Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr4
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: 30015117
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1306243 characters in sequence are not A, C, G, or T
File 18 of 85
Found at i:5969176 original size:81 final size:81
Alignment explanation
Indices: 5969003--5969225 Score: 326
Period size: 81 Copynumber: 2.8 Consensus size: 81
5968993 TTTTGAGCTT
** *
5969003 TCAGGGCTTTAGCGGCGTTTTTGAGAAAGC-ATGCTAATGCTCAGGGATTTAGCGGCGTTTTTGA
1 TCAGGGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCAGGGATTTAGCGGCGATTTTGA
*
5969067 GAAAGCATGCTAATGC
66 GAAAGCACGCTAATGC
**
5969083 TCAGGGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCA-GTCTTTAGCGGCGATTTTGA
1 TCAGGGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCAGGGATTTAGCGGCGATTTTGA
*
5969147 GAAAGCGCCGCTAATGC
66 GAAAGC-ACGCTAATGC
* * *
5969164 TCAGGGCCTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTTAGGGTTTTAGCGGC-ATTTT
1 TCAGGGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCAGGGATTTAGCGGCGATTTT
5969226 ACCGCTTTAA
Statistics
Matches: 129, Mismatches: 11, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
80 53 0.41
81 66 0.51
82 10 0.08
ACGTcount: A:0.21, C:0.19, G:0.30, T:0.30
Consensus pattern (81 bp):
TCAGGGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCAGGGATTTAGCGGCGATTTTGA
GAAAGCACGCTAATGC
Found at i:5969188 original size:41 final size:41
Alignment explanation
Indices: 5969003--5969225 Score: 326
Period size: 40 Copynumber: 5.5 Consensus size: 41
5968993 TTTTGAGCTT
**
5969003 TCAGGGCTTTAGCGGCGTTTTTGAGAAAGC-ATGCTAATGC
1 TCAGGGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGC
* **
5969043 TCAGGGATTTAGCGGCGTTTTTGAGAAAGC-ATGCTAATGC
1 TCAGGGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGC
5969083 TCAGGGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGC
1 TCAGGGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGC
* *
5969124 TCA-GTCTTTAGCGGCGATTTTGAGAAAGCGCCGCTAATGC
1 TCAGGGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGC
*
5969164 TCAGGGCCTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGC
1 TCAGGGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGC
* * *
5969205 TTAGGGTTTTAGCGGCATTTT
1 TCAGGGCTTTAGCGGCGTTTT
5969226 ACCGCTTTAA
Statistics
Matches: 168, Mismatches: 13, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
40 106 0.63
41 62 0.37
ACGTcount: A:0.21, C:0.19, G:0.30, T:0.30
Consensus pattern (41 bp):
TCAGGGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGC
Found at i:5969544 original size:7 final size:7
Alignment explanation
Indices: 5969532--5969585 Score: 54
Period size: 7 Copynumber: 7.6 Consensus size: 7
5969522 GTGTTACCAT
5969532 TTTATGG
1 TTTATGG
5969539 TTTATGG
1 TTTATGG
*
5969546 ATTATGGG
1 TTTAT-GG
*
5969554 TTTAGGG
1 TTTATGG
*
5969561 GTTATGG
1 TTTATGG
*
5969568 TTTAGGG
1 TTTATGG
*
5969575 TTTATAG
1 TTTATGG
5969582 TTTA
1 TTTA
5969586 AAGGCTGGGG
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
7 32 0.86
8 5 0.14
ACGTcount: A:0.19, C:0.00, G:0.31, T:0.50
Consensus pattern (7 bp):
TTTATGG
Found at i:5969557 original size:15 final size:14
Alignment explanation
Indices: 5969533--5969585 Score: 61
Period size: 14 Copynumber: 3.7 Consensus size: 14
5969523 TGTTACCATT
*
5969533 TTATGGTTTATGGA
1 TTATGGTTTAGGGA
*
5969547 TTATGGGTTTAGGGG
1 TTAT-GGTTTAGGGA
*
5969562 TTATGGTTTAGGGT
1 TTATGGTTTAGGGA
*
5969576 TTATAGTTTA
1 TTATGGTTTA
5969586 AAGGCTGGGG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
14 22 0.65
15 12 0.35
ACGTcount: A:0.19, C:0.00, G:0.32, T:0.49
Consensus pattern (14 bp):
TTATGGTTTAGGGA
Found at i:5969627 original size:29 final size:27
Alignment explanation
Indices: 5969593--5969664 Score: 74
Period size: 29 Copynumber: 2.6 Consensus size: 27
5969583 TTAAAGGCTG
5969593 GGGTTTAAGGTTTAGAGG-TTATGTGTTAA
1 GGGTTTAAGGTTTA-AGGTTTA-G-GTTAA
* *
5969622 GGGTTTATGGTTTTAAGGTTTAGGTTTA
1 GGGTTTAAGG-TTTAAGGTTTAGGTTAA
*
5969650 GGGTTTAAGATTTAA
1 GGGTTTAAGGTTTAA
5969665 TTAACTAGTT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
27 5 0.14
28 12 0.32
29 13 0.35
30 7 0.19
ACGTcount: A:0.24, C:0.00, G:0.32, T:0.44
Consensus pattern (27 bp):
GGGTTTAAGGTTTAAGGTTTAGGTTAA
Found at i:5969647 original size:21 final size:20
Alignment explanation
Indices: 5969623--5969663 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
5969613 ATGTGTTAAG
* *
5969623 GGTTTATGGTTTTAAGGTTTA
1 GGTTTA-GGGTTTAAGATTTA
5969644 GGTTTAGGGTTTAAGATTTA
1 GGTTTAGGGTTTAAGATTTA
5969664 ATTAACTAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.22, C:0.00, G:0.29, T:0.49
Consensus pattern (20 bp):
GGTTTAGGGTTTAAGATTTA
Found at i:5970133 original size:15 final size:15
Alignment explanation
Indices: 5970113--5970142 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5970103 ACTATTTTAA
*
5970113 GGTTTATGGATTATG
1 GGTTTAGGGATTATG
5970128 GGTTTAGGGATTATG
1 GGTTTAGGGATTATG
5970143 ATTTATAGTT
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:0.20, C:0.00, G:0.37, T:0.43
Consensus pattern (15 bp):
GGTTTAGGGATTATG
Found at i:5970197 original size:21 final size:21
Alignment explanation
Indices: 5970150--5970211 Score: 72
Period size: 21 Copynumber: 2.9 Consensus size: 21
5970140 ATGATTTATA
* *
5970150 GTTTAAAGGTTGGGGTTTAAG
1 GTTTAAGGGTTAGGGTTTAAG
5970171 GTTTAAGGGTTAGGGTTTAATG
1 GTTTAAGGGTTAGGGTTTAA-G
*
5970193 G-TTAAGGGTTTAGGATTTA
1 GTTTAAGGG-TTAGGGTTTA
5970212 TGATTTATGA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
21 25 0.69
22 11 0.31
ACGTcount: A:0.24, C:0.00, G:0.35, T:0.40
Consensus pattern (21 bp):
GTTTAAGGGTTAGGGTTTAAG
Found at i:5970211 original size:7 final size:7
Alignment explanation
Indices: 5970201--5970239 Score: 69
Period size: 7 Copynumber: 5.6 Consensus size: 7
5970191 TGGTTAAGGG
*
5970201 TTTAGGA
1 TTTATGA
5970208 TTTATGA
1 TTTATGA
5970215 TTTATGA
1 TTTATGA
5970222 TTTATGA
1 TTTATGA
5970229 TTTATGA
1 TTTATGA
5970236 TTTA
1 TTTA
5970240 GGGTTTAAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.28, C:0.00, G:0.15, T:0.56
Consensus pattern (7 bp):
TTTATGA
Found at i:5970246 original size:21 final size:21
Alignment explanation
Indices: 5970197--5970246 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
5970187 TTAATGGTTA
5970197 AGGGTTTAGGATTTATGATTT
1 AGGGTTTAGGATTTATGATTT
* * *
5970218 ATGATTTATGATTTATGATTT
1 AGGGTTTAGGATTTATGATTT
5970239 AGGGTTTA
1 AGGGTTTA
5970247 AGAGATAGGG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (21 bp):
AGGGTTTAGGATTTATGATTT
Found at i:5972604 original size:13 final size:13
Alignment explanation
Indices: 5972586--5972610 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5972576 AGTTCTTTAT
5972586 TGCTTTTGAGAAG
1 TGCTTTTGAGAAG
5972599 TGCTTTTGAGAA
1 TGCTTTTGAGAA
5972611 ATTTGAGTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.08, G:0.28, T:0.40
Consensus pattern (13 bp):
TGCTTTTGAGAAG
Found at i:5973163 original size:64 final size:64
Alignment explanation
Indices: 5973085--5973343 Score: 518
Period size: 64 Copynumber: 4.0 Consensus size: 64
5973075 GCAATATGCC
5973085 AAATTAGTGGACAGTCCACATCATTAACATTGCATACTGTTTTAAGATGAACAAGAATGGAACT
1 AAATTAGTGGACAGTCCACATCATTAACATTGCATACTGTTTTAAGATGAACAAGAATGGAACT
5973149 AAATTAGTGGACAGTCCACATCATTAACATTGCATACTGTTTTAAGATGAACAAGAATGGAACT
1 AAATTAGTGGACAGTCCACATCATTAACATTGCATACTGTTTTAAGATGAACAAGAATGGAACT
5973213 AAATTAGTGGACAGTCCACATCATTAACATTGCATACTGTTTTAAGATGAACAAGAATGGAACT
1 AAATTAGTGGACAGTCCACATCATTAACATTGCATACTGTTTTAAGATGAACAAGAATGGAACT
5973277 AAATTAGTGGACAGTCCACATCATTAACATTGCATACTGTTTTAAGATGAACAAGAATGGAACT
1 AAATTAGTGGACAGTCCACATCATTAACATTGCATACTGTTTTAAGATGAACAAGAATGGAACT
5973341 AAA
1 AAA
5973344 GTGTCTACCG
Statistics
Matches: 195, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 195 1.00
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (64 bp):
AAATTAGTGGACAGTCCACATCATTAACATTGCATACTGTTTTAAGATGAACAAGAATGGAACT
Found at i:5975714 original size:41 final size:40
Alignment explanation
Indices: 5975626--5975725 Score: 96
Period size: 41 Copynumber: 2.5 Consensus size: 40
5975616 TTTAAACAGA
* * *
5975626 TTCACTGGCACTTAGCCTGCTAGACTTAAAGCCTGATTCAG
1 TTCACCGGCACTTAGCCTGCTAGACATAAAGCCTGAAT-AG
* * *
5975667 TACACCGGCACTTAGCCTGCTAGACATATAGTCTGAA-ATG
1 TTCACCGGCACTTAGCCTGCTAGACATAAAGCCTGAATA-G
5975707 TTTCACCGGCA-TTAAGCCT
1 -TTCACCGGCACTT-AGCCT
5975726 NNNNNNNNNN
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
39 1 0.02
40 3 0.06
41 45 0.92
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.28
Consensus pattern (40 bp):
TTCACCGGCACTTAGCCTGCTAGACATAAAGCCTGAATAG
Found at i:5995247 original size:43 final size:43
Alignment explanation
Indices: 5995187--5995277 Score: 130
Period size: 43 Copynumber: 2.1 Consensus size: 43
5995177 CTTTGAGTTC
* * *
5995187 ATTA-CAAGATTTCCTTGATTAAGTAAATGTATTATATCTTTT
1 ATTACCAAGATTTACTTGATTAAGAAAATGCATTATATCTTTT
* *
5995229 ATTACCAAGATTTACTTGATTAAGAAAATGCATTGTATTTTTT
1 ATTACCAAGATTTACTTGATTAAGAAAATGCATTATATCTTTT
5995272 ATTACC
1 ATTACC
5995278 TTGCAATGTG
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
42 4 0.09
43 39 0.91
ACGTcount: A:0.34, C:0.11, G:0.10, T:0.45
Consensus pattern (43 bp):
ATTACCAAGATTTACTTGATTAAGAAAATGCATTATATCTTTT
Found at i:5995693 original size:43 final size:43
Alignment explanation
Indices: 5995628--5995822 Score: 173
Period size: 42 Copynumber: 4.6 Consensus size: 43
5995618 AATTTTTTTC
* * * *
5995628 AAAGGTAATGTT-TTTAGCGGCGTTTTTGCGAGAAGCACTGCT
