Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr8
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: 70076365
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3341059 characters in sequence are not A, C, G, or T
File 117 of 210
Found at i:39276946 original size:17 final size:17
Alignment explanation
Indices: 39276924--39276960 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
39276914 TAAAATGATT
39276924 AAATTGAAGTGATGGAA
1 AAATTGAAGTGATGGAA
39276941 AAATTGAAGTGATGGAA
1 AAATTGAAGTGATGGAA
39276958 AAA
1 AAA
39276961 GGAGGAGGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.51, C:0.00, G:0.27, T:0.22
Consensus pattern (17 bp):
AAATTGAAGTGATGGAA
Found at i:39279298 original size:25 final size:26
Alignment explanation
Indices: 39279270--39279329 Score: 63
Period size: 24 Copynumber: 2.4 Consensus size: 26
39279260 GTCTACTGGG
39279270 CCTCTGTTAAAAAG-GTAAAGGATTT
1 CCTCTGTTAAAAAGTGTAAAGGATTT
* * * *
39279295 CCTCT-AT-ATAAGTTTAAAGGGTTT
1 CCTCTGTTAAAAAGTGTAAAGGATTT
39279319 CCTCTGTTAAA
1 CCTCTGTTAAA
39279330 TGCTAAGGTA
Statistics
Matches: 26, Mismatches: 6, Indels: 5
0.70 0.16 0.14
Matches are distributed among these distances:
23 4 0.15
24 15 0.58
25 6 0.23
26 1 0.04
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.37
Consensus pattern (26 bp):
CCTCTGTTAAAAAGTGTAAAGGATTT
Found at i:39282954 original size:16 final size:16
Alignment explanation
Indices: 39282933--39282963 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
39282923 TTCACTATTA
*
39282933 TGTCTTTTGTATTTTC
1 TGTCTTTTATATTTTC
39282949 TGTCTTTTATATTTT
1 TGTCTTTTATATTTT
39282964 GCATGCATAG
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:0.10, C:0.10, G:0.10, T:0.71
Consensus pattern (16 bp):
TGTCTTTTATATTTTC
Found at i:39284180 original size:218 final size:218
Alignment explanation
Indices: 39283802--39284238 Score: 874
Period size: 218 Copynumber: 2.0 Consensus size: 218
39283792 TTTTCAATCA
39283802 TGGTACTTCTTGTGGACTGACTCCATGATTAAAGTAATTGCGAATTATCGGAACAATGCTTCTGG
1 TGGTACTTCTTGTGGACTGACTCCATGATTAAAGTAATTGCGAATTATCGGAACAATGCTTCTGG
39283867 ACATAATTGCAATCACTAGAGCCTAATTGTATATGTTCGATTTTTCCCTCCACTAGCTTAACAAA
66 ACATAATTGCAATCACTAGAGCCTAATTGTATATGTTCGATTTTTCCCTCCACTAGCTTAACAAA
39283932 AGCTCGACCGGATTGCATTTGAGAGCAGAAAATTCTATGACTTTAGGAATAATTTAATTGAGTTG
131 AGCTCGACCGGATTGCATTTGAGAGCAGAAAATTCTATGACTTTAGGAATAATTTAATTGAGTTG
39283997 ATTTATTCGATGTGAAATTAAAT
196 ATTTATTCGATGTGAAATTAAAT
39284020 TGGTACTTCTTGTGGACTGACTCCATGATTAAAGTAATTGCGAATTATCGGAACAATGCTTCTGG
1 TGGTACTTCTTGTGGACTGACTCCATGATTAAAGTAATTGCGAATTATCGGAACAATGCTTCTGG
39284085 ACATAATTGCAATCACTAGAGCCTAATTGTATATGTTCGATTTTTCCCTCCACTAGCTTAACAAA
66 ACATAATTGCAATCACTAGAGCCTAATTGTATATGTTCGATTTTTCCCTCCACTAGCTTAACAAA
39284150 AGCTCGACCGGATTGCATTTGAGAGCAGAAAATTCTATGACTTTAGGAATAATTTAATTGAGTTG
131 AGCTCGACCGGATTGCATTTGAGAGCAGAAAATTCTATGACTTTAGGAATAATTTAATTGAGTTG
39284215 ATTTATTCGATGTGAAATTAAAT
196 ATTTATTCGATGTGAAATTAAAT
39284238 T
1 T
39284239 AGGTGGCTGT
Statistics
Matches: 219, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
218 219 1.00
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Consensus pattern (218 bp):
TGGTACTTCTTGTGGACTGACTCCATGATTAAAGTAATTGCGAATTATCGGAACAATGCTTCTGG
ACATAATTGCAATCACTAGAGCCTAATTGTATATGTTCGATTTTTCCCTCCACTAGCTTAACAAA
AGCTCGACCGGATTGCATTTGAGAGCAGAAAATTCTATGACTTTAGGAATAATTTAATTGAGTTG
ATTTATTCGATGTGAAATTAAAT
Found at i:39284869 original size:20 final size:20
Alignment explanation
Indices: 39284828--39284886 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
39284818 AATTTAATAC
* *
39284828 TTATCTTAATAGT-AATTTA
1 TTATCTTAATATTAAAGTTA
39284847 TTAAT-TTAATATTAAAGTTA
1 TT-ATCTTAATATTAAAGTTA
39284867 TTATCTTAATATTAAAGTTA
1 TTATCTTAATATTAAAGTTA
39284887 ATGTAATGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
19 11 0.31
20 24 0.69
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (20 bp):
TTATCTTAATATTAAAGTTA
Found at i:39286770 original size:7 final size:7
Alignment explanation
Indices: 39286760--39286798 Score: 69
Period size: 7 Copynumber: 5.6 Consensus size: 7
39286750 AAAATTAAAA
39286760 AAAATCT
1 AAAATCT
*
39286767 AAAATAT
1 AAAATCT
39286774 AAAATCT
1 AAAATCT
39286781 AAAATCT
1 AAAATCT
39286788 AAAATCT
1 AAAATCT
39286795 AAAA
1 AAAA
39286799 AGAAATGTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.64, C:0.10, G:0.00, T:0.26
Consensus pattern (7 bp):
AAAATCT
Found at i:39292093 original size:15 final size:16
Alignment explanation
Indices: 39292063--39292095 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
39292053 TTTTTATTCA
*
39292063 TTTTTTTGTGTTTGAT
1 TTTTTTTGTGTCTGAT
39292079 TTTTTTTG-GTCTGAT
1 TTTTTTTGTGTCTGAT
39292094 TT
1 TT
39292096 GGGCCTGATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.06, C:0.03, G:0.18, T:0.73
Consensus pattern (16 bp):
TTTTTTTGTGTCTGAT
Found at i:39292480 original size:44 final size:44
Alignment explanation
Indices: 39292379--39293631 Score: 555
Period size: 44 Copynumber: 27.8 Consensus size: 44
39292369 GATTCATCGT
* * * * * ** *
39292379 TTTAATCCGCTCCACTGCAACTTTACGGAGATAGGAATAATAGC
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTATC
* * *
39292423 TTCAATATGCTCCACTGCAACTTCAAGGAGATAAGATTGGTATC
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTATC
* * * * * *
39292467 TTTAACCTTCTCCACTGCAACTTCAGGGATATAAGGTTTGTGTC
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTATC
* * * * * *
39292511 TTTAATATGCTCCACGGCAACTTTAAGGAGATGAGATTTGTAGCCTGTC
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTG--G--TATC
* *
39292560 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGCTTGGTTATC
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGG-TATC
** * * **
39292605 TTTTGTCTACTCCATTGCAACTTCAGGGAGATAAGACTT-GTAAA
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTGGTATC
* * * *
39292649 TTCAACCTGCTCCACTGCAACTTCAGGGAGATAAGGTT--T-GC
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTATC
* * * * * * * *
39292690 TATGATCTACTCTACTACAACTTCAGAGAGATAAGATCTGTAATTTATAG
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT-TG----GTAT-C
* * * *
39292740 TTTCAATCTGTTCCACTACAACTTCAGGGAAATAAGATTCGCTATC
1 TTT-AATCTGCTCCACTGCAACTTCAGGGAGATAAGATT-GGTATC
* * * * * **
39292786 TTCAGTCTGCTCCACTGCAACTTTAGGAAGGTAAGACTT-GTGGC
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTGGTATC
* * *
39292830 TTCAACCTGCCCCACTGCAACTTCAGGGAGATAA-ATT--T-TGC
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTAT-C
* * * * * *
39292871 TATGATCTGCTCTACTGCAACTTCAGAGAGATAAAATCTGTAATTTATAGC
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT-TG----GTAT--C
* * *
39292922 TTTAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTTGCTATC
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTGGTATC
* * * **
39292967 TTCAGTCTGCTCCACTGCAACTTCAGGGAGGTAAGACTT-GTAAA
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTGGTATC
* * * * *
39293011 TTCAACCTGCTCTACTGCAACTTCAGGGAGATAAGGTTTG-A--
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTATC
* * * ** * *
39293052 TATGATCTTCTTGACTGCAACTTCAGAGAGATAAGATCTGTAATTTATAGC
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT-TG----GTAT--C
* * * * *
39293103 TTTAACCTGTTGCACTGCAACTTCAGGGAAATAAGATTCGCTATC
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATT-GGTATC
* * * * **
39293148 TTCAGTCTGCTCCACTGCAACTTCCGAGAGATAAGACTT-GTGGC
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTGGTATC
* * *
39293192 TTCAACCTGCCCCACTGCAACTTCAGGGAGATAA-ATT--T-TGC
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTAT-C
* * * * * *
39293233 TATGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTGTAATTTATAGC
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT-TG----GTAT--C
* * *
39293284 TTTAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTCGCTATC
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATT-GGTATC
* * * *
39293329 TTCAGTCTGCTCCACTGCAACTTCAGAGAGATAAGACTT-GTAAC
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTGGTATC
* * * * * *
39293373 TTCAACCTGCCCCACTGCAACTTCAGAGAGATAAGGTT--T-GC
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTATC
* * * ** *
39293414 TATGATCTTCTTGACTGCAACTTCAGGGAGAT-AGAATCTGTAATTTATAGC
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAG-AT-TG----GTAT--C
* * * *
39293465 TTTAATCTGTTGCACTGCAACTTCAGGGAAATAAGATTCGCTATC
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATT-GGTATC
* * * * * **
39293510 TTCAGTCTACTCTACTGCAACTTCAGAGAGATAAGACTT-GTGGC
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTGGTATC
* * *
39293554 TTTAATCTGCTCCACTGCAACTTCATGGAGATAAGGTT--T-GC
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTATC
* * *
39293595 TATGATCTGCTCTACTGCAACTTCAGAGG-GATAAGAT
1 TTTAATCTGCTCCACTGCAACTTCAG-GGAGATAAGAT
39293632 CTATAATTTA
Statistics
Matches: 908, Mismatches: 230, Indels: 145
0.71 0.18 0.11
Matches are distributed among these distances:
40 2 0.00
41 169 0.19
42 16 0.02
43 13 0.01
44 288 0.32
45 186 0.20
46 13 0.01
47 17 0.02
48 5 0.01
49 35 0.04
50 8 0.01
51 153 0.17
52 3 0.00
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (44 bp):
TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTATC
Found at i:39292669 original size:138 final size:137
Alignment explanation
Indices: 39292422--39292680 Score: 329
Period size: 138 Copynumber: 1.9 Consensus size: 137
39292412 GGAATAATAG
*
39292422 CTTCAATATGCTCCACTGCAACTTCAAGGAGATAAGATTGGTATCTTTAACCTTCTCCACTGCAA
1 CTTCAATATGCTCCACTGCAACTTCAAGGAGATAAGATTGGTATCTTTAACCTACTCCACTGCAA
* ** *** * * *
39292487 CTTCAGGGATATAAGGTTTGTGTCTTTAATATGCTCCACGGCAACTTTAAGGAGATGAGATTTGT
66 CTTCAGGGAGATAAGACTTGTAAATTCAACATGCTCCACGGCAACTTCAAGGAGATGAGATTTGT
39292552 AGCCTGT
131 AGCCTGT
* * * *** *
39292559 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGCTTGGTTATCTTTTGTCTACTCCATTGCA
1 CTTCAATATGCTCCACTGCAACTTCAAGGAGATAAGATTGG-TATCTTTAACCTACTCCACTGCA
* * *
39292624 ACTTCAGGGAGATAAGACTTGTAAATTCAACCTGCTCCACTGCAACTTCAGGGAGAT
65 ACTTCAGGGAGATAAGACTTGTAAATTCAACATGCTCCACGGCAACTTCAAGGAGAT
39292681 AAGGTTTGCT
Statistics
Matches: 101, Mismatches: 20, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
137 38 0.38
138 63 0.62
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (137 bp):
CTTCAATATGCTCCACTGCAACTTCAAGGAGATAAGATTGGTATCTTTAACCTACTCCACTGCAA
CTTCAGGGAGATAAGACTTGTAAATTCAACATGCTCCACGGCAACTTCAAGGAGATGAGATTTGT
AGCCTGT
Found at i:39292823 original size:181 final size:182
Alignment explanation
Indices: 39292430--39293641 Score: 1608
Period size: 181 Copynumber: 6.7 Consensus size: 182
39292420 AGCTTCAATA
* * * * *
39292430 TGCTCCACTGCAACTTCAAG-GAGATAAGA-TTGGTATCTTTAACCTTCTCCACTGCAACTTCAG
1 TGCTCCACTGCAACTTCAGGAGAGATAAGACTT-GTAACTTCAACCTGCCCCACTGCAACTTCAG
* * * * * * * * * * ***
39292493 GGATATAAGGTTTGTGTCTTTAATATGCTCCACGGCAACTTTA-AGGAGATGAGATTTGTAGCCT
65 GGAGATAAGG-TT-TG-CTATGATCTACTCTACTGCAACTTCAGA-GAGATAAGATCTGTAATTT
* * * * * * * **
39292557 GT--CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGCTTGGTTATCTTTTGTC
126 ATAGCTTTAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTCAGTC
* * * *
39292612 TACTCCATTGCAACTTCAGG-GAGATAAGACTTGTAAATTCAACCTGCTCCACTGCAACTTCAGG
1 TGCTCCACTGCAACTTCAGGAGAGATAAGACTTGTAACTTCAACCTGCCCCACTGCAACTTCAGG
*
39292676 GAGATAAGGTTTGCTATGATCTACTCTACTACAACTTCAGAGAGATAAGATCTGTAATTTATAG-
66 GAGATAAGGTTTGCTATGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTGTAATTTATAGC
*
39292740 TTTCAATCTGTTCCACTACAACTTCAGGGAAATAAGATTCGCTATCTTCAGTC
131 TTT-AATCTGTTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTCAGTC
* * **
39292793 TGCTCCACTGCAACTTTAGGA-AGGTAAGACTTGTGGCTTCAACCTGCCCCACTGCAACTTCAGG
1 TGCTCCACTGCAACTTCAGGAGAGATAAGACTTGTAACTTCAACCTGCCCCACTGCAACTTCAGG
** * *
39292857 GAGATAAATTTTGCTATGATCTGCTCTACTGCAACTTCAGAGAGATAAAATCTGTAATTTATAGC
66 GAGATAAGGTTTGCTATGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTGTAATTTATAGC
*
39292922 TTTAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTTGCTATCTTCAGTC
131 TTTAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTCAGTC
* * * *
39292974 TGCTCCACTGCAACTTCAGG-GAGGTAAGACTTGTAAATTCAACCTGCTCTACTGCAACTTCAGG
1 TGCTCCACTGCAACTTCAGGAGAGATAAGACTTGTAACTTCAACCTGCCCCACTGCAACTTCAGG
* *
39293038 GAGATAAGGTTTGATATGATCTTCT-TGACTGCAACTTCAGAGAGATAAGATCTGTAATTTATAG
66 GAGATAAGGTTTGCTATGATCTACTCT-ACTGCAACTTCAGAGAGATAAGATCTGTAATTTATAG
* *
39293102 CTTTAACCTGTTGCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTCAGTC
