Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A01
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: 104050246
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4660000 characters in sequence are not A, C, G, or T
File 125 of 316
Found at i:39628779 original size:29 final size:28
Alignment explanation
Indices: 39628743--39628820 Score: 104
Period size: 29 Copynumber: 2.7 Consensus size: 28
39628733 TCATGAGATT
39628743 GGCACTAAGTGTGCGGGTTTAAATTGTACA
1 GGCACTAAGTGTGCGGGTTTAAA--GTACA
*
39628773 -GCACTAAGTGTGCGAGTTTAAAGTACA
1 GGCACTAAGTGTGCGGGTTTAAAGTACA
39628800 TGGCACTAAGTGTGCGCGGTT
1 -GGCACTAAGTGTGCG-GGTT
39628821 GATTATTAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
27 5 0.12
29 35 0.81
30 3 0.07
ACGTcount: A:0.26, C:0.15, G:0.31, T:0.28
Consensus pattern (28 bp):
GGCACTAAGTGTGCGGGTTTAAAGTACA
Found at i:39629038 original size:174 final size:174
Alignment explanation
Indices: 39628773--39629274 Score: 941
Period size: 174 Copynumber: 2.9 Consensus size: 174
39628763 AAATTGTACA
*
39628773 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGTGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
39628838 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACTTTACCGAGTCGA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACTTTACCGAGTCGA
39628903 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
131 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
* *
39628947 GCACTAAGTGTGTGAGTTTAAAGTGCATGGCACTAAGTGTGCGCGGTTGATTATTGAGCACTATG
1 GCACTAAGTGTGTGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
39629012 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACTTTACCGAGTCGA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACTTTACCGAGTCGA
39629077 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
131 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
39629121 GCACTAAGTGTGTGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGTGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
* * *
39629186 TGTGCGAACTCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACTTTACCGAGTCGA
*
39629251 TTTTGGACAACGGAAAAGGTAAGT
131 TTTTGGACAGCGGAAAAGGTAAGT
39629275 ACCTTGAGTT
Statistics
Matches: 319, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
174 319 1.00
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.31
Consensus pattern (174 bp):
GCACTAAGTGTGTGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACTTTACCGAGTCGA
TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
Found at i:39631632 original size:27 final size:26
Alignment explanation
Indices: 39631587--39631697 Score: 123
Period size: 27 Copynumber: 4.1 Consensus size: 26
39631577 TGGCTGCCAT
** *
39631587 AACAGATATTGTGATAGAGTCACCAG
1 AACAGATATTGTGGCAGAGCCACCAG
* *
39631613 ATACAGATATCGTGGCAGAGCCACTAG
1 A-ACAGATATTGTGGCAGAGCCACCAG
*
39631640 AACAGATATTTGTGGCATAGCCACCAG
1 AACAGATA-TTGTGGCAGAGCCACCAG
*
39631667 AAACAGATAATTGTGGCATAGCCACCAG
1 -AACAGAT-ATTGTGGCAGAGCCACCAG
39631695 AAC
1 AAC
39631698 GCTTCCTCGA
Statistics
Matches: 73, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
26 8 0.11
27 39 0.53
28 25 0.34
29 1 0.01
ACGTcount: A:0.37, C:0.21, G:0.23, T:0.20
Consensus pattern (26 bp):
AACAGATATTGTGGCAGAGCCACCAG
Found at i:39631680 original size:28 final size:28
Alignment explanation
Indices: 39631607--39631696 Score: 121
Period size: 28 Copynumber: 3.3 Consensus size: 28
39631597 GTGATAGAGT
* * *
39631607 CACCAGATACAGAT-ATCGTGGCAGAGC
1 CACCAGAAACAGATAATTGTGGCATAGC
* *
39631634 CACTAG-AACAGATATTTGTGGCATAGC
1 CACCAGAAACAGATAATTGTGGCATAGC
39631661 CACCAGAAACAGATAATTGTGGCATAGC
1 CACCAGAAACAGATAATTGTGGCATAGC
39631689 CACCAGAA
1 CACCAGAA
39631697 CGCTTCCTCG
Statistics
Matches: 54, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
26 6 0.11
27 20 0.37
28 28 0.52
ACGTcount: A:0.37, C:0.23, G:0.22, T:0.18
Consensus pattern (28 bp):
CACCAGAAACAGATAATTGTGGCATAGC
Found at i:39633080 original size:51 final size:51
Alignment explanation
Indices: 39633004--39633105 Score: 204
Period size: 51 Copynumber: 2.0 Consensus size: 51
39632994 TCACCACCAA
39633004 GCTCCTTTATCAGCTCCTAAGTTTCAGCCACCACCAATTTAAATCCCATCC
1 GCTCCTTTATCAGCTCCTAAGTTTCAGCCACCACCAATTTAAATCCCATCC
39633055 GCTCCTTTATCAGCTCCTAAGTTTCAGCCACCACCAATTTAAATCCCATCC
1 GCTCCTTTATCAGCTCCTAAGTTTCAGCCACCACCAATTTAAATCCCATCC
39633106 AAATTCCTTG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.25, C:0.37, G:0.08, T:0.29
Consensus pattern (51 bp):
GCTCCTTTATCAGCTCCTAAGTTTCAGCCACCACCAATTTAAATCCCATCC
Found at i:39644348 original size:39 final size:40
Alignment explanation
Indices: 39644144--39644366 Score: 236
Period size: 40 Copynumber: 5.6 Consensus size: 40
39644134 TTGAATGCTG
* * * * * *
39644144 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTACTAAA
** * * *
39644184 TCCGGACTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAA
*
39644224 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
**
39644264 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
* *
39644304 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
* * *
39644343 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
39644367 TGAACGAGGA
Statistics
Matches: 161, Mismatches: 19, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
39 35 0.22
40 118 0.73
41 8 0.05
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
Found at i:39644386 original size:79 final size:80
Alignment explanation
Indices: 39644219--39644401 Score: 226
Period size: 79 Copynumber: 2.3 Consensus size: 80
39644209 GTGCGAGATA
* * *
39644219 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
** **
39644284 CATTCGTGCGAGTTG
66 CATTCGAACGAGGAG
* * * *
39644299 TTAAATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
*
39644363 CATTTGAACGAGGAG
66 CATTCGAACGAGGAG
* *
39644378 CTATATCC-GGTTAAATCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGG
39644402 TACGTGATTT
Statistics
Matches: 87, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
78 14 0.16
79 46 0.53
80 27 0.31
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.26
Consensus pattern (80 bp):
CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
CATTCGAACGAGGAG
Found at i:39652219 original size:39 final size:40
Alignment explanation
Indices: 39652015--39652237 Score: 236
Period size: 40 Copynumber: 5.6 Consensus size: 40
39652005 TTGAATGCTG
* * * * * *
39652015 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTACTAAA
** * * *
39652055 TCCGGACTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAA
*
39652095 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
**
39652135 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
* *
39652175 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
* * *
39652214 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
39652238 TGAACGAGGA
Statistics
Matches: 161, Mismatches: 19, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
39 35 0.22
40 118 0.73
41 8 0.05
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
Found at i:39652257 original size:79 final size:80
Alignment explanation
Indices: 39652090--39652272 Score: 226
Period size: 79 Copynumber: 2.3 Consensus size: 80
39652080 GTGCGAGATA
* * *
39652090 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
** **
39652155 CATTCGTGCGAGTTG
66 CATTCGAACGAGGAG
* * * *
39652170 TTAAATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
*
39652234 CATTTGAACGAGGAG
66 CATTCGAACGAGGAG
* *
39652249 CTATATCC-GGTTAAATCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGG
39652273 TACGTGATTT
Statistics
Matches: 87, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
78 14 0.16
79 46 0.53
80 27 0.31
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.26
Consensus pattern (80 bp):
CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
CATTCGAACGAGGAG
Found at i:39663527 original size:27 final size:27
Alignment explanation
Indices: 39663494--39663579 Score: 109
Period size: 27 Copynumber: 3.2 Consensus size: 27
39663484 CAATTTACTG
* *
39663494 AAATACCCTCGACTTGTAAAATTACCA
1 AAATACCCTCAATTTGTAAAATTACCA
* * *
39663521 AAGTACCCCCAATTTATAAAATTACCA
1 AAATACCCTCAATTTGTAAAATTACCA
**
39663548 AAATATACTCAATTTGTAAAATTACCA
1 AAATACCCTCAATTTGTAAAATTACCA
39663575 AAATA
1 AAATA
39663580 AGATAGAATT
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 49 1.00
ACGTcount: A:0.47, C:0.21, G:0.05, T:0.28
Consensus pattern (27 bp):
AAATACCCTCAATTTGTAAAATTACCA
Found at i:39663613 original size:27 final size:27
Alignment explanation
Indices: 39663584--39663698 Score: 176
Period size: 27 Copynumber: 4.3 Consensus size: 27
39663574 AAAATAAGAT
**
39663584 AGAATTACCATTTTACCCTCGATTTGT
1 AGAATTACCATTTTACCCTCGATTTAC
*
39663611 AGAATTACCGTTTTACCCTCGATTTAC
1 AGAATTACCATTTTACCCTCGATTTAC
* *
39663638 AGATTTACCATTTTAACCTCGATTTAC
1 AGAATTACCATTTTACCCTCGATTTAC
39663665 AGAATTACCATTTTACCCTCGATTTAC
1 AGAATTACCATTTTACCCTCGATTTAC
*
39663692 AAAATTA
1 AGAATTA
39663699 TTGAAATACC
Statistics
Matches: 79, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 79 1.00
ACGTcount: A:0.30, C:0.23, G:0.09, T:0.38
Consensus pattern (27 bp):
AGAATTACCATTTTACCCTCGATTTAC
Found at i:39663708 original size:27 final size:27
Alignment explanation
Indices: 39663624--39663763 Score: 118
Period size: 27 Copynumber: 5.2 Consensus size: 27
39663614 ATTACCGTTT
* * ***
39663624 TACCCTCGATTTACAGATTTACCATTT
1 TACCCTCGATTTACAAAATTACCAAAA
* * ***
39663651 TAACCTCGATTTACAGAATTACCATTT
1 TACCCTCGATTTACAAAATTACCAAAA
***
39663678 TACCCTCGATTTACAAAATTATTGAAA
1 TACCCTCGATTTACAAAATTACCAAAA
* *
39663705 TACCCTTGGTTTACAAAATTACCAAAA
1 TACCCTCGATTTACAAAATTACCAAAA
** *
39663732 TACCCTCGATCAATAAAATTACCAAAA
1 TACCCTCGATTTACAAAATTACCAAAA
39663759 TACCC
1 TACCC
39663764 CTAGTTTGTG
Statistics
Matches: 93, Mismatches: 20, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 93 1.00
ACGTcount: A:0.37, C:0.24, G:0.06, T:0.32
Consensus pattern (27 bp):
TACCCTCGATTTACAAAATTACCAAAA
Found at i:39663805 original size:27 final size:27
Alignment explanation
Indices: 39663775--39663916 Score: 185
Period size: 27 Copynumber: 5.3 Consensus size: 27
39663765 TAGTTTGTGA
*
39663775 AATTACCGAAATACCCCTGTAGAGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
39663802 AATTACCGAAATACCCTTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
39663829 AATTACTGAAATACCCCTGTAGGGTAA
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
39663856 AATTATCGAAATACCCATGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * * * *
39663883 AATTGCCGAGATACCCTTGTGGGGTAA
1 AATTACCGAAATACCCCTGTAGGGTAG
39663910 AATTACC
1 AATTACC
39663917 ATTTTGCCCC
Statistics
Matches: 99, Mismatches: 16, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 99 1.00
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.25
Consensus pattern (27 bp):
AATTACCGAAATACCCCTGTAGGGTAG
Found at i:39663806 original size:54 final size:55
Alignment explanation
Indices: 39663745--39663916 Score: 181
Period size: 54 Copynumber: 3.2 Consensus size: 55
39663735 CCTCGATCAA
* **
39663745 TAAAATTACCAAAATACCCCTAGT-TTGT-GAAATTACCGAAATACCCCTGTAGAG
1 TAAAATTACCGAAATACCCCTAGTAGGGTAG-AATTACCGAAATACCCCTGTAGAG
* * * *
39663799 TAGAATTACCGAAATA-CCCTTGTAGGGTAGAATTACTGAAATACCCCTGTAGGG
1 TAAAATTACCGAAATACCCCTAGTAGGGTAGAATTACCGAAATACCCCTGTAGAG
* * * * * * *
39663853 TAAAATTATCGAAATACCCAT-GTAGGGTAGAATTGCCGAGATACCCTTGTGGGG
1 TAAAATTACCGAAATACCCCTAGTAGGGTAGAATTACCGAAATACCCCTGTAGAG
39663907 TAAAATTACC
1 TAAAATTACC
39663917 ATTTTGCCCC
Statistics
Matches: 99, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
53 6 0.06
54 89 0.90
55 4 0.04
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.26
Consensus pattern (55 bp):
TAAAATTACCGAAATACCCCTAGTAGGGTAGAATTACCGAAATACCCCTGTAGAG
Found at i:39663833 original size:81 final size:81
Alignment explanation
Indices: 39663745--39663917 Score: 222
Period size: 81 Copynumber: 2.1 Consensus size: 81
39663735 CCTCGATCAA
** * *
39663745 TAAAATTACCAAAATACCCCTAGT-TTGTGAAATTACCGAAATACCCCTGTAGAGTAGAATTACC
1 TAAAATTACCAAAATACCCCT-GTAGGGTAAAATTACCGAAATACCCATGTAGAGTAGAATTACC