1 AAAGGTTATGTTCTTTAGCGGCGTTTGTGAGAAAAGCACTGCT
* *
5995670 AAAGGTTATGTTCTTTAGCGGCGTTTGTGATAAAAGCTCTGCT
1 AAAGGTTATGTTCTTTAGCGGCGTTTGTGAGAAAAGCACTGCT
* * *
5995713 AAAGATT-TGTTCTTTAACGGCGTTTGTGATAAAAG-AGC-GCT
1 AAAGGTTATGTTCTTTAGCGGCGTTTGTGAGAAAAGCA-CTGCT
* * * * * * * *
5995754 AAAGGTCAAGATCTTTAGTGGCGTTTGTGATAAAAACGCCGCT
1 AAAGGTTATGTTCTTTAGCGGCGTTTGTGAGAAAAGCACTGCT
* * *
5995797 AAAGGTCATGATCTTTAGTGGCGTTT
1 AAAGGTTATGTTCTTTAGCGGCGTTT
5995823 TTCACATAAA
Statistics
Matches: 130, Mismatches: 18, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
41 8 0.06
42 63 0.48
43 59 0.45
ACGTcount: A:0.26, C:0.14, G:0.26, T:0.34
Consensus pattern (43 bp):
AAAGGTTATGTTCTTTAGCGGCGTTTGTGAGAAAAGCACTGCT
Found at i:5995834 original size:43 final size:43
Alignment explanation
Indices: 5995750--5995835 Score: 127
Period size: 43 Copynumber: 2.0 Consensus size: 43
5995740 GATAAAAGAG
* *
5995750 CGCTAAAGGTCAAGATCTTTAGTGGCGTTTGTGATAAAAACGC
1 CGCTAAAGGTCAAGATCTTTAGTGGCGTTTGTCACAAAAACGC
* * *
5995793 CGCTAAAGGTCATGATCTTTAGTGGCGTTTTTCACATAAACGC
1 CGCTAAAGGTCAAGATCTTTAGTGGCGTTTGTCACAAAAACGC
5995836 TGTTAAATTT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (43 bp):
CGCTAAAGGTCAAGATCTTTAGTGGCGTTTGTCACAAAAACGC
Found at i:6001801 original size:85 final size:85
Alignment explanation
Indices: 6001624--6001826 Score: 250
Period size: 85 Copynumber: 2.4 Consensus size: 85
6001614 GTCTCTGTTT
* *
6001624 TTTTTTTTTGCACTCAATTGTGTACTTGAACTTTTAAAATGCATAAAAAAGGCTTTCAAACTTTT
1 TTTTTTTTTGCACTCAATTGTGTATTTGAACTTTTAAAATACATAAAAAAGGCTTTCAAACTTTT
6001689 TCAAAAAAAGCAATAAAGACA
66 T-AAAAAAAGCAATAAAGACA
*
6001710 -TTTTTTTTGCACTCAATTGTGTATTTGAACTTTTAAAATACATCAAAAAGG-TTCTCAAACTTT
1 TTTTTTTTTGCACTCAATTGTGTATTTGAACTTTTAAAATACATAAAAAAGGCTT-TCAAACTTT
* * * *
6001773 TT-AAATAAGCAATTAAGTCC
65 TTAAAAAAAGCAATAAAGACA
** * *
6001793 TTACTTTTTTTTTACTCAATTGGGTATTTAAACT
1 TT--TTTTTTTGCACTCAATTGTGTATTTGAACT
6001827 GCCATAATGT
Statistics
Matches: 102, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
83 14 0.14
84 3 0.03
85 59 0.58
86 26 0.25
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.41
Consensus pattern (85 bp):
TTTTTTTTTGCACTCAATTGTGTATTTGAACTTTTAAAATACATAAAAAAGGCTTTCAAACTTTT
TAAAAAAAGCAATAAAGACA
Found at i:6001986 original size:10 final size:10
Alignment explanation
Indices: 6001949--6002058 Score: 54
Period size: 10 Copynumber: 11.3 Consensus size: 10
6001939 GACATGTGGC
*
6001949 AAAAAATGAT
1 AAAAAATTAT
*
6001959 AAAAAATCA-
1 AAAAAATTAT
6001968 ATAAAAATTAT
1 A-AAAAATTAT
6001979 AAAAAATTAT
1 AAAAAATTAT
* **
6001989 TAAATTTTAAT
1 AAAAAATT-AT
*
6002000 AAAAAAATAT
1 AAAAAATTAT
6002010 -AAAAATCGTA-
1 AAAAAAT--TAT
*
6002020 AAAAAATT-G
1 AAAAAATTAT
*
6002029 AAAATA-TAT
1 AAAAAATTAT
*
6002038 AAAATA-TAT
1 AAAAAATTAT
6002047 -AAAAATTAT
1 AAAAAATTAT
6002056 AAA
1 AAA
6002059 TTTTTATAAA
Statistics
Matches: 77, Mismatches: 13, Indels: 20
0.70 0.12 0.18
Matches are distributed among these distances:
8 5 0.06
9 24 0.31
10 33 0.43
11 15 0.19
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.28
Consensus pattern (10 bp):
AAAAAATTAT
Found at i:6001992 original size:20 final size:19
Alignment explanation
Indices: 6001950--6002058 Score: 80
Period size: 20 Copynumber: 5.6 Consensus size: 19
6001940 ACATGTGGCA
* *
6001950 AAAAATGATAAAAAATCAAT
1 AAAAATTATAAAAAAT-ATT
6001970 AAAAATTATAAAAAATTATT
1 AAAAATTATAAAAAA-TATT
**
6001990 AAATTTTAATAAAAAA-ATAT
1 AAAAATT-ATAAAAAATAT-T
**
6002010 AAAAATCGTAAAAAA-ATT
1 AAAAATTATAAAAAATATT
* *
6002028 GAAAA-TATATAAAATATAT
1 AAAAATTATAAAAAATAT-T
6002047 AAAAATTATAAA
1 AAAAATTATAAA
6002059 TTTTTATAAA
Statistics
Matches: 69, Mismatches: 14, Indels: 12
0.73 0.15 0.13
Matches are distributed among these distances:
17 6 0.09
18 7 0.10
19 16 0.23
20 31 0.45
21 9 0.13
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.28
Consensus pattern (19 bp):
AAAAATTATAAAAAATATT
Found at i:6002021 original size:19 final size:18
Alignment explanation
Indices: 6001999--6002126 Score: 73
Period size: 19 Copynumber: 6.9 Consensus size: 18
6001989 TAAATTTTAA
6001999 TAAAAAAATATAAAAATCG
1 TAAAAAAATATAAAAAT-G
* *
6002018 TAAAAAAAT-TGAAAATA
1 TAAAAAAATATAAAAATG
*
6002035 TATAAAATATATAAAAAT-
1 TA-AAAAAATATAAAAATG
* ** * *
6002053 TATAAATTTTTATAAAGTCG
1 TAAAAAAATATA-AAAAT-G
* *
6002073 TAAGGAAATTATAAAAATG
1 TAA-AAAAATATAAAAATG
*
6002092 T-AAAAAATATAAAATTAG
1 TAAAAAAATATAAAAAT-G
6002110 TAAAAAAATTATAAAAA
1 TAAAAAAA-TATAAAAA
6002127 ACATCGTACC
Statistics
Matches: 83, Mismatches: 17, Indels: 17
0.71 0.15 0.15
Matches are distributed among these distances:
17 20 0.24
18 21 0.25
19 23 0.28
20 13 0.16
21 6 0.07
ACGTcount: A:0.63, C:0.02, G:0.06, T:0.29
Consensus pattern (18 bp):
TAAAAAAATATAAAAATG
Found at i:6002059 original size:26 final size:26
Alignment explanation
Indices: 6002003--6002053 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
6001993 TTTTAATAAA
*
6002003 AAAATATAAAAATCGTAAAAAAATTG
1 AAAATATAAAAATCATAAAAAAATTG
*
6002029 AAAATATATAAAAT-ATATAAAAATT
1 AAAATATA-AAAATCATAAAAAAATT
6002054 ATAAATTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 17 0.77
27 5 0.23
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (26 bp):
AAAATATAAAAATCATAAAAAAATTG
Found at i:6002233 original size:10 final size:10
Alignment explanation
Indices: 6002218--6002255 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
6002208 AAAATCTTAA
6002218 AATTTTTTAT
1 AATTTTTTAT
6002228 AATTTTTT-T
1 AATTTTTTAT
*
6002237 ACTATTTTTAT
1 AAT-TTTTTAT
6002248 AATTTTTT
1 AATTTTTT
6002256 GCGATTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
9 3 0.12
10 18 0.75
11 3 0.12
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (10 bp):
AATTTTTTAT
Found at i:6002253 original size:19 final size:20
Alignment explanation
Indices: 6002221--6002266 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
6002211 ATCTTAAAAT
*
6002221 TTTTTATAATTTTTTTACTA
1 TTTTTATAATTTTTTTACGA
*
6002241 TTTTTATAA-TTTTTTGCGA
1 TTTTTATAATTTTTTTACGA
6002260 TTTTTAT
1 TTTTTAT
6002267 CAAAAATTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 15 0.62
20 9 0.38
ACGTcount: A:0.22, C:0.04, G:0.04, T:0.70
Consensus pattern (20 bp):
TTTTTATAATTTTTTTACGA
Found at i:6002264 original size:20 final size:21
Alignment explanation
Indices: 6002219--6002264 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
6002209 AAATCTTAAA
*
6002219 ATTTTTTATAATTTTTTTACT
1 ATTTTTTATAATTTTTTTACG
*
6002240 A-TTTTTATAA-TTTTTTGCG
1 ATTTTTTATAATTTTTTTACG
6002259 ATTTTT
1 ATTTTT
6002265 ATCAAAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 8 0.36
20 13 0.59
21 1 0.05
ACGTcount: A:0.22, C:0.04, G:0.04, T:0.70
Consensus pattern (21 bp):
ATTTTTTATAATTTTTTTACG
Found at i:6002322 original size:19 final size:19
Alignment explanation
Indices: 6002280--6002334 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 19
6002270 AAATTCTAAT
6002280 TTTTAATATTTTTATTAAA
1 TTTTAATATTTTTATTAAA
* *
6002299 ATTTAATAGTTTTTA-TAAC
1 TTTTAATA-TTTTTATTAAA
*
6002318 TTTTATTCATTTTTATT
1 TTTTAAT-ATTTTTATT
6002335 TTTTATAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
19 21 0.72
20 8 0.28
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.64
Consensus pattern (19 bp):
TTTTAATATTTTTATTAAA
Found at i:6003481 original size:11 final size:10
Alignment explanation
Indices: 6003455--6003480 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
6003445 GGGGAGAGCC
6003455 TTTTTTGAAG
1 TTTTTTGAAG
6003465 TTTTTTGAAG
1 TTTTTTGAAG
6003475 TTTTTT
1 TTTTTT
6003481 TAAAGGTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.15, C:0.00, G:0.15, T:0.69
Consensus pattern (10 bp):
TTTTTTGAAG
Found at i:6007788 original size:52 final size:52
Alignment explanation
Indices: 6007685--6007789 Score: 133
Period size: 51 Copynumber: 2.0 Consensus size: 52
6007675 CTACAGATTA
* * * * *
6007685 TTAACTCTTCTAAATAGTGTTTTTCTCATGTAAACCTGTTCTGCTCTTATTG
1 TTAACTCTTCTAAATAGTGCTATTCTCAAGTAAACCAGTTCTACTCTTATTG
6007737 TTAACT-TTCTAAATAGTGCTATTCTCAAGTAATACCAGTTCTACTAC-TATTG
1 TTAACTCTTCTAAATAGTGCTATTCTCAAGTAA-ACCAGTTCTACT-CTTATTG
6007789 T
1 T
6007790 CAACCATAGT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
51 23 0.50
52 22 0.48
53 1 0.02
ACGTcount: A:0.26, C:0.19, G:0.10, T:0.45
Consensus pattern (52 bp):
TTAACTCTTCTAAATAGTGCTATTCTCAAGTAAACCAGTTCTACTCTTATTG
Found at i:6007838 original size:51 final size:52
Alignment explanation
Indices: 6007777--6007875 Score: 137
Period size: 52 Copynumber: 1.9 Consensus size: 52
6007767 AATACCAGTT
*
6007777 CTACTACTATTGTCAACCATAGT-ACTGATGCTTTTTCTCATGTAACACCAA
1 CTACTACTATTGTCAACCATAGTAACTGATGCCTTTTCTCATGTAACACCAA
* * * * *
6007828 CTACTCCTATTGTTAACCCTAGTAACTGGTTCCTTTTCTCATGTAACA
1 CTACTACTATTGTCAACCATAGTAACTGATGCCTTTTCTCATGTAACA
6007876 GTTGTATCGT
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
51 20 0.49
52 21 0.51
ACGTcount: A:0.26, C:0.26, G:0.10, T:0.37
Consensus pattern (52 bp):
CTACTACTATTGTCAACCATAGTAACTGATGCCTTTTCTCATGTAACACCAA
Found at i:6017167 original size:2 final size:2
Alignment explanation
Indices: 6017160--6017187 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
6017150 AACTTGTTAA
6017160 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
6017188 ATCTATATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:6019139 original size:3 final size:3
Alignment explanation
Indices: 6019113--6019180 Score: 104
Period size: 3 Copynumber: 23.0 Consensus size: 3
