Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D13
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: 64892201
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1760000 characters in sequence are not A, C, G, or T
File 134 of 221
Found at i:41284915 original size:11 final size:11
Alignment explanation
Indices: 41284876--41284925 Score: 50
Period size: 11 Copynumber: 4.6 Consensus size: 11
41284866 CTTCTCCTAA
41284876 TTTCCTTTGTT
1 TTTCCTTTGTT
* * *
41284887 TTTCATTGGGT
1 TTTCCTTTGTT
41284898 TTT-CTTTGTT
1 TTTCCTTTGTT
41284908 TTTCCTTT-TAT
1 TTTCCTTTGT-T
41284919 TTTCCTT
1 TTTCCTT
41284926 AGGATTGAGT
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
10 8 0.26
11 23 0.74
ACGTcount: A:0.04, C:0.16, G:0.10, T:0.70
Consensus pattern (11 bp):
TTTCCTTTGTT
Found at i:41290919 original size:27 final size:27
Alignment explanation
Indices: 41290861--41291049 Score: 172
Period size: 27 Copynumber: 7.1 Consensus size: 27
41290851 GGGTATAACA
*
41290861 GTCATTTTACCCTAT-GAGGTATTTTG
1 GTCATTTTACCCTATAGAGGTATTTCG
*
41290887 GACATTTTACCCTATAGAGGTATTTCG
1 GTCATTTTACCCTATAGAGGTATTTCG
* * * **
41290914 GTCATTCTACCTTATAGGGGTATTTTA
1 GTCATTTTACCCTATAGAGGTATTTCG
*
41290941 GTAATTTTACCCTATA-AGGGTATTTCG
1 GTCATTTTACCCTATAGA-GGTATTTCG
* * *
41290968 ATCATTCTACCCCT-TAG-GGTATTT-A
1 GTCATTTTA-CCCTATAGAGGTATTTCG
* * *
41290993 GTCATTTTACCTTATGGGGGTATTTCG
1 GTCATTTTACCCTATAGAGGTATTTCG
* * *
41291020 GTCATTTTACCCTATTGGGGTATCTCG
1 GTCATTTTACCCTATAGAGGTATTTCG
41291047 GTC
1 GTC
41291050 GGGGGTATCT
Statistics
Matches: 130, Mismatches: 26, Indels: 13
0.77 0.15 0.08
Matches are distributed among these distances:
24 3 0.02
25 9 0.07
26 28 0.22
27 86 0.66
28 4 0.03
ACGTcount: A:0.21, C:0.18, G:0.20, T:0.42
Consensus pattern (27 bp):
GTCATTTTACCCTATAGAGGTATTTCG
Found at i:41291041 original size:79 final size:80
Alignment explanation
Indices: 41290848--41291042 Score: 218
Period size: 79 Copynumber: 2.5 Consensus size: 80
41290838 TTTCATCTCC
** * * *
41290848 TAGGGGTATAACAGTCATTTTACCCTA-TGAGGTATTTTGGACATTTTACCCTATAGAGGTATTT
1 TAGGGGTATTTCAGTCATTTTACCCTATTGGGGTA-TTTCGACATTCTACCCTATAGAGGTATTT
*
41290912 CGGTCATTCTACCTTA
65 CAGTCATTCTACCTTA
* * **
41290928 TAGGGGTATTTTAGTAATTTTACCCTATAAGGGTATTTCGATCATTCTACCCCT-TAG-GGTATT
1 TAGGGGTATTTCAGTCATTTTACCCTATTGGGGTATTTCGA-CATTCTA-CCCTATAGAGGTATT
*
41290991 T-AGTCATTTTACCTTA
64 TCAGTCATTCTACCTTA
* *
41291007 TGGGGGTATTTCGGTCATTTTACCCTATTGGGGTAT
1 TAGGGGTATTTCAGTCATTTTACCCTATTGGGGTAT
41291043 CTCGGTCGGG
Statistics
Matches: 95, Mismatches: 17, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
79 43 0.45
80 35 0.37
81 13 0.14
82 4 0.04
ACGTcount: A:0.23, C:0.16, G:0.20, T:0.41
Consensus pattern (80 bp):
TAGGGGTATTTCAGTCATTTTACCCTATTGGGGTATTTCGACATTCTACCCTATAGAGGTATTTC
AGTCATTCTACCTTA
Found at i:41291069 original size:42 final size:41
Alignment explanation
Indices: 41291008--41291090 Score: 130
Period size: 42 Copynumber: 2.0 Consensus size: 41
41290998 TTTACCTTAT
*
41291008 GGGGGTATTTCGGTCATTTTACCCTATTGGGGTATCTCGGTC
1 GGGGGTATCTCGGTCATTTTACCCTA-TGGGGTATCTCGGTC
* *
41291050 GGGGGTATCTCGGTTATTTTACCCTATGGGGTATTTCGGTC
1 GGGGGTATCTCGGTCATTTTACCCTATGGGGTATCTCGGTC
41291091 ATTTTACCCT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
41 14 0.37
42 24 0.63
ACGTcount: A:0.12, C:0.18, G:0.31, T:0.39
Consensus pattern (41 bp):
GGGGGTATCTCGGTCATTTTACCCTATGGGGTATCTCGGTC
Found at i:41291122 original size:26 final size:27
Alignment explanation
Indices: 41291050--41291121 Score: 110
Period size: 26 Copynumber: 2.7 Consensus size: 27
41291040 TATCTCGGTC
* *
41291050 GGGGGTATCTCGGTTATTTTACCCTAT
1 GGGGGTATTTCGGTCATTTTACCCTAT
*
41291077 -GGGGTATTTCGGTCATTTTACCCTGT
1 GGGGGTATTTCGGTCATTTTACCCTAT
41291103 GGGGGTATTTCGGTCATTT
1 GGGGGTATTTCGGTCATTT
41291122 ATTGACCTCT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
26 23 0.56
27 18 0.44
ACGTcount: A:0.12, C:0.17, G:0.29, T:0.42
Consensus pattern (27 bp):
GGGGGTATTTCGGTCATTTTACCCTAT
Found at i:41297387 original size:15 final size:15
Alignment explanation
Indices: 41297346--41297394 Score: 73
Period size: 15 Copynumber: 3.3 Consensus size: 15
41297336 AGAATAAGAT
41297346 TAAACATAAAT-ATAA
1 TAAACA-AAATAATAA
41297361 TAAACAAAATAATAA
1 TAAACAAAATAATAA
*
41297376 TAAACAAAATAAAAA
1 TAAACAAAATAATAA
41297391 TAAA
1 TAAA
41297395 AAGAAGGGGA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
14 4 0.12
15 28 0.88
ACGTcount: A:0.73, C:0.06, G:0.00, T:0.20
Consensus pattern (15 bp):
TAAACAAAATAATAA
Found at i:41298314 original size:12 final size:11
Alignment explanation
Indices: 41298289--41298327 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
41298279 GTGTGCACCC
*
41298289 TTTTTTTT-TA
1 TTTTTTTTCAA
41298299 TTTTTTTTCAA
1 TTTTTTTTCAA
*
41298310 TTTTTTTTCCA
1 TTTTTTTTCAA
41298321 TTTTTTT
1 TTTTTTT
41298328 AGAAAATAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
10 8 0.31
11 18 0.69
ACGTcount: A:0.10, C:0.08, G:0.00, T:0.82
Consensus pattern (11 bp):
TTTTTTTTCAA
Found at i:41301508 original size:36 final size:36
Alignment explanation
Indices: 41301359--41301508 Score: 194
Period size: 36 Copynumber: 4.2 Consensus size: 36
41301349 CAACCAAAAT
* *
41301359 ACACCAGAAGCTCATAACAGCTAATCCATCCGAAAC
1 ACACCAGATGCTCATAAGAGCTAATCCATCCGAAAC
* *
41301395 ACACC-GAATGCTCATAAGAGCTAACCCATTCGAAAC
1 ACACCAG-ATGCTCATAAGAGCTAATCCATCCGAAAC
* * * * **
41301431 AAACTAGATGCTCATAAGAGCTATTCTATCTTAAAC
1 ACACCAGATGCTCATAAGAGCTAATCCATCCGAAAC
41301467 ACACCAGATGCTCATAAGAGCTAATCCATCCGAAAC
1 ACACCAGATGCTCATAAGAGCTAATCCATCCGAAAC
41301503 ACACCA
1 ACACCA
41301509 AAATATGGAG
Statistics
Matches: 94, Mismatches: 18, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
35 1 0.01
36 92 0.98
37 1 0.01
ACGTcount: A:0.40, C:0.29, G:0.12, T:0.19
Consensus pattern (36 bp):
ACACCAGATGCTCATAAGAGCTAATCCATCCGAAAC
Found at i:41306290 original size:17 final size:17
Alignment explanation
Indices: 41306258--41306290 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
41306248 CAACCAAAGA
41306258 TAACAAATTTTATAAAT
1 TAACAAATTTTATAAAT
41306275 TAACACAATTTT-TAAA
1 TAACA-AATTTTATAAA
41306291 GTTTTACAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (17 bp):
TAACAAATTTTATAAAT
Found at i:41309680 original size:17 final size:17
Alignment explanation
Indices: 41309658--41309702 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
41309648 TTGCTAGGTG
41309658 TATGGATAAATATATTT
1 TATGGATAAATATATTT
** *
41309675 TATGGATCGACATATTT
1 TATGGATAAATATATTT
*
41309692 TAAGGATAAAT
1 TATGGATAAAT
41309703 CTTTAGTATG
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.40, C:0.04, G:0.16, T:0.40
Consensus pattern (17 bp):
TATGGATAAATATATTT
Found at i:41314962 original size:21 final size:21
Alignment explanation
Indices: 41314928--41314968 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
41314918 TTGCTAAATG
*
41314928 GTAAATTTGGTATTTGTGAAT
1 GTAAACTTGGTATTTGTGAAT
* *
41314949 GTAAACTTGTTATTTTTGAA
1 GTAAACTTGGTATTTGTGAA
41314969 CGCAAATTTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.02, G:0.20, T:0.49
Consensus pattern (21 bp):
GTAAACTTGGTATTTGTGAAT
Found at i:41319716 original size:40 final size:40
Alignment explanation
Indices: 41319672--41319759 Score: 122
Period size: 40 Copynumber: 2.2 Consensus size: 40
41319662 AAGTGTAACC
* * *
41319672 AGGGCACGAAAGTGAAATCAGGGGTACTGAAGTACAAACA
1 AGGGCACAAAAGTGAAATCAAGGGTACCGAAGTACAAACA
* *
41319712 AGGGCACAAAAGTGCAATCAAGTGTACCGAAGTACAAACA
1 AGGGCACAAAAGTGAAATCAAGGGTACCGAAGTACAAACA
*
41319752 GGGGCACA
1 AGGGCACA
41319760 TATGTCCAAC
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.42, C:0.18, G:0.28, T:0.11
Consensus pattern (40 bp):
AGGGCACAAAAGTGAAATCAAGGGTACCGAAGTACAAACA
Found at i:41319733 original size:20 final size:20
Alignment explanation
Indices: 41319672--41319733 Score: 52
Period size: 20 Copynumber: 3.1 Consensus size: 20
41319662 AAGTGTAACC
* *
41319672 AGGGCACGAAAGTGAAATCA
1 AGGGCACAAAAGTGCAATCA
* * ** * *
41319692 GGGGTACTGAAGTACAAACA
1 AGGGCACAAAAGTGCAATCA
41319712 AGGGCACAAAAGTGCAATCA
1 AGGGCACAAAAGTGCAATCA
41319732 AG
1 AG
41319734 TGTACCGAAG
Statistics
Matches: 29, Mismatches: 13, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.44, C:0.16, G:0.29, T:0.11
Consensus pattern (20 bp):
AGGGCACAAAAGTGCAATCA
Found at i:41332273 original size:19 final size:19
Alignment explanation
Indices: 41332226--41332275 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
41332216 AATCATATCT
** *
41332226 TCTAAGATTATATATCATA
1 TCTAAGATTGCATACCATA
41332245 TCTAAGATTGCATACCATA
1 TCTAAGATTGCATACCATA
41332264 TCTAAGATTGCA
1 TCTAAGATTGCA
41332276 GATCCTCGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.38, C:0.16, G:0.10, T:0.36
Consensus pattern (19 bp):
TCTAAGATTGCATACCATA
Found at i:41333295 original size:45 final size:43
Alignment explanation
Indices: 41332623--41333355 Score: 232
Period size: 44 Copynumber: 16.8 Consensus size: 43
41332613 GATTTGTTTA
* * * * * *
41332623 TTTAGTATGCCCCACTGCAATTTCAGGGGGATAAGGCTTGCTTTC
1 TTTAGTCTGCTCCACTGCAACTTCAGGGAGATAA-GATTGC-ATC
* * * *
41332668 TTGAGTCTGCTCCACTACAAATTCAGGGAGATAAGACT-CGAT-
1 TTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGATTGC-ATC
* * * * ** *
41332710 GTGA-TCTACTCTACTGCAACTTCAAAGAGATAAGATCTAAG-GT-
1 TTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGAT-T--GCATC
* ** * * * *
41332753 TTTAATCCACTCCACTGCAACTTTAGGAAGATAGGATTATCGA-C
1 TTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGATT-GC-ATC
** * * * *
41332797 TTTAACCTGCTCCACTGCAACTTCAGCGAGACAGGATTCGCCAAC
1 TTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGATT-G-CATC
* *
41332842 TTCAGTCTAC-CTCACTGCAACTTCA-GGAGGATAAGACTTG-AT-
1 TTTAGTCTGCTC-CACTGCAACTTCAGGGA-GATAAGA-TTGCATC
* * *
41332884 TACTTAGTGTGCTCCACTGCAACTTTAGGGAGATAAGACTAG-ATGC
1 T--TTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTGCAT-C
* * * * * * *
41332930 --GA-TCGGCT-CTCTACAACTTCAGAGAGATAAAATCTAAG-GT-
1 TTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGAT-T--GCATC
* ** * * *
41332970 TTTAATCCACTCCACTGCAACTTCAGGAAGATAGGATTATCGA-C
1 TTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGATT-GC-ATC
**
41333014 TTTAACCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATC
1 TTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTG-CATC
* * * * *
41333059 TTCAGTCTGC-CTCACTACAACTTTA-GAAGGATAAGACTTGCTTGC
1 TTTAGTCTGCTC-CACTGCAACTTCAGGGA-GATAAGA-TTGCAT-C
* * * *
41333104 -TTAGTCTGCTTCATTGCAACTTCAAGGAGATAAGACTAG-ATGC
1 TTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTGCAT-C
* ** *
41333147 TATA-TACT-CT---CTGCAACTTCAGAAAGATAAGATCTGAGAT-
1 TTTAGT-CTGCTCCACTGCAACTTCAGGGAGATAAGAT-TG-CATC
* * * **
41333187 TTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGTCGGC
1 TTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGATTG-CATC
* * *
41333231 TTTAATCTGCTCCCCTGCAACCTCAGGGAGATAAGATTTGCCATC
1 TTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTG-CATC
*
41333276 TTTAGTCTGGCT-CACTGCAACTTCA-GGAGGATAAGACTTGCTTAC
1 TTTAGTCT-GCTCCACTGCAACTTCAGGGA-GATAAGA-TTGCAT-C
*
41333321 -TTAGTCTGCTCCACTGCAACTTCAGGGAAATAAGA
1 TTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGA
41333356 CTAGATGCGA
Statistics
Matches: 511, Mismatches: 123, Indels: 109
0.69 0.17 0.15
Matches are distributed among these distances:
39 2 0.00
40 42 0.08
41 32 0.06
42 13 0.03
43 23 0.05
44 263 0.51
45 131 0.26
46 5 0.01
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.28
Consensus pattern (43 bp):
TTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGATTGCATC
Found at i:41333434 original size:217 final size:217
Alignment explanation
