Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008214.1 Hibiscus syriacus cultivar Beakdansim tig00110840_pilon, whole genome shotgun sequence
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: 2117680
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 11
Found at i:622324 original size:19 final size:18
Alignment explanation
Indices: 622300--622367 Score: 68
Period size: 18 Copynumber: 3.8 Consensus size: 18
622290 AGAAAAAGAA
622300 GAAGAAAAAATGGAAAAAG
1 GAAGAAAAAAT-GAAAAAG
*
622319 GAAGAAAAAATGAAAAAT
1 GAAGAAAAAATGAAAAAG
* *
622337 GAA-AAAAGA-GAAAAAT
1 GAAGAAAAAATGAAAAAG
* *
622353 GAAAAAAAAAAGAAA
1 GAAGAAAAAATGAAA
622368 TAAAAGGAGG
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
16 10 0.23
17 10 0.23
18 13 0.30
19 11 0.25
ACGTcount: A:0.75, C:0.00, G:0.19, T:0.06
Consensus pattern (18 bp):
GAAGAAAAAATGAAAAAG
Found at i:622349 original size:16 final size:15
Alignment explanation
Indices: 622275--622361 Score: 75
Period size: 16 Copynumber: 5.4 Consensus size: 15
622265 ATAATGATGG
*
622275 AAAAAACAAAAAGAA
1 AAAAAAGAAAAAGAA
*
622290 AGAAAAAGAAGAAGAA
1 A-AAAAAGAAAAAGAA
**
622306 AAAATGGAAAAAGGAA
1 AAAAAAGAAAAA-GAA
622322 GAAAAAATGAAAAATGAA
1 -AAAAAA-GAAAAA-GAA
*
622340 AAAAGAGAAAAATGAA
1 AAAAAAGAAAAA-GAA
622356 AAAAAA
1 AAAAAA
622362 AAGAAATAAA
Statistics
Matches: 58, Mismatches: 10, Indels: 7
0.77 0.13 0.09
Matches are distributed among these distances:
15 9 0.16
16 31 0.53
17 9 0.16
18 9 0.16
ACGTcount: A:0.77, C:0.01, G:0.17, T:0.05
Consensus pattern (15 bp):
AAAAAAGAAAAAGAA
Found at i:622368 original size:16 final size:16
Alignment explanation
Indices: 622331--622372 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
622321 AGAAAAAATG
*
622331 AAAAATGAAAAAAGAG
1 AAAAATGAAAAAAGAA
622347 AAAAATGAAAAAA-AA
1 AAAAATGAAAAAAGAA
622362 AAGAAAT-AAAA
1 AA-AAATGAAAA
622373 GGAGGGTTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 7 0.29
16 17 0.71
ACGTcount: A:0.81, C:0.00, G:0.12, T:0.07
Consensus pattern (16 bp):
AAAAATGAAAAAAGAA
Found at i:624018 original size:55 final size:55
Alignment explanation
Indices: 623724--624090 Score: 336
Period size: 51 Copynumber: 6.9 Consensus size: 55
623714 GAAGCAAACT
* * *
623724 CGTTTGTTGAAGA---TT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
1 CGTTTGTTGAAGATTGTTCGAGTCTTATACTCCCTGAAGGAATAGGGAGCAGACA
** * * * *
623775 AATTCGTTGAAGA---TT-GAGTCATATACTCTCTGAAGGAATAGGGAGCGGACA
1 CGTTTGTTGAAGATTGTTCGAGTCTTATACTCCCTGAAGGAATAGGGAGCAGACA
* * * *
623826 AGTTCGTTGAAGA---TT-GAGTCCTATACTCCCTGAAGGAATAGGGAGCGGACA
1 CGTTTGTTGAAGATTGTTCGAGTCTTATACTCCCTGAAGGAATAGGGAGCAGACA
* * * *
623877 CGTTTATTGAAGA----TCGAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACC
1 CGTTTGTTGAAGATTGTTCGAGTCTTATACTCCCTGAAGGAATAGGGAGCAGACA
* * * *
623928 CATTTTTTTGAAGATTGTTCGAGTCTTATACTCCCTGAACGAATAGGGAGCAGACT
1 C-GTTTGTTGAAGATTGTTCGAGTCTTATACTCCCTGAAGGAATAGGGAGCAGACA
* * * * *
623984 CGTTTGTTGAAGATTGTTTGAGTCTTATATTCCCTAAATGAATAGGGAGAAGACA
1 CGTTTGTTGAAGATTGTTCGAGTCTTATACTCCCTGAAGGAATAGGGAGCAGACA
** *
624039 CGTTTG-CCAAGGATTGTTCGAGTCTTATACTTCCTGAAGGAATAGGGAGCAG
1 CGTTTGTTGAA-GATTGTTCGAGTCTTATACTCCCTGAAGGAATAGGGAGCAG
624091 GCTCGTCATT
Statistics
Matches: 274, Mismatches: 35, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
50 1 0.00
51 139 0.51
52 10 0.04
54 2 0.01
55 87 0.32
56 35 0.13
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.29
Consensus pattern (55 bp):
CGTTTGTTGAAGATTGTTCGAGTCTTATACTCCCTGAAGGAATAGGGAGCAGACA
Found at i:634422 original size:27 final size:24
Alignment explanation
Indices: 634376--634432 Score: 69
Period size: 27 Copynumber: 2.2 Consensus size: 24
634366 AACTCGTCTT
*
634376 ATTTTTTATTTTTTTTAAAATTAA
1 ATTTTTTATTTTTTTTAAAAATAA
*
634400 TTTTTTTATTCTTTTTTTAAAAAATAA
1 ATTTTTTA-T-TTTTTTT-AAAAATAA
634427 ATTTTT
1 ATTTTT
634433 AAATGGACTC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 7 0.26
25 1 0.04
26 7 0.26
27 12 0.44
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.67
Consensus pattern (24 bp):
ATTTTTTATTTTTTTTAAAAATAA
Found at i:634424 original size:28 final size:24
Alignment explanation
Indices: 634377--634432 Score: 67
Period size: 28 Copynumber: 2.2 Consensus size: 24
634367 ACTCGTCTTA
*
634377 TTTTTTATTTTTTTTAAAATTAAT
1 TTTTTTATTTTTTTTAAAATAAAT
634401 TTTTTTATTCTTTTTTTAAAAAATAAAT
1 TTTTTTA-T-TTTTTTT--AAAATAAAT
634429 TTTT
1 TTTT
634433 AAATGGACTC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
24 7 0.26
25 1 0.04
26 7 0.26
28 12 0.44
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (24 bp):
TTTTTTATTTTTTTTAAAATAAAT
Found at i:635166 original size:18 final size:18
Alignment explanation
Indices: 635143--635187 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
635133 AACATTCCCA
635143 GTAATCTTATTCCCGTCG
1 GTAATCTTATTCCCGTCG
* * *
635161 GTAATCATATTTCTGTCG
1 GTAATCTTATTCCCGTCG
635179 GTAATCTTA
1 GTAATCTTA
635188 CATTCCGTGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.22, C:0.20, G:0.16, T:0.42
Consensus pattern (18 bp):
GTAATCTTATTCCCGTCG
Found at i:635579 original size:74 final size:73
Alignment explanation
Indices: 635458--635604 Score: 285
Period size: 74 Copynumber: 2.0 Consensus size: 73
635448 CCGTTTTACT
635458 TTTAATTTTATGCTAATTTCCTTCAACAACCTTATGTTGTTATTGCTTTGAAATAGAACATAACC
1 TTTAATTTTATGCTAATTTCCTTCAACAACCTTATGTTGTTATTGCTTTGAAATAGAACAT-ACC
635523 CCCCCCCCC
65 CCCCCCCCC
635532 TTTAATTTTATGCTAATTTCCTTCAACAACCTTATGTTGTTATTGCTTTGAAATAGAACATACCC
1 TTTAATTTTATGCTAATTTCCTTCAACAACCTTATGTTGTTATTGCTTTGAAATAGAACATACCC
635597 CCCCCCCC
66 CCCCCCCC
635605 AAAAAAACAC
Statistics
Matches: 73, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
73 12 0.16
74 61 0.84
ACGTcount: A:0.27, C:0.27, G:0.08, T:0.38
Consensus pattern (73 bp):
TTTAATTTTATGCTAATTTCCTTCAACAACCTTATGTTGTTATTGCTTTGAAATAGAACATACCC
CCCCCCCC
Found at i:656783 original size:44 final size:44
Alignment explanation
Indices: 656720--656810 Score: 182
Period size: 44 Copynumber: 2.1 Consensus size: 44
656710 CGAACAAACT
656720 ATGCCTCTCTTCACTCTGATTTTTAGGAAGCTTAGCTTTCTTCG
1 ATGCCTCTCTTCACTCTGATTTTTAGGAAGCTTAGCTTTCTTCG
656764 ATGCCTCTCTTCACTCTGATTTTTAGGAAGCTTAGCTTTCTTCG
1 ATGCCTCTCTTCACTCTGATTTTTAGGAAGCTTAGCTTTCTTCG
656808 ATG
1 ATG
656811 GACTGTAGCT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 47 1.00
ACGTcount: A:0.16, C:0.24, G:0.16, T:0.43
Consensus pattern (44 bp):
ATGCCTCTCTTCACTCTGATTTTTAGGAAGCTTAGCTTTCTTCG
Found at i:660276 original size:20 final size:20
Alignment explanation
Indices: 660247--660291 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
660237 TTTCACTTTT
*
660247 TTTCTCATCTATTCCTTTAA-
1 TTTCTAATCT-TTCCTTTAAC
*
660267 TTTCTAATCTTTTCTTTAAC
1 TTTCTAATCTTTCCTTTAAC
660287 TTTCT
1 TTTCT
660292 CACTAACCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.18, C:0.22, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTCTAATCTTTCCTTTAAC
Found at i:660311 original size:40 final size:40
Alignment explanation
Indices: 660267--660344 Score: 120
Period size: 40 Copynumber: 1.9 Consensus size: 40
660257 ATTCCTTTAA
** *
660267 TTTCTAATCTTTTCTTTAACTTTCTCACTAACCAAACAAG
1 TTTCTAATAATTTCTTCAACTTTCTCACTAACCAAACAAG
*
660307 TTTCTTATAATTTCTTCAACTTTCTCACTAACCAAACA
1 TTTCTAATAATTTCTTCAACTTTCTCACTAACCAAACA
660345 TACACAAAAG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.31, C:0.26, G:0.01, T:0.42
Consensus pattern (40 bp):
TTTCTAATAATTTCTTCAACTTTCTCACTAACCAAACAAG
Found at i:663837 original size:23 final size:23
Alignment explanation
Indices: 663806--663882 Score: 91
Period size: 23 Copynumber: 3.3 Consensus size: 23
663796 GTATAAATGC
* *
663806 ACCGAAGTACCATGTAGAATTGT
1 ACCGTAGTACCACGTAGAATTGT
663829 ACCGTAGTACCACGTAGAATTGT
1 ACCGTAGTACCACGTAGAATTGT
* * * * *
663852 ACCGTAGTGCCGCGTAAAAATGC
1 ACCGTAGTACCACGTAGAATTGT
663875 ACCGTAGT
1 ACCGTAGT
663883 GCCATATAAG
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 47 1.00
ACGTcount: A:0.31, C:0.22, G:0.23, T:0.23
Consensus pattern (23 bp):
ACCGTAGTACCACGTAGAATTGT
Found at i:663883 original size:23 final size:23
Alignment explanation
Indices: 663795--663886 Score: 76
Period size: 23 Copynumber: 4.0 Consensus size: 23
663785 CACCACAGCT
* * *
663795 CGTATAAATGCACCGAAGTACCA
1 CGTAAAAATGCACCGTAGTGCCA
* * * * *
663818 TGTAGAATTGTACCGTAGTACCA
1 CGTAAAAATGCACCGTAGTGCCA
* * * *
663841 CGTAGAATTGTACCGTAGTGCCG
1 CGTAAAAATGCACCGTAGTGCCA
663864 CGTAAAAATGCACCGTAGTGCCA
1 CGTAAAAATGCACCGTAGTGCCA
663887 TATAAGATTG
Statistics
Matches: 57, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 57 1.00
ACGTcount: A:0.32, C:0.23, G:0.23, T:0.23
Consensus pattern (23 bp):
CGTAAAAATGCACCGTAGTGCCA
Found at i:664645 original size:2 final size:2
Alignment explanation
Indices: 664638--664676 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
664628 ACTTATAAAC
664638 AT AT AT AT 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 AT AT AT AT A
664677 CTTCTATTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:667836 original size:23 final size:23