6019103 TTTTTTTAGT
*
6019113 TTA TT- TTA TTA GTA TTGA -TA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA
6019157 TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA
6019181 NNNNNNNNNN
Statistics
Matches: 60, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
2 3 0.05
3 56 0.93
4 1 0.02
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:6019265 original size:3 final size:3
Alignment explanation
Indices: 6019257--6019296 Score: 55
Period size: 3 Copynumber: 13.3 Consensus size: 3
6019247 ATTAATTTTG
*
6019257 TTA TTA TTA TTT TTA TTA TTA -TA TTA TATA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA T
6019297 ACCTACATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 28 0.85
4 3 0.09
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:6019265 original size:15 final size:15
Alignment explanation
Indices: 6019241--6019295 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
6019231 GTTTTTAGTC
6019241 TATT-TTATTAATTT
1 TATTATTATTAATTT
* *
6019255 TGTTATTATTATTTT
1 TATTATTATTAATTT
6019270 TATTATTA-T-ATTAT
1 TATTATTATTAATT-T
6019284 ATATTATTATTA
1 -TATTATTATTA
6019296 TACCTACATA
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
13 2 0.06
14 5 0.16
15 24 0.75
16 1 0.03
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (15 bp):
TATTATTATTAATTT
Found at i:6019272 original size:12 final size:12
Alignment explanation
Indices: 6019243--6019294 Score: 52
Period size: 12 Copynumber: 4.1 Consensus size: 12
6019233 TTTTAGTCTA
6019243 TTTTATTAATT-T
1 TTTTATT-ATTAT
*
6019255 TGTTATTATTAT
1 TTTTATTATTAT
6019267 TTTTATTATTAT
1 TTTTATTATTAT
6019279 ATTATATATTATTAT
1 -TT-T-TATTATTAT
6019294 T
1 T
6019295 ATACCTACAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
11 3 0.09
12 18 0.53
13 2 0.06
14 2 0.06
15 9 0.26
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (12 bp):
TTTTATTATTAT
Found at i:6020171 original size:25 final size:26
Alignment explanation
Indices: 6020143--6020200 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
6020133 TTGTTGGGAC
6020143 TTTAATATGTTA-ATGTAATTATTTT
1 TTTAATATGTTATATGTAATTATTTT
* * *
6020168 TTTATTTTTTTATATGTAATTATTTT
1 TTTAATATGTTATATGTAATTATTTT
6020194 TTATAAT
1 TT-TAAT
6020201 CTATACGTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 9 0.33
26 15 0.56
27 3 0.11
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (26 bp):
TTTAATATGTTATATGTAATTATTTT
Found at i:6028231 original size:13 final size:13
Alignment explanation
Indices: 6028213--6028237 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6028203 ACAAACAATA
6028213 AAATTTTCACACG
1 AAATTTTCACACG
6028226 AAATTTTCACAC
1 AAATTTTCACAC
6028238 ATATTAATTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:6040998 original size:12 final size:12
Alignment explanation
Indices: 6040981--6041006 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
6040971 TTCTTTTACC
6040981 ATATTTATTATT
1 ATATTTATTATT
6040993 ATATTTATTATT
1 ATATTTATTATT
6041005 AT
1 AT
6041007 TACTATTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
ATATTTATTATT
Found at i:6041246 original size:12 final size:12
Alignment explanation
Indices: 6041214--6041238 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
6041204 GTTATCATTG
6041214 TTATTATTTATT
1 TTATTATTTATT
6041226 TTATTATTTATT
1 TTATTATTTATT
6041238 T
1 T
6041239 ATTTATTTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (12 bp):
TTATTATTTATT
Found at i:6042386 original size:47 final size:48
Alignment explanation
Indices: 6042279--6042386 Score: 168
Period size: 48 Copynumber: 2.3 Consensus size: 48
6042269 TGGAAGAATA
6042279 TGGCAGTTTATCTGCAAAAGTAGTGGCTTGCCAACAAATTTGATTATG
1 TGGCAGTTTATCTGCAAAAGTAGTGGCTTGCCAACAAATTTGATTATG
*
6042327 TGGCAGTATATCTGCAAAAGT-GATGGCTTGTCC-AC-AATTTGATTATG
1 TGGCAGTTTATCTGCAAAAGTAG-TGGCTTG-CCAACAAATTTGATTATG
6042374 TGGCAGTTTATCT
1 TGGCAGTTTATCT
6042387 ACATTACTGT
Statistics
Matches: 56, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
47 25 0.45
48 29 0.52
49 2 0.04
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.35
Consensus pattern (48 bp):
TGGCAGTTTATCTGCAAAAGTAGTGGCTTGCCAACAAATTTGATTATG
Found at i:6045628 original size:101 final size:102
Alignment explanation
Indices: 6045496--6045680 Score: 302
Period size: 101 Copynumber: 1.8 Consensus size: 102
6045486 AAAGTGATGG
* * *
6045496 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGA-A-TGATGGGTCGCATATGTAGT
1 TCACGTGTGTAGTACTATGTGCAGGCGACTACATGTACCGGACAGTGAT-GGTCACATATGTAGT
6045559 ACTATGTGCAGGCTACTATGCATACCGGATAGCTTCGA
65 ACTATGTGCAGGCTACTATGCATACCGGATAGCTTCGA
* *
6045597 TCACGTGTGTAGTACTATGTGCAGGCGACTACATGTATCGGACAGTGATGGTCACATGTGTAGTA
1 TCACGTGTGTAGTACTATGTGCAGGCGACTACATGTACCGGACAGTGATGGTCACATATGTAGTA
6045662 CTATGTGCAGGCTACTATG
66 CTATGTGCAGGCTACTATG
6045681 TGAANNNNNN
Statistics
Matches: 77, Mismatches: 5, Indels: 3
0.91 0.06 0.04
Matches are distributed among these distances:
101 39 0.51
102 34 0.44
103 4 0.05
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.29
Consensus pattern (102 bp):
TCACGTGTGTAGTACTATGTGCAGGCGACTACATGTACCGGACAGTGATGGTCACATATGTAGTA
CTATGTGCAGGCTACTATGCATACCGGATAGCTTCGA
Found at i:6045657 original size:51 final size:51
Alignment explanation
Indices: 6045487--6045678 Score: 209
Period size: 51 Copynumber: 3.8 Consensus size: 51
6045477 GTAAAAGTGA
* *
6045487 AAGTGAT-GGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGG
1 AAGTGATCGGTCACATGTGTAGTACTATGTGCAGGCTACTACATGTACCGG
* * *
6045537 AA-TGATGGGTCGCATATGTAGTACTATGTGCAGGCTACT--ATGCATACCGG
1 AAGTGATCGGTCACATGTGTAGTACTATGTGCAGGCTACTACATG--TACCGG
* * * *
6045587 ATAGCT--TCGATCACGTGTGTAGTACTATGTGCAGGCGACTACATGTATCGG
1 A-AG-TGATCGGTCACATGTGTAGTACTATGTGCAGGCTACTACATGTACCGG
6045638 ACAGTGAT-GGTCACATGTGTAGTACTATGTGCAGGCTACTA
1 A-AGTGATCGGTCACATGTGTAGTACTATGTGCAGGCTACTA
6045679 TGTGAANNNN
Statistics
Matches: 117, Mismatches: 15, Indels: 19
0.77 0.10 0.13
Matches are distributed among these distances:
48 2 0.02
49 4 0.03
50 39 0.33
51 67 0.57
52 1 0.01
53 4 0.03
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.29
Consensus pattern (51 bp):
AAGTGATCGGTCACATGTGTAGTACTATGTGCAGGCTACTACATGTACCGG
Found at i:6058639 original size:13 final size:14
Alignment explanation
Indices: 6058621--6058658 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
6058611 CAAGTTGTTG
6058621 ATTTTACT-TAGTA
1 ATTTTACTGTAGTA
*
6058634 ATTTTATTGTAGTA
1 ATTTTACTGTAGTA
*
6058648 ATTTTATTGTA
1 ATTTTACTGTA
6058659 TTTGCGTTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 7 0.30
14 16 0.70
ACGTcount: A:0.29, C:0.03, G:0.11, T:0.58
Consensus pattern (14 bp):
ATTTTACTGTAGTA
Found at i:6058648 original size:14 final size:14
Alignment explanation
Indices: 6058629--6058658 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
6058619 TGATTTTACT
6058629 TAGTAATTTTATTG
1 TAGTAATTTTATTG
6058643 TAGTAATTTTATTG
1 TAGTAATTTTATTG
6058657 TA
1 TA
6058659 TTTGCGTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.30, C:0.00, G:0.13, T:0.57
Consensus pattern (14 bp):
TAGTAATTTTATTG
Found at i:6059272 original size:16 final size:18
Alignment explanation
Indices: 6059235--6059274 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
6059225 ATAAAGATGC
6059235 TTTATTTAAGTAAATTATA
1 TTTATTTAAGTAAA-TATA
6059254 TTTATTTAA-TAAA-ATA
1 TTTATTTAAGTAAATATA
6059270 TTTAT
1 TTTAT
6059275 AATTTAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 8 0.38
18 4 0.19
19 9 0.43
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (18 bp):
TTTATTTAAGTAAATATA
Found at i:6059855 original size:1 final size:1
Alignment explanation
Indices: 6059849--6059886 Score: 58
Period size: 1 Copynumber: 38.0 Consensus size: 1
6059839 TGTAATTCAC
* *
6059849 AAAAAAAAAAAAAAAAAAAAAACAAAAACAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
6059887 TTCATAAAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.95, C:0.05, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:6063914 original size:14 final size:14
Alignment explanation
Indices: 6063895--6063924 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
6063885 TCTCCTATGA
6063895 AAACTCAATAATTC
1 AAACTCAATAATTC
6063909 AAACTCAATAATTC
1 AAACTCAATAATTC
6063923 AA
1 AA
6063925 GAAATTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.53, C:0.20, G:0.00, T:0.27
Consensus pattern (14 bp):
AAACTCAATAATTC
Found at i:6064237 original size:14 final size:15
Alignment explanation
Indices: 6064218--6064251 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
6064208 GACACGGACG
*
6064218 AATTTCTGTTAAAA-
1 AATTTCTCTTAAAAC
6064232 AATTTCTCTTAAAAC
1 AATTTCTCTTAAAAC
6064247 AATTT
1 AATTT
6064252 TATATTAGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.41, C:0.12, G:0.03, T:0.44
Consensus pattern (15 bp):
AATTTCTCTTAAAAC
Found at i:6066170 original size:131 final size:131
Alignment explanation
Indices: 6065936--6066197 Score: 506
Period size: 131 Copynumber: 2.0 Consensus size: 131
6065926 ATTAGAAACA
*
6065936 ATAGCCCTTTTTGATACAGGAGCGGACCAAAACTGCATTAGAGAATGAATAATTCCAACAAAATA
1 ATAGCCCTTTTTGATACAGGAGCGGACCAAAACTGCATTAGAGAAGGAATAATTCCAACAAAATA
*
6066001 TTATAGTAAAACATCAGAATCTCTTAAGGCTGCAAATGGTAAAAAACTAAAAATTACTTACAAAA
66 TTATAATAAAACATCAGAATCTCTTAAGGCTGCAAATGGTAAAAAACTAAAAATTACTTACAAAA
6066066 T
131 T
6066067 ATAGCCCTTTTTGATACAGGAGCGGACCAAAACTGCATTAGAGAAGGAATAATTCCAACAAAATA
1 ATAGCCCTTTTTGATACAGGAGCGGACCAAAACTGCATTAGAGAAGGAATAATTCCAACAAAATA
6066132 TTATAATAAAACATCAGAATCTCTTAAGGCTGCAAATGGTAAAAAACTAAAAATTACTTACAAAA