Indices: 41332630--41333430 Score: 1098
Period size: 217 Copynumber: 3.7 Consensus size: 217
41332620 TTATTTAGTA
* * * * * * *
41332630 TGCCCCACTGCAATTTCAGGGGGATAAGGCTTGCTTTCTTGAGTCTGCTCCACTACAAATTCAGG
1 TGCCTCACTGCAACTTCAGGAGGATAAGACTTGCTTACTT-AGTCTGCTCCACTGCAACTTCAGG
* * * *
41332695 GAGATAAGACTCGATGTGATCTACTCTACTGCAACTTCAAAGAGATAAGATCTAAGGTTTTAATC
65 GAGATAAGACTAGATGCGATCTACTCT-CTACAACTTCAGAGAGATAAGATCTAAGGTTTTAATC
* *
41332760 CACTCCACTGCAACTTTAGGAAGATAGGATTATCGACTTTAACCTGCTCCACTGCAACTTCAGCG
129 CACTCCACTGCAACTTCAGGAAGATAGGATTATCGACTTTAACCTGCTCCACTGCAACTTCAGGG
* * * *
41332825 AGACAGGATTCGCCAACTTCAGTC
194 AGATAAGATTTGCCATCTTCAGTC
* * * *
41332849 TACCTCACTGCAACTTCAGGAGGATAAGACTTGATTACTTAGTGTGCTCCACTGCAACTTTAGGG
1 TGCCTCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGG
** *
41332914 AGATAAGACTAGATGCGATCGGCTCTCTACAACTTCAGAGAGATAAAATCTAAGGTTTTAATCCA
66 AGATAAGACTAGATGCGATCTACTCTCTACAACTTCAGAGAGATAAGATCTAAGGTTTTAATCCA
41332979 CTCCACTGCAACTTCAGGAAGATAGGATTATCGACTTTAACCTGCTCCACTGCAACTTCAGGGAG
131 CTCCACTGCAACTTCAGGAAGATAGGATTATCGACTTTAACCTGCTCCACTGCAACTTCAGGGAG
41333044 ATAAGATTTGCCATCTTCAGTC
196 ATAAGATTTGCCATCTTCAGTC
* * * * * * *
41333066 TGCCTCACTACAACTTTAGAAGGATAAGACTTGCTTGCTTAGTCTGCTTCATTGCAACTTCAAGG
1 TGCCTCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGG
* * * * * * *
41333131 AGATAAGACTAGATGCTATATACTCTCTGCAACTTCAGAAAGATAAGATCTGAGATTTTAATCCG
66 AGATAAGACTAGATGCGATCTACTCTCTACAACTTCAGAGAGATAAGATCTAAGGTTTTAATCCA
* * * * * *
41333196 CTCCACTGCAACTTCAGGGAGATAGGATTGTCGGCTTTAATCTGCTCCCCTGCAACCTCAGGGAG
131 CTCCACTGCAACTTCAGGAAGATAGGATTATCGACTTTAACCTGCTCCACTGCAACTTCAGGGAG
*
41333261 ATAAGATTTGCCATCTTTAGTC
196 ATAAGATTTGCCATCTTCAGTC
*
41333283 TGGCTCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGG
1 TGCCTCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGG
* * * * * **
41333348 AAATAAGACTAGATGCGATCTGCTCTCTACAACTTCAGAGATATACGATCCAAGGTTTTAATCTG
66 AGATAAGACTAGATGCGATCTACTCTCTACAACTTCAGAGAGATAAGATCTAAGGTTTTAATCCA
*
41333413 CTCCATTGCAACTTCAGG
131 CTCCACTGCAACTTCAGG
41333431 GAGACAAGGC
Statistics
Matches: 509, Mismatches: 73, Indels: 2
0.87 0.12 0.00
Matches are distributed among these distances:
217 433 0.85
218 43 0.08
219 33 0.06
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.28
Consensus pattern (217 bp):
TGCCTCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGG
AGATAAGACTAGATGCGATCTACTCTCTACAACTTCAGAGAGATAAGATCTAAGGTTTTAATCCA
CTCCACTGCAACTTCAGGAAGATAGGATTATCGACTTTAACCTGCTCCACTGCAACTTCAGGGAG
ATAAGATTTGCCATCTTCAGTC
Found at i:41333570 original size:132 final size:132
Alignment explanation
Indices: 41333426--41333706 Score: 447
Period size: 132 Copynumber: 2.1 Consensus size: 132
41333416 CATTGCAACT
*
41333426 TCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATATA-ATTTGCC
1 TCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGAAAAGATA-AGATTTGCC
** * * * *
41333490 GTTTTCGATCTGCTCCACTACTGCCTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGC
65 GTCCTCGATCTACTCCACTACTGCCTAGGAAAATAAGATCTACAATCCTCAACCTACTCCGCTGC
41333555 TGC
130 TGC
*
41333558 TCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGAAAAGATAAGATTTTCCG
1 TCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGAAAAGATAAGATTTGCCG
* * *
41333623 TCCTCGATCTACTCCACTACTGCTTAGGAAAATAAGATCTACGATCCTCAACCTACTCCGCTGTT
66 TCCTCGATCTACTCCACTACTGCCTAGGAAAATAAGATCTACAATCCTCAACCTACTCCGCTGCT
41333688 GC
131 GC
41333690 TCAGGGAGACAAGGCTT
1 TCAGGGAGACAAGGCTT
41333707 AGTGTTTTAC
Statistics
Matches: 137, Mismatches: 11, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
131 1 0.01
132 136 0.99
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28
Consensus pattern (132 bp):
TCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGAAAAGATAAGATTTGCCG
TCCTCGATCTACTCCACTACTGCCTAGGAAAATAAGATCTACAATCCTCAACCTACTCCGCTGCT
GC
Found at i:41341313 original size:29 final size:29
Alignment explanation
Indices: 41341271--41341329 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
41341261 GATTAAAATA
41341271 TACATATGATTTACAAATAAATTTTTGGG
1 TACATATGATTTACAAATAAATTTTTGGG
41341300 TACATATGATTTACAAATAAATTTTTGGG
1 TACATATGATTTACAAATAAATTTTTGGG
41341329 T
1 T
41341330 TATGGAACGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.37, C:0.07, G:0.14, T:0.42
Consensus pattern (29 bp):
TACATATGATTTACAAATAAATTTTTGGG
Found at i:41341685 original size:4 final size:4
Alignment explanation
Indices: 41341676--41341734 Score: 50
Period size: 4 Copynumber: 14.8 Consensus size: 4
41341666 ATTTGTTTTA
* * * *
41341676 AAAT AAAT AAAT AAAT AAAC AAAC AAAT ATATAT AAAT AAA- AACT AATT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT A-A-AT AAAT AAAT AAAT AAAT
41341725 AAA- AAAT AAA
1 AAAT AAAT AAA
41341735 AGAAATAATT
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
3 5 0.11
4 36 0.78
5 2 0.04
6 3 0.07
ACGTcount: A:0.73, C:0.05, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:41342352 original size:23 final size:22
Alignment explanation
Indices: 41342309--41342366 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
41342299 AAAGGGTATC
* *
41342309 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
41342330 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
*
41342353 TACATATCATATCT
1 TACAAATCATATCT
41342367 AATATTGCAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 3 0.09
22 18 0.56
23 11 0.34
ACGTcount: A:0.43, C:0.17, G:0.03, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:41342377 original size:19 final size:19
Alignment explanation
Indices: 41342345--41342419 Score: 114
Period size: 19 Copynumber: 3.8 Consensus size: 19
41342335 AATCATATCT
*
41342345 TCTAAGATTACATATCATA
1 TCTAAGATTGCATATCATA
*
41342364 TCTAATATTGCATATATCATA
1 TCTAAGATTGC--ATATCATA
41342385 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
41342404 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
41342420 CTCGAAGATT
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
19 33 0.65
21 18 0.35
ACGTcount: A:0.37, C:0.16, G:0.08, T:0.39
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:41342382 original size:21 final size:21
Alignment explanation
Indices: 41342356--41342418 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
41342346 CTAAGATTAC
*
41342356 ATATCATATCTAATATTGCAT
1 ATATCATATCTAAGATTGCAT
41342377 ATATCATATCTAAGATTGC--
1 ATATCATATCTAAGATTGCAT
41342396 ATATCATATCTAAGATTGCAT
1 ATATCATATCTAAGATTGCAT
41342417 AT
1 AT
41342419 CCTCGAAGAT
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
19 19 0.49
21 20 0.51
ACGTcount: A:0.38, C:0.14, G:0.08, T:0.40
Consensus pattern (21 bp):
ATATCATATCTAAGATTGCAT
Found at i:41346546 original size:12 final size:12
Alignment explanation
Indices: 41346529--41346553 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
41346519 GAACTCCTTT
41346529 AAAAAATTATAA
1 AAAAAATTATAA
41346541 AAAAAATTATAA
1 AAAAAATTATAA
41346553 A
1 A
41346554 TAATATAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
AAAAAATTATAA
Found at i:41348755 original size:30 final size:30
Alignment explanation
Indices: 41348719--41348777 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
41348709 TGGGTAACCT
41348719 TGATATAATACCAACTTGTGTGAGCAACTG
1 TGATATAATACCAACTTGTGTGAGCAACTG
* * *
41348749 TGATATAATATCAGCTTGTGTGAGGAACT
1 TGATATAATACCAACTTGTGTGAGCAACT
41348778 TATTCCCGCG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.32, C:0.14, G:0.22, T:0.32
Consensus pattern (30 bp):
TGATATAATACCAACTTGTGTGAGCAACTG
Found at i:41357854 original size:138 final size:138
Alignment explanation
Indices: 41357603--41358194 Score: 891
Period size: 138 Copynumber: 4.3 Consensus size: 138
41357593 TAGATAAAGC
* * * * * *
41357603 TAATAAATGAATTTAATTTATACAAAATATTAATTGTACATATTTTATCGAAA-TTATTAATAGA
1 TAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTA-CCAAATTTATTAATA-T
* * *
41357667 AAAAAATTATATTAATTAATTTCGGTCAAAATATAAAAGACATGGAAATTAATATTCTGTTGGAA
64 AAACAGTTATATTAATTAATTTCGGTCAAAATATAAAAGACATGGAAATTAATATTCTTTTGGAA
41357732 AGAATATAAT
129 AGAATATAAT
41357742 TAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTATT-CCAAATTTATTAATATA
1 TAATATATGAATTTGATTCATACAAAATATTAATTGTATATATT-TTACCAAATTTATTAATATA
* * * *
41357806 AATAGTTATATTAATTCATTTCGGTCAAAATATAAAAGACATGTAAATTAATATTCTTTTAGAAA
65 AACAGTTATATTAATTAATTTCGGTCAAAATATAAAAGACATGGAAATTAATATTCTTTTGGAAA
41357871 GAATATAAT
130 GAATATAAT
* *
41357880 TAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTATCGAATTTATTAATATAA
1 TAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCAAATTTATTAATATAA
* * * * *
41357945 ACATTTCTATTAATTAATTTCGATCAAAATATAAAGGACATGAAAATTAATATTCTTTTGGAAAG
66 ACAGTTATATTAATTAATTTCGGTCAAAATATAAAAGACATGGAAATTAATATTCTTTTGGAAAG
41358010 AATATAAT
131 AATATAAT
* * *
41358018 TAATATATGAATTTGATTCATATAAAATATTAATTGTATATATTTTACCGAATTTATGAATATAA
1 TAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCAAATTTATTAATATAA
* * *
41358083 ACAGTTATATTAATTAATTGCGGTCAAAATATTAAATACATGGAAATTAATATTCTTTTGGAAAG
66 ACAGTTATATTAATTAATTTCGGTCAAAATATAAAAGACATGGAAATTAATATTCTTTTGGAAAG
41358148 AATATAAT
131 AATATAAT
* *
41358156 TAATATATAAATTTTATTCATACAAAATATTAATTGTAT
1 TAATATATGAATTTGATTCATACAAAATATTAATTGTAT
41358195 TTATATAGAG
Statistics
Matches: 414, Mismatches: 36, Indels: 7
0.91 0.08 0.02
Matches are distributed among these distances:
137 2 0.00
138 361 0.87
139 49 0.12
140 2 0.00
ACGTcount: A:0.45, C:0.06, G:0.08, T:0.41
Consensus pattern (138 bp):
TAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCAAATTTATTAATATAA
ACAGTTATATTAATTAATTTCGGTCAAAATATAAAAGACATGGAAATTAATATTCTTTTGGAAAG
AATATAAT
Found at i:41357908 original size:71 final size:71
Alignment explanation
Indices: 41357693--41358047 Score: 185
Period size: 71 Copynumber: 5.1 Consensus size: 71
41357683 TAATTTCGGT
* * *
41357693 CAAAATATAAAAGACATGGAAATTAATATTCTGTTGGAAAGAATATAATTAATATATGAATTTGA
1 CAAAATATAAAAGACATGTAAATTAATATTCTTTTAGAAAGAATATAATTAATATATGAATTTGA
41357758 TTCATA
66 TTCATA
** * * * * * * *
41357764 CAAAATATTAATTG-TATATATTATTCCAA-ATT-TATTA-ATATAA-ATAGTT-ATAT-T-AA-
1 CAAAATA-TAAAAGACATGTA-AATT--AATATTCTTTTAGAAAGAATATAATTAATATATGAAT
* *
41357820 TTCATTTCGGT-
62 TTGA-TTC-ATA
41357831 CAAAATATAAAAGACATGTAAATTAATATTCTTTTAGAAAGAATATAATTAATATATGAATTTGA
1 CAAAATATAAAAGACATGTAAATTAATATTCTTTTAGAAAGAATATAATTAATATATGAATTTGA
41357896 TTCATA
66 TTCATA
* * * * * ** * * *
41357902 CAAAATAT--TA-A-TTGT--A-T-ATATT-TTATCGAATTTATTAATATAAACATTTCTATTAA
1 CAAAATATAAAAGACATGTAAATTAATATTCTTTTAGAA---A-GAATATAATTA-ATATATGAA
*
41357958 -TTAATTTCGAT-
61 TTTGA-TTC-ATA
* * *
41357969 CAAAATATAAAGGACATGAAAATTAATATTCTTTTGGAAAGAATATAATTAATATATGAATTTGA
1 CAAAATATAAAAGACATGTAAATTAATATTCTTTTAGAAAGAATATAATTAATATATGAATTTGA
41358034 TTCATA
66 TTCATA
*
41358040 TAAAATAT
1 CAAAATAT
41358048 TAATTGTATA
Statistics
Matches: 201, Mismatches: 49, Indels: 68
0.63 0.15 0.21
Matches are distributed among these distances:
62 6 0.03
63 5 0.02
64 3 0.01
65 5 0.02
66 25 0.12
67 40 0.20
68 10 0.05
69 9 0.04
70 10 0.05
71 45 0.22
72 24 0.12
73 5 0.02
74 3 0.01
75 5 0.02
76 6 0.03
ACGTcount: A:0.46, C:0.06, G:0.08, T:0.40
Consensus pattern (71 bp):
CAAAATATAAAAGACATGTAAATTAATATTCTTTTAGAAAGAATATAATTAATATATGAATTTGA
TTCATA
Found at i:41364187 original size:22 final size:22
Alignment explanation
Indices: 41364162--41364204 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
41364152 TGTATGTAAT
*
41364162 TATTTTCTT-TTTAAATATATAA
1 TATTTTATTATTTAAA-ATATAA
41364184 TATTTTATTATTTAAAATATA
1 TATTTTATTATTTAAAATATA
41364205 GTTTAAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (22 bp):
TATTTTATTATTTAAAATATAA
