53734799 original size:31 final size:31
Alignment explanation
Indices: 53734756--53734834 Score: 140
Period size: 31 Copynumber: 2.5 Consensus size: 31
53734746 TTTAACGGTT
*
53734756 ACTGGGCTGAAGCCTTTTCATAAATCATATC
1 ACTGGGCCGAAGCCTTTTCATAAATCATATC
53734787 ACTGGGCCGAAGCCTTTTCATAAATCATATC
1 ACTGGGCCGAAGCCTTTTCATAAATCATATC
*
53734818 ATTGGGCCGAAGCCTTT
1 ACTGGGCCGAAGCCTTT
53734835 ACTGTAAATG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (31 bp):
ACTGGGCCGAAGCCTTTTCATAAATCATATC
Found at i:53735123 original size:26 final size:26
Alignment explanation
Indices: 53735039--53735226 Score: 240
Period size: 26 Copynumber: 7.3 Consensus size: 26
53735029 CTGGAGGCCT
53735039 AGCCTCTTTT-AAT-AACTGGGGCA-A
1 AGCC-CTTTTCAATAAACTGGGGCATA
* * ** *
53735063 TGCTCTTTTCGGTAAACTAGGGCA-A
1 AGCCCTTTTCAATAAACTGGGGCATA
53735088 AGCCCTTTTCAATAAACTGGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
** *
53735114 AGCCCTTTTCGGTAAACTGGGCCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
*
53735140 AGCCCTTTTCAATAAACTAGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
**
53735166 AGCCCTTTTCGGTAAACTGGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
53735192 AGCCCTTTTCAATAAACTGGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
53735218 AGCCCTTTT
1 AGCCCTTTT
53735227 GCACTTCCTC
Statistics
Matches: 139, Mismatches: 22, Indels: 4
0.84 0.13 0.02
Matches are distributed among these distances:
23 5 0.04
24 3 0.02
25 29 0.21
26 102 0.73
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (26 bp):
AGCCCTTTTCAATAAACTGGGGCATA
Found at i:53735152 original size:52 final size:51
Alignment explanation
Indices: 53735039--53735226 Score: 285
Period size: 52 Copynumber: 3.7 Consensus size: 51
53735029 CTGGAGGCCT
* *
53735039 AGCCTCTTTT-AAT-AACTGGGGCA-ATGCTCTTTTCGGTAAACTAGGGCA-A
1 AGCC-CTTTTCAATAAACTGGGGCATAAGCCCTTTTCGGTAAACT-GGGCATA
53735088 AGCCCTTTTCAATAAACTGGGGCATAAGCCCTTTTCGGTAAACTGGGCCATA
1 AGCCCTTTTCAATAAACTGGGGCATAAGCCCTTTTCGGTAAACTGGG-CATA
*
53735140 AGCCCTTTTCAATAAACTAGGGCATAAGCCCTTTTCGGTAAACTGGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATAAGCCCTTTTCGGTAAACT-GGGCATA
53735192 AGCCCTTTTCAATAAACTGGGGCATAAGCCCTTTT
1 AGCCCTTTTCAATAAACTGGGGCATAAGCCCTTTT
53735227 GCACTTCCTC
Statistics
Matches: 129, Mismatches: 4, Indels: 9
0.91 0.03 0.06
Matches are distributed among these distances:
48 5 0.04
49 7 0.05
50 13 0.10
51 19 0.15
52 82 0.64
53 3 0.02
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (51 bp):
AGCCCTTTTCAATAAACTGGGGCATAAGCCCTTTTCGGTAAACTGGGCATA
Found at i:53736125 original size:27 final size:27
Alignment explanation
Indices: 53736029--53736116 Score: 124
Period size: 27 Copynumber: 3.3 Consensus size: 27
53736019 ATATTTGTCA
* *
53736029 TTTTACCATACAGGGG-TATTACGGTCA
1 TTTTACCCTACAGGGGCT-TTACGGTCT
* *
53736056 CTTTACCCTACAGGGGCTTTACGGTTT
1 TTTTACCCTACAGGGGCTTTACGGTCT
53736083 TTTTACCCTACAGGGGCTTTACGGTCT
1 TTTTACCCTACAGGGGCTTTACGGTCT
53736110 TTTTACC
1 TTTTACC
53736117 TAATAGGGGT
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
27 53 0.98
28 1 0.02
ACGTcount: A:0.18, C:0.24, G:0.20, T:0.38
Consensus pattern (27 bp):
TTTTACCCTACAGGGGCTTTACGGTCT
Found at i:53736200 original size:27 final size:27
Alignment explanation
Indices: 53736147--53736519 Score: 196
Period size: 27 Copynumber: 13.7 Consensus size: 27
53736137 TTTCATCCTA
* * * * *
53736147 CAAGGGTGTTTTGGTAAATCTACAAAC
1 CAAGGGTATTTTAGTAATTTTACAAAT
* ** *
53736174 CAAGGGTATTTCAGTAATTTTGTAAAC
1 CAAGGGTATTTTAGTAATTTTACAAAT
* * *
53736201 CAATGGTATTTCCA-TAATTTTTAGAAAGT
1 CAAGGGTATTT-TAGTAA-TTTTACAAA-T
* **
53736230 CAAGGGTATTTCT-GTAACTTTGTAAAT
1 CAAGGGTATTT-TAGTAATTTTACAAAT
* *
53736257 CAGGGGTATTTTGGTAATTTTACAAAT
1 CAAGGGTATTTTAGTAATTTTACAAAT
** * *
53736284 TGAGGGTATTTTGGTAATTTCACAAA-
1 CAAGGGTATTTTAGTAATTTTACAAAT
* *
53736310 CCAGTGGTATTTTGGTAATTTTACAAA-
1 CAAG-GGTATTTTAGTAATTTTACAAAT
* *
53736337 CTAGGGGTATTTTGGTAATTTTACAAAT
1 C-AAGGGTATTTTAGTAATTTTACAAAT
* ** *
53736365 CGAGGGTATTTTTTTAATTTTACAAAC
1 CAAGGGTATTTTAGTAATTTTACAAAT
**
53736392 CAAGGGTATTTTAGTAATTTTGTAAAT
1 CAAGGGTATTTTAGTAATTTTACAAAT
** **** **
53736419 TGAGGGTAAAACAGTAATTTTGTAAAT
1 CAAGGGTATTTTAGTAATTTTACAAAT
**** * *
53736446 CAAGGGTAAAACAGTAATTCTATAAAT
1 CAAGGGTATTTTAGTAATTTTACAAAT
* * * *
53736473 CGAGGGTACTTTGGTAATTTTACAATT
1 CAAGGGTATTTTAGTAATTTTACAAAT
** *
53736500 TGAGGGTATTTCAGTAATTT
1 CAAGGGTATTTTAGTAATTT
53736520 GGTAAACTAA
Statistics
Matches: 275, Mismatches: 63, Indels: 16
0.78 0.18 0.05
Matches are distributed among these distances:
26 3 0.01
27 241 0.88
28 17 0.06
29 14 0.05
ACGTcount: A:0.32, C:0.09, G:0.20, T:0.39
Consensus pattern (27 bp):
CAAGGGTATTTTAGTAATTTTACAAAT
Found at i:53736412 original size:54 final size:54
Alignment explanation
Indices: 53736149--53736525 Score: 238
Period size: 54 Copynumber: 6.9 Consensus size: 54
53736139 TCATCCTACA
* * * * * *
53736149 AGGGTGTTTTGGTAAATCTACAAACCAAGGGTATTTCAGTAATTTTGTAAACCA
1 AGGGTATTTTGGTAATTTTACAAACCAAGGGTATTTTAGTAATTTTGTAAATCG
* *** * * *
53736203 ATGGTATTTCCATAATTTTTAGAAAGTCAAGGGTATTTCT-GTAACTTTGTAAATC-
1 AGGGTATTTTGGTAA-TTTTACAAA-CCAAGGGTATTT-TAGTAATTTTGTAAATCG
*** * *** *
53736258 AGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTTGGTAATTTCACAAA-CC
1 A-GGGTATTTTGGTAATTTTACAAACCAAGGGTATTTTAGTAATTTTGTAAATCG
* * * **
53736312 AGTGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTACAAATCG
1 AG-GGTATTTTGGTAATTTTACAAACCAAGGGTATTTTAGTAATTTTGTAAATCG
** *
53736367 AGGGTATTTTTTTAATTTTACAAACCAAGGGTATTTTAGTAATTTTGTAAATTG
1 AGGGTATTTTGGTAATTTTACAAACCAAGGGTATTTTAGTAATTTTGTAAATCG
***** ** * **** * *
53736421 AGGGTAAAACAGTAATTTTGTAAATCAAGGGTAAAACAGTAATTCTATAAATCG
1 AGGGTATTTTGGTAATTTTACAAACCAAGGGTATTTTAGTAATTTTGTAAATCG
* **** * *
53736475 AGGGTACTTTGGTAATTTTACAATTTGAGGGTATTTCAGTAATTTGGTAAA
1 AGGGTATTTTGGTAATTTTACAAACCAAGGGTATTTTAGTAATTTTGTAAA
53736526 CTAAAGTATT
Statistics
Matches: 247, Mismatches: 68, Indels: 16
0.75 0.21 0.05
Matches are distributed among these distances:
53 3 0.01
54 192 0.78
55 18 0.07
56 34 0.14
ACGTcount: A:0.33, C:0.09, G:0.20, T:0.39
Consensus pattern (54 bp):
AGGGTATTTTGGTAATTTTACAAACCAAGGGTATTTTAGTAATTTTGTAAATCG
Found at i:53736426 original size:81 final size:79
Alignment explanation
Indices: 53736230--53736418 Score: 254
Period size: 81 Copynumber: 2.3 Consensus size: 79
53736220 TTTAGAAAGT
* *
53736230 CAAGGGTATTTCTGTAACTTTGTAAATCAGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTT
1 CAAGGGTATTT-TGTAATTTTGTAAAT-AGGGGTATTTTGGTAATTTTACAAATCGAGGGTATTT
53736295 TGGTAATTTCACAAAC
64 TGGTAATTTCACAAAC
**
53736311 C-AGTGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTACAAATCGAGGGTATT
1 CAAG-GGTATTTT-GTAATTTTGTAAA-TAGGGGTATTTTGGTAATTTTACAAATCGAGGGTATT
** *
53736375 TTTTTAATTTTACAAAC
63 TTGGTAATTTCACAAAC
53736392 CAAGGGTATTTTAGTAATTTTGTAAAT
1 CAAGGGTATTTT-GTAATTTTGTAAAT
53736419 TGAGGGTAAA
Statistics
Matches: 94, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
80 4 0.04
81 87 0.93
82 3 0.03
ACGTcount: A:0.30, C:0.08, G:0.20, T:0.42
Consensus pattern (79 bp):
CAAGGGTATTTTGTAATTTTGTAAATAGGGGTATTTTGGTAATTTTACAAATCGAGGGTATTTTG
GTAATTTCACAAAC
Found at i:53737588 original size:27 final size:27
Alignment explanation
Indices: 53737550--53737604 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
53737540 GCTCCATGGC
53737550 CTCCAAGTTTGAGAGAATTTCTTTAAA
1 CTCCAAGTTTGAGAGAATTTCTTTAAA
53737577 CTCCAAGTTTGAGAGAATTTCTTTAAA
1 CTCCAAGTTTGAGAGAATTTCTTTAAA
53737604 C
1 C
53737605 ACTATTAAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Consensus pattern (27 bp):
CTCCAAGTTTGAGAGAATTTCTTTAAA
Found at i:53746128 original size:27 final size:27
Alignment explanation
Indices: 53746048--53746135 Score: 97
Period size: 27 Copynumber: 3.3 Consensus size: 27
53746038 GGCCGTTAGG
* *
53746048 ACCCTTGTAGTGCAAAATTACTGAAAT
1 ACCCTCGTAGTGCAAAATTACCGAAAT
* *
53746075 ACCC-CTATAGTGCAAAATTATCGAAAT
1 ACCCTC-GTAGTGCAAAATTACCGAAAT
* *
53746102 ACCCTCGTAGTGTAAAATTACCAAAAT
1 ACCCTCGTAGTGCAAAATTACCGAAAT
*
53746129 AACCTCG
1 ACCCTCG
53746136 ATTTGTGAAA
Statistics
Matches: 50, Mismatches: 9, Indels: 4
0.79 0.14 0.06
Matches are distributed among these distances:
27 49 0.98
28 1 0.02
ACGTcount: A:0.39, C:0.23, G:0.12, T:0.26
Consensus pattern (27 bp):
ACCCTCGTAGTGCAAAATTACCGAAAT
Found at i:53749742 original size:24 final size:24
Alignment explanation
Indices: 53749706--53749756 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
53749696 TAACTGGATA
* *
53749706 CTCTGATTTGTTATAGGTGCGGTG
1 CTCTGATTGGTTATAAGTGCGGTG
53749730 CTCTGATTGGTTATAAGTGCGGTG
1 CTCTGATTGGTTATAAGTGCGGTG
53749754 CTC
1 CTC
53749757 GTGAAGTGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.14, C:0.16, G:0.31, T:0.39
Consensus pattern (24 bp):
CTCTGATTGGTTATAAGTGCGGTG
Found at i:53754731 original size:40 final size:40
Alignment explanation
Indices: 53754685--53754804 Score: 222
Period size: 40 Copynumber: 3.0 Consensus size: 40
53754675 GGATTTAGCT
* *
53754685 GGATATAACAACTCGCACAAATGCCTTCGGGTCCTAGCCC
1 GGATATAGCAACTCGCACAAATGCCTTCGGGTCTTAGCCC
53754725 GGATATAGCAACTCGCACAAATGCCTTCGGGTCTTAGCCC
1 GGATATAGCAACTCGCACAAATGCCTTCGGGTCTTAGCCC
53754765 GGATATAGCAACTCGCACAAATGCCTTCGGGTCTTAGCCC
1 GGATATAGCAACTCGCACAAATGCCTTCGGGTCTTAGCCC
53754805 AGTTATCATC
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
40 78 1.00
ACGTcount: A:0.26, C:0.31, G:0.22, T:0.22
Consensus pattern (40 bp):
GGATATAGCAACTCGCACAAATGCCTTCGGGTCTTAGCCC
Found at i:53759101 original size:64 final size:64
Alignment explanation
Indices: 53759020--53759203 Score: 176
Period size: 67 Copynumber: 2.8 Consensus size: 64
53759010 AGACATTATG
* **
53759020 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATTT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
** * * * * *
53759084 ATGTAGCTAGGTCGCATGCATGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
53759149 AA
63 AA
* * * *
53759151 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAGC
53759204 CGAACTATAT
Statistics
Matches: 95, Mismatches: 20, Indels: 11
0.75 0.16 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.20
64 20 0.21
65 8 0.08
66 15 0.16
67 30 0.32
68 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.29, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:53767532 original size:24 final size:23
Alignment explanation
Indices: 53767461--53767532 Score: 72
Period size: 25 Copynumber: 3.0 Consensus size: 23
53767451 GCTTTATCAT
**
53767461 ATAACTGGAGGCCTAGCCTCTTTTG
1 ATAACTGG-GGCAAAGCC-CTTTTG
*
53767486 ATAACTGGGGCAAACCCCTTTTTG
1 ATAACTGGGGCAAAGCCC-TTTTG
*
53767510 GTAAACTGGGGCAAAGCCCTTTT
1 AT-AACTGGGGCAAAGCCCTTTT
53767533 CGCACTTCCT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
23 1 0.03
24 16 0.40
25 23 0.57
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.29
Consensus pattern (23 bp):
ATAACTGGGGCAAAGCCCTTTTG
Found at i:53767602 original size:11 final size:11
Alignment explanation
Indices: 53767566--53767630 Score: 62
Period size: 11 Copynumber: 6.1 Consensus size: 11
53767556 ACCCAACCTA
*
53767566 TGCATATAATG
1 TGCATATCATG
* *
53767577 AGTATATCAT-
1 TGCATATCATG
*
53767587 AGCATATCATG
1 TGCATATCATG
*
53767598 TGCATCTCAT-
1 TGCATATCATG
*
53767608 TACATATCATG
1 TGCATATCATG
53767619 TGCATATCATG
1 TGCATATCATG
53767630 T
1 T
53767631 ATAACAATAT
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
10 17 0.40
11 26 0.60
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.37
Consensus pattern (11 bp):
TGCATATCATG
Found at i:53767607 original size:21 final size:20
Alignment explanation
Indices: 53767580--53767628 Score: 71
Period size: 21 Copynumber: 2.4 Consensus size: 20
53767570 TATAATGAGT
53767580 ATATCATAGCATATCATGTGC
1 ATATCATA-CATATCATGTGC
*
53767601 ATCTCATTACATATCATGTGC
