Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D11
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: 73211361
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1690000 characters in sequence are not A, C, G, or T
File 91 of 240
Found at i:28695062 original size:27 final size:27
Alignment explanation
Indices: 28695020--28695219 Score: 172
Period size: 27 Copynumber: 7.4 Consensus size: 27
28695010 GTAATGGGCC
* *
28695020 TAAAATGACCGAAATACCCCCAAAGGG
1 TAAAATGACTGAAATACCCCCGAAGGG
* *
28695047 TAAAATGACTGGAATACCCCCGAGGGG
1 TAAAATGACTGAAATACCCCCGAAGGG
* * **
28695074 TAAAATAACTTAAATACCGTCGAAGGG
1 TAAAATGACTGAAATACCCCCGAAGGG
** * **
28695101 TAAAATGACCAAAATATCCCTAAAGGG
1 TAAAATGACTGAAATACCCCCGAAGGG
*
28695128 TAAAATGA-TAGAAATACCCCCGAGGGG
1 TAAAATGACT-GAAATACCCCCGAAGGG
* * * *
28695155 TATAATGA-TAGAAATACACTCGAAGGT
1 TAAAATGACT-GAAATACCCCCGAAGGG
* *
28695182 TAAAATGACCGAAATACTCCC-ATAGGG
1 TAAAATGACTGAAATACCCCCGA-AGGG
28695209 TAAAATGACTG
1 TAAAATGACTG
28695220 TTATGCCCCT
Statistics
Matches: 135, Mismatches: 35, Indels: 6
0.77 0.20 0.03
Matches are distributed among these distances:
26 1 0.01
27 134 0.99
ACGTcount: A:0.42, C:0.18, G:0.20, T:0.18
Consensus pattern (27 bp):
TAAAATGACTGAAATACCCCCGAAGGG
Found at i:28695155 original size:81 final size:80
Alignment explanation
Indices: 28695020--28695219 Score: 253
Period size: 81 Copynumber: 2.5 Consensus size: 80
28695010 GTAATGGGCC
* *
28695020 TAAAATGACCGAAATACCCCCAAAGGGTAAAATGACTGGAATACCCCCGAGGGGTAAAATAACT-
1 TAAAATGACCGAAATA-TCCCAAAGGGTAAAATGACTGAAATACCCCCGAGGGGTAAAATAA-TA
*
28695084 TAAATAC-CGTCGAAGGG
64 GAAATACAC-TCGAAGGG
* * *
28695101 TAAAATGACCAAAATATCCCTAAAGGGTAAAATGA-TAGAAATACCCCCGAGGGGTATAATGATA
1 TAAAATGACCGAAATATCCC-AAAGGGTAAAATGACT-GAAATACCCCCGAGGGGTAAAATAATA
*
28695165 GAAATACACTCGAAGGT
64 GAAATACACTCGAAGGG
*
28695182 TAAAATGACCGAAATACTCCCATAGGGTAAAATGACTG
1 TAAAATGACCGAAATA-TCCCAAAGGGTAAAATGACTG
28695220 TTATGCCCCT
Statistics
Matches: 104, Mismatches: 9, Indels: 12
0.83 0.07 0.10
Matches are distributed among these distances:
80 5 0.05
81 93 0.89
82 6 0.06
ACGTcount: A:0.42, C:0.18, G:0.20, T:0.18
Consensus pattern (80 bp):
TAAAATGACCGAAATATCCCAAAGGGTAAAATGACTGAAATACCCCCGAGGGGTAAAATAATAGA
AATACACTCGAAGGG
Found at i:28695421 original size:26 final size:26
Alignment explanation
Indices: 28695392--28695468 Score: 109
Period size: 26 Copynumber: 3.0 Consensus size: 26
28695382 TTGCCACATA
*
28695392 TACTGTTACTGGCAGCTTTACTGCGT
1 TACTGTTACTGGCAGCTTTACTGCAT
* *
28695418 TACTGTTACTAGCAGCTTTGCTGCAT
1 TACTGTTACTGGCAGCTTTACTGCAT
* *
28695444 CACTATTACTGGCAGCTTTACTGCA
1 TACTGTTACTGGCAGCTTTACTGCA
28695469 ATATTGGTGT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 44 1.00
ACGTcount: A:0.19, C:0.25, G:0.19, T:0.36
Consensus pattern (26 bp):
TACTGTTACTGGCAGCTTTACTGCAT
Found at i:28702567 original size:27 final size:27
Alignment explanation
Indices: 28702527--28702640 Score: 140
Period size: 27 Copynumber: 4.2 Consensus size: 27
28702517 GTAATGGGCC
*
28702527 TAAAATGACTGAAATACCCCCGAAGGG
1 TAAAATGACTGAAATACCCCCAAAGGG
* *
28702554 TAAAATGA-TCGAAATACCCCTAAAAGG
1 TAAAATGACT-GAAATACCCCCAAAGGG
** *
28702581 TAAAATGACTGAAATACCCTTAAAGGA
1 TAAAATGACTGAAATACCCCCAAAGGG
**
28702608 TAAAATGACCAAAATACCCCCAAAGGG
1 TAAAATGACTGAAATACCCCCAAAGGG
28702635 TAAAAT
1 TAAAAT
28702641 AACTATTATA
Statistics
Matches: 74, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
26 1 0.01
27 72 0.97
28 1 0.01
ACGTcount: A:0.47, C:0.19, G:0.16, T:0.18
Consensus pattern (27 bp):
TAAAATGACTGAAATACCCCCAAAGGG
Found at i:28702612 original size:54 final size:54
Alignment explanation
Indices: 28702527--28702640 Score: 156
Period size: 54 Copynumber: 2.1 Consensus size: 54
28702517 GTAATGGGCC
* * * * *
28702527 TAAAATGACTGAAATACCCCCGAAGGGTAAAATGATCGAAATACCCCTAAAAGG
1 TAAAATGACTGAAATACCCCCAAAGGATAAAATGACCAAAATACCCCCAAAAGG
** *
28702581 TAAAATGACTGAAATACCCTTAAAGGATAAAATGACCAAAATACCCCCAAAGGG
1 TAAAATGACTGAAATACCCCCAAAGGATAAAATGACCAAAATACCCCCAAAAGG
28702635 TAAAAT
1 TAAAAT
28702641 AACTATTATA
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.47, C:0.19, G:0.16, T:0.18
Consensus pattern (54 bp):
TAAAATGACTGAAATACCCCCAAAGGATAAAATGACCAAAATACCCCCAAAAGG
Found at i:28720451 original size:167 final size:171
Alignment explanation
Indices: 28719868--28720599 Score: 654
Period size: 167 Copynumber: 4.4 Consensus size: 171
28719858 CTAAACGAAT
* * * * * **
28719868 ATTAAAATTAAATAAAATCTGTTTCAAGATTTACTCCCATCATTTAACAGA----TTTT-ATTCG
1 ATTAAAATTAAATAAAATCTATTTCGAGATTTATTCCCGTCATTTAACAAATTTTTTTTGATTTT
* * * * * *
28719928 ATTTTGTTTCTAAATT---A--AAAGTGAATAAAATTTGTTTCGGGATTTATTCCGGCCGTTCAA
66 ATTTTGTTTCCAAATTAGAATTAAATTAAATAAAATCTGTTTCAGGATTTATTCCTGCCGTTCAA
** * * * * *
28719988 TGA-ATTTTATTCCAATTTTGATTTTATTTCCAAAATGAGT
131 CAAGATTTTATTACGATTTTGATTTTGTTTCCAAAATAAGA
* * ** * **
28720028 ATTAAAATTAAAATAAAATCCATTTTGAGATTTATTCCTATCATTCAACGGATTTTATCCTTT--
1 ATTAAAATT-AAATAAAATCTATTTCGAGATTTATTCCCGTCATTTAACAAATTTT-T--TTTGA
* * * ** *
28720091 TTTTATTTTATTTCCAAATGAGAAATTAAAGTTAAATAAAATCTGTTTCGGGATTTATTCCCACT
62 TTTTATTTTGTTTCCAAATTAG-AATTAAA-TTAAATAAAATCTGTTTCAGGATTTATTCCTGCC
* * *
28720156 GTTCAAC-GGATTTTATTAC-ATTTTGATTTTGTTGCCAAAACAAGAA
125 GTTCAACAAGATTTTATTACGATTTTGATTTTGTTTCCAAAATAAG-A
* * * * *
28720202 ATTAAAATTAAATAAAATCTA-TTCTG-GATTTATTCCGGCCATTTAGCAAGATTTTATTCGATT
1 ATTAAAATTAAATAAAATCTATTTC-GAGATTTATTCCCGTCATTTAACAA-ATTTTTTTTGATT
* *
28720265 TTATTTTGTTTCTAAATTAGAATTAAATTAAATAAAATCTGTTTCAGGATTTATTCCTGCCGTTT
64 TTATTTTGTTTCCAAATTAGAATTAAATTAAATAAAATCTGTTTCAGGATTTATTCCTGCCGTTC
*
28720330 AACAAGATTTTATT-CGATTTT-ATTTTGTTTCC-AAATTAGA
129 AACAAGATTTTATTACGATTTTGATTTTGTTTCCAAAATAAGA
* * *
28720370 ATT-AAATTAAATAAAATTTGTTTCGAGATTTATTCCCGTCGTTTAACAAATTTTTTTTGATTTT
1 ATTAAAATTAAATAAAATCTATTTCGAGATTTATTCCCGTCATTTAACAAATTTTTTTTGATTTT
* * * *
28720434 ATTTTGTTTCCAAATTAGAATTAAATTAAATAAAATTTGTTTCAGGATTTATTACTGTCGTTTAA
66 ATTTTGTTTCCAAATTAGAATTAAATTAAATAAAATCTGTTTCAGGATTTATTCCTGCCGTTCAA
*
28720499 CAAGATTTTATT-CGATATTG-TTTTGTTTCCAAACA-AAGA
131 CAAGATTTTATTACGATTTTGATTTTGTTTCCAAA-ATAAGA
* * * * * *
28720538 CTT--AATCAAAT-AATTCTATTTCGGGATTTATTCCCGTCATTTAACAGATTCTATTTTGATTT
1 ATTAAAATTAAATAAAATCTATTTCGAGATTTATTCCCGTCATTTAACAAATT-TTTTTTGATTT
28720600 AATTATATAA
Statistics
Matches: 470, Mismatches: 73, Indels: 51
0.79 0.12 0.09
Matches are distributed among these distances:
160 9 0.02
161 34 0.07
166 34 0.07
167 150 0.32
168 36 0.08
169 6 0.01
170 49 0.10
171 22 0.05
172 37 0.08
173 41 0.09
174 52 0.11
ACGTcount: A:0.33, C:0.12, G:0.11, T:0.44
Consensus pattern (171 bp):
ATTAAAATTAAATAAAATCTATTTCGAGATTTATTCCCGTCATTTAACAAATTTTTTTTGATTTT
ATTTTGTTTCCAAATTAGAATTAAATTAAATAAAATCTGTTTCAGGATTTATTCCTGCCGTTCAA
CAAGATTTTATTACGATTTTGATTTTGTTTCCAAAATAAGA
Found at i:28720470 original size:83 final size:84
Alignment explanation
Indices: 28719872--28720592 Score: 545
Period size: 84 Copynumber: 8.7 Consensus size: 84
