Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 85040211
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: 85040211
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 160 characters in sequence are not A, C, G, or T
File 181 of 292
Found at i:53904002 original size:20 final size:20
Alignment explanation
Indices: 53903977--53904014 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
53903967 TTAGGATGTA
53903977 TATAAAATAAATAAATAATT
1 TATAAAATAAATAAATAATT
53903997 TATAAAATAAATAAATAA
1 TATAAAATAAATAAATAA
53904015 AAATAATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (20 bp):
TATAAAATAAATAAATAATT
Found at i:53904257 original size:23 final size:23
Alignment explanation
Indices: 53904210--53904257 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
53904200 TTGATTAAAT
* *
53904210 TAAAATTATTTTTATTTATTTTA
1 TAAAATAATTTTTATTTATTATA
53904233 TAAAATAATTTTTATTT-TGTATA
1 TAAAATAATTTTTATTTAT-TATA
53904256 TA
1 TA
53904258 TTTAAGAGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 1 0.05
23 21 0.95
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (23 bp):
TAAAATAATTTTTATTTATTATA
Found at i:53904632 original size:9 final size:9
Alignment explanation
Indices: 53904595--53904624 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
53904585 TAAATATTCA
53904595 TTTT-ATTT
1 TTTTAATTT
53904603 TTTTAATTT
1 TTTTAATTT
53904612 TTTTAATTT
1 TTTTAATTT
53904621 TTTT
1 TTTT
53904625 TTTATTTTGC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 4 0.19
9 17 0.81
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (9 bp):
TTTTAATTT
Found at i:53909257 original size:48 final size:48
Alignment explanation
Indices: 53909186--53909352 Score: 235
Period size: 48 Copynumber: 3.5 Consensus size: 48
53909176 GGGCCTTACA
* * * *
53909186 ATGTCCTAGATATGGTCTTACACTGGCATACATATCATCGCTGATGCC
1 ATGTCCCAGACATGGTCTTACACTGGCACACATATCATCGCCGATGCC
* * * *
53909234 ATGTCCCAGATATGGTTTTACACTGGCACATATATCATCACCGATGCC
1 ATGTCCCAGACATGGTCTTACACTGGCACACATATCATCGCCGATGCC
* * *
53909282 ATGTCCCAGACACGGTTTTACACTGGCACACAAATCATCGCCGATGCC
1 ATGTCCCAGACATGGTCTTACACTGGCACACATATCATCGCCGATGCC
53909330 ATGTCCCAGACATGGTCTTACAC
1 ATGTCCCAGACATGGTCTTACAC
53909353 AGAATCTCAT
Statistics
Matches: 106, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 106 1.00
ACGTcount: A:0.26, C:0.29, G:0.18, T:0.27
Consensus pattern (48 bp):
ATGTCCCAGACATGGTCTTACACTGGCACACATATCATCGCCGATGCC
Found at i:53914366 original size:40 final size:40
Alignment explanation
Indices: 53914311--53914536 Score: 382
Period size: 40 Copynumber: 5.7 Consensus size: 40
53914301 GATGATAATG
* * * *
53914311 GGGTTAAGTCCCGAAGACATTTGTGCTAGTGATTAATTCC
1 GGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCC
53914351 GGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCC
1 GGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCC
53914391 GGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCC
1 GGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCC
53914431 GGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCC
1 GGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCC
*
53914471 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT-ATATCC
1 GGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT-TCC
*
53914511 GGGCTAAGTCCCGAAGGCATTTGTGC
1 GGGTTAAGTCCCGAAGGCATTTGTGC
53914537 TAGTGACCAT
Statistics
Matches: 180, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
39 2 0.01
40 178 0.99
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.29
Consensus pattern (40 bp):
GGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCC
Found at i:53914549 original size:40 final size:40
Alignment explanation
Indices: 53914315--53914572 Score: 369
Period size: 40 Copynumber: 6.5 Consensus size: 40
53914305 ATAATGGGGT
* * * * *
53914315 TAAGTCCCGAAGACATTTGTGCTAGTGATTAATTCCGGGT
1 TAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCCGGGC
*
53914355 TAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCCGGGT
1 TAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCCGGGC
*
53914395 TAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCCGGGT
1 TAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCCGGGC
53914435 TAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCCGGGC
1 TAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCCGGGC
53914475 TAAGTCCCGAAGGCATTTGTGCGAGTTACT-ATATCCGGGC
1 TAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT-TCCGGGC
* * *
53914515 TAAGTCCCGAAGGCATTTGTGCTAGTGAC-CATATCCGGGC
1 TAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT-TCCGGGC
* *
53914555 TAAGGCCCGATGGC-TTTG
1 TAAGTCCCGAAGGCATTTG
53914573 CGAGTGGTTT
Statistics
Matches: 207, Mismatches: 9, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
39 6 0.03
40 201 0.97
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (40 bp):
TAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCCGGGC
Found at i:53922435 original size:40 final size:40
Alignment explanation
Indices: 53922380--53922605 Score: 346
Period size: 40 Copynumber: 5.7 Consensus size: 40
53922370 GATGATAACG
* * * *
53922380 GGGTTAAGTCCCGAAGACATTTGTGCTAGTGATTAATTCC
1 GGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCC
53922420 GGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCC
1 GGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCC
*
53922460 GGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACCAATTCC
1 GGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCC
* *
53922500 AGGTTAAGTCCCGAAGGCATTTGTGCTAGTTACTAATTCC
1 GGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCC
*
53922540 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT-ATATCC
1 GGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT-TCC
* *
53922580 GGGCTAAGTCCCGAATGCATTTGTGC
1 GGGTTAAGTCCCGAAGGCATTTGTGC
53922606 TAGTGACCAT
Statistics
Matches: 173, Mismatches: 12, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
39 2 0.01
40 171 0.99
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.30
Consensus pattern (40 bp):
GGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCC
Found at i:53922618 original size:40 final size:40
Alignment explanation
Indices: 53922384--53922641 Score: 333
Period size: 40 Copynumber: 6.5 Consensus size: 40
53922374 ATAACGGGGT
* * * * *
53922384 TAAGTCCCGAAGACATTTGTGCTAGTGATTAATTCCGGGT
1 TAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCCGGGC
*
53922424 TAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCCGGGT
1 TAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCCGGGC
* * *
53922464 TAAGTCCCGAAGGCATTTGTGCGAGTTACCAATTCCAGGT
1 TAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCCGGGC
*
53922504 TAAGTCCCGAAGGCATTTGTGCTAGTTACTAATTCCGGGC
1 TAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCCGGGC
53922544 TAAGTCCCGAAGGCATTTGTGCGAGTTACT-ATATCCGGGC
1 TAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT-TCCGGGC
* * * *
53922584 TAAGTCCCGAATGCATTTGTGCTAGTGAC-CATATCCGGGC
1 TAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT-TCCGGGC
* *
53922624 TAAGGCCCGATGGC-TTTG
1 TAAGTCCCGAAGGCATTTG
53922642 CGAGTGGTTA
Statistics
Matches: 199, Mismatches: 17, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
39 6 0.03
40 193 0.97
ACGTcount: A:0.23, C:0.22, G:0.26, T:0.29
Consensus pattern (40 bp):
TAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCCGGGC
Found at i:53922633 original size:120 final size:120
Alignment explanation
Indices: 53922384--53922641 Score: 369
Period size: 120 Copynumber: 2.2 Consensus size: 120
53922374 ATAACGGGGT
* * *
53922384 TAAGTCCCGAAGACATTTGTGCTAGTGATTAATTCCGGGTTAAGTCCCGAAGGCATTTGTGCGAG
1 TAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCCGGGCTAAGTCCCGAAGGCATTTGTGCGAG
* * *
53922449 TTACTAATTCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACCAATTCCAGGT
66 TTACTAATTCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACCAATTCCAGGC
*
53922504 TAAGTCCCGAAGGCATTTGTGCTAGTTACTAATTCCGGGCTAAGTCCCGAAGGCATTTGTGCGAG
1 TAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCCGGGCTAAGTCCCGAAGGCATTTGTGCGAG
* * *
53922569 TTACT-ATATCCGGGCTAAGTCCCGAATGCATTTGTGCTAGTGACC-ATATCCGGGC
66 TTACTAAT-TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACCAAT-TCCAGGC
* *
53922624 TAAGGCCCGATGGC-TTTG
1 TAAGTCCCGAAGGCATTTG
53922642 CGAGTGGTTA
Statistics
Matches: 124, Mismatches: 12, Indels: 5
0.88 0.09 0.04
Matches are distributed among these distances:
119 8 0.06
120 116 0.94
ACGTcount: A:0.23, C:0.22, G:0.26, T:0.29
Consensus pattern (120 bp):
TAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCCGGGCTAAGTCCCGAAGGCATTTGTGCGAG
TTACTAATTCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACCAATTCCAGGC
Found at i:53931723 original size:21 final size:20
Alignment explanation
Indices: 53931674--53931730 Score: 105
Period size: 20 Copynumber: 2.8 Consensus size: 20
53931664 AGCAGACAGA
53931674 GGCACACGCCCGTGTGGAAG
1 GGCACACGCCCGTGTGGAAG
53931694 GGCACACGCCCGTGTGGAAG
1 GGCACACGCCCGTGTGGAAG
53931714 GGCGACACGCCCGTGTG
1 GGC-ACACGCCCGTGTG
53931731 TCTTCTTAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.18, C:0.32, G:0.40, T:0.11
Consensus pattern (20 bp):
GGCACACGCCCGTGTGGAAG
Found at i:53933023 original size:48 final size:48
Alignment explanation
Indices: 53932952--53933366 Score: 359
Period size: 48 Copynumber: 8.7 Consensus size: 48
53932942 GGTAACTTAT
* * * * **
53932952 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCCCATGTCGAGGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCAATAC
* *
53933000 CGATGCCATGTCCCAGATATGGTCTTACACTAGCTCTCATCTCAATAC
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCAATAC
* * * *
53933048 CGATGCCATGTCCCAGACATGATCTTACACTAGCGCACATATCAACAC
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCAATAC
* * * *
53933096 TGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAACATTAC
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCAATAC
* * * ** *
53933144 TGATGCCATGTTCCAAACATGGTCTTACACTAGCTCTCAT-T-TGTGGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCAAT-AC
* * * * * * * *
53933191 TGACGCTATGTTCCAAACATGGTCTTACACTAGCGCACATATCAATGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCAATAC
* * ** * * **
53933239 CGATGCCATGTCCCAGAGATGTTCTTACACCGGCTCTCATAACATTGT
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCAATAC
* * * * * **
53933287 CGATGCCATGTTCCAAACGTGGTCTTACATTGGCTCTCATAT-TGTAGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCAATA-C
* * *
53933335 CGACGCCATGTTCCAAACATGGTCTTACACTA
1 CGATGCCATGTCCCAGACATGGTCTTACACTA
53933367 ACAGACATAT
Statistics
Matches: 299, Mismatches: 64, Indels: 8
0.81 0.17 0.02
Matches are distributed among these distances:
46 1 0.00
47 38 0.13
48 259 0.87
49 1 0.00
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.28
Consensus pattern (48 bp):
CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCAATAC
Found at i:53933294 original size:191 final size:192
Alignment explanation
Indices: 53932952--53933366 Score: 478
Period size: 191 Copynumber: 2.2 Consensus size: 192
53932942 GGTAACTTAT
* * * * *
53932952 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCCCATGTCGAGGCCGATGCCATGTCCCAGA
1 CGATGCCATGTTCCAAACATGGTCTTACACTAGCTCCCATGTCGAGGCCGACGCCATGTCCCAAA
* * * * *
53933017 TATGGTCTTACACTAGCTCTCATCTCAATACCGATGCCATGTCCCAGACATGATCTTACACTAGC
66 CATGGTCTTACACTAGCGCACATATCAATACCGATGCCATGTCCCAGACATGATCTTACACCAGC
* *
53933082 GCACATATCAACACTGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAACAT-TA-C
131 GCACATAACAACACTGATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCAT-A-ATGTAGC
* * * * * * *
53933144 TGATGCCATGTTCCAAACATGGTCTTACACTAGCTCTCAT-TTGTGGCTGACGCTATGTTCCAAA
1 CGATGCCATGTTCCAAACATGGTCTTACACTAGCTCCCATGTCGAGGCCGACGCCATGTCCCAAA
* * * *
53933208 CATGGTCTTACACTAGCGCACATATCAATGCCGATGCCATGTCCCAGAGATGTTCTTACACCGGC
66 CATGGTCTTACACTAGCGCACATATCAATACCGATGCCATGTCCCAGACATGATCTTACACCAGC
* * *** * * * *
53933273 TCTCATAAC-ATTGTCGATGCCATGTTCCAAACGTGGTCTTACATTGGCTCTCATATTGTAGC
131 GCACATAACAACACT-GATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCATAATGTAGC
*
53933335 CGACGCCATGTTCCAAACATGGTCTTACACTA
1 CGATGCCATGTTCCAAACATGGTCTTACACTA
53933367 ACAGACATAT
Statistics
Matches: 186, Mismatches: 34, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
189 1 0.01
190 5 0.03
191 145 0.78
192 35 0.19
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.28
Consensus pattern (192 bp):
CGATGCCATGTTCCAAACATGGTCTTACACTAGCTCCCATGTCGAGGCCGACGCCATGTCCCAAA
CATGGTCTTACACTAGCGCACATATCAATACCGATGCCATGTCCCAGACATGATCTTACACCAGC
GCACATAACAACACTGATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCATAATGTAGC
Found at i:53940812 original size:48 final size:48
Alignment explanation
Indices: 53940740--53941104 Score: 267
Period size: 48 Copynumber: 7.6 Consensus size: 48
53940730 GAAATTACCA
* * * *
53940740 ATGCCATGTCCCAGACATGATCTTACACTGACTCCCATGTCGAGGCCG
1 ATGCCATGTCCCAAACATGGTCTTACACTGACTCTCATATCGAGGCCG
* * * * * *
53940788 ATGCCATTTCCCAAACATGGTCTTATACT-AGCTCTCGTCTCAATGCCG
1 ATGCCATGTCCCAAACATGGTCTTACACTGA-CTCTCATATCGAGGCCG
* * *
53940836 ATGCCATGTCCCAGACATGGTCTTACACTTG-CTGTCATAAT--ATGGTCG
1 ATGCCATGTCCCAAACATGGTCTTACAC-TGACTCTCAT-ATCGA-GGCCG
* * * *
53940884 ACGCCATGTCCTAAACATGGTCTTACACT-AGCTCTCATATTGTGGCCG
1 ATGCCATGTCCCAAACATGGTCTTACACTGA-CTCTCATATCGAGGCCG
* * * * * * * * **
53940932 ACGCTATGTTCCAAACATGGTCTTATAC-AAGTGTACATATCAATACCG
1 ATGCCATGTCCCAAACATGGTCTTACACTGACTCT-CATATCGAGGCCG
* * * * *
53940980 ATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAAC-ATTGCTG
1 ATGCCATGTCCCAAACATGGTCTTACACTGACTCTCATATCGA-GGCCG
* * * * *
53941028 ATGCCATGTTCCAAACATGTTCTTACACTGGCTCTCATATTGTGGCCG
1 ATGCCATGTCCCAAACATGGTCTTACACTGACTCTCATATCGAGGCCG
* *
53941076 ACGCCATGTTCCAAACATGGTCTTACACT
1 ATGCCATGTCCCAAACATGGTCTTACACT
53941105 AGCACACATA
Statistics
Matches: 247, Mismatches: 56, Indels: 28
0.75 0.17 0.08
Matches are distributed among these distances:
47 8 0.03
48 235 0.95
49 4 0.02
ACGTcount: A:0.24, C:0.28, G:0.18, T:0.29
Consensus pattern (48 bp):
ATGCCATGTCCCAAACATGGTCTTACACTGACTCTCATATCGAGGCCG
Found at i:53940904 original size:96 final size:96
Alignment explanation
Indices: 53940783--53941117 Score: 327
Period size: 96 Copynumber: 3.5 Consensus size: 96
53940773 CCCATGTCGA
* * * * * *
53940783 GGCCGATGCCATTTCCCAAACATGGTCTTATACTAGCTCTCGTCTCAATGCCGATGCCATGTCCC
1 GGCCGACGCCATGTCCCAAACATGGTCTTACACTAGCTCTCATATCAATGCCGATGCCATGTTCC
* *
53940848 AGACATGGTCTTACACTTGCTGTCATAATAT
66 AAACATGGTCTTACACTAGCTGTCATAATAT
* * ** * *
53940879 GGTCGACGCCATGTCCTAAACATGGTCTTACACTAGCTCTCATAT-TGTGGCCGACGCTATGTTC
1 GGCCGACGCCATGTCCCAAACATGGTCTTACACTAGCTCTCATATCAAT-GCCGATGCCATGTTC
* *
53940943 CAAACATGGTCTTATACAAG-TGTACAT-ATCAAT
65 CAAACATGGTCTTACACTAGCTGT-CATAAT--AT
* * * * * * *
53940976 -ACCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAACATTGCTGATGCCATGTTCC
1 GGCCGACGCCATGTCCCAAACATGGTCTTACACTAGCTCTCATATCAATGCCGATGCCATGTTCC
* * * * *
53941040 AAACATGTTCTTACACTGGCTCTCATATTGT
66 AAACATGGTCTTACACTAGCTGTCATAATAT
* * *
53941071 GGCCGACGCCATGTTCCAAACATGGTCTTACACTAGCACACATATCA
1 GGCCGACGCCATGTCCCAAACATGGTCTTACACTAGCTCTCATATCA
53941118 CCCAAATGTC
Statistics
Matches: 188, Mismatches: 43, Indels: 16
0.76 0.17 0.06
Matches are distributed among these distances:
95 7 0.04
96 175 0.93
97 6 0.03
ACGTcount: A:0.25, C:0.28, G:0.18, T:0.29
Consensus pattern (96 bp):
GGCCGACGCCATGTCCCAAACATGGTCTTACACTAGCTCTCATATCAATGCCGATGCCATGTTCC
AAACATGGTCTTACACTAGCTGTCATAATAT
Found at i:53941114 original size:144 final size:144
Alignment explanation
Indices: 53940740--53941117 Score: 465
Period size: 144 Copynumber: 2.6 Consensus size: 144
53940730 GAAATTACCA
* * * * * * * *
53940740 ATGCCATGTCCCAGACATGATCTTACACTGACTCCCATGTCGAGGCCGATGCCAT-TTCCCAAAC
1 ATGCCATGTTCCAAACATGATCTTACACTGGCTCTCATATTGTGGCCGACGCCATGTT-CCAAAC
* * * * * *
53940804 ATGGTCTTATACTAGCTCTCGTCTCAATGCCGATGCCATGTCCCAGACATGGTCTTACACTTGCT
65 ATGGTCTTATACTAGCACACATATCAATACCGATGCCATGTCCCAGACATGGTCTTACACTGGCT
* * *
53940869 GTCATAATATGGTCG
130 CTCATAACATGCTCG
* * * *
53940884 ACGCCATG-TCCTAAACATGGTCTTACACTAGCTCTCATATTGTGGCCGACGCTATGTTCCAAAC
1 ATGCCATGTTCC-AAACATGATCTTACACTGGCTCTCATATTGTGGCCGACGCCATGTTCCAAAC
* ***
53940948 ATGGTCTTATACAAGTGTACATATCAATACCGATGCCATGTCCCAGACATGGTCTTACACTGGCT
65 ATGGTCTTATACTAGCACACATATCAATACCGATGCCATGTCCCAGACATGGTCTTACACTGGCT
53941013 CTCATAACATTGCT-G
130 CTCATAACA-TGCTCG
*
53941028 ATGCCATGTTCCAAACATGTTCTTACACTGGCTCTCATATTGTGGCCGACGCCATGTTCCAAACA
1 ATGCCATGTTCCAAACATGATCTTACACTGGCTCTCATATTGTGGCCGACGCCATGTTCCAAACA
*
53941093 TGGTCTTACACTAGCACACATATCA
66 TGGTCTTATACTAGCACACATATCA
53941118 CCCAAATGTC
Statistics
Matches: 197, Mismatches: 33, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
143 2 0.01
144 187 0.95
145 8 0.04
ACGTcount: A:0.25, C:0.29, G:0.17, T:0.29
Consensus pattern (144 bp):
ATGCCATGTTCCAAACATGATCTTACACTGGCTCTCATATTGTGGCCGACGCCATGTTCCAAACA
TGGTCTTATACTAGCACACATATCAATACCGATGCCATGTCCCAGACATGGTCTTACACTGGCTC
TCATAACATGCTCG
Found at i:53941115 original size:48 final size:48
Alignment explanation
Indices: 53940783--53941107 Score: 291
Period size: 48 Copynumber: 6.8 Consensus size: 48
53940773 CCCATGTCGA
* * * * *
53940783 GGCCGATGCCAT-TTCCCAAACATGGTCTTATACTAGCTCTCGTCTCAAT
1 GGCCGACGCCATGTT-CCAAACATGGTCTTACACTAGCTCTCATAT-TAT
* * * * * *
53940832 -GCCGATGCCATGTCCCAGACATGGTCTTACACTTGCTGTCATAATAT
1 GGCCGACGCCATGTTCCAAACATGGTCTTACACTAGCTCTCATATTAT
* *
53940879 GGTCGACGCCATG-TCCTAAACATGGTCTTACACTAGCTCTCATATTGT
1 GGCCGACGCCATGTTCC-AAACATGGTCTTACACTAGCTCTCATATTAT
* * * * *
53940927 GGCCGACGCTATGTTCCAAACATGGTCTTATACAAG-TGTACATATCAAT
1 GGCCGACGCCATGTTCCAAACATGGTCTTACACTAGCTCT-CATAT-TAT
* * * * * **
53940976 -ACCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAACAT
1 GGCCGACGCCATGTTCCAAACATGGTCTTACACTAGCTCTCATATTAT
* * * * * *
53941023 TGCTGATGCCATGTTCCAAACATGTTCTTACACTGGCTCTCATATTGT
1 GGCCGACGCCATGTTCCAAACATGGTCTTACACTAGCTCTCATATTAT
53941071 GGCCGACGCCATGTTCCAAACATGGTCTTACACTAGC
1 GGCCGACGCCATGTTCCAAACATGGTCTTACACTAGC
53941108 ACACATATCA
Statistics
Matches: 220, Mismatches: 48, Indels: 17
0.77 0.17 0.06
Matches are distributed among these distances:
47 8 0.04
48 205 0.93
49 7 0.03
ACGTcount: A:0.24, C:0.28, G:0.18, T:0.30
Consensus pattern (48 bp):
GGCCGACGCCATGTTCCAAACATGGTCTTACACTAGCTCTCATATTAT
Found at i:53947102 original size:24 final size:25
Alignment explanation
Indices: 53947062--53947118 Score: 98
Period size: 24 Copynumber: 2.3 Consensus size: 25
53947052 TATATTTTAT
*
53947062 ATATCATACCACAACAAAATACAAA
1 ATATTATACCACAACAAAATACAAA
53947087 ATATTATA-CACAACAAAATACAAA
1 ATATTATACCACAACAAAATACAAA
53947111 ATATTATA
1 ATATTATA
53947119 ATGTCAAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 24 0.77
25 7 0.23
ACGTcount: A:0.60, C:0.18, G:0.00, T:0.23
Consensus pattern (25 bp):
ATATTATACCACAACAAAATACAAA
Found at i:53948496 original size:19 final size:20
Alignment explanation
Indices: 53948460--53948505 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
53948450 AATATAAATT
*
53948460 ATATAAATTATTTAAAAAAA
1 ATATAAATTATATAAAAAAA
53948480 ATATAAATT-TATAAAAAAA
1 ATATAAATTATATAAAAAAA
*
53948499 TTATAAA
1 ATATAAA
53948506 AATTATTTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 15 0.62
20 9 0.38
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (20 bp):
ATATAAATTATATAAAAAAA
Found at i:53948506 original size:29 final size:29
Alignment explanation
Indices: 53948447--53948507 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 29
53948437 TTTTGAAATT
** *
53948447 AAAAATATAAATTATATAAATTATTTAAA
1 AAAAATATAAATTATATAAAAAAATTAAA
*
53948476 AAAAATATAAATT-TATAAAAAAATTATA
1 AAAAATATAAATTATATAAAAAAATTAAA
53948504 AAAA
1 AAAA
53948508 TTATTTCACA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 15 0.54
29 13 0.46
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (29 bp):
AAAAATATAAATTATATAAAAAAATTAAA
Found at i:53948511 original size:20 final size:20
Alignment explanation
Indices: 53948455--53948511 Score: 62
Period size: 19 Copynumber: 2.8 Consensus size: 20
53948445 TTAAAAATAT
*
53948455 AAATTATATAAATTATTTAAAA
1 AAATTATAAAAATTA--TAAAA
* *
53948477 AAAATAT-AAATTTATAAAA
1 AAATTATAAAAATTATAAAA
53948496 AAATTATAAAAATTAT
1 AAATTATAAAAATTAT
53948512 TTCACATCCA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
19 11 0.38
20 7 0.24
21 5 0.17
22 6 0.21
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
AAATTATAAAAATTATAAAA
Found at i:53948706 original size:2 final size:2
Alignment explanation
Indices: 53948701--53948731 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
53948691 TATAAGTTTA
53948701 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
53948732 AATTGTTTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:53949421 original size:7 final size:7
Alignment explanation
Indices: 53949409--53949433 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
53949399 CATGATTTTG
53949409 ATTTAAT
1 ATTTAAT
53949416 ATTTAAT
1 ATTTAAT
53949423 ATTTAAT
1 ATTTAAT
53949430 ATTT
1 ATTT
53949434 TATAATTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (7 bp):
ATTTAAT
Found at i:53949527 original size:27 final size:27
Alignment explanation
Indices: 53949473--53949546 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
53949463 TTAATTTTAA
* * *
53949473 TATATATTATTTTAATTTATAAAAAAT
1 TATATATTTTTTTTATTTTTAAAAAAT
* *
53949500 TATATATTTTTTTTATTTTTTAATAAT
1 TATATATTTTTTTTATTTTTAAAAAAT
* *
53949527 TTTATACTTTTTTATATTTT
1 TATATA-TTTTTTTTATTTT
53949547 GACAATGATG
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
27 27 0.69
28 12 0.31
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (27 bp):
TATATATTTTTTTTATTTTTAAAAAAT
Found at i:53949887 original size:24 final size:24
Alignment explanation
