Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D10
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: 67973905
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1760000 characters in sequence are not A, C, G, or T
File 184 of 228
Found at i:54806486 original size:24 final size:24
Alignment explanation
Indices: 54806459--54806521 Score: 67
Period size: 25 Copynumber: 2.6 Consensus size: 24
54806449 GGTATACCAT
54806459 TTAAAATTATTTATAAATATT-AAA
1 TTAAAATTATTTATAAA-ATTAAAA
* *
54806483 TTAATAATAATTAATAAAATTAAAA
1 TTAA-AATTATTTATAAAATTAAAA
54806508 TATAAAA-TATTTAT
1 T-TAAAATTATTTAT
54806522 CAATTACATA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
24 12 0.38
25 17 0.53
26 3 0.09
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (24 bp):
TTAAAATTATTTATAAAATTAAAA
Found at i:54806581 original size:48 final size:48
Alignment explanation
Indices: 54806492--54806583 Score: 116
Period size: 48 Copynumber: 1.9 Consensus size: 48
54806482 ATTAATAATA
* * *
54806492 ATTAATAAAATTAAAATATAAAATATTTATCAATTACATAAATTACTC
1 ATTAATAAAATTAAAACATAAAATATCTATCAATTAAATAAATTACTC
*
54806540 ATTAATAAACATTAACACATAAAA-ATCTATC-ATTCAAATAAATT
1 ATTAATAAA-ATTAAAACATAAAATATCTATCAATT-AAATAAATT
54806584 CAAAATTAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
47 3 0.08
48 23 0.61
49 12 0.32
ACGTcount: A:0.54, C:0.11, G:0.00, T:0.35
Consensus pattern (48 bp):
ATTAATAAAATTAAAACATAAAATATCTATCAATTAAATAAATTACTC
Found at i:54806741 original size:17 final size:17
Alignment explanation
Indices: 54806715--54806748 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
54806705 GAACGTGGTT
*
54806715 TTTTTGATTATATTTTA
1 TTTTTAATTATATTTTA
54806732 TTTTTAATTATATTTTA
1 TTTTTAATTATATTTTA
54806749 ATTGTGAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (17 bp):
TTTTTAATTATATTTTA
Found at i:54810215 original size:16 final size:16
Alignment explanation
Indices: 54810194--54810225 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
54810184 ATATTTTTAG
54810194 TATTTACCTTATAGTA
1 TATTTACCTTATAGTA
54810210 TATTTACCTTATAGTA
1 TATTTACCTTATAGTA
54810226 CAATATAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.12, G:0.06, T:0.50
Consensus pattern (16 bp):
TATTTACCTTATAGTA
Found at i:54811502 original size:17 final size:17
Alignment explanation
Indices: 54811480--54811513 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
54811470 ATTACAAAAT
54811480 CAAATCTTATAAGATTA
1 CAAATCTTATAAGATTA
*
54811497 CAAATCTTCTAAGATTA
1 CAAATCTTATAAGATTA
54811514 GTTTTTATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.15, G:0.06, T:0.35
Consensus pattern (17 bp):
CAAATCTTATAAGATTA
Found at i:54814779 original size:24 final size:24
Alignment explanation
Indices: 54814752--54814797 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
54814742 AAAAAGAAAC
*
54814752 AATTACCTTCACAATAATATAAAA
1 AATTACCTTCACAACAATATAAAA
54814776 AATTACCTTCACAACAATATAA
1 AATTACCTTCACAACAATATAA
54814798 TTTATTTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.52, C:0.20, G:0.00, T:0.28
Consensus pattern (24 bp):
AATTACCTTCACAACAATATAAAA
Found at i:54819337 original size:17 final size:17
Alignment explanation
Indices: 54819315--54819348 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
54819305 ATAATTATTT
54819315 GCCTACTTTTGGTAATA
1 GCCTACTTTTGGTAATA
54819332 GCCTACTTTTGGTAATA
1 GCCTACTTTTGGTAATA
54819349 TTGAAGTAAG
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:0.24, C:0.18, G:0.18, T:0.41
Consensus pattern (17 bp):
GCCTACTTTTGGTAATA
Found at i:54828119 original size:25 final size:25
Alignment explanation
Indices: 54828083--54828184 Score: 109
Period size: 25 Copynumber: 4.1 Consensus size: 25
54828073 GGACACACCA
* *
54828083 CAGCTCGA-ATGACCTTCCCATTGTT
1 CAGCTC-ACATGAGCTTCCCATTATT
*
54828108 CAGCTCACATGAGCTTCCCGA-TACT
1 CAGCTCACATGAGCTTCCC-ATTATT
**
54828133 CAGCTTGCATGAGCTTCCCATTATT
1 CAGCTCACATGAGCTTCCCATTATT
**
54828158 CAGCTCACATGAGCTTCCTGTTATT
1 CAGCTCACATGAGCTTCCCATTATT
54828183 CA
1 CA
54828185 ACTCGGAAGA
Statistics
Matches: 64, Mismatches: 10, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
24 2 0.03
25 61 0.95
26 1 0.02
ACGTcount: A:0.22, C:0.31, G:0.16, T:0.31
Consensus pattern (25 bp):
CAGCTCACATGAGCTTCCCATTATT
Found at i:54828197 original size:50 final size:50
Alignment explanation
Indices: 54828096--54828198 Score: 134
Period size: 50 Copynumber: 2.1 Consensus size: 50
54828086 CTCGAATGAC
* * * *
54828096 CTTCCCATTGTTCAGCTCACATGAGCTTCCCGATACTCAGCTTGCATGAG
1 CTTCCCATTATTCAGCTCACATGAGCTTCCCGATACTCAACTCGCAAGAG
* * * *
54828146 CTTCCCATTATTCAGCTCACATGAGCTTCCTGTTATTCAACTCGGAAGAG
1 CTTCCCATTATTCAGCTCACATGAGCTTCCCGATACTCAACTCGCAAGAG
54828196 CTT
1 CTT
54828199 ACTATTTATA
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
50 45 1.00
ACGTcount: A:0.21, C:0.30, G:0.17, T:0.32
Consensus pattern (50 bp):
CTTCCCATTATTCAGCTCACATGAGCTTCCCGATACTCAACTCGCAAGAG
Found at i:54829325 original size:17 final size:17
Alignment explanation
Indices: 54829303--54829336 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
54829293 CTGGGATACG
54829303 GTCGTGTGTCCCTATTT
1 GTCGTGTGTCCCTATTT
54829320 GTCGTGTGTCCCTATTT
1 GTCGTGTGTCCCTATTT
54829337 TGAATGCCCA
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:0.06, C:0.24, G:0.24, T:0.47
Consensus pattern (17 bp):
GTCGTGTGTCCCTATTT
Found at i:54836854 original size:23 final size:22
Alignment explanation
Indices: 54836814--54836856 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
54836804 AAATAAAAGA
54836814 AAAAATAACTTATATATTAATT
1 AAAAATAACTTATATATTAATT
* *
54836836 AAAAATTACTATATTTATTAA
1 AAAAATAACT-TATATATTAA
54836857 ATATTTTACT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (22 bp):
AAAAATAACTTATATATTAATT
Found at i:54837185 original size:20 final size:20
Alignment explanation
Indices: 54837146--54837185 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
54837136 TGAATTACTT
* **
54837146 ATTACAGCTCTATTTTATTA
1 ATTACAACTCTATTCCATTA
54837166 ATTACAACTCTATTCCATTA
1 ATTACAACTCTATTCCATTA
54837186 CAGCCATATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.20, G:0.03, T:0.45
Consensus pattern (20 bp):
ATTACAACTCTATTCCATTA
Found at i:54838647 original size:15 final size:15
Alignment explanation
Indices: 54838629--54838669 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
54838619 AATACTGAGC
54838629 AGAACAAAACAAAAT
1 AGAACAAAACAAAAT
* * *
54838644 AGAACAGAACAGAGT
1 AGAACAAAACAAAAT
54838659 AGAACAAAACA
1 AGAACAAAACA
54838670 TGTATGTTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.66, C:0.15, G:0.15, T:0.05
Consensus pattern (15 bp):
AGAACAAAACAAAAT
Found at i:54842921 original size:19 final size:19
Alignment explanation
Indices: 54842884--54842921 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
54842874 CTAATTAAGT
*
54842884 TTTAATTAGATGAATTTAG
1 TTTAATTAGATGAAATTAG
54842903 TTTAATTAAGA-GAAATTAG
1 TTTAATT-AGATGAAATTAG
54842922 GAAAAAAGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.42, C:0.00, G:0.16, T:0.42
Consensus pattern (19 bp):
TTTAATTAGATGAAATTAG
Found at i:54843409 original size:14 final size:14
Alignment explanation
Indices: 54843390--54843419 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
54843380 TAATTAAAAC
54843390 AATAAAGTAAATAA
1 AATAAAGTAAATAA
54843404 AATAAAGTAAATAA
1 AATAAAGTAAATAA
54843418 AA
1 AA
54843420 ACAAAAGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.73, C:0.00, G:0.07, T:0.20
Consensus pattern (14 bp):
AATAAAGTAAATAA
Found at i:54844739 original size:23 final size:23
Alignment explanation
Indices: 54844712--54844819 Score: 73
Period size: 23 Copynumber: 4.9 Consensus size: 23
54844702 CTTGCCGATT
*
54844712 AGGCACTTTATGTGTTGTATATC
1 AGGCACTTTATGTGTCGTATATC
* * *
54844735 AGGCAGTTTATGTGTCGTATTTT
1 AGGCACTTTATGTGTCGTATATC
* **
54844758 AGGCACCTCGTGTGTCG--TATC
1 AGGCACTTTATGTGTCGTATATC
* ** *
54844779 AGGCACCTCGTGTGTCGT-T-TT
1 AGGCACTTTATGTGTCGTATATC
*
54844800 AGGCAC-TTATGTGTCATATA
1 AGGCACTTTATGTGTCGTATA
54844820 CTTATCAGGT
Statistics
Matches: 68, Mismatches: 14, Indels: 7
0.76 0.16 0.08
Matches are distributed among these distances:
20 8 0.12
21 27 0.40
22 1 0.01
23 32 0.47
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.39
Consensus pattern (23 bp):
AGGCACTTTATGTGTCGTATATC
Found at i:54844782 original size:21 final size:21
Alignment explanation
Indices: 54844758--54844805 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
54844748 GTCGTATTTT
54844758 AGGCACCTCGTGTGTCGTATC
1 AGGCACCTCGTGTGTCGTATC
* *
54844779 AGGCACCTCGTGTGTCGTTTT
1 AGGCACCTCGTGTGTCGTATC
54844800 AGGCAC
1 AGGCAC
54844806 TTATGTGTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.15, C:0.27, G:0.29, T:0.29
Consensus pattern (21 bp):
AGGCACCTCGTGTGTCGTATC
Found at i:54846120 original size:28 final size:28
Alignment explanation
Indices: 54846088--54846249 Score: 130
Period size: 28 Copynumber: 5.8 Consensus size: 28
54846078 CGGTCGTGTC
*
54846088 TCCCCTATTTTTCATATTTTATAATTTT
1 TCCCCTATTTTTCAAATTTTATAATTTT
* * *
54846116 TCCCCTATTTTTCAAATTTTACAGTTTAG
1 TCCCCTATTTTTCAAATTTTATAATTT-T
** * *
54846145 TCTACTACTTTAT-AAATTTTATAGTTTT
1 TCCCCTA-TTTTTCAAATTTTATAATTTT
* * *
54846173 ACCCAT-TTTTTCTAGATTTTATAATTTT
1 TCCCCTATTTTTC-AAATTTTATAATTTT
* * * *
54846201 ACCCTTACTTTTCAAATTTTACAATTTT
1 TCCCCTATTTTTCAAATTTTATAATTTT
* *
54846229 TTCCCTATTTTTCAGATTTTA
1 TCCCCTATTTTTCAAATTTTA
54846250 GATGTTACCT
Statistics
Matches: 104, Mismatches: 25, Indels: 10
0.75 0.18 0.07
Matches are distributed among these distances:
26 4 0.04
28 73 0.70
29 23 0.22
30 4 0.04
ACGTcount: A:0.25, C:0.17, G:0.03, T:0.55
Consensus pattern (28 bp):
TCCCCTATTTTTCAAATTTTATAATTTT
Found at i:54852914 original size:24 final size:24
Alignment explanation
Indices: 54852886--54852939 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
54852876 TTTTTAGAAG
* *
54852886 ATTTAATATTAATTAGTATAATAT
1 ATTTAACATTAATTAGCATAATAT
* * *
54852910 ATTTAGCATTTATTAGCATAATTT
1 ATTTAACATTAATTAGCATAATAT
54852934 ATTTAA
1 ATTTAA
54852940 ACTACGAATT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.41, C:0.04, G:0.06, T:0.50
Consensus pattern (24 bp):
ATTTAACATTAATTAGCATAATAT
Found at i:54853636 original size:28 final size:28
Alignment explanation
Indices: 54853586--54853678 Score: 89
Period size: 28 Copynumber: 3.4 Consensus size: 28
54853576 CCTACTTTAC
* *
54853586 AAATTTTATAGA-TTGCCTTTATTTTTT
1 AAATTTTATAAATTTGCCCTTATTTTTT
54853613 AAATTTTATAAATTTGCCCTTATTTTTT
1 AAATTTTATAAATTTGCCCTTATTTTTT
** * ** * *
54853641 AGGTTTTACACTTTTGCCCCTATTTTTC
1 AAATTTTATAAATTTGCCCTTATTTTTT
*
54853669 AGATTTTATA
1 AAATTTTATA
54853679 GTTTTGCCTA
Statistics
Matches: 54, Mismatches: 11, Indels: 1
0.82 0.17 0.02