1 ATATCA-TACATATCATGTGC
53767622 ATATCAT
1 ATATCAT
53767629 GTATAACAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 1 0.04
21 22 0.88
22 2 0.08
ACGTcount: A:0.33, C:0.20, G:0.10, T:0.37
Consensus pattern (20 bp):
ATATCATACATATCATGTGC
Found at i:53768035 original size:21 final size:20
Alignment explanation
Indices: 53767980--53768036 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
53767970 TGGGCCCAAA
*
53767980 AGCCCATTGGGCCTAATTCC
1 AGCCCATTGGGCCCAATTCC
* *
53768000 AGCCCATTCGGCCCAATTCT
1 AGCCCATTGGGCCCAATTCC
53768020 AGCCCATTGAGGCCCAA
1 AGCCCATTG-GGCCCAA
53768037 CTTACCATCG
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 25 0.78
21 7 0.22
ACGTcount: A:0.23, C:0.37, G:0.19, T:0.21
Consensus pattern (20 bp):
AGCCCATTGGGCCCAATTCC
Found at i:53770908 original size:13 final size:13
Alignment explanation
Indices: 53770890--53770916 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
53770880 GGTTGTTTAT
53770890 TAAACTAATTAAC
1 TAAACTAATTAAC
53770903 TAAACTAATTAAC
1 TAAACTAATTAAC
53770916 T
1 T
53770917 GATTAAACTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.52, C:0.15, G:0.00, T:0.33
Consensus pattern (13 bp):
TAAACTAATTAAC
Found at i:53773850 original size:6 final size:6
Alignment explanation
Indices: 53773841--53773903 Score: 74
Period size: 6 Copynumber: 10.5 Consensus size: 6
53773831 AATAAAATTG
* * *
53773841 AAATGA AAATAA AAATAA AAATAG AGATAA AAATAA AAATAA AATATAA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AA-ATAA
*
53773890 AAA-AG AAATAA AAA
1 AAATAA AAATAA AAA
53773904 GATAGGAGGA
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
5 4 0.08
6 38 0.79
7 6 0.12
ACGTcount: A:0.78, C:0.00, G:0.06, T:0.16
Consensus pattern (6 bp):
AAATAA
Found at i:53779115 original size:79 final size:79
Alignment explanation
Indices: 53778994--53779167 Score: 280
Period size: 79 Copynumber: 2.2 Consensus size: 79
53778984 AACCAAAATG
*
53778994 AGAATCAGAATCAGTAACAGAATCAGAATCAGAATCAATATTAGTAACAGAATCAGAATCAGAAT
1 AGAATCAGAATCAGAAACAGAATCAGAATCAGAATCAATATTAGTAACAGAATCAGAATCAGAAT
*
53779059 CAGAATTAGGTGAC
66 CAGAATTACGTGAC
*
53779073 AGAATCAGAATCA-AAATCAGTAAT-AGAATCAGAATCAGTATTAGTAACAGAATCAGAATCAGA
1 AGAATCAGAATCAGAAA-CAG-AATCAGAATCAGAATCAATATTAGTAACAGAATCAGAATCAGA
53779136 ATCAGAATTACGTGAC
64 ATCAGAATTACGTGAC
*
53779152 AGAATCAGAACCAGAA
1 AGAATCAGAATCAGAA
53779168 TGTGAATACA
Statistics
Matches: 88, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
78 2 0.02
79 81 0.92
80 5 0.06
ACGTcount: A:0.49, C:0.14, G:0.17, T:0.20
Consensus pattern (79 bp):
AGAATCAGAATCAGAAACAGAATCAGAATCAGAATCAATATTAGTAACAGAATCAGAATCAGAAT
CAGAATTACGTGAC
Found at i:53779157 original size:31 final size:30
Alignment explanation
Indices: 53779072--53779168 Score: 108
Period size: 30 Copynumber: 3.2 Consensus size: 30
53779062 AATTAGGTGA
* *
53779072 CAGAATCAGAATCA-AAATCAGTAAT-AGAAT
1 CAGAATCAGAATTAGTAA-CAG-AATCAGAAT
*
53779102 CAGAATCAGTATTAGTAACAGAATCAGAAT
1 CAGAATCAGAATTAGTAACAGAATCAGAAT
* *
53779132 CAGAATCAGAATTACGTGACAGAATCAGAAC
1 CAGAATCAGAATTA-GTAACAGAATCAGAAT
53779163 CAGAAT
1 CAGAAT
53779169 GTGAATACAA
Statistics
Matches: 58, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
29 3 0.05
30 33 0.57
31 22 0.38
ACGTcount: A:0.48, C:0.15, G:0.16, T:0.20
Consensus pattern (30 bp):
CAGAATCAGAATTAGTAACAGAATCAGAAT
Found at i:53779161 original size:6 final size:6
Alignment explanation
Indices: 53778994--53779143 Score: 141
Period size: 6 Copynumber: 24.8 Consensus size: 6
53778984 AACCAAAATG
*
53778994 AGAATC AGAATC AGTAA-C AGAATC AGAATC AGAATC A-ATATT AGTAA-C
1 AGAATC AGAATC AG-AATC AGAATC AGAATC AGAATC AGA-ATC AG-AATC
* * *
53779042 AGAATC AGAATC AGAATC AGAATT AG-GTGAC AGAATC AGAATC AAAATC
1 AGAATC AGAATC AGAATC AGAATC AGAAT--C AGAATC AGAATC AGAATC
* *
53779091 AGTAAT- AGAATC AGAATC AGTATT AGTAA-C AGAATC AGAATC AGAATC
1 AG-AATC AGAATC AGAATC AGAATC AG-AATC AGAATC AGAATC AGAATC
53779139 AGAAT
1 AGAAT
53779144 TACGTGACAG
Statistics
Matches: 119, Mismatches: 12, Indels: 26
0.76 0.08 0.17
Matches are distributed among these distances:
5 11 0.09
6 97 0.82
7 9 0.08
8 2 0.02
ACGTcount: A:0.49, C:0.13, G:0.17, T:0.21
Consensus pattern (6 bp):
AGAATC
Found at i:53779330 original size:27 final size:26
Alignment explanation
Indices: 53779300--53779401 Score: 105
Period size: 27 Copynumber: 3.8 Consensus size: 26
53779290 GCTCAGTTAT
* *
53779300 CAGATATTGTGATAGAGTCACCAGATA
1 CAGATATTGTGACAGAGCCACCAGA-A
*
53779327 CAGATATTGTGGCAGAGCCACCAGAA
1 CAGATATTGTGACAGAGCCACCAGAA
* *
53779353 CAGATATTTGTGGCATAGCCACCAGAAA
1 CAGATA-TTGTGACAGAGCCACCAG-AA
* * *
53779381 CAGATAATGTGGCAAAGCCAC
1 CAGATATTGTGACAGAGCCAC
53779402 TTAACAAAAT
Statistics
Matches: 67, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
26 7 0.10
27 52 0.78
28 8 0.12
ACGTcount: A:0.36, C:0.21, G:0.24, T:0.20
Consensus pattern (26 bp):
CAGATATTGTGACAGAGCCACCAGAA
Found at i:53779587 original size:22 final size:23
Alignment explanation
Indices: 53779559--53779621 Score: 76
Period size: 22 Copynumber: 2.8 Consensus size: 23
53779549 GCAAATACGT
*
53779559 TTGGCACACAGCCATAAT-CAGG
1 TTGGCACAAAGCCATAATGCAGG
* *
53779581 TTGGCACAGAGCCAT-ATGTAGG
1 TTGGCACAAAGCCATAATGCAGG
*
53779603 TTGACACAAAGCCATAATG
1 TTGGCACAAAGCCATAATG
53779622 AGAAGGCTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
21 2 0.06
22 30 0.86
23 3 0.09
ACGTcount: A:0.33, C:0.22, G:0.24, T:0.21
Consensus pattern (23 bp):
TTGGCACAAAGCCATAATGCAGG
Found at i:53780106 original size:27 final size:27
Alignment explanation
Indices: 53780049--53780667 Score: 781
Period size: 27 Copynumber: 23.3 Consensus size: 27
53780039 AGGGCAAAAT
* * *
53780049 GGTAATTTTACCCCACA-AGGTATCTT-
1 GGTAATTCTACCCTACAGGGGTAT-TTC
* *
53780075 GGTAATTCCACCCTACAGGGGTATTTT
1 GGTAATTCTACCCTACAGGGGTATTTC
* * * *
53780102 AGTAATTCTACCTTATAGGGGTATTTT
1 GGTAATTCTACCCTACAGGGGTATTTC
*
53780129 AGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* * *
53780156 AGTAATTCTACCTTACAGGGGTATTGC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
53780183 GATAATTCTACCCTTCAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
***
53780210 GGTAATTCTACCCTACAAAAGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
53780237 GATAATTCTACCCTACAGGGGTATTGC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
53780264 GATAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
53780291 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
53780318 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
53780345 GGTAATTCTACCCTACAGGGGTATTGC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
53780372 GATAATTCTACCCTACA--GG------
1 GGTAATTCTACCCTACAGGGGTATTTC
*
53780391 GGTAATTCTACCGTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
53780418 GATAATTCTACCCTACTGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
53780445 GGTAATTCTACCCTACAAGGGTATTAC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
53780472 GATAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
53780499 GGTAATTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* * *
53780526 GGTTATTCTACCCTACAAGGGTAATTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* * *
53780553 GATAATTCTAACCTACAGGGGTATTCC
1 GGTAATTCTACCCTACAGGGGTATTTC
* * *
53780580 AGTAATTCTACCCTATAGGGGTATTCC
1 GGTAATTCTACCCTACAGGGGTATTTC
* * *
53780607 GGTAATTTTACCCTATAGGGGTATTCC
1 GGTAATTCTACCCTACAGGGGTATTTC
53780634 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
53780661 GGTAATT
1 GGTAATT
53780668 TTATAAACCA
Statistics
Matches: 520, Mismatches: 63, Indels: 19
0.86 0.10 0.03
Matches are distributed among these distances:
19 15 0.03
21 2 0.00
25 2 0.00
26 16 0.03
27 485 0.93
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.34
Consensus pattern (27 bp):
GGTAATTCTACCCTACAGGGGTATTTC
Found at i:53780398 original size:19 final size:19
Alignment explanation
Indices: 53780374--53780413 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
53780364 GGTATTGCGA
53780374 TAATTCTACCCTACAGGGG
1 TAATTCTACCCTACAGGGG
*
53780393 TAATTCTACCGTACAGGGG
1 TAATTCTACCCTACAGGGG
53780412 TA
1 TA
53780414 TTTCGATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.28
Consensus pattern (19 bp):
TAATTCTACCCTACAGGGG
Found at i:53780412 original size:46 final size:46
Alignment explanation
Indices: 53780345--53780494 Score: 183
Period size: 46 Copynumber: 3.1 Consensus size: 46
53780335 GGGGTATTTC
*
53780345 GGTAATTCTACCCTACAGGGGTATTGCGATAATTCTACCCTACAGG
1 GGTAATTCTACCCTACAGGGGTATTACGATAATTCTACCCTACAGG
* * *
53780391 GGTAATTCTACCGTACAGGGGTATTTCGATAATTCTACCCTACTGGGG
1 GGTAATTCTACCCTACAGGGGTATTACGATAATTCTACCCTAC--AGG
*
53780439 TATTTCGGTAATTCTACCCTACAAGGGTATTACGATAATTCTACCCTACAGG
1 ------GGTAATTCTACCCTACAGGGGTATTACGATAATTCTACCCTACAGG
53780491 GGTA
1 GGTA
53780495 TTTCGGTAAT
Statistics
Matches: 89, Mismatches: 7, Indels: 16
0.79 0.06 0.14
Matches are distributed among these distances:
46 45 0.51
48 2 0.02
52 2 0.02
54 40 0.45
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (46 bp):
GGTAATTCTACCCTACAGGGGTATTACGATAATTCTACCCTACAGG
Found at i:53780692 original size:54 final size:53
Alignment explanation
Indices: 53780409--53780725 Score: 220
Period size: 54 Copynumber: 5.9 Consensus size: 53
53780399 TACCGTACAG
* * * *
53780409 GGGTATTTCGATAATTCTACCCTACTGGGGTATTTCGGTAATTCTACCCT-A-CAA
1 GGGTATTCCGGTAATTCTACCCTACAGGGGTATTTCGGTAATTTTA---TAACCAA
* * *
53780463 GGGTATTACGATAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCCT-A-CAA
1 GGGTATTCCGGTAATTCTACCCTACAGGGGTATTTCGGTAATTTTA---TAACCAA
* * * * * *
53780517 GGGTATTTCGGTTATTCTACCCTACAAGGGTAATTCGATAA--TTCTAACCTACA
1 GGGTATTCCGGTAATTCTACCCTACAGGGGTATTTCGGTAATTTTATAACC-A-A
* * * *
53780570 GGGGTATTCCAGTAATTCTACCCTATAGGGGTATTCCGGTAA-TTT-TACCCTATA
1 -GGGTATTCCGGTAATTCTACCCTACAGGGGTATTTCGGTAATTTTATAACC-A-A
53780624 GGGGTATTCCGGTAATTCTACCCTACAGGGGTATTTCGGTAATTTTATAAACCAA
1 -GGGTATTCCGGTAATTCTACCCTACAGGGGTATTTCGGTAATTTTAT-AACCAA
* ** * ** * *
53780679 GGGCATTTTGGTAATTTTA-CAAACCAGTGGTATTTTGGTAATTTTAT
1 GGGTATTCCGGTAATTCTACCCTA-CAGGGGTATTTCGGTAATTTTAT
53780726 TGATCGAGGG
Statistics
Matches: 221, Mismatches: 32, Indels: 20
0.81 0.12 0.07
Matches are distributed among these distances:
49 1 0.00
50 1 0.00
51 1 0.00
52 2 0.01
53 3 0.01
54 202 0.91
55 6 0.03
56 2 0.01
57 3 0.01
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.35
Consensus pattern (53 bp):
GGGTATTCCGGTAATTCTACCCTACAGGGGTATTTCGGTAATTTTATAACCAA
Found at i:53781024 original size:27 final size:26
Alignment explanation
Indices: 53780652--53781029 Score: 224
Period size: 27 Copynumber: 14.1 Consensus size: 26
53780642 TACCCTACAG
* *
53780652 GGGTATTTCGGTAATTTTATAAACCAA
1 GGGTATTT-GGTAATTTTATAAATCGA
* * *
53780679 GGGCATTTTGGTAATTTTACAAA-CCA
1 GGGTA-TTTGGTAATTTTATAAATCGA
**
53780705 GTGGTATTTTGGTAATTTTATTGATCGA
1 G-GGTA-TTTGGTAATTTTATAAATCGA
* **
53780733 GGGTATTTCAGTAATTTTGCAAA-CTGA
1 GGGTATTT-GGTAATTTTATAAATC-GA
*
53780760 GGGTATTTCGGTAATTTTACAAATCGA
1 GGGTATTT-GGTAATTTTATAAATCGA
* *
53780787 GGATATTTGGGTAATTTTATAAATCGG
1 GGGTATTT-GGTAATTTTATAAATCGA
* * *
53780814 GGGTACTTTGGTAATTTTA-CAATTGG
1 GGGTA-TTTGGTAATTTTATAAATCGA
* *
53780840 GGGTATTTCAGTAATTTCAT-AATCGA
1 GGGTATTT-GGTAATTTTATAAATCGA
** *
53780866 GGGTAAAATGGTAATTTTTTAAATCGA
1 GGGT-ATTTGGTAATTTTATAAATCGA
**** * *
53780893 GGGTAAAACAGTAATTCTGTAAATCGA
1 GGGT-ATTTGGTAATTTTATAAATCGA
** *
53780920 GGGTAAAATGGTAATTCTATAAATCGA
1 GGGT-ATTTGGTAATTTTATAAATCGA
** *
53780947 GGGTAAAATGGTAATTTTGTAAATCGA
1 GGGT-ATTTGGTAATTTTATAAATCGA
*** * *
53780974 GGGTGAAACGGTAATTCTGTAAATCGA
1 GGGT-ATTTGGTAATTTTATAAATCGA
* *
53781001 GGGTACTTTGGTAATTTTACAAATTGA
1 GGGTA-TTTGGTAATTTTATAAATCGA
53781028 GG
1 GG
53781030 ACATTTTAGT
Statistics
Matches: 289, Mismatches: 50, Indels: 24