Indices: 53949855--53949900 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
53949845 GGTGACATCA
*
53949855 ATTACTGTAGCAATAAGATTAAGT
1 ATTAATGTAGCAATAAGATTAAGT
**
53949879 ATTAATGTAGTGATAAGATTAA
1 ATTAATGTAGCAATAAGATTAA
53949901 AATAAGTGAT
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:0.43, C:0.04, G:0.17, T:0.35
Consensus pattern (24 bp):
ATTAATGTAGCAATAAGATTAAGT
Found at i:53950148 original size:22 final size:22
Alignment explanation
Indices: 53950123--53950194 Score: 74
Period size: 23 Copynumber: 3.2 Consensus size: 22
53950113 TTATATTAAA
53950123 TAAATGAAAAAT-ATTAAAATTT
1 TAAAT-AAAAATAATTAAAATTT
* **
53950145 TAAATTAAAATAATTAAAAAGAT
1 TAAATAAAAATAATT-AAAATTT
*
53950168 TAATTAAAAATAATTACAAATTT
1 TAAATAAAAATAATTA-AAATTT
53950191 TAAA
1 TAAA
53950195 AAGGTTAATA
Statistics
Matches: 39, Mismatches: 8, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
21 5 0.13
22 9 0.23
23 25 0.64
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.35
Consensus pattern (22 bp):
TAAATAAAAATAATTAAAATTT
Found at i:53950183 original size:32 final size:32
Alignment explanation
Indices: 53950147--53950212 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 32
53950137 TAAAATTTTA
53950147 AATTA-AAATAATTAAAAAGATTAATTAAAA-AT
1 AATTACAAAT-ATTAAAAAGATTAA-TAAAACAT
* *
53950179 AATTACAAATTTTAAAAAGGTTAATAAAACAT
1 AATTACAAATATTAAAAAGATTAATAAAACAT
53950211 AA
1 AA
53950213 ATTGAAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
31 5 0.17
32 21 0.70
33 4 0.13
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.30
Consensus pattern (32 bp):
AATTACAAATATTAAAAAGATTAATAAAACAT
Found at i:53950385 original size:31 final size:30
Alignment explanation
Indices: 53950361--53950422 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
53950351 AATTACCTAC
53950361 AAAAAG-TATGGAAAACATATTAATTACGA
1 AAAAAGATATGGAAAACATATTAATTACGA
* *
53950390 AAAGAGATATGGAAAACATATTAATTATGA
1 AAAAAGATATGGAAAACATATTAATTACGA
53950420 AAA
1 AAA
53950423 TAGACATTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 5 0.17
30 25 0.83
ACGTcount: A:0.56, C:0.05, G:0.15, T:0.24
Consensus pattern (30 bp):
AAAAAGATATGGAAAACATATTAATTACGA
Found at i:53979311 original size:14 final size:14
Alignment explanation
Indices: 53979292--53979320 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
53979282 GTTCATCATA
53979292 ACAACAACAAAATT
1 ACAACAACAAAATT
53979306 ACAACAACAAAATT
1 ACAACAACAAAATT
53979320 A
1 A
53979321 AAAGGATAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.66, C:0.21, G:0.00, T:0.14
Consensus pattern (14 bp):
ACAACAACAAAATT
Found at i:53980385 original size:5 final size:5
Alignment explanation
Indices: 53980366--53980432 Score: 73
Period size: 5 Copynumber: 12.6 Consensus size: 5
53980356 CTCTTTCCCT
*
53980366 TTTTC TTTTC ATTTTC TTTTAC ATTTT- TATTC TTCTTTC TTTTC TTTTC
1 TTTTC TTTTC -TTTTC TTTT-C -TTTTC TTTTC -T-TTTC TTTTC TTTTC
53980415 TTTTC TTTTC TTTTC TTT
1 TTTTC TTTTC TTTTC TTT
53980433 CACTTGTTGA
Statistics
Matches: 54, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
4 3 0.06
5 36 0.67
6 8 0.15
7 7 0.13
ACGTcount: A:0.06, C:0.18, G:0.00, T:0.76
Consensus pattern (5 bp):
TTTTC
Found at i:53981047 original size:63 final size:63
Alignment explanation
Indices: 53980976--53981138 Score: 193
Period size: 63 Copynumber: 2.6 Consensus size: 63
53980966 CGTGTGGCAA
* *
53980976 GCCGTGTGACTCACTGTTTGCCATTAAGGACCACATGGGCCAGAGAC-TAGGGTGTGTGTTCAG
1 GCCGTGTGACTCACTGTTTGCAATTAAGGACCACATGGGCCAGAGACAT-GGGTGTGTGTCCAG
* * * * * **
53981039 GCTGTGTGACTTACTGTTTGCTATTAGGGACCATACAGGCCAGAGACATGGGTGTGTGTCCAG
1 GCCGTGTGACTCACTGTTTGCAATTAAGGACCACATGGGCCAGAGACATGGGTGTGTGTCCAG
* * * *
53981102 GCCGTATGACTCACTGTTTACAATTCAGGACAACATG
1 GCCGTGTGACTCACTGTTTGCAATTAAGGACCACATG
53981139 AGCAAATGAC
Statistics
Matches: 80, Mismatches: 19, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
63 79 0.99
64 1 0.01
ACGTcount: A:0.23, C:0.21, G:0.29, T:0.27
Consensus pattern (63 bp):
GCCGTGTGACTCACTGTTTGCAATTAAGGACCACATGGGCCAGAGACATGGGTGTGTGTCCAG
Found at i:53994067 original size:13 final size:13
Alignment explanation
Indices: 53994051--53994083 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
53994041 TTTGATTAAA
*
53994051 TTAGTTAATTAGT
1 TTAGATAATTAGT
53994064 TTAGATAATTAGT
1 TTAGATAATTAGT
53994077 TTA-ATAA
1 TTAGATAA
53994084 ACAAACCCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (13 bp):
TTAGATAATTAGT
Found at i:53994374 original size:5 final size:5
Alignment explanation
Indices: 53994364--53994389 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
53994354 TTTTTCTTGA
53994364 AATTT AATTT AATTT AATTT AATTT A
1 AATTT AATTT AATTT AATTT AATTT A
53994390 CTATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
AATTT
Found at i:53999519 original size:18 final size:17
Alignment explanation
Indices: 53999483--53999536 Score: 56
Period size: 18 Copynumber: 3.2 Consensus size: 17
53999473 AATCCTCCTA
*
53999483 TTTTATTTTATTCTTAT
1 TTTTCTTTTATTCTTAT
*
53999500 TTTTCTTTTGATTTTTAT
1 TTTTCTTTT-ATTCTTAT
**
53999518 TTTTCAATT-TTCTTAT
1 TTTTCTTTTATTCTTAT
53999534 TTT
1 TTT
53999537 GAAAGACATA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
16 9 0.29
17 8 0.26
18 14 0.45
ACGTcount: A:0.15, C:0.07, G:0.02, T:0.76
Consensus pattern (17 bp):
TTTTCTTTTATTCTTAT
Found at i:54002442 original size:13 final size:13
Alignment explanation
Indices: 54002426--54002458 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
54002416 TTTTATTAAA
*
54002426 TTAGTTAATTAGT
1 TTAGATAATTAGT
54002439 TTAGATAATTAGT
1 TTAGATAATTAGT
54002452 TTA-ATAA
1 TTAGATAA
54002459 ACAAACTCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (13 bp):
TTAGATAATTAGT
Found at i:54006894 original size:21 final size:22
Alignment explanation
Indices: 54006849--54006899 Score: 79
Period size: 21 Copynumber: 2.4 Consensus size: 22
54006839 AATTTTTTTA
54006849 AAATATCAAATATTAAAATATT
1 AAATATCAAATATTAAAATATT
54006871 AAA-ATCAAATATTAAAA-ATGT
1 AAATATCAAATATTAAAATAT-T
54006892 AAATATCA
1 AAATATCA
54006900 TTAAACATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
20 2 0.07
21 18 0.67
22 7 0.26
ACGTcount: A:0.61, C:0.06, G:0.02, T:0.31
Consensus pattern (22 bp):
AAATATCAAATATTAAAATATT
Found at i:54007028 original size:16 final size:17
Alignment explanation
Indices: 54006992--54007028 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
54006982 AATTTCACTT
*
54006992 TAATAATAAATTTTAAA
1 TAATAATAAATTGTAAA
54007009 -AATAAT-AATTGTAAA
1 TAATAATAAATTGTAAA
54007024 TAATA
1 TAATA
54007029 TTCTTCATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (17 bp):
TAATAATAAATTGTAAA
Found at i:54015994 original size:34 final size:34
Alignment explanation
Indices: 54015935--54016034 Score: 119
Period size: 34 Copynumber: 2.9 Consensus size: 34
54015925 TGCATACTAT
* * * *
54015935 ACTGATACTATTATTAAAATAGGCTCAGGCCCAG
1 ACTGCTACTGTTAATAAAATGGGCTCAGGCCCAG
* * *
54015969 ACTGCTACTGTTACTAAAATGGGCTCAAGCCTAG
1 ACTGCTACTGTTAATAAAATGGGCTCAGGCCCAG
* *
54016003 ACTGCAACTGTTAATAAAATGGGCTAAGGCCC
1 ACTGCTACTGTTAATAAAATGGGCTCAGGCCC
54016035 TAATTGAGAC
Statistics
Matches: 55, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
34 55 1.00
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (34 bp):
ACTGCTACTGTTAATAAAATGGGCTCAGGCCCAG
Found at i:54023395 original size:14 final size:15
Alignment explanation
Indices: 54023359--54023399 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
54023349 GATTAGTCCC
54023359 AAATCATAATAAACT
1 AAATCATAATAAACT
**
54023374 TGAT-ATAATAAA-T
1 AAATCATAATAAACT
54023387 AAATCATAATAAA
1 AAATCATAATAAA
54023400 ATATACCAGA
Statistics
Matches: 21, Mismatches: 4, Indels: 3
0.75 0.14 0.11
Matches are distributed among these distances:
13 3 0.14
14 16 0.76
15 2 0.10
ACGTcount: A:0.61, C:0.07, G:0.02, T:0.29
Consensus pattern (15 bp):
AAATCATAATAAACT
Found at i:54025164 original size:18 final size:18
Alignment explanation
Indices: 54025121--54025165 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
54025111 GATATTAATT
*
54025121 ATTATAAAATAATATTTT
1 ATTATAAAATAATATTTG
54025139 ATTATAAAATTAAT-TTTG
1 ATTATAAAA-TAATATTTG
*
54025157 ATTGTAAAA
1 ATTATAAAA
54025166 AAAAATTGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 20 0.83
19 4 0.17
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (18 bp):
ATTATAAAATAATATTTG
Found at i:54025753 original size:20 final size:20
Alignment explanation
Indices: 54025716--54025754 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
54025706 AAATATATAA
*
54025716 ATTAAAAAAACTTCAAAATT
1 ATTAAAAAAACTTAAAAATT
* *
54025736 ATTAATAAATCTTAAAAAT
1 ATTAAAAAAACTTAAAAAT
54025755 GCTAAATTAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.59, C:0.08, G:0.00, T:0.33
Consensus pattern (20 bp):
ATTAAAAAAACTTAAAAATT
Found at i:54031791 original size:104 final size:105
Alignment explanation
Indices: 54031577--54031762 Score: 288
Period size: 104 Copynumber: 1.8 Consensus size: 105
54031567 TGATTAAAAT
* * * *
54031577 TAATCACTTTAATATTAAATTAATATAATATTTATCAAGATAAATATTAGATTAAATTTAATATT
1 TAATCACTTTAATATTAAATTAATAAAATATCTATCAAGATAAATATTAAATTAAATTTAACATT
*
54031642 AAACCTTATTAAAATAATAAAATGTTTATAAACATTAAGA
66 AAACCTTATTAAAATAATAAAATGTTTAAAAACATTAAGA
* *
54031682 TAATCACTTTAATATTAAATTAATAAAATA-CTATTAAGATAAGTATTAAATTAAATTTAACATT
1 TAATCACTTTAATATTAAATTAATAAAATATCTATCAAGATAAATATTAAATTAAATTTAACATT
54031746 AAA-C-TATTAAAATAATA
66 AAACCTTATTAAAATAATA
54031763 TTATTTTTGA
Statistics
Matches: 75, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
102 13 0.17
103 1 0.01
104 32 0.43
105 29 0.39
ACGTcount: A:0.52, C:0.06, G:0.03, T:0.39
Consensus pattern (105 bp):
TAATCACTTTAATATTAAATTAATAAAATATCTATCAAGATAAATATTAAATTAAATTTAACATT
AAACCTTATTAAAATAATAAAATGTTTAAAAACATTAAGA
Found at i:54043060 original size:25 final size:25
Alignment explanation
Indices: 54043031--54043079 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
54043021 AGTTGTAAAT
*
54043031 TAGAAAAATATCTATAGAAAATTTC
1 TAGAAAAATATCTATAAAAAATTTC
* * *
54043056 TAGAATAATCTCTCTAAAAAATTT
1 TAGAAAAATATCTATAAAAAATTT
54043080 TCTCTCTACA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.49, C:0.10, G:0.06, T:0.35
Consensus pattern (25 bp):
TAGAAAAATATCTATAAAAAATTTC
Found at i:54046208 original size:40 final size:40
Alignment explanation
Indices: 54046081--54046210 Score: 129
Period size: 40 Copynumber: 3.2 Consensus size: 40
54046071 ATGCTGGAAA
* * * *
54046081 TTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATGG
* * * **
54046121 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGA-CA
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-ATGG
* *
54046161 TTCTATCCGGGCCAAGACCCGAAGGCATTTGTGC-ACATGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-ATGG
54046201 TTATATCCGG
1 TTATATCCGG
54046211 TTATATTCCG
Statistics
Matches: 70, Mismatches: 18, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
39 2 0.03
40 68 0.97