28719862 ACGAATATTA
* * * *
28719872 AAATTAAATAAAATCTGTTTCAAGATTTACTCCCATCATTTAAC-AGATTTTATTCG-----ATT
1 AAATTAAATAAAATCTGTTTCGAGATTTATTCCCGTCGTTTAACAAGATTTTATTCGATTTTATT
*
28719931 TTGTTTCTAAATT---A--
66 TTGTTTCCAAATTAGAATT
* * * * * * * ** *
28719945 AAAGTGAATAAAATTTGTTTCGGGATTTATTCCGGCCGTTCAATGA-ATTTTATTCCAATTTTGA
1 AAATTAAATAAAATCTGTTTCGAGATTTATTCCCGTCGTTTAACAAGATTTTATT-CGATTTT-A
* * *
28720009 TTTTATTTCCAAAATGAGTATT
64 TTTTGTTTCC-AAATTAGAATT
** * ** * * * * **
28720031 AAAATTAAAATAAAATCCATTTTGAGATTTATTCCTATCATTCAAC-GGATTTTATCCTTTTTTT
1 -AAATT-AAATAAAATCTGTTTCGAGATTTATTCCCGTCGTTTAACAAGATTTTATTC-GATTTT
* *
28720095 ATTTTATTTCCAAATGAGAAATT
63 ATTTTGTTTCCAAATTAG-AATT
* * * *
28720118 AAAGTTAAATAAAATCTGTTTCGGGATTTATTCCC-ACTGTTCAAC-GGATTTTATTAC-ATTTT
1 AAA-TTAAATAAAATCTGTTTCGAGATTTATTCCCGTC-GTTTAACAAGATTTTATT-CGATTTT
* **
28720180 GATTTTGTTGCCAAAACAAGAAATT
63 -ATTTTGTTTCC-AAATTAG-AATT
* * * * *
28720205 AAAATTAAATAAAATCT-ATTCTG-GATTTATTCCGGCCATTTAGCAAGATTTTATTCGATTTTA
1 -AAATTAAATAAAATCTGTTTC-GAGATTTATTCCCGTCGTTTAACAAGATTTTATTCGATTTTA
*
28720268 TTTTGTTTCTAAATTAGAATT
64 TTTTGTTTCCAAATTAGAATT
* *
28720289 AAATTAAATAAAATCTGTTTC-AGGATTTATTCCTGCCGTTTAACAAGATTTTATTCGATTTTAT
1 AAATTAAATAAAATCTGTTTCGA-GATTTATTCCCGTCGTTTAACAAGATTTTATTCGATTTTAT
28720353 TTTGTTTCCAAATTAGAATT
65 TTTGTTTCCAAATTAGAATT
* * *
28720373 AAATTAAATAAAATTTGTTTCGAGATTTATTCCCGTCGTTTAACAA-ATTTTTTTTGATTTTATT
1 AAATTAAATAAAATCTGTTTCGAGATTTATTCCCGTCGTTTAACAAGATTTTATTCGATTTTATT
28720437 TTGTTTCCAAATTAGAATT
66 TTGTTTCCAAATTAGAATT
* * * * *
28720456 AAATTAAATAAAATTTGTTTC-AGGATTTATTACTGTCGTTTAACAAGATTTTATTCGATATTGT
1 AAATTAAATAAAATCTGTTTCGA-GATTTATTCCCGTCGTTTAACAAGATTTTATTCGATTTTAT
** *
28720520 TTTGTTTCCAAACAAAGACTT
65 TTTGTTTCCAAA-TTAGAATT
* * * * * *
28720541 -AATCAAAT-AATTCTATTTCGGGATTTATTCCCGTCATTTAAC-AGATTCTATT
1 AAATTAAATAAAATCTGTTTCGAGATTTATTCCCGTCGTTTAACAAGATTTTATT
28720593 TTGATTTAAT
Statistics
Matches: 526, Mismatches: 85, Indels: 65
0.78 0.13 0.10
Matches are distributed among these distances:
73 40 0.08
74 2 0.00
80 9 0.02
81 4 0.01
82 10 0.02
83 119 0.23
84 138 0.26
85 16 0.03
86 85 0.16
87 61 0.12
88 42 0.08
ACGTcount: A:0.33, C:0.12, G:0.11, T:0.44
Consensus pattern (84 bp):
AAATTAAATAAAATCTGTTTCGAGATTTATTCCCGTCGTTTAACAAGATTTTATTCGATTTTATT
TTGTTTCCAAATTAGAATT
Found at i:28720610 original size:59 final size:59
Alignment explanation
Indices: 28720547--28720658 Score: 145
Period size: 59 Copynumber: 1.9 Consensus size: 59
28720537 ACTTAATCAA
* *
28720547 ATAATTCTATTTCGGGATTTATTCCCGTCATTTAACAGATTCT-ATTTTGATTTAATTAT
1 ATAATTCTATTTCGGGATTTAATCCCGTCATTTAACAAATT-TGATTTTGATTTAATTAT
* * * * *
28720606 ATAATTTTGTTTCGTGATTTAATCCTGTCGTTTAACAAATTTGATTTTGATTT
1 ATAATTCTATTTCGGGATTTAATCCCGTCATTTAACAAATTTGATTTTGATTT
28720659 TGTTTTAGAA
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
58 1 0.02
59 44 0.98
ACGTcount: A:0.26, C:0.12, G:0.12, T:0.51
Consensus pattern (59 bp):
ATAATTCTATTTCGGGATTTAATCCCGTCATTTAACAAATTTGATTTTGATTTAATTAT
Found at i:28720671 original size:59 final size:59
Alignment explanation
Indices: 28720556--28720672 Score: 137
Period size: 59 Copynumber: 2.0 Consensus size: 59
28720546 AATAATTCTA
* * *
28720556 TTTCGGGATTTATTCCCGTCATTTAACAGATTCTATTTTGATTTAATTATATAATTTTG
1 TTTCGGGATTTAATCCCGTCATTTAACAAATTCTATTTTGATTTAATTATAGAATTTTG
* * * ** *
28720615 TTTCGTGATTTAATCCTGTCGTTTAACAAATT-TGATTTTGATTTTGTTTTAGAATTTT
1 TTTCGGGATTTAATCCCGTCATTTAACAAATTCT-ATTTTGATTTAATTATAGAATTTT
28720673 AATTCTACCG
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
58 1 0.02
59 47 0.98
ACGTcount: A:0.24, C:0.10, G:0.13, T:0.53
Consensus pattern (59 bp):
TTTCGGGATTTAATCCCGTCATTTAACAAATTCTATTTTGATTTAATTATAGAATTTTG
Found at i:28723699 original size:27 final size:26
Alignment explanation
Indices: 28723668--28723845 Score: 169
Period size: 27 Copynumber: 6.6 Consensus size: 26
28723658 TAAATTGTAC
28723668 AGCACTAAGTGTGCGATTCGACTATGT
1 AGCACTAAGTGTGCGATT-GACTATGT
* * *
28723695 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCG-ATTGACTATGT
* *
28723721 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCG-ATTGACTATGT
*
28723749 GGCACTAAGTGTGCGAGTCTGACTATGT
1 AGCACTAAGTGTGCGA-T-TGACTATGT
* *
28723777 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGA-TTGACTATGT
* * *
28723804 GGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGA-TTGACTATGT
*
28723831 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
28723846 GGCTCAATAT
Statistics
Matches: 126, Mismatches: 20, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
26 1 0.01
27 100 0.79
28 25 0.20
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.29
Consensus pattern (26 bp):
AGCACTAAGTGTGCGATTGACTATGT
Found at i:28723784 original size:82 final size:81
Alignment explanation
Indices: 28723669--28723824 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 81
28723659 AAATTGTACA
* * *
28723669 GCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATGAT-GCACTAAGTG
1 GCACTAAGTGTGCGAGTCGACTATGTAGCACTAAGTGTGCGAAATGAATACG-TGGCACTAAGTG
28723733 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
28723750 GCACTAAGTGTGCGAGTCTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTGGCACTAAGTG
1 GCACTAAGTGTGCGAGTC-GACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTG
*
28723815 TGCGAGTTGA
65 TGCGAATTGA
28723825 TTATATAGCA
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 18 0.27
82 48 0.73
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.28
Consensus pattern (81 bp):
GCACTAAGTGTGCGAGTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:28723836 original size:82 final size:81
Alignment explanation
Indices: 28723665--28723845 Score: 220
Period size: 82 Copynumber: 2.2 Consensus size: 81
28723655 GATTAAATTG
* * *
28723665 TACAGCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGAGTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
28723730 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
28723746 TGCGGCACTAAGTGTGCGAGTCTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TGGCACT
1 TACAGCACTAAGTGTGCGAGTC-GACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
28723810 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
28723828 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
28723846 GGCTCAATAT
Statistics
Matches: 83, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
81 20 0.24
82 63 0.76
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.29
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGAGTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:28730424 original size:34 final size:35
Alignment explanation
Indices: 28730358--28730424 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
28730348 CAAACACCAG
*
28730358 AAAATATTTTCTAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCTAGTAAATCATTTTACAGAAAAGT
* *
28730393 AAAACATTTTCTAG-AAATTATTTTACGGAAAA
1 AAAACATTTTCTAGTAAATCATTTTACAGAAAA