0.80 0.14 0.07
Matches are distributed among these distances:
25 3 0.01
26 42 0.15
27 234 0.81
28 10 0.03
ACGTcount: A:0.32, C:0.08, G:0.24, T:0.36
Consensus pattern (26 bp):
GGGTATTTGGTAATTTTATAAATCGA
Found at i:53781042 original size:81 final size:81
Alignment explanation
Indices: 53780860--53781050 Score: 211
Period size: 81 Copynumber: 2.4 Consensus size: 81
53780850 GTAATTTCAT
** * *
53780860 AATCGAGGGTAAAATGGTAATTTTTTAAATCGAGGGTAAAACAGTAATTCTGTAAATCGAGGGTA
1 AATCGAGGACAAAATAGTAATTTTGTAAATCGAGGGTAAAACAGTAATTCTGTAAATCGAGGGTA
*
53780925 AAATGGTAATTCTATA
66 AAATGGTAATTCTACA
** * * *
53780941 AATCGAGGGTAAAATGGTAATTTTGTAAATCGAGGGTGAAACGGTAATTCTGTAAATCGAGGGTA
1 AATCGAGGACAAAATAGTAATTTTGTAAATCGAGGGTAAAACAGTAATTCTGTAAATCGAGGGTA
*** *
53781006 CTTTGGTAATTTTACA
66 AAATGGTAATTCTACA
* *** *
53781022 AATTGAGGACATTTTAGTAATTTGGTAAA
1 AATCGAGGACAAAATAGTAATTTTGTAAA
53781051 CTAAAGTATT
Statistics
Matches: 94, Mismatches: 16, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
81 94 1.00
ACGTcount: A:0.37, C:0.07, G:0.24, T:0.32
Consensus pattern (81 bp):
AATCGAGGACAAAATAGTAATTTTGTAAATCGAGGGTAAAACAGTAATTCTGTAAATCGAGGGTA
AAATGGTAATTCTACA
Found at i:53782955 original size:13 final size:13
Alignment explanation
Indices: 53782937--53782963 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
53782927 GGTTGTTTAT
53782937 TAAACTAATTAAC
1 TAAACTAATTAAC
53782950 TAAACTAATTAAC
1 TAAACTAATTAAC
53782963 T
1 T
53782964 GATTAAACTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.52, C:0.15, G:0.00, T:0.33
Consensus pattern (13 bp):
TAAACTAATTAAC
Found at i:53783740 original size:24 final size:24
Alignment explanation
Indices: 53783685--53783732 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
53783675 AAAAGTTTTG
53783685 GAGGAGGGCCCCTTTCTAAGTCAT
1 GAGGAGGGCCCCTTTCTAAGTCAT
53783709 GAGGAGGGCCCCTTTCTAAGTCAT
1 GAGGAGGGCCCCTTTCTAAGTCAT
53783733 ACTTAGGGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.21, C:0.25, G:0.29, T:0.25
Consensus pattern (24 bp):
GAGGAGGGCCCCTTTCTAAGTCAT
Found at i:53786717 original size:27 final size:27
Alignment explanation
Indices: 53786665--53786717 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
53786655 TATTTTTGGG
*
53786665 TTTGATTTTGTAATAAGGGCACTTGAA
1 TTTGATTTTGTAATAAGGCCACTTGAA
* *
53786692 TTTGATTTTTTAATAAGGCCATTTGA
1 TTTGATTTTGTAATAAGGCCACTTGA
53786718 GGTTAACTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.28, C:0.08, G:0.19, T:0.45
Consensus pattern (27 bp):
TTTGATTTTGTAATAAGGCCACTTGAA
Found at i:53787152 original size:28 final size:29
Alignment explanation
Indices: 53787097--53787167 Score: 76
Period size: 29 Copynumber: 2.5 Consensus size: 29
53787087 GACTATGGAA
* *
53787097 TGGGTTTTTAAAA-TCTTTTCTCTCAAAT
1 TGGGTTTTGAAAAGTCTTTTCTCTAAAAT
53787125 TAGGGTTTTGAAAAGT-TTTTCT-TAAAAT
1 T-GGGTTTTGAAAAGTCTTTTCTCTAAAAT
*
53787153 TTGGTTTTGGAAAAG
1 TGGGTTTT-GAAAAG
53787168 ATGATTTCAA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
27 6 0.16
28 13 0.35
29 17 0.46
30 1 0.03
ACGTcount: A:0.28, C:0.07, G:0.18, T:0.46
Consensus pattern (29 bp):
TGGGTTTTGAAAAGTCTTTTCTCTAAAAT
Found at i:53795250 original size:40 final size:40
Alignment explanation
Indices: 53795205--53795504 Score: 342
Period size: 40 Copynumber: 7.5 Consensus size: 40
53795195 CATTTGAATG
* * *
53795205 ATATCCGGGATAAGTCCCGAAGGCAATTGTGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
* * *
53795245 TTATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATT
* *
53795285 ATATCCGGGCTAAGTCCCGAAGGCAATTGTGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
* * * *
53795325 TTATTCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATT
* * *
53795365 ATACCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
* *
53795405 TTATCCGGGCTAAGA-CCGAAGGCATTTGTGCGAGTTGA-T
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATT
* * *
53795444 ATATCCGGGCTAAGACCTGAAGGCATTTGTGCTTGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
53795484 ATATCC-GGCTAA-ACTCCGAAG
1 ATATCCGGGCTAAGAC-CCGAAG
53795505 AAACTTGGGT
Statistics
Matches: 217, Mismatches: 35, Indels: 17
0.81 0.13 0.06
Matches are distributed among these distances:
38 2 0.01
39 49 0.23
40 162 0.75
41 4 0.02
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
Found at i:53795503 original size:79 final size:80
Alignment explanation
Indices: 53795205--53795504 Score: 462
Period size: 80 Copynumber: 3.8 Consensus size: 80
53795195 CATTTGAATG
* *
53795205 ATATCCGGGATAAGTCCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCA
53795270 TTTGTGCGAGTTGCT
66 TTTGTGCGAGTTGCT
* *
53795285 ATATCCGGGCTAAGTCCCGAAGGCAATTGTGCTAGTGATTTTATTCGGGCTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCA
53795350 TTTGTGCGAGTTGCT
66 TTTGTGCGAGTTGCT
* *
53795365 ATACCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAAGA-CCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCA
*
53795429 TTTGTGCGAGTTGAT
66 TTTGTGCGAGTTGCT
* * * * *
53795444 ATATCCGGGCTAAGACCTGAAGGCATTTGTGCTTGTGGTTATATCC-GGCTAA-ACTCCGAAG
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAAGAC-CCGAAG
53795505 AAACTTGGGT
Statistics
Matches: 204, Mismatches: 14, Indels: 5
0.91 0.06 0.02
Matches are distributed among these distances:
77 1 0.00
78 6 0.03
79 68 0.33
80 129 0.63
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (80 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCA
TTTGTGCGAGTTGCT
Found at i:53803407 original size:40 final size:40
Alignment explanation
Indices: 53803362--53803661 Score: 342
Period size: 40 Copynumber: 7.5 Consensus size: 40
53803352 CATTTGAATG
* * *
53803362 ATATCCGGGATAAGTCCCGAAGGCAATTGTGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
* * *
53803402 TTATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATT
* * *
53803442 ATATCCGGGCTAAGTCTCGAAGGCAATTGTGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
* * *
53803482 TTATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATT
* * * *
53803522 ATACCCGGGTTAAGAGCCGAAGGCAATTGTGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
* *
53803562 TTATCCGGGCTAAGA-CCGAAGGCATTTGTGCGAGTTGA-T
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATT
* *
53803601 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTTGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
53803641 ATATCC-GGCTAA-ACTCCGAAG
1 ATATCCGGGCTAAGAC-CCGAAG
53803662 AAACTTGGGT
Statistics
Matches: 218, Mismatches: 34, Indels: 17
0.81 0.13 0.06
Matches are distributed among these distances:
38 2 0.01
39 50 0.23
40 162 0.74
41 4 0.02
ACGTcount: A:0.24, C:0.20, G:0.29, T:0.27
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
Found at i:53803660 original size:79 final size:80
Alignment explanation
Indices: 53803362--53803661 Score: 462
Period size: 80 Copynumber: 3.8 Consensus size: 80
53803352 CATTTGAATG
* *
53803362 ATATCCGGGATAAGTCCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCA
53803427 TTTGTGCGAGTTGCT
66 TTTGTGCGAGTTGCT
* *
53803442 ATATCCGGGCTAAGTCTCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCA
53803507 TTTGTGCGAGTTGCT
66 TTTGTGCGAGTTGCT
* * *
53803522 ATACCCGGGTTAAGAGCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAAGA-CCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCA
*
53803586 TTTGTGCGAGTTGAT
66 TTTGTGCGAGTTGCT
* * * *
53803601 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTTGTGGTTATATCC-GGCTAA-ACTCCGAAG
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAAGAC-CCGAAG
53803662 AAACTTGGGT
Statistics
Matches: 203, Mismatches: 15, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
77 1 0.00
78 6 0.03
79 68 0.33
80 128 0.63
ACGTcount: A:0.24, C:0.20, G:0.29, T:0.27
Consensus pattern (80 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCA
TTTGTGCGAGTTGCT
Found at i:53805787 original size:27 final size:27
Alignment explanation
Indices: 53805716--53805793 Score: 104
Period size: 27 Copynumber: 2.9 Consensus size: 27
53805706 TTGGAGGAAG
* *
53805716 TTCTGTACTAGTGGCTTTGCCACGTAT
1 TTCTGTACTGGTGGCTTTGCCACATAT
*
53805743 TTGCTGTACTGGTGGCTTAGCCACATA-
1 TT-CTGTACTGGTGGCTTTGCCACATAT
53805770 TTCTGATACTGGTGGCTTTGCCAC
1 TTCTG-TACTGGTGGCTTTGCCAC
53805794 GATACTGTTA
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
26 3 0.07
27 21 0.47
28 21 0.47
ACGTcount: A:0.15, C:0.23, G:0.24, T:0.37
Consensus pattern (27 bp):
TTCTGTACTGGTGGCTTTGCCACATAT
Found at i:53807144 original size:30 final size:29
Alignment explanation
Indices: 53807005--53807154 Score: 158
Period size: 29 Copynumber: 5.1 Consensus size: 29
53806995 TGTGCTAAAC
** * * *
53807005 GATGGTTGAAACCATCTCTTTTCATTAATC
1 GATGGTTGTCACCATCCCTTTTCA-TAGTT
** *
53807035 GATGGTCATCACCATCCCTTTTCAAAGTT
1 GATGGTTGTCACCATCCCTTTTCATAGTT
* * *
53807064 GATGGTCGTCACTATCTCTTTTCATAGTT
1 GATGGTTGTCACCATCCCTTTTCATAGTT
53807093 GATGGTTGTCACCATCCCTTTTCATAGTT
1 GATGGTTGTCACCATCCCTTTTCATAGTT
*
53807122 GATGGCTT-TTACCATCCCCTTTTCATAGTT
1 GATGG-TTGTCACCAT-CCCTTTTCATAGTT
53807152 GAT
1 GAT
53807155 AGTCAAAAAC
Statistics
Matches: 102, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
29 64 0.63
30 38 0.37
ACGTcount: A:0.21, C:0.23, G:0.15, T:0.41
Consensus pattern (29 bp):
GATGGTTGTCACCATCCCTTTTCATAGTT
Found at i:53808347 original size:22 final size:22
Alignment explanation
Indices: 53808308--53808357 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
53808298 CCTTTAGCCA
* *
53808308 TCCTGTCTATGACGTTGAG-CTG
1 TCCTGTCTACGACATTGAGTC-G
*
53808330 TCCTGTCTACGATATTGAGTCG
1 TCCTGTCTACGACATTGAGTCG
53808352 TCCTGT
1 TCCTGT
53808358 TGACTTAGTG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 23 0.96
23 1 0.04
ACGTcount: A:0.14, C:0.24, G:0.24, T:0.38
Consensus pattern (22 bp):
TCCTGTCTACGACATTGAGTCG
Found at i:53811823 original size:22 final size:22
Alignment explanation
Indices: 53811795--53811849 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
53811785 TACGGCCTTT
53811795 AGCCATCCTGTCTACTG-CGTTA
1 AGCCATCCTGTCTAC-GACGTTA
* *
53811817 AGCCATCCTGCCTACGATGTTA
1 AGCCATCCTGTCTACGACGTTA
*
53811839 AGCCTTCCTGT
1 AGCCATCCTGT
53811850 TGACTTAGTG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 1 0.04
22 27 0.96
ACGTcount: A:0.18, C:0.33, G:0.18, T:0.31
Consensus pattern (22 bp):
AGCCATCCTGTCTACGACGTTA
Found at i:53812814 original size:29 final size:29
Alignment explanation
Indices: 53812756--53812826 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
53812746 GGTCATTACC
* * **
53812756 ATTCCTTTTCATAGTTGATGGTTGCCACT
1 ATTCCTTTTCATAGTTGATAGTCGAAACT
*
53812785 ATTCCTTTTCATCGTTGATAGTCGAAACT
1 ATTCCTTTTCATAGTTGATAGTCGAAACT
53812814 A-TCCATTTTCATA
1 ATTCC-TTTTCATA
53812827 TTCGATGCTC
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
28 3 0.09
29 32 0.91
ACGTcount: A:0.23, C:0.21, G:0.13, T:0.44
Consensus pattern (29 bp):
ATTCCTTTTCATAGTTGATAGTCGAAACT
Found at i:53825882 original size:24 final size:24
Alignment explanation
Indices: 53825846--53825891 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
53825836 TCGACCACCC
*
53825846 ACTTTTTGACTTTTCAGCCTTTCG
1 ACTTTTCGACTTTTCAGCCTTTCG
*
53825870 ACTTTTCGGCTTTTCAGCCTTT
1 ACTTTTCGACTTTTCAGCCTTT
53825892 GTCGTTTCAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.11, C:0.26, G:0.13, T:0.50
Consensus pattern (24 bp):
ACTTTTCGACTTTTCAGCCTTTCG
Found at i:53837138 original size:28 final size:28
Alignment explanation
Indices: 53837075--53837225 Score: 214
Period size: 28 Copynumber: 5.4 Consensus size: 28
53837065 ATATTAAGTC
*
53837075 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
53837102 TGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
53837130 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
53837158 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
53837186 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