66 TTATAATAAAACATCAGAATCTCTTAAGGCTGCAAATGGTAAAAAACTAAAAATTACTTACAAAA
6066197 T
131 T
6066198 TCCCCATACA
Statistics
Matches: 129, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
131 129 1.00
ACGTcount: A:0.45, C:0.16, G:0.14, T:0.25
Consensus pattern (131 bp):
ATAGCCCTTTTTGATACAGGAGCGGACCAAAACTGCATTAGAGAAGGAATAATTCCAACAAAATA
TTATAATAAAACATCAGAATCTCTTAAGGCTGCAAATGGTAAAAAACTAAAAATTACTTACAAAA
T
Found at i:6066557 original size:21 final size:22
Alignment explanation
Indices: 6066533--6066577 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
6066523 AGAAAAAGAG
6066533 AAATACAAAAAAG-AATAG-ATC
1 AAAT-CAAAAAAGAAATAGAATC
*
6066554 AAATCAAGAAAGAAATAGAATC
1 AAATCAAAAAAGAAATAGAATC
6066576 AA
1 AA
6066578 CAATTTGTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 7 0.33
21 9 0.43
22 5 0.24
ACGTcount: A:0.67, C:0.09, G:0.11, T:0.13
Consensus pattern (22 bp):
AAATCAAAAAAGAAATAGAATC
Found at i:6070717 original size:15 final size:15
Alignment explanation
Indices: 6070697--6070728 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
6070687 CATTTCACTA
*
6070697 TTATGTCTTTTGTAT
1 TTATGTCTTTTATAT
6070712 TTATGTCTTTTATAT
1 TTATGTCTTTTATAT
6070727 TT
1 TT
6070729 TTGTATGCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.06, G:0.09, T:0.69
Consensus pattern (15 bp):
TTATGTCTTTTATAT
Found at i:6071937 original size:21 final size:21
Alignment explanation
Indices: 6071906--6071954 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
6071896 AAATTAATTA
6071906 AAATT-ATATGATATTTTTGG
1 AAATTAATATGATATTTTTGG
6071926 AAATTAATATGATATTTTTGG
1 AAATTAATATGATATTTTTGG
6071947 AAATTAAT
1 AAATTAAT
6071955 TTTTAAGTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 5 0.18
21 23 0.82
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (21 bp):
AAATTAATATGATATTTTTGG
Found at i:6084711 original size:28 final size:26
Alignment explanation
Indices: 6084667--6084718 Score: 77
Period size: 28 Copynumber: 1.9 Consensus size: 26
6084657 ATATTATTAA
6084667 TATAATATATAAATGTTATAATAAGG
1 TATAATATATAAATGTTATAATAAGG
*
6084693 TATAATATATTATTATGTTATAATAA
1 TATAATATA-TA-AATGTTATAATAA
6084719 ACATTAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 9 0.39
27 2 0.09
28 12 0.52
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (26 bp):
TATAATATATAAATGTTATAATAAGG
Found at i:6085668 original size:25 final size:25
Alignment explanation
Indices: 6085640--6085701 Score: 106
Period size: 25 Copynumber: 2.5 Consensus size: 25
6085630 TTATCCTAGT
6085640 AGGCTTTATGCCAGTGAATTATAAC
1 AGGCTTTATGCCAGTGAATTATAAC
* *
6085665 AGGCTTTATGCCGGTGAATTATATC
1 AGGCTTTATGCCAGTGAATTATAAC
6085690 AGGCTTTATGCC
1 AGGCTTTATGCC
6085702 TAGCAGACTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.34
Consensus pattern (25 bp):
AGGCTTTATGCCAGTGAATTATAAC
Found at i:6089340 original size:18 final size:18
Alignment explanation
Indices: 6089317--6089353 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
6089307 NNNNNAATAT
6089317 TTTTTACAATTTTTATAA
1 TTTTTACAATTTTTATAA
*
6089335 TTTTTACAATTTTTGTAA
1 TTTTTACAATTTTTATAA
6089353 T
1 T
6089354 AAGATTATTA
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:0.30, C:0.05, G:0.03, T:0.62
Consensus pattern (18 bp):
TTTTTACAATTTTTATAA
Found at i:6089347 original size:8 final size:9
Alignment explanation
Indices: 6089317--6089348 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
6089307 NNNNNAATAT
6089317 TTTTTACAA
1 TTTTTACAA
*
6089326 TTTTTATAA
1 TTTTTACAA
6089335 TTTTTACAA
1 TTTTTACAA
6089344 TTTTT
1 TTTTT
6089349 GTAATAAGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.66
Consensus pattern (9 bp):
TTTTTACAA
Found at i:6089444 original size:18 final size:19
Alignment explanation
Indices: 6089405--6089453 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
6089395 TTTTTAAAAT
6089405 TTTTTATG-ATTTATATT-
1 TTTTTATGAATTTATATTA
*
6089422 TTTTTCTAGAATTTATA-TA
1 TTTTTAT-GAATTTATATTA
6089441 TTTTTATGAATTT
1 TTTTTATGAATTT
6089454 TTTATATATT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.02, G:0.06, T:0.65
Consensus pattern (19 bp):
TTTTTATGAATTTATATTA
Found at i:6095054 original size:40 final size:40
Alignment explanation
Indices: 6095003--6095089 Score: 115
Period size: 40 Copynumber: 2.2 Consensus size: 40
6094993 AATTATGGAA
* * *
6095003 TACTGAATATTGTTTTG-AGTACTG-AGTTGAATTGTGAAGT
1 TACTGAATATTGTTATGTA-TACTGCA-TTGAACTGTGAAAT
6095043 TACTGAATATTGTTATGTATACTGCATTGAACTGTGAAAT
1 TACTGAATATTGTTATGTATACTGCATTGAACTGTGAAAT
6095083 TACTGAA
1 TACTGAA
6095090 GTAATGAATT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
40 40 0.95
41 2 0.05
ACGTcount: A:0.31, C:0.08, G:0.21, T:0.40
Consensus pattern (40 bp):
TACTGAATATTGTTATGTATACTGCATTGAACTGTGAAAT
Found at i:6095338 original size:45 final size:45
Alignment explanation
Indices: 6095272--6095443 Score: 208
Period size: 45 Copynumber: 3.9 Consensus size: 45
6095262 TTACTGATTA
* * *
6095272 GGCAC-TTGTGTGCCGACTACTGTTACTATTACTGTTACCAATTT
1 GGCACTTTGTGTGTCGAATACTGTTACTATTACTGTTACCAATTC
* *
6095316 GGCACTTTGTGTGTCGAATACTGTTACTGTTACTGTTACCGATTC
1 GGCACTTTGTGTGTCGAATACTGTTACTATTACTGTTACCAATTC
*
6095361 GGCACTTTGTGTGTCGAATACTGTTA--ACGTACTGTTA-CAGATTC
1 GGCACTTTGTGTGTCGAATACTGTTACTA-TTACTGTTACCA-ATTC
* * * *
6095405 AGCACTTTGTGTGTTGAATACTGTTACTGTTACTTTTAC
1 GGCACTTTGTGTGTCGAATACTGTTACTATTACTGTTAC
6095444 TGCTACCGTT
Statistics
Matches: 109, Mismatches: 13, Indels: 10
0.83 0.10 0.08
Matches are distributed among these distances:
43 1 0.01
44 41 0.38
45 67 0.61
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.40
Consensus pattern (45 bp):
GGCACTTTGTGTGTCGAATACTGTTACTATTACTGTTACCAATTC
Found at i:6095397 original size:89 final size:88
Alignment explanation
Indices: 6095262--6095443 Score: 233
Period size: 89 Copynumber: 2.0 Consensus size: 88
6095252 TTTTGTCGGC
* * * **
6095262 TTACTGATTAGGCACTTGTGTGCCGACTACTGTTACTATTACTGTTACCA-ATTTGGCACTTTGT
1 TTACCGATTAGGCACTTGTGTGCCGAATACTGTTAC-AGTACTGTTA-CAGATTCAGCACTTTGT
6095326 GTGTCGAATACTGTTACTGTTACTG
64 GTGTCGAATACTGTTACTGTTACTG
* *
6095351 TTACCGATTCGGCACTTTGTGTGTCGAATACTGTTA-ACGTACTGTTACAGATTCAGCACTTTGT
1 TTACCGATTAGGCAC-TTGTGTGCCGAATACTGTTACA-GTACTGTTACAGATTCAGCACTTTGT
* *
6095415 GTGTTGAATACTGTTACTGTTACTT
64 GTGTCGAATACTGTTACTGTTACTG
6095440 TTAC
1 TTAC
6095444 TGCTACCGTT
Statistics
Matches: 81, Mismatches: 9, Indels: 6
0.84 0.09 0.06
Matches are distributed among these distances:
88 3 0.04
89 60 0.74
90 18 0.22
ACGTcount: A:0.21, C:0.19, G:0.20, T:0.41
Consensus pattern (88 bp):
TTACCGATTAGGCACTTGTGTGCCGAATACTGTTACAGTACTGTTACAGATTCAGCACTTTGTGT
GTCGAATACTGTTACTGTTACTG
Found at i:6095434 original size:6 final size:6
Alignment explanation
Indices: 6095423--6095466 Score: 52
Period size: 6 Copynumber: 7.2 Consensus size: 6
6095413 GTGTGTTGAA
* * *
6095423 TACTGT TACTGT TACTTT TACTGC TACCGT TACTGAT TACTGT T
1 TACTGT TACTGT TACTGT TACTGT TACTGT TACTG-T TACTGT T
6095467 TAGGTACTGT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
6 25 0.81
7 6 0.19
ACGTcount: A:0.18, C:0.20, G:0.14, T:0.48
Consensus pattern (6 bp):
TACTGT
Found at i:6104769 original size:18 final size:18
Alignment explanation
Indices: 6104735--6104769 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
6104725 ATATATGTTA
**
6104735 AAATAATAAAAGTAAAAC
1 AAATAATAAAACAAAAAC
6104753 AAATAATAAAACAAAAA
1 AAATAATAAAACAAAAA
6104770 GACAACCATT
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:0.77, C:0.06, G:0.03, T:0.14
Consensus pattern (18 bp):
AAATAATAAAACAAAAAC
Found at i:6106155 original size:18 final size:18
Alignment explanation
Indices: 6106122--6106174 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
6106112 ATTCACCTAA
*
6106122 ACCCAATCCAAACCCAAGT
1 ACCCAA-CCCAACCCAAGT
** *
6106141 ATTCAACCCAACCCAATT
1 ACCCAACCCAACCCAAGT
6106159 ACCCAACCCAACCCAA
1 ACCCAACCCAACCCAA
6106175 TCATAAAAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
18 24 0.86
19 4 0.14
ACGTcount: A:0.42, C:0.45, G:0.02, T:0.11
Consensus pattern (18 bp):
ACCCAACCCAACCCAAGT
Found at i:6106324 original size:9 final size:9
Alignment explanation
Indices: 6106266--6106323 Score: 80
Period size: 9 Copynumber: 6.4 Consensus size: 9
6106256 GTAGTGATTC
6106266 AATTCGGTT
1 AATTCGGTT
6106275 AATTCGGTT
1 AATTCGGTT
*
6106284 AATTCGGGT
1 AATTCGGTT
*
6106293 AATCCGGTT
1 AATTCGGTT
*
6106302 AATTCAGTT
1 AATTCGGTT
*
6106311 AATTTGGTT
1 AATTCGGTT
6106320 AATT
1 AATT
6106324 TTTAACCAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 42 1.00
ACGTcount: A:0.26, C:0.10, G:0.21, T:0.43
Consensus pattern (9 bp):
AATTCGGTT
Found at i:6108199 original size:20 final size:20
Alignment explanation
Indices: 6108100--6108201 Score: 82
Period size: 20 Copynumber: 5.1 Consensus size: 20
6108090 GCATCATAGA
* *
6108100 TGTGTAATAGAGACACCAAAG
1 TGTG-AATAGAGGCACCGAAG
*
6108121 TGCAGAA-AGAGGCACCGAAG
1 TG-TGAATAGAGGCACCGAAG
** * * *
6108141 TGCAAACAGAGACACCAAAG
1 TGTGAATAGAGGCACCGAAG
**
6108161 TGT-AATAGAGGCATTGAAG
1 TGTGAATAGAGGCACCGAAG
6108180 TGTGAATAGAGGCACCGAAG
1 TGTGAATAGAGGCACCGAAG
6108200 TG
1 TG
6108202 CAAACCCGTA
Statistics
Matches: 63, Mismatches: 15, Indels: 7
0.74 0.18 0.08
Matches are distributed among these distances:
19 16 0.25
20 42 0.67
21 4 0.06
22 1 0.02
ACGTcount: A:0.40, C:0.16, G:0.29, T:0.15
Consensus pattern (20 bp):
TGTGAATAGAGGCACCGAAG
Found at i:6116134 original size:5 final size:5
Alignment explanation
Indices: 6116124--6116160 Score: 74