Found at i:41364533 original size:13 final size:13
Alignment explanation
Indices: 41364476--41364536 Score: 50
Period size: 13 Copynumber: 4.7 Consensus size: 13
41364466 ACCAAAATTT
*
41364476 TCAAAAGTACTTC
1 TCAAAAGCACTTC
* *
41364489 TCAAAATCACTTT
1 TCAAAAGCACTTC
* * * *
41364502 TCCACAGCATTTT
1 TCAAAAGCACTTC
*
41364515 TTAAAAGCACTTC
1 TCAAAAGCACTTC
41364528 TCAAAAGCA
1 TCAAAAGCA
41364537 ATGCTAAACT
Statistics
Matches: 35, Mismatches: 13, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
13 35 1.00
ACGTcount: A:0.38, C:0.25, G:0.07, T:0.31
Consensus pattern (13 bp):
TCAAAAGCACTTC
Found at i:41390814 original size:23 final size:23
Alignment explanation
Indices: 41390784--41390828 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
41390774 CATTATTATT
41390784 ATTTTTTACTT-TTCTTTGTTTAA
1 ATTTTTTACTTCTTC-TTGTTTAA
41390807 ATTTTTTACTTCTTCTTGTTTA
1 ATTTTTTACTTCTTCTTGTTTA
41390829 TTTAAGTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 18 0.86
24 3 0.14
ACGTcount: A:0.16, C:0.11, G:0.04, T:0.69
Consensus pattern (23 bp):
ATTTTTTACTTCTTCTTGTTTAA
Found at i:41390873 original size:17 final size:18
Alignment explanation
Indices: 41390851--41390884 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
41390841 TGTAGTTTTT
*
41390851 TTTTCA-AATATTTTTAG
1 TTTTCATAAAATTTTTAG
41390868 TTTTCATAAAATTTTTA
1 TTTTCATAAAATTTTTA
41390885 AACTATTATG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.32, C:0.06, G:0.03, T:0.59
Consensus pattern (18 bp):
TTTTCATAAAATTTTTAG
Found at i:41393337 original size:14 final size:14
Alignment explanation
Indices: 41393315--41393346 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
41393305 TTATATACGT
*
41393315 TTTATGATTTAGGG
1 TTTAGGATTTAGGG
41393329 TTTAGGATTTAGGG
1 TTTAGGATTTAGGG
41393343 TTTA
1 TTTA
41393347 TATATGTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.22, C:0.00, G:0.28, T:0.50
Consensus pattern (14 bp):
TTTAGGATTTAGGG
Found at i:41395565 original size:66 final size:65
Alignment explanation
Indices: 41395441--41395567 Score: 155
Period size: 66 Copynumber: 1.9 Consensus size: 65
41395431 TTTGGTATTT
* * *
41395441 GGTTAATGCTGCTGCAAGTTCTTTTTTGCTGGAAGTTCTGCTTAATGTTGCTGGTTAATGTTAGG
1 GGTTAATGCTGCTGCAAGTTCTTTTTTGCTGCAAGTTCTGCTTAATATTGCTGCTTAATGTTAGG
* * * * * * *
41395506 GGTTAATGTTGTTGCAAGTTATTTTTTTGTTGCACGTTGTGGTTAATATTGCTGCTTAATGT
1 GGTTAATGCTGCTGCAAGTT-CTTTTTTGCTGCAAGTTCTGCTTAATATTGCTGCTTAATGT
41395568 ATTTATTTCT
Statistics
Matches: 51, Mismatches: 10, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
65 18 0.35
66 33 0.65
ACGTcount: A:0.17, C:0.10, G:0.26, T:0.46
Consensus pattern (65 bp):
GGTTAATGCTGCTGCAAGTTCTTTTTTGCTGCAAGTTCTGCTTAATATTGCTGCTTAATGTTAGG
Found at i:41396423 original size:9 final size:9
Alignment explanation
Indices: 41396396--41396443 Score: 64
Period size: 9 Copynumber: 5.6 Consensus size: 9
41396386 GTTCAAATTT
41396396 CATAACTTA
1 CATAACTTA
* *
41396405 CGTAATTTA
1 CATAACTTA
41396414 CATAACTTA
1 CATAACTTA
41396423 CATAA-TT-
1 CATAACTTA
41396430 CATAACTTA
1 CATAACTTA
41396439 CATAA
1 CATAA
41396444 TTTAAATTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
7 5 0.15
8 4 0.12
9 24 0.73
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (9 bp):
CATAACTTA
Found at i:41396435 original size:16 final size:16
Alignment explanation
Indices: 41396394--41396472 Score: 83
Period size: 16 Copynumber: 5.0 Consensus size: 16
41396384 AAGTTCAAAT
*
41396394 TTCATAACTTACGTAA
1 TTCATAACTTACATAA
41396410 TTTACATAACTTACATAA
1 -TT-CATAACTTACATAA
41396428 TTCATAACTTACATAA
1 TTCATAACTTACATAA
* *
41396444 TT--TAAATT-TATAA
1 TTCATAACTTACATAA
*
41396457 TACATAACTTACATAA
1 TTCATAACTTACATAA
41396473 ATTATTAATA
Statistics
Matches: 52, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
13 5 0.10
14 5 0.10
15 5 0.10
16 20 0.38
17 4 0.08
18 13 0.25
ACGTcount: A:0.44, C:0.15, G:0.01, T:0.39
Consensus pattern (16 bp):
TTCATAACTTACATAA
Found at i:41396501 original size:19 final size:18
Alignment explanation
Indices: 41396477--41396530 Score: 69
Period size: 17 Copynumber: 3.1 Consensus size: 18
41396467 ACATAAATTA
41396477 TTAATATTTATATATAGTT
1 TTAATATTTATATATA-TT
41396496 TTAATA--TATATATA-T
1 TTAATATTTATATATATT
*
41396511 TTAAAATTTATATATATT
1 TTAATATTTATATATATT
41396529 TT
1 TT
41396531 TAAAAATTGA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
15 6 0.19
17 16 0.52
18 3 0.10
19 6 0.19
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (18 bp):
TTAATATTTATATATATT
Found at i:41396659 original size:9 final size:9
Alignment explanation
Indices: 41396616--41397008 Score: 63
Period size: 9 Copynumber: 44.0 Consensus size: 9
41396606 AAATTTGTAA
*
41396616 TACATAATAA
1 TACATAA-AT
**
41396626 TACATAACC
1 TACATAAAT
41396635 TACATAAAT
1 TACATAAAT
* *
41396644 TAAATAAGT
1 TACATAAAT
41396653 TACAT-AA-
1 TACATAAAT
* *
41396660 TACACAAAAA
1 TACA-TAAAT
* *
41396670 AACAAAAACT
1 TACATAAA-T
*
41396680 TACATAACT
1 TACATAAAT
41396689 TACATAATAT
1 TACATAA-AT
41396699 CCTACATAATAACT
1 --TACAT-A-AA-T
*
41396713 TACATAATAA
1 TACATAA-AT
**
41396723 TACATAACC
1 TACATAAAT
41396732 TACATAAAT
1 TACATAAAT
* *
41396741 TAAATAAGT
1 TACATAAAT
41396750 TACAT-AA-
1 TACATAAAT
*
41396757 TACACAAA-
1 TACATAAAT
* *
41396765 AACAAAAACT
1 TACATAAA-T
*
41396775 TACATAACT
1 TACATAAAT
41396784 TACAT-AA-
1 TACATAAAT
*
41396791 TACATAACT
1 TACATAAAT
**
41396800 TACATAACC
1 TACATAAAT
*
41396809 TAC-TTAA-
1 TACATAAAT
*
41396816 TACATAACT
1 TACATAAAT
41396825 TACATAACA-
1 TACATAA-AT
* * *
41396834 CACACAACT
1 TACATAAAT
*
41396843 TACATAACT
1 TACATAAAT
*
41396852 TACATAACT
1 TACATAAAT
*
41396861 TATATAAGACAACT
1 TACAT---A-AA-T
41396875 TACAT-AAT
1 TACATAAAT
*
41396883 GTAC-TTAA-
1 -TACATAAAT
*
41396891 TACATAACT
1 TACATAAAT
**
41396900 TACATAACC
1 TACATAAAT
41396909 TACAT-AA-
1 TACATAAAT
* *
41396916 GACATAACT
1 TACATAAAT
*
41396925 TACATAAGT
1 TACATAAAT
*
41396934 TTCAT-AA-
1 TACATAAAT
* *
41396941 TACACAACT
1 TACATAAAT
*
41396950 TACATAACT
1 TACATAAAT
41396959 TACAT-AA-
1 TACATAAAT
*
41396966 TACATAACT
1 TACATAAAT
*
41396975 TACATAATT
1 TACATAAAT
*
41396984 TAC-TTAA-
1 TACATAAAT
*
41396991 TACATAACT
1 TACATAAAT
*
41397000 TACACAAAT
1 TACATAAAT
41397009 ATATGATGTG
Statistics
Matches: 277, Mismatches: 69, Indels: 75
0.66 0.16 0.18
Matches are distributed among these distances:
7 34 0.12
8 30 0.11
9 161 0.58
10 29 0.10
11 2 0.01
12 11 0.04
13 3 0.01
14 7 0.03
ACGTcount: A:0.50, C:0.19, G:0.02, T:0.29
Consensus pattern (9 bp):
TACATAAAT
Found at i:41396660 original size:34 final size:34
Alignment explanation
Indices: 41396622--41396981 Score: 142
Period size: 34 Copynumber: 10.6 Consensus size: 34
41396612 GTAATACATA
*
41396622 ATAATACATAACCTACATAAATTAAATAAGTTAC
1 ATAATACATAACCTACATAAATTAAATAACTTAC
* *** * *
41396656 ATAATACACAAAAAAACAAAAACTTACATAACTTAC
1 ATAATACA-TAACCTACATAAA-TTAAATAACTTAC
* * *
41396692 ATAAT--AT--CCTACAT-AA-TAACTTACATA-
1 ATAATACATAACCTACATAAATTAAATAACTTAC
*
41396719 ATAATACATAACCTACATAAATTAAATAAGTTAC
1 ATAATACATAACCTACATAAATTAAATAACTTAC
* ** * *
41396753 ATAATACACAA-AAACAAAAACTTACATAACTTAC
1 ATAATACATAACCTACATAAA-TTAAATAACTTAC
*
41396787 ATAATACATAACTTACATAACCTACTTAATACATAACTTAC
1 ATAATACATAACCTACATAA---A-TT-A-A-ATAACTTAC
* * * * * *
41396828 ATAACACACACAACTTACATAACTTACATAACTTAT
1 AT-A-ATACATAACCTACATAAATTAAATAACTTAC
* * **
41396864 ATAAGAC--AACTTACAT-AATGTACTTAA--TAC
1 ATAATACATAACCTACATAAAT-TAAATAACTTAC
* *
41396894 ATAACTTACATAACCTACAT-AA-GACATAACTTAC
1 ATAA--TACATAACCTACATAAATTAAATAACTTAC
* * * *
41396928 ATAAGTTTCATAA--TACACAACTTACATAACTTAC
1 ATAA--TACATAACCTACATAAATTAAATAACTTAC
*
41396962 ATAATACATAACTTACATAA
1 ATAATACATAACCTACATAA
41396982 TTTACTTAAT
Statistics
Matches: 245, Mismatches: 51, Indels: 60
0.69 0.14 0.17
Matches are distributed among these distances:
27 5 0.02
28 7 0.03
29 2 0.01
30 8 0.03
31 12 0.05
32 34 0.14
33 14 0.06
34 88 0.36
35 14 0.06
36 26 0.11
38 5 0.02
39 3 0.01
41 11 0.04
42 1 0.00
43 15 0.06
ACGTcount: A:0.51, C:0.19, G:0.02, T:0.28
Consensus pattern (34 bp):
ATAATACATAACCTACATAAATTAAATAACTTAC
Found at i:41396706 original size:12 final size:12
Alignment explanation
Indices: 41396683--41396722 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
41396673 AAAAACTTAC
*
41396683 ATAACTTACATA
1 ATAACCTACATA
*
41396695 ATATCCTACATA
1 ATAACCTACATA
*
41396707 ATAACTTACATA
1 ATAACCTACATA
41396719 ATAA
1 ATAA
41396723 TACATAACCT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (12 bp):
ATAACCTACATA
Found at i:41396728 original size:97 final size:95
Alignment explanation
Indices: 41396616--41396792 Score: 336
Period size: 97 Copynumber: 1.8 Consensus size: 95
41396606 AAATTTGTAA
41396616 TACATAATAATACATAACCTACATAAATTAAATAAGTTACATAATACACAAAAAAACAAAAACTT
1 TACATAATAATACATAACCTACATAAATTAAATAAGTTACATAATACAC--AAAAACAAAAACTT
41396681 ACATAACTTACATAATATCCTACATAATAACT
64 ACATAACTTACATAATATCCTACATAATAACT
41396713 TACATAATAATACATAACCTACATAAATTAAATAAGTTACATAATACACAAAAACAAAAACTTAC
1 TACATAATAATACATAACCTACATAAATTAAATAAGTTACATAATACACAAAAACAAAAACTTAC
41396778 ATAACTTACATAATA
66 ATAACTTACATAATA
41396793 CATAACTTAC
Statistics
Matches: 80, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
95 31 0.39
97 49 0.61
ACGTcount: A:0.55, C:0.17, G:0.01, T:0.27
Consensus pattern (95 bp):
TACATAATAATACATAACCTACATAAATTAAATAAGTTACATAATACACAAAAACAAAAACTTAC
ATAACTTACATAATATCCTACATAATAACT
Found at i:41396796 original size:16 final size:16
Alignment explanation
Indices: 41396775--41396982 Score: 127
Period size: 16 Copynumber: 13.1 Consensus size: 16
41396765 AACAAAAACT
41396775 TACATAACTTACATAA
1 TACATAACTTACATAA
41396791 TACATAACTTACAT-A
1 TACATAACTTACATAA
*
41396806 -AC----C-TACTTAA
1 TACATAACTTACATAA
41396816 TACATAACTTACATAACA
1 TACATAACTTACAT-A-A
* *
41396834 CACACAACTTACATAA
1 TACATAACTTACATAA
*
41396850 CTTACATAACTTATATAA
1 --TACATAACTTACATAA
*
41396868 GAC--AACTTACATAA
1 TACATAACTTACATAA
*
41396882 TGTACTTAA--TACATAA
1 --TACATAACTTACATAA
*
41396898 CTTACATAACCTACATAA
1 --TACATAACTTACATAA
*
41396916 GACATAACTTACATAA
1 TACATAACTTACATAA
* *
41396932 GTTTCATAA--TACACAA
1 --TACATAACTTACATAA
41396948 CTTACATAACTTACATAA
1 --TACATAACTTACATAA
41396966 TACATAACTTACATAA
1 TACATAACTTACATAA
41396982 T
1 T
41396983 TTACTTAATA
Statistics
Matches: 150, Mismatches: 21, Indels: 42
0.70 0.10 0.20
Matches are distributed among these distances:
9 4 0.03
10 2 0.01
11 2 0.01
14 12 0.08
15 2 0.01
16 80 0.53
17 2 0.01
18 46 0.31
ACGTcount: A:0.47, C:0.21, G:0.02, T:0.30
Consensus pattern (16 bp):
TACATAACTTACATAA
Found at i:41396799 original size:25 final size:25
Alignment explanation
Indices: 41396771--41397003 Score: 283
Period size: 25 Copynumber: 9.3 Consensus size: 25
41396761 CAAAAACAAA
41396771 AACTTACATAACTTACATAATACAT
1 AACTTACATAACTTACATAATACAT
* *
41396796 AACTTACATAACCTACTTAATACAT
1 AACTTACATAACTTACATAATACAT
** *
41396821 AACTTACATAACACACACAACTTACAT
1 AACTTACATAACTTACATAA--TACAT
* *
41396848 AACTTACATAACTTATATAAGAC--
1 AACTTACATAACTTACATAATACAT
*
41396871 AACTTACATAA-TGTACTTAATACAT
1 AACTTACATAACT-TACATAATACAT
* *
41396896 AACTTACATAACCTACATAAGACAT
1 AACTTACATAACTTACATAATACAT
* * *
41396921 AACTTACATAAGTTTCATAATACAC
1 AACTTACATAACTTACATAATACAT
41396946 AACTTACATAACTTACATAATACAT
1 AACTTACATAACTTACATAATACAT
* *
41396971 AACTTACATAATTTACTTAATACAT
1 AACTTACATAACTTACATAATACAT
41396996 AACTTACA
1 AACTTACA
41397004 CAAATATATG
Statistics
Matches: 175, Mismatches: 27, Indels: 12
0.82 0.13 0.06
Matches are distributed among these distances:
22 1 0.01
23 18 0.10
25 135 0.77
27 21 0.12
ACGTcount: A:0.46, C:0.21, G:0.02, T:0.31
Consensus pattern (25 bp):
