Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D01
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: 64473564
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1880000 characters in sequence are not A, C, G, or T
File 177 of 213
Found at i:53480083 original size:45 final size:44
Alignment explanation
Indices: 53479937--53480179 Score: 186
Period size: 45 Copynumber: 5.5 Consensus size: 44
53479927 AATCCACTCT
* * * ** * * * *
53479937 ACTGCAACTTCAAGGAGATAGGATTATTGGCTTTAATCTGCACT
1 ACTGCAACTTCAGGGAGATAAGATTACTATCTTCAGTCTGCTCC
* * * * *
53479981 ACTGCAACTTCAAGGACATAAGGTTCACCATCTTCAGTCTGCCCC
1 ACTGCAACTTCAGGGAGATAAGATT-ACTATCTTCAGTCTGCTCC
* *
53480026 ACTGCAACTTCAGGGGGATAAGACTTGCTATCTTCAGTCTGCTCC
1 ACTGCAACTTCAGGGAGATAAGA-TTACTATCTTCAGTCTGCTCC
* * * ** * *
53480071 ACTGCAACTTCAGGGAAATAGGATTATTGGCTTTAATCTGCTCC
1 ACTGCAACTTCAGGGAGATAAGATTACTATCTTCAGTCTGCTCC
** * * *
53480115 ACTGCAACTTCAGGGAGATAAGATT-C-GCCTTGA-ACTGCTCT
1 ACTGCAACTTCAGGGAGATAAGATTACTATCTTCAGTCTGCTCC
*
53480156 ACTGCAACTTCAGAGAGATAAGAT
1 ACTGCAACTTCAGGGAGATAAGAT
53480180 CTGTGACTTA
Statistics
Matches: 162, Mismatches: 35, Indels: 7
0.79 0.17 0.03
Matches are distributed among these distances:
41 29 0.18
42 5 0.03
44 60 0.37
45 66 0.41
46 2 0.01
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (44 bp):
ACTGCAACTTCAGGGAGATAAGATTACTATCTTCAGTCTGCTCC
Found at i:53480123 original size:44 final size:44
Alignment explanation
Indices: 53479923--53480175 Score: 181
Period size: 44 Copynumber: 5.8 Consensus size: 44
53479913 CGTCTTGTTT
** * *
53479923 CTTCAATCCACTCTACTGCAACTTCAAGGAGATAGGATTATTGG
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAGGATTATTGG
* * * * * ****
53479967 CTTTAATCTGCACTACTGCAACTTCAAGGACATAAGG-TTCACCAT
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGAT-AGGATT-ATTGG
* * * * ** **
53480012 CTTCAGTCTGCCCCACTGCAACTTCAGGGGGATAAGACTTGCTAT
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAGGA-TTATTGG
* *
53480057 CTTCAGTCTGCTCCACTGCAACTTCAGGGAAATAGGATTATTGG
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAGGATTATTGG
* * * *
53480101 CTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-T-TCGC
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAGGATTATTGG
* * *
53480143 CTTGAA-CTGCTCTACTGCAACTTCAGAGAGATA
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATA
53480176 AGATCTGTGA
Statistics
Matches: 169, Mismatches: 36, Indels: 11
0.78 0.17 0.05
Matches are distributed among these distances:
41 25 0.15
42 7 0.04
43 1 0.01
44 68 0.40
45 66 0.39
46 2 0.01
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.28
Consensus pattern (44 bp):
CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAGGATTATTGG
Found at i:53480240 original size:46 final size:46
Alignment explanation
Indices: 53480191--53481070 Score: 758
Period size: 46 Copynumber: 18.3 Consensus size: 46
53480181 TGTGACTTAT
* * *
53480191 AGCTTTAATCTATTGCAATGCCAGGGAAACAAGATTCGCTGCCTTT
1 AGCTTTAATCTATTGCAACGCCAGGGAAATAAGATTCGCTGCCTTC
* * * *
53480237 AGCTTTAATCTGTTCCACTACAACGCCAAGGAAATAAGATTCGCTGTCTTC
1 AGCTTTAATC---T--ATTGCAACGCCAGGGAAATAAGATTCGCTGCCTTC
* * * *
53480288 AGCTCTAATTTACTGCAACGCCAGGGAAATAAGATTTGCTGCCTTC
1 AGCTTTAATCTATTGCAACGCCAGGGAAATAAGATTCGCTGCCTTC
* * * * * * *
53480334 AGCATTAATCTGTTCCACTGCAACACCAAGGAAATAAGATTTGTTGTCTTC
1 AGCTTTAATC---T--ATTGCAACGCCAGGGAAATAAGATTCGCTGCCTTC
* *
53480385 AGCTTTAATCTATTGCAACGCCAGGGAAACAAGATTCACTGCCTTC
1 AGCTTTAATCTATTGCAACGCCAGGGAAATAAGATTCGCTGCCTTC
* *
53480431 AGCTTCAATCTATTGCAACGCCAGGGAAACAAG--TCGCTGCCTTC
1 AGCTTTAATCTATTGCAACGCCAGGGAAATAAGATTCGCTGCCTTC
* * * * * *
53480475 AGCTTTAATCTGTTCCACTGCAACGGCAAGGAAATAAGATTCGTTTCCATC
1 AGCTTTAATC---T--ATTGCAACGCCAGGGAAATAAGATTCGCTGCCTTC
* * * *
53480526 AGCTTTAATCTATTGCAAAGCAAGGGAAACAAGATTTGCTGCCTTC
1 AGCTTTAATCTATTGCAACGCCAGGGAAATAAGATTCGCTGCCTTC
* * * *
53480572 AGCTTTAATTTGTTCCACTGCAACGCCAAGGACATAAGATTCGCTGCCTTC
1 AGCTTTAA-----TCTATTGCAACGCCAGGGAAATAAGATTCGCTGCCTTC
* *
53480623 AGCTTTAATCTATTGCAACGCTAGGGAAACAAGA-TCTGCTGCCTTC
1 AGCTTTAATCTATTGCAACGCCAGGGAAATAAGATTC-GCTGCCTTC
* * *
53480669 AGCTTTAATCTATTCCACTGCAATGCCAAGGAAATAAGATTCGCTACCTTC
1 AGCTTTAATCTA-T----TGCAACGCCAGGGAAATAAGATTCGCTGCCTTC
* * * ** *
53480720 AGCTTTAATCTGTTCCACTGTAATGCCAAAGAAATAAGATTCTCTGCCTTC
1 AGCTTTAATC---T--ATTGCAACGCCAGGGAAATAAGATTCGCTGCCTTC
* * *
53480771 AGCTTTAATCTATTGCAACGCTAGGGAAACAAGATTCGCTGACTTC
1 AGCTTTAATCTATTGCAACGCCAGGGAAATAAGATTCGCTGCCTTC
* * *
53480817 AGCTTTAATCTATTGGAACGCCAGAGAAACAAGATTCGCTGCCTTC
1 AGCTTTAATCTATTGCAACGCCAGGGAAATAAGATTCGCTGCCTTC
* * * *
53480863 AGCTTTAATTTGTTCCACTGCAACGCCAAGGAAATAAGATTCACTGCCTTC
1 AGCTTTAA-----TCTATTGCAACGCCAGGGAAATAAGATTCGCTGCCTTC
* *
53480914 AACTTTAATCTATTGCAACGCCAGGGAAACAAGATTCGCTGCCTTC
1 AGCTTTAATCTATTGCAACGCCAGGGAAATAAGATTCGCTGCCTTC
* * * ** *
53480960 AGATTTAATCTGTTCCACTACAACGCCAAAGAAATAATATTCGCTGCCTTC
1 AGCTTTAATC---T--ATTGCAACGCCAGGGAAATAAGATTCGCTGCCTTC
* *
53481011 AGGTTTAATCTATTGCAACGCCAGGGAGATAAGATTCGCTGCCTTC
1 AGCTTTAATCTATTGCAACGCCAGGGAAATAAGATTCGCTGCCTTC
*
53481057 AGCTTTAATGTATT
1 AGCTTTAATCTATT
53481071 CCACTGCAAC
Statistics
Matches: 674, Mismatches: 116, Indels: 88
0.77 0.13 0.10
Matches are distributed among these distances:
44 19 0.03
45 2 0.00
46 339 0.50
47 2 0.00
48 5 0.01
49 21 0.03
51 282 0.42
52 2 0.00
54 1 0.00
56 1 0.00
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (46 bp):
AGCTTTAATCTATTGCAACGCCAGGGAAATAAGATTCGCTGCCTTC
Found at i:53480342 original size:97 final size:98
Alignment explanation
Indices: 53480204--53481097 Score: 754
Period size: 97 Copynumber: 9.2 Consensus size: 98
53480194 TTTAATCTAT
* * * *
53480204 TGCAATGCCAGGGAAACAAGATTCGCTGCCTTTAGCTTTAATCTGTTCCACTACAACGCCAAGGA
1 TGCAACGCCAGGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTGTT--ACTGCAACGCCAAGGA
* * *
53480269 AATAAGATTCGCTGTCTTCAGCTCTAA-T-TT-AC
64 AACAAGATTCGCTGCCTTCAGCTTTAATTGTTCAC
* * *
53480301 TGCAACGCCAGGGAAATAAGATTTGCTGCCTTCAGCATTAATCTGTTCCACTGCAACACCAAGGA
1 TGCAACGCCAGGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTGTT--ACTGCAACGCCAAGGA
* * * * * *
53480366 AATAAGATTTGTTGTCTTCAGCTTTAA-T-CT-AT
64 AACAAGATTCGCTGCCTTCAGCTTTAATTGTTCAC
* * * * *
53480398 TGCAACGCCAGGGAAACAAGATTCACTGCCTTCAGCTTCAATC---TATTGCAACGCCAGGGAAA
1 TGCAACGCCAGGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTGTTACTGCAACGCCAAGGAAA
53480460 CAAG--TCGCTGCCTTCAGCTTTAATCTGTTCCAC
66 CAAGATTCGCTGCCTTCAGCTTTAAT-TGTT-CAC
* * * * * * *
53480493 TGCAACGGCAAGGAAATAAGATTCGTTTCCATCAGCTTTAATC---TATTGCAAAG-CAAGGGAA
1 TGCAACGCCAGGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTGTTACTGCAACGCCAA-GGAA
*
53480554 ACAAGATTTGCTGCCTTCAGCTTTAATTTGTTCCAC
65 ACAAGATTCGCTGCCTTCAGCTTTAA-TTGTT-CAC
* * * * *
53480590 TGCAACGCCAAGGACATAAGATTCGCTGCCTTCAGCTTTAATC---TATTGCAACGCTAGGGAAA
1 TGCAACGCCAGGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTGTTACTGCAACGCCAAGGAAA
*
53480652 CAAGA-TCTGCTGCCTTCAGCTTTAATCTATTCCAC
66 CAAGATTC-GCTGCCTTCAGCTTTAAT-TGTT-CAC
* * * * * *
53480687 TGCAATGCCAAGGAAATAAGATTCGCTACCTTCAGCTTTAATCTGTTCCACTGTAATGCCAAAGA
1 TGCAACGCCAGGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTGTT--ACTGCAACGCCAAGGA
* * * *
53480752 AATAAGATTCTCTGCCTTCAGCTTTAA-T-CT-AT
64 AACAAGATTCGCTGCCTTCAGCTTTAATTGTTCAC
* * * * *
53480784 TGCAACGCTAGGGAAACAAGATTCGCTGACTTCAGCTTTAATC---TATTGGAACGCC-AGAGAA
1 TGCAACGCCAGGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTGTTACTGCAACGCCAAG-GAA
53480845 ACAAGATTCGCTGCCTTCAGCTTTAATTTGTTCCAC
65 ACAAGATTCGCTGCCTTCAGCTTTAA-TTGTT-CAC
* * * * *
53480881 TGCAACGCCAAGGAAATAAGATTCACTGCCTTCAACTTTAATC---TATTGCAACGCCAGGGAAA
1 TGCAACGCCAGGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTGTTACTGCAACGCCAAGGAAA
*
53480943 CAAGATTCGCTGCCTTCAGATTTAATCTGTTCCAC
66 CAAGATTCGCTGCCTTCAGCTTTAAT-TGTT-CAC
* ** * * * * *
53480978 TACAACGCCAAAGAAATAATATTCGCTGCCTTCAGGTTTAATC---TATTGCAACGCCAGGGAGA
1 TGCAACGCCAGGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTGTTACTGCAACGCCAAGGAAA
* *
53481040 TAAGATTCGCTGCCTTCAGCTTTAATGTATTCCAC
66 CAAGATTCGCTGCCTTCAGCTTTAAT-TGTT-CAC
* * *
53481075 TGCAACACCCGGGAAAAAAGATT
1 TGCAACGCCAGGGAAATAAGATT
53481098 TGCCATAATG
Statistics
Matches: 670, Mismatches: 101, Indels: 52
0.81 0.12 0.06
Matches are distributed among these distances:
90 16 0.02
91 1 0.00
92 54 0.08
93 1 0.00
94 5 0.01
95 55 0.08
96 3 0.00
97 495 0.74
98 3 0.00
99 1 0.00
100 2 0.00
102 32 0.05
103 2 0.00
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.28
Consensus pattern (98 bp):
TGCAACGCCAGGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTGTTACTGCAACGCCAAGGAAA
CAAGATTCGCTGCCTTCAGCTTTAATTGTTCAC
Found at i:53480728 original size:194 final size:193
Alignment explanation
Indices: 53480204--53481080 Score: 892
Period size: 194 Copynumber: 4.5 Consensus size: 193
53480194 TTTAATCTAT
* * * * * *
53480204 TGCAATGCCAGGGAAACAAGATTCGCTGCCTTTAGCTTTAATCTGTTCCACTACAACGCCAAGGA
1 TGCAACGCCAAGGAAACAAGATTCGCTGCCTTCAGCTTTAATC---T--ATTGCAACGCCAGGGA
* * * * * *
53480269 AATAAGATTCGCTGTCTTCAGCTCTAA--T-TT--ACTGCAACGCCAGGGAAATAAGATTTGCTG
61 AACAAGATTCGCTGCCTTCAGCTTTAATCTATTCCACTGCAACGCCAAGGAAATAAGATTCGCTA
* * * * * *
53480329 CCTTCAGCATTAATCTGTTCCACTGCAACACCAA-GGAAATAAGATTTGTTGTCTTCAGCTTTAA
126 CCTTCAGCTTTAATC---T--ATTGCAA-AGCAAGGGAAACAAGATTTGCTGCCTTCAGCTTTAA
* *
53480393 ----TCTAT
185 TTGTTCCAC
* * *
53480398 TGCAACGCCAGGGAAACAAGATTCACTGCCTTCAGCTTCAATCTATTGCAACGCCAGGGAAACAA
1 TGCAACGCCAAGGAAACAAGATTCGCTGCCTTCAGCTTTAATCTATTGCAACGCCAGGGAAACAA
* * * * *
53480463 G--TCGCTGCCTTCAGCTTTAATCTGTTCCACTGCAACGGCAAGGAAATAAGATTCGTTTCCATC
66 GATTCGCTGCCTTCAGCTTTAATCTATTCCACTGCAACGCCAAGGAAATAAGATTCGCTACCTTC
53480526 AGCTTTAATCTATTGCAAAGCAAGGGAAACAAGATTTGCTGCCTTCAGCTTTAATTTGTTCCAC
131 AGCTTTAATCTATTGCAAAGCAAGGGAAACAAGATTTGCTGCCTTCAGCTTTAA-TTGTTCCAC
* * *
53480590 TGCAACGCCAAGGACATAAGATTCGCTGCCTTCAGCTTTAATCTATTGCAACGCTAGGGAAACAA
1 TGCAACGCCAAGGAAACAAGATTCGCTGCCTTCAGCTTTAATCTATTGCAACGCCAGGGAAACAA
*
53480655 GA-TCTGCTGCCTTCAGCTTTAATCTATTCCACTGCAATGCCAAGGAAATAAGATTCGCTACCTT
66 GATTC-GCTGCCTTCAGCTTTAATCTATTCCACTGCAACGCCAAGGAAATAAGATTCGCTACCTT
* * * *
53480719 CAGCTTTAATCTGTTCCACTGTAATGCCAA-AGAAATAAGATTCT-CTGCCTTCAGCTTTAA---
130 CAGCTTTAATCTATTGCA----AA-G-CAAGGGAAACAAGATT-TGCTGCCTTCAGCTTTAATTG
* *
53480779 -TCTAT
188 TTCCAC
* * * * *
53480784 TGCAACGCTAGGGAAACAAGATTCGCTGACTTCAGCTTTAATCTATTGGAACGCCAGAGAAACAA
1 TGCAACGCCAAGGAAACAAGATTCGCTGCCTTCAGCTTTAATCTATTGCAACGCCAGGGAAACAA
* * * *
53480849 GATTCGCTGCCTTCAGCTTTAATTTGTTCCACTGCAACGCCAAGGAAATAAGATTCACTGCCTTC
66 GATTCGCTGCCTTCAGCTTTAATCTATTCCACTGCAACGCCAAGGAAATAAGATTCGCTACCTTC
* * * * *
53480914 AACTTTAATCTATTGCAACGCCAGGGAAACAAGATTCGCTGCCTTCAGATTTAATCTGTTCCAC
131 AGCTTTAATCTATTGCAAAGCAAGGGAAACAAGATTTGCTGCCTTCAGCTTTAAT-TGTTCCAC
* * * * * * *
53480978 TACAACGCCAAAGAAATAATATTCGCTGCCTTCAGGTTTAATCTATTGCAACGCCAGGGAGATAA
1 TGCAACGCCAAGGAAACAAGATTCGCTGCCTTCAGCTTTAATCTATTGCAACGCCAGGGAAACAA
*
53481043 GATTCGCTGCCTTCAGCTTTAATGTATTCCACTGCAAC
66 GATTCGCTGCCTTCAGCTTTAATCTATTCCACTGCAAC
53481081 ACCCGGGAAA
Statistics
Matches: 575, Mismatches: 80, Indels: 56
0.81 0.11 0.08
Matches are distributed among these distances:
186 4 0.01
187 50 0.09
188 2 0.00
189 46 0.08
190 3 0.01
191 1 0.00
192 101 0.18
193 2 0.00
194 331 0.58
195 2 0.00
198 2 0.00
199 27 0.05
200 4 0.01
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.29
Consensus pattern (193 bp):
TGCAACGCCAAGGAAACAAGATTCGCTGCCTTCAGCTTTAATCTATTGCAACGCCAGGGAAACAA
GATTCGCTGCCTTCAGCTTTAATCTATTCCACTGCAACGCCAAGGAAATAAGATTCGCTACCTTC
AGCTTTAATCTATTGCAAAGCAAGGGAAACAAGATTTGCTGCCTTCAGCTTTAATTGTTCCAC
Found at i:53482350 original size:14 final size:15
Alignment explanation
Indices: 53482326--53482361 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
53482316 GCCTCTCTAT
53482326 TTTTTACTTTTTTCA
1 TTTTTACTTTTTTCA
*
53482341 TTTTTA-TTTTTTTA
1 TTTTTACTTTTTTCA
53482355 TTTTTAC
1 TTTTTAC
53482362 GACTCAAAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
14 13 0.68
15 6 0.32
ACGTcount: A:0.14, C:0.08, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTTTACTTTTTTCA
Found at i:53482402 original size:49 final size:50
Alignment explanation
Indices: 53482348--53482447 Score: 146
Period size: 50 Copynumber: 2.0 Consensus size: 50
53482338 TCATTTTTAT
* *
53482348 TTTTTTATTTTTACGACTCAAAGCACCCTTTGCAGGTTTTCACCTTGGTC