39663809 GAAATACCCTTGTAGGG
65 GAAATACCCTTGTAGGG
* ** * * *
39663826 TAGAATTACTGAAATACCCCTGTAGGGTAAAATTATCGAAATACCCATGTAGGGTAGAATTGCCG
1 TAAAATTACCAAAATACCCCTGTAGGGTAAAATTACCGAAATACCCATGTAGAGTAGAATTACCG
* *
39663891 AGATACCCTTGTGGGG
66 AAATACCCTTGTAGGG
39663907 TAAAATTACCA
1 TAAAATTACCA
39663918 TTTTGCCCCT
Statistics
Matches: 76, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
80 2 0.03
81 74 0.97
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (81 bp):
TAAAATTACCAAAATACCCCTGTAGGGTAAAATTACCGAAATACCCATGTAGAGTAGAATTACCG
AAATACCCTTGTAGGG
Found at i:39664345 original size:31 final size:31
Alignment explanation
Indices: 39664310--39664386 Score: 102
Period size: 31 Copynumber: 2.5 Consensus size: 31
39664300 TTGCATTCAC
* *
39664310 ATTCTGATTTTGATTCTGTTACCTGA-TACTG
1 ATTCTGATTCTGATTCTGTCACCTGATTA-TG
*
39664341 ATTCTGATTCTAATTCTGTCACCTGATTATG
1 ATTCTGATTCTGATTCTGTCACCTGATTATG
*
39664372 ATTATGATTCTGATT
1 ATTCTGATTCTGATT
39664387 TTGATTCTAG
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
31 38 0.95
32 2 0.05
ACGTcount: A:0.22, C:0.16, G:0.14, T:0.48
Consensus pattern (31 bp):
ATTCTGATTCTGATTCTGTCACCTGATTATG
Found at i:39664349 original size:6 final size:6
Alignment explanation
Indices: 39664310--39664403 Score: 59
Period size: 6 Copynumber: 15.3 Consensus size: 6
39664300 TTGCATTCAC
* * *
39664310 ATTCTG ATTTTG ATTCTG -TTACCTG ATACTG ATTCTG ATTCTA ATTCTG
1 ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG ATTCTG
* * * *
39664359 -TCACCTG ATTATG ATTATG ATTCTG ATTTTG ATTCT- AGTTCTG AT
1 AT--TCTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG A-TTCTG AT
39664404 AATGTTTCTT
Statistics
Matches: 68, Mismatches: 12, Indels: 16
0.71 0.12 0.17
Matches are distributed among these distances:
5 4 0.06
6 55 0.81
7 7 0.10
8 2 0.03
ACGTcount: A:0.21, C:0.15, G:0.15, T:0.49
Consensus pattern (6 bp):
ATTCTG
Found at i:39666387 original size:27 final size:27
Alignment explanation
Indices: 39666356--39666450 Score: 102
Period size: 27 Copynumber: 3.5 Consensus size: 27
39666346 TTAGTTTACG
** *
39666356 AAATTACTGAAATACCCTCGACTTGTA
1 AAATTACCCAAATACCCTCGATTTGTA
* *
39666383 AAATTA-CCAAAGTACCCCCGATTTATA
1 AAATTACCCAAA-TACCCTCGATTTGTA
* *
39666410 AAATTACCCAAATATCCTCTATTTGTA
1 AAATTACCCAAATACCCTCGATTTGTA
*
39666437 AAATTACCGAAATA
1 AAATTACCCAAATA
39666451 AGATTGAATT
Statistics
Matches: 56, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
26 3 0.05
27 48 0.86
28 5 0.09
ACGTcount: A:0.41, C:0.22, G:0.07, T:0.29
Consensus pattern (27 bp):
AAATTACCCAAATACCCTCGATTTGTA
Found at i:39666486 original size:27 final size:27
Alignment explanation
Indices: 39666456--39666569 Score: 183
Period size: 27 Copynumber: 4.2 Consensus size: 27
39666446 AAATAAGATT
39666456 GAATTACCATTTTACCCTCGATTTACA
1 GAATTACCATTTTACCCTCGATTTACA
* * *
39666483 GAATTATCGTTTTACCCTCGATTTATA
1 GAATTACCATTTTACCCTCGATTTACA
39666510 GAATTACCATTTTACCCTCGATTTACA
1 GAATTACCATTTTACCCTCGATTTACA
*
39666537 TAATTACCATTTTACCCTCGATTTACA
1 GAATTACCATTTTACCCTCGATTTACA
*
39666564 AAATTA
1 GAATTA
39666570 TTGAAATACC
Statistics
Matches: 79, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 79 1.00
ACGTcount: A:0.31, C:0.23, G:0.07, T:0.39
Consensus pattern (27 bp):
GAATTACCATTTTACCCTCGATTTACA
Found at i:39666579 original size:27 final size:27
Alignment explanation
Indices: 39666468--39666659 Score: 134
Period size: 27 Copynumber: 7.1 Consensus size: 27
39666458 ATTACCATTT
* * ****
39666468 TACCCTCGATTTACAGAATTATCGTTT
1 TACCCTCGATTTACAAAATTACCAAAA
* * ***
39666495 TACCCTCGATTTATAGAATTACCATTT
1 TACCCTCGATTTACAAAATTACCAAAA
* ***
39666522 TACCCTCGATTTACATAATTACCATTT
1 TACCCTCGATTTACAAAATTACCAAAA
***
39666549 TACCCTCGATTTACAAAATTATTGAAA
1 TACCCTCGATTTACAAAATTACCAAAA
* *
39666576 TACCCTTGGTTTACAAAATTACCAAAA
1 TACCCTCGATTTACAAAATTACCAAAA
** *
39666603 TACCCTCGATCAATAAAATTACCAAAA
1 TACCCTCGATTTACAAAATTACCAAAA
* **
39666630 TACCC-CTAGTTTGTAAAATTACCAAAA
1 TACCCTCGA-TTTACAAAATTACCAAAA
39666657 TAC
1 TAC
39666660 ATCTGATTTG
Statistics
Matches: 138, Mismatches: 26, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
26 2 0.01
27 136 0.99
ACGTcount: A:0.36, C:0.23, G:0.07, T:0.34
Consensus pattern (27 bp):
TACCCTCGATTTACAAAATTACCAAAA
Found at i:39666580 original size:54 final size:54
Alignment explanation
Indices: 39666457--39666634 Score: 151
Period size: 54 Copynumber: 3.3 Consensus size: 54
39666447 AATAAGATTG
** * * * * *
39666457 AATTACCATTTTACCCTCGATTTACAGAATTATCGTTTTACCCTCGATTTATAG
1 AATTACCATAATACCCTCGATTTACAAAATTACCATTTTACCCTCGATTTACAA
** *
39666511 AATTACCATTTTACCCTCGATTTACATAATTACCATTTTACCCTCGATTTACAA
1 AATTACCATAATACCCTCGATTTACAAAATTACCATTTTACCCTCGATTTACAA
** * * *** ** *
39666565 AATTATTGA-AATACCCTTGGTTTACAAAATTACCAAAATACCCTCGATCAATAA
1 AATTA-CCATAATACCCTCGATTTACAAAATTACCATTTTACCCTCGATTTACAA
*
39666619 AATTACCAAAATACCC
1 AATTACCATAATACCC
39666635 CTAGTTTGTA
Statistics
Matches: 102, Mismatches: 20, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
53 1 0.01
54 100 0.98
55 1 0.01
ACGTcount: A:0.35, C:0.24, G:0.06, T:0.35
Consensus pattern (54 bp):
AATTACCATAATACCCTCGATTTACAAAATTACCATTTTACCCTCGATTTACAA
Found at i:39666607 original size:81 final size:81
Alignment explanation
Indices: 39666457--39666612 Score: 204
Period size: 81 Copynumber: 1.9 Consensus size: 81
39666447 AATAAGATTG
* *** * * ***
39666457 AATTACCATTTTACCCTCGATTTACAGAATTATCGTTTTACCCTCGATTTATAGAATTACCATTT
1 AATTACCATTTTACCCTCGATTTACAAAATTATCGAAATACCCTCGATTTACAAAATTACCAAAA
39666522 TACCCTCGATTTACAT
66 TACCCTCGATTTACAT
* * *
39666538 AATTACCATTTTACCCTCGATTTACAAAATTATTGAAATACCCTTGGTTTACAAAATTACCAAAA
1 AATTACCATTTTACCCTCGATTTACAAAATTATCGAAATACCCTCGATTTACAAAATTACCAAAA
39666603 TACCCTCGAT
66 TACCCTCGAT
39666613 CAATAAAATT
Statistics
Matches: 63, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
81 63 1.00
ACGTcount: A:0.33, C:0.23, G:0.07, T:0.37
Consensus pattern (81 bp):
AATTACCATTTTACCCTCGATTTACAAAATTATCGAAATACCCTCGATTTACAAAATTACCAAAA
TACCCTCGATTTACAT
Found at i:39666691 original size:27 final size:28
Alignment explanation
Indices: 39666590--39666691 Score: 104
Period size: 27 Copynumber: 3.8 Consensus size: 28
39666580 CTTGGTTTAC
***
39666590 AAAATTACCAAAATACC-CTCGA-TCAAT
1 AAAATTACCAAAATACCTCT-GAGTTTGT
*
39666617 AAAATTACCAAAATACCCCT-AGTTTGT
1 AAAATTACCAAAATACCTCTGAGTTTGT
*
39666644 AAAATTACCAAAATACATCTGA-TTTGT
1 AAAATTACCAAAATACCTCTGAGTTTGT
* *
39666671 GAAATTACCGAAATACCTCTG
1 AAAATTACCAAAATACCTCTG
39666692 TAGGGTAGAA
Statistics
Matches: 64, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
26 1 0.02
27 60 0.94
28 3 0.05
ACGTcount: A:0.43, C:0.22, G:0.08, T:0.27
Consensus pattern (28 bp):
AAAATTACCAAAATACCTCTGAGTTTGT
Found at i:39666703 original size:27 final size:26
Alignment explanation
Indices: 39666673--39666814 Score: 185
Period size: 27 Copynumber: 5.3 Consensus size: 26
39666663 TGATTTGTGA
39666673 AATTACCGAAATACCTCTGTAGGGTAG
1 AATTACCGAAATACC-CTGTAGGGTAG
39666700 AATTACCGAAATACCCTTGTAGGGTAG
1 AATTACCGAAATACCC-TGTAGGGTAG
* *
39666727 AATTACTGAAATACCCCTGTAGGGTAA
1 AATTACCGAAATA-CCCTGTAGGGTAG
*
39666754 AATTATCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATA-CCCTGTAGGGTAG
* * *
39666781 AATTACCGAGATACCCTTGTGGGGTAA
1 AATTACCGAAATACCC-TGTAGGGTAG
39666808 AATTACC
1 AATTACC
39666815 ATTTTGCCCC
Statistics
Matches: 103, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
26 4 0.04
27 96 0.93
28 3 0.03
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Consensus pattern (26 bp):
AATTACCGAAATACCCTGTAGGGTAG
Found at i:39666731 original size:81 final size:81
Alignment explanation
Indices: 39666642--39666815 Score: 224
Period size: 81 Copynumber: 2.1 Consensus size: 81
39666632 CCCCTAGTTT
* ** * *
39666642 GTAAAATTACCAAAATACATCTG-ATTTGTGAAATTACCGAAATACCTCTGTAGGGTAGAATTAC
1 GTAAAATTACCAAAATACACCTGTA-GGGTAAAATTACCGAAATACCCCTGTAGGGTAGAATTAC
39666706 CGAAATACCCTTGTAGG
65 CGAAATACCCTTGTAGG
* ** * *
39666723 GTAGAATTACTGAAATACCCCTGTAGGGTAAAATTATCGAAATACCCCTGTAGGGTAGAATTACC
1 GTAAAATTACCAAAATACACCTGTAGGGTAAAATTACCGAAATACCCCTGTAGGGTAGAATTACC
* *
39666788 GAGATACCCTTGTGGG
66 GAAATACCCTTGTAGG
39666804 GTAAAATTACCA
1 GTAAAATTACCA
39666816 TTTTGCCCCT
Statistics
Matches: 77, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
81 76 0.99
82 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.27
Consensus pattern (81 bp):
GTAAAATTACCAAAATACACCTGTAGGGTAAAATTACCGAAATACCCCTGTAGGGTAGAATTACC
GAAATACCCTTGTAGG
Found at i:39667244 original size:31 final size:31
Alignment explanation
Indices: 39667209--39667287 Score: 104
Period size: 31 Copynumber: 2.5 Consensus size: 31
39667199 TTGCATTCAC
* *
39667209 ATTCTGATTTTGATTCTGTTACCTGATACTG
1 ATTCTGATTCTGATTCTGTCACCTGATACTG
* **
39667240 ATTCTGATTCTAATTCTGTCACCTGATTTTG
1 ATTCTGATTCTGATTCTGTCACCTGATACTG
*
39667271 ATTATGATTCTGATTCT
1 ATTCTGATTCTGATTCT
39667288 AGTTTTGATA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.20, C:0.16, G:0.14, T:0.49
Consensus pattern (31 bp):
ATTCTGATTCTGATTCTGTCACCTGATACTG
Found at i:39667248 original size:6 final size:6
Alignment explanation
Indices: 39667209--39667287 Score: 54
Period size: 6 Copynumber: 12.8 Consensus size: 6
39667199 TTGCATTCAC
* * *
39667209 ATTCTG ATTTTG ATTCTG -TTACCTG ATACTG ATTCTG ATTCTA ATTCTG
1 ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG ATTCTG
* * *
39667258 -TCACCTG ATTTTG ATTATG ATTCTG ATTCT
1 AT--TCTG ATTCTG ATTCTG ATTCTG ATTCT
39667288 AGTTTTGATA
Statistics
Matches: 56, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
5 3 0.05
6 45 0.80
7 6 0.11
8 2 0.04
ACGTcount: A:0.20, C:0.16, G:0.14, T:0.49
Consensus pattern (6 bp):
ATTCTG
Found at i:39667305 original size:24 final size:24
Alignment explanation
Indices: 39667266--39667311 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
39667256 TGTCACCTGA
*
39667266 TTTTGATTATGATTCTGATTCTAG
1 TTTTGATAATGATTCTGATTCTAG
* *
39667290 TTTTGATAATGTTTCTTATTCT
1 TTTTGATAATGATTCTGATTCT
39667312 GTAATGGGTT
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:0.20, C:0.09, G:0.13, T:0.59
Consensus pattern (24 bp):
TTTTGATAATGATTCTGATTCTAG
Found at i:39668727 original size:76 final size:76
Alignment explanation
Indices: 39668584--39668757 Score: 172
Period size: 76 Copynumber: 2.3 Consensus size: 76
39668574 TACACCAGCG
* * * *
39668584 CGAAGCCTGCTAAGTACAGAGCCCGAATATCACTGAAACAGAGCCTACTAAGCACAGAATCTGAA
1 CGAAGCCTGCTAGGCACAGAGCCCGAATATCACCGAAACAGAGCCTACTAAGCACAGAATCTAAA
* **
39668649 TAACATTGGCA
66 TAACATCGAAA
* * * * * * **
39668660 CGAAGCCTGCTAGGCACAGAGCCCGGATATCACCGACACATAGCTTGCTAGGCACAG-GGCTCAA
1 CGAAGCCTGCTAGGCACAGAGCCCGAATATCACCGAAACAGAGCCTACTAAGCACAGAATCT-AA
39668724 ATAACATCGAAA
65 ATAACATCGAAA
*
39668736 C-AGAGCCTACTAGGCACAGAGC
1 CGA-AGCCTGCTAGGCACAGAGC
39668758 TTGAATAAAA
Statistics
Matches: 80, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
75 3 0.04
76 77 0.96
ACGTcount: A:0.35, C:0.28, G:0.22, T:0.15
Consensus pattern (76 bp):
CGAAGCCTGCTAGGCACAGAGCCCGAATATCACCGAAACAGAGCCTACTAAGCACAGAATCTAAA
TAACATCGAAA
Found at i:39668765 original size:38 final size:38
Alignment explanation
Indices: 39668599--39668765 Score: 115
Period size: 38 Copynumber: 4.4 Consensus size: 38
39668589 CCTGCTAAGT
* * *
39668599 ACAGAGCCCGAATATCA-CTGAAACAGAGCCTACTAAGC
1 ACAGAGCTCGAATAACATC-GAAACAGAGCCTACTAGGC
* * ** *
39668637 ACAGA-ATCTGAATAACATTGGCAC-GAAGCCTGCTAGGC
1 ACAGAGCTC-GAATAACATCGAAACAG-AGCCTACTAGGC
* * * * * * * *
39668675 ACAGAGCCCGGATATCACCGACACATAGCTTGCTAGGC
1 ACAGAGCTCGAATAACATCGAAACAGAGCCTACTAGGC
* *
39668713 ACAGGGCTCAAATAACATCGAAACAGAGCCTACTAGGC
1 ACAGAGCTCGAATAACATCGAAACAGAGCCTACTAGGC
*
39668751 ACAGAGCTTGAATAA
1 ACAGAGCTCGAATAA
39668766 AACTGGCATA
Statistics
Matches: 94, Mismatches: 30, Indels: 10
0.70 0.22 0.07
Matches are distributed among these distances:
37 2 0.02
38 91 0.97
39 1 0.01
ACGTcount: A:0.37, C:0.26, G:0.22, T:0.16
Consensus pattern (38 bp):
ACAGAGCTCGAATAACATCGAAACAGAGCCTACTAGGC
Found at i:39668798 original size:16 final size:16
Alignment explanation