28730425 TATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 16 0.55
35 13 0.45
ACGTcount: A:0.46, C:0.09, G:0.09, T:0.36
Consensus pattern (35 bp):
AAAACATTTTCTAGTAAATCATTTTACAGAAAAGT
Found at i:28731379 original size:13 final size:13
Alignment explanation
Indices: 28731363--28731441 Score: 115
Period size: 13 Copynumber: 6.1 Consensus size: 13
28731353 TTTAAACTAA
28731363 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
*
28731376 ACTTCTCAAAAGC
1 ACTTTTCAAAAGC
*
28731389 ACTTTTCCATAA-C
1 ACTTTT-CAAAAGC
*
28731402 ACTTTTTAAAAGC
1 ACTTTTCAAAAGC
28731415 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
28731428 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
28731441 A
1 A
28731442 ATGAAGAACT
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
12 3 0.05
13 51 0.88
14 4 0.07
ACGTcount: A:0.38, C:0.24, G:0.06, T:0.32
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:28733516 original size:234 final size:234
Alignment explanation
Indices: 28733107--28733558 Score: 877
Period size: 234 Copynumber: 1.9 Consensus size: 234
28733097 AATCTGAACT
*
28733107 AAACGATTTATTCACTTGTGTCTTGATCCGTAGAAATCCCTAAATTATGTTAATATCTCTTTCGT
1 AAACGATTTATTCACTTGTGTCTTGATCCGTAGAAATCCCTAAATTATGTTAATATCTCTTTCGA
*
28733172 GAGTAAGAACAACTGACTCTAGGTTGATTAATTGAAATCTCTTTCTAGTTAAAACATCTATCGTT
66 GAGTAAGAACAACTGACTCTAGGTTGATTAATTGAAATCTCTTTCTAGTTAAAACATCTATCGTC
*
28733237 GCATTAACTTGATCTATGGATTCCCCTATTAGATTTGACTCTAATCCGGTAGATTTATGTCGTCC
131 GCATTAACTCGATCTATGGATTCCCCTATTAGATTTGACTCTAATCCGGTAGATTTATGTCGTCC
28733302 TATTTCCAGGATTGCACGCAACTCCACCTATTATTATGA
196 TATTTCCAGGATTGCACGCAACTCCACCTATTATTATGA
28733341 AAACGATTTATTCACTTGTGTCTTGATCCGTAGAAATCCCTAAATTATGTTAATATCTCTTTCGA
1 AAACGATTTATTCACTTGTGTCTTGATCCGTAGAAATCCCTAAATTATGTTAATATCTCTTTCGA
28733406 GAGTAAGAACAACTGACTCTAGGTTGATTAATTGAAATCTCTTTCTAGTTAAAACATCTATCGTC
66 GAGTAAGAACAACTGACTCTAGGTTGATTAATTGAAATCTCTTTCTAGTTAAAACATCTATCGTC
28733471 GCATTAACTCGATCTATGGATTCCCCTATTAGATTTGACTCTAATCCGGTAGATTTATGTCGTCC
131 GCATTAACTCGATCTATGGATTCCCCTATTAGATTTGACTCTAATCCGGTAGATTTATGTCGTCC
28733536 TATTTCCAGGATTGCACGCAACT
196 TATTTCCAGGATTGCACGCAACT
28733559 TCACTCAATT
Statistics
Matches: 215, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
234 215 1.00
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.37
Consensus pattern (234 bp):
AAACGATTTATTCACTTGTGTCTTGATCCGTAGAAATCCCTAAATTATGTTAATATCTCTTTCGA
GAGTAAGAACAACTGACTCTAGGTTGATTAATTGAAATCTCTTTCTAGTTAAAACATCTATCGTC
GCATTAACTCGATCTATGGATTCCCCTATTAGATTTGACTCTAATCCGGTAGATTTATGTCGTCC
TATTTCCAGGATTGCACGCAACTCCACCTATTATTATGA
Found at i:28739554 original size:15 final size:15
Alignment explanation
Indices: 28739536--28739566 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
28739526 TGGTTTAAAT
28739536 TTATATATTATCATC
1 TTATATATTATCATC
*
28739551 TTATATATTATTATC
1 TTATATATTATCATC
28739566 T
1 T
28739567 ATGTTAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.32, C:0.10, G:0.00, T:0.58
Consensus pattern (15 bp):
TTATATATTATCATC
Found at i:28740570 original size:107 final size:107
Alignment explanation
Indices: 28740292--28740698 Score: 556
Period size: 103 Copynumber: 3.9 Consensus size: 107
28740282 AGGTTTTTCT
*
28740292 AAATAAGGCAATATTTCGCGTTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGATT
1 AAATAAGGCAATATTTCGCATTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGATT
*
28740357 TCTCGTTCGACCAAATAGCCAAATATCATTTTTAAACTTTTA
66 TCTCGTTCGACCAAATAGCCAAATATCCTTTTTAAACTTTTA
*
28740399 AAAT----CAATATTTCGCATTTGAAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGATT
1 AAATAAGGCAATATTTCGCATTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGATT
*
28740460 TCTCCTTCGACCAAATAGCCAAATATCCTTTTTAAACTTTTA
66 TCTCGTTCGACCAAATAGCCAAATATCCTTTTTAAACTTTTA
* * * * * * *
28740502 AAATAAGGCAATATTTAGCGTTTGGAAAATCAAGGAAACGTACCCTAACGTGTTGGGTTTCGACT
1 AAATAAGGCAATATTTCGCATTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGATT
* **
28740567 TCTCGTTTGACCAAATAGCCAAATATCC-TTTTAAACTTTCG
66 TCTCGTTCGACCAAATAGCCAAATATCCTTTTTAAACTTTTA
* * * * * * * *
28740608 AAGTGAGGCAATATTT-GCATTTGGAAATTTGAGAGAACGTGCTCTAACGTGCTGGGTCTCAATT
1 AAATAAGGCAATATTTCGCATTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGATT
* *
28740672 TCTCATTTGACCAAATAGCCAAATATC
66 TCTCGTTCGACCAAATAGCCAAATATC
28740699 TTCTTAACTT
Statistics
Matches: 265, Mismatches: 31, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
103 99 0.37
105 62 0.23
106 25 0.09
107 79 0.30
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (107 bp):
AAATAAGGCAATATTTCGCATTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGATT
TCTCGTTCGACCAAATAGCCAAATATCCTTTTTAAACTTTTA
Found at i:28745415 original size:41 final size:40
Alignment explanation
Indices: 28745310--28745417 Score: 99
Period size: 41 Copynumber: 2.6 Consensus size: 40
28745300 ACCGGCACGT
* ** * *
28745310 AGCCTACTAGGCCTGAAGCCTGATTTAGTTCACCGGCATAA
1 AGCCTACTAGGCATG-AGCCTGAAATAATTCACCAGCATAA
* * * * *
28745351 AGCCTGCTAGACATAAAGTCTGAAATAATTCACCAGCATTA
1 AGCCTACTAGGCAT-GAGCCTGAAATAATTCACCAGCATAA
28745392 AGCCTACTAGGCATCGAGCCTGAAAT
1 AGCCTACTAGGCAT-GAGCCTGAAAT
28745418 CACAGATACG
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.23
Consensus pattern (40 bp):
AGCCTACTAGGCATGAGCCTGAAATAATTCACCAGCATAA
Found at i:28773906 original size:46 final size:46
Alignment explanation
Indices: 28773844--28774020 Score: 284
Period size: 46 Copynumber: 3.8 Consensus size: 46
28773834 ATGAATTGAC
28773844 GTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGTTGTGAAAA
1 GTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGTTGTGAAAA
* * *
28773890 GTAGATATGGTGTTTCAGTGAAGAAAACTATACTGAGTTGTGAAAA
1 GTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGTTGTGAAAA
* *
28773936 GTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGTTGTAAAAA
1 GTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGTTGTGAAAA
*
28773982 GTAGGTATGATATTTCCA-TGAAGAAAACCATACTGAGTT
1 GTAGGTATGGTATTT-CAGTGAAGAAAACCATACTGAGTT
28774021 ATAGCAATGT
Statistics
Matches: 122, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
46 120 0.98
47 2 0.02
ACGTcount: A:0.37, C:0.09, G:0.25, T:0.29
Consensus pattern (46 bp):
GTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGTTGTGAAAA
Found at i:28777274 original size:27 final size:26
Alignment explanation
Indices: 28777245--28777306 Score: 97
Period size: 26 Copynumber: 2.4 Consensus size: 26
28777235 ACCCCCATAA
*
28777245 AAAATTTTGACGATTTTACCCCTGAT
1 AAAATTTTGACAATTTTACCCCTGAT
* *
28777271 AAAATTTTGACAAATTTACCCCTGGT
1 AAAATTTTGACAATTTTACCCCTGAT
28777297 AAAATTTTGA
1 AAAATTTTGA
28777307 GAAAATATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.37
Consensus pattern (26 bp):
AAAATTTTGACAATTTTACCCCTGAT
Found at i:28787704 original size:19 final size:19
Alignment explanation
Indices: 28787676--28787712 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
28787666 TACTCTTCCT
*
28787676 ATCAATTAAAAAAAATTTG