AACTTACATAACTTACATAATACAT
Found at i:41400318 original size:87 final size:87
Alignment explanation
Indices: 41400167--41400343 Score: 246
Period size: 87 Copynumber: 2.0 Consensus size: 87
41400157 GAACACATTT
* * * * *
41400167 GAGGTTCAAAGGAAATATGAAGAACTTCAGCTACAACTTAAAGTAAAGGTGGCAGCGAGGGAAGC
1 GAGGTTCAAAAGAAATATGAAGAACTCCAGCTACAACTTAAAGCAAAGGCGGCAGCGAGAGAAGC
*
41400232 AAAGGCTGCAGCGAGAAAAGCA
66 AAACGCTGCAGCGAGAAAAGCA
* * *
41400254 GAGGTTCAAAAGAAATATGAAGAACTCCAGCTACAACTTAAAGCAGATGCGGCATCGAGAGAAGC
1 GAGGTTCAAAAGAAATATGAAGAACTCCAGCTACAACTTAAAGCAAAGGCGGCAGCGAGAGAAGC
* **
41400319 AGACGCTGCAGCGAGGGAAGCA
66 AAACGCTGCAGCGAGAAAAGCA
41400341 GAG
1 GAG
41400344 CAGAGCAGAA
Statistics
Matches: 78, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
87 78 1.00
ACGTcount: A:0.40, C:0.17, G:0.30, T:0.13
Consensus pattern (87 bp):
GAGGTTCAAAAGAAATATGAAGAACTCCAGCTACAACTTAAAGCAAAGGCGGCAGCGAGAGAAGC
AAACGCTGCAGCGAGAAAAGCA
Found at i:41400320 original size:21 final size:21
Alignment explanation
Indices: 41400294--41400342 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
41400284 CTACAACTTA
* *
41400294 AAGCAGATGCGGCATCGAGAG
1 AAGCAGACGCGGCAGCGAGAG
* *
41400315 AAGCAGACGCTGCAGCGAGGG
1 AAGCAGACGCGGCAGCGAGAG
41400336 AAGCAGA
1 AAGCAGA
41400343 GCAGAGCAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.35, C:0.20, G:0.39, T:0.06
Consensus pattern (21 bp):
AAGCAGACGCGGCAGCGAGAG
Found at i:41400782 original size:43 final size:43
Alignment explanation
Indices: 41400692--41401003 Score: 306
Period size: 43 Copynumber: 7.3 Consensus size: 43
41400682 ACTAAACAAA
* *
41400692 TAGCGGCGTTTGTGGAAAAAGCGCTGCTAAAAGAACATGACCTT
1 TAGCGGCGTTTGTGGAAAAAGCGCCGCT-AAAGAACATGATCTT
* *
41400736 TAGCAGCGTTTGTGGAAGAAGCGCCGCTAAAGAACATGATCTT
1 TAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGAACATGATCTT
* * * * * *
41400779 TAGCGGCATTTGTGGAAAAATCACCACTAAGGAGCATGATCTT
1 TAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGAACATGATCTT
*
41400822 TAGCGGCGTTTGTGGAACAAGCGCCGCTAAAGAACATGATCTT
1 TAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGAACATGATCTT
* * * * * *
41400865 CAACGGCGTTTGTTGAAAAAGCGGCTCTAAAGAACATGACCTT
1 TAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGAACATGATCTT
* * * *
41400908 TAACGGCGTTTGTAGG-AAAAGCGCTGCTAAAGACCCTGA-CTTT
1 TAGCGGCGTTTGT-GGAAAAAGCGCCGCTAAAGAACATGATC-TT
* ****** * *
41400951 TAGCGGTGTTT-TTTCTGTAGCGTCGCTAAAGAACATGACCTT
1 TAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGAACATGATCTT
41400993 TAGCGGCGTTT
1 TAGCGGCGTTT
41401004 ATAAAAATAA
Statistics
Matches: 219, Mismatches: 45, Indels: 10
0.80 0.16 0.04
Matches are distributed among these distances:
42 30 0.14
43 163 0.74
44 26 0.12
ACGTcount: A:0.29, C:0.20, G:0.26, T:0.26
Consensus pattern (43 bp):
TAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGAACATGATCTT
Found at i:41401140 original size:22 final size:22
Alignment explanation
Indices: 41401097--41401140 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
41401087 TAGTGGCGCT
* **
41401097 AAAAAGCGCCGCTAAAGGCCTG
1 AAAAAACGCCGCTAAAAACCTG
41401119 AAAAAACGCCGCTAAAAACCTG
1 AAAAAACGCCGCTAAAAACCTG
41401141 TTTTGGTGTA
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:0.27, G:0.20, T:0.09
Consensus pattern (22 bp):
AAAAAACGCCGCTAAAAACCTG
Found at i:41401622 original size:18 final size:15
Alignment explanation
Indices: 41401578--41401610 Score: 50
Period size: 14 Copynumber: 2.2 Consensus size: 15
41401568 CTTGGATGAG
41401578 AATAAATTTTTAATTA
1 AATAAA-TTTTAATTA
41401594 AATAAA-TTTAATTA
1 AATAAATTTTAATTA
41401608 AAT
1 AAT
41401611 CAAAAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 11 0.65
16 6 0.35
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AATAAATTTTAATTA
Found at i:41402814 original size:41 final size:40
Alignment explanation
Indices: 41402755--41403123 Score: 407
Period size: 41 Copynumber: 9.0 Consensus size: 40
41402745 AGTTTTCGGG
* * *
41402755 GGCTTTACCGGTGTTTTTGAGGAAGC-CCAGCTAATGCTCA
1 GGCTTTAGCGGCGTTTTTGAGAAAGCGCC-GCTAATGCTCA
* *
41402795 GGCTTTTAGCGGCATTTTTGAAAAAGCGCCGCTAATGCTCA
1 GGC-TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCA
* *
41402836 GGCCTTTAGCGGTGTTTTTGACAAAGCGCCGCTAATGCTCA
1 GG-CTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCA
* * * *
41402877 GGGCTTTAGCGGCGTTTTTGAGGAAGTGCCACTAATGGTCA
1 -GGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCA
* * *
41402918 GAGCTTTAGCAGCATTTTTGAGGAAGCGCCGCTAATGCTCA
1 G-GCTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCA
** * *
41402959 GGGCTTTAGCGGTATTTTTGATAAAGTGCCGCTAATGCTCA
1 -GGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCA
* *
41403000 GGGCTTTAGCGGCGTTTTTGATAAAGCGCCGCTGATGCTCA
1 -GGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCA
* * * *
41403041 GGGCTTTAGCAGCGTTTTTGGGAAAGTGCCGCTAATGCTTA
1 -GGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCA
* * *
41403082 GGGTTTTAGCGGTGTTTTTAAGAAAGCGCCGCTAATGCTCA
1 -GGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCA
41403123 G
1 G
41403124 AAGCGCCGCT
Statistics
Matches: 282, Mismatches: 41, Indels: 12
0.84 0.12 0.04
Matches are distributed among these distances:
40 5 0.02
41 271 0.96
42 6 0.02
ACGTcount: A:0.21, C:0.20, G:0.29, T:0.30
Consensus pattern (40 bp):
GGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCA
Found at i:41402895 original size:82 final size:82
Alignment explanation
Indices: 41402754--41403123 Score: 474
Period size: 82 Copynumber: 4.5 Consensus size: 82
41402744 GAGTTTTCGG
* * *
41402754 GGGCTTTACCGGTGTTTTTGAGGAAGC-CCAGCTAATGCTCA-GGCTTTTAGCGGCATTTTTGAA
1 GGGCTTTAGCGGTGTTTTTGAGAAAGCGCC-GCTAATGCTCAGGGC-TTTAGCGGCATTTTTGAG
*
41402817 AAAGCGCCGCTAATGCTCA
64 AAAGTGCCGCTAATGCTCA
* * * *
41402836 GGCCTTTAGCGGTGTTTTTGACAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGAGGA
1 GGGCTTTAGCGGTGTTTTTGAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCATTTTTGAGAA
* *
41402901 AGTGCCACTAATGGTCA
66 AGTGCCGCTAATGCTCA
* * ** * * *
41402918 GAGCTTTAGCAGCATTTTTGAGGAAGCGCCGCTAATGCTCAGGGCTTTAGCGGTATTTTTGATAA
1 GGGCTTTAGCGGTGTTTTTGAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCATTTTTGAGAA
41402983 AGTGCCGCTAATGCTCA
66 AGTGCCGCTAATGCTCA
* * * * * *
41403000 GGGCTTTAGCGGCGTTTTTGATAAAGCGCCGCTGATGCTCAGGGCTTTAGCAGCGTTTTTGGGAA
1 GGGCTTTAGCGGTGTTTTTGAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCATTTTTGAGAA
*
41403065 AGTGCCGCTAATGCTTA
66 AGTGCCGCTAATGCTCA
* *
41403082 GGGTTTTAGCGGTGTTTTTAAGAAAGCGCCGCTAATGCTCAG
1 GGGCTTTAGCGGTGTTTTTGAGAAAGCGCCGCTAATGCTCAG
41403124 AAGCGCCGCT
Statistics
Matches: 246, Mismatches: 40, Indels: 4
0.85 0.14 0.01
Matches are distributed among these distances:
82 241 0.98
83 5 0.02
ACGTcount: A:0.21, C:0.20, G:0.29, T:0.30
Consensus pattern (82 bp):
GGGCTTTAGCGGTGTTTTTGAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCATTTTTGAGAA
AGTGCCGCTAATGCTCA
Found at i:41402977 original size:123 final size:121
Alignment explanation
Indices: 41402754--41403123 Score: 481
Period size: 123 Copynumber: 3.0 Consensus size: 121
41402744 GAGTTTTCGG
* * * * **
41402754 GGGCTTTACCGGTGTTTTTGAGGAAGCCCAGCTAATGCTCAGGCTTTTAGCGGCATTTTTGAAAA
1 GGGCTTTAGCGGCGTTTTTGAGGAAGGCCA-CTAATGCTCAGGC-TTTAGCAGCATTTTTGAGGA
*
41402819 AGCGCCGCTAATGCTCAGGCCTTTAGCGGTGTTTTTGACAAAGCGCCGCTAATGCTCA
64 AGCGCCGCTAATGCTCAGGGCTTTAGCGGTGTTTTTGACAAAGCGCCGCTAATGCTCA
*
41402877 GGGCTTTAGCGGCGTTTTTGAGGAAGTGCCACTAATGGTCAGAGCTTTAGCAGCATTTTTGAGGA
1 GGGCTTTAGCGGCGTTTTTGAGGAAG-GCCACTAATGCTCAG-GCTTTAGCAGCATTTTTGAGGA
* * *
41402942 AGCGCCGCTAATGCTCAGGGCTTTAGCGGTATTTTTGATAAAGTGCCGCTAATGCTCA
64 AGCGCCGCTAATGCTCAGGGCTTTAGCGGTGTTTTTGACAAAGCGCCGCTAATGCTCA
** * * *
41403000 GGGCTTTAGCGGCGTTTTTGATAAAGCGCCGCTGATGCTCAGGGCTTTAGCAGCGTTTTTG-GGA
1 GGGCTTTAGCGGCGTTTTTGAGGAAG-GCCACTAATGCTCA-GGCTTTAGCAGCATTTTTGAGG-
* * * * *
41403064 AAGTGCCGCTAATGCTTAGGGTTTTAGCGGTGTTTTTAAGAAAGCGCCGCTAATGCTCA
63 AAGCGCCGCTAATGCTCAGGGCTTTAGCGGTGTTTTTGACAAAGCGCCGCTAATGCTCA
41403123 G
1 G
41403124 AAGCGCCGCT
Statistics
Matches: 218, Mismatches: 25, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
122 2 0.01
123 210 0.96
124 6 0.03
ACGTcount: A:0.21, C:0.20, G:0.29, T:0.30
Consensus pattern (121 bp):
GGGCTTTAGCGGCGTTTTTGAGGAAGGCCACTAATGCTCAGGCTTTAGCAGCATTTTTGAGGAAG
CGCCGCTAATGCTCAGGGCTTTAGCGGTGTTTTTGACAAAGCGCCGCTAATGCTCA
Found at i:41403129 original size:19 final size:19
Alignment explanation
Indices: 41403105--41403142 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
41403095 GTTTTTAAGA
41403105 AAGCGCCGCTAATGCTCAG
1 AAGCGCCGCTAATGCTCAG
41403124 AAGCGCCGCTAATGCTCAG
1 AAGCGCCGCTAATGCTCAG
41403143 GGCTTTAACG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.32, G:0.26, T:0.16
Consensus pattern (19 bp):
AAGCGCCGCTAATGCTCAG
Found at i:41403561 original size:14 final size:14
Alignment explanation
Indices: 41403516--41403565 Score: 57
Period size: 14 Copynumber: 3.5 Consensus size: 14
41403506 TTAAAGGCTT
*
41403516 GGGTTTAAGGTTTA
1 GGGTTTATGGTTTA
*
41403530 GAGG-TTATGTGTTAA
1 G-GGTTTATG-GTTTA
41403545 GGGTTTATGGTTTA
1 GGGTTTATGGTTTA
41403559 GGGTTTA
1 GGGTTTA
41403566 GATTAACTAG
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
14 18 0.60
15 12 0.40
ACGTcount: A:0.20, C:0.00, G:0.36, T:0.44
Consensus pattern (14 bp):
GGGTTTATGGTTTA
Found at i:41403873 original size:14 final size:14
Alignment explanation
Indices: 41403856--41403889 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
41403846 GATTTAAGGT
*
41403856 TTAGGGGTTAGGAG
1 TTAGGGGTTAAGAG
*
41403870 TTAGGGGTTAATAG
1 TTAGGGGTTAAGAG
41403884 TTAGGG
1 TTAGGG
41403890 ATTTAGGGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.44, T:0.32
Consensus pattern (14 bp):
TTAGGGGTTAAGAG
Found at i:41404371 original size:14 final size:14
Alignment explanation
Indices: 41404352--41404379 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
41404342 TTATCAAAAT
41404352 TTTAAATAATATTA
1 TTTAAATAATATTA
41404366 TTTAAATAATATTA
1 TTTAAATAATATTA
41404380 ATAATGATAT
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):
TTTAAATAATATTA
Found at i:41404672 original size:83 final size:81
Alignment explanation
Indices: 41404522--41404724 Score: 226
Period size: 83 Copynumber: 2.4 Consensus size: 81
41404512 GCGTTTGGTC
* * * *
41404522 AAAAATGCCGCAAAAAATATATTTAAAATTTAACCAAACGGCGCCGTTTCATTGACGAATTAAAT
1 AAAAACGCC-CAAAAAATATA-TTAAAATTTAACAAAACAGCACCGTTTCATTGACGAATTAAAT
*
41404587 ATTAATGGTGTTTTGTAT
64 ATTAATGGCGTTTTGTAT
* * * *
41404605 ACAAACGCCACAAAAAATATATTAAGAATTTAACAAAACAGCACCGTTTTATTGATGAATTATAT
1 AAAAACGCC-CAAAAAATATATTAA-AATTTAACAAAACAGCACCGTTTCATTGACGAATTAAAT
* *
41404670 ATTAGTGGCGTTTTTTAT
64 ATTAATGGCGTTTTGTAT
* * * *
41404688 AAAAATGCCGAAAAAATACATTAAAAATTTAAAAAAA
1 AAAAACGCCCAAAAAATATATT-AAAATTTAACAAAA
41404725 TGGCGCTGTT
Statistics
Matches: 101, Mismatches: 17, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
82 26 0.26
83 75 0.74
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.31
Consensus pattern (81 bp):
AAAAACGCCCAAAAAATATATTAAAATTTAACAAAACAGCACCGTTTCATTGACGAATTAAATAT
TAATGGCGTTTTGTAT
Found at i:41407151 original size:21 final size:21
Alignment explanation
Indices: 41407127--41407170 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
41407117 TAGTTGGAGT
41407127 TTCTAGTTTTATAGTTTCTAA
1 TTCTAGTTTTATAGTTTCTAA
41407148 TTCTAGTTTTATAGTTTCTAA
1 TTCTAGTTTTATAGTTTCTAA
41407169 TT
1 TT
41407171 TTACCCGTCC
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:0.23, C:0.09, G:0.09, T:0.59
Consensus pattern (21 bp):
TTCTAGTTTTATAGTTTCTAA
Found at i:41409230 original size:42 final size:43
Alignment explanation
