Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr3
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: 26558743
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1281270 characters in sequence are not A, C, G, or T
File 13 of 79
Found at i:4424136 original size:95 final size:97
Alignment explanation
Indices: 4424007--4424205 Score: 240
Period size: 96 Copynumber: 2.1 Consensus size: 97
4423997 TTTGACACGA
* * * * ** *
4424007 AAAAAAAAATTAAATTGTACTGGGTGCCGACCATTGACAGGCTAGCACC-TCAAAAATTTTTTTT
1 AAAAAAAAATTAAATTGTACTAGGTGCCGACCATTGACAGACCAACACCAAAAAAAATATTTTTT
* *
4424071 ATTTTTTTCGTATTCTAATACCTGATTCTGAC
66 ACTTGTTTCGTATTCTAATACCTGATTCTGAC
* * *
4424103 AAAAAACAATT-AATTGTACTAGGTGTCGGCCATTGACAGACCAACACCAAAAAAAATATTTTTT
1 AAAAAAAAATTAAATTGTACTAGGTGCCGACCATTGACAGACCAACACCAAAAAAAATATTTTTT
* **
4424167 ACTTGTTTCGTATTCTGATATTTGATTCTGAC
66 ACTTGTTTCGTATTCTAATACCTGATTCTGAC
*
4424199 AAGAAAA
1 AAAAAAA
4424206 TTTTTTATTT
Statistics
Matches: 85, Mismatches: 17, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
95 31 0.36
96 54 0.64
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.34
Consensus pattern (97 bp):
AAAAAAAAATTAAATTGTACTAGGTGCCGACCATTGACAGACCAACACCAAAAAAAATATTTTTT
ACTTGTTTCGTATTCTAATACCTGATTCTGAC
Found at i:4424221 original size:44 final size:45
Alignment explanation
Indices: 4424153--4424249 Score: 126
Period size: 44 Copynumber: 2.2 Consensus size: 45
4424143 CCAACACCAA
* *
4424153 AAAAAATATTTTTTACTTGTTTCGTAT-TCTGATATTTGATTCTGAC
1 AAAAAA-ATTTTTTACTTGTTTCGTATAT-TGATATCTAATTCTGAC
* *
4424199 AAGAAAATTTTTTA-TTTTTTCGTATATTGATATCTAATTCTGAC
1 AAAAAAATTTTTTACTTGTTTCGTATATTGATATCTAATTCTGAC
4424243 AAAAAAA
1 AAAAAAA
4424250 AAATTTTTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
44 31 0.69
45 9 0.20
46 5 0.11
ACGTcount: A:0.35, C:0.09, G:0.09, T:0.46
Consensus pattern (45 bp):
AAAAAAATTTTTTACTTGTTTCGTATATTGATATCTAATTCTGAC
Found at i:4426744 original size:17 final size:17
Alignment explanation
Indices: 4426722--4426777 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
4426712 GTTTCTTACG
4426722 TATTTGTTTTGTATATA
1 TATTTGTTTTGTATATA
*
4426739 TATTTGCTATTTTGT-TACA
1 TATTTG---TTTTGTATATA
*
4426758 TTTTTGTTTTGTATATA
1 TATTTGTTTTGTATATA
4426775 TAT
1 TAT
4426778 ATATCTGATT
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
16 6 0.19
17 11 0.35
19 8 0.26
20 6 0.19
ACGTcount: A:0.21, C:0.04, G:0.11, T:0.64
Consensus pattern (17 bp):
TATTTGTTTTGTATATA
Found at i:4427094 original size:39 final size:39
Alignment explanation
Indices: 4427002--4427094 Score: 100
Period size: 39 Copynumber: 2.4 Consensus size: 39
4426992 GTGACACAGG
* *
4427002 TTTAGCTCGGACGAGTAACCTGATGTGCCATTATAAAGG
1 TTTAGCTCGGACGAGTAACCTGATATGCCATTATAAAGA
* * *
4427041 TTTATC-CTGGACGAGTAACCTGATATG-CATATATATATA
1 TTTAGCTC-GGACGAGTAACCTGATATGCCAT-TATAAAGA
*
4427080 TTTAGCTCGAACGAG
1 TTTAGCTCGGACGAG
4427095 CAACTGGTGT
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
38 4 0.09
39 39 0.89
40 1 0.02
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Consensus pattern (39 bp):
TTTAGCTCGGACGAGTAACCTGATATGCCATTATAAAGA
Found at i:4429917 original size:109 final size:109
Alignment explanation
Indices: 4429728--4430060 Score: 508
Period size: 109 Copynumber: 3.1 Consensus size: 109
4429718 AAGATATAAG
* * * *
4429728 AGGATATTTGACTATGTGGTCCAACGAG--AAATCGAAACCCAGCACATTAGGGCACGTTTTCTC
1 AGGATATTCGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTC
*
4429791 GAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATTTTTAAA
66 GAATTTCCAAAAGCAAAACATTGCCTTATTTTGAAATTTTTAAA
* *
4429835 AGGATATTCGGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCATGTTTTCTC
1 AGGATATTCGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTC
* *
4429900 GAATTTCCAAAAGCAAAATATTGCCTTATTTTAAAATTTTTAAA
66 GAATTTCCAAAAGCAAAACATTGCCTTATTTTGAAATTTTTAAA
* *
4429944 AGGATATTTGGCTATTTGGTCGCACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTC
1 AGGATATTCGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTC
* * * **
4430009 GAATTTCCAAATGCAAAACATTACCTTACTTTGAAATTTTTTTA
66 GAATTTCCAAAAGCAAAACATTGCCTTATTTTGAAATTTTTAAA
4430053 AGGATATT
1 AGGATATT
4430061 AATATGCATA
Statistics
Matches: 204, Mismatches: 20, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
107 23 0.11
109 181 0.89
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Consensus pattern (109 bp):
AGGATATTCGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTC
GAATTTCCAAAAGCAAAACATTGCCTTATTTTGAAATTTTTAAA
Found at i:4430691 original size:16 final size:16
Alignment explanation
Indices: 4430672--4430702 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4430662 ATGAATAAAC
4430672 AATAACAATAATAATT
1 AATAACAATAATAATT
*
4430688 AATAATAATAATAAT
1 AATAACAATAATAAT
4430703 AGTATTAGAT
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:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (16 bp):
AATAACAATAATAATT
Found at i:4432232 original size:44 final size:42
Alignment explanation
Indices: 4432179--4432432 Score: 165
Period size: 44 Copynumber: 5.9 Consensus size: 42
4432169 TCCTCGTTTT
* * *
4432179 AATCCGCTCCACTGCAACTTTAGGGAGATAGGATTAGTAGCATC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATT-GT-GCATC
* * *
4432223 AGTCTGCTCCATTGCAACTTCAGGGAGATAAGACTG-G-ATGC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGTGCAT-C
* * * * *
4432264 AATCTGCTCTATTGCAACTTCAGAGAGATAAGATCTGTGGCTTTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGAT-TGT-GC-ATC
* * * * *
4432309 AATCCGCTCCACTGCAATTTCAGGGAGATAGGATTGGTTTCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATT-G-TGCATC
** * *
4432353 TGTCTGCTCCACTGTAACTTCAGGGAGATAAGACTG-G-ATGC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGTGCAT-C
* * * **
4432394 GATCTGCTCTATTGCAACTTCAAAGAGATAAGATCTGTG
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGAT-TGTG
4432433 ATTTTTTTTT
Statistics
Matches: 162, Mismatches: 37, Indels: 23
0.73 0.17 0.10
Matches are distributed among these distances:
40 3 0.02
41 59 0.36
42 4 0.02
43 3 0.02
44 61 0.38
45 30 0.19
46 2 0.01
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.29
Consensus pattern (42 bp):
AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGTGCATC
Found at i:4432282 original size:41 final size:41
Alignment explanation
Indices: 4432225--4432426 Score: 154
Period size: 41 Copynumber: 4.8 Consensus size: 41
4432215 GTAGCATCAG
*
4432225 TCTGCTCCATTGCAACTTCAGGGAGATAAGACTGGATGCAA
1 TCTGCTCTATTGCAACTTCAGGGAGATAAGACTGGATGCAA
* * **
4432266 TCTGCTCTATTGCAACTTCAGAGAGATAAGATCTGTGGCTTTTAA
1 TCTGCTCTATTGCAACTTCAGGGAGATAAGA-C--TGG-ATGCAA
* * * * * * * * *
4432311 TCCGCTCCACTGCAATTTCAGGGAGATAGGATTGGTTTC-T
1 TCTGCTCTATTGCAACTTCAGGGAGATAAGACTGGATGCAA
* * *
4432351 TCTGTCTGCTCCACTGTAACTTCAGGGAGATAAGACTGGATGCGA
1 TCTG-CT-CT--ATTGCAACTTCAGGGAGATAAGACTGGATGCAA
**
4432396 TCTGCTCTATTGCAACTTCAAAGAGATAAGA
1 TCTGCTCTATTGCAACTTCAGGGAGATAAGA
4432427 TCTGTGATTT
Statistics
Matches: 125, Mismatches: 27, Indels: 18
0.74 0.16 0.11
Matches are distributed among these distances:
40 3 0.02
41 53 0.42
42 5 0.04
43 2 0.02
44 30 0.24
45 32 0.26
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.30
Consensus pattern (41 bp):
TCTGCTCTATTGCAACTTCAGGGAGATAAGACTGGATGCAA
Found at i:4432408 original size:130 final size:130
Alignment explanation
Indices: 4432175--4432432 Score: 419
Period size: 130 Copynumber: 2.0 Consensus size: 130
4432165 GGGTTCCTCG
*
4432175 TTTTAATCCGCTCCACTGCAACTTTAGGGAGATAGGATTAGTAGCATCAGTCTGCTCCATTGCAA
1 TTTTAATCCGCTCCACTGCAACTTTAGGGAGATAGGATTAGTAGCATCAGTCTGCTCCACTGCAA
*
4432240 CTTCAGGGAGATAAGACTGGATGCAATCTGCTCTATTGCAACTTCAGAGAGATAAGATCTGTGGC
66 CTTCAGGGAGATAAGACTGGATGCAATCTGCTCTATTGCAACTTCAAAGAGATAAGATCTGTGGC
* ** * * *
4432305 TTTTAATCCGCTCCACTGCAA-TTTCAGGGAGATAGGATTGGTTTCTTCTGTCTGCTCCACTGTA
1 TTTTAATCCGCTCCACTGCAACTTT-AGGGAGATAGGATTAGTAGCATCAGTCTGCTCCACTGCA
*
4432369 ACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTATTGCAACTTCAAAGAGATAAGATCTGTG
65 ACTTCAGGGAGATAAGACTGGATGCAATCTGCTCTATTGCAACTTCAAAGAGATAAGATCTGTG
4432433 ATTTTTTTTT
Statistics
Matches: 118, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
129 3 0.03
130 115 0.97
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (130 bp):
TTTTAATCCGCTCCACTGCAACTTTAGGGAGATAGGATTAGTAGCATCAGTCTGCTCCACTGCAA
CTTCAGGGAGATAAGACTGGATGCAATCTGCTCTATTGCAACTTCAAAGAGATAAGATCTGTGGC
Found at i:4442775 original size:16 final size:16
Alignment explanation
Indices: 4442743--4442776 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
4442733 TTTATGATGT
* *
4442743 AATGCCATGTAGTCAA
1 AATGCCATGCAGCCAA
4442759 AATGCCATGCAGCCAA
1 AATGCCATGCAGCCAA
4442775 AA
1 AA
4442777 CAAAACACCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.41, C:0.24, G:0.18, T:0.18
Consensus pattern (16 bp):
AATGCCATGCAGCCAA
Found at i:4443885 original size:109 final size:109
Alignment explanation
Indices: 4443696--4444028 Score: 481
Period size: 109 Copynumber: 3.1 Consensus size: 109
4443686 AAGATATAAG
* * * *
4443696 AGGATATTTGGCTATTTGGTCCAACGAG--AAATCAAAACTCAGCACATTAGGGTACGTTTTCTC
1 AGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTC
* *
4443759 GAATTTTCAAATGCAAAACATTGCCTTATTTTGAAATTTTTAAA
66 GAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATTTTTAAA
* * * *
4443803 AGGATATTCGGCTATTTAGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCATGTTTTCTC
1 AGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTC
* * *
4443868 AAATTTCCAAACGCAAAATATTGCCTTATTTTAAAATTTTTAAA
66 GAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATTTTTAAA
* * *
4443912 AGGATATTTGACAATTTGGTCGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTT
1 AGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTC
* **
4443977 GAATTTCCAAACGCAAAACATTGCCTTACTTTGAAATTTTTTTA
66 GAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATTTTTAAA
4444021 AGGATATT
1 AGGATATT