130 CTTTAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTCAGTC
* **
39293155 TGCTCCACTGCAACTTC-CGAGAGATAAGACTTGTGGCTTCAACCTGCCCCACTGCAACTTCAGG
1 TGCTCCACTGCAACTTCAGGAGAGATAAGACTTGTAACTTCAACCTGCCCCACTGCAACTTCAGG
**
39293219 GAGATAAATTTTGCTATGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTGTAATTTATAGC
66 GAGATAAGGTTTGCTATGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTGTAATTTATAGC
39293284 TTTAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTCAGTC
131 TTTAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTCAGTC
*
39293336 TGCTCCACTGCAACTTCA-GAGAGATAAGACTTGTAACTTCAACCTGCCCCACTGCAACTTCAGA
1 TGCTCCACTGCAACTTCAGGAGAGATAAGACTTGTAACTTCAACCTGCCCCACTGCAACTTCAGG
* *
39293400 GAGATAAGGTTTGCTATGATCTTCT-TGACTGCAACTTCAGGGAGAT-AGAATCTGTAATTTATA
66 GAGATAAGGTTTGCTATGATCTACTCT-ACTGCAACTTCAGAGAGATAAG-ATCTGTAATTTATA
*
39293463 GCTTTAATCTGTTGCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTCAGTC
129 GCTTTAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTCAGTC
* * ** * * * *
39293517 TACTCTACTGCAACTTCA-GAGAGATAAGACTTGTGGCTTTAATCTGCTCCACTGCAACTTCATG
1 TGCTCCACTGCAACTTCAGGAGAGATAAGACTTGTAACTTCAACCTGCCCCACTGCAACTTCAGG
* * *
39293581 GAGATAAGGTTTGCTATGATCTGCTCTACTGCAACTTCAGAGGGATAAGATCTATAATTTA
66 GAGATAAGGTTTGCTATGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTGTAATTTA
39293642 ATTTGTTCTA
Statistics
Matches: 920, Mismatches: 94, Indels: 33
0.88 0.09 0.03
Matches are distributed among these distances:
179 33 0.04
180 10 0.01
181 806 0.88
182 69 0.08
183 2 0.00
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (182 bp):
TGCTCCACTGCAACTTCAGGAGAGATAAGACTTGTAACTTCAACCTGCCCCACTGCAACTTCAGG
GAGATAAGGTTTGCTATGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTGTAATTTATAGC
TTTAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTCAGTC
Found at i:39293306 original size:51 final size:49
Alignment explanation
Indices: 39293246--39293501 Score: 138
Period size: 51 Copynumber: 5.5 Consensus size: 49
39293236 GATCTACTCT
39293246 ACTGCAACTTCAGAGAGATAAGATCTGTAATTTATAGCTTTAATCTGTTCC
1 ACTGCAACTTCAGAGAGATAAGATCTGT--TTTATAGCTTTAATCTGTTCC
* * * * * *
39293297 ACTGCAACTTCAGGGAAATAAGAT-TCG--CTAT--CTTCAGTCTGCTCC
1 ACTGCAACTTCAGAGAGATAAGATCT-GTTTTATAGCTTTAATCTGTTCC
* * * **
39293342 ACTGCAACTTCAGAGAGATAAGA-C--TTGTA-A-CTTCAACCTGCCCC
1 ACTGCAACTTCAGAGAGATAAGATCTGTTTTATAGCTTTAATCTGTTCC
* * **
39293386 ACTGCAACTTCAGAGAGATAAG----G--TT-T-GCTATGATCT-TCTTG
1 ACTGCAACTTCAGAGAGATAAGATCTGTTTTATAGCTTTAATCTGT-TCC
* *
39293427 ACTGCAACTTCAGGGAGAT-AGAATCTGTAATTTATAGCTTTAATCTGTTGC
1 ACTGCAACTTCAGAGAGATAAG-ATCTGT--TTTATAGCTTTAATCTGTTCC
* *
39293478 ACTGCAACTTCAGGGAAATAAGAT
1 ACTGCAACTTCAGAGAGATAAGAT
39293502 TCGCTATCTT
Statistics
Matches: 156, Mismatches: 27, Indels: 44
0.69 0.12 0.19
Matches are distributed among these distances:
40 2 0.01
41 24 0.15
44 35 0.22
45 33 0.21
47 3 0.02
49 2 0.01
50 2 0.01
51 52 0.33
52 3 0.02
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.30
Consensus pattern (49 bp):
ACTGCAACTTCAGAGAGATAAGATCTGTTTTATAGCTTTAATCTGTTCC
Found at i:39293615 original size:41 final size:44
Alignment explanation
Indices: 39293519--39293630 Score: 142
Period size: 41 Copynumber: 2.6 Consensus size: 44
39293509 CTTCAGTCTA
*
39293519 CTCTACTGCAACTTCAGAGAGATAAGACTTGTGGCTTTAATCTG
1 CTCTACTGCAACTTCAGAGAGATAAGACTTGTGGCTATAATCTG
* * *
39293563 CTCCACTGCAACTTCATG-GAGATAAG-GTT-T-GCTATGATCTG
1 CTCTACTGCAACTTCA-GAGAGATAAGACTTGTGGCTATAATCTG
*
39293604 CTCTACTGCAACTTCAGAGGGATAAGA
1 CTCTACTGCAACTTCAGAGAGATAAGA
39293631 TCTATAATTT
Statistics
Matches: 59, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
40 1 0.02
41 31 0.53
42 1 0.02
43 2 0.03
44 23 0.39
45 1 0.02
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.29
Consensus pattern (44 bp):
CTCTACTGCAACTTCAGAGAGATAAGACTTGTGGCTATAATCTG
Found at i:39295771 original size:42 final size:42
Alignment explanation
Indices: 39295707--39295789 Score: 148
Period size: 42 Copynumber: 2.0 Consensus size: 42
39295697 TGATAGATCG
*
39295707 TCAAACTTCACGATGCCTATCTTGATAAACCTTTCAACTAAT
1 TCAAACTTCACGATGCCCATCTTGATAAACCTTTCAACTAAT
*
39295749 TCAAACTTCACGATGCCCATCTTGATGAACCTTTCAACTAA
1 TCAAACTTCACGATGCCCATCTTGATAAACCTTTCAACTAA
39295790 CTTTTTAAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.33, C:0.28, G:0.08, T:0.31
Consensus pattern (42 bp):
TCAAACTTCACGATGCCCATCTTGATAAACCTTTCAACTAAT
Found at i:39301068 original size:44 final size:44
Alignment explanation
Indices: 39301020--39301332 Score: 227
Period size: 44 Copynumber: 7.1 Consensus size: 44
39301010 CCTCAGAGGT
* *
39301020 ATAGGATTCATCGTTTTAATCTGCTCCACTGCAACTTCAGGGAG
1 ATAGGATTTATCGTTTCAATCTGCTCCACTGCAACTTCAGGGAG
* * *
39301064 ATAGGA-TTAGTAGTTTCAATATGCTCCACTGCAACTTCAGCGAG
1 ATAGGATTTA-TCGTTTCAATCTGCTCCACTGCAACTTCAGGGAG
* * * *
39301108 ATAAGATTGGTATC--TTCAACCTGCTCTACTGCAACTTCAGGGAT
1 ATAGGATT--TATCGTTTCAATCTGCTCCACTGCAACTTCAGGGAG
* * *
39301152 ATAAGG-TTTGTGGCTTT-AATCTGCTCCACTGAAACTTCAGGGAG
1 AT-AGGATTTATCG-TTTCAATCTGCTCCACTGCAACTTCAGGGAG
*
39301196 ATAAGATTTGTATCCTGTCTTCAATCTGCTCCA-TAGCAACTTCAGGGAG
1 ATAGGA-TT-TAT-C-GT-TTCAATCTGCTCCACT-GCAACTTCAGGGAG
* * *
39301245 ATAAGACTTGTAAC--TTCAACCTGCTCCACTGCAACTTCAGGGAG
1 ATAGGA-TT-TATCGTTTCAATCTGCTCCACTGCAACTTCAGGGAG
* * * * *
39301289 ATAAGG-TTT-GC-TAT-GATCTGCTCTACTGCAACTTCAGAGAG
1 AT-AGGATTTATCGTTTCAATCTGCTCCACTGCAACTTCAGGGAG
39301330 ATA
1 ATA
39301333 AGATCTGCAA
Statistics
Matches: 217, Mismatches: 33, Indels: 42
0.74 0.11 0.14
Matches are distributed among these distances:
40 1 0.00
41 26 0.12
42 4 0.02
43 6 0.03
44 124 0.57
45 10 0.05
46 3 0.01
47 3 0.01
48 5 0.02
49 35 0.16
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (44 bp):
ATAGGATTTATCGTTTCAATCTGCTCCACTGCAACTTCAGGGAG
Found at i:39301263 original size:137 final size:129
Alignment explanation
Indices: 39301034--39301336 Score: 394
Period size: 137 Copynumber: 2.3 Consensus size: 129
39301024 GATTCATCGT
*
39301034 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAGGATTAGTAGTTTCAATATGCTCCACTGCAAC
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTAGTAGTTTCAATATGCTCCACTGCAAC
* * *
39301099 TTCAGCGAGATAAGATTGGTATCTTCAACCTGCTCTACTGCAACTTCAGGGATATAAGGTTTGTG
66 TTCAGCGAGATAAGATTGGTAACTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAGG-TT-T-
39301164 GC
128 GC
* * *
39301166 TTTAATCTGCTCCACTGAAACTTCAGGGAGATAAGATTTGTATCCTGTCTTCAATCTGCTCCA-T
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTAGTA----GT-TTCAATATGCTCCACT
*
39301230 AGCAACTTCAGGGAGATAAGACTT-GTAACTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAG
61 -GCAACTTCAGCGAGATAAGA-TTGGTAACTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAG
39301294 GTTTGC
124 GTTTGC
* * * *
39301300 TATGATCTGCTCTACTGCAACTTCAGAGAGATAAGAT
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
39301337 CTGCAATTTA
Statistics
Matches: 151, Mismatches: 13, Indels: 12
0.86 0.07 0.07
Matches are distributed among these distances:
132 39 0.26
134 34 0.23
135 1 0.01
136 5 0.03
137 70 0.46
138 2 0.01
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (129 bp):
TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTAGTAGTTTCAATATGCTCCACTGCAAC
TTCAGCGAGATAAGATTGGTAACTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGC
Found at i:39301269 original size:93 final size:87
Alignment explanation
Indices: 39301037--39301336 Score: 313
Period size: 93 Copynumber: 3.4 Consensus size: 87
39301027 TCATCGTTTT
* * *
39301037 AATCTGCTCCACTGCAACTTCAGGGAGATAGGATTAGTAGTTTCAATATGCTCCACTGCAACTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATT-GTAGCTTCAATCTGCTCCACTGCAACTTC
* *
39301102 AGCGAGATAAGATTGGTATCTTC
65 AGGGAGATAAGATTTGTATCTTC
* * * * * * *
39301125 AACCTGCTCTACTGCAACTTCAGGGATATAAGGTTTGTGGCTTTAATCTGCTCCACTGAAACTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAA-GATTGTAGCTTCAATCTGCTCCACTGCAACTTC
39301190 AGGGAGATAAGATTTGTATCCTGTCTTC
65 AGGGAGATAAGATTTGTA-----TCTTC
* *
39301218 AATCTGCTCCA-TAGCAACTTCAGGGAGATAAGACTTGTAACTTCAACCTGCTCCACTGCAACTT
1 AATCTGCTCCACT-GCAACTTCAGGGAGATAAGA-TTGTAGCTTCAATCTGCTCCACTGCAACTT
*
39301282 CAGGGAGATAAGGTTTG---CTAT-
64 CAGGGAGATAAGATTTGTATCT-TC
* * *
39301303 GATCTGCTCTACTGCAACTTCAGAGAGATAAGAT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
39301337 CTGCAATTTA
Statistics
Matches: 177, Mismatches: 25, Indels: 24
0.78 0.11 0.11
Matches are distributed among these distances:
84 1 0.01
85 30 0.17
86 2 0.01
88 67 0.38
89 3 0.02
92 2 0.01
93 72 0.41
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (87 bp):
AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGTAGCTTCAATCTGCTCCACTGCAACTTCA
GGGAGATAAGATTTGTATCTTC
Found at i:39302221 original size:30 final size:29
Alignment explanation
Indices: 39302179--39302235 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 29
39302169 CTGTACTTTG
39302179 GGGAAAAATGTAAATATG-CAAAAGTTTA
1 GGGAAAAATGTAAATATGTCAAAAGTTTA
* *
39302207 GGGACAAAATTGTAATTTTGTCAAAAGTT
1 GGGA-AAAA-TGTAAATATGTCAAAAGTT
39302236 GAGTCGAGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 4 0.17
29 4 0.17
30 8 0.33
31 8 0.33
ACGTcount: A:0.44, C:0.05, G:0.21, T:0.30
Consensus pattern (29 bp):
GGGAAAAATGTAAATATGTCAAAAGTTTA
Found at i:39302869 original size:50 final size:50
Alignment explanation
Indices: 39302706--39302891 Score: 205
Period size: 51 Copynumber: 3.7 Consensus size: 50
39302696 CTATAAACAT
* * *
39302706 GTGTGTAGTACTAAT-TGCAGGCTACTACGTGTATCGATAGATAATGGTCAC
1 GTGTGTAGTACT-ATGTGCAGGCTACTACGTGTATAGAAAGAT-TTGGTCAC
* * * * * *
39302757 TTGTGTAGTACAATGTGCAGGCTACTATGTGTACCAGAAGGCTTTGGTCAC
1 GTGTGTAGTACTATGTGCAGGCTACTACGTGTA-TAGAAAGATTTGGTCAC
* * *
39302808 GTGTGTAGTACTATGTGCAGGCTACTACGTGAATTGGAAAG-TTTGATCAC
1 GTGTGTAGTACTATGTGCAGGCTACTACGTGTA-TAGAAAGATTTGGTCAC
*
39302858 GTGTGTAGTACTATGTGAAGGCTACTACGTGTAT
1 GTGTGTAGTACTATGTGCAGGCTACTACGTGTAT
39302892 CGAATGATAA
Statistics
Matches: 113, Mismatches: 20, Indels: 6
0.81 0.14 0.04
Matches are distributed among these distances:
49 1 0.01
50 41 0.36
51 67 0.59
52 4 0.04
ACGTcount: A:0.25, C:0.15, G:0.27, T:0.32
Consensus pattern (50 bp):
GTGTGTAGTACTATGTGCAGGCTACTACGTGTATAGAAAGATTTGGTCAC
Found at i:39304454 original size:44 final size:44
Alignment explanation
Indices: 39304169--39304703 Score: 408
Period size: 44 Copynumber: 11.9 Consensus size: 44
39304159 CTTCAATTTA
* * * * * *
39304169 TAGCTTTAATCTGTTCCACTGTAACTTCAGGGAAATAAGATTCTC
1 TAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACT-TG
* * * *
39304214 TATCTTCAGTCTGCTCCATTGCAACTTCAGGTAGATAAGACTTG
1 TAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTG
* * * *
39304258 TAACTTCAACCTGC-CCTACTGCAACTTTAGGGAGATAA-AGTT-
1 TAGCTTCAATCTGCTCC-ACTGCAACTTCAGGGAGATAAGACTTG
* *
39304300 T-GCTAT-GATCTGCTCTACTGCAACTTCAGGGAGATAAGA-TATG
1 TAGCT-TCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACT-TG
* * * * *
39304343 TAATTTATAGCTTTAATCTGTTCCACTACAACTTCAGGGAAATAAGATTTG
1 -------TAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTG
* * * *
39304394 CTATCTTCAGTCTGCTCCTCTGCAACTTCAGGGAGATGAGACTTG
1 -TAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTG
* *
39304439 TGGCTTCAATCTGCTCCACTGCAACTTCAAGGAGATAAGA-TT-
1 TAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTG
* * * * *
39304481 T-GCTAT-GATCTGCTCTACTACAACTTCAGAGAGATAAGATCTATAATTTA
1 TAGCT-TCAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-C------TTG
* * * *
39304531 TAGCTTTAATCTGTTCCACTGCAACTTCAGGGAAATAAGA-TTCAA
1 TAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTT--G
* * *
39304576 TATCTTCAGTCTGCTCCACTGCAACTTTAGGGAGATAAGACTTG
1 TAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTG
* * *
39304620 TGGCTTCAATCTGCTCCATTGCAACTTTAGGGAGATAAGACTTG
1 TAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTG
*
39304664 TGGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGA
1 TAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGA
39304704 TTCACCATGA
Statistics
Matches: 392, Mismatches: 67, Indels: 63
0.75 0.13 0.12
Matches are distributed among these distances:
41 59 0.15
42 7 0.02
43 9 0.02
44 142 0.36
45 103 0.26
46 2 0.01
49 2 0.01
50 4 0.01
51 63 0.16
52 1 0.00
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (44 bp):
TAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTG
Found at i:39304475 original size:181 final size:180
Alignment explanation
Indices: 39304163--39304704 Score: 779
Period size: 181 Copynumber: 3.0 Consensus size: 180