1 TTTTTTGTTTTAACGACTCAAAGCACCCTTTGCAGGTTTTCACCTTGGTC
* * * *
53482398 TTTTTTGTTTTAAGGACTCTAGGCACCCTTTGCGGGTTTTCACCTTGGTC
1 TTTTTTGTTTTAACGACTCAAAGCACCCTTTGCAGGTTTTCACCTTGGTC
53482448 CCTTCTCCTT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 44 1.00
ACGTcount: A:0.15, C:0.23, G:0.18, T:0.44
Consensus pattern (50 bp):
TTTTTTGTTTTAACGACTCAAAGCACCCTTTGCAGGTTTTCACCTTGGTC
Found at i:53488673 original size:13 final size:14
Alignment explanation
Indices: 53488642--53488676 Score: 54
Period size: 13 Copynumber: 2.5 Consensus size: 14
53488632 ATGAAACGAA
53488642 TTAAAATAAATCAAT
1 TTAAAA-AAATCAAT
53488657 TTAAAAAAATC-AT
1 TTAAAAAAATCAAT
53488670 TTAAAAA
1 TTAAAAA
53488677 TACATGTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 9 0.45
14 5 0.25
15 6 0.30
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (14 bp):
TTAAAAAAATCAAT
Found at i:53495634 original size:18 final size:19
Alignment explanation
Indices: 53495604--53495657 Score: 51
Period size: 18 Copynumber: 3.0 Consensus size: 19
53495594 TTTACTTAGC
53495604 ATTTTA-TTAATTTAATTT
1 ATTTTACTTAATTTAATTT
*
53495622 ATTTTACTT-ATTTTA-TT
1 ATTTTACTTAATTTAATTT
* * *
53495639 ATTATGCTTCATTTAATTT
1 ATTTTACTTAATTTAATTT
53495658 TTATTTTATC
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
17 9 0.31
18 16 0.55
19 4 0.14
ACGTcount: A:0.28, C:0.06, G:0.02, T:0.65
Consensus pattern (19 bp):
ATTTTACTTAATTTAATTT
Found at i:53495673 original size:21 final size:24
Alignment explanation
Indices: 53495632--53495674 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
53495622 ATTTTACTTA
53495632 TTTTATTATTATGCTTCATTTAAT
1 TTTTATTATTATGCTTCATTTAAT
53495656 TTTTATT-TTAT-CTT-ATTTA
1 TTTTATTATTATGCTTCATTTA
53495675 TGATATTTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.26
22 3 0.16
23 4 0.21
24 7 0.37
ACGTcount: A:0.23, C:0.07, G:0.02, T:0.67
Consensus pattern (24 bp):
TTTTATTATTATGCTTCATTTAAT
Found at i:53511296 original size:28 final size:28
Alignment explanation
Indices: 53511231--53511381 Score: 205
Period size: 28 Copynumber: 5.4 Consensus size: 28
53511221 GAGATTGGCG
* * * *
53511231 CTAAGTGTGCGGGTTTAAATTGTACAGCA
1 CTAAGTGTGCGAGTTT-GATTATATAGCA
*
53511260 CTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
* *
53511288 CTAAGTGTGCGAGCTTGATTATCTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
53511316 CTAAGTGTGCGAGTTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
*
53511344 CTAAGTGTGTGAG-TTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
*
53511371 CTGAGTGTGCG
1 CTAAGTGTGCG
53511382 GACTTAATAT
Statistics
Matches: 110, Mismatches: 12, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
27 23 0.21
28 72 0.65
29 15 0.14
ACGTcount: A:0.26, C:0.13, G:0.28, T:0.34
Consensus pattern (28 bp):
CTAAGTGTGCGAGTTTGATTATATAGCA
Found at i:53513458 original size:29 final size:29
Alignment explanation
Indices: 53513425--53513480 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
53513415 TCCTTAACTC
*
53513425 AAACTTTTTCAAATTACAATTTTGCCCCT
1 AAACTTTTGCAAATTACAATTTTGCCCCT
* *
53513454 AAACTTTTGCATATTACACTTTTGCCC
1 AAACTTTTGCAAATTACAATTTTGCCC
53513481 TTGGCTCGGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.29, C:0.25, G:0.05, T:0.41
Consensus pattern (29 bp):
AAACTTTTGCAAATTACAATTTTGCCCCT
Found at i:53521318 original size:27 final size:27
Alignment explanation
Indices: 53521288--53521465 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
53521278 ATATCGAGTC
* * * *
53521288 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
*
53521315 CGCACACTTAGTGCTACATAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
*
53521342 CGCACACTTAGTGCTTCATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
53521370 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
53521397 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
53521424 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
53521451 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
53521466 GTACAATTTA
Statistics
Matches: 131, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
27 107 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:53521427 original size:82 final size:81
Alignment explanation
Indices: 53521309--53521464 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
53521299 TGCTATATAA
**
53521309 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCTTCATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
53521374 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
53521391 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
53521455 CACTTAGTGC
65 CACTTAGTGC
53521465 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:53529347 original size:27 final size:27
Alignment explanation
Indices: 53529317--53529494 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
53529307 ATATCGAGTC
* * * *
53529317 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
*
53529344 CGCACACTTAGTGCTACATAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
*
53529371 CGCACACTTAGTGCTTCATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
53529399 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
53529426 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
53529453 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
53529480 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
53529495 GTACAATTTA
Statistics
Matches: 131, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
27 107 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:53529456 original size:82 final size:81
Alignment explanation
Indices: 53529338--53529493 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
53529328 TGCTATATAA
**
53529338 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCTTCATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
53529403 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
53529420 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
53529484 CACTTAGTGC
65 CACTTAGTGC
53529494 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:53535865 original size:25 final size:25
Alignment explanation
Indices: 53535831--53535878 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
53535821 ACCACATAAA
53535831 CAAAATTACTTTTAATGTTATCAGT
1 CAAAATTACTTTTAATGTTATCAGT
53535856 CAAAATTACTTTTAATGTTATCA
1 CAAAATTACTTTTAATGTTATCA
53535879 TATCATGCGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.38, C:0.12, G:0.06, T:0.44
Consensus pattern (25 bp):
CAAAATTACTTTTAATGTTATCAGT
Found at i:53541671 original size:17 final size:17
Alignment explanation
Indices: 53541645--53541690 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
53541635 TATAACTAAG
*
53541645 ATATAGATAAATAAAAA
1 ATATATATAAATAAAAA
53541662 ATATATAT-AATAAAAA
1 ATATATATAAATAAAAA
53541678 ATTATAATATAAA
1 A-TAT-ATATAAA
53541691 GAATTGTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
16 9 0.36
17 10 0.40
18 4 0.16
19 2 0.08
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (17 bp):
ATATATATAAATAAAAA
Found at i:53541675 original size:16 final size:18
Alignment explanation
Indices: 53541654--53541689 Score: 58
Period size: 16 Copynumber: 2.1 Consensus size: 18
53541644 GATATAGATA
53541654 AATAAAAAA-TAT-ATAT
1 AATAAAAAATTATAATAT
53541670 AATAAAAAATTATAATAT
1 AATAAAAAATTATAATAT
53541688 AA
1 AA
53541690 AGAATTGTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.50
17 3 0.17
18 6 0.33
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
AATAAAAAATTATAATAT
Found at i:53542155 original size:39 final size:39
Alignment explanation
Indices: 53542098--53542172 Score: 132
Period size: 39 Copynumber: 1.9 Consensus size: 39
53542088 TAATTTGGCA
53542098 GAAGTTTGTTTGGCAGTTAAATTGCATTATCATAATAAG
1 GAAGTTTGTTTGGCAGTTAAATTGCATTATCATAATAAG
* *
53542137 GAAGTTTGTTTGGTAGTTAAATTGTATTATCATAAT
1 GAAGTTTGTTTGGCAGTTAAATTGCATTATCATAAT
53542173 TCGACAATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.32, C:0.05, G:0.20, T:0.43
Consensus pattern (39 bp):
GAAGTTTGTTTGGCAGTTAAATTGCATTATCATAATAAG
Found at i:53547899 original size:69 final size:69
Alignment explanation
Indices: 53547774--53548252 Score: 381
Period size: 69 Copynumber: 6.9 Consensus size: 69
53547764 TTTATAGCTA
** * * * * * **
53547774 GGAGCTTTGCTCTCGCTAGTTGTGCTAGAGGTCATGGCTTTTTGCCTGGGGTCCTTAATTTTACA
1 GGAGCTTTGCTCTCGCTAACTGTGCTGGAGGTCGTGGCTCTTCGCCTGCGAACCTTAATTTTACA
*
53547839 GTTG
66 ATTG
* * * * * * * *
53547843 GGAGCTTTTCCCTCGCTAACTGTGTTAGAGGTCATGGCACTTCACCTGCGAACCTTAGTTTTACA
1 GGAGCTTTGCTCTCGCTAACTGTGCTGGAGGTCGTGGCTCTTCGCCTGCGAACCTTAATTTTACA
53547908 GA-TG
66 -ATTG
* * * * ** *
53547912 GGAGCTTTGCTCTCACTAACTATGTTGCAGGTCGTGGCTCTTCGCCT-ATAGGCCTTAATTTTAC
1 GGAGCTTTGCTCTCGCTAACTGTGCTGGAGGTCGTGGCTCTTCGCCTGCGA-ACCTTAATTTTAC
53547976 AATTG
65 AATTG
* * ***** *
53547981 AGAGCTTTGCTCTTGCTAACTGTGCTGGAGGTTACACCTCTTCGCCTGTGAACCTTAATTTTACA
1 GGAGCTTTGCTCTCGCTAACTGTGCTGGAGGTCGTGGCTCTTCGCCTGCGAACCTTAATTTTACA
53548046 ATTG
66 ATTG
* * * * * *
53548050 GGAACTTTGCTCTCGCTACCTATGCTGGAGGTTGTGCCTCTTCGCCTGC-AACCCTTAATTTTAT
1 GGAGCTTTGCTCTCGCTAACTGTGCTGGAGGTCGTGGCTCTTCGCCTGCGAA-CCTTAATTTTAC
** *
53548114 AGCTA
65 AATTG
* * * * *
53548119 GGAGCTTTGCTCTC-ATTACTTGTGCTGGAGGTCGCGGCTCTTCACCTGCAAACCTTAATTTTAC
1 GGAGCTTTGCTCTCGCTAAC-TGTGCTGGAGGTCGTGGCTCTTCGCCTGCGAACCTTAATTTTAC
*
53548183 AACTG
65 AATTG
* * ** * * * **
53548188 GGAGCTTTGTTCTTGCTAACCATGCTGAAGGTTGCGGCTCTTCGCCTGTAAACCTTAATTTTACA
1 GGAGCTTTGCTCTCGCTAACTGTGCTGGAGGTCGTGGCTCTTCGCCTGCGAACCTTAATTTTACA
53548253 GGTAACATTT
Statistics
Matches: 326, Mismatches: 76, Indels: 16
0.78 0.18 0.04
Matches are distributed among these distances:
68 6 0.02
69 314 0.96
70 6 0.02
ACGTcount: A:0.18, C:0.24, G:0.23, T:0.35
Consensus pattern (69 bp):
GGAGCTTTGCTCTCGCTAACTGTGCTGGAGGTCGTGGCTCTTCGCCTGCGAACCTTAATTTTACA
ATTG
Found at i:53547999 original size:138 final size:138
Alignment explanation
Indices: 53547826--53548253 Score: 450
Period size: 138 Copynumber: 3.1 Consensus size: 138
53547816 TGCCTGGGGT
* * * * * * * *
53547826 CCTTAATTTTACAGTTGGGAGCTTTTCCCTCGCTAACTGTGTTAGAGGTCATGGCACTTCACCTG
1 CCTTAATTTTACAGTTGAGAGCTTTGCTCTTGCTAACTGTGCTGGAGGTCACGGCTCTTCACCTG
* * * * *
53547891 CGAACCTTAGTTTTACAGA-TGGGAGCTTTGCTCTCACTAACTATGTTGCAGGTCGTGGCTCTTC
66 CGAACCTTAATTTTACA-ACTGGGAGCTTTGCTCTCGCTAACTATGCTGAAGGTTGTGGCTCTTC
* **
53547955 GCCTATAGG
130 GCCTGTAAA
* * ** *
53547964 CCTTAATTTTACAATTGAGAGCTTTGCTCTTGCTAACTGTGCTGGAGGTTACACCTCTTCGCCTG
1 CCTTAATTTTACAGTTGAGAGCTTTGCTCTTGCTAACTGTGCTGGAGGTCACGGCTCTTCACCTG
* * * * * *
53548029 TGAACCTTAATTTTACAATTGGGAACTTTGCTCTCGCTACCTATGCTGGAGGTTGTGCCTCTTCG
66 CGAACCTTAATTTTACAACTGGGAGCTTTGCTCTCGCTAACTATGCTGAAGGTTGTGGCTCTTCG
* *
53548094 CCTGCAAC
131 CCTGTAAA
* * * *
53548102 CCTTAATTTTATAGCT-AGGAGCTTTGCTC-T-CATTACTTGTGCTGGAGGTCGCGGCTCTTCAC
1 CCTTAATTTTACAGTTGA-GAGCTTTGCTCTTGC-TAAC-TGTGCTGGAGGTCACGGCTCTTCAC
* * * * *
53548164 CTGCAAACCTTAATTTTACAACTGGGAGCTTTGTTCTTGCTAACCATGCTGAAGGTTGCGGCTCT
63 CTGCGAACCTTAATTTTACAACTGGGAGCTTTGCTCTCGCTAACTATGCTGAAGGTTGTGGCTCT
53548229 TCGCCTGTAAA
128 TCGCCTGTAAA
53548240 CCTTAATTTTACAG
1 CCTTAATTTTACAG
53548254 GTAACATTTT
Statistics
Matches: 237, Mismatches: 49, Indels: 8
0.81 0.17 0.03
Matches are distributed among these distances:
136 1 0.00
137 6 0.03
138 230 0.97
ACGTcount: A:0.19, C:0.24, G:0.21, T:0.35
Consensus pattern (138 bp):
CCTTAATTTTACAGTTGAGAGCTTTGCTCTTGCTAACTGTGCTGGAGGTCACGGCTCTTCACCTG
CGAACCTTAATTTTACAACTGGGAGCTTTGCTCTCGCTAACTATGCTGAAGGTTGTGGCTCTTCG
CCTGTAAA
Found at i:53548177 original size:207 final size:207
Alignment explanation
Indices: 53547826--53548252 Score: 491
Period size: 207 Copynumber: 2.1 Consensus size: 207
53547816 TGCCTGGGGT
* * * * * *
53547826 CCTTAATTTTACAGTTGGGAGCTTTTCCCTCGCTAACTGTGTTAGAGGTCATGGCACTTCACCTG
1 CCTTAATTTTACAATTGGGAACTTTGCCCTCGCTAACTATGCTAGAGGTCATGCCACTTCACCTG
* * * *
53547891 CGAACCTTAGTTTTACAGATGGGAGCTTTGCTCTCACTAACTATGTTGCAGGTCGTGGCTCTTCG
66 CGAACCTTAATTTTACAGATAGGAGCTTTGCTCTCACTAACTATGTTGCAGGTCGCGGCTCTTCA
* ** * ** *
53547956 CCTATAGGCCTTAATTTTACAATTGAGAGCTTTGCTCTTGCTAACTGTGCTGGAGGTTACACCTC
131 CCTACAAACCTTAATTTTACAACTGAGAGCTTTGCTCTTGCTAACCATGCTGAAGGTTACACCTC
*
53548021 TTCGCCTGTGAA
196 TTCGCCTGTAAA
* * * ** * *
53548033 CCTTAATTTTACAATTGGGAACTTTGCTCTCGCTACCTATGCTGGAGGTTGTGCCTCTTCGCCTG
1 CCTTAATTTTACAATTGGGAACTTTGCCCTCGCTAACTATGCTAGAGGTCATGCCACTTCACCTG
* * * *
53548098 C-AACCCTTAATTTTATAGCTAGGAGCTTTGCTCTCA-TTACT-TGTGCTGGAGGTCGCGGCTCT