Indices: 39668779--39668812 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
39668769 TGGCATAAAT
39668779 CCTGCTAGGCACAGAG
1 CCTGCTAGGCACAGAG
*
39668795 CCTGCTGGGCACAGAG
1 CCTGCTAGGCACAGAG
39668811 CC
1 CC
39668813 CGAATATCAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.21, C:0.35, G:0.32, T:0.12
Consensus pattern (16 bp):
CCTGCTAGGCACAGAG
Found at i:39668818 original size:54 final size:54
Alignment explanation
Indices: 39668735--39668845 Score: 132
Period size: 54 Copynumber: 2.1 Consensus size: 54
39668725 TAACATCGAA
** * * * *
39668735 ACAGAGCCTACTAGGCACAGAGCTTGAATAAAACTGGCATAAATCCTGCTAGGC
1 ACAGAGCCTACTAGGCACAGAGCCCGAATAAAACCGACACAAAGCCTGCTAGGC
* * **
39668789 ACAGAGCCTGCTGGGCACAGAGCCCGAATATCACCGACACAAAGCCTGCTAGGC
1 ACAGAGCCTACTAGGCACAGAGCCCGAATAAAACCGACACAAAGCCTGCTAGGC
39668843 ACA
1 ACA
39668846 AAGCTTGAAT
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
54 47 1.00
ACGTcount: A:0.33, C:0.29, G:0.23, T:0.14
Consensus pattern (54 bp):
ACAGAGCCTACTAGGCACAGAGCCCGAATAAAACCGACACAAAGCCTGCTAGGC
Found at i:39669122 original size:28 final size:28
Alignment explanation
Indices: 39669089--39669144 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
39669079 ATTTATAGAG
39669089 TAAAATTATTTATTTCATGCAATTTGGT
1 TAAAATTATTTATTTCATGCAATTTGGT
39669117 TAAAATTATTTATTTCATGCAATTTGGT
1 TAAAATTATTTATTTCATGCAATTTGGT
39669145 CATTTTTACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.32, C:0.07, G:0.11, T:0.50
Consensus pattern (28 bp):
TAAAATTATTTATTTCATGCAATTTGGT
Found at i:39669407 original size:21 final size:20
Alignment explanation
Indices: 39669383--39669422 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
39669373 ATACTTTTAA
39669383 TTATCAATCAACATTCAAAAT
1 TTATCAATCAACA-TCAAAAT
* *
39669404 TTATCATTTAACATCAAAA
1 TTATCAATCAACATCAAAA
39669423 ATCACAAGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.47, C:0.17, G:0.00, T:0.35
Consensus pattern (20 bp):
TTATCAATCAACATCAAAAT
Found at i:39671394 original size:17 final size:18
Alignment explanation
Indices: 39671362--39671395 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
39671352 GTTGGACCGA
*
39671362 AATGGGCCTTGTGGGCCC
1 AATGGGCCTCGTGGGCCC
39671380 AATGGG-CTCGTGGGCC
1 AATGGGCCTCGTGGGCC
39671396 ACACACAGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.12, C:0.26, G:0.41, T:0.21
Consensus pattern (18 bp):
AATGGGCCTCGTGGGCCC
Found at i:39677073 original size:38 final size:37
Alignment explanation
Indices: 39677023--39677295 Score: 260
Period size: 38 Copynumber: 7.2 Consensus size: 37
39677013 TAATATTGGA
* * ** *
39677023 ACAAAGCTTACTAGGCACAGAGCTCGAATGTCACCAGC
1 ACAAAGCCTGCTAGGCACAGAGC-CGAATAACACCGGC
* * * *
39677061 ATAGAGCCTACTAGGCACAGAGCCCGAATATCACCGGC
1 ACAAAGCCTGCTAGGCACAGAG-CCGAATAACACCGGC
* * *
39677099 ATAAAGCTTGCTAGGCACAAAGCCGGAATAACACCGGC
1 ACAAAGCCTGCTAGGCACAGAGCC-GAATAACACCGGC
*
39677137 ACAAAGCCTGCTAGGCACAGAGCTCGAATAACACCGGA
1 ACAAAGCCTGCTAGGCACAGAGC-CGAATAACACCGGC
* *
39677175 ACAAA-CCTACTAGACACAGAGCCAGAATAACACCGGC
1 ACAAAGCCTGCTAGGCACAGAGCC-GAATAACACCGGC
** * * * *
39677212 ATGAAGCCTGCTAGGCACGGAGCCTGAATATCTCCAGC
1 ACAAAGCCTGCTAGGCACAGAGCC-GAATAACACCGGC
* * *
39677250 ACAAAGCCTGCTAGGCACAAAGCTTGAATAACACAGGC
1 ACAAAGCCTGCTAGGCACAGAGC-CGAATAACACCGGC
39677288 ACAAAGCC
1 ACAAAGCC
39677296 GGCCAGGTGT
Statistics
Matches: 194, Mismatches: 35, Indels: 12
0.80 0.15 0.05
Matches are distributed among these distances:
36 1 0.01
37 32 0.16
38 159 0.82
39 2 0.01
ACGTcount: A:0.36, C:0.29, G:0.22, T:0.13
Consensus pattern (37 bp):
ACAAAGCCTGCTAGGCACAGAGCCGAATAACACCGGC
Found at i:39677220 original size:151 final size:152
Alignment explanation
Indices: 39677020--39677295 Score: 378
Period size: 151 Copynumber: 1.8 Consensus size: 152
39677010 AAATAATATT
* * **
39677020 GGAACAAAGCTTACTAGGCACAGAGCTCGAATGTCACCAGCATAGAGCCTACTAGGCACAGAGCC
1 GGAACAAAGCCTACTAGACACAGAGCTCGAATAACACCAGCATAGAGCCTACTAGGCACAGAGCC
* * * *
39677085 CGAATATCACCGGCATAAAGCTTGCTAGGCACAAAGCCGGAATAACACCGGCACAAAGCCTGCTA
66 CGAATATCACCAGCACAAAGCCTGCTAGGCACAAAGCCGGAATAACACAGGCACAAAGCCTGCTA
39677150 GGCACAGAGCTCGAATAACACC
131 GGCACAGAGCTCGAATAACACC
* * *
39677172 GGAACAAA-CCTACTAGACACAGAGC-CAGAATAACACCGGCAT-GAAGCCTGCTAGGCACGGAG
1 GGAACAAAGCCTACTAGACACAGAGCTC-GAATAACACCAGCATAG-AGCCTACTAGGCACAGAG
* * **
39677234 CCTGAATATCTCCAGCACAAAGCCTGCTAGGCACAAAGCTTGAATAACACAGGCACAAAGCC
64 CCCGAATATCACCAGCACAAAGCCTGCTAGGCACAAAGCCGGAATAACACAGGCACAAAGCC
39677296 GGCCAGGTGT
Statistics
Matches: 107, Mismatches: 15, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
150 2 0.02
151 97 0.91
152 8 0.07
ACGTcount: A:0.36, C:0.29, G:0.22, T:0.13
Consensus pattern (152 bp):
GGAACAAAGCCTACTAGACACAGAGCTCGAATAACACCAGCATAGAGCCTACTAGGCACAGAGCC
CGAATATCACCAGCACAAAGCCTGCTAGGCACAAAGCCGGAATAACACAGGCACAAAGCCTGCTA
GGCACAGAGCTCGAATAACACC
Found at i:39677227 original size:113 final size:113
Alignment explanation
Indices: 39677023--39677292 Score: 333
Period size: 113 Copynumber: 2.4 Consensus size: 113
39677013 TAATATTGGA
* * ** * * * * *
39677023 ACAAAGCTTACTAGGCACAGAGCTCGAATGTCACCAGCATAGAGCCTACTAGGCACAGAGCCCGA
1 ACAAAGCCTGCTAGGCACAGAGCTCGAATAACACCGGCACA-AACCTACTAGACACAGAGCCAGA
* * *
39677088 ATATCACCGGCATAAAGCTTGCTAGGCACAAAGCCGGAATAACACCGGC
65 ATAACACCGGCATAAAGCCTGCTAGGCACAAAGCCGGAATAACACCAGC
*
39677137 ACAAAGCCTGCTAGGCACAGAGCTCGAATAACACCGGAACAAACCTACTAGACACAGAGCCAGAA
1 ACAAAGCCTGCTAGGCACAGAGCTCGAATAACACCGGCACAAACCTACTAGACACAGAGCCAGAA
* ** * * *
39677202 TAACACCGGCATGAAGCCTGCTAGGCACGGAGCCTGAATATCTCCAGC
66 TAACACCGGCATAAAGCCTGCTAGGCACAAAGCCGGAATAACACCAGC
* * *
39677250 ACAAAGCCTGCTAGGCACAAAGCTTGAATAACACAGGCACAAA
1 ACAAAGCCTGCTAGGCACAGAGCTCGAATAACACCGGCACAAA
39677293 GCCGGCCAGG
Statistics
Matches: 133, Mismatches: 23, Indels: 1
0.85 0.15 0.01
Matches are distributed among these distances:
113 99 0.74
114 34 0.26
ACGTcount: A:0.36, C:0.29, G:0.22, T:0.13
Consensus pattern (113 bp):
ACAAAGCCTGCTAGGCACAGAGCTCGAATAACACCGGCACAAACCTACTAGACACAGAGCCAGAA
TAACACCGGCATAAAGCCTGCTAGGCACAAAGCCGGAATAACACCAGC
Found at i:39693160 original size:46 final size:47
Alignment explanation
Indices: 39693092--39693215 Score: 164
Period size: 46 Copynumber: 2.7 Consensus size: 47
39693082 TTACTAGTGT
* *
39693092 GCCAGTGTAAGACATGTCTGGGACATGGCATCGGCGTAGA-GATGAGT-
1 GCCAGTGTAAGACATGTCTGGGACAT-GCATCGCCCTAGACGATGA-TA
* * *
39693139 G-TAGTGTAAGACATGTTTGGGACATGCATCGCCCTCGACGATGATA
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGCCCTAGACGATGATA
39693185 GCCAGTGTAAGACATGTCTGGGACATGCATC
1 GCCAGTGTAAGACATGTCTGGGACATGCATC
39693216 AGCACGTATA
Statistics
Matches: 67, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
45 11 0.16
46 28 0.42
47 28 0.42
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.23
Consensus pattern (47 bp):
GCCAGTGTAAGACATGTCTGGGACATGCATCGCCCTAGACGATGATA
Found at i:39693201 original size:47 final size:46
Alignment explanation
Indices: 39693090--39693215 Score: 166
Period size: 47 Copynumber: 2.7 Consensus size: 46
39693080 GATTACTAGT
* *
39693090 GTGCCAGTGTAAGACATGTCTGGGACATGGCATCGGCGTAGAGATGA
1 GTGCCAGTGTAAGACATGTCTGGGACAT-GCATCGCCCTAGAGATGA
* * *
39693137 GTG-TAGTGTAAGACATGTTTGGGACATGCATCGCCCTCGACGATGA
1 GTGCCAGTGTAAGACATGTCTGGGACATGCATCGCCCTAGA-GATGA
39693183 -TAGCCAGTGTAAGACATGTCTGGGACATGCATC
1 GT-GCCAGTGTAAGACATGTCTGGGACATGCATC
39693216 AGCACGTATA
Statistics
Matches: 69, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
45 11 0.16
46 28 0.41
47 30 0.43
ACGTcount: A:0.25, C:0.19, G:0.32, T:0.24
Consensus pattern (46 bp):
GTGCCAGTGTAAGACATGTCTGGGACATGCATCGCCCTAGAGATGA
Found at i:39694114 original size:55 final size:55
Alignment explanation
Indices: 39694029--39694161 Score: 158
Period size: 55 Copynumber: 2.4 Consensus size: 55
39694019 GCACTTAAAA
* * * * * ** * * *
39694029 TTTTAAAGTCAGTGCTGTACATGGGTAGGCCACACGGGAGTGTGTCATGGTCGTG
1 TTTTAAAGTCAGTGTTGTACACGAGAAGGCCACACAGGAGTGTCACATAGCCATG
*
39694084 TTTTAAAGTCAGTGTTGTACACGAGAAGGCCACACAGGCGTGTCACATAGCCATG
1 TTTTAAAGTCAGTGTTGTACACGAGAAGGCCACACAGGAGTGTCACATAGCCATG
*
39694139 TTTTAAAGTCAGTGTTGCACACG
1 TTTTAAAGTCAGTGTTGTACACG
39694162 GGCTAAAGGC
Statistics
Matches: 66, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
55 66 1.00
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.28
Consensus pattern (55 bp):
TTTTAAAGTCAGTGTTGTACACGAGAAGGCCACACAGGAGTGTCACATAGCCATG
Found at i:39695996 original size:25 final size:25
Alignment explanation
Indices: 39695968--39696018 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
39695958 GGGGCATAAA
39695968 ATTTGCTTTTAAAATTAATTTGTTT
1 ATTTGCTTTTAAAATTAATTTGTTT
*
39695993 ATTTGCTTTTAAAATTAATTTTTTT
1 ATTTGCTTTTAAAATTAATTTGTTT
39696018 A
1 A
39696019 CATCCATTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.29, C:0.04, G:0.06, T:0.61
Consensus pattern (25 bp):
ATTTGCTTTTAAAATTAATTTGTTT
Found at i:39696810 original size:32 final size:33
Alignment explanation
Indices: 39696776--39696859 Score: 89
Period size: 32 Copynumber: 2.5 Consensus size: 33
39696766 CGGGCCTAAG
*
39696776 CCCATTCAGATAACAGTGATACTGGGCCAGAGC
1 CCCATTCAGATAACAGTGAAACTGGGCCAGAGC
* * * **
39696809 CCCTTTCAGATTACA-TTAAACTGGGCCTTAGC
1 CCCATTCAGATAACAGTGAAACTGGGCCAGAGC
39696841 CCCTTATTCAGATAACAGT
1 CCC--ATTCAGATAACAGT
39696860 ATGGCCCATA
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
32 16 0.40
33 13 0.32
34 10 0.25
35 1 0.03
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.26
Consensus pattern (33 bp):
CCCATTCAGATAACAGTGAAACTGGGCCAGAGC
Found at i:39697221 original size:26 final size:26
Alignment explanation
Indices: 39697170--39697222 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
39697160 TTAAACATGC
*
39697170 ATTTTGGTCAATTTACTCATAGGGGT
1 ATTTTGGTCAATTTACTCATAAGGGT
* *
39697196 ATTTTGGT-ACTTTATCTCCTAAGGGT
1 ATTTTGGTCAATTTA-CTCATAAGGGT
39697222 A
1 A
39697223 AAACTATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 5 0.22
26 18 0.78
ACGTcount: A:0.23, C:0.13, G:0.21, T:0.43
Consensus pattern (26 bp):
ATTTTGGTCAATTTACTCATAAGGGT
Found at i:39698494 original size:24 final size:23
Alignment explanation
Indices: 39698466--39698564 Score: 126
Period size: 24 Copynumber: 4.1 Consensus size: 23
39698456 CCAAATCCAG
*
39698466 CTCCTTGATCAGCTCCTAAATCTT
1 CTCCTT-ATCAGCTCCTAAATCCT
*
39698490 CTCCTTTATTAGCTCCTAAATCCT
1 CTCC-TTATCAGCTCCTAAATCCT
*
39698514 CTCCCTTACCAGCTCCTAAATCCT
1 CT-CCTTATCAGCTCCTAAATCCT
*
39698538 CTCCCTTATCAGCTCCTAAATCTT
1 CT-CCTTATCAGCTCCTAAATCCT
39698562 CTC
1 CTC
39698565 TTGATAGCCT
Statistics
Matches: 67, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
23 1 0.01
24 62 0.93
25 4 0.06
ACGTcount: A:0.20, C:0.38, G:0.05, T:0.36
Consensus pattern (23 bp):
CTCCTTATCAGCTCCTAAATCCT
Found at i:39702080 original size:40 final size:40
Alignment explanation
Indices: 39701996--39702220 Score: 260
Period size: 40 Copynumber: 5.7 Consensus size: 40
39701986 TTGAATGATG
* * * *
39701996 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * * * *
39702036 TTCGGACTAAGAT-CCGAAGGTATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
39702076 TTCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
39702115 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
39702155 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGCTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
39702196 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
39702221 AACGAGGAGC
Statistics
Matches: 160, Mismatches: 20, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
39 32 0.20
40 118 0.74
41 10 0.06
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:39702238 original size:80 final size:79
Alignment explanation
Indices: 39702078--39702243 Score: 203
Period size: 80 Copynumber: 2.1 Consensus size: 79
39702068 ATACTAATTT
* * * **
39702078 CGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTG
1 CGGGTTAAGCCCGAAGGCATTGGTGCGAGCTACTAAATCCGGGCTAAGTCCCGAAGGCATTTGAA
*
39702143 CGAGTTACTAAATC
66 CGAGTGACTAAATC
* *
39702157 CGGGTTAAGTCCCGAAGGCATTTGTGCGAGCTACTATAA-CCGGGCTATGTCCCGAAGGCATTTG