Period size: 5 Copynumber: 7.4 Consensus size: 5
6116114 TCTATAATAG
6116124 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AA
6116161 TTACATTTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:6119929 original size:24 final size:24
Alignment explanation
Indices: 6119878--6119945 Score: 75
Period size: 24 Copynumber: 2.8 Consensus size: 24
6119868 ATTGTAAAGT
* * **
6119878 ATCTTAGAATGACGAAATAATAGG
1 ATCTTAGAATTACCAAATAATAAA
6119902 ATCTTAGAATTACCAAATAATAAA
1 ATCTTAGAATTACCAAATAATAAA
6119926 ATCTT-GTAAATTACCAAATA
1 ATCTTAG--AATTACCAAATA
6119946 TTTTCCTTCT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
23 1 0.03
24 25 0.66
25 12 0.32
ACGTcount: A:0.49, C:0.12, G:0.10, T:0.29
Consensus pattern (24 bp):
ATCTTAGAATTACCAAATAATAAA
Found at i:6120079 original size:15 final size:15
Alignment explanation
Indices: 6120055--6120084 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
6120045 TAAAATTAGT
*
6120055 TAAATTAATAATAAA
1 TAAATAAATAATAAA
6120070 TAAATAAATAATAAA
1 TAAATAAATAATAAA
6120085 AAAGGATAGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
TAAATAAATAATAAA
Found at i:6120425 original size:31 final size:31
Alignment explanation
Indices: 6120387--6120476 Score: 153
Period size: 32 Copynumber: 2.9 Consensus size: 31
6120377 AGGCAAATTA
6120387 CAAGAGTAATTGAATCCTAATAAAACTATTT
1 CAAGAGTAATTGAATCCTAATAAAACTATTT
*
6120418 CAAGAGTAATTGAATCCTAATAAAAACTCTTT
1 CAAGAGTAATTGAATCCTAAT-AAAACTATTT
*
6120450 AAAGAGTAATTGAATCCTAATAAAACT
1 CAAGAGTAATTGAATCCTAATAAAACT
6120477 CTTTAAAATT
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
31 27 0.48
32 29 0.52
ACGTcount: A:0.47, C:0.13, G:0.10, T:0.30
Consensus pattern (31 bp):
CAAGAGTAATTGAATCCTAATAAAACTATTT
Found at i:6120478 original size:31 final size:31
Alignment explanation
Indices: 6120388--6120483 Score: 165
Period size: 31 Copynumber: 3.1 Consensus size: 31
6120378 GGCAAATTAC
* *
6120388 AAGAGTAATTGAATCCTAATAAAACTATTTC
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
6120419 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAAT-AAAACTCTTTA
6120451 AAGAGTAATTGAATCCTAATAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
6120482 AA
1 AA
6120484 ATTATCTAAG
Statistics
Matches: 62, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
31 33 0.53
32 29 0.47
ACGTcount: A:0.47, C:0.12, G:0.09, T:0.31
Consensus pattern (31 bp):
AAGAGTAATTGAATCCTAATAAAACTCTTTA
Found at i:6128070 original size:18 final size:20
Alignment explanation
Indices: 6128047--6128084 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
6128037 AAGAGTCTAT
6128047 AAAT-CCTTC-CGCACTCTC
1 AAATCCCTTCACGCACTCTC
*
6128065 AAATCCCTTCACTCACTCTC
1 AAATCCCTTCACGCACTCTC
6128085 CCCCTATCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.24
19 5 0.29
20 8 0.47
ACGTcount: A:0.24, C:0.45, G:0.03, T:0.29
Consensus pattern (20 bp):
AAATCCCTTCACGCACTCTC
Found at i:6136630 original size:32 final size:32
Alignment explanation
Indices: 6136587--6136662 Score: 98
Period size: 32 Copynumber: 2.4 Consensus size: 32
6136577 CAAAATAAAT
* *
6136587 TATGAAAAGTTACGAATGTGAAGAGACTTGAA
1 TATGAAAAGTTAAGAATGCGAAGAGACTTGAA
* *
6136619 TATGAAGAGTTAATAATGCGAAGAGACTTGAA
1 TATGAAAAGTTAAGAATGCGAAGAGACTTGAA
* *
6136651 GACGAAAAGTTA
1 TATGAAAAGTTA
6136663 CACACATGCA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.45, C:0.07, G:0.25, T:0.24
Consensus pattern (32 bp):
TATGAAAAGTTAAGAATGCGAAGAGACTTGAA
Found at i:6141104 original size:32 final size:32
Alignment explanation
Indices: 6141062--6141137 Score: 107
Period size: 32 Copynumber: 2.4 Consensus size: 32
6141052 AAAATAAATT
*
6141062 ATGAAAAGTTACGAATGTGAAGAGACTTGAAC
1 ATGAAAAGTTACGAATGCGAAGAGACTTGAAC
* ** *
6141094 ATGAATAGTTAATAATGCGAAGAGACTTGAAG
1 ATGAAAAGTTACGAATGCGAAGAGACTTGAAC
6141126 ATGAAAAGTTAC
1 ATGAAAAGTTAC
6141138 ACACATGCAT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.45, C:0.08, G:0.24, T:0.24
Consensus pattern (32 bp):
ATGAAAAGTTACGAATGCGAAGAGACTTGAAC
Found at i:6141918 original size:20 final size:19
Alignment explanation
Indices: 6141889--6141941 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 19
6141879 AAATGGTAAG
6141889 AAATAAAAGTTTAGGGGGA
1 AAATAAAAGTTTAGGGGGA
*
6141908 AAATAAAAAGTTT-TGGGG-
1 AAAT-AAAAGTTTAGGGGGA
6141926 -AATAAAAGTTTGAGGG
1 AAATAAAAGTTT-AGGG
6141942 AAAGTAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
16 8 0.28
17 3 0.10
18 2 0.07
19 8 0.28
20 8 0.28
ACGTcount: A:0.45, C:0.00, G:0.30, T:0.25
Consensus pattern (19 bp):
AAATAAAAGTTTAGGGGGA
Found at i:6142977 original size:22 final size:22
Alignment explanation
Indices: 6142951--6142992 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
6142941 ATTGCACCAT
6142951 CAATAATGAAACAAAATTATAC
1 CAATAATGAAACAAAATTATAC
* * *
6142973 CAATATTTAAAGAAAATTAT
1 CAATAATGAAACAAAATTAT
6142993 TCTATAAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.57, C:0.10, G:0.05, T:0.29
Consensus pattern (22 bp):
CAATAATGAAACAAAATTATAC
Found at i:6149777 original size:37 final size:39
Alignment explanation
Indices: 6149731--6149829 Score: 121
Period size: 37 Copynumber: 2.5 Consensus size: 39
6149721 TTTAATCAAT
6149731 TTAATATTAAATTAATATAATACTTA-T-CAAGATAAATA
1 TTAA-ATTAAATTAATATAATACTTACTACAAGATAAATA
* * *
6149769 TTAGATTAAATTAATAGAATATTTATCTACAAGATAAATA
1 TTAAATTAAATTAATATAATACTTA-CTACAAGATAAATA
*
6149809 TTAAATTAAAATTAAAATAAT
1 TTAAATT-AAATTAATATAAT
6149830 CGCATTAATA
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
37 19 0.37
38 3 0.06
39 1 0.02
40 17 0.33
41 11 0.22
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.38
Consensus pattern (39 bp):
TTAAATTAAATTAATATAATACTTACTACAAGATAAATA
Found at i:6150518 original size:22 final size:22
Alignment explanation
Indices: 6150490--6150534 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
6150480 TGACAATGTC
6150490 TGGCTTGGTCCCACCATTCGAT
1 TGGCTTGGTCCCACCATTCGAT
6150512 TGGCTTGGTCCCACCATTCGAT
1 TGGCTTGGTCCCACCATTCGAT
6150534 T
1 T
6150535 TTCGAGACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.13, C:0.31, G:0.22, T:0.33
Consensus pattern (22 bp):
TGGCTTGGTCCCACCATTCGAT
Found at i:6151527 original size:26 final size:25
Alignment explanation
Indices: 6151491--6151554 Score: 74
Period size: 26 Copynumber: 2.5 Consensus size: 25
6151481 AAATTCCCCG
* * *
6151491 TGTTTACTGTCCCGATGGACTACCC
1 TGTTTATTGTCCCAATGAACTACCC
6151516 ATGTTTATTGTCCCAATGAACTACCC
1 -TGTTTATTGTCCCAATGAACTACCC
*
6151542 CGTCTTATTGTCC
1 TGT-TTATTGTCC
6151555 AAGCAGACTC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
25 2 0.06
26 31 0.94
ACGTcount: A:0.19, C:0.30, G:0.16, T:0.36
Consensus pattern (25 bp):
TGTTTATTGTCCCAATGAACTACCC
Found at i:6154207 original size:19 final size:19
Alignment explanation
Indices: 6154163--6154209 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
6154153 CTAAACCGAG
6154163 ACTAATTTTTATTCTTCAT
1 ACTAATTTTTATTCTTCAT
* *
6154182 ATTTAATTTTATATT-TTTAT
1 A-CTAATTTT-TATTCTTCAT
6154202 ACTAATTT
1 ACTAATTT
6154210 CATTTTAAGC
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 7 0.30
20 12 0.52
21 4 0.17
ACGTcount: A:0.30, C:0.09, G:0.00, T:0.62
Consensus pattern (19 bp):
ACTAATTTTTATTCTTCAT
Found at i:6166254 original size:8 final size:8
Alignment explanation
Indices: 6166241--6166266 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
6166231 CACAAAGGTT
6166241 CATATATA
1 CATATATA
6166249 CATATATA
1 CATATATA
6166257 CATATATA
1 CATATATA
6166265 CA
1 CA
6166267 CACGTACATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (8 bp):
CATATATA
Found at i:6167182 original size:33 final size:33
Alignment explanation
Indices: 6167110--6167187 Score: 90
Period size: 34 Copynumber: 2.4 Consensus size: 33
6167100 GATATTACAA
*
6167110 ATATTTAAAAAAATGCAAAAATACAAAAATATT
1 ATATTTAAAAAAATGCAAAAAAACAAAAATATT
*
6167143 AAATTTATAAAAAATAG-AAAAAAACTAAAAA-A-T
1 ATATTTA-AAAAAAT-GCAAAAAAAC-AAAAATATT
6167176 ATATTTAAAAAA
1 ATATTTAAAAAA
6167188 TTACTAAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
32 5 0.13
33 13 0.33
34 15 0.38
35 6 0.15
ACGTcount: A:0.68, C:0.04, G:0.03, T:0.26
Consensus pattern (33 bp):
ATATTTAAAAAAATGCAAAAAAACAAAAATATT
Found at i:6170581 original size:32 final size:30
Alignment explanation
Indices: 6170508--6170573 Score: 114
Period size: 30 Copynumber: 2.2 Consensus size: 30
6170498 ATTATGGAGC
6170508 ACACGGCTGTGTGACACACACGGCCTGAGT
1 ACACGGCTGTGTGACACACACGGCCTGAGT
* *
6170538 ATACAGCTGTGTGACACACACGGCCTGAGT
1 ACACGGCTGTGTGACACACACGGCCTGAGT
6170568 ACACGG
1 ACACGG
6170574 TCATGTGTCA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.26, C:0.29, G:0.29, T:0.17
Consensus pattern (30 bp):
ACACGGCTGTGTGACACACACGGCCTGAGT
Found at i:6174461 original size:18 final size:17
Alignment explanation
Indices: 6174433--6174466 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
6174423 AGTAAAATAC
*
6174433 TAAAAATTAATGTATTT
1 TAAAAATTAATATATTT
6174450 TAAAATATTAATATATT
1 TAAAA-ATTAATATATT
6174467 AATATAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (17 bp):
TAAAAATTAATATATTT
Found at i:6174706 original size:78 final size:79
Alignment explanation
Indices: 6174617--6174774 Score: 309
Period size: 78 Copynumber: 2.0 Consensus size: 79
6174607 TTTACTGTTG
6174617 TTTAATTTTTTTTGTACAATCTTTTGCAATTTCTAATAATTTTTATATTTTTTAAAATACTTTAA
1 TTTAATTTTTTTTGTACAATCTTTTGCAATTTCTAATAATTTTTATATTTTTTAAAATACTTTAA
6174682 GA-TTCTAATAGTT
66 GATTTCTAATAGTT
6174695 TTTAATTTTTTTTGTACAATCTTTTGCAATTTCTAATAATTTTTATATTTTTTAAAATACTTTAA