Indices: 41409095--41409293 Score: 251
Period size: 43 Copynumber: 4.7 Consensus size: 43
41409085 ACCAAAGTGT
* *
41409095 CGCTAAAGGTCTTGAGCTATAGCGGTGTTTGTAGGAAAA-CTGC
1 CGCTAAAGGTCTTGAGCTATAGCGGCGTTTGTGGGAAAAGC-GC
* * *
41409138 CGCTAAAGGTCTTGATCTATCGCGGCGTTTGTGGTAAAAGCGC
1 CGCTAAAGGTCTTGAGCTATAGCGGCGTTTGTGGGAAAAGCGC
* *
41409181 CGCTAAAGGTCTTGAGCTATAGCAGCGTTTGT-GTAAAAGCGC
1 CGCTAAAGGTCTTGAGCTATAGCGGCGTTTGTGGGAAAAGCGC
* * *
41409223 CCCTAAAGGTCCTGATCTATAGCGGCGTTTGTGGGAAAAGCGC
1 CGCTAAAGGTCTTGAGCTATAGCGGCGTTTGTGGGAAAAGCGC
* * *
41409266 CGCTAAAGATCAT-ATCTATAGCGGCGTT
1 CGCTAAAGGTCTTGAGCTATAGCGGCGTT
41409294 GACAACAGCG
Statistics
Matches: 138, Mismatches: 16, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
42 53 0.38
43 84 0.61
44 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.29, T:0.27
Consensus pattern (43 bp):
CGCTAAAGGTCTTGAGCTATAGCGGCGTTTGTGGGAAAAGCGC
Found at i:41409255 original size:85 final size:86
Alignment explanation
Indices: 41409095--41409273 Score: 272
Period size: 85 Copynumber: 2.1 Consensus size: 86
41409085 ACCAAAGTGT
* * * * *
41409095 CGCTAAAGGTCTTGAGCTATAGCGGTGTTTGTAGGAAAACTGCCGCTAAAGGTCTTGATCTATCG
1 CGCTAAAGGTCTTGAGCTATAGCAGCGTTTGTAGGAAAACTGCCCCTAAAGGTCCTGATCTATAG
*
41409160 CGGCGTTTGTGGTAAAAGCGC
66 CGGCGTTTGTGGGAAAAGCGC
*
41409181 CGCTAAAGGTCTTGAGCTATAGCAGCGTTTGT-GTAAAAGC-GCCCCTAAAGGTCCTGATCTATA
1 CGCTAAAGGTCTTGAGCTATAGCAGCGTTTGTAGGAAAA-CTGCCCCTAAAGGTCCTGATCTATA
41409244 GCGGCGTTTGTGGGAAAAGCGC
65 GCGGCGTTTGTGGGAAAAGCGC
41409266 CGCTAAAG
1 CGCTAAAG
41409274 ATCATATCTA
Statistics
Matches: 85, Mismatches: 7, Indels: 3
0.89 0.07 0.03
Matches are distributed among these distances:
85 54 0.64
86 31 0.36
ACGTcount: A:0.25, C:0.20, G:0.30, T:0.26
Consensus pattern (86 bp):
CGCTAAAGGTCTTGAGCTATAGCAGCGTTTGTAGGAAAACTGCCCCTAAAGGTCCTGATCTATAG
CGGCGTTTGTGGGAAAAGCGC
Found at i:41409961 original size:57 final size:57
Alignment explanation
Indices: 41409881--41410017 Score: 175
Period size: 57 Copynumber: 2.4 Consensus size: 57
41409871 TTATTTCTAC
** * * **
41409881 ATTTATGTTGTCTTAATGTAATTTATAGATGTTGTCAAAATGTCTCTTAATGTGCAT
1 ATTTATGTTGTCAAAATGGAATTTATAGATGTTGCCAAAATGTCTCTTAATGCACAT
* * *
41409938 ATTTATGTAGTCCAAATGGAATTTATAGATGTTGCCATAATGTCTCTTAATGCACAT
1 ATTTATGTTGTCAAAATGGAATTTATAGATGTTGCCAAAATGTCTCTTAATGCACAT
*
41409995 ATTTTTGTTGTCAAAATGTGAAT
1 ATTTATGTTGTCAAAATG-GAAT
41410018 AATAGTTGTT
Statistics
Matches: 68, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
57 64 0.94
58 4 0.06
ACGTcount: A:0.30, C:0.10, G:0.16, T:0.44
Consensus pattern (57 bp):
ATTTATGTTGTCAAAATGGAATTTATAGATGTTGCCAAAATGTCTCTTAATGCACAT
Found at i:41412494 original size:50 final size:51
Alignment explanation
Indices: 41412419--41412607 Score: 197
Period size: 50 Copynumber: 3.7 Consensus size: 51
41412409 GGGAATGAGG
**
41412419 TCCCATGTAAGACCATGTCTGGGACATGGTGTTGGCACCGAGATAAGA-GT-
1 TCCCATG-AAGACCATGTCTGGGACATGGCATTGGCACCGAGATAAGAGGTC
* *
41412469 TCCCATGGAAGACCATGTCTAGGACATGGCATTGGCACCGAGATGAGAGGTC
1 TCCCAT-GAAGACCATGTCTGGGACATGGCATTGGCACCGAGATAAGAGGTC
* * * * **
41412521 CCCCAT-AAGACCATGTCTGGGACATGGCATGGGCACTGATATAAGA-AAC
1 TCCCATGAAGACCATGTCTGGGACATGGCATTGGCACCGAGATAAGAGGTC
* * *
41412570 ATCCCATGTAAGACCATATCTAGGATATGGCATTGGCA
1 -TCCCATG-AAGACCATGTCTGGGACATGGCATTGGCA
41412608 GTACAAGAAA
Statistics
Matches: 116, Mismatches: 17, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
49 1 0.01
50 82 0.71
51 3 0.03
52 30 0.26
ACGTcount: A:0.29, C:0.22, G:0.27, T:0.22
Consensus pattern (51 bp):
TCCCATGAAGACCATGTCTGGGACATGGCATTGGCACCGAGATAAGAGGTC
Found at i:41412628 original size:49 final size:51
Alignment explanation
Indices: 41412526--41412646 Score: 138
Period size: 49 Copynumber: 2.4 Consensus size: 51
41412516 AGGTCCCCCA
* * *
41412526 TAAGACCATGTCTGGGACATGGCATGGGCACTGATATAAGAAACATCCCATG
1 TAAGACCATATCTAGGACATGGCATGGGCAC-GATACAAGAAACATCCCATG
* * *
41412578 TAAGACCATATCTAGGATATGGCATTGGCA-G-TACAAGAAACATCTCATG
1 TAAGACCATATCTAGGACATGGCATGGGCACGATACAAGAAACATCCCATG
* * *
41412627 TAAGACTATGTCTGGGACAT
1 TAAGACCATATCTAGGACAT
41412647 AGCTTTGGCA
Statistics
Matches: 59, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
49 32 0.54
50 1 0.02
52 26 0.44
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.24
Consensus pattern (51 bp):
TAAGACCATATCTAGGACATGGCATGGGCACGATACAAGAAACATCCCATG
Found at i:41412655 original size:49 final size:51
Alignment explanation
Indices: 41412419--41412656 Score: 184
Period size: 50 Copynumber: 4.7 Consensus size: 51
41412409 GGGAATGAGG
** * * **
41412419 TCCCATGTAAGACCATGTCTGGGACATGGTGTTGGCACCGAGATAAG--AGT
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CGATACAAGAAACA
* * * ** **
41412469 TCCCATGGAAGACCATGTCTAGGACATGGCATTGGCACCGAGATGAGAGGTC-
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CGATACAAGA-AACA
* * *
41412521 CCCCA--TAAGACCATGTCTGGGACATGGCATGGGCACTGATATAAGAAACA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAC-GATACAAGAAACA
* * *
41412571 TCCCATGTAAGACCATATCTAGGATATGGCATTGGCA-G-TACAAGAAACA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACGATACAAGAAACA
* * * *
41412620 TCTCATGTAAGACTATGTCTGGGACATAGCTTTGGCA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
41412657 TCTTATATTC
Statistics
Matches: 153, Mismatches: 28, Indels: 15
0.78 0.14 0.08
Matches are distributed among these distances:
49 42 0.27
50 81 0.53
52 30 0.20
ACGTcount: A:0.30, C:0.21, G:0.26, T:0.23
Consensus pattern (51 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACGATACAAGAAACA
Found at i:41415077 original size:15 final size:15
Alignment explanation
Indices: 41415057--41415090 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
41415047 AAATGGCAAA
41415057 TCAATTGATAACACT
1 TCAATTGATAACACT
*
41415072 TCAATTGATAATACT
1 TCAATTGATAACACT
41415087 TCAA
1 TCAA
41415091 GCCAACCACC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.41, C:0.18, G:0.06, T:0.35
Consensus pattern (15 bp):
TCAATTGATAACACT
Found at i:41417895 original size:21 final size:21
Alignment explanation
Indices: 41417871--41417950 Score: 133
Period size: 21 Copynumber: 3.8 Consensus size: 21
41417861 ACGTGTTCCC
*
41417871 CCTTCATACGGGCGTGTGTGG
1 CCTTCACACGGGCGTGTGTGG
41417892 CCTTCACACGGGCGTGTGTGG
1 CCTTCACACGGGCGTGTGTGG
41417913 CCTTCACACGGGCGTGTGTGG
1 CCTTCACACGGGCGTGTGTGG
**
41417934 CCTTCACATAGGCGTGT
1 CCTTCACACGGGCGTGT
41417951 AGACCCTCAC
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 56 1.00
ACGTcount: A:0.11, C:0.28, G:0.35, T:0.26
Consensus pattern (21 bp):
CCTTCACACGGGCGTGTGTGG
Found at i:41418132 original size:22 final size:22
Alignment explanation
Indices: 41418107--41418150 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
41418097 GGCTAGGACT
41418107 TATGAGTTATTTATAATCGTTA
1 TATGAGTTATTTATAATCGTTA
41418129 TATGAGTTATTTATAATCGTTA
1 TATGAGTTATTTATAATCGTTA
41418151 CACTAGGATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.05, G:0.14, T:0.50
Consensus pattern (22 bp):
TATGAGTTATTTATAATCGTTA
Found at i:41422374 original size:16 final size:16
Alignment explanation
Indices: 41422353--41422424 Score: 108
Period size: 16 Copynumber: 4.5 Consensus size: 16
41422343 TGTTTAGTTT
41422353 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
*
41422369 GCTGTAATTGAATAGA
1 GCTGTAATGGAATAGA
*
41422385 GTTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
* *
41422401 GCTATAATAGAATAGA
1 GCTGTAATGGAATAGA
41422417 GCTGTAAT
1 GCTGTAAT
41422425 AGGTATTCTT
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 49 1.00
ACGTcount: A:0.39, C:0.06, G:0.26, T:0.29
Consensus pattern (16 bp):
GCTGTAATGGAATAGA
Found at i:41422647 original size:17 final size:18
Alignment explanation
Indices: 41422612--41422659 Score: 62
Period size: 19 Copynumber: 2.7 Consensus size: 18
41422602 TTATTATTAA
41422612 ATATAATTTAATAAAAAAT
1 ATATAATTTAAT-AAAAAT
*
41422631 ATATAATTTAATAAAATT
1 ATATAATTTAATAAAAAT
*
41422649 CT-TAATTTAAT
1 ATATAATTTAAT
41422660 TATTCTTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
17 9 0.33
18 6 0.22
19 12 0.44
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (18 bp):
ATATAATTTAATAAAAAT
Found at i:41422676 original size:56 final size:56
Alignment explanation
Indices: 41422561--41422689 Score: 136
Period size: 56 Copynumber: 2.3 Consensus size: 56
41422551 AATAAGATTA
* *
41422561 TTAATATAAATAATAAATAATTTAATCATATTTTAACATAATTATTATTAAATATAAT
1 TTAATA-AAATAATAAATAATTTAATAAAATTTTAACATAATTATTATT-AATATAAT
* ** *
41422619 TTAATAAAA-AATATATAATTTAATAAAATTCTTAATTTAATTATTCTT-ATATGAAT
1 TTAATAAAATAATAAATAATTTAATAAAATT-TTAACATAATTATTATTAATAT-AAT
* *
41422675 TTACTAAAATCATAA
1 TTAATAAAATAATAA
41422690 TATATAATAA
Statistics
Matches: 59, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
55 4 0.07
56 29 0.49
57 20 0.34
58 6 0.10
ACGTcount: A:0.50, C:0.05, G:0.01, T:0.44
Consensus pattern (56 bp):
TTAATAAAATAATAAATAATTTAATAAAATTTTAACATAATTATTATTAATATAAT
Found at i:41424245 original size:20 final size:20
Alignment explanation
Indices: 41424207--41424250 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
41424197 GCAGAAATCG
*
41424207 AGAGAAAATCAAAGAAAAAT
1 AGAGAAAATCAAAGAAAAAA
*
41424227 AGAGAAAAT-AAGAGGAAAAA
1 AGAGAAAATCAA-AGAAAAAA
41424247 AGAG
1 AGAG
41424251 GGATTCGACG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 2 0.10
20 19 0.90
ACGTcount: A:0.68, C:0.02, G:0.23, T:0.07
Consensus pattern (20 bp):
AGAGAAAATCAAAGAAAAAA
Found at i:41425262 original size:15 final size:15
Alignment explanation
Indices: 41425229--41425266 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
41425219 TAGGAAAATG
41425229 TTAATATATTATTAT
1 TTAATATATTATTAT
*
41425244 TTAATTTATTATTCA-
1 TTAATATATTATT-AT
41425259 TTAATATA
1 TTAATATA
41425267 CATTTTTCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 19 0.95
16 1 0.05
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (15 bp):
TTAATATATTATTAT
Found at i:41425575 original size:17 final size:17
Alignment explanation
Indices: 41425553--41425586 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
41425543 AAAAAGAAAA
41425553 AAATTTACT-TATTTATG
1 AAATTTA-TATATTTATG
41425570 AAATTTATATATTTATG
1 AAATTTATATATTTATG
41425587 TGTATGGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 1 0.06
17 15 0.94
ACGTcount: A:0.38, C:0.03, G:0.06, T:0.53
Consensus pattern (17 bp):
AAATTTATATATTTATG
Found at i:41429066 original size:21 final size:21
Alignment explanation
Indices: 41429041--41429093 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
41429031 AGCGGTGGTA
*
41429041 GTGAGATTAGTTACTGTAGCG
1 GTGAGATTAGATACTGTAGCG
*
41429062 GTGAGATTGGATACTGTAGCG
1 GTGAGATTAGATACTGTAGCG
41429083 GTGAGATTAGA
1 GTGAGATTAGA
41429094 AACAATGGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.26, C:0.08, G:0.36, T:0.30
Consensus pattern (21 bp):
GTGAGATTAGATACTGTAGCG
Found at i:41436223 original size:21 final size:22
Alignment explanation
Indices: 41436186--41436238 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
41436176 TTTTAAAATA
* **
41436186 TTTTTAAAAT-ACTTTTTTTTG
1 TTTTTAAAATAAATTTTTGGTG
41436207 TTTTTAAAATAAATTTTTGGTG
1 TTTTTAAAATAAATTTTTGGTG
41436229 TTTATTAAAA
1 TTT-TTAAAA
41436239 AATGGGCCGG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 10 0.37
22 11 0.41
23 6 0.22
ACGTcount: A:0.32, C:0.02, G:0.08, T:0.58
Consensus pattern (22 bp):
TTTTTAAAATAAATTTTTGGTG
Found at i:41437916 original size:21 final size:21
Alignment explanation
Indices: 41437892--41437955 Score: 94
Period size: 21 Copynumber: 3.0 Consensus size: 21
41437882 TGTAGATCAA
41437892 ACTTATCATAATACA-TGTCAT
1 ACTTATCATAATACAGT-TCAT
*
41437913 ACTTATCATAACACAGTTCAT
1 ACTTATCATAATACAGTTCAT