1 CGGGTTAAG-CCCGAAGGCATTGGTGCGAGCTACTA-AATCCGGGCTAAGTCCCGAAGGCATTTG
*
39702221 AACGAG-GAGCTATATC
64 AACGAGTGA-CTAAATC
39702237 C-GGTTAA
1 CGGGTTAA
39702244 ATTTCGAAGG
Statistics
Matches: 75, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
79 15 0.20
80 58 0.77
81 2 0.03
ACGTcount: A:0.25, C:0.22, G:0.29, T:0.24
Consensus pattern (79 bp):
CGGGTTAAGCCCGAAGGCATTGGTGCGAGCTACTAAATCCGGGCTAAGTCCCGAAGGCATTTGAA
CGAGTGACTAAATC
Found at i:39710097 original size:40 final size:40
Alignment explanation
Indices: 39710013--39710237 Score: 278
Period size: 40 Copynumber: 5.7 Consensus size: 40
39710003 TTGAATGATG
* * * *
39710013 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * * *
39710053 TCCGGACTAAGAT-CCGAAGGTATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
39710093 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
39710132 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
39710172 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGCTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
39710213 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
39710238 AACGAGGAGC
Statistics
Matches: 162, Mismatches: 18, Indels: 10
0.85 0.09 0.05
Matches are distributed among these distances:
39 33 0.20
40 119 0.73
41 10 0.06
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:39710255 original size:80 final size:80
Alignment explanation
Indices: 39710013--39710270 Score: 217
Period size: 80 Copynumber: 3.2 Consensus size: 80
39710003 TTGAATGATG
* * * * * * *
39710013 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAG-TGACCATATCCGGACTAAGAT-CCGAAGGTA
1 TCCGGGTTAAGTCCCGAAGGCATTGGTGC-GAGCT-ACTAAATCCGGGCTAAG-TCCCGAAGGCA
** *
39710075 TTTGTGCGAGAT-ACTAAT
63 TTTGAACGAG-TGACTAAA
* * *
39710093 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCATTGGTGCGAGCTACTAAATCCGGGCTAAGTCCCGAAGGCATTT
** *
39710157 GTGCGAGTTACTAAA
66 GAACGAGTGACTAAA
* *
39710172 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGCTACTATAA-CCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATTGGTGCGAGCTACTA-AATCCGGGCTAAGTCCCGAAGGCATT
*
39710236 TGAACGAG-GAGCTATA
65 TGAACGAGTGA-CTAAA
* *
39710252 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
39710271 TACGTGATTT
Statistics
Matches: 152, Mismatches: 19, Indels: 15
0.82 0.10 0.08
Matches are distributed among these distances:
78 2 0.01
79 72 0.47
80 76 0.50
81 2 0.01
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCATTGGTGCGAGCTACTAAATCCGGGCTAAGTCCCGAAGGCATTT
GAACGAGTGACTAAA
Found at i:39710259 original size:119 final size:119
Alignment explanation
Indices: 39710013--39710270 Score: 274
Period size: 119 Copynumber: 2.2 Consensus size: 119
39710003 TTGAATGATG
* * *
39710013 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGTATTT
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
* ** *
39710078 GTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAAA
66 GTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTGACTAAA
* * * **
39710132 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCAT
* * * *
39710195 TTGTGCGAGCTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTATA
64 TTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTGA-CTAAA
* *
39710252 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
39710271 TACGTGATTT
Statistics
Matches: 116, Mismatches: 18, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
118 3 0.03
119 82 0.71
120 31 0.27
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (119 bp):
TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
GTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTGACTAAA
Found at i:39711635 original size:25 final size:25
Alignment explanation
Indices: 39711605--39711690 Score: 113
Period size: 25 Copynumber: 3.5 Consensus size: 25
39711595 ACGAGCTACA
*
39711605 AACGGGAAGCTCCTCCGAGCTGAAT
1 AACGGGAAGCTCCTGCGAGCTGAAT
* *
39711630 AACGGGAAGCTCATGTGAGCTGAAT
1 AACGGGAAGCTCCTGCGAGCTGAAT
39711655 AACGGGAAGCT-CTGCGAGCT-ATAT
1 AACGGGAAGCTCCTGCGAGCTGA-AT
*
39711679 AACGAGAAGCTC
1 AACGGGAAGCTC
39711691 ATAAGAGTTT
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
23 1 0.02
24 19 0.36
25 33 0.62
ACGTcount: A:0.31, C:0.22, G:0.29, T:0.17
Consensus pattern (25 bp):
AACGGGAAGCTCCTGCGAGCTGAAT
Found at i:39713340 original size:20 final size:20
Alignment explanation
Indices: 39713315--39713362 Score: 64
Period size: 18 Copynumber: 2.5 Consensus size: 20
39713305 AAGGAATAAA
*
39713315 TATTGATACTTTATGGTAAG
1 TATTGATACTTTATAGTAAG
39713335 TATTGATA--TTATAGTAAG
1 TATTGATACTTTATAGTAAG
*
39713353 TATGGATACT
1 TATTGATACT
39713363 GTTTTGGCAG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
18 16 0.67
20 8 0.33
ACGTcount: A:0.33, C:0.04, G:0.19, T:0.44
Consensus pattern (20 bp):
TATTGATACTTTATAGTAAG
Found at i:39713559 original size:22 final size:22
Alignment explanation
Indices: 39713534--39713602 Score: 74
Period size: 22 Copynumber: 3.3 Consensus size: 22
39713524 ACAATTAAAC
39713534 TACAAAGAACTTATTCAATCCA
1 TACAAAGAACTTATTCAATCCA
* * *
39713556 TACAAACACAC-AATT-AA-AC-
1 TACAAAGA-ACTTATTCAATCCA
39713575 TACAAAGAACTTATTCAATCCA
1 TACAAAGAACTTATTCAATCCA
39713597 TACAAA
1 TACAAA
39713603 CATACAACCA
Statistics
Matches: 36, Mismatches: 6, Indels: 10
0.69 0.12 0.19
Matches are distributed among these distances:
18 2 0.06
19 10 0.28
20 3 0.08
21 3 0.08
22 16 0.44
23 2 0.06
ACGTcount: A:0.51, C:0.23, G:0.03, T:0.23
Consensus pattern (22 bp):
TACAAAGAACTTATTCAATCCA
Found at i:39713571 original size:41 final size:41
Alignment explanation
Indices: 39713522--39713609 Score: 167
Period size: 41 Copynumber: 2.1 Consensus size: 41
39713512 ACATATAGGT
39713522 ACACAATTAAACTACAAAGAACTTATTCAATCCATACAAAC
1 ACACAATTAAACTACAAAGAACTTATTCAATCCATACAAAC
39713563 ACACAATTAAACTACAAAGAACTTATTCAATCCATACAAAC
1 ACACAATTAAACTACAAAGAACTTATTCAATCCATACAAAC
*
39713604 ATACAA
1 ACACAA
39713610 CCAATATGCC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 46 1.00
ACGTcount: A:0.52, C:0.24, G:0.02, T:0.22
Consensus pattern (41 bp):
ACACAATTAAACTACAAAGAACTTATTCAATCCATACAAAC
Found at i:39715533 original size:23 final size:25
Alignment explanation
Indices: 39715502--39715592 Score: 77
Period size: 24 Copynumber: 3.8 Consensus size: 25
39715492 TTCCCGTTAC
39715502 ATGGCTCTTTGTAAGCTTCCT-GAT
1 ATGGCTCTTTGTAAGCTTCCTCGAT
**
39715526 A-GGCTCTTCATAAGCTT-CTCGAT
1 ATGGCTCTTTGTAAGCTTCCTCGAT
* *
39715549 ATGGTTCTTTGTGAA-CTTCC-CAATT
1 ATGGCTCTTTGT-AAGCTTCCTCGA-T
*
39715574 ATGGCTC-TTATAAGCTTCC
1 ATGGCTCTTTGTAAGCTTCC
39715593 CATTATATAC
Statistics
Matches: 53, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
22 2 0.04
23 20 0.38
24 21 0.40
25 10 0.19
ACGTcount: A:0.20, C:0.23, G:0.18, T:0.40
Consensus pattern (25 bp):
ATGGCTCTTTGTAAGCTTCCTCGAT
Found at i:39715734 original size:44 final size:45
Alignment explanation
Indices: 39715685--39715770 Score: 147
Period size: 44 Copynumber: 1.9 Consensus size: 45
39715675 CTCGAGAGTA
*
39715685 TGCTTCCCGGTTATGTGCCCCAATGGTCA-CCCCGTATATGATTT
1 TGCTTCCCGGTTATGTGCCCCAATGGGCACCCCCGTATATGATTT
*
39715729 TGCTTCCCGGTTATGTGCCCTAATGGGCACCCCCGTATATGA
1 TGCTTCCCGGTTATGTGCCCCAATGGGCACCCCCGTATATGA
39715771 ATTGAGGATC
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
44 27 0.69
45 12 0.31
ACGTcount: A:0.16, C:0.30, G:0.22, T:0.31
Consensus pattern (45 bp):
TGCTTCCCGGTTATGTGCCCCAATGGGCACCCCCGTATATGATTT
Found at i:39717651 original size:21 final size:22
Alignment explanation
Indices: 39717607--39717658 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
39717597 TCAATCATAT
39717607 AACATTTCAATTCACTTAATTC
1 AACATTTCAATTCACTTAATTC
39717629 AACATTTCAATTCACTT-ATTC
1 AACATTTCAATTCACTTAATTC
39717650 AACATTTCA
1 AACATTTCA
39717659 TTATCATTCC
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 13 0.43
22 17 0.57
ACGTcount: A:0.37, C:0.23, G:0.00, T:0.40
Consensus pattern (22 bp):
AACATTTCAATTCACTTAATTC
Found at i:39718010 original size:12 final size:12
Alignment explanation
Indices: 39717993--39718045 Score: 56
Period size: 12 Copynumber: 4.5 Consensus size: 12
39717983 TCATTCCACA
39717993 ATTTCATATTTC
1 ATTTCATATTTC
*
39718005 ATTTCACATTTC
1 ATTTCATATTTC
*
39718017 ACTTCA-ATTTC
1 ATTTCATATTTC
*
39718028 ATATCAT-TTTCC
1 ATTTCATATTT-C
39718040 ATTTCA
1 ATTTCA
39718046 AATATTAGAT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
11 12 0.35
12 22 0.65
ACGTcount: A:0.26, C:0.23, G:0.00, T:0.51
Consensus pattern (12 bp):
ATTTCATATTTC
Found at i:39733748 original size:39 final size:39
Alignment explanation
Indices: 39733679--39733899 Score: 288
Period size: 39 Copynumber: 5.6 Consensus size: 39
39733669 NNNNNNNNNN
* * * *
39733679 AAATGCCTTTGGGACTTAACCCGGATTTAGTAACTCGCAC
1 AAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCAC
39733719 AAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCAC
1 AAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCAC
*
39733758 AAATGCCTTCGGGCTTAGCCCGAAATTAGTATCTCGCAC
1 AAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCAC
39733797 AAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCAC
1 AAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCAC
* * *
39733836 AAATGCCTTCGGATCTTAGTCCGGATATT-GTCA-CTTAGCAC
1 AAATGCCTTCGG-GCTTAGCCCGGA-ATTAGT-ATC-TCGCAC
39733877 -AA-GCCTTCGGGACTTAGCCCGGA
1 AAATGCCTTCGGG-CTTAGCCCGGA
39733900 CATCATTCAA
Statistics
Matches: 165, Mismatches: 11, Indels: 11
0.88 0.06 0.06
Matches are distributed among these distances:
39 129 0.78
40 27 0.16
41 9 0.05
ACGTcount: A:0.24, C:0.27, G:0.22, T:0.26
Consensus pattern (39 bp):
AAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCAC
Found at i:39744340 original size:11 final size:11
Alignment explanation
Indices: 39744324--39744365 Score: 59
Period size: 11 Copynumber: 3.8 Consensus size: 11
39744314 CCTAAGGATG
*
39744324 AAATAAAATTA
1 AAATAAAAATA
39744335 AAATAAAAGA-A
1 AAATAAAA-ATA
39744346 AAATAAAAATA
1 AAATAAAAATA
39744357 AAATAAAAA
1 AAATAAAAA
39744366 GTAGTTTTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
10 1 0.04
11 27 0.96
ACGTcount: A:0.81, C:0.00, G:0.02, T:0.17
Consensus pattern (11 bp):
AAATAAAAATA
Found at i:39744354 original size:17 final size:17
Alignment explanation
Indices: 39744328--39744365 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
39744318 AGGATGAAAT
*
39744328 AAAATTAAAATAAAAGA
1 AAAATAAAAATAAAAGA
*
39744345 AAAATAAAAATAAAATA
1 AAAATAAAAATAAAAGA
39744362 AAAA
1 AAAA
39744366 GTAGTTTTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.16
Consensus pattern (17 bp):
AAAATAAAAATAAAAGA
Found at i:39744392 original size:14 final size:13
Alignment explanation
Indices: 39744382--39744418 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 13
39744372 TTGAAAAGAT
39744382 AAAAATAAAAATA
1 AAAAATAAAAATA
39744395 AAAACATAAAAATA
1 AAAA-ATAAAAATA
*
39744409 ATAAATAAAA
1 AAAAATAAAA
39744419 GTCTTTAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.81, C:0.03, G:0.00, T:0.16
Consensus pattern (13 bp):
AAAAATAAAAATA
Found at i:39744397 original size:5 final size:6
Alignment explanation
Indices: 39744324--39744418 Score: 61
Period size: 6 Copynumber: 15.3 Consensus size: 6
39744314 CCTAAGGATG
* * *
39744324 AAAT-A AAATTA AAAT-A AAAGAA AAATAA AAAT-A AAATAA AAAGTAG
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAA-TAA
***
39744370 TTTTGAA AAGATAA AAATAA AAATAAA AACATAA AAATAA TAAATAA AA
1 AAAT-AA AA-ATAA AAATAA AAAT-AA AA-ATAA AAATAA -AAATAA AA
39744419 GTCTTTAAAC
Statistics
Matches: 71, Mismatches: 10, Indels: 17
0.72 0.10 0.17
Matches are distributed among these distances:
5 13 0.18
6 34 0.48
7 21 0.30
8 3 0.04
ACGTcount: A:0.74, C:0.01, G:0.05, T:0.20
Consensus pattern (6 bp):
AAATAA
Found at i:39744398 original size:20 final size:21
Alignment explanation
Indices: 39744375--39744418 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
39744365 AGTAGTTTTG
*
39744375 AAAAGATAAAAATAA-AAATA
1 AAAACATAAAAATAATAAATA
39744395 AAAACATAAAAATAATAAATA
1 AAAACATAAAAATAATAAATA
39744416 AAA
1 AAA