Alignment explanation
Indices: 667810--667857 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
667800 ATAAAGTACA
*
667810 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
667833 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
667856 AT
1 AT
667858 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:668261 original size:21 final size:22
Alignment explanation
Indices: 668236--668287 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
668226 ACACTTTACA
*
668236 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
668259 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
668282 ATATAA
1 ATATAA
668288 GGGCTACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:668272 original size:23 final size:23
Alignment explanation
Indices: 668246--668308 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
668236 ATATAACCAC
668246 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
668269 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
668292 TACCTATTACATCATAT
1 TACCTATTACATTATAT
668309 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:668785 original size:39 final size:39
Alignment explanation
Indices: 668710--668834 Score: 225
Period size: 39 Copynumber: 3.2 Consensus size: 39
668700 TCAAGTTGTA
668710 GATTTTGATTTCCTTTTGCTT-GCATCATATGAGATTTG
1 GATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTG
668748 GATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTG
1 GATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTG
* *
668787 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTG
1 GATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTG
668826 GATTTTGAT
1 GATTTTGAT
668835 GAGCATCGGA
Statistics
Matches: 84, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
38 21 0.25
39 63 0.75
ACGTcount: A:0.18, C:0.14, G:0.20, T:0.49
Consensus pattern (39 bp):
GATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTG
Found at i:669115 original size:18 final size:18
Alignment explanation
Indices: 669092--669128 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
669082 CGAAATATAT
669092 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
669110 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
669128 A
1 A
669129 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:669405 original size:25 final size:25
Alignment explanation
Indices: 669377--669427 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
669367 TTAATCCAAA
*
669377 TAATGTACCCATAACAATGTTCAAT
1 TAATGTACCCACAACAATGTTCAAT
*
669402 TAATGTACCCACAACAATGTTTAAT
1 TAATGTACCCACAACAATGTTCAAT
669427 T
1 T
669428 GATTTGTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.39, C:0.20, G:0.08, T:0.33
Consensus pattern (25 bp):
TAATGTACCCACAACAATGTTCAAT
Found at i:669720 original size:21 final size:22
Alignment explanation
Indices: 669695--669746 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
669685 ACACTTTACA
*
669695 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
669718 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
669741 ATATAA
1 ATATAA
669747 GGGCTACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:669731 original size:23 final size:23
Alignment explanation
Indices: 669705--669767 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
669695 ATATAACCAC
669705 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
669728 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
669751 TACCTATTACATCATAT
1 TACCTATTACATTATAT
669768 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:670160 original size:23 final size:23
Alignment explanation
Indices: 670134--670196 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
670124 ATATAACCAC
670134 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
670157 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
670180 TACCTATTACATCATAT
1 TACCTATTACATTATAT
670197 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:670263 original size:429 final size:431
Alignment explanation
Indices: 669456--670295 Score: 1614
Period size: 429 Copynumber: 2.0 Consensus size: 431
669446 CAATTTGAAT
669456 TATTGATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAAT
1 TATTGATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAAT
* *
669521 ATTTAGAATTTTTAATTTAATAATAATATATATCGTAACGTAAAAAATAAATCATTATACGCCTA
66 ATTTAGAATTTTTAATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTA
669586 TAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGT
131 TAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGT
669651 GAAAAAAGTATGGACACTTTTATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACA
196 GAAAAAAGTATGGACACTTTTATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACA
669716 TTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTAT
261 TTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTAT
669781 ATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTATGTAATTTATG
326 ATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTATGTAATTTATG
669846 TTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAA
391 TTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAA
* *
669887 TATTGA-TTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATT
1 TATTGATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAAT
669951 ATTTAGAATTTTTAATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTA
66 ATTTAGAATTTTTAATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTA
670016 TAATTACTAAATTAATATCTTAAAACTCACTC-AAAGATAACCTTAAATTAATGTTTTCCACAGT
131 TAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGT
670080 GAAAAAAAGTATGGACACTTTTAT-AAAAGGATAGACACTTTACAATATAACCACTACCTATTAC
196 G-AAAAAAGTATGGACACTTTTATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTAC
670144 ATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTA
260 ATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTA
670209 TATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTATGTAATTTAT
325 TATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTATGTAATTTAT
670274 GTTTCAATTTTTTTAACAGTGT
390 GTTTCAATTTTTTTAACAGTGT
670296 ACTGCGAATT
Statistics
Matches: 404, Mismatches: 4, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
429 225 0.56
430 173 0.43
431 6 0.01
ACGTcount: A:0.39, C:0.13, G:0.08, T:0.40
Consensus pattern (431 bp):
TATTGATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAAT
ATTTAGAATTTTTAATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTA
TAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGT
GAAAAAAGTATGGACACTTTTATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACA
TTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTAT
ATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTATGTAATTTATG
TTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAA
Found at i:672527 original size:17 final size:17
Alignment explanation
Indices: 672505--672547 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 17
672495 ATATATCCGG
672505 TATCATTTTACCGGTTT
1 TATCATTTTACCGGTTT
672522 TATCATTTTTTTACCGGTTT
1 TATCA---TTTTACCGGTTT
672542 TATCAT
1 TATCAT
672548 ATTTTTACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
17 6 0.26
20 17 0.74
ACGTcount: A:0.19, C:0.16, G:0.09, T:0.56
Consensus pattern (17 bp):
TATCATTTTACCGGTTT
Found at i:672565 original size:20 final size:20
Alignment explanation
Indices: 672510--672556 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
672500 TCCGGTATCA
*
672510 TTTTACCGGTTTTATCATTT
1 TTTTACCGGTTTTATCATAT
672530 TTTTACCGGTTTTATCATAT
1 TTTTACCGGTTTTATCATAT
672550 TTTTACC
1 TTTTACC
672557 TGTTATATCG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.17, C:0.17, G:0.09, T:0.57
Consensus pattern (20 bp):
TTTTACCGGTTTTATCATAT
Found at i:672704 original size:20 final size:20
Alignment explanation
Indices: 672678--672723 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
672668 CACTTTTAAA
672678 TTTACCGGTTTTATCAT-TT
1 TTTACCGGTTTTATCATATT
672697 TGTTACCGGTTTTATCATATT
1 T-TTACCGGTTTTATCATATT
672718 TTTACC
1 TTTACC
672724 TGGTATATCG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.54
Consensus pattern (20 bp):
TTTACCGGTTTTATCATATT
Found at i:674085 original size:20 final size:19
Alignment explanation
Indices: 674057--674100 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
674047 AGAAAACACT
*
674057 TTGAAAGTGAATTGTGAATG
1 TTGAAAGTGAATTGAGAA-G
* *
674077 TTGAGAGTGAGTTGAGAAG
1 TTGAAAGTGAATTGAGAAG
674096 TTGAA
1 TTGAA
674101 TATAGCCCTC
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.34, C:0.00, G:0.34, T:0.32
Consensus pattern (19 bp):
TTGAAAGTGAATTGAGAAG
Found at i:674295 original size:22 final size:22
Alignment explanation
Indices: 674247--674300 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
674237 TTCAGCTGTT
* *
674247 ATAACTCCTGAAATTATATCAT
1 ATAACTCCTGAAATTAAATCAA
* * *
674269 GTAACCCCTGGAATTAAATCAA
1 ATAACTCCTGAAATTAAATCAA
674291 ATAACTCCTG
1 ATAACTCCTG
674301 TAACTCCTGA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.39, C:0.22, G:0.09, T:0.30