53837215 CGCACACTTAG
1 CGCACACTTAG
53837226 CGCCAATCTC
Statistics
Matches: 113, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
27 21 0.19
28 76 0.67
29 16 0.14
ACGTcount: A:0.34, C:0.28, G:0.12, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:53842489 original size:33 final size:33
Alignment explanation
Indices: 53842417--53842489 Score: 85
Period size: 33 Copynumber: 2.2 Consensus size: 33
53842407 CCCAGATAAG
* *
53842417 TAACAGTCTGGGCCTGAGCCCATTACAGAACAG
1 TAACAGTCTGGGCCTGAGCCCAATACAGAACAA
* * *
53842450 TAACAGTGTGGGCCTTAGCCCAATGCAGTAACAA
1 TAACAGTCTGGGCCTGAGCCCAATACAG-AACAA
53842484 T-ACAGT
1 TAACAGT
53842490 ATAATAATGC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
33 29 0.85
34 5 0.15
ACGTcount: A:0.32, C:0.25, G:0.23, T:0.21
Consensus pattern (33 bp):
TAACAGTCTGGGCCTGAGCCCAATACAGAACAA
Found at i:53842616 original size:26 final size:26
Alignment explanation
Indices: 53842583--53842686 Score: 91
Period size: 26 Copynumber: 4.0 Consensus size: 26
53842573 CCAACACACC
*
53842583 AATATTGTAGCAAAGCTGCTAGTAAT
1 AATATTGTAGCAAAGCTGCCAGTAAT
*
53842609 AATATTGTAGCAAAGCTGCCAGTATT
1 AATATTGTAGCAAAGCTGCCAGTAAT
* ** * * *
53842635 AGTAACGCAGCAAAGCTACCAGTAAC
1 AATATTGTAGCAAAGCTGCCAGTAAT
* * **
53842661 AGTATATGTGGCAAAGCCACCAGTAA
1 AATAT-TGTAGCAAAGCTGCCAGTAA
53842687 AACACACTTC
Statistics
Matches: 63, Mismatches: 14, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
26 47 0.75
27 16 0.25
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.23
Consensus pattern (26 bp):
AATATTGTAGCAAAGCTGCCAGTAAT
Found at i:53846937 original size:6 final size:6
Alignment explanation
Indices: 53846907--53846954 Score: 62
Period size: 6 Copynumber: 8.0 Consensus size: 6
53846897 TTCACAATAA
* *
53846907 AATACTC AAT-TC AATTTC GATATC AATATC AATATC AATATC AATATC
1 AATA-TC AATATC AATATC AATATC AATATC AATATC AATATC AATATC
53846955 CATTTTATGA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
5 5 0.14
6 29 0.78
7 3 0.08
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (6 bp):
AATATC
Found at i:53848164 original size:11 final size:12
Alignment explanation
Indices: 53848129--53848166 Score: 51
Period size: 11 Copynumber: 3.1 Consensus size: 12
53848119 TGTTTAATTC
53848129 TAATAATAATATAA
1 TAAT-ATAATAT-A
53848143 TAATATAATAT-
1 TAATATAATATA
53848154 TAATATAATATA
1 TAATATAATATA
53848166 T
1 T
53848167 TTACTTAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 11 0.48
12 1 0.04
13 7 0.30
14 4 0.17
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
TAATATAATATA
Found at i:53850073 original size:60 final size:60
Alignment explanation
Indices: 53850002--53850121 Score: 222
Period size: 60 Copynumber: 2.0 Consensus size: 60
53849992 ATTTCTTATT
* *
53850002 TTCTTAGAAGTCTTTCCTTAGTAGAATTACTTTCTTAGCAAGTTTTAAATTTCAGTTGAA
1 TTCTTAAAAGTCTTTCCTTAGTAGAATTACTTTCTTAGCAAGTTTTAAATTTCAATTGAA
53850062 TTCTTAAAAGTCTTTCCTTAGTAGAATTACTTTCTTAGCAAGTTTTAAATTTCAATTGAA
1 TTCTTAAAAGTCTTTCCTTAGTAGAATTACTTTCTTAGCAAGTTTTAAATTTCAATTGAA
53850122 CTCTATAATC
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 58 1.00
ACGTcount: A:0.30, C:0.13, G:0.12, T:0.45
Consensus pattern (60 bp):
TTCTTAAAAGTCTTTCCTTAGTAGAATTACTTTCTTAGCAAGTTTTAAATTTCAATTGAA
Found at i:53853385 original size:43 final size:46
Alignment explanation
Indices: 53853330--53853463 Score: 139
Period size: 43 Copynumber: 2.9 Consensus size: 46
53853320 GAGATATGTG
* *
53853330 GCATCTGAGCTCGTTTAGAGGTCCGAGTTCATTATGGATGC-A-A-
1 GCATCCGAGCTCGTTGAGAGGTCCGAGTTCATTATGGATGCGATAT
* **
53853373 GCATCCGAGCTCGTTGAGTGGTCCGAGTTCACAATGGATGCGATTCAT
1 GCATCCGAGCTCGTTGAGAGGTCCGAGTTCATTATGGATGCGA-T-AT
**
53853421 GTAACATCCGAGCTCGTTGAGAGGTTTGAGTTCATTATGGATG
1 G---CATCCGAGCTCGTTGAGAGGTCCGAGTTCATTATGGATG
53853464 TGTTACATTT
Statistics
Matches: 73, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
43 36 0.49
44 1 0.01
47 1 0.01
48 1 0.01
51 34 0.47
ACGTcount: A:0.22, C:0.19, G:0.29, T:0.30
Consensus pattern (46 bp):
GCATCCGAGCTCGTTGAGAGGTCCGAGTTCATTATGGATGCGATAT
Found at i:53856917 original size:46 final size:44
Alignment explanation
Indices: 53856867--53856979 Score: 147
Period size: 46 Copynumber: 2.5 Consensus size: 44
53856857 GACAAGAGCT
* *
53856867 AGTGTAAGACATGTCTGGGAGATGCATCAGCCT-CGAGATGTAAGCC
1 AGTGTAAGACATGTCTGGGACAAGCATC-GCCTACGAGATGT--GCC
*
53856913 AGTGTAAGACATGTCTGGGACAAGCATCGGCTACGAGATGTGCC
1 AGTGTAAGACATGTCTGGGACAAGCATCGCCTACGAGATGTGCC
*
53856957 AGTGTAAGACCATGTATGGGACA
1 AGTGTAAGA-CATGTCTGGGACA
53856980 TGACATTGGC
Statistics
Matches: 61, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
44 12 0.20
45 15 0.25
46 34 0.56
ACGTcount: A:0.29, C:0.19, G:0.31, T:0.21
Consensus pattern (44 bp):
AGTGTAAGACATGTCTGGGACAAGCATCGCCTACGAGATGTGCC
Found at i:53857131 original size:96 final size:94
Alignment explanation
Indices: 53856821--53857135 Score: 286
Period size: 96 Copynumber: 3.3 Consensus size: 94
53856811 TGAGAACCAA
* * *
53856821 TGTAAGACCATGTCTAGGACATGGCATCGGCATTGAGACAAGAGCTAGTGTAAGA-CATGTCTGG
1 TGTAAGACCATGTCTAGGACATGGCATCGGCCTCGAGACAATAGC-AGTGTAAGACCATGTCTGG
* * * * * * *
53856885 GAGAT-GCATCAGCCTCGAGATGTAAGCCAG
65 GACATGGCAT-TGACTAGAGATATTAGCCTG
* * ** *
53856915 TGTAAGA-CATGTCTGGGACA-AGCATCGG-CTACGAGA-TGT-GCCAGTGTAAGACCATGTATG
1 TGTAAGACCATGTCTAGGACATGGCATCGGCCT-CGAGACAATAG-CAGTGTAAGACCATGTCTG
* * * *
53856975 GGACATGACATTGGC-ACAGATATGTGAGAGCTAG
64 GGACATGGCATTGACTAGAGATAT-T-AG-CCT-G
53857009 TGTAAGACCATGTCTAGGACATGGCATCGGCCTCGATGACAATAGTCAGTGTAAGACCATGTCTG
1 TGTAAGACCATGTCTAGGACATGGCATCGGCCTCGA-GACAATAG-CAGTGTAAGACCATGTCTG
*
53857074 GGACATGGCATTGACTTGAGATATTAGCCTG
64 GGACATGGCATTGACTAGAGATATTAGCCTG
* *
53857105 TGTAAGACCAGGTCTGGGACATGGCATCGGC
1 TGTAAGACCATGTCTAGGACATGGCATCGGC
53857136 ACCTTACCCA
Statistics
Matches: 175, Mismatches: 31, Indels: 28
0.75 0.13 0.12
Matches are distributed among these distances:
90 15 0.09
91 16 0.09
92 16 0.09
93 13 0.07
94 15 0.09
95 12 0.07
96 40 0.23
97 6 0.03
98 3 0.02
99 33 0.19
100 6 0.03
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.23
Consensus pattern (94 bp):
TGTAAGACCATGTCTAGGACATGGCATCGGCCTCGAGACAATAGCAGTGTAAGACCATGTCTGGG
ACATGGCATTGACTAGAGATATTAGCCTG
Found at i:53865391 original size:79 final size:81
Alignment explanation
Indices: 53865282--53865464 Score: 223
Period size: 79 Copynumber: 2.3 Consensus size: 81
53865272 TACTCGTTCA
* *
53865282 AATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCACACAAATGCCTTCGGGA-CTTAACCCGG
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCACACAAATGCCTTC-GGATCTTAACCCGG
* *
53865345 ATTTAGTAAC-TCGCACC
65 ATATAGTAACTTAGCA-C
* **
53865362 AATGCCTTCGGG-CTTAGCCCGGAAT-TAGTAACTCTCACAAATGCCTTCGGATCTTAGTCCGGA
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCACACAAATGCCTTCGGATCTTAACCCGGA
* *
53865425 TATGGTCACTTAGCAC
66 TATAGTAACTTAGCAC
*
53865441 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
53865465 CATCATTCGA
Statistics
Matches: 89, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 3 0.03
79 58 0.65
80 28 0.31
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (81 bp):
AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCACACAAATGCCTTCGGATCTTAACCCGGA
TATAGTAACTTAGCAC
Found at i:53865464 original size:40 final size:40
Alignment explanation
Indices: 53865280--53865464 Score: 200
Period size: 40 Copynumber: 4.7 Consensus size: 40
53865270 GCTACTCGTT
* * *
53865280 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCACA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTTACA
* * **
53865320 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTTACA
*
53865360 CCAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTAACTCT-CA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACT-TACA
* * *
53865399 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAACTTA-CA
53865440 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
53865465 CATCATTCGA
Statistics
Matches: 123, Mismatches: 14, Indels: 16
0.80 0.09 0.10
Matches are distributed among these distances:
38 2 0.02
39 31 0.25
40 80 0.65
41 10 0.08
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTTACA
Found at i:53873574 original size:79 final size:80
Alignment explanation
Indices: 53873465--53873645 Score: 217
Period size: 79 Copynumber: 2.3 Consensus size: 80
53873455 TACTCGTTCA
* **
53873465 AATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGAGA-CTTAACCCGGA
1 AATGCCTTCGGGACTTAGCCCGAATATAGTAACTCGCACAAATGCCTTCG-GATCTTAACCCGGA
* *
53873529 TTTAGTAAC-TCGCACC
65 TATAGTAACTTAGCA-C
**
53873545 AATGCCTTCGGG-CTTAGCCCGAA-ATTAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGGA
1 AATGCCTTCGGGACTTAGCCCGAATA-TAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
* *
53873608 TATGGTCACTTAGCAC
65 TATAGTAACTTAGCAC
*
53873624 AAAGCCTTCGGGACTTAGCCCG
1 AATGCCTTCGGGACTTAGCCCG
53873646 GACATCATTC
Statistics
Matches: 87, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
78 3 0.03
79 59 0.68
80 25 0.29
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (80 bp):
AATGCCTTCGGGACTTAGCCCGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGAT
ATAGTAACTTAGCAC
Found at i:53873647 original size:40 final size:40
Alignment explanation
Indices: 53873444--53873647 Score: 220
Period size: 40 Copynumber: 5.1 Consensus size: 40
53873434 CAGAATTTAA
** *
53873444 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
53873484 CCGGTTATAGTAACTCGCACAAATGCCTTCGAGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
53873524 CCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
53873563 CC-GAAATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
53873603 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
53873643 CCGGA
1 CCGGA
53873648 CATCATTCGA
Statistics
Matches: 137, Mismatches: 20, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
38 4 0.03
39 30 0.22
40 89 0.65
41 14 0.10
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:53880666 original size:46 final size:43
Alignment explanation
Indices: 53880581--53880700 Score: 134
Period size: 46 Copynumber: 2.6 Consensus size: 43
53880571 TTTGTGCGCT
*
53880581 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGTAAACC
1 AGTGTAAGACATGTCT-GGACATGCATCGGCCTCAAGATGT--ACC
**
53880627 AGTGTAAGACATGTCTGTGACATGCATCGG-CTACAAGATGTGTC
1 AGTGTAAGACATGTCTG-GACATGCATCGGCCT-CAAGATGTACC
53880671 AGTGTAAGACCATGTCTAGGACATGGCATC
1 AGTGTAAGA-CATGTCT-GGACAT-GCATC
53880701 AGCACGTATA
Statistics
Matches: 66, Mismatches: 3, Indels: 10
0.84 0.04 0.13
Matches are distributed among these distances:
44 10 0.15
45 15 0.23
46 41 0.62
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (43 bp):
AGTGTAAGACATGTCTGGACATGCATCGGCCTCAAGATGTACC
Found at i:53880731 original size:48 final size:50
Alignment explanation
Indices: 53880666--53880795 Score: 135
Period size: 48 Copynumber: 2.6 Consensus size: 50
53880656 GCTACAAGAT
* *
53880666 GTGTCAGTGTAAGACCATGTCTAGGACATGGCATCAGCACGTATA-GAG-
1 GTGTCAGTGTAAAACCATGTCTAGGACATGGCATCAGCACATATATGAGA
* ** *
53880714 GTGTCAGTGTAAAACCATGT-TGGGGACATGGCATTGGCACATATATGTGA
1 GTGTCAGTGTAAAACCATGTCT-AGGACATGGCATCAGCACATATATGAGA
*
53880764 GAG-CTAGTG-AAAGACCATGTCTAGGACATGGC
1 GTGTC-AGTGTAAA-ACCATGTCTAGGACATGGC
53880796 GTCGACCTCG
Statistics
Matches: 68, Mismatches: 8, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
47 1 0.01
48 38 0.56
49 6 0.09
50 22 0.32
51 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.30, T:0.24
Consensus pattern (50 bp):
GTGTCAGTGTAAAACCATGTCTAGGACATGGCATCAGCACATATATGAGA
Found at i:53896448 original size:59 final size:59
Alignment explanation
Indices: 53896348--53896514 Score: 183
Period size: 59 Copynumber: 2.8 Consensus size: 59
53896338 TGCATTGATT
* * * * *
53896348 TTTTTAATATATTTGTACAAGTTGTTTTTATATTGTTTCATTTAATAAAACAGAAGTTG