ACGTcount: A:0.25, C:0.25, G:0.28, T:0.23
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATGG
Found at i:54054155 original size:40 final size:40
Alignment explanation
Indices: 54054070--54054220 Score: 134
Period size: 40 Copynumber: 3.8 Consensus size: 40
54054060 AATTGAATGA
* * *
54054070 TATCCGGGCTAA-ATCCCGAAGACAATTATGCTG-GAAATTA-
1 TATCCGGGCTAAGA-CCCGAAGGCAATTGTGC-GAGACA-TAC
* * *
54054110 TATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGC-TAC
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGC--GAGACATAC
*
54054151 -ATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGACATTC
1 TATCCGGGCTAAGACCCGAAGGCAATT-GTGCGAGACATAC
*
54054190 TATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGC
54054221 ACATGGTTAT
Statistics
Matches: 92, Mismatches: 11, Indels: 16
0.77 0.09 0.13
Matches are distributed among these distances:
38 3 0.03
39 5 0.05
40 79 0.86
41 4 0.04
42 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.26, T:0.23
Consensus pattern (40 bp):
TATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGACATAC
Found at i:54054234 original size:40 final size:40
Alignment explanation
Indices: 54054107--54054236 Score: 138
Period size: 40 Copynumber: 3.2 Consensus size: 40
54054097 ATGCTGGAAA
* * * *
54054107 TTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATGG
* * * **
54054147 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGA-CA
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-ATGG
*
54054187 TTCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACATGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-ATGG
54054227 TTATATCCGG
1 TTATATCCGG
54054237 TTATATTCCG
Statistics
Matches: 71, Mismatches: 17, Indels: 4
0.77 0.18 0.04
Matches are distributed among these distances:
39 2 0.03
40 69 0.97
ACGTcount: A:0.25, C:0.24, G:0.28, T:0.24
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATGG
Found at i:54058644 original size:50 final size:50
Alignment explanation
Indices: 54058569--54058701 Score: 189
Period size: 50 Copynumber: 2.7 Consensus size: 50
54058559 AGCTATTGTG
**
54058569 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGG-TGGTT
1 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTA-CAGGATAATT
* *
54058619 AGGTCATGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
1 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACAGGATAATT
* *
54058669 -GGTCGCATGTGTAGTACTAAGTGCAGGCTACTA
1 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTA
54058702 TGCGTACCAG
Statistics
Matches: 75, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
49 33 0.44
50 42 0.56
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.29
Consensus pattern (50 bp):
AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACAGGATAATT
Found at i:54061425 original size:16 final size:15
Alignment explanation
Indices: 54061387--54061425 Score: 60
Period size: 15 Copynumber: 2.5 Consensus size: 15
54061377 TGGATTCTCG
*
54061387 TATCATGGATTTCTT
1 TATCTTGGATTTCTT
54061402 TATCTTGGATTTCTT
1 TATCTTGGATTTCTT
54061417 TATTCTTGG
1 TA-TCTTGG
54061426 CTTCTTGTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 16 0.73
16 6 0.27
ACGTcount: A:0.15, C:0.13, G:0.15, T:0.56
Consensus pattern (15 bp):
TATCTTGGATTTCTT
Found at i:54063499 original size:30 final size:30
Alignment explanation
Indices: 54063465--54063521 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
54063455 CCCGAGCCTA
54063465 GGGCAAAA-GTGTAATTATGCAAAAGTTTAG
1 GGGCAAAATG-GTAATTATGCAAAAGTTTAG
* *
54063495 GGGCAAAATGGTAATTTTGCCAAAGTT
1 GGGCAAAATGGTAATTATGCAAAAGTT
54063522 CGTATTAAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 23 0.96
31 1 0.04
ACGTcount: A:0.37, C:0.09, G:0.26, T:0.28
Consensus pattern (30 bp):
GGGCAAAATGGTAATTATGCAAAAGTTTAG
Found at i:54064246 original size:50 final size:50
Alignment explanation
Indices: 54064168--54064300 Score: 189
Period size: 50 Copynumber: 2.7 Consensus size: 50
54064158 AGCTATTGTG
**
54064168 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGG-TGGTT
1 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTA-CAGGATAATT
* *
54064218 AGGTCACGTGTGTAGTACTAAGTTCAGGCTACTACGTGTACCGGATAATT
1 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACAGGATAATT
* *
54064268 -GGTCGCATGTGTAGTACTAAGTGCAGGCTACTA
1 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTA
54064301 TGCGTACCAG
Statistics
Matches: 75, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
49 33 0.44
50 42 0.56
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.29
Consensus pattern (50 bp):
AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACAGGATAATT
Found at i:54065627 original size:16 final size:16
Alignment explanation
Indices: 54065606--54065645 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
54065596 CTTATCAACA
54065606 GAGTACCAGCACAGAG
1 GAGTACCAGCACAGAG
54065622 GAGTACCAGCACAGAG
1 GAGTACCAGCACAGAG
*
54065638 GCGTACCA
1 GAGTACCA
54065646 ACAAACTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.35, C:0.28, G:0.30, T:0.07
Consensus pattern (16 bp):
GAGTACCAGCACAGAG
Found at i:54066147 original size:62 final size:62
Alignment explanation
Indices: 54066050--54066182 Score: 205
Period size: 62 Copynumber: 2.1 Consensus size: 62
54066040 TAGGCACACA
* * *
54066050 CCCATGTCCCTGGTCTTGTGGTTCTAAAGTGTAAATAAT-ATGTTGCACGACCTGGACACATG
1 CCCATGTCCCTGGCCGTGTGGTTCTAAAGTGTAAATAATGA-GTTACACGACCTGGACACATG
* *
54066112 CCCATGTCCCTGGCCGTGTGGTTCTAAAGTGTAAATAGTGAGTTACACGGCCTGGACACATG
1 CCCATGTCCCTGGCCGTGTGGTTCTAAAGTGTAAATAATGAGTTACACGACCTGGACACATG
54066174 CCCATGTCC
1 CCCATGTCC
54066183 TTGCCCGTAT
Statistics
Matches: 65, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
62 64 0.98
63 1 0.02
ACGTcount: A:0.23, C:0.26, G:0.24, T:0.28
Consensus pattern (62 bp):
CCCATGTCCCTGGCCGTGTGGTTCTAAAGTGTAAATAATGAGTTACACGACCTGGACACATG
Found at i:54076543 original size:39 final size:39
Alignment explanation
Indices: 54076489--54076612 Score: 196
Period size: 39 Copynumber: 3.2 Consensus size: 39
54076479 TGTGAATGAA
54076489 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
54076528 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
* * *
54076567 TGTGC-AAGTTGTGATATCCGAGTTAAGTCCCGAAGGCATT
1 TGTGCGAA-TTGTGATATCCGGGCTAAG-CCCGAAGGCAAT
54076607 TGTGCG
1 TGTGCG
54076613 GGTTACCATA
Statistics
Matches: 79, Mismatches: 3, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
38 2 0.03
39 61 0.77
40 16 0.20
ACGTcount: A:0.24, C:0.19, G:0.31, T:0.26
Consensus pattern (39 bp):
TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
Found at i:54078514 original size:12 final size:11
Alignment explanation
Indices: 54078480--54078517 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
54078470 ATTAGCCAGA
54078480 AAAAATTATAT
1 AAAAATTATAT
54078491 AATAAATT-TAT
1 AA-AAATTATAT
54078502 AAAAATTGATAT
1 AAAAATT-ATAT
54078514 AAAA
1 AAAA
54078518 TGTTAATATG
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
10 5 0.21
11 7 0.29
12 12 0.50
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (11 bp):
AAAAATTATAT
Found at i:54082633 original size:38 final size:38
Alignment explanation
Indices: 54082591--54082707 Score: 112
Period size: 38 Copynumber: 3.1 Consensus size: 38
54082581 TATTGTTAAC
54082591 ACTGCGACTGTTAAACT-AAAAGCATGTGAAGCATGTCT
1 ACTGCGACTGTTAAACTGAAAA-CATGTGAAGCATGTCT
* * * *
54082629 ACTGCGACTATTGAACTGAATACATGTTAAGCATGTCT
1 ACTGCGACTGTTAAACTGAAAACATGTGAAGCATGTCT
* ** * * *
54082667 ATTGTTACTGTTAAATTGAATACATGCT-AAACATGTCT
1 ACTGCGACTGTTAAACTGAAAACATG-TGAAGCATGTCT
54082705 ACT
1 ACT
54082708 ATTTTGTATT
Statistics
Matches: 65, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
38 61 0.94
39 4 0.06
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Consensus pattern (38 bp):
ACTGCGACTGTTAAACTGAAAACATGTGAAGCATGTCT
Found at i:54082865 original size:22 final size:22
Alignment explanation
Indices: 54082799--54082865 Score: 66
Period size: 22 Copynumber: 3.0 Consensus size: 22
54082789 AATAATTTGT
*
54082799 AAACACTAGTGGTTCATCCA-A
1 AAACACTGGTGGTTCATCCACA
* * *
54082820 AACTCACTGG-GGATTTATCTACA
1 AA-ACACTGGTGG-TTCATCCACA
54082843 AAACACTGGTGGTTCATCCACA
1 AAACACTGGTGGTTCATCCACA
54082865 A
1 A
54082866 CCTACTAGTA
Statistics
Matches: 35, Mismatches: 7, Indels: 7
0.71 0.14 0.14
Matches are distributed among these distances:
21 4 0.11
22 26 0.74
23 5 0.14
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.25
Consensus pattern (22 bp):
AAACACTGGTGGTTCATCCACA
Found at i:54084573 original size:91 final size:91
Alignment explanation
Indices: 54084403--54084575 Score: 231
Period size: 91 Copynumber: 1.9 Consensus size: 91
54084393 TTTGTAGATA
* * * *
54084403 AACCACCAAAAGGTGTAGGTTAATATGCTGCCAGATGGTTGTGAATACATAACATAATTACATAT
1 AACCACCAAAAGGTGTAGGTTAATACGCTACCAGATGGTTATGAATACATAACATAATTACAGAT
*
54084468 AAAAGATGCTAGATAATGGGTGGGCG
66 AAAAGATGCCAGATAATGGGTGGGCG
* * **
54084494 AACCACC-AAAGGTTGTAGTTTAATACGCTATCAGATGGTTATGAATACATAACATTTTTACAGA
1 AACCACCAAAAGG-TGTAGGTTAATACGCTACCAGATGGTTATGAATACATAACATAATTACAGA
* *
54084558 TAGAAGTTGCCAGATAAT
65 TAAAAGATGCCAGATAAT
54084576 ATGTGGATGA
Statistics
Matches: 70, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
90 5 0.07
91 65 0.93
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.28
Consensus pattern (91 bp):
AACCACCAAAAGGTGTAGGTTAATACGCTACCAGATGGTTATGAATACATAACATAATTACAGAT
AAAAGATGCCAGATAATGGGTGGGCG
Found at i:54094317 original size:26 final size:26
Alignment explanation
Indices: 54094281--54094330 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
54094271 GCACTAATTA
54094281 GTATCGCAGCAAAGCTGCCAGTAACG
1 GTATCGCAGCAAAGCTGCCAGTAACG
* * *
54094307 GTATCGTAGCAATGCTTCCAGTAA
1 GTATCGCAGCAAAGCTGCCAGTAA
54094331 TCAGTATAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.30, C:0.24, G:0.24, T:0.22
Consensus pattern (26 bp):
GTATCGCAGCAAAGCTGCCAGTAACG
Found at i:54095959 original size:23 final size:23
Alignment explanation
Indices: 54095915--54095959 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
54095905 ATCTCTCCAT
**
54095915 AATCCTCTCCTTGATTTTCTCCC
1 AATCCTCTCCTTGATTCCCTCCC
54095938 AATCCTCTCCTTGATTCCCTCC
1 AATCCTCTCCTTGATTCCCTCC
54095960 ACATAACACT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.13, C:0.42, G:0.04, T:0.40
Consensus pattern (23 bp):
AATCCTCTCCTTGATTCCCTCCC
Found at i:54107252 original size:24 final size:24
Alignment explanation
Indices: 54107225--54107271 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
54107215 TCCTAAAATC
*
54107225 TCTCCATAATCCTCTCCTTGATTT
1 TCTCCACAATCCTCTCCTTGATTT
* *
54107249 TCTCCCCAATCCTCTTCTTGATT
1 TCTCCACAATCCTCTCCTTGATT
54107272 CCCTTAACAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.15, C:0.36, G:0.04, T:0.45
Consensus pattern (24 bp):
TCTCCACAATCCTCTCCTTGATTT
Found at i:54112615 original size:268 final size:252
Alignment explanation
Indices: 54112216--54112988 Score: 1161