39304153 AAAACACTTC
*
39304163 AATTTATAGCTTTAATCTGTTCCACTGTAACTTCAGGGAAATAAGATTCTCTATCTTCAGTCTGC
1 AATTTATAGCTTTAATCTGTTCCACTGCAACTTCAGGGAAATAAGATT-TCTATCTTCAGTCTGC
* ** *
39304228 TCCAT-TGCAACTTCAGGTAGATAAGACTTGTAACTTCAACCTGC-CCTACTGCAACTTTAGGGA
65 TCC-TCTGCAACTTCAGGGAGATAAGACTTGTGGCTTCAATCTGCTCC-ACTGCAACTTTAGGGA
*
39304291 GATAAAGTTTGCTATGATCTGCTCTACTGCAACTTCAGGGAGATAAGATATGT
128 GATAAAGTTTGCTATGATCTGCTCTACTGCAACTTCAGGGAGATAAGATATAT
*
39304344 AATTTATAGCTTTAATCTGTTCCACTACAACTTCAGGGAAATAAGATTTGCTATCTTCAGTCTGC
1 AATTTATAGCTTTAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTT-CTATCTTCAGTCTGC
* * *
39304409 TCCTCTGCAACTTCAGGGAGATGAGACTTGTGGCTTCAATCTGCTCCACTGCAACTTCAAGGAGA
65 TCCTCTGCAACTTCAGGGAGATAAGACTTGTGGCTTCAATCTGCTCCACTGCAACTTTAGGGAGA
* * *
39304474 T-AAGATTTGCTATGATCTGCTCTACTACAACTTCAGAGAGATAAGATCTAT
130 TAAAG-TTTGCTATGATCTGCTCTACTGCAACTTCAGGGAGATAAGATATAT
39304525 AATTTATAGCTTTAATCTGTTCCACTGCAACTTCAGGGAAATAAGA-TTCAATATCTTCAGTCTG
1 AATTTATAGCTTTAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTTC--TATCTTCAGTCTG
* * *
39304589 CTCCACTGCAACTTTAGGGAGATAAGACTTGTGGCTTCAATCTGCTCCATTGCAACTTTAGGGAG
64 CTCCTCTGCAACTTCAGGGAGATAAGACTTGTGGCTTCAATCTGCTCCACTGCAACTTTAGGGAG
* * *
39304654 ATAAGACTTGTGGCT-TCAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
129 ATAA-AGTT-T-GCTAT-GATCTGCTCTACTGCAACTTCAGGGAGATAAGAT
39304705 TCACCATGAT
Statistics
Matches: 325, Mismatches: 25, Indels: 19
0.88 0.07 0.05
Matches are distributed among these distances:
179 1 0.00
180 7 0.02
181 276 0.85
182 5 0.02
183 3 0.01
184 33 0.10
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (180 bp):
AATTTATAGCTTTAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTTCTATCTTCAGTCTGCT
CCTCTGCAACTTCAGGGAGATAAGACTTGTGGCTTCAATCTGCTCCACTGCAACTTTAGGGAGAT
AAAGTTTGCTATGATCTGCTCTACTGCAACTTCAGGGAGATAAGATATAT
Found at i:39304559 original size:92 final size:91
Alignment explanation
Indices: 39304163--39304704 Score: 385
Period size: 89 Copynumber: 6.0 Consensus size: 91
39304153 AAAACACTTC
* *
39304163 AATTTATAGCTTTAATCTGTTCCACTGTAACTTCAGGGAAATAAGATTCT-CTATCTTCAGTCTG
1 AATTTATAGCTTTAATCTGTTCCACTGCAACTTCAGGGAAATAAGATT-TGCTA---TGA-TCTG
* * *
39304227 CTCCATTGCAACTTCAGGTAGATAAGA-C-T
61 CTCTACTGCAACTTCAGGGAGATAAGATCTT
* * * * * *
39304256 --TGTA-A-CTTCAACCTG-CCCTACTGCAACTTTAGGGAGATAA-AGTTTGCTATGATCTGCTC
1 AATTTATAGCTTTAATCTGTTCC-ACTGCAACTTCAGGGAAATAAGA-TTTGCTATGATCTGCTC
*
39304315 TACTGCAACTTCAGGGAGATAAGATATGT
64 TACTGCAACTTCAGGGAGATAAGATCT-T
* *
39304344 AATTTATAGCTTTAATCTGTTCCACTACAACTTCAGGGAAATAAGATTTGCTATCTTCAGTCTGC
1 AATTTATAGCTTTAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTTGCTA---TGA-TCTGC
*
39304409 TCCT-CTGCAACTTCAGGGAGATGAGA-C--
62 T-CTACTGCAACTTCAGGGAGATAAGATCTT
* * * * * *
39304436 ---TTGTGGCTTCAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTTGCTATGATCTGCTCTA
1 AATTTATAGCTTTAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTTGCTATGATCTGCTCTA
* *
39304498 CTACAACTTCAGAGAGATAAGATCTAT
66 CTGCAACTTCAGGGAGATAAGATCT-T
* *
39304525 AATTTATAGCTTTAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTCAATATCT-TCAGTCTG
1 AATTTATAGCTTTAATCTGTTCCACTGCAACTTCAGGGAAATAAGATT---T-GCTATGA-TCTG
* *
39304589 CTCCACTGCAACTTTAGGGAGATAAGA-C--
61 CTCTACTGCAACTTCAGGGAGATAAGATCTT
* * * * * * * *
39304617 ---TTGTGGCTTCAATCTGCTCCATTGCAACTTTAGGGAGATAAGACTTGTGGCT-TCAATCTGC
1 AATTTATAGCTTTAATCTGTTCCACTGCAACTTCAGGGAAATAAGA-TT-T-GCTAT-GATCTGC
*
39304678 TCCACTGCAACTTCAGGGAGATAAGAT
62 TCTACTGCAACTTCAGGGAGATAAGAT
39304705 TCACCATGAT
Statistics
Matches: 359, Mismatches: 57, Indels: 70
0.74 0.12 0.14
Matches are distributed among these distances:
84 2 0.01
85 53 0.15
86 5 0.01
88 39 0.11
89 111 0.31
90 6 0.02
91 4 0.01
92 72 0.20
93 3 0.01
95 6 0.02
96 56 0.16
97 2 0.01
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (91 bp):
AATTTATAGCTTTAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTTGCTATGATCTGCTCTA
CTGCAACTTCAGGGAGATAAGATCTT
Found at i:39306344 original size:19 final size:17
Alignment explanation
Indices: 39306301--39306373 Score: 60
Period size: 17 Copynumber: 4.1 Consensus size: 17
39306291 AAATCAAAAT
*
39306301 AATTTTTAAAATTTTAA
1 AATTTATAAAATTTTAA
39306318 ATATTTATAAAATAATTTAA
1 A-ATTTATAAAAT--TTTAA
*
39306338 AATTTAT--ATTTTTAAAA
1 AATTTATAAAATTTT--AA
*
39306355 AAATTATAAAATTTTAA
1 AATTTATAAAATTTTAA
39306372 AA
1 AA
39306374 AAAATCTAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 14
0.71 0.06 0.22
Matches are distributed among these distances:
15 3 0.07
17 15 0.33
18 10 0.22
19 11 0.24
20 6 0.13
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
AATTTATAAAATTTTAA
Found at i:39306351 original size:27 final size:26
Alignment explanation
Indices: 39306296--39306368 Score: 76
Period size: 26 Copynumber: 2.7 Consensus size: 26
39306286 AAAAAAAATC
39306296 AAAATAATTTTTAAAATTTTAAATATTTA
1 AAAATAA--TTTAAAA-TTTAAATATTTA
* *
39306325 TAAAATAATTTAAAATTTATATTTTTA
1 -AAAATAATTTAAAATTTAAATATTTA
39306352 AAAA-AATTATAAAATTT
1 AAAATAATT-TAAAATTT
39306369 TAAAAAAAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
25 4 0.10
26 12 0.30
27 10 0.25
28 7 0.17
30 7 0.17
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (26 bp):
AAAATAATTTAAAATTTAAATATTTA
Found at i:39306370 original size:27 final size:26
Alignment explanation
Indices: 39306305--39306370 Score: 80
Period size: 25 Copynumber: 2.5 Consensus size: 26
39306295 CAAAATAATT
*
39306305 TTTAAAATTTTAAATATTTATAAAATAA
1 TTTAAAATTTT--ATATTTATAAAAAAA
*
39306333 TTTAAAA-TTTATATTTTTAAAAAAA
1 TTTAAAATTTTATATTTATAAAAAAA
39306358 TTATAAAATTTTA
1 TT-TAAAATTTTA
39306371 AAAAAAATCT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
25 15 0.44
26 5 0.15
27 7 0.21
28 7 0.21
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (26 bp):
TTTAAAATTTTATATTTATAAAAAAA
Found at i:39306383 original size:19 final size:19
Alignment explanation
Indices: 39306347--39306383 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
39306337 AAATTTATAT
*
39306347 TTTTAAAAAAATTATAAAA
1 TTTTAAAAAAAATATAAAA
*
39306366 TTTTAAAAAAAATCTAAA
1 TTTTAAAAAAAATATAAA
39306384 GAAGATATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (19 bp):
TTTTAAAAAAAATATAAAA
Found at i:39311304 original size:437 final size:437
Alignment explanation
Indices: 39310490--39311364 Score: 1750
Period size: 437 Copynumber: 2.0 Consensus size: 437
39310480 ACGCTTTTGG
39310490 GATATGTTCAACTCTACGAGTCATTTGGTGTGTTGGAGATCCATGTATCCGATGTGTGGTGGTAG
1 GATATGTTCAACTCTACGAGTCATTTGGTGTGTTGGAGATCCATGTATCCGATGTGTGGTGGTAG
39310555 AGCCCACTCTTATGTTTCATAACCCCAAGTGCCAATTTAACATTAAATGTGATATTATGATATGT
66 AGCCCACTCTTATGTTTCATAACCCCAAGTGCCAATTTAACATTAAATGTGATATTATGATATGT
39310620 GATGTGTATATATATGTGTGGTTGTAATGCTAGAGGAGTTGATAAATAATGCACGATTAATATGT
131 GATGTGTATATATATGTGTGGTTGTAATGCTAGAGGAGTTGATAAATAATGCACGATTAATATGT
39310685 TCGTTCTTATAGTTAATCAAGTATGTGAATGTGTCTGAGTCGTTTTCATTTAACGTATGTTTTCT
196 TCGTTCTTATAGTTAATCAAGTATGTGAATGTGTCTGAGTCGTTTTCATTTAACGTATGTTTTCT
39310750 TGTTTAGTTAGTGGTAATTCTGATCATTCACAGAGCTTGTTAAGCTCACTTACTCTTTTCTAAAC
261 TGTTTAGTTAGTGGTAATTCTGATCATTCACAGAGCTTGTTAAGCTCACTTACTCTTTTCTAAAC
39310815 TTTGCAGACAGTTAGTGACTTCATTGTGAGCAGTGCGAAAAAATTCCAAGGGACTGATCCAAGTA
326 TTTGCAGACAGTTAGTGACTTCATTGTGAGCAGTGCGAAAAAATTCCAAGGGACTGATCCAAGTA
39310880 GTTTTTAGCTTTTGCGTAGGTGATTTATAGTTGTTATTTTAAATTAT
391 GTTTTTAGCTTTTGCGTAGGTGATTTATAGTTGTTATTTTAAATTAT
39310927 GATATGTTCAACTCTACGAGTCATTTGGTGTGTTGGAGATCCATGTATCCGATGTGTGGTGGTAG
1 GATATGTTCAACTCTACGAGTCATTTGGTGTGTTGGAGATCCATGTATCCGATGTGTGGTGGTAG
39310992 AGCCCACTCTTATGTTTCATAACCCCAAGTGCCAATTTAACATTAAATGTGATATTATGATATGT
66 AGCCCACTCTTATGTTTCATAACCCCAAGTGCCAATTTAACATTAAATGTGATATTATGATATGT
39311057 GATGTGTATATATATGTGTGGTTGTAATGCTAGAGGAGTTGATAAATAATGCACGATTAATATGT
131 GATGTGTATATATATGTGTGGTTGTAATGCTAGAGGAGTTGATAAATAATGCACGATTAATATGT
39311122 TCGTTCTTATAGTTAATCAAGTATGTGAATGTGTCTGAGTCGTTTTCATTTAACGTATGTTTTCT
196 TCGTTCTTATAGTTAATCAAGTATGTGAATGTGTCTGAGTCGTTTTCATTTAACGTATGTTTTCT
39311187 TGTTTAGTTAGTGGTAATTCTGATCATTCACAGAGCTTGTTAAGCTCACTTACTCTTTTCTAAAC
261 TGTTTAGTTAGTGGTAATTCTGATCATTCACAGAGCTTGTTAAGCTCACTTACTCTTTTCTAAAC
39311252 TTTGCAGACAGTTAGTGACTTCATTGTGAGCAGTGCGAAAAAATTCCAAGGGACTGATCCAAGTA
326 TTTGCAGACAGTTAGTGACTTCATTGTGAGCAGTGCGAAAAAATTCCAAGGGACTGATCCAAGTA
39311317 GTTTTTAGCTTTTGCGTAGGTGATTTATAGTTGTTATTTTAAATTAT
391 GTTTTTAGCTTTTGCGTAGGTGATTTATAGTTGTTATTTTAAATTAT
39311364 G
1 G
39311365 GGAATAAGGC
Statistics
Matches: 438, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
437 438 1.00
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.39
Consensus pattern (437 bp):
GATATGTTCAACTCTACGAGTCATTTGGTGTGTTGGAGATCCATGTATCCGATGTGTGGTGGTAG
AGCCCACTCTTATGTTTCATAACCCCAAGTGCCAATTTAACATTAAATGTGATATTATGATATGT
GATGTGTATATATATGTGTGGTTGTAATGCTAGAGGAGTTGATAAATAATGCACGATTAATATGT
TCGTTCTTATAGTTAATCAAGTATGTGAATGTGTCTGAGTCGTTTTCATTTAACGTATGTTTTCT
TGTTTAGTTAGTGGTAATTCTGATCATTCACAGAGCTTGTTAAGCTCACTTACTCTTTTCTAAAC
TTTGCAGACAGTTAGTGACTTCATTGTGAGCAGTGCGAAAAAATTCCAAGGGACTGATCCAAGTA
GTTTTTAGCTTTTGCGTAGGTGATTTATAGTTGTTATTTTAAATTAT
Found at i:39313074 original size:49 final size:49
Alignment explanation
Indices: 39313015--39313137 Score: 174
Period size: 49 Copynumber: 2.5 Consensus size: 49
39313005 TCATTAGGGA
* * *
39313015 TTACCAATTGCAGCTCGTGAGAGCTTATCGATACTCAGCTCGTATGAGC
1 TTACCGATTGCAGCTCGTAAGAGCTTATCGATACTCAGCTCATATGAGC
*
39313064 TTACCGATTGCAGCTCGTAAGAGCTTATCGATTCTCAGCTCATATGAGC
1 TTACCGATTGCAGCTCGTAAGAGCTTATCGATACTCAGCTCATATGAGC
* **
39313113 TTACTGATTTATAGCTCGTAAGAGC
1 TTACCGA-TTGCAGCTCGTAAGAGC
39313138 ATACCAATTC
Statistics
Matches: 66, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
49 51 0.77
50 15 0.23
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.31
Consensus pattern (49 bp):
TTACCGATTGCAGCTCGTAAGAGCTTATCGATACTCAGCTCATATGAGC
Found at i:39313121 original size:25 final size:25
Alignment explanation
Indices: 39313025--39313115 Score: 114
Period size: 25 Copynumber: 3.7 Consensus size: 25
39313015 TTACCAATTG
*
39313025 CAGCTCGTGA-GAGCTTATCGATACT
1 CAGCTCGT-ATGAGCTTATCGATTCT
* *
39313050 CAGCTCGTATGAGCTTACCGATT-G
1 CAGCTCGTATGAGCTTATCGATTCT
*
39313074 CAGCTCGTAAGAGCTTATCGATTCT
1 CAGCTCGTATGAGCTTATCGATTCT
*
39313099 CAGCTCATATGAGCTTA
1 CAGCTCGTATGAGCTTA
39313116 CTGATTTATA
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
24 22 0.39
25 34 0.61
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.30
Consensus pattern (25 bp):
CAGCTCGTATGAGCTTATCGATTCT
Found at i:39313137 original size:25 final size:24
Alignment explanation
Indices: 39313025--39313137 Score: 95
Period size: 25 Copynumber: 4.6 Consensus size: 24
39313015 TTACCAATTG
* *
39313025 CAGCTCGTGAGAGCTTA-TCGATACT
1 CAGCTCGTAAGAGCTTACT-GAT-TT
* * *
39313050 CAGCTCGTATGAGCTTACCGATTG
1 CAGCTCGTAAGAGCTTACTGATTT
39313074 CAGCTCGTAAGAGCTTA-TCGATTCT
1 CAGCTCGTAAGAGCTTACT-GATT-T
* *
39313099 CAGCTCATATGAGCTTACTGATTT
1 CAGCTCGTAAGAGCTTACTGATTT
*
39313123 ATAGCTCGTAAGAGC
1 -CAGCTCGTAAGAGC
39313138 ATACCAATTC
Statistics
Matches: 70, Mismatches: 13, Indels: 10
0.75 0.14 0.11
Matches are distributed among these distances:
24 21 0.30
25 48 0.69
26 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.30
Consensus pattern (24 bp):
CAGCTCGTAAGAGCTTACTGATTT
Found at i:39313160 original size:50 final size:49
Alignment explanation
Indices: 39313050--39313162 Score: 136
Period size: 50 Copynumber: 2.3 Consensus size: 49
39313040 TATCGATACT
* * * * *
39313050 CAGCTCGTATGAGCTTACCGATTGCAGCTCGTAAGAGCTTATCGATTCT
1 CAGCTCGTATGAGCTTACCGATTACAGCTCGTAAGAGCATACCAATTCA
* * *
39313099 CAGCTCATATGAGCTTACTGATTTATAGCTCGTAAGAGCATACCAATTCA
1 CAGCTCGTATGAGCTTACCGA-TTACAGCTCGTAAGAGCATACCAATTCA
*
39313149 CAGGTCGTATGAGC
1 CAGCTCGTATGAGC
39313163 ATACATGTAC
Statistics
Matches: 53, Mismatches: 10, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
49 19 0.36
50 34 0.64
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (49 bp):
CAGCTCGTATGAGCTTACCGATTACAGCTCGTAAGAGCATACCAATTCA
Found at i:39321035 original size:19 final size:20
Alignment explanation
Indices: 39320993--39321035 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
39320983 TCATGCTTTC
*
39320993 TATTCACATTTTCATATTCA
1 TATTCACATTTTCAAATTCA
39321013 -ATTCACATTTTCAAATT-A
1 TATTCACATTTTCAAATTCA
39321031 TATTC
1 TATTC
39321036 CACTTAGTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 1 0.05
19 20 0.95
ACGTcount: A:0.33, C:0.19, G:0.00, T:0.49