1 TTTTGAATATATTTGTACAAATTATTTTTATATTGTGTCATTTAATAAAACAGAAGTTC
* * *
53896407 TTTTGAATATTTTTGTACAAATTATTTTTATATTGTGTCATTTAATAAAATATAAGTTC
1 TTTTGAATATATTTGTACAAATTATTTTTATATTGTGTCATTTAATAAAACAGAAGTTC
**** * * *
53896466 TTTTGAATA-AGACAATACAAATTATTTTTTTATAGTTTCATTTAATAAA
1 TTTTGAATATA-TTTGTACAAATTATTTTTATATTGTGTCATTTAATAAA
53896515 TTATGAACTA
Statistics
Matches: 91, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
59 91 1.00
ACGTcount: A:0.35, C:0.05, G:0.09, T:0.50
Consensus pattern (59 bp):
TTTTGAATATATTTGTACAAATTATTTTTATATTGTGTCATTTAATAAAACAGAAGTTC
Found at i:53899510 original size:24 final size:25
Alignment explanation
Indices: 53899444--53899512 Score: 95
Period size: 25 Copynumber: 2.8 Consensus size: 25
53899434 CAACTTATAC
* * **
53899444 CTTCTCAACTTCTTTAATTCCTATT
1 CTTCTGAACTTCTTCAATTTATATT
53899469 CTTCTGAACTTCTTCAATTTATATT
1 CTTCTGAACTTCTTCAATTTATATT
53899494 CTTCTGAA-TTCTTCAATTT
1 CTTCTGAACTTCTTCAATTT
53899513 CTCTTATTGT
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
24 11 0.28
25 29 0.73
ACGTcount: A:0.22, C:0.23, G:0.03, T:0.52
Consensus pattern (25 bp):
CTTCTGAACTTCTTCAATTTATATT
Found at i:53899822 original size:125 final size:124
Alignment explanation
Indices: 53899610--53899906 Score: 418
Period size: 125 Copynumber: 2.4 Consensus size: 124
53899600 TGAAAAGAGC
* * *
53899610 GTCCAATTGGGAGCTTTTTTCGGTACTTTTGCTAACAGTGCATCCTACTTGAAGCATTTTTCAAC
1 GTCCAATTGGGAGC-TTTTTCAGTACTTTTGATGACAGTGCATCCTACTTGAAGCATTTTTCAAC
* * *
53899675 TTATTTTTTCAGAACTAACTTCTCAAAATTATTTTTTCAAAATAAACTATGCAAAAAAAA
65 CTATTTTTTCAGAACCAACTTCTCAAAATTATTTTTTCAAAATAAACTATACAAAAAAAA
* * * *
53899735 GTCCAACTGGGAGCCTTTTTCAGTACTTTTGTTGACAATGCATCCTGCTTGAAGCATTTTTCAAC
1 GTCCAATTGGGAG-CTTTTTCAGTACTTTTGATGACAGTGCATCCTACTTGAAGCATTTTTCAAC
* * *
53899800 CTATTTTTTCAGAACCATCTTCTCAAAATTATTTTTTCAGAATCAACTATACAAAAAAAA
65 CTATTTTTTCAGAACCAACTTCTCAAAATTATTTTTTCAAAATAAACTATACAAAAAAAA
* * *
53899860 -TCCAGTTGGGAG-TTTTTCAGTAATTTTGATGACAGTGCATTCTACTT
1 GTCCAATTGGGAGCTTTTTCAGTACTTTTGATGACAGTGCATCCTACTT
53899907 ACAGTGTTTT
Statistics
Matches: 152, Mismatches: 19, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
122 30 0.20
124 10 0.07
125 111 0.73
126 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (124 bp):
GTCCAATTGGGAGCTTTTTCAGTACTTTTGATGACAGTGCATCCTACTTGAAGCATTTTTCAACC
TATTTTTTCAGAACCAACTTCTCAAAATTATTTTTTCAAAATAAACTATACAAAAAAAA
Found at i:53899854 original size:28 final size:28
Alignment explanation
Indices: 53899801--53899855 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
53899791 TTTTTCAACC
* *
53899801 TATTTTTTCAGAACCATCTTCTCAAAAT
1 TATTTTTTCAGAACCAACTTCACAAAAT
*
53899829 TATTTTTTCAGAATCAACTAT-ACAAAA
1 TATTTTTTCAGAACCAACT-TCACAAAA
53899856 AAAATCCAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 22 0.96
29 1 0.04
ACGTcount: A:0.38, C:0.18, G:0.04, T:0.40
Consensus pattern (28 bp):
TATTTTTTCAGAACCAACTTCACAAAAT
Found at i:53900196 original size:27 final size:28
Alignment explanation
Indices: 53900127--53900200 Score: 105
Period size: 28 Copynumber: 2.7 Consensus size: 28
53900117 AAAAAAACCC
* *
53900127 TAAAACCCCTAAACCCAAATTTATTTTT
1 TAAAAACCCTAAACCCTAATTTATTTTT
53900155 TAAAAACCCTAAACCCTAATTTATTTTT
1 TAAAAACCCTAAACCCTAATTTATTTTT
* *
53900183 TCAACACCCT-AACCCTAA
1 TAAAAACCCTAAACCCTAA
53900201 ACCATAAATC
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
27 8 0.19
28 34 0.81
ACGTcount: A:0.39, C:0.28, G:0.00, T:0.32
Consensus pattern (28 bp):
TAAAAACCCTAAACCCTAATTTATTTTT
Found at i:53900849 original size:23 final size:24
Alignment explanation
Indices: 53900795--53900850 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 24
53900785 TTTTTTATTT
* *
53900795 TTTTTATTTATATTTTTGTGCTTA
1 TTTTTATTTATATTTTTGTACCTA
* * *
53900819 ATTGTATTT-TCTTTTTGTACCTA
1 TTTTTATTTATATTTTTGTACCTA
53900842 TTTTTATTT
1 TTTTTATTT
53900851 GAACTAAAAT
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
23 18 0.72
24 7 0.28
ACGTcount: A:0.16, C:0.07, G:0.07, T:0.70
Consensus pattern (24 bp):
TTTTTATTTATATTTTTGTACCTA
Found at i:53900985 original size:7 final size:7
Alignment explanation
Indices: 53900959--53901000 Score: 61
Period size: 7 Copynumber: 6.3 Consensus size: 7
53900949 ATAAGGTTTG
53900959 TTGATTT
1 TTGATTT
*
53900966 TT-AGTT
1 TTGATTT
53900972 TTG-TTT
1 TTGATTT
53900978 TTGATTT
1 TTGATTT
53900985 TTGATTT
1 TTGATTT
53900992 TTGATTT
1 TTGATTT
53900999 TT
1 TT
53901001 CAATGCGTCA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
6 10 0.32
7 21 0.68
ACGTcount: A:0.12, C:0.00, G:0.14, T:0.74
Consensus pattern (7 bp):
TTGATTT
Found at i:53902600 original size:17 final size:17
Alignment explanation
Indices: 53902578--53902612 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
53902568 AAGATTGATG
53902578 CCCATAGAGGAAAGACC
1 CCCATAGAGGAAAGACC
53902595 CCCATAGAGGAAAGACC
1 CCCATAGAGGAAAGACC
53902612 C
1 C
53902613 TTAAAGACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.40, C:0.31, G:0.23, T:0.06
Consensus pattern (17 bp):
CCCATAGAGGAAAGACC
Found at i:53906778 original size:43 final size:43
Alignment explanation
Indices: 53906730--53906905 Score: 257
Period size: 43 Copynumber: 4.1 Consensus size: 43
53906720 CCGGCATTAC
*
53906730 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCAGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCAGCACTAA
* *
53906773 GCCTGCTGGGCACGAAGGCCCGAATACACATCACCGGCACTAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCAGCACTAA
* * *
53906816 GCTTGCTAGGCACAAAGGCCCGAATACACATCACCGGCACTAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCAGCACTAA
* * *
53906859 GCCTACTAGGCACGAAGGCCCGAATATA-AT-ACCAGCACTAG
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCAGCACTAA
53906900 GCCTGC
1 GCCTGC
53906906 GGGATTTATC
Statistics
Matches: 120, Mismatches: 13, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
41 14 0.12
42 2 0.02
43 104 0.87
ACGTcount: A:0.31, C:0.34, G:0.23, T:0.12
Consensus pattern (43 bp):
GCCTGCTAGGCACGAAGGCCCGAATACACATCACCAGCACTAA
Found at i:53906925 original size:38 final size:38
Alignment explanation
Indices: 53906877--53906960 Score: 132
Period size: 38 Copynumber: 2.2 Consensus size: 38
53906867 GGCACGAAGG
* * *
53906877 CCCGAATATAATACCAGCACTAGGCCTGCGGGATTTAT
1 CCCGAATATAATACCAGCACAAAGCCTGCGGGATTTAA
*
53906915 CCCGGATATAATACCAGCACAAAGCCTGCGGGATTTAA
1 CCCGAATATAATACCAGCACAAAGCCTGCGGGATTTAA
53906953 CCCGAATA
1 CCCGAATA
53906961 CACATCAAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.32, C:0.27, G:0.20, T:0.20
Consensus pattern (38 bp):
CCCGAATATAATACCAGCACAAAGCCTGCGGGATTTAA
Found at i:53923870 original size:8 final size:8
Alignment explanation
Indices: 53923857--53923883 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
53923847 CTCCTAAGTC
53923857 CAAAAATT
1 CAAAAATT
53923865 CAAAAATT
1 CAAAAATT
53923873 CAAAAATT
1 CAAAAATT
53923881 CAA
1 CAA
53923884 CCAGGTTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.63, C:0.15, G:0.00, T:0.22
Consensus pattern (8 bp):
CAAAAATT
Found at i:53934850 original size:19 final size:19
Alignment explanation
Indices: 53934813--53934850 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
53934803 ACCTGATAGA
*
53934813 AGAAAATAAATGAAGAATT
1 AGAAAATAAATGAAAAATT
53934832 AGAAAATAAAAT-AAAAATT
1 AGAAAAT-AAATGAAAAATT
53934851 TAAATTGCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.68, C:0.00, G:0.11, T:0.21
Consensus pattern (19 bp):
AGAAAATAAATGAAAAATT
Found at i:53937757 original size:49 final size:49
Alignment explanation
Indices: 53937685--53937864 Score: 247
Period size: 49 Copynumber: 3.7 Consensus size: 49
53937675 CTGGTACGCA
*
53937685 TAGTAGCCTGCACATAGTACTACACATGCGACCAATTATCCAGTACACG
1 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCAGTACACG
* * *
53937734 TAGTAGCCTACACTTAGTACTACACATGTGACCAATTATCCGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCAGTACACG
* * * * *
53937783 TAGTAGCCTGCACTTAGTACTACACACGTGACC--TAACCTCTGATACACG
1 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATC-CAG-TACACG
53937832 TAGTAGCCTGCACTTAGTACTACACATGCGACC
1 TAGTAGCCTGCACTTAGTACTACACATGCGACC
53937865 TCACAATAGA
Statistics
Matches: 118, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
47 3 0.03
48 2 0.02
49 113 0.96
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.24
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCAGTACACG
Found at i:53939574 original size:30 final size:30
Alignment explanation
Indices: 53939538--53939595 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
53939528 TAAGAAAACT
*
53939538 GAATAAAGAAATCCAAGA-TAGAGAAACCCA
1 GAATAAAGAAA-CCAAGAGTAAAGAAACCCA
*
53939568 GAATAAAGAAACCCAGAGTAAAGAAACC
1 GAATAAAGAAACCAAGAGTAAAGAAACC
53939596 TAAGATACGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 5 0.20
30 20 0.80
ACGTcount: A:0.57, C:0.17, G:0.17, T:0.09
Consensus pattern (30 bp):
GAATAAAGAAACCAAGAGTAAAGAAACCCA
Found at i:53939577 original size:15 final size:15
Alignment explanation
Indices: 53939538--53939595 Score: 73
Period size: 15 Copynumber: 3.9 Consensus size: 15
53939528 TAAGAAAACT
*
53939538 GAATAAAGAAATCCA
1 GAATAAAGAAACCCA
*
53939553 -AGATAGAGAAACCCA
1 GA-ATAAAGAAACCCA
53939568 GAATAAAGAAACCCA
1 GAATAAAGAAACCCA
*
53939583 GAGTAAAGAAACC
1 GAATAAAGAAACC
53939596 TAAGATACGA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
14 1 0.03
15 35 0.95
16 1 0.03
ACGTcount: A:0.57, C:0.17, G:0.17, T:0.09
Consensus pattern (15 bp):
GAATAAAGAAACCCA
Found at i:53942658 original size:49 final size:49
Alignment explanation
Indices: 53942602--53942826 Score: 263
Period size: 49 Copynumber: 4.5 Consensus size: 49
53942592 CTGGTACGCA
* * * *
53942602 TAGTAGCCTACACATAGTACTACACATGCGACCAATTATCCAGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCAGTACACG
*
53942651 TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCAGTACACG
* ** **
53942700 TAATAGCCTGCACTTAGTACTACACACGTGACCTAACCAT-TTGATACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACC-AATTATCCAG-TACACG
* * * * *
53942750 TAGTAGCCTGCACTTAGTACTACACACGTGATCACAGTTTTCGAGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACACGTGA-C-CAATTATCCAGTACACG
*
53942801 TAGTAGCCTACACTTAGTACTACACA
1 TAGTAGCCTGCACTTAGTACTACACA
53942827 TGCGACCTCA
Statistics
Matches: 151, Mismatches: 20, Indels: 8
0.84 0.11 0.04
Matches are distributed among these distances:
49 77 0.51
50 40 0.26
51 32 0.21
52 2 0.01
ACGTcount: A:0.31, C:0.28, G:0.16, T:0.25
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCAGTACACG
Found at i:53942766 original size:99 final size:101
Alignment explanation
Indices: 53942645--53942826 Score: 280
Period size: 99 Copynumber: 1.8 Consensus size: 101
53942635 AATTATCCAG
*
53942645 TACACGTAGTAGCCTGCACTTAGTACTACACACGTGA-C-CAATTATCCG-GTACACGTAATAGC
1 TACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCACAATT-TCCGAGTACACATAATAGC
*
53942707 CTGCACTTAGTACTACACACGTGACCTAACCATTTGA
65 CTACACTTAGTACTACACACGTGACCTAACCATTTGA
* * * *
53942744 TACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCACAGTTTTCGAGTACGCATAGTAGCC
1 TACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCACAATTTCCGAGTACACATAATAGCC
53942809 TACACTTAGTACTACACA
66 TACACTTAGTACTACACA
53942827 TGCGACCTCA
Statistics
Matches: 74, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
99 37 0.50
100 4 0.05
101 33 0.45
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.26
Consensus pattern (101 bp):
TACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCACAATTTCCGAGTACACATAATAGCC
TACACTTAGTACTACACACGTGACCTAACCATTTGA
Found at i:53957771 original size:48 final size:48
Alignment explanation
Indices: 53957708--53958465 Score: 1156
Period size: 48 Copynumber: 16.1 Consensus size: 48
53957698 TATATATGTG