Period size: 268 Copynumber: 3.0 Consensus size: 252
54112206 CCAAATGGTG
* * * *
54112216 CAACGGGCACAGTGATGTTACAAGAATGTACGAGTTCGATATGAACCAGTACAGGTATGTATGTA
1 CAACGGGCACAATAATGTTACGAGAATGTACGAGTTCGATATGAACCAGTACAGGTATGTATATA
54112281 TGTAAATCATGTA-AAATTTGGATCTATGAATTTGTGATTCCATAATTAACTTTGTTGGTGATTA
66 TGTAAA-CATGTAGAAA-TTGGATCTATGAATTTGTGATTCCATAATTAACTTTGTTGGTGATTA
* * * *
54112345 CATGTTATGTTAATGAGACTAAATTGAGTTGCATTATAATTTAAATTGCTCGCTTAATTATGGTT
129 CATGTTAGGTTAATGAGACTAAATTGAGTTGCATTATAATTTAAATTACTTGCTTAATTGTGGTT
* * *
54112410 TATTGGTAAGTTATATTTGCAGTTATACAAACTTACTAAGCCTAATTGCTTACTGTGTT
194 GATTGGTAAGTTATATTTGCAGTTATACGAACTTACTAAGCCTAATTGCTTACTTTGTT
* ** *
54112469 CAACGGGCACAATGATGTTACGAGAATGTATTAGTTCGATATGGACCAGTACAAGTATGTATGTA
1 CAACGGGCACAATAATGTTACGAGAATGTACGAGTTCGATATGAACCAGTAC-AG---GTATGTA
*
54112534 TGTATGTAAATCATGTAGAAATTGGATCTATGAAATTTCTATGAATTTGTGATTCCATAATTAAC
62 TATATGTAAA-CATGTAGAAATT-G------G--A--TCTATGAATTTGTGATTCCATAATTAAC
* *
54112599 TTTGTTGGAGATTACATGTTAGGTTAATGAGACTGAATTGAGTTGCATTATAATTTAAATTACTT
115 TTTGTTGGTGATTACATGTTAGGTTAATGAGACTAAATTGAGTTGCATTATAATTTAAATTACTT
*
54112664 GCTTAATTGTGGTTGATTGGTCAGTTATATTTGCAGTTATACGAACTTACTAAGCCTAATTGCTT
180 GCTTAATTGTGGTTGATTGGTAAGTTATATTTGCAGTTATACGAACTTACTAAGCCTAATTGCTT
54112729 ACTTTGTT
245 ACTTTGTT
*
54112737 CAACGGGCACAGTAATGTTACGAGAATGTACGAGTTCGATATGAACCAGTACAGGTATGTATATA
1 CAACGGGCACAATAATGTTACGAGAATGTACGAGTTCGATATGAACCAGTACAGGTATGTATATA
*
54112802 TGTAAACATGTAGAAATTGGATCTATGAATTTGTGATTTCATAATTAACTTTGTTGGTGATTACA
66 TGTAAACATGTAGAAATTGGATCTATGAATTTGTGATTCCATAATTAACTTTGTTGGTGATTACA
* *
54112867 TGTTAGGTTAATGAGACTAAATTGAGTTGCATTATAATTTAAAATACTTGTTTAATTGTGGTTGA
131 TGTTAGGTTAATGAGACTAAATTGAGTTGCATTATAATTTAAATTACTTGCTTAATTGTGGTTGA
*
54112932 TTGGTAATTTATATTTGCAGTTATACGAACTTACTAAGCCTAATTGCTTACTTTGTT
196 TTGGTAAGTTATATTTGCAGTTATACGAACTTACTAAGCCTAATTGCTTACTTTGTT
54112989 TACTTTTCTG
Statistics
Matches: 476, Mismatches: 28, Indels: 33
0.89 0.05 0.06
Matches are distributed among these distances:
252 159 0.33
253 47 0.10
254 3 0.01
256 1 0.00
257 26 0.05
258 4 0.01
262 1 0.00
263 12 0.03
264 17 0.04
266 1 0.00
267 2 0.00
268 203 0.43
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.39
Consensus pattern (252 bp):
CAACGGGCACAATAATGTTACGAGAATGTACGAGTTCGATATGAACCAGTACAGGTATGTATATA
TGTAAACATGTAGAAATTGGATCTATGAATTTGTGATTCCATAATTAACTTTGTTGGTGATTACA
TGTTAGGTTAATGAGACTAAATTGAGTTGCATTATAATTTAAATTACTTGCTTAATTGTGGTTGA
TTGGTAAGTTATATTTGCAGTTATACGAACTTACTAAGCCTAATTGCTTACTTTGTT
Found at i:54123307 original size:46 final size:46
Alignment explanation
Indices: 54123257--54123432 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
54123247 TGGTTGAGCA
54123257 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
54123303 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
54123348 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
54123396 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
54123433 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 63 0.57
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:54123413 original size:93 final size:93
Alignment explanation
Indices: 54123254--54123425 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
54123244 GGATGGTTGA
* *
54123254 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
54123319 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
54123347 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
54123412 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
54123426 CTTATGGGCG
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:54130828 original size:46 final size:46
Alignment explanation
Indices: 54130778--54130906 Score: 222
Period size: 46 Copynumber: 2.8 Consensus size: 46
54130768 TGGTTGAGCA
*
54130778 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
54130824 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
* * *
54130870 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
54130907 GCGGGTTACA
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 79 1.00
ACGTcount: A:0.19, C:0.22, G:0.29, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
Found at i:54136697 original size:24 final size:24
Alignment explanation
Indices: 54136665--54136749 Score: 161
Period size: 24 Copynumber: 3.5 Consensus size: 24
54136655 AATCTCAAAT
54136665 GCACTATGTGTGCGATTTACTATG
1 GCACTATGTGTGCGATTTACTATG
*
54136689 GCACTATGTGTGCGATTTACTATA
1 GCACTATGTGTGCGATTTACTATG
54136713 GCACTATGTGTGCGATTTACTATG
1 GCACTATGTGTGCGATTTACTATG
54136737 GCACTATGTGTGC
1 GCACTATGTGTGC
54136750 TAACATAATA
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 59 1.00
ACGTcount: A:0.21, C:0.18, G:0.25, T:0.36
Consensus pattern (24 bp):
GCACTATGTGTGCGATTTACTATG
Found at i:54136764 original size:48 final size:48
Alignment explanation
Indices: 54136665--54136772 Score: 164
Period size: 48 Copynumber: 2.2 Consensus size: 48
54136655 AATCTCAAAT
* ** *
54136665 GCACTATGTGTGCGATTTACTATGGCACTATGTGTGCGATTTACTATA
1 GCACTATGTGTGCGATTTACTATGGCACTATGTGTGCAACATAATATA
54136713 GCACTATGTGTGCGATTTACTATGGCACTATGTGTGCTAACATAATA-A
1 GCACTATGTGTGCGATTTACTATGGCACTATGTGTGC-AACATAATATA
54136761 GCACTATGTGTG
1 GCACTATGTGTG
54136773 TAACGTTTGG
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
48 50 0.91
49 5 0.09
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.35
Consensus pattern (48 bp):
GCACTATGTGTGCGATTTACTATGGCACTATGTGTGCAACATAATATA
Found at i:54144279 original size:38 final size:38
Alignment explanation
Indices: 54144237--54144321 Score: 100
Period size: 38 Copynumber: 2.3 Consensus size: 38
54144227 AAGCATATGG
* * * * *
54144237 AGCATGTCTATTGCAACTGTTGAACTAAATATATGTTA
1 AGCATATCTATTACAACTGTTAAACTAAATACATGTCA
**
54144275 AGCATATCTATTATTACTGTTAAACTAAATACATGTCA
1 AGCATATCTATTACAACTGTTAAACTAAATACATGTCA
54144313 AGC-TATCTA
1 AGCATATCTA
54144322 CTGTTTTTGT
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
37 6 0.15
38 34 0.85
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.36
Consensus pattern (38 bp):
AGCATATCTATTACAACTGTTAAACTAAATACATGTCA
Found at i:54145021 original size:113 final size:113
Alignment explanation
Indices: 54144823--54145048 Score: 434
Period size: 113 Copynumber: 2.0 Consensus size: 113
54144813 AAAGCTCGTA
54144823 AAGCACACCCCCTTGATTTTCATCTTTACAAATAACCCACTAGGTTAGGATGTGGACTCAACATC
1 AAGCACACCCCCTTGATTTTCATCTTTACAAATAACCCACTAGGTTAGGATGTGGACTCAACATC
54144888 CAGAAAGTCTCAGCTCGAAGTAATATTTTCATTAAAAGTATTTTAGAC
66 CAGAAAGTCTCAGCTCGAAGTAATATTTTCATTAAAAGTATTTTAGAC
54144936 AAGCACACCCCCTTGATTTTCATCTTTACAAATAACCCACTAGGTTAGGATGTGGACTCAACATC
1 AAGCACACCCCCTTGATTTTCATCTTTACAAATAACCCACTAGGTTAGGATGTGGACTCAACATC
* *
54145001 CAGAAGGTCTCAGCTGGAAGTAATATTTTCATTAAAAGTATTTTAGAC
66 CAGAAAGTCTCAGCTCGAAGTAATATTTTCATTAAAAGTATTTTAGAC
54145049 TTTGAATTAT
Statistics
Matches: 111, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
113 111 1.00
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (113 bp):
AAGCACACCCCCTTGATTTTCATCTTTACAAATAACCCACTAGGTTAGGATGTGGACTCAACATC
CAGAAAGTCTCAGCTCGAAGTAATATTTTCATTAAAAGTATTTTAGAC
Found at i:54146383 original size:28 final size:30
Alignment explanation
Indices: 54146341--54146423 Score: 93
Period size: 29 Copynumber: 2.9 Consensus size: 30
54146331 TGTAAAGTAG
* *
54146341 GGGGAAAAACTATAAAATA-T-GAAAAATA
1 GGGGCAAAACTATAAAATAGTAAAAAAATA
*
54146369 GGGGCAAAACCATAAAA-AGTAAAAAAATA
1 GGGGCAAAACTATAAAATAGTAAAAAAATA
* *
54146398 AGGGCAAAACTATAAAAT-CTAAAAAA
1 GGGGCAAAACTATAAAATAGTAAAAAA
54146424 CAGGGACAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
27 1 0.02
28 16 0.35
29 29 0.63
ACGTcount: A:0.61, C:0.08, G:0.16, T:0.14
Consensus pattern (30 bp):
GGGGCAAAACTATAAAATAGTAAAAAAATA
Found at i:54146514 original size:28 final size:28
Alignment explanation
Indices: 54146341--54146701 Score: 97
Period size: 28 Copynumber: 13.1 Consensus size: 28
54146331 TGTAAAGTAG
* *
54146341 GGGGAAAAACTATAAAAT-ATGAAAAATA
1 GGGGCAAAACTATAAAATCA-AAAAAATA
*
54146369 GGGGCAAAACCATAAAAAGT-AAAAAAATA
1 GGGGCAAAACTAT-AAAA-TCAAAAAAATA
* * *
54146398 AGGGCAAAACTATAAAATCTAAAAAACA
1 GGGGCAAAACTATAAAATCAAAAAAATA
* * * * *
54146426 -GGG-ACAATTGTCAAATCTAAAAAATA
1 GGGGCAAAACTATAAAATCAAAAAAATA
* * **
54146452 GAAGG-AAAA-TGA-AAATTTTGAAAAAATA
1 G-GGGCAAAACT-ATAAA-ATCAAAAAAATA
***
54146480 ATAGCAAAACTATAAAATCAAAAAAATA
1 GGGGCAAAACTATAAAATCAAAAAAATA
* * * *
54146508 GGGGCAAAATTCTAAAATTTGAAAATAA-A
1 GGGGCAAAACTATAAAA--TCAAAAAAATA
* * *
54146537 -GGGTAAAACTGTAAAATC-TAAAAA-A
1 GGGGCAAAACTATAAAATCAAAAAAATA
* * * * **
54146562 ---GAAAAATTGTCAAATCTGAAAAATA
1 GGGGCAAAACTATAAAATCAAAAAAATA
** * ***
54146587 GACGCAAAATTATAAAAT-TTGAAAATA
1 GGGGCAAAACTATAAAATCAAAAAAATA
*
54146614 GGGGTAAAACTATAAAATCAAAAAAATA
1 GGGGCAAAACTATAAAATCAAAAAAATA
* * * * *
54146642 TGGG-AAAATTGTAAAATTTAGAAAAATA
1 GGGGCAAAACTATAAAA-TCAAAAAAATA
* * ** *
54146670 GGGGTAAAATTATAAAATTTAAGAAATA
1 GGGGCAAAACTATAAAATCAAAAAAATA
54146698 GGGG
1 GGGG
54146702 ACACATGGCC
Statistics
Matches: 249, Mismatches: 64, Indels: 40
0.71 0.18 0.11
Matches are distributed among these distances:
23 13 0.05
24 5 0.02
25 6 0.02
26 19 0.08
27 39 0.16
28 120 0.48
29 38 0.15
30 9 0.04
ACGTcount: A:0.57, C:0.07, G:0.16, T:0.21
Consensus pattern (28 bp):
GGGGCAAAACTATAAAATCAAAAAAATA
Found at i:54146576 original size:23 final size:23
Alignment explanation
Indices: 54146541--54146584 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
54146531 AATAAAGGGT
54146541 AAAACTGTAAAATCTAAAAAAGA
1 AAAACTGTAAAATCTAAAAAAGA
* * *
54146564 AAAATTGTCAAATCTGAAAAA
1 AAAACTGTAAAATCTAAAAAA
54146585 TAGACGCAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.61, C:0.09, G:0.09, T:0.20
Consensus pattern (23 bp):
AAAACTGTAAAATCTAAAAAAGA
Found at i:54146697 original size:56 final size:54
Alignment explanation
Indices: 54146592--54146702 Score: 150
Period size: 56 Copynumber: 2.0 Consensus size: 54
54146582 AAATAGACGC
*
54146592 AAAATTATAAAATTTGAAAATAGGGGTAAAACTATAAAATCAAAAAAATATGGG
1 AAAATTATAAAATTTGAAAATAGGGGTAAAACTATAAAATCAAAAAAATAGGGG
* * ** *
54146646 AAAATTGTAAAATTTAGAAAAATAGGGGTAAAATTATAAAATTTAAGAAATAGGGG
1 AAAATTATAAAATTT-G-AAAATAGGGGTAAAACTATAAAATCAAAAAAATAGGGG
54146702 A
1 A
54146703 CACATGGCCA
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
54 14 0.29
55 1 0.02
56 34 0.69
ACGTcount: A:0.56, C:0.02, G:0.17, T:0.25
Consensus pattern (54 bp):
AAAATTATAAAATTTGAAAATAGGGGTAAAACTATAAAATCAAAAAAATAGGGG
Found at i:54149166 original size:26 final size:26
Alignment explanation
Indices: 54149121--54149193 Score: 83
Period size: 26 Copynumber: 2.8 Consensus size: 26
54149111 TCACATCCCT
* * *
54149121 ATTTTACCCTTAGCATAATTTTGAAG
1 ATTTTACCCATAGTAAAATTTTGAAG
* *
54149147 ATTTTACCCCTAGTAAAATTTTGACG
1 ATTTTACCCATAGTAAAATTTTGAAG
* *
54149173 ATTTTGCCCATTGTAAAATTT
1 ATTTTACCCATAGTAAAATTT
54149194 CTAGAAAACA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.30, C:0.16, G:0.11, T:0.42