1 ATCAACTAAAAAAAATTTG
*
28787695 ATCAACTAAAAATAATTT
1 ATCAACTAAAAAAAATTT
28787713 CACAAATTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.57, C:0.08, G:0.03, T:0.32
Consensus pattern (19 bp):
ATCAACTAAAAAAAATTTG
Found at i:28788191 original size:110 final size:111
Alignment explanation
Indices: 28788027--28788459 Score: 500
Period size: 113 Copynumber: 3.9 Consensus size: 111
28788017 TAAATTAATC
* *
28788027 AAACCTAATAAAACACAACAACAAAAATAATTTTTCCTTCAATACGAAAAACTAATATAAGATAC
1 AAACCTAATAAAACACAACAACAAAAAT-ATTTTTCCTTAAATACAAAAAACTAATATAAGATAC
* * *
28788092 CACAAAAATATTAATAAAACAAATTAATAAAACCTTAATACAAACTT
65 CACAAAAACATTAATAAAACAAATTAATCATACCTTAATACAAACTT
28788139 AAACCTAATAAAACACAACAA-AAATAAT-TTTTTCCTTAAATACAAAAAACTAATATAAGATAC
1 AAACCTAATAAAACACAACAACAAA-AATATTTTTCCTTAAATACAAAAAACTAATATAAGATAC
*
28788202 CACAAAAATATTAATAAAACAAATTAATCATACCTTTAATACAAA-TCT
65 CACAAAAACATTAATAAAACAAATTAATCATACC-TTAATACAAACT-T
** * ** * *
28788250 AAAATTAGTAAAACACAACAA-AAAAAT-TCCTTCCCCTTAAATACAAAAAAGTTGATATAAGAT
1 AAACCTAATAAAACACAACAACAAAAATAT--TTTTCCTTAAATACAAAAAA-CTAATATAAGAT
* * * *
28788313 ACAACAAAAGCATTAATAAAACAAACTAATCATACATTTAATACAAACTT
63 ACCACAAAAACATTAATAAAACAAATTAATCATAC-CTTAATACAAACTT
* * * ** *
28788363 AAATCTAATAAAACACAACAACAAAAA-ATCTTTCTTTTAAATACAAAAAACTGTTATAAGATAT
1 AAACCTAATAAAACACAACAACAAAAATATTTTTC-CTTAAATACAAAAAACTAATATAAGATAC
* * * *
28788427 CATAAAAACAATAGTAAAACAAATAAATCATAC
65 CACAAAAACATTAATAAAACAAATTAATCATAC
28788460 TTTTTTTTGT
Statistics
Matches: 277, Mismatches: 33, Indels: 22
0.83 0.10 0.07
Matches are distributed among these distances:
110 70 0.25
111 35 0.13
112 81 0.29
113 84 0.30
114 7 0.03
ACGTcount: A:0.56, C:0.16, G:0.03, T:0.25
Consensus pattern (111 bp):
AAACCTAATAAAACACAACAACAAAAATATTTTTCCTTAAATACAAAAAACTAATATAAGATACC
ACAAAAACATTAATAAAACAAATTAATCATACCTTAATACAAACTT
Found at i:28798039 original size:30 final size:30
Alignment explanation
Indices: 28798003--28798060 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
28797993 GCATTTGTAC
28798003 AAGACCATAAGTACCAATTTGCTATGACAT
1 AAGACCATAAGTACCAATTTGCTATGACAT
28798033 AAGACCATAAGTACCAATTTGCTATGAC
1 AAGACCATAAGTACCAATTTGCTATGAC
28798061 TGGCATGGTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.40, C:0.21, G:0.14, T:0.26
Consensus pattern (30 bp):
AAGACCATAAGTACCAATTTGCTATGACAT
Found at i:28799156 original size:32 final size:32
Alignment explanation
Indices: 28799118--28799204 Score: 95
Period size: 33 Copynumber: 2.7 Consensus size: 32
28799108 AACTTTTCCG
** *
28799118 GAAAATATTTTCAAGAAATCTGTCAAACAGCA
1 GAAAATATTTTCAAGAAATCAATCAAACACCA
*
28799150 GAAAATATTTTACACAG-ATTCAATCAAACACCA
1 GAAAATATTTT-CA-AGAAATCAATCAAACACCA
*
28799183 GAAAATATTTTCCAGTAAATCA
1 GAAAATATTTTCAAG-AAATCA
28799205 TTTTACAGAA
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
31 2 0.04
32 12 0.27
33 29 0.64
34 2 0.04
ACGTcount: A:0.47, C:0.17, G:0.09, T:0.26
Consensus pattern (32 bp):
GAAAATATTTTCAAGAAATCAATCAAACACCA
Found at i:28799242 original size:34 final size:35
Alignment explanation
Indices: 28799184--28799250 Score: 118
Period size: 34 Copynumber: 1.9 Consensus size: 35
28799174 CAAACACCAG
28799184 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
*
28799219 AAAATATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAATATTTTCCAGTAAATCATTTTACAGAAAA
28799251 TATTTTACGG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 17 0.55
35 14 0.45
ACGTcount: A:0.46, C:0.12, G:0.09, T:0.33
Consensus pattern (35 bp):
AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:28799249 original size:14 final size:14
Alignment explanation
Indices: 28799232--28799272 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
28799222 ATATTTTCCA
28799232 GAAATCATTTTACG
1 GAAATCATTTTACG
28799246 GAAAAT-ATTTTACG
1 G-AAATCATTTTACG
*
28799260 GAAAACATTTTAC
1 GAAATCATTTTAC
28799273 TGGCAATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
13 3 0.12
14 17 0.71
15 4 0.17
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.34
Consensus pattern (14 bp):
GAAATCATTTTACG
Found at i:28799263 original size:28 final size:28
Alignment explanation
Indices: 28799219--28799272 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
28799209 ACAGAAAAGT
* *
28799219 AAAATATTTTCCAGAAATCATTTTACGG
1 AAAATATTTTACAGAAAACATTTTACGG
*
28799247 AAAATATTTTACGGAAAACATTTTAC
1 AAAATATTTTACAGAAAACATTTTAC
28799273 TGGCAATTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.43, C:0.13, G:0.09, T:0.35
Consensus pattern (28 bp):
AAAATATTTTACAGAAAACATTTTACGG
Found at i:28801435 original size:27 final size:27
Alignment explanation
Indices: 28801404--28801461 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
28801394 TAAAATTATT
* *
28801404 ATTTAAAAGAAATACATTTTTAATAAA
1 ATTTAAAAGAAATACAATTCTAATAAA
* **
28801431 ATTTAAAATAAATTTAATTCTAATAAA
1 ATTTAAAAGAAATACAATTCTAATAAA
28801458 ATTT
1 ATTT
28801462 CTACTAAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.41
Consensus pattern (27 bp):
ATTTAAAAGAAATACAATTCTAATAAA
Found at i:28808032 original size:17 final size:17
Alignment explanation
Indices: 28808010--28808045 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
28808000 GTTATTCGAG
28808010 ATGTAAAATTCAATTCA
1 ATGTAAAATTCAATTCA
28808027 ATGTAAAATTCAATTCA
1 ATGTAAAATTCAATTCA
28808044 AT
1 AT
28808046 TCAAACTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.47, C:0.11, G:0.06, T:0.36
Consensus pattern (17 bp):
ATGTAAAATTCAATTCA
Found at i:28809738 original size:33 final size:32
Alignment explanation
Indices: 28809666--28809741 Score: 89
Period size: 33 Copynumber: 2.3 Consensus size: 32
28809656 ATGTTTAAAT
* *
28809666 GTAAGACCATAACTGGGCTATGACATTTTAAT
1 GTAAGACCATAACTGGGCTATGACATTTGAAC
* * *
28809698 GAAAAGACCATAACTGGGTTATGGCACTTTGAAC
1 G-TAAGACCATAACTGGGCTATGACA-TTTGAAC
28809732 GTAAGACCAT
1 GTAAGACCAT
28809742 GGTTGGACCA
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
32 1 0.03
33 29 0.81
34 6 0.17
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.26
Consensus pattern (32 bp):
GTAAGACCATAACTGGGCTATGACATTTGAAC
Found at i:28809842 original size:33 final size:32
Alignment explanation
Indices: 28809770--28809846 Score: 91
Period size: 33 Copynumber: 2.3 Consensus size: 32
28809760 TAGATATATG
* **
28809770 TGTAAGACCATAACTGGGCTATGGCATTCTGA
1 TGTAAGACCATAACTGGGCTATGGCATACAAA
* *
28809802 TGATAAGATCATAACTGGGTTATGGCACTACAAA
1 TG-TAAGACCATAACTGGGCTATGGCA-TACAAA
28809836 TGTAAGACCAT
1 TGTAAGACCAT
28809847 GGCAAGGCCA
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
32 2 0.05
33 30 0.81
34 5 0.14
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.27
Consensus pattern (32 bp):
TGTAAGACCATAACTGGGCTATGGCATACAAA
Found at i:28809858 original size:105 final size:105
Alignment explanation
Indices: 28809665--28809858 Score: 273
Period size: 105 Copynumber: 1.8 Consensus size: 105
28809655 AATGTTTAAA
* ***