4444029 AATATGCATA
Statistics
Matches: 198, Mismatches: 26, Indels: 2
0.88 0.12 0.01
Matches are distributed among these distances:
107 24 0.12
109 174 0.88
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.33
Consensus pattern (109 bp):
AGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTC
GAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATTTTTAAA
Found at i:4446376 original size:31 final size:31
Alignment explanation
Indices: 4446338--4446400 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
4446328 AACAGCCCCT
4446338 GCGTGGCACAAAAATCTGATGTAAATATATA
1 GCGTGGCACAAAAATCTGATGTAAATATATA
4446369 GCGTGGCACAAAAATCTGATGTAAATATATA
1 GCGTGGCACAAAAATCTGATGTAAATATATA
4446400 G
1 G
4446401 TTATTTACAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.41, C:0.13, G:0.21, T:0.25
Consensus pattern (31 bp):
GCGTGGCACAAAAATCTGATGTAAATATATA
Found at i:4447661 original size:68 final size:69
Alignment explanation
Indices: 4447501--4447729 Score: 233
Period size: 64 Copynumber: 3.3 Consensus size: 69
4447491 TGTATGATAC
* * * * *
4447501 AAGTTCTTTGAGCTGAACTTAATATTATGAATTATATATATATATGCACATATGGTTCGAATATA
1 AAGTTCTTTGAGCTGAATTTAAT-GTATGAATTTTATATATATAT--ATATGTGGTTC-AA-ATA
*
4447566 TATA-TT-TA
61 TA-AGTTACA
*
4447574 AAGTTC-TTGAGCTGAATTTAATGTATGAATTTTATATATATATATATGTGGTTCAAATATAGGT
1 AAGTTCTTTGAGCTGAATTTAATGTATGAATTTTATATATATATATATGTGGTTCAAATATAAGT
4447638 TACA
66 TACA
* * *
4447642 AAGTTC-TTGAGCTGAATTTAATGTATGAA--TT-T-TACATACATATGTGGTTCGAATATAAGT
1 AAGTTCTTTGAGCTGAATTTAATGTATGAATTTTATATATATATATATGTGGTTCAAATATAAGT
4447702 TACA
66 TACA
*
4447706 AA-TTCTTTGAACTGAATTTTAATG
1 AAGTTCTTTGAGCTGAA-TTTAATG
4447730 CTGTAAATTA
Statistics
Matches: 140, Mismatches: 12, Indels: 16
0.83 0.07 0.10
Matches are distributed among these distances:
63 3 0.02
64 39 0.28
65 8 0.06
66 2 0.01
67 7 0.05
68 32 0.23
69 9 0.06
71 19 0.14
72 15 0.11
73 6 0.04
ACGTcount: A:0.35, C:0.08, G:0.15, T:0.42
Consensus pattern (69 bp):
AAGTTCTTTGAGCTGAATTTAATGTATGAATTTTATATATATATATATGTGGTTCAAATATAAGT
TACA
Found at i:4447721 original size:64 final size:63
Alignment explanation
Indices: 4447573--4447757 Score: 207
Period size: 64 Copynumber: 2.9 Consensus size: 63
4447563 ATATATATTT
* * *
4447573 AAAGTTCTTGAGCTGAATTTAATGTATGAATTTTATATATATATATATGTGGTTCAAATATAGGT
1 AAAGTTCTTGAGCTGAATTTAATGTATGAA--TT-T-TA-ATACATATGTGGTTCGAATATAAGT
4447638 TAC
61 TAC
4447641 AAAGTTCTTGAGCTGAATTTAATGTATGAATTTTACATACATATGTGGTTCGAATATAAGTTAC
1 AAAGTTCTTGAGCTGAATTTAATGTATGAATTTTA-ATACATATGTGGTTCGAATATAAGTTAC
* * *
4447705 AAA-TTCTTTGAACTGAATTTTAATG-CTGTAA-ATT-ATACATATGTGGTTCGAAT
1 AAAGTTC-TTGAGCTGAA-TTTAATGTATG-AATTTTAATACATATGTGGTTCGAAT
4447758 GTTTGTTTGC
Statistics
Matches: 107, Mismatches: 7, Indels: 12
0.85 0.06 0.10
Matches are distributed among these distances:
62 19 0.18
63 3 0.03
64 43 0.40
65 10 0.09
66 2 0.02
68 30 0.28
ACGTcount: A:0.35, C:0.08, G:0.16, T:0.41
Consensus pattern (63 bp):
AAAGTTCTTGAGCTGAATTTAATGTATGAATTTTAATACATATGTGGTTCGAATATAAGTTAC
Found at i:4449395 original size:91 final size:90
Alignment explanation
Indices: 4449220--4449395 Score: 237
Period size: 91 Copynumber: 1.9 Consensus size: 90
4449210 ATATTTTTTC
* * ***
4449220 AAAAAAGAGATTCGAGTTCTAAAATTAAATAATTAAAAATGTTGAAATGGCCTCGACAGAAATCT
1 AAAAAAGAGATTCAAGTTCTAAAATCAAATAATTAAAAATGTTGAAACAACCTCGACAGAAATCT
* *
4449285 CGAAGCTCTCTTATATTTTTTTTAA
66 CGAAGCTCACTCATATTTTTTTTAA
* * *
4449310 AAAAAAGAGATTCAAGTTTTAAAATCAAATAAATTGAAAATGTTGAAACAACCTCGACTGAAATC
1 AAAAAAGAGATTCAAGTTCTAAAATCAAAT-AATTAAAAATGTTGAAACAACCTCGACAGAAATC
4449375 TCGAAGCTCAACTCAT-TTTTT
65 TCGAAGCTC-ACTCATATTTTT
4449396 AGAAAATGAA
Statistics
Matches: 74, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
90 27 0.36
91 43 0.58
92 4 0.05
ACGTcount: A:0.43, C:0.14, G:0.12, T:0.31
Consensus pattern (90 bp):
AAAAAAGAGATTCAAGTTCTAAAATCAAATAATTAAAAATGTTGAAACAACCTCGACAGAAATCT
CGAAGCTCACTCATATTTTTTTTAA
Found at i:4451069 original size:21 final size:21
Alignment explanation
Indices: 4451043--4451098 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
4451033 AACAGCGGTG
*
4451043 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGATACTGTA
*
4451064 GCGGTGAGATTGGATACTGTA
1 GCGGTGAGATTAGATACTGTA
*
4451085 GCAGTGAGATTAGA
1 GCGGTGAGATTAGA
4451099 AACAGCGGTG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.27, C:0.09, G:0.36, T:0.29
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTGTA
Found at i:4453994 original size:25 final size:25
Alignment explanation
Indices: 4453966--4454017 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
4453956 GAATATGCTG
4453966 AGAAAAGAAG-ATGAAGAACGGAAGA
1 AGAAAA-AAGAATGAAGAACGGAAGA
*
4453991 AGAAAAAGGAATGAAGAACGGAAGA
1 AGAAAAAAGAATGAAGAACGGAAGA
4454016 AG
1 AG
4454018 GAGAAGGAGC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 2 0.08
25 23 0.92
ACGTcount: A:0.60, C:0.04, G:0.33, T:0.04
Consensus pattern (25 bp):
AGAAAAAAGAATGAAGAACGGAAGA
Found at i:4454108 original size:18 final size:18
Alignment explanation
Indices: 4454085--4454120 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
4454075 TTTGCAACCC
4454085 AAGGGGAAGGCGAAAGGG
1 AAGGGGAAGGCGAAAGGG
*
4454103 AAGGGGAAGGGGAAAGGG
1 AAGGGGAAGGCGAAAGGG
4454121 GAGAAGAAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.39, C:0.03, G:0.58, T:0.00
Consensus pattern (18 bp):
AAGGGGAAGGCGAAAGGG
Found at i:4455572 original size:19 final size:19
Alignment explanation
Indices: 4455548--4455660 Score: 172
Period size: 19 Copynumber: 5.8 Consensus size: 19
4455538 AATTTTTGAG
4455548 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
**
4455567 GATATGCAATCCAAGATAT
1 GATATGCAATCTTAGATAT
4455586 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
4455607 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
**
4455626 GATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
4455645 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
4455661 ATATATGATT
Statistics
Matches: 84, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
19 67 0.80
21 17 0.20
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.35
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:4455593 original size:40 final size:40
Alignment explanation
Indices: 4455549--4455655 Score: 182
Period size: 40 Copynumber: 2.7 Consensus size: 40
4455539 ATTTTTGAGG
4455549 ATATGCAATCTTAGATATGATATGCAATCCAAGATATGAT
1 ATATGCAATCTTAGATATGATATGCAATCCAAGATATGAT
**
4455589 ATATGCAATCTTAGATATGATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGATATGCAATCCAAGATATGAT
4455629 ATAT--AATCTTAGATATGATATGCAATC
1 ATATGCAATCTTAGATATGATATGCAATC
4455656 TTAGAATATA
Statistics
Matches: 65, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
38 23 0.35
40 42 0.65
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (40 bp):
ATATGCAATCTTAGATATGATATGCAATCCAAGATATGAT
Found at i:4455615 original size:59 final size:56
Alignment explanation
Indices: 4455548--4455667 Score: 170
Period size: 59 Copynumber: 2.1 Consensus size: 56
4455538 AATTTTTGAG
*
4455548 GATATGCAATCTTAGATATGATATGCAATCCAAGATATGATATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATATGATATACAATCCAAGATATG--ATATGCAATCTTAGA-AT
* **
4455607 GATATGCAATCTTAGATATGATATATAATCTTAGATATGATATGCAATCTTAGAAT
1 GATATGCAATCTTAGATATGATATACAATCCAAGATATGATATGCAATCTTAGAAT
4455663 -ATATG
1 GATATG
4455668 ATTTTGTAAT
Statistics
Matches: 57, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
55 5 0.09
56 2 0.04
57 15 0.26
59 35 0.61
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (56 bp):
GATATGCAATCTTAGATATGATATACAATCCAAGATATGATATGCAATCTTAGAAT
Found at i:4469257 original size:1 final size:1
Alignment explanation
Indices: 4469251--4469284 Score: 50
Period size: 1 Copynumber: 34.0 Consensus size: 1
4469241 TGTTTAATTC
* *
4469251 TTTTTTTTTCTTTTTTTTCTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
4469285 GCATGCACCT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.06, G:0.00, T:0.94
Consensus pattern (1 bp):
T
Found at i:4469263 original size:10 final size:10
Alignment explanation
Indices: 4469248--4469284 Score: 60
Period size: 9 Copynumber: 3.9 Consensus size: 10
4469238 TGCTGTTTAA
4469248 TTCTTTTTTT
1 TTCTTTTTTT
4469258 TTC-TTTTTT
1 TTCTTTTTTT
4469267 TTCTTTTTTT
1 TTCTTTTTTT
4469277 TT-TTTTTT
1 TTCTTTTTT
4469285 GCATGCACCT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
9 15 0.58
10 11 0.42
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (10 bp):
TTCTTTTTTT
Found at i:4469270 original size:19 final size:18
Alignment explanation
Indices: 4469248--4469284 Score: 65
Period size: 19 Copynumber: 2.0 Consensus size: 18
4469238 TGCTGTTTAA
4469248 TTCTTTTTTTTTCTTTTTT
1 TTCTTTTTTTTT-TTTTTT
4469267 TTCTTTTTTTTTTTTTTT
1 TTCTTTTTTTTTTTTTTT
4469285 GCATGCACCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (18 bp):
TTCTTTTTTTTTTTTTTT
Found at i:4469612 original size:22 final size:22
Alignment explanation
Indices: 4469577--4469622 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
4469567 CAAATTCCAA
4469577 TCAAGTTTCAAAAGTCCAAA-AT
1 TCAAGTTTCAAAAGT-CAAATAT
4469599 TCAA-TTTCACAAAGTCAAATAT
1 TCAAGTTTCA-AAAGTCAAATAT
4469621 TC
1 TC
4469623 TAGTCTAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.43, C:0.20, G:0.07, T:0.30
Consensus pattern (22 bp):
TCAAGTTTCAAAAGTCAAATAT
Found at i:4473025 original size:15 final size:15
Alignment explanation
Indices: 4473005--4473035 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
4472995 AAAATAAAGC
4473005 AAATAATAGGCTGTT
1 AAATAATAGGCTGTT
4473020 AAATAATAGGCTGTT
1 AAATAATAGGCTGTT
4473035 A
1 A
4473036 TGAAACAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.42, C:0.06, G:0.19, T:0.32
Consensus pattern (15 bp):
AAATAATAGGCTGTT
Found at i:4475236 original size:35 final size:36
Alignment explanation
Indices: 4475181--4475249 Score: 131
Period size: 35 Copynumber: 1.9 Consensus size: 36