Consensus pattern (20 bp):
TATTCACATTTTCAAATTCA
Found at i:39321353 original size:101 final size:101
Alignment explanation
Indices: 39321172--39321356 Score: 275
Period size: 101 Copynumber: 1.8 Consensus size: 101
39321162 GTTCGGTTCA
* * * **
39321172 CATAGTATCCTACACATAGTACTACACATGTGACCATTACCATCCGATACATGTAGTAGCCTGCA
1 CATAGTAGCCTACACACAGTACTACACATGCGACCATTA-CATCCGATACACATAGTAGCCTGCA
39321237 CATAGTACTACACACGTGATCGAAACTATCCAGTACG
65 CATAGTACTACACACGTGATCGAAACTATCCAGTACG
*
39321274 CATAGTAGCCTACACACAGTACTACACATGCGACCCA-T-CATTCCGGTACACATAGTAGCCTGC
1 CATAGTAGCCTACACACAGTACTACACATGCGA-CCATTACA-TCCGATACACATAGTAGCCTGC
39321337 ACATAGTACTACACACGTGA
64 ACATAGTACTACACACGTGA
39321357 CCATCACTTT
Statistics
Matches: 75, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
100 2 0.03
101 39 0.52
102 31 0.41
103 3 0.04
ACGTcount: A:0.33, C:0.29, G:0.15, T:0.23
Consensus pattern (101 bp):
CATAGTAGCCTACACACAGTACTACACATGCGACCATTACATCCGATACACATAGTAGCCTGCAC
ATAGTACTACACACGTGATCGAAACTATCCAGTACG
Found at i:39321379 original size:101 final size:101
Alignment explanation
Indices: 39321170--39321394 Score: 267
Period size: 101 Copynumber: 2.2 Consensus size: 101
39321160 ATGTTCGGTT
* * * **
39321170 CACATAGTATCCTACACATAGTACTACACATGTGACCATTACCATCCGATACATGTAGTAGCCTG
1 CACATAGTAGCCTACACACAGTACTACACATGCGACCATTA-CATCCGATACACATAGTAGCCTG
* *
39321235 CACATAGTACTACACACGTGATCGAAACTATCCAGTA
65 CACATAGTACTACACACGTGATCCAAACTATCAAGTA
* *
39321272 CGCATAGTAGCCTACACACAGTACTACACATGCGACCCA-T-CATTCCGGTACACATAGTAGCCT
1 CACATAGTAGCCTACACACAGTACTACACATGCGA-CCATTACA-TCCGATACACATAGTAGCCT
* * * *
39321335 GCACATAGTACTACACACGTGA-CCATCACTTTCAATTT
64 GCACATAGTACTACACACGTGATCCA-AACTATCAAGTA
*
39321373 TACATAGTAGCCTACACACAGT
1 CACATAGTAGCCTACACACAGT
39321395 CCGTGCCACA
Statistics
Matches: 105, Mismatches: 15, Indels: 7
0.83 0.12 0.06
Matches are distributed among these distances:
100 4 0.04
101 66 0.63
102 32 0.30
103 3 0.03
ACGTcount: A:0.33, C:0.29, G:0.14, T:0.24
Consensus pattern (101 bp):
CACATAGTAGCCTACACACAGTACTACACATGCGACCATTACATCCGATACACATAGTAGCCTGC
ACATAGTACTACACACGTGATCCAAACTATCAAGTA
Found at i:39321384 original size:51 final size:52
Alignment explanation
Indices: 39321170--39321390 Score: 193
Period size: 51 Copynumber: 4.3 Consensus size: 52
39321160 ATGTTCGGTT
* * * **
39321170 CACATAGTATCCTACACATAGTACTACACATGTGA-CCATTACCATCC-GATA
1 CACATAGTAGCCTACACATAGTACTACACACGTGACCCATCACTTTCCAG-TA
** * * * * *
39321221 CATGTAGTAGCCTGCACATAGTACTACACACGTGATCGA-AACTATCCAGTA
1 CACATAGTAGCCTACACATAGTACTACACACGTGACCCATCACTTTCCAGTA
* * * * *
39321272 CGCATAGTAGCCTACACACAGTACTACACATGCGACCCATCA--TTCCGGTA
1 CACATAGTAGCCTACACATAGTACTACACACGTGACCCATCACTTTCCAGTA
* * * *
39321322 CACATAGTAGCCTGCACATAGTACTACACACGTGA-CCATCACTTTCAATTT
1 CACATAGTAGCCTACACATAGTACTACACACGTGACCCATCACTTTCCAGTA
*
39321373 TACATAGTAGCCTACACA
1 CACATAGTAGCCTACACA
39321391 CAGTCCGTGC
Statistics
Matches: 134, Mismatches: 31, Indels: 10
0.77 0.18 0.06
Matches are distributed among these distances:
49 6 0.04
50 36 0.27
51 88 0.66
52 4 0.03
ACGTcount: A:0.33, C:0.29, G:0.14, T:0.24
Consensus pattern (52 bp):
CACATAGTAGCCTACACATAGTACTACACACGTGACCCATCACTTTCCAGTA
Found at i:39332655 original size:25 final size:25
Alignment explanation
Indices: 39332621--39332670 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
39332611 ATTCCAAACG
39332621 CTTCACTTCCTCCAAAATTTTGGTT
1 CTTCACTTCCTCCAAAATTTTGGTT
* *
39332646 CTTCACTTCCTCTAAATTTTTGGTT
1 CTTCACTTCCTCCAAAATTTTGGTT
39332671 TTCTCCACTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.18, C:0.26, G:0.08, T:0.48
Consensus pattern (25 bp):
CTTCACTTCCTCCAAAATTTTGGTT
Found at i:39333583 original size:16 final size:15
Alignment explanation
Indices: 39333518--39333583 Score: 64
Period size: 16 Copynumber: 4.3 Consensus size: 15
39333508 GAGTATCAGT
*
39333518 ATCTATAGTTTTTCGA
1 ATCTATAG-TTTTCAA
*
39333534 ATCTATAG-TTTCAT
1 ATCTATAGTTTTCAA
*
39333548 A-GTATAGTTTTCAGA
1 ATCTATAGTTTTCA-A
39333563 ATCTATAGTTTTCAA
1 ATCTATAGTTTTCAA
39333578 AGTCTA
1 A-TCTA
39333584 AGGTATACTA
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
13 5 0.12
14 10 0.24
15 3 0.07
16 23 0.56
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.45
Consensus pattern (15 bp):
ATCTATAGTTTTCAA
Found at i:39335774 original size:106 final size:106
Alignment explanation
Indices: 39335589--39336008 Score: 662
Period size: 106 Copynumber: 4.0 Consensus size: 106
39335579 AAAAATTTCA
*
39335589 AAGGCAATATTTTGCGTTTCGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGATTTCTC
1 AAGGCAATATTTTGCGTTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGATTTCTC
39335654 GTTCGACCAAATAGCCAAATATCCTTTTAAAATTTCAAAGC
66 GTTCGACCAAATAGCCAAATATCCTTTTAAAATTTCAAAGC
* * *
39335695 AAGGCACTATTTTACGTTTGGAAATTCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGATTTCTC
1 AAGGCAATATTTTGCGTTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGATTTCTC
*
39335760 GTTCGACCAAATAGCCAAATATCCTTTTAAAATTTCAAAGT
66 GTTCGACCAAATAGCCAAATATCCTTTTAAAATTTCAAAGC
* * * * *
39335801 AAGGTAATATTTTGTGTTTGGAAAATCGAGAAAATGTGCCCTAACATGCTGGGTTTCAATTTCTC
1 AAGGCAATATTTTGCGTTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGATTTCTC
* *
39335866 GTTCGACCAAATAGCCAAATATCCTTTAAAAATTTTAAAGC
66 GTTCGACCAAATAGCCAAATATCCTTTTAAAATTTCAAAGC
* * *
39335907 AAGGTAATATTTTGCGTTTGGAAATTCGAGAAAACGTACCCTAACGTGCTGGGTTTCGATTTCTC
1 AAGGCAATATTTTGCGTTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGATTTCTC
* * * *
39335972 GTTCAACCAAATTGCAAAATATCCTCTT-AAATTTCAA
66 GTTCGACCAAATAGCCAAATATCCTTTTAAAATTTCAA
39336009 TCCATGTTAT
Statistics
Matches: 286, Mismatches: 28, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
105 8 0.03
106 278 0.97
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (106 bp):
AAGGCAATATTTTGCGTTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGATTTCTC
GTTCGACCAAATAGCCAAATATCCTTTTAAAATTTCAAAGC
Found at i:39347507 original size:44 final size:44
Alignment explanation
Indices: 39347459--39347596 Score: 131
Period size: 44 Copynumber: 3.2 Consensus size: 44
39347449 TCCTATCTCC
* *
39347459 CTGAAGTTACAGTGGAGCGGATTAAAACCACAAATCTTATCCCT
1 CTGAAGTTGCAGTGGAGTGGATTAAAACCACAAATCTTATCCCT
* * *** * * *
39347503 CTGAAGTTGCAGTAGAGTAGA-TCGCATC-C-AGTTTTATCTCC-
1 CTGAAGTTGCAGTGGAGTGGATTAAAACCACAAATCTTATC-CCT
* *
39347544 CTGAAGTTGCAGTGGAGTGGATTAAAACCACAGATCTTATCTCT
1 CTGAAGTTGCAGTGGAGTGGATTAAAACCACAAATCTTATCCCT
39347588 CTGAAGTTG
1 CTGAAGTTG
39347597 AAGTAGAGAA
Statistics
Matches: 69, Mismatches: 20, Indels: 10
0.70 0.20 0.10
Matches are distributed among these distances:
41 26 0.38
42 6 0.09
43 5 0.07
44 32 0.46
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (44 bp):
CTGAAGTTGCAGTGGAGTGGATTAAAACCACAAATCTTATCCCT
Found at i:39347548 original size:41 final size:41
Alignment explanation
Indices: 39347493--39347641 Score: 147
Period size: 41 Copynumber: 3.6 Consensus size: 41
39347483 AAACCACAAA
39347493 TCTTATC-CCTCTGAAGTTGCAGTAGAGTAGATCGCATCCAG
1 TCTTATCTCC-CTGAAGTTGCAGTAGAGTAGATCGCATCCAG
* * * *** *
39347534 TTTTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAACCACAG
1 TCTTATCTCCCTGAAGTTGCAGTAGAGTAGA-TCGCATC-CAG
* * * *
39347577 ATCTTATCTCTCTGAAGTTGAAGTAGAGAAGATCGCATCAAG
1 -TCTTATCTCCCTGAAGTTGCAGTAGAGTAGATCGCATCCAG
*
39347619 CCTTATCTCCCTGAAGTTGCAGT
1 TCTTATCTCCCTGAAGTTGCAGT
39347642 GGAGCAGGTT
Statistics
Matches: 83, Mismatches: 21, Indels: 8
0.74 0.19 0.07
Matches are distributed among these distances:
41 45 0.54
42 7 0.08
43 6 0.07
44 25 0.30
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.30
Consensus pattern (41 bp):
TCTTATCTCCCTGAAGTTGCAGTAGAGTAGATCGCATCCAG
Found at i:39347557 original size:85 final size:85
Alignment explanation
Indices: 39347444--39347646 Score: 309
Period size: 85 Copynumber: 2.4 Consensus size: 85
39347434 GACAGAAGAA
* *
39347444 ATCAATCC-TATCTCCCTGAAGTTACAGTGGAGCGGATTAAAACCACAAATCTTATCCCTCTGAA
1 ATCAAGCCTTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAAATCTTATCCCTCTGAA
* *
39347508 GTTGCAGTAGAGTAGATCGC
66 GTTGAAGTAGAGAAGATCGC
* ** * * *
39347528 ATCCAGTTTTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAACCACAGATCTTATCTCTCTGAA
1 ATCAAGCCTTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAAATCTTATCCCTCTGAA
39347593 GTTGAAGTAGAGAAGATCGC
66 GTTGAAGTAGAGAAGATCGC
39347613 ATCAAGCCTTATCTCCCTGAAGTTGCAGTGGAGC
1 ATCAAGCCTTATCTCCCTGAAGTTGCAGTGGAGC
39347647 AGGTTGAAGA
Statistics
Matches: 104, Mismatches: 14, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
84 4 0.04
85 100 0.96
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.28
Consensus pattern (85 bp):
ATCAAGCCTTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAAATCTTATCCCTCTGAA
GTTGAAGTAGAGAAGATCGC
Found at i:39347670 original size:85 final size:82
Alignment explanation
Indices: 39347444--39347681 Score: 273
Period size: 85 Copynumber: 2.8 Consensus size: 82
39347434 GACAGAAGAA
* * *
39347444 ATCAATCC-TATCTCCCTGAAGTTACAGTGGAGCGGATTAAAACCACAAATCTTATCCCTCTGAA
1 ATCAAGCCTTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAA-C-C-AATCTTATCTCTCTGAA
* *
39347508 GTTGCAGTAGAGTAGATCGC
63 GTTGAAGTAGAGAAGATCGC
* ** *
39347528 ATCCAGTTTTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAACCACAGATCTTATCTCTCTGAA
1 ATCAAGCCTTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAA-C-CA-ATCTTATCTCTCTGAA
39347593 GTTGAAGTAGAGAAGATCGC
63 GTTGAAGTAGAGAAGATCGC
* *
39347613 ATCAAGCCTTATCTCCCTGAAGTTGCAGTGGAGCAGG-TTGAAGATACCAATCCTATCTCCCTGA
1 ATCAAGCCTTATCTCCCTGAAGTTGCAGTGGAGC-GGATT-AA-A-ACCAATCTTATCTCTCTGA
39347677 AGTTG
62 AGTTG
39347682 CAGCGGAGCA
Statistics
Matches: 133, Mismatches: 15, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
84 5 0.04
85 119 0.89
86 6 0.05
87 2 0.02
88 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.28
Consensus pattern (82 bp):
ATCAAGCCTTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCAATCTTATCTCTCTGAAGTT
GAAGTAGAGAAGATCGC
Found at i:39347674 original size:44 final size:44
Alignment explanation
Indices: 39347622--39347722 Score: 148
Period size: 44 Copynumber: 2.3 Consensus size: 44
39347612 CATCAAGCCT
* *
39347622 TATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGATACCAATCC
1 TATCTCCCTGAAGTTGCAGCGGAGCAGATTGAAGATACCAATCC
* * **
39347666 TATCTCCCTGAAGTTGCAGCGGAGCATATTGAAGTTATTAATCC
1 TATCTCCCTGAAGTTGCAGCGGAGCAGATTGAAGATACCAATCC
39347710 TATCTCCCTGAAG
1 TATCTCCCTGAAG
39347723 CTAGAATAGA
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 51 1.00
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.29
Consensus pattern (44 bp):
TATCTCCCTGAAGTTGCAGCGGAGCAGATTGAAGATACCAATCC
Found at i:39347970 original size:66 final size:67
Alignment explanation
Indices: 39347846--39347970 Score: 171
Period size: 66 Copynumber: 1.9 Consensus size: 67
39347836 AGATACTAGT
* * * *
39347846 CGTATCTCTCTGAAGTTGTAGTGGAGTGAATCGAAGCAAGAAGACACGGTAGATTGAAGCTACAA
1 CGTATCTCTCTGAAGTTGTAGTGGAATGAATCGAAGCAACAAGACACAGTAGACTGAAGCTACAA
39347911 GC
66 GC
* * * *
39347913 CGTATCTCTCTGAAG-TGTAGTGGAATGGATCGAAGTAACAAGACATAGTGGACTGAAG
1 CGTATCTCTCTGAAGTTGTAGTGGAATGAATCGAAGCAACAAGACACAGTAGACTGAAG
39347971 GAGGCCACCT
Statistics
Matches: 50, Mismatches: 8, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
66 35 0.70
67 15 0.30
ACGTcount: A:0.33, C:0.15, G:0.29, T:0.23
Consensus pattern (67 bp):
CGTATCTCTCTGAAGTTGTAGTGGAATGAATCGAAGCAACAAGACACAGTAGACTGAAGCTACAA
GC
Found at i:39349484 original size:23 final size:22
Alignment explanation
Indices: 39349458--39349502 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
39349448 ACAATTCGCA
39349458 ATCTAATTTATATTTT-TTATTTT
1 ATCTAATTT-T-TTTTGTTATTTT
*
39349481 ATCTTATTTTTTTTGTTATTTT
1 ATCTAATTTTTTTTGTTATTTT
39349503 CATTGGTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 4 0.20
22 8 0.40
23 8 0.40
ACGTcount: A:0.20, C:0.04, G:0.02, T:0.73
Consensus pattern (22 bp):
ATCTAATTTTTTTTGTTATTTT
Found at i:39351367 original size:36 final size:36
Alignment explanation
Indices: 39351327--39351429 Score: 170
Period size: 36 Copynumber: 2.9 Consensus size: 36
39351317 TTTTATCACA
39351327 ATGGCATGCTTAACATGCAAATCAGAATATCAGAAT
1 ATGGCATGCTTAACATGCAAATCAGAATATCAGAAT
* * *
39351363 ATGGCAAGCTTAACATGCAAATCAGAACATTAGAAT
1 ATGGCATGCTTAACATGCAAATCAGAATATCAGAAT
*
39351399 ATGTCATGCTTAACATGCAAATCAGAATATC
1 ATGGCATGCTTAACATGCAAATCAGAATATC
39351430 GATAATCATA