Matches are distributed among these distances:
27 11 0.20
28 43 0.80
ACGTcount: A:0.25, C:0.13, G:0.08, T:0.55
Consensus pattern (28 bp):
AAATTTTATAAATTTGCCCTTATTTTTT
Found at i:54853683 original size:28 final size:28
Alignment explanation
Indices: 54853568--54853686 Score: 87
Period size: 28 Copynumber: 4.2 Consensus size: 28
54853558 GACATTACAA
* *
54853568 TTTTGTCCCCTACTTTACAAATTTTATAG
1 TTTTG-CCCCTATTTTTCAAATTTTATAG
* ** * *
54853597 -ATTGCCTTTATTTTTTAAATTTTATAA
1 TTTTGCCCCTATTTTTCAAATTTTATAG
* * * ** * *
54853624 ATTTGCCCTTATTTTTTAGGTTTTACAC
1 TTTTGCCCCTATTTTTCAAATTTTATAG
*
54853652 TTTTGCCCCTATTTTTCAGATTTTATAG
1 TTTTGCCCCTATTTTTCAAATTTTATAG
54853680 TTTTGCC
1 TTTTGCC
54853687 TAAGAAATTC
Statistics
Matches: 70, Mismatches: 19, Indels: 3
0.76 0.21 0.03
Matches are distributed among these distances:
27 17 0.24
28 53 0.76
ACGTcount: A:0.21, C:0.17, G:0.08, T:0.54
Consensus pattern (28 bp):
TTTTGCCCCTATTTTTCAAATTTTATAG
Found at i:54856460 original size:90 final size:90
Alignment explanation
Indices: 54856226--54856461 Score: 301
Period size: 90 Copynumber: 2.6 Consensus size: 90
54856216 TTATTTATAC
* * * * *
54856226 ATATGTTGTGCATTCACAATCATCTAACAGTGTATTAACCTGCAACACTGGTGGTTCATCCACCT
1 ATATGTTGTGCATTCACAACCATCTAGCAGCGTATTAACCTGCAACATTGGTGGTTCATCCACCC
**
54856291 ATTTTCTGGCAGCTCTCATCTACAA
66 ACATTCTGGCAGCTCTCATCTACAA
* * * * *
54856316 ATATGTTGTGTATTCACAACCATATGGCAACGTATTAACCTGCAAAATTGGTGGTTCATCCACCC
1 ATATGTTGTGCATTCACAACCATCTAGCAGCGTATTAACCTGCAACATTGGTGGTTCATCCACCC
**
54856381 ACATTCTGGCAGCTCTCATCTGTAA
66 ACATTCTGGCAGCTCTCATCTACAA
* * * * *
54856406 ATATGTTATACATTCACAACCATCTAGCAGCATATTAACCTGCAACTTTTGTGGTT
1 ATATGTTGTGCATTCACAACCATCTAGCAGCGTATTAACCTGCAACATTGGTGGTT
54856462 TATTCACAAC
Statistics
Matches: 122, Mismatches: 24, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
90 122 1.00
ACGTcount: A:0.28, C:0.24, G:0.15, T:0.33
Consensus pattern (90 bp):
ATATGTTGTGCATTCACAACCATCTAGCAGCGTATTAACCTGCAACATTGGTGGTTCATCCACCC
ACATTCTGGCAGCTCTCATCTACAA
Found at i:54856580 original size:51 final size:51
Alignment explanation
Indices: 54856511--54856613 Score: 197
Period size: 51 Copynumber: 2.0 Consensus size: 51
54856501 GAATTCTTAC
54856511 TATGGTGTGTAGCGATGGGGTAAGATCTTCTTTTATAAACCGAAACTATGT
1 TATGGTGTGTAGCGATGGGGTAAGATCTTCTTTTATAAACCGAAACTATGT
*
54856562 TATGGTGTGTAGCGATGGGGTAGGATCTTCTTTTATAAACCGAAACTATGT
1 TATGGTGTGTAGCGATGGGGTAAGATCTTCTTTTATAAACCGAAACTATGT
54856613 T
1 T
54856614 GCATTCATGA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.26, C:0.12, G:0.26, T:0.36
Consensus pattern (51 bp):
TATGGTGTGTAGCGATGGGGTAAGATCTTCTTTTATAAACCGAAACTATGT
Found at i:54857279 original size:22 final size:23
Alignment explanation
Indices: 54857236--54857279 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
54857226 AGCTCTTGGG
*
54857236 TTCTTCTAAAAATAGACTAAATT
1 TTCTTCTAAAAATAAACTAAATT
* *
54857259 TTCTTTTAAAAGTAAAC-AAAT
1 TTCTTCTAAAAATAAACTAAAT
54857280 GTTTTAATAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.45, C:0.11, G:0.05, T:0.39
Consensus pattern (23 bp):
TTCTTCTAAAAATAAACTAAATT
Found at i:54858214 original size:28 final size:28
Alignment explanation
Indices: 54858182--54858238 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
54858172 TATTTATGAC
54858182 ATCATTTCTTATATATAAATTAATTTTA
1 ATCATTTCTTATATATAAATTAATTTTA
54858210 ATCATTTCTTATATATAAATTAATTTTA
1 ATCATTTCTTATATATAAATTAATTTTA
54858238 A
1 A
54858239 CTTTAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (28 bp):
ATCATTTCTTATATATAAATTAATTTTA
Found at i:54859505 original size:58 final size:58
Alignment explanation
Indices: 54859415--54859528 Score: 192
Period size: 58 Copynumber: 2.0 Consensus size: 58
54859405 AAAAAAACTG
* *
54859415 AAATTATTTGATATTCAAATTGATAGTGATTTGATGATTTGGGCAACCTTAGAATATT
1 AAATTATTTGATATTCAAATTGAGAGTGATTTGATCATTTGGGCAACCTTAGAATATT
* *
54859473 AAATTATTTGATATTCAAATTTAGAGTGATTTGTTCATTTGGGCAACCTTAGAATA
1 AAATTATTTGATATTCAAATTGAGAGTGATTTGATCATTTGGGCAACCTTAGAATA
54859529 ATTTAAAATC
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
58 52 1.00
ACGTcount: A:0.34, C:0.08, G:0.17, T:0.41
Consensus pattern (58 bp):
AAATTATTTGATATTCAAATTGAGAGTGATTTGATCATTTGGGCAACCTTAGAATATT
Found at i:54859894 original size:29 final size:27
Alignment explanation
Indices: 54859833--54859901 Score: 84
Period size: 29 Copynumber: 2.5 Consensus size: 27
54859823 ATTTTTTTTC
* * *
54859833 TAAAATTTTAAAACTTTATAATTTATT
1 TAAAATATTAAAACTTTATAATCTAGT
54859860 TAAAATTTATTAAAACTTTATAATCTAGT
1 TAAAA--TATTAAAACTTTATAATCTAGT
*
54859889 TCAAATATTAAAA
1 TAAAATATTAAAA
54859902 AAATTAATTA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
27 13 0.36
29 23 0.64
ACGTcount: A:0.48, C:0.06, G:0.01, T:0.45
Consensus pattern (27 bp):
TAAAATATTAAAACTTTATAATCTAGT
Found at i:54860341 original size:20 final size:20
Alignment explanation
Indices: 54860299--54860340 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
54860289 TTATGAACTA
*
54860299 TTTATATAGTATTTTAAAAT
1 TTTATATAGTATATTAAAAT
54860319 TTTA-ATAGTATATTAAAAT
1 TTTATATAGTATATTAAAAT
54860338 TTT
1 TTT
54860341 TTAAAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (20 bp):
TTTATATAGTATATTAAAAT
Found at i:54869735 original size:96 final size:96
Alignment explanation
Indices: 54869623--54869814 Score: 384
Period size: 96 Copynumber: 2.0 Consensus size: 96
54869613 CTGCAAGATA
54869623 AAAATTTGTGGCTGAAATTAAACAATGAAACAACTATCAATTTTGTTAGTTAGTACATCTGAAAT
1 AAAATTTGTGGCTGAAATTAAACAATGAAACAACTATCAATTTTGTTAGTTAGTACATCTGAAAT
54869688 TTCCCCATGTTTTCAATATTTTCGGCATTCT
66 TTCCCCATGTTTTCAATATTTTCGGCATTCT
54869719 AAAATTTGTGGCTGAAATTAAACAATGAAACAACTATCAATTTTGTTAGTTAGTACATCTGAAAT
1 AAAATTTGTGGCTGAAATTAAACAATGAAACAACTATCAATTTTGTTAGTTAGTACATCTGAAAT
54869784 TTCCCCATGTTTTCAATATTTTCGGCATTCT
66 TTCCCCATGTTTTCAATATTTTCGGCATTCT
54869815 TTTTTGTGTG
Statistics
Matches: 96, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
96 96 1.00
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.39
Consensus pattern (96 bp):
AAAATTTGTGGCTGAAATTAAACAATGAAACAACTATCAATTTTGTTAGTTAGTACATCTGAAAT
TTCCCCATGTTTTCAATATTTTCGGCATTCT
Found at i:54871698 original size:109 final size:109
Alignment explanation
Indices: 54871506--54871814 Score: 478
Period size: 109 Copynumber: 2.8 Consensus size: 109
54871496 AAGATATAAG
* * *
54871506 AGGATATTTGGCTATTTGATCCAACGAGAAAAATCGAAACCCAGCACATTGGGGCACGTTTTCTC
1 AGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTC
* *
54871571 GAATTTCCAAACGCAAAACACTGCTTTATTTTGAAAATT-TTAAA
66 GAATTTCCAAACGCAAAACACTGCCTTACTTTG-AAATTATTAAA
*
54871615 AGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAGCACATTAGGACACGTTTTCTC
1 AGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTC
* * *
54871680 GAATTTCCAAACGTAAAACATTGCCTTACTTTGAATTTATTAAA
66 GAATTTCCAAACGCAAAACACTGCCTTACTTTGAAATTATTAAA
* * *
54871724 AGGATATTTGGCTATTTGGTCGAATGAGAAAAATAGAAACCCAACACATTAGGGCACGTTTTCT-
1 AGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTC
*
54871788 GAATTTCCAAACGCAAAACATTGCCTT
66 GAATTTCCAAACGCAAAACACTGCCTT
54871815 TGAAAATTTT
Statistics
Matches: 185, Mismatches: 14, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
108 30 0.16
109 155 0.84
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (109 bp):
AGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTC
GAATTTCCAAACGCAAAACACTGCCTTACTTTGAAATTATTAAA
Found at i:54871877 original size:20 final size:21
Alignment explanation
Indices: 54871845--54871889 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
54871835 GTATGGTGTT
54871845 AATATGCATAATG-AAATAATA
1 AATATGCATAATGTAAATAA-A
54871866 AATATG-ATAATGTAAATAAA
1 AATATGCATAATGTAAATAAA
54871886 AATA
1 AATA
54871890 ATACGAGCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 11 0.48
21 12 0.52
ACGTcount: A:0.60, C:0.02, G:0.09, T:0.29
Consensus pattern (21 bp):
AATATGCATAATGTAAATAAA
Found at i:54874338 original size:50 final size:49
Alignment explanation
Indices: 54874178--54874760 Score: 310
Period size: 50 Copynumber: 11.7 Consensus size: 49
54874168 TTCAATGTTG
* * *
54874178 GGGAAGTAAGATTCGCCGTCGTAGCTTCAATATATTCCACTACACTGCCT
1 GGGAAGTAAGATTCGCCGTCGTAGCTTCAATCT-TTTCACTGCACTGCCT
* * * * * * * * * *
54874228 AGGAAGTAAGATTTC-CTGTTGTGGCCTCAATCTTTTAATTGCAATGTCG
1 GGGAAGTAAGA-TTCGCCGTCGTAGCTTCAATCTTTTCACTGCACTGCCT
* * * **
54874277 GGGAAGTAAGATTCGTCGTCGTAGCTTCAATCTATTCCGCTGCACCACCT
1 GGGAAGTAAGATTCGCCGTCGTAGCTTCAATCT-TTTCACTGCACTGCCT
* * * * * * * * *
54874327 GGGAAGTAAGATTCGTCGTTGTGGCCTCAATCTTTTAATTGCAATGTCG
1 GGGAAGTAAGATTCGCCGTCGTAGCTTCAATCTTTTCACTGCACTGCCT
** * *
54874376 GGGAAACAAGATTCACCGTCGTAGCTTCAATCTGTTTCGCTGCACTGCCT
1 GGGAAGTAAGATTCGCCGTCGTAGCTTCAATCT-TTTCACTGCACTGCCT
* * * * * * * * * *
54874426 GGGAAGTAAGATTTGCCGTTGTGGCCTCAATCTTTTAATTGTAATGTCA
1 GGGAAGTAAGATTCGCCGTCGTAGCTTCAATCTTTTCACTGCACTGCCT
* ** * * *
54874475 GGGAAGCAAGATTCATCGTTGTAGCTTCAATCTGTTCCACTGTACTGCCT
1 GGGAAGTAAGATTCGCCGTCGTAGCTTCAATCT-TTTCACTGCACTGCCT
* * * * * * * * * **
54874525 GGGAAGTAAAATTCACCATTGTGGCTTCAATCTTTTTAATTGTAAT-TTT
1 GGGAAGTAAGATTCGCCGTCGTAGCTTCAATC-TTTTCACTGCACTGCCT
* * * ** *
54874574 GGGGAAGCAAGATTCACCGTCGTAGCTTCAAT-TTGTTCCGCTGCACCACTT
1 -GGGAAGTAAGATTCGCCGTCGTAGCTTCAATCTT-TT-CACTGCACTGCCT
* * * * * * *
54874625 GGGAAGTAAGATTCGCCGTGGTGGCTTCAATCTTTTTAATTACAATG-TT
1 GGGAAGTAAGATTCGCCGTCGTAGCTTCAATC-TTTTCACTGCACTGCCT
* * * * *
54874674 GGGGAAGCAAGATTCGCCGTCGTAGCTTCAATCTATTCCGCTGCACCGTCT
1 -GGGAAGTAAGATTCGCCGTCGTAGCTTCAATCT-TTTCACTGCACTGCCT
* ** *
54874725 GGGAAGTAAGATTCACCGTTATGGCTTCAATCTTTT
1 GGGAAGTAAGATTCGCCGTCGTAGCTTCAATCTTTT
54874761 TAATTGCAAA
Statistics
Matches: 388, Mismatches: 130, Indels: 31
0.71 0.24 0.06
Matches are distributed among these distances:
48 5 0.01
49 109 0.28
50 263 0.68
51 9 0.02
52 2 0.01
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (49 bp):
GGGAAGTAAGATTCGCCGTCGTAGCTTCAATCTTTTCACTGCACTGCCT
Found at i:54874611 original size:100 final size:99
Alignment explanation
Indices: 54874162--54874769 Score: 734
Period size: 99 Copynumber: 6.1 Consensus size: 99
54874152 CTTCTGTCTA
* * * * * * *
54874162 TTTAACTT-CAATGTTGGGGAAGTAAGATTCGCCGTCGTAGCTTCAATATATTCCACTACACTGC
1 TTTAA-TTGCAATGTCGGGGAAGCAAGATTCACCGTCGTAGCTTCAATCTATTCCGCTGCACCGC
* *
54874226 CTAGGAAGTAAGATTTC-CTGTTGTGGCCTCAATCT
65 CTGGGAAGTAAGA-TTCGCCGTTGTGGCCTCAATCT
* ** *
54874261 TTTAATTGCAATGTCGGGGAAGTAAGATTCGTCGTCGTAGCTTCAATCTATTCCGCTGCACCACC
1 TTTAATTGCAATGTCGGGGAAGCAAGATTCACCGTCGTAGCTTCAATCTATTCCGCTGCACCGCC
*
54874326 TGGGAAGTAAGATTCGTCGTTGTGGCCTCAATCT
66 TGGGAAGTAAGATTCGCCGTTGTGGCCTCAATCT
* * * *
54874360 TTTAATTGCAATGTCGGGGAAACAAGATTCACCGTCGTAGCTTCAATCTGTTTCGCTGCACTGCC
1 TTTAATTGCAATGTCGGGGAAGCAAGATTCACCGTCGTAGCTTCAATCTATTCCGCTGCACCGCC