66 CGAA-CCTTAATTTTACAGATAGGAGCTTTGCTCTCACTAACTATGT--TGCAGGTCGCGGCTCT
* * * * **
53548160 TCACCTGCAAACCTTAATTTTACAACTGGGAGCTTTGTTCTTGCTAACCATGCTGAAGGTTGCGG
128 TCACCTACAAACCTTAATTTTACAACTGAGAGCTTTGCTCTTGCTAACCATGCTGAAGGTTACAC
53548225 CTCTTCGCCTGTAAA
193 CTCTTCGCCTGTAAA
53548240 CCTTAATTTTACA
1 CCTTAATTTTACA
53548253 GGTAACATTT
Statistics
Matches: 182, Mismatches: 35, Indels: 6
0.82 0.16 0.03
Matches are distributed among these distances:
205 3 0.02
206 6 0.03
207 173 0.95
ACGTcount: A:0.19, C:0.24, G:0.21, T:0.35
Consensus pattern (207 bp):
CCTTAATTTTACAATTGGGAACTTTGCCCTCGCTAACTATGCTAGAGGTCATGCCACTTCACCTG
CGAACCTTAATTTTACAGATAGGAGCTTTGCTCTCACTAACTATGTTGCAGGTCGCGGCTCTTCA
CCTACAAACCTTAATTTTACAACTGAGAGCTTTGCTCTTGCTAACCATGCTGAAGGTTACACCTC
TTCGCCTGTAAA
Found at i:53552627 original size:26 final size:25
Alignment explanation
Indices: 53552610--53552670 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
53552600 AAGCTCTTTC
53552610 GAGCTGAAATAACGGTAAGCTCATAT
1 GAGCTG-AATAACGGTAAGCTCATAT
* * *
53552636 GAGCTGAGTATCGGTAAGCTCATAA
1 GAGCTGAATAACGGTAAGCTCATAT
53552661 GAGCTTGAAT
1 GAGC-TGAAT
53552671 CGATAACCCT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
25 20 0.67
26 10 0.33
ACGTcount: A:0.34, C:0.15, G:0.26, T:0.25
Consensus pattern (25 bp):
GAGCTGAATAACGGTAAGCTCATAT
Found at i:53560202 original size:25 final size:25
Alignment explanation
Indices: 53560154--53560245 Score: 91
Period size: 25 Copynumber: 3.7 Consensus size: 25
53560144 GTACATGTAT
*
53560154 GCTCATACGAGC-G-ATAAATGGTAA
1 GCTCATATGAGCTGAAT-AATGGTAA
* *
53560178 GCTCTTCTGAGCTGAATAATGGTAA
1 GCTCATATGAGCTGAATAATGGTAA
*
53560203 GCTCATATGAGCTGAGT-ATCGGTAA
1 GCTCATATGAGCTGAATAAT-GGTAA
*
53560228 GCTCATAAGAGCTTGAAT
1 GCTCATATGAGC-TGAAT
53560246 CAATAACCCT
Statistics
Matches: 56, Mismatches: 8, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
24 11 0.20
25 39 0.70
26 6 0.11
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.27
Consensus pattern (25 bp):
GCTCATATGAGCTGAATAATGGTAA
Found at i:53565615 original size:111 final size:111
Alignment explanation
Indices: 53565418--53565747 Score: 617
Period size: 111 Copynumber: 3.0 Consensus size: 111
53565408 ATATAAAAAT
53565418 ATTCTTCTATAATTAACATTTCATGCTTATAACTCTTAATTTCTGATATCTGTAATTGAATCATT
1 ATTCTTCTATAATTAACATTTCATGCTTATAACTCTTAATTTCTGATATCTGTAATTGAATCATT
*
53565483 AAAGTATTAGTTACACGCTGTACCATTCAACCATCACATTTGAATC
66 AAAGTATTAGTTACACACTGTACCATTCAACCATCACATTTGAATC
53565529 ATTCTTCTATAATTAACATTTCATGCTTATAACTCTTAATTTCTGATATCTGTAATTGAATCATT
1 ATTCTTCTATAATTAACATTTCATGCTTATAACTCTTAATTTCTGATATCTGTAATTGAATCATT
*
53565594 AAAGTATTAGTCACACACTGTACCATTCAACCATCACATTTGAATC
66 AAAGTATTAGTTACACACTGTACCATTCAACCATCACATTTGAATC
*
53565640 ATTCTTCTATAATTAACATTTCATGCTTATAACTCTTAATTTCTGATATCTATAATTGAATCATT
1 ATTCTTCTATAATTAACATTTCATGCTTATAACTCTTAATTTCTGATATCTGTAATTGAATCATT
53565705 AAAGTATTAGTTACACGA-TGTACCATTCAACCATCACATTTGA
66 AAAGTATTAGTTACAC-ACTGTACCATTCAACCATCACATTTGA
53565748 CCTATCAGTT
Statistics
Matches: 214, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
111 213 1.00
112 1 0.00
ACGTcount: A:0.33, C:0.19, G:0.08, T:0.40
Consensus pattern (111 bp):
ATTCTTCTATAATTAACATTTCATGCTTATAACTCTTAATTTCTGATATCTGTAATTGAATCATT
AAAGTATTAGTTACACACTGTACCATTCAACCATCACATTTGAATC
Found at i:53567876 original size:33 final size:33
Alignment explanation
Indices: 53567839--53567904 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
53567829 TATCCTGATC
53567839 TATACTTTAAAATATAATTTGGATGACCAAAAT
1 TATACTTTAAAATATAATTTGGATGACCAAAAT
53567872 TATACTTTAAAATATAATTTGGATGACCAAAAT
1 TATACTTTAAAATATAATTTGGATGACCAAAAT
53567905 ATAGGAATCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.36
Consensus pattern (33 bp):
TATACTTTAAAATATAATTTGGATGACCAAAAT
Found at i:53567970 original size:21 final size:21
Alignment explanation
Indices: 53567944--53567987 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
53567934 GGACGGGTAA
53567944 AATTAGAAACTATAAAACTAG
1 AATTAGAAACTATAAAACTAG
53567965 AATTAGAAACTATAAAACTAG
1 AATTAGAAACTATAAAACTAG
53567986 AA
1 AA
53567988 ACTCCAACTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.59, C:0.09, G:0.09, T:0.23
Consensus pattern (21 bp):
AATTAGAAACTATAAAACTAG
Found at i:53570604 original size:84 final size:82
Alignment explanation
Indices: 53570431--53570659 Score: 323
Period size: 84 Copynumber: 2.7 Consensus size: 82
53570421 TAACTTTTGC
* ** * * *
53570431 TTTAATTCGTCAATGAAACAGTGCCATTTTGTTAAATTTTTAATATATTTTTTGCGGCATTTTTA
1 TTTAATTCATCAATGAAAC-GAACCGTTTTGTTAAATTTTTAATATATTTTTTGCGGCGTTTGTA
*
53570496 TAGAAAACGCCACTAATA
65 TACAAAACGCCACTAATA
*
53570514 TTTAATTCATCAATGAAACGACACCGTTTTATTAAATTTTTAATATATTTTTTTGCGGCGTTTGT
1 TTTAATTCATCAATGAAACGA-ACCGTTTTGTTAAATTTTTAATATA-TTTTTTGCGGCGTTTGT
*
53570579 ATACAAAACGCCACTGATA
64 ATACAAAACGCCACTAATA
* *
53570598 TTTAATTCATCAATGAAACGTATCCGTTTTGTTAAATTTTAAATATATTTTTTGCGGCGTTT
1 TTTAATTCATCAATGAAACG-AACCGTTTTGTTAAATTTTTAATATATTTTTTGCGGCGTTT
53570660 TTGACCAAAC
Statistics
Matches: 131, Mismatches: 12, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
82 1 0.01
83 55 0.42
84 74 0.56
85 1 0.01
ACGTcount: A:0.31, C:0.14, G:0.12, T:0.43
Consensus pattern (82 bp):
TTTAATTCATCAATGAAACGAACCGTTTTGTTAAATTTTTAATATATTTTTTGCGGCGTTTGTAT
ACAAAACGCCACTAATA
Found at i:53570831 original size:14 final size:14
Alignment explanation
Indices: 53570814--53570841 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
53570804 ATGACATTAT
53570814 TAATATTATTTAAA
1 TAATATTATTTAAA
53570828 TAATATTATTTAAA
1 TAATATTATTTAAA
53570842 ATTTTGATAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TAATATTATTTAAA
Found at i:53571364 original size:21 final size:20
Alignment explanation
Indices: 53571338--53571419 Score: 74
Period size: 21 Copynumber: 4.0 Consensus size: 20
53571328 TAACAAATCA
53571338 TAAACCCTAAACTCTAAACTC
1 TAAACCCTAAACTCTAAAC-C
*
53571359 TAAACCCCAAACTCATAAACC
1 TAAACCCTAAACTC-TAAACC
** *
53571380 TGTTACCCTAAACACTAAACC
1 T-AAACCCTAAACTCTAAACC
* * *
53571401 TACACCATAAACCCTAAAC
1 TAAACCCTAAACTCTAAAC
53571420 TCAAAATTAT
Statistics
Matches: 50, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
20 14 0.28
21 22 0.44
22 14 0.28
ACGTcount: A:0.44, C:0.35, G:0.01, T:0.20
Consensus pattern (20 bp):
TAAACCCTAAACTCTAAACC
Found at i:53571418 original size:7 final size:7
Alignment explanation
Indices: 53571338--53571419 Score: 51
Period size: 7 Copynumber: 11.7 Consensus size: 7
53571328 TAACAAATCA
53571338 TAAACCC
1 TAAACCC
*
53571345 TAAACTC
1 TAAACCC
*
53571352 TAAACTC
1 TAAACCC
53571359 TAAACCC
1 TAAACCC
* *
53571366 CAAACTCA
1 TAAAC-CC
53571374 TAAA-CC
1 TAAACCC
**
53571380 TGTTACCC
1 T-AAACCC
*
53571388 TAAACAC
1 TAAACCC
53571395 TAAA-CC
1 TAAACCC
* *
53571401 TACACCA
1 TAAACCC
53571408 TAAACCC
1 TAAACCC
53571415 TAAAC
1 TAAAC
53571420 TCAAAATTAT
Statistics
Matches: 55, Mismatches: 16, Indels: 8
0.70 0.20 0.10
Matches are distributed among these distances:
6 6 0.11
7 42 0.76
8 7 0.13
ACGTcount: A:0.44, C:0.35, G:0.01, T:0.20
Consensus pattern (7 bp):
TAAACCC
Found at i:53572297 original size:41 final size:42
Alignment explanation
Indices: 53572249--53572592 Score: 299
Period size: 41 Copynumber: 8.5 Consensus size: 42
53572239 TATTTTTTGA
*
53572249 GGCGCTTTCA-CAAAAACACCGCTAAAAACCCGAGCATTAGC
1 GGCGCTTTCATCAAAAACGCCGCTAAAAACCCGAGCATTAGC
* * * *
53572290 GGTGCTTT-TTCAAAAACGCTC-CTAAAAACCCAACCATTAGC
1 GGCGCTTTCATCAAAAACGC-CGCTAAAAACCCGAGCATTAGC
* * * ***
53572331 AGCACTTTC-TCAAAAACGCCGCTAAAATCTAAAGCATTAGC
1 GGCGCTTTCATCAAAAACGCCGCTAAAAACCCGAGCATTAGC
* * *
53572372 AGCGC-TTC-TCTAAAAACGCCGCTAAAACCCCCAGCATTAGC
1 GGCGCTTTCATC-AAAAACGCCGCTAAAAACCCGAGCATTAGC
* * * *
53572413 GGTG-TTT-AGT-ATTAAATGTCGCT-AAAACCCTGAGCATTAGC
1 GGCGCTTTCA-TCA-AAAACGCCGCTAAAAACCC-GAGCATTAGC
*
53572454 GGCGC-TTCATCGAAAACGCCGCT-AAAACCCAGAGCATTAGC
1 GGCGCTTTCATCAAAAACGCCGCTAAAAACCC-GAGCATTAGC
* *
53572495 GGCGC-TTCATCGAAAACGCCGCT-AAAATCC-AGCATTAGC
1 GGCGCTTTCATCAAAAACGCCGCTAAAAACCCGAGCATTAGC
*
53572534 GGCGCTTT-ATCAAAAACGCCGCTAAAACCCCGAGCATTAGC
1 GGCGCTTTCATCAAAAACGCCGCTAAAAACCCGAGCATTAGC
* *
53572575 GACGC-TTCATGAAAAACG
1 GGCGCTTTCATCAAAAACG
53572593 TCTCTAAAGC
Statistics
Matches: 250, Mismatches: 36, Indels: 34
0.78 0.11 0.11
Matches are distributed among these distances:
39 28 0.11
40 22 0.09
41 197 0.79
42 3 0.01
ACGTcount: A:0.33, C:0.29, G:0.18, T:0.20
Consensus pattern (42 bp):
GGCGCTTTCATCAAAAACGCCGCTAAAAACCCGAGCATTAGC
Found at i:53572414 original size:123 final size:123
Alignment explanation
Indices: 53572250--53572592 Score: 348
Period size: 123 Copynumber: 2.8 Consensus size: 123
53572240 ATTTTTTGAG
* * *
53572250 GCGCTTTCA-CAAAAACACCGCTAAAAACCCGAGCATTAGCGGTGCTTTTTCAAAAACGCTC-CT
1 GCGC-TTCATCAAAAACGCCGCT-AAAACCCCAGCATTAGCGGTGCTTTATCAAAAACGCTCGCT
* * * *
53572313 AAAAACCCAACCATTAGCAGCACTTTC-TCAAAAACGCCGCTAAAATCTAAAGCATTAGCA
64 AAAAACCCGAGCATTAGCAGCAC-TTCATCAAAAACGCCGCTAAAACCCAAAGCATTAGCA
* *
53572373 GCGCTTC-TCTAAAAACGCCGCTAAAACCCCCAGCATTAGCGGTG-TTTAGT-ATTAAATG-TCG
1 GCGCTTCATC-AAAAACGCCGCTAAAA-CCCCAGCATTAGCGGTGCTTTA-TCA-AAAACGCTCG
* * * * *
53572434 CT-AAAACCCTGAGCATTAGCGGCGCTTCATCGAAAACGCCGCTAAAACCCAGAGCATTAGCG
62 CTAAAAACCC-GAGCATTAGCAGCACTTCATCAAAAACGCCGCTAAAACCCAAAGCATTAGCA
* * *
53572496 GCGCTTCATCGAAAACGCCGCTAAAA-TCCAGCATTAGCGGCGCTTTATCAAAAACGC-CGCTAA
1 GCGCTTCATCAAAAACGCCGCTAAAACCCCAGCATTAGCGGTGCTTTATCAAAAACGCTCGCTAA
* * *
53572559 AACCCCGAGCATTAGC-GACGCTTCATGAAAAACG
66 AAACCCGAGCATTAGCAG-CACTTCATCAAAAACG
53572593 TCTCTAAAGC
Statistics
Matches: 184, Mismatches: 22, Indels: 30
0.78 0.09 0.13
Matches are distributed among these distances:
120 1 0.01
121 47 0.26
122 35 0.19
123 99 0.54
124 2 0.01
ACGTcount: A:0.34, C:0.29, G:0.17, T:0.20
Consensus pattern (123 bp):
GCGCTTCATCAAAAACGCCGCTAAAACCCCAGCATTAGCGGTGCTTTATCAAAAACGCTCGCTAA
AAACCCGAGCATTAGCAGCACTTCATCAAAAACGCCGCTAAAACCCAAAGCATTAGCA
Found at i:53581723 original size:26 final size:26
Alignment explanation
Indices: 53581694--53581750 Score: 87
Period size: 26 Copynumber: 2.2 Consensus size: 26
53581684 AGTAATTATT
*
53581694 AATATATGTACCAAGTTGTTGATTTG
1 AATATATGTACAAAGTTGTTGATTTG
* *
53581720 AATATGTTTACAAAGTTGTTGATTTG
1 AATATATGTACAAAGTTGTTGATTTG
53581746 AATAT
1 AATAT
53581751 GTTTACATGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.33, C:0.05, G:0.18, T:0.44
Consensus pattern (26 bp):
AATATATGTACAAAGTTGTTGATTTG
Found at i:53581751 original size:26 final size:26
Alignment explanation
Indices: 53581706--53581757 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
53581696 TATATGTACC
53581706 AAGTTGTTGATTTGAATATGTTTACA
1 AAGTTGTTGATTTGAATATGTTTACA
53581732 AAGTTGTTGATTTGAATATGTTTACA
1 AAGTTGTTGATTTGAATATGTTTACA
53581758 TGTATGGCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.31, C:0.04, G:0.19, T:0.46
Consensus pattern (26 bp):
AAGTTGTTGATTTGAATATGTTTACA
Found at i:53591227 original size:14 final size:16
Alignment explanation
Indices: 53591197--53591228 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
53591187 TTATAAGGCC
53591197 TTTATAATTTCTGGAT
1 TTTATAATTTCTGGAT
53591213 TTTA-AATTT-TGGAT
1 TTTATAATTTCTGGAT
53591227 TT
1 TT
53591229 GCTTTGATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 5 0.31
16 4 0.25
ACGTcount: A:0.25, C:0.03, G:0.12, T:0.59
Consensus pattern (16 bp):
TTTATAATTTCTGGAT
Found at i:53594568 original size:3 final size:3
Alignment explanation
Indices: 53594560--53594592 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
53594550 CTGAAAGAGG
53594560 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
53594593 CTTTTCTTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:53599264 original size:21 final size:21
Alignment explanation
Indices: 53599240--53599284 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
53599230 ATCAGTACCA
53599240 AAACATGACAAAATTAAGGAT
1 AAACATGACAAAATTAAGGAT
53599261 AAACATGACAAAATTAAGGAT
1 AAACATGACAAAATTAAGGAT
53599282 AAA
1 AAA
53599285 TTAAGGATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.60, C:0.09, G:0.13, T:0.18
Consensus pattern (21 bp):
AAACATGACAAAATTAAGGAT
Found at i:53599287 original size:11 final size:11
Alignment explanation
Indices: 53599271--53599295 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
53599261 AAACATGACA
53599271 AAATTAAGGAT
1 AAATTAAGGAT
53599282 AAATTAAGGAT