1 TTTAATTTTTTTTGTACAATCTTTTGCAATTTCTAATAATTTTTATATTTTTTAAAATACTTTAA
6174760 GATTTCTAATAGTT
66 GATTTCTAATAGTT
6174774 T
1 T
6174775 CATTTTTTAT
Statistics
Matches: 79, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
78 67 0.85
79 12 0.15
ACGTcount: A:0.30, C:0.08, G:0.05, T:0.57
Consensus pattern (79 bp):
TTTAATTTTTTTTGTACAATCTTTTGCAATTTCTAATAATTTTTATATTTTTTAAAATACTTTAA
GATTTCTAATAGTT
Found at i:6174794 original size:25 final size:26
Alignment explanation
Indices: 6174766--6174817 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
6174756 TTAAGATTTC
* *
6174766 TAATAGTT-TCATTTTTTATATTTTT
1 TAATAATTATCATTTTTTACATTTTT
*
6174791 TAATAATTATTATTTTTTACATTTTT
1 TAATAATTATCATTTTTTACATTTTT
6174817 T
1 T
6174818 TAAAAGTGCT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 7 0.30
26 16 0.70
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (26 bp):
TAATAATTATCATTTTTTACATTTTT
Found at i:6174869 original size:26 final size:26
Alignment explanation
Indices: 6174778--6174871 Score: 68
Period size: 27 Copynumber: 3.5 Consensus size: 26
6174768 ATAGTTTCAT
* * *
6174778 TTTTTATATTTTTTAATAATTAT-TA
1 TTTTTATAATTTTTAAAAATTATACA
*
6174803 TTTTT-TACATTTTTTTAAAAGTGCTA-ACA
1 TTTTTATA-A--TTTTTAAAAAT--TATACA
*
6174832 TTTTTTTGAATTTTTAAAAATTATACA
1 TTTTTAT-AATTTTTAAAAATTATACA
6174859 TTTTTATAATTTT
1 TTTTTATAATTTT
6174872 ATTTATATTT
Statistics
Matches: 54, Mismatches: 6, Indels: 17
0.70 0.08 0.22
Matches are distributed among these distances:
24 2 0.04
25 5 0.09
26 8 0.15
27 18 0.33
28 10 0.19
29 8 0.15
30 2 0.04
31 1 0.02
ACGTcount: A:0.32, C:0.04, G:0.03, T:0.61
Consensus pattern (26 bp):
TTTTTATAATTTTTAAAAATTATACA
Found at i:6175476 original size:22 final size:20
Alignment explanation
Indices: 6175443--6175485 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 20
6175433 ATTGAATAAA
*
6175443 GAAAAAAAAAAACTTTGATG
1 GAAAAAAAAAAACGTTGATG
6175463 GAAAAAATAGAAAACGTTGATG
1 GAAAAAA-A-AAAACGTTGATG
6175485 G
1 G
6175486 CTAAAGGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 7 0.35
21 1 0.05
22 12 0.60
ACGTcount: A:0.56, C:0.05, G:0.21, T:0.19
Consensus pattern (20 bp):
GAAAAAAAAAAACGTTGATG
Found at i:6175729 original size:21 final size:21
Alignment explanation
Indices: 6175703--6175755 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
6175693 CGCTATTTCT
*
6175703 AATCTCACTGCTACAATACCC
1 AATCTCACTGCTACAATAACC
* * * *
6175724 AATCTCACCGCTATAGTAACT
1 AATCTCACTGCTACAATAACC
6175745 AATCTCACTGC
1 AATCTCACTGC
6175756 CACCGCTGTT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.32, C:0.34, G:0.08, T:0.26
Consensus pattern (21 bp):
AATCTCACTGCTACAATAACC
Found at i:6178450 original size:20 final size:19
Alignment explanation
Indices: 6178425--6178462 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
6178415 CATCCTCTTA
6178425 AGAAAGAAAAAAACAGAAAT
1 AGAAAGAAAAAAA-AGAAAT
*
6178445 AGAAAGAAGAAAAAGAAA
1 AGAAAGAAAAAAAAGAAA
6178463 GCCTCCTACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03
Consensus pattern (19 bp):
AGAAAGAAAAAAAAGAAAT
Found at i:6185192 original size:15 final size:14
Alignment explanation
Indices: 6185171--6185206 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
6185161 ATAATCCTTA
6185171 ATAATTATCTCAAT
1 ATAATTATCTCAAT
*
6185185 ATTAATTATCTTAAT
1 A-TAATTATCTCAAT
6185200 ATAATTA
1 ATAATTA
6185207 AAATAGAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (14 bp):
ATAATTATCTCAAT
Found at i:6186940 original size:29 final size:29
Alignment explanation
Indices: 6186898--6186955 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
6186888 AAAAAAAGTG
6186898 GTAGAGGATCTTTCACATTGAAGTTAGAT
1 GTAGAGGATCTTTCACATTGAAGTTAGAT
6186927 GTAGAGGATCTTTCACATTGAAGTTAGAT
1 GTAGAGGATCTTTCACATTGAAGTTAGAT
6186956 ATGAGTAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.31, C:0.10, G:0.24, T:0.34
Consensus pattern (29 bp):
GTAGAGGATCTTTCACATTGAAGTTAGAT
Found at i:6195485 original size:15 final size:15
Alignment explanation
Indices: 6195461--6195515 Score: 56
Period size: 16 Copynumber: 3.5 Consensus size: 15
6195451 TTTTAAAAAT
6195461 TTTAAAAATATTTTA
1 TTTAAAAATATTTTA
*
6195476 TTTAACAATATTTTTA
1 TTTAAAAATA-TTTTA
* *
6195492 TCTCAAAAATATATTTT
1 T-TTAAAAATAT-TTTA
6195509 TTTAAAA
1 TTTAAAA
6195516 TCAATGTTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
15 9 0.28
16 12 0.38
17 11 0.34
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (15 bp):
TTTAAAAATATTTTA
Found at i:6196340 original size:16 final size:17
Alignment explanation
Indices: 6196311--6196352 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
6196301 TTATATGATA
*
6196311 TTTAATATTTTTTAAAT
1 TTTAATATTATTTAAAT
6196328 TTTAAT-TTATTTAAAT
1 TTTAATATTATTTAAAT
*
6196344 ATT-ATATTA
1 TTTAATATTA
6196353 CAATTTAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 2 0.09
16 14 0.64
17 6 0.27
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTAATATTATTTAAAT
Found at i:6197347 original size:25 final size:26
Alignment explanation
Indices: 6197311--6197361 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
6197301 TTTTTATGAC
6197311 AGTTTTTATTTATTT-ACTTTTTTTA
1 AGTTTTTATTTATTTGACTTTTTTTA
* *
6197336 AGTTTTTTTTTATTTGTCTTTTTTTA
1 AGTTTTTATTTATTTGACTTTTTTTA
6197362 TTTGTTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 14 0.61
26 9 0.39
ACGTcount: A:0.16, C:0.04, G:0.06, T:0.75
Consensus pattern (26 bp):
AGTTTTTATTTATTTGACTTTTTTTA
Found at i:6197357 original size:14 final size:13
Alignment explanation
Indices: 6197312--6197381 Score: 61
Period size: 13 Copynumber: 5.3 Consensus size: 13
6197302 TTTTATGACA
6197312 GTTTTTATTTATTT
1 GTTTTT-TTTATTT
** **
6197326 ACTTTTTTTAAGT
1 GTTTTTTTTATTT
6197339 -TTTTTTTTATTT
1 GTTTTTTTTATTT
6197351 GTCTTTTTTTATTT
1 GT-TTTTTTTATTT
* *
6197365 GTTTTATTTGTTT
1 GTTTTTTTTATTT
6197378 GTTT
1 GTTT
6197382 ATTGTTGATT
Statistics
Matches: 45, Mismatches: 9, Indels: 5
0.76 0.15 0.08
Matches are distributed among these distances:
12 9 0.20
13 19 0.42
14 17 0.38
ACGTcount: A:0.11, C:0.03, G:0.09, T:0.77
Consensus pattern (13 bp):
GTTTTTTTTATTT
Found at i:6197357 original size:15 final size:14
Alignment explanation
Indices: 6197340--6197379 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
6197330 TTTTTAAGTT
6197340 TTTTTTTATTTGTC
1 TTTTTTTATTTGTC
6197354 TTTTTTTATTTGT-
1 TTTTTTTATTTGTC
* *
6197367 TTTATTTGTTTGT
1 TTTTTTTATTTGT
6197380 TTATTGTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 11 0.46
14 13 0.54
ACGTcount: A:0.07, C:0.03, G:0.10, T:0.80
Consensus pattern (14 bp):
TTTTTTTATTTGTC
Found at i:6197444 original size:24 final size:24
Alignment explanation
Indices: 6197417--6197484 Score: 75
Period size: 24 Copynumber: 2.7 Consensus size: 24
6197407 ATTTTTTATA
6197417 ATATTATTTTTTAAAATTTTAAAT
1 ATATTATTTTTTAAAATTTTAAAT
*
6197441 ATATT-TTTTTTATAATTTTTAAAT
1 ATATTATTTTTTA-AAATTTTAAAT
*
6197465 ATTTTTAATTTTTTTAAAAT
1 A-TATT-A-TTTTTTAAAAT
6197485 ATATTATTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
23 7 0.19
24 16 0.44
25 3 0.08
27 3 0.08
28 7 0.19
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (24 bp):
ATATTATTTTTTAAAATTTTAAAT
Found at i:6197448 original size:22 final size:22
Alignment explanation
Indices: 6197410--6197470 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 22
6197400 AATTGAAATT
6197410 TTTTATAATAT-TATTTTTTAAAA
1 TTTTA-AATATAT-TTTTTTAAAA
*
6197433 TTTTAAATATATTTTTTTTATAA
1 TTTTAAATATA-TTTTTTTAAAA
*
6197456 TTTTTAA-ATATTTTT
1 TTTTAAATATATTTTT
6197471 AATTTTTTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
21 5 0.15
22 8 0.24
23 20 0.59
24 1 0.03
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (22 bp):
TTTTAAATATATTTTTTTAAAA
Found at i:6197584 original size:30 final size:28
Alignment explanation
Indices: 6197536--6197614 Score: 88
Period size: 30 Copynumber: 2.7 Consensus size: 28
6197526 TTTTTACAAT
* * *
6197536 ATTTTAAATGTATATTTTAAATATTCTTTA
1 ATTTTAAATATAT-TTTTAAA-ATTATTAA
6197566 ATTTTAAATATAATTTTTATAAATTATTAA
1 ATTTTAAATAT-ATTTTTA-AAATTATTAA
6197596 ATTTTAAA-ATATTTTTAAA
1 ATTTTAAATATATTTTTAAA
6197615 GATATTCAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
27 2 0.05
28 7 0.16
29 2 0.05
30 29 0.66
31 4 0.09
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (28 bp):
ATTTTAAATATATTTTTAAAATTATTAA
Found at i:6197649 original size:19 final size:21
Alignment explanation
Indices: 6197625--6197664 Score: 66
Period size: 19 Copynumber: 2.0 Consensus size: 21
6197615 GATATTCAAA
6197625 AAAATTTT-AAATT-ATATTT
1 AAAATTTTAAAATTAATATTT
6197644 AAAATTTTAAAATTAATATTT
1 AAAATTTTAAAATTAATATTT
6197665 TATTTGGTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 8 0.42
20 5 0.26
21 6 0.32
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
AAAATTTTAAAATTAATATTT
Found at i:6197962 original size:86 final size:85
Alignment explanation
Indices: 6197817--6198001 Score: 334
Period size: 86 Copynumber: 2.2 Consensus size: 85
6197807 GCATATATAG
*
6197817 AATGGTGAAATTGTTGTGTTCAATAGGAGAGTTTAAAAATTCTGTTGAAGATGAATAATGAGGTG
1 AATGGTGAAATTGTTGTGTTCAATAGGAGAGTTAAAAAATTCTGTTGAAGATGAATAATGAGGTG
6197882 TTTTTGGTGTATATTTTTTTT
66 TTTTTGGTGTATA-TTTTTTT
* *
6197903 AATGGCGAAATTGTTGTGTTCAGTAGGAGAGTTAAAAAATTCTGTTGAAGATGAATAATGAGGTG
1 AATGGTGAAATTGTTGTGTTCAATAGGAGAGTTAAAAAATTCTGTTGAAGATGAATAATGAGGTG
6197968 TTTTTGGTGTATATTTTTTT
66 TTTTTGGTGTATATTTTTTT
6197988 AATGGTGAAATTGT
1 AATGGTGAAATTGT
6198002 AGAAGGTGAT
Statistics