*
41437934 ACTTATCATAATACAGATCAT
1 ACTTATCATAATACAGTTCAT
41437955 A
1 A
41437956 TTGAGCATAT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
21 38 0.97
22 1 0.03
ACGTcount: A:0.41, C:0.20, G:0.05, T:0.34
Consensus pattern (21 bp):
ACTTATCATAATACAGTTCAT
Found at i:41458406 original size:29 final size:28
Alignment explanation
Indices: 41458370--41458477 Score: 83
Period size: 29 Copynumber: 3.8 Consensus size: 28
41458360 AAAGGACAAC
41458370 CTTTGTGGCAAAACTCTAAAAGGGTAAG
1 CTTTGTGGCAAAACTCTAAAAGGGTAAG
* * * * ** *
41458398 CGTATGTGGCGAACCTATTAAAA-GACAGG
1 C-TTTGTGGCAAAACT-CTAAAAGGGTAAG
* *
41458427 CTTTGTGGCAAAAATCTAGAAGGGTAAG
1 CTTTGTGGCAAAACTCTAAAAGGGTAAG
* *
41458455 CCTTTGTGGCAAACCTCTTAAAG
1 -CTTTGTGGCAAAACTCTAAAAG
41458478 AATGACTTTA
Statistics
Matches: 56, Mismatches: 20, Indels: 7
0.67 0.24 0.08
Matches are distributed among these distances:
27 4 0.07
28 14 0.25
29 33 0.59
30 5 0.09
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (28 bp):
CTTTGTGGCAAAACTCTAAAAGGGTAAG
Found at i:41458470 original size:57 final size:57
Alignment explanation
Indices: 41458314--41458476 Score: 209
Period size: 57 Copynumber: 2.9 Consensus size: 57
41458304 AAGAAAAACT
* * ** *
41458314 TTTGTGGCAAAAATCTGGAAAGGTAAGCCTATGTGGCGAACCGGTTAAAGGACAACC
1 TTTGTGGCAAAAATCTAGAAGGGTAAGCCTATGTGGCGAACCTATTAAAAGACAACC
* * * **
41458371 TTTGTGGCAAAACTCTAAAAGGGTAAGCGTATGTGGCGAACCTATTAAAAGACAGGC
1 TTTGTGGCAAAAATCTAGAAGGGTAAGCCTATGTGGCGAACCTATTAAAAGACAACC
* * *
41458428 TTTGTGGCAAAAATCTAGAAGGGTAAGCCTTTGTGGCAAACCTCTTAAA
1 TTTGTGGCAAAAATCTAGAAGGGTAAGCCTATGTGGCGAACCTATTAAA
41458477 GAATGACTTT
Statistics
Matches: 90, Mismatches: 16, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
57 90 1.00
ACGTcount: A:0.34, C:0.17, G:0.26, T:0.24
Consensus pattern (57 bp):
TTTGTGGCAAAAATCTAGAAGGGTAAGCCTATGTGGCGAACCTATTAAAAGACAACC
Found at i:41459435 original size:26 final size:26
Alignment explanation
Indices: 41459398--41459461 Score: 101
Period size: 26 Copynumber: 2.4 Consensus size: 26
41459388 TAATGATCAA
41459398 TTGAGTGATTTTATACTTGGTAAAATT
1 TTGA-TGATTTTATACTTGGTAAAATT
41459425 TTGATGATTTTATACTTGGTAAAATT
1 TTGATGATTTTATACTTGGTAAAATT
* *
41459451 TTAACGATTTT
1 TTGATGATTTT
41459462 GCCCCCTGGC
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
26 31 0.89
27 4 0.11
ACGTcount: A:0.30, C:0.05, G:0.16, T:0.50
Consensus pattern (26 bp):
TTGATGATTTTATACTTGGTAAAATT
Found at i:41463423 original size:25 final size:25
Alignment explanation
Indices: 41463389--41463440 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
41463379 TGCCCCCTAA
41463389 ATTGAAAGATCCTGGGAGCTTTACC
1 ATTGAAAGATCCTGGGAGCTTTACC
41463414 ATTGAAAGATCCTGGGAGCTTTACC
1 ATTGAAAGATCCTGGGAGCTTTACC
41463439 AT
1 AT
41463441 CCCATGATCG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (25 bp):
ATTGAAAGATCCTGGGAGCTTTACC
Found at i:41465247 original size:15 final size:15
Alignment explanation
Indices: 41465227--41465256 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
41465217 CCCAGCCCAT
*
41465227 AACCAAATTAATAAA
1 AACCAAAATAATAAA
41465242 AACCAAAATAATAAA
1 AACCAAAATAATAAA
41465257 TTAAATGTCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.70, C:0.13, G:0.00, T:0.17
Consensus pattern (15 bp):
AACCAAAATAATAAA
Found at i:41471387 original size:10 final size:9
Alignment explanation
Indices: 41471372--41471402 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
41471362 TATGAGTTTT
41471372 AAAAAAATC
1 AAAAAAATC
41471381 AAAAAAATC
1 AAAAAAATC
*
41471390 AAAAAAATG
1 AAAAAAATC
41471399 AAAA
1 AAAA
41471403 TAATGGAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.81, C:0.06, G:0.03, T:0.10
Consensus pattern (9 bp):
AAAAAAATC
Found at i:41471417 original size:6 final size:6
Alignment explanation
Indices: 41471408--41471447 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
41471398 GAAAATAATG
* *
41471408 GAAAAA G-AAAA GAAAAA GAAAAG GAAAAA GAAAAG GAAAA
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAA
41471448 GGAGAGGCCA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
5 5 0.17
6 25 0.83
ACGTcount: A:0.78, C:0.00, G:0.23, T:0.00
Consensus pattern (6 bp):
GAAAAA
Found at i:41471422 original size:11 final size:11
Alignment explanation
Indices: 41471408--41471448 Score: 64
Period size: 11 Copynumber: 3.6 Consensus size: 11
41471398 GAAAATAATG
41471408 GAAAAAGAAAA
1 GAAAAAGAAAA
41471419 GAAAAAGAAAA
1 GAAAAAGAAAA
41471430 GGAAAAAGAAAA
1 -GAAAAAGAAAA
*
41471442 GGAAAAG
1 GAAAAAG
41471449 GAGAGGCCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
11 17 0.61
12 11 0.39
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (11 bp):
GAAAAAGAAAA
Found at i:41471434 original size:12 final size:12
Alignment explanation
Indices: 41471407--41471447 Score: 75
Period size: 12 Copynumber: 3.5 Consensus size: 12
41471397 TGAAAATAAT
41471407 GGAAAAAGAAAA
1 GGAAAAAGAAAA
41471419 -GAAAAAGAAAA
1 GGAAAAAGAAAA
41471430 GGAAAAAGAAAA
1 GGAAAAAGAAAA
41471442 GGAAAA
1 GGAAAA
41471448 GGAGAGGCCA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 11 0.39
12 17 0.61
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (12 bp):
GGAAAAAGAAAA
Found at i:41471438 original size:18 final size:18
Alignment explanation
Indices: 41471415--41471450 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
41471405 ATGGAAAAAG
41471415 AAAAGAAAAAGAAAAGGA
1 AAAAGAAAAAGAAAAGGA
*
41471433 AAAAGAAAAGGAAAAGGA
1 AAAAGAAAAAGAAAAGGA
41471451 GAGGCCAAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (18 bp):
AAAAGAAAAAGAAAAGGA
Found at i:41473681 original size:45 final size:45
Alignment explanation
Indices: 41473633--41474259 Score: 831
Period size: 45 Copynumber: 13.9 Consensus size: 45
41473623 AAAAAAATAG
* * *
41473633 CAGATCTTGTCTTTCTGTATTGGCAGTGAAGTAGATCGAAGATAG
1 CAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAA
* *
41473678 CAGATCTTGTCTTCCTGTATTGGCAGTGAAGTAGATCAAAGATAA
1 CAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAA
* * * *
41473723 TAGATCTTGTCTTCCTATATTGGCAGCAAAGTAGATCGAAGACAA
1 CAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAA
* * * * * *
41473768 CAAATCTTGTCTTCCTATATTGGTAGCGAAGTACATCAAAGATAG
1 CAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAA
* * * *
41473813 CAGATCTTGTTTTCCTGTACTGCCAGCGAAGTAGATTGAAGATAA
1 CAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAA
* * *
41473858 CAGATCTTGTCTTCCTATATTGGCAGCAAAGTAGATCAAAGATAA
1 CAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAA
* * *
41473903 CAGATCTTGTCTTTCTGTATTGGCAGCGAAGCAGATTGAAGATAA
1 CAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAA
* * *
41473948 TAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCAAAGAGAA
1 CAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAA
* * * * * *
41473993 TAGATCTTGTCTTCCTGCATTTGCAACAAAGTAGATTGAAGATAA
1 CAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAA
*
41474038 TAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAA
1 CAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAA
* * * *
41474083 TAGATCTTGTCTTCCTGTATTTGCAGTGAAGTAGATCAAAGATAA
1 CAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAA
* * * *
41474128 TAGATCTTGTCTTCTTGTATTGGCTGCTAAGTAGATCGAAGATAA
1 CAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAA
* * *
41474173 CAGATCTTGTCTTTCTGTATTGACAGCGAAGTAGATCGAAGATAG
1 CAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAA
*
41474218 TAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGA
1 CAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGA
41474260 CCCAAGCCTT
Statistics
Matches: 505, Mismatches: 77, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 505 1.00
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (45 bp):
CAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAA
Found at i:41474422 original size:132 final size:132
Alignment explanation
Indices: 41474271--41474609 Score: 520
Period size: 132 Copynumber: 2.6 Consensus size: 132
41474261 CCAAGCCTTA
**
41474271 TCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTCCCAAGGTAGTAGGGAA
1 TCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGTGAATCTTATCTTCCCAAGGTAGTAGGGAA
* ** *
41474336 ACAGATTTAAGCCACCAGTCCTGTCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTATGGATCT
66 ACAGATTTAAGCCACCAGTCCTGTCTCCCTAAGCAGCAGTGGAGTAGGTTGAAGATTATACATCC
41474401 TG
131 TG
41474403 TCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGTGAAT-TGTATCTTCCCAAGGTAGTA-GGA
1 TCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGTGAATCT-TATCTTCCCAAGGTAGTAGGGA
* * * * *
41474466 AAGCAGGTTTAAGCCATCAGTCCTGTCTCCCTAAGCAGCTGTGGAGTAGGTTGAGGATTGTACAT
65 AA-CAGATTTAAGCCACCAGTCCTGTCTCCCTAAGCAGCAGTGGAGTAGGTTGAAGATTATACAT
41474531 CCTG
129 CCTG
* *
41474535 TCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGTGAATCTTATCTTTCCAAGGTAGTAGAGAA
1 TCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGTGAATCTTATCTTCCCAAGGTAGTAGGGAA
*
41474600 GCAGATTTAA
66 ACAGATTTAA
41474610 AACACCGGTC
Statistics
Matches: 188, Mismatches: 15, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
131 6 0.03
132 178 0.95
133 4 0.02
ACGTcount: A:0.29, C:0.20, G:0.26, T:0.25
Consensus pattern (132 bp):
TCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGTGAATCTTATCTTCCCAAGGTAGTAGGGAA
ACAGATTTAAGCCACCAGTCCTGTCTCCCTAAGCAGCAGTGGAGTAGGTTGAAGATTATACATCC
TG
Found at i:41474719 original size:50 final size:50
Alignment explanation
Indices: 41474635--41474775 Score: 156
Period size: 50 Copynumber: 2.8 Consensus size: 50
41474625 TCTTTTGCAT
* * *
41474635 TACAGTGGAACAGATTGAAGCTACAATAGCGAATCTTACTTCCCAGGCAC
1 TACAGTGGAACAGATTGAAGCTACAACAACGAATCTTACTTCCCAGACAC
** * *** *
41474685 TGTAGTGGAACAGATTGAAGCTACAACAATGAATCTCGTTTCCCAGACAT
1 TACAGTGGAACAGATTGAAGCTACAACAACGAATCTTACTTCCCAGACAC
** * *
41474735 TACAGTTAAATAGATTGAAGTTACAACAACGAATCTTACTT
1 TACAGTGGAACAGATTGAAGCTACAACAACGAATCTTACTT
41474776 TCCTAGCGTT
Statistics
Matches: 71, Mismatches: 20, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
50 71 1.00
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26
Consensus pattern (50 bp):
TACAGTGGAACAGATTGAAGCTACAACAACGAATCTTACTTCCCAGACAC
Found at i:41474837 original size:44 final size:43
Alignment explanation
Indices: 41474787--41474929 Score: 128
Period size: 44 Copynumber: 3.2 Consensus size: 43
41474777 CCTAGCGTTG
* *
41474787 CAGTGGAACAAGTTGAAGATAAAAGCCTTATCTCCTTGAAGTTA
1 CAGTGGAGCAAG-TGAAGATAAAAGTCTTATCTCCTTGAAGTTA
* * * *
41474831 CAGTGGAGCAGGCTGAAGATAACGAA-TCTTTTGTCCTAGAAGTTA
1 CAGTGGAGCAAG-TGAAGATAA--AAGTCTTATCTCCTTGAAGTTA
** * *
41474876 C-GTGGAGCAGAGTGAAGATTGCAAGTCTTATCCCCTTGAAGTTG
1 CAGTGGAGCA-AGTGAAGA-TAAAAGTCTTATCTCCTTGAAGTTA
41474920 CAGTGGAGCA
1 CAGTGGAGCA
41474930 GAAAGAAGAT
Statistics
Matches: 78, Mismatches: 15, Indels: 11
0.75 0.14 0.11
Matches are distributed among these distances:
43 2 0.03
44 48 0.62
45 26 0.33
46 2 0.03
ACGTcount: A:0.31, C:0.17, G:0.27, T:0.26
Consensus pattern (43 bp):
CAGTGGAGCAAGTGAAGATAAAAGTCTTATCTCCTTGAAGTTA
Found at i:41474953 original size:45 final size:45
Alignment explanation
Indices: 41474813--41474955 Score: 139
Period size: 45 Copynumber: 3.2 Consensus size: 45
41474803 AGATAAAAGC
* ** *
41474813 CTTATCTCCTTGAAGTTACAGTGGAGCAGGCTGAAGATAACGAAT
1 CTTATCCCCTTGAAGTTACAGTGGAGCAGAATGAAGATGACGAAT
* ** * *
41474858 CTTTTGTCCTAGAAGTTAC-GTGGAGCAGAGTGAAGATTG-C-AAGT
1 CTTATCCCCTTGAAGTTACAGTGGAGCAGAATGAAGA-TGACGAA-T
* *
41474902 CTTATCCCCTTGAAGTTGCAGTGGAGCAGAAAGAAGATGACGAAT
1 CTTATCCCCTTGAAGTTACAGTGGAGCAGAATGAAGATGACGAAT
*
41474947 CCTATCCCC
1 CTTATCCCC
41474956 CTGACGTGGC
Statistics
Matches: 79, Mismatches: 14, Indels: 10