1 AAATTAAGGAT
53599293 AAA
1 AAA
53599296 CATCGCACCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.60, C:0.00, G:0.16, T:0.24
Consensus pattern (11 bp):
AAATTAAGGAT
Found at i:53602145 original size:10 final size:10
Alignment explanation
Indices: 53602124--53602153 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
53602114 GCTTCCACCG
53602124 ATCTCG-TCC
1 ATCTCGCTCC
53602133 ATCTCGCTCC
1 ATCTCGCTCC
53602143 ATCTCGCTCC
1 ATCTCGCTCC
53602153 A
1 A
53602154 GATTATCAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 6 0.30
10 14 0.70
ACGTcount: A:0.13, C:0.47, G:0.10, T:0.30
Consensus pattern (10 bp):
ATCTCGCTCC
Found at i:53609590 original size:17 final size:16
Alignment explanation
Indices: 53609559--53609592 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
53609549 AAATATTATG
53609559 AAATAAAAACAAACAA
1 AAATAAAAACAAACAA
*
53609575 AAATAAACATCAAACAA
1 AAATAAA-AACAAACAA
53609592 A
1 A
53609593 CACCATCCCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.76, C:0.15, G:0.00, T:0.09
Consensus pattern (16 bp):
AAATAAAAACAAACAA
Found at i:53618960 original size:5 final size:5
Alignment explanation
Indices: 53618952--53618989 Score: 76
Period size: 5 Copynumber: 7.6 Consensus size: 5
53618942 ATATTATAAC
53618952 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAA
53618990 TATATGTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
TAAAA
Found at i:53620317 original size:12 final size:11
Alignment explanation
Indices: 53620300--53620356 Score: 57
Period size: 10 Copynumber: 5.2 Consensus size: 11
53620290 AACAAATCCT
53620300 CTCTCATATTTC
1 CTCTCA-ATTTC
53620312 CTCTCAA-TTC
1 CTCTCAATTTC
53620322 CTCTCAATTTC
1 CTCTCAATTTC
*
53620333 CT-TCCAAAATT-
1 CTCT-C-AATTTC
53620344 CTCTCAATTTC
1 CTCTCAATTTC
53620355 CT
1 CT
53620357 TCTAAAATTC
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
10 15 0.39
11 12 0.32
12 11 0.29
ACGTcount: A:0.21, C:0.35, G:0.00, T:0.44
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:53620347 original size:22 final size:22
Alignment explanation
Indices: 53620317--53620372 Score: 94
Period size: 22 Copynumber: 2.5 Consensus size: 22
53620307 ATTTCCTCTC
53620317 AATTCCTCTCAATTTCCTTCCAA
1 AATT-CTCTCAATTTCCTTCCAA
*
53620340 AATTCTCTCAATTTCCTTCTAA
1 AATTCTCTCAATTTCCTTCCAA
53620362 AATTCTCTCAA
1 AATTCTCTCAA
53620373 ATCTATATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 28 0.88
23 4 0.12
ACGTcount: A:0.29, C:0.30, G:0.00, T:0.41
Consensus pattern (22 bp):
AATTCTCTCAATTTCCTTCCAA
Found at i:53620401 original size:51 final size:51
Alignment explanation
Indices: 53620344--53620459 Score: 205
Period size: 51 Copynumber: 2.3 Consensus size: 51
53620334 TTCCAAAATT
* *
53620344 CTCTCAATTTCCTTCTAAAATTCTCTCAAATCTATATTTAATTTCAATTTC
1 CTCTCAATTTCCTTCAAAAATTCTCTCAAATCCATATTTAATTTCAATTTC
53620395 CTCTCAATTTCCTTCAAAAATTCTCTCAAATCCATATTTAATTTCAATTTC
1 CTCTCAATTTCCTTCAAAAATTCTCTCAAATCCATATTTAATTTCAATTTC
*
53620446 TTCTCAATTTCCTT
1 CTCTCAATTTCCTT
53620460 TTTTAAAATA
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
51 62 1.00
ACGTcount: A:0.28, C:0.25, G:0.00, T:0.47
Consensus pattern (51 bp):
CTCTCAATTTCCTTCAAAAATTCTCTCAAATCCATATTTAATTTCAATTTC
Found at i:53621600 original size:7 final size:7
Alignment explanation
Indices: 53621588--53621612 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
53621578 ATTTGATTGA
53621588 TATTTAG
1 TATTTAG
53621595 TATTTAG
1 TATTTAG
53621602 TATTTAG
1 TATTTAG
53621609 TATT
1 TATT
53621613 ATGTATGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:53625963 original size:22 final size:22
Alignment explanation
Indices: 53625947--53625991 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
53625937 TATAACATCA
53625947 ACCAAGACATGGCATAAAACAT
1 ACCAAGACATGGCATAAAACAT
*
53625969 ACTAAGACATGGCATAAAACAT
1 ACCAAGACATGGCATAAAACAT
53625991 A
1 A
53625992 TCAACATTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.51, C:0.20, G:0.13, T:0.16
Consensus pattern (22 bp):
ACCAAGACATGGCATAAAACAT
Found at i:53626470 original size:41 final size:41
Alignment explanation
Indices: 53626357--53626496 Score: 167
Period size: 41 Copynumber: 3.4 Consensus size: 41
53626347 GTACAACTTA
* * *
53626357 CCTGATACAATACACCAGTACGAAGCCTGCTAAGC-TCAAAG
1 CCTGATATAATACACCAGCACGAAGCCTGCTAGGCAT-AAAG
* * *
53626398 CCTAATATAACACACC-GACACAAAGCCTGCTAGGCATAAAG
1 CCTGATATAATACACCAG-CACGAAGCCTGCTAGGCATAAAG
* *
53626439 CCTGATATAATACACCAGCGCGAAGCTTGCTAGGCATAAAG
1 CCTGATATAATACACCAGCACGAAGCCTGCTAGGCATAAAG
*
53626480 CCCGATATAATACACCA
1 CCTGATATAATACACCA
53626497 TAACATCACG
Statistics
Matches: 84, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
40 1 0.01
41 81 0.96
42 2 0.02
ACGTcount: A:0.38, C:0.29, G:0.16, T:0.17
Consensus pattern (41 bp):
CCTGATATAATACACCAGCACGAAGCCTGCTAGGCATAAAG
Found at i:53626798 original size:45 final size:45
Alignment explanation
Indices: 53626749--53626873 Score: 153
Period size: 46 Copynumber: 2.8 Consensus size: 45
53626739 ATTTGATTTG
* *
53626749 TGATGCCATAGCGTCTTTCAGCTATGGACTTAC-ACGATAGAATCA
1 TGATGCCATAACGTCTTTCAGCTATGGTCTTACTA-GATAGAATCA
* * * * *
53626794 TGATGCCATATATGGCTTTCACCTATGGTCTGACTAGATAGAATCG
1 TGATGCCATA-ACGTCTTTCAGCTATGGTCTTACTAGATAGAATCA
*
53626840 TGATGCCATAACGTCTTTTAGCTATGGTCTTACT
1 TGATGCCATAACGTCTTTCAGCTATGGTCTTACT
53626874 CGTTTTTGCT
Statistics
Matches: 66, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
45 29 0.44
46 36 0.55
47 1 0.02
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.34
Consensus pattern (45 bp):
TGATGCCATAACGTCTTTCAGCTATGGTCTTACTAGATAGAATCA
Found at i:53626901 original size:45 final size:45
Alignment explanation
Indices: 53626843--53626958 Score: 108
Period size: 45 Copynumber: 2.6 Consensus size: 45
53626833 AGAATCGTGA
* * *
53626843 TGCCATA-ACGTCTTTTAGCTATGGTCTTACTCGTTTTTGCTATGG
1 TGCCATAGA-GTCTTTTAGCTATGGTCTTACTCATTTCTGCTATAG
* * * * * * * *
53626888 TGCCATAGTGTCTTTCAACTTTGTTCTTATTTATTTCTGGTATAG
1 TGCCATAGAGTCTTTTAGCTATGGTCTTACTCATTTCTGCTATAG
*
53626933 TGTCATAGAGTCTTTTAGCTATGGTC
1 TGCCATAGAGTCTTTTAGCTATGGTC
53626959 CTAATAATTT
Statistics
Matches: 53, Mismatches: 17, Indels: 2
0.74 0.24 0.03
Matches are distributed among these distances:
45 53 1.00
ACGTcount: A:0.17, C:0.17, G:0.19, T:0.47
Consensus pattern (45 bp):
TGCCATAGAGTCTTTTAGCTATGGTCTTACTCATTTCTGCTATAG
Found at i:53636494 original size:45 final size:45
Alignment explanation
Indices: 53636438--53636593 Score: 143
Period size: 45 Copynumber: 3.5 Consensus size: 45
53636428 TGTCATTGTT
* * **
53636438 TCTTTCAACTATGGTCTTA-TTCGTTTGATTCATGATACAATAGTG
1 TCTTTCAACTATGGTCTTACTT-GATTGAATCATGATACAATAACG
* * *
53636483 TCTTTCAACTATGCTCTTACTTGATTGAATCATGATGCCATAACG
1 TCTTTCAACTATGGTCTTACTTGATTGAATCATGATACAATAACG
* * * * * *
53636528 TCTTTCACCTATGGTCTTCCTAGATAGAATCATGATGCCATAACG
1 TCTTTCAACTATGGTCTTACTTGATTGAATCATGATACAATAACG
* * * *
53636573 TCCTTCATCTCTTGTCTTACT
1 TCTTTCAACTATGGTCTTACT
53636594 CGTTTCTGGT
Statistics
Matches: 93, Mismatches: 17, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
45 91 0.98
46 2 0.02
ACGTcount: A:0.24, C:0.22, G:0.13, T:0.40
Consensus pattern (45 bp):
TCTTTCAACTATGGTCTTACTTGATTGAATCATGATACAATAACG
Found at i:53641121 original size:12 final size:12
Alignment explanation
Indices: 53641096--53641134 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
53641086 ACTCGCTTCT
* *
53641096 TTACTTACTCAC
1 TTACTTGCTTAC
*
53641108 TTACTTGTTTAC
1 TTACTTGCTTAC
53641120 TTACTTGCTTAC
1 TTACTTGCTTAC
53641132 TTA
1 TTA
53641135 AATAACTCAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.21, C:0.23, G:0.05, T:0.51
Consensus pattern (12 bp):
TTACTTGCTTAC
Found at i:53641458 original size:50 final size:50
Alignment explanation
Indices: 53641383--53641630 Score: 262
Period size: 50 Copynumber: 4.8 Consensus size: 50
53641373 TTTTCTGTAC
* * * ** *
53641383 TGCCAATGCCATATCCTAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGA
* * ** * *
53641433 TGCCCATGCCATGTCCCAAACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGA
* * *
53641483 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGAACCTCTCATCTCGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGA
*
53641533 TGCCAATGCTATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC---GA
* * * *
53641589 TGCCGATGCCATGTCCCATACATGGTCTTATATGGGATCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
53641631 TTACCCAAAT
Statistics
Matches: 166, Mismatches: 26, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
50 125 0.75
53 2 0.01
56 39 0.23
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.28
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGA
Found at i:53645655 original size:41 final size:41
Alignment explanation
Indices: 53645598--53645839 Score: 260
Period size: 41 Copynumber: 5.9 Consensus size: 41
53645588 ATAATTAATT
53645598 ATACCC-TGAATTGCACATATGTGCCCCTATTTGTACTTCG
1 ATACCCTTGAATTGCACATATGTGCCCCTATTTGTACTTCG
* * * *
53645638 GTACCCTTGCATTGCACATATGTGTCCCTATTCGTACTTCG
1 ATACCCTTGAATTGCACATATGTGCCCCTATTTGTACTTCG
*
53645679 ATACCCTTGAATTGCACATATATGCCCCTATTTGTACTTCG
1 ATACCCTTGAATTGCACATATGTGCCCCTATTTGTACTTCG
* * * *
53645720 GTACTGC-TGAATT-C-CATATGCGTGCCCCTGTTTGTACTTTG
1 ATAC-CCTTGAATTGCACATAT--GTGCCCCTATTTGTACTTCG
* * * *
53645761 ATA-GCTCTGAATTGCACATAAGTCCCCCTGTTTGTACTTCG
1 ATACCCT-TGAATTGCACATATGTGCCCCTATTTGTACTTCG
* * * *
53645802 ATACCCCTGAATAGCACATATATGCCCCTATTTATACT
1 ATACCCTTGAATTGCACATATGTGCCCCTATTTGTACT
53645840 CTGGTAACTT
Statistics
Matches: 167, Mismatches: 26, Indels: 17
0.80 0.12 0.08
Matches are distributed among these distances:
39 7 0.04
40 6 0.04
41 147 0.88
42 3 0.02
43 4 0.02
ACGTcount: A:0.22, C:0.27, G:0.15, T:0.36
Consensus pattern (41 bp):
ATACCCTTGAATTGCACATATGTGCCCCTATTTGTACTTCG
Found at i:53654645 original size:54 final size:54
Alignment explanation
Indices: 53654586--53654709 Score: 133
Period size: 54 Copynumber: 2.3 Consensus size: 54
53654576 ATGTCCTCAC
** *
53654586 CCGTGTAACTCACTGAGAAGGGTTACACGGCCATGTCG-CAAGCCGTGTGCCAGG
1 CCGTGTAACTCACTGAGAAGCCTTACACAGCCATGT-GTCAAGCCGTGTGCCAGG
* * ** * * * *
53654640 TCGTGTAACTCTCTGAGTTGCCTTACACAGTCGTGTGTCAGGCCGTGTGCTAGG
1 CCGTGTAACTCACTGAGAAGCCTTACACAGCCATGTGTCAAGCCGTGTGCCAGG
53654694 CCGTGTAACTCACTGA
1 CCGTGTAACTCACTGA
53654710 ATTAAAATGC
Statistics
Matches: 56, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
53 1 0.02
54 55 0.98
ACGTcount: A:0.19, C:0.27, G:0.29, T:0.25
Consensus pattern (54 bp):
CCGTGTAACTCACTGAGAAGCCTTACACAGCCATGTGTCAAGCCGTGTGCCAGG
Found at i:53657322 original size:18 final size:18
Alignment explanation
Indices: 53657299--53657338 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
53657289 ATTGAATTTG
* *
53657299 AAACAAAATTAAAAGAAA
1 AAACAAAAATAAAAAAAA
53657317 AAACAAAAATAAAAAAAA
1 AAACAAAAATAAAAAAAA
53657335 AAAC
1 AAAC
53657339 TGAGGGCCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.82, C:0.07, G:0.03, T:0.07
Consensus pattern (18 bp):
AAACAAAAATAAAAAAAA
Found at i:53658809 original size:88 final size:88
Alignment explanation
Indices: 53658638--53658815 Score: 214
Period size: 88 Copynumber: 2.0 Consensus size: 88
53658628 GGACCATGAG
* *
53658638 CTACTTCACTGTCGATGCAGGAAGGCAAGACCAGCTATCTTCAACCTGCTCCACTACAACCGAGG
1 CTACTTCACTGTCGATGCAGGAAGGCAAGACCAGCTATCTTCAACCTACTCCACTACAACCAAGG
* * *
53658703 GAGGCAAGCCTTGTGTCTTTGAT
66 GAGGCAAGCCTAGGGTCTTCGAT
* * * * * **
53658726 CTACTTCGCTGTCGATGTAGGAAGG-AAGGATCTGCTATCTTCAACCTATTCTGCTACAACCAAG
1 CTACTTCACTGTCGATGCAGGAAGGCAA-GACCAGCTATCTTCAACCTACTCCACTACAACCAAG
* *
53658790 GGAGGGAAGGCTAGGGTCTTCGAT
65 GGAGGCAAGCCTAGGGTCTTCGAT
53658814 CT
1 CT
53658816 GCTCCACTAC
Statistics
Matches: 75, Mismatches: 14, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
87 2 0.03
88 73 0.97
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.25
Consensus pattern (88 bp):
CTACTTCACTGTCGATGCAGGAAGGCAAGACCAGCTATCTTCAACCTACTCCACTACAACCAAGG
GAGGCAAGCCTAGGGTCTTCGAT
Found at i:53658909 original size:44 final size:44
Alignment explanation
Indices: 53658862--53659122 Score: 342
Period size: 44 Copynumber: 5.9 Consensus size: 44
53658852 TTCAACCTGC
** * * *
53658862 TCCACTGCTACTCAGGGAGCTAGGACTTACAATCTTCTACCTAC
1 TCCACTGCTGGTCAGGGAGCTAGGATTTACAATCTTCCACCTAT
*
53658906 TCCACTACTGGTCAGGGAGCTAGGATTTACAATCTTCCACCTAT
1 TCCACTGCTGGTCAGGGAGCTAGGATTTACAATCTTCCACCTAT
* * * *
53658950 TCCACTGCTGGTCAAGGAGCTAGGTTTTATAATCTTCCGCCTAT