39744419 GTCTTTAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.80, C:0.02, G:0.02, T:0.16
Consensus pattern (21 bp):
AAAACATAAAAATAATAAATA
Found at i:39751480 original size:23 final size:25
Alignment explanation
Indices: 39751454--39751506 Score: 58
Period size: 23 Copynumber: 2.2 Consensus size: 25
39751444 TATCGAGAAC
39751454 TAAATACAAAAATAAAT-AACAAA-
1 TAAATACAAAAATAAATAAACAAAT
* * *
39751477 TAAA-ACACAAATGACTAAACAAAT
1 TAAATACAAAAATAAATAAACAAAT
39751501 TAAATA
1 TAAATA
39751507 AATCAAGAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
22 9 0.38
23 10 0.42
24 4 0.17
25 1 0.04
ACGTcount: A:0.68, C:0.11, G:0.02, T:0.19
Consensus pattern (25 bp):
TAAATACAAAAATAAATAAACAAAT
Found at i:39758536 original size:47 final size:47
Alignment explanation
Indices: 39758433--39758625 Score: 273
Period size: 47 Copynumber: 4.1 Consensus size: 47
39758423 TTAGGATTTT
* * *
39758433 ATGTGATGAATGTGAATGA-GTATATATGAGATAA-GCCGAATGGCCA
1 ATGTGATGAATGTGAA-CATGCATATATGTGATAAGGCCGAATGGCCA
39758479 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
39758526 ATGTGATGAATGTGAGCATGCATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * * * *
39758573 ATGTGGTGAATATGAACATGCATATATGTGGTAAAGCCGAATGGCTA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
39758620 ATGTGA
1 ATGTGA
39758626 AATATATATG
Statistics
Matches: 132, Mismatches: 13, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
45 1 0.01
46 29 0.22
47 102 0.77
ACGTcount: A:0.34, C:0.11, G:0.29, T:0.26
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
Found at i:39758581 original size:25 final size:25
Alignment explanation
Indices: 39758506--39758581 Score: 63
Period size: 23 Copynumber: 3.2 Consensus size: 25
39758496 ATGCATATAT
39758506 GTGATAAGGCCGAATGGCCAATGTG
1 GTGATAAGGCCGAATGGCCAATGTG
* * * *
39758531 ATGA-ATGTG-AGCAT-G-CATATGT-
1 GTGATAAG-GCCGAATGGCCA-ATGTG
39758553 GTGATAAGGCCGAATGGCCAATGTG
1 GTGATAAGGCCGAATGGCCAATGTG
39758578 GTGA
1 GTGA
39758582 ATATGAACAT
Statistics
Matches: 36, Mismatches: 8, Indels: 14
0.62 0.14 0.24
Matches are distributed among these distances:
22 6 0.17
23 10 0.28
24 10 0.28
25 10 0.28
ACGTcount: A:0.29, C:0.13, G:0.34, T:0.24
Consensus pattern (25 bp):
GTGATAAGGCCGAATGGCCAATGTG
Found at i:39758750 original size:98 final size:96
Alignment explanation
Indices: 39758600--39758779 Score: 317
Period size: 98 Copynumber: 1.9 Consensus size: 96
39758590 ATGCATATAT
39758600 GTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAGATATGTATATGTGGTAAAGCCGAATGG
1 GTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAGATATGTATATGTGGTAAAGCCGAATGG
39758665 CTAATGTGAAATATGTATGAGATATGCATAC
66 CTAATGTGAAATATGTATGAGATATGCATAC
39758696 GTGGTAAAGCCGAATGG-TCAATGTGAAATATATATATGAGATATGTATATGTGGTAAAGCCGAA
1 GTGGTAAAGCCGAATGGCT-AATGTG-AA-ATATATATGAGATATGTATATGTGGTAAAGCCGAA
*
39758760 TGGCTAGTGTGAAATATGTA
63 TGGCTAATGTGAAATATGTA
39758780 GGCGATGTGC
Statistics
Matches: 80, Mismatches: 1, Indels: 4
0.94 0.01 0.05
Matches are distributed among these distances:
95 1 0.01
96 23 0.29
97 2 0.03
98 54 0.68
ACGTcount: A:0.36, C:0.08, G:0.27, T:0.29
Consensus pattern (96 bp):
GTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAGATATGTATATGTGGTAAAGCCGAATGG
CTAATGTGAAATATGTATGAGATATGCATAC
Found at i:39758795 original size:50 final size:48
Alignment explanation
Indices: 39758595--39758776 Score: 294
Period size: 48 Copynumber: 3.8 Consensus size: 48
39758585 TGAACATGCA
39758595 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAGATATG
1 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAGATATG
*
39758643 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATG
1 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAGATATG
* *
39758691 CATACGTGGTAAAGCCGAATGG-TCAATGTGAAATATATATATGAGATATG
1 TATATGTGGTAAAGCCGAATGGCT-AATGTG-AA-ATATATATGAGATATG
*
39758741 TATATGTGGTAAAGCCGAATGGCTAGTGTGAAATAT
1 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATAT
39758777 GTAGGCGATG
Statistics
Matches: 123, Mismatches: 7, Indels: 8
0.89 0.05 0.06
Matches are distributed among these distances:
47 1 0.01
48 77 0.63
49 4 0.03
50 40 0.33
51 1 0.01
ACGTcount: A:0.36, C:0.08, G:0.26, T:0.30
Consensus pattern (48 bp):
TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAGATATG
Found at i:39759108 original size:37 final size:37
Alignment explanation
Indices: 39758934--39759107 Score: 285
Period size: 37 Copynumber: 4.7 Consensus size: 37
39758924 ATTCCGGATG
39758934 AGACCCGATGACTACGTGTGGAGATTATGTCCGGGTA
1 AGACCCGATGACTACGTGTGGAGATTATGTCCGGGTA
*
39758971 AGACCCGATGACTACGTGTGGGGATTATGTCCGGGTA
1 AGACCCGATGACTACGTGTGGAGATTATGTCCGGGTA
* * *
39759008 AGACCCGATGACTACGTGTGGGGAGTATGTTCGGGTA
1 AGACCCGATGACTACGTGTGGAGATTATGTCCGGGTA
*
39759045 AGACCCGATGACTACGTGTGGAGATTTTGTCCGGGTA
1 AGACCCGATGACTACGTGTGGAGATTATGTCCGGGTA
* *
39759082 AGACCCGATAACTTCGTGTGGAGATT
1 AGACCCGATGACTACGTGTGGAGATT
39759108 TCGTCTGAGC
Statistics
Matches: 128, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 128 1.00
ACGTcount: A:0.23, C:0.18, G:0.33, T:0.25
Consensus pattern (37 bp):
AGACCCGATGACTACGTGTGGAGATTATGTCCGGGTA
Found at i:39760992 original size:42 final size:42
Alignment explanation
Indices: 39760938--39761034 Score: 158
Period size: 42 Copynumber: 2.3 Consensus size: 42
39760928 ATAGTCCAGC
* *
39760938 TATGGTCTTACACGAAGTCTCATATCGATGCCACATCTCAAA
1 TATGGTCTTACACGAAGTCTCATATAGATGCCACATCCCAAA
* *
39760980 TATGGTCTTACACGAAGTCTCATATAGATGCCATATCCCAGA
1 TATGGTCTTACACGAAGTCTCATATAGATGCCACATCCCAAA
39761022 TATGGTCTTACAC
1 TATGGTCTTACAC
39761035 ATAGCCTTAG
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 51 1.00
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30
Consensus pattern (42 bp):
TATGGTCTTACACGAAGTCTCATATAGATGCCACATCCCAAA
Found at i:39779065 original size:3 final size:3
Alignment explanation
Indices: 39779059--39779088 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
39779049 TTGGTGATAT
39779059 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
39779089 TGAAATAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:39785394 original size:40 final size:40
Alignment explanation
Indices: 39785330--39785582 Score: 136
Period size: 40 Copynumber: 6.3 Consensus size: 40
39785320 CGATATCTAT
* ** * **
39785330 TGAATCTACTGAAGTGTATATGCTTTTGAGCCATACCTAC
1 TGAATCTACTAAAACGTATGTGCTTTCAAGCCATACCTAC
* * ** *** * **
39785370 TGAATCTACTCATACGTATGTGCTTTTGAGTGGTATCTGT
1 TGAATCTACTAAAACGTATGTGCTTTCAAGCCATACCTAC
* *
39785410 TAAATCTACTAAAACGTATGTGCTTTCAAGCCATACCTAT
1 TGAATCTACTAAAACGTATGTGCTTTCAAGCCATACCTAC
* **
39785450 TGAATCTACTGAAACGTATGCACTTTCAAGCCATACCTAC
1 TGAATCTACTAAAACGTATGTGCTTTCAAGCCATACCTAC
* * * * * * * *
39785490 -CAGTCCCACTGAAATGTATGTGCTATCGAGCCTTACCTAC
1 TGAAT-CTACTAAAACGTATGTGCTTTCAAGCCATACCTAC
* * * * *
39785530 T-ATTTCTACTGAAA-GTATGCT-TTTTCGAGCCATACCTAA
1 TGA-ATCTACTAAAACGTATG-TGCTTTCAAGCCATACCTAC
*
39785569 TGATTCTACTAAAA
1 TGAATCTACTAAAA
39785583 GTAGCTCAAA
Statistics
Matches: 166, Mismatches: 42, Indels: 11
0.76 0.19 0.05
Matches are distributed among these distances:
39 32 0.19
40 133 0.80
41 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.34
Consensus pattern (40 bp):
TGAATCTACTAAAACGTATGTGCTTTCAAGCCATACCTAC
Found at i:39785681 original size:37 final size:39
Alignment explanation
Indices: 39785589--39785693 Score: 119
Period size: 37 Copynumber: 2.8 Consensus size: 39
39785579 AAAAGTAGCT
* * *
39785589 CAAATGAG-AAAATTTTACTGTTATACTG-ATGTGAAGCT
1 CAAATGAGTAAAA-TCTACTGTTATACTGAATGAGAAGCA
*
39785627 CAAATGAGTAAATTCTACTGTTATACTGAAT-AG-AGCA
1 CAAATGAGTAAAATCTACTGTTATACTGAATGAGAAGCA
* *
39785664 CAAATGAGTAAAATCTACAGATATACTGAA
1 CAAATGAGTAAAATCTACTGTTATACTGAA
39785694 ATAAAGCTCA
Statistics
Matches: 58, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
37 30 0.52
38 23 0.40
39 5 0.09
ACGTcount: A:0.42, C:0.12, G:0.16, T:0.30
Consensus pattern (39 bp):
CAAATGAGTAAAATCTACTGTTATACTGAATGAGAAGCA
Found at i:39795246 original size:26 final size:26
Alignment explanation
Indices: 39795210--39795352 Score: 214
Period size: 26 Copynumber: 5.5 Consensus size: 26
39795200 AACACATTAG
39795210 AAAATGGAAGCCTTTGTGGCATATCT
1 AAAATGGAAGCCTTTGTGGCATATCT
*
39795236 GAAATGGAAGCCTTTGTGGCATATCT
1 AAAATGGAAGCCTTTGTGGCATATCT
* * *
39795262 AAAATGGAAGTCTTTGCGGTATATCT
1 AAAATGGAAGCCTTTGTGGCATATCT
*
39795288 AAAATGGAAGCCTATGTGGCATATCT
1 AAAATGGAAGCCTTTGTGGCATATCT
* *
39795314 AAAATGGAAGCCTTTGTAGCGTATCT
1 AAAATGGAAGCCTTTGTGGCATATCT
*
39795340 GAAATGGAAGCCT
1 AAAATGGAAGCCT
39795353 CTATGGCGAA
Statistics
Matches: 104, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 104 1.00
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.29
Consensus pattern (26 bp):
AAAATGGAAGCCTTTGTGGCATATCT
Found at i:39805563 original size:40 final size:40
Alignment explanation
Indices: 39805481--39805663 Score: 221
Period size: 40 Copynumber: 4.6 Consensus size: 40
39805471 TATTCGAATG
* * *
39805481 ATATTCGGGCTAAG-TCCCGAAGGCTTTTATGCTAGTGACT
1 ATATCCGGGCTAAGAT-CCGAAGGCATTTGTGCTAGTGACT
* *
39805521 ATATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGATCCGAAGGCATTTGTGCTAG-TGACT
*
39805561 ATATCCGGGCTAAGA-CCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAGATCCGAAGGCATTTGTGCTAGTGACT
* *
39805600 ATATCCGGGCTAAG-TCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGAT-CCGAAGGCATTTGTGCTAGTGACT
* *
39805640 ATATCCGGGCTAAGACCCAAAGGC
1 ATATCCGGGCTAAGATCCGAAGGC
39805664 CTTGTGTGAG
Statistics
Matches: 124, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
38 1 0.01
39 34 0.27
40 86 0.69
41 3 0.02
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGATCCGAAGGCATTTGTGCTAGTGACT
Found at i:39805669 original size:79 final size:80
Alignment explanation
Indices: 39805481--39805663 Score: 237
Period size: 79 Copynumber: 2.3 Consensus size: 80
39805471 TATTCGAATG
* * * * *
39805481 ATATTCGGGCTAAGTCCCGAAGGCTTTTATGCTAGTGACTATATCCGGACTAAGATCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGACTATATCCGGACTAAGATCCGAAGGCA
* *
39805546 TTTGTGCGAGTTGCT
66 TTTATGCGAGTTGCC
*
39805561 ATATCCGGGCTAAGA-CCGAAGGCATTTGTGCTAGCGACTATATCCGGGCTAAG-TCCCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGACTATATCCGGACTAAGAT-CCGAAGGC
*
39805624 ATTTATGCTAG-TGACC
65 ATTTATGCGAGTTG-CC
*
39805640 ATATCCGGGCTAAGACCCAAAGGC
1 ATATCCGGGCTAAGACCCGAAGGC
39805664 CTTGTGTGAG
Statistics
Matches: 90, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
78 3 0.03
79 67 0.74
80 20 0.22
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.25
Consensus pattern (80 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGACTATATCCGGACTAAGATCCGAAGGCA
TTTATGCGAGTTGCC
Found at i:39807911 original size:27 final size:27
Alignment explanation
Indices: 39807880--39808057 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
39807870 TAAATTGTAC
39807880 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
39807907 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
39807933 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
39807961 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
39807989 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
39808016 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
39808043 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
39808058 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:39807994 original size:82 final size:81
Alignment explanation
Indices: 39807881--39808036 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
39807871 AAATTGTACA
* *
39807881 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
39807945 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
39807962 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
39808027 TGCGAGTTGA
65 TGCGAATTGA
39808037 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:39808048 original size:82 final size:81
Alignment explanation
Indices: 39807877--39808057 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
39807867 GATTAAATTG
* *
39807877 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
39807942 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