Consensus pattern (22 bp):
ATAACTCCTGAAATTAAATCAA
Found at i:676994 original size:12 final size:12
Alignment explanation
Indices: 676977--677016 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
676967 TCATATTTAT
676977 TAATATAAAATA
1 TAATATAAAATA
676989 TAATAT--AATA
1 TAATATAAAATA
676999 TAATATGAAAA-A
1 TAATAT-AAAATA
677011 TAATAT
1 TAATAT
677017 TATGATCTCG
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
10 10 0.40
12 13 0.52
13 2 0.08
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (12 bp):
TAATATAAAATA
Found at i:677118 original size:17 final size:17
Alignment explanation
Indices: 677098--677130 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
677088 TATTATATTA
*
677098 AATAATTATATTTTTAC
1 AATAATAATATTTTTAC
677115 AATAATAATATTTTTA
1 AATAATAATATTTTTA
677131 GCTCATAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (17 bp):
AATAATAATATTTTTAC
Found at i:678986 original size:23 final size:24
Alignment explanation
Indices: 678960--679011 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
678950 ATTTATGTTT
*
678960 TAAATTTTATAAAATAAAA-TATA
1 TAAATTATATAAAATAAAATTATA
* * *
678983 TAAATTATATGAATTAAAATTTTA
1 TAAATTATATAAAATAAAATTATA
679007 TAAAT
1 TAAAT
679012 AAAAATTAGG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 16 0.67
24 8 0.33
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (24 bp):
TAAATTATATAAAATAAAATTATA
Found at i:680921 original size:34 final size:36
Alignment explanation
Indices: 680825--680911 Score: 124
Period size: 36 Copynumber: 2.5 Consensus size: 36
680815 CAAAATGGTC
* *
680825 ATTTCTAATACTAGTGGAATAACCTAATTTGAGTAT
1 ATTTCTAATACTAGTGGAATAACCTAATCTGAGCAT
* *
680861 ATTTCAAATACTAGTGGGATAACCTAA-CT-AGCAT
1 ATTTCTAATACTAGTGGAATAACCTAATCTGAGCAT
680895 ATTTCTAATACTAGTGG
1 ATTTCTAATACTAGTGG
680912 TATGGCCTAA
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
34 20 0.43
35 1 0.02
36 25 0.54
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.36
Consensus pattern (36 bp):
ATTTCTAATACTAGTGGAATAACCTAATCTGAGCAT
Found at i:685198 original size:22 final size:23
Alignment explanation
Indices: 685173--685217 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
685163 CATACATTAT
685173 TATGCATTATTAT-AATAAAACG
1 TATGCATTATTATCAATAAAACG
685195 TATGCATTATTATGCAATAAAAC
1 TATGCATTATTAT-CAATAAAAC
685218 CCCCACACAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 13 0.62
24 8 0.38
ACGTcount: A:0.44, C:0.11, G:0.09, T:0.36
Consensus pattern (23 bp):
TATGCATTATTATCAATAAAACG
Found at i:685915 original size:34 final size:36
Alignment explanation
Indices: 685835--685921 Score: 106
Period size: 36 Copynumber: 2.5 Consensus size: 36
685825 CAAAATGATC
* * * *
685835 ATTTCCAATACTAGTGAAATAACCTAATTTGAGTAT
1 ATTTCAAATACTAGTGGAATAACCTAATCTGAGCAT
*
685871 ATTTCAAATACTAGTGGGATAACCTAA-CT-AGCAT
1 ATTTCAAATACTAGTGGAATAACCTAATCTGAGCAT
*
685905 ATTTCTAATACTAGTGG
1 ATTTCAAATACTAGTGG
685922 TATGGCCTAA
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
34 20 0.44
35 1 0.02
36 24 0.53
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Consensus pattern (36 bp):
ATTTCAAATACTAGTGGAATAACCTAATCTGAGCAT
Found at i:687599 original size:2 final size:2
Alignment explanation
Indices: 687592--687637 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
687582 TTGCATTTTG
687592 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
687634 AT AT
1 AT AT
687638 CAAAGTATTA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:688083 original size:10 final size:9
Alignment explanation
Indices: 688066--688149 Score: 58
Period size: 8 Copynumber: 9.9 Consensus size: 9
688056 ATTTATTTAT
688066 TAATATAT-
1 TAATATATA
688074 TAATATATA
1 TAATATATA
688083 TAATA-ATA
1 TAATATATA
688091 TAATATA-A
1 TAATATATA
*
688099 T-AT-T-TT
1 TAATATATA
688105 TAATATTATA
1 TAATA-TATA
*
688115 TAAAATA-A
1 TAATATATA
688123 TCAATTATATA
1 T-AA-TATATA
688134 TAATA-ATA
1 TAATATATA
*
688142 TAAGATAT
1 TAATATAT
688150 TATATTTTTA
Statistics
Matches: 60, Mismatches: 5, Indels: 21
0.70 0.06 0.24
Matches are distributed among these distances:
6 2 0.03
7 4 0.07
8 27 0.45
9 15 0.25
10 10 0.17
11 2 0.03
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (9 bp):
TAATATATA
Found at i:688086 original size:17 final size:17
Alignment explanation
Indices: 688066--688138 Score: 55
Period size: 19 Copynumber: 4.3 Consensus size: 17
688056 ATTTATTTAT
688066 TAATATATTAATATATA
1 TAATATATTAATATATA
688083 TAATA-A-T-ATA-ATA
1 TAATATATTAATATATA
*
688096 TAATATTTTTAATATTATA
1 TAATA-TATTAATA-TATA
* *
688115 TAAAATAATCAATTATATA
1 TAATAT-ATTAA-TATATA
688134 TAATA
1 TAATA
688139 ATATAAGATA
Statistics
Matches: 43, Mismatches: 5, Indels: 14
0.69 0.08 0.23
Matches are distributed among these distances:
13 8 0.19
14 3 0.07
15 1 0.02
16 2 0.05
17 8 0.19
18 1 0.02
19 18 0.42
20 2 0.05
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.45
Consensus pattern (17 bp):
TAATATATTAATATATA
Found at i:688110 original size:29 final size:28
Alignment explanation
Indices: 688077--688226 Score: 97
Period size: 29 Copynumber: 5.5 Consensus size: 28
688067 AATATATTAA
688077 TATATATAATAATATAATATAATATTTT
1 TATATATAATAATATAATATAATATTTT
* *
688105 TA-ATAT--T-ATATAAAATAATCA--AT
1 TATATATAATAATATAATATAAT-ATTTT
*
688128 TATATATAATAATATAAGATATTATATTTT
1 TATATATAATAATAT-A-ATATAATATTTT
* *
688158 TAT-TTTAATAATAT-A-ATAATTTTTT
1 TATATATAATAATATAATATAATATTTT
* *
688183 TATATTTAATAATGAATAATAT--TATTTA
1 TATATATAATAAT--ATAATATAATATTTT
*
688211 TATATTTTAATAATAT
1 TATA-TATAATAATAT
688227 TTTAATAAAG
Statistics
Matches: 97, Mismatches: 10, Indels: 31
0.70 0.07 0.22
Matches are distributed among these distances:
23 3 0.03
24 15 0.15
25 13 0.13
26 11 0.11
27 10 0.10
28 14 0.14
29 25 0.26
30 6 0.06
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (28 bp):
TATATATAATAATATAATATAATATTTT
Found at i:688174 original size:51 final size:48
Alignment explanation
Indices: 688050--688178 Score: 145
Period size: 51 Copynumber: 2.6 Consensus size: 48
688040 TTTTAATCAA
* *
688050 AATATTATTTA-TTTATTAATATATTAA-TATATATAATAATATAATAT
1 AATATT-TTTATTTTAATAATATAATAATTATATATAATAATATAATAT
* *
688097 AATATTTTTAATATTATATAAAATAATCAATTATATATAATAATATAAGATAT
1 AATATTTTT-ATTTTA-ATAATATAAT-AATTATATATAATAATAT-A-ATAT
*
688150 TATATTTTTATTTTAATAATATAATAATT
1 AATATTTTTATTTTAATAATATAATAATT
688179 TTTTTATATT
Statistics
Matches: 68, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
46 3 0.04
47 7 0.10
48 3 0.04
49 7 0.10
50 6 0.09
51 24 0.35
52 6 0.09
53 12 0.18
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.50
Consensus pattern (48 bp):
AATATTTTTATTTTAATAATATAATAATTATATATAATAATATAATAT
Found at i:688242 original size:14 final size:11
Alignment explanation
Indices: 688197--688234 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
688187 TTTAATAATG
688197 AATAATATTATT
1 AATAATATT-TT
*
688209 TAT-ATATTTT
1 AATAATATTTT
688219 AATAATATTTT
1 AATAATATTTT
688230 AATAA
1 AATAA
688235 AGATATTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
10 4 0.17
11 17 0.74
12 2 0.09
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
AATAATATTTT
Found at i:688249 original size:23 final size:23
Alignment explanation
Indices: 688229--688273 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
688219 AATAATATTT
688229 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
688252 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
688274 ATATAACATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:688636 original size:14 final size:15
Alignment explanation
Indices: 688615--688656 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 15
688605 TTTCAGAAAT
688615 GTAATTCATTTTCTA
1 GTAATTCATTTTCTA
**
688630 G-AATTCAAATTCTA
1 GTAATTCATTTTCTA
688644 GTAATTCATTTTC
1 GTAATTCATTTTC
688657 CAATTCCAGT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.31, C:0.14, G:0.07, T:0.48
Consensus pattern (15 bp):
GTAATTCATTTTCTA
Found at i:699345 original size:15 final size:15
Alignment explanation
Indices: 699325--699358 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
699315 TCTATTTAAG
* *
699325 ATTACATTTTATAAA
1 ATTACATTATAAAAA
699340 ATTACATTATAAAAA
1 ATTACATTATAAAAA
699355 ATTA
1 ATTA
699359 ATCTAATCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (15 bp):
ATTACATTATAAAAA
Found at i:702180 original size:20 final size:20
Alignment explanation
Indices: 702155--702196 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
702145 TTTATGAATT
702155 TTATTGTTCTAA-ACTTAATA
1 TTATTGTT-TAAGACTTAATA
*
702175 TTATTGTTTAAGTCTTAATA
1 TTATTGTTTAAGACTTAATA
702195 TT
1 TT
702197 TCACTTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 3 0.15
20 17 0.85
ACGTcount: A:0.31, C:0.07, G:0.07, T:0.55
Consensus pattern (20 bp):
TTATTGTTTAAGACTTAATA
Found at i:707729 original size:15 final size:17
Alignment explanation
Indices: 707709--707748 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
707699 AAAACTCGTG
707709 TATTTTAT-AT-TTCTA
1 TATTTTATCATATTCTA
