Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D07
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: 58101237
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1550000 characters in sequence are not A, C, G, or T
File 185 of 199
Found at i:53744436 original size:17 final size:18
Alignment explanation
Indices: 53744403--53744437 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
53744393 AGGTTTTTAA
*
53744403 TTTAATTAAATTAGGGTT
1 TTTAATTAAAGTAGGGTT
53744421 TTTAATT-AAGTAGGGTT
1 TTTAATTAAAGTAGGGTT
53744438 AGGGATTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.31, C:0.00, G:0.20, T:0.49
Consensus pattern (18 bp):
TTTAATTAAAGTAGGGTT
Found at i:53746843 original size:22 final size:22
Alignment explanation
Indices: 53746813--53746854 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
53746803 ATTTGGAGAT
*
53746813 TTTTTGAAGGAAATTGAGAGGA
1 TTTTGGAAGGAAATTGAGAGGA
*
53746835 TTTTGGAAGGAATTTGAGAG
1 TTTTGGAAGGAAATTGAGAG
53746855 TTTGAGAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (22 bp):
TTTTGGAAGGAAATTGAGAGGA
Found at i:53746881 original size:22 final size:23
Alignment explanation
Indices: 53746856--53746947 Score: 104
Period size: 22 Copynumber: 4.2 Consensus size: 23
53746846 ATTTGAGAGT
53746856 TTGAGAG-AATTTTGGAAGGAAA
1 TTGAGAGAAATTTTGGAAGGAAA
*
53746878 TTGATG-GAAATTTT-GAAGGGAA
1 TTGA-GAGAAATTTTGGAAGGAAA
*
53746900 TTGAGAGAAATTTTGAAAGG-AA
1 TTGAGAGAAATTTTGGAAGGAAA
* *
53746922 TTGAGAG-AATTTTTGAAAGAAA
1 TTGAGAGAAATTTTGGAAGGAAA
53746944 TTGA
1 TTGA
53746948 TATTGAATTT
Statistics
Matches: 60, Mismatches: 5, Indels: 10
0.80 0.07 0.13
Matches are distributed among these distances:
21 10 0.17
22 39 0.65
23 11 0.18
ACGTcount: A:0.41, C:0.00, G:0.28, T:0.30
Consensus pattern (23 bp):
TTGAGAGAAATTTTGGAAGGAAA
Found at i:53746896 original size:52 final size:51
Alignment explanation
Indices: 53746804--53746906 Score: 122
Period size: 52 Copynumber: 2.0 Consensus size: 51
53746794 TTAATATGGA
* * *
53746804 TTTGGAGATTTTTTGAAGGAAATTGAGAGGATTTTGGAA-GGAATTTGAGAG
1 TTTGGAGAATTTTGGAAGGAAATTGAGAGAATTTTGGAAGGGAA-TTGAGAG
53746855 TTTGAGAGAATTTTGGAAGGAAATTGATG-GAAATTTT-GAAGGGAATTGAGAG
1 TTTG-GAGAATTTTGGAAGGAAATTGA-GAG-AATTTTGGAAGGGAATTGAGAG
53746907 AAATTTTGAA
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
51 4 0.09
52 31 0.69
53 10 0.22
ACGTcount: A:0.34, C:0.00, G:0.33, T:0.33
Consensus pattern (51 bp):
TTTGGAGAATTTTGGAAGGAAATTGAGAGAATTTTGGAAGGGAATTGAGAG
Found at i:53746904 original size:44 final size:44
Alignment explanation
Indices: 53746856--53746947 Score: 116
Period size: 44 Copynumber: 2.1 Consensus size: 44
53746846 ATTTGAGAGT
* * *
53746856 TTGAGAG-AATTTTGGAAGGAAATTGATG-GAAATTTTGAAGGGAA
1 TTGAGAGAAATTTTGAAAGG-AATTGA-GAGAAATTTTGAAAGAAA
*
53746900 TTGAGAGAAATTTTGAAAGGAATTGAGAGAATTTTTGAAAGAAA
1 TTGAGAGAAATTTTGAAAGGAATTGAGAGAAATTTTGAAAGAAA
53746944 TTGA
1 TTGA
53746948 TATTGAATTT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
43 1 0.02
44 30 0.71
45 11 0.26
ACGTcount: A:0.41, C:0.00, G:0.28, T:0.30
Consensus pattern (44 bp):
TTGAGAGAAATTTTGAAAGGAATTGAGAGAAATTTTGAAAGAAA
Found at i:53765494 original size:37 final size:38
Alignment explanation
Indices: 53765448--53765521 Score: 123
Period size: 37 Copynumber: 2.0 Consensus size: 38
53765438 TACAATCACA
*
53765448 ACCACTTATAATCAATATTAGATAAAATTATCATAGAT
1 ACCACTTATAATCAAAATTAGATAAAATTATCATAGAT
*
53765486 ACCA-TTATAATCAAAATTAGATAAAATTATTATAGA
1 ACCACTTATAATCAAAATTAGATAAAATTATCATAGA
53765522 ACGTCTCTGT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
37 30 0.88
38 4 0.12
ACGTcount: A:0.50, C:0.11, G:0.05, T:0.34
Consensus pattern (38 bp):
ACCACTTATAATCAAAATTAGATAAAATTATCATAGAT
Found at i:53770205 original size:31 final size:30
Alignment explanation
Indices: 53770170--53770229 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
53770160 GGAGGTGGGA
*
53770170 TGGGAAGGGAATAAAAGTTTTAGGGGAAAAG
1 TGGG-AGGGAATAAAAATTTTAGGGGAAAAG
* * *
53770201 TGGGAGGTAGTAAAAATTTTGGGGGAAAA
1 TGGGAGGGAATAAAAATTTTAGGGGAAAA
53770230 TAAAAGGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.40, C:0.00, G:0.38, T:0.22
Consensus pattern (30 bp):
TGGGAGGGAATAAAAATTTTAGGGGAAAAG
Found at i:53770436 original size:18 final size:18
Alignment explanation
Indices: 53770413--53770448 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
53770403 ATAGTTTGAC
53770413 ATTCGAATTATTTGAATT
1 ATTCGAATTATTTGAATT
*
53770431 ATTCGAGTTATTTGAATT
1 ATTCGAATTATTTGAATT
53770449 CAAAAACTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.31, C:0.06, G:0.14, T:0.50
Consensus pattern (18 bp):
ATTCGAATTATTTGAATT
Found at i:53770518 original size:9 final size:9
Alignment explanation
Indices: 53770501--53770531 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
53770491 TCGAGTTGAT
53770501 TCGAATAAC
1 TCGAATAAC
*
53770510 TCGATTAAC
1 TCGAATAAC
53770519 TCGAATAAC
1 TCGAATAAC
53770528 TCGA
1 TCGA
53770532 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:53771822 original size:57 final size:57
Alignment explanation
Indices: 53771734--53771841 Score: 137
Period size: 57 Copynumber: 1.9 Consensus size: 57
53771724 TTAATAAACT
* * * * *
53771734 ATTTGGTACTTGAATTTGGTTTCAATGTTCAATTTAGTATTTGAATTTTTTGTCCGA
1 ATTTGGTACGTGAATTTGGCTTCAATATTCAAATTAGTACTTGAATTTTTTGTCCGA
* *
53771791 ATTTGGTACGT-AAGTTTGGCTTCAATATTCAAATTGGTACTTGAGTTTTTT
1 ATTTGGTACGTGAA-TTTGGCTTCAATATTCAAATTAGTACTTGAATTTTTT
53771842 CAATTTGATA
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
56 2 0.05
57 41 0.95
ACGTcount: A:0.23, C:0.09, G:0.19, T:0.49
Consensus pattern (57 bp):
ATTTGGTACGTGAATTTGGCTTCAATATTCAAATTAGTACTTGAATTTTTTGTCCGA
Found at i:53782811 original size:25 final size:27
Alignment explanation
Indices: 53782778--53782827 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
53782768 AAATAACATA
*
53782778 GAAAGCAATTTAAA-TAGGTAATATAT
1 GAAAGCAATTTAAAGTAGCTAATATAT
53782804 GAAA-CAATTTAAAGTAGCTAATAT
1 GAAAGCAATTTAAAGTAGCTAATAT
53782828 CAAACATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 9 0.41
26 13 0.59
ACGTcount: A:0.50, C:0.06, G:0.14, T:0.30
Consensus pattern (27 bp):
GAAAGCAATTTAAAGTAGCTAATATAT
Found at i:53782832 original size:24 final size:25
Alignment explanation
Indices: 53782783--53782839 Score: 64
Period size: 24 Copynumber: 2.3 Consensus size: 25
53782773 ACATAGAAAG
* *
53782783 CAATTTAAATAGGTAATATATGAAA
1 CAATTTAAATAGCTAATATATCAAA
53782808 CAATTTAAAGTAGCT-A-ATATCAAA
1 CAATTTAAA-TAGCTAATATATCAAA
*
53782832 CATTTTAA
1 CAATTTAA
53782840 TATGAATAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 14 0.50
25 10 0.36
26 4 0.14
ACGTcount: A:0.49, C:0.09, G:0.09, T:0.33
Consensus pattern (25 bp):
CAATTTAAATAGCTAATATATCAAA
Found at i:53784469 original size:44 final size:44
Alignment explanation
Indices: 53784420--53784542 Score: 140
Period size: 44 Copynumber: 2.8 Consensus size: 44
53784410 TGGTTTTAGT
* * * *
53784420 CTGCTCCATTGCAACTTTATGAAGATAAGACTTGTCGCTTCAAC
1 CTGCTCCACTGCAACTTCAGGAAGATAAGACTTGTAGCTTCAAC
* * * * *
53784464 CTGCTCCACTGCGACTTCAGGGAGATAGGA-TTAGTAGCTTTAAT
1 CTGCTCCACTGCAACTTCAGGAAGATAAGACTT-GTAGCTTCAAC
*
53784508 ATGCTCCACTGCAACTTCAGGAAGATAAGACTTGT
1 CTGCTCCACTGCAACTTCAGGAAGATAAGACTTGT
53784543 TATGATAGAT
Statistics
Matches: 64, Mismatches: 13, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
43 2 0.03
44 60 0.94
45 2 0.03
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (44 bp):
CTGCTCCACTGCAACTTCAGGAAGATAAGACTTGTAGCTTCAAC
Found at i:53784793 original size:129 final size:129
Alignment explanation
Indices: 53784595--53784890 Score: 434
Period size: 129 Copynumber: 2.3 Consensus size: 129
53784585 AGATTCATTG
* * *
53784595 TTTTAATCTGCTCCACTGCAACTTCAGGGAGATAGAATTGGTTTTTTCTGTCTACTCCACTGCAA
1 TTTTAATCTGCTCCACTGCAACTTCAGGAAGATAGGATTGGTTTCTTCTGTCTACTCCACTGCAA
* * *
53784660 CTTTAGGGAGATAAGACTGGATGCGATATGCTCTACTGCAACTTCAGAGAAG-TAAGATCTGTGT
66 CTTTAGAGAGATAAGACTGGATGCGATATGCTCTACTGCAACTTCAGA-AAGAGAAGATCTGTAT
**
53784724 TTTTAATCCACTCCACTGCAACTTCAGGAAGATAGGATTGGTTTCTTCTGTCTACTCCACTGCAA
1 TTTTAATCTGCTCCACTGCAACTTCAGGAAGATAGGATTGGTTTCTTCTGTCTACTCCACTGCAA
* * * *
53784789 CTTTAGAGAGATAAGACTGGATGCGATCTGCTCTACTGTAACTTTAGAAAGAGAAGATTTGTAT
66 CTTTAGAGAGATAAGACTGGATGCGATATGCTCTACTGCAACTTCAGAAAGAGAAGATCTGTAT
* *
53784853 TTTTAATCTGCACCACTGCAACTTTA-GAGAGATAGGAT
1 TTTTAATCTGCTCCACTGCAACTTCAGGA-AGATAGGAT
53784891 CTGTGTTTTT
Statistics
Matches: 149, Mismatches: 16, Indels: 4
0.88 0.09 0.02
Matches are distributed among these distances:
128 5 0.03
129 144 0.97
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.32
Consensus pattern (129 bp):
TTTTAATCTGCTCCACTGCAACTTCAGGAAGATAGGATTGGTTTCTTCTGTCTACTCCACTGCAA
CTTTAGAGAGATAAGACTGGATGCGATATGCTCTACTGCAACTTCAGAAAGAGAAGATCTGTAT
Found at i:53784873 original size:173 final size:173
Alignment explanation
Indices: 53784694--53785185 Score: 599
Period size: 173 Copynumber: 2.8 Consensus size: 173
53784684 GATATGCTCT
* * * *
53784694 ACTGCAACTTCAGAGA-AGTAAGATCTGTGTTTTTAATCCACTCCACTGCAACTTCAGGAAGATA
1 ACTGCAACTTTAGAGAGA-TAGGATCTGTGTTTTTAATCCGCTCCACTGCAACTTCAGGGAGATA
* * *
53784758 GGATTGGTTTCTTCTGTCTACTCCACTGCAACTTTAGAGAGATAAGACTGGATGCGATCTGCTCT
65 GGATTGGTTTCTTCTATCTGCTCCACTGCAACTTTAGGGAGATAAGACTGGATGCGATCTGCTCT
* * * *
53784823 ACTGTAACTTTAGAAAGAGAAGATTTGTATTTTTAATCTGCACC
130 ACTGCAACTTCAGAAAGAGAAGATCTGTATTTTTAATCCGCACC
* **
53784867 ACTGCAACTTTAGAGAGATAGGATCTGTGTTTTTAATCTGCTCCACTATAACTTCAGGGAGATAG
1 ACTGCAACTTTAGAGAGATAGGATCTGTGTTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAG
* * *
53784932 GATTGGTTTTTTCTATCTGCTCCACTGCAACTTTAGGGAGATAAGACTGGATGTGATCTGTTCTA
66 GATTGGTTTCTTCTATCTGCTCCACTGCAACTTTAGGGAGATAAGACTGGATGCGATCTGCTCTA
* * * * **
53784997 TTGCAACTTCAGATAGATAAGATCTGTGTTTTTAATCCGTTCC
131 CTGCAACTTCAGAAAGAGAAGATCTGTATTTTTAATCCGCACC
* * * * *
53785040 ACTACAACTTTAGGGAGATAGGATCTGTGTTTTAAATTCGCTCAACTGCAACTTCAGGGAGATAG
1 ACTGCAACTTTAGAGAGATAGGATCTGTGTTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAG
* ** * * * * * * *
53785105 GATTAGTAGCTTCAATCTGCTCCGCTGCAACTTCAGGGAGATAAGATTGGTATCTTCAACCTGCT
66 GATTGGTTTCTTCTATCTGCTCCACTGCAACTTTAGGGAGATAAGACTGG-A--TGCGATCTGCT
53785170 CTACTGCAACTTCAGA
128 CTACTGCAACTTCAGA
53785186 TAGATAAGGT
Statistics
Matches: 270, Mismatches: 45, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
173 247 0.91
174 2 0.01
176 21 0.08
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.33
Consensus pattern (173 bp):
ACTGCAACTTTAGAGAGATAGGATCTGTGTTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAG
GATTGGTTTCTTCTATCTGCTCCACTGCAACTTTAGGGAGATAAGACTGGATGCGATCTGCTCTA
CTGCAACTTCAGAAAGAGAAGATCTGTATTTTTAATCCGCACC
Found at i:53785274 original size:44 final size:44
Alignment explanation
Indices: 53784602--53785340 Score: 313
Period size: 44 Copynumber: 17.0 Consensus size: 44
53784592 TTGTTTTAAT
* * ***
53784602 CTGCTCCACTGCAACTTCAGGGAGAT-AGAATTGGTTTTTTCTGT
1 CTGCTCCACTGCAACTTCAGGGAGATAAG-ATTGGTATCTTCAAC
* * * * * *
53784646 CTACTCCACTGCAACTTTAGGGAGATAAGACTGG-A--TGCGAT
1 CTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTATCTTCAAC
* * * *