1 TCCACTGCTGGTCAGGGAGCTAGGATTTACAATCTTCCACCTAT
* * * * * *
53658994 TCCACTGTTGTTCAGGGAACTAGGACTTATAGTCTTCCACCTAT
1 TCCACTGCTGGTCAGGGAGCTAGGATTTACAATCTTCCACCTAT
* *
53659038 TCCACTGCTAGTCAGGGAGCTAGGATTTACAATCTTCTACCTAT
1 TCCACTGCTGGTCAGGGAGCTAGGATTTACAATCTTCCACCTAT
* *
53659082 TCCACTGCTGGTCAGGGAGCTAGGATTTATAGTCTTCCACC
1 TCCACTGCTGGTCAGGGAGCTAGGATTTACAATCTTCCACC
53659123 GGTTTGTTCT
Statistics
Matches: 186, Mismatches: 31, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
44 186 1.00
ACGTcount: A:0.23, C:0.27, G:0.19, T:0.31
Consensus pattern (44 bp):
TCCACTGCTGGTCAGGGAGCTAGGATTTACAATCTTCCACCTAT
Found at i:53658913 original size:88 final size:87
Alignment explanation
Indices: 53658817--53659122 Score: 317
Period size: 88 Copynumber: 3.5 Consensus size: 87
53658807 CTTCGATCTG
* * * * ** *
53658817 CTCCACTACTGCTTAGGGAGATAAGATTTGTAATTTTCAACCTGCTCCACTGCTACTCAGGGAGC
1 CTCCACTACTG-TTAGGGAGATAGGATTTATAATCTTCCACCTATTCCACTGCTAGTCAGGGAGC
*
53658882 TAGGACTTACAATCTTCTACCTA
65 TAGGATTTACAATCTTCTACCTA
* * * * *
53658905 CTCCACTACTGGTCAGGGAGCTAGGATTTACAATCTTCCACCTATTCCACTGCTGGTCAAGGAGC
1 CTCCACTACT-GTTAGGGAGATAGGATTTATAATCTTCCACCTATTCCACTGCTAGTCAGGGAGC
* * **
53658970 TAGGTTTTATAATCTTCCGCCTA
65 TAGGATTTACAATCTTCTACCTA
* ** * *
53658993 TTCCACTGTTGTTCAGGGA-ACTAGGACTTATAGTCTTCCACCTATTCCACTGCTAGTCAGGGAG
1 CTCCACTACTGTT-AGGGAGA-TAGGATTTATAATCTTCCACCTATTCCACTGCTAGTCAGGGAG
53659057 CTAGGATTTACAATCTTCTACCTA
64 CTAGGATTTACAATCTTCTACCTA
* * * * *
53659081 TTCCACTGCTGGTCAGGGAGCTAGGATTTATAGTCTTCCACC
1 CTCCACTACT-GTTAGGGAGATAGGATTTATAATCTTCCACC
53659123 GGTTTGTTCT
Statistics
Matches: 178, Mismatches: 35, Indels: 10
0.80 0.16 0.04
Matches are distributed among these distances:
87 2 0.01
88 173 0.97
89 3 0.02
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.31
Consensus pattern (87 bp):
CTCCACTACTGTTAGGGAGATAGGATTTATAATCTTCCACCTATTCCACTGCTAGTCAGGGAGCT
AGGATTTACAATCTTCTACCTA
Found at i:53659009 original size:132 final size:132
Alignment explanation
Indices: 53658873--53659119 Score: 395
Period size: 132 Copynumber: 1.9 Consensus size: 132
53658863 CCACTGCTAC
* * *
53658873 TCAGGGAGCTAGGACTTACAATCTTCTACCTACTCCACTACTGGTCAGGGAGCTAGGATTTACAA
1 TCAGGGAACTAGGACTTACAATCTTCCACCTACTCCACTACTAGTCAGGGAGCTAGGATTTACAA
*
53658938 TCTTCCACCTATTCCACTGCTGGTCAAGGAGCTAGGTTTTATAATCTTCCGCCTATTCCACTGTT
66 TCTTCCACCTATTCCACTGCTGGTCAAGGAGCTAGGATTTATAATCTTCCGCCTATTCCACTGTT
53659003 GT
131 GT
* * * *
53659005 TCAGGGAACTAGGACTTATAGTCTTCCACCTATTCCACTGCTAGTCAGGGAGCTAGGATTTACAA
1 TCAGGGAACTAGGACTTACAATCTTCCACCTACTCCACTACTAGTCAGGGAGCTAGGATTTACAA
* * *
53659070 TCTTCTACCTATTCCACTGCTGGTCAGGGAGCTAGGATTTATAGTCTTCC
66 TCTTCCACCTATTCCACTGCTGGTCAAGGAGCTAGGATTTATAATCTTCC
53659120 ACCGGTTTGT
Statistics
Matches: 104, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
132 104 1.00
ACGTcount: A:0.23, C:0.26, G:0.20, T:0.32
Consensus pattern (132 bp):
TCAGGGAACTAGGACTTACAATCTTCCACCTACTCCACTACTAGTCAGGGAGCTAGGATTTACAA
TCTTCCACCTATTCCACTGCTGGTCAAGGAGCTAGGATTTATAATCTTCCGCCTATTCCACTGTT
GT
Found at i:53670346 original size:33 final size:31
Alignment explanation
Indices: 53670266--53670546 Score: 142
Period size: 33 Copynumber: 8.7 Consensus size: 31
53670256 GAATATAAAG
53670266 GGGGTTGCTAAGTGCTGATTCCCC-A--A--
1 GGGGTTGCTAAGTGCTGATTCCCCGATCATT
* * *
53670292 GGGGTTGCTAAGTGTTAATTCCCTGACTCATT
1 GGGGTTGCTAAGTGCTGATTCCCCGA-TCATT
53670324 GGTGGTTGCTAAGTGCTGATTCCACCGTATCTTGAATAT
1 GG-GGTTGCTAAGTGCTGATTCC-CCG-ATC----AT-T
* *
53670363 AAAGGGGTTGCTAAGTGTTGATT-CCC--T-A-A
1 ---GGGGTTGCTAAGTGCTGATTCCCCGATCATT
*
53670392 GGGGTTGCTAAGTGCTGATTCCCTGATTCATT
1 GGGGTTGCTAAGTGCTGATTCCCCGA-TCATT
*
53670424 GGTGGTTGCTAAGTGCTGA-TCCACCGTATTTTAAATGT
1 GG-GGTTGCTAAGTGCTGATTCC-CCG-A---T-CAT-T
*
53670462 GAAGGGGTTGCTAAGTGCTGATT-CCC-A-CA-A
1 ---GGGGTTGCTAAGTGCTGATTCCCCGATCATT
*
53670492 GGGGTTGCTAAGTGCTCATTCCCCGAATCATT
1 GGGGTTGCTAAGTGCTGATTCCCCG-ATCATT
53670524 GGTGGTTGCTAAGTGCTGATTCC
1 GG-GGTTGCTAAGTGCTGATTCC
53670547 ACCATATCTT
Statistics
Matches: 197, Mismatches: 18, Indels: 73
0.68 0.06 0.25
Matches are distributed among these distances:
26 40 0.20
27 22 0.11
28 3 0.02
30 3 0.02
31 4 0.02
32 10 0.05
33 55 0.28
34 5 0.03
35 1 0.01
36 3 0.02
37 3 0.02
38 3 0.02
39 5 0.03
40 18 0.09
41 20 0.10
42 2 0.01
ACGTcount: A:0.20, C:0.19, G:0.28, T:0.33
Consensus pattern (31 bp):
GGGGTTGCTAAGTGCTGATTCCCCGATCATT
Found at i:53670393 original size:26 final size:26
Alignment explanation
Indices: 53670364--53670415 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
53670354 CTTGAATATA
*
53670364 AAGGGGTTGCTAAGTGTTGATTCCCT
1 AAGGGGTTGCTAAGTGCTGATTCCCT
53670390 AAGGGGTTGCTAAGTGCTGATTCCCT
1 AAGGGGTTGCTAAGTGCTGATTCCCT
53670416 GATTCATTGG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.19, C:0.17, G:0.31, T:0.33
Consensus pattern (26 bp):
AAGGGGTTGCTAAGTGCTGATTCCCT
Found at i:53670428 original size:100 final size:100
Alignment explanation
Indices: 53670254--53670590 Score: 496
Period size: 100 Copynumber: 3.3 Consensus size: 100
53670244 CCTGAGTACA
* *
53670254 TTGAATATAAAGGGGGTTGCTAAGTGCTGATTCCCCAAGGGGTTGCTAAGTGTTAATTCCCTGAC
1 TTGAATATAAA-GGGGTTGCTAAGTGCTGATTCCCCAAGGGGTTGCTAAGTGCTAATTCCCTGAA
53670319 TCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
65 TCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
* * * *
53670355 TTGAATATAAAGGGGTTGCTAAGTGTTGATTCCCTAAGGGGTTGCTAAGTGCTGATTCCCTGATT
1 TTGAATATAAAGGGGTTGCTAAGTGCTGATTCCCCAAGGGGTTGCTAAGTGCTAATTCCCTGAAT
*
53670420 CATTGGTGGTTGCTAAGTGCTGA-TCCACCGTATT
66 CATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
* * * * *
53670454 TTAAATGTGAAGGGGTTGCTAAGTGCTGATTCCCACAAGGGGTTGCTAAGTGCTCATTCCCCGAA
1 TTGAATATAAAGGGGTTGCTAAGTGCTGATTCCC-CAAGGGGTTGCTAAGTGCTAATTCCCTGAA
*
53670519 TCATTGGTGGTTGCTAAGTGCTGATTCCACCATATC
65 TCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
* *
53670555 TTTGAATGTGAAAGGGGTTGCTAAGTGGTGATTCCC
1 -TTGAATAT-AAAGGGGTTGCTAAGTGCTGATTCCC
53670591 GAATCACTGG
Statistics
Matches: 213, Mismatches: 19, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
99 40 0.19
100 122 0.57
101 20 0.09
102 7 0.03
103 24 0.11
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.33
Consensus pattern (100 bp):
TTGAATATAAAGGGGTTGCTAAGTGCTGATTCCCCAAGGGGTTGCTAAGTGCTAATTCCCTGAAT
CATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
Found at i:53670501 original size:27 final size:29
Alignment explanation
Indices: 53670463--53670546 Score: 100
Period size: 27 Copynumber: 2.8 Consensus size: 29
53670453 TTTAAATGTG
53670463 AAGGGGTTGCTAAGTGCTGATTCCC-A-C
1 AAGGGGTTGCTAAGTGCTGATTCCCAATC
*
53670490 AAGGGGTTGCTAAGTGCTCATTCCCCGAATC
1 AAGGGGTTGCTAAGTGCTGATT-CCC-AATC
*
53670521 ATTGGTGGTTGCTAAGTGCTGATTCC
1 A-AGG-GGTTGCTAAGTGCTGATTCC
53670547 ACCATATCTT
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
27 21 0.44
28 3 0.06
30 1 0.02
31 2 0.04
32 4 0.08
33 17 0.35
ACGTcount: A:0.20, C:0.21, G:0.29, T:0.30
Consensus pattern (29 bp):
AAGGGGTTGCTAAGTGCTGATTCCCAATC
Found at i:53682156 original size:27 final size:30
Alignment explanation
Indices: 53682120--53682200 Score: 89
Period size: 27 Copynumber: 2.7 Consensus size: 30
53682110 GAATATAAAG
53682120 GGGGTTGCTAAGTGCTGATTCCC-C-CA-A
1 GGGGTTGCTAAGTGCTGATTCCCACTCATA
* *
53682147 GGGGTTGCTAAGTG-TTATTCCCTGACTCATT
1 GGGGTTGCTAAGTGCTGATTCCC--ACTCATA
53682178 GGTGGTTGCTAAGTGCTGATTCC
1 GG-GGTTGCTAAGTGCTGATTCC
53682201 ACCGTATCTT
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
26 7 0.16
27 14 0.32
29 1 0.02
30 2 0.05
31 2 0.05
32 12 0.27
33 6 0.14
ACGTcount: A:0.16, C:0.21, G:0.30, T:0.33
Consensus pattern (30 bp):
GGGGTTGCTAAGTGCTGATTCCCACTCATA
Found at i:53682277 original size:96 final size:98
Alignment explanation
Indices: 53682108--53682437 Score: 456
Period size: 96 Copynumber: 3.4 Consensus size: 98
53682098 CCTGAGTACA
*
53682108 TTGAATAT-AAAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGTTATTCCCTGA
1 TTGAATATGAAA-GGGGTTGCTAAGTGCTGATT-CCCCAA-GGGTTGCTAAGTGCTATTCCC-GA
*
53682172 CTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
62 ATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
* *
53682209 TTGAATAT-AAAGGGGTTGCTAAGTG-TGA-TCCCTAAGGGTTGCTAAGTGCTGATTCCCGATTC
1 TTGAATATGAAAGGGGTTGCTAAGTGCTGATTCCCCAAGGGTTGCTAAGTGCT-ATTCCCGAATC
* *
53682271 ATTGGTGGTTGCTAAGTGCTGATCCCACCGTATT
65 ATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
* * *
53682305 TTAAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCAAGGG-TGCTAA-TGCTATTCCCGAATCA
1 TTGAATATGAAAGGGGTTGCTAAGTGCTGATTCCCCAAGGGTTGCTAAGTGCTATTCCCGAATCA
*
53682368 TTGGTGGTTGCTAAGTGCTGATTCCACCATATC
66 TTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
* *
53682401 TTTGAATGTGAAAGGGGTTGCTAAGTGGTGATTCCCC
1 -TTGAATATGAAAGGGGTTGCTAAGTGCTGATTCCCC
53682438 GAATCACTGG
Statistics
Matches: 208, Mismatches: 16, Indels: 14
0.87 0.07 0.06
Matches are distributed among these distances:
96 97 0.47
97 64 0.31
98 10 0.05
99 12 0.06
100 14 0.07
101 11 0.05
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.32
Consensus pattern (98 bp):
TTGAATATGAAAGGGGTTGCTAAGTGCTGATTCCCCAAGGGTTGCTAAGTGCTATTCCCGAATCA
TTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
Found at i:53689675 original size:27 final size:31
Alignment explanation
Indices: 53689639--53689720 Score: 91
Period size: 27 Copynumber: 2.7 Consensus size: 31
53689629 GAATATAAAG
53689639 GGGGTTGCTAAGTGCTGATTCC-C-C-CA-A
1 GGGGTTGCTAAGTGCTGATTCCTCACTCATA
* * *
53689666 GGGGTTGCTAAGTGTTGGTTCCTCGACTCATT
1 GGGGTTGCTAAGTGCTGATTCCTC-ACTCATA
53689698 GGTGGTTGCTAAGTGCTGATTCC
1 GG-GGTTGCTAAGTGCTGATTCC
53689721 ACCATATCTT
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
27 20 0.45
28 1 0.02
30 1 0.02
31 2 0.05
32 2 0.05
33 18 0.41
ACGTcount: A:0.15, C:0.21, G:0.32, T:0.33
Consensus pattern (31 bp):
GGGGTTGCTAAGTGCTGATTCCTCACTCATA
Found at i:53689775 original size:26 final size:26
Alignment explanation
Indices: 53689741--53689790 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
53689731 GAATATAAAG
53689741 GGGGTTGCTAAGTGCTGATTCCCCAA
1 GGGGTTGCTAAGTGCTGATTCCCCAA
*
53689767 GGGGTTGCTAAGTGTTGATTCCCC
1 GGGGTTGCTAAGTGCTGATTCCCC
53689791 GATTCATTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.16, C:0.22, G:0.32, T:0.30
Consensus pattern (26 bp):
GGGGTTGCTAAGTGCTGATTCCCCAA
Found at i:53689806 original size:33 final size:34
Alignment explanation
Indices: 53689769--53689977 Score: 129
Period size: 33 Copynumber: 5.8 Consensus size: 34
53689759 TTCCCCAAGG
*
53689769 GGTTGCTAAGTGTTGATTCC-CCGATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCACCGATTCATTGGT
* * * *
53689802 GGTTGCTAAGTGCTGATCCCACCATATTTTAAATGTGAAGG
1 GGTTGCTAAGTGCTGATTCCACC-GA--TT-CAT-TG--GT
*
53689843 GGTTGCTAAGTGCTGATTCC-CCGAATCATTGGT
1 GGTTGCTAAGTGCTGATTCCACCGATTCATTGGT
*
53689876 GGTTGCTAGGTGCTGATTCCACC-ATATCTTTTAATGTGAAAGT
1 GGTTGCTAAGTGCTGATTCCACCGAT-TC-----AT-TG---GT
* * * *
53689919 GGTTGCTAAGTGTTGATTCC-CCGAATCACTGTT
1 GGTTGCTAAGTGCTGATTCCACCGATTCATTGGT
*
53689952 GGTTGCTAAGTGCTGAATCCACCGAT
1 GGTTGCTAAGTGCTGATTCCACCGAT
53689978 AACGGTTAAT
Statistics
Matches: 135, Mismatches: 20, Indels: 41
0.69 0.10 0.21
Matches are distributed among these distances:
33 58 0.43
34 10 0.07
35 3 0.02
36 4 0.03
37 4 0.03
38 2 0.01
39 5 0.04
40 4 0.03
41 20 0.15
42 4 0.03
43 21 0.16
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.34
Consensus pattern (34 bp):
GGTTGCTAAGTGCTGATTCCACCGATTCATTGGT
Found at i:53689806 original size:101 final size:101
Alignment explanation
Indices: 53689627--53689864 Score: 388
Period size: 101 Copynumber: 2.4 Consensus size: 101
53689617 CCGGAGTACA
* *
53689627 TTGAATATAAAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGTTGGTTCCTCGA
1 TTGAATATAAAGGGGGTTGCTAAGTGCTGATT-CCCCAAGGGGTTGCTAAGTGTTGATTCCCCGA
*
53689692 CTCATTGGTGGTTGCTAAGTGCTGATTCCACCATATC
65 CTCATTGGTGGTTGCTAAGTGCTGATCCCACCATATC
*
53689729 TTGAATATAAAGGGGGTTGCTAAGTGCTGATTCCCCAAGGGGTTGCTAAGTGTTGATTCCCCGAT
1 TTGAATATAAAGGGGGTTGCTAAGTGCTGATTCCCCAAGGGGTTGCTAAGTGTTGATTCCCCGAC
*
53689794 TCATTGGTGGTTGCTAAGTGCTGATCCCACCATATT
66 TCATTGGTGGTTGCTAAGTGCTGATCCCACCATATC
* * *
53689830 TTAAATGTGAA-GGGGTTGCTAAGTGCTGATTCCCC
1 TTGAATATAAAGGGGGTTGCTAAGTGCTGATTCCCC
53689865 GAATCATTGG
Statistics
Matches: 128, Mismatches: 8, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
100 24 0.19
101 72 0.56
102 32 0.25