39807958 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
39808022 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
39808040 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
39808058 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:39836277 original size:27 final size:27
Alignment explanation
Indices: 39836247--39836424 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
39836237 ATATTGAGTC
* * * *
39836247 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
39836274 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
39836301 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
39836329 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
39836356 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
39836383 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
39836410 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
39836425 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:39836386 original size:82 final size:81
Alignment explanation
Indices: 39836268--39836423 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
39836258 TGCTATATAA
* *
39836268 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
39836333 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
39836350 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
39836414 CACTTAGTGC
65 CACTTAGTGC
39836424 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:39852848 original size:68 final size:67
Alignment explanation
Indices: 39852771--39852956 Score: 175
Period size: 67 Copynumber: 2.8 Consensus size: 67
39852761 CATCATGTGT
* * *
39852771 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGT-GATACAA-TG-TGTACACC
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACC
39852833 ATGTAG
62 ATGTAG
* ** * *
39852839 ACAAAAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
39852904 AG
66 AG
* * * * *
39852906 ACAAGAGAGCTACGAGATAAAT-TGGCTAGGTCACATGGGTGG-TACTAAGTG
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATAC-AAGTG
39852957 TTCACCATGT
Statistics
Matches: 99, Mismatches: 15, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
64 20 0.20
65 10 0.10
66 26 0.26
67 31 0.31
68 12 0.12
ACGTcount: A:0.33, C:0.16, G:0.29, T:0.22
Consensus pattern (67 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
AG
Found at i:39852875 original size:64 final size:64
Alignment explanation
Indices: 39852795--39852966 Score: 186
Period size: 67 Copynumber: 2.7 Consensus size: 64
39852785 AGACATTATG
* *
39852795 ATGTAGCTAGGTCGCATGGGTGATACAATGTGTACACCATGTAGACAAAAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACAATGTGTACACCATGTAGACAAAAGAGCTACGAGATAA
* * * * * *
39852859 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATACAA-TG-TGTACACCATGTAGACAAAAGAGCTACGAGAT
39852924 AA
63 AA
* * * *
39852926 AT-TGGCTAGGTCACATGGGTGGTACTAA-GTGTTCACCATGT
1 ATGTAGCTAGGTCGCATGGGTGATAC-AATGTGTACACCATGT
39852967 GTACAAGAGA
Statistics
Matches: 88, Mismatches: 16, Indels: 9
0.78 0.14 0.08
Matches are distributed among these distances:
63 9 0.10
64 21 0.24
65 8 0.09
66 19 0.22
67 31 0.35
ACGTcount: A:0.30, C:0.17, G:0.29, T:0.24
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACAATGTGTACACCATGTAGACAAAAGAGCTACGAGATAA
Found at i:39858045 original size:11 final size:11
Alignment explanation
Indices: 39858029--39858058 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
39858019 AAATTGAGAA
*
39858029 ATGTGAAAATT
1 ATGTGAAAAAT
39858040 ATGTGAAAAAT
1 ATGTGAAAAAT
39858051 ATGTGAAA
1 ATGTGAAA
39858059 TAATGAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.20, T:0.30
Consensus pattern (11 bp):
ATGTGAAAAAT
Found at i:39864872 original size:27 final size:26
Alignment explanation
Indices: 39864816--39864872 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 26
39864806 CAACCTTAAC
* *
39864816 CCTAGGGGTATATCAGTAATTTTACT
1 CCTAGGGGTAAATCAGTAATTTTACA
** *
39864842 CCTAGGGGTAAATTTGTAAATTTTCCA
1 CCTAGGGGTAAATCAGT-AATTTTACA
39864869 CCTA
1 CCTA
39864873 TAAAGGTGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
26 14 0.56
27 11 0.44
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.37
Consensus pattern (26 bp):
CCTAGGGGTAAATCAGTAATTTTACA
Found at i:39875028 original size:27 final size:26
Alignment explanation
Indices: 39874972--39875028 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 26
39874962 CAACCTTAAC
* *
39874972 CCTAAGGGTATATCAGTAATTTTACT
1 CCTAAGGGTAAATCAGTAATTTTACA
* * *
39874998 CCTAGGGGTAAATCTGTAAATTTTCCA
1 CCTAAGGGTAAATCAGT-AATTTTACA
39875025 CCTA
1 CCTA
39875029 TAAAGGTGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
26 14 0.56
27 11 0.44
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (26 bp):
CCTAAGGGTAAATCAGTAATTTTACA
Found at i:39880905 original size:46 final size:46
Alignment explanation
Indices: 39880838--39880929 Score: 175
Period size: 46 Copynumber: 2.0 Consensus size: 46
39880828 AAAGCAAAGG
*
39880838 AAGTTGGTGTATTGAAGATAATTATTTTGAAGATCCGATTGAAGCT
1 AAGTTGGTGTATTGAAGATAATTATTCTGAAGATCCGATTGAAGCT
39880884 AAGTTGGTGTATTGAAGATAATTATTCTGAAGATCCGATTGAAGCT
1 AAGTTGGTGTATTGAAGATAATTATTCTGAAGATCCGATTGAAGCT
39880930 GAGTCTAGGG
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.33, C:0.08, G:0.24, T:0.36
Consensus pattern (46 bp):
AAGTTGGTGTATTGAAGATAATTATTCTGAAGATCCGATTGAAGCT
Found at i:39882428 original size:18 final size:19
Alignment explanation
Indices: 39882405--39882440 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
39882395 TGTGATGTTG
39882405 ATATGTTT-AATTTAATTA
1 ATATGTTTCAATTTAATTA
39882423 ATATGTTTCAATTTAATT
1 ATATGTTTCAATTTAATT
39882441 TGTGTTAGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.36, C:0.03, G:0.06, T:0.56
Consensus pattern (19 bp):
ATATGTTTCAATTTAATTA
Found at i:39885138 original size:47 final size:45
Alignment explanation
Indices: 39884973--39885240 Score: 192
Period size: 47 Copynumber: 5.7 Consensus size: 45
39884963 CTGTTTTATC
*
39884973 CCGATGCCATGTCCCAGACATGGTCTTACACTGGC-TCTCATATACGCGTG
1 CCGATG-CATGTCCCAGACAT-GTCTTACACTGGCATCTC-T-T-CGAG-G
* * *
39885023 CTGATGCATGTCCCAGACATGTCTTACACTAGCACAACTCTT--A-G
1 CCGATGCATGTCCCAGACATGTCTTACACT-G-GCATCTCTTCGAGG
* *
39885067 CCGATGCGTGTCCCAGACACGTCTTACACTGGCTATCTCTGTCGAGG
1 CCGATGCATGTCCCAGACATGTCTTACACTGGC-ATCTCT-TCGAGG
* *
39885114 CCGATGCATGTCCCAAACATGTCTTACACTGGCA-CTCATCTCTG-TG
1 CCGATGCATGTCCCAGACATGTCTTACACTGGCATCTC-T-TC-GAGG
** * * *
39885160 TTGATGCCATATCCTAGACATGGTCTTACACTGGC-TCTCATAAT-GTGG
1 CCGATG-CATGTCCCAGACAT-GTCTTACACTGGCATCTC-T--TCGAGG
*
39885208 CCGAAGCATGTCCCAGACATGTCTTACACTGGC
1 CCGATGCATGTCCCAGACATGTCTTACACTGGC
39885241 GCACAAATCA
Statistics
Matches: 177, Mismatches: 26, Indels: 34
0.75 0.11 0.14
Matches are distributed among these distances:
42 1 0.01
43 6 0.03
44 29 0.16
45 3 0.02
46 23 0.13
47 56 0.32
48 32 0.18
49 17 0.10
50 7 0.04
51 3 0.02
ACGTcount: A:0.22, C:0.30, G:0.21, T:0.27
Consensus pattern (45 bp):
CCGATGCATGTCCCAGACATGTCTTACACTGGCATCTCTTCGAGG
Found at i:39885219 original size:94 final size:92
Alignment explanation
Indices: 39884973--39885240 Score: 294
Period size: 94 Copynumber: 2.9 Consensus size: 92
39884963 CTGTTTTATC
* * *
39884973 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATATACGCGTGCTGATGCATGTCCCA
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATA-ATGAG-GCCGATGCATGTCCCA
*
39885038 GACATGTCTTACACTAGCACAACTCTTAG
64 GACATGTCTTACACTGGCACAACTCTTAG
* * *
39885067 CCGATG-CGTGTCCCAGACA-CGTCTTACACTGGCTATCTC-T-GTCGAGGCCGATGCATGTCCC
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGC--TCTCATAAT-GAGGCCGATGCATGTCCC
* *
39885128 AAACATGTCTTACACTGGCACTCATCTCTGT-G
63 AGACATGTCTTACACTGGCA--CAACTCT-TAG
** * * * *
39885160 TTGATGCCATATCCTAGACATGGTCTTACACTGGCTCTCATAATGTGGCCGAAGCATGTCCCAGA
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGAGGCCGATGCATGTCCCAGA
39885225 CATGTCTTACACTGGC
66 CATGTCTTACACTGGC
39885241 GCACAAATCA
Statistics
Matches: 145, Mismatches: 19, Indels: 20
0.79 0.10 0.11
Matches are distributed among these distances:
91 32 0.22
92 15 0.10
93 28 0.19
94 56 0.39
95 14 0.10
ACGTcount: A:0.22, C:0.30, G:0.21, T:0.27
Consensus pattern (92 bp):
CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGAGGCCGATGCATGTCCCAGA
CATGTCTTACACTGGCACAACTCTTAG
Found at i:39885621 original size:30 final size:30
Alignment explanation
Indices: 39885580--39885637 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
39885570 AAATTTACAT
* *
39885580 CTTTGGTAAAATGACCATTTTGCCCCTAGA
1 CTTTGGCAAAATGACCATTTTACCCCTAGA
39885610 CTTTGGCAAAATGACCATTTTACCCCTA
1 CTTTGGCAAAATGACCATTTTACCCCTA
39885638 TGCCTGAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.33
Consensus pattern (30 bp):
CTTTGGCAAAATGACCATTTTACCCCTAGA
Found at i:39888278 original size:13 final size:14
Alignment explanation
Indices: 39888262--39888290 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
39888252 TTGTAAATAT
39888262 TTATAAT-GTTTAA
1 TTATAATGGTTTAA
39888275 TTATAATGGTTTAA
1 TTATAATGGTTTAA
39888289 TT
1 TT
39888291 CATTGTTAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.55
Consensus pattern (14 bp):
TTATAATGGTTTAA
Found at i:39888708 original size:22 final size:21
Alignment explanation
Indices: 39888683--39888723 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
39888673 AACAACTTAG
39888683 AGCGGAGGCAGCAGAGGGAGGC
1 AGCGGAGGCAGC-GAGGGAGGC
**
39888705 AGCGGCTGCAGCGAGGGAG
1 AGCGGAGGCAGCGAGGGAG
39888724 TTAGCGGCAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.24, C:0.20, G:0.54, T:0.02
Consensus pattern (21 bp):
AGCGGAGGCAGCGAGGGAGGC
Found at i:39888722 original size:21 final size:21
Alignment explanation
Indices: 39888690--39888760 Score: 70
Period size: 21 Copynumber: 3.3 Consensus size: 21
39888680 TAGAGCGGAG
*
39888690 GCAGCAGAGGGAGGCAGCGGCT
1 GCAGC-GAGGGAGGCAGCGGCA
**
39888712 GCAGCGAGGGAGTTAGCGGCA
1 GCAGCGAGGGAGGCAGCGGCA
* * **
39888733 GTAGCGAGAGAGGCAGAAGCA
1 GCAGCGAGGGAGGCAGCGGCA
39888754 GCAGCGA
1 GCAGCGA
39888761 TGGTAGTAGA
Statistics
Matches: 39, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
21 34 0.87
22 5 0.13
ACGTcount: A:0.28, C:0.20, G:0.46, T:0.06
Consensus pattern (21 bp):
GCAGCGAGGGAGGCAGCGGCA
Found at i:39889028 original size:32 final size:31
Alignment explanation
Indices: 39888992--39889076 Score: 98
Period size: 31 Copynumber: 2.7 Consensus size: 31
39888982 TTAGATTTAA
* * *
39888992 TGTTTTTTATTGTATTTTTATGCTACATTTGC
1 TGTTTTTGATTGGA-TTTCATGCTACATTTGC
* *
39889024 TGTTTTTGGTTGGATTTCATGCTATATTTGC
1 TGTTTTTGATTGGATTTCATGCTACATTTGC
* *
39889055 TGTTTTTGGTTGGATTTAATGC
1 TGTTTTTGATTGGATTTCATGC
39889077 AGGAAGGGTT
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
31 36 0.77
32 11 0.23
ACGTcount: A:0.14, C:0.08, G:0.20, T:0.58
Consensus pattern (31 bp):
TGTTTTTGATTGGATTTCATGCTACATTTGC
Found at i:39889046 original size:31 final size:31
Alignment explanation
Indices: 39889011--39889076 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 31
39889001 TTGTATTTTT
*
39889011 ATGCTACATTTGCTGTTTTTGGTTGGATTTC
1 ATGCTACATTTGCTGTTTTTGGTTGGATTTA
*
39889042 ATGCTATATTTGCTGTTTTTGGTTGGATTTA
1 ATGCTACATTTGCTGTTTTTGGTTGGATTTA
39889073 ATGC
1 ATGC
39889077 AGGAAGGGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.15, C:0.11, G:0.23, T:0.52
Consensus pattern (31 bp):
ATGCTACATTTGCTGTTTTTGGTTGGATTTA
Found at i:39893218 original size:37 final size:37
Alignment explanation
Indices: 39893151--39893262 Score: 161
Period size: 37 Copynumber: 3.0 Consensus size: 37
39893141 CCTTTAGCTT
* * *
39893151 GGACGAAATCTCCACACGAAGTTATCGGGTCTTACCC
1 GGACAAAATCTCCACACGTAGTCATCGGGTCTTACCC
*
39893188 GGACAAAATCTCCACACGTAGTCATTGGGTCTTACCC
1 GGACAAAATCTCCACACGTAGTCATCGGGTCTTACCC
* * *
39893225 GGACATACTCTCCACACGTAGTCATCGGGTCTCACCC
1 GGACAAAATCTCCACACGTAGTCATCGGGTCTTACCC
39893262 G
1 G
39893263 AAATATATTT
Statistics
Matches: 67, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 67 1.00
ACGTcount: A:0.25, C:0.32, G:0.21, T:0.22
Consensus pattern (37 bp):
GGACAAAATCTCCACACGTAGTCATCGGGTCTTACCC
Found at i:39893479 original size:47 final size:47