707724 TATTTTATCATATTCTA
1 TATTTTATCATATTCTA
707741 -ATTTTATC
1 TATTTTATC
707749 TAATTTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 8 0.35
16 10 0.43
17 5 0.22
ACGTcount: A:0.28, C:0.10, G:0.00, T:0.62
Consensus pattern (17 bp):
TATTTTATCATATTCTA
Found at i:709151 original size:2 final size:2
Alignment explanation
Indices: 709144--709191 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
709134 AACCTTACTT
709144 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
709186 TA TA TA
1 TA TA TA
709192 GTAGATGAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:711329 original size:30 final size:30
Alignment explanation
Indices: 711294--711477 Score: 160
Period size: 30 Copynumber: 6.2 Consensus size: 30
711284 CTGTTATAGC
* * *
711294 CCTTTAAGTTTTTATTTTTGCCATTTTATT
1 CCTTTAAGTTTATATTTTTGCTATTTTAGT
* * *
711324 CCTTTAAATTTAT-GTTTTGCTGTTTTAGT
1 CCTTTAAGTTTATATTTTTGCTATTTTAGT
* * * * *
711353 CCCTTAAATTTATGTTTTTACTATTTTAATT
1 CCTTTAAGTTTATATTTTTGCTATTTT-AGT
**
711384 CC-TTAAGTTTCGATTTTTGCTATTTTAGT
1 CCTTTAAGTTTATATTTTTGCTATTTTAGT
*
711413 CCTTTTAA-TTTATATTTTTTCTATTTTAGT
1 CC-TTTAAGTTTATATTTTTGCTATTTTAGT
* * *
711443 CCCTTAAGTTTCT-TTTTCTGCTATTTTGGT
1 CCTTTAAGTTTATATTTT-TGCTATTTTAGT
711473 CCTTT
1 CCTTT
711478 TAAATAAGAA
Statistics
Matches: 123, Mismatches: 25, Indels: 12
0.77 0.16 0.08
Matches are distributed among these distances:
29 36 0.29
30 79 0.64
31 8 0.07
ACGTcount: A:0.17, C:0.14, G:0.09, T:0.60
Consensus pattern (30 bp):
CCTTTAAGTTTATATTTTTGCTATTTTAGT
Found at i:711475 original size:60 final size:59
Alignment explanation
Indices: 711296--711480 Score: 190
Period size: 60 Copynumber: 3.1 Consensus size: 59
711286 GTTATAGCCC
* * * * * * * * * *
711296 TTTAAGTTTTTATTTTTGCCATTTTATTCCTTTAAATTTATGTTTTGCTGTTTTAGTCCC
1 TTTAA-TTTATATTTTTACTATTTTAATCCCTTAAGTTTCTTTTTTGCTATTTTAGTCCT
* * * *
711356 TTAAATTTATGTTTTTACTATTTTAATTCCTTAAGTTTCGATTTTTGCTATTTTAGTCCT
1 TTTAATTTATATTTTTACTATTTTAATCCCTTAAGTTTC-TTTTTTGCTATTTTAGTCCT
* * *
711416 TTTAATTTATATTTTTTCTATTTTAGTCCCTTAAGTTTCTTTTTCTGCTATTTTGGTCCT
1 TTTAATTTATATTTTTACTATTTTAATCCCTTAAGTTTCTTTTT-TGCTATTTTAGTCCT
711476 TTTAA
1 TTTAA
711481 ATAAGAATAT
Statistics
Matches: 102, Mismatches: 21, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
59 29 0.28
60 73 0.72
ACGTcount: A:0.18, C:0.13, G:0.09, T:0.60
Consensus pattern (59 bp):
TTTAATTTATATTTTTACTATTTTAATCCCTTAAGTTTCTTTTTTGCTATTTTAGTCCT
Found at i:720324 original size:25 final size:25
Alignment explanation
Indices: 720277--720325 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
720267 CCTTCCTGCA
* * *
720277 AGAAGACACAATGTGTGGTATCTCG
1 AGAAGACACAATATGGGGCATCTCG
720302 AGAAGACACAATATGGGGCATCTC
1 AGAAGACACAATATGGGGCATCTC
720326 ACATCATTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.35, C:0.18, G:0.27, T:0.20
Consensus pattern (25 bp):
AGAAGACACAATATGGGGCATCTCG
Found at i:720814 original size:14 final size:15
Alignment explanation
Indices: 720776--720819 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
720766 AAACAAATTA
* *
720776 CAAAGAGGAAAAAAT
1 CAAAGAGAAAAAAAC
720791 CAAAGAGAAAAAAAC
1 CAAAGAGAAAAAAAC
720806 CAAAG-GAAAGAAAA
1 CAAAGAGAAA-AAAA
720820 AAAAAGCAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
14 4 0.15
15 22 0.85
ACGTcount: A:0.70, C:0.09, G:0.18, T:0.02
Consensus pattern (15 bp):
CAAAGAGAAAAAAAC
Found at i:720821 original size:20 final size:20
Alignment explanation
Indices: 720792--720829 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
720782 GGAAAAAATC
*
720792 AAAGAGAAAAAAACCAAAGG
1 AAAGAAAAAAAAACCAAAGG
*
720812 AAAGAAAAAAAAAGCAAA
1 AAAGAAAAAAAAACCAAA
720830 AACAATGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.76, C:0.08, G:0.16, T:0.00
Consensus pattern (20 bp):
AAAGAAAAAAAAACCAAAGG
Found at i:720842 original size:12 final size:12
Alignment explanation
Indices: 720796--720866 Score: 56
Period size: 12 Copynumber: 5.6 Consensus size: 12
720786 AAAATCAAAG
720796 AGAAAAAAACCAA
1 AGAAAAAAA-CAA
720809 AGGAAAGAAAA-AA
1 A-GAAA-AAAACAA
720822 A-AAGCAAAAACAA
1 AGAA--AAAAACAA
*
720835 TGAAAAAAACAAA
1 AGAAAAAAAC-AA
720848 AGAAAAAAACAA
1 AGAAAAAAACAA
*
720860 ATAAAAA
1 AGAAAAA
720867 GAAGACAAGA
Statistics
Matches: 48, Mismatches: 3, Indels: 15
0.73 0.05 0.23
Matches are distributed among these distances:
11 2 0.04
12 18 0.38
13 18 0.38
14 6 0.12
15 4 0.08
ACGTcount: A:0.79, C:0.08, G:0.10, T:0.03
Consensus pattern (12 bp):
AGAAAAAAACAA
Found at i:724255 original size:62 final size:62
Alignment explanation
Indices: 724135--724259 Score: 207
Period size: 62 Copynumber: 2.0 Consensus size: 62
724125 AGGGTCGAGG
* * *
724135 GTTTACCTATGTTCTTCGGGACATATGGACTGTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACTGTTTACCTAGGTTCTTCAGAACATATGGACT
724197 GTTTACCTATGTTCTTCGGGACATATGGACTGTTTACCTAGGTTCTTCAGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACTGTTTACCTAGGTTCTTCAGAA-CATATGGACT
724259 G
1 G
724260 GTCCTTCGGG
Statistics
Matches: 59, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
62 58 0.98
63 1 0.02
ACGTcount: A:0.20, C:0.19, G:0.22, T:0.38
Consensus pattern (62 bp):
GTTTACCTATGTTCTTCGGGACATATGGACTGTTTACCTAGGTTCTTCAGAACATATGGACT
Found at i:724259 original size:31 final size:31
Alignment explanation
Indices: 724135--724244 Score: 211
Period size: 31 Copynumber: 3.5 Consensus size: 31
724125 AGGGTCGAGG
724135 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
724166 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
724197 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
724228 GTTTACCTAGGTTCTTC
1 GTTTACCTATGTTCTTC
724245 AGAATCTATG
Statistics
Matches: 78, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
31 78 1.00
ACGTcount: A:0.18, C:0.20, G:0.22, T:0.40
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:728373 original size:31 final size:31
Alignment explanation
Indices: 728335--728459 Score: 207
Period size: 31 Copynumber: 4.0 Consensus size: 31
728325 AGGGTCGAGG
728335 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
728366 GTTTACCTATGTTCTTCGGGACATATGGATT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
728397 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
728428 GTTTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
728459 G
1 G
728460 GTCCTTCGGG
Statistics
Matches: 89, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
31 88 0.99
32 1 0.01
ACGTcount: A:0.19, C:0.18, G:0.23, T:0.39
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:731408 original size:31 final size:29
Alignment explanation
Indices: 731373--731447 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 29
731363 CCTTGAGGCA
*
731373 GTTTCTTTGGAAACACAAA-ATCTTTTAGTTT
1 GTTTCTTT-GAAACA-AAACATCTTTGAG-TT
731404 GTTTCTCTTGAAACAAAACCATCTTTGAGTT
1 GTTTCT-TTGAAACAAAA-CATCTTTGAGTT
*
731435 GTTTCCTTGAAAC
1 GTTTCTTTGAAAC
731448 GAATTTTGTC
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
30 10 0.26
31 19 0.49
32 10 0.26
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.41
Consensus pattern (29 bp):
GTTTCTTTGAAACAAAACATCTTTGAGTT
Found at i:731851 original size:40 final size:41
Alignment explanation
Indices: 731668--731851 Score: 131
Period size: 40 Copynumber: 4.4 Consensus size: 41
731658 TGGCCTGCCT
* ** *
731668 TCCTCATCGCGTAGGAACTATGCCATCCCCCGACCAGACC-
1 TCCTCATCACGTAGGAACCGTGTCATCCCCCGACCAGACCG
* * * ** * *
731708 TCCTCATCACGTAGGAGCCGTATCAACCCTAGATAACAAACCG
1 TCCTCATCACGTAGGAACCGTGTCATCCCCCG--ACCAGACCG
* ** * *
731751 TCCTCATCACGTAGGAACCGTGTTATCATTCCTA-AAGATGGCCTG
1 TCCTCATCACGTAGGAACCGTGTCATC-CCCCGACCAGA---CC-G
*
731796 TCCTCATCACGTAGGAACTGTGTCATCCCCCGACCAGACC-
1 TCCTCATCACGTAGGAACCGTGTCATCCCCCGACCAGACCG
731836 TCCTCATCACGTAGGA
1 TCCTCATCACGTAGGA
731852 GCCGCGTTAA
Statistics
Matches: 107, Mismatches: 28, Indels: 18
0.70 0.18 0.12
Matches are distributed among these distances:
40 39 0.36
41 2 0.02
42 9 0.08
43 23 0.21
44 5 0.05
45 29 0.27
ACGTcount: A:0.26, C:0.35, G:0.18, T:0.22
Consensus pattern (41 bp):
TCCTCATCACGTAGGAACCGTGTCATCCCCCGACCAGACCG
Found at i:731852 original size:128 final size:129
Alignment explanation
Indices: 731519--731986 Score: 546
Period size: 131 Copynumber: 3.6 Consensus size: 129
731509 AGACATTATC
* * *
731519 CCTAAAGATGACATGTCATCCTCATCACGTAGGAA-TCGTGTCATCCCCCGACTAGACCTCCTCA
1 CCTAAAGATGGCCTG-C-TCCTCATCACGTAGGAACT-GTGTCATCCCCCGACCAGACCTCCTCA
* * * * * *
731583 TCACGTAGTAGCTGCGTCAACCCTAGATAACCAACAGTCCTTATCATGTAGGAACAATGTTATCA
63 TCACGTAGGAGCCGCGTCAACCCTAGATAACCAACCGTCCTCATCACGTAGGAACCATGTTATCA
731648 TT
128 TT
* * * *
731650 -TTCAAAGATGGCCTGCCTTCCTCATCGCGTAGGAACTATGCCATCCCCCGACCAGACCTCCTCA
1 CCT-AAAGATGGCCTG-C-TCCTCATCACGTAGGAACTGTGTCATCCCCCGACCAGACCTCCTCA
** * *
731714 TCACGTAGGAGCCGTATCAACCCTAGATAACAAACCGTCCTCATCACGTAGGAACCGTGTTATCA
63 TCACGTAGGAGCCGCGTCAACCCTAGATAACCAACCGTCCTCATCACGTAGGAACCATGTTATCA
731779 TT
128 TT
731781 CCTAAAGATGGCCTG-TCCTCATCACGTAGGAACTGTGTCATCCCCCGACCAGACCTCCTCATCA