*
54874425 TGGGAAGTAAGATTTGCCGTTGTGGCCTCAATCT
66 TGGGAAGTAAGATTCGCCGTTGTGGCCTCAATCT
* * * * * * * *
54874459 TTTAATTGTAATGTCAGGGAAGCAAGATTCATCGTTGTAGCTTCAATCTGTTCCACTGTACTGCC
1 TTTAATTGCAATGTCGGGGAAGCAAGATTCACCGTCGTAGCTTCAATCTATTCCGCTGCACCGCC
* * * *
54874524 TGGGAAGTAAAATTCACCATTGTGGCTTCAATCTT
66 TGGGAAGTAAGATTCGCCGTTGTGGCCTCAATC-T
* * * * * * *
54874559 TTTAATTGTAATTTTGGGGAAGCAAGATTCACCGTCGTAGCTTCAATTTGTTCCGCTGCACCACT
1 TTTAATTGCAATGTCGGGGAAGCAAGATTCACCGTCGTAGCTTCAATCTATTCCGCTGCACCGCC
* *
54874624 TGGGAAGTAAGATTCGCCGTGGTGGCTTCAATCTT
66 TGGGAAGTAAGATTCGCCGTTGTGGCCTCAATC-T
* * * *
54874659 TTTAATTACAATGTTGGGGAAGCAAGATTCGCCGTCGTAGCTTCAATCTATTCCGCTGCACCGTC
1 TTTAATTGCAATGTCGGGGAAGCAAGATTCACCGTCGTAGCTTCAATCTATTCCGCTGCACCGCC
* * *
54874724 TGGGAAGTAAGATTCACCGTTATGGCTTCAATCTT
66 TGGGAAGTAAGATTCGCCGTTGTGGCCTCAATC-T
54874759 TTTAATTGCAA
1 TTTAATTGCAA
54874770 ACTATGGTTT
Statistics
Matches: 445, Mismatches: 61, Indels: 5
0.87 0.12 0.01
Matches are distributed among these distances:
98 5 0.01
99 256 0.58
100 184 0.41
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.33
Consensus pattern (99 bp):
TTTAATTGCAATGTCGGGGAAGCAAGATTCACCGTCGTAGCTTCAATCTATTCCGCTGCACCGCC
TGGGAAGTAAGATTCGCCGTTGTGGCCTCAATCT
Found at i:54880481 original size:254 final size:254
Alignment explanation
Indices: 54880032--54880540 Score: 921
Period size: 254 Copynumber: 2.0 Consensus size: 254
54880022 ATGTGGGGGA
54880032 AAGTCATAGGTTCCCAATCAACTTCTTCTCCACTCAAACGCGCCTTCCTTCTCTCTTGTCTTTTC
1 AAGTCATAGGTTCCCAATCAACTTCTTCTCCACTCAAACGCGCCTTCCTTCTCTCTTGTCTTTTC
*
54880097 TCTAACTCTTCCCTTCTTTGTCTAGCATTTGGCTTCAATCCTAAACCAAAGTGGTCTTATTTATC
66 TCTAACTCTTCCCTTCTTTGTCTAGCATTTGGCTTCAATCCTAAACCAAAGTAGTCTTATTTATC
*
54880162 TTTCACCATTGGTGCCTCTATCATTCCTTGAAGGTATATTCCAAGTCCTCTTCCAGGCACAGCTC
131 TTTCACCATTGGTGCCTCTATCATTCCTTGAAGGCATATTCCAAGTCCTCTTCCAGGCACAGCTC
* *
54880227 CTTTCCCAACAATCATTTGTAGTCTCATCCTCGTGGCTCTAGATATGCTGGCCATCGGG
196 CTTTCCCAACAATCATTTGTAGTCCCATCCTCGTGGCTCTAGATATGCTGGCCACCGGG
54880286 AAGTCATAGGTTCCCAATCAACTTCTTCTCCACTCAAACGCGCCTT-CTTCCTCTCTTGTCTTTT
1 AAGTCATAGGTTCCCAATCAACTTCTTCTCCACTCAAACGCGCCTTCCTT-CTCTCTTGTCTTTT
* * *
54880350 CTCTAACTCTTTCTTTTTTTGTCTAGCATTTGGCTTCAATCCTAAACCAAAGTAGTCTTATTTAT
65 CTCTAACTCTTCCCTTCTTTGTCTAGCATTTGGCTTCAATCCTAAACCAAAGTAGTCTTATTTAT
* *
54880415 CTTTCACCATTGGTGCCTCTATCCTTCCTTGAAGGCATCTTCCAAGTCCTCTTCCAGGCACAGCT
130 CTTTCACCATTGGTGCCTCTATCATTCCTTGAAGGCATATTCCAAGTCCTCTTCCAGGCACAGCT
54880480 CCTTTCCCAACAATCATTTGTAGTCCCATCCTCGTGGCTCTAGATATGCTGGCCACCGGG
195 CCTTTCCCAACAATCATTTGTAGTCCCATCCTCGTGGCTCTAGATATGCTGGCCACCGGG
54880540 A
1 A
54880541 TCTTCTTTCC
Statistics
Matches: 245, Mismatches: 9, Indels: 2
0.96 0.04 0.01
Matches are distributed among these distances:
253 3 0.01
254 242 0.99
ACGTcount: A:0.20, C:0.31, G:0.14, T:0.36
Consensus pattern (254 bp):
AAGTCATAGGTTCCCAATCAACTTCTTCTCCACTCAAACGCGCCTTCCTTCTCTCTTGTCTTTTC
TCTAACTCTTCCCTTCTTTGTCTAGCATTTGGCTTCAATCCTAAACCAAAGTAGTCTTATTTATC
TTTCACCATTGGTGCCTCTATCATTCCTTGAAGGCATATTCCAAGTCCTCTTCCAGGCACAGCTC
CTTTCCCAACAATCATTTGTAGTCCCATCCTCGTGGCTCTAGATATGCTGGCCACCGGG
Found at i:54886974 original size:109 final size:109
Alignment explanation
Indices: 54886783--54887208 Score: 674
Period size: 109 Copynumber: 3.9 Consensus size: 109
54886773 GATATAAGAA
* * * **
54886783 GATATTTGGCTATTTGATCCAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTTGA
1 GATATTTGGCTATTTGGTCGAATGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCCCGA
*
54886848 ATTTCCAAACGCAAAACATTGCCTTATTTTGAAAATT-TTAAAAG
66 ATTTCCAAACGCAAAACATTGCCTTACTTTG-AAATTATTAAAAG
* ** * * * *
54886892 GATATTTAGCTATTTGGTCGAAAAAGAAAAATCGAAACCCTGCACATTAGGACACGTTTTCTCTA
1 GATATTTGGCTATTTGGTCGAATGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCCCGA
* * *
54886957 ATTTCTAAACGTAAAACATTGCCTTACTTTGAATTTATTAAAAG
66 ATTTCCAAACGCAAAACATTGCCTTACTTTGAAATTATTAAAAG
*
54887001 GATATTTGGCTATTTGGTCGAATGAGAAAAACCGAAACCCAGCACATTAGGGCACGTTTTCCCGA
1 GATATTTGGCTATTTGGTCGAATGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCCCGA
54887066 ATTTCCAAACGCAAAACATTGCCTTACTTTGAAATTATTAAAAG
66 ATTTCCAAACGCAAAACATTGCCTTACTTTGAAATTATTAAAAG
*
54887110 GATATTTGGCTATTTGGTCGAATGAGAAAAATCAAAACCCAGCACATTAGGGCACGTTTTCCCGA
1 GATATTTGGCTATTTGGTCGAATGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCCCGA
54887175 ATTTCCAAACGCAAAACATTGCCTTACTTTGAAA
66 ATTTCCAAACGCAAAACATTGCCTTACTTTGAAA
54887209 ATTTTTCTTT
Statistics
Matches: 290, Mismatches: 26, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
108 4 0.01
109 286 0.99
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30
Consensus pattern (109 bp):
GATATTTGGCTATTTGGTCGAATGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCCCGA
ATTTCCAAACGCAAAACATTGCCTTACTTTGAAATTATTAAAAG
Found at i:54887266 original size:20 final size:21
Alignment explanation
Indices: 54887234--54887278 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
54887224 GTATGGTGTT
54887234 AATATGCATAATG-AAATAATA
1 AATATGCATAATGTAAATAA-A
54887255 AATATG-ATAATGTAAATAAA
1 AATATGCATAATGTAAATAAA
54887275 AATA
1 AATA
54887279 ATACGAGCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 11 0.48
21 12 0.52
ACGTcount: A:0.60, C:0.02, G:0.09, T:0.29
Consensus pattern (21 bp):
AATATGCATAATGTAAATAAA
Found at i:54887435 original size:18 final size:18
Alignment explanation
Indices: 54887394--54887436 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
54887384 AACACGTAAT
54887394 AAATAAACAACAAATAAGA
1 AAAT-AACAACAAATAAGA
*
54887413 CAATAACAAC-AATAATGA
1 AAATAACAACAAATAA-GA
54887431 AAATAA
1 AAATAA
54887437 ATAAAATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 5 0.24
18 13 0.62
19 3 0.14
ACGTcount: A:0.70, C:0.12, G:0.05, T:0.14
Consensus pattern (18 bp):
AAATAACAACAAATAAGA
Found at i:54888619 original size:20 final size:19
Alignment explanation
Indices: 54888594--54888636 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
54888584 TTTTTGTATT
54888594 CAAAAA-AAAAGAAGAAAAAC
1 CAAAAACAAAA-AA-AAAAAC
54888614 CAAAAACTAAAAAAAAAAAC
1 CAAAAAC-AAAAAAAAAAAC
54888634 CAA
1 CAA
54888637 TTTTGATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 15 0.71
21 2 0.10
22 4 0.19
ACGTcount: A:0.79, C:0.14, G:0.05, T:0.02
Consensus pattern (19 bp):
CAAAAACAAAAAAAAAAAC
Found at i:54889639 original size:9 final size:9
Alignment explanation
Indices: 54889620--54889651 Score: 55
Period size: 9 Copynumber: 3.4 Consensus size: 9
54889610 TCCTTTTTTT
54889620 AGATATCCCG
1 AGAT-TCCCG
54889630 AGATTCCCG
1 AGATTCCCG
54889639 AGATTCCCG
1 AGATTCCCG
54889648 AGAT
1 AGAT
54889652 ATTTTCAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 18 0.82
10 4 0.18
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (9 bp):
AGATTCCCG
Found at i:54897625 original size:15 final size:15
Alignment explanation
Indices: 54897605--54897634 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
54897595 TACATAAAGA
54897605 GTTTTTTTGGTTTTT
1 GTTTTTTTGGTTTTT
*
54897620 GTTTTTTTTGTTTTT
1 GTTTTTTTGGTTTTT
54897635 AAATATATAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (15 bp):
GTTTTTTTGGTTTTT
Found at i:54900676 original size:2 final size:2
Alignment explanation
Indices: 54900671--54900699 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
54900661 TTTCCTCTAT
54900671 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
54900700 TTTGTTCAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:54900742 original size:15 final size:16
Alignment explanation
Indices: 54900722--54900751 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
54900712 TTTTAAAGAA
54900722 TTAAAAAATG-ATAAT
1 TTAAAAAATGCATAAT
54900737 TTAAAAAATGCATAA
1 TTAAAAAATGCATAA
54900752 AAATTTCAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.60, C:0.03, G:0.07, T:0.30
Consensus pattern (16 bp):
TTAAAAAATGCATAAT
Found at i:54902292 original size:33 final size:33
Alignment explanation
Indices: 54902239--54902301 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
54902229 CAAAAGCTAG
54902239 AACCCTTCAGCAGAGCAGATACGATTTCAACGT
1 AACCCTTCAGCAGAGCAGATACGATTTCAACGT
* * *
54902272 AACCTTTCAGCGGAGTAGATACGATTTCAA
1 AACCCTTCAGCAGAGCAGATACGATTTCAA
54902302 TGTTGTTTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (33 bp):
AACCCTTCAGCAGAGCAGATACGATTTCAACGT
Found at i:54905159 original size:13 final size:13
Alignment explanation
Indices: 54905141--54905178 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
54905131 TATATTTTAA
54905141 ATGAAAAATAAAT
1 ATGAAAAATAAAT
54905154 ATGAAAAATAAAT
1 ATGAAAAATAAAT
*
54905167 AAGAAAAATAAA
1 ATGAAAAATAAA
54905179 AAAATAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.74, C:0.00, G:0.08, T:0.18
Consensus pattern (13 bp):
ATGAAAAATAAAT
Found at i:54907120 original size:5 final size:5
Alignment explanation
Indices: 54907110--54907134 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
54907100 ACCATAGGTT
54907110 TTTTA TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA
54907135 AATTAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:54912272 original size:21 final size:22
Alignment explanation
Indices: 54912246--54912286 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
54912236 ATATTGTCTC
*
54912246 AATTTAG-TCTTAATTTTTAAA
1 AATTTAGCTCTTAATGTTTAAA
54912267 AATTTAGCTCTTAATGTTTA
1 AATTTAGCTCTTAATGTTTA
54912287 CATATTATCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.34, C:0.07, G:0.07, T:0.51
Consensus pattern (22 bp):
AATTTAGCTCTTAATGTTTAAA
Found at i:54912392 original size:18 final size:18
Alignment explanation
Indices: 54912355--54912389 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
54912345 TAAATTAGAA
54912355 ATAAAACAAAAATATTTT
1 ATAAAACAAAAATATTTT
*
54912373 ATAAAA-AAATATATTTT
1 ATAAAACAAAAATATTTT
54912390 TATTAAACTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (18 bp):
ATAAAACAAAAATATTTT
Found at i:54913035 original size:20 final size:18
Alignment explanation
Indices: 54912996--54913040 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
54912986 TGAAAACAAC
54912996 AAAAAATGATTTTTGAAA
1 AAAAAATGATTTTTGAAA
* *
54913014 AATAAATCGATTTTTTAGAA
1 AAAAAAT-GATTTTTGA-AA
54913034 AAAAAAT
1 AAAAAAT
54913041 TATTATTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 6 0.27
19 8 0.36
20 8 0.36
ACGTcount: A:0.56, C:0.02, G:0.09, T:0.33
Consensus pattern (18 bp):
AAAAAATGATTTTTGAAA
Found at i:54913049 original size:20 final size:22
Alignment explanation
Indices: 54913004--54913049 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
54912994 ACAAAAAATG
*
54913004 ATTTTTGAAAAATAAATCGATT
1 ATTTTAGAAAAATAAATCGATT
*
54913026 -TTTTAGAAAAA-AAAT-TATT
1 ATTTTAGAAAAATAAATCGATT
54913045 ATTTT
1 ATTTT