53784687 ATGCTCTACTGCAACTTCAGAGA-AGTAAGATCTGTGT-T-TTTAATC
1 CTGCTCCACTGCAACTTCAGGGAGA-TAAGAT-TG-GTATCTTCAA-C
* * * * ***
53784732 C-ACTCCACTGCAACTTCAGGAAGATAGGATTGGTTTCTTCTGT
1 CTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTATCTTCAAC
* * * * * * *
53784775 CTACTCCACTGCAACTTTAGAGAGATAAGACTGG-A--TGCGAT
1 CTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTATCTTCAAC
* * * ** * * * * *
53784816 CTGCTCTACTGTAACTTTAGAAAGAGAAGATTTGTATTTTTAAT
1 CTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTATCTTCAAC
* * * * * *
53784860 CTGCACCACTGCAACTTTAGAGAGATAGGATCTGTGT-T-TTTAAT
1 CTGCTCCACTGCAACTTCAGGGAGATAAGAT-TG-GTATCTTCAAC
** * * * * *
53784904 CTGCTCCACTATAACTTCAGGGAGATAGGATTGGTTTTTTCTAT
1 CTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTATCTTCAAC
* * * * *
53784948 CTGCTCCACTGCAACTTTAGGGAGATAAGACTGG-AT-GT-GAT
1 CTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTATCTTCAAC
* * * ** *
53784989 CTGTTCTATTGCAACTTCAGATAGATAAGATCTGTGT-T-TTTAATC
1 CTGCTCCACTGCAACTTCAGGGAGATAAGAT-TG-GTATCTTCAA-C
* * * * *
53785034 C-GTTCCACTACAACTTTAGGGAGATAGGATCTGTGT-T-TT-AAA
1 CTGCTCCACTGCAACTTCAGGGAGATAAGAT-TG-GTATCTTCAAC
* * * * * *
53785076 TTCGCTCAACTGCAACTTCAGGGAGATAGGATTAGTAGCTTCAAT
1 CT-GCTCCACTGCAACTTCAGGGAGATAAGATTGGTATCTTCAAC
*
53785121 CTGCTCCGCTGCAACTTCAGGGAGATAAGATTGGTATCTTCAAC
1 CTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTATCTTCAAC
* ** * * **
53785165 CTGCTCTACTGCAACTTCAGATAGATAAGGTTGGTTACCTTCAGT
1 CTGCTCCACTGCAACTTCAGGGAGATAAGATTGG-TATCTTCAAC
*
53785210 CTGCTCCACTGCAACTTCAGGGAGATAAGACTT-GTATTTTCAAC
1 CTGCTCCACTGCAACTTCAGGGAGATAAGA-TTGGTATCTTCAAC
* * * * * *
53785254 CTGCCCCATTGCAACTTCAGGGGGATAAGGTTTGTCAT-TTTAATC
1 CTGCTCCACTGCAACTTCAGGGAGATAAGATTGGT-ATCTTCAA-C
* * * *
53785299 C-GCTCCACTGCAACTTTAGGGAGATAGGATTAGTAGCTTCAA
1 CTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTATCTTCAA
53785341 TCTATTTAAT
Statistics
Matches: 530, Mismatches: 131, Indels: 68
0.73 0.18 0.09
Matches are distributed among these distances:
40 1 0.00
41 82 0.15
42 12 0.02
43 18 0.03
44 366 0.69
45 47 0.09
46 4 0.01
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (44 bp):
CTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTATCTTCAAC
Found at i:53785324 original size:133 final size:127
Alignment explanation
Indices: 53784592--53785329 Score: 383
Period size: 129 Copynumber: 5.7 Consensus size: 127
53784582 ATAAGATTCA
* * * ** **
53784592 TTGT-TTT-AATCTGCTCCACTGCAACTTCAGGGAGAT-AGAATTGGTTTTTTCTGTCTACTCCA
1 TTGTATTTCAATCTGCTCCATTGCAACTTCAGGGAGATAAG-ATTTGTATTTT-AATCCGCTCCA
* * * * * * * * *
53784654 CTGCAACTTTAGGGAGATAAGACTGG-ATGCGATATGCTCTACTGCAACTTCAGAGA-AGTAAGA
64 CTACAACTTCAGGGAGATAGGATTGGTTTTC-ATCTGCTCCACTGCAACTTCAGGGAGA-TAAGA
53784717 TC
127 -C
* ** * * * * ** **
53784719 TGTGT-TTTTAATCCACTCCACTGCAACTTCAGGAAGATAGGATTGGT-TTCTTCTGTCTACTCC
1 T-TGTATTTCAATCTGCTCCATTGCAACTTCAGGGAGATAAGATTTGTATT-TT-AATCCGCTCC
* * * * * * * * * * ** *
53784782 ACTGCAACTTTAGAGAGATAAGACTGG-ATGCGATCTGCTCTACTGTAACTTTAGAAAGAGAAGA
63 ACTACAACTTCAGGGAGATAGGATTGGTTTTC-ATCTGCTCCACTGCAACTTCAGGGAGATAAGA
*
53784846 T
127 C
* * * * * * *
53784847 TTGTATTTTTAATCTGCACCACTGCAACTTTAGAGAGATAGGATCTGTGT-TTTTAATCTGCTCC
1 TTGTA-TTTCAATCTGCTCCATTGCAACTTCAGGGAGATAAGAT-T-TGTATTTTAATCCGCTCC
* *
53784911 ACTATAACTTCAGGGAGATAGGATTGGTTTTTTCTATCTGCTCCACTGCAACTTTAGGGAGATAA
63 ACTACAACTTCAGGGAGATAGGATTGG--TTTTC-ATCTGCTCCACTGCAACTTCAGGGAGATAA
53784976 GAC
125 GAC
* * * * * ** *
53784979 -TGGATGT-GATCTGTTCTATTGCAACTTCAGATAGATAAGATCTGTGT-TTTTAATCCGTTCCA
1 TTGTATTTCAATCTGCTCCATTGCAACTTCAGGGAGATAAGAT-T-TGTATTTTAATCCGCTCCA
* * * *
53785041 CTACAACTTTAGGGAGATAGGATCTGTGTTTTAAAT-TCGCTCAACTGCAACTTCAGGGAGATAG
64 CTACAACTTCAGGGAGATAGGAT-TG-GTTTT-CATCT-GCTCCACTGCAACTTCAGGGAGATAA
53785105 GA-
125 GAC
* ** * *
53785107 TTAGTAGCTTCAATCTGCTCCGCTGCAACTTCAGGGAGATAAGATTGGTATCTTCAA-CCTGCTC
1 TT-GTA-TTTCAATCTGCTCCATTGCAACTTCAGGGAGATAAGATTTGTAT-TTTAATCC-GCTC
* * **
53785171 TACTGCAACTTCAGATAGATAAGG-TTGGTTACCTTCAGTCTGCTCCACTGCAACTTCAGGGAGA
62 CACTACAACTTCAGGGAGAT-AGGATTGGTT---TTCA-TCTGCTCCACTGCAACTTCAGGGAGA
53785235 TAAGAC
122 TAAGAC
* * * *
53785241 TTGTATTTTCAACCTGCCCCATTGCAACTTCAGGGGGATAAGGTTTGTCATTTTAATCCGCTCCA
1 TTGTA-TTTCAATCTGCTCCATTGCAACTTCAGGGAGATAAGATTTGT-ATTTTAATCCGCTCCA
* *
53785306 CTGCAACTTTAGGGAGATAGGATT
64 CTACAACTTCAGGGAGATAGGATT
53785330 AGTAGCTTCA
Statistics
Matches: 489, Mismatches: 89, Indels: 60
0.77 0.14 0.09
Matches are distributed among these distances:
127 4 0.01
128 10 0.02
129 259 0.53
130 16 0.03
131 15 0.03
132 83 0.17
133 95 0.19
134 7 0.01
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.33
Consensus pattern (127 bp):
TTGTATTTCAATCTGCTCCATTGCAACTTCAGGGAGATAAGATTTGTATTTTAATCCGCTCCACT
ACAACTTCAGGGAGATAGGATTGGTTTTCATCTGCTCCACTGCAACTTCAGGGAGATAAGAC
Found at i:53785389 original size:50 final size:50
Alignment explanation
Indices: 53785331--53786299 Score: 695
Period size: 50 Copynumber: 19.4 Consensus size: 50
53785321 GATAGGATTA
* * * * *
53785331 GTAGCTTCAATCTATTTAATTGCAATGTCGGGGAAGGAAGATTCGCTGTT
1 GTAGCTTCAATCTTTTTAATTGCAATGTCAGGGAAGTAAGATTCACCGTT
* ** * ** * **
53785381 GTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATTTGCCGTT
1 GTAGCTTCAATCTTTTTAATTGCAATGTCAGGGAAGTAAGATTCACCGTT
* *
53785431 GTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGTAAGATTCACCGTT
1 GTAGCTTCAATCTTTTTAATTGCAATGTCAGGGAAGTAAGATTCACCGTT
* ** * *
53785481 GTAGCTTCAATCTATTCCACTGCACCA-CT-AGGGAAGTAAGATTCACCGTT
1 GTAGCTTCAATCTTTTTAATTGCA--ATGTCAGGGAAGTAAGATTCACCGTT
* * * *
53785531 GTGGCTTCAATCTTTTTAATTGTAATGTCAGGGAAGCAAGATTCACCATT
1 GTAGCTTCAATCTTTTTAATTGCAATGTCAGGGAAGTAAGATTCACCGTT
* * ** * ** * **
53785581 GTAGATTCAATCTATTCCACTGCACCGCCAGGGAAGTAAGATTTGCCGTT
1 GTAGCTTCAATCTTTTTAATTGCAATGTCAGGGAAGTAAGATTCACCGTT
* * ** **
53785631 GTGGCTTCAATCTTTTTAATTGCAATATCTTGGAAGTAAGATTTGCCGTT
1 GTAGCTTCAATCTTTTTAATTGCAATGTCAGGGAAGTAAGATTCACCGTT
* * ** * * * *
53785681 GTAACTTCAATCTGTTCCATTACACTGCCAGGGAAGTAAGATTCACTGTT
1 GTAGCTTCAATCTTTTTAATTGCAATGTCAGGGAAGTAAGATTCACCGTT
* * * *
53785731 GTGGCTTCAATCTTTTTAATTGTAATGTC-GGAGAAGCAAGATTCACTGTT
1 GTAGCTTCAATCTTTTTAATTGCAATGTCAGG-GAAGTAAGATTCACCGTT
* ** * ** * * *
53785781 GTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAGTAAAATTCGCCGTT
1 GTAGCTTCAATCTTTTTAATTGCAATGTCAGGGAAGTAAGATTCACCGTT
* * * * *
53785831 GTGGCTTCAATCTTTTTAATTGCCATGTCGGGGAAGCAAGATTCACTGTT
1 GTAGCTTCAATCTTTTTAATTGCAATGTCAGGGAAGTAAGATTCACCGTT
* ** * ** * * *
53785881 GTAGCTTCAATCTATTCCACTGCACCGCCAGGGAAGTAAGATTCGCAGTT
1 GTAGCTTCAATCTTTTTAATTGCAATGTCAGGGAAGTAAGATTCACCGTT
* * * * * * *
53785931 TTGGCTTCAATCTTTTTAATTGCAATATCGGGGAAGCAAGATTCGCTGTT
1 GTAGCTTCAATCTTTTTAATTGCAATGTCAGGGAAGTAAGATTCACCGTT
* ** * * ** * * *
53785981 GTAGCTTCAATCTGTTCCACTACACCGCCAGGGAAGTAAGGTTCACTGTT
1 GTAGCTTCAATCTTTTTAATTGCAATGTCAGGGAAGTAAGATTCACCGTT
* * * * * *
53786031 GTGGCTTCAATCTTTTTAATTGCAATTTCGGGGAAGCAAGATTCGCTGTT
1 GTAGCTTCAATCTTTTTAATTGCAATGTCAGGGAAGTAAGATTCACCGTT
* * * *
53786081 GTGGCTTCAATCTTTTTAATTGCAATATCGGGGAAGTGAGATTCACCGTT
1 GTAGCTTCAATCTTTTTAATTGCAATGTCAGGGAAGTAAGATTCACCGTT
* ** * * * **
53786131 GTAGCTTCAATCTGTTCCACT-AAACCGTCAGGGAAGTAAGATTTTCCGTT
1 GTAGCTTCAATCTTTTTAATTGCAA-TGTCAGGGAAGTAAGATTCACCGTT
* * * * ** *
53786181 ATGGCTTCAATCGTTTTAATTACAATGTCAGGGAAACAAGATTCGCCGTT
1 GTAGCTTCAATCTTTTTAATTGCAATGTCAGGGAAGTAAGATTCACCGTT
* * ** * * ** * * *
53786231 GTAGTTTCAATCTGTTCCACTACACCGCCAAGGAAGTAAGATTCGCCGTT
1 GTAGCTTCAATCTTTTTAATTGCAATGTCAGGGAAGTAAGATTCACCGTT
* *
53786281 GTGGTTTCAATCTTTTTAA
1 GTAGCTTCAATCTTTTTAA
53786300 CTGTAACCTA
Statistics
Matches: 693, Mismatches: 218, Indels: 16
0.75 0.24 0.02
Matches are distributed among these distances:
48 1 0.00
49 5 0.01
50 681 0.98
51 5 0.01
52 1 0.00
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (50 bp):
GTAGCTTCAATCTTTTTAATTGCAATGTCAGGGAAGTAAGATTCACCGTT
Found at i:53785472 original size:100 final size:100
Alignment explanation
Indices: 53785334--53786093 Score: 1106
Period size: 100 Copynumber: 7.6 Consensus size: 100
53785324 AGGATTAGTA
* * *
53785334 GCTTCAATCTATTTAATTGCAATGTCGGGGAAGGAAGATTCGCTGTTGTAGCTTCAATCTGTTCC
1 GCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCACTGTTGTAGCTTCAATCTGTTCC
*
53785399 ACTGCACCGCCAGGGAAGTAAGATTTGCCGTTGTG
66 ACTGCACCGCCAGGGAAGTAAGATTCGCCGTTGTG
* * *
53785434 GCTTCAATCTTTTTAATTGCAATGTCGGGGAAGTAAGATTCACCGTTGTAGCTTCAATCTATTCC
1 GCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCACTGTTGTAGCTTCAATCTGTTCC
* * *
53785499 ACTGCACCACTAGGGAAGTAAGATTCACCGTTGTG
66 ACTGCACCGCCAGGGAAGTAAGATTCGCCGTTGTG
* * ** * *
53785534 GCTTCAATCTTTTTAATTGTAATGTCAGGGAAGCAAGATTCACCATTGTAGATTCAATCTATTCC
1 GCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCACTGTTGTAGCTTCAATCTGTTCC
*
53785599 ACTGCACCGCCAGGGAAGTAAGATTTGCCGTTGTG
66 ACTGCACCGCCAGGGAAGTAAGATTCGCCGTTGTG
* ** * ** * *
53785634 GCTTCAATCTTTTTAATTGCAATATCTTGGAAGTAAGATTTGCCGTTGTAACTTCAATCTGTTCC
1 GCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCACTGTTGTAGCTTCAATCTGTTCC
* * * * *
53785699 ATTACACTGCCAGGGAAGTAAGATTCACTGTTGTG
66 ACTGCACCGCCAGGGAAGTAAGATTCGCCGTTGTG
* *
53785734 GCTTCAATCTTTTTAATTGTAATGTCGGAGAAGCAAGATTCACTGTTGTAGCTTCAATCTGTTCC
1 GCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCACTGTTGTAGCTTCAATCTGTTCC
*
53785799 ACTGCACCGCCAGGGAAGTAAAATTCGCCGTTGTG
66 ACTGCACCGCCAGGGAAGTAAGATTCGCCGTTGTG
* *
53785834 GCTTCAATCTTTTTAATTGCCATGTCGGGGAAGCAAGATTCACTGTTGTAGCTTCAATCTATTCC
1 GCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCACTGTTGTAGCTTCAATCTGTTCC
* *
53785899 ACTGCACCGCCAGGGAAGTAAGATTCGCAGTTTTG
66 ACTGCACCGCCAGGGAAGTAAGATTCGCCGTTGTG
* *
53785934 GCTTCAATCTTTTTAATTGCAATATCGGGGAAGCAAGATTCGCTGTTGTAGCTTCAATCTGTTCC
1 GCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCACTGTTGTAGCTTCAATCTGTTCC
* * * *
53785999 ACTACACCGCCAGGGAAGTAAGGTTCACTGTTGTG
66 ACTGCACCGCCAGGGAAGTAAGATTCGCCGTTGTG
* * *
53786034 GCTTCAATCTTTTTAATTGCAATTTCGGGGAAGCAAGATTCGCTGTTGTGGCTTCAATCT
1 GCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCACTGTTGTAGCTTCAATCT
53786094 TTTTAATTGC
Statistics
Matches: 591, Mismatches: 69, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
100 591 1.00
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (100 bp):
GCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCACTGTTGTAGCTTCAATCTGTTCC
ACTGCACCGCCAGGGAAGTAAGATTCGCCGTTGTG
Found at i:53786894 original size:45 final size:45
Alignment explanation
Indices: 53786808--53786894 Score: 111
Period size: 45 Copynumber: 1.9 Consensus size: 45
53786798 AGCTCGAAAT
* * *
53786808 GAATGAATTAATCAAGATAGTAAATTTTGCTAGAATACAAAATGA
1 GAATAAATTAATCAAGATAGTAAATTTTGCCAAAATACAAAATGA
* ** *
53786853 GAATAAATTAATCAAGATGGTGTATTTTGCCAAAATCCAAAA
1 GAATAAATTAATCAAGATAGTAAATTTTGCCAAAATACAAAA
53786895 ATGAATAAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
45 35 1.00
ACGTcount: A:0.47, C:0.09, G:0.15, T:0.29
Consensus pattern (45 bp):
GAATAAATTAATCAAGATAGTAAATTTTGCCAAAATACAAAATGA
Found at i:53787189 original size:13 final size:13
Alignment explanation
Indices: 53787171--53787229 Score: 52
Period size: 13 Copynumber: 4.6 Consensus size: 13