Matches: 95, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
85 20 0.21
86 75 0.79
ACGTcount: A:0.30, C:0.03, G:0.25, T:0.42
Consensus pattern (85 bp):
AATGGTGAAATTGTTGTGTTCAATAGGAGAGTTAAAAAATTCTGTTGAAGATGAATAATGAGGTG
TTTTTGGTGTATATTTTTTT
Found at i:6201104 original size:30 final size:30
Alignment explanation
Indices: 6201069--6201174 Score: 106
Period size: 30 Copynumber: 3.6 Consensus size: 30
6201059 CAGTGGTTGC
* *
6201069 TCTGGGTGAAATGAACTCGAACCGCCTATG
1 TCTGGGTGATATGAACTCGAACCGCCCATG
* * * *
6201099 TCTGGGTGATACGAACTCCAACCACCCAAG
1 TCTGGGTGATATGAACTCGAACCGCCCATG
* * *
6201129 TC-CGGTGATATGAACTTGAACTGCCCATG
1 TCTGGGTGATATGAACTCGAACCGCCCATG
* *
6201158 TCAGGGTGATACGAACT
1 TCTGGGTGATATGAACT
6201175 GCTTTGCGAC
Statistics
Matches: 60, Mismatches: 15, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
29 22 0.37
30 38 0.63
ACGTcount: A:0.27, C:0.25, G:0.25, T:0.23
Consensus pattern (30 bp):
TCTGGGTGATATGAACTCGAACCGCCCATG
Found at i:6203901 original size:20 final size:20
Alignment explanation
Indices: 6203876--6203959 Score: 88
Period size: 20 Copynumber: 4.3 Consensus size: 20
6203866 NNNNNNNTTA
6203876 TTAAAAATATATTTAAAATT
1 TTAAAAATATATTTAAAATT
* *
6203896 TTAAAAATAATTTTTAAATTT
1 TTAAAAAT-ATATTTAAAATT
6203917 TTAAAAA-ATAATTTAAAA--
1 TTAAAAATAT-ATTTAAAATT
*
6203935 --AAGAATATATTTAAAATT
1 TTAAAAATATATTTAAAATT
6203953 TTAAAAA
1 TTAAAAA
6203960 AGTAATATTA
Statistics
Matches: 51, Mismatches: 6, Indels: 14
0.72 0.08 0.20
Matches are distributed among these distances:
16 12 0.24
17 2 0.04
19 2 0.04
20 18 0.35
21 17 0.33
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (20 bp):
TTAAAAATATATTTAAAATT
Found at i:6203911 original size:21 final size:21
Alignment explanation
Indices: 6203876--6203930 Score: 76
Period size: 21 Copynumber: 2.6 Consensus size: 21
6203866 NNNNNNNTTA
*
6203876 TTAAAAAT-ATATTTAAAATT
1 TTAAAAATAATTTTTAAAATT
*
6203896 TTAAAAATAATTTTTAAATTT
1 TTAAAAATAATTTTTAAAATT
6203917 TTAAAAAATAATTT
1 TT-AAAAATAATTT
6203931 AAAAAAGAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 8 0.26
21 12 0.39
22 11 0.35
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
TTAAAAATAATTTTTAAAATT
Found at i:6203967 original size:23 final size:25
Alignment explanation
Indices: 6203928--6203974 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
6203918 TAAAAAATAA
6203928 TTTAAAAAAGAATATATT-TAAAAT
1 TTTAAAAAAGAATATATTATAAAAT
*
6203952 TTTAAAAAAGTA-ATATTATAAAA
1 TTTAAAAAAGAATATATTATAAAA
6203975 CATTTCAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (25 bp):
TTTAAAAAAGAATATATTATAAAAT
Found at i:6205659 original size:27 final size:27
Alignment explanation
Indices: 6205619--6205673 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
6205609 AATATATTGG
*
6205619 ATTTATACTCTTGACTTTTGTTTGTCA
1 ATTTATACTATTGACTTTTGTTTGTCA
*
6205646 ATTTGTACTATTGACTTTTGTTTGTCA
1 ATTTATACTATTGACTTTTGTTTGTCA
6205673 A
1 A
6205674 CTTCTCTCGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.20, C:0.13, G:0.13, T:0.55
Consensus pattern (27 bp):
ATTTATACTATTGACTTTTGTTTGTCA
Found at i:6211002 original size:18 final size:18
Alignment explanation
Indices: 6210964--6211002 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
6210954 TCCAAAACCA
*
6210964 AAACAGTCCAAAATGTCC
1 AAACAGTCCAAAATGTAC
*
6210982 AAACAGTCCAAAATTTAC
1 AAACAGTCCAAAATGTAC
6211000 AAA
1 AAA
6211003 ACTCTCCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.51, C:0.23, G:0.08, T:0.18
Consensus pattern (18 bp):
AAACAGTCCAAAATGTAC
Found at i:6212557 original size:40 final size:40
Alignment explanation
Indices: 6212513--6212590 Score: 113
Period size: 40 Copynumber: 1.9 Consensus size: 40
6212503 TTTAATAAAT
6212513 AAATACATATTCTTTA-TTTTTTAATTTTAAAATATTTTAA
1 AAATACAT-TTCTTTATTTTTTTAATTTTAAAATATTTTAA
* * *
6212553 AAATATATTTTTTTATTTTTTTATTTTTAAAATATTTT
1 AAATACATTTCTTTATTTTTTTAATTTTAAAATATTTT
6212591 TTTGTGTTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
39 6 0.18
40 28 0.82
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (40 bp):
AAATACATTTCTTTATTTTTTTAATTTTAAAATATTTTAA
Found at i:6213289 original size:42 final size:41
Alignment explanation
Indices: 6213190--6213394 Score: 243
Period size: 42 Copynumber: 4.9 Consensus size: 41
6213180 ACTTACAGGG
* * ***
6213190 AAAACGCCGCTAAATCTCATGTTCTTTAGTGGCGCTACCG-A
1 AAAACGCCGCTAAA-ATCATGTTCTTTAGCGGCGCTTGGGAA
6213231 AAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTGGGAA
1 AAAACGCCGCTAAA-ATCATGTTCTTTAGCGGCGCTTGGGAA
* *
6213273 AAAACGCCGCTAAAGATCATGTTCTTTAGCAGCGCTTAGGAA
1 AAAACGCCGCTAAA-ATCATGTTCTTTAGCGGCGCTTGGGAA
* *
6213315 GAAAACGCCGCTAAAAGTAATGTTCTTTAGCGGCGCTTGGTAA
1 -AAAACGCCGCTAAAA-TCATGTTCTTTAGCGGCGCTTGGGAA
*
6213358 AAAGCGCCGCTAAAAGT-AGTGTTCTTTAGCGGCGCTT
1 AAAACGCCGCTAAAA-TCA-TGTTCTTTAGCGGCGCTT
6213395 ATTTCACAAA
Statistics
Matches: 147, Mismatches: 13, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
41 35 0.24
42 76 0.52
43 36 0.24
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.25
Consensus pattern (41 bp):
AAAACGCCGCTAAAATCATGTTCTTTAGCGGCGCTTGGGAA
Found at i:6213351 original size:85 final size:83
Alignment explanation
Indices: 6213190--6213395 Score: 258
Period size: 85 Copynumber: 2.4 Consensus size: 83
6213180 ACTTACAGGG
* * *
6213190 AAAACGCCGCTAAATCTCATGTTCTTTAGTGGCGC-TACCGAAAAACGCCGCTAAAGATCATGTT
1 AAAACGCCGCTAAA-ATCATGTTCTTTAGCGGCGCTTACCGAAAAACGCCGCTAAAGATAATGTT
6213254 CTTTAGCGGCGCTTGGGAA
65 CTTTAGCGGCGCTTGGGAA
* *
6213273 AAAACGCCGCTAAAGATCATGTTCTTTAGCAGCGCTTA-GGAAGAAAACGCCGCTAAA-AGTAAT
1 AAAACGCCGCTAAA-ATCATGTTCTTTAGCGGCGCTTACCG-A-AAAACGCCGCTAAAGA-TAAT
*
6213336 GTTCTTTAGCGGCGCTTGGTAA
62 GTTCTTTAGCGGCGCTTGGGAA
*
6213358 AAAGCGCCGCTAAAAGT-AGTGTTCTTTAGCGGCGCTTA
1 AAAACGCCGCTAAAA-TCA-TGTTCTTTAGCGGCGCTTA
6213396 TTTCACAAAC
Statistics
Matches: 108, Mismatches: 9, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
83 32 0.30
84 6 0.06
85 70 0.65
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.25
Consensus pattern (83 bp):
AAAACGCCGCTAAAATCATGTTCTTTAGCGGCGCTTACCGAAAAACGCCGCTAAAGATAATGTTC
TTTAGCGGCGCTTGGGAA
Found at i:6213840 original size:21 final size:21
Alignment explanation
Indices: 6213816--6213887 Score: 101
Period size: 21 Copynumber: 3.4 Consensus size: 21
6213806 TTCTTTTGAA
* *
6213816 CCTCTACTTCTCTCGCTGCGG
1 CCTCTGCTTCTCTCGCTGCAG
6213837 CCTCTGCTTCTCTCGCTGCAG
1 CCTCTGCTTCTCTCGCTGCAG
*
6213858 CCTCTGCTTCCCTCGCTGCCA-
1 CCTCTGCTTCTCTCGCTG-CAG
6213879 CCTCTGCTT
1 CCTCTGCTT
6213888 TAAGTTGTTG
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
21 45 0.96
22 2 0.04
ACGTcount: A:0.04, C:0.46, G:0.17, T:0.33
Consensus pattern (21 bp):
CCTCTGCTTCTCTCGCTGCAG
Found at i:6216581 original size:74 final size:74
Alignment explanation
Indices: 6216459--6216615 Score: 194
Period size: 74 Copynumber: 2.1 Consensus size: 74
6216449 TAATACTATA
* *
6216459 CTTTAGCGGCGTTTTAATATAAGCGTCACTAATGCTACTATACATCAAGACCAAAGCGCTGCGTT
1 CTTT-GCGGCGTTTTAATATAAGCGCCACTAATGCTAATATACATCAAGACCAAA-CGCTGCGTT
*
6216524 TTGGTTAATAT
64 TTGGTTAAGAT
* * * *
6216535 -TTTGCGGCGTTTTTCA-ATAAGCGCCACTAACT-CTAATCTACCTCAAGACCAAACGGTGCGTT
1 CTTTGCGGCG-TTTTAATATAAGCGCCACTAA-TGCTAATATACATCAAGACCAAACGCTGCGTT
6216597 TTGGTTAAGAT
64 TTGGTTAAGAT
6216608 CTTTGCGG
1 CTTTGCGG
6216616 TGCTTTTTGT
Statistics
Matches: 71, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
73 18 0.25
74 44 0.62
75 9 0.13
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.32
Consensus pattern (74 bp):
CTTTGCGGCGTTTTAATATAAGCGCCACTAATGCTAATATACATCAAGACCAAACGCTGCGTTTT
GGTTAAGAT
Found at i:6216726 original size:188 final size:188
Alignment explanation
Indices: 6216363--6216754 Score: 463
Period size: 188 Copynumber: 2.1 Consensus size: 188
6216353 AACTGCATTT
* * *
6216363 ATAAGCGCCACTAATGCTAGTGTACCTCAAGACCAAACTCTGCGTTTTGGTTAAGAAATATTGCG
1 ATAAGCGCCACTAATGCTAATCTACCTCAAGACCAAACGCTGCGTTTTGGTTAAGAAATATTGCG
** * *
6216428 GCGCTTTTCAGTTCTCGCCGCTAATACTATACTTTAGCGGCGTTTTAATATAAGCGTCACTAATG
66 GCGCTTTTCAGTAATCGCCGCTAATACTATACTTTAGCGGCGTTTTAATATAAACGCCACTAATG
* *
6216493 CTACTATACATCAAGACCAAAGCGCTGCGTTTTGGTTAATATTTTGCGGCGTTTTTCA
131 CTAATATACATCAAAACCAAAGCGCTGCGTTTTGGTTAATATTTTGCGGCGTTTTTCA
* **
6216551 ATAAGCGCCACTAACT-CTAATCTACCTCAAGACCAAACGGTGCGTTTTGGTTAAGATCT-TTGC
1 ATAAGCGCCACTAA-TGCTAATCTACCTCAAGACCAAACGCTGCGTTTTGGTTAAGAAATATTGC
* * * * * *
6216614 GGTGCTTTT-TGTAATACGCCGCTAATACTGTTCTTTAGCGGCGTTTT-CTCGTAAACGCCACTA
65 GGCGCTTTTCAGTAAT-CGCCGCTAATACTATACTTTAGCGGCGTTTTAAT-ATAAACGCCACTA
* * * * * *
6216677 ATTCTAATATGCCTCAAAACCAAA-TGCTGCGTTTTGGTTAAGGTATTTTGCGGCG-CTTACAA
128 ATGCTAATATACATCAAAACCAAAGCGCTGCGTTTTGGTTAA--TATTTTGCGGCGTTTTTC-A
*
6216739 ATAAACGCCACTAATG
1 ATAAGCGCCACTAATG
6216755 ATGTTCTTTT
Statistics
Matches: 172, Mismatches: 25, Indels: 14
0.82 0.12 0.07
Matches are distributed among these distances:
186 20 0.12
187 74 0.43
188 77 0.45
189 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.32
Consensus pattern (188 bp):
ATAAGCGCCACTAATGCTAATCTACCTCAAGACCAAACGCTGCGTTTTGGTTAAGAAATATTGCG
GCGCTTTTCAGTAATCGCCGCTAATACTATACTTTAGCGGCGTTTTAATATAAACGCCACTAATG
CTAATATACATCAAAACCAAAGCGCTGCGTTTTGGTTAATATTTTGCGGCGTTTTTCA
Found at i:6216787 original size:114 final size:113
Alignment explanation
Indices: 6216534--6216790 Score: 270
Period size: 113 Copynumber: 2.3 Consensus size: 113
6216524 TTGGTTAATA
* * * * * *
6216534 TTTTGCGGCGTTTTTCAATAAGCGCCACTAACTCTAATCTACCTCAAGACCAAACGGTGCGTTTT