Consensus pattern (26 bp):
ATTTTACCCATAGTAAAATTTTGAAG
Found at i:54149357 original size:6 final size:6
Alignment explanation
Indices: 54149342--54149376 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
54149332 GCAAATGGGT
* *
54149342 CATTTC CATTTT CATTTA CATTTC CATTTC CATTT
1 CATTTC CATTTC CATTTC CATTTC CATTTC CATTT
54149377 TTGGAAACCT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.20, C:0.26, G:0.00, T:0.54
Consensus pattern (6 bp):
CATTTC
Found at i:54149365 original size:18 final size:18
Alignment explanation
Indices: 54149342--54149376 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
54149332 GCAAATGGGT
*
54149342 CATTTCCATTTTCATTTA
1 CATTTCCATTTCCATTTA
54149360 CATTTCCATTTCCATTT
1 CATTTCCATTTCCATTT
54149377 TTGGAAACCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.26, G:0.00, T:0.54
Consensus pattern (18 bp):
CATTTCCATTTCCATTTA
Found at i:54158171 original size:2 final size:2
Alignment explanation
Indices: 54158164--54158199 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
54158154 GAGGCTAGTC
54158164 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
54158200 GTCATGATAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:54162891 original size:23 final size:24
Alignment explanation
Indices: 54162840--54162892 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 24
54162830 TTCTTTGTTG
54162840 AATATGTTAAAAATGTTTCAATTAT
1 AATAT-TTAAAAATGTTTCAATTAT
* *
54162865 --TATTTGAAAAT-TTTCTATTAT
1 AATATTTAAAAATGTTTCAATTAT
54162886 AATATTT
1 AATATTT
54162893 TAATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
21 9 0.38
22 7 0.29
23 8 0.33
ACGTcount: A:0.40, C:0.04, G:0.06, T:0.51
Consensus pattern (24 bp):
AATATTTAAAAATGTTTCAATTAT
Found at i:54163425 original size:14 final size:16
Alignment explanation
Indices: 54163394--54163426 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
54163384 TTTATTCATA
54163394 AATATTTATATCATTG
1 AATATTTATATCATTG
54163410 AATA-TTATAT-ATTG
1 AATATTTATATCATTG
54163424 AAT
1 AAT
54163427 TTAAGTCTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.41
15 6 0.35
16 4 0.24
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.48
Consensus pattern (16 bp):
AATATTTATATCATTG
Found at i:54166757 original size:23 final size:23
Alignment explanation
Indices: 54166721--54166800 Score: 144
Period size: 23 Copynumber: 3.5 Consensus size: 23
54166711 TTTATTGTTT
*
54166721 GAAAA-CATAGTCGTGTTTTTAG
1 GAAAATCATTGTCGTGTTTTTAG
54166743 GAAAATCATTGTCGTGTTTTTAG
1 GAAAATCATTGTCGTGTTTTTAG
54166766 GAAAATCATTGTCGTGTTTTTAG
1 GAAAATCATTGTCGTGTTTTTAG
54166789 GAAAATCATTGT
1 GAAAATCATTGT
54166801 TTGCATAAAA
Statistics
Matches: 56, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
22 5 0.09
23 51 0.91
ACGTcount: A:0.30, C:0.09, G:0.21, T:0.40
Consensus pattern (23 bp):
GAAAATCATTGTCGTGTTTTTAG
Found at i:54167158 original size:26 final size:26
Alignment explanation
Indices: 54167122--54167178 Score: 82
Period size: 26 Copynumber: 2.2 Consensus size: 26
54167112 GCAAACAAAA
54167122 ACAAATACAG-ATCCAGATTCAGATAT
1 ACAAATACAGAAT-CAGATTCAGATAT
54167148 -CAAATTACAGAATCAGATTCAGATAT
1 ACAAA-TACAGAATCAGATTCAGATAT
54167174 ACAAA
1 ACAAA
54167179 ATCCTACCCC
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
25 4 0.14
26 18 0.64
27 6 0.21
ACGTcount: A:0.49, C:0.18, G:0.11, T:0.23
Consensus pattern (26 bp):
ACAAATACAGAATCAGATTCAGATAT
Found at i:54167181 original size:20 final size:20
Alignment explanation
Indices: 54167140--54167181 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
54167130 AGATCCAGAT
*
54167140 TCAGATATCAAATTACAGAA
1 TCAGATATCAAATTACAAAA
*
54167160 TCAGAT-TCAGATATACAAAA
1 TCAGATATCAAAT-TACAAAA
54167180 TC
1 TC
54167182 CTACCCCCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.48, C:0.17, G:0.10, T:0.26
Consensus pattern (20 bp):
TCAGATATCAAATTACAAAA
Found at i:54167617 original size:18 final size:18
Alignment explanation
Indices: 54167594--54167629 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
54167584 CAGTATAATA
* *
54167594 GGCCCACATGTCCGTGTG
1 GGCCCACACGCCCGTGTG
54167612 GGCCCACACGCCCGTGTG
1 GGCCCACACGCCCGTGTG
54167630 ACATGCTCGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.11, C:0.39, G:0.33, T:0.17
Consensus pattern (18 bp):
GGCCCACACGCCCGTGTG
Found at i:54168314 original size:15 final size:16
Alignment explanation
Indices: 54168278--54168324 Score: 60
Period size: 15 Copynumber: 2.9 Consensus size: 16
54168268 AAAAAGGTTG
54168278 AAAGAAAACTAGAAAATA
1 AAAGAAAA-TA-AAAATA
54168296 AAAGAAAATAAAAAT-
1 AAAGAAAATAAAAATA
*
54168311 AAAGTAAATAAAAA
1 AAAGAAAATAAAAA
54168325 CTATATCCCA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
15 13 0.46
16 5 0.18
17 2 0.07
18 8 0.29
ACGTcount: A:0.77, C:0.02, G:0.09, T:0.13
Consensus pattern (16 bp):
AAAGAAAATAAAAATA
Found at i:54169454 original size:23 final size:22
Alignment explanation
Indices: 54169396--54169454 Score: 68
Period size: 25 Copynumber: 2.6 Consensus size: 22
54169386 CAATCCTATA
54169396 AGTATTTCTG-AA-ACTTAGAT
1 AGTATTTCTGAAACACTTAGAT
*
54169416 AGTATATTTTGAAAACACTATAGAT
1 AGTAT-TTCTG-AAACACT-TAGAT
54169441 AGTATTTCTGAAAC
1 AGTATTTCTGAAAC
54169455 TGTATTGAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
20 5 0.16
21 4 0.12
23 6 0.19
24 7 0.22
25 10 0.31
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.37
Consensus pattern (22 bp):
AGTATTTCTGAAACACTTAGAT
Found at i:54174552 original size:5 final size:5
Alignment explanation
Indices: 54174544--54174569 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
54174534 TTTTATTTTA
54174544 TCTTT TCTTT TCTTT TCTTT TCTTT T
1 TCTTT TCTTT TCTTT TCTTT TCTTT T
54174570 TTGATTTTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TCTTT
Found at i:54177421 original size:42 final size:42
Alignment explanation
Indices: 54177361--54177443 Score: 157
Period size: 42 Copynumber: 2.0 Consensus size: 42
54177351 ATGACTTCAT
54177361 TTTTTTTCATTTCATTTTTACACAAATACCCATTTATATCCA
1 TTTTTTTCATTTCATTTTTACACAAATACCCATTTATATCCA
*
54177403 TTTTTTTCATTTCGTTTTTACACAAATACCCATTTATATCC
1 TTTTTTTCATTTCATTTTTACACAAATACCCATTTATATCC
54177444 TACTGGCTTT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.27, C:0.22, G:0.01, T:0.51
Consensus pattern (42 bp):
TTTTTTTCATTTCATTTTTACACAAATACCCATTTATATCCA
Found at i:54181809 original size:43 final size:42
Alignment explanation
Indices: 54181761--54181916 Score: 152
Period size: 43 Copynumber: 3.7 Consensus size: 42
54181751 AGCTCATACA
* * *
54181761 ATGCCAACGTCCCATACATAGTCTTACATGTAATCAAATTTCG
1 ATGCCAACATCCCAGACATGGTCTTACATGTAATCAAA-TTCG
*** * * * *
54181804 ATGCCATTGTCCCAAACAGGGTCTTACATGAAATCAAATACG
1 ATGCCAACATCCCAGACATGGTCTTACATGTAATCAAATTCG
* * * *
54181846 ATGTCAACATCCCAGACGT-GTCTTACACGTAAATCATAAGTCG
1 ATGCCAACATCCCAGACATGGTCTTACATGT-AATCA-AATTCG
54181889 ATGCCAACATCCCAGACATGGTCTTACA
1 ATGCCAACATCCCAGACATGGTCTTACA
54181917 CGATATCACT
Statistics
Matches: 90, Mismatches: 20, Indels: 5
0.78 0.17 0.04
Matches are distributed among these distances:
41 9 0.10
42 20 0.22
43 53 0.59
44 8 0.09
ACGTcount: A:0.33, C:0.26, G:0.15, T:0.26
Consensus pattern (42 bp):
ATGCCAACATCCCAGACATGGTCTTACATGTAATCAAATTCG
Found at i:54184195 original size:277 final size:275
Alignment explanation
Indices: 54183651--54184209 Score: 978
Period size: 277 Copynumber: 2.0 Consensus size: 275
54183641 TTAAGAAAAA
54183651 AAAGAGGAAATAACATAAAATAATTTGTGATATAAAATTTAGGATTACCTTAAGTCGATAGAGAA
1 AAAGAGGAAATAACATAAAATAATTTGTGATATAAAATTTAGGATTACCTTAAGTCGATAGAGAA
* * *
54183716 ATTAAATTCGATTCCTCCTAAGAATTTTAAGCAAATTGTTGTACAAGTTTGAACCCCTCTTTTTT
66 ATTAAATTCGATTCCTCCCAAGAATTTTAAGCAAATTGCTGCACAAGTTTGAACCCCTCTTTTTT
*
54183781 CATCAATTTTGGGTAGCCAAGCAATCAATTTGAATGCTAGGTTAGAAAAATAATGAAAGTAATTC
131 CATCAATTTTGGGTAGCCAAGCAACCAATTTGAATGCTAGGTTAGAAAAATAATGAAAGTAATTC
* *
54183846 AACGGGAGATTAAAAATGGATAGAAAGCAATTGAGGTATGGGTTTCAAATTTTTTTGGTGGGTAT
196 AACGGGAGATTAAAAATGGATAGAAAGCAATTAAGGTATGGGTTTCAAATTTTTTTGGTAGGTAT
54183911 CAAATGAAAAATAAG
261 CAAATGAAAAATAAG
54183926 AAAGAGGAAATAACATAAAATAATTTGTGATATAAAATTTAGGATTACCTTAAGTCGATAGAGAA
1 AAAGAGGAAATAACATAAAATAATTTGTGATATAAAATTTAGGATTACCTTAAGTCGATAGAGAA
*
54183991 ATTAAATTCGATTCCTCCCAAGAATTTTAAGTAAATTGCTGCACAAGTTTGAACCCCTCTTTTTT
66 ATTAAATTCGATTCCTCCCAAGAATTTTAAGCAAATTGCTGCACAAGTTTGAACCCCTC--TTTT
*
54184056 TTTATCAATTTTGGGTAGCCAAGCAACCAATTTGAATGCTAGGTTAGAAAAATAATGAAAGTAAT
129 TTCATCAATTTTGGGTAGCCAAGCAACCAATTTGAATGCTAGGTTAGAAAAATAATGAAAGTAAT
*
54184121 TCAACGGGGGATTAGAAAAT-GATAGAAAGCAATTAAGGTATGGGTTTCGAAA-TTTTTTGGTAG
194 TCAACGGGAGATTA-AAAATGGATAGAAAGCAATTAAGGTATGGGTTTC-AAATTTTTTTGGTAG
54184184 GTATCAAATGAAAAATAAG
257 GTATCAAATGAAAAATAAG
*
54184203 AATGAGG
1 AAAGAGG
54184210 TGGGTTTAGA
Statistics
Matches: 270, Mismatches: 10, Indels: 6
0.94 0.03 0.02
Matches are distributed among these distances:
275 120 0.44
277 142 0.53
278 8 0.03
ACGTcount: A:0.40, C:0.10, G:0.19, T:0.31
Consensus pattern (275 bp):
AAAGAGGAAATAACATAAAATAATTTGTGATATAAAATTTAGGATTACCTTAAGTCGATAGAGAA
ATTAAATTCGATTCCTCCCAAGAATTTTAAGCAAATTGCTGCACAAGTTTGAACCCCTCTTTTTT
CATCAATTTTGGGTAGCCAAGCAACCAATTTGAATGCTAGGTTAGAAAAATAATGAAAGTAATTC
AACGGGAGATTAAAAATGGATAGAAAGCAATTAAGGTATGGGTTTCAAATTTTTTTGGTAGGTAT
CAAATGAAAAATAAG
Found at i:54184452 original size:20 final size:20
Alignment explanation
Indices: 54184429--54184468 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
54184419 AATTTAAAGT
54184429 ACATTAAAACTTTATCTTTA
1 ACATTAAAACTTTATCTTTA
54184449 ACATTAAAACTTTATCTTTA
1 ACATTAAAACTTTATCTTTA
54184469 TCATGATGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.15, G:0.00, T:0.45
Consensus pattern (20 bp):
ACATTAAAACTTTATCTTTA
Found at i:54189930 original size:58 final size:57
Alignment explanation
Indices: 54189835--54189947 Score: 217
Period size: 58 Copynumber: 2.0 Consensus size: 57
54189825 AGGGGAGTAT
54189835 GTTAGCATAATAGTGAAAAAAAATACAAGTCATAATATATAGAATTGACTTGTAAAG
1 GTTAGCATAATAGTGAAAAAAAATACAAGTCATAATATATAGAATTGACTTGTAAAG
54189892 GTTAGCATAATAGTGAAAAAAAAATACAAGTCATAATATATAGAATTGACTTGTAA
1 GTTAGCATAATAGTG-AAAAAAAATACAAGTCATAATATATAGAATTGACTTGTAA
54189948 CAAGAATGTT
Statistics
Matches: 55, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
57 15 0.27
58 40 0.73
ACGTcount: A:0.50, C:0.07, G:0.15, T:0.28
Consensus pattern (57 bp):
GTTAGCATAATAGTGAAAAAAAATACAAGTCATAATATATAGAATTGACTTGTAAAG
Found at i:54197735 original size:50 final size:50
Alignment explanation
Indices: 54197680--54197782 Score: 188
Period size: 50 Copynumber: 2.1 Consensus size: 50
54197670 TTAAAAGAAA
* *
54197680 AAAGAAAATATCCATAGATATTCAAATGAGTACGGTGTATTTTGCAATTC
1 AAAGAAAATATCCATAGATATTCAAACGAGTACGGTGTATTTTGAAATTC
54197730 AAAGAAAATATCCATAGATATTCAAACGAGTACGGTGTATTTTGAAATTC
1 AAAGAAAATATCCATAGATATTCAAACGAGTACGGTGTATTTTGAAATTC
54197780 AAA
1 AAA
54197783 TGATAACAAC