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 60 1.00
ACGTcount: A:0.42, C:0.17, G:0.16, T:0.25
Consensus pattern (36 bp):
ATGGCATGCTTAACATGCAAATCAGAATATCAGAAT
Found at i:39354006 original size:25 final size:25
Alignment explanation
Indices: 39353972--39354045 Score: 76
Period size: 25 Copynumber: 3.0 Consensus size: 25
39353962 AGCCCTCTCT
* *
39353972 CGAGCCATATAACAGGAAGCTCATG
1 CGAGCTATATAACAGGAAGCTCATC
* * *
39353997 TGAGCTATATAACGGGAAGCTTATC
1 CGAGCTATATAACAGGAAGCTCATC
* * *
39354022 CGGGTTGTATAACAGGAAGCTCAT
1 CGAGCTATATAACAGGAAGCTCAT
39354046 AAGAGCCAAT
Statistics
Matches: 38, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.32, C:0.19, G:0.26, T:0.23
Consensus pattern (25 bp):
CGAGCTATATAACAGGAAGCTCATC
Found at i:39354066 original size:24 final size:24
Alignment explanation
Indices: 39354030--39354082 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
39354020 TCCGGGTTGT
*
39354030 ATAACAGGAAGCTCATAAGAGCCA
1 ATAACAGGAAGCTCAGAAGAGCCA
* * *
39354054 ATAATAGGTAGCTCCGAAGAGCCA
1 ATAACAGGAAGCTCAGAAGAGCCA
*
39354078 TTAAC
1 ATAAC
39354083 GAGAAACTCC
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.42, C:0.21, G:0.21, T:0.17
Consensus pattern (24 bp):
ATAACAGGAAGCTCAGAAGAGCCA
Found at i:39354134 original size:23 final size:23
Alignment explanation
Indices: 39354103--39354150 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
39354093 AGATAGCCAT
* *
39354103 ATATCGGGAAGTTCAAGCGAGCC
1 ATATCGGGAAGCTCAAGAGAGCC
* *
39354126 ATATGGGGAAGCTCTAGAGAGCC
1 ATATCGGGAAGCTCAAGAGAGCC
39354149 AT
1 AT
39354151 TAATCAAGAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.31, C:0.19, G:0.31, T:0.19
Consensus pattern (23 bp):
ATATCGGGAAGCTCAAGAGAGCC
Found at i:39361895 original size:24 final size:24
Alignment explanation
Indices: 39361858--39362001 Score: 119
Period size: 24 Copynumber: 5.8 Consensus size: 24
39361848 TTGTATAACA
** *
39361858 GGAAGCTCATAAGAGCCACTAATG
1 GGAAGCTCCGAAGAGCCATTAATG
* *
39361882 GGTAGCTCCGAAGAGCCATTAACG
1 GGAAGCTCCGAAGAGCCATTAATG
* *
39361906 GGAAGCTCCGGATAGCCA-TATATCG
1 GGAAGCTCCGAAGAGCCATTA-AT-G
* *
39361931 GGAAGCTCCGGAGAGCCATTAATCA
1 GGAAGCTCCGAAGAGCCATTAAT-G
* * *
39361956 GGAAGCTCACAAAGAGACTTTAATCG
1 GGAAGCTC-CGAAGAGCCATTAAT-G
39361982 GGAAGCTCACGAAGAGCCAT
1 GGAAGCTC-CGAAGAGCCAT
39362002 ATATCGGGAC
Statistics
Matches: 97, Mismatches: 19, Indels: 6
0.80 0.16 0.05
Matches are distributed among these distances:
23 2 0.02
24 35 0.36
25 29 0.30
26 31 0.32
ACGTcount: A:0.33, C:0.23, G:0.27, T:0.17
Consensus pattern (24 bp):
GGAAGCTCCGAAGAGCCATTAATG
Found at i:39362007 original size:26 final size:26
Alignment explanation
Indices: 39361858--39362016 Score: 129
Period size: 26 Copynumber: 6.3 Consensus size: 26
39361848 TTGTATAACA
*
39361858 GGAAGCTCA-TAAGAGCCACTA-AT-G
1 GGAAGCTCACGAAGAGCCA-TATATCG
* *
39361882 GGTAGCTC-CGAAGAGCCAT-TAACG
1 GGAAGCTCACGAAGAGCCATATATCG
* *
39361906 GGAAGCTC-CGGATAGCCATATATCG
1 GGAAGCTCACGAAGAGCCATATATCG
* *
39361931 GGAAGCTC-CGGAGAGCCAT-TAATCA
1 GGAAGCTCACGAAGAGCCATAT-ATCG
* * *
39361956 GGAAGCTCACAAAGAGAC-TTTAATCG
1 GGAAGCTCACGAAGAGCCATAT-ATCG
39361982 GGAAGCTCACGAAGAGCCATATATCG
1 GGAAGCTCACGAAGAGCCATATATCG
*
39362008 GGACGCTCA
1 GGAAGCTCA
39362017 TTAGAGTTGT
Statistics
Matches: 110, Mismatches: 17, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
23 2 0.02
24 33 0.30
25 34 0.31
26 39 0.35
27 2 0.02
ACGTcount: A:0.33, C:0.23, G:0.27, T:0.17
Consensus pattern (26 bp):
GGAAGCTCACGAAGAGCCATATATCG
Found at i:39363711 original size:37 final size:36
Alignment explanation
Indices: 39363649--39363822 Score: 190
Period size: 37 Copynumber: 4.7 Consensus size: 36
39363639 GTCCAACTGA
* * *
39363649 AACACGCCAAACGCTCATAAGAGCTAATCTAACCAAT
1 AACACACCAAATGCTCATAAGAGCTAATCCAACC-AT
* *
39363686 AACGCACCGAATGCTCATAAGAGCTAATCCAACCAT
1 AACACACCAAATGCTCATAAGAGCTAATCCAACCAT
* *
39363722 AA-ACATGTCAAATGCTCATAAGAGCTAATCCAACCGT
1 AACACA--CCAAATGCTCATAAGAGCTAATCCAACCAT
* *
39363759 AAACACGCCAAATGCTCATAAGAGCTAATCCAACCGT
1 -AACACACCAAATGCTCATAAGAGCTAATCCAACCAT
*
39363796 AA-ACACGTCAAATGCTCAGAAGAGCTA
1 AACACAC--CAAATGCTCATAAGAGCTA
39363823 TACATCCGCC
Statistics
Matches: 118, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
35 5 0.04
36 6 0.05
37 103 0.87
38 2 0.02
39 2 0.02
ACGTcount: A:0.41, C:0.28, G:0.14, T:0.17
Consensus pattern (36 bp):
AACACACCAAATGCTCATAAGAGCTAATCCAACCAT
Found at i:39363773 original size:74 final size:74
Alignment explanation
Indices: 39363648--39363822 Score: 244
Period size: 74 Copynumber: 2.4 Consensus size: 74
39363638 AGTCCAACTG
* * * * *
39363648 AAACACGCCAAACGCTCATAAGAGCTAATCTAACCAATAACGCACCGAATGCTCATAAGAGCTAA
1 AAACACGTCAAATGCTCATAAGAGCTAATCCAACCAATAACACACCAAATGCTCATAAGAGCTAA
39363713 TCCAACCAT
66 TCCAACCAT
* * *
39363722 AAACATGTCAAATGCTCATAAGAGCTAATCCAACC-GTAAACACGCCAAATGCTCATAAGAGCTA
1 AAACACGTCAAATGCTCATAAGAGCTAATCCAACCAAT-AACACACCAAATGCTCATAAGAGCTA
*
39363786 ATCCAACCGT
65 ATCCAACCAT
*
39363796 AAACACGTCAAATGCTCAGAAGAGCTA
1 AAACACGTCAAATGCTCATAAGAGCTA
39363823 TACATCCGCC
Statistics
Matches: 89, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
73 1 0.01
74 88 0.99
ACGTcount: A:0.42, C:0.27, G:0.14, T:0.17
Consensus pattern (74 bp):
AAACACGTCAAATGCTCATAAGAGCTAATCCAACCAATAACACACCAAATGCTCATAAGAGCTAA
TCCAACCAT
Found at i:39372111 original size:12 final size:13
Alignment explanation
Indices: 39372078--39372116 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
39372068 TATTTCTTCA
*
39372078 AAAAATACTTAGT
1 AAAAATATTTAGT
39372091 AAAATATATTTAGT
1 AAAA-ATATTTAGT
39372105 AAAATATATTTA
1 AAAA-ATATTTA
39372117 TTTTAAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 4 0.17
14 20 0.83
ACGTcount: A:0.54, C:0.03, G:0.05, T:0.38
Consensus pattern (13 bp):
AAAAATATTTAGT
Found at i:39372125 original size:16 final size:14
Alignment explanation
Indices: 39372086--39372116 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
39372076 CAAAAAATAC
39372086 TTAGTAAAATATAT
1 TTAGTAAAATATAT
39372100 TTAGTAAAATATAT
1 TTAGTAAAATATAT
39372114 TTA
1 TTA
39372117 TTTTAAAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (14 bp):
TTAGTAAAATATAT
Found at i:39375212 original size:49 final size:50
Alignment explanation
Indices: 39375116--39375212 Score: 124
Period size: 49 Copynumber: 2.0 Consensus size: 50
39375106 CTATAAATAG
* * * * **
39375116 AATATTATGGTCGAGCCACTAGATAATTGCAGATATACTGTCAGATACAA
1 AATATTATGGTCAAGCCACCAGAAAATTACAGATATACTACCAGATACAA
*
39375166 AATATTGTGGTCAAGCCACCA-AAAATTACAGATATACTACCAGATAC
1 AATATTATGGTCAAGCCACCAGAAAATTACAGATATACTACCAGATAC
39375213 TTCCTCCGTA
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
49 22 0.55
50 18 0.45
ACGTcount: A:0.40, C:0.19, G:0.15, T:0.26
Consensus pattern (50 bp):
AATATTATGGTCAAGCCACCAGAAAATTACAGATATACTACCAGATACAA
Found at i:39375417 original size:35 final size:35
Alignment explanation
Indices: 39375326--39375418 Score: 98
Period size: 35 Copynumber: 2.7 Consensus size: 35
39375316 AACACAGTGA
* * * ** *
39375326 CATGTTTAACATGTGAATCAGAATCAGAATTATGG
1 CATGCTTAACATGTGAATCATAAGCAGAACAATAG
* *
39375361 CATGCTTAACATG-CAAGTCATAGGCAGAACAATAG
1 CATGCTTAACATGTGAA-TCATAAGCAGAACAATAG
39375396 CATGCTTAACATGTGAATCATAA
1 CATGCTTAACATGTGAATCATAA
39375419 TCAAAATATT
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
34 2 0.04
35 42 0.91
36 2 0.04
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.27
Consensus pattern (35 bp):
CATGCTTAACATGTGAATCATAAGCAGAACAATAG
Found at i:39381205 original size:161 final size:162
Alignment explanation
Indices: 39380939--39381264 Score: 627
Period size: 161 Copynumber: 2.0 Consensus size: 162
39380929 TGATATTGGT
39380939 GGTATTGCCATTAAAGACGAAACCTCAAACTGCAGCGATAGTAGCAAGAATGGTGGTTTTCCCTG
1 GGTATTGCCATTAAAGACGAAACCTCAAACTGCAGCGATAGTAGCAAGAATGGTGGTTTTCCCTG
39381004 GAAAGATAAACATCCAAATAATGCTACCTTTGTAGATCAGGCTACTGTTGGTTCTTTGACTTTCA
66 GAAAGATAAACATCCAAATAATGCTACCTTTGTAGATCAGGCTACTGTTGGTTCTTTGACTTTCA
39381069 ATGTTATTGATGCTTCATGTTTGAAATCATCA
131 ATGTTATTGATGCTTCATGTTTGAAATCATCA
* *
39381101 GGTATTGCCATTAAAGACG-ATCCTCAAACTGCAGCGATAGTAGTAAGAATGGTGGTTTTCCCTG
1 GGTATTGCCATTAAAGACGAAACCTCAAACTGCAGCGATAGTAGCAAGAATGGTGGTTTTCCCTG
39381165 GAAAGATAAACATCCAAATAATGCTACCTTTGTAGATCAGGCTACTGTTGGTTCTTTGACTTTCA
66 GAAAGATAAACATCCAAATAATGCTACCTTTGTAGATCAGGCTACTGTTGGTTCTTTGACTTTCA
39381230 ATGTTATTGATGCTTCATGTTTGAAATCATCA
131 ATGTTATTGATGCTTCATGTTTGAAATCATCA
39381262 GGT
1 GGT
39381265 GAATCATCAA
Statistics
Matches: 162, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
161 143 0.88
162 19 0.12
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.33
Consensus pattern (162 bp):
GGTATTGCCATTAAAGACGAAACCTCAAACTGCAGCGATAGTAGCAAGAATGGTGGTTTTCCCTG
GAAAGATAAACATCCAAATAATGCTACCTTTGTAGATCAGGCTACTGTTGGTTCTTTGACTTTCA
ATGTTATTGATGCTTCATGTTTGAAATCATCA
Found at i:39383321 original size:17 final size:18
Alignment explanation
Indices: 39383290--39383324 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
39383280 TGTTCTTTAT
39383290 TGCTTATGGCACCAAAAG
1 TGCTTATGGCACCAAAAG
*
39383308 TGCTT-TGGCTCCAAAAG
1 TGCTTATGGCACCAAAAG
39383325 CACTTTTAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.26
Consensus pattern (18 bp):
TGCTTATGGCACCAAAAG
Found at i:39383629 original size:17 final size:17
Alignment explanation
Indices: 39383607--39383639 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
39383597 CAAGCCACAT
39383607 AGGAGACTGAAG-ATTTG
1 AGGAGA-TGAAGCATTTG
39383624 AGGAGATGAAGCATTT
1 AGGAGATGAAGCATTT
39383640 TTAGGACCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.36, C:0.06, G:0.33, T:0.24
Consensus pattern (17 bp):
AGGAGATGAAGCATTTG
Found at i:39390747 original size:43 final size:43
Alignment explanation
Indices: 39390684--39390847 Score: 199
Period size: 43 Copynumber: 3.9 Consensus size: 43
39390674 GTACCGTAAA
* * * *
39390684 ATGCC-ATATCCCAGATATGGTCTTACATGTAATCTCATATCG
1 ATGCCAATAGCCCAGACATGGTCTTACACGAAATCTCATATCG
* * *
39390726 ATGCCAATAGCCCAGCCATGGTCTTACAAGAAATCACATATCG
1 ATGCCAATAGCCCAGACATGGTCTTACACGAAATCTCATATCG
*
39390769 ATGCCAAT-GTCCTAGACATGGTCTTACACGAAATCTCATATCG
1 ATGCCAATAG-CCCAGACATGGTCTTACACGAAATCTCATATCG
* * *
39390812 ATGCC-ATATCCCAGATATGGTCTTACACGTAATCTC
1 ATGCCAATAGCCCAGACATGGTCTTACACGAAATCTC
39390848 GGTAACCCTA
Statistics
Matches: 105, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
42 32 0.30
43 73 0.70
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.28
Consensus pattern (43 bp):
ATGCCAATAGCCCAGACATGGTCTTACACGAAATCTCATATCG
Found at i:39392977 original size:38 final size:38
Alignment explanation
Indices: 39392935--39393013 Score: 158
Period size: 38 Copynumber: 2.1 Consensus size: 38
39392925 ATGAGATAGC
39392935 TAAGTAAGTTCTGGAAAGTGGCAGACAATGGTAAAAAA
1 TAAGTAAGTTCTGGAAAGTGGCAGACAATGGTAAAAAA
39392973 TAAGTAAGTTCTGGAAAGTGGCAGACAATGGTAAAAAA
1 TAAGTAAGTTCTGGAAAGTGGCAGACAATGGTAAAAAA
39393011 TAA
1 TAA
39393014 CTCAATTCTG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.46, C:0.08, G:0.25, T:0.22
Consensus pattern (38 bp):
TAAGTAAGTTCTGGAAAGTGGCAGACAATGGTAAAAAA
Found at i:39393023 original size:38 final size:38
Alignment explanation
Indices: 39392939--39393023 Score: 145
Period size: 38 Copynumber: 2.2 Consensus size: 38
39392929 GATAGCTAAG
*
39392939 TAAGTTCTGGAAAGTGGCAGACAATGGTAAAAAATAAG
1 TAAGTTCTGGAAAGTGGCAGACAATGGTAAAAAATAAC
39392977 TAAGTTCTGGAAAGTGGCAGACAATGGTAAAAAATAAC
1 TAAGTTCTGGAAAGTGGCAGACAATGGTAAAAAATAAC
39393015 TCAA-TTCTG
1 T-AAGTTCTG
39393024 ATGTGACGTT
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
38 43 0.96
39 2 0.04
ACGTcount: A:0.42, C:0.11, G:0.24, T:0.24
Consensus pattern (38 bp):
TAAGTTCTGGAAAGTGGCAGACAATGGTAAAAAATAAC
Found at i:39393924 original size:54 final size:54
Alignment explanation
Indices: 39393833--39393999 Score: 232
Period size: 54 Copynumber: 3.1 Consensus size: 54
39393823 TGGTCATGGC
* *
39393833 AAGAAGACTATATAGTGTAAGACCTAGTCTGGGATTATGGCATCATATGGGGAA
1 AAGAAGACCATATAGTGTAAGACCTAGTTTGGGATTATGGCATCATATGGGGAA
*
39393887 TAA-AATACCATATAGTGTAAGACCTAGTTTGGGATTATGGCATCATATGGGGAA
1 -AAGAAGACCATATAGTGTAAGACCTAGTTTGGGATTATGGCATCATATGGGGAA
* * * * *
39393941 AAGAAGACCACATAGTGTAAGACCTAGTTT-GGACTATGGTACCATGTGGGG-A
1 AAGAAGACCATATAGTGTAAGACCTAGTTTGGGATTATGGCATCATATGGGGAA
39393993 AAGAAGA
1 AAGAAGA
39394000 TAAATGACGA
Statistics
Matches: 102, Mismatches: 9, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
52 8 0.08
53 19 0.19
54 73 0.72
55 2 0.02