28809665 TGTAAGACCATAACTGGGCTATGACATTTTAATGAAAAGACCATAACTGGGTTATGGCACTTTGA
1 TGTAAGACCATAACTGGGCTATGACATTCTAATGAAAAGACCATAACTGGGTTATGGCACTACAA
**
28809730 ACGTAAGACCATGGTTGGACCATGGCATTATAGATATATG
66 ACGTAAGACCATGGAAGGACCATGGCATTATAGATATATG
* * * *
28809770 TGTAAGACCATAACTGGGCTATGGCATTCTGATGATAAGATCATAACTGGGTTATGGCACTACAA
1 TGTAAGACCATAACTGGGCTATGACATTCTAATGAAAAGACCATAACTGGGTTATGGCACTACAA
*
28809835 ATGTAAGACCATGGCAAGG-CCATG
66 ACGTAAGACCATGG-AAGGACCATG
28809859 ACAATGCATG
Statistics
Matches: 77, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
105 75 0.97
106 2 0.03
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.27
Consensus pattern (105 bp):
TGTAAGACCATAACTGGGCTATGACATTCTAATGAAAAGACCATAACTGGGTTATGGCACTACAA
ACGTAAGACCATGGAAGGACCATGGCATTATAGATATATG
Found at i:28811053 original size:16 final size:17
Alignment explanation
Indices: 28811032--28811064 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
28811022 AAAGGGTCAG
28811032 AAAAAGA-AAAATTACA
1 AAAAAGACAAAATTACA
*
28811048 AAAAAGACCAAATTACA
1 AAAAAGACAAAATTACA
28811065 TAATGTATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.70, C:0.12, G:0.06, T:0.12
Consensus pattern (17 bp):
AAAAAGACAAAATTACA
Found at i:28814841 original size:14 final size:14
Alignment explanation
Indices: 28814822--28814850 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
28814812 AAATGAGAAA
28814822 AGCAACTTAGATAG
1 AGCAACTTAGATAG
28814836 AGCAACTTAGATAG
1 AGCAACTTAGATAG
28814850 A
1 A
28814851 ACTAAATGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.14, G:0.21, T:0.21
Consensus pattern (14 bp):
AGCAACTTAGATAG
Found at i:28816756 original size:24 final size:23
Alignment explanation
Indices: 28816726--28816785 Score: 68
Period size: 24 Copynumber: 2.6 Consensus size: 23
28816716 TTATATATAA
28816726 TAATTATTTTATAAAAAATAATT
1 TAATTATTTTATAAAAAATAATT
* *
28816749 TAATT-TATATATCAAAATATAATT
1 TAATTAT-TTTAT-AAAAAATAATT
*
28816773 TAATAATTTTATA
1 TAATTATTTTATA
28816786 TTTGAGTTGG
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
22 1 0.03
23 10 0.33
24 18 0.60
25 1 0.03
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (23 bp):
TAATTATTTTATAAAAAATAATT
Found at i:28822054 original size:13 final size:14
Alignment explanation
Indices: 28822034--28822073 Score: 57
Period size: 13 Copynumber: 3.0 Consensus size: 14
28822024 TCCTTATTAT
28822034 TCGAATTATAAAGG
1 TCGAATTATAAAGG
*
28822048 T-GAATTAT-AATG
1 TCGAATTATAAAGG
28822060 TCGAATTATAAAGG
1 TCGAATTATAAAGG
28822074 CACTCCGATG
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
12 4 0.18
13 14 0.64
14 4 0.18
ACGTcount: A:0.42, C:0.05, G:0.20, T:0.33
Consensus pattern (14 bp):
TCGAATTATAAAGG
Found at i:28824269 original size:28 final size:28
Alignment explanation
Indices: 28824228--28824282 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
28824218 ATGACTGTAT
* *
28824228 AAAATTTTTTAATAAATAAAA-AATATAC
1 AAAATTATTAAAT-AATAAAATAATATAC
*
28824256 AAAATTATTAAATATTAAAATAATATA
1 AAAATTATTAAATAATAAAATAATATA
28824283 ATATAAATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 6 0.26
28 17 0.74
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (28 bp):
AAAATTATTAAATAATAAAATAATATAC
Found at i:28825430 original size:32 final size:30
Alignment explanation
Indices: 28825377--28825441 Score: 94
Period size: 32 Copynumber: 2.1 Consensus size: 30
28825367 ATTTATTTTA
*
28825377 TTGTTAATTTTGTTATTATTTTAAAGGCAT
1 TTGTTAATTTTATTATTATTTTAAAGGCAT
*
28825407 TTGTTAATTTATTATTATTATTTTAGAGGCAT
1 TTGTTAA-TT-TTATTATTATTTTAAAGGCAT
28825439 TTG
1 TTG
28825442 CTTGTTAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 7 0.23
31 2 0.06
32 22 0.71
ACGTcount: A:0.26, C:0.03, G:0.14, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTATTATTATTTTAAAGGCAT
Found at i:28826073 original size:34 final size:32
Alignment explanation
Indices: 28826029--28826142 Score: 108
Period size: 34 Copynumber: 3.5 Consensus size: 32
28826019 CAATATTTAA
*
28826029 AAAAAAACTAAATCCAATTTTAATTAATTTTCTT
1 AAAAACACTAAATCCAA-TTTAATTAATTTT-TT
*
28826063 AAAAACACTAAAACCAAATTTAATTAATTTATTT
1 AAAAACACTAAATCC-AATTTAATTAATTT-TTT
* * *
28826097 AAAATCCCTAAA-CCGTAATTTAATTAA--TTTA
1 AAAAACACTAAATCC--AATTTAATTAATTTTTT
28826128 AAAAACACTAAATCC
1 AAAAACACTAAATCC
28826143 TGATTTATTT
Statistics
Matches: 68, Mismatches: 8, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
31 12 0.18
32 3 0.04
33 2 0.03
34 48 0.71
35 3 0.04
ACGTcount: A:0.50, C:0.15, G:0.01, T:0.34
Consensus pattern (32 bp):
AAAAACACTAAATCCAATTTAATTAATTTTTT
Found at i:28826203 original size:21 final size:21
Alignment explanation
Indices: 28826174--28826244 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 21
28826164 TAAAACCTAG
* *
28826174 AACCTTAAATTATTTTAACAA
1 AACCCTAAATTATTCTAACAA
** * * **
28826195 AACCCTAAATCCTACAAACCT
1 AACCCTAAATTATTCTAACAA
28826216 AACCCTAAATTATTCTAACAA
1 AACCCTAAATTATTCTAACAA
28826237 AACCCTAA
1 AACCCTAA
28826245 CCCTAAAAAA
Statistics
Matches: 36, Mismatches: 14, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.46, C:0.27, G:0.00, T:0.27
Consensus pattern (21 bp):
AACCCTAAATTATTCTAACAA
Found at i:28826256 original size:42 final size:43
Alignment explanation
Indices: 28826165--28826263 Score: 121
Period size: 42 Copynumber: 2.3 Consensus size: 43
28826155 AAAAATTTCT
* * *
28826165 AAAACCTAGAACCTTAAATTATTTTAACAAAACCCTAAATCCTA
1 AAAACCTA-AACCCTAAATTATTCTAACAAAACCCTAAACCCTA
*
28826209 CAAACCT-AACCCTAAATTATTCTAACAAAACCCT-AACCCTAA
1 AAAACCTAAACCCTAAATTATTCTAACAAAACCCTAAACCCT-A
28826251 AAAACCCTAAACC
1 AAAA-CCTAAACC
28826264 AAAAAACCCT
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
41 5 0.11
42 29 0.62
43 3 0.06
44 10 0.21
ACGTcount: A:0.47, C:0.29, G:0.01, T:0.22
Consensus pattern (43 bp):
AAAACCTAAACCCTAAATTATTCTAACAAAACCCTAAACCCTA
Found at i:28826267 original size:15 final size:16
Alignment explanation
Indices: 28826230--28826274 Score: 65
Period size: 16 Copynumber: 2.8 Consensus size: 16
28826220 CTAAATTATT
*
28826230 CTAACAAAACCCTAACC
1 CTAA-AAAACCCTAAAC
28826247 CTAAAAAACCCTAAAC
1 CTAAAAAACCCTAAAC
28826263 C-AAAAAACCCTA
1 CTAAAAAACCCTA
28826275 GGGACTAAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
15 11 0.41
16 12 0.44
17 4 0.15
ACGTcount: A:0.53, C:0.36, G:0.00, T:0.11
Consensus pattern (16 bp):
CTAAAAAACCCTAAAC
Found at i:28834957 original size:17 final size:16
Alignment explanation
Indices: 28834923--28834972 Score: 50
Period size: 17 Copynumber: 3.1 Consensus size: 16
28834913 TTGTAAAATA
28834923 AAAACAAATAACAA-A-
1 AAAACAAATAA-AACAT
*
28834938 AAATCAAATAAAACAT
1 AAAACAAATAAAACAT
*
28834954 AAAACTAAATAAAATAT
1 AAAAC-AAATAAAACAT
28834971 AA
1 AA
28834973 GTAATTCAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
14 2 0.07
15 11 0.38
16 4 0.14
17 12 0.41
ACGTcount: A:0.74, C:0.10, G:0.00, T:0.16
Consensus pattern (16 bp):
AAAACAAATAAAACAT
Found at i:28835235 original size:30 final size:30
Alignment explanation