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.43, C:0.12, G:0.16, T:0.30
Consensus pattern (50 bp):
AAAGAAAATATCCATAGATATTCAAACGAGTACGGTGTATTTTGAAATTC
Found at i:54208522 original size:13 final size:13
Alignment explanation
Indices: 54208504--54208563 Score: 54
Period size: 13 Copynumber: 4.7 Consensus size: 13
54208494 AAATAATTCA
54208504 AAATTTAAAAATT
1 AAATTTAAAAATT
*
54208517 AAATTT--AAACT
1 AAATTTAAAAATT
*
54208528 AGAATTT-AAATTT
1 A-AATTTAAAAATT
*
54208541 AAAATTTAAAAATC
1 -AAATTTAAAAATT
54208555 AAATTTAAA
1 AAATTTAAA
54208564 CTAGAATTTA
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
11 5 0.13
12 5 0.13
13 23 0.61
14 5 0.13
ACGTcount: A:0.58, C:0.03, G:0.02, T:0.37
Consensus pattern (13 bp):
AAATTTAAAAATT
Found at i:54208535 original size:12 final size:12
Alignment explanation
Indices: 54208518--54208579 Score: 63
Period size: 12 Copynumber: 5.0 Consensus size: 12
54208508 TTAAAAATTA
54208518 AATTTAAACTAG
1 AATTTAAACTAG
* *
54208530 AATTTAAATTTAA
1 AATTTAAA-CTAG
*
54208543 AATTTAAAAATCA-
1 AATTT-AAACT-AG
54208556 AATTTAAACTAG
1 AATTTAAACTAG
54208568 AATTTAAACTAG
1 AATTTAAACTAG
54208580 TTACAGAGTT
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
11 1 0.02
12 24 0.57
13 13 0.31
14 4 0.10
ACGTcount: A:0.53, C:0.06, G:0.05, T:0.35
Consensus pattern (12 bp):
AATTTAAACTAG
Found at i:54208546 original size:38 final size:38
Alignment explanation
Indices: 54208498--54208575 Score: 138
Period size: 38 Copynumber: 2.1 Consensus size: 38
54208488 ATCACTAAAT
*
54208498 AATTCAAAATTTAAAAATTAAATTTAAACTAGAATTTA
1 AATTCAAAATTTAAAAATCAAATTTAAACTAGAATTTA
*
54208536 AATTTAAAATTTAAAAATCAAATTTAAACTAGAATTTA
1 AATTCAAAATTTAAAAATCAAATTTAAACTAGAATTTA
54208574 AA
1 AA
54208576 CTAGTTACAG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.56, C:0.05, G:0.03, T:0.36
Consensus pattern (38 bp):
AATTCAAAATTTAAAAATCAAATTTAAACTAGAATTTA
Found at i:54209146 original size:23 final size:23
Alignment explanation
Indices: 54209120--54209183 Score: 92
Period size: 23 Copynumber: 2.7 Consensus size: 23
54209110 TTCATTTAAT
*
54209120 TTAATTGGACATGTTCATGAACA
1 TTAATTGAACATGTTCATGAACA
*
54209143 TTAAATGAACATGTTCATGAACA
1 TTAATTGAACATGTTCATGAACA
*
54209166 TATAATTGAACATATTCA
1 T-TAATTGAACATGTTCA
54209184 CAATGTTAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
23 22 0.61
24 14 0.39
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.34
Consensus pattern (23 bp):
TTAATTGAACATGTTCATGAACA
Found at i:54209162 original size:12 final size:12
Alignment explanation
Indices: 54209128--54209166 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
54209118 ATTTAATTGG
54209128 ACATGTTCATGA
1 ACATGTTCATGA
**
54209140 ACAT-TAAATGA
1 ACATGTTCATGA
54209151 ACATGTTCATGA
1 ACATGTTCATGA
54209163 ACAT
1 ACAT
54209167 ATAATTGAAC
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
11 9 0.41
12 13 0.59
ACGTcount: A:0.41, C:0.15, G:0.13, T:0.31
Consensus pattern (12 bp):
ACATGTTCATGA
Found at i:54210791 original size:22 final size:22
Alignment explanation
Indices: 54210763--54210804 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
54210753 TGAATAAACC
* *
54210763 AAATAAACTTTATTTCTGTAGA
1 AAATAAACTTAATATCTGTAGA
54210785 AAATAAACTTAATATCTGTA
1 AAATAAACTTAATATCTGTA
54210805 AATTGAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.45, C:0.10, G:0.07, T:0.38
Consensus pattern (22 bp):
AAATAAACTTAATATCTGTAGA
Found at i:54219969 original size:25 final size:25
Alignment explanation
Indices: 54219939--54219987 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
54219929 TCATGGACTC
* *
54219939 AGTTTACCTTTTTGACTAAATCTCA
1 AGTTTACCTTTTCGACCAAATCTCA
54219964 AGTTTACCTTTTCGACCAAATCTC
1 AGTTTACCTTTTCGACCAAATCTC
54219988 GATACCTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.27, C:0.24, G:0.08, T:0.41
Consensus pattern (25 bp):
AGTTTACCTTTTCGACCAAATCTCA
Found at i:54230261 original size:13 final size:13
Alignment explanation
Indices: 54230243--54230270 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
54230233 GCAATAGAAG
54230243 ATGAATTAGCTGA
1 ATGAATTAGCTGA
54230256 ATGAATTAGCTGA
1 ATGAATTAGCTGA
54230269 AT
1 AT
54230271 ATAGAACAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.07, G:0.21, T:0.32
Consensus pattern (13 bp):
ATGAATTAGCTGA
Found at i:54232130 original size:98 final size:98
Alignment explanation
Indices: 54231961--54232158 Score: 369
Period size: 98 Copynumber: 2.0 Consensus size: 98
54231951 AAAGATATCT
54231961 TATTGAATAATGATTATAAACATATATTCACACAAACTATAATCATGCATTAGTCCTCAAAATCA
1 TATTGAATAATGATTATAAACATATATTCACACAAACTATAATCATGCATTAGTCCTCAAAATCA
54232026 TTGATATGCATATAATATAAATACACACAATTA
66 TTGATATGCATATAATATAAATACACACAATTA
* *
54232059 TATTGAATAATGGTTATAAGCATATATTCACACAAACTATAATCATGCATTAGTCCTCAAAATCA
1 TATTGAATAATGATTATAAACATATATTCACACAAACTATAATCATGCATTAGTCCTCAAAATCA
*
54232124 TTGATATGCATATAATATATATACACACAATTA
66 TTGATATGCATATAATATAAATACACACAATTA
54232157 TA
1 TA
54232159 ATAATAGAAA
Statistics
Matches: 97, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
98 97 1.00
ACGTcount: A:0.44, C:0.15, G:0.07, T:0.33
Consensus pattern (98 bp):
TATTGAATAATGATTATAAACATATATTCACACAAACTATAATCATGCATTAGTCCTCAAAATCA
TTGATATGCATATAATATAAATACACACAATTA
Found at i:54232812 original size:2 final size:2
Alignment explanation
Indices: 54232805--54232843 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
54232795 GCAAAGCCTT
* *
54232805 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
54232844 GCGTACTGCA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (2 bp):
TA
Found at i:54234811 original size:29 final size:28
Alignment explanation
Indices: 54234751--54234852 Score: 141
Period size: 29 Copynumber: 3.6 Consensus size: 28
54234741 GTTGAGAGAT
* *
54234751 TGGCACTGAGTGTACGAGTTGAAATGCA
1 TGGCACTAAGTGTGCGAGTTGAAATGCA
54234779 TGGCACTAAGTGTGCGAGCTTGAAATGCA
1 TGGCACTAAGTGTGCGAG-TTGAAATGCA
* **
54234808 TGGCACTAAGTGTGCGAGTTTAAAGTATA
1 TGGCACTAAGTGTGCGAGTTGAAA-TGCA
54234837 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
54234853 CGGCTGATTA
Statistics
Matches: 67, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
28 21 0.31
29 46 0.69
ACGTcount: A:0.27, C:0.15, G:0.31, T:0.26
Consensus pattern (28 bp):
TGGCACTAAGTGTGCGAGTTGAAATGCA
Found at i:54236719 original size:31 final size:31
Alignment explanation
Indices: 54236679--54236744 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
54236669 AACCCTTCCT
*
54236679 GCATTAAATCCAACCAAAAACAACAAATATA
1 GCATGAAATCCAACCAAAAACAACAAATATA
* * *
54236710 GCATGAAATCCAACCAAAAAGAGCAAATGTA
1 GCATGAAATCCAACCAAAAACAACAAATATA
54236741 GCAT
1 GCAT
54236745 AAAAAATACA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.53, C:0.21, G:0.11, T:0.15
Consensus pattern (31 bp):
GCATGAAATCCAACCAAAAACAACAAATATA
Found at i:54237478 original size:13 final size:14
Alignment explanation
Indices: 54237452--54237480 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
54237442 ACTAACCACG
54237452 AATTAAACCATTAT
1 AATTAAACCATTAT
54237466 AATTAAA-CATTAT
1 AATTAAACCATTAT
54237479 AA
1 AA
54237481 ATATTTGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.34
Consensus pattern (14 bp):
AATTAAACCATTAT
Found at i:54242558 original size:9 final size:9
Alignment explanation
Indices: 54242540--54242957 Score: 132
Period size: 9 Copynumber: 45.7 Consensus size: 9
54242530 TAAGTATAAT
54242540 TAAGTTATG
1 TAAGTTATG
*
54242549 TAAGTCATG
1 TAAGTTATG
54242558 T-A-TTATG
1 TAAGTTATG
54242565 TAAGTTATG
1 TAAGTTATG
*
54242574 TAAATTATG
1 TAAGTTATG
54242583 TAAGTTATG
1 TAAGTTATG
* *
54242592 -AATTTTGATCTT
1 TAA-GTT-A--TG
*
54242604 TAAATTATG
1 TAAGTTATG
54242613 TAAGTTATG
1 TAAGTTATG
54242622 T-A-TTATG
1 TAAGTTATG
54242629 TAAGTTATG
1 TAAGTTATG
* * *
54242638 AAATTTGATCTT
1 TAAGTT-A--TG
*
54242650 TAAATTATTATG
1 T-AA--GTTATG
54242662 TAAGTTATG
1 TAAGTTATG
*
54242671 TAAATTATG
1 TAAGTTATG
*
54242680 TAACTTATG
1 TAAGTTATG
* *
54242689 AAATTTGATGG
1 TAAGTT-AT-G
*
54242700 ATTAAATTATG
1 --TAAGTTATG
54242711 TAAGTTATG
1 TAAGTTATG
*
54242720 -AAATT-TG
1 TAAGTTATG
* **
54242727 -AACTTTAAA
1 TAA-GTTATG
*
54242736 TTA-TTATG
1 TAAGTTATG
54242744 TAAGTTATG
1 TAAGTTATG
*
54242753 TAAATTATG
1 TAAGTTATG
*
54242762 TAACTTATG
1 TAAGTTATG
* * * *
54242771 AAATTTGGTCTT
1 TAA---GTTATG
*
54242783 TAAATTATG
1 TAAGTTATG
54242792 TAAGTTATG
1 TAAGTTATG
*
54242801 T-A-TCATG
1 TAAGTTATG
54242808 TAAGTTATG
1 TAAGTTATG
* * *
54242817 AAATTTGATCTT
1 TAAGTT-A--TG
*
54242829 TAAATTATG
1 TAAGTTATG
*
54242838 TAAGTCATG
1 TAAGTTATG
54242847 T-A-TTATG
1 TAAGTTATG
54242854 TAAGTTATG
1 TAAGTTATG
54242863 T-A-TTATG
1 TAAGTTATG
*
54242870 TAAGTTAAG
1 TAAGTTATG
*
54242879 TAAATTATG
1 TAAGTTATG
54242888 TAAGTTATG
1 TAAGTTATG
* * *
54242897 AAATTTGAACTT
1 TAAGTT--A-TG
*
54242909 TAAATTATG
1 TAAGTTATG
54242918 TAAGTTATG
1 TAAGTTATG
54242927 T-A-TTATG
1 TAAGTTATG
*
54242934 TAAATTATG
1 TAAGTTATG
*
54242943 TAAATTATG
1 TAAGTTATG
*
54242952 TGAGTT
1 TAAGTT
54242958 GCTGGTGAAC
Statistics
Matches: 301, Mismatches: 68, Indels: 80
0.67 0.15 0.18
Matches are distributed among these distances:
7 37 0.12
8 25 0.08
9 192 0.64
10 7 0.02
11 7 0.02
12 22 0.07
13 8 0.03
14 1 0.00
15 2 0.01
ACGTcount: A:0.36, C:0.03, G:0.16, T:0.46
Consensus pattern (9 bp):
TAAGTTATG
Found at i:54242565 original size:16 final size:16
Alignment explanation
Indices: 54242544--54242944 Score: 135
Period size: 16 Copynumber: 25.0 Consensus size: 16
54242534 TATAATTAAG
*
54242544 TTATGTAAGTCATGTA
1 TTATGTAAGTTATGTA
54242560 TTATGTAAGTTATGTAAA
1 TTATGTAAGTTATGT--A
*
54242578 TTATGTAAGTTATGAA
1 TTATGTAAGTTATGTA
* ** **
54242594 TTTTG-ATCTT-TAAA
1 TTATGTAAGTTATGTA
54242608 TTATGTAAGTTATGTA
1 TTATGTAAGTTATGTA
*
54242624 TTATGTAAGTTATGAAA
1 TTATGTAAGTTATG-TA
**
54242641 TT-TG-ATCTTTAAAT-TA
1 TTATGTA-AGTT--ATGTA
54242657 TTATGTAAGTTATGTAAA
1 TTATGTAAGTTATGT--A
* *
54242675 TTATGTAACTTATGAAA
1 TTATGTAAGTTATG-TA
* *
54242692 TT-TG-ATGGATTA--AA
1 TTATGTA-AG-TTATGTA
*
54242706 TTATGTAAGTTATGAAA
1 TTATGTAAGTTATG-TA
*
54242723 TT-TG-AACTTTAAAT-TA
1 TTATGTAA-GTT--ATGTA
54242739 TTATGTAAGTTATGTAAA
1 TTATGTAAGTTATGT--A
* *
54242757 TTATGTAACTTATGAAA
1 TTATGTAAGTTATG-TA
* **
54242774 TT-TG---GTCTTTAAA
1 TTATGTAAGT-TATGTA
54242787 TTATGTAAGTTATGTA
1 TTATGTAAGTTATGTA
* *
54242803 TCATGTAAGTTATGAAA
1 TTATGTAAGTTATG-TA
** **
54242820 TT-TG-ATCTT-TAAA
1 TTATGTAAGTTATGTA
*
54242833 TTATGTAAGTCATGTA
1 TTATGTAAGTTATGTA
54242849 TTATGTAAGTTATGTA
1 TTATGTAAGTTATGTA
*
54242865 TTATGTAAGTTAAGTAAA
1 TTATGTAAGTTATGT--A
*
54242883 TTATGTAAGTTATGAAA
1 TTATGTAAGTTATG-TA
* **
54242900 TT-TG-AACTT-TAAA
1 TTATGTAAGTTATGTA
54242913 TTATGTAAGTTATGTA
1 TTATGTAAGTTATGTA
*
54242929 TTATGTAAATTATGTA
1 TTATGTAAGTTATGTA
54242945 AATTATGTGA
Statistics
Matches: 286, Mismatches: 54, Indels: 90
0.67 0.13 0.21
Matches are distributed among these distances:
13 13 0.05
14 24 0.08
15 30 0.10
16 124 0.43
17 31 0.11