4475171 AATTGAGAAA
4475181 AAAAATCAATGTTTAAATCGGTTTACAATTTTTTTT
1 AAAAATCAATGTTTAAATCGGTTTACAATTTTTTTT
4475217 AAAAATCAAT-TTTAAATCGGTTTACAATTTTTT
1 AAAAATCAATGTTTAAATCGGTTTACAATTTTTT
4475250 AGGCTTAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 23 0.70
36 10 0.30
ACGTcount: A:0.38, C:0.09, G:0.07, T:0.46
Consensus pattern (36 bp):
AAAAATCAATGTTTAAATCGGTTTACAATTTTTTTT
Found at i:4475480 original size:16 final size:16
Alignment explanation
Indices: 4475459--4475501 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
4475449 GTCTTTAATT
4475459 ATTTTAAGAAATTA-AA
1 ATTTTAA-AAATTATAA
*
4475475 ATTTTAAATATATATAA
1 ATTTTAAAAAT-TATAA
4475492 ATTTTAAAAA
1 ATTTTAAAAA
4475502 ATTTTGAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 3 0.13
16 9 0.39
17 11 0.48
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (16 bp):
ATTTTAAAAATTATAA
Found at i:4476493 original size:18 final size:19
Alignment explanation
Indices: 4476470--4476515 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 19
4476460 AACTCTTTTT
4476470 ATTCTCTCTAAA-CTC-CAA
1 ATTCTCTC-AAATCTCTCAA
4476488 ATTCTCTCAAATCTCTCAA
1 ATTCTCTCAAATCTCTCAA
4476507 ATT-TCTCAA
1 ATTCTCTCAA
4476516 TTTTTGTTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
17 3 0.12
18 17 0.65
19 6 0.23
ACGTcount: A:0.33, C:0.30, G:0.00, T:0.37
Consensus pattern (19 bp):
ATTCTCTCAAATCTCTCAA
Found at i:4480306 original size:50 final size:50
Alignment explanation
Indices: 4480203--4480395 Score: 242
Period size: 50 Copynumber: 3.7 Consensus size: 50
4480193 GGGAATGAGA
4480203 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATC---GAG---ATGAGAGG
*
4480259 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCATCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGAGATGAGAGG
** * * * **
4480309 TCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGAGATGAGAGG
* *
4480359 TCCCATGTAAGACCATATCTGGGATATGGCATTGGCA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
4480396 ATACAGAAAA
Statistics
Matches: 123, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
50 82 0.67
53 3 0.02
56 38 0.31
ACGTcount: A:0.26, C:0.22, G:0.29, T:0.23
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGAGATGAGAGG
Found at i:4487281 original size:31 final size:31
Alignment explanation
Indices: 4487246--4487308 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
4487236 ACATGCCAAA
4487246 GCCATGTCCTAGACATGGTCTTACATGGGGT
1 GCCATGTCCTAGACATGGTCTTACATGGGGT
4487277 GCCATGTCCTAGACATGGTCTTACATGGGGT
1 GCCATGTCCTAGACATGGTCTTACATGGGGT
4487308 G
1 G
4487309 TTCTCATATC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.19, C:0.22, G:0.30, T:0.29
Consensus pattern (31 bp):
GCCATGTCCTAGACATGGTCTTACATGGGGT
Found at i:4487388 original size:50 final size:50
Alignment explanation
Indices: 4487276--4487462 Score: 239
Period size: 50 Copynumber: 3.7 Consensus size: 50
4487266 TTACATGGGG
* *** * * *
4487276 TGCCATGTCCTAGACATGGTCTTACATGGGGTGTTCTCATATCGGTGCCCA
1 TGCCATGTCCCAGACATGGTCTTACAT-GGGACCTCTAATCTCGGTGCCAA
* * **
4487327 TGCCATATCCCAGATATGGTCTTACGGGGGACCTCTAATCTCGGTGCCAA
1 TGCCATGTCCCAGACATGGTCTTACATGGGACCTCTAATCTCGGTGCCAA
* * *
4487377 CGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTTGGTGCCAA
1 TGCCATGTCCCAGACATGGTCTTACATGGGACCTCTAATCTCGGTGCCAA
4487427 TGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
1 TGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
4487463 TTACCCAAAT
Statistics
Matches: 117, Mismatches: 19, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
50 95 0.81
51 22 0.19
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.28
Consensus pattern (50 bp):
TGCCATGTCCCAGACATGGTCTTACATGGGACCTCTAATCTCGGTGCCAA
Found at i:4487451 original size:100 final size:101
Alignment explanation
Indices: 4487277--4487462 Score: 266
Period size: 100 Copynumber: 1.9 Consensus size: 101
4487267 TACATGGGGT
* *** * *
4487277 GCCATGTCCTAGACATGGTCTTACATGGGGTGTTCTCATATCGGTGCCCATGCCATATCCCAGAT
1 GCCATGTCCCAGACATGGTCTTACATGGGGACCTCTCATATCGGTGCCAATGCCATATCCCAGAC
*
4487342 ATGGTCTTACGGGGGACCTCTAATCTCGGTGCCAAC
66 ATGGTCTTACAGGGGACCTCTAATCTCGGTGCCAAC
* * *
4487378 GCCATGTCCCAGACATGGTCTTACAT-GGGACCTCTCATCTTGGTGCCAATGCCATGTCCCAGAC
1 GCCATGTCCCAGACATGGTCTTACATGGGGACCTCTCATATCGGTGCCAATGCCATATCCCAGAC
*
4487442 ATGGTCTTACATGGGACCTCT
66 ATGGTCTTACAGGGGACCTCT
4487463 TTACCCAAAT
Statistics
Matches: 74, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
100 49 0.66
101 25 0.34
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.27
Consensus pattern (101 bp):
GCCATGTCCCAGACATGGTCTTACATGGGGACCTCTCATATCGGTGCCAATGCCATATCCCAGAC
ATGGTCTTACAGGGGACCTCTAATCTCGGTGCCAAC
Found at i:4501823 original size:87 final size:88
Alignment explanation
Indices: 4501714--4501895 Score: 348
Period size: 87 Copynumber: 2.1 Consensus size: 88
4501704 GTTAATTTCA
4501714 GTAAATGTGATCTCAAACTTTGAAATATTTTAATTAAAATTTTAAAATATTAGTTTTGTATTATT
1 GTAAATGTGATCTCAAACTTTGAAATATTTTAATTAAAATTTTAAAATATTAGTTTTGTATTATT
4501779 AGTTTTTTTTTGTTAATTTAGAT
66 AGTTTTTTTTTGTTAATTTAGAT
4501802 GTAAATGTGAT-TCAAACTTTGAAATATTTTAATTAAAATTTTAAAATATTAGTTTTGTATTATT
1 GTAAATGTGATCTCAAACTTTGAAATATTTTAATTAAAATTTTAAAATATTAGTTTTGTATTATT
4501866 AGTTTTTTTTTGTTAATTTAGAT
66 AGTTTTTTTTTGTTAATTTAGAT
4501889 GCTAAAT
1 G-TAAAT
4501896 ACTAATTTAT
Statistics
Matches: 93, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
87 77 0.83
88 16 0.17
ACGTcount: A:0.35, C:0.03, G:0.10, T:0.52
Consensus pattern (88 bp):
GTAAATGTGATCTCAAACTTTGAAATATTTTAATTAAAATTTTAAAATATTAGTTTTGTATTATT
AGTTTTTTTTTGTTAATTTAGAT
Found at i:4503252 original size:31 final size:31
Alignment explanation
Indices: 4503179--4503252 Score: 94
Period size: 31 Copynumber: 2.4 Consensus size: 31
4503169 CAAACTGAAA
* * *
4503179 AAACTCAAGTACCAAAATAAATATCGAAGCT
1 AAACTCAAGTATCAAAATAAATATCAAAGCC
* *
4503210 AAACTCAAGTATCAAAGTAAATATTAAAGCC
1 AAACTCAAGTATCAAAATAAATATCAAAGCC
*
4503241 AAACTTAAGTAT
1 AAACTCAAGTAT
4503253 TAAATTAGAA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.51, C:0.16, G:0.09, T:0.23
Consensus pattern (31 bp):
AAACTCAAGTATCAAAATAAATATCAAAGCC
Found at i:4505681 original size:17 final size:17
Alignment explanation
Indices: 4505661--4505693 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
4505651 CTCTTTTTTT
*
4505661 TTTCTTTTAAATTATTG
1 TTTCATTTAAATTATTG
4505678 TTTCATTTAAATTATT
1 TTTCATTTAAATTATT
4505694 TGTCTCATCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.06, G:0.03, T:0.64
Consensus pattern (17 bp):
TTTCATTTAAATTATTG
Found at i:4505701 original size:18 final size:17
Alignment explanation
Indices: 4505666--4505701 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
4505656 TTTTTTTTCT
*
4505666 TTTAAATTATTGTTTCA
1 TTTAAATTATTGTCTCA
4505683 TTTAAATTATTTGTCTCA
1 TTTAAATTA-TTGTCTCA
4505701 T
1 T
4505702 CTCCACTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.28, C:0.08, G:0.06, T:0.58
Consensus pattern (17 bp):
TTTAAATTATTGTCTCA
Found at i:4505861 original size:12 final size:14
Alignment explanation
Indices: 4505832--4505860 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
4505822 CATGCATGAG
4505832 AAATATAAAGATAA
1 AAATATAAAGATAA
4505846 AAATA-AAAGATAA
1 AAATATAAAGATAA
4505859 AA
1 AA
4505861 TGGAGAGGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.17
Consensus pattern (14 bp):
AAATATAAAGATAA
Found at i:4506184 original size:129 final size:130
Alignment explanation
Indices: 4506016--4506274 Score: 511
Period size: 129 Copynumber: 2.0 Consensus size: 130
4506006 TTTTTATATT
4506016 AATATATTAAATGTTAATGGTATAATAAATTTTTTGGCCCTCAAATTTTACAAAAAAAAAATCAT
1 AATATATTAAATGTTAATGGTATAATAAATTTTTTGGCCCTCAAATTTTACAAAAAAAAAATCAT
4506081 TTTAGCCATTTGTTTAATTTTTTTTGCATCTTTTAGCTATTGAACTTGCATTATTTGTCAAATCA
66 TTTAGCCATTTGTTTAATTTTTTTTGCATCTTTTAGCTATTGAACTTGCATTATTTGTCAAATCA
4506146 AATATATT-AATGTTAATGGTATAATAAATTTTTTGGCCCTCAAATTTTACAAAAAAAAAATCAT
1 AATATATTAAATGTTAATGGTATAATAAATTTTTTGGCCCTCAAATTTTACAAAAAAAAAATCAT
4506210 TTTAGCCATTTGTTTAATTTTTTTTGCATCTTTTAGCTATTGAACTTGCATTATTTGTCAAATCA
66 TTTAGCCATTTGTTTAATTTTTTTTGCATCTTTTAGCTATTGAACTTGCATTATTTGTCAAATCA
4506275 CCCTAAAGTG
Statistics
Matches: 129, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
129 121 0.94
130 8 0.06
ACGTcount: A:0.34, C:0.12, G:0.09, T:0.45
Consensus pattern (130 bp):
AATATATTAAATGTTAATGGTATAATAAATTTTTTGGCCCTCAAATTTTACAAAAAAAAAATCAT
TTTAGCCATTTGTTTAATTTTTTTTGCATCTTTTAGCTATTGAACTTGCATTATTTGTCAAATCA
Found at i:4517589 original size:13 final size:12
Alignment explanation
Indices: 4517563--4517621 Score: 50
Period size: 12 Copynumber: 4.8 Consensus size: 12
4517553 AGGCAACCCA
4517563 ATTTTTATTTTT
1 ATTTTTATTTTT
*
4517575 ATTTTTGTTTATT
1 ATTTTTATTT-TT
*
4517588 ATTTATT-TATTT
1 ATTT-TTATTTTT
4517600 ATTTATTA-TTTT
1 ATTT-TTATTTTT
4517612 ATTATTTATT
1 ATT-TTTATT
4517622 ACTTATTTGG
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
12 27 0.69
13 10 0.26
14 2 0.05
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (12 bp):
ATTTTTATTTTT
Found at i:4517591 original size:19 final size:18
Alignment explanation
Indices: 4517563--4517621 Score: 66
Period size: 19 Copynumber: 3.2 Consensus size: 18
4517553 AGGCAACCCA
*
4517563 ATTT-TTATTTTTATTTTT
1 ATTTATTATTTTT-TATTT
*
4517581 GTTTATTATTTATTTATTT
1 ATTTATTATTT-TTTATTT
4517600 ATTTATTATTTTATTATTT
1 ATTTATTATTTT-TTATTT
4517619 ATT
1 ATT
4517622 ACTTATTTGG
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
18 4 0.11
19 29 0.83
20 2 0.06
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (18 bp):
ATTTATTATTTTTTATTT
Found at i:4517595 original size:4 final size:4
Alignment explanation
Indices: 4517582--4517621 Score: 50
Period size: 4 Copynumber: 10.5 Consensus size: 4
4517572 TTTATTTTTG
4517582 TTTA -TTA TTTA TTTA TTTA TTTA -TTA TTT- TATTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA T-TTA TTTA TT
4517622 ACTTATTTGG