Indices: 28835201--28835261 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
28835191 TCCATGTGCT
* *
28835201 AAGCCATGTGAGCCATATGGCAGTGTGGCC
1 AAGCCATGTGAGCCACATGACAGTGTGGCC
*
28835231 AAGCCATGTGAGCCACATGACCGTGTGGCC
1 AAGCCATGTGAGCCACATGACAGTGTGGCC
28835261 A
1 A
28835262 GACCGTGTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.25, C:0.26, G:0.31, T:0.18
Consensus pattern (30 bp):
AAGCCATGTGAGCCACATGACAGTGTGGCC
Found at i:28835577 original size:13 final size:13
Alignment explanation
Indices: 28835559--28835588 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
28835549 GACACACCCA
28835559 TGTGTCCAAACCG
1 TGTGTCCAAACCG
*
28835572 TGTGTCCAAGCCG
1 TGTGTCCAAACCG
28835585 TGTG
1 TGTG
28835589 AATTCTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.27, G:0.30, T:0.27
Consensus pattern (13 bp):
TGTGTCCAAACCG
Found at i:28838087 original size:5 final size:6
Alignment explanation
Indices: 28838065--28838095 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
28838055 AATTGAAACA
28838065 AAAATAT AAAAAT AAAAAT AAAAAT AAAAAT
1 AAAA-AT AAAAAT AAAAAT AAAAAT AAAAAT
28838096 GGCTAAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 20 0.83
7 4 0.17
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (6 bp):
AAAAAT
Found at i:28838093 original size:25 final size:26
Alignment explanation
Indices: 28838037--28838093 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 26
28838027 AACAAAAAAC
* * *
28838037 AATAGAATATAAAAATTAAATTGAAA
1 AATAAAATATAAAAATAAAAATGAAA
*
28838063 CA-AAAATATAAAAATAAAAAT-AAA
1 AATAAAATATAAAAATAAAAATGAAA
28838087 AATAAAA
1 AATAAAA
28838094 ATGGCTAAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
24 4 0.16
25 20 0.80
26 1 0.04
ACGTcount: A:0.74, C:0.02, G:0.04, T:0.21
Consensus pattern (26 bp):
AATAAAATATAAAAATAAAAATGAAA
Found at i:28839784 original size:18 final size:19
Alignment explanation
Indices: 28839763--28839799 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
28839753 CACTGCTTGT
*
28839763 GTTAGAATTAC-TGAAAAG
1 GTTACAATTACATGAAAAG
28839781 GTTACAATTACATGAAAAG
1 GTTACAATTACATGAAAAG
28839800 ACACTCTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.46, C:0.08, G:0.19, T:0.27
Consensus pattern (19 bp):
GTTACAATTACATGAAAAG
Found at i:28842121 original size:22 final size:22
Alignment explanation
Indices: 28842096--28842140 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
28842086 GCATTGAGAA
28842096 TGAGATTAAAATATGTTACTTT
1 TGAGATTAAAATATGTTACTTT
28842118 TGAGATTAAAATATGTTACTTT
1 TGAGATTAAAATATGTTACTTT
28842140 T
1 T
28842141 AGCACTTATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (22 bp):
TGAGATTAAAATATGTTACTTT
Found at i:28858999 original size:20 final size:20
Alignment explanation
Indices: 28858974--28859020 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
28858964 AATATCCAAA
28858974 CAATAATAATAAAATAGTAG
1 CAATAATAATAAAATAGTAG
* *
28858994 CAATAATAGTAAAATTGTAG
1 CAATAATAATAAAATAGTAG
28859014 CAA-AATA
1 CAATAATA
28859021 GTGAGAAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 4 0.16
20 21 0.84
ACGTcount: A:0.57, C:0.06, G:0.11, T:0.26
Consensus pattern (20 bp):
CAATAATAATAAAATAGTAG
Found at i:28865399 original size:24 final size:24
Alignment explanation
Indices: 28865372--28865420 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
28865362 ATTTAAGCGC
28865372 TTAATTTTGATTTTGACTTTATGT
1 TTAATTTTGATTTTGACTTTATGT
28865396 TTAATTTTGATTTTGACTTTATGT
1 TTAATTTTGATTTTGACTTTATGT
28865420 T
1 T
28865421 GGGGGTTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.20, C:0.04, G:0.12, T:0.63
Consensus pattern (24 bp):
TTAATTTTGATTTTGACTTTATGT
Found at i:28875958 original size:49 final size:49
Alignment explanation
Indices: 28875901--28875995 Score: 181
Period size: 49 Copynumber: 1.9 Consensus size: 49
28875891 ACAGAATCGT
*
28875901 AGGAAAGAAGAGGAAAAGAAAAATGGCAGGGAATAGAGAAACTAACAAA
1 AGGAAAGAAGAGGAAAAGAAAAATGGCAGGGAACAGAGAAACTAACAAA
28875950 AGGAAAGAAGAGGAAAAGAAAAATGGCAGGGAACAGAGAAACTAAC
1 AGGAAAGAAGAGGAAAAGAAAAATGGCAGGGAACAGAGAAACTAAC
28875996 GCCAGATTGT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.58, C:0.07, G:0.29, T:0.05
Consensus pattern (49 bp):
AGGAAAGAAGAGGAAAAGAAAAATGGCAGGGAACAGAGAAACTAACAAA
Found at i:28879670 original size:20 final size:19
Alignment explanation
Indices: 28879639--28879708 Score: 68
Period size: 20 Copynumber: 3.3 Consensus size: 19
28879629 CTTGCGTTTC
28879639 TTCTTTCTTTCTTTTTTTT
1 TTCTTTCTTTCTTTTTTTT
28879658 TTCTTTCCTTTCTATTTCATTTTGT
1 TTCTTT-CTTTC--TTT--TTTT-T
*
28879683 TTCTTTCTTTCTCTTTTTAT
1 TTCTTTCTTTCT-TTTTTTT
28879703 TTCTTT
1 TTCTTT
28879709 TTCTTTTACT
Statistics
Matches: 43, Mismatches: 1, Indels: 13
0.75 0.02 0.23
Matches are distributed among these distances:
19 6 0.14
20 12 0.28
21 3 0.07
22 4 0.09
23 2 0.05
24 9 0.21
25 7 0.16
ACGTcount: A:0.04, C:0.19, G:0.01, T:0.76
Consensus pattern (19 bp):
TTCTTTCTTTCTTTTTTTT
Found at i:28879776 original size:8 final size:8
Alignment explanation
Indices: 28879763--28879819 Score: 50
Period size: 8 Copynumber: 7.2 Consensus size: 8
28879753 TTTTAAGTTT
28879763 TAATATTA
1 TAATATTA
28879771 TAATATTA
1 TAATATTA
28879779 TAATA-TA
1 TAATATTA
*
28879786 T-ATATTT
1 TAATATTA
28879793 TAACT-TTA
1 TAA-TATTA
28879801 -AATATTTA
1 TAATA-TTA
28879809 TAATATATA
1 TAATAT-TA
28879818 TA
1 TA
28879820 CACTTATGCC
Statistics
Matches: 40, Mismatches: 2, Indels: 13
0.73 0.04 0.24
Matches are distributed among these distances:
6 4 0.10
7 7 0.17
8 20 0.50
9 9 0.22
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (8 bp):
TAATATTA
Found at i:28880422 original size:21 final size:21
Alignment explanation
Indices: 28880398--28880448 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
28880388 GTGTCCCCTC
*
28880398 CACACGGGTATGTGTGGCCTT
1 CACACGGGCATGTGTGGCCTT
28880419 CACACGGGCATGTGTGGCCTT
1 CACACGGGCATGTGTGGCCTT
*
28880440 CACATGGGC
1 CACACGGGC
28880449 GTGTAGACCC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.16, C:0.27, G:0.33, T:0.24
Consensus pattern (21 bp):
CACACGGGCATGTGTGGCCTT
Found at i:28884270 original size:21 final size:21
Alignment explanation
Indices: 28884245--28884286 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
28884235 AAACTTACAA
28884245 AAACCCCATAAAACTCATTTC
1 AAACCCCATAAAACTCATTTC
28884266 AAACCCCATAAAACTCATTTC
1 AAACCCCATAAAACTCATTTC
28884287 TTAGGCAGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.33, G:0.00, T:0.24
Consensus pattern (21 bp):
AAACCCCATAAAACTCATTTC
Found at i:28885370 original size:13 final size:13
Alignment explanation
Indices: 28885352--28885377 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
28885342 CAATAGTTAA
28885352 ATATATTAATAAT
1 ATATATTAATAAT
28885365 ATATATTAATAAT
1 ATATATTAATAAT
28885378 GGAACTTTAT
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):
ATATATTAATAAT
Found at i:28889984 original size:17 final size:16
Alignment explanation
Indices: 28889962--28890006 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