ACGTcount: A:0.21, C:0.19, G:0.27, T:0.32
Consensus pattern (101 bp):
TTGAATATAAAGGGGGTTGCTAAGTGCTGATTCCCCAAGGGGTTGCTAAGTGTTGATTCCCCGAC
TCATTGGTGGTTGCTAAGTGCTGATCCCACCATATC
Found at i:53689946 original size:76 final size:74
Alignment explanation
Indices: 53689765--53689974 Score: 321
Period size: 74 Copynumber: 2.8 Consensus size: 74
53689755 CTGATTCCCC
* *
53689765 AAGGGGTTGCTAAGTGTTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATCCCACCATATT
1 AAGGGGTTGCTAAGTGTTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCATATT
53689830 TTAAATGTG
66 TTAAATGTG
* *
53689839 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAGGTGCTGATTCCACCATATC
1 AAGGGGTTGCTAAGTGTTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCATAT-
*
53689904 TTTTAATGTG
65 TTTAAATGTG
* * * *
53689914 AAAGTGGTTGCTAAGTGTTGATTCCCCGAATCACTGTTGGTTGCTAAGTGCTGAATCCACC
1 -AAGGGGTTGCTAAGTGTTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACC
53689975 GATAACGGTT
Statistics
Matches: 123, Mismatches: 11, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
74 60 0.49
75 9 0.07
76 54 0.44
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.34
Consensus pattern (74 bp):
AAGGGGTTGCTAAGTGTTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCATATT
TTAAATGTG
Found at i:53697503 original size:2 final size:2
Alignment explanation
Indices: 53697496--53697537 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
53697486 ACAAGCAAAA
53697496 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
53697538 CTCTCAATTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:53701252 original size:792 final size:791
Alignment explanation
Indices: 53699700--53701292 Score: 2875
Period size: 792 Copynumber: 2.0 Consensus size: 791
53699690 TATCCAACCT
*
53699700 CAACTCCTTACTATCGACATTCAGTACATAGGCTAGATAAGCTTCGTAACCTTTCCAGACCAACT
1 CAACTCCTTACTATCGACATTCAATACATAGGCTAGATAAGCTTCGTAACCTTTCCAGACCAACT
53699765 TCTCAGCTCTAAGCGAAGAAATCACATTAGAAAGCAACTCCAACTTCTCTCCAACAACAACAACT
66 TCTCAGCTCTAAGCGAAGAAATCACATTAGAAAGCAACTCCAACTTCTCTCCAACAACAACAACT
* * *
53699830 TCGAAACCATCCGCGCAACACAAAATCACCATAATTACCTCACAATCAACCTTCGCTCGATGCTC
131 TCGAAACCATCCACGCAACACAAAATCACCATAATTACCTCACAATAAACCTTCGCTCAATGCTC
* * *
53699895 GGTCAACCAATCCATCCTGAGGATAACATAGAACCCTTAGAACGGTAATTCTAAAAGATCTATAG
196 GGTCAACCAATCCATCCTAAGGATAACATAAAACCCTTAAAACGGTAATTCTAAAAGATCTATAG
53699960 GAAACACTTGTCCCTAAACCATTAGAGAACAACGACGGTAAACCCAATCCACCACTACACTATCA
261 GAAACACTTGTCCCTAAACCATTAGAGAACAACGACGGTAAACCCAATCCACCACTACACTATCA
53700025 CCTAGAGGGATCTTAATCATAACACCTAACCTAGATGTCTCTACAGGAATCCTTAACTTTCTAAC
326 CCTAGAGGGATCTTAATCATAACACCTAACCTAGATGTCTCTACAGGAATCCTTAACTTTCTAAC
53700090 TACATCACTCAGAATAAACGATCCCATAGCACCCGAATCAACTAAAGCTAAAAGAGGAAAAGATT
391 TACATCACTCAGAATAAACGATCCCATAGCACCCGAATCAACTAAAGCTAAAAGAGGAAAAGATT
* *
53700155 GTAGCATGAAAGTACCCGCGATGACATCCGTAGCCTCTTTTGTCTAAGGCTCTCTAACTGTGTAA
456 GTAGCATGAAAGTACCCGCGATGACATCCGTAGCCTCTCTTATCTAAGGCTCTCTAACTGTGTAA
* * *
53700220 ACTCTGGCTGGACCTTCATTACCATCGTGAGCAATTTTACGCTAACCAACATCTCTACCACCACC
521 ACTCTGGCTGGACCTCCATTACCACCCTGAGCAATTTTACGCTAACCAACATCTCTACCACCACC
*
53700285 TCTGTCAAGGCCCCTCCCTCAAGCCGAAACAGGTGCAGCAGCAACAACAATAGCAATAGGTTGGT
586 TCTGTCAAGGCCCCTCCCTCAAGCCGAAACAGATGCAGCAGCAACAACAATAGCAATAGGTTGGT
* * *
53700350 CCATCAAGCCGAACCACAACTGCTCTTCTCGGACAATTACTAACATGATGCTTCATCGATCCGTA
651 CCATCAAGCCGAACCACAACTGCTCTCCTCGGACAATAACTAACACGATGCTTCATCGATCCGTA
*
53700415 AAGAAGATAAGTGCCACTCATCCTCCAACACTCACC-ATGATGATGACGACCACAATGCTCACAT
716 AAGAAGATAAATGCCACTCATCCTCCAACACTCACCAATGAT-A-GACGACCACAATGCTCACAT
53700479 AACAGCCATGTAA
779 AACAGCCATGTAA
*
53700492 CAACTCCTTACTATCGACATTCAATACATAGGCTAGATAAGCTTCGTAACCTTTCTAGACCAACT
1 CAACTCCTTACTATCGACATTCAATACATAGGCTAGATAAGCTTCGTAACCTTTCCAGACCAACT
* *
53700557 TCTCAGCTCTAAGTGAAGAAATCACATTAGAAAGCAACTCCAACTTCTCTCCAATAACAACAACT
66 TCTCAGCTCTAAGCGAAGAAATCACATTAGAAAGCAACTCCAACTTCTCTCCAACAACAACAACT
*
53700622 TCGAAACCATCCACGCAACACAAAATCACCATAATTGCCTCACAATAAACCTTCGCTCAATGCTC
131 TCGAAACCATCCACGCAACACAAAATCACCATAATTACCTCACAATAAACCTTCGCTCAATGCTC
*
53700687 GGTCAACCAATCCATCCTAAGGATAACATAAAACCCTTAAAATGGTAATTCTAAAAGATCTATAG
196 GGTCAACCAATCCATCCTAAGGATAACATAAAACCCTTAAAACGGTAATTCTAAAAGATCTATAG
53700752 GAAACACTTGTCCCTAAACCATTAGAGAACAACGACGGTAAACCCAATCCACCACTACACTATCA
261 GAAACACTTGTCCCTAAACCATTAGAGAACAACGACGGTAAACCCAATCCACCACTACACTATCA
*
53700817 CCTAGAGGGCTCTTAATCATAACACCTAACCTAGATGTCTCTACAGGAATCCTTAACTTTCTAAC
326 CCTAGAGGGATCTTAATCATAACACCTAACCTAGATGTCTCTACAGGAATCCTTAACTTTCTAAC
53700882 TACATCACTCAGAATAAACGATCCCATAGCACCCGAATCAACTAAAGCTAAAAGAGGAAAAGATT
391 TACATCACTCAGAATAAACGATCCCATAGCACCCGAATCAACTAAAGCTAAAAGAGGAAAAGATT
*
53700947 GTAGCATGAAAGTACCCGCGATGACATCCGTGGCCTCTCTTATCTAAGGCTCTCTAACTGTGTAA
456 GTAGCATGAAAGTACCCGCGATGACATCCGTAGCCTCTCTTATCTAAGGCTCTCTAACTGTGTAA
*
53701012 ACTCTGGCTGGACCTCCATTACCACCCTGAGCAGTTTTACGCTAACCAACATCTCTACCACCACC
521 ACTCTGGCTGGACCTCCATTACCACCCTGAGCAATTTTACGCTAACCAACATCTCTACCACCA-C
*
53701077 ACATCTGTCAAGGCCCCTCCCTCGAGCCGAAACAGATGCAGCAGCAACAACAATAGCAATAGGTT
585 -C-TCTGTCAAGGCCCCTCCCTCAAGCCGAAACAGATGCAGCAGCAACAACAATAGCAATAGGTT
53701142 GGTCCATCAAGCCGAACCACAACTGCTCTCCTCGGACAATAACTAACACGATGCTTCATCGATCC
648 GGTCCATCAAGCCGAACCACAACTGCTCTCCTCGGACAATAACTAACACGATGCTTCATCGATCC
53701207 GTAAAGAAGATAAATGCCACTCATCCTCCAACACTCACC-ATGATGACGACGACCACAATGCTCA
713 GTAAAGAAGATAAATGCCACTCATCCTCCAACACTCACCAATGAT-A-GACGACCACAATGCTCA
53701271 CATAACAGCCATGTAA
776 CATAACAGCCATGTAA
53701287 CAACTC
1 CAACTC
53701293 TTTGATCACT
Statistics
Matches: 771, Mismatches: 27, Indels: 3
0.96 0.03 0.00
Matches are distributed among these distances:
792 563 0.73
793 1 0.00
794 1 0.00
795 206 0.27
ACGTcount: A:0.35, C:0.30, G:0.14, T:0.22
Consensus pattern (791 bp):
CAACTCCTTACTATCGACATTCAATACATAGGCTAGATAAGCTTCGTAACCTTTCCAGACCAACT
TCTCAGCTCTAAGCGAAGAAATCACATTAGAAAGCAACTCCAACTTCTCTCCAACAACAACAACT
TCGAAACCATCCACGCAACACAAAATCACCATAATTACCTCACAATAAACCTTCGCTCAATGCTC
GGTCAACCAATCCATCCTAAGGATAACATAAAACCCTTAAAACGGTAATTCTAAAAGATCTATAG
GAAACACTTGTCCCTAAACCATTAGAGAACAACGACGGTAAACCCAATCCACCACTACACTATCA
CCTAGAGGGATCTTAATCATAACACCTAACCTAGATGTCTCTACAGGAATCCTTAACTTTCTAAC
TACATCACTCAGAATAAACGATCCCATAGCACCCGAATCAACTAAAGCTAAAAGAGGAAAAGATT
GTAGCATGAAAGTACCCGCGATGACATCCGTAGCCTCTCTTATCTAAGGCTCTCTAACTGTGTAA
ACTCTGGCTGGACCTCCATTACCACCCTGAGCAATTTTACGCTAACCAACATCTCTACCACCACC
TCTGTCAAGGCCCCTCCCTCAAGCCGAAACAGATGCAGCAGCAACAACAATAGCAATAGGTTGGT
CCATCAAGCCGAACCACAACTGCTCTCCTCGGACAATAACTAACACGATGCTTCATCGATCCGTA
AAGAAGATAAATGCCACTCATCCTCCAACACTCACCAATGATAGACGACCACAATGCTCACATAA
CAGCCATGTAA
Found at i:53703782 original size:22 final size:22
Alignment explanation
Indices: 53703757--53703800 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
53703747 TCAACTTTTA
*
53703757 ACACAAACATTCAATTATATTG
1 ACACAAACAATCAATTATATTG
* *
53703779 ACACAACCAATCAATTCTATTG
1 ACACAAACAATCAATTATATTG
53703801 GCATAGTGCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.43, C:0.23, G:0.05, T:0.30
Consensus pattern (22 bp):
ACACAAACAATCAATTATATTG
Found at i:53707326 original size:13 final size:14
Alignment explanation
Indices: 53707308--53707337 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
53707298 AAACCTAAGA
53707308 AAAGAA-AAAGACT
1 AAAGAATAAAGACT
53707321 AAAGAATAAAGACT
1 AAAGAATAAAGACT
53707335 AAA
1 AAA
53707338 TCTAACAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.70, C:0.07, G:0.13, T:0.10
Consensus pattern (14 bp):
AAAGAATAAAGACT
Found at i:53709135 original size:132 final size:132
Alignment explanation
Indices: 53708898--53709166 Score: 520
Period size: 132 Copynumber: 2.0 Consensus size: 132
53708888 CTTTCAATTG
*
53708898 ATTTGCTCATTTCCAATTAGACTAATGATATGTTTAGGTTCATCTACTAATACAAGTTGTCTTTC
1 ATTTGCTCATTTCCAATTAGACTAATGATATGTGTAGGTTCATCTACTAATACAAGTTGTCTTTC
53708963 TGTATTACGATCTGACCACGTGAAACCGCTTAGTATTAGTTAAATACTAGATAACCAGTGAGCCC
66 TGTATTACGATCTGACCACGTGAAACCGCTTAGTATTAGTTAAATACTAGATAACCAGTGAGCCC
53709028 AT
131 AT
*
53709030 ATTTGCTTATTTCCAATTAGACTAATGATATGTGTAGGTTCATCTACTAATACAAGTTGTCTTTC
1 ATTTGCTCATTTCCAATTAGACTAATGATATGTGTAGGTTCATCTACTAATACAAGTTGTCTTTC
53709095 TGTATTACGATCTGACCACGTGAAACCGCTTAGTATTAGTTAAATACTAGATAACCAGTGAGCCC
66 TGTATTACGATCTGACCACGTGAAACCGCTTAGTATTAGTTAAATACTAGATAACCAGTGAGCCC
53709160 AT
131 AT
53709162 ATTTG
1 ATTTG
53709167 TTTTCATTTT
Statistics
Matches: 135, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
132 135 1.00
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.36
Consensus pattern (132 bp):
ATTTGCTCATTTCCAATTAGACTAATGATATGTGTAGGTTCATCTACTAATACAAGTTGTCTTTC
TGTATTACGATCTGACCACGTGAAACCGCTTAGTATTAGTTAAATACTAGATAACCAGTGAGCCC
AT
Found at i:53710191 original size:27 final size:27
Alignment explanation
Indices: 53710127--53710192 Score: 105
Period size: 27 Copynumber: 2.4 Consensus size: 27
53710117 GGTCGAGGGC
53710127 CTGCCACAGGCGGCACCAAAGGTGCCA
1 CTGCCACAGGCGGCACCAAAGGTGCCA
* * *
53710154 GTGGCAGAGGCGGCACCAAAGGTGCCA
1 CTGCCACAGGCGGCACCAAAGGTGCCA
53710181 CTGCCACAGGCG
1 CTGCCACAGGCG
53710193 ACATCCCAGC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.24, C:0.33, G:0.35, T:0.08
Consensus pattern (27 bp):
CTGCCACAGGCGGCACCAAAGGTGCCA
Found at i:53710269 original size:3 final size:3
Alignment explanation
Indices: 53710241--53710292 Score: 56
Period size: 3 Copynumber: 17.7 Consensus size: 3
53710231 TGCACGAAAG
*
53710241 AGA AGAA AGA A-A AGGA A-A AG- AGA AGA AGA AGA AGA AGA AGA AAA
1 AGA AG-A AGA AGA A-GA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
53710285 AGA AGA AG
1 AGA AGA AG
53710293 GGGAAGGAGG
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
2 6 0.14
3 31 0.74
4 5 0.12
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:53715417 original size:11 final size:11
Alignment explanation
Indices: 53715371--53715438 Score: 68
Period size: 11 Copynumber: 6.2 Consensus size: 11
53715361 TAAATCATTT
*
53715371 CTCTC-AATTT
1 CTCTCAAATTC
53715381 CTCTCTAATATT-
1 CTCTC-AA-ATTC
53715393 CTCTCAAATTC
1 CTCTCAAATTC
* *
53715404 CTCCCAATTTC
1 CTCTCAAATTC
*
53715415 CTCTCAAGTTC
1 CTCTCAAATTC
53715426 CTCTCAAATTC
1 CTCTCAAATTC
53715437 CT
1 CT
53715439 ATTTAAAAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 7
0.80 0.08 0.11
Matches are distributed among these distances:
10 8 0.16
11 32 0.65
12 6 0.12
13 3 0.06
ACGTcount: A:0.22, C:0.35, G:0.01, T:0.41
Consensus pattern (11 bp):
CTCTCAAATTC
Found at i:53715492 original size:30 final size:29
Alignment explanation
Indices: 53715443--53715499 Score: 71
Period size: 31 Copynumber: 1.9 Consensus size: 29
53715433 ATTCCTATTT
* *
53715443 AAAAAAGTTTTAATTTTTTAATTATTTTTTA
1 AAAAAAATTTTAATATTTT-ATT-TTTTTTA
53715474 AAAAAAATTTTAA-ATTTTATTTTTTT
1 AAAAAAATTTTAATATTTTATTTTTTT
53715500 GAATTTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 5 0.21
29 3 0.12
30 4 0.17
31 12 0.50
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (29 bp):
AAAAAAATTTTAATATTTTATTTTTTTTA
Found at i:53716624 original size:7 final size:7
Alignment explanation
Indices: 53716612--53716637 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
53716602 AAGTCGATTG
53716612 GTATTTA
1 GTATTTA
53716619 GTATTTA
1 GTATTTA
53716626 GTATTTA
1 GTATTTA
53716633 GTATT
1 GTATT
53716638 ATGTATTGTG
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:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (7 bp):
GTATTTA
Found at i:53716643 original size:7 final size:7
Alignment explanation
Indices: 53716633--53716664 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
53716623 TTAGTATTTA
53716633 GTATTAT
1 GTATTAT
*
53716640 GTATTGT
1 GTATTAT
53716647 GTATTAT
1 GTATTAT
53716654 GTATTAT
1 GTATTAT
53716661 GTAT
1 GTAT
53716665 ATAACTAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.25, C:0.00, G:0.19, T:0.56
Consensus pattern (7 bp):
GTATTAT
Found at i:53716643 original size:14 final size:14
Alignment explanation
Indices: 53716612--53716658 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
53716602 AAGTCGATTG
53716612 GTATTTAGTATT-T
1 GTATTTAGTATTAT
53716625 AGTATTTAGTATTAT
1 -GTATTTAGTATTAT
53716640 GTATTGT-GTATTAT
1 GTATT-TAGTATTAT
53716654 GTATT
1 GTATT
53716659 ATGTATATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
14 29 0.94
15 2 0.06
ACGTcount: A:0.26, C:0.00, G:0.17, T:0.57
Consensus pattern (14 bp):
GTATTTAGTATTAT
Found at i:53717245 original size:30 final size:30