ACGTcount: A:0.36, C:0.12, G:0.27, T:0.25
Consensus pattern (54 bp):
AAGAAGACCATATAGTGTAAGACCTAGTTTGGGATTATGGCATCATATGGGGAA
Found at i:39396564 original size:37 final size:36
Alignment explanation
Indices: 39396515--39396590 Score: 93
Period size: 37 Copynumber: 2.1 Consensus size: 36
39396505 GATAATCACT
*
39396515 TTAATATTAAA-TTAATAAAATACTATTAAGATAAGTA
1 TTAATATTAAATTTAATAAAA-ACTATTAAAATAA-TA
*
39396552 TTAA-ATTAAAATTTAATATAAACTATTAAAATAATA
1 TTAATATT-AAATTTAATAAAAACTATTAAAATAATA
39396588 TTA
1 TTA
39396591 TTTTTTGAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
36 8 0.23
37 19 0.54
38 8 0.23
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (36 bp):
TTAATATTAAATTTAATAAAAACTATTAAAATAATA
Found at i:39397887 original size:16 final size:16
Alignment explanation
Indices: 39397866--39397901 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
39397856 CAACAATGTT
39397866 AGCTTAATTTTATTTA
1 AGCTTAATTTTATTTA
39397882 AGCTTAATTTTATTTA
1 AGCTTAATTTTATTTA
39397898 AGCT
1 AGCT
39397902 AGGATGATTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.31, C:0.08, G:0.08, T:0.53
Consensus pattern (16 bp):
AGCTTAATTTTATTTA
Found at i:39398650 original size:24 final size:24
Alignment explanation
Indices: 39398618--39398667 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
39398608 CCCTGAGGAG
39398618 ACGATAACTCGATACTTACTTATT
1 ACGATAACTCGATACTTACTTATT
39398642 ACGATAACTCGATACTTACTTATT
1 ACGATAACTCGATACTTACTTATT
39398666 AC
1 AC
39398668 TTGATAACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.34, C:0.22, G:0.08, T:0.36
Consensus pattern (24 bp):
ACGATAACTCGATACTTACTTATT
Found at i:39416932 original size:344 final size:344
Alignment explanation
Indices: 39416305--39416992 Score: 1376
Period size: 344 Copynumber: 2.0 Consensus size: 344
39416295 TTCCTATGTA
39416305 ATTTATCACCTTTCTACTTAAATCCATTGTTAAAACAAAGTAATTGTGTAATAAATTAATGAAAT
1 ATTTATCACCTTTCTACTTAAATCCATTGTTAAAACAAAGTAATTGTGTAATAAATTAATGAAAT
39416370 ATGTGAAAATATGAAATTAGGACATAGAAATTATTAAAATGTGATTTTCTGCTTTATTATATGGT
66 ATGTGAAAATATGAAATTAGGACATAGAAATTATTAAAATGTGATTTTCTGCTTTATTATATGGT
39416435 TTTCATGCAACAAATGACTTATTCTATATTAATTTGAATATATTATATTTTTAAGACATAAAGTG
131 TTTCATGCAACAAATGACTTATTCTATATTAATTTGAATATATTATATTTTTAAGACATAAAGTG
39416500 GGCCATGCATCATTAAATTAAATAATAAAATATAAAATTATATTTAATAATTCATTTTAAAATAT
196 GGCCATGCATCATTAAATTAAATAATAAAATATAAAATTATATTTAATAATTCATTTTAAAATAT
39416565 TTCATTAATAATTAGGGTTTTAATTAATTAATTAAATTTGACAAAATTTAATTCTTTGGTCCTCT
261 TTCATTAATAATTAGGGTTTTAATTAATTAATTAAATTTGACAAAATTTAATTCTTTGGTCCTCT
39416630 AACTTGTTGATTTATTTTG
326 AACTTGTTGATTTATTTTG
39416649 ATTTATCACCTTTCTACTTAAATCCATTGTTAAAACAAAGTAATTGTGTAATAAATTAATGAAAT
1 ATTTATCACCTTTCTACTTAAATCCATTGTTAAAACAAAGTAATTGTGTAATAAATTAATGAAAT
39416714 ATGTGAAAATATGAAATTAGGACATAGAAATTATTAAAATGTGATTTTCTGCTTTATTATATGGT
66 ATGTGAAAATATGAAATTAGGACATAGAAATTATTAAAATGTGATTTTCTGCTTTATTATATGGT
39416779 TTTCATGCAACAAATGACTTATTCTATATTAATTTGAATATATTATATTTTTAAGACATAAAGTG
131 TTTCATGCAACAAATGACTTATTCTATATTAATTTGAATATATTATATTTTTAAGACATAAAGTG
39416844 GGCCATGCATCATTAAATTAAATAATAAAATATAAAATTATATTTAATAATTCATTTTAAAATAT
196 GGCCATGCATCATTAAATTAAATAATAAAATATAAAATTATATTTAATAATTCATTTTAAAATAT
39416909 TTCATTAATAATTAGGGTTTTAATTAATTAATTAAATTTGACAAAATTTAATTCTTTGGTCCTCT
261 TTCATTAATAATTAGGGTTTTAATTAATTAATTAAATTTGACAAAATTTAATTCTTTGGTCCTCT
39416974 AACTTGTTGATTTATTTTG
326 AACTTGTTGATTTATTTTG
39416993 GACAGGTCTG
Statistics
Matches: 344, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
344 344 1.00
ACGTcount: A:0.39, C:0.08, G:0.10, T:0.42
Consensus pattern (344 bp):
ATTTATCACCTTTCTACTTAAATCCATTGTTAAAACAAAGTAATTGTGTAATAAATTAATGAAAT
ATGTGAAAATATGAAATTAGGACATAGAAATTATTAAAATGTGATTTTCTGCTTTATTATATGGT
TTTCATGCAACAAATGACTTATTCTATATTAATTTGAATATATTATATTTTTAAGACATAAAGTG
GGCCATGCATCATTAAATTAAATAATAAAATATAAAATTATATTTAATAATTCATTTTAAAATAT
TTCATTAATAATTAGGGTTTTAATTAATTAATTAAATTTGACAAAATTTAATTCTTTGGTCCTCT
AACTTGTTGATTTATTTTG
Found at i:39419261 original size:82 final size:83
Alignment explanation
Indices: 39419154--39419318 Score: 323
Period size: 82 Copynumber: 2.0 Consensus size: 83
39419144 ATCCAAGGCT
39419154 CTCTTTATATAGGGAGAGTTTAGAGAGTTCAACTACGATTAAACTTTATTGCTTTAATATTAAGT
1 CTCTTTATATAGGGAGAGTTTAGAGAGTTCAACTACGATTAAACTTTATTGCTTTAATATTAAGT
39419219 TAATATAATATTTATCAA
66 TAATATAATATTTATCAA
39419237 CTCTTTATAT-GGGAGAGTTTAGAGAGTTCAACTACGATTAAACTTTATTGCTTTAATATTAAGT
1 CTCTTTATATAGGGAGAGTTTAGAGAGTTCAACTACGATTAAACTTTATTGCTTTAATATTAAGT
39419301 TAATATAATATTTATCAA
66 TAATATAATATTTATCAA
39419319 GATAAATAAA
Statistics
Matches: 82, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
82 72 0.88
83 10 0.12
ACGTcount: A:0.36, C:0.10, G:0.13, T:0.41
Consensus pattern (83 bp):
CTCTTTATATAGGGAGAGTTTAGAGAGTTCAACTACGATTAAACTTTATTGCTTTAATATTAAGT
TAATATAATATTTATCAA
Found at i:39424864 original size:19 final size:19
Alignment explanation
Indices: 39424840--39424880 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
39424830 TATTTTAAAG
*
39424840 TTATTTAGGTAGATAAATC
1 TTATTTAAGTAGATAAATC
*
39424859 TTATTTAAGTATATAAATC
1 TTATTTAAGTAGATAAATC
39424878 TTA
1 TTA
39424881 GAATAAATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.39, C:0.05, G:0.10, T:0.46
Consensus pattern (19 bp):
TTATTTAAGTAGATAAATC
Found at i:39425030 original size:16 final size:16
Alignment explanation
Indices: 39425009--39425043 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
39424999 AAATGCTCTC
39425009 TTATAGAACAGTTTTA
1 TTATAGAACAGTTTTA
39425025 TTATAGAACAGTTTTA
1 TTATAGAACAGTTTTA
39425041 TTA
1 TTA
39425044 AATGCTCTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.37, C:0.06, G:0.11, T:0.46
Consensus pattern (16 bp):
TTATAGAACAGTTTTA
Found at i:39428714 original size:19 final size:19
Alignment explanation
Indices: 39428687--39428727 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
39428677 TAATTTAAAG
*
39428687 TTATTTAGGTAGATAAATC
1 TTATATAGGTAGATAAATC
39428706 TTATATAGGTAGATAAATC
1 TTATATAGGTAGATAAATC
39428725 TTA
1 TTA
39428728 AAATAAATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.39, C:0.05, G:0.15, T:0.41
Consensus pattern (19 bp):
TTATATAGGTAGATAAATC
Found at i:39434275 original size:15 final size:15
Alignment explanation
Indices: 39434255--39434283 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
39434245 TTAAGGTAAT
39434255 CACTTTTTTCGAAAC
1 CACTTTTTTCGAAAC
39434270 CACTTTTTTCGAAA
1 CACTTTTTTCGAAA
39434284 ATAAAAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.24, G:0.07, T:0.41
Consensus pattern (15 bp):
CACTTTTTTCGAAAC
Found at i:39436718 original size:37 final size:36
Alignment explanation
Indices: 39436666--39436741 Score: 93
Period size: 37 Copynumber: 2.1 Consensus size: 36
39436656 TATTACAACT
*
39436666 TTAATATTAAATTAATA-AAATACTATTAAGATAAGTA
1 TTAATATTAAATTAATACAAA-ACTATTAAAATAA-TA
*
39436703 TTAA-ATTAAATTTAATACTAAACTATTAAAATAATA
1 TTAATATTAAA-TTAATACAAAACTATTAAAATAATA
39436739 TTA
1 TTA
39436742 TTTTTGGAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
36 11 0.31
37 22 0.63
38 2 0.06
ACGTcount: A:0.54, C:0.04, G:0.03, T:0.39
Consensus pattern (36 bp):
TTAATATTAAATTAATACAAAACTATTAAAATAATA
Found at i:39441218 original size:51 final size:52
Alignment explanation
Indices: 39441153--39441256 Score: 192
Period size: 51 Copynumber: 2.0 Consensus size: 52
39441143 TGTCCGGTTG
39441153 ATTTGTTTCTTGATCTAAATAATAGTTTTAACCCAATTAACCATTTAAAACA
1 ATTTGTTTCTTGATCTAAATAATAGTTTTAACCCAATTAACCATTTAAAACA
*
39441205 ATTT-TTTCTTGATCTAAATAATAGTTTTAACTCAATTAACCATTTAAAACA
1 ATTTGTTTCTTGATCTAAATAATAGTTTTAACCCAATTAACCATTTAAAACA
39441256 A
1 A
39441257 ATTAAATAAT
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
51 47 0.92
52 4 0.08
ACGTcount: A:0.39, C:0.14, G:0.05, T:0.41
Consensus pattern (52 bp):
ATTTGTTTCTTGATCTAAATAATAGTTTTAACCCAATTAACCATTTAAAACA
Found at i:39443504 original size:27 final size:29
Alignment explanation
Indices: 39443474--39443542 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 29
39443464 TACAGAATAC
*
39443474 GCCACAAAGG-T-GATCCATATAGAGCAT
1 GCCACAAAGGCTAGATCCATATAAAGCAT
* **
39443501 GCCACAAAGGCTATATGTATATAAAGCAT
1 GCCACAAAGGCTAGATCCATATAAAGCAT
39443530 GCCACAAAGGCTA
1 GCCACAAAGGCTA
39443543 ACACGATACG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
27 10 0.28
28 1 0.03
29 25 0.69
ACGTcount: A:0.39, C:0.22, G:0.20, T:0.19
Consensus pattern (29 bp):
GCCACAAAGGCTAGATCCATATAAAGCAT
Found at i:39447275 original size:10 final size:10
Alignment explanation
Indices: 39447253--39447305 Score: 58
Period size: 9 Copynumber: 5.5 Consensus size: 10
39447243 AATAACATAA
*
39447253 AAAAATT-TA
1 AAAAATTATT
39447262 AAAAATTATT
1 AAAAATTATT
39447272 -AAAATTATT
1 AAAAATTATT
*
39447281 AAAATTTA-T
1 AAAAATTATT
39447290 AAAAATTAATT
1 AAAAATT-ATT
39447301 AAAAA
1 AAAAA
39447306 CATAAAATGT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
9 23 0.62
10 8 0.22
11 6 0.16
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (10 bp):
AAAAATTATT
Found at i:39447277 original size:18 final size:19
Alignment explanation
Indices: 39447253--39447297 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
39447243 AATAACATAA
39447253 AAAAATT-TAAAAAATTAT
1 AAAAATTATAAAAAATTAT
* * *
39447271 TAAAATTATTAAAATTTAT
1 AAAAATTATAAAAAATTAT
39447290 AAAAATTA
1 AAAAATTA
39447298 ATTAAAAACA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
AAAAATTATAAAAAATTAT
Found at i:39447318 original size:29 final size:28
Alignment explanation
Indices: 39447254--39447318 Score: 80
Period size: 28 Copynumber: 2.3 Consensus size: 28
39447244 ATAACATAAA
**
39447254 AAAATTTA-AAAAATTATTAAAATTATT
1 AAAATTTATAAAAATTATTAAAAACATT
39447281 AAAATTTATAAAAATTAATTAAAAACA-T
1 AAAATTTATAAAAATT-ATTAAAAACATT
39447309 AAAATGTTAT
1 AAAAT-TTAT
39447319 NNNNNNNNNN
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 8 0.24
28 13 0.39
29 12 0.36
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (28 bp):
AAAATTTATAAAAATTATTAAAAACATT
Found at i:39448257 original size:15 final size:16
Alignment explanation
Indices: 39448231--39448266 Score: 65
Period size: 15 Copynumber: 2.3 Consensus size: 16
39448221 ATTAATGGTG
39448231 ATTAAGGATTAAATTA
1 ATTAAGGATTAAATTA
39448247 ATTAA-GATTAAATTA
1 ATTAAGGATTAAATTA
39448262 ATTAA
1 ATTAA
39448267 ACAAGGTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 15 0.75
16 5 0.25
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.39
Consensus pattern (16 bp):
ATTAAGGATTAAATTA
Found at i:39453661 original size:16 final size:18
Alignment explanation
Indices: 39453634--39453666 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
39453624 ATCCTAAACC
39453634 CATCCTCTTGGT-GATTT
1 CATCCTCTTGGTCGATTT
39453651 CATCC-CTTGGTCGATT
1 CATCCTCTTGGTCGATT
39453667 AGTATATTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.12, C:0.27, G:0.18, T:0.42
Consensus pattern (18 bp):
CATCCTCTTGGTCGATTT
Found at i:39454943 original size:18 final size:18
Alignment explanation
Indices: 39454908--39454943 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
39454898 TTCATGATTA
* *
39454908 TGGATTTTTATTATCTTT
1 TGGATTTTTATGAACTTT
39454926 TGGATTTTTATGAACTTT
1 TGGATTTTTATGAACTTT
39454944 ATAAATTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.19, C:0.06, G:0.14, T:0.61
Consensus pattern (18 bp):
TGGATTTTTATGAACTTT
Found at i:39455546 original size:16 final size:16
Alignment explanation
Indices: 39455520--39455562 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
39455510 TTATAGATTG
*
39455520 TAGATTGTGAAAACTA
1 TAGACTGTGAAAACTA
* *
39455536 TAGACTTTGAAAACTC
1 TAGACTGTGAAAACTA
39455552 TAGACTGTGAA
1 TAGACTGTGAA
39455563 GACAATAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.30
Consensus pattern (16 bp):
TAGACTGTGAAAACTA
Found at i:39462340 original size:12 final size:12
Alignment explanation
Indices: 39462323--39462349 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
39462313 ATTTTTTTTT
39462323 TAACCCTAGGTA
1 TAACCCTAGGTA
39462335 TAACCCTAGGTA
1 TAACCCTAGGTA
39462347 TAA
1 TAA
39462350 ATTTTAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.37, C:0.22, G:0.15, T:0.26
Consensus pattern (12 bp):
TAACCCTAGGTA
Found at i:39467387 original size:56 final size:56
Alignment explanation
Indices: 39467323--39467438 Score: 178
Period size: 56 Copynumber: 2.1 Consensus size: 56
39467313 TGACTAGTAA
* *
39467323 ATTTAAATAAAAATATTTACAAACATACTTGTCAGAATTGTAGTCTCGAAACCACT