28889952 TAGAATCAAG
*
28889962 TTGAGAAAATTATTTAA
1 TTGAG-AAATTAATTAA
28889979 TTGAGAAATTAATTAA
1 TTGAGAAATTAATTAA
28889995 TT-A-AAATTAATT
1 TTGAGAAATTAATT
28890007 TATGATGAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 9 0.33
15 1 0.04
16 12 0.44
17 5 0.19
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.42
Consensus pattern (16 bp):
TTGAGAAATTAATTAA
Found at i:28890016 original size:132 final size:131
Alignment explanation
Indices: 28889875--28890144 Score: 513
Period size: 132 Copynumber: 2.1 Consensus size: 131
28889865 TCATAGTGAA
* *
28889875 TATGTTGAATGTAGAAATATTAAATGTATTTTCTCATAGGTTTTTTTACAGTAAAATTGTCACGG
1 TATGATGAATGTAGAAATATTAAATGTATTTTCTCATAGGTTTTTTTACAGTAAAATTGTCACGA
28889940 TTTTAAGAGAATTAGAATCAAGTTGAGAAAATTATTTAATTGAGAAATTAATTAATTAAAATTAA
66 TTTTAAGAGAATTAGAATCAAGTTGAGAAAATTATTTAATTGAGAAATTAATT-ATTAAAATTAA
28890005 TT
130 TT
28890007 TATGATGAATGTAGAAATATTAAATGTATTTTCTCATAGGTTTTTTTACAGTAAAATTGTCACGA
1 TATGATGAATGTAGAAATATTAAATGTATTTTCTCATAGGTTTTTTTACAGTAAAATTGTCACGA
28890072 TTTTAAGAGAATTAGAATCAAGTTGAGAAAATTATTTAATTGAGAAATTAATTATTAAAATTAAT
66 TTTTAAGAGAATTAGAATCAAGTTGAGAAAATTATTTAATTGAGAAATTAATTATTAAAATTAAT
28890137 T
131 T
28890138 TATGATG
1 TATGATG
28890145 TTTATTTTGG
Statistics
Matches: 136, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
131 20 0.15
132 116 0.85
ACGTcount: A:0.40, C:0.04, G:0.14, T:0.41
Consensus pattern (131 bp):
TATGATGAATGTAGAAATATTAAATGTATTTTCTCATAGGTTTTTTTACAGTAAAATTGTCACGA
TTTTAAGAGAATTAGAATCAAGTTGAGAAAATTATTTAATTGAGAAATTAATTATTAAAATTAAT
T
Found at i:28897473 original size:18 final size:19
Alignment explanation
Indices: 28897450--28897488 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
28897440 CTTTTATGAT
28897450 TTAGTCCCTAAATCG-TAA
1 TTAGTCCCTAAATCGATAA
*
28897468 TTAGTCCCTAATTCGATAA
1 TTAGTCCCTAAATCGATAA
28897487 TT
1 TT
28897489 TTACCTATCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.31, C:0.21, G:0.10, T:0.38
Consensus pattern (19 bp):
TTAGTCCCTAAATCGATAA
Found at i:28898188 original size:13 final size:13
Alignment explanation
Indices: 28898170--28898196 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
28898160 TCAAAGGATA
28898170 GATTTCTTTTATT
1 GATTTCTTTTATT
28898183 GATTTCTTTTATT
1 GATTTCTTTTATT
28898196 G
1 G
28898197 GTTTAGTTTA
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:0.15, C:0.07, G:0.11, T:0.67
Consensus pattern (13 bp):
GATTTCTTTTATT
Found at i:28899561 original size:31 final size:31
Alignment explanation
Indices: 28899526--28899586 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
28899516 TTAATAGCCT
* *
28899526 AATGACTTAAATAAAAACTTTTGAATAATTG
1 AATGACTTAAAGAAAAACTTTTAAATAATTG
* *
28899557 AATGACTTAAAGGAAAATTTTTAAATAATT
1 AATGACTTAAAGAAAAACTTTTAAATAATT
28899587 CAGTGACCAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.49, C:0.05, G:0.10, T:0.36
Consensus pattern (31 bp):
AATGACTTAAAGAAAAACTTTTAAATAATTG
Found at i:28904997 original size:123 final size:123
Alignment explanation
Indices: 28904770--28905003 Score: 319
Period size: 123 Copynumber: 1.9 Consensus size: 123
28904760 ATTAATTATA
* *
28904770 CCCTGAATTGCACATACGTGCCTCTGTTTGTACTTCGGTACTCCTGAATTACACATACATGCCCC
1 CCCTAAATTGCACATACATGCCTCTGTTTGTACTTCGGTACTCCTGAATTACACATACATGCCCC
* ** *
28904835 TATTTGTACTTTGGTACCCCTGAATTGCACATACATGCCCTTATTTGTACTTTGGTAC
66 TATTTGTACTTCGGTACCCCTGAATAACACATACATGCCCCTATTTGTACTTTGGTAC
* * * *
28904893 CCCTAAATTGCACATACATGCC-CTTGTTTGTACTTTGGTAC-CATTGAATTGCACATAGATGCC
1 CCCTAAATTGCACATACATGCCTC-TGTTTGTACTTCGGTACTC-CTGAATTACACATACATGCC
* * *
28904956 CTTATTTGTACTTCGGTACCCTTGAATAACACATACGTGCCCCTATTT
64 CCTATTTGTACTTCGGTACCCCTGAATAACACATACATGCCCCTATTT
28905004 ACACTTCAAT
Statistics
Matches: 96, Mismatches: 13, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
122 2 0.02
123 94 0.98
ACGTcount: A:0.23, C:0.27, G:0.15, T:0.35
Consensus pattern (123 bp):
CCCTAAATTGCACATACATGCCTCTGTTTGTACTTCGGTACTCCTGAATTACACATACATGCCCC
TATTTGTACTTCGGTACCCCTGAATAACACATACATGCCCCTATTTGTACTTTGGTAC
Found at i:28905010 original size:41 final size:41
Alignment explanation
Indices: 28904770--28905003 Score: 288
Period size: 41 Copynumber: 5.7 Consensus size: 41
28904760 ATTAATTATA
* * *
28904770 CCCTGAATTGCACATACGTGCCTCTGTTTGTACTTCGGTAC
1 CCCTGAATTGCACATACATGCCCCTATTTGTACTTCGGTAC
* * *
28904811 TCCTGAATTACACATACATGCCCCTATTTGTACTTTGGTAC
1 CCCTGAATTGCACATACATGCCCCTATTTGTACTTCGGTAC
* *
28904852 CCCTGAATTGCACATACATGCCCTTATTTGTACTTTGGTAC
1 CCCTGAATTGCACATACATGCCCCTATTTGTACTTCGGTAC
* * * *
28904893 CCCTAAATTGCACATACATGCCCTTGTTTGTACTTTGGTAC
1 CCCTGAATTGCACATACATGCCCCTATTTGTACTTCGGTAC
** * *
28904934 CATTGAATTGCACATAGATGCCCTTATTTGTACTTCGGTAC
1 CCCTGAATTGCACATACATGCCCCTATTTGTACTTCGGTAC
* ** *
28904975 CCTTGAATAACACATACGTGCCCCTATTT
1 CCCTGAATTGCACATACATGCCCCTATTT
28905004 ACACTTCAAT
Statistics
Matches: 170, Mismatches: 23, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 170 1.00
ACGTcount: A:0.23, C:0.27, G:0.15, T:0.35
Consensus pattern (41 bp):
CCCTGAATTGCACATACATGCCCCTATTTGTACTTCGGTAC
Found at i:28913952 original size:30 final size:30
Alignment explanation
Indices: 28913918--28913980 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
28913908 ACTTAACAAG
28913918 CAAATGCCTCTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
*
28913948 CAAATGCCTTTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
28913978 CAA
1 CAA
28913981 TAAAATAAGC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.57, C:0.16, G:0.03, T:0.24
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAATAACAAAATTAA
Found at i:28916370 original size:104 final size:104
Alignment explanation
Indices: 28916189--28916541 Score: 535
Period size: 97 Copynumber: 3.5 Consensus size: 104
28916179 GGGTTGTTGT
* * **
28916189 GTGCTGATTCCCCGATTCATTGGTGGTGCTATGTGCG-TGATCCACCATATCTTTGAAATGTGAA
1 GTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGAT-ATCCACCGTATCTTTGAAATGAAAA
*
28916253 AGGGGGTTGCTATGTGTTGATTCCCCCGAGGGGTTGCTAA
65 AGGGGGTTGCTATGTGCTGATTCCCCCGAGGGGTTGCTAA
28916293 GTGCTGATTCCCCGATTTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCTTTGAAATG-AAA
1 GTGCTGATTCCCCGA-TTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCTTTGAAATGAAAA
28916357 AGGGGGTTGCTATGTGCTGATTCCCCCCGAGGGGTTGCTAA
65 AGGGGGTTGCTATGTGCTGATT-CCCCCGAGGGGTTGCTAA
*
28916398 GTGCCGA-T------TTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCTTTGAAATGAAAAA
1 GTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCTTTGAAATGAAAAA
28916456 GGGGGTTGCTATGTGCTGATTCCCCCGAGGGGTTGCTAA
66 GGGGGTTGCTATGTGCTGATTCCCCCGAGGGGTTGCTAA
* **
28916495 GTGCTGATTCCCCGATTCAGTGGTGGTGCTAAGTGCGGGATCCACCG
1 GTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCG
28916542 ATAACGGTTA
Statistics
Matches: 229, Mismatches: 9, Indels: 22
0.88 0.03 0.08
Matches are distributed among these distances:
97 69 0.30
98 26 0.11
104 68 0.30
105 65 0.28
106 1 0.00