0.77 0.14 0.10
Matches are distributed among these distances:
43 2 0.03
44 33 0.42
45 42 0.53
46 2 0.03
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.26
Consensus pattern (45 bp):
CTTATCCCCTTGAAGTTACAGTGGAGCAGAATGAAGATGACGAAT
Found at i:41475182 original size:15 final size:15
Alignment explanation
Indices: 41475162--41475191 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
41475152 CCCAGCCCAT
*
41475162 AACCAAATTAATAAA
1 AACCAAAATAATAAA
41475177 AACCAAAATAATAAA
1 AACCAAAATAATAAA
41475192 TTAAATGTCC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.70, C:0.13, G:0.00, T:0.17
Consensus pattern (15 bp):
AACCAAAATAATAAA
Found at i:41475321 original size:18 final size:19
Alignment explanation
Indices: 41475292--41475327 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
41475282 ACCCGTATGG
*
41475292 CCCAATACCCAATTACATA
1 CCCAATACCCAAATACATA
41475311 CCCAA-ACCCAAATACAT
1 CCCAATACCCAAATACAT
41475328 CAAGCCCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.44, C:0.39, G:0.00, T:0.17
Consensus pattern (19 bp):
CCCAATACCCAAATACATA
Found at i:41477479 original size:60 final size:60
Alignment explanation
Indices: 41477386--41477507 Score: 235
Period size: 60 Copynumber: 2.0 Consensus size: 60
41477376 TTGTTTACAC
41477386 AAAAGTTTTCAAAAATAATGCGATACTCGAAATTTGGGGTCCTCAAGAAGATTGTACCCT
1 AAAAGTTTTCAAAAATAATGCGATACTCGAAATTTGGGGTCCTCAAGAAGATTGTACCCT
*
41477446 AAAAGTTTTCAAAAATAATGCGATACTCGAAATTTGGGGTCCTCAAGAAGATTTTACCCT
1 AAAAGTTTTCAAAAATAATGCGATACTCGAAATTTGGGGTCCTCAAGAAGATTGTACCCT
41477506 AA
1 AA
41477508 CTCATTGGGT
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 61 1.00
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.29
Consensus pattern (60 bp):
AAAAGTTTTCAAAAATAATGCGATACTCGAAATTTGGGGTCCTCAAGAAGATTGTACCCT
Found at i:41482596 original size:17 final size:17
Alignment explanation
Indices: 41482574--41482628 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 17
41482564 TATTCTATTA
41482574 ATTTATTAAGATTTAAT
1 ATTTATTAAGATTTAAT
* *
41482591 ATTTATCAAGA-TAAAT
1 ATTTATTAAGATTTAAT
* *
41482607 ATTAGATTGA-ATTTAAT
1 ATT-TATTAAGATTTAAT
41482624 ATTTA
1 ATTTA
41482629 AGTGATTAAG
Statistics
Matches: 29, Mismatches: 7, Indels: 5
0.71 0.17 0.12
Matches are distributed among these distances:
16 9 0.31
17 20 0.69
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (17 bp):
ATTTATTAAGATTTAAT
Found at i:41484997 original size:21 final size:21
Alignment explanation
Indices: 41484958--41484997 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
41484948 AACCTTATTT
*
41484958 TGTTTTTTTTTCTTATTTCAA
1 TGTTTTTTTTTATTATTTCAA
41484979 TGTTTTTTATTTATT-TTTC
1 TGTTTTTT-TTTATTATTTC
41484998 TAACAATCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.12, C:0.07, G:0.05, T:0.75
Consensus pattern (21 bp):
TGTTTTTTTTTATTATTTCAA
Found at i:41487431 original size:17 final size:17
Alignment explanation
Indices: 41487409--41487463 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 17
41487399 TATTCTATTA
41487409 ATTTATTAAGATTTAAT
1 ATTTATTAAGATTTAAT
* *
41487426 ATTTATCAAGA-TAAAT
1 ATTTATTAAGATTTAAT
* *
41487442 ATTAGATTGA-ATTTAAT
1 ATT-TATTAAGATTTAAT
41487459 ATTTA
1 ATTTA
41487464 AGTGATTAAG
Statistics
Matches: 29, Mismatches: 7, Indels: 5
0.71 0.17 0.12
Matches are distributed among these distances:
16 9 0.31
17 20 0.69
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (17 bp):
ATTTATTAAGATTTAAT
Found at i:41489832 original size:21 final size:21
Alignment explanation
Indices: 41489793--41489832 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
41489783 AACCTTATTT
*
41489793 TGTTTTTTTTTCTTATTTCAA
1 TGTTTTTTTTTATTATTTCAA
41489814 TGTTTTTTATTTATT-TTTC
1 TGTTTTTT-TTTATTATTTC
41489833 TAACAATCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.12, C:0.07, G:0.05, T:0.75
Consensus pattern (21 bp):
TGTTTTTTTTTATTATTTCAA
Found at i:41492264 original size:17 final size:17
Alignment explanation
Indices: 41492242--41492296 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 17
41492232 TATTCTATTA
41492242 ATTTATTAAGATTTAAT
1 ATTTATTAAGATTTAAT
* *
41492259 ATTTATCAAGA-TAAAT
1 ATTTATTAAGATTTAAT
* *
41492275 ATTAGATTGA-ATTTAAT
1 ATT-TATTAAGATTTAAT
41492292 ATTTA
1 ATTTA
41492297 AGTGATTAAG
Statistics
Matches: 29, Mismatches: 7, Indels: 5
0.71 0.17 0.12
Matches are distributed among these distances:
16 9 0.31
17 20 0.69
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (17 bp):
ATTTATTAAGATTTAAT
Found at i:41494663 original size:20 final size:20
Alignment explanation
Indices: 41494626--41494663 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
41494616 AACCTTATTT
*
41494626 TGTTTTTTTTCTTATTTCAA
1 TGTTTTTTTTATTATTTCAA
41494646 TGTTTTTATTTATT-TTTC
1 TGTTTTT-TTTATTATTTC
41494664 TAACAATCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.13, C:0.08, G:0.05, T:0.74
Consensus pattern (20 bp):
TGTTTTTTTTATTATTTCAA
Found at i:41497097 original size:17 final size:17
Alignment explanation
Indices: 41497075--41497129 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 17
41497065 TATTCTATTA
41497075 ATTTATTAAGATTTAAT
1 ATTTATTAAGATTTAAT
* *
41497092 ATTTATCAAGA-TAAAT
1 ATTTATTAAGATTTAAT
* *
41497108 ATTAGATTGA-ATTTAAT
1 ATT-TATTAAGATTTAAT
41497125 ATTTA
1 ATTTA
41497130 AGTGATTAAG
Statistics
Matches: 29, Mismatches: 7, Indels: 5
0.71 0.17 0.12
Matches are distributed among these distances:
16 9 0.31
17 20 0.69
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (17 bp):
ATTTATTAAGATTTAAT
Found at i:41501933 original size:17 final size:17
Alignment explanation
Indices: 41501911--41501965 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 17
41501901 TATTCTATTA
41501911 ATTTATTAAGATTTAAT
1 ATTTATTAAGATTTAAT
* *
41501928 ATTTATCAAGA-TAAAT
1 ATTTATTAAGATTTAAT
* *
41501944 ATTAGATTGA-ATTTAAT
1 ATT-TATTAAGATTTAAT
41501961 ATTTA
1 ATTTA
41501966 AGTGATTAAG
Statistics
Matches: 29, Mismatches: 7, Indels: 5
0.71 0.17 0.12
Matches are distributed among these distances:
16 9 0.31
17 20 0.69
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (17 bp):
ATTTATTAAGATTTAAT
Found at i:41504336 original size:21 final size:21
Alignment explanation
Indices: 41504297--41504336 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
41504287 AACCTTATTT
*
41504297 TGTTTTTTTTTCTTATTTCAA
1 TGTTTTTTTTTATTATTTCAA
41504318 TGTTTTTTATTTATT-TTTC
1 TGTTTTTT-TTTATTATTTC
41504337 TAACAATCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.12, C:0.07, G:0.05, T:0.75
Consensus pattern (21 bp):
TGTTTTTTTTTATTATTTCAA
Found at i:41506771 original size:17 final size:17
Alignment explanation
Indices: 41506749--41506803 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 17
41506739 TATTCTATTA
41506749 ATTTATTAAGATTTAAT
1 ATTTATTAAGATTTAAT
* *
41506766 ATTTATCAAGA-TAAAT
1 ATTTATTAAGATTTAAT
* *
41506782 ATTAGATTGA-ATTTAAT
1 ATT-TATTAAGATTTAAT
41506799 ATTTA
1 ATTTA
41506804 AGTGATTAAG
Statistics
Matches: 29, Mismatches: 7, Indels: 5
0.71 0.17 0.12
Matches are distributed among these distances:
16 9 0.31
17 20 0.69
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (17 bp):
ATTTATTAAGATTTAAT
Found at i:41509014 original size:43 final size:44
Alignment explanation
Indices: 41508952--41509050 Score: 164
Period size: 43 Copynumber: 2.3 Consensus size: 44
41508942 CAGTGTTTAT
**
41508952 ATGTAAGACCATAGTTGGGCTATTGGCATCGATTTGAGATTT-C
1 ATGTAAGACCATAGTTGGGCTATTGGCATCGATACGAGATTTCC
*
41508995 GTGTAAGACCATAGTTGGGCTATTGGCATCGATACGAGATTTCC
1 ATGTAAGACCATAGTTGGGCTATTGGCATCGATACGAGATTTCC
41509039 ATGTAAGACCAT
1 ATGTAAGACCAT
41509051 GTCTCTGACT
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
43 39 0.76
44 12 0.24
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.31
Consensus pattern (44 bp):
ATGTAAGACCATAGTTGGGCTATTGGCATCGATACGAGATTTCC
Found at i:41517667 original size:39 final size:39
Alignment explanation
Indices: 41517569--41517729 Score: 159
Period size: 40 Copynumber: 4.1 Consensus size: 39
41517559 AATGATGTCT
*
41517569 GGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGC-AAGT-ACTATATCC
*
41517609 GGACTAAGAT-CCGAAGGCATTTGTGCAAGATACTA-ATTCC
1 GGGCTAAG-TCCCGAAGGCATTTGTGCAAG-TACTATA-TCC
* *
41517649 GGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTATAACC
1 GGGCTAAGTCCCGAAGGCATTTGTGCAAG-TACTATATCC
* ** *
41517688 GGGCTATGTCCCGAAGGCATTTGAACGAGTAGCTATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCAAGTA-CTATATCC
41517728 GG
1 GG
41517730 TTAAATTCCG
Statistics
Matches: 103, Mismatches: 10, Indels: 16
0.80 0.08 0.12
Matches are distributed among these distances:
39 35 0.34
40 59 0.57
41 9 0.09
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.24
Consensus pattern (39 bp):
GGGCTAAGTCCCGAAGGCATTTGTGCAAGTACTATATCC
Found at i:41518004 original size:47 final size:47
Alignment explanation
Indices: 41517935--41518292 Score: 626
Period size: 47 Copynumber: 7.6 Consensus size: 47
41517925 AAGGGTTGGT
41517935 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
41517982 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
41518029 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG
41518078 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
41518125 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
41518172 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* * * * * *
41518219 AATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
41518266 GATGTGAAAGTGTATAAATGTGATAAG
1 AATGTGAAAGTGTATATATGTGATAAG
41518293 TCCCGAAGGG
Statistics
Matches: 299, Mismatches: 10, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
47 252 0.84
49 47 0.16
ACGTcount: A:0.32, C:0.08, G:0.30, T:0.29
Consensus pattern (47 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
Found at i:41518237 original size:143 final size:142
Alignment explanation
Indices: 41517935--41518292 Score: 628
Period size: 143 Copynumber: 2.5 Consensus size: 142
41517925 AAGGGTTGGT
41517935 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
41518000 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAAT
66 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG-ATATATATGTGATAAGGCCTAAT
41518065 GGCCGATGTGATG
130 GGCCGATGTGATG
41518078 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
41518143 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG-TATATATGTGATAAGGCCTAATG
66 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGATATATATGTGATAAGGCCTAATG
41518207 GCCGATGTGATG
131 GCCGATGTGATG
* * * * * * * *
41518219 AATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATAAA
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
41518284 TGTGATAAG
66 TGTGATAAG
41518293 TCCCGAAGGG
Statistics
Matches: 207, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
141 101 0.49
143 106 0.51
ACGTcount: A:0.32, C:0.08, G:0.30, T:0.29
Consensus pattern (142 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGATATATATGTGATAAGGCCTAATG
GCCGATGTGATG
Found at i:41518467 original size:37 final size:37
Alignment explanation
Indices: 41518411--41518489 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
41518401 CCGAGCTCTA
* * *
41518411 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
41518448 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
41518485 AAGAC
1 AAGAC
41518490 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:41521010 original size:40 final size:40
Alignment explanation
Indices: 41520950--41521040 Score: 139
Period size: 40 Copynumber: 2.3 Consensus size: 40
41520940 GTTCTGTTTT
* *
41520950 TAGCAGGCTTATTGTCAGTGAATTTTTTAGACTTAATGTC
1 TAGCAGGCTTATTGTCAGTGAAATTTTCAGACTTAATGTC
*