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
3 7 0.22
4 24 0.75
5 1 0.03
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:4517599 original size:27 final size:27
Alignment explanation
Indices: 4517572--4517629 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 27
4517562 AATTTTTATT
4517572 TTTATTT-TT-GTTTATTATTTATTTA
1 TTTATTTATTAGTTTATTATTTATTTA
*
4517597 TTTATTTATTATTTTATTATTTA-TTA
1 TTTATTTATTAGTTTATTATTTATTTA
*
4517623 CTTATTT
1 TTTATTT
4517630 GGATATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 7 0.24
26 11 0.38
27 11 0.38
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.74
Consensus pattern (27 bp):
TTTATTTATTAGTTTATTATTTATTTA
Found at i:4517602 original size:15 final size:15
Alignment explanation
Indices: 4517572--4517629 Score: 59
Period size: 15 Copynumber: 3.9 Consensus size: 15
4517562 AATTTTTATT
*
4517572 TTTATT-TTTGTTTA
1 TTTATTATTTATTTA
4517586 -TTATTTATTTATTTA
1 TTTA-TTATTTATTTA
4517601 TTTATTATTT-TATTA
1 TTTATTATTTAT-TTA
*
4517616 TTTATTACTTATTT
1 TTTATTATTTATTT
4517630 GGATATTAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
13 3 0.08
14 3 0.08
15 27 0.73
16 4 0.11
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.74
Consensus pattern (15 bp):
TTTATTATTTATTTA
Found at i:4517622 original size:7 final size:7
Alignment explanation
Indices: 4517563--4517628 Score: 61
Period size: 7 Copynumber: 10.0 Consensus size: 7
4517553 AGGCAACCCA
4517563 ATTT-TT
1 ATTTATT
4517569 ATTT-TT
1 ATTTATT
4517575 ATTT-TT
1 ATTTATT
*
4517581 GTTTATT
1 ATTTATT
4517588 ATTTATT
1 ATTTATT
*
4517595 -TAT-TT
1 ATTTATT
4517600 ATTTATT
1 ATTTATT
4517607 ATTTTATT
1 A-TTTATT
4517615 ATTTATT
1 ATTTATT
*
4517622 ACTTATT
1 ATTTATT
4517629 TGGATATTAA
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
5 2 0.04
6 19 0.37
7 23 0.45
8 7 0.14
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.74
Consensus pattern (7 bp):
ATTTATT
Found at i:4517808 original size:22 final size:23
Alignment explanation
Indices: 4517780--4517830 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 23
4517770 AGAACGCCTC
* *
4517780 CAGCCAAACTACCC-TATTCCTG
1 CAGCCAAACCACCCTTATCCCTG
4517802 CAGCC-AACCACCCTTATCCCTG
1 CAGCCAAACCACCCTTATCCCTG
4517824 CAGCCAA
1 CAGCCAA
4517831 GCATCACCCC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 7 0.28
22 17 0.68
23 1 0.04
ACGTcount: A:0.27, C:0.45, G:0.10, T:0.18
Consensus pattern (23 bp):
CAGCCAAACCACCCTTATCCCTG
Found at i:4518935 original size:99 final size:100
Alignment explanation
Indices: 4518764--4518954 Score: 280
Period size: 99 Copynumber: 1.9 Consensus size: 100
4518754 TTTAAGAACA
*
4518764 TGTTGGGCTGAGTAACCGGGGTAAGGTGCTTGGCTGTCATCTCTCTTCGCGTCAAAAGGTTCGAT
1 TGTTGGGCTGAGTAACCGGGGTAAGGTACTTGGCTGTCATCTCTCTTCGCGTCAAAAGGTTCGAT
* *
4518829 GTGTTCCT-AAG-AAAAAAATAATAAATTAGGAGTC
66 ATATTCCTAAAGCAAAAAAAT-ATAAATTAGGAGTC
* **
4518863 TGTTGGGCTGAGTAATCGGGGTGGGGTACTTGGCTGTCATCTCTCTTCGCGTCAAAAGGTTC-AG
1 TGTTGGGCTGAGTAACCGGGGTAAGGTACTTGGCTGTCATCTCTCTTCGCGTCAAAAGGTTCGA-
*
4518927 TATATTCCTAAAGCATAAAAATATAAAT
65 TATATTCCTAAAGCAAAAAAATATAAAT
4518955 AATAAATAAA
Statistics
Matches: 82, Mismatches: 7, Indels: 5
0.87 0.07 0.05
Matches are distributed among these distances:
98 1 0.01
99 65 0.79
100 9 0.11
101 7 0.09
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.30
Consensus pattern (100 bp):
TGTTGGGCTGAGTAACCGGGGTAAGGTACTTGGCTGTCATCTCTCTTCGCGTCAAAAGGTTCGAT
ATATTCCTAAAGCAAAAAAATATAAATTAGGAGTC
Found at i:4518963 original size:19 final size:18
Alignment explanation
Indices: 4518941--4518982 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
4518931 TTCCTAAAGC
4518941 ATAAAAATATAAATAATAA
1 ATAAAAATATAAA-AATAA
*
4518960 AT--AAATATCAAAATAA
1 ATAAAAATATAAAAATAA
4518976 ATAAAAA
1 ATAAAAA
4518983 AGAAAAAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 5
0.77 0.04 0.19
Matches are distributed among these distances:
16 7 0.35
17 8 0.40
18 3 0.15
19 2 0.10
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (18 bp):
ATAAAAATATAAAAATAA
Found at i:4518976 original size:16 final size:17
Alignment explanation
Indices: 4518945--4518980 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
4518935 TAAAGCATAA
4518945 AAATATAAATAATAAAT
1 AAATATAAATAATAAAT
*
4518962 AAATATCAA-AATAAAT
1 AAATATAAATAATAAAT
4518978 AAA
1 AAA
4518981 AAAGAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (17 bp):
AAATATAAATAATAAAT
Found at i:4519586 original size:15 final size:15
Alignment explanation
Indices: 4519566--4519595 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
4519556 TATTTTAAAT
*
4519566 ATATTAGGATAATTA
1 ATATTAAGATAATTA
4519581 ATATTAAGATAATTA
1 ATATTAAGATAATTA
4519596 TTCAGGATTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (15 bp):
ATATTAAGATAATTA
Found at i:4521998 original size:5 final size:5
Alignment explanation
Indices: 4521988--4522012 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
4521978 TTTATAAAGC
4521988 TTATA TTATA TTATA TTATA TTATA
1 TTATA TTATA TTATA TTATA TTATA
4522013 AAGTTATTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TTATA
Found at i:4525707 original size:18 final size:18
Alignment explanation
Indices: 4525684--4525718 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
4525674 GTTGGTTTTC
*
4525684 AAAAATAGAAACGGAAAT
1 AAAAATAAAAACGGAAAT
*
4525702 AAAAATAAAAATGGAAA
1 AAAAATAAAAACGGAAA
4525719 CTTGCAATCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.71, C:0.03, G:0.14, T:0.11
Consensus pattern (18 bp):
AAAAATAAAAACGGAAAT
Found at i:4525885 original size:26 final size:25
Alignment explanation
Indices: 4525856--4525928 Score: 69
Period size: 25 Copynumber: 2.9 Consensus size: 25
4525846 AATTTTGTAG
4525856 AAATTTTATCAAGGGT-AAATTCGTCA
1 AAATTTTAT-AAGGGTAAAATT-GTCA
**
4525882 AAATTTTATGGGGGTAAAATTGTCA
1 AAATTTTATAAGGGTAAAATTGTCA
* *
4525907 AATTTTTAT-TGAGGTAAAATTG
1 AAATTTTATAAG-GGTAAAATTG
4525929 GGGTGAGAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
24 1 0.02
25 26 0.63
26 14 0.34
ACGTcount: A:0.37, C:0.05, G:0.19, T:0.38
Consensus pattern (25 bp):
AAATTTTATAAGGGTAAAATTGTCA
Found at i:4525906 original size:25 final size:25
Alignment explanation
Indices: 4525868--4525928 Score: 79
Period size: 25 Copynumber: 2.4 Consensus size: 25
4525858 ATTTTATCAA
4525868 GGGT-AAATTCGTCAAAATTTTATGG
1 GGGTAAAATT-GTCAAAATTTTATGG
* *
4525893 GGGTAAAATTGTCAAATTTTTATTG
1 GGGTAAAATTGTCAAAATTTTATGG
*
4525918 AGGTAAAATTG
1 GGGTAAAATTG
4525929 GGGTGAGAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
25 27 0.84
26 5 0.16
ACGTcount: A:0.34, C:0.05, G:0.23, T:0.38
Consensus pattern (25 bp):
GGGTAAAATTGTCAAAATTTTATGG
Found at i:4532745 original size:29 final size:31
Alignment explanation
Indices: 4532670--4532745 Score: 77
Period size: 31 Copynumber: 2.5 Consensus size: 31
4532660 ATGTTTGTTT
* * *
4532670 TGAATTGAAATGTATATGTTTTATATATTAC
1 TGAATTGAATTGTATATGTATTATATAGTAC
* *
4532701 TGAATTGATTTATATATGATATT-TATAGT-C
1 TGAATTGAATTGTATATG-TATTATATAGTAC
4532731 -GAATTGAATTGTATA
1 TGAATTGAATTGTATA
4532746 CGAATATACG
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
29 13 0.35
30 1 0.03
31 20 0.54
32 3 0.08
ACGTcount: A:0.36, C:0.03, G:0.14, T:0.47
Consensus pattern (31 bp):
TGAATTGAATTGTATATGTATTATATAGTAC
Found at i:4532833 original size:64 final size:64
Alignment explanation
Indices: 4532759--4532898 Score: 217
Period size: 64 Copynumber: 2.2 Consensus size: 64
4532749 ATATACGTTG
*
4532759 CCGAATTGAATTGTATAGGTACACACCTATTGCCGAATTGAAATGTATATATATACTTATATTA
1 CCGAATTGAATTGTATAGGTACACACCTATTGCCGAATTGAAATATATATATATACTTATATTA
* ** * * *
4532823 CCGAAATGAATTGTATAGGTATGCACCTATTGCCGAATTGAATTATATATGTATACTTATATTG
1 CCGAATTGAATTGTATAGGTACACACCTATTGCCGAATTGAAATATATATATATACTTATATTA
4532887 CCGAATTGAATT
1 CCGAATTGAATT
4532899 TTATTTGTAT
Statistics
Matches: 68, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
64 68 1.00
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (64 bp):
CCGAATTGAATTGTATAGGTACACACCTATTGCCGAATTGAAATATATATATATACTTATATTA
Found at i:4532908 original size:32 final size:32
Alignment explanation
Indices: 4532671--4532919 Score: 163
Period size: 32 Copynumber: 8.0 Consensus size: 32
4532661 TGTTTGTTTT
* * * *
4532671 GAATTGAAATGTATATGT-T-TTATATATTACT
1 GAATTGAATTGTATATGTATACT-TATATTGCC
* * * *
4532702 GAATTGATTTATATATG-ATA-TT-TATAGTC
1 GAATTGAATTGTATATGTATACTTATATTGCC
* * **
4532731 GAATTGAATTGTATACGAATA--TACGTTGCC
1 GAATTGAATTGTATATGTATACTTATATTGCC
* * ***
4532761 GAATTGAATTGTATAGGTACACACCTATTGCC
1 GAATTGAATTGTATATGTATACTTATATTGCC
* * *
4532793 GAATTGAAATGTATATATATACTTATATTACC
1 GAATTGAATTGTATATGTATACTTATATTGCC
* * * ***
4532825 GAAATGAATTGTATAGGTATGCACCTATTGCC
1 GAATTGAATTGTATATGTATACTTATATTGCC
*
4532857 GAATTGAATTATATATGTATACTTATATTGCC
1 GAATTGAATTGTATATGTATACTTATATTGCC
* *
4532889 GAATTGAATTTTATTTGTATA-TATATATTGC
1 GAATTGAATTGTATATGTATACT-TATATTGC
4532920 TGATTTGATT
Statistics
Matches: 164, Mismatches: 47, Indels: 13
0.73 0.21 0.06
Matches are distributed among these distances:
29 18 0.11
30 25 0.15
31 17 0.10
32 104 0.63
ACGTcount: A:0.34, C:0.10, G:0.15, T:0.41
Consensus pattern (32 bp):
GAATTGAATTGTATATGTATACTTATATTGCC
Found at i:4533963 original size:16 final size:17
Alignment explanation
Indices: 4533942--4533974 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
4533932 TTGAGCAAGT
*
4533942 AAAATG-TGTTTGGTTA
1 AAAATGTTGTTTAGTTA
4533958 AAAATGTTGTTTAGTTA
1 AAAATGTTGTTTAGTTA
4533975 CGAAATTGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.45
Consensus pattern (17 bp):
AAAATGTTGTTTAGTTA
Found at i:4544146 original size:40 final size:40
Alignment explanation
Indices: 4544085--4544217 Score: 132
Period size: 40 Copynumber: 3.5 Consensus size: 40
4544075 CGAAAGTTGC
* *
4544085 GCCCAGCACTAGTCGGGTAAACCGACAAATATAATGGTGT
1 GCCCAGCACTAGTCAGATAAACCGACAAATATAATGGTGT
* * **
4544125 GCCCAACACTAGTCAGATAAACTGACAAAGGT--T-GTG-