54913050 TCGGTGTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
19 3 0.14
20 8 0.38
21 10 0.48
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.46
Consensus pattern (22 bp):
ATTTTAGAAAAATAAATCGATT
Found at i:54914065 original size:10 final size:10
Alignment explanation
Indices: 54914050--54914078 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
54914040 CACTTTTAGT
54914050 ACTTGGCATG
1 ACTTGGCATG
54914060 ACTTGGCATG
1 ACTTGGCATG
54914070 ACTTGGCAT
1 ACTTGGCAT
54914079 TACACACCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.31
Consensus pattern (10 bp):
ACTTGGCATG
Found at i:54927152 original size:16 final size:18
Alignment explanation
Indices: 54927126--54927158 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
54927116 TCAAATTAAC
54927126 TAAATTAATTTT-TCAAT
1 TAAATTAATTTTCTCAAT
54927143 TAAA-TAATTTTCTCAA
1 TAAATTAATTTTCTCAA
54927159 CCCAATTCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.48
Consensus pattern (18 bp):
TAAATTAATTTTCTCAAT
Found at i:54928870 original size:101 final size:102
Alignment explanation
Indices: 54928750--54928934 Score: 257
Period size: 101 Copynumber: 1.8 Consensus size: 102
54928740 AAAGTGATGG
* ** * *
54928750 TCACGTGTGTAGTACTATGTGTATTCTACTACGTGTACAGGAATGAT-A-GGTCGCATGTGTAGT
1 TCACGTGTGTAGTACTATGTGCACGCTACTACATGTACAGG-ATGATAATGGTCACATGTGTAGT
54928813 ACTATGTGCAAGCTACTATGCGTACCGGATAGTTTCGA
65 ACTATGTGCAAGCTACTATGCGTACCGGATAGTTTCGA
** *
54928851 TCACGTGTGTAGTACTATGTGCACGCTACTACATGTATTGGATGGTAATGGTCACATGTGTAGTA
1 TCACGTGTGTAGTACTATGTGCACGCTACTACATGTACAGGATGATAATGGTCACATGTGTAGTA
* *
54928916 CTATGTGTAGGCTACTATG
66 CTATGTGCAAGCTACTATG
54928935 TGAACCAAAC
Statistics
Matches: 72, Mismatches: 10, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
100 4 0.06
101 36 0.50
102 32 0.44
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.34
Consensus pattern (102 bp):
TCACGTGTGTAGTACTATGTGCACGCTACTACATGTACAGGATGATAATGGTCACATGTGTAGTA
CTATGTGCAAGCTACTATGCGTACCGGATAGTTTCGA
Found at i:54928911 original size:51 final size:50
Alignment explanation
Indices: 54928746--54928932 Score: 169
Period size: 51 Copynumber: 3.7 Consensus size: 50
54928736 AGTGAAAGTG
* * ** *
54928746 ATGGTCACGTGTGTAGTACTATGTGTATTCTACTACGTGTACAGGAATGAT
1 ATGGTCACATGTGTAGTACTATGTGCAAGCTACTACGTGTACAGG-ATGGT
* * * * *
54928797 A-GGTCGCATGTGTAGTACTATGTGCAAGCTACTATGCGTACCGGATAGT
1 ATGGTCACATGTGTAGTACTATGTGCAAGCTACTACGTGTACAGGATGGT
* * * * * **
54928846 TTCGATCACGTGTGTAGTACTATGTGCACGCTACTACATGTATTGGATGGT
1 AT-GGTCACATGTGTAGTACTATGTGCAAGCTACTACGTGTACAGGATGGT
* *
54928897 AATGGTCACATGTGTAGTACTATGTGTAGGCTACTA
1 -ATGGTCACATGTGTAGTACTATGTGCAAGCTACTA
54928933 TGTGAACCAA
Statistics
Matches: 107, Mismatches: 26, Indels: 6
0.77 0.19 0.04
Matches are distributed among these distances:
49 3 0.03
50 35 0.33
51 68 0.64
52 1 0.01
ACGTcount: A:0.25, C:0.16, G:0.26, T:0.33
Consensus pattern (50 bp):
ATGGTCACATGTGTAGTACTATGTGCAAGCTACTACGTGTACAGGATGGT
Found at i:54928994 original size:45 final size:45
Alignment explanation
Indices: 54928943--54929029 Score: 147
Period size: 45 Copynumber: 1.9 Consensus size: 45
54928933 TGTGAACCAA
* * *
54928943 ACATCATTGATTAGTAAGGTGGTTGCTATGTGCTGATTCCACCGG
1 ACATCATTGATTAATAAGGTGGTTGATATGTGCTGAATCCACCGG
54928988 ACATCATTGATTAATAAGGTGGTTGATATGTGCTGAATCCAC
1 ACATCATTGATTAATAAGGTGGTTGATATGTGCTGAATCCAC
54929030 TGAGTATCTG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.33
Consensus pattern (45 bp):
ACATCATTGATTAATAAGGTGGTTGATATGTGCTGAATCCACCGG
Found at i:54934318 original size:59 final size:58
Alignment explanation
Indices: 54934223--54934361 Score: 201
Period size: 59 Copynumber: 2.4 Consensus size: 58
54934213 AAGATACGTA
54934223 GTGTAAGACCATGGATGAAAGACGCCATGACAGCATGGTACAAGGTAAAACGGTATATAG
1 GTGTAAGACCATGGATGAAAGACGCCATGACAGCATGGTACAAGGTAAAA-GGTATAT-G
* * *
54934283 G-GTAAGACCATGGATAAAAGACGCCATGGA-GGCATGGTACAAGGTATAAGGTATATG
1 GTGTAAGACCATGGATGAAAGACGCCAT-GACAGCATGGTACAAGGTAAAAGGTATATG
*
54934340 GTGTAAGACCATAGATGAAAGA
1 GTGTAAGACCATGGATGAAAGA
54934362 TGTTATGACA
Statistics
Matches: 72, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
57 2 0.03
58 25 0.35
59 42 0.58
60 3 0.04
ACGTcount: A:0.39, C:0.13, G:0.29, T:0.19
Consensus pattern (58 bp):
GTGTAAGACCATGGATGAAAGACGCCATGACAGCATGGTACAAGGTAAAAGGTATATG
Found at i:54934607 original size:33 final size:33
Alignment explanation
Indices: 54934502--54934608 Score: 85
Period size: 33 Copynumber: 3.2 Consensus size: 33
54934492 CCACTGCGAC
* * * ** *
54934502 AGTAAACATAGAACAAAGATAGTCCGTTGTGAC
1 AGTAAACATAAAACAGAGATAGTCAGTTAAGAT
* *
54934535 AGTAAACATATAAGA-AG-GATAGTCCA-CTAGGAT
1 AGTAAACATA-AA-ACAGAGATAGT-CAGTTAAGAT
*
54934568 AATAAACATAAAACAGAGATAGTCAGTTAAGAT
1 AGTAAACATAAAACAGAGATAGTCAGTTAAGAT
54934601 AGTAAACA
1 AGTAAACA
54934609 CAGATGAAGT
Statistics
Matches: 57, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
31 1 0.02
32 6 0.11
33 46 0.81
34 3 0.05
35 1 0.02
ACGTcount: A:0.49, C:0.12, G:0.19, T:0.21
Consensus pattern (33 bp):
AGTAAACATAAAACAGAGATAGTCAGTTAAGAT
Found at i:54940237 original size:16 final size:16
Alignment explanation
Indices: 54940216--54940247 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
54940206 AATTGGGTTG
*
54940216 AGAAAATTATTTAATT
1 AGAAAATTAATTAATT
54940232 AGAAAATTAATTAATT
1 AGAAAATTAATTAATT
54940248 TAAATTAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (16 bp):
AGAAAATTAATTAATT
Found at i:54941962 original size:49 final size:47
Alignment explanation
Indices: 54941872--54941972 Score: 118
Period size: 49 Copynumber: 2.1 Consensus size: 47
54941862 AGCTCTTATA
*
54941872 AACTTCCCGATATATGGCTCTCCGTGAGCTTTTTGATATGGCTCGCTTG
1 AACTTCCCGATATATGGCTATCCGTGAGCTTTTTGATATGGCT--CTTG
*
54941921 AACTTTCCGATATATGGCTATCCG-GAGCTTTCCATT-A-ATGGCTCTTG
1 AACTTCCCGATATATGGCTATCCGTGAGCTTT---TTGATATGGCTCTTG
54941968 AACTT
1 AACTT
54941973 ACCTAAAATG
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
47 9 0.19
48 7 0.15
49 28 0.60
50 1 0.02
51 2 0.04
ACGTcount: A:0.20, C:0.24, G:0.20, T:0.37
Consensus pattern (47 bp):
AACTTCCCGATATATGGCTATCCGTGAGCTTTTTGATATGGCTCTTG
Found at i:54944604 original size:16 final size:16
Alignment explanation
Indices: 54944569--54944618 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
54944559 TTTTGAATAG
* *
54944569 AGTTATTCATGAAGAAT
1 AGTTATTC-TAAATAAT
54944586 AGTTATTCTAAATAAT
1 AGTTATTCTAAATAAT
* *
54944602 AGTTGTTCCAAATAAT
1 AGTTATTCTAAATAAT
54944618 A
1 A
54944619 ATCATTTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
16 21 0.72
17 8 0.28
ACGTcount: A:0.42, C:0.08, G:0.12, T:0.38
Consensus pattern (16 bp):
AGTTATTCTAAATAAT
Found at i:54944765 original size:3 final size:3
Alignment explanation
Indices: 54944757--54944796 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
54944747 AATTATCCTA
54944757 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
54944797 ATGTCTTGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:54944998 original size:5 final size:5
Alignment explanation
Indices: 54944988--54945019 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
54944978 GGAGAGGTAC
54944988 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT AT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT AT
54945020 GTAAATTCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (5 bp):
ATTTT
Found at i:54945072 original size:13 final size:13
Alignment explanation
Indices: 54945039--54945070 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
54945029 ACTGTTTTAG
54945039 TTTT-AAATTATT
1 TTTTAAAATTATT
54945051 TTTTAAAATT-TT
1 TTTTAAAATTATT
54945063 TTTTAAAA
1 TTTTAAAA
54945071 ATATCTAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 14 0.74
13 5 0.26
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TTTTAAAATTATT
Found at i:54954610 original size:5 final size:5
Alignment explanation
Indices: 54954602--54954633 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
54954592 TATTTTTTTC
*
54954602 ATTCG ATTCG ATTCG ATTCG ATTCA ATTCG AT
1 ATTCG ATTCG ATTCG ATTCG ATTCG ATTCG AT
54954634 CAAACACTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.25, C:0.19, G:0.16, T:0.41
Consensus pattern (5 bp):
ATTCG
Found at i:54966975 original size:27 final size:27
Alignment explanation
Indices: 54966943--54967120 Score: 178
Period size: 27 Copynumber: 6.6 Consensus size: 27
54966933 ATATTGAGTC
* *
54966943 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* * *
54966970 CACACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
54966997 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
54967025 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
54967052 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* * *
54967079 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
54967106 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
54967121 GTACAATTTA
Statistics
Matches: 127, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
27 103 0.81
28 24 0.19
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:54967103 original size:54 final size:55
Alignment explanation
Indices: 54966943--54967120 Score: 200
Period size: 54 Copynumber: 3.3 Consensus size: 55
54966933 ATATTGAGTC
* * * * * * *
54966943 CGCACACTCAGTGCTATATAATC-AACTCACACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAACTCGCACACTTAGTGCAACATAGTCAAAT
** * *
54966997 CGCACACTTAGTGCTACATAGTCAAACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAACTCGCACACTTAGTGCAACATAGTCAAAT
* **
54967052 CGCACACTTAGTGC-ATCATATTC-ATTTCGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTA-CATAGTCAAACTCGCACACTTAGTGCAACATAGTCAAAT
54967106 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
54967121 GTACAATTTA
Statistics
Matches: 104, Mismatches: 17, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
54 60 0.58
55 44 0.42
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (55 bp):
CGCACACTTAGTGCTACATAGTCAAACTCGCACACTTAGTGCAACATAGTCAAAT
Found at i:54975062 original size:27 final size:27
Alignment explanation
Indices: 54975032--54975209 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
54975022 ATATTGAGTC
* * * *
54975032 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
54975059 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
54975086 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
54975114 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
54975141 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
54975168 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
54975195 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
54975210 GTACAATTCA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:54975171 original size:82 final size:81
Alignment explanation