** *
53957708 TGTGGTAAAGTTGAATGGCTAATGTGAAATATGTATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
* *
53957756 TGTGGTAAAGCTGAATGGCTAGTGTGAAATATGTATGAGACATGTATA
1 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
*
53957804 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATATATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
*
53957852 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATATATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
*
53957900 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGAATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
53957948 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
53957996 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
* * *
53958044 TGTGGTAAAGCCAAATGGCTAGTGTGAAATATGCATGAGAGATGTATA
1 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
*
53958092 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATATATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
53958140 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
*
53958188 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATA-GCCGA-A
1 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATG--TATA
* ** * * * *
53958236 TG-GCTAGTG-TGAAAT--ATA-TATG--AGA--TAT--G-TAT----A
1 TGTGGTAAAGCCG-AATGGCTAGTGTGAAATATGTATGAGATATGTATA
53958269 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
53958317 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
*
53958365 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATATATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
* *
53958413 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTAGGAGATGTGTATA
1 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
53958461 TGTGG
1 TGTGG
53958466 AAGAGGTCGT
Statistics
Matches: 654, Mismatches: 36, Indels: 40
0.90 0.05 0.05
Matches are distributed among these distances:
33 3 0.00
34 7 0.01
35 1 0.00
36 2 0.00
37 5 0.01
38 1 0.00
39 2 0.00
40 3 0.00
41 3 0.00
42 2 0.00
43 1 0.00
44 6 0.01
45 2 0.00
46 1 0.00
47 8 0.01
48 606 0.93
49 1 0.00
ACGTcount: A:0.34, C:0.06, G:0.29, T:0.31
Consensus pattern (48 bp):
TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
Found at i:53957883 original size:144 final size:144
Alignment explanation
Indices: 53957708--53958465 Score: 1294
Period size: 144 Copynumber: 5.4 Consensus size: 144
53957698 TATATATGTG
** * *
53957708 TGTGGTAAAGTTGAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCTGAATG
1 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATG
*
53957773 GCTAGTGTGAAATATGTATGAGACATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATAT
66 GCTAGTGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATAT
53957838 ATGAGATATGTATA
131 ATGAGATATGTATA
*
53957852 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATATATGAGATATGTATATGTGGTAAAGCCGAATG
1 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATG
* *
53957917 GCTAGTGTGAAATATGAATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGT
66 GCTAGTGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATAT
53957982 ATGAGATATGTATA
131 ATGAGATATGTATA
*
53957996 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCAAATG
1 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATG
* *
53958061 GCTAGTGTGAAATATGCATGAGAGATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATAT
66 GCTAGTGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATAT
53958126 ATGAGATATGTATA
131 ATGAGATATGTATA
53958140 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATG
1 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATG
53958205 GCTAGTGTGAAATATGTAT--G--A-G---A-----T--AGCCGAATGGCTAGTGTGAAATATAT
66 GCTAGTGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATAT
53958255 ATGAGATATGTATA
131 ATGAGATATGTATA
53958269 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATG
1 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATG
53958334 GCTAGTGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATAT
66 GCTAGTGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATAT
53958399 ATGAGATATGTATA
131 ATGAGATATGTATA
* *
53958413 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTAGGAGATGTGTATATGTGG
1 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATATGTGG
53958466 AAGAGGTCGT
Statistics
Matches: 582, Mismatches: 17, Indels: 30
0.93 0.03 0.05
Matches are distributed among these distances:
129 124 0.21
131 2 0.00
133 1 0.00
134 1 0.00
136 1 0.00
137 1 0.00
139 1 0.00
140 1 0.00
142 2 0.00
144 448 0.77
ACGTcount: A:0.34, C:0.06, G:0.29, T:0.31
Consensus pattern (144 bp):
TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATG
GCTAGTGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATAT
ATGAGATATGTATA
Found at i:53958236 original size:33 final size:33
Alignment explanation
Indices: 53958196--53958262 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
53958186 TATGTGGTAA
*
53958196 AGCCGAATGGCTAGTGTGAAATATGTATGAGAT
1 AGCCGAATGGCTAGTGTGAAATATATATGAGAT
53958229 AGCCGAATGGCTAGTGTGAAATATATATGAGAT
1 AGCCGAATGGCTAGTGTGAAATATATATGAGAT
53958262 A
1 A
53958263 TGTATATGTG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.36, C:0.09, G:0.28, T:0.27
Consensus pattern (33 bp):
AGCCGAATGGCTAGTGTGAAATATATATGAGAT
Found at i:53958242 original size:81 final size:81
Alignment explanation
Indices: 53958148--53958310 Score: 317
Period size: 81 Copynumber: 2.0 Consensus size: 81
53958138 TATGTGGTAA
*
53958148 AGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGT
1 AGCCGAATGGCTAGTGTGAAATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGT
53958213 GAAATATGTATGAGAT
66 GAAATATGTATGAGAT
53958229 AGCCGAATGGCTAGTGTGAAATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGT
1 AGCCGAATGGCTAGTGTGAAATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGT
53958294 GAAATATGTATGAGAT
66 GAAATATGTATGAGAT
53958310 A
1 A
53958311 TGTATATGTG
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
81 81 1.00
ACGTcount: A:0.34, C:0.07, G:0.29, T:0.29
Consensus pattern (81 bp):
AGCCGAATGGCTAGTGTGAAATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGT
GAAATATGTATGAGAT
Found at i:53958287 original size:177 final size:177
Alignment explanation
Indices: 53957860--53958406 Score: 853
Period size: 177 Copynumber: 3.0 Consensus size: 177
53957850 TATGTGGTAA
* * *
53957860 AGCCGAATGGCTAGTGTGAAATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGT
1 AGCCAAATGGCTAGTGTGAAATATACATGAGAGATGTATATGTGGTAAAGCCGAATGGCTAGTGT
53957925 GAAATATGA-ATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGAT
66 GAAATAT-ATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGAT
*
53957989 ATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATATGTGGTAA
130 ATGTATATGTGGTAAAGCCGAATGGCTAGTGTG-AA-A--TAT---ATATG---A----G-AT
*
53958052 AGCCAAATGGCTAGTGTGAAATATGCATGAGAGATGTATATGTGGTAAAGCCGAATGGCTAGTGT
1 AGCCAAATGGCTAGTGTGAAATATACATGAGAGATGTATATGTGGTAAAGCCGAATGGCTAGTGT
53958117 GAAATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATA
66 GAAATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATA
*
53958182 TGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGAT
131 TGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATATATGAGAT
* * *
53958229 AGCCGAATGGCTAGTGTGAAATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGT
1 AGCCAAATGGCTAGTGTGAAATATACATGAGAGATGTATATGTGGTAAAGCCGAATGGCTAGTGT
*
53958294 GAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATA
66 GAAATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATA
53958359 TGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATATATGAGAT
131 TGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATATATGAGAT
53958406 A
1 A
53958407 TGTATATGTG
Statistics
Matches: 342, Mismatches: 12, Indels: 17
0.92 0.03 0.05
Matches are distributed among these distances:
177 173 0.51
178 1 0.00
182 1 0.00
185 4 0.01
188 3 0.01
190 1 0.00
191 3 0.01
192 156 0.46
ACGTcount: A:0.35, C:0.07, G:0.29, T:0.30
Consensus pattern (177 bp):
AGCCAAATGGCTAGTGTGAAATATACATGAGAGATGTATATGTGGTAAAGCCGAATGGCTAGTGT
GAAATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATA
TGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATATATGAGAT
Found at i:53958395 original size:225 final size:225
Alignment explanation
Indices: 53958004--53958453 Score: 837
Period size: 225 Copynumber: 2.0 Consensus size: 225
53957994 TATGTGGTAA
*
53958004 AGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCAAATGGCTAGTGT
1 AGCCGAATGGCTAGTGTGAAATATATATGAGATATGTATATGTGGTAAAGCCAAATGGCTAGTGT
53958069 GAAATATGCATGAGAGATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATATATGAGATA
66 GAAATATGCATGAGAGATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATATATGAGATA
*
53958134 TGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATATGTGGTAAAGC
131 TGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATATATGAGATATGTATATGTGGTAAAGC
*
53958199 CGAATGGCTAGTGTGAAATATGTATGAGAT
196 CGAATGGCTAGTGTGAAATATGTAGGAGAT
*
53958229 AGCCGAATGGCTAGTGTGAAATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGT
1 AGCCGAATGGCTAGTGTGAAATATATATGAGATATGTATATGTGGTAAAGCCAAATGGCTAGTGT
* * *
53958294 GAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATA
66 GAAATATGCATGAGAGATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATATATGAGATA
53958359 TGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATATATGAGATATGTATATGTGGTAAAGC
131 TGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATATATGAGATATGTATATGTGGTAAAGC
53958424 CGAATGGCTAGTGTGAAATATGTAGGAGAT
196 CGAATGGCTAGTGTGAAATATGTAGGAGAT
53958454 GTGTATATGT
Statistics
Matches: 218, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
225 218 1.00
ACGTcount: A:0.34, C:0.07, G:0.29, T:0.30
Consensus pattern (225 bp):
AGCCGAATGGCTAGTGTGAAATATATATGAGATATGTATATGTGGTAAAGCCAAATGGCTAGTGT
GAAATATGCATGAGAGATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATATATGAGATA
TGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATATATGAGATATGTATATGTGGTAAAGC
CGAATGGCTAGTGTGAAATATGTAGGAGAT
Found at i:53959850 original size:46 final size:46
Alignment explanation
Indices: 53959797--53959972 Score: 184
Period size: 46 Copynumber: 3.8 Consensus size: 46
53959787 TATTTGGGCA
53959797 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
*
53959843 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGA--TA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATGGATGCGAA-T--G
* * * * *
53959888 CATCTGAGCTCGTTGAATTGAGTCTGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
*
53959936 -CCTGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCC-GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
53959973 GCGGGTTACA
Statistics
Matches: 108, Mismatches: 10, Indels: 24
0.76 0.07 0.17
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 4 0.04
46 62 0.57
47 26 0.24
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.22, C:0.19, G:0.28, T:0.31
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:53959952 original size:93 final size:93
Alignment explanation
Indices: 53959793--53959964 Score: 274
Period size: 93 Copynumber: 1.8 Consensus size: 93
53959783 AGGATATTTG
* *
53959793 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAATTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAG
53959858 TTGAGTCCGAGTTCGATAGATGTAACTA
66 TTGAGTCCGAGTTCGATAGATGTAACTA
* * * *
53959886 GGCATCTGAGCTCGTTGAATTGAGTCTGAGTTCACTTATGGATGCGAACG-CCTGAGCTCGTTGA
1 GGCATCCGAACTCGTTGAATTGAGTCCGAGTTCACTTATGGATGCGAACGTCC-GAACTCGTTGA
53959950 GTTGAGTCCGAGTTC
65 GTTGAGTCCGAGTTC
53959965 ACTTATGGGC
Statistics
Matches: 72, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
92 2 0.03
93 70 0.97
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.30
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAATTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAG
TTGAGTCCGAGTTCGATAGATGTAACTA
Found at i:53966142 original size:28 final size:28
Alignment explanation
Indices: 53966110--53966179 Score: 99
Period size: 28 Copynumber: 2.5 Consensus size: 28
53966100 AATGAGATTG
53966110 GCACTAAGTGTGCGAGTTT-AAT-TGTATA
1 GCACTAAGTGTGCGAGTTTGAATAT-TA-A
*
53966138 GCACTAAGTGTGCGAGTTTGACTATTAA
1 GCACTAAGTGTGCGAGTTTGAATATTAA
53966166 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
53966180 GACTTACTAT
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 34 0.87
29 4 0.10
30 1 0.03
ACGTcount: A:0.27, C:0.14, G:0.27, T:0.31
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGAATATTAA
Found at i:53969944 original size:18 final size:18
Alignment explanation
Indices: 53969921--53969964 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
53969911 ATTTTGTGAA
53969921 CTCGTGAGCGTGTGAGCG
1 CTCGTGAGCGTGTGAGCG
*
53969939 CTCGTGAGTGTGTGAGCG
1 CTCGTGAGCGTGTGAGCG
53969957 CTCGTGAG
1 CTCGTGAG
53969965 ACAGTTGTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.11, C:0.20, G:0.43, T:0.25
Consensus pattern (18 bp):
CTCGTGAGCGTGTGAGCG
Found at i:53970379 original size:27 final size:26
Alignment explanation
Indices: 53970335--53970386 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
53970325 TTCGCTGCAA
*
53970335 TCTGGTGGCCTCGCCACATATATCTGT
1 TCTGGTGACCTCGCCACA-ATATCTGT
* *
53970362 TCTGGTGACTTCGTCACAATATCTG
1 TCTGGTGACCTCGCCACAATATCTG
53970387 GCAGCCTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.17, C:0.27, G:0.21, T:0.35
Consensus pattern (26 bp):
TCTGGTGACCTCGCCACAATATCTGT
Found at i:53972242 original size:31 final size:28
Alignment explanation
Indices: 53972218--53972428 Score: 163
Period size: 29 Copynumber: 7.2 Consensus size: 28
53972208 TTTTCTTTTA
*
53972218 ATTGATGGTCAAAACCATCCCTTTTCAT
1 ATTGATGGTCGAAACCATCCCTTTTCAT
*
53972246 ATTCGATGGTCGAAGCCATCCCTTTTCAT
1 ATT-GATGGTCGAAACCATCCCTTTTCAT
* ** *
53972275 ATTCGATGATCGTCACCATCTCTTTTCAT
1 ATT-GATGGTCGAAACCATCCCTTTTCAT
*
53972304 AGTTGATGGTC-ATCACCATCCCTTTTCAT
1 A-TTGATGGTCGA-AACCATCCCTTTTCAT
* * *
53972333 AGTTGATAGTCGAAACTATCCCTTTTAATT
1 A-TTGATGGTCGAAACCATCCCTTTTCA-T
* * ** *
53972363 AATCGATGGTTGTCACAATCCCTTTTCAT
1 -ATTGATGGTCGAAACCATCCCTTTTCAT
* * * *
53972392 AGTTGATAGTTGAAACTATCCATTTTCAT
1 A-TTGATGGTCGAAACCATCCCTTTTCAT
53972421 ATTCGATG
1 ATT-GATG
53972429 CTTGTCTATA
Statistics
Matches: 147, Mismatches: 28, Indels: 15
0.77 0.15 0.08
Matches are distributed among these distances:
28 6 0.04
29 117 0.80
30 23 0.16
31 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.14, T:0.38
Consensus pattern (28 bp):
ATTGATGGTCGAAACCATCCCTTTTCAT
Found at i:53972358 original size:58 final size:57
Alignment explanation
Indices: 53972219--53972428 Score: 185
Period size: 58 Copynumber: 3.6 Consensus size: 57
53972209 TTTCTTTTAA
* *
53972219 TTGATGGTCAAAACCATCCCTTTTCATATTCGATGGTCGA--AGCCATCCCTTTTCATA-
1 TTGATAGTCGAAACCATCCCTTTTCATATT-GATGGTC-ATCA-CCATCCCTTTTCATAG
** *
53972276 TTCGAT-GATCGTCACCATCTCTTTTCATAGTTGATGGTCATCACCATCCCTTTTCATAG
1 TT-GATAG-TCGAAACCATCCCTTTTCATA-TTGATGGTCATCACCATCCCTTTTCATAG
* * * ** *
53972335 TTGATAGTCGAAACTATCCCTTTTAATTAATCGATGGTTGTCACAATCCCTTTTCATAG
1 TTGATAGTCGAAACCATCCCTTTTCA-T-ATTGATGGTCATCACCATCCCTTTTCATAG
* * *
53972394 TTGATAGTTGAAACTATCCATTTTCATATTCGATG
1 TTGATAGTCGAAACCATCCCTTTTCATATT-GATG
53972429 CTTGTCTATA
Statistics
Matches: 126, Mismatches: 17, Indels: 19
0.78 0.10 0.12
Matches are distributed among these distances:
57 6 0.05
58 64 0.51
59 55 0.44
60 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.14, T:0.39
Consensus pattern (57 bp):
TTGATAGTCGAAACCATCCCTTTTCATATTGATGGTCATCACCATCCCTTTTCATAG
Found at i:53972400 original size:59 final size:58
Alignment explanation
Indices: 53972316--53972434 Score: 175
Period size: 59 Copynumber: 2.0 Consensus size: 58
53972306 TTGATGGTCA
* * *
53972316 TCACCATCCCTTTTCATAGTTGATAGTCGAAACTATCCCTTTTAATTAATCGATGGTTG
1 TCACAATCCCTTTTCATAGTTGATAGTCGAAACTATCCATTTTAA-TAATCGATGCTTG
* * *
53972375 TCACAATCCCTTTTCATAGTTGATAGTTGAAACTATCCATTTTCATATTCGATGCTTG
1 TCACAATCCCTTTTCATAGTTGATAGTCGAAACTATCCATTTTAATAATCGATGCTTG
53972433 TC
1 TC
53972435 TATACGTCTT
Statistics
Matches: 54, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
58 13 0.24
59 41 0.76
ACGTcount: A:0.25, C:0.22, G:0.13, T:0.40
Consensus pattern (58 bp):
TCACAATCCCTTTTCATAGTTGATAGTCGAAACTATCCATTTTAATAATCGATGCTTG
Found at i:53973210 original size:5 final size:5
Alignment explanation
Indices: 53973200--53973236 Score: 74
Period size: 5 Copynumber: 7.4 Consensus size: 5
53973190 AGATTTTCGG
53973200 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TT
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TT
53973237 ATCAAATTGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TTTAA
Found at i:53977826 original size:40 final size:39
Alignment explanation
Indices: 53977771--53977857 Score: 138
Period size: 40 Copynumber: 2.2 Consensus size: 39
53977761 ATACTATTTG
* *
53977771 ATTCAGTGATACCAAAGTACAAACAGGGTCACGTATGTGC
1 ATTCAG-GATACCAAAGTACAAACAGGGGCACATATGTGC
53977811 ATTCAGGCATACCAAAGTACAAACAGGGGCACATATGTGC
1 ATTCAGG-ATACCAAAGTACAAACAGGGGCACATATGTGC
53977851 ATTCAGG
1 ATTCAGG
53977858 GGCACTGAAG
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
39 1 0.02
40 43 0.98
ACGTcount: A:0.36, C:0.21, G:0.23, T:0.21
Consensus pattern (39 bp):
ATTCAGGATACCAAAGTACAAACAGGGGCACATATGTGC
Found at i:53977869 original size:40 final size:40
Alignment explanation
Indices: 53977781--53977877 Score: 131
Period size: 40 Copynumber: 2.4 Consensus size: 40
53977771 ATTCAGTGAT
* * *
53977781 ACCAAAGTACAAACAGGGTCACGTATGTGCATTCAGGCAT
1 ACCAAAGTACAAACAGGGGCACATATGTGCATTCAGGCAC
**
53977821 ACCAAAGTACAAACAGGGGCACATATGTGCATTCAGGGGC
1 ACCAAAGTACAAACAGGGGCACATATGTGCATTCAGGCAC
**
53977861 ACTGAAGTACAAACAGG
1 ACCAAAGTACAAACAGG
53977878 AGCATGTATG
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 50 1.00
ACGTcount: A:0.37, C:0.22, G:0.25, T:0.16
Consensus pattern (40 bp):
ACCAAAGTACAAACAGGGGCACATATGTGCATTCAGGCAC
Found at i:53977877 original size:20 final size:20
Alignment explanation
Indices: 53977825--53977877 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
53977815 AGGCATACCA
53977825 AAGTACAAACAGGGGCACAT
1 AAGTACAAACAGGGGCACAT
* * **
53977845 ATGTGCATTCAGGGGCAC-T
1 AAGTACAAACAGGGGCACAT
53977864 GAAGTACAAACAGG
1 -AAGTACAAACAGG
53977878 AGCATGTATG
Statistics
Matches: 24, Mismatches: 8, Indels: 2
0.71 0.24 0.06
Matches are distributed among these distances:
19 1 0.04
20 23 0.96
ACGTcount: A:0.38, C:0.19, G:0.28, T:0.15
Consensus pattern (20 bp):
AAGTACAAACAGGGGCACAT
Found at i:53981733 original size:29 final size:28
Alignment explanation
Indices: 53981691--53981780 Score: 128
Period size: 29 Copynumber: 3.1 Consensus size: 28
53981681 GTGTACTAAA
*
53981691 CGATGGTCAAAACCATCCCTTCTCATATT
1 CGATGGTC-AAACCATCCCTTTTCATATT
53981720 CGATGGTCGAAACCATCCCTTTTCATATT
1 CGATGGTC-AAACCATCCCTTTTCATATT
*
53981749 CGATGGTCATCACCATCCCTTTTC-TATT
1 CGATGGTCA-AACCATCCCTTTTCATATT
53981777 CGAT
1 CGAT
53981781 AGGTGTCGAT
Statistics
Matches: 57, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
28 9 0.16
29 48 0.84
ACGTcount: A:0.23, C:0.30, G:0.12, T:0.34
Consensus pattern (28 bp):
CGATGGTCAAACCATCCCTTTTCATATT
Found at i:53983100 original size:16 final size:16
Alignment explanation
Indices: 53983079--53983111 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
53983069 CTGAATCGAG
53983079 AGAAATGAACAGCCCA
1 AGAAATGAACAGCCCA
*
53983095 AGAAATGGACAGCCCA
1 AGAAATGAACAGCCCA
53983111 A
1 A
53983112 AACTATCCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.48, C:0.24, G:0.21, T:0.06
Consensus pattern (16 bp):
AGAAATGAACAGCCCA
Found at i:53985881 original size:25 final size:25
Alignment explanation
Indices: 53985834--53985881 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
53985824 TTATAATATG
* * *
53985834 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
*
53985859 AAAATGACCATTATACCCTTAGG
1 AAAATGACCATTATACCCCTAGG
53985882 GTTTAAATAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:53985947 original size:20 final size:20
Alignment explanation
Indices: 53985918--53985964 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
53985908 ATTTTGATAA
*
53985918 ACATGGTATGTATGATATGC
1 ACATGATATGTATGATATGC
53985938 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
53985958 ACATGAT
1 ACATGAT
53985965 GTATTCATAA
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:0.11, G:0.21, T:0.34
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:53986083 original size:23 final size:24
Alignment explanation
Indices: 53986013--53986108 Score: 142
Period size: 24 Copynumber: 4.0 Consensus size: 24
53986003 GGAGGAAGTG
53986013 TAAAAGGGCTTATGCCCCAGTTAT
1 TAAAAGGGCTTATGCCCCAGTTAT
*
53986037 TAAAAGGGCTTATGCCCCAATTAT
1 TAAAAGGGCTTATGCCCCAGTTAT
53986061 TAAAAGGGCTT-TGCCCCAGTTAT
1 TAAAAGGGCTTATGCCCCAGTTAT
*
53986084 TAAAAGAGGC-TAGGCCTCCAGTTAT
1 TAAAAG-GGCTTATGCC-CCAGTTAT
53986109 ATGAAAAAGC
Statistics
Matches: 66, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
23 18 0.27
24 40 0.61
25 8 0.12
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (24 bp):
TAAAAGGGCTTATGCCCCAGTTAT
Found at i:53986357 original size:31 final size:31
Alignment explanation
Indices: 53986303--53986363 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
53986293 CGTTTACAGT
*
53986303 AAAGGCTTCGGCCCAGTAATATGAGATATGG
1 AAAGGCTTCGGCCCAGTAATATGAAATATGG
* * **
53986334 AAAGGTTTCGGCCTAGTGTTATGAAATATG
1 AAAGGCTTCGGCCCAGTAATATGAAATATG
53986364 AAAATTGAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.31, C:0.13, G:0.28, T:0.28
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGG
Found at i:53990559 original size:27 final size:27
Alignment explanation
Indices: 53990464--53990550 Score: 131
Period size: 27 Copynumber: 3.2 Consensus size: 27
53990454 CATTCGTCAT
* *
53990464 TTTACCATACAGGGG-TATTACGGTCAC
1 TTTACCCTACAGGGGCT-TTACGGTCTC
53990491 TTTACCCTACAGGGGCTTTACGGTCTC
1 TTTACCCTACAGGGGCTTTACGGTCTC
*
53990518 TTTACCCTACAGGGGCTTTACGGTCTT
1 TTTACCCTACAGGGGCTTTACGGTCTC
53990545 TTTACC
1 TTTACC
53990551 TAATAGGGGT
Statistics
Matches: 56, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
27 55 0.98
28 1 0.02
ACGTcount: A:0.18, C:0.26, G:0.21, T:0.34
Consensus pattern (27 bp):
TTTACCCTACAGGGGCTTTACGGTCTC
Found at i:53990708 original size:27 final size:27
Alignment explanation
Indices: 53990688--53990898 Score: 205
Period size: 27 Copynumber: 7.9 Consensus size: 27
53990678 GTAACTTTGT
53990688 AAATTAGGGGTATTTTGGTAATTTTAC
1 AAATTAGGGGTATTTTGGTAATTTTAC
* *
53990715 AAATT-GAGGGTATTTCGGTAATTTCAC
1 AAATTAG-GGGTATTTTGGTAATTTTAC
** *
53990742 AAACCAGTGGTATTTTGGTAATTTTAC
1 AAATTAGGGGTATTTTGGTAATTTTAC
* *
53990769 AAACTAGGGATATTTTGGTAATTTTAC
1 AAATTAGGGGTATTTTGGTAATTTTAC
*
53990796 AAATT-GAGGGTATTTCGGTAATTTTAC
1 AAATTAG-GGGTATTTTGGTAATTTTAC
** * * *
53990823 AAACCAAGGGTATTTTAGCAATTTTAC
1 AAATTAGGGGTATTTTGGTAATTTTAC
* *
53990850 AGACTA-GGGTATTTTGGTAATTTTAC
1 AAATTAGGGGTATTTTGGTAATTTTAC
** *
53990876 TGA-TCGAGGGTATTTTGGTAATT
1 AAATTAG-GGGTATTTTGGTAATT
53990899 CTGTAAACCG
Statistics
Matches: 153, Mismatches: 25, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
25 1 0.01
26 22 0.14
27 129 0.84
28 1 0.01
ACGTcount: A:0.30, C:0.09, G:0.21, T:0.40
Consensus pattern (27 bp):
AAATTAGGGGTATTTTGGTAATTTTAC
Found at i:53990755 original size:54 final size:53
Alignment explanation
Indices: 53990695--53990927 Score: 234
Period size: 54 Copynumber: 4.3 Consensus size: 53
53990685 TGTAAATTAG
** * *
53990695 GGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAACCA
1 GGGTATTTTGGTAATTTTACAAACCGAGGGTATTTTGGTAATTTTACAAACCA
* **