1 GCCCAGCACTAGTCAGATAAACCGACAAATATAATGGTGT
* * *
4544161 G-CCAGCGCTAGTCGGGTAAACCGACAAATATAATGGTGT
1 GCCCAGCACTAGTCAGATAAACCGACAAATATAATGGTGT
* *
4544200 GTCCAGCACTAGTTAGAT
1 GCCCAGCACTAGTCAGAT
4544218 GTACCAACGA
Statistics
Matches: 71, Mismatches: 17, Indels: 10
0.72 0.17 0.10
Matches are distributed among these distances:
35 23 0.32
36 1 0.01
37 4 0.06
38 4 0.06
39 1 0.01
40 38 0.54
ACGTcount: A:0.32, C:0.22, G:0.25, T:0.21
Consensus pattern (40 bp):
GCCCAGCACTAGTCAGATAAACCGACAAATATAATGGTGT
Found at i:4544146 original size:75 final size:73
Alignment explanation
Indices: 4544046--4544261 Score: 263
Period size: 75 Copynumber: 2.9 Consensus size: 73
4544036 GTATAAAAAA
*
4544046 GTGTGCCCAGCACTAGTCAGGTAAACTGACGAAAGTTGCGCCCAGCACTAGTCGGGTAAACCGAC
1 GTGTGCCCAGCACTAGTCAGATAAACTGACGAAAGTTGCG-CCAGC-CTAGTCGGGTAAACCGAC
4544111 AAATATAATG
64 AAATATAATG
* *
4544121 GTGTGCCCAACACTAGTCAGATAAACTGAC-AAAGGTTGTGGCCAGCGCTAGTCGGGTAAACCGA
1 GTGTGCCCAGCACTAGTCAGATAAACTGACGAAA-GTTG-CGCCAGC-CTAGTCGGGTAAACCGA
4544185 CAAATATAATG
63 CAAATATAATG
* * ** ** * * *
4544196 GTGTGTCCAGCACTAGTTAGATGTACCAACGATGAGTTGCGCCAGCGTAGTCGAGTAAACCGACA
1 GTGTGCCCAGCACTAGTCAGATAAACTGACGA-AAGTTGCGCCAGCCTAGTCGGGTAAACCGACA
4544261 A
65 A
4544262 TATCGATTGC
Statistics
Matches: 122, Mismatches: 15, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
74 21 0.17
75 94 0.77
76 6 0.05
77 1 0.01
ACGTcount: A:0.31, C:0.23, G:0.26, T:0.20
Consensus pattern (73 bp):
GTGTGCCCAGCACTAGTCAGATAAACTGACGAAAGTTGCGCCAGCCTAGTCGGGTAAACCGACAA
ATATAATG
Found at i:4544181 original size:35 final size:34
Alignment explanation
Indices: 4544043--4544188 Score: 123
Period size: 35 Copynumber: 4.1 Consensus size: 34
4544033 CAGGTATAAA
*
4544043 AAAG-TGTGCCCAGCACTAGTCAGGTAAACTGAC
1 AAAGTTGTGCCCAGCACTAGTCAGGTAAACCGAC
* *
4544076 GAAAGTTGCGCCCAGCACTAGTCGGGTAAACCGAC
1 -AAAGTTGTGCCCAGCACTAGTCAGGTAAACCGAC
* * * *
4544111 AAATATAATGGTGTGCCCAACACTAGTCAGATAAACTGAC
1 ----A-AA-GTTGTGCCCAGCACTAGTCAGGTAAACCGAC
* * *
4544151 AAAGGTTGTGGCCAGCGCTAGTCGGGTAAACCGAC
1 AAA-GTTGTGCCCAGCACTAGTCAGGTAAACCGAC
4544186 AAA
1 AAA
4544189 TATAATGGTG
Statistics
Matches: 88, Mismatches: 18, Indels: 11
0.75 0.15 0.09
Matches are distributed among these distances:
34 4 0.05
35 55 0.62
36 1 0.01
38 1 0.01
39 2 0.02
40 25 0.28
ACGTcount: A:0.34, C:0.23, G:0.25, T:0.18
Consensus pattern (34 bp):
AAAGTTGTGCCCAGCACTAGTCAGGTAAACCGAC
Found at i:4544630 original size:35 final size:35
Alignment explanation
Indices: 4544584--4544665 Score: 137
Period size: 35 Copynumber: 2.3 Consensus size: 35
4544574 CTGGCCCGGT
*
4544584 CCGAAATATGGGAGGGTTCAGATAAAAATACAGGC
1 CCGAAATATGGGAGGGTCCAGATAAAAATACAGGC
* *
4544619 CCGAAATATGGGAGGGTCCAGGTAAAAATATAGGC
1 CCGAAATATGGGAGGGTCCAGATAAAAATACAGGC
4544654 CCGAAATATGGG
1 CCGAAATATGGG
4544666 TTTGGGCAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 44 1.00
ACGTcount: A:0.38, C:0.15, G:0.30, T:0.17
Consensus pattern (35 bp):
CCGAAATATGGGAGGGTCCAGATAAAAATACAGGC
Found at i:4547405 original size:18 final size:18
Alignment explanation
Indices: 4547382--4547444 Score: 58
Period size: 18 Copynumber: 3.6 Consensus size: 18
4547372 GAATATAATA
4547382 ATAATAATAATCATCATT
1 ATAATAATAATCATCATT
* *
4547400 ATAATAATAA-CATTAAT
1 ATAATAATAATCATCATT
* *
4547417 ATTAATAATCAT-ATCATG
1 A-TAATAATAATCATCATT
*
4547435 GTAATAATAA
1 ATAATAATAA
4547445 ATAAATGATG
Statistics
Matches: 35, Mismatches: 8, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
17 14 0.40
18 21 0.60
ACGTcount: A:0.52, C:0.08, G:0.03, T:0.37
Consensus pattern (18 bp):
ATAATAATAATCATCATT
Found at i:4547572 original size:10 final size:10
Alignment explanation
Indices: 4547557--4547597 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
4547547 AAATAACGAG
4547557 AATAATAAAT
1 AATAATAAAT
4547567 AATAATAAA-
1 AATAATAAAT
4547576 ATATAAT-AAT
1 A-ATAATAAAT
*
4547586 GATAATAAAT
1 AATAATAAAT
4547596 AA
1 AA
4547598 AAAATTGCAC
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
9 8 0.31
10 18 0.69
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.29
Consensus pattern (10 bp):
AATAATAAAT
Found at i:4547697 original size:15 final size:15
Alignment explanation
Indices: 4547665--4547703 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 15
4547655 AGTAATACAT
4547665 AAATATAAATAGATAA
1 AAATA-AAATAGATAA
4547681 AAATAAAATA-ATAAA
1 AAATAAAATAGAT-AA
4547696 AAATAAAA
1 AAATAAAA
4547704 CAAATAAGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 2 0.09
15 15 0.68
16 5 0.23
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.21
Consensus pattern (15 bp):
AAATAAAATAGATAA
Found at i:4547820 original size:18 final size:18
Alignment explanation
Indices: 4547797--4547833 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
4547787 ATAAGTAAAT
4547797 AAATAAATAAAAGAATTA
1 AAATAAATAAAAGAATTA
*
4547815 AAATAAATAAAAGACTTA
1 AAATAAATAAAAGAATTA
4547833 A
1 A
4547834 TCATAACTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.70, C:0.03, G:0.05, T:0.22
Consensus pattern (18 bp):
AAATAAATAAAAGAATTA
Found at i:4548182 original size:47 final size:48
Alignment explanation
Indices: 4548113--4548207 Score: 156
Period size: 47 Copynumber: 2.0 Consensus size: 48
4548103 CTTCTTAAGA
* *
4548113 AAAAACACGTGGATCCCAGAAGTAGATCAGGTCAGGCCACCGGTCGCG
1 AAAAACACGAGGATCCCAGAAGTAGATCAGGTCAGGCCACCGGCCGCG
*
4548161 AAAAA-ACGAGGATCCCAGAAGTAGATCAGGTCGGGCCACCGGCCGCG
1 AAAAACACGAGGATCCCAGAAGTAGATCAGGTCAGGCCACCGGCCGCG
4548208 GCAAAACAAC
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
47 39 0.89
48 5 0.11
ACGTcount: A:0.32, C:0.27, G:0.31, T:0.11
Consensus pattern (48 bp):
AAAAACACGAGGATCCCAGAAGTAGATCAGGTCAGGCCACCGGCCGCG
Found at i:4550704 original size:18 final size:20
Alignment explanation
Indices: 4550667--4550716 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
4550657 TAAACTATAA
*
4550667 ATTTTGAAATTTTCATAAA-T
1 ATTTTG-AATTTTCAAAAATT
4550687 ATTTTGAATTTT-AAAAATT
1 ATTTTGAATTTTCAAAAATT
4550706 ATTTTG-ATTTT
1 ATTTTGAATTTT
4550717 TTTTCGTAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 9 0.32
19 13 0.46
20 6 0.21
ACGTcount: A:0.36, C:0.02, G:0.06, T:0.56
Consensus pattern (20 bp):
ATTTTGAATTTTCAAAAATT
Found at i:4557618 original size:18 final size:18
Alignment explanation
Indices: 4557585--4557619 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
4557575 AAAATGAATC
**
4557585 AAAACCAAAACCGAAAAG
1 AAAACCAAAAAAGAAAAG
4557603 AAAACCAAAAAAGAAAA
1 AAAACCAAAAAAGAAAA
4557620 AAAGGAAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.74, C:0.17, G:0.09, T:0.00
Consensus pattern (18 bp):
AAAACCAAAAAAGAAAAG
Found at i:4564755 original size:17 final size:17
Alignment explanation
Indices: 4564733--4564781 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
4564723 CCTGGGCAGT
*
4564733 AGAAGAAGAAGAGAATA
1 AGAAGAAGAAGAGAAGA
*
4564750 AGAAGAATAAGAGAAGA
1 AGAAGAAGAAGAGAAGA
4564767 A-ATAGAAGAAGAGAA
1 AGA-AGAAGAAGAGAA
4564782 AATGGAAGGA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
16 1 0.04
17 27 0.96
ACGTcount: A:0.65, C:0.00, G:0.29, T:0.06
Consensus pattern (17 bp):
AGAAGAAGAAGAGAAGA
Found at i:4565860 original size:21 final size:21
Alignment explanation
Indices: 4565834--4565876 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
4565824 CAACGTGGCA
4565834 AGTTAACTGGCCACATCAGCT
1 AGTTAACTGGCCACATCAGCT
*
4565855 AGTTAACTGGCCACGTCAGCT
1 AGTTAACTGGCCACATCAGCT
4565876 A
1 A
4565877 TCCCATTAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (21 bp):
AGTTAACTGGCCACATCAGCT
Found at i:4569391 original size:50 final size:51
Alignment explanation
Indices: 4569305--4569498 Score: 153
Period size: 50 Copynumber: 3.8 Consensus size: 51
4569295 CGATTTCTTA
* *
4569305 TCGTAAGCCTCCCCCCATGCGTCTAGGAGTAGGGATATTATTAAACATCGT
1 TCGTAAGCCTCCCCCCATGCGTCTAGGAGCAAGGATATTATTAAACATCGT
* * * ** *
4569356 TCGTAAGTCT-CCCTCATGCGTCTATGAGCAAGGATATTATTAAACCCCAT
1 TCGTAAGCCTCCCCCCATGCGTCTAGGAGCAAGGATATTATTAAACATCGT
* * ** ** * * * **
4569406 TTGTAAG-CTTCCCTTATATGTCTAGGAACAGGGGTATTATTAAACCCCG-
1 TCGTAAGCCTCCCCCCATGCGTCTAGGAGCAAGGATATTATTAAACATCGT
* *
4569455 TCTGTAAGCCTCCCTCCATGCGTCTGGGAGC-AGGATATTCATTA
1 TC-GTAAGCCTCCCCCCATGCGTCTAGGAGCAAGGATATT-ATTA
4569499 CTCTCCACGA
Statistics
Matches: 111, Mismatches: 28, Indels: 8
0.76 0.19 0.05
Matches are distributed among these distances:
49 3 0.03
50 81 0.73
51 27 0.24
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.30
Consensus pattern (51 bp):
TCGTAAGCCTCCCCCCATGCGTCTAGGAGCAAGGATATTATTAAACATCGT
Found at i:4569641 original size:58 final size:58
Alignment explanation
Indices: 4569578--4569710 Score: 169
Period size: 58 Copynumber: 2.3 Consensus size: 58
4569568 GAGCTCTTGG
* * * * *
4569578 CGGAGGTGAGACATATCTTCTATATTTGGGACCCTCCAG-GAACCCTTTGGGCTCTCAA
1 CGGAGGTGAGGCATATCTTCTACATTCGAGACCCTCC-GTGAACCCTTTAGGCTCTCAA
* * *
4569636 CGGAGGTGAGGCGTATCTTCTACATTCGAGCCCCTCCGTGAACCCTTTAGGCTTTCAA
1 CGGAGGTGAGGCATATCTTCTACATTCGAGACCCTCCGTGAACCCTTTAGGCTCTCAA
*
4569694 TGGAGGTGAGGCATATC
1 CGGAGGTGAGGCATATC
4569711 ATCTTCATAA
Statistics
Matches: 64, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
57 1 0.02
58 63 0.98
ACGTcount: A:0.21, C:0.26, G:0.26, T:0.27
Consensus pattern (58 bp):
CGGAGGTGAGGCATATCTTCTACATTCGAGACCCTCCGTGAACCCTTTAGGCTCTCAA
Found at i:4572347 original size:24 final size:25
Alignment explanation
Indices: 4572320--4572368 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
4572310 TAACAGGTAA
*
4572320 CTCCGAAGAGCTAT-TATCAGGAAG
1 CTCCGAAGAGCCATATATCAGGAAG
* *
4572344 CTCCGGATAGCCATATATCAGGAAG
1 CTCCGAAGAGCCATATATCAGGAAG
4572369 TTCAAGTGAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.33, C:0.22, G:0.24, T:0.20
Consensus pattern (25 bp):
CTCCGAAGAGCCATATATCAGGAAG
Found at i:4580859 original size:16 final size:16
Alignment explanation
Indices: 4580838--4580879 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