53787161 CCTTGTCCTC
53787171 TCTTTTTTCTTTT
1 TCTTTTTTCTTTT
53787184 TCTTTTTTCGTTTT
1 TCTTTTTTC-TTTT
* *
53787198 TATTTTATT-TTCT
1 TCTTTT-TTCTTTT
*
53787211 T-TTTTTTC-GTT
1 TCTTTTTTCTTTT
53787222 TCTTTTTT
1 TCTTTTTT
53787230 AAGTGAAGTA
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
11 4 0.11
12 10 0.26
13 13 0.34
14 9 0.24
15 2 0.05
ACGTcount: A:0.03, C:0.12, G:0.03, T:0.81
Consensus pattern (13 bp):
TCTTTTTTCTTTT
Found at i:53787217 original size:14 final size:13
Alignment explanation
Indices: 53787173--53787229 Score: 51
Period size: 14 Copynumber: 4.0 Consensus size: 13
53787163 TTGTCCTCTC
*
53787173 TTTTTTCTTTTTC
1 TTTTTTCTTTTTT
53787186 TTTTTTCGTTTTTATT
1 TTTTTTC--TTTT-TT
53787202 TTATTTTCTTTTTT
1 TT-TTTTCTTTTTT
*
53787216 TTCGTTTCTTTTTT
1 TT-TTTTCTTTTTT
53787230 AAGTGAAGTA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
13 7 0.19
14 14 0.38
15 8 0.22
16 3 0.08
17 5 0.14
ACGTcount: A:0.04, C:0.11, G:0.04, T:0.82
Consensus pattern (13 bp):
TTTTTTCTTTTTT
Found at i:53787700 original size:15 final size:14
Alignment explanation
Indices: 53787660--53787702 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
53787650 CCCCGGTAGA
53787660 GTTTTTTTGTTTTTT
1 GTTTTTTT-TTTTTT
*
53787675 CTTTTCTTTTTTTTT
1 GTTTT-TTTTTTTTT
53787690 GTTTTTATTTTTT
1 GTTTTT-TTTTTT
53787703 GCCTCCACTG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
14 1 0.04
15 20 0.83
16 3 0.12
ACGTcount: A:0.02, C:0.05, G:0.07, T:0.86
Consensus pattern (14 bp):
GTTTTTTTTTTTTT
Found at i:53790895 original size:25 final size:27
Alignment explanation
Indices: 53790861--53790911 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 27
53790851 AAAATAACAT
*
53790861 TGAAAGCAATTTAAA-TAGGTAATATA
1 TGAAAGCAATTTAAAGTAGCTAATATA
53790887 TGAAA-CAATTTAAAGTAGCTAATAT
1 TGAAAGCAATTTAAAGTAGCTAATAT
53790912 CAAACATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 9 0.39
26 14 0.61
ACGTcount: A:0.49, C:0.06, G:0.14, T:0.31
Consensus pattern (27 bp):
TGAAAGCAATTTAAAGTAGCTAATATA
Found at i:53790916 original size:24 final size:25
Alignment explanation
Indices: 53790867--53790923 Score: 64
Period size: 24 Copynumber: 2.3 Consensus size: 25
53790857 ACATTGAAAG
* *
53790867 CAATTTAAATAGGTAATATATGAAA
1 CAATTTAAATAGCTAATATATCAAA
53790892 CAATTTAAAGTAGCT-A-ATATCAAA
1 CAATTTAAA-TAGCTAATATATCAAA
*
53790916 CATTTTAA
1 CAATTTAA
53790924 TATGAATAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 14 0.50
25 10 0.36
26 4 0.14
ACGTcount: A:0.49, C:0.09, G:0.09, T:0.33
Consensus pattern (25 bp):
CAATTTAAATAGCTAATATATCAAA
Found at i:53795015 original size:24 final size:23
Alignment explanation
Indices: 53794970--53795020 Score: 75
Period size: 24 Copynumber: 2.2 Consensus size: 23
53794960 CTTTTTACTA
**
53794970 AAAATATTTAAAAATATCTATAAT
1 AAAATATTTAAAAATAAATAT-AT
53794994 AAAATATTTAAAAATAAATATAT
1 AAAATATTTAAAAATAAATATAT
53795017 AAAA
1 AAAA
53795021 AATGAAATAC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 6 0.24
24 19 0.76
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (23 bp):
AAAATATTTAAAAATAAATATAT
Found at i:53800992 original size:24 final size:24
Alignment explanation
Indices: 53800971--53801022 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
53800961 AATTAATGTC
*
53800971 AAATATATTATGCTAATAAATGCT
1 AAATATATTATACTAATAAATGCT
*
53800995 AAATATATTATACTAATAAATACT
1 AAATATATTATACTAATAAATGCT
53801019 AAAT
1 AAAT
53801023 CTTCTAGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.52, C:0.08, G:0.04, T:0.37
Consensus pattern (24 bp):
AAATATATTATACTAATAAATGCT
Found at i:53802887 original size:100 final size:100
Alignment explanation
Indices: 53802706--53802901 Score: 275
Period size: 100 Copynumber: 2.0 Consensus size: 100
53802696 GCTTCAAAAA
* * * * * *
53802706 AAGTAGATGTTTCTTGATTTGCATCTATATCTTCATCCACGTTTAAACCATAAATAGCTAGATCA
1 AAGTAAATGTTTCTTAATTTACATATATATCTTCATCCACGTTTAAACCATAAACAACTAGATCA
*
53802771 GCCTCAGCATATCTCTTTAAAGGTTTAATTTTAAT
66 GCCTCAGCATACCTCTTTAAAGGTTTAATTTTAAT
* *
53802806 AAGTAAATGTTTCTTAATTTACATATATATCTTCATCCACGTTTAAAGCATAAGCAACTAGATCA
1 AAGTAAATGTTTCTTAATTTACATATATATCTTCATCCACGTTTAAACCATAAACAACTAGATCA
* * **
53802871 GCCTCGGCGTACCTCTTTGGAGGTTTAATTT
66 GCCTCAGCATACCTCTTTAAAGGTTTAATTT
53802902 CTTTTTTATG
Statistics
Matches: 83, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
100 83 1.00
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (100 bp):
AAGTAAATGTTTCTTAATTTACATATATATCTTCATCCACGTTTAAACCATAAACAACTAGATCA
GCCTCAGCATACCTCTTTAAAGGTTTAATTTTAAT
Found at i:53805488 original size:24 final size:24
Alignment explanation
Indices: 53805442--53805506 Score: 76
Period size: 24 Copynumber: 2.5 Consensus size: 24
53805432 TAATAAATAT
*
53805442 TAATAAATATTAAATCTTAATATTATGC
1 TAATAAATATT-AA--TT-ATATTATAC
*
53805470 TAATAAATCTTAATTATATTATAC
1 TAATAAATATTAATTATATTATAC
53805494 TAATAAATATTAA
1 TAATAAATATTAA
53805507 ATCTTCTAGA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
24 20 0.59
25 2 0.06
27 2 0.06
28 10 0.29
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.43
Consensus pattern (24 bp):
TAATAAATATTAATTATATTATAC
Found at i:53819673 original size:18 final size:19
Alignment explanation
Indices: 53819641--53819678 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
53819631 AAAATTTATG
53819641 ATAATTATACATTTA-AAA
1 ATAATTATACATTTATAAA
53819659 ATAATTATA-ATTTTATAAA
1 ATAATTATACA-TTTATAAA
53819678 A
1 A
53819679 AATGTGATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 1 0.06
18 13 0.72
19 4 0.22
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (19 bp):
ATAATTATACATTTATAAA
Found at i:53819934 original size:19 final size:19
Alignment explanation
Indices: 53819910--53819947 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
53819900 AGTGTTAATT
53819910 TTATTAATGT-AAAATAGAA
1 TTATTAAT-TAAAAATAGAA
53819929 TTATTAATTAAAAATAGAA
1 TTATTAATTAAAAATAGAA
53819948 CTCTAAGCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 1 0.06
19 17 0.94
ACGTcount: A:0.55, C:0.00, G:0.08, T:0.37
Consensus pattern (19 bp):
TTATTAATTAAAAATAGAA
Found at i:53822070 original size:38 final size:38
Alignment explanation
Indices: 53822027--53822121 Score: 145
Period size: 38 Copynumber: 2.5 Consensus size: 38
53822017 TGTAATAGAA
* *
53822027 CAATTCAACACTAGCAGTACTCATGCTTAACATGTATT
1 CAATTCAACACTAGCAATAATCATGCTTAACATGTATT
* *
53822065 TAATTCAACACTAGTAATAATCATGCTTAACATGTATT
1 CAATTCAACACTAGCAATAATCATGCTTAACATGTATT
*
53822103 CAATTCAATACTAGCAATA
1 CAATTCAACACTAGCAATA
53822122 GACATGTTTT
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 50 1.00
ACGTcount: A:0.39, C:0.20, G:0.08, T:0.33
Consensus pattern (38 bp):
CAATTCAACACTAGCAATAATCATGCTTAACATGTATT
Found at i:53822527 original size:9 final size:9
Alignment explanation
Indices: 53822513--53822624 Score: 152
Period size: 9 Copynumber: 12.4 Consensus size: 9
53822503 GTAGTGATTC
*
53822513 AATTTGGTT
1 AATTCGGTT
*
53822522 AATTTGGTT
1 AATTCGGTT
*
53822531 AATTCGGGT
1 AATTCGGTT
53822540 AATTCGGTT
1 AATTCGGTT
*
53822549 AATTCGGGT
1 AATTCGGTT
53822558 AATTCGGTT
1 AATTCGGTT
*
53822567 AATTCGGGT
1 AATTCGGTT
*
53822576 AATTCGGGT
1 AATTCGGTT
53822585 AATTCGGTT
1 AATTCGGTT
* *
53822594 GATTCGGGT
1 AATTCGGTT
53822603 AATTCGGTT
1 AATTCGGTT
53822612 AATTCGGTT
1 AATTCGGTT
53822621 AATT
1 AATT
53822625 TTTAACCAAA
Statistics
Matches: 92, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 92 1.00
ACGTcount: A:0.22, C:0.09, G:0.27, T:0.42
Consensus pattern (9 bp):
AATTCGGTT
Found at i:53831674 original size:6 final size:6
Alignment explanation
Indices: 53831660--53831700 Score: 73
Period size: 6 Copynumber: 6.7 Consensus size: 6
53831650 TCATGTTATA
53831660 TTTGAAT TTTGAT TTTGAT TTTGAT TTTGAT TTTGAT TTTG
1 TTTG-AT TTTGAT TTTGAT TTTGAT TTTGAT TTTGAT TTTG
53831701 TGCAATTTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 30 0.88
7 4 0.12
ACGTcount: A:0.17, C:0.00, G:0.17, T:0.66
Consensus pattern (6 bp):
TTTGAT
Found at i:53834249 original size:30 final size:31
Alignment explanation
Indices: 53834197--53834254 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 31
53834187 CACCCTTAAA
* *
53834197 TATTTACACTATTGGTCCTTCAAATTTTTTG
1 TATTTACACTATTAGCCCTTCAAATTTTTTG
53834228 TATTTACACT-TTAGCCCTTCAAATTTT
1 TATTTACACTATTAGCCCTTCAAATTTT
53834255 GAATATTTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 15 0.60
31 10 0.40
ACGTcount: A:0.24, C:0.19, G:0.07, T:0.50
Consensus pattern (31 bp):
TATTTACACTATTAGCCCTTCAAATTTTTTG
Found at i:53834262 original size:30 final size:31
Alignment explanation
Indices: 53834195--53834264 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 31
53834185 TCCACCCTTA
* * *
53834195 AATATTTACACTATTGGTCCTTCAAATTTTT
1 AATATTTACACTATTAGCCCTTCAAATTTTG
**
53834226 TGTATTTACACT-TTAGCCCTTCAAATTTTG
1 AATATTTACACTATTAGCCCTTCAAATTTTG
53834256 AATATTTAC
1 AATATTTAC
53834265 TCTTGGGCAA
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
30 22 0.69
31 10 0.31
ACGTcount: A:0.29, C:0.17, G:0.07, T:0.47
Consensus pattern (31 bp):
AATATTTACACTATTAGCCCTTCAAATTTTG
Found at i:53839911 original size:18 final size:16
Alignment explanation
Indices: 53839888--53839924 Score: 56
Period size: 18 Copynumber: 2.2 Consensus size: 16
53839878 GCTGTTTATA
53839888 ATATATTATATTATATTT
1 ATATATTAT-TTA-ATTT
53839906 ATATATTATTTAATTT
1 ATATATTATTTAATTT
53839922 ATA
1 ATA
53839925 ACACAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.37
17 3 0.16
18 9 0.47
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
ATATATTATTTAATTT
Found at i:53856206 original size:49 final size:49
Alignment explanation
Indices: 53856134--53856231 Score: 196
Period size: 49 Copynumber: 2.0 Consensus size: 49
53856124 TCTCCAAAAA
53856134 CACATGTGTGATTTTGGTAAAAGGTTTATTGCTATAAATATCATAAATC
1 CACATGTGTGATTTTGGTAAAAGGTTTATTGCTATAAATATCATAAATC
53856183 CACATGTGTGATTTTGGTAAAAGGTTTATTGCTATAAATATCATAAATC
1 CACATGTGTGATTTTGGTAAAAGGTTTATTGCTATAAATATCATAAATC
53856232 AATTCAGTTT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.35, C:0.10, G:0.16, T:0.39
Consensus pattern (49 bp):
CACATGTGTGATTTTGGTAAAAGGTTTATTGCTATAAATATCATAAATC
Found at i:53859232 original size:14 final size:14
Alignment explanation
Indices: 53859209--53859243 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
53859199 AACTAAAAGG
53859209 TTAATTATGTT-AA
1 TTAATTATGTTAAA
53859222 TTAAGTTATGTTAAA
1 TTAA-TTATGTTAAA
53859237 TTAATTA
1 TTAATTA
53859244 ATCTAGGTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 4 0.20
14 10 0.50
15 6 0.30
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (14 bp):
TTAATTATGTTAAA
Found at i:53870607 original size:15 final size:17
Alignment explanation
Indices: 53870587--53870618 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
53870577 TTAAAATATT
53870587 CATATAT-TA-TAAAAA
1 CATATATCTATTAAAAA
53870602 CATATATCTATTAAAAA
1 CATATATCTATTAAAAA
53870619 AATGCATGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 2 0.13
17 6 0.40
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.34
Consensus pattern (17 bp):
CATATATCTATTAAAAA