1 TTTTACGGCGTTTTTTAATAAACGCCACTAACTCTAATATACCTCAAAACCAAACGCTGCGTTTT
* **** *
6216599 GGTTAAGATCTTTGCGGTGCTTTTTGTAATACGCCGCTAATACTGTTC
66 GGTTAAGATCTTTGCGGCGCTTCAAATAATACGCCACTAATACTGTTC
* ** * * *
6216647 -TTTAGCGGCGTTTTCTCGTAAACGCCACTAATTCTAATATGCCTCAAAACCAAATGCTGCGTTT
1 TTTTA-CGGCGTTTTTTAATAAACGCCACTAACTCTAATATACCTCAAAACCAAACGCTGCGTTT
6216711 TGGTTAAGGTAT-TTTGCGGCGCTTACAAATAA-ACGCCACTAATGA-TGTTC
65 TGGTTAA-G-ATCTTTGCGGCGCTT-CAAATAATACGCCACTAAT-ACTGTTC
*
6216761 TTTTACGGCGTTTTTTAAAAAACGCCACTA
1 TTTTACGGCGTTTTTTAATAAACGCCACTA
6216791 GATGTTCGGG
Statistics
Matches: 116, Mismatches: 22, Indels: 11
0.78 0.15 0.07
Matches are distributed among these distances:
112 3 0.03
113 55 0.47
114 48 0.41
115 10 0.09
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.34
Consensus pattern (113 bp):
TTTTACGGCGTTTTTTAATAAACGCCACTAACTCTAATATACCTCAAAACCAAACGCTGCGTTTT
GGTTAAGATCTTTGCGGCGCTTCAAATAATACGCCACTAATACTGTTC
Found at i:6217469 original size:13 final size:14
Alignment explanation
Indices: 6217446--6217478 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
6217436 GTTGAGAGAG
6217446 GAAGAAAGAAAAAA
1 GAAGAAAGAAAAAA
6217460 GAAG-AAGAAAAAA
1 GAAGAAAGAAAAAA
6217473 G-AGAAA
1 GAAGAAA
6217479 TGGTGGAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 2 0.11
13 12 0.67
14 4 0.22
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (14 bp):
GAAGAAAGAAAAAA
Found at i:6217718 original size:29 final size:30
Alignment explanation
Indices: 6217666--6217742 Score: 93
Period size: 29 Copynumber: 2.5 Consensus size: 30
6217656 TGTTAAAAAA
* **
6217666 AAGTACCAAACTAGTTGACAAAAAAAAAGTTT
1 AAGTACCAATCTAG--GACAAAAAAAAACCTT
*
6217698 AGGTACCAATCTAGGAC-AAAAAAAACCTT
1 AAGTACCAATCTAGGACAAAAAAAAACCTT
6217727 AAGTACCAATCTAGGA
1 AAGTACCAATCTAGGA
6217743 GAAGTGGACA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
29 25 0.62
30 3 0.08
32 12 0.30
ACGTcount: A:0.49, C:0.17, G:0.14, T:0.19
Consensus pattern (30 bp):
AAGTACCAATCTAGGACAAAAAAAAACCTT
Found at i:6228088 original size:2 final size:2
Alignment explanation
Indices: 6228081--6228117 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
6228071 GTAACCAGCA
6228081 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
6228118 AAAGAAAGGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:6228981 original size:24 final size:24
Alignment explanation
Indices: 6228954--6228999 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
6228944 CAAATCTACA
* *
6228954 CATGAAAACAGACATGTGCAGACT
1 CATGAAAACACACATATGCAGACT
* *
6228978 CATGCATACACACATATGCAGA
1 CATGAAAACACACATATGCAGA
6229000 AGAATATCAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.41, C:0.24, G:0.17, T:0.17
Consensus pattern (24 bp):
CATGAAAACACACATATGCAGACT
Found at i:6231199 original size:60 final size:59
Alignment explanation
Indices: 6231125--6231249 Score: 196
Period size: 60 Copynumber: 2.1 Consensus size: 59
6231115 CATAAATCTA
** * *
6231125 AAAATTCAACAAATTTAGCCCTCAATGTTTACAAAATTTGTCATTTTAGTTCTAATTCTT
1 AAAATTCAACAAATTTAGCCCTCAACATTTACAAAATTTGTCAATTTAATTCTAATTC-T
*
6231185 AAAATTCAATAAATTTAGCCCTCAACATTTACAAAATTTGTCAATTTAATTCTAATTCT
1 AAAATTCAACAAATTTAGCCCTCAACATTTACAAAATTTGTCAATTTAATTCTAATTCT
6231244 AAAATT
1 AAAATT
6231250 TTAAAAAAAG
Statistics
Matches: 60, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
59 7 0.12
60 53 0.88
ACGTcount: A:0.39, C:0.16, G:0.05, T:0.40
Consensus pattern (59 bp):
AAAATTCAACAAATTTAGCCCTCAACATTTACAAAATTTGTCAATTTAATTCTAATTCT
Found at i:6235860 original size:84 final size:84
Alignment explanation
Indices: 6235641--6235885 Score: 438
Period size: 83 Copynumber: 2.9 Consensus size: 84
6235631 ATACCATATT
* *
6235641 ATCCTAACCCAATCAAAACTAAGAATAATATGTTCAACAATCTCATCCTCAATACCACATAAACA
1 ATCCTATCCCAATCAAAACTAAGAATAATATGTTCAACAATCTCATCTTCAATACCACATAAACA
6235706 ACAAATTAGGTTCAAAAAA
66 ACAAATTAGGTTCAAAAAA
* * *
6235725 ATCCTGTCCCAATC-AAACTAAAAATAATATGTTCAACAATCACATCTTCAATACCACATAAACA
1 ATCCTATCCCAATCAAAACTAAGAATAATATGTTCAACAATCTCATCTTCAATACCACATAAACA
6235789 ACAAATTAGGTTCAAAAAA
66 ACAAATTAGGTTCAAAAAA
6235808 ATCCTATCCCAATCAAAACTAAGAATAATATGTTCAACAATCTCATCTTCAATACCACATAAACA
1 ATCCTATCCCAATCAAAACTAAGAATAATATGTTCAACAATCTCATCTTCAATACCACATAAACA
6235873 ACAAATTAGGTTC
66 ACAAATTAGGTTC
6235886 GAAACACACT
Statistics
Matches: 152, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
83 79 0.52
84 73 0.48
ACGTcount: A:0.47, C:0.24, G:0.05, T:0.24
Consensus pattern (84 bp):
ATCCTATCCCAATCAAAACTAAGAATAATATGTTCAACAATCTCATCTTCAATACCACATAAACA
ACAAATTAGGTTCAAAAAA
Found at i:6242258 original size:690 final size:690
Alignment explanation
Indices: 6240885--6242261 Score: 2093
Period size: 690 Copynumber: 2.0 Consensus size: 690
6240875 TACCAAAGAC
6240885 AAAAAGTATAGGCATAGCCGTTGTGTTGTAGGCGAGGTCTTTTGGTTAGAAAAAAAGTACACATT
1 AAAAAGTATAGGCATAGCCGTTGTGTTGTAGGCGAGGTCTTTTGGTTAGAAAAAAAGTACACATT
* * *
6240950 TCTTTCTGTAAAAACTGAAAAGGTAAACTGTATCACAAAGATAACTTGCAGAAGTAAAGTTGATA
66 TCTTTCTATAAAAACTGAAAAGGTAAACTATATCACAAAGATAACTTGCAGAAATAAAGTTGATA
*
6241015 TTATTCCTAATACACCATTTGTGAATGAAGGCATGTTGTATTGAACTTGTGAGACCTTGAAAGTA
131 TTATTCCTAATACACCATTTGTGAATGAAGGCATGTTGTATTGAACTTGCGAGACCTTGAAAGTA
* * * **
6241080 AAGTATGAACACAGAACGCGTAACTTTGAAGATAAAGTGTGAATGTAAAATTTGGTACTAAAGTT
196 AAGTATGAACACACAACGCGTAACTTTGAAGATAAAGTATGAATGCAAAAAGTGGTACTAAAGTT
* * *
6241145 TTGTTGAAAGGGTCGAAAAGGTGAAAAGTGAAATTATATGTAAGGAGGTTAAAATCTTGAAATCA
261 TTGTTGAAAGGCTCGAAAAGGTGAAAAGTGAAATTATATGTAAGAAGGTTAAAATCTTGAAATAA
* *
6241210 AAGTGACTAAAAAAGGTGCACAACTGAAGAAGGTGAAGACCTGAAAACATAAAGAGATCCTTGGA
326 AAGTGACTAAAAAAGGTGCACAACTGAAGAAGGTGAAGACCTGAAAACATAAAGAGATCCCTAGA
*
6241275 TCCATACTTCAAAAAGGATAAATATGTAGAAAATTACATGACCTGAAAAGATCAAGAGTTGGGTG
391 TCCATACTTCAAAAAGGATAAATAAGTAGAAAATTACATGACCTGAAAAGATCAAGAGTTGGGTG
** * * *
6241340 GCTTGATGCTTAGAAAATCTTAAGTAAGTGTTGACGAGTGATGTGAATTGTGGCTATATATGCCC
456 GCTTGATGCCCAGAAAAGCTTAAGTAAGTCTTGACGAGTGATGTGAATTGTGGCTATACATGCCC
* * **
6241405 AATAAGACAAATGGGAGAAAATAGTAAAATAAGTTTTGATAACCTTAATGCTTGCATCAATAGTG
521 AATAAGACAAATGGGAGAAAATAGTAAAATAAATTTCGATAACCTTAATGCTCACATCAATAGTG
* * *
6241470 GGTCAAGGACTACTAGTGCAATTGGGGAAATATTAGCTATTGCTAGCACATATATAATATATATA
586 GGCCAAGGACTACTAGTGCAATTGGGGAAATATTAACTATTGCTAGAACATATATAATATATATA
6241535 AATTGGGGCATTGTCAACCAATATATAAATATATATAATT
651 AATTGGGGCATTGTCAACCAATATATAAATATATATAATT
*
6241575 AAAAAGGTATAGGCATAGCCGTTGTGTTGTAGGCGAGGTCTTTTGGTTAGAAAAAAAAATTACAC
1 AAAAA-GTATAGGCATAGCCGTTGTGTTGTAGGCGAGGTCTTTTGGTTAG--AAAAAAAGTACAC
* ** *
6241640 ATTTCTTTTTATAAAAGTTGAAAAGGTAAACTATATCACAAAGATCACTTGC-GAAAATAAAGTT
63 ATTTCTTTCTATAAAAACTGAAAAGGTAAACTATATCACAAAGATAACTTGCAG-AAATAAAGTT
* ** *
6241704 GATATTATTCTTAATACACTGTTTGTGAATGAAGGCATGTTGTATTGAACTTGCGA-ACCTTGAG
127 GATATTATTCCTAATACACCATTTGTGAATGAAGGCATGTTGTATTGAACTTGCGAGACCTTGAA
*
6241768 AGTAAAGTATGAACACACAGCGCGTAACTTTGAAGATAAAGTATGAATGCAAAAAGTGGTACTAA
192 AGTAAAGTATGAACACACAACGCGTAACTTTGAAGATAAAGTATGAATGCAAAAAGTGGTACTAA
** * *
6241833 A-TTTT-TTTTAAGAGCT-GAAAAGGTGAAATGTGAAATTATATGTAAGAATGTTAAAATCTTGA
257 AGTTTTGTTGAAAG-GCTCGAAAAGGTGAAAAGTGAAATTATATGTAAGAAGGTTAAAATCTTGA
* * *
6241895 AATAAAAGTGACTAAAAAAGGTGCGCAACTTAAGAAGGTGAAGACCTGAAAATATAAAGAGATCC
321 AATAAAAGTGACTAAAAAAGGTGCACAACTGAAGAAGGTGAAGACCTGAAAACATAAAGAGATCC
* * * * * *
6241960 CTAGCTTCATGCTTCAAAATGGATAAATAAGTAGAAAATTACATGACTTGAAAAGATTAAGAGTT
386 CTAGATCCATACTTCAAAAAGGATAAATAAGTAGAAAATTACATGACCTGAAAAGATCAAGAGTT
* *
6242025 GGGTGGCTTGATGCCCGGAAAAGCTTAAGTAAGTACTT-ACGAG-GCATGTGAATTGTGGCTATG
451 GGGTGGCTTGATGCCCAGAAAAGCTTAAGTAAGT-CTTGACGAGTG-ATGTGAATTGTGGCTATA
* * * * *
6242088 CGTGCCCTATAAGACAAATTGGAGAGAATAGTAAAATAAATTTCGATAACCTTAATGCTCACATT
514 CATGCCCAATAAGACAAATGGGAGAAAATAGTAAAATAAATTTCGATAACCTTAATGCTCACATC
* * * *
6242153 AATAGTGGGCCAGGGACTATTAGTGCAATTGGGGAAATATTAATTATTGCTAGAACATATATAGT
579 AATAGTGGGCCAAGGACTACTAGTGCAATTGGGGAAATATTAACTATTGCTAGAACATATATAAT
6242218 ATATATAAATTGGGGCATTGTCAACCAATATATAAATATATATA
644 ATATATAAATTGGGGCATTGTCAACCAATATATAAATATATATA
6242262 TAACTTGCCA
Statistics
Matches: 619, Mismatches: 61, Indels: 14
0.89 0.09 0.02
Matches are distributed among these distances:
689 1 0.00
690 379 0.61
691 52 0.08
692 68 0.11
693 119 0.19
ACGTcount: A:0.39, C:0.11, G:0.21, T:0.29
Consensus pattern (690 bp):
AAAAAGTATAGGCATAGCCGTTGTGTTGTAGGCGAGGTCTTTTGGTTAGAAAAAAAGTACACATT
TCTTTCTATAAAAACTGAAAAGGTAAACTATATCACAAAGATAACTTGCAGAAATAAAGTTGATA
TTATTCCTAATACACCATTTGTGAATGAAGGCATGTTGTATTGAACTTGCGAGACCTTGAAAGTA
AAGTATGAACACACAACGCGTAACTTTGAAGATAAAGTATGAATGCAAAAAGTGGTACTAAAGTT
TTGTTGAAAGGCTCGAAAAGGTGAAAAGTGAAATTATATGTAAGAAGGTTAAAATCTTGAAATAA
AAGTGACTAAAAAAGGTGCACAACTGAAGAAGGTGAAGACCTGAAAACATAAAGAGATCCCTAGA
TCCATACTTCAAAAAGGATAAATAAGTAGAAAATTACATGACCTGAAAAGATCAAGAGTTGGGTG
GCTTGATGCCCAGAAAAGCTTAAGTAAGTCTTGACGAGTGATGTGAATTGTGGCTATACATGCCC
AATAAGACAAATGGGAGAAAATAGTAAAATAAATTTCGATAACCTTAATGCTCACATCAATAGTG
GGCCAAGGACTACTAGTGCAATTGGGGAAATATTAACTATTGCTAGAACATATATAATATATATA
AATTGGGGCATTGTCAACCAATATATAAATATATATAATT
Found at i:6247388 original size:21 final size:20
Alignment explanation
Indices: 6247364--6247408 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
6247354 CACTCAGTAA
*
6247364 GAGAAGAACAACTCTCATTTT
1 GAGAAGAA-AACTCTCATTTC
*
6247385 GAG-AGAAAATTCTCATTTC
1 GAGAAGAAAACTCTCATTTC
6247404 GAGAA
1 GAGAA
6247409 ACAATACATG
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
19 13 0.62
20 5 0.24
21 3 0.14
ACGTcount: A:0.40, C:0.16, G:0.18, T:0.27
Consensus pattern (20 bp):
GAGAAGAAAACTCTCATTTC
Done.