4580828 TCAATATCCA
4580838 ATTATCATATTCACAC
1 ATTATCATATTCACAC
* *
4580854 ATTATCACATTTACAC
1 ATTATCATATTCACAC
4580870 A-TAT-ATATTC
1 ATTATCATATTC
4580880 TTTTCAATTC
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 4 0.18
15 3 0.14
16 15 0.68
ACGTcount: A:0.38, C:0.21, G:0.00, T:0.40
Consensus pattern (16 bp):
ATTATCATATTCACAC
Found at i:4594319 original size:24 final size:24
Alignment explanation
Indices: 4594292--4594337 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
4594282 AGAACAATCC
* *
4594292 CAAAAGGAAATGCACGAGCAGCTT
1 CAAAAGCAAATGAACGAGCAGCTT
*
4594316 CAAAAGCAAATGAATGAGCAGC
1 CAAAAGCAAATGAACGAGCAGC
4594338 AAAAAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.46, C:0.20, G:0.24, T:0.11
Consensus pattern (24 bp):
CAAAAGCAAATGAACGAGCAGCTT
Found at i:4600149 original size:38 final size:39
Alignment explanation
Indices: 4600107--4600191 Score: 145
Period size: 40 Copynumber: 2.2 Consensus size: 39
4600097 AATTTTTGAG
4600107 GATATGCAATCTTAGATATG-ATATGCAATCCTAGATAT
1 GATATGCAATCTTAGATATGAATATGCAATCCTAGATAT
*
4600145 GATATGCAATCTTAGATATGATATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATATGA-ATATGCAATCCTAGATAT
4600185 GATATGC
1 GATATGC
4600192 NNNNNNNNNN
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
38 20 0.45
40 24 0.55
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.35
Consensus pattern (39 bp):
GATATGCAATCTTAGATATGAATATGCAATCCTAGATAT
Found at i:4600172 original size:21 final size:19
Alignment explanation
Indices: 4600107--4600191 Score: 143
Period size: 19 Copynumber: 4.4 Consensus size: 19
4600097 AATTTTTGAG
4600107 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
4600126 GATATGCAATCCTAGATAT
1 GATATGCAATCTTAGATAT
4600145 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
4600164 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
4600185 GATATGC
1 GATATGC
4600192 NNNNNNNNNN
Statistics
Matches: 62, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
19 43 0.69
21 19 0.31
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.35
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:4607312 original size:18 final size:18
Alignment explanation
Indices: 4607281--4607339 Score: 50
Period size: 18 Copynumber: 3.1 Consensus size: 18
4607271 GCAGAGTACA
4607281 GATGAAGA-GAATGAAGGT
1 GATGAAGATG-ATGAAGGT
*
4607299 GATGAAGATGATGATGATGAT
1 GATGAAGATGATGA--A-GGT
4607320 GATGACA-ATGATGAAGGT
1 GATGA-AGATGATGAAGGT
4607338 GA
1 GA
4607340 AGATGACAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
18 16 0.47
19 2 0.06
20 1 0.03
21 14 0.41
22 1 0.03
ACGTcount: A:0.41, C:0.02, G:0.36, T:0.22
Consensus pattern (18 bp):
GATGAAGATGATGAAGGT
Found at i:4614085 original size:31 final size:31
Alignment explanation
Indices: 4614011--4614086 Score: 80
Period size: 31 Copynumber: 2.5 Consensus size: 31
4614001 GGTATTGTCG
* *
4614011 TTAAAAACTATTTTCATTTGAGGCAATACCA
1 TTAAAAACTGTTTTCATTTCAGGCAATACCA
** * * **
4614042 TTAAAATTTGTTTTCATTTCAGGTAGTTTCA
1 TTAAAAACTGTTTTCATTTCAGGCAATACCA
4614073 TTAAAAACTGTTTT
1 TTAAAAACTGTTTT
4614087 TGTAATAAAA
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.33, C:0.12, G:0.11, T:0.45
Consensus pattern (31 bp):
TTAAAAACTGTTTTCATTTCAGGCAATACCA
Found at i:4616614 original size:14 final size:14
Alignment explanation
Indices: 4616595--4616622 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
4616585 TAGTAAATTA
4616595 TTAAAAATATATAT
1 TTAAAAATATATAT
4616609 TTAAAAATATATAT
1 TTAAAAATATATAT
4616623 CATTTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TTAAAAATATATAT
Found at i:4624835 original size:2 final size:2
Alignment explanation
Indices: 4624828--4624869 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
4624818 CAAGAGCTCA
4624828 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4624870 GCGCATTTAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4634182 original size:16 final size:16
Alignment explanation
Indices: 4634133--4634185 Score: 88
Period size: 16 Copynumber: 3.3 Consensus size: 16
4634123 TTGGTTGGCT
*
4634133 GTAATGGAATAGATGT
1 GTAATGGAATAGATGC
4634149 GTAATGGAATAGATGC
1 GTAATGGAATAGATGC
*
4634165 GTAATGGAATAGAGGC
1 GTAATGGAATAGATGC
4634181 GTAAT
1 GTAAT
4634186 AGGTAATCTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.38, C:0.04, G:0.32, T:0.26
Consensus pattern (16 bp):
GTAATGGAATAGATGC
Found at i:4634220 original size:45 final size:44
Alignment explanation
Indices: 4634165--4634252 Score: 122
Period size: 44 Copynumber: 2.0 Consensus size: 44
4634155 GAATAGATGC
* *
4634165 GTAATGGAATAGAGGCGTAATAGGTAATCTTTTGTTTGATTGAAT
1 GTAATGGAATAGAGGCATAAT-GGTAATCTTGTGTTTGATTGAAT
* * *
4634210 GTAATTGAATAGAGGCATAATGGTATTCTTGTGTTTGGTTGAA
1 GTAATGGAATAGAGGCATAATGGTAATCTTGTGTTTGATTGAA
4634253 AGGAATAGAG
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
44 19 0.50
45 19 0.50
ACGTcount: A:0.30, C:0.05, G:0.27, T:0.39
Consensus pattern (44 bp):
GTAATGGAATAGAGGCATAATGGTAATCTTGTGTTTGATTGAAT
Found at i:4637721 original size:51 final size:52
Alignment explanation
Indices: 4637643--4637743 Score: 136
Period size: 51 Copynumber: 2.0 Consensus size: 52
4637633 AATTTATCAC
* *
4637643 ATTAAAAAATTTATTTTTTCTTATTTT-GGAATACTGATGGCCGACACCAAGT
1 ATTAAAAAATTTATGTTTTCTTATTTTGGGAAT-CAGATGGCCGACACCAAGT
*
4637695 ATTAAAAAA-TTA-GTTTTCTTAATTTTGGGAATCAGATGGCTGACACCAA
1 ATTAAAAAATTTATGTTTTCTT-ATTTTGGGAATCAGATGGCCGACACCAA
4637744 ACCCTGTGTA
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
50 7 0.16
51 23 0.52
52 14 0.32
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.38
Consensus pattern (52 bp):
ATTAAAAAATTTATGTTTTCTTATTTTGGGAATCAGATGGCCGACACCAAGT
Found at i:4638103 original size:14 final size:14
Alignment explanation
Indices: 4638084--4638115 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
4638074 TAATTTCTAT
4638084 ATTTTCGTGTATTA
1 ATTTTCGTGTATTA
4638098 ATTTTCGTGTATTA
1 ATTTTCGTGTATTA
4638112 ATTT
1 ATTT
4638116 AGTATGTGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.22, C:0.06, G:0.12, T:0.59
Consensus pattern (14 bp):
ATTTTCGTGTATTA
Found at i:4638341 original size:90 final size:90
Alignment explanation
Indices: 4638228--4638553 Score: 492
Period size: 90 Copynumber: 3.6 Consensus size: 90
4638218 TTGTATCTGC
*
4638228 AAATTTAATTTAGTCTGTATTATATGTAGTTTGAATTTAAAATTTTCGTGTATTAATTTTACCCA
1 AAATTTAATTTAGTCCGTATTATATGTAGTTTGAATTTAAAATTTTCGTGTATTAATTTTACCCA
4638293 TCTGTTTGTAGTTTGTTGGGTGTTT
66 TCTGTTTGTAGTTTGTTGGGTGTTT
** * * * * * *
4638318 AAATTTAATTTAGTATGTGTTATATATAGTTTGAATTTAAAATTTTCGTGCACTAATGTTATCCA
1 AAATTTAATTTAGTCCGTATTATATGTAGTTTGAATTTAAAATTTTCGTGTATTAATTTTACCCA
* *
4638383 TCAGTTTGTAGTTTGTTGGATGTTT
66 TCTGTTTGTAGTTTGTTGGGTGTTT
*
4638408 AAATTTAATTTAGTCCGTATTATATGTAGTTTGAATTTAAAATTTTCATGTATTAATTTTACCCA
1 AAATTTAATTTAGTCCGTATTATATGTAGTTTGAATTTAAAATTTTCGTGTATTAATTTTACCCA
4638473 TCTGTTTGTAGTTTGTTGGGTGTTT
66 TCTGTTTGTAGTTTGTTGGGTGTTT
* * * * *
4638498 AAATTTAATTTAGTGCGTATTATAT-TTGTTTGAATTTTATATTTTTGTGTATTAAT
1 AAATTTAATTTAGTCCGTATTATATGTAGTTTGAATTTAAAATTTTCGTGTATTAAT
4638554 ATTCTAGAAT
Statistics
Matches: 210, Mismatches: 26, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
89 26 0.12
90 184 0.88
ACGTcount: A:0.26, C:0.06, G:0.16, T:0.52
Consensus pattern (90 bp):
AAATTTAATTTAGTCCGTATTATATGTAGTTTGAATTTAAAATTTTCGTGTATTAATTTTACCCA
TCTGTTTGTAGTTTGTTGGGTGTTT
Found at i:4641644 original size:25 final size:25
Alignment explanation
Indices: 4641565--4641644 Score: 72
Period size: 25 Copynumber: 3.2 Consensus size: 25
4641555 TCTTTCGAGC
* *
4641565 CATATAACGGGAAGCTCATATGAGT
1 CATATAACGGGAAGCTTATAAGAGT
* * * ** *
4641590 CATGTAAAGGGAAACTTATCCG-GG
1 CATATAACGGGAAGCTTATAAGAGT
4641614 CGATATAACGGGAAGCTTATAAGAGT
1 C-ATATAACGGGAAGCTTATAAGAGT
4641640 CATAT
1 CATAT
4641645 TCAAAAAACT
Statistics
Matches: 40, Mismatches: 13, Indels: 4
0.70 0.23 0.07
Matches are distributed among these distances:
24 2 0.05
25 36 0.90
26 2 0.05
ACGTcount: A:0.36, C:0.15, G:0.25, T:0.24
Consensus pattern (25 bp):
CATATAACGGGAAGCTTATAAGAGT
Found at i:4641727 original size:25 final size:25
Alignment explanation
Indices: 4641699--4641749 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
4641689 ATTAATCAGA
*
4641699 AAGCTCCAGATAGCCATATATCGGG
1 AAGCTCCAGAGAGCCATATATCGGG
*
4641724 AAGCTCCGGAGAGCCATATATCGGG
1 AAGCTCCAGAGAGCCATATATCGGG
4641749 A
1 A
4641750 CACTCATAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.31, C:0.24, G:0.27, T:0.18
Consensus pattern (25 bp):
AAGCTCCAGAGAGCCATATATCGGG
Found at i:4641761 original size:25 final size:25
Alignment explanation
Indices: 4641710--4641762 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
4641700 AGCTCCAGAT
* *
4641710 AGCCATATATCGGGAAGCTCCGGAG
1 AGCCATATATCGGGAAGCTCAGAAG
*
4641735 AGCCATATATCGGGACA-CTCATAAG
1 AGCCATATATCGGGA-AGCTCAGAAG
4641760 AGC
1 AGC
4641763 TGTGGTGTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 23 0.96
26 1 0.04
ACGTcount: A:0.32, C:0.25, G:0.26, T:0.17
Consensus pattern (25 bp):
AGCCATATATCGGGAAGCTCAGAAG
Found at i:4641850 original size:25 final size:25
Alignment explanation
Indices: 4641822--4641881 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
4641812 AAAGAGCTAT
4641822 TAACGGGAAGAT-TGCAAGAACCATA
1 TAACGGGAAGATCT-CAAGAACCATA
* * *
4641847 TAACAGGAAGCTCTTAAGAACCATA
1 TAACGGGAAGATCTCAAGAACCATA
*
4641872 TACCGGGAAG
1 TAACGGGAAG
4641882 CTCGAGAGGG
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
25 28 0.97
26 1 0.03
ACGTcount: A:0.42, C:0.18, G:0.23, T:0.17
Consensus pattern (25 bp):
TAACGGGAAGATCTCAAGAACCATA
Found at i:4641882 original size:25 final size:25
Alignment explanation
Indices: 4641837--4641884 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
4641827 GGAAGATTGC
4641837 AAGAACCATATAACAGGAAGCTCTT
1 AAGAACCATATAACAGGAAGCTCTT
* *
4641862 AAGAACCATATACCGGGAAGCTC
1 AAGAACCATATAACAGGAAGCTC