Indices: 54975053--54975208 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
54975043 TGCTATATAA
* *
54975053 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
54975118 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
54975135 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
54975199 CACTTAGTGC
65 CACTTAGTGC
54975209 TGTACAATTC
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:54975221 original size:82 final size:83
Alignment explanation
Indices: 54975032--54975221 Score: 221
Period size: 82 Copynumber: 2.3 Consensus size: 83
54975022 ATATTGAGTC
* * * * *
54975032 CGCACACTCAGTGCTATATAA-TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTA
1 CGCACACTTAGTGCTGTACAATTCAATTCGCACACTTAGTGCTACATAATCAAATCGCACACTTA
*
54975096 GTGCTACATAGTCAAACT
66 GTGCAACATAGTCAAACT
* * **
54975114 CGCACACTTAGTGCCG--C-ATGGTCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACAC
1 CGCACACTTAGTGCTGTACAAT--TCAATTCGCACACTTAGTGCTA-CATAATCAAATCGCACAC
54975175 TTAGTGCAACATAGTCAAA-T
63 TTAGTGCAACATAGTCAAACT
54975195 CGCACACTTAGTGCTGTACAATTCAAT
1 CGCACACTTAGTGCTGTACAATTCAAT
54975222 CCCGCGCACT
Statistics
Matches: 90, Mismatches: 11, Indels: 14
0.78 0.10 0.12
Matches are distributed among these distances:
79 1 0.01
81 17 0.19
82 69 0.77
83 1 0.01
84 2 0.02
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.27
Consensus pattern (83 bp):
CGCACACTTAGTGCTGTACAATTCAATTCGCACACTTAGTGCTACATAATCAAATCGCACACTTA
GTGCAACATAGTCAAACT
Found at i:54981424 original size:3 final size:3
Alignment explanation
Indices: 54981416--54981440 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
54981406 GTATGTATTA
54981416 TGT TGT TGT TGT TGT TGT TGT TGT T
1 TGT TGT TGT TGT TGT TGT TGT TGT T
54981441 TAGGAACAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TGT
Found at i:54999770 original size:27 final size:27
Alignment explanation
Indices: 54999740--54999916 Score: 160
Period size: 27 Copynumber: 6.6 Consensus size: 27
54999730 ATATTGAGTC
* *
54999740 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* *
54999767 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
54999794 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
54999822 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
54999849 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* * * *
54999876 CGCACACTTAATGCAACATAGT-AAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
54999902 CGCACACATAGTGCT
1 CGCACACTTAGTGCT
54999917 GTACAATTTA
Statistics
Matches: 125, Mismatches: 22, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
26 14 0.11
27 87 0.70
28 24 0.19
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:54999832 original size:55 final size:54
Alignment explanation
Indices: 54999740--54999916 Score: 187
Period size: 55 Copynumber: 3.3 Consensus size: 54
54999730 ATATTGAGTC
* * * * *
54999740 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
* ** * *
54999794 CGCACACTTAGTGCTACATAGTCAAACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATC-AACTCGCACACTTAGTGCAACATAGTCAAAT
* ** *
54999849 CGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAATGCAACATAGT-AAAT
1 CGCACACTTAGTGCTA-CATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
*
54999902 CGCACACATAGTGCT
1 CGCACACTTAGTGCT
54999917 GTACAATTTA
Statistics
Matches: 102, Mismatches: 18, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
53 16 0.16
54 41 0.40
55 45 0.44
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.27
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
Found at i:54999879 original size:82 final size:80
Alignment explanation
Indices: 54999761--54999915 Score: 204
Period size: 82 Copynumber: 1.9 Consensus size: 80
54999751 TGCTATATAA
* * *
54999761 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAATGCAACATAGT-AAA-TCGCA
*
54999826 CACTTAGTGCCGCATGG
64 CACATAGTGCCGCATGG
* * **
54999843 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAATGCAACATAGTAAATCGCAC
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAATGCAACATAGTAAATCGCAC
54999907 ACATAGTGC
65 ACATAGTGC
54999916 TGTACAATTT
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
80 14 0.22
81 4 0.06
82 46 0.72
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.26
Consensus pattern (80 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAATGCAACATAGTAAATCGCACA
CATAGTGCCGCATGG
Found at i:55007854 original size:27 final size:27
Alignment explanation
Indices: 55007822--55007999 Score: 178
Period size: 27 Copynumber: 6.6 Consensus size: 27
55007812 ATATTGAGTC
* *
55007822 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* * *
55007849 CACACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
55007876 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
55007904 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
55007931 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* * *
55007958 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
55007985 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
55008000 GTACAATTTA
Statistics
Matches: 127, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
27 103 0.81
28 24 0.19
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:55007982 original size:54 final size:55
Alignment explanation
Indices: 55007822--55007999 Score: 200
Period size: 54 Copynumber: 3.3 Consensus size: 55
55007812 ATATTGAGTC
* * * * * * *
55007822 CGCACACTCAGTGCTATATAATC-AACTCACACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAACTCGCACACTTAGTGCAACATAGTCAAAT
** * *
55007876 CGCACACTTAGTGCTACATAGTCAAACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAACTCGCACACTTAGTGCAACATAGTCAAAT
* **
55007931 CGCACACTTAGTGC-ATCATATTC-ATTTCGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTA-CATAGTCAAACTCGCACACTTAGTGCAACATAGTCAAAT
55007985 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
55008000 GTACAATTTA
Statistics
Matches: 104, Mismatches: 17, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
54 60 0.58
55 44 0.42
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (55 bp):
CGCACACTTAGTGCTACATAGTCAAACTCGCACACTTAGTGCAACATAGTCAAAT
Found at i:55011943 original size:13 final size:13
Alignment explanation
Indices: 55011925--55011951 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
55011915 CCAAACTGCA
55011925 ATTCACATATAAT
1 ATTCACATATAAT
55011938 ATTCACATATAAT
1 ATTCACATATAAT
55011951 A
1 A
55011952 CGACTCTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.15, G:0.00, T:0.37
Consensus pattern (13 bp):
ATTCACATATAAT
Found at i:55017117 original size:95 final size:95
Alignment explanation
Indices: 55016862--55017201 Score: 351
Period size: 95 Copynumber: 3.6 Consensus size: 95
55016852 GGTGATTAGA
* * *
55016862 AAATCAGCTAACACAGATGAGATTGTTCATGATAG-TAAATCAAATG-ACTTAGGCTGCGATCTT
1 AAATCAGCTAACTCAGATAAGATTGTTCATGAT-GTTAAATAAAATGAACTTAGGCTGCGATCTT
* * * *
55016925 AAATCAGCAAGCCATTTGAAGCAGCAATGTT
65 AAATCAGCAAGCCGTTTGGAGTAGCGATGTT
* * * * * **
55016956 AAATTAGTTAACTCAGATAAGTTTGTTCATGATGTTAAATAGAATTAACTTAGGCCACGATCTTA
1 AAATCAGCTAACTCAGATAAGATTGTTCATGATGTTAAATAAAATGAACTTAGGCTGCGATCTTA
*** *
55017021 AATCAATGAGCCGTTTGGAGTAGTGATGTT
66 AATCAGCAAGCCGTTTGGAGTAGCGATGTT
* * * *
55017051 AAATCAGCTAACTCAGATAAGATTGCTCATGATGTTAAATAAAATGAACTTAGGTTGTGATATTA
1 AAATCAGCTAACTCAGATAAGATTGTTCATGATGTTAAATAAAATGAACTTAGGCTGCGATCTTA
* * * * *
55017116 AATTAGCAAGTCGTTTCGAGTACCGATTTT
66 AATCAGCAAGCCGTTTGGAGTAGCGATGTT
* * * * * * *
55017146 AAATCAGCAAACTCGGATAAAATTGTTCATGATGTTGAATAGAACGAACATAGGCT
1 AAATCAGCTAACTCAGATAAGATTGTTCATGATGTTAAATAAAATGAACTTAGGCT
55017202 ATAATCTTAA
Statistics
Matches: 197, Mismatches: 47, Indels: 3
0.80 0.19 0.01
Matches are distributed among these distances:
93 1 0.01
94 36 0.18
95 160 0.81
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.31
Consensus pattern (95 bp):
AAATCAGCTAACTCAGATAAGATTGTTCATGATGTTAAATAAAATGAACTTAGGCTGCGATCTTA
AATCAGCAAGCCGTTTGGAGTAGCGATGTT
Found at i:55017211 original size:190 final size:189
Alignment explanation
Indices: 55016862--55017213 Score: 420
Period size: 190 Copynumber: 1.9 Consensus size: 189
55016852 GGTGATTAGA
* * * *
55016862 AAATCAGCTAACACAGATGAGATTGTTCATGATAGTAAATCAAATGACTTAGGCTGCGATCTTAA
1 AAATCAGCTAACACAGATAAGATTGCTCATGATAGTAAATAAAATGACTTAGGCTGCGATATTAA
* * ** **
55016927 ATCAGCAAGCCATTTGAAGCAGCAATGTTAAATTAGTTAACTCAGATAAGTTTGTTCATGATGTT
66 ATCAGCAAGCCATTTGAAGCACCAATGTTAAATCAGCAAACTCAGATAAAATTGTTCATGATGTT
** * *
55016992 AAATAGAATTAACTTAGGCCACGATCTTAAATCAATGAGCCGTTTGGAGTAGTGATGTT
131 AAATAGAACGAACATAGGCCACAATCTTAAATCAATGAGCCGTTTGGAGTAGTGATGTT
* * *
55017051 AAATCAGCTAACTCAGATAAGATTGCTCATGAT-GTTAAATAAAATGAACTTAGGTTGTGATATT
1 AAATCAGCTAACACAGATAAGATTGCTCATGATAG-TAAATAAAATG-ACTTAGGCTGCGATATT
* * * * * * *
55017115 AAATTAGCAAGTCGTTTCG-AGTACCGATTTTAAATCAGCAAACTCGGATAAAATTGTTCATGAT
64 AAATCAGCAAGCCATTT-GAAGCACCAATGTTAAATCAGCAAACTCAGATAAAATTGTTCATGAT
* * *
55017179 GTTGAATAGAACGAACATAGGCTATAATCTTAAAT
128 GTTAAATAGAACGAACATAGGCCACAATCTTAAAT
55017214 TAGCGAGCCT
Statistics
Matches: 133, Mismatches: 27, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
188 1 0.01
189 40 0.30
190 91 0.68
191 1 0.01
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.31
Consensus pattern (189 bp):
AAATCAGCTAACACAGATAAGATTGCTCATGATAGTAAATAAAATGACTTAGGCTGCGATATTAA
ATCAGCAAGCCATTTGAAGCACCAATGTTAAATCAGCAAACTCAGATAAAATTGTTCATGATGTT
AAATAGAACGAACATAGGCCACAATCTTAAATCAATGAGCCGTTTGGAGTAGTGATGTT
Found at i:55017399 original size:130 final size:131
Alignment explanation
Indices: 55017145--55017481 Score: 408
Period size: 130 Copynumber: 2.6 Consensus size: 131
55017135 GTACCGATTT
* * * * * * * * *
55017145 TAAATCAGCAAACTCGGATAAAATTGTTCATGATGTTGAAT-AGAACGAACATAGGCTATAATCT
1 TAAATCAACTAACTCAGAAAAAATTGTTCATAATATTAAATCA-AATGAACATAGGCTACAATCT
* * *
55017209 TAAATTAGCGAGCCTTAACGATATCAGCTGCGATCTTACATCAGCGAGCTATTTAGATTAGCAAT
65 TAAATTAACGAGCCTTAACGATATCAGCTGCGATCTTAAATCAACGAGCTATTTAGATTAGCAAT
55017274 AG
130 AG
* * * *
55017276 TAAATCAACTAACTCAG-AACAATTGTTCATAATATTAAATTAAATGAACTTAGGCTACGATCTT
1 TAAATCAACTAACTCAGAAAAAATTGTTCATAATATTAAATCAAATGAACATAGGCTACAATCTT
* * * * * *
55017340 AAGTTAACGAGCCTTAACGATATCAGTTGCGATCTTAAATCAATGAGCTGTTTATATTAGCGATA
66 AAATTAACGAGCCTTAACGATATCAGCTGCGATCTTAAATCAACGAGCTATTTAGATTAGCAATA
55017405 G
131 G
* * * *
55017406 TAAATCAACTAACTCAGAAAAAATTGTTCATGATATTAAATCAAATGAACCTAAGCTGCAATCTT
1 TAAATCAACTAACTCAGAAAAAATTGTTCATAATATTAAATCAAATGAACATAGGCTACAATCTT
*
55017471 AAATCAACGAG
66 AAATTAACGAG
55017482 TTGTTTAGAG
Statistics
Matches: 174, Mismatches: 30, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
130 110 0.63
131 64 0.37
ACGTcount: A:0.39, C:0.16, G:0.15, T:0.29
Consensus pattern (131 bp):