Alignment explanation
Indices: 39893427--39893894 Score: 713
Period size: 47 Copynumber: 10.0 Consensus size: 47
39893417 TTTCACACTA
* * * *
39893427 GCCATTCGGCTTTACCACATATATGCATGTTCATATTCACCACATTG
1 GCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCACATTG
*
39893474 GCCATTCGGCCTTATCACACATATGCATGCTT-ACATTCATCACATTG
1 GCCATTCGGCCTTATCACATATATGCATG-TTCACATTCATCACATTG
*
39893521 GCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCACATAG
1 GCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCACATTG
* *
39893568 GCCATTCGGCCTTATCACATATATGCATGTTCATATTCACCACATTG
1 GCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCACATTG
* * *
39893615 GCCATTCGGCCTTGTCACACATATGCATGCTCACATTCATCACATTG
1 GCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCACATTG
*
39893662 GCCATTCGGCCTTATCACATATATGCATGCTCACATTCATCACATTG
1 GCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCACATTG
* * *
39893709 GCCATTCTGCCTCATCACATATATGCATGTTCACATTCATCACATAG
1 GCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCACATTG
*
39893756 GCCATTCGGCCTTATCACATATATGCATGTTCACATTCACCACATTG
1 GCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCACATTG
* *
39893803 GCCATTCGGCCTTATCACACATATGCATGCTCACATTCATCACATTG
1 GCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCACATTG
* * * **
39893850 GTCATTCGGCCTTATCACAAATATACACATTCACATTCATCACAT
1 GCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCACAT
39893895 AAAATCCTAA
Statistics
Matches: 385, Mismatches: 34, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
46 2 0.01
47 381 0.99
48 2 0.01
ACGTcount: A:0.26, C:0.29, G:0.12, T:0.32
Consensus pattern (47 bp):
GCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCACATTG
Found at i:39893491 original size:25 final size:25
Alignment explanation
Indices: 39893463--39893538 Score: 61
Period size: 23 Copynumber: 3.2 Consensus size: 25
39893453 ATGTTCATAT
39893463 TCACCACATTGGCCATTCGGCCTTA
1 TCACCACATTGGCCATTCGGCCTTA
* *** *
39893488 TCA-CACATAT-G-CATGCTTACAT-
1 TCACCACAT-TGGCCATTCGGCCTTA
*
39893510 TCATCACATTGGCCATTCGGCCTTA
1 TCACCACATTGGCCATTCGGCCTTA
39893535 TCAC
1 TCAC
39893539 ATATATGCAT
Statistics
Matches: 35, Mismatches: 11, Indels: 10
0.62 0.20 0.18
Matches are distributed among these distances:
22 4 0.11
23 12 0.34
24 12 0.34
25 7 0.20
ACGTcount: A:0.24, C:0.33, G:0.13, T:0.30
Consensus pattern (25 bp):
TCACCACATTGGCCATTCGGCCTTA
Found at i:39893754 original size:25 final size:25
Alignment explanation
Indices: 39893675--39893800 Score: 76
Period size: 25 Copynumber: 5.3 Consensus size: 25
39893665 ATTCGGCCTT
*
39893675 ATCACATATATGCATGCTCACATTC
1 ATCACATATATGCATGTTCACATTC
*
39893700 ATCACAT-T-GGCCAT-TCTGC-C--TC
1 ATCACATATATG-CATGT-T-CACATTC
39893722 ATCACATATATGCATGTTCACATTC
1 ATCACATATATGCATGTTCACATTC
* * *
39893747 ATCAC--ATAGGCCA--TTCGGCCTT-
1 ATCACATATATG-CATGTTC-ACATTC
39893769 ATCACATATATGCATGTTCACATTC
1 ATCACATATATGCATGTTCACATTC
*
39893794 ACCACAT
1 ATCACAT
39893801 TGGCCATTCG
Statistics
Matches: 75, Mismatches: 10, Indels: 32
0.64 0.09 0.27
Matches are distributed among these distances:
22 18 0.24
23 16 0.21
24 17 0.23
25 24 0.32
ACGTcount: A:0.29, C:0.29, G:0.10, T:0.32
Consensus pattern (25 bp):
ATCACATATATGCATGTTCACATTC
Found at i:39919213 original size:46 final size:46
Alignment explanation
Indices: 39919163--39919335 Score: 181
Period size: 46 Copynumber: 3.7 Consensus size: 46
39919153 TTGAGCATCT
*
39919163 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCC
* * * *
39919209 GAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCATCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CGTCC
* * * *
39919256 GAACTCGATGAGTTGAGTCCGAGTTCACTCATGGATGCGAACGCCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCC
* * *
39919302 GAGCTCGTTGAGTTGAGTCTGAGTTCGCTTATGG
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
39919336 GCGGGTTACA
Statistics
Matches: 103, Mismatches: 17, Indels: 14
0.77 0.13 0.10
Matches are distributed among these distances:
43 6 0.06
45 3 0.03
46 58 0.56
47 28 0.27
48 3 0.03
50 5 0.05
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.28
Consensus pattern (46 bp):
GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCC
Found at i:39919316 original size:93 final size:93
Alignment explanation
Indices: 39919157--39919328 Score: 272
Period size: 93 Copynumber: 1.8 Consensus size: 93
39919147 GGATGGTTGA
* * * * *
39919157 GCATCTGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGATGAGTTGAGTCCGAGTTCACTCATGGATGCAAACGCCCGAACTCGTTGAGT
39919222 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* *
39919250 GCATCCGAACTCGATGAGTTGAGTCCGAGTTCACTCATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGATGAGTTGAGTCCGAGTTCACTCATGGATGCAAACGCCCGAACTCGTTGAGT
*
39919315 TGAGTCTGAGTTCG
66 TGAGTCCGAGTTCG
39919329 CTTATGGGCG
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGATGAGTTGAGTCCGAGTTCACTCATGGATGCAAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:39925471 original size:41 final size:44
Alignment explanation
Indices: 39925274--39925483 Score: 180
Period size: 44 Copynumber: 4.8 Consensus size: 44
39925264 CTTTCATGTA
** * *
39925274 TCTTCAATGTGCTCCACTGCAACTTCAGAGAGATAAGGTTCGTA
1 TCTTCAACCTGCTCCACTGCAACTTCAGAGAGATAAGGTTTGTT
* ** * * * * *
39925318 ACTTCAGTCTGCCCCACTGCAACTTCA-AGGGGATAAGATTTCTGA
1 TCTTCAACCTGCTCCACTGCAACTTCAGA-GAGATAAGGTTTGT-T
* * *
39925363 T-TTCAACCTACTCCATTGTAACTTCA-AGGAGATAAGGTTTGTT
1 TCTTCAACCTGCTCCACTGCAACTTCAGA-GAGATAAGGTTTGTT
*
39925406 TCTTCAACCTGCTCCACTGTAACTTCAGAGAGATAAGGTTTG-T
1 TCTTCAACCTGCTCCACTGCAACTTCAGAGAGATAAGGTTTGTT
* * *
39925449 T-TT-GATCTGCTCTACTGCAACTTCAGAGAGATAAG
1 TCTTCAACCTGCTCCACTGCAACTTCAGAGAGATAAG
39925484 ATCTGTGATT
Statistics
Matches: 137, Mismatches: 25, Indels: 11
0.79 0.14 0.06
Matches are distributed among these distances:
41 28 0.20
42 2 0.01
43 4 0.03
44 101 0.74
45 2 0.01
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.31
Consensus pattern (44 bp):
TCTTCAACCTGCTCCACTGCAACTTCAGAGAGATAAGGTTTGTT
Found at i:39925595 original size:28 final size:28
Alignment explanation
Indices: 39925554--39925611 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 28
39925544 CTTCAGTCTG
* *
39925554 CTCCACTGCATCTTTTTGCTTTGATCCA
1 CTCCACTGCATCTTGTTACTTTGATCCA
* *
39925582 CTCCACTTCGTCTTGTTACTTTGATCCA
1 CTCCACTGCATCTTGTTACTTTGATCCA
39925610 CT
1 CT
39925612 TCATGCAACT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.14, C:0.33, G:0.10, T:0.43
Consensus pattern (28 bp):
CTCCACTGCATCTTGTTACTTTGATCCA
Found at i:39925925 original size:88 final size:89
Alignment explanation
Indices: 39925801--39926643 Score: 872
Period size: 88 Copynumber: 9.7 Consensus size: 89
39925791 CGCCATTTCA
* * *
39925801 AGGA-GATGAGAT-TTGTAATTTCCAGCCTGTTACCCTACTGCTTAGGGAGTT-AGGTCCCGTCA
1 AGGATGATAAGATCTTGTAATTTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGG-CCCGTCA
* *
39925863 TCTTCGATCTGCTCCCCTCCTGCTT
65 TCTTCGATCTGTTCCCCTACTGCTT
* * * * * *
39925888 AAGATGATAAGATC-TATAATTTTCAGTCTGTTACCCTACTGCTTAAGGGGTTAAGGCCCATCGT
1 AGGATGATAAGATCTTGTAATTTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCCCGTCAT
* * *
39925952 CTTCGGTTTGTTCCACTACTGCTT
66 CTTCGATCTGTTCCCCTACTGCTT
* * * * *
39925976 AGGGA-GACAAGATC-TATAATCTTCCGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCCCATCA
1 A-GGATGATAAGATCTTGTAATTTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCCCGTCA
*
39926039 TCTTCTATCTGTTCCCCTACTGCTT
65 TCTTCGATCTGTTCCCCTACTGCTT
* * ** * * *
39926064 AGGGTGATAAGATCTTGTAAATTT-AATCTGTTACCCTACTACTTAGGGGGTTAAGGCTCATCAT
1 AGGATGATAAGATCTTGTAATTTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCCCGTCAT
*
39926128 CTTCGATCTGTTCCCCCACTGCTT
66 CTTCGATCTGTTCCCCTACTGCTT
* * * * * * *
39926152 AGGGTGATAAGATCTTGTAAATTT-AGCCTTTTACCCTACTACTTAGGGGGTTAAGGCTCATCGT
1 AGGATGATAAGATCTTGTAATTTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCCCGTCAT
* * **
39926216 CTTCAATCTGCTCCAATACTGCTT
66 CTTCGATCTGTTCCCCTACTGCTT
* * * * *
39926240 AGGGA-GATAAGATC-TGTAATTTCCAACATGTTACTCTACTGCTTATGGGGTTAAGGCCCGTCA
1 A-GGATGATAAGATCTTGTAATTTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCCCGTCA
* *
39926303 TTTTCGATCTGTTCCCTTACTGCTT
65 TCTTCGATCTGTTCCCCTACTGCTT
* * * * * *
39926328 AAGG-TGATAAGATCTTGTAA-ATTCAGCCTGCTACCCTACTGCTTAGGGGATTAAGGCTCGCCG
1 -AGGATGATAAGATCTTGTAATTTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCCCGTCA
* *
39926391 TCTTCGATCTGCTCCACTACTGCTT
65 TCTTCGATCTGTTCCCCTACTGCTT
* * *
39926416 AGGGA-GATAAGATC-TATAATTTCCAACCTGTTACCCTACTGCTTAGGGGGTTAAGGCCCGTCA
1 A-GGATGATAAGATCTTGTAATTTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCCCGTCA
39926479 TCTTCGATCTGTTCCCCTACTGCTT
65 TCTTCGATCTGTTCCCCTACTGCTT
* * * * *
39926504 AGGGTGATAAGATCTTGTAA-ATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCGCCGT
1 AGGATGATAAGATCTTGTAATTTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCCCGTCAT
39926568 CTTCGATCTG--------CT-CTT
66 CTTCGATCTGTTCCCCTACTGCTT
* * * *
39926583 AGGAAGACAAGATC-TGTAATTTCCAACCTGTTACCCTACTGCTTAGGGGGTTAAGGCCCGT
1 AGGATGATAAGATCTTGTAATTTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCCCGT
39926644 GAATTCACCA
Statistics
Matches: 634, Mismatches: 105, Indels: 42
0.81 0.13 0.05
Matches are distributed among these distances:
78 5 0.01
79 50 0.08
80 2 0.00
87 19 0.03
88 535 0.84
89 23 0.04
ACGTcount: A:0.22, C:0.24, G:0.21, T:0.33
Consensus pattern (89 bp):
AGGATGATAAGATCTTGTAATTTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCCCGTCAT
CTTCGATCTGTTCCCCTACTGCTT
Found at i:39925971 original size:44 final size:43
Alignment explanation
Indices: 39925913--39926064 Score: 135
Period size: 44 Copynumber: 3.4 Consensus size: 43
39925903 ATAATTTTCA
* *
39925913 GTCTGTTACCCTACTGCTTAAGGGGTTAAGGCCCATCGTCTTCG
1 GTCTGTT-CCCTACTGCTTAAGGGGTTAAGGCCCATCATCTTCC
* ** ** * *
39925957 GTTTGTTCCACTACTGCTT-AGGGAGACAAGATCTATAATCTTCC
1 GTCTGTTCC-CTACTGCTTAAGGG-GTTAAGGCCCATCATCTTCC
* * *
39926001 GCCTGTTACCCTACTGCTTAGGGGGTTAAGGCCCATCATCTTCT
1 GTCTGTT-CCCTACTGCTTAAGGGGTTAAGGCCCATCATCTTCC
*
39926045 ATCTGTTCCCCTACTGCTTA
1 GTCTGTT-CCCTACTGCTTA
39926065 GGGTGATAAG
Statistics
Matches: 82, Mismatches: 22, Indels: 8
0.73 0.20 0.07
Matches are distributed among these distances:
43 6 0.07
44 71 0.87
45 5 0.06
ACGTcount: A:0.18, C:0.28, G:0.20, T:0.34
Consensus pattern (43 bp):
GTCTGTTCCCTACTGCTTAAGGGGTTAAGGCCCATCATCTTCC
Found at i:39926119 original size:176 final size:175
Alignment explanation
Indices: 39925809--39926641 Score: 960
Period size: 176 Copynumber: 4.8 Consensus size: 175
39925799 CAAGGAGATG
* *
39925809 AGAT-TTGTAATTTCCAGCCTGTTACCCTACTGCTTAGGGAGTT-AGGTCCCGTCATCTTCGATC
1 AGATCTTGTAATTT-CAGCCTGTTACCCTACTGCTTAGGGGGTTAAGG-CCCATCATCTTCGATC
* * * * *
39925872 TGCTCCCCTCCTGCTTA-AGATGATAAGATCTATAATTTTCAGTCTGTTACCCTACTGCTTAAGG
64 TGCTCCACTACTGCTTAGGGA-GATAAGATCTATAA-TTTCAATCTGTTACCCTACTGCTTAGGG
* * * * * *
39925936 GGTTAAGGCCCATCGTCTTCGGTTTGTTCCACTACTGCTTAGGGAGACA
127 GGTTAAGGCCCATCATCTTCGATCTGTTCCCCTACTGCTTAGGGTGATA
* * *
39925985 AGATC-TATAATCTTCCGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCCCATCATCTTCTATCT
1 AGATCTTGTAAT-TTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCCCATCATCTTCGATCT
* * * * *
39926049 GTTCCCCTACTGCTTAGGGTGATAAGATCTTGTAAATTT-AATCTGTTACCCTACTACTTAGGGG
65 GCTCCACTACTGCTTAGGGAGATAAGATC-TAT-AATTTCAATCTGTTACCCTACTGCTTAGGGG
* *
39926113 GTTAAGGCTCATCATCTTCGATCTGTTCCCCCACTGCTTAGGGTGATA
128 GTTAAGGCCCATCATCTTCGATCTGTTCCCCTACTGCTTAGGGTGATA
* * * * *
39926161 AGATCTTGTAAATTT-AGCCTTTTACCCTACTACTTAGGGGGTTAAGGCTCATCGTCTTCAATCT
1 AGATCTTGT-AATTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCCCATCATCTTCGATCT
* * * *
39926225 GCTCCAATACTGCTTAGGGAGATAAGATCTGTAATTTCCAA-CATGTTACTCTACTGCTTATGGG
65 GCTCCACTACTGCTTAGGGAGATAAGATCTATAATTT-CAATC-TGTTACCCTACTGCTTAGGGG
* * * *
39926289 GTTAAGGCCCGTCATTTTCGATCTGTTCCCTTACTGCTTAAGGTGATA
128 GTTAAGGCCCATCATCTTCGATCTGTTCCCCTACTGCTTAGGGTGATA
* * * * ** *
39926337 AGATCTTGTAAATTCAGCCTGCTACCCTACTGCTTAGGGGATTAAGGCTCGCCGTCTTCGATCTG