Found at i:53873253 original size:19 final size:19
Alignment explanation
Indices: 53873222--53873460 Score: 83
Period size: 18 Copynumber: 12.8 Consensus size: 19
53873212 GATCCGATTA
53873222 AAACACGAG-ATTTTTTTT
1 AAACACGAGAATTTTTTTT
*
53873240 AAACACGAGAA--TTTTGT
1 AAACACGAGAATTTTTTTT
* * * *
53873257 -AACACTATAATAATTTTTG
1 AAACACGAGAAT-TTTTTTT
*
53873276 AAACACGAGAATTTTTTTG
1 AAACACGAGAATTTTTTTT
* *
53873295 AAA-AC-ATGAAATTTTTTG
1 AAACACGA-GAATTTTTTTT
* *
53873313 AAACAC-A-AGTTTTTTTGA
1 AAACACGAGAATTTTTTT-T
* *
53873331 AAACGCGAAAATTTTTTTT
1 AAACACGAGAATTTTTTTT
* * *
53873350 -TACATGAGAATTTTTTTGA
1 AAACACGAGAATTTTTTT-T
* * *
53873369 AAACACTA-AA-ATTTTTA
1 AAACACGAGAATTTTTTTT
* *
53873386 AAACACGA-ACA-ATTTTTG
1 AAACACGAGA-ATTTTTTTT
* *
53873404 AAAGCGCGA-ATTTTTTTTT
1 AAA-CACGAGAATTTTTTTT
*
53873423 AAAACACGAGATTTGTTTTTT
1 -AAACACGAGAATT-TTTTTT
*
53873444 GAAACACGAAAATTTTT
1 -AAACACGAGAATTTTT
53873461 GAAAAGAAGT
Statistics
Matches: 169, Mismatches: 34, Indels: 34
0.71 0.14 0.14
Matches are distributed among these distances:
16 8 0.05
17 22 0.13
18 57 0.34
19 34 0.20
20 31 0.18
21 17 0.10
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (19 bp):
AAACACGAGAATTTTTTTT
Found at i:53873308 original size:36 final size:37
Alignment explanation
Indices: 53873233--53873402 Score: 136
Period size: 36 Copynumber: 4.6 Consensus size: 37
53873223 AACACGAGAT
* * *
53873233 TTTTTTTAAACACGAGAA-TTTTGT-AACACTATAATAA
1 TTTTTTGAAACACGAGAATTTTTTTGAAAAC-ATAA-AA
*
53873270 -TTTTTGAAACACGAGAATTTTTTTGAAAACATGAAA
1 TTTTTTGAAACACGAGAATTTTTTTGAAAACATAAAA
* **
53873306 TTTTTTGAAACAC-A-AGTTTTTTTGAAAACGCGAAAA
1 TTTTTTGAAACACGAGAATTTTTTTGAAAAC-ATAAAA
*** *
53873342 TTTTTTTTTACATGAGAATTTTTTTGAAAACACTAAAA
1 TTTTTTGAAACACGAGAATTTTTTTGAAAACA-TAAAA
* *
53873380 -TTTTTAAAACACGAACAATTTTT
1 TTTTTTGAAACACG-AGAATTTTT
53873403 GAAAGCGCGA
Statistics
Matches: 105, Mismatches: 20, Indels: 15
0.75 0.14 0.11
Matches are distributed among these distances:
35 14 0.13
36 31 0.30
37 30 0.29
38 30 0.29
ACGTcount: A:0.39, C:0.10, G:0.10, T:0.41
Consensus pattern (37 bp):
TTTTTTGAAACACGAGAATTTTTTTGAAAACATAAAA
Found at i:53873346 original size:35 final size:37
Alignment explanation
Indices: 53873268--53873464 Score: 152
Period size: 38 Copynumber: 5.3 Consensus size: 37
53873258 ACACTATAAT
*
53873268 AATTTTTGAAACACGAGAATTTTTTTGAAAACATGAA
1 AATTTTTGAAACACGAGAATTTTTTTGAAAACACGAA
* * *
53873305 ATTTTTTGAAACAC-A-AGTTTTTTTGAAAACGCGAA
1 AATTTTTGAAACACGAGAATTTTTTTGAAAACACGAA
*** * *
53873340 AATTTTTTTTTACATGAGAATTTTTTTGAAAACACTAA
1 AA-TTTTTGAAACACGAGAATTTTTTTGAAAACACGAA
* * * *
53873378 AATTTTTAAAACACGA-ACA-ATTTTTGAAAGCGCGAA
1 AATTTTTGAAACACGAGA-ATTTTTTTGAAAACACGAA
** * *
53873414 TTTTTTTTTAAAACACGAGATTTGTTTTTTG-AAACACGAA
1 --AATTTTTGAAACACGAGA-AT-TTTTTTGAAAACACGAA
53873454 AATTTTTGAAA
1 AATTTTTGAAA
53873465 AGAAGTATCG
Statistics
Matches: 121, Mismatches: 30, Indels: 17
0.72 0.18 0.10
Matches are distributed among these distances:
35 18 0.15
36 23 0.19
37 25 0.21
38 41 0.34
39 1 0.01
40 7 0.06
41 6 0.05
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (37 bp):
AATTTTTGAAACACGAGAATTTTTTTGAAAACACGAA
Found at i:53873360 original size:73 final size:72
Alignment explanation
Indices: 53873282--53873423 Score: 189
Period size: 73 Copynumber: 2.0 Consensus size: 72
53873272 TTTGAAACAC
* * ***
53873282 GAGAATTTTTTTGAAAACA-TGAAATTTTTTGAAACAC-AAGTTTTTTTGAAAACGCGAAAATTT
1 GAGAATTTTTTTGAAAACACT-AAAATTTTTAAAACACGAACAATTTTTGAAAACGCG--AATTT
53873345 TTTTTTACAT
63 TTTTTTACAT
*
53873355 GAGAATTTTTTTGAAAACACTAAAATTTTTAAAACACGAACAATTTTTGAAAGCGCGAATTTTTT
1 GAGAATTTTTTTGAAAACACTAAAATTTTTAAAACACGAACAATTTTTGAAAACGCGAATTTTTT
53873420 TTTA
66 TTTA
53873424 AAACACGAGA
Statistics
Matches: 61, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
72 12 0.20
73 33 0.54
74 16 0.26
ACGTcount: A:0.38, C:0.09, G:0.12, T:0.41
Consensus pattern (72 bp):
GAGAATTTTTTTGAAAACACTAAAATTTTTAAAACACGAACAATTTTTGAAAACGCGAATTTTTT
TTTACAT
Found at i:53873441 original size:21 final size:20
Alignment explanation
Indices: 53873413--53873452 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
53873403 GAAAGCGCGA
53873413 ATTTTTTTTTAAAACACGAG
1 ATTTTTTTTTAAAACACGAG
*
53873433 ATTTGTTTTTTGAAACACGA
1 ATTT-TTTTTTAAAACACGA
53873453 AAATTTTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.33, C:0.10, G:0.12, T:0.45
Consensus pattern (20 bp):
ATTTTTTTTTAAAACACGAG
Found at i:53874200 original size:7 final size:7
Alignment explanation
Indices: 53874188--53874256 Score: 58
Period size: 7 Copynumber: 10.3 Consensus size: 7
53874178 GTGATATTAT
53874188 TTTTTTC
1 TTTTTTC
53874195 TTTTTTC
1 TTTTTTC
*
53874202 --TTCTC
1 TTTTTTC
53874207 -TTTTTC
1 TTTTTTC
53874213 TTTTTTC
1 TTTTTTC
*
53874220 -TTTCTC
1 TTTTTTC
53874226 -TTTTTC
1 TTTTTTC
*
53874232 TTCTTTC
1 TTTTTTC
53874239 TTTTTCTTC
1 -TTTT-TTC
53874248 TTTTTTC
1 TTTTTTC
53874255 TT
1 TT
53874257 CCTTTTTCTT
Statistics
Matches: 51, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
5 4 0.08
6 14 0.27
7 23 0.45
8 7 0.14
9 3 0.06
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (7 bp):
TTTTTTC
Found at i:53874205 original size:10 final size:10
Alignment explanation
Indices: 53874187--53874268 Score: 80
Period size: 10 Copynumber: 8.0 Consensus size: 10
53874177 TGTGATATTA
53874187 TTTTT-TTCT
1 TTTTTCTTCT
53874196 TTTTTCTTC-
1 TTTTTCTTCT
*
53874205 TCTTT-TTCT
1 TTTTTCTTCT
53874214 TTTTTCTTTCT
1 TTTTTC-TTCT
53874225 CTTTTTCTTCTTT
1 -TTTTTCTTC--T
53874238 CTTTTTCTTCT
1 -TTTTTCTTCT
*
53874249 TTTTTCTTCC
1 TTTTTCTTCT
53874259 TTTTTCTTCT
1 TTTTTCTTCT
53874269 CCTTCTTCTT
Statistics
Matches: 62, Mismatches: 4, Indels: 13
0.78 0.05 0.16
Matches are distributed among these distances:
8 3 0.05
9 13 0.21
10 21 0.34
11 8 0.13
12 6 0.10
13 11 0.18
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (10 bp):
TTTTTCTTCT
Found at i:53874217 original size:19 final size:18
Alignment explanation
Indices: 53874189--53874266 Score: 108
Period size: 19 Copynumber: 4.4 Consensus size: 18
53874179 TGATATTATT
53874189 TTTTTCTTTTTTCTTCTC
1 TTTTTCTTTTTTCTTCTC
53874207 TTTTTCTTTTTTCTTTCTC
1 TTTTTCTTTTTTC-TTCTC
*
53874226 TTTTTCTTCTTTCTT-T-
1 TTTTTCTTTTTTCTTCTC
*
53874242 TTCTTCTTTTTTCTTC-C
1 TTTTTCTTTTTTCTTCTC
53874259 TTTTTCTT
1 TTTTTCTT
53874267 CTCCTTCTTC
Statistics
Matches: 53, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
16 13 0.25
17 8 0.15
18 15 0.28
19 17 0.32
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTTTCTTTTTTCTTCTC
Found at i:53874221 original size:13 final size:13
Alignment explanation
Indices: 53874188--53874266 Score: 67
Period size: 13 Copynumber: 6.2 Consensus size: 13
53874178 GTGATATTAT
53874188 TTTTTTCTTTTT-
1 TTTTTTCTTTTTC
* *
53874200 TCTTCTCTTTTTC
1 TTTTTTCTTTTTC
*
53874213 TTTTTTCTTTCTC
1 TTTTTTCTTTTTC
53874226 -TTTTTCTTCTTTC
1 TTTTTTCTT-TTTC
53874239 -TTTTTCTTCTTT-
1 TTTTTTCTT-TTTC
*
53874251 TTTCTTCCTTTTTC
1 TTT-TTTCTTTTTC
53874265 TT
1 TT
53874267 CTCCTTCTTC
Statistics
Matches: 55, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
12 18 0.33
13 30 0.55
14 7 0.13
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (13 bp):
TTTTTTCTTTTTC
Found at i:53874268 original size:13 final size:13
Alignment explanation
Indices: 53874195--53874278 Score: 50
Period size: 13 Copynumber: 6.5 Consensus size: 13
53874185 TATTTTTTTC
53874195 TTTT-TTCTTCTCT
1 TTTTCTTCTTC-CT
* *
53874208 TTTTCTTTTTTCT
1 TTTTCTTCTTCCT
* *
53874221 TTCTCTT-TTTCT
1 TTTTCTTCTTCCT
*
53874233 TCTTTCTT-TTTCT
1 T-TTTCTTCTTCCT
*
53874246 TCTTTTTTCTTCCT
1 T-TTTCTTCTTCCT
53874260 TTTTCTTC-TCCT
1 TTTTCTTCTTCCT
*
53874272 TCTTCTT
1 TTTTCTT
53874279 TGGGCCGAAC
Statistics
Matches: 60, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
12 16 0.27
13 35 0.58
14 9 0.15
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (13 bp):
TTTTCTTCTTCCT
Found at i:53874930 original size:30 final size:31
Alignment explanation
Indices: 53874896--53874959 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 31
53874886 AAAATACTAG
*
53874896 GGGTCAAGATGAAAATTTGGGAAAAG-TTAA
1 GGGTCAAAATGAAAATTTGGGAAAAGTTTAA
* * **
53874926 GGGTCAAAATGTAATTTTTTGAAAAGTTTAA
1 GGGTCAAAATGAAAATTTGGGAAAAGTTTAA
53874957 GGG
1 GGG
53874960 CTAAACTGTA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
30 21 0.75
31 7 0.25
ACGTcount: A:0.39, C:0.03, G:0.28, T:0.30
Consensus pattern (31 bp):
GGGTCAAAATGAAAATTTGGGAAAAGTTTAA
Found at i:53875446 original size:75 final size:75
Alignment explanation
Indices: 53875342--53876222 Score: 977
Period size: 75 Copynumber: 11.7 Consensus size: 75
53875332 CCTAGCGTAC
* * * * *
53875342 GACCCGAGGCTCAACTCACCTCACGCATTATGAGTTGATTCTTGAAAAACAAG-ACTTGAAAATA
1 GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAA-AAGAAATTAAAAATA
*
53875406 CCTCGGCATGC
65 CCTCGGCATGT
* * * * * * * *
53875417 GGCCCAAGGCTCAACTCACCTCT-GACATTATGAGTTGATATTTGGAAAACAGAAAATAAAGATA
1 GACCCGAGGCTCAACTCACCTCTCG-CAATATGAGTTGATTTTTGAAAAAAAGAAATTAAAAATA
*
53875481 CCTTGGCA--T
65 CCTCGGCATGT
* * * *
53875490 GATCC-AGGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTTGAAAAATAGAAATTGAAAA
1 GACCCGA-GGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAAAAAGAAATTAAAAA
*
53875554 TACCTCAGC--GT
63 TACCTCGGCATGT
* * * *
53875565 GACCCGAGGCTCAACTCGCTTCTCGCAATATGAGTTGATTTTTGAAAAATAGAAATTAAAGATAC
1 GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAAAGAAATTAAAAATAC
*
53875630 CTCGGTATGT
66 CTCGGCATGT
* ** *
53875640 GACCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTTGAAAAGCAGAAATTAAAGATAC
1 GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAAAGAAATTAAAAATAC
*
53875705 CTCGGTATGT
66 CTCGGCATGT
** *
53875715 GACCTAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTGAAAAATAGAAATTAAAA
1 GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA----TTTTTGAAAAAAAGAAATT-AAA
*
53875780 AATACCTCGGCGTGT
61 AATACCTCGGCATGT
* * *
53875795 GACCCGAGGCTCAACCCACCTCTGGCAATATGAGTTGATTTTTGAAAAATAGAAATTTAAAAGAA
1 GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAAAGAAA-TT--AA-AA
*
53875860 ATACCTCGACATGT
62 ATACCTCGGCATGT
* *
53875874 G-TCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTT----AAAA-AAATTGAAAATAC
1 GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAAAGAAATTAAAAATAC
* *
53875932 CTCAGCGTGT
66 CTCGGCATGT
* *
53875942 GACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTTGAAAAACAGAAATTAAAAAA
1 GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAAAAAGAAATT-AAAAA
*
53876007 TACCTCGGCGTGT
63 TACCTCGGCATGT
* *
53876020 GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTGTTTTTGAAAAAAATAAA--AGAAA
1 GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA---TTTTTGAAAAAAAGAAATTAAAAA
53876083 TACCTCGGCATGT
63 TACCTCGGCATGT
* * *
53876096 G-TCCGAGGCTCAACTCACCTCTCGCAATATGAGTCGATTTTTGAAAAACAAGAATTTAAAAAAT
1 GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAA-AAGAAATT-AAAAAT
* *
53876160 ACCTCGGTATAT
64 ACCTCGGCATGT
53876172 GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAAA
1 GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAAA
53876223 AACAGAAATT