TAAATCAACTAACTCAGAAAAAATTGTTCATAATATTAAATCAAATGAACATAGGCTACAATCTT
AAATTAACGAGCCTTAACGATATCAGCTGCGATCTTAAATCAACGAGCTATTTAGATTAGCAATA
G
Found at i:55021286 original size:11 final size:11
Alignment explanation
Indices: 55021270--55021304 Score: 61
Period size: 11 Copynumber: 3.1 Consensus size: 11
55021260 ATTGTGTTAC
55021270 AATAAAATAAA
1 AATAAAATAAA
55021281 AATAAAATAAA
1 AATAAAATAAA
55021292 AATAAAATGAAA
1 AATAAAAT-AAA
55021304 A
1 A
55021305 CAAATAGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 19 0.83
12 4 0.17
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (11 bp):
AATAAAATAAA
Found at i:55023854 original size:19 final size:18
Alignment explanation
Indices: 55023822--55023868 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 18
55023812 GTGACCCCTG
*
55023822 TTTTCAAAATTTTTAGAT
1 TTTTCAAAACTTTTAGAT
55023840 TTTTCTAAAACTTTTAGAT
1 TTTTC-AAAACTTTTAGAT
55023859 CTATTTCAAA
1 -T-TTTCAAA
55023869 TTAGTCCCTG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 5 0.20
19 12 0.48
20 4 0.16
21 4 0.16
ACGTcount: A:0.34, C:0.11, G:0.04, T:0.51
Consensus pattern (18 bp):
TTTTCAAAACTTTTAGAT
Found at i:55047454 original size:13 final size:14
Alignment explanation
Indices: 55047435--55047472 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 14
55047425 CGATGGCATA
55047435 GAAATAATATAAAC
1 GAAATAATATAAAC
55047449 -AAATAA-ATAAAC
1 GAAATAATATAAAC
55047461 GAAACTAATATA
1 GAAA-TAATATA
55047473 CATAAGAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 6 0.29
13 9 0.43
14 3 0.14
15 3 0.14
ACGTcount: A:0.66, C:0.08, G:0.05, T:0.21
Consensus pattern (14 bp):
GAAATAATATAAAC
Found at i:55047605 original size:22 final size:23
Alignment explanation
Indices: 55047566--55047611 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
55047556 TAAACAAATG
*
55047566 AAAGAAATAAACAAAAAA-ATAT
1 AAAGAAAAAAACAAAAAATATAT
* *
55047588 AAAGAAAAAAATACAAAATATAT
1 AAAGAAAAAAACAAAAAATATAT
55047611 A
1 A
55047612 TATTGAAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.76, C:0.04, G:0.04, T:0.15
Consensus pattern (23 bp):
AAAGAAAAAAACAAAAAATATAT
Found at i:55048212 original size:14 final size:14
Alignment explanation
Indices: 55048193--55048227 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
55048183 AAATAAAATT
55048193 TAATAAACAATAAA
1 TAATAAACAATAAA
55048207 TAATAAACAATAAA
1 TAATAAACAATAAA
55048221 TAATAAA
1 TAATAAA
55048228 TAAAAAAGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.23
Consensus pattern (14 bp):
TAATAAACAATAAA
Found at i:55048228 original size:7 final size:7
Alignment explanation
Indices: 55048143--55048230 Score: 63
Period size: 7 Copynumber: 12.1 Consensus size: 7
55048133 TAAAATATAC
55048143 ATAAATGA
1 ATAAAT-A
*
55048151 ATATATA
1 ATAAATA
55048158 ATAACAATA
1 AT-A-AATA
**
55048167 ATACTTA
1 ATAAATA
55048174 ATAAA-A
1 ATAAATA
55048180 ATAAAATA
1 AT-AAATA
*
55048188 A-AATTTA
1 ATAA-ATA
*
55048195 ATAAACA
1 ATAAATA
55048202 ATAAATA
1 ATAAATA
*
55048209 ATAAACA
1 ATAAATA
55048216 ATAAATA
1 ATAAATA
55048223 ATAAATA
1 ATAAATA
55048230 A
1 A
55048231 AAAAGACTAA
Statistics
Matches: 62, Mismatches: 12, Indels: 13
0.71 0.14 0.15
Matches are distributed among these distances:
6 5 0.08
7 41 0.66
8 11 0.18
9 5 0.08
ACGTcount: A:0.67, C:0.05, G:0.01, T:0.27
Consensus pattern (7 bp):
ATAAATA
Found at i:55051494 original size:57 final size:57
Alignment explanation
Indices: 55051354--55051463 Score: 166
Period size: 57 Copynumber: 1.9 Consensus size: 57
55051344 TAAATTCATG
* * * * *
55051354 GATAGAATATGGAGTTGAGATGAGTTATGTATATTTGATATAAATTTATGGATAGAC
1 GATAGAATATGAAATTGATATGAGTTATGTATATTTGATATAAATTCATAGATAGAC
*
55051411 GATAGAATATGAAATTGATATGAGTTATGTGTATTTGATATAAATTCATAGAT
1 GATAGAATATGAAATTGATATGAGTTATGTATATTTGATATAAATTCATAGAT
55051464 TGATGATAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
57 47 1.00
ACGTcount: A:0.38, C:0.02, G:0.22, T:0.38
Consensus pattern (57 bp):
GATAGAATATGAAATTGATATGAGTTATGTATATTTGATATAAATTCATAGATAGAC
Found at i:55053888 original size:25 final size:25
Alignment explanation
Indices: 55053859--55053914 Score: 112
Period size: 25 Copynumber: 2.2 Consensus size: 25
55053849 ATGGAAAGTA
55053859 TGAATTCAATGGCATTATGTTAATG
1 TGAATTCAATGGCATTATGTTAATG
55053884 TGAATTCAATGGCATTATGTTAATG
1 TGAATTCAATGGCATTATGTTAATG
55053909 TGAATT
1 TGAATT
55053915 TACCTTATCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.32, C:0.07, G:0.20, T:0.41
Consensus pattern (25 bp):
TGAATTCAATGGCATTATGTTAATG
Found at i:55061251 original size:16 final size:17
Alignment explanation
Indices: 55061230--55061267 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
55061220 TTCTATAGGG
*
55061230 ATTTTACT-TTTATTTT
1 ATTTTACTATGTATTTT
55061246 ATTTTACTACTGTATTTT
1 ATTTTACTA-TGTATTTT
55061264 ATTT
1 ATTT
55061268 AAATAATGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 8 0.42
18 11 0.58
ACGTcount: A:0.21, C:0.08, G:0.03, T:0.68
Consensus pattern (17 bp):
ATTTTACTATGTATTTT
Found at i:55065442 original size:21 final size:23
Alignment explanation
Indices: 55065406--55065450 Score: 67
Period size: 21 Copynumber: 2.0 Consensus size: 23
55065396 TAAAAAAATT
55065406 TAAAATTATTAAAATTTT-AATA
1 TAAAATTATTAAAATTTTCAATA
*
55065428 TAAAA-TATTATAATTTTCAATA
1 TAAAATTATTAAAATTTTCAATA
55065450 T
1 T
55065451 TATTAAACGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (23 bp):
TAAAATTATTAAAATTTTCAATA
Found at i:55065535 original size:13 final size:13
Alignment explanation
Indices: 55065517--55065542 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
55065507 TTTCATTTTT
55065517 ATTTTAATAATAA
1 ATTTTAATAATAA
55065530 ATTTTAATAATAA
1 ATTTTAATAATAA
55065543 TACTCTTCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
ATTTTAATAATAA
Found at i:55068453 original size:2 final size:2
Alignment explanation
Indices: 55068446--55068562 Score: 85
Period size: 2 Copynumber: 58.5 Consensus size: 2
55068436 CAATATGAGC
55068446 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG -G
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
* * * * * * * * * * *
55068487 GG GG GG AC A- ATG AC AG GG AC AG GG AG GG AG AG AG AG GG GG AG
1 AG AG AG AG AG A-G AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
* *
55068529 AG AG GG AG AG AG GG AG AG AG AG AG AG AG ATG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A-G AG A
55068563 ATAAGAAGGA
Statistics
Matches: 93, Mismatches: 18, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
1 2 0.02
2 88 0.95
3 3 0.03
ACGTcount: A:0.41, C:0.03, G:0.55, T:0.02
Consensus pattern (2 bp):
AG
Found at i:55070471 original size:21 final size:23
Alignment explanation
Indices: 55070447--55070498 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 23
55070437 TTCTATTAAG
55070447 TTTTTCTGTCTT-TTGACACGCTT
1 TTTTTCTGTCTTGTTGACACGC-T
55070470 TTTCTTCTGTCTTGTTGACACGCT
1 TTT-TTCTGTCTTGTTGACACGCT
*
55070494 CTTTT
1 TTTTT
55070499 GGTTTTTCTG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
23 5 0.19
24 12 0.46
25 9 0.35
ACGTcount: A:0.08, C:0.23, G:0.13, T:0.56
Consensus pattern (23 bp):
TTTTTCTGTCTTGTTGACACGCT
Found at i:55070481 original size:24 final size:26
Alignment explanation
Indices: 55070450--55070498 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 26
55070440 TATTAAGTTT
55070450 TTCTGTCTT-TTGACACGCT-TTTTC
1 TTCTGTCTTGTTGACACGCTCTTTTC
55070474 TTCTGTCTTGTTGACACGCTCTTTT
1 TTCTGTCTTGTTGACACGCTCTTTT
55070499 GGTTTTTCTG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 9 0.39
25 10 0.43
26 4 0.17
ACGTcount: A:0.08, C:0.24, G:0.14, T:0.53
Consensus pattern (26 bp):
TTCTGTCTTGTTGACACGCTCTTTTC
Found at i:55090601 original size:112 final size:112
Alignment explanation
Indices: 55090404--55090620 Score: 371
Period size: 112 Copynumber: 1.9 Consensus size: 112
55090394 TTAACATCCC
* *
55090404 GGTGATAGAAAAAGGCAATATTCGTTCGTTGATCGCTGCAGAGGTGTTACTATTTTGATCATAAT
1 GGTGATAGAAAAAAGCAATATTCGTTCGTTGATCGCTGCAGAGGTGTTACTACTTTGATCATAAT
* *
55090469 GTTGTTATATCTTGGAAGACATTCGACCAACGTTTCTTCAGCAATAA
66 GCTGTTATATCCTGGAAGACATTCGACCAACGTTTCTTCAGCAATAA
* *
55090516 GGTGATAGAAAAAAGCAATGTTCGTTCGTTGATCGCTGCAGAGGTGTTACTACTTTGATCATAGT
1 GGTGATAGAAAAAAGCAATATTCGTTCGTTGATCGCTGCAGAGGTGTTACTACTTTGATCATAAT
*
55090581 GCTGTTATATCCTGGGAGACATTCGACCAACGTTTCTTCA
66 GCTGTTATATCCTGGAAGACATTCGACCAACGTTTCTTCA
55090621 ACCGTAAGAG
Statistics
Matches: 98, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
112 98 1.00
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.33
Consensus pattern (112 bp):
GGTGATAGAAAAAAGCAATATTCGTTCGTTGATCGCTGCAGAGGTGTTACTACTTTGATCATAAT
GCTGTTATATCCTGGAAGACATTCGACCAACGTTTCTTCAGCAATAA
Found at i:55091140 original size:88 final size:86
Alignment explanation
Indices: 55090924--55091408 Score: 382
Period size: 87 Copynumber: 5.6 Consensus size: 86
55090914 AAAAAAATTG
* * * * *
55090924 AAAA-TAAATAAAATTTGTTTCGGGATTAATTCCCGCCATTCAACTGATTTTATTCTTTATTTTG
1 AAAATTAAATAAAATCTGTTTCGGGATTTATTCCCGCCGTTCAACAGATTTTATTC--CATTTTG
*
55090988 -TTTTTATTTCCAAACA-A-ATATT
64 ATTTTT-TTT-CAAAAATAGATATT
* * ** * *
55091010 AAAATTAAAAAAAATATGTTTCAAGATTTATTCCCGCTGTTCAACGGATTTTATTCCAATTTTGA
1 AAAATTAAATAAAATCTGTTTCGGGATTTATTCCCGCCGTTCAACAGATTTTATTCC-ATTTTGA
*
55091075 TTTTTTTTTAAAAAT-GATTATT
65 TTTTTTTTCAAAAATAGA-TATT
* * * * *
55091097 AAAATTAAAATAAAATCTGTTTCGAGATTTATTCCCGCCGTTCAACGGATTTCATTACATTCTGA
1 AAAATT-AAATAAAATCTGTTTCGGGATTTATTCCCGCCGTTCAACAGATTTTATTCCATTTTGA
* *
55091162 TTTTTTTGCAAAAACTAGAAATT
65 TTTTTTTTCAAAAA-TAGATATT
* * ** * *
55091185 CAAATTAAATAAAATCTATTTCGGGATTTATTCCTACCGTTTAACAAGATTTTATTCGA-TTTGA
1 AAAATTAAATAAAATCTGTTTCGGGATTTATTCCCGCCGTTCAAC-AGATTTTATTCCATTTTGA
* * * *
55091249 TGTTGTTTCCAAATTAGA-ATT
65 TTTTTTTTCAAAAATAGATATT
* * * * * *
55091270 AAAATTAAATAAAATCTATTTCGGGATTTATTCTCGCAGTTTAACAAGATTTTATTCGATATTG-
1 AAAATTAAATAAAATCTGTTTCGGGATTTATTCCCGCCGTTCAAC-AGATTTTATTCCATTTTGA
* *
55091334 TTTTGTTTCCAAACAA-AGA-CTT
65 TTTT-TTTTCAAA-AATAGATATT
* * * * * *
55091356 --AATCAAATAAAATCTGTTTTGGGATTTATTCCCGTCATTTAACATATTTTATT
1 AAAATTAAATAAAATCTGTTTCGGGATTTATTCCCGCCGTTCAACAGATTTTATT
55091409 AAATCCCGAA
Statistics
Matches: 329, Mismatches: 57, Indels: 29
0.79 0.14 0.07
Matches are distributed among these distances:
83 9 0.03
84 36 0.11
85 64 0.19
86 31 0.09
87 124 0.38
88 63 0.19
89 2 0.01
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.42
Consensus pattern (86 bp):
AAAATTAAATAAAATCTGTTTCGGGATTTATTCCCGCCGTTCAACAGATTTTATTCCATTTTGAT
TTTTTTTCAAAAATAGATATT
Found at i:55091290 original size:85 final size:83
Alignment explanation
Indices: 55091094--55091387 Score: 292
Period size: 85 Copynumber: 3.4 Consensus size: 83
55091084 AAAAATGATT
* * * * * *
55091094 ATTAAAATTAAAATAAAATCTGTTTCGAGATTTATTCCCGCCGTTCAAC-GGATTTCATTAC-AT