1 CCTAAAGATGGCCTGCTCCTCATCACGTAGGAACTGTGTCATCCCCCGACCAGACCTCCTCATCA
* * * * *
731845 CGTAGGAGCCGCGTTAACCCTAGATAACCAACCGTCATCATCGCGTAGGAATCATGTTATCGCCC
66 CGTAGGAGCCGCGTCAACCCTAGATAACCAACCGTCCTCATCACGTAGGAACCATGTTAT---CA
731910 TT
128 TT
* * * * * * * *
731912 CCTAAAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCTTCCACCGACCAGATCTCCTCAT
1 CCTAAAGATGGCCTG--CTCCTCATCACGTAGGAACTGTGTCATCCCCCGACCAGACCTCCTCAT
731977 CACGTAGGAG
64 CACGTAGGAG
731987 TCGTGTCACC
Statistics
Matches: 288, Mismatches: 40, Indels: 15
0.84 0.12 0.04
Matches are distributed among these distances:
128 98 0.34
130 1 0.00
131 137 0.48
132 2 0.01
134 50 0.17
ACGTcount: A:0.26, C:0.32, G:0.18, T:0.24
Consensus pattern (129 bp):
CCTAAAGATGGCCTGCTCCTCATCACGTAGGAACTGTGTCATCCCCCGACCAGACCTCCTCATCA
CGTAGGAGCCGCGTCAACCCTAGATAACCAACCGTCCTCATCACGTAGGAACCATGTTATCATT
Found at i:732031 original size:43 final size:41
Alignment explanation
Indices: 731923--732036 Score: 124
Period size: 43 Copynumber: 2.8 Consensus size: 41
731913 CTAAAGATGG
* *
731923 CCAGAACTCTTCATCACGTATGAGCCGTGT-CTTCCACCGA
1 CCAGAACTCTTCATCACGTATGAGTCGTGTCCTTCCAACGA
* * * *
731963 CCAGATCTCCTCATCACGTAGGAGTCGTGTCACCTT-TAGACGA
1 CCAGAACTCTTCATCACGTATGAGTCGTGT--CCTTCCA-ACGA
*
732006 CCAGAACTCTTCATCGCGTATGAGTCGTGTC
1 CCAGAACTCTTCATCACGTATGAGTCGTGTC
732037 GTCCCCAAAT
Statistics
Matches: 60, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
40 26 0.43
41 1 0.02
42 1 0.02
43 32 0.53
ACGTcount: A:0.22, C:0.32, G:0.20, T:0.26
Consensus pattern (41 bp):
CCAGAACTCTTCATCACGTATGAGTCGTGTCCTTCCAACGA
Found at i:732507 original size:13 final size:13
Alignment explanation
Indices: 732489--732522 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
732479 ATCCAGCTGC
732489 TACCGCTGATTGT
1 TACCGCTGATTGT
732502 TACCGCTGATTGT
1 TACCGCTGATTGT
*
732515 TTCCGCTG
1 TACCGCTG
732523 CCATTGACAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.12, C:0.26, G:0.24, T:0.38
Consensus pattern (13 bp):
TACCGCTGATTGT
Found at i:733848 original size:29 final size:28
Alignment explanation
Indices: 733816--733878 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 28
733806 TTTCAGTTTT
* *
733816 TTTTTCCATTTTATTCCTTTAAATTTCTA
1 TTTTT-CATTTTAGTCCCTTAAATTTCTA
**
733845 TTTTGTTGTTTTAGTCCCTTAAATTTCTA
1 TTTT-TCATTTTAGTCCCTTAAATTTCTA
733874 TTTTT
1 TTTTT
733879 ACTGTATTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
28 1 0.03
29 27 0.93
30 1 0.03
ACGTcount: A:0.17, C:0.14, G:0.05, T:0.63
Consensus pattern (28 bp):
TTTTTCATTTTAGTCCCTTAAATTTCTA
Found at i:734282 original size:5 final size:5
Alignment explanation
Indices: 734265--734307 Score: 59
Period size: 5 Copynumber: 8.2 Consensus size: 5
734255 TTTTCAACTC
*
734265 ATTTT ACTTTT ATTTT ATTTT GTTTT ATTTT ATTTT ATCTTT A
1 ATTTT A-TTTT ATTTT ATTTT ATTTT ATTTT ATTTT AT-TTT A
734308 CGAAAATTGC
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
5 25 0.74
6 9 0.26
ACGTcount: A:0.19, C:0.05, G:0.02, T:0.74
Consensus pattern (5 bp):
ATTTT
Found at i:735481 original size:19 final size:19
Alignment explanation
Indices: 735459--735501 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
735449 CTAATTTCTT
*
735459 TAAAATTACAAAAAATCCC
1 TAAAATTACAAAAAATACC
* *
735478 T-AAATTTCTAAAAATACC
1 TAAAATTACAAAAAATACC
735496 TAAAAT
1 TAAAAT
735502 CAACCCTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.56, C:0.16, G:0.00, T:0.28
Consensus pattern (19 bp):
TAAAATTACAAAAAATACC
Found at i:738380 original size:27 final size:28
Alignment explanation
Indices: 738349--738406 Score: 82
Period size: 29 Copynumber: 2.1 Consensus size: 28
738339 TTTTTTTTAT
738349 TATAACTA-AAACAATATAAAATTAATA
1 TATAACTAGAAACAATATAAAATTAATA
* *
738376 TATAATTATGAAACTATATAAAATTAATA
1 TATAACTA-GAAACAATATAAAATTAATA
738405 TA
1 TA
738407 ATCTTAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 7 0.26
29 20 0.74
ACGTcount: A:0.59, C:0.05, G:0.02, T:0.34
Consensus pattern (28 bp):
TATAACTAGAAACAATATAAAATTAATA
Found at i:739165 original size:21 final size:21
Alignment explanation
Indices: 739140--739193 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
739130 ATTCAAGTCG
*
739140 TTGGGCTTAATTTGGATGGTC
1 TTGGGCCTAATTTGGATGGTC
739161 TTGGGCCTAATTTGGATGGTC
1 TTGGGCCTAATTTGGATGGTC
739182 TTGGGCCTAATT
1 TTGGGCCTAATT
739194 AGCCATAAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.15, C:0.13, G:0.31, T:0.41
Consensus pattern (21 bp):
TTGGGCCTAATTTGGATGGTC
Found at i:741020 original size:12 final size:12
Alignment explanation
Indices: 741003--741035 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
740993 CTTATTTTAA
741003 TCTTGTTTCTTT
1 TCTTGTTTCTTT
741015 TCTTGTTTCTTT
1 TCTTGTTTCTTT
741027 TCTTGTTTC
1 TCTTGTTTC
741036 CAGCACCAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.00, C:0.18, G:0.09, T:0.73
Consensus pattern (12 bp):
TCTTGTTTCTTT
Found at i:741386 original size:17 final size:17
Alignment explanation
Indices: 741363--741405 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
741353 ATTTTTTCAA
* *
741363 AAAAAAATAAAAAAATCC
1 AAAAAAA-ACAAAAAGCC
741381 AAAAAAAACAAAAAGCC
1 AAAAAAAACAAAAAGCC
741398 AAAAAAAA
1 AAAAAAAA
741406 AGCCAAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 16 0.70
18 7 0.30
ACGTcount: A:0.81, C:0.12, G:0.02, T:0.05
Consensus pattern (17 bp):
AAAAAAAACAAAAAGCC
Found at i:741405 original size:12 final size:13
Alignment explanation
Indices: 741385--741413 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
741375 AAATCCAAAA
741385 AAAACAAAAAGCC
1 AAAACAAAAAGCC
741398 AAAA-AAAAAGCC
1 AAAACAAAAAGCC
741410 AAAA
1 AAAA
741414 TTTCAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.76, C:0.17, G:0.07, T:0.00
Consensus pattern (13 bp):
AAAACAAAAAGCC
Found at i:747200 original size:50 final size:50
Alignment explanation
Indices: 747146--747272 Score: 245
Period size: 50 Copynumber: 2.5 Consensus size: 50
747136 CACACTCCAA
*
747146 TTTGCCTTTTCATCGCGACTAGGAGGGTTGGTTAGAGCCATATTATCGTG
1 TTTGCCTTTTCATTGCGACTAGGAGGGTTGGTTAGAGCCATATTATCGTG
747196 TTTGCCTTTTCATTGCGACTAGGAGGGTTGGTTAGAGCCATATTATCGTG
1 TTTGCCTTTTCATTGCGACTAGGAGGGTTGGTTAGAGCCATATTATCGTG
747246 TTTGCCTTTTCATTGCGACTAGGAGGG
1 TTTGCCTTTTCATTGCGACTAGGAGGG
747273 CTCGATAGGA
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
50 76 1.00
ACGTcount: A:0.17, C:0.17, G:0.28, T:0.37
Consensus pattern (50 bp):
TTTGCCTTTTCATTGCGACTAGGAGGGTTGGTTAGAGCCATATTATCGTG
Found at i:752028 original size:39 final size:39
Alignment explanation
Indices: 751985--752062 Score: 95
Period size: 39 Copynumber: 2.0 Consensus size: 39
751975 TGTTATTTTT
* **
751985 TTATTGTAAAT-ATATTTTAGGTTTTAATCGAAAATGTTA
1 TTATT-TAAATAATATTTTAGATTACAATCGAAAATGTTA
**
752024 TTATTTTTATAATATTTTAGATTACAATCGAAAATGTTA
1 TTATTTAAATAATATTTTAGATTACAATCGAAAATGTTA
752063 AAAATTATGA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
38 3 0.09
39 30 0.91
ACGTcount: A:0.37, C:0.04, G:0.10, T:0.49
Consensus pattern (39 bp):
TTATTTAAATAATATTTTAGATTACAATCGAAAATGTTA
Found at i:752300 original size:26 final size:25
Alignment explanation
Indices: 752257--752310 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
752247 AATATTTCAG
*
752257 AAAATAAAAAAATTAAATTATTTATA
1 AAAATAAAAAAA-TAAAATATTTATA
** *
752283 AAAATAAAAGTATAAAATATTTTTA
1 AAAATAAAAAAATAAAATATTTATA
752308 AAA
1 AAA
752311 GGCAAACACA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
25 14 0.58
26 10 0.42
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (25 bp):
AAAATAAAAAAATAAAATATTTATA
Found at i:752891 original size:23 final size:23
Alignment explanation
Indices: 752864--752910 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
752854 TTTCTGGAAA
*
752864 TTTTAAATTTTCATA-TAATTATT
1 TTTTAAATTTT-ATACTAATAATT
*
752887 TTTTATATTTTATACTAATAATT
1 TTTTAAATTTTATACTAATAATT
752910 T
1 T
752911 GCTTTCGTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 3 0.14
23 18 0.86
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (23 bp):
TTTTAAATTTTATACTAATAATT
Found at i:755382 original size:3 final size:3
Alignment explanation
Indices: 755374--755400 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
755364 ATTTTCGGTG
755374 GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA
755401 CGAATGAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:763841 original size:20 final size:20
Alignment explanation
Indices: 763816--763871 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
763806 TTTATTTAGG
763816 AATTTAGAGGGAAATTGGAA
1 AATTTAGAGGGAAATTGGAA
*
763836 AATTTAGAGGG-AA-TAGAA
1 AATTTAGAGGGAAATTGGAA
*
763854 AATTTTGAAGGGAAATTG
1 AATTTAG-AGGGAAATTG
763872 AGAATTGAGA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
18 10 0.33
19 6 0.20
20 13 0.43
21 1 0.03
ACGTcount: A:0.45, C:0.00, G:0.29, T:0.27
Consensus pattern (20 bp):
AATTTAGAGGGAAATTGGAA
Found at i:764086 original size:2 final size:2
Alignment explanation
Indices: 764079--764114 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
764069 ATCTATAGAT
764079 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