Alignment explanation
Indices: 53717174--53717247 Score: 76
Period size: 30 Copynumber: 2.5 Consensus size: 30
53717164 CAACGTGGCC
* * * * *
53717174 CACCCGACCCATCATCAGCACCTATACAAT
1 CACCCGACCCAGCAACAACACCGACACAAT
* * *
53717204 CACCAGGCCCAGCAACAACACCGACACAGT
1 CACCCGACCCAGCAACAACACCGACACAAT
53717234 CACCCGACCCAGCA
1 CACCCGACCCAGCA
53717248 GTTCAACCGA
Statistics
Matches: 34, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.34, C:0.46, G:0.12, T:0.08
Consensus pattern (30 bp):
CACCCGACCCAGCAACAACACCGACACAAT
Found at i:53717320 original size:18 final size:18
Alignment explanation
Indices: 53717297--53717335 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
53717287 ATGCCAGGTG
* *
53717297 TGTATCATAGCCCTTTTA
1 TGTATCATAACCCTTATA
*
53717315 TGTATCCTAACCCTTATA
1 TGTATCATAACCCTTATA
53717333 TGT
1 TGT
53717336 TTCCTTTTTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.23, C:0.23, G:0.10, T:0.44
Consensus pattern (18 bp):
TGTATCATAACCCTTATA
Found at i:53719167 original size:126 final size:126
Alignment explanation
Indices: 53718873--53719283 Score: 646
Period size: 126 Copynumber: 3.3 Consensus size: 126
53718863 CATGCACTAT
* * * * *
53718873 TGTAGCAAAAACGCATCCACGTGGGAGCTTCTTTCAATACT-TCTACTGACAAAACATCCTGCTT
1 TGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTAT-TGCTGACAAAGCATCCTGCTT
* * *
53718937 AAAGCTTTTTTAACACTATTTGCTCAGAAACGTCTACTCAAAATTA-TTTTTCATGAGCTAC
65 AAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCAAAATTATTTTTTCAGGAGCTAC
*
53718998 TGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTATTGCTGACAAAGCATCTTGCTTA
1 TGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTATTGCTGACAAAGCATCCTGCTTA
* * *
53719063 AAGCGTTTTTGACACTATTTGCTCAAAAACGTCTACTCGAAATTATTTTTTTAGGAGCTAC
66 AAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCAAAATTATTTTTTCAGGAGCTAC
* * *
53719124 AGTAACGAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTATTGCTGACAAAGCATCCTGCTTA
1 TGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTATTGCTGACAAAGCATCCTGCTTA
53719189 AAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCAAAATTATTTTTTCAGGAGCTAC
66 AAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCAAAATTATTTTTTCAGGAGCTAC
* *
53719250 TGTAGCAAAAGCGCGTCCACGTGAGAACTTCTTT
1 TGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTT
53719284 AAATTAACAA
Statistics
Matches: 260, Mismatches: 24, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
125 98 0.38
126 162 0.62
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.32
Consensus pattern (126 bp):
TGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTATTGCTGACAAAGCATCCTGCTTA
AAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCAAAATTATTTTTTCAGGAGCTAC
Found at i:53719466 original size:96 final size:95
Alignment explanation
Indices: 53719322--53719594 Score: 329
Period size: 96 Copynumber: 2.9 Consensus size: 95
53719312 CCTCAACCAC
*
53719322 AAACCCTAATTTATTTGAGTTTTTACTTAAAAACCCTAAACACTAAACCATAATCTAATTTTTTA
1 AAACCCTAATTTATTTGA-TTTTTTCTTAAAAACCCTAAACACTAAACC-TAATCTAATTTTTTA
*
53719387 AAAATTTATAATTAATTTATTCAAGTAACCCT
64 AAAATTTATAATTAATTTACTCAAGTAACCCT
* * * * *
53719419 GAACCCTAATTTATTTGATTTTTTCATAAAAACCCTTAACTCTAAACCCTAATCTATTTTTTTTA
1 AAACCCTAATTTATTTGATTTTTTCTTAAAAACCCTAAACACTAAA-CCTAATCTA-ATTTTTTA
** * *
53719484 AAAAAAT-TAATTAAATTACTCAAGTAACCTT
64 AAAATTTATAATTAATTTACTCAAGTAACCCT
* ** * *
53719515 AAACCCTAATTTAATT--TTTTTTCTTAAAAAACAATAAACACGAAACCTAATCTAA-TTTTGAA
1 AAACCCTAATTTATTTGATTTTTTCTT-AAAAACCCTAAACACTAAACCTAATCTAATTTTTTAA
53719577 AAATTTATAATTAATTTA
65 AAATTTATAATTAATTTA
53719595 ATTGACAAAC
Statistics
Matches: 148, Mismatches: 24, Indels: 12
0.80 0.13 0.07
Matches are distributed among these distances:
92 10 0.07
93 10 0.07
94 17 0.11
95 14 0.09
96 66 0.45
97 31 0.21
ACGTcount: A:0.42, C:0.16, G:0.03, T:0.40
Consensus pattern (95 bp):
AAACCCTAATTTATTTGATTTTTTCTTAAAAACCCTAAACACTAAACCTAATCTAATTTTTTAAA
AATTTATAATTAATTTACTCAAGTAACCCT
Found at i:53725139 original size:28 final size:28
Alignment explanation
Indices: 53725078--53725143 Score: 82
Period size: 27 Copynumber: 2.4 Consensus size: 28
53725068 TTTTAGGATG
* * *
53725078 ATTTTTATTTTAATATTTATTTTTAATT
1 ATTTTTATTTAAATATTTATTTTAAAAT
53725106 ATTTTTATTTAAATA-TTATTTTAAAAT
1 ATTTTTATTTAAATATTTATTTTAAAAT
*
53725133 ATATTT-TTTAA
1 ATTTTTATTTAA
53725144 GAATTTAATT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
26 5 0.15
27 15 0.44
28 14 0.41
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (28 bp):
ATTTTTATTTAAATATTTATTTTAAAAT
Found at i:53728702 original size:4 final size:4
Alignment explanation
Indices: 53728685--53728718 Score: 50
Period size: 4 Copynumber: 8.0 Consensus size: 4
53728675 CAAATTATTT
53728685 TTAA TTATA TTAA TTAA TTAA TTAA TTAAA TTAA
1 TTAA TTA-A TTAA TTAA TTAA TTAA TT-AA TTAA
53728719 CATATTTATT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
TTAA
Found at i:53728707 original size:17 final size:17
Alignment explanation
Indices: 53728685--53728718 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
53728675 CAAATTATTT
53728685 TTAATTATATT-AATTAA
1 TTAATTA-ATTAAATTAA
53728702 TTAATTAATTAAATTAA
1 TTAATTAATTAAATTAA
53728719 CATATTTATT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TTAATTAATTAAATTAA
Found at i:53736973 original size:44 final size:44
Alignment explanation
Indices: 53736910--53737067 Score: 199
Period size: 44 Copynumber: 3.4 Consensus size: 44
53736900 TACTTCTAAC
* *
53736910 CAGTGAAAAGTGATAAGTGGTAGCTTTAGCTACGCTTATCTGAT
1 CAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
*
53736954 CAGTGACAAGTGATAAGTGGTAGCTTTAGTTACACTTATCTGAT
1 CAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
*
53736998 CAGTGACAAGTAACAAGTGATAAGTGGTAGCTTTAGCTACACTTATTTGAT
1 CAGT-----G--ACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
* *
53737049 CAGGGACAAGTGACAAGTG
1 CAGTGACAAGTGATAAGTG
53737068 ATAAATGTGA
Statistics
Matches: 100, Mismatches: 7, Indels: 14
0.83 0.06 0.12
Matches are distributed among these distances:
44 58 0.58
46 1 0.01
49 1 0.01
51 40 0.40
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.30
Consensus pattern (44 bp):
CAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
Found at i:53737014 original size:51 final size:51
Alignment explanation
Indices: 53736959--53737071 Score: 190
Period size: 51 Copynumber: 2.2 Consensus size: 51
53736949 CTGATCAGTG
* *
53736959 ACAAGTGATAAGTGGTAGCTTTAGTTACACTTATCTGATCAGTGACAAGTA
1 ACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGGGACAAGTA
* *
53737010 ACAAGTGATAAGTGGTAGCTTTAGCTACACTTATTTGATCAGGGACAAGTG
1 ACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGGGACAAGTA
53737061 ACAAGTGATAA
1 ACAAGTGATAA
53737072 ATGTGATCCG
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 58 1.00
ACGTcount: A:0.35, C:0.13, G:0.23, T:0.29
Consensus pattern (51 bp):
ACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGGGACAAGTA
Found at i:53738224 original size:14 final size:14
Alignment explanation
Indices: 53738205--53738231 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
53738195 GTTTCGTCAT
53738205 CGAATACGGGTTAC
1 CGAATACGGGTTAC
53738219 CGAATACGGGTTA
1 CGAATACGGGTTA
53738232 GGGGTGTTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.19, G:0.30, T:0.22
Consensus pattern (14 bp):
CGAATACGGGTTAC
Found at i:53745554 original size:41 final size:42
Alignment explanation
Indices: 53745479--53745566 Score: 103
Period size: 42 Copynumber: 2.1 Consensus size: 42
53745469 AATTCACGTT
53745479 AAATTCATAAAAATTCAAAAAAAATATATAAAAAACATTTTA-
1 AAATTCATAAAAATTCAAAAAAAATATATAAAAAAC-TTTTAG
* *
53745521 AAATTCA-ATAAATTTCAAAAAAAGT-TCAT-AAAAACTTTTAG
1 AAATTCATA-AAAATTCAAAAAAAATAT-ATAAAAAACTTTTAG
53745562 AAATT
1 AAATT
53745567 TTATTTATGT
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
40 5 0.12
41 13 0.32
42 23 0.56
ACGTcount: A:0.59, C:0.08, G:0.02, T:0.31
Consensus pattern (42 bp):
AAATTCATAAAAATTCAAAAAAAATATATAAAAAACTTTTAG
Found at i:53745895 original size:16 final size:16
Alignment explanation
Indices: 53745874--53745907 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
53745864 TAAATAAATT
*
53745874 AAAATAATAGACAATA
1 AAAATAAAAGACAATA
*
53745890 AAAATAAAAGATAATA
1 AAAATAAAAGACAATA
53745906 AA
1 AA
53745908 TCACGAATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.74, C:0.03, G:0.06, T:0.18
Consensus pattern (16 bp):
AAAATAAAAGACAATA
Found at i:53749676 original size:20 final size:20
Alignment explanation
Indices: 53749651--53749693 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
53749641 CTAAAATTGT
* *
53749651 AAATTGAGCCCAAGAGCCCA
1 AAATTGAGACCAAGACCCCA
*
53749671 AAATTGAGATCAAGACCCCA
1 AAATTGAGACCAAGACCCCA
53749691 AAA
1 AAA
53749694 ACTAGTCGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.47, C:0.26, G:0.16, T:0.12
Consensus pattern (20 bp):
AAATTGAGACCAAGACCCCA
Found at i:53750024 original size:48 final size:48
Alignment explanation
Indices: 53749959--53750077 Score: 150
Period size: 48 Copynumber: 2.4 Consensus size: 48
53749949 AAAATAATGT
*
53749959 TATTTTAATAGATTTAATATTAAATTAAATTTAATATTTATCTTAATAG-
1 TATTTTATTA-ATTTAATATTAAATTAAATTTAATATTTATCTT-ATAGA
* *
53750008 TATTTTATTAATTTAATATTAAATTTAATTTAATGTTTATCTTATAGA
1 TATTTTATTAATTTAATATTAAATTAAATTTAATATTTATCTTATAGA
53750056 TAAATATTCTATTAATTTAATA
1 T--AT-TT-TATTAATTTAATA
53750078 ATATTTAATA
Statistics
Matches: 62, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
47 4 0.06
48 32 0.52
49 9 0.15
50 2 0.03
51 2 0.03
52 13 0.21
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (48 bp):
TATTTTATTAATTTAATATTAAATTAAATTTAATATTTATCTTATAGA
Found at i:53750037 original size:17 final size:17
Alignment explanation
Indices: 53749970--53750041 Score: 62
Period size: 17 Copynumber: 4.4 Consensus size: 17
53749960 ATTTTAATAG
*
53749970 ATTTAATATTAAATTAA
1 ATTTAATATTAAATTTA
*
53749987 ATTTAATATT-TATCTTA
1 ATTTAATATTAAAT-TTA
* **
53750004 A--TAGTATTTTA-TTA
1 ATTTAATATTAAATTTA
53750018 ATTTAATATTAAATTTA
1 ATTTAATATTAAATTTA
53750035 ATTTAAT
1 ATTTAAT
53750042 GTTTATCTTA
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
14 4 0.09
15 6 0.14
16 11 0.25
17 23 0.52
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (17 bp):
ATTTAATATTAAATTTA
Found at i:53757269 original size:24 final size:24
Alignment explanation
Indices: 53757242--53757326 Score: 90
Period size: 24 Copynumber: 3.6 Consensus size: 24
53757232 TGTGGCAAGG
53757242 GAAAACTTTATCCTTATGTTATAT
1 GAAAACTTTATCCTTATGTTATAT
*
53757266 GAAATA-TAAATTAT--TTAT-TTAGA-
1 GAAA-ACT---TTATCCTTATGTTATAT
53757289 GAAAACTTTATCCTTATGTTATAT
1 GAAAACTTTATCCTTATGTTATAT
53757313 GAAAACTTTATCCT
1 GAAAACTTTATCCT
53757327 AATTGTTGTT
Statistics
Matches: 50, Mismatches: 2, Indels: 18
0.71 0.03 0.26
Matches are distributed among these distances:
20 4 0.08
22 5 0.10
23 9 0.18
24 23 0.46
25 5 0.10
27 4 0.08
ACGTcount: A:0.38, C:0.11, G:0.08, T:0.44
Consensus pattern (24 bp):
GAAAACTTTATCCTTATGTTATAT
Found at i:53757489 original size:159 final size:160
Alignment explanation
Indices: 53757164--53757473 Score: 419
Period size: 159 Copynumber: 1.9 Consensus size: 160
53757154 TCTAAAGGCA
53757164 CCTAATTGTTGTTATCTTTTTAAATGGGAGGTTCAAAGATGAAAATAAGACCAAAATTCAAGATA
1 CCTAATTGTTGTTATCTTTTTAAATGGGAGGTTCAAAGATGAAAATAAGACCAAAATTCAAGATA
* *
53757229 ATGTGTGGCAAGGGAAAACTTTATCCTTATGTTATATGAAATATAAATTATTTATTTAGAGAAAA
66 ATGGGTGGCAAGGGAAAACTTTATCCTTATGTTATATGAAATATAAATTATTTATTTAAAGAAAA
*** ** * * ** *
53757294 CTTTATCCTTATGTTATATGAAAACTTTAT
131 AGGTAAACTTATATAATACCAAAACTATAT
* * *
53757324 CCTAATTGTTGTTGTCTTTTTAAATGGGAGGTTTAAAGATG-CAATAAGACCAAAATTCAAGATA
1 CCTAATTGTTGTTATCTTTTTAAATGGGAGGTTCAAAGATGAAAATAAGACCAAAATTCAAGATA
* *
53757388 GTGGGTGGCAATGGAAAACTTTATCCTTATGTTATATGAAATATAAATTATTTATTTAAATGTTA
66 ATGGGTGGCAAGGGAAAACTTTATCCTTATGTTATATGAAATATAAATTATTTATTTAAA-G--A
53757453 AAAAGGTAAAC-TA-ATAATACC
128 AAAAGGTAAACTTATATAATACC
53757474 TTAATATATG
Statistics
Matches: 131, Mismatches: 16, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
159 78 0.60
160 44 0.34
161 2 0.02
162 7 0.05
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.36
Consensus pattern (160 bp):
CCTAATTGTTGTTATCTTTTTAAATGGGAGGTTCAAAGATGAAAATAAGACCAAAATTCAAGATA
ATGGGTGGCAAGGGAAAACTTTATCCTTATGTTATATGAAATATAAATTATTTATTTAAAGAAAA
AGGTAAACTTATATAATACCAAAACTATAT