Statistics
Matches: 694, Mismatches: 78, Indels: 67
0.83 0.09 0.08
Matches are distributed among these distances:
68 14 0.02
69 35 0.05
71 2 0.00
72 19 0.03
73 68 0.10
74 4 0.01
75 254 0.37
76 56 0.08
77 56 0.08
78 89 0.13
79 48 0.07
80 49 0.07
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (75 bp):
GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAAAGAAATTAAAAATAC
CTCGGCATGT
Found at i:53875619 original size:148 final size:149
Alignment explanation
Indices: 53875344--53876220 Score: 900
Period size: 148 Copynumber: 5.8 Consensus size: 149
53875334 TAGCGTACGA
* * * * *
53875344 CCCGAGGCTCAACTCACCTCACGCATTATGAGTTGATTCTTGAAAAACA-AGACTT-GAAAATAC
1 CCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGA-AATTAAAAAATAC
* * * * * * *
53875407 CTCGG-CATGCGGCCCAAGGCTCAACTCACCTCT-GACATTATGAGTTGATATTTGGAAAACAGA
65 CTCGGAC-TGTGACCCGAGGCTCAACTCACCTCTCG-CAATATGAGTTGATTTTTGAAAAATAGA
*
53875470 AAATAAAGATACCTTGGCATGAT
128 AAATAAAGATACCTCGGCATG-T
* * * *
53875493 CCAG-GGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTTGAAAAATAGAAATT-GAAAATA
1 CCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAAACAGAAATTAAAAAATA
* * *
53875556 CCTCAG-C-GTGACCCGAGGCTCAACTCGCTTCTCGCAATATGAGTTGATTTTTGAAAAATAGAA
64 CCTCGGACTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAGAA
* *
53875619 ATTAAAGATACCTCGGTATGT
129 AATAAAGATACCTCGGCATGT
* * *
53875640 GACCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTTGAAAAGCAGAAATT-AAAGATA
1 --CCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAAATA
**
53875704 CCTCGGTA-TGTGACCTAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTGAAAAA
64 CCTCGG-ACTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA----TTTTTGAAAAA
* * *
53875768 TAGAAATTAAAAAATACCTCGGCGTGT
124 TAGAAAAT-AAAGATACCTCGGCATGT
* * *
53875795 GACCCGAGGCTCAACCCACCTCTGGCAATATGAGTTGATTTTTGAAAAATAGAAATTTAAAAGAA
1 --CCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAA-TT-AAA-AA
*
53875860 ATACCTC-GACATGTG-TCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTT---AAA-
61 ATACCTCGGAC-TGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAT
* * *
53875918 A-AAATTGAAA-ATACCTCAGCGTGT
125 AGAAAAT-AAAGATACCTCGGCATGT
*
53875942 GACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTTGAAAAACAGAAATTAAAAAA
1 --CCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAAACAGAAATTAAAAAA
53876007 TACCTCGG-CGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTGTTTTTGAAAA
62 TACCTCGGAC-TGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA---TTTTTGAAAA
* * *
53876071 AAATAAAA-GAA-ATACCTCGGCATGT
123 ATAGAAAATAAAGATACCTCGGCATGT
* * *
53876096 GTCCGAGGCTCAACTCACCTCTCGCAATATGAGTCGATTTTTGAAAAACAAGAATTTAAAAAATA
1 -CCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAC-AGAAATTAAAAAATA
*
53876161 CCTCGGTA-TATGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAA
64 CCTCGG-ACTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAA
53876221 AAAACAGAAA
Statistics
Matches: 632, Mismatches: 59, Indels: 74
0.83 0.08 0.10
Matches are distributed among these distances:
146 14 0.02
147 88 0.14
148 129 0.20
149 35 0.06
150 95 0.15
151 17 0.03
152 60 0.09
153 37 0.06
154 36 0.06
155 67 0.11
156 5 0.01
157 1 0.00
158 36 0.06
159 12 0.02
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.27
Consensus pattern (149 bp):
CCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAAATACC
TCGGACTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAGAAAA
TAAAGATACCTCGGCATGT
Found at i:53875849 original size:230 final size:227
Alignment explanation
Indices: 53875342--53876214 Score: 1078
Period size: 223 Copynumber: 3.8 Consensus size: 227
53875332 CCTAGCGTAC
* * * * * *
53875342 GACCCGAGGCTCAACTCACCTCACGCATTATGAGTTGATTCTTGAAAAACA-AGACTTGAAAATA
1 GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAGA-AATTAAAAATA
* * * *
53875406 CCTCGGCATGCGGCCCAAGGCTCAACTCACCTCT-GACATTATGAGTTGATATTTGGAAAACAGA
65 CCTCGGCATG-TGCCCGAGGCTCAACTCACCTCTCG-CAATATGAGTTGAT-TTTTGAAAACAGA
* * * * *
53875470 AAAT-AAAGATACCTTGGCA--TGATCCAGGGCTCAACTCACCTCTCGCATTATGAGTTGATTTT
127 AATTAAAAGATACCTCGGCATGTGACCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
* *
53875532 TTTGAAAAATAGAAATT-GAAAATACCTCAGC--GT
192 TTTGAAAAATAGAAATTAAAAAATACCTCGGCGTGT
* * *
53875565 GACCCGAGGCTCAACTCGCTTCTCGCAATATGAGTTGATTTTTGAAAAATAGAAATTAAAGATAC
1 GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAGAAATTAAAAATAC
* *
53875630 CTCGGTATGTGACCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTTGAAAAGCAGAAA
66 CTCGGCATGTG-CCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAA-CAGAAA
* *
53875695 TT-AAAGATACCTCGGTATGTGACCTAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
129 TTAAAAGATACCTCGGCATGTGACCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTT
53875759 TTTGAAAAATAGAAATTAAAAAATACCTCGGCGTGT
192 TTTGAAAAATAGAAATTAAAAAATACCTCGGCGTGT
* *
53875795 GACCCGAGGCTCAACCCACCTCTGGCAATATGAGTTGATTTTTGAAAAATAGAAATTTAAAAGAA
1 GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAGAAA-TT--AA-AA
* *
53875860 ATACCTCGACATGTGTCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTT--AAA-A-A
62 ATACCTCGGCATGTGCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGA
* * * * *
53875920 AATTGAAA-ATACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTT
127 AATTAAAAGATACCTCGGCATGTGACCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
*
53875984 TTTGAAAAACAGAAATTAAAAAATACCTCGGCGTGT
192 TTTGAAAAATAGAAATTAAAAAATACCTCGGCGTGT
* * *
53876020 GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTGTTTTTGAAAAAAATAAA--AGAAA
1 GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA---TTTTTGAAAAATAGAAATTAAAAA
* *
53876083 TACCTCGGCATGTGTCCGAGGCTCAACTCACCTCTCGCAATATGAGTCGATTTTTGAAAAACAAG
63 TACCTCGGCATGTGCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG-AAAAC-AG
* * * * *
53876148 AATTTAAAAAATACCTCGGTATATGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
126 AAATTAAAAGATACCTCGGCATGTGACCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
53876213 TT
191 TT
53876215 GAAAAAAAAA
Statistics
Matches: 570, Mismatches: 53, Indels: 47
0.85 0.08 0.07
Matches are distributed among these distances:
222 60 0.11
223 120 0.21
224 2 0.00
225 110 0.19
226 3 0.01
227 72 0.13
228 32 0.06
229 7 0.01
230 108 0.19
231 2 0.00
232 4 0.01
233 36 0.06
234 14 0.02
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.27
Consensus pattern (227 bp):
GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAGAAATTAAAAATAC
CTCGGCATGTGCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATT
AAAAGATACCTCGGCATGTGACCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTG
AAAAATAGAAATTAAAAAATACCTCGGCGTGT
Found at i:53877154 original size:6 final size:7
Alignment explanation
Indices: 53877137--53877162 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
53877127 TCCTAATCTT
53877137 TTTTTTG
1 TTTTTTG
53877144 TTTTTTG
1 TTTTTTG
53877151 TTTTTTG
1 TTTTTTG
53877158 TTTTT
1 TTTTT
53877163 AGGCATAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (7 bp):
TTTTTTG
Found at i:53888031 original size:24 final size:23
Alignment explanation
Indices: 53887980--53888033 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 23
53887970 CTTTAAATCA
* *
53887980 ATATACTAAATTAGTATATTACT
1 ATATACTAAAATAGTATATTAAT
53888003 A-ATACATAAAATAGTA-ATATAAT
1 ATATAC-TAAAATAGTATAT-TAAT
53888026 ATATACTA
1 ATATACTA
53888034 GGATTATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
22 6 0.23
23 16 0.62
24 4 0.15
ACGTcount: A:0.52, C:0.07, G:0.04, T:0.37
Consensus pattern (23 bp):
ATATACTAAAATAGTATATTAAT
Found at i:53888508 original size:16 final size:17
Alignment explanation
Indices: 53888489--53888521 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
53888479 TATATAATGT
53888489 ACTACTATTAT-ATATA
1 ACTACTATTATAATATA
*
53888505 ACTATTATTATAATATA
1 ACTACTATTATAATATA
53888522 TATATAAGGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.45, C:0.09, G:0.00, T:0.45
Consensus pattern (17 bp):
ACTACTATTATAATATA
Found at i:53889183 original size:9 final size:9
Alignment explanation
Indices: 53889159--53889195 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
53889149 TAAGTTTTCA
*
53889159 AATTCAAAT
1 AATTCGAAT
*
53889168 AACTCGAAT
1 AATTCGAAT
53889177 AATTCGAAT
1 AATTCGAAT
53889186 AATTCGAAT
1 AATTCGAAT
53889195 A
1 A
53889196 TCAAACTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.49, C:0.14, G:0.08, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:53889272 original size:21 final size:21
Alignment explanation
Indices: 53889231--53889273 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
53889221 ACCCCAAACT
* *
53889231 CTCAAACCTTTTTACTTTTCC
1 CTCAAAACTTTTTACTCTTCC
53889252 CTCAAAAC-TTTTACTCCTTCC
1 CTCAAAACTTTTTACT-CTTCC
53889273 C
1 C
53889274 ACTTTCCCCC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.21, C:0.37, G:0.00, T:0.42
Consensus pattern (21 bp):
CTCAAAACTTTTTACTCTTCC
Found at i:53889280 original size:29 final size:31
Alignment explanation
Indices: 53889244--53889304 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 31
53889234 AAACCTTTTT
* *
53889244 ACTTTTCCCTCAAAACTTTTACTCCT-TCCC
1 ACTTTCCCCCCAAAACTTTTACTCCTCTCCC
53889274 ACTTTCCCCCCAAAACTTTTACTCCTCTCCC
1 ACTTTCCCCCCAAAACTTTTACTCCTCTCCC
53889305 CTCCCAACCC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
30 24 0.86
31 4 0.14
ACGTcount: A:0.20, C:0.44, G:0.00, T:0.36
Consensus pattern (31 bp):
ACTTTCCCCCCAAAACTTTTACTCCTCTCCC
Found at i:53891220 original size:100 final size:100
Alignment explanation
Indices: 53891069--53891249 Score: 231
Period size: 100 Copynumber: 1.8 Consensus size: 100
53891059 TTCGGTGCCA
* * * *
53891069 CCACTTCACATGGAGTCACCAAAAACAGTAAAAAAAAAATCATAATGCCTAC-TCTAGATGTGGC
1 CCACTTCAAATGGAGTCACCAAAAACAATAAAAAAAAAATCATAATCCCTACTTC-AGATATGGC
*
53891133 GGCACCAGTAATTTTTTTTAAAGTTTTTTGGTGTTG
65 GGCACCAGTAAATTTTTTTAAAGTTTTTTGGTGTTG
* ** * * *
53891169 CCACTTCAAATGGAGTCACTAAAAACAAT-AAAAAAATTTCCCTAGTCCCTACTTCAGATATGGT
1 CCACTTCAAATGGAGTCACCAAAAACAATAAAAAAAAAAT-CATAATCCCTACTTCAGATATGGC
53891233 GGCACCAGTAAATTTTT
65 GGCACCAGTAAATTTTT
53891250 AAAAAAATTT
Statistics
Matches: 68, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
99 8 0.12
100 58 0.85
101 2 0.03
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.30
Consensus pattern (100 bp):
CCACTTCAAATGGAGTCACCAAAAACAATAAAAAAAAAATCATAATCCCTACTTCAGATATGGCG
GCACCAGTAAATTTTTTTAAAGTTTTTTGGTGTTG
Found at i:53893620 original size:13 final size:14
Alignment explanation
Indices: 53893604--53893645 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
53893594 TTTCAATTTT
53893604 ATTTTAATAATA-A
1 ATTTTAATAATATA
*
53893617 ATTTTAAAAATAATA
1 ATTTTAATAAT-ATA
53893632 ATTTTAAATAATAT
1 ATTTT-AATAATAT
53893646 TCTTCACGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 8 0.33
16 5 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTTTAATAATATA
Found at i:53893630 original size:16 final size:16
Alignment explanation
Indices: 53893608--53893644 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
53893598 AATTTTATTT
53893608 TAATAATAAATTTTAAA