764115 GAAACACTAT
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):
TA
Found at i:764337 original size:2 final size:2
Alignment explanation
Indices: 764278--764329 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
764268 AAACCATGTG
764278 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
764320 TA TA TA TA TA
1 TA TA TA TA TA
764330 ACTATATAAG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:764428 original size:7 final size:7
Alignment explanation
Indices: 764413--764470 Score: 53
Period size: 7 Copynumber: 8.3 Consensus size: 7
764403 AGTTTTATAG
*
764413 AAACTCT
1 AAACCCT
764420 AAACCCT
1 AAACCCT
*
764427 AAACCAT
1 AAACCCT
**
764434 AAACATT
1 AAACCCT
764441 AAACCCT
1 AAACCCT
*
764448 AAATCCT
1 AAACCCT
**
764455 AAACTAT
1 AAACCCT
764462 AAACCCT
1 AAACCCT
764469 AA
1 AA
764471 TATAAATGAA
Statistics
Matches: 39, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
7 39 1.00
ACGTcount: A:0.50, C:0.29, G:0.00, T:0.21
Consensus pattern (7 bp):
AAACCCT
Found at i:764436 original size:14 final size:14
Alignment explanation
Indices: 764419--764470 Score: 59
Period size: 14 Copynumber: 3.7 Consensus size: 14
764409 ATAGAAACTC
764419 TAAACCCTAAACCA
1 TAAACCCTAAACCA
** *
764433 TAAACATTAAACCC
1 TAAACCCTAAACCA
* *
764447 TAAATCCTAAACTA
1 TAAACCCTAAACCA
764461 TAAACCCTAA
1 TAAACCCTAA
764471 TATAAATGAA
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.50, C:0.29, G:0.00, T:0.21
Consensus pattern (14 bp):
TAAACCCTAAACCA
Found at i:764443 original size:21 final size:21
Alignment explanation
Indices: 764413--764470 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
764403 AGTTTTATAG
*
764413 AAACTCTAAACCCTAAA-CCAT
1 AAACTATAAACCCTAAATCC-T
764434 AAAC-ATTAAACCCTAAATCCT
1 AAACTA-TAAACCCTAAATCCT
764455 AAACTATAAACCCTAA
1 AAACTATAAACCCTAA
764471 TATAAATGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
21 30 0.91
22 3 0.09
ACGTcount: A:0.50, C:0.29, G:0.00, T:0.21
Consensus pattern (21 bp):
AAACTATAAACCCTAAATCCT
Found at i:764874 original size:23 final size:24
Alignment explanation
Indices: 764839--764883 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
764829 ATAAACCGTG
764839 TATAGTATATATAAACTATATATA
1 TATAGTATATATAAACTATATATA
*
764863 TATA-TATATATAACCTATATA
1 TATAGTATATATAAACTATATA
764884 AAGTAAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (24 bp):
TATAGTATATATAAACTATATATA
Found at i:764966 original size:7 final size:7
Alignment explanation
Indices: 764956--765034 Score: 72
Period size: 7 Copynumber: 11.4 Consensus size: 7
764946 ATAGTTTATA
764956 TAAACCC
1 TAAACCC
764963 TAAA-CC
1 TAAACCC
764969 TAAACCC
1 TAAACCC
***
764976 TAAAATT
1 TAAACCC
*
764983 TAAACCA
1 TAAACCC
764990 TAAACCC
1 TAAACCC
**
764997 TAATA-TT
1 TAA-ACCC
765004 TAAACCC
1 TAAACCC
765011 TAAACCC
1 TAAACCC
*
765018 TAAACCA
1 TAAACCC
765025 TAAACCC
1 TAAACCC
765032 TAA
1 TAA
765035 TATATGTATT
Statistics
Matches: 56, Mismatches: 13, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
6 7 0.12
7 48 0.86
8 1 0.02
ACGTcount: A:0.48, C:0.30, G:0.00, T:0.22
Consensus pattern (7 bp):
TAAACCC
Found at i:764995 original size:21 final size:20
Alignment explanation
Indices: 764963--765021 Score: 91
Period size: 21 Copynumber: 2.9 Consensus size: 20
764953 ATATAAACCC
764963 TAAACCTAAACCCTAAAATT
1 TAAACCTAAACCCTAAAATT
*
764983 TAAACCATAAACCCTAATATT
1 TAAACC-TAAACCCTAAAATT
765004 TAAACCCTAAACCCTAAA
1 TAAA-CCTAAACCCTAAA
765022 CCATAAACCC
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
20 6 0.17
21 27 0.77
22 2 0.06
ACGTcount: A:0.49, C:0.27, G:0.00, T:0.24
Consensus pattern (20 bp):
TAAACCTAAACCCTAAAATT
Found at i:765056 original size:17 final size:16
Alignment explanation
Indices: 765034--765073 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
765024 ATAAACCCTA
765034 ATATATGTATTACATGC
1 ATATATGTA-TACATGC
*
765051 ATATATGTATATATGC
1 ATATATGTATACATGC
765067 ATA-ATGT
1 ATATATGT
765074 GTGTATTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 4 0.18
16 9 0.41
17 9 0.41
ACGTcount: A:0.38, C:0.07, G:0.12, T:0.42
Consensus pattern (16 bp):
ATATATGTATACATGC
Found at i:765320 original size:23 final size:23
Alignment explanation
Indices: 765288--765339 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
765278 GTATGATACA
*
765288 TATGT-TATATGCATATATTATG
1 TATGTATATATGCATATATGATG
* *
765310 TATGTATATATGTATGTATGATG
1 TATGTATATATGCATATATGATG
*
765333 CATGTAT
1 TATGTAT
765340 TAAAATTTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
22 5 0.20
23 20 0.80
ACGTcount: A:0.31, C:0.04, G:0.17, T:0.48
Consensus pattern (23 bp):
TATGTATATATGCATATATGATG
Found at i:765334 original size:34 final size:35
Alignment explanation
Indices: 765264--765341 Score: 88
Period size: 34 Copynumber: 2.2 Consensus size: 35
765254 TATTATAAAA
*
765264 ATATATTGATGTGTGTATGATACATATGTTATATGC
1 ATATATT-ATGTATGTATGATACATATGTTATATGC
**
765300 ATATATTATGTATGTAT-ATATGTATG-TATGATGC
1 ATATATTATGTATGTATGATACATATGTTAT-ATGC
*
765334 ATGTATTA
1 ATATATTA
765342 AAATTTTAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
33 3 0.08
34 18 0.49
35 9 0.24
36 7 0.19
ACGTcount: A:0.32, C:0.04, G:0.18, T:0.46
Consensus pattern (35 bp):
ATATATTATGTATGTATGATACATATGTTATATGC
Found at i:765833 original size:22 final size:22
Alignment explanation
Indices: 765779--765913 Score: 111
Period size: 22 Copynumber: 6.1 Consensus size: 22
765769 CACATTCTTA
*
765779 ATATATAATATAAAGTAATAAAGT
1 ATATA-AATATAAA-TATTAAAGT
*
765803 GAT-TGAATATAAATATTAAAGT
1 -ATATAAATATAAATATTAAAGT
*
765825 ATATAAATATAAGTATTAAA-T
1 ATATAAATATAAATATTAAAGT
* *
765846 ATA-AAGTATATAAGTACTAAAGT
1 ATATAA--ATATAAATATTAAAGT
*
765869 ATAT-AATATAAACTATTAAACT
1 ATATAAATATAAA-TATTAAAGT
*
765891 ATAT-AATATAAGTATTAAA-T
1 ATATAAATATAAATATTAAAGT
765911 ATA
1 ATA
765914 AAGTATTAAA
Statistics
Matches: 95, Mismatches: 9, Indels: 17
0.79 0.07 0.14
Matches are distributed among these distances:
20 6 0.06
21 19 0.20
22 54 0.57
23 13 0.14
24 1 0.01
25 2 0.02
ACGTcount: A:0.55, C:0.02, G:0.07, T:0.36
Consensus pattern (22 bp):
ATATAAATATAAATATTAAAGT
Found at i:765868 original size:8 final size:7
Alignment explanation
Indices: 765787--765956 Score: 88
Period size: 8 Copynumber: 23.6 Consensus size: 7
765777 TAATATATAA
765787 TATAAAG
1 TATAAAG
765794 TAATAAAG
1 T-ATAAAG
*
765802 TGATTGAA-
1 T-A-TAAAG
765810 TATAAA-
1 TATAAAG
765816 TATTAAAG
1 TA-TAAAG
*
765824 TATATAAA
1 TATA-AAG
765832 TAT-AAG
1 TATAAAG
765838 TATTAAA-
1 TA-TAAAG
765845 TATAAAG
1 TATAAAG
765852 TATATAAG
1 TATA-AAG
765860 TACTAAAG
1 TA-TAAAG
765868 TATATAA-
1 TATA-AAG
*
765875 TATAAAC
1 TATAAAG
*
765882 TATTAAAC
1 TA-TAAAG
765890 TATATAA-
1 TATA-AAG
765897 TAT-AAG
1 TATAAAG
765903 TATTAAA-
1 TA-TAAAG
765910 TATAAAG
1 TATAAAG
765917 TATTAAAG
1 TA-TAAAG
*
765925 TATATAAA
1 TATA-AAG
765933 TAT-AAG
1 TATAAAG
* *
765939 TATTAAT
1 TATAAAG
765946 TATAAAG
1 TATAAAG
765953 TATA
1 TATA
765957 TTAATTATCA
Statistics
Matches: 132, Mismatches: 10, Indels: 42
0.72 0.05 0.23
Matches are distributed among these distances:
5 2 0.02
6 26 0.20
7 46 0.35
8 53 0.40
9 5 0.04
ACGTcount: A:0.54, C:0.02, G:0.08, T:0.36
Consensus pattern (7 bp):
TATAAAG
Found at i:765877 original size:65 final size:65
Alignment explanation
Indices: 765778--765932 Score: 210
Period size: 65 Copynumber: 2.4 Consensus size: 65
765768 ACACATTCTT
*
765778 AATATATAA-TATAAAGTAATAAAGTGATTGAATATAAA-TATTAAAGTATATAAATATAAGTAT
1 AATATA-AAGTATAAAGTAATAAAGTGATTGAATATAAACTATTAAACTATAT-AATATAAGTAT
765841 TA
64 TA
*
765843 AATATAAAGTATATAAGTACTAAAGT-ATAT-AATATAAACTATTAAACTATATAATATAAGTAT
1 AATATAAAGTATA-AAGTAATAAAGTGAT-TGAATATAAACTATTAAACTATATAATATAAGTAT
765906 TA
64 TA
765908 AATATAAAGTATTAAAGTATATAAA
1 AATATAAAGTA-TAAAGTA-ATAAA
765933 TATAAGTATT
Statistics
Matches: 81, Mismatches: 3, Indels: 11
0.85 0.03 0.12
Matches are distributed among these distances:
64 2 0.02
65 49 0.60
66 30 0.37
ACGTcount: A:0.55, C:0.02, G:0.08, T:0.35
Consensus pattern (65 bp):
AATATAAAGTATAAAGTAATAAAGTGATTGAATATAAACTATTAAACTATATAATATAAGTATTA
Found at i:765942 original size:36 final size:36
Alignment explanation
Indices: 765847--765955 Score: 141
Period size: 36 Copynumber: 3.0 Consensus size: 36
765837 GTATTAAATA
* *
765847 TAAAGTATATAAGTACTAAAGTA-TATAATATAAACTAT
1 TAAAGTATATAAATA-T-AAGTATTA-AATATAAAGTAT
*
765885 TAAACTATAT-AATATAAGTATTAAATATAAAGTAT
1 TAAAGTATATAAATATAAGTATTAAATATAAAGTAT
*
765920 TAAAGTATATAAATATAAGTATTAATTATAAAGTAT
1 TAAAGTATATAAATATAAGTATTAAATATAAAGTAT
765956 ATTAATTATC
Statistics
Matches: 64, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
35 25 0.39
36 27 0.42
37 3 0.05
38 9 0.14
ACGTcount: A:0.53, C:0.03, G:0.07, T:0.37
Consensus pattern (36 bp):
TAAAGTATATAAATATAAGTATTAAATATAAAGTAT
Found at i:765957 original size:22 final size:22
Alignment explanation
Indices: 765831--765941 Score: 108
Period size: 22 Copynumber: 5.1 Consensus size: 22
765821 AAGTATATAA
765831 ATATAAGTATTAAATATAAAGT
1 ATATAAGTATTAAATATAAAGT