1 ATTAAAATT-AAATAAAATCTATTTCGGGATTTATT-CCTCCGTTTAACAAGATTTTATT-CGAT
* *
55091157 TCTGATTTTTTTGCAAAAACTAGAA
63 T-TGATTTGTTT-CCAAAA-TAG-A
*
55091182 ATTCAAATTAAATAAAATCTATTTCGGGATTTATTCCTACCGTTTAACAAGATTTTATTCGATTT
1 ATTAAAATTAAATAAAATCTATTTCGGGATTTATTCCT-CCGTTTAACAAGATTTTATTCGATTT
*
55091247 GATGTTGTTTCCAAATTAGA
65 GAT-TTGTTTCCAAAATAGA
55091267 ATTAAAATTAAATAAAATCTATTTCGGGATTTATT-CTCGCAGTTTAACAAGATTTTATTCGATA
1 ATTAAAATTAAATAAAATCTATTTCGGGATTTATTCCTC-C-GTTTAACAAGATTTTATTCGAT-
* *
55091331 TTGTTTTGTTTCCAAACAAAGA
63 TTGATTTGTTTCCAAA-ATAGA
* * * *
55091353 CTT--AATCAAATAAAATCTGTTTTGGGATTTATTCC
1 ATTAAAATTAAATAAAATCTATTTCGGGATTTATTCC
55091388 CGTCATTTAA
Statistics
Matches: 179, Mismatches: 18, Indels: 21
0.82 0.08 0.10
Matches are distributed among these distances:
83 1 0.01
84 30 0.17
85 69 0.39
86 14 0.08
87 41 0.23
88 24 0.13
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.40
Consensus pattern (83 bp):
ATTAAAATTAAATAAAATCTATTTCGGGATTTATTCCTCCGTTTAACAAGATTTTATTCGATTTG
ATTTGTTTCCAAAATAGA
Found at i:55091689 original size:91 final size:93
Alignment explanation
Indices: 55091589--55091764 Score: 225
Period size: 91 Copynumber: 1.9 Consensus size: 93
55091579 ATCAAAATGT
* * * *
55091589 AATATAATCCATTGAACGGTAG-GAATAAATCCCGAAACAAAATTTA-TTTAACTTTAAT-TTCT
1 AATAAAATCCATAGAACGG-AGAGAATAAATCCCGAAACAAAATTTATTTTAACTTTAATACTCG
55091651 TGTTTGGAAATAAAAT-AAAATAAAAAAAG
65 T-TTTGGAAATAAAATCAAAATAAAAAAAG
* * * * *
55091680 AATAAAATCCGTAGAACGGCGAGAATAAATCCCGAAACATATTTTATTTTAATTTTAATACTCGT
1 AATAAAATCCATAGAACGGAGAGAATAAATCCCGAAACAAAATTTATTTTAACTTTAATACTCGT
55091745 TTTGGAAATAAAATCAAAAT
66 TTTGGAAATAAAATCAAAAT
55091765 TAGAATAAAA
Statistics
Matches: 72, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
90 1 0.01
91 38 0.53
92 25 0.35
93 8 0.11
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.31
Consensus pattern (93 bp):
AATAAAATCCATAGAACGGAGAGAATAAATCCCGAAACAAAATTTATTTTAACTTTAATACTCGT
TTTGGAAATAAAATCAAAATAAAAAAAG
Found at i:55091832 original size:87 final size:87
Alignment explanation
Indices: 55091611--55091908 Score: 271
Period size: 87 Copynumber: 3.4 Consensus size: 87
55091601 TGAACGGTAG
* * * * * * * *
55091611 GAATAAATCCCGAAACAAAATTTATTTAACTTTAATTTCTTGTTTGGAAATAAAATAAAATAAAA
1 GAATAAATCCCGAAACAGATTTTATTTAATTTTAA-TACTCGTTTAGAAAT-AAA-AACA-AAAT
** * **
55091676 AAAGAATAAAATCCGTAGAACGGCGA
62 AAAGAATAAAATCTATTGAACAACGA
* * * *
55091702 GAATAAATCCCGAAACATATTTTATTTTAATTTTAATACTCGTTTTGGAAATAAAATCAAAAT-T
1 GAATAAATCCCGAAACAGATTTTA-TTTAATTTTAATACTCG-TTTAGAAATAAAAACAAAATAA
55091766 AGAATAAAAT-TCATTGAACAACTG-
64 AGAATAAAATCT-ATTGAACAAC-GA
* * * * *
55091790 GAATAAATTCTGAAATAGATTTTATTTAATTTTAATATTCGTTTAGAAATAAAAACAATATAAAG
1 GAATAAATCCCGAAACAGATTTTATTTAATTTTAATACTCGTTTAGAAATAAAAACAAAATAAAG
* *
55091855 AATATAATCTGTTGAACAACGA
66 AATAAAATCTATTGAACAACGA
*
55091877 GAATTAATCCCGAAACAGATTTTATTT-ATTTT
1 GAATAAATCCCGAAACAGATTTTATTTAATTTT
55091909 CAAAATTTAT
Statistics
Matches: 171, Mismatches: 29, Indels: 19
0.78 0.13 0.09
Matches are distributed among these distances:
86 23 0.13
87 57 0.33
88 37 0.22
89 4 0.02
90 2 0.01
91 29 0.17
92 19 0.11
ACGTcount: A:0.46, C:0.10, G:0.10, T:0.34
Consensus pattern (87 bp):
GAATAAATCCCGAAACAGATTTTATTTAATTTTAATACTCGTTTAGAAATAAAAACAAAATAAAG
AATAAAATCTATTGAACAACGA
Found at i:55091918 original size:13 final size:13
Alignment explanation
Indices: 55091900--55091924 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55091890 AACAGATTTT
55091900 ATTTATTTTCAAA
1 ATTTATTTTCAAA
55091913 ATTTATTTTCAA
1 ATTTATTTTCAA
55091925 TTTTTTTCTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (13 bp):
ATTTATTTTCAAA
Found at i:55097990 original size:31 final size:31
Alignment explanation
Indices: 55097927--55098248 Score: 273
Period size: 31 Copynumber: 10.4 Consensus size: 31
55097917 ATCCAATGCT
*
55097927 CAAATCAA-TTCAATAATATATATATTCATATA
1 CAAATCAATTTCAATAATGTATA-A-TCATATA
55097959 CAAATCAATTTCAATAATGTATAATCATATA
1 CAAATCAATTTCAATAATGTATAATCATATA
* * *
55097990 CAAATTAATTTCAACAATGAATAATCATATA
1 CAAATCAATTTCAATAATGTATAATCATATA
* *
55098021 CGAATCAATTTTAATAATGTATAATCATATA
1 CAAATCAATTTCAATAATGTATAATCATATA
* ** *
55098052 CAAATTAATTTCAGCAATGAATAATCATATA
1 CAAATCAATTTCAATAATGTATAATCATATA
* * * * *
55098083 -AGAACCAA-TTCGACAGCT-TAT-ATCCTTATA
1 CA-AATCAATTTCAATA-ATGTATAAT-CATATA
*
55098113 CAAATCAATTTCAATAATGTGTAATCATATA
1 CAAATCAATTTCAATAATGTATAATCATATA
* ** *
55098144 CAAATTAATTTCAGCAATGAATAATCATATA
1 CAAATCAATTTCAATAATGTATAATCATATA
* * * * *
55098175 CGAATCAATTTGACA-ACT-TATATTCATTTA
1 CAAATCAATTTCA-ATAATGTATAATCATATA
* *
55098205 CAAATCAATTTCAATAATGAATAA-CTATAAA
1 CAAATCAATTTCAATAATGTATAATC-ATATA
*
55098236 CAAATTAATTTCA
1 CAAATCAATTTCA
55098249 GCAATGAATA
Statistics
Matches: 229, Mismatches: 49, Indels: 25
0.76 0.16 0.08
Matches are distributed among these distances:
29 3 0.01
30 42 0.18
31 160 0.70
32 11 0.05
33 13 0.06
ACGTcount: A:0.47, C:0.14, G:0.05, T:0.34
Consensus pattern (31 bp):
CAAATCAATTTCAATAATGTATAATCATATA
Found at i:55098276 original size:92 final size:91
Alignment explanation
Indices: 55097927--55098267 Score: 382
Period size: 92 Copynumber: 3.7 Consensus size: 91
55097917 ATCCAATGCT
* * ** *
55097927 CAAATCAA-TTCAATAATATATATATTCATATACAAATCAATTTCAATAATGTATAATCATATAC
1 CAAATCAATTTCAATAATGTATA-A-TCATATACAAATTAATTTCAGCAATGAATAATCATATAC
* ** * * *
55097991 AAATTAATTTCAACAA-TGAATAATCATATA
64 GAACCAA-TTCGACAACT-TAT-ATCATTTA
* * *
55098021 CGAATCAATTTTAATAATGTATAATCATATACAAATTAATTTCAGCAATGAATAATCATATAAGA
1 CAAATCAATTTCAATAATGTATAATCATATACAAATTAATTTCAGCAATGAATAATCATATACGA
* *
55098086 ACCAATTCGACAGCTTATATCCTTATA
66 ACCAATTCGACAACTTATATCATT-TA
*
55098113 CAAATCAATTTCAATAATGTGTAATCATATACAAATTAATTTCAGCAATGAATAATCATATACGA
1 CAAATCAATTTCAATAATGTATAATCATATACAAATTAATTTCAGCAATGAATAATCATATACGA
* *
55098178 ATCAATTTGACAACTTATATTCATTTA
66 ACCAATTCGACAACTTATA-TCATTTA
* * * *
55098205 CAAATCAATTTCAATAATGAATAA-CTATAAACAAATTAATTTCAGCAATGAATATTGATATAC
1 CAAATCAATTTCAATAATGTATAATC-ATATACAAATTAATTTCAGCAATGAATAATCATATAC
55098268 CCAACAATTC
Statistics
Matches: 213, Mismatches: 29, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
91 5 0.02
92 145 0.68
93 43 0.20
94 8 0.04
95 12 0.06
ACGTcount: A:0.46, C:0.14, G:0.06, T:0.34
Consensus pattern (91 bp):
CAAATCAATTTCAATAATGTATAATCATATACAAATTAATTTCAGCAATGAATAATCATATACGA
ACCAATTCGACAACTTATATCATTTA
Found at i:55098303 original size:92 final size:89
Alignment explanation
Indices: 55097927--55098332 Score: 350
Period size: 92 Copynumber: 4.4 Consensus size: 89
55097917 ATCCAATGCT
* * ** *
55097927 CAAATCAA-TTCAATAATATATATATTCATATACAAATCAATTTCAATAATGTATAATCATATAC
1 CAAATCAATTTCAATAATGTATA-A-TCATATACAAATTAATTTCAGCAATGAATAATCATATAC
* ** * * *
55097991 AAATTAATTTCAACAATGAATAATCATATA
64 GAACCAA-TTCGACAAT-TAT-ATC-CATA
* * *
55098021 CGAATCAATTTTAATAATGTATAATCATATACAAATTAATTTCAGCAATGAATAATCATATAAGA
1 CAAATCAATTTCAATAATGTATAATCATATACAAATTAATTTCAGCAATGAATAATCATATACGA
*
55098086 ACCAATTCGACAGCTTATATCCTTATA
66 ACCAATTCGACA-ATTATATCC--ATA
*
55098113 CAAATCAATTTCAATAATGTGTAATCATATACAAATTAATTTCAGCAATGAATAATCATATACGA
1 CAAATCAATTTCAATAATGTATAATCATATACAAATTAATTTCAGCAATGAATAATCATATACGA
* * *
55098178 ATCAATTTGACAACTTATATTCATTTA
66 ACCAATTCGACAA-TTATATCCA--TA
* * * *
55098205 CAAATCAATTTCAATAATGAATAA-CTATAAACAAATTAATTTCAGCAATGAATATTGATATACC
1 CAAATCAATTTCAATAATGTATAATC-ATATACAAATTAATTTCAGCAATGAATAATCATATA-C
* * *
55098269 CAA-CAATTCGGCAATGTATAACCACTCA
64 GAACCAATTCGACAAT-TATATCCA-T-A
* * ** * *
55098297 CGAATCAAGTTCAGCAATGTATAATTATACACAAAT
1 CAAATCAATTTCAATAATGTATAATCATATACAAAT
55098333 CAAATTCGGC
Statistics
Matches: 259, Mismatches: 41, Indels: 26
0.79 0.13 0.08
Matches are distributed among these distances:
90 1 0.00
91 6 0.02
92 190 0.73
93 42 0.16
94 8 0.03
95 12 0.05
ACGTcount: A:0.46, C:0.15, G:0.06, T:0.33
Consensus pattern (89 bp):
CAAATCAATTTCAATAATGTATAATCATATACAAATTAATTTCAGCAATGAATAATCATATACGA
ACCAATTCGACAATTATATCCATA
Found at i:55098334 original size:31 final size:31
Alignment explanation
Indices: 55097927--55098335 Score: 207
Period size: 31 Copynumber: 13.3 Consensus size: 31
55097917 ATCCAATGCT
** *
55097927 CAAATCAA-TTCAATAATATATATATTCATATA
1 CAAATCAATTTCAGCAATGTATA-ATT-ATATA
** *
55097959 CAAATCAATTTCAATAATGTATAATCATATA
1 CAAATCAATTTCAGCAATGTATAATTATATA
* * * *
55097990 CAAATTAATTTCAACAATGAATAATCATATA
1 CAAATCAATTTCAGCAATGTATAATTATATA
* * ** *
55098021 CGAATCAATTTTAATAATGTATAATCATATA
1 CAAATCAATTTCAGCAATGTATAATTATATA
* * *
55098052 CAAATTAATTTCAGCAATGAATAATCATATA
1 CAAATCAATTTCAGCAATGTATAATTATATA
* *
55098083 -AGAACCAA-TTC-GACAGCT-TAT-ATCCT-TATA
1 CA-AATCAATTTCAG-CA-ATGTATAAT--TATATA
** * *
55098113 CAAATCAATTTCAATAATGTGTAATCATATA
1 CAAATCAATTTCAGCAATGTATAATTATATA
* * *
55098144 CAAATTAATTTCAGCAATGAATAATCATATA
1 CAAATCAATTTCAGCAATGTATAATTATATA
* * *
55098175 CGAATCAATTTGA-CAACT-TAT-ATTCATTTA
1 CAAATCAATTTCAGCAA-TGTATAATT-ATATA
** * * *
55098205 CAAATCAATTTCAATAATGAATAACTATAAA
1 CAAATCAATTTCAGCAATGTATAATTATATA
* *
55098236 CAAATTAATTTCAGCAATGAAT-ATTGATATA
1 CAAATCAATTTCAGCAATGTATAATT-ATATA
* * ** *
55098267 CCCAA-CAA-TTCGGCAATGTATAACCACT-CA
1 -CAAATCAATTTCAGCAATGTATAATTA-TATA
* * *
55098297 CGAATCAAGTTCAGCAATGTATAATTATACA
1 CAAATCAATTTCAGCAATGTATAATTATATA
55098328 CAAATCAA
1 CAAATCAA
55098336 ATTCGGCATC
Statistics
Matches: 291, Mismatches: 62, Indels: 49
0.72 0.15 0.12
Matches are distributed among these distances:
29 8 0.03
30 58 0.20
31 195 0.67
32 17 0.06
33 13 0.04
ACGTcount: A:0.46, C:0.15, G:0.06, T:0.33
Consensus pattern (31 bp):
CAAATCAATTTCAGCAATGTATAATTATATA
Found at i:55098513 original size:91 final size:90
Alignment explanation
Indices: 55098418--55098703 Score: 263
Period size: 91 Copynumber: 3.1 Consensus size: 90
55098408 AGGTAAAACT
* * * * *
55098418 ATATACGAATCAATGCATCAACTTAAATCCATATACCAAACAGTTCGGCAATATATAACCATACA
1 ATATACAAATCAATGCGTCAACTTATATCCATATACCAAACAATTCGACAATATATAACCATACA
55098483 CGAATCAAGTTCAATATTGTATACTC
66 C-AATCAAGTTCAATATTGTATACTC
* * * * * * *
55098509 ATATACAAATCCAATTCGGC-ATTCTATATTCATA-AACAATTCAATATCGACAATTTATAACCA
1 ATATACAAAT-CAATGCGTCAACT-TATATCCATATACCAA-ACAAT-TCGACAATATATAACCA
** * * ** ** *
55098572 TGTACAATTAAATTTCAGCAAGGTAAAACT-
62 TACACAA-TCAAGTTCAATATTGT-ATACTC
*
55098602 ATATACGAATCAATGCGTCAACTTATATCCATATACCAAACAATTCGACAATATATAACCATACA
1 ATATACAAATCAATGCGTCAACTTATATCCATATACCAAACAATTCGACAATATATAACCATACA
* *
55098667 CAAATCAAGTTCGATCTTGTATACTC
66 C-AATCAAGTTCAATATTGTATACTC
55098693 ATATACAAATC
1 ATATACAAATC
55098704 CAATTCGGCA
Statistics
Matches: 144, Mismatches: 41, Indels: 20
0.70 0.20 0.10
Matches are distributed among these distances:
90 4 0.03
91 52 0.36
92 41 0.28
93 43 0.30