1 TAATAAT-AATTTTAAA
53893625 -AATAATAATTTTAAA
1 TAATAATAATTTTAAA
53893640 TAATA
1 TAATA
53893645 TTCTTCACGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATAATTTTAAA
Found at i:53895742 original size:15 final size:15
Alignment explanation
Indices: 53895718--53895747 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
53895708 ATAGTTATAG
*
53895718 TAACATTAATAATAA
1 TAACAGTAATAATAA
53895733 TAACAGTAATAATAA
1 TAACAGTAATAATAA
53895748 AAATAGTTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.60, C:0.07, G:0.03, T:0.30
Consensus pattern (15 bp):
TAACAGTAATAATAA
Found at i:53897377 original size:31 final size:31
Alignment explanation
Indices: 53897316--53897382 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 31
53897306 TCGTGACCTT
* ** *
53897316 GTAACCACTGCCAATAGGAACTATTGACCGC
1 GTAACCACTACCAATAAAAACTATTAACCGC
*
53897347 GTAACCACTACCAATAAAAACTCTTAACCGC
1 GTAACCACTACCAATAAAAACTATTAACCGC
53897378 GTAAC
1 GTAAC
53897383 TAATACCTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.37, C:0.30, G:0.13, T:0.19
Consensus pattern (31 bp):
GTAACCACTACCAATAAAAACTATTAACCGC
Found at i:53898776 original size:5 final size:5
Alignment explanation
Indices: 53898766--53898820 Score: 83
Period size: 5 Copynumber: 11.0 Consensus size: 5
53898756 AACTATTAAT
* * *
53898766 ATATG ATATG ATATG ATATG ATATG ATATG ATATA ATATA ATATA ATATG
1 ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG
53898816 ATATG
1 ATATG
53898821 TGTTAGAGTT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 48 1.00
ACGTcount: A:0.45, C:0.00, G:0.15, T:0.40
Consensus pattern (5 bp):
ATATG
Found at i:53898930 original size:24 final size:24
Alignment explanation
Indices: 53898898--53898949 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
53898888 TTTCCAGAAG
*
53898898 ATTTAGCATTTATGAGTATAATAT
1 ATTTAGCATTTATGAGAATAATAT
*
53898922 ATTTAGCATTTATTAGAATAATAT
1 ATTTAGCATTTATGAGAATAATAT
53898946 ATTT
1 ATTT
53898950 GACTTTGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.38, C:0.04, G:0.10, T:0.48
Consensus pattern (24 bp):
ATTTAGCATTTATGAGAATAATAT
Found at i:53903276 original size:24 final size:24
Alignment explanation
Indices: 53903242--53903294 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
53903232 TTTCTAGAAA
* *
53903242 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATGAGCATAATAT
*
53903266 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGCATTTATGAGCATAATAT
53903290 ATTTA
1 ATTTA
53903295 ACTTTGATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.38, C:0.04, G:0.09, T:0.49
Consensus pattern (24 bp):
ATTTAGCATTTATGAGCATAATAT
Found at i:53903304 original size:24 final size:24
Alignment explanation
Indices: 53903249--53903305 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
53903239 AAAATTTAGT
* * *
53903249 ATTTATGAGTATAATATATTTAGC
1 ATTTATTAGCATAATATATTTAAC
53903273 ATTTATTAGCATAATATATTTAAC
1 ATTTATTAGCATAATATATTTAAC
53903297 -TTTGATTAG
1 ATTT-ATTAG
53903306 ATTTAGGTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 3 0.10
24 26 0.90
ACGTcount: A:0.37, C:0.05, G:0.11, T:0.47
Consensus pattern (24 bp):
ATTTATTAGCATAATATATTTAAC
Found at i:53903648 original size:17 final size:18
Alignment explanation
Indices: 53903626--53903672 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
53903616 TCATTGATGC
53903626 ATATATATAAACTAT-TA
1 ATATATATAAACTATCTA
* *
53903643 ATATATTATATACTATCTG
1 ATATA-TATAAACTATCTA
53903662 ATATGATATAA
1 ATAT-ATATAA
53903673 CATTATAGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
17 5 0.21
18 9 0.38
19 9 0.38
20 1 0.04
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (18 bp):
ATATATATAAACTATCTA
Found at i:53905806 original size:18 final size:18
Alignment explanation
Indices: 53905775--53905822 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
53905765 TGTCGTTCGT
*
53905775 TTTCAAAACATTATTC-A
1 TTTCAAAACGTTATTCAA
*
53905792 TTTACAAATCGTTATTCAA
1 TTT-CAAAACGTTATTCAA
53905811 TTTCAAAACGTT
1 TTTCAAAACGTT
53905823 TTCTTATTGC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 3 0.12
18 19 0.73
19 4 0.15
ACGTcount: A:0.38, C:0.17, G:0.04, T:0.42
Consensus pattern (18 bp):
TTTCAAAACGTTATTCAA
Found at i:53909058 original size:6 final size:6
Alignment explanation
Indices: 53909047--53909078 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
53909037 AATAAAGTGC
53909047 ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA AT
1 ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA AT
53909079 GAATGTAGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (6 bp):
ATTAAA
Found at i:53910411 original size:13 final size:14
Alignment explanation
Indices: 53910393--53910421 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
53910383 TTACTTTTTG
53910393 TTCAAGCCTAT-TT
1 TTCAAGCCTATATT
53910406 TTCAAGCCTATATT
1 TTCAAGCCTATATT
53910420 TT
1 TT
53910422 TACCCAAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.24, C:0.21, G:0.07, T:0.48
Consensus pattern (14 bp):
TTCAAGCCTATATT
Found at i:53920668 original size:26 final size:25
Alignment explanation
Indices: 53920626--53920701 Score: 73
Period size: 26 Copynumber: 3.0 Consensus size: 25
53920616 CTCATCCTAA
* * *
53920626 ATTTT-ACCTCTAGTAAAACTTTGATG
1 ATTTTAACC-CTAATAAAATTTTGA-C
*
53920652 ATTTTAACCCTGATAAAATTTTTGAC
1 ATTTTAACCCTAATAAAA-TTTTGAC
*
53920678 ATTTTACCCCTAATAAAATTTTGA
1 ATTTTAACCCTAATAAAATTTTGA
53920702 GAAAATATTT
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
25 6 0.14
26 28 0.67
27 8 0.19
ACGTcount: A:0.34, C:0.16, G:0.08, T:0.42
Consensus pattern (25 bp):
ATTTTAACCCTAATAAAATTTTGAC
Found at i:53923403 original size:34 final size:34
Alignment explanation
Indices: 53923363--53923448 Score: 163
Period size: 34 Copynumber: 2.5 Consensus size: 34
53923353 ATTTAATTAA
*
53923363 ATAATATATTAATAATAATTAAATTAGTTATTTT
1 ATAATATTTTAATAATAATTAAATTAGTTATTTT
53923397 ATAATATTTTAATAATAATTAAATTAGTTATTTT
1 ATAATATTTTAATAATAATTAAATTAGTTATTTT
53923431 ATAATATTTTAATAATAA
1 ATAATATTTTAATAATAA
53923449 AATGATAATA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 51 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (34 bp):
ATAATATTTTAATAATAATTAAATTAGTTATTTT
Found at i:53923413 original size:11 final size:11
Alignment explanation
Indices: 53923362--53923447 Score: 59
Period size: 11 Copynumber: 7.6 Consensus size: 11
53923352 TATTTAATTA
*
53923362 AATAATATATT
1 AATAATATTTT
* *
53923373 AATAATAATTA
1 AATAATATTTT
*
53923384 AATTAGTTATTTT
1 AA-TA-ATATTTT
53923397 -ATAATATTTT
1 AATAATATTTT
* *
53923407 AATAATAATTA
1 AATAATATTTT
*
53923418 AATTAGTTATTTT
1 AA-TA-ATATTTT
53923431 -ATAATATTTT
1 AATAATATTTT
53923441 AATAATA
1 AATAATA
53923448 AAATGATAAT
Statistics
Matches: 56, Mismatches: 13, Indels: 12
0.69 0.16 0.15
Matches are distributed among these distances:
10 12 0.21
11 30 0.54
12 6 0.11
13 8 0.14
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (11 bp):
AATAATATTTT
Found at i:53925132 original size:17 final size:18
Alignment explanation
Indices: 53925112--53925146 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
53925102 TAATTGAGTA
*
53925112 AAAGGATTAAA-TTGAAT
1 AAAGGATAAAAGTTGAAT
53925129 AAAGGATAAAAGTTGAAT
1 AAAGGATAAAAGTTGAAT
53925147 TATAGATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.54, C:0.00, G:0.20, T:0.26
Consensus pattern (18 bp):
AAAGGATAAAAGTTGAAT
Found at i:53925807 original size:9 final size:9
Alignment explanation
Indices: 53925793--53925830 Score: 60
Period size: 9 Copynumber: 4.3 Consensus size: 9
53925783 AACAGGGAGA
53925793 AAAGAAAGG
1 AAAGAAAGG
*
53925802 AAAGAAAGA
1 AAAGAAAGG
53925811 AAAGAAA-G
1 AAAGAAAGG
53925819 AAAGAAAGG
1 AAAGAAAGG
53925828 AAA
1 AAA
53925831 AATTAGGGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
8 7 0.27
9 19 0.73
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (9 bp):
AAAGAAAGG
Found at i:53925808 original size:4 final size:4
Alignment explanation
Indices: 53925793--53925826 Score: 50
Period size: 4 Copynumber: 8.0 Consensus size: 4
53925783 AACAGGGAGA
53925793 AAAG AAAGG AAAG AAAG AAAAG AAAG AAAG AAAG
1 AAAG AAA-G AAAG AAAG -AAAG AAAG AAAG AAAG
53925827 GAAAAATTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 20 0.71
5 8 0.29
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:53925811 original size:13 final size:13
Alignment explanation
Indices: 53925793--53925830 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
53925783 AACAGGGAGA
53925793 AAAGAAAGGAAAG
1 AAAGAAAGGAAAG
*
53925806 AAAGAAAAGAAAG
1 AAAGAAAGGAAAG
53925819 AAAGAAAGGAAA
1 AAAGAAAGGAAA
53925831 AATTAGGGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (13 bp):
AAAGAAAGGAAAG
Found at i:53926221 original size:17 final size:18
Alignment explanation
Indices: 53926199--53926232 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
53926189 TAAATGAGTT
53926199 AATTAGGAT-TAAATTGG
1 AATTAGGATATAAATTGG
*
53926216 AATTAGGGTATAAATTG
1 AATTAGGATATAAATTG
53926233 AAAAGAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.41, C:0.00, G:0.24, T:0.35
Consensus pattern (18 bp):
AATTAGGATATAAATTGG
Found at i:53926644 original size:13 final size:13
Alignment explanation
Indices: 53926626--53926651 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
53926616 TATTTGCTAT
53926626 CTGCTTCACCTCC
1 CTGCTTCACCTCC
53926639 CTGCTTCACCTCC
1 CTGCTTCACCTCC
53926652 AACTTGGTCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.08, C:0.54, G:0.08, T:0.31
Consensus pattern (13 bp):
CTGCTTCACCTCC
Found at i:53927191 original size:5 final size:4
Alignment explanation
Indices: 53927155--53927188 Score: 50
Period size: 4 Copynumber: 8.0 Consensus size: 4
53927145 CTAGTTTTTC
53927155 CTTT CTTT CTTT CTTT CTTT CCTTT CCTTT CTTT
1 CTTT CTTT CTTT CTTT CTTT -CTTT -CTTT CTTT
53927189 TCTACTTGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 20 0.69
5 9 0.31
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (4 bp):
CTTT
Found at i:53927908 original size:17 final size:17
Alignment explanation
Indices: 53927886--53927919 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
53927876 TTAATCTATA
53927886 ATTCAACTTT-ATCCTTT
1 ATTCAA-TTTAATCCTTT
53927903 ATTCAATTTAATCCTTT
1 ATTCAATTTAATCCTTT
53927920 TACGCAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 3 0.19
17 13 0.81
ACGTcount: A:0.26, C:0.21, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTCAATTTAATCCTTT
Found at i:53929318 original size:17 final size:17
Alignment explanation
Indices: 53929298--53929331 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
53929288 TTTATATATT
*
53929298 TTTAGATTTTTTTAAAA
1 TTTAGAATTTTTTAAAA
*
53929315 TTTATAATTTTTTAAAA
1 TTTAGAATTTTTTAAAA
53929332 ATATAAATTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (17 bp):
TTTAGAATTTTTTAAAA
Found at i:53929336 original size:16 final size:18
Alignment explanation
Indices: 53929305--53929342 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
53929295 ATTTTTAGAT
*
53929305 TTTTTTAAAATTTAT-AA
1 TTTTTTAAAATATATAAA
53929322 TTTTTTAAAA-ATATAAA
1 TTTTTTAAAATATATAAA
53929339 TTTT
1 TTTT