*
765853 ATATAAGTACTAAAGTATATAA-T
1 ATATAAGTATTAAA-TATA-AAGT
* *
765876 ATA-AACTATTAAACTATATA--
1 ATATAAGTATTAAA-TATAAAGT
765896 ATATAAGTATTAAATATAAAGT
1 ATATAAGTATTAAATATAAAGT
765918 AT-TAAAGTATATAAATAT-AAGT
1 ATAT-AAGTAT-TAAATATAAAGT
765940 AT
1 AT
765942 TAATTATAAA
Statistics
Matches: 75, Mismatches: 7, Indels: 14
0.78 0.07 0.15
Matches are distributed among these distances:
20 8 0.11
21 11 0.15
22 39 0.52
23 15 0.20
24 2 0.03
ACGTcount: A:0.54, C:0.03, G:0.07, T:0.36
Consensus pattern (22 bp):
ATATAAGTATTAAATATAAAGT
Found at i:765960 original size:16 final size:16
Alignment explanation
Indices: 765920--765964 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 16
765910 TATAAAGTAT
*
765920 TAAAGTATA-TAAATA
1 TAAAGTATATTAATTA
765935 T-AAG--TATTAATTA
1 TAAAGTATATTAATTA
765948 TAAAGTATATTAATTA
1 TAAAGTATATTAATTA
765964 T
1 T
765965 CATAATTAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
12 2 0.08
13 6 0.24
14 6 0.24
15 1 0.04
16 10 0.40
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAGTATATTAATTA
Found at i:765979 original size:21 final size:21
Alignment explanation
Indices: 765953--766023 Score: 62
Period size: 21 Copynumber: 3.6 Consensus size: 21
765943 AATTATAAAG
765953 TATATTAATTATCATAATTAA
1 TATATTAATTATCATAATTAA
* *
765974 TATATTAA--AT-ATATTTAT
1 TATATTAATTATCATAATTAA
*
765992 TA-ATTTAATTATCTTAATTAA
1 TATA-TTAATTATCATAATTAA
*
766013 TAT-TTTATTAT
1 TATATTAATTAT
766024 AACATTTAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 11
0.70 0.11 0.20
Matches are distributed among these distances:
17 1 0.03
18 12 0.31
19 2 0.05
20 9 0.23
21 15 0.38
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (21 bp):
TATATTAATTATCATAATTAA
Found at i:765980 original size:73 final size:73
Alignment explanation
Indices: 765825--765986 Score: 176
Period size: 73 Copynumber: 2.2 Consensus size: 73
765815 ATATTAAAGT
* *
765825 ATATAAATA-TAAGTATTAAA-TA-TAAAGTATATAAGTACTAAAGTATATAATATAAACTATTA
1 ATATAAATATTAAATA-TAAAGTATTAAAGTATATAAATACTAAAGTATATAATATAAACTATTA
765887 AACTATATA
65 AACTATATA
* *
765896 ATATAAGTATTAAATATAAAGTATTAAAGTATATAAATA-T-AAGTAT-TAATTATAAAGTATAT
1 ATATAAATATTAAATATAAAGTATTAAAGTATATAAATACTAAAGTATATAA-TATAAACTAT-T
* *
765958 TAATTATCATA
64 AAACTAT-ATA
765969 AT-TAATATATTAAATATA
1 ATATAA-ATATTAAATATA
765987 TTTATTAATT
Statistics
Matches: 77, Mismatches: 7, Indels: 12
0.80 0.07 0.12
Matches are distributed among these distances:
70 3 0.04
71 27 0.35
72 17 0.22
73 30 0.39
ACGTcount: A:0.54, C:0.02, G:0.06, T:0.38
Consensus pattern (73 bp):
ATATAAATATTAAATATAAAGTATTAAAGTATATAAATACTAAAGTATATAATATAAACTATTAA
ACTATATA
Found at i:766011 original size:18 final size:19
Alignment explanation
Indices: 765954--766016 Score: 65
Period size: 18 Copynumber: 3.3 Consensus size: 19
765944 ATTATAAAGT
*
765954 ATATTAATTATCATAATTAA
1 ATATTAATTATCTTAATT-A
* * *
765974 TATATTAAATATATTTATTA
1 -ATATTAATTATCTTAATTA
765994 AT-TTAATTATCTTAATTA
1 ATATTAATTATCTTAATTA
766012 ATATT
1 ATATT
766017 TTATTATAAC
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
18 15 0.44
19 4 0.12
20 1 0.03
21 14 0.41
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.52
Consensus pattern (19 bp):
ATATTAATTATCTTAATTA
Found at i:776174 original size:82 final size:82
Alignment explanation
Indices: 775994--776533 Score: 247
Period size: 82 Copynumber: 6.7 Consensus size: 82
775984 AAAAGAATTC
* * * *
775994 CCTT-TAATGAGGGAA-TGATGTTAGAATTTACAGCTTTAAGGTTGAAGTT-CAACAAAAAGAGT
1 CCTTATAATGA-GGAACTGAAGTTAGAATTTACAGCTTTAAGGTTGAA-TTGAAACTAAAAGAAT
*
776056 TAATTAAATTGGAATTTTA
64 TAATTAAATTGAAATTTTA
* *
776075 CTTTATAATGAGGAACTGAAGTTAGAATTTACAGCTTTAAGGTTTAATTGAAACTAAAAGAATTA
1 CCTTATAATGAGGAACTGAAGTTAGAATTTACAGCTTTAAGGTTGAATTGAAACTAAAAGAATTA
** *
776140 ATTATGTTGAAATTTTCC
66 ATTAAATTGAAATTTT-A
* * * * * * * *
776158 CCTT-TACTG-GGAAACTGAAGTTACAGTTCAGAGCTTTATGGTCGAGTTGAAACTAAAAG----
1 CCTTATAATGAGG-AACTGAAGTTAGAATTTACAGCTTTAAGGTTGAATTGAAACTAAAAGAATT
* * * *
776217 AGTGAAATTCAAA-ATT-
65 AATTAAATTGAAATTTTA
* * * ** *
776233 -CTT-TAACGAGGAAATGAAGTTA-ATTATGTTGAAATTTTTAATGTTGAATTTGAAACT-----
1 CCTTATAATGAGGAACTGAAGTTAGA--AT-TT-ACAGCTTTAAGGTTGAA-TTGAAACTAAAAG
*
776290 -A-T-ACTAAATTGAAA-TTTA
61 AATTAATTAAATTGAAATTTTA
* * * * * * ** *
776308 CCTGT-TAACGAAGAACTGAAGTTAGAATTTAGAGCTTTATGGTTTAATTCAAACTAAAAGTGTC
1 CCT-TATAATGAGGAACTGAAGTTAGAATTTACAGCTTTAAGGTTGAATTGAAACTAAAAGAATT
*
776372 AATTTAA-TGCATAATTTTA
65 AATTAAATTG-A-AATTTTA
* * * * * * *
776391 CCCCTT-GAA-GAGGAACTGAAGTTAGAATTTAGATCTTTTAGGTTGAACTGAAACTTAAAGAAC
1 --CCTTATAATGAGGAACTGAAGTTAGAATTTACAGCTTTAAGGTTGAATTGAAACTAAAAGAAT
*
776454 TGATTAAATTGAAAATTTTA
64 TAATTAAATTG-AAATTTTA
* * * * * * *
776474 CCTTTTAATGAAGAAATGAAGGTACG-ATTTAGAG-TGTAAGGTTGAATTGAAACTTAAAGA
1 CCTTATAATGAGGAACTGAAGTTA-GAATTTACAGCTTTAAGGTTGAATTGAAACTAAAAGA
776534 TTCGATTAAT
Statistics
Matches: 345, Mismatches: 80, Indels: 67
0.70 0.16 0.14
Matches are distributed among these distances:
73 8 0.02
74 37 0.11
75 5 0.01
76 5 0.01
77 30 0.09
78 17 0.05
80 2 0.01
81 20 0.06
82 130 0.38
83 81 0.23
84 7 0.02
85 3 0.01
ACGTcount: A:0.38, C:0.09, G:0.18, T:0.34
Consensus pattern (82 bp):
CCTTATAATGAGGAACTGAAGTTAGAATTTACAGCTTTAAGGTTGAATTGAAACTAAAAGAATTA
ATTAAATTGAAATTTTA
Found at i:782821 original size:18 final size:17
Alignment explanation
Indices: 782789--782822 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
782779 TCAGCCGGTC
782789 CGGTTTGAACGGTTCAG
1 CGGTTTGAACGGTTCAG
*
782806 CGGTTCTGACCGGTTCA
1 CGGTT-TGAACGGTTCA
782823 CTAGTAACGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.15, C:0.24, G:0.32, T:0.29
Consensus pattern (17 bp):
CGGTTTGAACGGTTCAG
Found at i:787363 original size:18 final size:18
Alignment explanation
Indices: 787342--787377 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
787332 TGTAGCATTT
*
787342 CAATGCTATGGAGCATCC
1 CAATGCTATAGAGCATCC
*
787360 CAATGCTGTAGAGCATCC
1 CAATGCTATAGAGCATCC
787378 GATGACTCAG
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:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (18 bp):
CAATGCTATAGAGCATCC
Found at i:802337 original size:2 final size:2
Alignment explanation
Indices: 802330--802361 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
802320 TACTCATATG
802330 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
802362 TTATTGGACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:803117 original size:26 final size:27
Alignment explanation
Indices: 803088--803142 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 27
803078 GTCAGTTGTC
*
803088 ACATTAAG-TATCCTTGCTCATTCATA
1 ACATTAAGTTATCCTTACTCATTCATA
* * *
803114 ACATTTAGTTGTCTTTACTCATTCATA
1 ACATTAAGTTATCCTTACTCATTCATA
803141 AC
1 AC
803143 GTTTCATTCC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 7 0.29
27 17 0.71
ACGTcount: A:0.29, C:0.22, G:0.07, T:0.42
Consensus pattern (27 bp):
ACATTAAGTTATCCTTACTCATTCATA
Found at i:805195 original size:22 final size:22
Alignment explanation
Indices: 805155--805205 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
805145 AGATTCAATC
* **
805155 TAAAATTTTGAATCTTAAAGTT
1 TAAAATTTTAAATCTTAAACCT
805177 TAAAATTTTAAAT-TATAAACCT
1 TAAAATTTTAAATCT-TAAACCT
805199 TAAAATT
1 TAAAATT
805206 GACAATATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 1 0.04
22 24 0.96
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (22 bp):
TAAAATTTTAAATCTTAAACCT
Found at i:806728 original size:189 final size:183
Alignment explanation
Indices: 806395--806786 Score: 601
Period size: 189 Copynumber: 2.1 Consensus size: 183
806385 TTTTCTAATT
* * * *
806395 TATATAA-AAATTAAATGTTTTTTAATTAAAAAAAGTTTATAATTAATTTAAATAATATATAATT
1 TATATAATATATTTAATATTTTTTAATTAAAAAAAGTTTACAATTAATTTAAATAATATATAATT
* *
806459 ATAAAATAAAAATTTCAGATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTG
66 ATAAAATAAAAATTTCAGATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAATTATTA
*
806524 GATCTTAAATTATTAATTGGGTTTTAAATGGTTTGAGCTT-AGCCCATATGTTATA
131 AATCTTAAATTATTAATTGGGTTTTAAATGGTTTG-GCTTGAGCCCATATG-T-TA
806579 TATATAATATATTTAATATTTTTTAATTAAAAAAACAGTTTACAATTAATTTAAATAATATATAT
1 TATATAATATATTTAATATTTTTTAATT-AAAAAA-AGTTTACAATTAATTTAAAT-A-ATATAT
* *
806644 AATTATAAAATAAAAAATTT-ATATAATTTTTTTAATTAATTAATATTGATTTAGGTTTAAAAAT
62 AATTATAAAAT-AAAAATTTCAGATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAAT
*
806708 TATTAAATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGGTTGAGCCCATATGTTA
126 TATTAAATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGCTTGAGCCCATATGTTA
806766 TATATAATATATTTAATATTT
1 TATATAATATATTTAATATTT
806787 AAAATTTAAT
Statistics
Matches: 191, Mismatches: 10, Indels: 11
0.90 0.05 0.05
Matches are distributed among these distances:
184 7 0.04
185 17 0.09
186 6 0.03
187 42 0.22
188 5 0.03
189 106 0.55
190 8 0.04
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.46
Consensus pattern (183 bp):
TATATAATATATTTAATATTTTTTAATTAAAAAAAGTTTACAATTAATTTAAATAATATATAATT
ATAAAATAAAAATTTCAGATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAATTATTA
AATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGCTTGAGCCCATATGTTA
Found at i:807093 original size:2 final size:2
Alignment explanation
Indices: 807086--807116 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
807076 TCTTCTAGAA
807086 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
807117 GACTTTTCAA
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:808547 original size:2 final size:2
Alignment explanation
Indices: 808542--808572 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
808532 TATATGTGTG
808542 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
808573 TATTCTTTTA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:809211 original size:2 final size:2
Alignment explanation
Indices: 809206--809240 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
809196 TTCGTGTGTT
809206 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
809241 GTATGCATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:812958 original size:5 final size:5
Alignment explanation
Indices: 812948--812982 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
812938 AATTATTTTT
*
812948 TATTA TATTA TATTA TATTA TATTTA TTTTA TATT
1 TATTA TATTA TATTA TATTA TA-TTA TATTA TATT
812983 TAATTATTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
5 23 0.85
6 4 0.15
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (5 bp):
TATTA
Found at i:812989 original size:15 final size:15
Alignment explanation
Indices: 812938--812991 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 15
812928 TATAAGGTAA
*
812938 AATTATTTTTTA-TT
1 AATTATTTTATATTT
*
812952 ATATTATATTATATTAT
1 A-ATTATTTTATATT-T
*
812969 ATTTATTTTATATTT
1 AATTATTTTATATTT
812984 AATTATTT
1 AATTATTT
812992 GAATAAATTT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
14 1 0.03
15 17 0.53
16 12 0.38
17 2 0.06
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
AATTATTTTATATTT
Found at i:816439 original size:19 final size:19
Alignment explanation
Indices: 816401--816440 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
816391 ACAAACAATA
* *
816401 TAAATAAAAAGTTCATAAT
1 TAAATAAAAACTTCAAAAT
*
816420 TAAATAAAAACTTTAAAAT
1 TAAATAAAAACTTCAAAAT
816439 TA
1 TA
816441 CTTTTCAACA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.60, C:0.05, G:0.03, T:0.33
Consensus pattern (19 bp):
TAAATAAAAACTTCAAAAT
Found at i:816590 original size:3 final size:3
Alignment explanation
Indices: 816582--816617 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
816572 CTCTTTAGTC
*
816582 TCA TCA TCA TCA TCA TCA TCA TCA TTA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
816618 GGAGCAGTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.33, C:0.31, G:0.00, T:0.36
Consensus pattern (3 bp):
TCA
Found at i:816976 original size:21 final size:21
Alignment explanation
Indices: 816952--817019 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
816942 AGCGGTGGCT
* *
816952 TCTGATCTGACTACAGTGGTA
1 TCTGATATGACTACAGTGATA
* *
816973 TCTGAAATGGCTACAGTGATA
1 TCTGATATGACTACAGTGATA
* * * *
816994 TCTGATACGACTGCGGTGACA
1 TCTGATATGACTACAGTGATA
817015 TCTGA
1 TCTGA
817020 AACGGTTACG
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.29
Consensus pattern (21 bp):
TCTGATATGACTACAGTGATA
Found at i:818833 original size:24 final size:24
Alignment explanation
Indices: 818806--818867 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
818796 CGTTCGTGAA
818806 CGTTCAGTTATGTTCGTTTATGTT
1 CGTTCAGTTATGTTCGTTTATGTT
818830 CGTTC-GATTATGTTCGTTTATGTT
1 CGTTCAG-TTATGTTCGTTTATGTT
* *
818854 CATTCATTTATGTT
1 CGTTCAGTTATGTT
818868 TACCCAATCT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
23 1 0.03
24 33 0.97
ACGTcount: A:0.15, C:0.13, G:0.18, T:0.55
Consensus pattern (24 bp):
CGTTCAGTTATGTTCGTTTATGTT
Found at i:818834 original size:14 final size:14
Alignment explanation
Indices: 818817--818847 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
818807 GTTCAGTTAT
*
818817 GTTCGTTTATGTTC
1 GTTCGATTATGTTC
818831 GTTCGATTATGTTC
1 GTTCGATTATGTTC
818845 GTT
1 GTT
818848 TATGTTCATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.10, C:0.13, G:0.23, T:0.55
Consensus pattern (14 bp):
GTTCGATTATGTTC
Found at i:819303 original size:63 final size:63
Alignment explanation
Indices: 819225--819351 Score: 245
Period size: 63 Copynumber: 2.0 Consensus size: 63
819215 AGAAAACATC
819225 ATACTTCTTTCTAGAAATAGATAGGAATATAAAGGTAACAATCGGAAGTATACGAGCATCAGT
1 ATACTTCTTTCTAGAAATAGATAGGAATATAAAGGTAACAATCGGAAGTATACGAGCATCAGT
*
819288 ATACTTCTTTCTAGAAATAGATGGGAATATAAAGGTAACAATCGGAAGTATACGAGCATCAGT
1 ATACTTCTTTCTAGAAATAGATAGGAATATAAAGGTAACAATCGGAAGTATACGAGCATCAGT
819351 A
1 A
819352 AAGAGAAAAA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 63 1.00
ACGTcount: A:0.41, C:0.13, G:0.20, T:0.27
Consensus pattern (63 bp):
ATACTTCTTTCTAGAAATAGATAGGAATATAAAGGTAACAATCGGAAGTATACGAGCATCAGT
Found at i:819680 original size:16 final size:16
Alignment explanation
Indices: 819659--819725 Score: 102
Period size: 16 Copynumber: 4.3 Consensus size: 16
819649 GTCTCCAACG
819659 TTTATGTTCGTGTTCA
1 TTTATGTTCGTGTTCA
*
819675 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
*
819691 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
819707 TTTATGTTCGT-TT-A
1 TTTATGTTCGTGTTCA
819721 TTTAT
1 TTTAT
819726 TAAATGAACG
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
14 5 0.10
15 2 0.04
16 42 0.86
ACGTcount: A:0.10, C:0.10, G:0.19, T:0.60
Consensus pattern (16 bp):
TTTATGTTCGTGTTCA
Found at i:819698 original size:32 final size:32
Alignment explanation
Indices: 819657--819717 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
819647 GGGTCTCCAA
819657 CGTTTATGTTCGTGTTCATTTATGTTCGTGTT
1 CGTTTATGTTCGTGTTCATTTATGTTCGTGTT
*
819689 CGTTTATGTTCGTGTTCGTTTATGTTCGT
1 CGTTTATGTTCGTGTTCATTTATGTTCGT
819718 TTATTTATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.08, C:0.13, G:0.23, T:0.56
Consensus pattern (32 bp):
CGTTTATGTTCGTGTTCATTTATGTTCGTGTT
Found at i:819808 original size:16 final size:16
Alignment explanation
Indices: 819787--819819 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
819777 AATTTTTTTT
819787 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
819803 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
819819 T
1 T
819820 CTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:837471 original size:36 final size:36
Alignment explanation
Indices: 837431--837537 Score: 196
Period size: 36 Copynumber: 3.0 Consensus size: 36
837421 CACCGCGTTT
* *
837431 ACTCTCAGACAGACGATCAGTCATAGTGCGTTATTC
1 ACTCTCAGACAGATGATCAGTCAGAGTGCGTTATTC
837467 ACTCTCAGACAGATGATCAGTCAGAGTGCGTTATTC
1 ACTCTCAGACAGATGATCAGTCAGAGTGCGTTATTC
837503 ACTCTCAGACAGATGATCAGTCAGAGTGCGTTATT
1 ACTCTCAGACAGATGATCAGTCAGAGTGCGTTATT
837538 GATTTTGAGG
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 69 1.00
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.28
Consensus pattern (36 bp):
ACTCTCAGACAGATGATCAGTCAGAGTGCGTTATTC
Found at i:841366 original size:121 final size:122
Alignment explanation
Indices: 841204--841422 Score: 309
Period size: 121 Copynumber: 1.8 Consensus size: 122
841194 TTCTAATTTT
* * *
841204 AATCATAAATAATTTAATAAATCTAATTCTCTACTAAGATGATGACATATTATTATACAAATTGA
1 AATCATAAATAATTTAATAAATCTAATTCTCTAATAAGATGATGACACACTATTATACAAATT-A
*
841269 TA-GAATATGTAAGTAATAAGGACCAAATGTGTTATTATATAATTTTTTTTTAACTAA
65 TACGAATATGTAAGTAACAAGGACCAAATGTGTTATTATATAATTTTTTTTTAACTAA
* * *
841326 AATCA-AAATAATTTAATAAATTTAA-TCTTTTAATAAGATGATGACACACTATTATACAAATTT
1 AATCATAAATAATTTAATAAATCTAATTC-TCTAATAAGATGATGACACACTATTATACAAATTA
* * *
841389 TACGAGTATGTAAGTAACAAGGATCAAATTTGTT
65 TACGAATATGTAAGTAACAAGGACCAAATGTGTT
841423 CGTAATTTCG
Statistics
Matches: 85, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
120 4 0.05
121 76 0.89
122 5 0.06
ACGTcount: A:0.44, C:0.09, G:0.10, T:0.38
Consensus pattern (122 bp):
AATCATAAATAATTTAATAAATCTAATTCTCTAATAAGATGATGACACACTATTATACAAATTAT
ACGAATATGTAAGTAACAAGGACCAAATGTGTTATTATATAATTTTTTTTTAACTAA
Found at i:847364 original size:21 final size:21
Alignment explanation
Indices: 847323--847361 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
847313 ATGCATAAAG
847323 TTATAAATTTTAAAAATAATT
1 TTATAAATTTTAAAAATAATT
847344 TTAT-AATTTTAAAAATAA
1 TTATAAATTTTAAAAATAA
847362 ATTGTGAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
TTATAAATTTTAAAAATAATT
Found at i:847982 original size:22 final size:22
Alignment explanation
Indices: 847923--847983 Score: 61
Period size: 25 Copynumber: 2.6 Consensus size: 22
847913 AAAGGAAGCA
847923 TGTATATACAAATCATTGTTTT
1 TGTATATACAAATCATTGTTTT
* *
847945 TGCTTATTAAAAAAATCATT-TTCTT
1 TG--TA-TATACAAATCATTGTT-TT
847970 TGTATATACAAATC
1 TGTATATACAAATC
847984 TTTAAATTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
22 10 0.32
23 2 0.06
24 4 0.13
25 15 0.48
ACGTcount: A:0.36, C:0.11, G:0.07, T:0.46
Consensus pattern (22 bp):
TGTATATACAAATCATTGTTTT
Done.