1 AGATCTTGTAATTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCCCATCATCTTCGATCTG
*
39926402 CTCCACTACTGCTTAGGGAGATAAGATCTATAATTTCCAACCTGTTACCCTACTGCTTAGGGGGT
66 CTCCACTACTGCTTAGGGAGATAAGATCTATAATTT-CAATCTGTTACCCTACTGCTTAGGGGGT
*
39926467 TAAGGCCCGTCATCTTCGATCTGTTCCCCTACTGCTTAGGGTGATA
130 TAAGGCCCATCATCTTCGATCTGTTCCCCTACTGCTTAGGGTGATA
* * ** *
39926513 AGATCTTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCGCCGTCTTCGATCTG
1 AGATCTTGTAATTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCCCATCATCTTCGATCTG
* * * *
39926578 --------CT-CTTAGGAAGACAAGATCTGTAATTTCCAACCTGTTACCCTACTGCTTAGGGGGT
66 CTCCACTACTGCTTAGGGAGATAAGATCTATAATTT-CAATCTGTTACCCTACTGCTTAGGGGGT
39926634 TAAGGCCC
130 TAAGGCCC
39926642 GTGAATTCAC
Statistics
Matches: 583, Mismatches: 61, Indels: 35
0.86 0.09 0.05
Matches are distributed among these distances:
167 59 0.10
168 2 0.00
174 5 0.01
175 8 0.01
176 488 0.84
177 16 0.03
178 5 0.01
ACGTcount: A:0.21, C:0.24, G:0.21, T:0.33
Consensus pattern (175 bp):
AGATCTTGTAATTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCCCATCATCTTCGATCTG
CTCCACTACTGCTTAGGGAGATAAGATCTATAATTTCAATCTGTTACCCTACTGCTTAGGGGGTT
AAGGCCCATCATCTTCGATCTGTTCCCCTACTGCTTAGGGTGATA
Found at i:39926297 original size:264 final size:264
Alignment explanation
Indices: 39925800--39926639 Score: 960
Period size: 264 Copynumber: 3.2 Consensus size: 264
39925790 ACGCCATTTC
* * * * * *
39925800 AAGGAGATGAGAT-TTGTAATTTCCAGCCTGTTACCCTACTGCTTAGGGAGTT-AGGTCCCGTCA
1 AAGGTGATAAGATCTTGTAAATT-CAACCTGTTACCCTACTGCTTAGGGGGTTAAGG-CTCGTCA
* * * *
39925863 TCTTCGATCTGCTCCCCTC-CTGCTTAAGATGATAAGATCTATAATTTTCAGTCTGTTACCCTAC
64 TCTTCGATCTGCTCCCC-CACTGCTTAGGGTGATAAGATCTATAAATTTCAGCCTGTTACCCTAC
* * * * *
39925927 TGCTTAAGGGGTTAAGGCCCATCGTCTTCGGTTTGTTCCACTACTGCTTAGGGAGACAAGATCTA
128 TGCTTAGGGGGTTAAGGCCCATCGTCTTCGATCTGTTCCACTACTGCTTAGGGAGATAAGATCTG
*
39925992 TAATCTTCC-GCCTGTTACCCTACTGCTTAGGGGGTTAAGGCCCATCATCTTCTATCTGTTCCCC
193 TAAT-TTCCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCCCATCATCTTCGATCTGTTCCCC
39926056 TACTGCTT
257 TACTGCTT
* * * * *
39926064 AGGGTGATAAGATCTTGTAAATTTAATCTGTTACCCTACTACTTAGGGGGTTAAGGCTCATCATC
1 AAGGTGATAAGATCTTGTAAATTCAACCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCGTCATC
* * * *
39926129 TTCGATCTGTTCCCCCACTGCTTAGGGTGATAAGATCTTGTAAATTT-AGCCTTTTACCCTACTA
66 TTCGATCTGCTCCCCCACTGCTTAGGGTGATAAGATC-TATAAATTTCAGCCTGTTACCCTACTG
* * * *
39926193 CTTAGGGGGTTAAGGCTCATCGTCTTCAATCTGCTCCAATACTGCTTAGGGAGATAAGATCTGTA
130 CTTAGGGGGTTAAGGCCCATCGTCTTCGATCTGTTCCACTACTGCTTAGGGAGATAAGATCTGTA
* * * * * * *
39926258 ATTTCCAACATGTTACTCTACTGCTTATGGGGTTAAGGCCCGTCATTTTCGATCTGTTCCCTTAC
195 ATTTCCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCCCATCATCTTCGATCTGTTCCCCTAC
39926323 TGCTT
260 TGCTT
* * * * *
39926328 AAGGTGATAAGATCTTGTAAATTCAGCCTGCTACCCTACTGCTTAGGGGATTAAGGCTCGCCGTC
1 AAGGTGATAAGATCTTGTAAATTCAACCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCGTCATC
* * * *
39926393 TTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTAT-AATTTCCAACCTGTTACCCTACTG
66 TTCGATCTGCTCCCCCACTGCTTAGGGTGATAAGATCTATAAATTT-CAGCCTGTTACCCTACTG
* * * *
39926457 CTTAGGGGGTTAAGGCCCGTCATCTTCGATCTGTTCCCCTACTGCTTAGGGTGATAAGATCTTGT
130 CTTAGGGGGTTAAGGCCCATCGTCTTCGATCTGTTCCACTACTGCTTAGGGAGATAAGATC-TGT
* * ** *
39926522 AAATT-CAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCGCCGTCTTCGATCTG--------
194 AATTTCCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCCCATCATCTTCGATCTGTTCCCCTA
39926578 CT-CTT
259 CTGCTT
* * *
39926583 -AGGAAGACAAGATC-TGTAATTTCCAACCTGTTACCCTACTGCTTAGGGGGTTAAGGC
1 AAGG-TGATAAGATCTTGTAAATT-CAACCTGTTACCCTACTGCTTAGGGGGTTAAGGC
39926640 CCGTGAATTC
Statistics
Matches: 489, Mismatches: 77, Indels: 29
0.82 0.13 0.05
Matches are distributed among these distances:
254 10 0.02
255 42 0.09
256 2 0.00
262 5 0.01
263 7 0.01
264 398 0.81
265 25 0.05
ACGTcount: A:0.22, C:0.24, G:0.21, T:0.33
Consensus pattern (264 bp):
AAGGTGATAAGATCTTGTAAATTCAACCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCGTCATC
TTCGATCTGCTCCCCCACTGCTTAGGGTGATAAGATCTATAAATTTCAGCCTGTTACCCTACTGC
TTAGGGGGTTAAGGCCCATCGTCTTCGATCTGTTCCACTACTGCTTAGGGAGATAAGATCTGTAA
TTTCCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCCCATCATCTTCGATCTGTTCCCCTACT
GCTT
Found at i:39926535 original size:44 final size:44
Alignment explanation
Indices: 39926046--39926551 Score: 195
Period size: 44 Copynumber: 11.5 Consensus size: 44
39926036 TCATCTTCTA
* * *
39926046 TCTGTTCCCCTACTGCTTAGGGTGATAAGATCTTGTAAATTTAA
1 TCTGTTACCCTACTGCTTAGGGTGATAAGATCTTGTAAATTCAG
* * * * * * **
39926090 TCTGTTACCCTACTACTTAGGGGGTTAAGGCTCAT-CATCTTC-G
1 TCTGTTACCCTACTGCTTAGGGTGATAA-GATCTTGTAAATTCAG
* * *
39926133 ATCTGTTCCCCCACTGCTTAGGGTGATAAGATCTTGTAAATTTAG
1 -TCTGTTACCCTACTGCTTAGGGTGATAAGATCTTGTAAATTCAG
* * * * * * * * *
39926178 CCTTTTACCCTACTACTTAGGGGGTTAAGGCTCATCGT--CTTCAA
1 TCTGTTACCCTACTGCTTAGGGTGATAA-GATC-TTGTAAATTCAG
* * * *
39926222 TCTGCT-CCAATACTGCTTAGGGAGATAAGATC-TGTAATTTCCA-
1 TCTGTTACC-CTACTGCTTAGGGTGATAAGATCTTGTAAATT-CAG
* * * * ** **
39926265 ACATGTTACTCTACTGCTTATGGG-GTTAAG-GCCCGTCATTTTC-G
1 TC-TGTTACCCTACTGCTTA-GGGTGATAAGATCTTGT-AAATTCAG
*
39926309 ATCTGTT-CCCTTACTGCTTAAGGTGATAAGATCTTGTAAATTCAG
1 -TCTGTTACCC-TACTGCTTAGGGTGATAAGATCTTGTAAATTCAG
* * * ** *
39926354 CCTGCTACCCTACTGCTTAGGG-GATTAAGGCTCGCCGT--CTTC-G
1 TCTGTTACCCTACTGCTTAGGGTGA-TAA-GATC-TTGTAAATTCAG
* * * * *
39926397 ATCTGCT-CCACTACTGCTTAGGGAGATAAGATC-TATAATTTCCAA
1 -TCTGTTACC-CTACTGCTTAGGGTGATAAGATCTTGTAAATT-CAG
* * * * ** **
39926442 CCTGTTACCCTACTGCTTAGGGGGTTAAG-GCCCGTCATCTTC-G
1 TCTGTTACCCTACTGCTTAGGGTGATAAGATCTTGT-AAATTCAG
*
39926485 ATCTGTTCCCCTACTGCTTAGGGTGATAAGATCTTGTAAATTCAG
1 -TCTGTTACCCTACTGCTTAGGGTGATAAGATCTTGTAAATTCAG
*
39926530 CCTGTTACCCTACTGCTTAGGG
1 TCTGTTACCCTACTGCTTAGGG
39926552 GGTTAAGGCT
Statistics
Matches: 329, Mismatches: 95, Indels: 76
0.66 0.19 0.15
Matches are distributed among these distances:
41 3 0.01
43 28 0.09
44 255 0.78
45 38 0.12
46 5 0.02
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.34
Consensus pattern (44 bp):
TCTGTTACCCTACTGCTTAGGGTGATAAGATCTTGTAAATTCAG
Found at i:39937545 original size:18 final size:18
Alignment explanation
Indices: 39937483--39937546 Score: 65
Period size: 18 Copynumber: 3.4 Consensus size: 18
39937473 GCTCTGATGA
*
39937483 GCTTCAGTTAGCCTTCGG
1 GCTTCAGTTAGACTTCGG
* * *
39937501 GCTTCCGTTTAGCACTTATGT
1 GCTTCAG-TTAG-ACTT-CGG
39937522 GCTTCAGTTAGACTTCGG
1 GCTTCAGTTAGACTTCGG
39937540 GCTTCAG
1 GCTTCAG
39937547 ATCACAATGA
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
18 14 0.39
19 8 0.22
20 7 0.19
21 7 0.19
ACGTcount: A:0.14, C:0.25, G:0.25, T:0.36
Consensus pattern (18 bp):
GCTTCAGTTAGACTTCGG
Found at i:39941432 original size:12 final size:13
Alignment explanation
Indices: 39941415--39941447 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
39941405 ATAAAATAAA
39941415 ATAAATAAAT-AC
1 ATAAATAAATGAC
39941427 ATAAATAAATGAC
1 ATAAATAAATGAC
*
39941440 ATATATAA
1 ATAAATAA
39941448 GAATAAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 10 0.53
13 9 0.47
ACGTcount: A:0.64, C:0.06, G:0.03, T:0.27
Consensus pattern (13 bp):
ATAAATAAATGAC
Found at i:39941569 original size:17 final size:17
Alignment explanation
Indices: 39941528--39941632 Score: 81
Period size: 17 Copynumber: 5.9 Consensus size: 17
39941518 ACAATAAAAA
*
39941528 TAATAATAAAATAAT-G
1 TAATAATAATATAATAG
* *
39941544 TACTAATAATGTAATAG
1 TAATAATAATATAATAG
39941561 TAATAATAAAATATAATAG
1 TAATAAT--AATATAATAG
39941580 TTAAT-ATAATATTAA-AG
1 -TAATAATAATA-TAATAG
*
39941597 TAATACTAAATATAATATG
1 TAATAAT-AATATAATA-G
39941616 ATAATAATAATTATAAT
1 -TAATAATAA-TATAAT
39941633 GCAGTACAAA
Statistics
Matches: 71, Mismatches: 7, Indels: 18
0.74 0.07 0.19
Matches are distributed among these distances:
16 16 0.23
17 17 0.24
18 8 0.11
19 14 0.20
20 16 0.23
ACGTcount: A:0.56, C:0.02, G:0.06, T:0.36
Consensus pattern (17 bp):
TAATAATAATATAATAG
Found at i:39941623 original size:23 final size:22
Alignment explanation
Indices: 39941573--39941624 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
39941563 ATAATAAAAT
* * *
39941573 ATAATAGTTAATATAATATTAA
1 ATAATACTAAATATAATATGAA
39941595 AGTAATACTAAATATAATATGATA
1 A-TAATACTAAATATAATATGA-A
39941619 ATAATA
1 ATAATA
39941625 ATTATAATGC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
22 1 0.04
23 22 0.88
24 2 0.08
ACGTcount: A:0.56, C:0.02, G:0.06, T:0.37
Consensus pattern (22 bp):
ATAATACTAAATATAATATGAA
Found at i:39943868 original size:32 final size:32
Alignment explanation
Indices: 39943819--39943891 Score: 94
Period size: 32 Copynumber: 2.2 Consensus size: 32
39943809 TTATATATAT
*
39943819 TTTTATATGTTATATATACTTTTAATATTGTA
1 TTTTATATGATATATATACTTTTAATATTGTA
* *
39943851 TTTTATAT-ATATCATATATTTTTAATGTTGTA
1 TTTTATATGATAT-ATATACTTTTAATATTGTA
39943883 TTATTATAT
1 TT-TTATAT
39943892 TTTAATATTA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
31 3 0.08
32 27 0.75
33 6 0.17
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.60
Consensus pattern (32 bp):
TTTTATATGATATATATACTTTTAATATTGTA
Found at i:39943912 original size:53 final size:50
Alignment explanation
Indices: 39943805--39943915 Score: 118
Period size: 53 Copynumber: 2.1 Consensus size: 50
39943795 ACTTAGGTAT
* * **
39943805 TATATTATATATATTTTTATATGTTATATATACTTTTAATATTGTATTTTA
1 TATA-TATATATATTTTTATATGTTATATATACTTTTAATATTATACTACA
39943856 TATATATCATATATTTTTA-ATGTTGTATTATTATA-TTTTAATATTATACTACA
1 TATATAT-ATATATTTTTATATG-T-TA-TA-TATACTTTTAATATTATACTACA
39943909 TATATAT
1 TATATAT
39943916 TTTCATATTA
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
50 6 0.12
51 16 0.31
52 2 0.04
53 23 0.45
54 4 0.08
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.58
Consensus pattern (50 bp):
TATATATATATATTTTTATATGTTATATATACTTTTAATATTATACTACA
Found at i:39943933 original size:22 final size:22
Alignment explanation
Indices: 39943864--39943934 Score: 56
Period size: 24 Copynumber: 3.2 Consensus size: 22
39943854 TATATATATC
* **
39943864 ATATAT-TTTTAATGTTGTATT
1 ATATATATTTTAATATTACATT
* *
39943885 AT-TATATTTTAATATTATACTAC
1 ATATATATTTTAATATTACA-T-T
*
39943908 ATATATATTTTCATATTACATT
1 ATATATATTTTAATATTACATT
39943930 ATATA
1 ATATA
39943935 CATATATTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
20 3 0.08
21 13 0.32
22 6 0.15
23 3 0.08
24 15 0.38
ACGTcount: A:0.37, C:0.06, G:0.03, T:0.55
Consensus pattern (22 bp):
ATATATATTTTAATATTACATT
Found at i:39943939 original size:24 final size:24
Alignment explanation
Indices: 39943888--39943939 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
39943878 TTGTATTATT
* *
39943888 ATATTTTAATATTATACTACATAT
1 ATATTTTAATATTACACTACATAC
* * *
39943912 ATATTTTCATATTACATTATATAC
1 ATATTTTAATATTACACTACATAC
39943936 ATAT
1 ATAT
39943940 ATTTTTATAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (24 bp):
ATATTTTAATATTACACTACATAC
Found at i:39943949 original size:26 final size:26
Alignment explanation
Indices: 39943898--39943988 Score: 85
Period size: 26 Copynumber: 3.3 Consensus size: 26
39943888 ATATTTTAAT
39943898 ATTATACTACATATATATTTTCATATTAC
1 ATTATA-TACATATAT-TTTT-ATATTAC
*
39943927 ATTATATACATATATTTTTATA-TAT
1 ATTATATACATATATTTTTATATTAC
** *
39943952 ATTATCATGTATATATTTTGATATTAC
1 ATTAT-ATACATATATTTTTATATTAC
39943979 TAGTTATATA
1 -A-TTATATA
39943989 TTACTTATAT
Statistics
Matches: 52, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
25 7 0.13
26 17 0.33
27 6 0.12
28 12 0.23
29 10 0.19
ACGTcount: A:0.37, C:0.08, G:0.03, T:0.52
Consensus pattern (26 bp):
ATTATATACATATATTTTTATATTAC
Found at i:39945339 original size:12 final size:13
Alignment explanation
Indices: 39945322--39945354 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
39945312 AAAAAATAAA
39945322 ATAAATAAAT-AC
1 ATAAATAAATGAC
39945334 ATAAATAAATGAC
1 ATAAATAAATGAC
*
39945347 ATATATAA
1 ATAAATAA
39945355 GAATAAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 10 0.53
13 9 0.47
ACGTcount: A:0.64, C:0.06, G:0.03, T:0.27
Consensus pattern (13 bp):
ATAAATAAATGAC
Done.