53990748 GTGGTATTTTGGTAATTTTACAAA-CTAGGGATATTTTGGTAATTTTACAAATTGA
1 G-GGTATTTTGGTAATTTTACAAACCGAGGG-TATTTTGGTAATTTTACAAA-CCA
* * * * * *
53990803 GGGTATTTCGGTAATTTTACAAACCAAGGGTATTTTAGCAATTTTACAGACTA
1 GGGTATTTTGGTAATTTTACAAACCGAGGGTATTTTGGTAATTTTACAAACCA
** * * **
53990856 GGGTATTTTGGTAATTTTACTGATCGAGGGTATTTTGGTAATTCTGTAAACCGA
1 GGGTATTTTGGTAATTTTACAAACCGAGGGTATTTTGGTAATTTTACAAACC-A
* *
53990910 AGGTATTTTAGTAATTTT
1 GGGTATTTTGGTAATTTT
53990928 GTAAATCAAG
Statistics
Matches: 148, Mismatches: 27, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
53 46 0.31
54 95 0.64
55 7 0.05
ACGTcount: A:0.29, C:0.09, G:0.21, T:0.41
Consensus pattern (53 bp):
GGGTATTTTGGTAATTTTACAAACCGAGGGTATTTTGGTAATTTTACAAACCA
Found at i:53990783 original size:81 final size:80
Alignment explanation
Indices: 53990695--53990898 Score: 311
Period size: 81 Copynumber: 2.5 Consensus size: 80
53990685 TGTAAATTAG
*
53990695 GGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAACC-AGTGGTATTTTG
1 GGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAACCAAG-GGTATTTTA
*
53990759 GTAATTTTACAAACTA
65 GCAATTTTACAAACTA
*
53990775 GGGATATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTTACAAACCAAGGGTATTTTA
1 GGG-TATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAACCAAGGGTATTTTA
*
53990840 GCAATTTTACAGACTA
65 GCAATTTTACAAACTA
** * *
53990856 GGGTATTTTGGTAATTTTACTGATCGAGGGTATTTTGGTAATT
1 GGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATT
53990899 CTGTAAACCG
Statistics
Matches: 114, Mismatches: 8, Indels: 4
0.90 0.06 0.03
Matches are distributed among these distances:
80 39 0.34
81 73 0.64
82 2 0.02
ACGTcount: A:0.29, C:0.09, G:0.22, T:0.41
Consensus pattern (80 bp):
GGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAACCAAGGGTATTTTAG
CAATTTTACAAACTA
Found at i:53990941 original size:27 final size:27
Alignment explanation
Indices: 53990581--53991009 Score: 204
Period size: 27 Copynumber: 15.8 Consensus size: 27
53990571 TTTCATCCTA
* * * * *
53990581 CAAGGGTGTTTTGGTAAATCTACAAAC
1 CAAGGGTATTTTGGTAATTTTATAAAT
** * *
53990608 CAAGGGTATTTCAGTAATTTTGTTAAAC
1 CAAGGGTATTTTGGTAATTTT-ATAAAT
* *** *
53990636 CAATGGTATTTCCATAATTTTTAGAAAGT
1 CAAGGGTATTTTGGTAA-TTTTATAAA-T
* * *
53990665 CAAAGGTATTTCT-GTAACTTTGTAAAT
1 CAAGGGTATTT-TGGTAATTTTATAAAT
* * *
53990692 TAGGGGTATTTTGGTAATTTTACAAAT
1 CAAGGGTATTTTGGTAATTTTATAAAT
** * * *
53990719 TGAGGGTATTTCGGTAATTTCACAAA-
1 CAAGGGTATTTTGGTAATTTTATAAAT
* *
53990745 CCAGTGGTATTTTGGTAATTTTACAAA-
1 CAAG-GGTATTTTGGTAATTTTATAAAT
* *
53990772 CTAGGGATATTTTGGTAATTTTACAAAT
1 CAAGGG-TATTTTGGTAATTTTATAAAT
** * * *
53990800 TGAGGGTATTTCGGTAATTTTACAAAC
1 CAAGGGTATTTTGGTAATTTTATAAAT
* * * *
53990827 CAAGGGTATTTTAGCAATTTTACAGA-
1 CAAGGGTATTTTGGTAATTTTATAAAT
* *
53990853 CTAGGGTATTTTGGTAATTTTACT-GAT
1 CAAGGGTATTTTGGTAATTTTA-TAAAT
* * * *
53990880 CGAGGGTATTTTGGTAATTCTGTAAAC
1 CAAGGGTATTTTGGTAATTTTATAAAT
* *
53990907 CGAA-GGTATTTTAGTAATTTTGTAAAT
1 C-AAGGGTATTTTGGTAATTTTATAAAT
***** * *
53990934 CAAGGGTAAAACAGTAATTCTGTAAAT
1 CAAGGGTATTTTGGTAATTTTATAAAT
*** * *
53990961 CAAGGGTAAAATAGTAATTCTATAAAT
1 CAAGGGTATTTTGGTAATTTTATAAAT
* *
53990988 CGAGGGTACTTTGGTAATTTTA
1 CAAGGGTATTTTGGTAATTTTA
53991010 CAATTTGAAG
Statistics
Matches: 319, Mismatches: 70, Indels: 26
0.77 0.17 0.06
Matches are distributed among these distances:
26 29 0.09
27 241 0.76
28 32 0.10
29 17 0.05
ACGTcount: A:0.32, C:0.10, G:0.20, T:0.38
Consensus pattern (27 bp):
CAAGGGTATTTTGGTAATTTTATAAAT
Found at i:53993123 original size:28 final size:28
Alignment explanation
Indices: 53993060--53993157 Score: 128
Period size: 27 Copynumber: 3.5 Consensus size: 28
53993050 ATATTAAGTC
*
53993060 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
53993087 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * *
53993115 CGCACACTTAGTGCTGA-ACAATTTAAACC
1 CGCACACTTAGTGCT-ATATAA-TCAAACT
53993144 CGCACACTTAGTGC
1 CGCACACTTAGTGC
53993158 CAATCTCATG
Statistics
Matches: 64, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
27 22 0.34
28 22 0.34
29 20 0.31
ACGTcount: A:0.33, C:0.29, G:0.13, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:54001399 original size:28 final size:28
Alignment explanation
Indices: 54001336--54001433 Score: 128
Period size: 27 Copynumber: 3.5 Consensus size: 28
54001326 ATATTAAGTC
*
54001336 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
54001363 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * *
54001391 CGCACACTTAGTGCTGA-ACAATTTAAACC
1 CGCACACTTAGTGCT-ATATAA-TCAAACT
54001420 CGCACACTTAGTGC
1 CGCACACTTAGTGC
54001434 CAATCTCATG
Statistics
Matches: 64, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
27 22 0.34
28 22 0.34
29 20 0.31
ACGTcount: A:0.33, C:0.29, G:0.13, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:54019303 original size:48 final size:48
Alignment explanation
Indices: 54019241--54019617 Score: 673
Period size: 48 Copynumber: 7.9 Consensus size: 48
54019231 TATATATGTG
54019241 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA
54019289 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA
54019337 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA
54019385 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA
*
54019433 TGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA
* *
54019481 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATATATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA
* *
54019529 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATG
1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA
* * * *
54019577 TGTGGTAACGCCGAATGGCTAGTGTGAACTATGTAGGAGAT
1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGAT
54019618 GTGTGTATAT
Statistics
Matches: 322, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 322 1.00
ACGTcount: A:0.34, C:0.07, G:0.28, T:0.31
Consensus pattern (48 bp):
TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA
Found at i:54019808 original size:37 final size:37
Alignment explanation
Indices: 54019758--54019860 Score: 188
Period size: 37 Copynumber: 2.8 Consensus size: 37
54019748 GGAAATATAT
54019758 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
*
54019795 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
*
54019832 TCCGGGTAAGACCCGATAACTACGTGTGG
1 TCCGGGTAAGACCCGATGACTACGTGTGG
54019861 GGACTATTCG
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 64 1.00
ACGTcount: A:0.23, C:0.20, G:0.32, T:0.24
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
Found at i:54023963 original size:12 final size:11
Alignment explanation
Indices: 54023941--54023968 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
54023931 CATCATTACC
54023941 TTTTTTCTTTT
1 TTTTTTCTTTT
54023952 TTTTTTCTTTT
1 TTTTTTCTTTT
54023963 TTTTTT
1 TTTTTT
54023969 ATCTCAACTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (11 bp):
TTTTTTCTTTT
Found at i:54024728 original size:15 final size:16
Alignment explanation
Indices: 54024699--54024732 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
54024689 ACTTCGACTC
54024699 TTTGTTTTTTCTTTTT
1 TTTGTTTTTTCTTTTT
54024715 TTTGTTTTTGT-TTTTT
1 TTTGTTTTT-TCTTTTT
54024731 TT
1 TT
54024733 AAGTATCCGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 16 0.94
17 1 0.06
ACGTcount: A:0.00, C:0.03, G:0.09, T:0.88
Consensus pattern (16 bp):
TTTGTTTTTTCTTTTT
Found at i:54030806 original size:19 final size:20
Alignment explanation
Indices: 54030760--54030808 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
54030750 AATCATTAAC
54030760 AATCTAATTTTATAAAAGAG
1 AATCTAATTTTATAAAAGAG
**
54030780 GTTCTAATTTTATTAAAA-A-
1 AATCTAATTTTA-TAAAAGAG
54030799 AATCTAATTT
1 AATCTAATTT
54030809 AATTGTTCCT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 8 0.33
20 11 0.46
21 5 0.21
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.43
Consensus pattern (20 bp):
AATCTAATTTTATAAAAGAG
Found at i:54031580 original size:8 final size:8
Alignment explanation
Indices: 54031567--54031617 Score: 57
Period size: 8 Copynumber: 5.9 Consensus size: 8
54031557 TTTAAGATTT
54031567 ATTATAAA
1 ATTATAAA
54031575 ATTATAAA
1 ATTATAAA
54031583 ATTATTAAAA
1 ATTA-T-AAA
*
54031593 ATTTATCAA
1 A-TTATAAA
54031602 ATTATAAA
1 ATTATAAA
54031610 ATCTATAA
1 AT-TATAA
54031618 GAAGTATTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
8 20 0.54
9 9 0.24
10 5 0.14
11 3 0.08
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (8 bp):
ATTATAAA
Found at i:54031589 original size:19 final size:19
Alignment explanation
Indices: 54031565--54031639 Score: 66
Period size: 19 Copynumber: 4.0 Consensus size: 19
54031555 TTTTTAAGAT
54031565 TTATTATAAAA-TTATAAAA
1 TTATTA-AAAATTTATAAAA
*
54031584 TTATTAAAAATTTATCAAA
1 TTATTAAAAATTTATAAAA
*
54031603 TTA-T-AAAATCTATAAGAA
1 TTATTAAAAATTTATAA-AA
* * *
54031621 GTATTAAAACTATATAAAA
1 TTATTAAAAATTTATAAAA
54031640 AAAAGACATA
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
17 9 0.20
18 9 0.20
19 19 0.41
20 9 0.20
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.37
Consensus pattern (19 bp):
TTATTAAAAATTTATAAAA
Found at i:54031950 original size:28 final size:28
Alignment explanation
Indices: 54031902--54031981 Score: 74
Period size: 28 Copynumber: 2.9 Consensus size: 28
54031892 TTGTGCATTT
* ** *
54031902 TTATAATTTTATTTTTTTATAATTTTTAC
1 TTATGATTTTATAATTTTATAAATTTT-C
54031931 TT-T-ATTTTGATAATTTTATAAATTTTC
1 TTATGATTTT-ATAATTTTATAAATTTTC
* *
54031958 TTATGATTTTATAATCTCATAAAT
1 TTATGATTTTATAATTTTATAAAT
54031982 GAATATAATA
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
27 8 0.19
28 28 0.65
29 7 0.16
ACGTcount: A:0.31, C:0.05, G:0.03, T:0.61
Consensus pattern (28 bp):
TTATGATTTTATAATTTTATAAATTTTC
Found at i:54038929 original size:31 final size:31
Alignment explanation
Indices: 54038891--54038952 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
54038881 GTTGTTAGGC
*
54038891 GTATTTTAGGTAGTATAAAAAATTAATAAGG
1 GTATTTTAGGTAGTATAAAAAATCAATAAGG
* *
54038922 GTATTTTAGGTAGTATCAATAATCAATAAGG
1 GTATTTTAGGTAGTATAAAAAATCAATAAGG
54038953 ATAATTTAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.42, C:0.03, G:0.19, T:0.35
Consensus pattern (31 bp):
GTATTTTAGGTAGTATAAAAAATCAATAAGG
Found at i:54041964 original size:144 final size:144
Alignment explanation
Indices: 54041704--54041984 Score: 508
Period size: 144 Copynumber: 2.0 Consensus size: 144
54041694 GATCATCTAA
* * *
54041704 GACTTCGTTACCAAGTCTCTAGATACGCACACGACTAAAAAAGAAAATCAAGATTTACTTTCTTG
1 GACTTCGTTACCAAGTCCCTAGATACGCACACAACTAAAAAAGAAAATCAAGATTCACTTTCTTG
*
54041769 TTTTCAAGAAAATTAAGAAACTAAATCTTGGTCAAATTTTATTGTTTCAGACAATTTCAAGAATC
66 TTTTCAAGAAAATTAAGAAACTAAACCTTGGTCAAATTTTATTGTTTCAGACAATTTCAAGAATC
54041834 AAGATTTCAAAGAT
131 AAGATTTCAAAGAT
*
54041848 GACTTCGTTACCAAGTCCCTAGATACGCACACAACTGAAAAAGAAAATCAAGATTCACTTTCTTG
1 GACTTCGTTACCAAGTCCCTAGATACGCACACAACTAAAAAAGAAAATCAAGATTCACTTTCTTG
*
54041913 TTTTCAAGAAAATTAAGAAACTAAACCTTGGTCAAATTTTGTTGTTTCAGACAATTTCAAGAATC
66 TTTTCAAGAAAATTAAGAAACTAAACCTTGGTCAAATTTTATTGTTTCAGACAATTTCAAGAATC
54041978 AAGATTT
131 AAGATTT
54041985 TAAATCTTGG
Statistics
Matches: 131, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
144 131 1.00
ACGTcount: A:0.39, C:0.17, G:0.13, T:0.31
Consensus pattern (144 bp):
GACTTCGTTACCAAGTCCCTAGATACGCACACAACTAAAAAAGAAAATCAAGATTCACTTTCTTG
TTTTCAAGAAAATTAAGAAACTAAACCTTGGTCAAATTTTATTGTTTCAGACAATTTCAAGAATC
AAGATTTCAAAGAT
Found at i:54045012 original size:12 final size:12
Alignment explanation
Indices: 54044995--54045019 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
54044985 GAAGGTGAAA
54044995 ATGTAAGTAATT
1 ATGTAAGTAATT
54045007 ATGTAAGTAATT
1 ATGTAAGTAATT
54045019 A
1 A
54045020 CACCTAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.16, T:0.40
Consensus pattern (12 bp):
ATGTAAGTAATT
Done.