1 ATTTAAATAAAAATATTTACAAACATACTTGTCAGAATTGTAGCCCCGAAACCACT
* * * *
39467379 ATTTAAATAAAAATATTTACGAACTTACTTGTTAGACTTGTAGCCCCGAAACCACT
1 ATTTAAATAAAAATATTTACAAACATACTTGTCAGAATTGTAGCCCCGAAACCACT
39467435 ATTT
1 ATTT
39467439 CCAACAGCAT
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
56 54 1.00
ACGTcount: A:0.40, C:0.17, G:0.09, T:0.34
Consensus pattern (56 bp):
ATTTAAATAAAAATATTTACAAACATACTTGTCAGAATTGTAGCCCCGAAACCACT
Found at i:39471751 original size:13 final size:13
Alignment explanation
Indices: 39471733--39471777 Score: 60
Period size: 13 Copynumber: 3.7 Consensus size: 13
39471723 TCCTCTATAC
39471733 CAAAATGAACATA
1 CAAAATGAACATA
39471746 CAAAATG--CA-A
1 CAAAATGAACATA
*
39471756 CAAAATGATCATA
1 CAAAATGAACATA
39471769 CAAAATGAA
1 CAAAATGAA
39471778 ACCTAGATGC
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
10 8 0.29
11 2 0.07
12 2 0.07
13 16 0.57
ACGTcount: A:0.60, C:0.16, G:0.09, T:0.16
Consensus pattern (13 bp):
CAAAATGAACATA
Found at i:39483437 original size:49 final size:51
Alignment explanation
Indices: 39483380--39483521 Score: 189
Period size: 51 Copynumber: 2.8 Consensus size: 51
39483370 AGGTGGAAGT
* * *
39483380 AGTGGCAGTATATCTACAAATCAATGGTGGCTTGTCCACAAAA-T-TTATC
1 AGTGGCAGTATATCTGCAAATCAGTGGTGGCTTGTCCACAAAAGTGTAATC
**
39483429 AGTGGCAGTATATCTGCGTATCAGTGGTGGCTTGTCCACAAAAGTGTAATC
1 AGTGGCAGTATATCTGCAAATCAGTGGTGGCTTGTCCACAAAAGTGTAATC
* * * *
39483480 AGTGGCAGTTTATATGTAAGTCAGTGGTGGCTTGTCCACAAA
1 AGTGGCAGTATATCTGCAAATCAGTGGTGGCTTGTCCACAAA
39483522 TGGTGTTACG
Statistics
Matches: 80, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
49 39 0.49
50 1 0.01
51 40 0.50
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (51 bp):
AGTGGCAGTATATCTGCAAATCAGTGGTGGCTTGTCCACAAAAGTGTAATC
Found at i:39483504 original size:51 final size:48
Alignment explanation
Indices: 39483380--39483521 Score: 160
Period size: 49 Copynumber: 2.9 Consensus size: 48
39483370 AGGTGGAAGT
* ** * *
39483380 AGTGGCAGTATATCTACAAATCAATGGTGGCTTGTCCACAAAATTTATC
1 AGTGGCAGTATATAT-CGTATCAGTGGTGGCTTGTCCACAAAATTAATC
*
39483429 AGTGGCAGTATATCTGCGTATCAGTGGTGGCTTGTCCACAAAAGTGTAATC
1 AGTGGCAGTATATAT-CGTATCAGTGGTGGCTTGTCCACAAAA-T-TAATC
*
39483480 AGTGGCAGTTTATAT-GTAAGTCAGTGGTGGCTTGTCCACAAA
1 AGTGGCAGTATATATCGT-A-TCAGTGGTGGCTTGTCCACAAA
39483522 TGGTGTTACG
Statistics
Matches: 82, Mismatches: 7, Indels: 6
0.86 0.07 0.06
Matches are distributed among these distances:
49 41 0.50
50 2 0.02
51 39 0.48
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (48 bp):
AGTGGCAGTATATATCGTATCAGTGGTGGCTTGTCCACAAAATTAATC
Found at i:39484919 original size:19 final size:19
Alignment explanation
Indices: 39484895--39484938 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
39484885 TAATACCAAG
39484895 TGACTTAGCATGAAGATCA
1 TGACTTAGCATGAAGATCA
* *
39484914 TGACTTAGCGTGACGATCA
1 TGACTTAGCATGAAGATCA
39484933 TG-CTTA
1 TGACTTA
39484939 TATTGTGTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.30
Consensus pattern (19 bp):
TGACTTAGCATGAAGATCA
Found at i:39493022 original size:24 final size:24
Alignment explanation
Indices: 39492995--39493041 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
39492985 ATTGAAATGG
39492995 ATTG-ATTTAGTATTTGA-TGAATTT
1 ATTGAATTTA-TA-TTGATTGAATTT
39493019 ATTGAATTTATATTGATTGAATT
1 ATTGAATTTATATTGATTGAATT
39493042 GGTATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 4 0.19
24 12 0.57
25 5 0.24
ACGTcount: A:0.32, C:0.00, G:0.15, T:0.53
Consensus pattern (24 bp):
ATTGAATTTATATTGATTGAATTT
Found at i:39499743 original size:75 final size:75
Alignment explanation
Indices: 39499616--39499944 Score: 394
Period size: 75 Copynumber: 4.4 Consensus size: 75
39499606 TACGCAAGCC
**
39499616 ATTT-TCAGTTTATCCGACTAGCGCTGGGCGCAACTTTTGTCAGTTTATCTGACTAGTGCTGGGC
1 ATTTGTCAGTTTATCCGACTAGCGCTGGGCGCAACTTTCATCAGTTTATCTGACTAGTGCTGGGC
39499680 ACACCATTAT
66 ACACCATTAT
* * * * *
39499690 ATTTGTCAGTTCATCC-AGCTAGCACTGGGCGCAAATTTCATCAATTTATCTGACTAGTGCTAGG
1 ATTTGTCAGTTTATCCGA-CTAGCGCTGGGCGCAACTTTCATCAGTTTATCTGACTAGTGCTGGG
39499754 CACACCATTAT
65 CACACCATTAT
* * * * * *
39499765 ATTTTTCAATTTATCCGACTAG-GGTAGGGTGCAACTTTCATCAGCTTATCTGACTAGTGATGGG
1 ATTTGTCAGTTTATCCGACTAGCGCT-GGGCGCAACTTTCATCAGTTTATCTGACTAGTGCTGGG
39499829 CACACCATTAT
65 CACACCATTAT
* * * * * * * *
39499840 ATTTTTTAGTTTATCTGACTACCGTTGGGTGCAACTTTCGTCAGTTTATCTAACTAGTGCTGGGC
1 ATTTGTCAGTTTATCCGACTAGCGCTGGGCGCAACTTTCATCAGTTTATCTGACTAGTGCTGGGC
*
39499905 ACATCATTAT
66 ACACCATTAT
* * *
39499915 ATCTGTCGGTTTATCCGACTAGCGCAGGGC
1 ATTTGTCAGTTTATCCGACTAGCGCTGGGC
39499945 ATAAAACTTT
Statistics
Matches: 213, Mismatches: 37, Indels: 9
0.82 0.14 0.03
Matches are distributed among these distances:
74 6 0.03
75 204 0.96
76 3 0.01
ACGTcount: A:0.23, C:0.22, G:0.20, T:0.35
Consensus pattern (75 bp):
ATTTGTCAGTTTATCCGACTAGCGCTGGGCGCAACTTTCATCAGTTTATCTGACTAGTGCTGGGC
ACACCATTAT
Found at i:39503068 original size:23 final size:23
Alignment explanation
Indices: 39503038--39503082 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
39503028 GAATTAAAAG
39503038 AAAGATTTTTTATAAACTATACC
1 AAAGATTTTTTATAAACTATACC
39503061 AAAGATTTTTTATAAACTATAC
1 AAAGATTTTTTATAAACTATAC
39503083 TAAAAATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.44, C:0.11, G:0.04, T:0.40
Consensus pattern (23 bp):
AAAGATTTTTTATAAACTATACC
Found at i:39509225 original size:5 final size:5
Alignment explanation
Indices: 39509215--39509241 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
39509205 AAATTTGATG
39509215 AATTA AATTA AATTA AATTA AATTA AA
1 AATTA AATTA AATTA AATTA AATTA AA
39509242 CAAAAGCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (5 bp):
AATTA
Found at i:39515397 original size:17 final size:17
Alignment explanation
Indices: 39515335--39515399 Score: 53
Period size: 19 Copynumber: 3.7 Consensus size: 17
39515325 ATAATATATT
39515335 CATA-TTTTTA-ACATA
1 CATATTTTTTATACATA
* *
39515350 AATATTTTTTTTATAAATA
1 CATA--TTTTTTATACATA
*
39515369 TGCATATATTTTATACATA
1 --CATATTTTTTATACATA
39515388 CATATTTTTTAT
1 CATATTTTTTAT
39515400 TTTATTTACC
Statistics
Matches: 38, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
15 3 0.08
17 11 0.29
18 6 0.16
19 15 0.39
21 3 0.08
ACGTcount: A:0.37, C:0.08, G:0.02, T:0.54
Consensus pattern (17 bp):
CATATTTTTTATACATA
Found at i:39516131 original size:104 final size:99
Alignment explanation
Indices: 39516016--39516273 Score: 314
Period size: 98 Copynumber: 2.6 Consensus size: 99
39516006 CACGTTGTGT
39516016 CCTAACGTATTGGATGTGACGCATTGATTTCTCGAAA-TGAATAAGTGGATGTTCTTTTAAAGTA
1 CCTAACGTATTGG-TGTGA-G---TGATTTCT-GAAATTGAATAAGTGGATGTTCTTTTAAAGTA
39516080 AAGGAAATATTCCGAGTTTGGGATTCTAGAGGAATCGTGC
60 AAGGAAATATTCCGAGTTTGGGATTCTAGAGGAATCGTGC
* *
39516120 CCTAACGTATTGG-GT--GTGATTTCTTAAATCTTGGATAAGTGGATGTTCTTTTAAAGTAAAGG
1 CCTAACGTATTGGTGTGAGTGATTTCTGAAA--TTGAATAAGTGGATGTTCTTTTAAAGTAAAGG
39516182 AAATATTCCGAGTTTGGGATTCTAGAGGAATCGTGC
64 AAATATTCCGAGTTTGGGATTCTAGAGGAATCGTGC
* * * * *
39516218 CCTAGCGTATTGG-GT--GTGATTTCTTAAATCTTGGATAAGCGGATATTCTTTTAAAG
1 CCTAACGTATTGGTGTGAGTGATTTCTGAAA--TTGAATAAGTGGATGTTCTTTTAAAG
39516274 ATTTATTGTA
Statistics
Matches: 146, Mismatches: 5, Indels: 12
0.90 0.03 0.07
Matches are distributed among these distances:
95 3 0.02
96 8 0.05
98 119 0.82
99 1 0.01
102 2 0.01
104 13 0.09
ACGTcount: A:0.28, C:0.12, G:0.25, T:0.35
Consensus pattern (99 bp):
CCTAACGTATTGGTGTGAGTGATTTCTGAAATTGAATAAGTGGATGTTCTTTTAAAGTAAAGGAA
ATATTCCGAGTTTGGGATTCTAGAGGAATCGTGC
Found at i:39516171 original size:98 final size:98
Alignment explanation
Indices: 39516056--39516273 Score: 409
Period size: 98 Copynumber: 2.2 Consensus size: 98
39516046 CTCGAAATGA
39516056 ATAAGTGGATGTTCTTTTAAAGTAAAGGAAATATTCCGAGTTTGGGATTCTAGAGGAATCGTGCC
1 ATAAGTGGATGTTCTTTTAAAGTAAAGGAAATATTCCGAGTTTGGGATTCTAGAGGAATCGTGCC
39516121 CTAACGTATTGGGTGTGATTTCTTAAATCTTGG
66 CTAACGTATTGGGTGTGATTTCTTAAATCTTGG
39516154 ATAAGTGGATGTTCTTTTAAAGTAAAGGAAATATTCCGAGTTTGGGATTCTAGAGGAATCGTGCC
1 ATAAGTGGATGTTCTTTTAAAGTAAAGGAAATATTCCGAGTTTGGGATTCTAGAGGAATCGTGCC
*
39516219 CTAGCGTATTGGGTGTGATTTCTTAAATCTTGG
66 CTAACGTATTGGGTGTGATTTCTTAAATCTTGG
* *
39516252 ATAAGCGGATATTCTTTTAAAG
1 ATAAGTGGATGTTCTTTTAAAG
39516274 ATTTATTGTA
Statistics
Matches: 117, Mismatches: 3, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
98 117 1.00
ACGTcount: A:0.28, C:0.11, G:0.25, T:0.36
Consensus pattern (98 bp):
ATAAGTGGATGTTCTTTTAAAGTAAAGGAAATATTCCGAGTTTGGGATTCTAGAGGAATCGTGCC
CTAACGTATTGGGTGTGATTTCTTAAATCTTGG
Found at i:39518711 original size:32 final size:32
Alignment explanation
Indices: 39518660--39518859 Score: 251
Period size: 32 Copynumber: 6.3 Consensus size: 32
39518650 GAATTGCTAC
* * *
39518660 AAGCCATAAGT-ACAGTAATATGATTGGCACA
1 AAGCCATCAGTAATAGTAATATGATCGGCACA
*
39518691 AAGCCATCAGTAGTAGTAATATGATCGGCACA
1 AAGCCATCAGTAATAGTAATATGATCGGCACA
* * *
39518723 CAGCCATCAGTAATCGTAGTATGATCGGCACA
1 AAGCCATCAGTAATAGTAATATGATCGGCACA
* *
39518755 AAGCCATCAATAGTAGTAATATGATCGGCACA
1 AAGCCATCAGTAATAGTAATATGATCGGCACA
* * * *
39518787 CAGCCATTAGTAATGGTAATATGATCGGTACA
1 AAGCCATCAGTAATAGTAATATGATCGGCACA
*
39518819 CAA-CCATCAGTAATGGTAATATGATCGGCACA
1 -AAGCCATCAGTAATAGTAATATGATCGGCACA
39518851 AAGCCATCA
1 AAGCCATCA
39518860 ATAGCATCGC
Statistics
Matches: 144, Mismatches: 22, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
31 12 0.08
32 131 0.91
33 1 0.01
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.23
Consensus pattern (32 bp):
AAGCCATCAGTAATAGTAATATGATCGGCACA
Found at i:39518792 original size:96 final size:96
Alignment explanation
Indices: 39518673--39518863 Score: 301
Period size: 96 Copynumber: 2.0 Consensus size: 96
39518663 CCATAAGTAC
* * *
39518673 AGTAATATGATTGGCACAAAGCCATCAGTAGTAGTAATATGATCGGCACACAGCCATCAGTAATC
1 AGTAATATGATCGGCACAAAGCCATCAGTAATAGTAATATGATCGGCACACAACCATCAGTAATC
*
39518738 GTAGTATGATCGGCACAAAGCCATCAATAGT
66 GTAATATGATCGGCACAAAGCCATCAATAGT
* * * * *
39518769 AGTAATATGATCGGCACACAGCCATTAGTAATGGTAATATGATCGGTACACAACCATCAGTAATG
1 AGTAATATGATCGGCACAAAGCCATCAGTAATAGTAATATGATCGGCACACAACCATCAGTAATC
39518834 GTAATATGATCGGCACAAAGCCATCAATAG
66 GTAATATGATCGGCACAAAGCCATCAATAG
39518864 CATCGCAGCA
Statistics
Matches: 86, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
96 86 1.00
ACGTcount: A:0.37, C:0.19, G:0.20, T:0.23
Consensus pattern (96 bp):
AGTAATATGATCGGCACAAAGCCATCAGTAATAGTAATATGATCGGCACACAACCATCAGTAATC
GTAATATGATCGGCACAAAGCCATCAATAGT
Found at i:39518894 original size:26 final size:26
Alignment explanation
Indices: 39518865--39518918 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
39518855 CATCAATAGC
* *
39518865 ATCGCAGCAAAGCTGCCAGCAACAGT
1 ATCGCAACAAAGCTCCCAGCAACAGT
*
39518891 ATCGCAACAAAGCTCCCAGTAACAGT
1 ATCGCAACAAAGCTCCCAGCAACAGT
39518917 AT
1 AT
39518919 ATGTGGCGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.37, C:0.30, G:0.19, T:0.15
Consensus pattern (26 bp):
ATCGCAACAAAGCTCCCAGCAACAGT
Found at i:39518936 original size:27 final size:27
Alignment explanation
Indices: 39518906--39518965 Score: 79
Period size: 27 Copynumber: 2.2 Consensus size: 27
39518896 AACAAAGCTC
39518906 CCAGTAACAGT-ATATGTGGC-GAAGCCA
1 CCAGTAACAGTGAT-TGTGGCAG-AGCCA
*
39518933 CCAGTTACAGTGATTGTGGCAGAGCCA
1 CCAGTAACAGTGATTGTGGCAGAGCCA
39518960 CCAGTA
1 CCAGTA
39518966 TAGTACTTCC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 26 0.90
28 3 0.10
ACGTcount: A:0.30, C:0.23, G:0.27, T:0.20
Consensus pattern (27 bp):
CCAGTAACAGTGATTGTGGCAGAGCCA
Found at i:39519108 original size:24 final size:24
Alignment explanation
Indices: 39519048--39519134 Score: 86
Period size: 24 Copynumber: 3.6 Consensus size: 24
39519038 AGTGATACAA
39519048 ATCACAGACAAATCAGTCATTTTA-
1 ATCACAGACAAATCAGTCA-TTTAC
*
39519072 ATCACAGAAAAATCAGTCATTTAC
1 ATCACAGACAAATCAGTCATTTAC
*** * *
39519096 ATCTTGGACAAATCATTTATTTAC
1 ATCACAGACAAATCAGTCATTTAC
* *
39519120 ATCGCAGGCAAATCA
1 ATCACAGACAAATCA
39519135 ATGGTTTAAC
Statistics
Matches: 51, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
23 4 0.08
24 47 0.92
ACGTcount: A:0.40, C:0.21, G:0.10, T:0.29
Consensus pattern (24 bp):
ATCACAGACAAATCAGTCATTTAC
Found at i:39519221 original size:27 final size:27
Alignment explanation
Indices: 39519191--39519251 Score: 88
Period size: 27 Copynumber: 2.3 Consensus size: 27
39519181 CATTACGGTC
*
39519191 ATTTTACCCTTCAAGGGTATTTCGA-TA
1 ATTTTACCCTTCAAGGGTA-TTCCATTA
*
39519218 ATTTTACCCTTCGAGGGTATTCCATTA