4641885 GAGAGGGTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.42, C:0.23, G:0.19, T:0.17
Consensus pattern (25 bp):
AAGAACCATATAACAGGAAGCTCTT
Found at i:4644176 original size:5 final size:5
Alignment explanation
Indices: 4644168--4644222 Score: 65
Period size: 5 Copynumber: 10.0 Consensus size: 5
4644158 AACTTTTTTT
4644168 TTTCA TTTCA TTTCTA CTTTCA TTTCCA TTTCA TTTCA TTTACA TTTTCA
1 TTTCA TTTCA TTTC-A -TTTCA TTT-CA TTTCA TTTCA TTT-CA -TTTCA
4644218 TTTCA
1 TTTCA
4644223 CTTAAATTAT
Statistics
Matches: 45, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
5 27 0.60
6 11 0.24
7 7 0.16
ACGTcount: A:0.20, C:0.22, G:0.00, T:0.58
Consensus pattern (5 bp):
TTTCA
Found at i:4644190 original size:12 final size:11
Alignment explanation
Indices: 4644171--4644222 Score: 61
Period size: 11 Copynumber: 4.6 Consensus size: 11
4644161 TTTTTTTTTT
4644171 CATTTCATTTC
1 CATTTCATTTC
*
4644182 TACTTTCATTTC
1 CA-TTTCATTTC
4644194 CATTTCATTT-
1 CATTTCATTTC
*
4644204 CATTTACATTTT
1 CATTT-CATTTC
4644216 CATTTCA
1 CATTTCA
4644223 CTTAAATTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
10 5 0.14
11 16 0.44
12 15 0.42
ACGTcount: A:0.21, C:0.23, G:0.00, T:0.56
Consensus pattern (11 bp):
CATTTCATTTC
Found at i:4644201 original size:28 final size:28
Alignment explanation
Indices: 4644168--4644221 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
4644158 AACTTTTTTT
4644168 TTTCATTTCATTT-CTACTTTCATTTCCA
1 TTTCATTTCATTTAC-ACTTTCATTTCCA
*
4644196 TTTCATTTCATTTACATTTTCATTTC
1 TTTCATTTCATTTACACTTTCATTTC
4644222 ACTTAAATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 23 0.96
29 1 0.04
ACGTcount: A:0.19, C:0.22, G:0.00, T:0.59
Consensus pattern (28 bp):
TTTCATTTCATTTACACTTTCATTTCCA
Found at i:4644275 original size:17 final size:17
Alignment explanation
Indices: 4644162--4644306 Score: 89
Period size: 17 Copynumber: 8.2 Consensus size: 17
4644152 CCTTTCAACT
4644162 TTTTTTTTTCATTTC-A
1 TTTTTTTTTCATTTCAA
** *
4644178 TTTCTACTTTCATTTCCA
1 TTT-TTTTTTCATTTCAA
**
4644196 -TTTCATTTCATTT-ACA
1 TTTTTTTTTCATTTCA-A
** * *
4644212 TTTTCATTTCACTTAAA
1 TTTTTTTTTCATTTCAA
*
4644229 TTATTTTTTTCCATTTAAA
1 TT-TTTTTTT-CATTTCAA
4644248 TTTAATTTTTTCTCATTTCAA
1 -TT--TTTTTT-TCATTTCAA
*
4644269 TTTTTTTTTCATTTCAGT
1 TTTTTTTTTCATTTCA-A
4644287 TTTTTTTTTCATTTCAA
1 TTTTTTTTTCATTTCAA
4644304 TTT
1 TTT
4644307 GTAATTTATT
Statistics
Matches: 106, Mismatches: 12, Indels: 21
0.76 0.09 0.15
Matches are distributed among these distances:
16 13 0.12
17 38 0.36
18 29 0.27
19 7 0.07
20 4 0.04
21 14 0.13
22 1 0.01
ACGTcount: A:0.20, C:0.15, G:0.01, T:0.64
Consensus pattern (17 bp):
TTTTTTTTTCATTTCAA
Found at i:4644589 original size:21 final size:21
Alignment explanation
Indices: 4644547--4644589 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
4644537 TGTCAGGGTC
*
4644547 ATTTAAAATTTTTCATATTTT
1 ATTTAAAATTTTTCATAATTT
*
4644568 ATTTAAATTTTTTC-TCAATTT
1 ATTTAAAATTTTTCAT-AATTT
4644589 A
1 A
4644590 AAAATCATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (21 bp):
ATTTAAAATTTTTCATAATTT
Found at i:4644832 original size:27 final size:27
Alignment explanation
Indices: 4644768--4644973 Score: 128
Period size: 27 Copynumber: 8.2 Consensus size: 27
4644758 GCCTATCCTT
*
4644768 TCTTTTTTTTTCATTTAATTT-AATT-
1 TCTTTTTTTTTCATTTCATTTAAATTA
**
4644793 TCATTTCCATTTTCATTTCATTTAAATTA
1 TC-TTT-TTTTTTCATTTCATTTAAATTA
4644822 TC--TTTTTTT--TTTCATTTAAATTTA
1 TCTTTTTTTTTCATTTCATTTAAA-TTA
* * **
4644846 AC-TTTTTTCTCATTTTGTTTAAATTA
1 TCTTTTTTTTTCATTTCATTTAAATTA
4644872 TC--TTTTTTTC----CATTTAAATT-
1 TCTTTTTTTTTCATTTCATTTAAATTA
* *
4644892 TAATTTTTTTCTCATTTCATTTAAATTA
1 T-CTTTTTTTTTCATTTCATTTAAATTA
*
4644920 TC-TTTTTTTTCATTT-A---AATTTAA
1 TCTTTTTTTTTCATTTCATTTAAATT-A
*
4644943 T-TTTTTTTCTCATTTCATTTAAATTA
1 TCTTTTTTTTTCATTTCATTTAAATTA
4644969 TCTTT
1 TCTTT
4644974 CTTTCCATTT
Statistics
Matches: 138, Mismatches: 20, Indels: 44
0.68 0.10 0.22
Matches are distributed among these distances:
20 1 0.01
21 8 0.06
22 4 0.03
23 32 0.23
24 5 0.04
25 20 0.14
26 22 0.16
27 39 0.28
28 5 0.04
29 2 0.01
ACGTcount: A:0.23, C:0.12, G:0.00, T:0.65
Consensus pattern (27 bp):
TCTTTTTTTTTCATTTCATTTAAATTA
Found at i:4644853 original size:21 final size:21
Alignment explanation
Indices: 4644827--4644951 Score: 81
Period size: 26 Copynumber: 5.4 Consensus size: 21
4644817 AATTATCTTT
4644827 TTTTTTTCATTTAAATTTAAC
1 TTTTTTTCATTTAAATTTAAC
*
4644848 TTTTTTCTCATTTTGTTTAAA-TTATC
1 TTTTTT-TCA-----TTTAAATTTAAC
*
4644874 TTTTTTTCCATTTAAATTTAAT
1 TTTTTTT-CATTTAAATTTAAC
* *
4644896 TTTTTTCTCATTTCATTTAAATTATC
1 TTTTTT-TCATTT-A---AATTTAAC
*
4644922 TTTTTTTTCATTTAAATTTAAT
1 -TTTTTTTCATTTAAATTTAAC
4644944 TTTTTTTC
1 TTTTTTTC
4644952 TCATTTCATT
Statistics
Matches: 81, Mismatches: 9, Indels: 28
0.69 0.08 0.24
Matches are distributed among these distances:
21 20 0.25
22 22 0.27
23 2 0.02
25 2 0.02
26 23 0.28
27 12 0.15
ACGTcount: A:0.23, C:0.10, G:0.01, T:0.66
Consensus pattern (21 bp):
TTTTTTTCATTTAAATTTAAC
Found at i:4644927 original size:49 final size:48
Alignment explanation
Indices: 4644805--4645000 Score: 284
Period size: 48 Copynumber: 4.0 Consensus size: 48
4644795 ATTTCCATTT
* *
4644805 TCATTTCATTTAAATTATCTTTTTTTTTTCATTTAAATTTAACTTTTTTC
1 TCATTTCATTTAAATTATC--TTTTTTTCCATTTAAATTTAATTTTTTTC
**
4644855 TCATTTTGTTTAAATTATCTTTTTTTCCATTTAAATTTAATTTTTTTC
1 TCATTTCATTTAAATTATCTTTTTTTCCATTTAAATTTAATTTTTTTC
*
4644903 TCATTTCATTTAAATTATCTTTTTTTTCATTTAAATTTAATTTTTTTTC
1 TCATTTCATTTAAATTATCTTTTTTTCCATTTAAATTTAA-TTTTTTTC
* * *
4644952 TCATTTCATTTAAATTATCTTTCTTTCCATTTTAATTTATGTTTTTTTC
1 TCATTTCATTTAAATTATCTTTTTTTCCATTTAAATTTA-ATTTTTTTC
4645001 ATATTAATTT
Statistics
Matches: 133, Mismatches: 11, Indels: 5
0.89 0.07 0.03
Matches are distributed among these distances:
48 64 0.48
49 52 0.39
50 17 0.13
ACGTcount: A:0.23, C:0.12, G:0.01, T:0.64
Consensus pattern (48 bp):
TCATTTCATTTAAATTATCTTTTTTTCCATTTAAATTTAATTTTTTTC
Found at i:4644979 original size:97 final size:98
Alignment explanation
Indices: 4644805--4645000 Score: 306
Period size: 97 Copynumber: 2.0 Consensus size: 98
4644795 ATTTCCATTT
**
4644805 TCATTTCATTTAAATTATCTTTTTTTTTTCATTTAAATTTAACTTTTTTCTCATTTTGTTTAAAT
1 TCATTTCATTTAAATTATC-TTTTTTTTTCATTTAAATTTAACTTTTTTCTCATTTCATTTAAAT
*
4644870 TATCTTTTTTTCCATTTAAATTTA-ATTTTTTTC
65 TATCTTTCTTTCCATTTAAATTTATATTTTTTTC
*
4644903 TCATTTCATTTAAATTATC-TTTTTTTTCATTTAAATTTAATTTTTTTTCTCATTTCATTTAAAT
1 TCATTTCATTTAAATTATCTTTTTTTTTCATTTAAATTTAA-CTTTTTTCTCATTTCATTTAAAT
* *
4644967 TATCTTTCTTTCCATTTTAATTTATGTTTTTTTC
65 TATCTTTCTTTCCATTTAAATTTATATTTTTTTC
4645001 ATATTAATTT
Statistics
Matches: 90, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
96 21 0.23
97 42 0.47
98 27 0.30
ACGTcount: A:0.23, C:0.12, G:0.01, T:0.64
Consensus pattern (98 bp):
TCATTTCATTTAAATTATCTTTTTTTTTCATTTAAATTTAACTTTTTTCTCATTTCATTTAAATT
ATCTTTCTTTCCATTTAAATTTATATTTTTTTC
Found at i:4645007 original size:21 final size:21
Alignment explanation
Indices: 4644889--4645010 Score: 70
Period size: 21 Copynumber: 5.4 Consensus size: 21
4644879 TTCCATTTAA
4644889 ATTTAATTT-T-TTTCTCATTTC
1 ATTTAATTTATCTTTCT--TTTC
* *
4644910 ATTTAAATTATCTTTTTTTTC
1 ATTTAATTTATCTTTCTTTTC
*
4644931 ATTTAAATTTAATTTTTTTTCTCATTTC
1 ATTT-AATTT-A---TCTTTCT--TTTC
* *
4644959 ATTTAAATTATCTTTCTTTCC
1 ATTTAATTTATCTTTCTTTTC
*
4644980 ATTTTAATTTATGTTT-TTTTC
1 A-TTTAATTTATCTTTCTTTTC
4645001 ATATTAATTT
1 AT-TTAATTT
4645011 TTCTCTAATT
Statistics
Matches: 79, Mismatches: 11, Indels: 22
0.71 0.10 0.20
Matches are distributed among these distances:
20 1 0.01
21 32 0.41
22 17 0.22
23 11 0.14
26 6 0.08
27 4 0.05
28 8 0.10
ACGTcount: A:0.24, C:0.11, G:0.01, T:0.65
Consensus pattern (21 bp):
ATTTAATTTATCTTTCTTTTC
Found at i:4645226 original size:44 final size:44
Alignment explanation
Indices: 4645033--4645228 Score: 275
Period size: 44 Copynumber: 4.5 Consensus size: 44
4645023 AATTTATTTC
* * * *
4645033 ATTTAATGTGTTTTAAGTTAAATATGTAAGTCTGTTGTATTATA
1 ATTTAATGTGTTTTAAATTAAATATGTATGTATATTGTATTATA
* *
4645077 ATTTAACGTGTTTTAAAATAAATATGTATGTATATTGTATTATA
1 ATTTAATGTGTTTTAAATTAAATATGTATGTATATTGTATTATA
* * *
4645121 GTTTAATGTGTTTTAAAATAAATATGTATGTATATTGTATTTTA
1 ATTTAATGTGTTTTAAATTAAATATGTATGTATATTGTATTATA
* *
4645165 ATTTAATGTGCTTTAAATTAAATATGCATGTATATTGTATTATA
1 ATTTAATGTGTTTTAAATTAAATATGTATGTATATTGTATTATA
* *
4645209 ATTTAACGTATTTTAAATTA
1 ATTTAATGTGTTTTAAATTA
4645229 GGAACAAGAA
Statistics
Matches: 135, Mismatches: 17, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 135 1.00
ACGTcount: A:0.36, C:0.03, G:0.12, T:0.49
Consensus pattern (44 bp):
ATTTAATGTGTTTTAAATTAAATATGTATGTATATTGTATTATA
Found at i:4649084 original size:46 final size:44
Alignment explanation
Indices: 4649033--4649141 Score: 125
Period size: 46 Copynumber: 2.4 Consensus size: 44
4649023 TTTTGACATA
*
4649033 TAGTATTATTTAATATTTAAGCT-TAAC-ATTGTTTTAAATTTATCAT
1 TAGTATTATTTAATATTTAA--TAT-ACTATTATTTTAAA-TTATCAT
*
4649079 TAGTATTATTTTAATATTTAATATACTATTATTTTAAATTATTAT
1 TAGTATTA-TTTAATATTTAATATACTATTATTTTAAATTATCAT
*
4649124 TAATATTATTTAA-ATTTA
1 TAGTATTATTTAATATTTA
4649142 TCATATGTCA
Statistics
Matches: 57, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
43 5 0.09
44 5 0.09
45 16 0.28
46 19 0.33
47 12 0.21
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.55
Consensus pattern (44 bp):
TAGTATTATTTAATATTTAATATACTATTATTTTAAATTATCAT
Found at i:4649142 original size:22 final size:23
Alignment explanation
Indices: 4649055--4649142 Score: 92
Period size: 23 Copynumber: 3.9 Consensus size: 23
4649045 ATATTTAAGC
* * *
4649055 TTAACATTGTTTTAAATTTATCA
1 TTAATATTATTTTAAATTTATTA
* *
4649078 TTAGTATTATTTTAATATTTAATA
1 TTAATATTATTTTAA-ATTTATTA
*
4649102 -TACTATTATTTTAAA-TTATTA
1 TTAATATTATTTTAAATTTATTA
4649123 TTAATATTA-TTTAAATTTAT
1 TTAATATTATTTTAAATTTAT
4649143 CATATGTCAA
Statistics
Matches: 54, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