18 64 0.22
ACGTcount: A:0.36, C:0.03, G:0.15, T:0.46
Consensus pattern (16 bp):
TTATGTAAGTTATGTA
Found at i:54242639 original size:46 final size:46
Alignment explanation
Indices: 54242559--54242862 Score: 328
Period size: 46 Copynumber: 6.7 Consensus size: 46
54242549 TAAGTCATGT
*
54242559 ATTATGTAAGTTATGTAAATTATGTAAGTTATGAATTTTGATCTTTAA
1 ATTATGTAAGTTATGT--ATTATGTAAGTTATGAAATTTGATCTTTAA
54242607 ATTATGTAAGTTATGTATTATGTAAGTTATGAAATTTGATCTTTAAA
1 ATTATGTAAGTTATGTATTATGTAAGTTATGAAATTTGATCTTT-AA
* **
54242654 TTATTATGTAAGTTATGTAAATTATGTAACTTATGAAATTTGATGGATTAA
1 --ATTATGTAAGTTATGT--ATTATGTAAGTTATGAAATTTGAT-CTTTAA
* **
54242705 ATTATGTAAGTTATG----A---AA-TT-TGAACTTT-A-AATT-A
1 ATTATGTAAGTTATGTATTATGTAAGTTATGAAATTTGATCTTTAA
* *
54242739 -TTATGTAAGTTATGTAAATTATGTAACTTATGAAATTTGGTCTTTAA
1 ATTATGTAAGTTATGT--ATTATGTAAGTTATGAAATTTGATCTTTAA
*
54242786 ATTATGTAAGTTATGTATCATGTAAGTTATGAAATTTGATCTTTAA
1 ATTATGTAAGTTATGTATTATGTAAGTTATGAAATTTGATCTTTAA
*
54242832 ATTATGTAAGTCATGTATTATGTAAGTTATG
1 ATTATGTAAGTTATGTATTATGTAAGTTATG
54242863 TATTATGTAA
Statistics
Matches: 220, Mismatches: 15, Indels: 44
0.79 0.05 0.16
Matches are distributed among these distances:
33 14 0.06
34 1 0.00
35 3 0.01
37 1 0.00
38 7 0.03
39 3 0.01
40 2 0.01
42 2 0.01
43 3 0.01
44 7 0.03
46 85 0.39
47 3 0.01
48 31 0.14
49 31 0.14
51 25 0.11
52 2 0.01
ACGTcount: A:0.36, C:0.03, G:0.15, T:0.46
Consensus pattern (46 bp):
ATTATGTAAGTTATGTATTATGTAAGTTATGAAATTTGATCTTTAA
Found at i:54242725 original size:82 final size:81
Alignment explanation
Indices: 54242623--54242800 Score: 311
Period size: 82 Copynumber: 2.2 Consensus size: 81
54242613 TAAGTTATGT
*
54242623 ATTATGTAAGTTATGAAATTTGATCTTTAAATTATTATGTAAGTTATGTAAATTATGTAACTTAT
1 ATTATGTAAGTTATGAAATTTGAACTTTAAATTATTATGTAAGTTATGTAAATTATGTAACTTAT
*
54242688 GAAATTTGATGGATTAA
66 GAAATTTGAT-CATTAA
54242705 ATTATGTAAGTTATGAAATTTGAACTTTAAATTATTATGTAAGTTATGTAAATTATGTAACTTAT
1 ATTATGTAAGTTATGAAATTTGAACTTTAAATTATTATGTAAGTTATGTAAATTATGTAACTTAT
* *
54242770 GAAATTTGGTCTTTAA
66 GAAATTTGATCATTAA
54242786 ATTATGTAAGTTATG
1 ATTATGTAAGTTATG
54242801 TATCATGTAA
Statistics
Matches: 92, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
81 19 0.21
82 73 0.79
ACGTcount: A:0.37, C:0.03, G:0.15, T:0.46
Consensus pattern (81 bp):
ATTATGTAAGTTATGAAATTTGAACTTTAAATTATTATGTAAGTTATGTAAATTATGTAACTTAT
GAAATTTGATCATTAA
Found at i:54242897 original size:80 final size:78
Alignment explanation
Indices: 54242786--54242944 Score: 255
Period size: 80 Copynumber: 2.0 Consensus size: 78
54242776 TGGTCTTTAA
* *
54242786 ATTATGTAAGTTATGTATCATGTAAGTTATGAAATTTGATCTTTAAATTATGTAAGTCATGTATT
1 ATTATGTAAGTTAAGTATCATGTAAGTTATGAAATTTGAACTTTAAATTATGTAAGTCATGTATT
*
54242851 ATGTAAGTTATGT
66 ATGTAAATTATGT
* *
54242864 ATTATGTAAGTTAAGTAAATTATGTAAGTTATGAAATTTGAACTTTAAATTATGTAAGTTATGTA
1 ATTATGTAAGTTAAGT--ATCATGTAAGTTATGAAATTTGAACTTTAAATTATGTAAGTCATGTA
54242929 TTATGTAAATTATGT
64 TTATGTAAATTATGT
54242944 A
1 A
54242945 AATTATGTGA
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
78 15 0.20
80 59 0.80
ACGTcount: A:0.36, C:0.03, G:0.16, T:0.45
Consensus pattern (78 bp):
ATTATGTAAGTTAAGTATCATGTAAGTTATGAAATTTGAACTTTAAATTATGTAAGTCATGTATT
ATGTAAATTATGT
Found at i:54242926 original size:30 final size:30
Alignment explanation
Indices: 54242671--54242842 Score: 102
Period size: 31 Copynumber: 5.5 Consensus size: 30
54242661 GTAAGTTATG
* ***
54242671 TAAATTATGTAACTTATGAAATTTGATGGAT
1 TAAATTATGTAAGTTATGAAATTTGA-ACTT
54242702 TAAATTATGTAAGTTATGAAATTTGAACTT
1 TAAATTATGTAAGTTATGAAATTTGAACTT
54242732 TAAATTATTATGTAAGTTATGTAAATTATGTAACTT
1 T-AA--ATTATGTAAGTTATG-AAATT-TG-AACTT
* *
54242768 ATGAAATT-TG---GTCT-TTAAATTATGTAAGTT
1 -T-AAATTATGTAAGT-TATGAAATT-TG-AACTT
** * *
54242798 ATGTATCATGTAAGTTATGAAATTTGATCTT
1 -TAAATTATGTAAGTTATGAAATTTGAACTT
54242829 TAAATTATGTAAGT
1 TAAATTATGTAAGT
54242843 CATGTATTAT
Statistics
Matches: 112, Mismatches: 16, Indels: 27
0.72 0.10 0.17
Matches are distributed among these distances:
29 2 0.02
30 30 0.27
31 33 0.29
32 4 0.04
33 23 0.21
34 7 0.06
35 5 0.04
36 5 0.04
37 3 0.03
ACGTcount: A:0.37, C:0.03, G:0.15, T:0.45
Consensus pattern (30 bp):
TAAATTATGTAAGTTATGAAATTTGAACTT
Found at i:54242999 original size:17 final size:17
Alignment explanation
Indices: 54242977--54243010 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
54242967 CTTGAAAAAA
54242977 ATATATTACTTTTGAAT
1 ATATATTACTTTTGAAT
54242994 ATATATTACTTTTGAAT
1 ATATATTACTTTTGAAT
54243011 TAGAAACATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.06, G:0.06, T:0.53
Consensus pattern (17 bp):
ATATATTACTTTTGAAT
Found at i:54244471 original size:14 final size:14
Alignment explanation
Indices: 54244449--54244482 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
54244439 TTAGTATACA
54244449 ATATAATTTTACTTC
1 ATAT-ATTTTACTTC
54244464 ATATATTTTACTTC
1 ATATATTTTACTTC
54244478 ATATA
1 ATATA
54244483 ATTATTATAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 15 0.79
15 4 0.21
ACGTcount: A:0.35, C:0.12, G:0.00, T:0.53
Consensus pattern (14 bp):
ATATATTTTACTTC
Found at i:54245484 original size:27 final size:27
Alignment explanation
Indices: 54245449--54245524 Score: 82
Period size: 27 Copynumber: 2.8 Consensus size: 27
54245439 ATATTTTAGT
*
54245449 TTACCAAATTACTGAAATACCCTCGAC
1 TTACAAAATTACTGAAATACCCTCGAC
** * *
54245476 TTGTAAAATTAC-CAAAGTACCCTCGAT
1 TTACAAAATTACTGAAA-TACCCTCGAC
*
54245503 TTACAAAATTATTGAAATACCC
1 TTACAAAATTACTGAAATACCC
54245525 CTGTAGGGTA
Statistics
Matches: 38, Mismatches: 9, Indels: 4
0.75 0.18 0.08
Matches are distributed among these distances:
26 3 0.08
27 32 0.84
28 3 0.08
ACGTcount: A:0.39, C:0.24, G:0.08, T:0.29
Consensus pattern (27 bp):
TTACAAAATTACTGAAATACCCTCGAC
Found at i:54245539 original size:27 final size:27
Alignment explanation
Indices: 54245516--54245650 Score: 180
Period size: 27 Copynumber: 5.0 Consensus size: 27
54245506 CAAAATTATT
*
54245516 GAAATACCCCTGTAGGGTAGAATTACT
1 GAAATACCCCTGTAGGGTAGAATTACC
*
54245543 GAAATACCCCTATAGGGTAGAATTACC
1 GAAATACCCCTGTAGGGTAGAATTACC
* *
54245570 GAAATACCCCTGTAGGGTAAAAATACC
1 GAAATACCCCTGTAGGGTAGAATTACC
* *
54245597 GAAATACCCCTATAGGGTAGAATTATC
1 GAAATACCCCTGTAGGGTAGAATTACC
* * * *
54245624 GAGATACCCTTGTGGGGTAAAATTACC
1 GAAATACCCCTGTAGGGTAGAATTACC
54245651 ATTTTGCCCC
Statistics
Matches: 93, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 93 1.00
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.24
Consensus pattern (27 bp):
GAAATACCCCTGTAGGGTAGAATTACC
Found at i:54245567 original size:54 final size:54
Alignment explanation
Indices: 54245509--54245650 Score: 212
Period size: 54 Copynumber: 2.6 Consensus size: 54
54245499 CGATTTACAA
* * *
54245509 AATTATTGAAATACCCCTGTAGGGTAGAATTACTGAAATACCCCTATAGGGTAG
1 AATTATCGAAATACCCCTGTAGGGTAAAATTACCGAAATACCCCTATAGGGTAG
* *
54245563 AATTACCGAAATACCCCTGTAGGGTAAAAATACCGAAATACCCCTATAGGGTAG
1 AATTATCGAAATACCCCTGTAGGGTAAAATTACCGAAATACCCCTATAGGGTAG
* * *
54245617 AATTATCGAGATACCCTTGTGGGGTAAAATTACC
1 AATTATCGAAATACCCCTGTAGGGTAAAATTACC
54245651 ATTTTGCCCC
Statistics
Matches: 78, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 78 1.00
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.25
Consensus pattern (54 bp):
AATTATCGAAATACCCCTGTAGGGTAAAATTACCGAAATACCCCTATAGGGTAG
Found at i:54246010 original size:26 final size:27
Alignment explanation
Indices: 54245974--54246040 Score: 82
Period size: 27 Copynumber: 2.5 Consensus size: 27
54245964 ACCGATCGAT
*
54245974 GGCTGAGTGCCAATCAT-GTTACCGAA
1 GGCTGTGTGCCAATCATAGTTACCGAA
* * * *
54246000 GGCTGTGTGCCAAACATATTTGCCTAA
1 GGCTGTGTGCCAATCATAGTTACCGAA
54246027 GGCTGTGTGCCAAT
1 GGCTGTGTGCCAAT
54246041 ATATGATTAT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
26 15 0.44
27 19 0.56
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (27 bp):
GGCTGTGTGCCAATCATAGTTACCGAA
Found at i:54246076 original size:32 final size:32
Alignment explanation
Indices: 54246039--54246104 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
54246029 CTGTGTGCCA
54246039 ATATATGATTATTGATGACTCGTGTCTATCAT
1 ATATATGATTATTGATGACTCGTGTCTATCAT
*
54246071 ATATATGATTATTGATGACTCGTGTTTATCAT
1 ATATATGATTATTGATGACTCGTGTCTATCAT
54246103 AT
1 AT
54246105 TTACTCAAGG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.29, C:0.11, G:0.15, T:0.45
Consensus pattern (32 bp):
ATATATGATTATTGATGACTCGTGTCTATCAT
Found at i:54246247 original size:22 final size:22
Alignment explanation
Indices: 54246195--54246257 Score: 76
Period size: 22 Copynumber: 2.9 Consensus size: 22
54246185 GCCAATTATT
*
54246195 CTGATTATGGCTTTGCGCCAAC
1 CTGATTATGGCTTTGTGCCAAC
*
54246217 CT-ACGTATGGCTTTGTGCCAAC
1 CTGA-TTATGGCTTTGTGCCAAC
54246239 CTGATTATGG-TTGTGTGCC
1 CTGATTATGGCTT-TGTGCC
54246258 GTTATTGTGG
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
21 3 0.09
22 31 0.89
23 1 0.03
ACGTcount: A:0.16, C:0.24, G:0.25, T:0.35
Consensus pattern (22 bp):
CTGATTATGGCTTTGTGCCAAC
Found at i:54246354 original size:27 final size:27
Alignment explanation
Indices: 54246324--54246404 Score: 103
Period size: 27 Copynumber: 3.0 Consensus size: 27
54246314 ATTCTGTTAA
* *
54246324 GTGGCTTTGCCACATTATCTGATTCTG
1 GTGGCTCTGCCACAATATCTGATTCTG
54246351 GTGGCTCTGCCACAATATCTG-TATCTG
1 GTGGCTCTGCCACAATATCTGAT-TCTG
* *
54246378 GTGACTCTGTCACAATATCT-ATTCTG
1 GTGGCTCTGCCACAATATCTGATTCTG
54246404 G
1 G
54246405 CAGCCATGCT
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
26 6 0.12
27 42 0.88
ACGTcount: A:0.19, C:0.23, G:0.21, T:0.37
Consensus pattern (27 bp):
GTGGCTCTGCCACAATATCTGATTCTG
Found at i:54246531 original size:6 final size:6
Alignment explanation
Indices: 54246522--54246626 Score: 65
Period size: 6 Copynumber: 16.8 Consensus size: 6
54246512 TTGCATTCAC
* **
54246522 ATTCTG ATTCTG ATTCTG -TTACCTG ATAT-TG ATTCTG ATTCTG -TCACCAA
1 ATTCTG ATTCTG ATTCTG ATT--CTG AT-TCTG ATTCTG ATTCTG AT--TCTG
* *
54246572 ATTCTG ATTCTG ATTTTGG ATTCTG ATTCTG -TCACTTG ATTCTG ATTCTG
1 ATTCTG ATTCTG ATTCT-G ATTCTG ATTCTG AT-TC-TG ATTCTG ATTCTG
54246622 ATTCT
1 ATTCT
54246627 CATTTTAATT
Statistics
Matches: 77, Mismatches: 10, Indels: 24
0.69 0.09 0.22
Matches are distributed among these distances:
5 5 0.06
6 56 0.73
7 12 0.16
8 3 0.04
9 1 0.01
ACGTcount: A:0.19, C:0.18, G:0.15, T:0.48
Consensus pattern (6 bp):
ATTCTG
Found at i:54246579 original size:25 final size:25
Alignment explanation
Indices: 54246522--54246586 Score: 87
Period size: 25 Copynumber: 2.6 Consensus size: 25
54246512 TTGCATTCAC
* **
54246522 ATTCTGATTCTGATTCTGTTACCTG
1 ATTCTGATTCTGATTCTGTCACCAA
54246547 ATAT-TGATTCTGATTCTGTCACCAA
1 AT-TCTGATTCTGATTCTGTCACCAA
54246572 ATTCTGATTCTGATT
1 ATTCTGATTCTGATT
54246587 TTGGATTCTG
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
24 1 0.03
25 33 0.94
26 1 0.03
ACGTcount: A:0.22, C:0.18, G:0.14, T:0.46
Consensus pattern (25 bp):
ATTCTGATTCTGATTCTGTCACCAA
Done.