94 4 0.03
ACGTcount: A:0.42, C:0.21, G:0.08, T:0.29
Consensus pattern (90 bp):
ATATACAAATCAATGCGTCAACTTATATCCATATACCAAACAATTCGACAATATATAACCATACA
CAATCAAGTTCAATATTGTATACTC
Found at i:55098640 original size:184 final size:184
Alignment explanation
Indices: 55098262--55098783 Score: 821
Period size: 184 Copynumber: 2.8 Consensus size: 184
55098252 ATGAATATTG
* * ** * * *
55098262 ATATACCCAACAATTCGGCAATGTATAACCACT-CACGAATCAAGTTCAGCAATGTATAATTATA
1 ATATACCAAACAATTCGGCAATATATAACCA-TACACGAATCAAGTTCAATATTGTATACTCATA
* * * *
55098326 CACAAATCAAATTCGGCATCCTATATACATAAACAATGCAATATCGACAATATATATAACCATGT
65 TACAAATCCAATTCGGCATCCTATATTCATAAACAATTCAATATCGACAAT-T-TATAACCATGT
55098391 ACAATTAAATTTCAGCAAGGTAAAACTATATACGAATCAATGCATCAACTTAAATCC
128 ACAATTAAATTTCAGCAAGGTAAAACTATATACGAATCAATGCATCAACTTAAATCC
*
55098448 ATATACCAAACAGTTCGGCAATATATAACCATACACGAATCAAGTTCAATATTGTATACTCATAT
1 ATATACCAAACAATTCGGCAATATATAACCATACACGAATCAAGTTCAATATTGTATACTCATAT
*
55098513 ACAAATCCAATTCGGCATTCTATATTCATAAACAATTCAATATCGACAATTTATAACCATGTACA
66 ACAAATCCAATTCGGCATCCTATATTCATAAACAATTCAATATCGACAATTTATAACCATGTACA
* *
55098578 ATTAAATTTCAGCAAGGTAAAACTATATACGAATCAATGCGTCAACTTATATCC
131 ATTAAATTTCAGCAAGGTAAAACTATATACGAATCAATGCATCAACTTAAATCC
* * * *
55098632 ATATACCAAACAATTCGACAATATATAACCATACACAAATCAAGTTCGATCTTGTATACTCATAT
1 ATATACCAAACAATTCGGCAATATATAACCATACACGAATCAAGTTCAATATTGTATACTCATAT
* *
55098697 ACAAATCCAATTCGGCATCCTATATTCATAAACAATTCAATATCGATAATTTATAACCATGAACA
66 ACAAATCCAATTCGGCATCCTATATTCATAAACAATTCAATATCGACAATTTATAACCATGTACA
55098762 ATTAAATTTCAGCAAGGTAAAA
131 ATTAAATTTCAGCAAGGTAAAA
55098784 ACATTATATT
Statistics
Matches: 312, Mismatches: 23, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
184 210 0.67
185 2 0.01
186 100 0.32
ACGTcount: A:0.43, C:0.20, G:0.08, T:0.28
Consensus pattern (184 bp):
ATATACCAAACAATTCGGCAATATATAACCATACACGAATCAAGTTCAATATTGTATACTCATAT
ACAAATCCAATTCGGCATCCTATATTCATAAACAATTCAATATCGACAATTTATAACCATGTACA
ATTAAATTTCAGCAAGGTAAAACTATATACGAATCAATGCATCAACTTAAATCC
Found at i:55117871 original size:3 final size:3
Alignment explanation
Indices: 55117859--55117935 Score: 61
Period size: 3 Copynumber: 26.3 Consensus size: 3
55117849 TTCAGTTTAA
* * * * * *
55117859 TAT T-T TAT TAT TAT TAT TAT TAT TAT TAA TAG TAG TAG TAT TAA TAC
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
55117906 TAT TAT TAT TAT TGGT T-T TAT TAT T-T TAT T
1 TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT T
55117936 TTTGTTTATA
Statistics
Matches: 63, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
2 6 0.10
3 55 0.87
4 2 0.03
ACGTcount: A:0.31, C:0.01, G:0.06, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:55121420 original size:9 final size:9
Alignment explanation
Indices: 55121407--55121471 Score: 62
Period size: 9 Copynumber: 7.0 Consensus size: 9
55121397 AAATTAAAAA
55121407 AATATTTTT
1 AATATTTTT
*
55121416 TATATTTTT
1 AATATTTTT
55121425 AATAATTTTT
1 AAT-ATTTTT
*
55121435 AAATAATTTT
1 -AATATTTTT
55121445 AATATTTTTT
1 AATA-TTTTT
55121455 AAT-TTTTAT
1 AATATTTT-T
55121464 AA-ATTTTT
1 AATATTTTT
55121472 GTTTTTAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 11
0.76 0.06 0.18
Matches are distributed among these distances:
8 5 0.11
9 21 0.45
10 18 0.38
11 3 0.06
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (9 bp):
AATATTTTT
Found at i:55121438 original size:29 final size:27
Alignment explanation
Indices: 55121406--55121471 Score: 80
Period size: 29 Copynumber: 2.4 Consensus size: 27
55121396 AAAATTAAAA
*
55121406 AAATATTTTTTATATTTTTAATAATTTTT
1 AAATATTTTTAATATTTTT--TAATTTTT
*
55121435 AAATAATTTTAATATTTTTTAATTTTT
1 AAATATTTTTAATATTTTTTAATTTTT
55121462 ATAA-ATTTTT
1 A-AATATTTTT
55121472 GTTTTTAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
27 14 0.42
28 2 0.06
29 17 0.52
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (27 bp):
AAATATTTTTAATATTTTTTAATTTTT
Found at i:55121439 original size:11 final size:10
Alignment explanation
Indices: 55121410--55121457 Score: 55
Period size: 10 Copynumber: 4.9 Consensus size: 10
55121400 TTAAAAAAAT
*
55121410 ATTTTTTAT-
1 ATTTTTAATA
55121419 ATTTTTAATA
1 ATTTTTAATA
55121429 ATTTTTAAATA
1 ATTTTT-AATA
55121440 A-TTTTAATA
1 ATTTTTAATA
*
55121449 TTTTTTAAT
1 ATTTTTAAT
55121458 TTTTATAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
9 12 0.35
10 17 0.50
11 5 0.15
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (10 bp):
ATTTTTAATA
Found at i:55123151 original size:19 final size:18
Alignment explanation
Indices: 55123135--55123168 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
55123125 GCTGAAAATG
55123135 AAAAGAGAA-GATAAAAA
1 AAAAGAGAATGATAAAAA
*
55123152 ACAAGAGAATGATAAAA
1 AAAAGAGAATGATAAAA
55123169 TTTGAATTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.71, C:0.03, G:0.18, T:0.09
Consensus pattern (18 bp):
AAAAGAGAATGATAAAAA
Found at i:55123577 original size:17 final size:17
Alignment explanation
Indices: 55123557--55123590 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
55123547 TCATTATTGA
55123557 AATTATATATATATTTG
1 AATTATATATATATTTG
*
55123574 AATTATTTATATATTTG
1 AATTATATATATATTTG
55123591 TTTCTATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (17 bp):
AATTATATATATATTTG
Found at i:55129624 original size:20 final size:20
Alignment explanation
Indices: 55129590--55129631 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
55129580 AACTATTTAA
** *
55129590 ATAATATTATTTGAATAGTT
1 ATAATATTAAATGAATAATT
55129610 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
55129630 AT
1 AT
55129632 GTGTTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Found at i:55139670 original size:19 final size:20
Alignment explanation
Indices: 55139643--55139680 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
55139633 GAATTATAAA
55139643 AAAACTATTTTAAT-TTTTG
1 AAAACTATTTTAATCTTTTG
*
55139662 AAAATTATTTTAATCTTTT
1 AAAACTATTTTAATCTTTT
55139681 TGTAATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.37, C:0.05, G:0.03, T:0.55
Consensus pattern (20 bp):
AAAACTATTTTAATCTTTTG
Found at i:55144580 original size:26 final size:27
Alignment explanation
Indices: 55144524--55144584 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 27
55144514 TTTGGAGACA
*
55144524 ATTTTGTTTATAGAATGAATGCATTCATG
1 ATTTTGTTTATAAAATG-ATGCATT-ATG
55144553 ATTTTGTTTATAAAAATG-TGCATT-TG
1 ATTTTGTTTAT-AAAATGATGCATTATG
55144579 ATTTTG
1 ATTTTG
55144585 ATACAAAATC
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
26 8 0.27
28 6 0.20
29 11 0.37
30 5 0.17
ACGTcount: A:0.30, C:0.05, G:0.16, T:0.49
Consensus pattern (27 bp):
ATTTTGTTTATAAAATGATGCATTATG
Found at i:55145101 original size:21 final size:21
Alignment explanation
Indices: 55145075--55145115 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
55145065 TCAAAACAAC
*
55145075 ATAGTTTTGCCTTTTAACTTG
1 ATAGTTTTGACTTTTAACTTG
55145096 ATAGTTTTGACTTTTAACTT
1 ATAGTTTTGACTTTTAACTT
55145116 TAGGAAAGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.22, C:0.12, G:0.12, T:0.54
Consensus pattern (21 bp):
ATAGTTTTGACTTTTAACTTG
Found at i:55146686 original size:25 final size:24
Alignment explanation
Indices: 55146658--55146746 Score: 79
Period size: 25 Copynumber: 3.6 Consensus size: 24
55146648 ATTTGGGAAT
*
55146658 GCTCATACGAGCACATAAACAAGAA
1 GCTCATACGAGC-CATAAACGAGAA
* * * *
55146683 GCTCTTTCGAGCTATATAACGGGAA
1 GCTCATACGAGCCATA-AACGAGAA
** *
55146708 GCTCATGTGAGCCATGTAACGAGAA
1 GCTCATACGAGCCAT-AAACGAGAA
55146733 GCTCATACGAGCCA
1 GCTCATACGAGCCA
55146747 ATATCGGGAA
Statistics
Matches: 49, Mismatches: 13, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
24 3 0.06
25 46 0.94
ACGTcount: A:0.35, C:0.24, G:0.22, T:0.19
Consensus pattern (24 bp):
GCTCATACGAGCCATAAACGAGAA
Found at i:55146809 original size:25 final size:25
Alignment explanation
Indices: 55146779--55146847 Score: 70
Period size: 26 Copynumber: 2.7 Consensus size: 25
55146769 CCAATATCGA
55146779 GAAGCTCCAGAGAGCCATTAATCAG
1 GAAGCTCCAGAGAGCCATTAATCAG
* *
55146804 GAAGCTCACA-ATGAGCCTTTAATCGG
1 GAAGCTC-CAGA-GAGCCATTAATCAG
*
55146830 GAAG-TTCACGAGAGCCAT
1 GAAGCTCCA-GAGAGCCAT
55146848 ATATCGAGAT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
24 2 0.06
25 15 0.42
26 19 0.53
ACGTcount: A:0.33, C:0.23, G:0.25, T:0.19
Consensus pattern (25 bp):
GAAGCTCCAGAGAGCCATTAATCAG
Found at i:55146853 original size:25 final size:25
Alignment explanation
Indices: 55146691--55146862 Score: 77
Period size: 25 Copynumber: 6.9 Consensus size: 25
55146681 AAGCTCTTTC
* * * *
55146691 GAGCTATATAACGGGAAGCTCATGT
1 GAGCCATATATCGGGAAGCTCACGA
* * * *
55146716 GAGCCATGTAACGAGAAGCTCA-TA
1 GAGCCATATATCGGGAAGCTCACGA
* * * *
55146740 CGAGCCA-ATATCGGGAAGGTTAAAGC
1 -GAGCCATATATCGGGAA-GCTCACGA
*
55146766 GAGCCA-ATATCGAGAAGCTC-CAGA
1 GAGCCATATATCGGGAAGCTCAC-GA
* *
55146790 GAGCCAT-TAATCAGGAAGCTCACAA
1 GAGCCATAT-ATCGGGAAGCTCACGA
* *
55146815 TGAGCC-TTTAATCGGGAAGTTCACGA
1 -GAGCCATAT-ATCGGGAAGCTCACGA
* *
55146841 GAGCCATATATCGAGATGCTCA
1 GAGCCATATATCGGGAAGCTCA
55146863 TAAGAGCTAC
Statistics
Matches: 110, Mismatches: 27, Indels: 20
0.70 0.17 0.13
Matches are distributed among these distances:
24 17 0.15
25 70 0.64
26 23 0.21
ACGTcount: A:0.34, C:0.21, G:0.26, T:0.19
Consensus pattern (25 bp):
GAGCCATATATCGGGAAGCTCACGA
Found at i:55148544 original size:19 final size:19
Alignment explanation
Indices: 55148522--55148569 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 19
55148512 TTTTATAAAA
*
55148522 TTTT-AAAATTTTTATATTT
1 TTTTAAAAATTTATA-ATTT
55148541 TTTTAAAAATTTATAATTT
1 TTTTAAAAATTTATAATTT
55148560 TTTTAAAAAT
1 TTTTAAAAAT
55148570 ACAAATTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 18 0.67
20 9 0.33
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TTTTAAAAATTTATAATTT
Found at i:55148547 original size:27 final size:29
Alignment explanation
Indices: 55148507--55148561 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 29
55148497 ATTCCAAAAT
*
55148507 TATTATTTTATAAAATTTTAAAATTTTTA
1 TATTATTTTATAAAAATTTAAAATTTTTA
*
55148536 TATT-TTTT-TAAAAATTTATAATTTTT
1 TATTATTTTATAAAAATTTAAAATTTTT
55148562 TTAAAAATAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 16 0.67
28 4 0.17
29 4 0.17
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (29 bp):
TATTATTTTATAAAAATTTAAAATTTTTA
Found at i:55148576 original size:18 final size:19
Alignment explanation
Indices: 55148537--55148578 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
55148527 AAATTTTTAT
**
55148537 ATTTTTTTAAAAATTTATA
1 ATTTTTTTAAAAATACATA
55148556 ATTTTTTTAAAAATACA-A
1 ATTTTTTTAAAAATACATA
55148574 ATTTT
1 ATTTT
55148579 AGAATTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (19 bp):
ATTTTTTTAAAAATACATA
Done.