53929343 AGAATTTCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 3 0.16
17 16 0.84
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TTTTTTAAAATATATAAA
Found at i:53929340 original size:17 final size:18
Alignment explanation
Indices: 53929303--53929342 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
53929293 ATATTTTTAG
* *
53929303 ATTTTTTTAAAATTTATA
1 ATTTTTTAAAAATATATA
53929321 ATTTTTTAAAAATATA-A
1 ATTTTTTAAAAATATATA
53929338 ATTTT
1 ATTTT
53929343 AGAATTTCTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
ATTTTTTAAAAATATATA
Found at i:53929382 original size:20 final size:19
Alignment explanation
Indices: 53929359--53929403 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
53929349 TCTATAAATA
*
53929359 TTTTAAATCTTAAAAATTAT
1 TTTTAAAT-TTAAAAATTAC
*
53929379 TTTTAAAATTTGAAAATTAC
1 TTTT-AAATTTAAAAATTAC
53929399 TTTTA
1 TTTTA
53929404 TTTTTTTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 1 0.05
20 17 0.77
21 4 0.18
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.51
Consensus pattern (19 bp):
TTTTAAATTTAAAAATTAC
Found at i:53950790 original size:3 final size:3
Alignment explanation
Indices: 53950782--53950811 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
53950772 GCTATGATTT
*
53950782 TTA TTA TTA TTA CTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
53950812 CTACCACTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:53957136 original size:15 final size:15
Alignment explanation
Indices: 53957110--53957145 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
53957100 AACAAGAAAA
*
53957110 AATAAATTTCAATAT
1 AATAAATGTCAATAT
*
53957125 AGTAAATGTCAATAT
1 AATAAATGTCAATAT
53957140 AATAAA
1 AATAAA
53957146 AAATAAAATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.56, C:0.06, G:0.06, T:0.33
Consensus pattern (15 bp):
AATAAATGTCAATAT
Found at i:53963393 original size:75 final size:75
Alignment explanation
Indices: 53963303--53963467 Score: 312
Period size: 75 Copynumber: 2.2 Consensus size: 75
53963293 TTTTCTGCTT
*
53963303 CTTTCATGCATGCTGGTTCACGGGTCCATTATTTCTTTGCTCTGCTACATGCAAACAAAACACTA
1 CTTTCATGCATGCTGGTTCAAGGGTCCATTATTTCTTTGCTCTGCTACATGCAAACAAAACACTA
53963368 CATTTTCCTG
66 CATTTTCCTG
*
53963378 CTTTCATGCATGCTGGTTCAAGGGTTCATTATTTCTTTGCTCTGCTACATGCAAACAAAACACTA
1 CTTTCATGCATGCTGGTTCAAGGGTCCATTATTTCTTTGCTCTGCTACATGCAAACAAAACACTA
53963443 CATTTTCCTG
66 CATTTTCCTG
53963453 CTTTCATGCATGCTG
1 CTTTCATGCATGCTG
53963468 CCACGGGTTC
Statistics
Matches: 88, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
75 88 1.00
ACGTcount: A:0.22, C:0.25, G:0.15, T:0.37
Consensus pattern (75 bp):
CTTTCATGCATGCTGGTTCAAGGGTCCATTATTTCTTTGCTCTGCTACATGCAAACAAAACACTA
CATTTTCCTG
Found at i:53967801 original size:16 final size:16
Alignment explanation
Indices: 53967780--53967811 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
53967770 AAATGTCAAT
53967780 TTGAAAATGTTAAAAA
1 TTGAAAATGTTAAAAA
53967796 TTGAAAATGTTAAAAA
1 TTGAAAATGTTAAAAA
53967812 AAATAAGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.12, T:0.31
Consensus pattern (16 bp):
TTGAAAATGTTAAAAA
Found at i:53968154 original size:16 final size:16
Alignment explanation
Indices: 53968133--53968173 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
53968123 ATATTTGATA
53968133 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
53968149 TAATTTCAATAACAAT
1 TAATTTTAATAACAAT
*
53968165 TAGTTTTAA
1 TAATTTTAA
53968174 GTAAAAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.44
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:53969067 original size:42 final size:43
Alignment explanation
Indices: 53969008--53969175 Score: 223
Period size: 43 Copynumber: 4.0 Consensus size: 43
53968998 TAAGCGCTGT
* * *
53969008 TATAGATCATGACCTTTAGCGGCGCTTTT-GCATAAACGCCGC
1 TATAGATCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCGC
*
53969050 TATAGGTCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCGC
1 TATAGATCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCGC
* *
53969093 TATAGCTCGAGACCTTTAGCGGCGCTTTTCCCACAAACGCCGC
1 TATAGATCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCGC
* * * * *
53969136 TATAGAACAA-ACCTTTAGCGACGCTTCTCGCAAAAACGCC
1 TATAGATCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCC
53969176 ACTAAAAACA
Statistics
Matches: 112, Mismatches: 13, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
42 53 0.47
43 59 0.53
ACGTcount: A:0.26, C:0.31, G:0.20, T:0.24
Consensus pattern (43 bp):
TATAGATCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCGC
Found at i:53969120 original size:85 final size:85
Alignment explanation
Indices: 53969018--53969175 Score: 228
Period size: 85 Copynumber: 1.9 Consensus size: 85
53969008 TATAGATCAT
* * ** * *
53969018 GACCTTTAGCGGCGCTTTT-GCATAAACGCCGCTATAGGTCAAGACCTTTAGCGGCGCTTTTCCC
1 GACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGAACAA-ACCTTTAGCGACGCTTCTCCC
*
53969082 ACAAACGCCGCTATAGCTCGA
65 AAAAACGCCGCTATAGCTCGA
*
53969103 GACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGAACAAACCTTTAGCGACGCTTCTCGCA
1 GACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGAACAAACCTTTAGCGACGCTTCTCCCA
53969168 AAAACGCC
66 AAAACGCC
53969176 ACTAAAAACA
Statistics
Matches: 64, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
85 45 0.70
86 19 0.30
ACGTcount: A:0.25, C:0.32, G:0.20, T:0.23
Consensus pattern (85 bp):
GACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGAACAAACCTTTAGCGACGCTTCTCCCA
AAAACGCCGCTATAGCTCGA
Found at i:53971319 original size:25 final size:25
Alignment explanation
Indices: 53971291--53971362 Score: 144
Period size: 25 Copynumber: 2.9 Consensus size: 25
53971281 GGAGTTTAGC
53971291 GTGCTCTCTGATTACTAGCACGTCA
1 GTGCTCTCTGATTACTAGCACGTCA
53971316 GTGCTCTCTGATTACTAGCACGTCA
1 GTGCTCTCTGATTACTAGCACGTCA
53971341 GTGCTCTCTGATTACTAGCACG
1 GTGCTCTCTGATTACTAGCACG
53971363 CTCTCTGTTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 47 1.00
ACGTcount: A:0.19, C:0.28, G:0.21, T:0.32
Consensus pattern (25 bp):
GTGCTCTCTGATTACTAGCACGTCA
Found at i:53971390 original size:22 final size:22
Alignment explanation
Indices: 53971362--53971417 Score: 85
Period size: 22 Copynumber: 2.5 Consensus size: 22
53971352 TTACTAGCAC
*
53971362 GCTCTCTGTTTAGCACATTCGT
1 GCTCTCTGTTTAGCACATTAGT
* *
53971384 GCTCTCTGTATAGCACTTTAGT
1 GCTCTCTGTTTAGCACATTAGT
53971406 GCTCTCTGTTTA
1 GCTCTCTGTTTA
53971418 ATAGTGCATA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.14, C:0.25, G:0.18, T:0.43
Consensus pattern (22 bp):
GCTCTCTGTTTAGCACATTAGT
Found at i:53972712 original size:47 final size:50
Alignment explanation
Indices: 53972653--53972756 Score: 135
Period size: 47 Copynumber: 2.1 Consensus size: 50
53972643 AAAATATGAT
* *
53972653 TATGTGATTTCCGGGTAAGACCATATCTGGGA-TATGGCATC-G-GTGTGA
1 TATGTGATTTCCGGGTAAGACCATAGCT-GGACTATAGCATCGGTGTGTGA
* *
53972701 TATGTG-TTTCCGTGTAAGACCATAGCTGGACTATAGCTTCGGTGTGTGA
1 TATGTGATTTCCGGGTAAGACCATAGCTGGACTATAGCATCGGTGTGTGA
53972750 TATGTGA
1 TATGTGA
53972757 CAATGTGCAA
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
46 3 0.06
47 26 0.54
48 7 0.15
49 12 0.25
ACGTcount: A:0.22, C:0.14, G:0.30, T:0.34
Consensus pattern (50 bp):
TATGTGATTTCCGGGTAAGACCATAGCTGGACTATAGCATCGGTGTGTGA
Found at i:53978911 original size:19 final size:21
Alignment explanation
Indices: 53978882--53978923 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
53978872 AAATTGTCGT
53978882 AAATATTAAAAT-AAAAATAA
1 AAATATTAAAATCAAAAATAA
*
53978902 AAAT-TTAAAATCAAAACTAA
1 AAATATTAAAATCAAAAATAA
53978922 AA
1 AA
53978924 TAAATAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (21 bp):
AAATATTAAAATCAAAAATAA
Found at i:53982874 original size:50 final size:50
Alignment explanation
Indices: 53982780--53982875 Score: 120
Period size: 50 Copynumber: 1.9 Consensus size: 50
53982770 CTAATTAATC
* * * * **
53982780 TAAAACCTAAACCCTTAACCCTTAACCCCTATCCTTTAAACCTTAAATTA
1 TAAAACATAAACCCTTAACCCCTAACCCATAACCCCTAAACCTTAAATTA
* *
53982830 TAAAACATAAATCCTTAACCCCTAACCCATAACCCCTAACCCTTAA
1 TAAAACATAAACCCTTAACCCCTAACCCATAACCCCTAAACCTTAA
53982876 CCCTTAAACC
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
50 38 1.00
ACGTcount: A:0.40, C:0.34, G:0.00, T:0.26
Consensus pattern (50 bp):
TAAAACATAAACCCTTAACCCCTAACCCATAACCCCTAAACCTTAAATTA
Found at i:53982879 original size:7 final size:7
Alignment explanation
Indices: 53982842--53982889 Score: 60
Period size: 7 Copynumber: 6.9 Consensus size: 7
53982832 AAACATAAAT
53982842 CCTTAAC
1 CCTTAAC
*
53982849 CCCTAAC
1 CCTTAAC
*
53982856 CCATAAC
1 CCTTAAC
*
53982863 CCCTAAC
1 CCTTAAC
53982870 CCTTAAC
1 CCTTAAC
*
53982877 CCTTAAA
1 CCTTAAC
53982884 CCTTAA
1 CCTTAA
53982890 ATCCTAACCT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
7 36 1.00
ACGTcount: A:0.33, C:0.44, G:0.00, T:0.23
Consensus pattern (7 bp):
CCTTAAC
Found at i:53982897 original size:21 final size:21
Alignment explanation
Indices: 53982873--53982913 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
53982863 CCCTAACCCT
53982873 TAACCCTTAAACCT-TAAATCC
1 TAACCCTTAAA-CTATAAATCC
*
53982894 TAACCTTTAAACTATAAATC
1 TAACCCTTAAACTATAAATC
53982914 ATAAACCATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.41, C:0.27, G:0.00, T:0.32
Consensus pattern (21 bp):
TAACCCTTAAACTATAAATCC
Found at i:53984040 original size:41 final size:41
Alignment explanation
Indices: 53983924--53984168 Score: 221
Period size: 41 Copynumber: 6.0 Consensus size: 41
53983914 TAAATTATTT
* * * *
53983924 TAAATCCCTGAGCATTAGTGGCGCTT-TTTAGAAAACGCCGC
1 TAAAGCCCTGAGCATTAGCGGCGCTTCCTCA-AAAACGCCGC
** ** *
53983965 TAAA--AATAGAGCATTAGCAACGCTTTCTCAAAAAACGCCGC
1 TAAAGCCCT-GAGCATTAGCGGCGCTTCCTC-AAAAACGCCGC
*
53984006 TAAAGCCCTGAGCATTTGCGGCGCTTCCTCAAAAACGCCGC
1 TAAAGCCCTGAGCATTAGCGGCGCTTCCTCAAAAACGCCGC
* * *
53984047 TAAAGCCCT-AGCATTAGCGGAGCCTCCTCAAAAACGCCTC
1 TAAAGCCCTGAGCATTAGCGGCGCTTCCTCAAAAACGCCGC
* * * *
53984087 TAAATCCCCGAGCATTAGCGGCTCCTT-CACAAAAACGCCGC
1 TAAAGCCCTGAGCATTAGCGGC-GCTTCCTCAAAAACGCCGC
* * ** *
53984128 TATAGCCCTGAGCATTAGCGACGCTTTATTAAAAACGCCGC
1 TAAAGCCCTGAGCATTAGCGGCGCTTCCTCAAAAACGCCGC
53984169 AAAATCCCCG
Statistics
Matches: 164, Mismatches: 32, Indels: 16
0.77 0.15 0.08
Matches are distributed among these distances:
39 1 0.01
40 51 0.31
41 91 0.55
42 20 0.12
43 1 0.01
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.21
Consensus pattern (41 bp):
TAAAGCCCTGAGCATTAGCGGCGCTTCCTCAAAAACGCCGC
Found at i:53984120 original size:81 final size:82
Alignment explanation
Indices: 53983995--53984147 Score: 220
Period size: 81 Copynumber: 1.9 Consensus size: 82
53983985 CGCTTTCTCA
* * * *
53983995 AAAAACGCCGCTAAAGCCCTGAGCATTTGCGGCGCTTCCTCAAAAACGCCGCTAAAGCCCT-AGC
1 AAAAACGCCGCTAAAGCCCCGAGCATTAGCGGCCCTTCCACAAAAACGCCGCTAAAGCCCTGAGC
53984059 ATTAGCGGAGCCTCCTC
66 ATTAGCGGAGCCTCCTC
* * *
53984076 AAAAACGCCTCTAAATCCCCGAGCATTAGCGGCTCCTT-CACAAAAACGCCGCTATAGCCCTGAG
1 AAAAACGCCGCTAAAGCCCCGAGCATTAGCGGC-CCTTCCACAAAAACGCCGCTAAAGCCCTGAG
53984140 CATTAGCG
65 CATTAGCG
53984148 ACGCTTTATT
Statistics
Matches: 63, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
81 50 0.79
82 13 0.21