41520990 TAGCAGGCTTATTG-CTAGTGAAATTTTCAGACTTAATGTG
1 TAGCAGGCTTATTGTC-AGTGAAATTTTCAGACTTAATGTC
41521030 TAGCAGGCTTA
1 TAGCAGGCTTA
41521041 ATGCCGGTGT
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
39 1 0.02
40 46 0.98
ACGTcount: A:0.26, C:0.13, G:0.22, T:0.38
Consensus pattern (40 bp):
TAGCAGGCTTATTGTCAGTGAAATTTTCAGACTTAATGTC
Found at i:41531012 original size:41 final size:40
Alignment explanation
Indices: 41530967--41531106 Score: 106
Period size: 40 Copynumber: 3.5 Consensus size: 40
41530957 AGCGGCACTT
* *
41530967 TTAGCGGCGTTTGGACAAAAAACGCCACTAACA-ATCGAGCA
1 TTAGCGGCGTTT-GACAAAAAACACC-CTAAAATATCGAGCA
* * * *
41531008 TTAGCGGCATTTTACAAAAAACACCGTAAAATATTGAGCA
1 TTAGCGGCGTTTGACAAAAAACACCCTAAAATATCGAGCA
* ** * * *
41531048 TTAGCGGCGCTACATAAAAAACACCGCT-AAA-ACCAAGCA
1 TTAGCGGCGTTTGACAAAAAACACC-CTAAAATATCGAGCA
* *
41531087 TTAGCAGCGTTTTACAAAAA
1 TTAGCGGCGTTTGACAAAAA
41531107 GCGCCGCAAT
Statistics
Matches: 77, Mismatches: 20, Indels: 6
0.75 0.19 0.06
Matches are distributed among these distances:
39 24 0.31
40 41 0.53
41 12 0.16
ACGTcount: A:0.41, C:0.22, G:0.17, T:0.20
Consensus pattern (40 bp):
TTAGCGGCGTTTGACAAAAAACACCCTAAAATATCGAGCA
Found at i:41531287 original size:98 final size:95
Alignment explanation
Indices: 41531113--41531395 Score: 403
Period size: 98 Copynumber: 3.0 Consensus size: 95
41531103 AAAAGCGCCG
*
41531113 CAATAGAGTAACACAGAACGACGCCGTTTTCATATATTTGGGAACATTAGTGGCGGTTTTTCCCA
1 CAATAGAGTAACACAGAACGACGCCGTTTTCATATATTTGGGAACATTAGTGGCGGTTTTGCCCA
* * *
41531178 AGCACCGCTAATACTCCCTTCTTCAGCGGCG
66 AGCGCCGCTAATACTCCGTTCTTCAGCGG-A
* * *
41531209 CTTTATGGAGTAACACAGAACGACACCGTTTTCATATATTTGGGAACATTAGTGGCGGTTTTGCC
1 C--AATAGAGTAACACAGAACGACGCCGTTTTCATATATTTGGGAACATTAGTGGCGGTTTTGCC
*
41531274 CAAGCGCCGCTAATACTTCGTTCTTCA----A
64 CAAGCGCCGCTAATACTCCGTTCTTCAGCGGA
* **
41531302 CAATAGAGTAACACAGAACGACGCCGTTTTCATATATTTGGGAACACTAGTGATGGTTTTGCCCA
1 CAATAGAGTAACACAGAACGACGCCGTTTTCATATATTTGGGAACATTAGTGGCGGTTTTGCCCA
*
41531367 AACGCCGCTAATACTCCGTTCTTCAGCGG
66 AGCGCCGCTAATACTCCGTTCTTCAGCGG
41531396 TGTTTGGCGT
Statistics
Matches: 165, Mismatches: 16, Indels: 13
0.85 0.08 0.07
Matches are distributed among these distances:
91 81 0.49
93 1 0.01
96 1 0.01
98 82 0.50
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.28
Consensus pattern (95 bp):
CAATAGAGTAACACAGAACGACGCCGTTTTCATATATTTGGGAACATTAGTGGCGGTTTTGCCCA
AGCGCCGCTAATACTCCGTTCTTCAGCGGA
Found at i:41531373 original size:91 final size:91
Alignment explanation
Indices: 41531216--41531391 Score: 298
Period size: 91 Copynumber: 1.9 Consensus size: 91
41531206 GCGCTTTATG
* * *
41531216 GAGTAACACAGAACGACACCGTTTTCATATATTTGGGAACATTAGTGGCGGTTTTGCCCAAGCGC
1 GAGTAACACAGAACGACACCGTTTTCATATATTTGGGAACACTAGTGACGGTTTTGCCCAAACGC
*
41531281 CGCTAATACTTCGTTCTTCAACAATA
66 CGCTAATACTCCGTTCTTCAACAATA
* *
41531307 GAGTAACACAGAACGACGCCGTTTTCATATATTTGGGAACACTAGTGATGGTTTTGCCCAAACGC
1 GAGTAACACAGAACGACACCGTTTTCATATATTTGGGAACACTAGTGACGGTTTTGCCCAAACGC
41531372 CGCTAATACTCCGTTCTTCA
66 CGCTAATACTCCGTTCTTCA
41531392 GCGGTGTTTG
Statistics
Matches: 79, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
91 79 1.00
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (91 bp):
GAGTAACACAGAACGACACCGTTTTCATATATTTGGGAACACTAGTGACGGTTTTGCCCAAACGC
CGCTAATACTCCGTTCTTCAACAATA
Found at i:41531612 original size:41 final size:41
Alignment explanation
Indices: 41531549--41531626 Score: 113
Period size: 41 Copynumber: 1.9 Consensus size: 41
41531539 CTAATGTTCC
* * *
41531549 GGTCTATAGCGGCGTTCTTGTAACAGCGCCGGTAATTCTTG
1 GGTCTATAGCGGCGTTCTTGTAAAAACGCCGCTAATTCTTG
41531590 GGTCTATAGCGGCGTT-TGTGTAAAAACGCCGCTAATT
1 GGTCTATAGCGGCGTTCT-TGTAAAAACGCCGCTAATT
41531627 AGAAAATCTA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
40 1 0.03
41 32 0.97
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.31
Consensus pattern (41 bp):
GGTCTATAGCGGCGTTCTTGTAAAAACGCCGCTAATTCTTG
Found at i:41531668 original size:8 final size:8
Alignment explanation
Indices: 41531655--41531716 Score: 61
Period size: 8 Copynumber: 7.1 Consensus size: 8
41531645 TTTCATTCTT
41531655 TTATATTA
1 TTATATTA
41531663 TTATATTA
1 TTATATTA
*
41531671 TTATAATAA
1 TTAT-ATTA
41531680 GTTATATTA
1 -TTATATTA
*
41531689 TTATGTTTGAA
1 TTAT-ATT--A
41531700 TTATATTA
1 TTATATTA
41531708 TTATATTA
1 TTATATTA
41531716 T
1 T
41531717 AAGTTATATA
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
8 26 0.58
9 8 0.18
10 6 0.13
11 5 0.11
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (8 bp):
TTATATTA
Found at i:41531728 original size:19 final size:20
Alignment explanation
Indices: 41531663--41531730 Score: 83
Period size: 19 Copynumber: 3.6 Consensus size: 20
41531653 TTTTATATTA
41531663 TTATATTATTATA--ATAAG
1 TTATATTATTATATTATAAG
*
41531681 TTATATTATTATGTT-TGAA-
1 TTATATTATTATATTAT-AAG
41531700 TTATATTATTATATTATAAG
1 TTATATTATTATATTATAAG
41531720 TTATA-TATTAT
1 TTATATTATTAT
41531731 GAAGCATATA
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
18 12 0.28
19 23 0.53
20 8 0.19
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (20 bp):
TTATATTATTATATTATAAG
Found at i:41531747 original size:37 final size:38
Alignment explanation
Indices: 41531659--41531752 Score: 93
Period size: 38 Copynumber: 2.4 Consensus size: 38
41531649 ATTCTTTTAT
* **
41531659 ATTATTATATTATTATAATAAGTTATATTATTATGTTTGA
1 ATTA-TATATTA-TATTATAAGTTATATTATTATGTAAGA
*
41531699 ATTATATTATTATATTATAAGTTATA-TATTATG-AAGC
1 ATTATA-TATTATATTATAAGTTATATTATTATGTAAGA
41531736 ATATATATATTAATATT
1 AT-TATATATT-ATATT
41531753 GTGTTAGTTA
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
37 7 0.15
38 16 0.34
39 15 0.32
40 9 0.19
ACGTcount: A:0.40, C:0.01, G:0.06, T:0.52
Consensus pattern (38 bp):
ATTATATATTATATTATAAGTTATATTATTATGTAAGA
Found at i:41534119 original size:16 final size:16
Alignment explanation
Indices: 41534095--41534125 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
41534085 ATTTTTCCTC
41534095 TTCTAAAATCCCTAAG
1 TTCTAAAATCCCTAAG
*
41534111 TTCTGAAATCCCTAA
1 TTCTAAAATCCCTAA
41534126 CTCCATTTAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.26, G:0.06, T:0.32
Consensus pattern (16 bp):
TTCTAAAATCCCTAAG
Found at i:41541677 original size:21 final size:21
Alignment explanation
Indices: 41541651--41541701 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
41541641 CTACAACTTA
* *
41541651 AAGCAGATGCGGCAGCGAGAG
1 AAGCAGAGGCAGCAGCGAGAG
41541672 AAGCAGAGGCAGCAGCGAGAG
1 AAGCAGAGGCAGCAGCGAGAG
*
41541693 AAGCTGAGG
1 AAGCAGAGG
41541702 TTCAACGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.35, C:0.18, G:0.43, T:0.04
Consensus pattern (21 bp):
AAGCAGAGGCAGCAGCGAGAG
Found at i:41541696 original size:87 final size:87
Alignment explanation
Indices: 41541585--41541782 Score: 256
Period size: 87 Copynumber: 2.3 Consensus size: 87
41541575 ACACAACTTA
* * * *
41541585 AAGCGGAGGCAACATCGAGAGAAGCTGAGGTTCAA-AAAAGATATGAAGAACTCCAGCTA-CAAC
1 AAGCAGAGGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAG-TATGAACAACTCCAGC-AGCAAC
*
41541648 TTAAAGCAGATGCGGCAGCGAGAG
64 TTAAAGCAGATGCGACAGCGAGAG
* * *
41541672 AAGCAGAGGCAGCAGCGAGAGAAGCTGAGGTTCAACGAAAGTATGAACAACTCCAGCAGTAGCTT
1 AAGCAGAGGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAGTATGAACAACTCCAGCAGCAACTT
41541737 AAAGCAGATGCGACAGCGAGAG
66 AAAGCAGATGCGACAGCGAGAG
* * * *
41541759 AAGCAGCGGCTGCAGTGAGGGAAG
1 AAGCAGAGGCAGCAGCGAGAGAAG
41541783 TAGAGGCTGC
Statistics
Matches: 97, Mismatches: 12, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
86 1 0.01
87 92 0.95
88 4 0.04
ACGTcount: A:0.38, C:0.19, G:0.32, T:0.12
Consensus pattern (87 bp):
AAGCAGAGGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAGTATGAACAACTCCAGCAGCAACTT
AAAGCAGATGCGACAGCGAGAG
Found at i:41541782 original size:21 final size:21
Alignment explanation
Indices: 41541758--41541807 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
41541748 GACAGCGAGA
*
41541758 GAAGCAGCGGCTGCAGTGAGG
1 GAAGCAGAGGCTGCAGTGAGG
*
41541779 GAAGTAGAGGCTGCAGTGAGG
1 GAAGCAGAGGCTGCAGTGAGG
41541800 GAAGCAGA
1 GAAGCAGA
41541808 ACAACTTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.30, C:0.14, G:0.46, T:0.10
Consensus pattern (21 bp):
GAAGCAGAGGCTGCAGTGAGG
Found at i:41542209 original size:43 final size:42
Alignment explanation
Indices: 41542142--41542606 Score: 457
Period size: 43 Copynumber: 10.8 Consensus size: 42
41542132 GGTGTTTTTT
* * *
41542142 AAGCACCGCTAAAGACCAAGGTCTATAGCGGCGTTTGATGGGA
1 AAGCGCCGCGAAAGACC-TGGTCTATAGCGGCGTTTGATGGGA
* * **
41542185 AAGCGCCGCGAAAGATCCTAGTCTATAGCGGCGTTTTATGGTT
1 AAGCGCCGCGAAAGA-CCTGGTCTATAGCGGCGTTTGATGGGA
* *
41542228 AAGCGCCGCGAAAGATCCTGGTCTATAGCGGCATTTTATGGGA
1 AAGCGCCGCGAAAGA-CCTGGTCTATAGCGGCGTTTGATGGGA
*
41542271 AAGCGCCGCGAAAGATCCTGGTCTATAGCGGCGTTTTATGGGA
1 AAGCGCCGCGAAAGA-CCTGGTCTATAGCGGCGTTTGATGGGA
* * *
41542314 AAGCGCCGCGAAAGATCCTGGTCTATAGCGGCATTTTATGGAA
1 AAGCGCCGCGAAAGA-CCTGGTCTATAGCGGCGTTTGATGGGA
* * *
41542357 AAGCACCGCGAAAGATCCTGGTCTATAGCGGCGTTTGACGGGT
1 AAGCGCCGCGAAAGA-CCTGGTCTATAGCGGCGTTTGATGGGA
* * **
41542400 AAGCGCCGCTAAAGACCATGGTCTATCGCGGCGTTTGATGCAA
1 AAGCGCCGCGAAAGACC-TGGTCTATAGCGGCGTTTGATGGGA
* * * * **
41542443 AAGTGCCGCTAAAGACCATGGTCTATGGCGGCGATTGATGCCA
1 AAGCGCCGCGAAAGACC-TGGTCTATAGCGGCGTTTGATGGGA
* * * * **
41542486 AAGCGCTGCTAAAGACCACGGTCTATAGTGGCGTTTGATGCAA
1 AAGCGCCGCGAAAGACC-TGGTCTATAGCGGCGTTTGATGGGA
* * * **
41542529 AAGCGCCCCTAAAGACCACGGTCTATAGCGGCGTTT-AT-TTA
1 AAGCGCCGCGAAAGACC-TGGTCTATAGCGGCGTTTGATGGGA
* *
41542570 TAAGCGCCGCTAAAGACCATTGTCTATAGCGGCGTTT
1 -AAGCGCCGCGAAAGACC-TGGTCTATAGCGGCGTTT
41542607 ATTGTAAAAA
Statistics
Matches: 373, Mismatches: 46, Indels: 7
0.88 0.11 0.02
Matches are distributed among these distances:
41 1 0.00
42 37 0.10
43 333 0.89
44 2 0.01
ACGTcount: A:0.26, C:0.23, G:0.29, T:0.23
Consensus pattern (42 bp):
AAGCGCCGCGAAAGACCTGGTCTATAGCGGCGTTTGATGGGA
Found at i:41542269 original size:86 final size:86
Alignment explanation
Indices: 41542141--41542628 Score: 529
Period size: 86 Copynumber: 5.7 Consensus size: 86
41542131 CGGTGTTTTT
* * * *
41542141 TAAGCACCGCTAAAGACCAAGGTCTATAGCGGCGTTTGATGGGAAAGCGCCGCGAAAGATCCTAG
1 TAAGCGCCGCTAAAGACCATGGTCTATAGCGGCGTTTGATGGAAAAGCGCCGCGAAAGATCCTGG
*
41542206 TCTATAGCGGCGTTTTATGGT
66 TCTATAGCGGCGTTTTATGGG
* * * *
41542227 TAAGCGCCGCGAAAGATCC-TGGTCTATAGCGGCATTTTATGGGAAAGCGCCGCGAAAGATCCTG
1 TAAGCGCCGCTAAAGA-CCATGGTCTATAGCGGCGTTTGATGGAAAAGCGCCGCGAAAGATCCTG
41542291 GTCTATAGCGGCGTTTTATGGG
65 GTCTATAGCGGCGTTTTATGGG
* * * * *
41542313 AAAGCGCCGCGAAAGATCC-TGGTCTATAGCGGCATTTTATGGAAAAGCACCGCGAAAGATCCTG
1 TAAGCGCCGCTAAAGA-CCATGGTCTATAGCGGCGTTTGATGGAAAAGCGCCGCGAAAGATCCTG
* *
41542377 GTCTATAGCGGCGTTTGACGGG
65 GTCTATAGCGGCGTTTTATGGG
* * * *
41542399 TAAGCGCCGCTAAAGACCATGGTCTATCGCGGCGTTTGATGCAAAAGTGCCGCTAAAGA-CCATG
1 TAAGCGCCGCTAAAGACCATGGTCTATAGCGGCGTTTGATGGAAAAGCGCCGCGAAAGATCC-TG
* * * **
41542463 GTCTATGGCGGCGATTGATGCC
65 GTCTATAGCGGCGTTTTATGGG
* * * * * * * *
41542485 AAAGCGCTGCTAAAGACCACGGTCTATAGTGGCGTTTGATGCAAAAGCGCCCCTAAAGA-CCACG
1 TAAGCGCCGCTAAAGACCATGGTCTATAGCGGCGTTTGATGGAAAAGCGCCGCGAAAGATCC-TG
***
41542549 GTCTATAGCGGCG-TTTATTTA
65 GTCTATAGCGGCGTTTTATGGG
* * *
41542570 TAAGCGCCGCTAAAGACCATTGTCTATAGCGGCGTTT-ATTGTAAAAAGCGGCGCGAAAG
1 TAAGCGCCGCTAAAGACCATGGTCTATAGCGGCGTTTGA-TG-GAAAAGCGCCGCGAAAG
41542629 TTACCGACGC
Statistics
Matches: 349, Mismatches: 48, Indels: 10
0.86 0.12 0.02
Matches are distributed among these distances:
84 1 0.00
85 42 0.12
86 304 0.87
87 2 0.01
ACGTcount: A:0.26, C:0.22, G:0.29, T:0.23
Consensus pattern (86 bp):
TAAGCGCCGCTAAAGACCATGGTCTATAGCGGCGTTTGATGGAAAAGCGCCGCGAAAGATCCTGG
TCTATAGCGGCGTTTTATGGG
Done.