1 ATTTTACCCTTCAAGGGTATTCCATTA
39519245 ATTTTAC
1 ATTTTAC
39519252 AACCTTTCTG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
26 4 0.13
27 27 0.87
ACGTcount: A:0.25, C:0.20, G:0.13, T:0.43
Consensus pattern (27 bp):
ATTTTACCCTTCAAGGGTATTCCATTA
Found at i:39521324 original size:26 final size:26
Alignment explanation
Indices: 39521284--39521338 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
39521274 GGATCTCGAC
39521284 TTTATTTTATCTATGTTCTTAGGTTA
1 TTTATTTTATCTATGTTCTTAGGTTA
* *
39521310 TTTATTTTATTTATGTTTTTAGGTTA
1 TTTATTTTATCTATGTTCTTAGGTTA
39521336 TTT
1 TTT
39521339 TAGGATAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.18, C:0.04, G:0.11, T:0.67
Consensus pattern (26 bp):
TTTATTTTATCTATGTTCTTAGGTTA
Found at i:39524553 original size:15 final size:15
Alignment explanation
Indices: 39524533--39524570 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
39524523 AACTCGACAT
39524533 TTACTTGTCACTTTA
1 TTACTTGTCACTTTA
39524548 TTACTTGTCACTTTA
1 TTACTTGTCACTTTA
39524563 TTACTTGT
1 TTACTTGT
39524571 TATGATTGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.18, C:0.18, G:0.08, T:0.55
Consensus pattern (15 bp):
TTACTTGTCACTTTA
Found at i:39528329 original size:26 final size:26
Alignment explanation
Indices: 39528294--39528355 Score: 81
Period size: 26 Copynumber: 2.4 Consensus size: 26
39528284 GCAGCTCTTA
* *
39528294 TGAGCGTCCCG-TTATATGGCTCTTCG
1 TGAGCTTCCCGATTA-AAGGCTCTTCG
*
39528320 TGAGCTTCCCGATTAAAGGCTCTTTG
1 TGAGCTTCCCGATTAAAGGCTCTTCG
39528346 TGAGCTTCCC
1 TGAGCTTCCC
39528356 TTTAGTGCTC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
26 29 0.91
27 3 0.09
ACGTcount: A:0.15, C:0.27, G:0.24, T:0.34
Consensus pattern (26 bp):
TGAGCTTCCCGATTAAAGGCTCTTCG
Found at i:39535747 original size:25 final size:24
Alignment explanation
Indices: 39535699--39535756 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 24
39535689 AGCCCTCGCA
*
39535699 AGCTTCCCATTATAATGTTCTTGC
1 AGCTTCCCATTATAATGCTCTTGC
*
39535723 GAGCTTCCCGTTA-AATGCTCTTTGC
1 -AGCTTCCCATTATAATGCTC-TTGC
*
39535748 AGCATCCCA
1 AGCTTCCCA
39535757 ATCGGTTGTG
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
24 13 0.46
25 15 0.54
ACGTcount: A:0.21, C:0.29, G:0.16, T:0.34
Consensus pattern (24 bp):
AGCTTCCCATTATAATGCTCTTGC
Found at i:39535945 original size:24 final size:24
Alignment explanation
Indices: 39535909--39536018 Score: 114
Period size: 24 Copynumber: 4.5 Consensus size: 24
39535899 TCTGGTGCTT
* *
39535909 CCCGTTAACTGCTCTTCGGAGGTA
1 CCCGTTAATTGCTCTTCGGAGCTA
39535933 CCCGTTAATTGCTCTTCGGAGCTA
1 CCCGTTAATTGCTCTTCGGAGCTA
* *
39535957 CCCATTAATTGCTCTTTGGAGCTA
1 CCCGTTAATTGCTCTTCGGAGCTA
* * * *
39535981 CCCATT-ATAGGCTCTTTGTGAGCTT
1 CCCGTTAAT-TGCTCTTCG-GAGCTA
39536006 CCCGTTATATTGC
1 CCCGTTA-ATTGC
39536019 CTGGATAAGC
Statistics
Matches: 74, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
23 2 0.03
24 58 0.78
25 10 0.14
26 2 0.03
27 2 0.03
ACGTcount: A:0.17, C:0.27, G:0.20, T:0.35
Consensus pattern (24 bp):
CCCGTTAATTGCTCTTCGGAGCTA
Found at i:39537511 original size:22 final size:22
Alignment explanation
Indices: 39537483--39537534 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
39537473 CTTTTTTTAA
*
39537483 GGTGGTGATACGGTGGTGCTAG
1 GGTGGTGATACAGTGGTGCTAG
* ** *
39537505 GGTGGTGGTGTAGTGGTGCTAT
1 GGTGGTGATACAGTGGTGCTAG
39537527 GGTGGTGA
1 GGTGGTGA
39537535 AGTGGTGGTG
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.12, C:0.06, G:0.52, T:0.31
Consensus pattern (22 bp):
GGTGGTGATACAGTGGTGCTAG
Found at i:39537542 original size:22 final size:22
Alignment explanation
Indices: 39537494--39537544 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
39537484 GTGGTGATAC
**
39537494 GGTGGTGCTAGGGTGGTGGTGT
1 GGTGGTGCTAGGGTGGTGAAGT
* *
39537516 AGTGGTGCTATGGTGGTGAAGT
1 GGTGGTGCTAGGGTGGTGAAGT
39537538 GGTGGTG
1 GGTGGTG
39537545 ATCAAGGAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.10, C:0.04, G:0.55, T:0.31
Consensus pattern (22 bp):
GGTGGTGCTAGGGTGGTGAAGT
Found at i:39538279 original size:17 final size:17
Alignment explanation
Indices: 39538257--39538322 Score: 60
Period size: 17 Copynumber: 3.5 Consensus size: 17
39538247 AAAAGGATTT
*
39538257 TAAAAATATTTTAAAAA
1 TAAAAAAATTTTAAAAA
39538274 TAAAAAAATTTTAAAAAAGTA
1 TAAAAAAATTTT--AAAA--A
39538295 TTTAAAAAATATTTTAAAAA
1 --TAAAAAA-ATTTTAAAAA
39538315 TAAAAAAA
1 TAAAAAAA
39538323 ATAAAAAATA
Statistics
Matches: 41, Mismatches: 1, Indels: 14
0.73 0.02 0.25
Matches are distributed among these distances:
17 12 0.29
18 7 0.17
19 4 0.10
20 1 0.02
21 1 0.02
22 4 0.10
23 7 0.17
24 5 0.12
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.32
Consensus pattern (17 bp):
TAAAAAAATTTTAAAAA
Found at i:39538290 original size:41 final size:41
Alignment explanation
Indices: 39538245--39538322 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
39538235 TAAAAAAATA
*
39538245 AAAAAAGGATTTTAAAAATATTTTAAAAATAAAAAAATTTT
1 AAAAAAGGATTTAAAAAATATTTTAAAAATAAAAAAATTTT
*
39538286 AAAAAAGTATTTAAAAAATATTTTAAAAATAAAAAAA
1 AAAAAAGGATTTAAAAAATATTTTAAAAATAAAAAAA
39538323 ATAAAAAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (41 bp):
AAAAAAGGATTTAAAAAATATTTTAAAAATAAAAAAATTTT
Found at i:39538315 original size:11 final size:11
Alignment explanation
Indices: 39538253--39538316 Score: 66
Period size: 11 Copynumber: 6.1 Consensus size: 11
39538243 TAAAAAAAGG
39538253 ATTTTAAAAAT
1 ATTTTAAAAAT
39538264 ATTTTAAAAAT
1 ATTTTAAAAAT
39538275 A----AAAAA-
1 ATTTTAAAAAT
39538281 ATTTTAAAAAAGT
1 ATTTT-AAAAA-T
*
39538294 ATTTAAAAAAT
1 ATTTTAAAAAT
39538305 ATTTTAAAAAT
1 ATTTTAAAAAT
39538316 A
1 A
39538317 AAAAAAATAA
Statistics
Matches: 44, Mismatches: 2, Indels: 14
0.73 0.03 0.23
Matches are distributed among these distances:
6 1 0.02
7 5 0.11
11 29 0.66
12 5 0.11
13 4 0.09
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (11 bp):
ATTTTAAAAAT
Found at i:39543272 original size:9 final size:9
Alignment explanation
Indices: 39543255--39543285 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
39543245 TCAGGTTGAT
39543255 TCGAATAAC
1 TCGAATAAC
*
39543264 TCGATTAAC
1 TCGAATAAC
39543273 TCGAATAAC
1 TCGAATAAC
39543282 TCGA
1 TCGA
39543286 TTTGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:39545542 original size:16 final size:16
Alignment explanation
Indices: 39545521--39545551 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
39545511 AGTCTTACAG
39545521 AGTCTCAATTTCACAC
1 AGTCTCAATTTCACAC
39545537 AGTCTCAATTTCACA
1 AGTCTCAATTTCACA
39545552 ACCCTAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.29, G:0.06, T:0.32
Consensus pattern (16 bp):
AGTCTCAATTTCACAC
Found at i:39549391 original size:43 final size:44
Alignment explanation
Indices: 39549300--39549384 Score: 102
Period size: 44 Copynumber: 2.0 Consensus size: 44
39549290 GTGAGATGTC
* * * *
39549300 TCATCTCTCTTGGTAGAACTAACCGAAAGCCAAGGCGAGAGGCA
1 TCATCTCGCTTGGTAGAACTAACCGAAAGACAAGGCAAAAGGCA
*
39549344 TCATCTCGCTTGGTAGAA-TCAACC-TAAGACAAGGCAAAAGG
1 TCATCTCGCTTGGTAGAACT-AACCGAAAGACAAGGCAAAAGG
39549385 TTTCATCCCT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
43 14 0.40
44 21 0.60
ACGTcount: A:0.34, C:0.24, G:0.24, T:0.19
Consensus pattern (44 bp):
TCATCTCGCTTGGTAGAACTAACCGAAAGACAAGGCAAAAGGCA
Found at i:39553645 original size:18 final size:17
Alignment explanation
Indices: 39553612--39553649 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
39553602 CAATCTCTTG
39553612 ATATTTATTTCTTTATT
1 ATATTTATTTCTTTATT
39553629 ATATTATATTT-TATTATT
1 ATATT-TATTTCT-TTATT
39553647 ATA
1 ATA
39553650 GAAATCTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (17 bp):
ATATTTATTTCTTTATT
Found at i:39554192 original size:75 final size:75
Alignment explanation
Indices: 39554064--39554210 Score: 204
Period size: 75 Copynumber: 2.0 Consensus size: 75
39554054 GAAAAGCAAG
* * * ** * *
39554064 ATTATTCCCTTATTAATATAGAAGTCAAATGGAAAGTTAAAAAAATTATTTATATTCTTTCTAAA
1 ATTATTCCCTTATTAATAGAGAAGACAAATCGAAAGTTAAAAAAAGGAATTATATTCTTTCCAAA
39554129 AGAATATAGA
66 AGAATATAGA
* * *
39554139 ATTATTCTCTTATTAATAGAGAAGACAAATCGAAAGTTAGAAAAAGGAATTATATTTTTTCCAAA
1 ATTATTCCCTTATTAATAGAGAAGACAAATCGAAAGTTAAAAAAAGGAATTATATTCTTTCCAAA
39554204 AGAATAT
66 AGAATAT
39554211 TAATTTCTAA
Statistics
Matches: 62, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
75 62 1.00
ACGTcount: A:0.46, C:0.08, G:0.11, T:0.35
Consensus pattern (75 bp):
ATTATTCCCTTATTAATAGAGAAGACAAATCGAAAGTTAAAAAAAGGAATTATATTCTTTCCAAA
AGAATATAGA
Found at i:39554389 original size:115 final size:116
Alignment explanation
Indices: 39554186--39554413 Score: 311
Period size: 115 Copynumber: 2.0 Consensus size: 116
39554176 TAGAAAAAGG
* * * *
39554186 AATTATATTTTTTCCAAAAGAATATTAATTTCTAAGTCTTTTATATTTTGACCGAAATTAATTAT
1 AATTATATTCTTTCCAAAAGAATATTAATTTCCAAGTCTTTTATATTTTAACCGAAATTAATTAA
* ***
39554251 TATAATTGTTTATATTAATAAATTTGATAAAATATATA-ATATTAATATCTT
66 TAAAACAATTTATATTAATAAATTTGATAAAATATATACA-ATTAATATCTT
*
39554302 AATTATATTCTTTCCAAACA-AATATTAATTTCCATA-TC-TTTATATTTTAACTGAAATTAATT
1 AATTATATTCTTTCCAAA-AGAATATTAATTTCCA-AGTCTTTTATATTTTAACCGAAATTAATT
*
39554364 AATAAAACAATTTATATTAATAAATTTGGTAAAATATATACAATTAATAT
64 AATAAAACAATTTATATTAATAAATTTGATAAAATATATACAATTAATAT
39554414 TTTGTATGAA
Statistics
Matches: 99, Mismatches: 10, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
115 64 0.65
116 33 0.33
117 2 0.02
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (116 bp):
AATTATATTCTTTCCAAAAGAATATTAATTTCCAAGTCTTTTATATTTTAACCGAAATTAATTAA
TAAAACAATTTATATTAATAAATTTGATAAAATATATACAATTAATATCTT
Found at i:39554552 original size:136 final size:135
Alignment explanation
Indices: 39554295--39554581 Score: 429
Period size: 136 Copynumber: 2.1 Consensus size: 135
39554285 TATAATATTA
* *
39554295 ATATCTTAATTATATTCTTTCCAAACAAATATTAATTTCCATATCTTTATATTTTAACTGAAATT
1 ATATATTAATTATATTCTTTCCAAACAAATATTAATTTCCATATCTTTATATTTTAACCGAAATT
*
39554360 AATTAATAAAACAATTTATATTAATAAATTTGGTAAAATATATACAATTAATATTTTGTATGAAT
66 AATTAAT-AAACAATTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAAT
39554425 CAAATTC
130 CAAA-TC
* *
39554432 ATATATTAATTATATTCTTTCCAAA-AGAATATTAATTTCCATGTCTTTTATATTTTGACCGAAA
1 ATATATTAATTATATTCTTTCCAAACA-AATATTAATTTCCATATC-TTTATATTTTAACCGAAA
**
39554496 TTAA-T-AT-AACTGTTTATATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATG
64 TTAATTAATAAAC-AATT-TATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATG
39554558 AATCAAATC
127 AATCAAATC
39554567 ATATATTAATTATAT
1 ATATATTAATTATAT
39554582 CTATGTTTTC
Statistics
Matches: 139, Mismatches: 7, Indels: 10
0.89 0.04 0.06
Matches are distributed among these distances:
134 3 0.02
135 19 0.14
136 55 0.40
137 42 0.30
138 20 0.14
ACGTcount: A:0.42, C:0.09, G:0.05, T:0.44
Consensus pattern (135 bp):
ATATATTAATTATATTCTTTCCAAACAAATATTAATTTCCATATCTTTATATTTTAACCGAAATT
AATTAATAAACAATTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATC
AAATC
Found at i:39557305 original size:25 final size:25
Alignment explanation
Indices: 39557277--39557360 Score: 73
Period size: 25 Copynumber: 3.4 Consensus size: 25
39557267 TATGCTAATA
39557277 CGAGCTATGAATCGGTATGCTCACT
1 CGAGCTATGAATCGGTATGCTCACT
* ** * *
39557302 CGAGCTGT-AGATCTATATGCTCTCA
1 CGAGCTATGA-ATCGGTATGCTCACT
* *
39557327 CGAGCTATAAATTGGTATGCTCACAT
1 CGAGCTATGAATCGGTATGCTCAC-T
39557353 -GAGCTATG
1 CGAGCTATG
39557361 GGTTGGAACG
Statistics
Matches: 44, Mismatches: 12, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
24 1 0.02
25 42 0.95
26 1 0.02
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (25 bp):
CGAGCTATGAATCGGTATGCTCACT
Found at i:39558981 original size:51 final size:50
Alignment explanation
Indices: 39558862--39559005 Score: 162
Period size: 51 Copynumber: 2.9 Consensus size: 50
39558852 CGAAACACCA
* * * *
39558862 TTTGTGGACAAGCCACCACTAATTTGCGGATAAACTGCCACTGATAACAC
1 TTTGTGGACAAGCCACCACTGATTTGCAGATATACTACCACTGATAACAC
* * * * * * * *
39558912 ATTGTGGACAAACGACCACTGGTATACAGATATACTACCACTGATATATAT
1 TTTGTGGACAAGCCACCACTGATTTGCAGATATACTACCACTGATA-ACAC
*
39558963 TTTGTGGACAAGCCACCACTGATTTGTAGATATACTACCACTG
1 TTTGTGGACAAGCCACCACTGATTTGCAGATATACTACCACTG
39559006 CTTTCACCTT
Statistics
Matches: 74, Mismatches: 19, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
50 36 0.49
51 38 0.51
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27
Consensus pattern (50 bp):
TTTGTGGACAAGCCACCACTGATTTGCAGATATACTACCACTGATAACAC
Done.