ACGTcount: A:0.29, C:0.34, G:0.20, T:0.18
Consensus pattern (82 bp):
AAAAACGCCGCTAAAGCCCCGAGCATTAGCGGCCCTTCCACAAAAACGCCGCTAAAGCCCTGAGC
ATTAGCGGAGCCTCCTC
Found at i:53984284 original size:39 final size:40
Alignment explanation
Indices: 53984232--53984347 Score: 128
Period size: 40 Copynumber: 3.0 Consensus size: 40
53984222 CGCTTTCTGG
* * *
53984232 AAAA-CGCCTCTAATGCT-TATTTTTAGCGGCGTTTTTCA
1 AAAAGCGCCGCTAATGCTAGATCTTTAGCGGCGTTTTTCA
* * * * * *
53984270 TAATGCGCCGCTAATGCTAGATCTTTAACAGCATTTTCCA
1 AAAAGCGCCGCTAATGCTAGATCTTTAGCGGCGTTTTTCA
*
53984310 AAAAGCGCCGCTAATGCTCGATCTTTAGCGGCGTTTTT
1 AAAAGCGCCGCTAATGCTAGATCTTTAGCGGCGTTTTT
53984348 TATCCAAATG
Statistics
Matches: 60, Mismatches: 16, Indels: 2
0.77 0.21 0.03
Matches are distributed among these distances:
38 2 0.03
39 12 0.20
40 46 0.77
ACGTcount: A:0.24, C:0.23, G:0.18, T:0.34
Consensus pattern (40 bp):
AAAAGCGCCGCTAATGCTAGATCTTTAGCGGCGTTTTTCA
Found at i:53985036 original size:13 final size:13
Alignment explanation
Indices: 53985003--53985027 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
53984993 CAACCTCAAT
53985003 GTTAAACACTAGG
1 GTTAAACACTAGG
53985016 GTTAAACACTAG
1 GTTAAACACTAG
53985028 AGGTGAACAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.16, G:0.20, T:0.24
Consensus pattern (13 bp):
GTTAAACACTAGG
Found at i:53987123 original size:19 final size:20
Alignment explanation
Indices: 53987085--53987124 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
53987075 TATTAATAAC
*
53987085 ATTTATCAAATTAAATTTAT
1 ATTTATCAAATTAAAATTAT
*
53987105 ATTTTTCAAA-TAAAATTAT
1 ATTTATCAAATTAAAATTAT
53987124 A
1 A
53987125 GTTAATTTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (20 bp):
ATTTATCAAATTAAAATTAT
Found at i:53989265 original size:22 final size:23
Alignment explanation
Indices: 53989232--53989290 Score: 77
Period size: 24 Copynumber: 2.6 Consensus size: 23
53989222 AGAATGATAC
*
53989232 ATGA-AAACTTAAAATAAT-TAT
1 ATGATAAATTTAAAATAATATAT
53989253 ATGATAAATTTAAAATAATAATAT
1 ATGATAAATTTAAAATAAT-ATAT
*
53989277 GTGATAAATTTAAA
1 ATGATAAATTTAAA
53989291 CAACATTCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
21 4 0.12
22 13 0.39
24 16 0.48
ACGTcount: A:0.56, C:0.02, G:0.07, T:0.36
Consensus pattern (23 bp):
ATGATAAATTTAAAATAATATAT
Found at i:54010634 original size:45 final size:45
Alignment explanation
Indices: 54010570--54010691 Score: 226
Period size: 45 Copynumber: 2.7 Consensus size: 45
54010560 GCCATATCCT
54010570 TCTTCCTCGGATCTACCATAACTTGGCTTCCTATATCCTTCTGCC
1 TCTTCCTCGGATCTACCATAACTTGGCTTCCTATATCCTTCTGCC
*
54010615 TCTTCCTCGGATCTACCATAACTTGGCTTCCTATATCCTTCTTCC
1 TCTTCCTCGGATCTACCATAACTTGGCTTCCTATATCCTTCTGCC
*
54010660 TCTTCCTCGGATCTACCATAACTTGGTTTCCT
1 TCTTCCTCGGATCTACCATAACTTGGCTTCCT
54010692 CTCATACCCG
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
45 75 1.00
ACGTcount: A:0.16, C:0.34, G:0.11, T:0.39
Consensus pattern (45 bp):
TCTTCCTCGGATCTACCATAACTTGGCTTCCTATATCCTTCTGCC
Found at i:54011008 original size:54 final size:54
Alignment explanation
Indices: 54010943--54011054 Score: 172
Period size: 54 Copynumber: 2.1 Consensus size: 54
54010933 TGTTCGCCAT
*
54010943 ATTCGGGTCTCCGGCCATACCCAGATT-CAAATTCAGGAGGCGGAGGCTGCTCAA
1 ATTCGGGTCTCCGGCCATACCCAG-TTCCAAACTCAGGAGGCGGAGGCTGCTCAA
* * *
54010997 ATTCGGGTCTCCGTCGATACCCAGTTCCAAACTCAGGCGGCGGAGGCTGCTCAA
1 ATTCGGGTCTCCGGCCATACCCAGTTCCAAACTCAGGAGGCGGAGGCTGCTCAA
54011051 ATTC
1 ATTC
54011055 TGATCTACGG
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
53 2 0.04
54 51 0.96
ACGTcount: A:0.22, C:0.29, G:0.27, T:0.21
Consensus pattern (54 bp):
ATTCGGGTCTCCGGCCATACCCAGTTCCAAACTCAGGAGGCGGAGGCTGCTCAA
Found at i:54015088 original size:30 final size:30
Alignment explanation
Indices: 54015054--54015157 Score: 86
Period size: 30 Copynumber: 3.5 Consensus size: 30
54015044 AATGTGACCA
*
54015054 ATTACAGGCTATGACAGGCAAATGCAAATG
1 ATTACAGGCTATGACAGGAAAATGCAAATG
* ** ****
54015084 ATTACAAGG-TATGAAAATAAAAATGTGTCTG
1 ATTAC-AGGCTATG-ACAGGAAAATGCAAATG
*
54015115 ATTACAGGCTATGACAGGTAAATGCAAATG
1 ATTACAGGCTATGACAGGAAAATGCAAATG
*
54015145 ATT-CAGGGTATGA
1 ATTACAGGCTATGA
54015158 TAATGCAAAT
Statistics
Matches: 54, Mismatches: 17, Indels: 7
0.69 0.22 0.09
Matches are distributed among these distances:
29 9 0.17
30 24 0.44
31 21 0.39
ACGTcount: A:0.40, C:0.12, G:0.23, T:0.25
Consensus pattern (30 bp):
ATTACAGGCTATGACAGGAAAATGCAAATG
Found at i:54015125 original size:61 final size:61
Alignment explanation
Indices: 54015025--54015157 Score: 214
Period size: 61 Copynumber: 2.2 Consensus size: 61
54015015 TAGTACAGTG
54015025 TACAGGGTATGAAAATAAAAATGTGACCAATTACAGGCTATGACAGGCAAATGCAAATGAT
1 TACAGGGTATGAAAATAAAAATGTGACCAATTACAGGCTATGACAGGCAAATGCAAATGAT
* * ** *
54015086 TACAAGGTATGAAAATAAAAATGTGTCTGATTACAGGCTATGACAGGTAAATGCAAATGAT
1 TACAGGGTATGAAAATAAAAATGTGACCAATTACAGGCTATGACAGGCAAATGCAAATGAT
54015147 T-CAGGGTATGA
1 TACAGGGTATGA
54015158 TAATGCAAAT
Statistics
Matches: 66, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
60 9 0.14
61 57 0.86
ACGTcount: A:0.42, C:0.11, G:0.23, T:0.24
Consensus pattern (61 bp):
TACAGGGTATGAAAATAAAAATGTGACCAATTACAGGCTATGACAGGCAAATGCAAATGAT
Found at i:54028592 original size:13 final size:13
Alignment explanation
Indices: 54028574--54028600 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
54028564 ATATATTTTT
54028574 AGATTTAAAATTA
1 AGATTTAAAATTA
54028587 AGATTTAAAATTA
1 AGATTTAAAATTA
54028600 A
1 A
54028601 CAATAATAAT
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:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (13 bp):
AGATTTAAAATTA
Found at i:54034909 original size:11 final size:11
Alignment explanation
Indices: 54034884--54034923 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
54034874 TTCACACATT
54034884 ATTTCT-TTAA
1 ATTTCTCTTAA
*
54034894 TTTTCTCTTAA
1 ATTTCTCTTAA
54034905 ATTTCTCTCTAA
1 ATTTCTCT-TAA
54034917 ATTTCTC
1 ATTTCTC
54034924 AAAGCTTTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
10 5 0.19
11 11 0.42
12 10 0.38
ACGTcount: A:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (11 bp):
ATTTCTCTTAA
Found at i:54037231 original size:93 final size:92
Alignment explanation
Indices: 54037070--54037263 Score: 343
Period size: 93 Copynumber: 2.1 Consensus size: 92
54037060 CAACATTGAT
* * *
54037070 TTTTTAATATATTTGTACAAACTATTTTTATATTGTTTTATTTAGTAAAATAAAAGTTGTTTTAA
1 TTTTTAATATATTTGTACAAACTATTTTTATATTGTTTCATTTAATAAAATAAAAGTTATTTTAA
54037135 ATATTTTAATAGTAATTTATTTTTTATA
66 ATATTTTAATAGTAATTTA-TTTTTATA
*
54037163 TTTTTAATATATTTGTACAAACTATTTTTATATTGTTTCATTTAATAAAATAAAAGTTATTTTTA
1 TTTTTAATATATTTGTACAAACTATTTTTATATTGTTTCATTTAATAAAATAAAAGTTATTTTAA
54037228 ATATTTTAATAGTAATTTATTTTTATA
66 ATATTTTAATAGTAATTTATTTTTATA
54037255 TTTTTAATA
1 TTTTTAATA
54037264 AAATAGAAGT
Statistics
Matches: 97, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
92 17 0.18
93 80 0.82
ACGTcount: A:0.36, C:0.03, G:0.05, T:0.56
Consensus pattern (92 bp):
TTTTTAATATATTTGTACAAACTATTTTTATATTGTTTCATTTAATAAAATAAAAGTTATTTTAA
ATATTTTAATAGTAATTTATTTTTATA
Found at i:54037305 original size:8 final size:9
Alignment explanation
Indices: 54037289--54037318 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
54037279 TGAATAAGAC
54037289 AATATTTTT
1 AATATTTTT
54037298 AATATTTTT
1 AATATTTTT
54037307 -ATATTTTT
1 AATATTTTT
54037315 AATA
1 AATA
54037319 AAATAGAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (9 bp):
AATATTTTT
Found at i:54040585 original size:126 final size:126
Alignment explanation
Indices: 54040354--54040752 Score: 552
Period size: 126 Copynumber: 3.2 Consensus size: 126
54040344 GCCAAGCAGG
* ** * *
54040354 AACTACTGTAGAAAAAGAGCGCCCACGTGGGAGCTTTTTTTAGTAATTTTGTTGACAGTGCATCC
1 AACTACTGTAGAAAAAGAACATCCACATGGGAGCTTTTTTTAGTAATTTTGCTGACAGTGCATCC
* * * * *
54040419 TGCTTAAAGCATTTTTGACACTATTTGTTCAAAACCGTCTTCTCAAAATTATTTTTTTAGA
66 TGCTTGAAGCGTTTTTTACACTATTTGTTCAGAACTGTCTTCTCAAAATTATTTTTTTAGA
54040480 AACTACTGTAGAAAAAGAACATCCACATGGGAGCTTTTTTTAGTAATTTTGCTGACAGTGCATCC
1 AACTACTGTAGAAAAAGAACATCCACATGGGAGCTTTTTTTAGTAATTTTGCTGACAGTGCATCC
* *
54040545 TGCTTGAAGCGTTTTTTACACTATTTGTTCAGAACTGTCTTCTCAAAATTATTTTTTCAGG
66 TGCTTGAAGCGTTTTTTACACTATTTGTTCAGAACTGTCTTCTCAAAATTATTTTTTTAGA
* * * *
54040606 AACTACTGTAGAAAAA-AAGTATCCA-AGTGGGAGCTTTCTTCAGTAATTTTGCTAACAGTGCAT
1 AACTACTGTAGAAAAAGAA-CATCCACA-TGGGAGCTTTTTTTAGTAATTTTGCTGACAGTGCAT
* * * *
54040669 CCTGCTTGAAGCGTTTTTTACATTATCTT-TTTAGAATTGTTTTCTCAAAATTATTTTTTTAGA
64 CCTGCTTGAAGCGTTTTTTACACTAT-TTGTTCAGAACTGTCTTCTCAAAATTATTTTTTTAGA
* *
54040732 AACTAATGTAGAAAAAAAACA
1 AACTACTGTAGAAAAAGAACA
54040753 AAAAATTTTA
Statistics
Matches: 245, Mismatches: 24, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
125 3 0.01
126 238 0.97
127 4 0.02
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.38
Consensus pattern (126 bp):
AACTACTGTAGAAAAAGAACATCCACATGGGAGCTTTTTTTAGTAATTTTGCTGACAGTGCATCC
TGCTTGAAGCGTTTTTTACACTATTTGTTCAGAACTGTCTTCTCAAAATTATTTTTTTAGA
Found at i:54040849 original size:34 final size:32
Alignment explanation
Indices: 54040803--54040925 Score: 149
Period size: 33 Copynumber: 3.7 Consensus size: 32
54040793 TTAAACACAA
*
54040803 AATTATTTTAAAAAAACTAAACCATAATTTAATT
1 AATT-TTTTAAAAAACCTAAACC-TAATTTAATT
*
54040837 AATTTTCTTAAAAACCCTAAACCCTAATTTAATT
1 AATTTT-TTAAAAAACCTAAA-CCTAATTTAATT
*
54040871 AATTTATTT-AAAACCCTAAAACCTAATTTAATT
1 AATTT-TTTAAAAAACCT-AAACCTAATTTAATT
54040904 AATTTTTTAAAAAACCTTAAAC
1 AATTTTTTAAAAAACC-TAAAC
54040926 TACTAAAAAC
Statistics
Matches: 80, Mismatches: 3, Indels: 13
0.83 0.03 0.14
Matches are distributed among these distances:
32 3 0.04
33 37 0.46
34 37 0.46
35 3 0.04
ACGTcount: A:0.47, C:0.15, G:0.00, T:0.38
Consensus pattern (32 bp):
AATTTTTTAAAAAACCTAAACCTAATTTAATT
Found at i:54040850 original size:33 final size:31
Alignment explanation
Indices: 54040803--54040918 Score: 133
Period size: 34 Copynumber: 3.5 Consensus size: 31
54040793 TTAAACACAA
54040803 AATTATTTTAAAAAAACTAAACCATAATTTAATT
1 AATT-TTTT-AAAAAACTAAACC-TAATTTAATT
*
54040837 AATTTTCTTAAAAACCCTAAACCCTAATTTAATT
1 AATTTT-TTAAAAA-ACTAAA-CCTAATTTAATT
**
54040871 AATTTATTTAAAACCCTAAAACCTAATTTAATT
1 AATTT-TTTAAAAAACT-AAACCTAATTTAATT
54040904 AATTTTTTAAAAAAC
1 AATTTTTTAAAAAAC
54040919 CTTAAACTAC
Statistics
Matches: 73, Mismatches: 4, Indels: 12
0.82 0.04 0.13
Matches are distributed among these distances:
32 8 0.11
33 27 0.37
34 35 0.48
35 3 0.04
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.39
Consensus pattern (31 bp):
AATTTTTTAAAAAACTAAACCTAATTTAATT
Found at i:54044363 original size:31 final size:30
Alignment explanation
Indices: 54044327--54044390 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
54044317 TTATTAAAAG
* *
54044327 TAAAATTTTACTTTAA-TCTCCTAAAAATGA
1 TAAAAATTTAATTTAATTCT-CTAAAAATGA
* *
54044357 TAAAAATTTAATTTAATTCTTTAAAAATTA
1 TAAAAATTTAATTTAATTCTCTAAAAATGA
54044387 TAAA
1 TAAA
54044391 GATATAGACT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 26 0.90
31 3 0.10
ACGTcount: A:0.48, C:0.08, G:0.02, T:0.42
Consensus pattern (30 bp):
TAAAAATTTAATTTAATTCTCTAAAAATGA
Done.