Found at i:53761706 original size:15 final size:16
Alignment explanation
Indices: 53761688--53761721 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
53761678 AAATTAAATT
53761688 AATTAA-CTAAATGAA
1 AATTAACCTAAATGAA
*
53761703 AATTAACCTAAATGCA
1 AATTAACCTAAATGAA
53761719 AAT
1 AAT
53761722 GAGATGAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.56, C:0.12, G:0.06, T:0.26
Consensus pattern (16 bp):
AATTAACCTAAATGAA
Found at i:53766482 original size:85 final size:84
Alignment explanation
Indices: 53766339--53766533 Score: 257
Period size: 85 Copynumber: 2.3 Consensus size: 84
53766329 AATAAAAAGA
* ** *
53766339 GGTTGCTAAGTGCTGATCCCACCTTATCTTTGATTATGAAAGGGGTTGCTAAGTGCTGATTCCCC
1 GGTTGCTAAGTGCTGATTCCACCGAATCTTTAATTATGAAAGGGGTTGCTAAGTGCTGATTCCCC
53766404 GTATCACTAAATATAAAGGT
66 GTATCACTAAAT-TAAAGGT
* * *
53766424 GGTTGCTAAGTGCTGATTCCACCGAAT-TCTTAATTGTGAAAGGGGTTGCTATGTGCTGATTCCT
1 GGTTGCTAAGTGCTGATTCCACCGAATCT-TTAATTATGAAAGGGGTTGCTAAGTGCTGATTCCC
* * *
53766488 CGTATCACTGAATTTATGGT
65 CGTATCACTAAATTAAAGGT
*
53766508 GGTTGCTAAAGTGCTGAATCCACCGA
1 GGTTGCT-AAGTGCTGATTCCACCGA
53766534 GTAACGGATA
Statistics
Matches: 97, Mismatches: 11, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
84 13 0.13
85 84 0.87
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.33
Consensus pattern (84 bp):
GGTTGCTAAGTGCTGATTCCACCGAATCTTTAATTATGAAAGGGGTTGCTAAGTGCTGATTCCCC
GTATCACTAAATTAAAGGT
Found at i:53766485 original size:43 final size:43
Alignment explanation
Indices: 53766334--53766532 Score: 178
Period size: 43 Copynumber: 4.7 Consensus size: 43
53766324 TATTGAATAA
* * * * *
53766334 AAAGAGGTTGCTAAGTGCTGATCCCACCTTATCTTTGATTATG
1 AAAGGGGTTGCTAAGTGCTGATTCCACCGTATCATTAATTATG
* *
53766377 AAAGGGGTTGCTAAGTGCTGATTCC-CCGTATCACTAAATAT-
1 AAAGGGGTTGCTAAGTGCTGATTCCACCGTATCATTAATTATG
* *
53766418 AAAGGTGGTTGCTAAGTGCTGATTCCACCGAATTC-TTAATTGTG
1 AAAGG-GGTTGCTAAGTGCTGATTCCACCGTA-TCATTAATTATG
* * *
53766462 AAAGGGGTTGCTATGTGCTGATTCC-TCGTATCACTGAATTTATG
1 AAAGGGGTTGCTAAGTGCTGATTCCACCGTATCA-TTAA-TTATG
* *
53766506 ---GTGGTTGCTAAAGTGCTGAATCCACCG
1 AAAGGGGTTGCT-AAGTGCTGATTCCACCG
53766533 AGTAACGGAT
Statistics
Matches: 127, Mismatches: 20, Indels: 18
0.77 0.12 0.11
Matches are distributed among these distances:
41 15 0.12
42 45 0.35
43 56 0.44
44 11 0.09
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (43 bp):
AAAGGGGTTGCTAAGTGCTGATTCCACCGTATCATTAATTATG
Found at i:53768955 original size:23 final size:22
Alignment explanation
Indices: 53768912--53768957 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
53768902 TTTGTTTTTA
*
53768912 ACTTTAACTTTTATTTAAAAAC
1 ACTTTAACTTTTATATAAAAAC
* *
53768934 ACTTTAATTTGTTATATCAAAAC
1 ACTTTAACTT-TTATATAAAAAC
53768957 A
1 A
53768958 TATTATCAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.41, C:0.13, G:0.02, T:0.43
Consensus pattern (22 bp):
ACTTTAACTTTTATATAAAAAC
Found at i:53780895 original size:33 final size:33
Alignment explanation
Indices: 53780853--53780923 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 33
53780843 ATGACATTCG
* *
53780853 CAGATATAGTCTGCTGAGAAAGTAAACACAGAA
1 CAGAGATAGTCCGCTGAGAAAGTAAACACAGAA
* * * *
53780886 TAGAGATAGTCCGTTGGGACAGTAAACACAGAA
1 CAGAGATAGTCCGCTGAGAAAGTAAACACAGAA
53780919 CAGAG
1 CAGAG
53780924 TAAGTTCGTC
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.42, C:0.15, G:0.25, T:0.17
Consensus pattern (33 bp):
CAGAGATAGTCCGCTGAGAAAGTAAACACAGAA
Found at i:53780943 original size:33 final size:33
Alignment explanation
Indices: 53780873--53780946 Score: 96
Period size: 33 Copynumber: 2.2 Consensus size: 33
53780863 CTGCTGAGAA
* *
53780873 AGTAAACACAGAATAGAGATAGTCCGTTGGGAC
1 AGTAAACACAGAACAGAGATAGTCCGTCGGGAC
* *
53780906 AGTAAACACAGAACAGAG-TAAGTTCGTCGGGAG
1 AGTAAACACAGAACAGAGAT-AGTCCGTCGGGAC
53780939 AGTAAACA
1 AGTAAACA
53780947 TGAGGTGAGC
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
32 1 0.03
33 35 0.97
ACGTcount: A:0.42, C:0.15, G:0.27, T:0.16
Consensus pattern (33 bp):
AGTAAACACAGAACAGAGATAGTCCGTCGGGAC
Found at i:53782544 original size:29 final size:29
Alignment explanation
Indices: 53782484--53782572 Score: 79
Period size: 29 Copynumber: 3.0 Consensus size: 29
53782474 CATAACAAAA
* * * *
53782484 CAACCACAAGGGCTTCCGCATATAACATATT
1 CAACCACAAAGGC-T-CACATATAATAGATT
53782515 CAACCACAAAGGCTCACATATAATAGATT
1 CAACCACAAAGGCTCACATATAATAGATT
** * * *
53782544 CTGCCACTATGGCTCACATATAATTGATT
1 CAACCACAAAGGCTCACATATAATAGATT
53782573 TCGCCACTAG
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
29 36 0.73
30 1 0.02
31 12 0.24
ACGTcount: A:0.36, C:0.26, G:0.12, T:0.26
Consensus pattern (29 bp):
CAACCACAAAGGCTCACATATAATAGATT
Found at i:53782578 original size:29 final size:29
Alignment explanation
Indices: 53782525--53782595 Score: 92
Period size: 29 Copynumber: 2.4 Consensus size: 29
53782515 CAACCACAAA
*
53782525 GGCTCACATATAATAGATTCTGCCACTAT
1 GGCTCACATATAATAGATTCTGCCACTAG
*
53782554 GGCTCACATATAATTGATT-TCGCCACTAG
1 GGCTCACATATAATAGATTCT-GCCACTAG
53782583 GGC-CTACATATAA
1 GGCTC-ACATATAA
53782596 CTCAATGTCT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
28 2 0.05
29 36 0.95
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.30
Consensus pattern (29 bp):
GGCTCACATATAATAGATTCTGCCACTAG
Found at i:53790657 original size:25 final size:25
Alignment explanation
Indices: 53790565--53790677 Score: 113
Period size: 25 Copynumber: 4.5 Consensus size: 25
53790555 ATTCATGTAT
* * *
53790565 GCTCATACGAGCTATGAATCAGTAT
1 GCTCATACGAGCTATAAATCAGGAA
* *
53790590 GCTC-TCACGAGTTATGAATCAGGAA
1 GCTCAT-ACGAGCTATAAATCAGGAA
* *
53790615 GCTCATACGAGCTGTAAATCGGGAA
1 GCTCATACGAGCTATAAATCAGGAA
*
53790640 GCTCATACGAGCTATAAAT-TGGAAA
1 GCTCATACGAGCTATAAATCAGG-AA
*
53790665 GCTCATACAAGCT
1 GCTCATACGAGCT
53790678 GTGGTGTGTC
Statistics
Matches: 75, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
24 3 0.04
25 71 0.95
26 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.24
Consensus pattern (25 bp):
GCTCATACGAGCTATAAATCAGGAA
Found at i:53796181 original size:12 final size:12
Alignment explanation
Indices: 53796166--53796191 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
53796156 TAGTTATATA
53796166 TATTTCTATAAT
1 TATTTCTATAAT
53796178 TATTTCTATAAT
1 TATTTCTATAAT
53796190 TA
1 TA
53796192 ATATTTTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.08, G:0.00, T:0.58
Consensus pattern (12 bp):
TATTTCTATAAT
Found at i:53797186 original size:29 final size:29
Alignment explanation
Indices: 53797114--53797199 Score: 77
Period size: 29 Copynumber: 2.9 Consensus size: 29
53797104 TTAAAACTAA
* *
53797114 ATTTTATTAGTTTTTAAT-AATTTTAAATT
1 ATTTTA-TATTTTTTTATAAATTTTAAATT
* *
53797143 CTTTTATATTCTTTTATAAATTTTAAATT
1 ATTTTATATTTTTTTATAAATTTTAAATT
* *
53797172 ATTTTCT-TTATTTTTATAATTATTTAAA
1 ATTTTATATT-TTTTTATAAAT-TTTAAA
53797200 AAATTATTTT
Statistics
Matches: 46, Mismatches: 8, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
28 10 0.22
29 30 0.65
30 6 0.13
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.63
Consensus pattern (29 bp):
ATTTTATATTTTTTTATAAATTTTAAATT
Found at i:53800211 original size:3 final size:3
Alignment explanation
Indices: 53800203--53800250 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
53800193 TGTTTTCATA
53800203 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
53800251 CTACCGGTAC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:53804593 original size:18 final size:18
Alignment explanation
Indices: 53804572--53804609 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
53804562 GCAGCATTTA
53804572 GAAGAACTGGATGATGCT
1 GAAGAACTGGATGATGCT
53804590 GAAGAACTGGATGATGCT
1 GAAGAACTGGATGATGCT
53804608 GA
1 GA
53804610 GTTTACAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.34, C:0.11, G:0.34, T:0.21
Consensus pattern (18 bp):
GAAGAACTGGATGATGCT
Found at i:53815515 original size:25 final size:25
Alignment explanation
Indices: 53815487--53815608 Score: 103
Period size: 24 Copynumber: 5.0 Consensus size: 25
53815477 TATGAGTGTC
**
53815487 TCGATATATGGCTCTCCGGAGCTTT
1 TCGATATATGGCTCTCATGAGCTTT
53815512 TCGATATATGGCT-TGCATGAGC-TT
1 TCGATATATGGCTCT-CATGAGCTTT
*
53815536 CCAGAT-TAATGGCTCTCCA-GAGCTTT
1 TC-GATAT-ATGGCTCT-CATGAGCTTT
* * *
53815562 TCGATAT-TTGCTCACATGAGCTTC
1 TCGATATATGGCTCTCATGAGCTTT
*
53815586 TCGAT-TATGGCTCTTATGAGCTT
1 TCGATATATGGCTCTCATGAGCTT
53815609 CCCGTATATG
Statistics
Matches: 78, Mismatches: 11, Indels: 17
0.74 0.10 0.16
Matches are distributed among these distances:
23 3 0.04
24 34 0.44
25 34 0.44
26 7 0.09
ACGTcount: A:0.20, C:0.22, G:0.21, T:0.37
Consensus pattern (25 bp):
TCGATATATGGCTCTCATGAGCTTT
Found at i:53815553 original size:50 final size:48
Alignment explanation
Indices: 53815485--53815599 Score: 151
Period size: 50 Copynumber: 2.3 Consensus size: 48
53815475 CTTATGAGTG
* **
53815485 TCTCGATATATGGCTCTCCGGAGCTTTTCGATATATGGCTTGCATGAGCT
1 TCTCGAT-TATGGCTCTCCAGAGCTTTTCGATAT-TGGCTCACATGAGCT
*
53815535 TC-CAGATTAATGGCTCTCCAGAGCTTTTCGATATTTGCTCACATGAGCT
1 TCTC-GATT-ATGGCTCTCCAGAGCTTTTCGATATTGGCTCACATGAGCT
53815584 TCTCGATTATGGCTCT
1 TCTCGATTATGGCTCT
53815600 TATGAGCTTC
Statistics
Matches: 58, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
48 8 0.14
49 20 0.34
50 30 0.52
ACGTcount: A:0.19, C:0.23, G:0.21, T:0.37
Consensus pattern (48 bp):
TCTCGATTATGGCTCTCCAGAGCTTTTCGATATTGGCTCACATGAGCT
Found at i:53815598 original size:24 final size:24
Alignment explanation
Indices: 53815472--53815609 Score: 97
Period size: 25 Copynumber: 5.6 Consensus size: 24
53815462 ACACACCGCA
*
53815472 GCTCTTATGAG-TGTCTCGATATATG
1 GCTCTCATGAGCT-TCTCGAT-TATG
** *
53815497 GCTCTCCGGAGCTTTTCGATATATG
1 GCTCTCATGAGCTTCTCGAT-TATG
53815522 GCT-TGCATGAGCTTC-CAGATTAATG
1 GCTCT-CATGAGCTTCTC-GATT-ATG
* *
53815547 GCTCTCCA-GAGCTTTTCGA-TATTT
1 GCTCT-CATGAGCTTCTCGATTA-TG
*
53815571 GCTCACATGAGCTTCTCGATTATG
1 GCTCTCATGAGCTTCTCGATTATG
*
53815595 GCTCTTATGAGCTTC
1 GCTCTCATGAGCTTC
53815610 CCGTATATGT
Statistics
Matches: 89, Mismatches: 15, Indels: 19
0.72 0.12 0.15
Matches are distributed among these distances:
23 3 0.03
24 33 0.37
25 48 0.54
26 5 0.06
ACGTcount: A:0.19, C:0.22, G:0.22, T:0.37
Consensus pattern (24 bp):
GCTCTCATGAGCTTCTCGATTATG
Found at i:53815618 original size:24 final size:25
Alignment explanation
Indices: 53815577--53815623 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
53815567 ATTTGCTCAC
*
53815577 ATGAGCTTCTCGATTATG-GCTCTT
1 ATGAGCTTCCCGATTATGTGCTCTT
53815601 ATGAGCTTCCCG-TATATGTGCTC
1 ATGAGCTTCCCGAT-TATGTGCTC
53815624 GAACAAGCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 1 0.05
24 15 0.75
25 4 0.20
ACGTcount: A:0.17, C:0.23, G:0.21, T:0.38
Consensus pattern (25 bp):
ATGAGCTTCCCGATTATGTGCTCTT
Found at i:53815623 original size:49 final size:49
Alignment explanation
Indices: 53815494--53815623 Score: 113
Period size: 49 Copynumber: 2.6 Consensus size: 49
53815484 GTCTCGATAT
* ** * **
53815494 ATGGCTCTCCGGAGCTTTTCGATATATGGCTTGCATGAGCTTCCAGATTA
1 ATGGCTCTCCAGAGCTTCCCGATATGT-GCTCACATGAGCTTCCAGATTA
** *
53815544 ATGGCTCTCCAGAGCTTTTCGATATTTGCTCACATGAGCTTCTC-GATT-
1 ATGGCTCTCCAGAGCTTCCCGATATGTGCTCACATGAGCTTC-CAGATTA
*
53815592 ATGGCTCT-TATGAGCTTCCCGTATATGTGCTC
1 ATGGCTCTCCA-GAGCTTCCCG-ATATGTGCTC
53815624 GAACAAGCAT
Statistics
Matches: 69, Mismatches: 8, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
47 1 0.01
48 16 0.23
49 26 0.38
50 26 0.38
ACGTcount: A:0.18, C:0.24, G:0.22, T:0.36
Consensus pattern (49 bp):
ATGGCTCTCCAGAGCTTCCCGATATGTGCTCACATGAGCTTCCAGATTA
Found at i:53819599 original size:50 final size:49
Alignment explanation
Indices: 53819521--53819659 Score: 179
Period size: 50 Copynumber: 2.8 Consensus size: 49
53819511 CGAGTGAAGT
*
53819521 TGATAGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAA
1 TGATAGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGCGTACCGG-A
* * * *
53819571 TGATAGGTCGCATGTGTAGTACTGTGTGCAGGCTACTATGCGTACCGGA
1 TGATAGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGCGTACCGGA
* * *
53819620 TAGCTTCGATCACGTGTGTAGTACTATGTGCAGGCTACTA
1 T-G-ATAGGTCACGTGTGTAGTACTATGTGCAGGCTACTA
53819660 TGTGAATCGA
Statistics
Matches: 76, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
49 2 0.03
50 44 0.58
51 30 0.39
ACGTcount: A:0.22, C:0.19, G:0.29, T:0.29
Consensus pattern (49 bp):
TGATAGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGCGTACCGGA
Done.