21 11 0.20
22 12 0.22
23 25 0.46
24 6 0.11
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.57
Consensus pattern (23 bp):
TTAATATTATTTTAAATTTATTA
Found at i:4656619 original size:31 final size:32
Alignment explanation
Indices: 4656581--4656647 Score: 109
Period size: 31 Copynumber: 2.1 Consensus size: 32
4656571 CTTTAAATCC
4656581 ATACATTTGAATCAAAATCAAAATTT-TATGT
1 ATACATTTGAATCAAAATCAAAATTTATATGT
*
4656612 ATACATTTGAATTAAAATCAAAATTTAATATGT
1 ATACATTTGAATCAAAATCAAAATTT-ATATGT
4656645 ATA
1 ATA
4656648 ATTGCAAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
31 25 0.76
33 8 0.24
ACGTcount: A:0.48, C:0.07, G:0.06, T:0.39
Consensus pattern (32 bp):
ATACATTTGAATCAAAATCAAAATTTATATGT
Found at i:4657214 original size:28 final size:28
Alignment explanation
Indices: 4657182--4657241 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 28
4657172 GACGTGTAAC
*
4657182 ATAAAATGTAAAT-TTAAG-TACTAAATTA
1 ATAAAA-G-AAATCTTAAGATACCAAATTA
*
4657210 ATAAAAGAAATCTTAAGATACCAAATTC
1 ATAAAAGAAATCTTAAGATACCAAATTA
4657238 ATAA
1 ATAA
4657242 TTTCCAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 4 0.14
27 6 0.21
28 18 0.64
ACGTcount: A:0.55, C:0.08, G:0.07, T:0.30
Consensus pattern (28 bp):
ATAAAAGAAATCTTAAGATACCAAATTA
Found at i:4657614 original size:31 final size:32
Alignment explanation
Indices: 4657576--4657642 Score: 109
Period size: 31 Copynumber: 2.1 Consensus size: 32
4657566 CTTTAAATCC
4657576 ATACATTTGAATCAAAATCAAAATTT-TATGT
1 ATACATTTGAATCAAAATCAAAATTTATATGT
*
4657607 ATACATTTGAATTAAAATCAAAATTTAATATGT
1 ATACATTTGAATCAAAATCAAAATTT-ATATGT
4657640 ATA
1 ATA
4657643 ATTGCAAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
31 25 0.76
33 8 0.24
ACGTcount: A:0.48, C:0.07, G:0.06, T:0.39
Consensus pattern (32 bp):
ATACATTTGAATCAAAATCAAAATTTATATGT
Found at i:4658209 original size:28 final size:28
Alignment explanation
Indices: 4658177--4658236 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 28
4658167 GACGTGTAAC
*
4658177 ATAAAATGTAAAT-TTAAG-TACTAAATTA
1 ATAAAA-G-AAATCTTAAGATACCAAATTA
*
4658205 ATAAAAGAAATCTTAAGATACCAAATTC
1 ATAAAAGAAATCTTAAGATACCAAATTA
4658233 ATAA
1 ATAA
4658237 TTTCCAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 4 0.14
27 6 0.21
28 18 0.64
ACGTcount: A:0.55, C:0.08, G:0.07, T:0.30
Consensus pattern (28 bp):
ATAAAAGAAATCTTAAGATACCAAATTA
Found at i:4661186 original size:15 final size:15
Alignment explanation
Indices: 4661142--4661188 Score: 60
Period size: 16 Copynumber: 3.1 Consensus size: 15
4661132 TTACTCTTCA
4661142 AATTTTTTAAA-TTT
1 AATTTTTTAAATTTT
*
4661156 AATTTTTAAGAATTTT
1 AATTTTTTA-AATTTT
*
4661172 TATTTTTTAAATTTT
1 AATTTTTTAAATTTT
4661187 AA
1 AA
4661189 ATTCAGATTC
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
14 8 0.30
15 9 0.33
16 10 0.37
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (15 bp):
AATTTTTTAAATTTT
Found at i:4668635 original size:20 final size:19
Alignment explanation
Indices: 4668601--4668651 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 19
4668591 TTCATTCTAG
* *
4668601 ATGTATATATTTTTATTAA
1 ATGTAAATATTTTTAATAA
4668620 ATGTAAATACTTTTTAATAA
1 ATGTAAATA-TTTTTAATAA
*
4668640 ATTTAAA-ATTTT
1 ATGTAAATATTTT
4668652 CAAAAAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 4 0.14
19 9 0.32
20 15 0.54
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (19 bp):
ATGTAAATATTTTTAATAA
Found at i:4681379 original size:22 final size:24
Alignment explanation
Indices: 4681356--4681460 Score: 101
Period size: 25 Copynumber: 4.3 Consensus size: 24
4681346 CACTAATGAA
4681356 CAGAGAGCACAGATGTGCTA-AA-
1 CAGAGAGCACAGATGTGCTATAAT
* *
4681378 CAGAGAGCACTGACGTGCTAGTAAT
1 CAGAGAGCACAGATGTGCTA-TAAT
*
4681403 CAAAGAGCACTA-ATGTGCTAATAAT
1 CAGAGAGCAC-AGATGTGCT-ATAAT
*
4681428 CAGAGAGCACCA-ACGTGCTAATAAT
1 CAGAGAGCA-CAGATGTGCT-ATAAT
4681453 CAGAGAGC
1 CAGAGAGC
4681461 GCGCTAAAAT
Statistics
Matches: 70, Mismatches: 7, Indels: 9
0.81 0.08 0.10
Matches are distributed among these distances:
22 18 0.26
24 2 0.03
25 48 0.69
26 2 0.03
ACGTcount: A:0.39, C:0.20, G:0.24, T:0.17
Consensus pattern (24 bp):
CAGAGAGCACAGATGTGCTATAAT
Found at i:4681411 original size:25 final size:25
Alignment explanation
Indices: 4681378--4681460 Score: 121
Period size: 25 Copynumber: 3.3 Consensus size: 25
4681368 ATGTGCTAAA
* *
4681378 CAGAGAGCACTGACGTGCTAGTAAT
1 CAGAGAGCACTAACGTGCTAATAAT
* *
4681403 CAAAGAGCACTAATGTGCTAATAAT
1 CAGAGAGCACTAACGTGCTAATAAT
*
4681428 CAGAGAGCACCAACGTGCTAATAAT
1 CAGAGAGCACTAACGTGCTAATAAT
4681453 CAGAGAGC
1 CAGAGAGC
4681461 GCGCTAAAAT
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 51 1.00
ACGTcount: A:0.39, C:0.20, G:0.23, T:0.18
Consensus pattern (25 bp):
CAGAGAGCACTAACGTGCTAATAAT
Found at i:4681412 original size:47 final size:50
Alignment explanation
Indices: 4681359--4681460 Score: 131
Period size: 50 Copynumber: 2.1 Consensus size: 50
4681349 TAATGAACAG
** *
4681359 AGAGCAC-AGATGTGCT-A-AA-CAGAGAGCACTGACGTGCTAGTAATCAA
1 AGAGCACTA-ATGTGCTAATAATCAGAGAGCACCAACGTGCTAATAATCAA
*
4681406 AGAGCACTAATGTGCTAATAATCAGAGAGCACCAACGTGCTAATAATCAG
1 AGAGCACTAATGTGCTAATAATCAGAGAGCACCAACGTGCTAATAATCAA
4681456 AGAGC
1 AGAGC
4681461 GCGCTAAAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
47 14 0.30
48 2 0.04
49 2 0.04
50 29 0.62
ACGTcount: A:0.39, C:0.20, G:0.24, T:0.18
Consensus pattern (50 bp):
AGAGCACTAATGTGCTAATAATCAGAGAGCACCAACGTGCTAATAATCAA
Found at i:4682426 original size:5 final size:5
Alignment explanation
Indices: 4682416--4682443 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
4682406 TTATTTCTTT
4682416 TATAA TATAA TATAA TATAA TATAA TAT
1 TATAA TATAA TATAA TATAA TATAA TAT
4682444 TTATACTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (5 bp):
TATAA
Found at i:4702490 original size:16 final size:16
Alignment explanation
Indices: 4702466--4702501 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
4702456 GATTTGCTAT
*
4702466 TACACCTCTAATCCAA
1 TACAACTCTAATCCAA
4702482 TACAACTCTAATCCAA
1 TACAACTCTAATCCAA
4702498 TACA
1 TACA
4702502 GTGAACCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.42, C:0.33, G:0.00, T:0.25
Consensus pattern (16 bp):
TACAACTCTAATCCAA
Found at i:4703219 original size:53 final size:53
Alignment explanation
Indices: 4703134--4703238 Score: 142
Period size: 53 Copynumber: 2.0 Consensus size: 53
4703124 ATCAAATTCT
*
4703134 CATATTACTCATTTTGATATATTTATTGTGTT-AAATATTGAGATTTAATGGATC
1 CATATTACTCA-TTTGATATATCTATTGTGTTAAAAT-TTGAGATTTAATGGATC
* *
4703188 CATATTACTCGA-TTGATTTATCTATTTTGTTAAAATTTGAGATTTAATGGA
1 CATATTACTC-ATTTGATATATCTATTGTGTTAAAATTTGAGATTTAATGGA
4703239 GCAATTAAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
53 31 0.67
54 14 0.30
55 1 0.02
ACGTcount: A:0.31, C:0.08, G:0.13, T:0.48
Consensus pattern (53 bp):
CATATTACTCATTTGATATATCTATTGTGTTAAAATTTGAGATTTAATGGATC
Found at i:4703343 original size:54 final size:54
Alignment explanation
Indices: 4703261--4703366 Score: 176
Period size: 54 Copynumber: 2.0 Consensus size: 54
4703251 ACCAAACCCT
* *
4703261 TATATTACTCGTTTTGGTCCATCTATTGTGTTAAATATTGAGATTTAATGGATC
1 TATATTACTCATTTTGATCCATCTATTGTGTTAAATATTGAGATTTAATGGATC
* *
4703315 TATATTACTCATTTTGATCTATCTATTGTGTTAAATTTTGAGATTTAATGGA
1 TATATTACTCATTTTGATCCATCTATTGTGTTAAATATTGAGATTTAATGGA
4703367 GCAATTAACT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 48 1.00
ACGTcount: A:0.27, C:0.09, G:0.15, T:0.48
Consensus pattern (54 bp):
TATATTACTCATTTTGATCCATCTATTGTGTTAAATATTGAGATTTAATGGATC
Found at i:4703351 original size:127 final size:128
Alignment explanation
Indices: 4703103--4703437 Score: 448
Period size: 127 Copynumber: 2.6 Consensus size: 128
4703093 CTAATCAAAT
* * ** * * *
4703103 TTTAATGGAGCGATTAAATCCATCAAATTCTCATATTACTCATTTTGATATATTTATTGTGTTAA
1 TTTAATGGAGCAATTAAATCCACCAAACCCTCATATTACTCGTTTTGATCTATCTATTGTGTTAA
* *
4703168 ATATTGAGATTTAATGGATCCATATTACTCGATTGATTTATCTATTTTGTTAAAA-TTTGAGA
66 ATATTGAGATTTAATGGATCCATATTACTCGATTGATCTATCTATTGTGTTAAAATTTTGAGA
* * * *
4703230 TTTAATGGAGCAATTAAATTCACCAAACCCTTATATTACTCGTTTTGGTCCATCTATTGTGTTAA
1 TTTAATGGAGCAATTAAATCCACCAAACCCTCATATTACTCGTTTTGATCTATCTATTGTGTTAA
*
4703295 ATATTGAGATTTAATGGATCTATATTACTC-ATTTTGATCTATCTATTGTGTT-AAATTTTGAGA
66 ATATTGAGATTTAATGGATCCATATTACTCGA--TTGATCTATCTATTGTGTTAAAATTTTGAGA
* *
4703358 TTTAATGGAGCAATTAACTCCACCAAACCC-CA-A-TACTCGTTTTCATCTATCTATTGTGTTAA
1 TTTAATGGAGCAATTAAATCCACCAAACCCTCATATTACTCGTTTTGATCTATCTATTGTGTTAA
* *
4703420 ATTTTGAGATTTTATGGA
66 ATATTGAGATTTAATGGA
4703438 GCGATTAAAT
Statistics
Matches: 183, Mismatches: 22, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
125 42 0.23
126 2 0.01
127 87 0.48
128 52 0.28
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.43
Consensus pattern (128 bp):
TTTAATGGAGCAATTAAATCCACCAAACCCTCATATTACTCGTTTTGATCTATCTATTGTGTTAA
ATATTGAGATTTAATGGATCCATATTACTCGATTGATCTATCTATTGTGTTAAAATTTTGAGA
Found at i:4703502 original size:76 final size:72
Alignment explanation
Indices: 4703317--4703510 Score: 264
Period size: 71 Copynumber: 2.7 Consensus size: 72
4703307 AATGGATCTA
* *
4703317 TATTACTCATTTTGATCTATCTATTGTGTTAAATTTTGAGATTTAATGGAGCAATTAACTCCACC
1 TATTACTCGTTTTGATCTATCTATTGTGTTAAATTTTGAGATTTAATGGAGCAATTAAATCCACC
4703382 AAACCCC
66 AAACCCC
* * * *
4703389 -AATACTCGTTTTCATCTATCTATTGTGTTAAATTTTGAGATTTTATGGAGCGATTAAATCCACC
1 TATTACTCGTTTTGATCTATCTATTGTGTTAAATTTTGAGATTTAATGGAGCAATTAAATCCACC
4703453 AAACCCCGCC
66 AAA--CC-CC
* * *
4703463 GTATTATTCGTTTTGATCTATCTAATGTGTTGAATTTTGAGATTTAAT
1 -TATTACTCGTTTTGATCTATCTATTGTGTTAAATTTTGAGATTTAAT
4703511 TTTTAAGTAT
Statistics
Matches: 105, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
71 61 0.58
73 2 0.02
74 2 0.02
76 40 0.38
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.41
Consensus pattern (72 bp):
TATTACTCGTTTTGATCTATCTATTGTGTTAAATTTTGAGATTTAATGGAGCAATTAAATCCACC
AAACCCC
Done.