ACGTcount: A:0.19, C:0.20, G:0.30, T:0.30
Consensus pattern (104 bp):
GTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCTTTGAAATGAAAAA
GGGGGTTGCTATGTGCTGATTCCCCCGAGGGGTTGCTAA
Found at i:28918421 original size:92 final size:92
Alignment explanation
Indices: 28918283--28919157 Score: 1401
Period size: 92 Copynumber: 9.5 Consensus size: 92
28918273 ATCCAATGCT
* * * *
28918283 CAAATCAA-TTCAACAATATATATTCATATACGAATCAAATTCGGCAACTTATCTTCATATACAA
1 CAAATAAATTTCAGCAATGTATAATCATATACGAATC-AATTCGGCAACTTATCTTCATATACAA
* * *
28918347 ATCGATTTCGATAATGTATAATCATATA
65 ATCAATTTCGATAATATATAACCATATA
*
28918375 CAAATAAATTTCAGCAATGTATAATCATATACGAATCAATTCGGCAACTTATCTTCATATATAAA
1 CAAATAAATTTCAGCAATGTATAATCATATACGAATCAATTCGGCAACTTATCTTCATATACAAA
*
28918440 TCAATTTCGATAATGTATAACCATATA
66 TCAATTTCGATAATATATAACCATATA
* *
28918467 CAAATAAATTTCAGCAATGTATAATTATATACGAATCAATTTGGCAACTTATCTTCATATACAAA
1 CAAATAAATTTCAGCAATGTATAATCATATACGAATCAATTCGGCAACTTATCTTCATATACAAA
*
28918532 TCAATTTCTATAATATATAACCATATA
66 TCAATTTCGATAATATATAACCATATA
* * **
28918559 CAAATAAATTTCAGCAATGTATAATTATATACAAATCAATTCAACAACTTATCTTCATATACAAA
1 CAAATAAATTTCAGCAATGTATAATCATATACGAATCAATTCGGCAACTTATCTTCATATACAAA
28918624 TCAATTTCGATAATATATAACCATATA
66 TCAATTTCGATAATATATAACCATATA
* *
28918651 CAAATAAATTTCAGCAATATATAATCATATACGAATCAATTCGGCAACTTATCTTCATATATAAA
1 CAAATAAATTTCAGCAATGTATAATCATATACGAATCAATTCGGCAACTTATCTTCATATACAAA
*
28918716 TCAATTTCGATAATGTATAACCATATA
66 TCAATTTCGATAATATATAACCATATA
* * *
28918743 CAAATAAATTTCAGCAATGTATAATTATGTACGAATCAATTTGGCAACTTATCTTCATATACAAA
1 CAAATAAATTTCAGCAATGTATAATCATATACGAATCAATTCGGCAACTTATCTTCATATACAAA
*
28918808 TCAATTTCTATAATATATAACCATATA
66 TCAATTTCGATAATATATAACCATATA
* * *
28918835 CAAATAAATTTCAGCAATGTATAATTATATACAAATCAATTCGACAACTTATCTTCATATACAAA
1 CAAATAAATTTCAGCAATGTATAATCATATACGAATCAATTCGGCAACTTATCTTCATATACAAA
28918900 TCAATTTCGATAATATATAACCATATA
66 TCAATTTCGATAATATATAACCATATA
* *
28918927 CAAATAAATTTCAGCAATGTATAATCATATACGAATCCATTCGACAACTTATCTTCATATACAAA
1 CAAATAAATTTCAGCAATGTATAATCATATACGAATCAATTCGGCAACTTATCTTCATATACAAA
28918992 TCAATTTCGATAATATATAACCATATA
66 TCAATTTCGATAATATATAACCATATA
* *
28919019 TAAATAAATTTCAGCAATGTATAATCATATATGAATCAATTCGGCAACTTATCTTCATATACAAA
1 CAAATAAATTTCAGCAATGTATAATCATATACGAATCAATTCGGCAACTTATCTTCATATACAAA
*
28919084 TCAATTTCGATAATGTATAACCATATA
66 TCAATTTCGATAATATATAACCATATA
** ** * *
28919111 CAAATAAATTTCAATAATGTATAATTGTATACGAATTAATTTGGCAA
1 CAAATAAATTTCAGCAATGTATAATCATATACGAATCAATTCGGCAA
28919158 TGTATAAAAC
Statistics
Matches: 730, Mismatches: 52, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
92 705 0.97
93 25 0.03
ACGTcount: A:0.44, C:0.16, G:0.06, T:0.34
Consensus pattern (92 bp):
CAAATAAATTTCAGCAATGTATAATCATATACGAATCAATTCGGCAACTTATCTTCATATACAAA
TCAATTTCGATAATATATAACCATATA
Found at i:28919152 original size:31 final size:31
Alignment explanation
Indices: 28918338--28919134 Score: 356
Period size: 31 Copynumber: 26.0 Consensus size: 31
28918328 AACTTATCTT
** * *
28918338 CATATACAAATCGATTTCGATAATGTATAAT
1 CATATACAAATAAATTTCAATAATGTATAAC
** *
28918369 CATATACAAATAAATTTCAGCAATGTATAAT
1 CATATACAAATAAATTTCAATAATGTATAAC
* * *** ***
28918400 CATATACGAATCAA-TTCGGCAACT-TATCTT
1 CATATACAAATAAATTTCAATAA-TGTATAAC
* * *
28918430 CATATATAAATCAATTTCGATAATGTATAAC
1 CATATACAAATAAATTTCAATAATGTATAAC
** *
28918461 CATATACAAATAAATTTCAGCAATGTATAAT
1 CATATACAAATAAATTTCAATAATGTATAAC
* * * * *
28918492 TATATACGAATCAATTTGGCAACTTATCT-T---
1 CATATACAAATAAATTT--CAA-TAATGTATAAC
* * *
28918522 CATATACAAATCAATTTCTATAATATATAAC
1 CATATACAAATAAATTTCAATAATGTATAAC
** *
28918553 CATATACAAATAAATTTCAGCAATGTATAAT
1 CATATACAAATAAATTTCAATAATGTATAAC
* * * ***
28918584 TATATACAAATCAA-TTCAACAACT-TATCTT
1 CATATACAAATAAATTTCAATAA-TGTATAAC
* * *
28918614 CATATACAAATCAATTTCGATAATATATAAC
1 CATATACAAATAAATTTCAATAATGTATAAC
** * *
28918645 CATATACAAATAAATTTCAGCAATATATAAT
1 CATATACAAATAAATTTCAATAATGTATAAC
* * *** ***
28918676 CATATACGAATCAA-TTCGGCAACT-TATCTT
1 CATATACAAATAAATTTCAATAA-TGTATAAC
* * *
28918706 CATATATAAATCAATTTCGATAATGTATAAC
1 CATATACAAATAAATTTCAATAATGTATAAC
** *
28918737 CATATACAAATAAATTTCAGCAATGTATAAT
1 CATATACAAATAAATTTCAATAATGTATAAC
* * * * * *
28918768 TATGTACGAATCAATTTGGCAACTTATCT-T---
1 CATATACAAATAAATTT--CAA-TAATGTATAAC
* * *
28918798 CATATACAAATCAATTTCTATAATATATAAC
1 CATATACAAATAAATTTCAATAATGTATAAC
** *
28918829 CATATACAAATAAATTTCAGCAATGTATAAT
1 CATATACAAATAAATTTCAATAATGTATAAC
* * * * ***
28918860 TATATACAAATCAA-TTCGACAACT-TATCTT
1 CATATACAAATAAATTTCAATAA-TGTATAAC
* * *
28918890 CATATACAAATCAATTTCGATAATATATAAC
1 CATATACAAATAAATTTCAATAATGTATAAC
** *
28918921 CATATACAAATAAATTTCAGCAATGTATAAT
1 CATATACAAATAAATTTCAATAATGTATAAC
* ** * * ***
28918952 CATATACGAATCCA-TTCGACAACT-TATCTT
1 CATATACAAATAAATTTCAATAA-TGTATAAC
* * *
28918982 CATATACAAATCAATTTCGATAATATATAAC
1 CATATACAAATAAATTTCAATAATGTATAAC
* ** *
28919013 CATATATAAATAAATTTCAGCAATGTATAAT
1 CATATACAAATAAATTTCAATAATGTATAAC
** * *** ***
28919044 CATATATGAATCAA-TTCGGCAACT-TATCTT
1 CATATACAAATAAATTTCAATAA-TGTATAAC
* *
28919074 CATATACAAATCAATTTCGATAATGTATAAC
1 CATATACAAATAAATTTCAATAATGTATAAC
28919105 CATATACAAATAAATTTCAATAATGTATAA
1 CATATACAAATAAATTTCAATAATGTATAA
28919135 TTGTATACGA
Statistics
Matches: 588, Mismatches: 146, Indels: 64
0.74 0.18 0.08
Matches are distributed among these distances:
27 8 0.01
28 6 0.01
30 173 0.29
31 389 0.66
33 6 0.01
34 6 0.01
ACGTcount: A:0.44, C:0.16, G:0.06, T:0.34
Consensus pattern (31 bp):
CATATACAAATAAATTTCAATAATGTATAAC
Found at i:28921244 original size:73 final size:73
Alignment explanation
Indices: 28921167--28921329 Score: 177
Period size: 73 Copynumber: 2.2 Consensus size: 73
28921157 TGTATAACGT
* * * *
28921167 GAAGCT-CATAAGAGTCATAT-TTAGGAAACTCATGCGAGCCAATAACGGGTAGCTTCAAAGAGC
1 GAAGCTCCA-AAGAGCCATATATTAGGAAACTCAAGCGAGCC-ATAACGGGAAGCTCCAAAGAGC
28921230 CATTAATTAG
64 CATTAATTAG
* * ** * * *
28921240 GAAGCTCCAAATAGCCATATATTGGGAAGTTCAAGCGAGCCATATCGGGAAGCTCCGAAGGGCCA
1 GAAGCTCCAAAGAGCCATATATTAGGAAACTCAAGCGAGCCATAACGGGAAGCTCCAAAGAGCCA
28921305 TTAATTAG
66 TTAATTAG
*
28921313 GAAGCTTACAAAGAGCC
1 GAAGC-TCCAAAGAGCC
28921330 TTTAATCGGG
Statistics
Matches: 74, Mismatches: 13, Indels: 5
0.80 0.14 0.05
Matches are distributed among these distances:
73 47 0.64
74 27 0.36
ACGTcount: A:0.36, C:0.20, G:0.24, T:0.21
Consensus pattern (73 bp):
GAAGCTCCAAAGAGCCATATATTAGGAAACTCAAGCGAGCCATAACGGGAAGCTCCAAAGAGCCA
TTAATTAG
Found at i:28921250 original size:25 final size:25
Alignment explanation
Indices: 28921217--28921345 Score: 95
Period size: 25 Copynumber: 5.2 Consensus size: 25
28921207 AATAACGGGT
* *
28921217 AGCTTCAAAGAGCCATTAATTAGGA
1 AGCTCCAAAGAGCCATTAATTGGGA
*
28921242 AGCTCCAAATAGCCA-TATATTGGGA
1 AGCTCCAAAGAGCCATTA-ATTGGGA
* * *
28921267 AG-TTCAAGCGAGCCA-T-ATCGGGA
1 AGCTCCAA-AGAGCCATTAATTGGGA
* * *
28921290 AGCTCCGAAGGGCCATTAATTAGGA
1 AGCTCCAAAGAGCCATTAATTGGGA
* * *
28921315 AGCTTACAAAGAGCCTTTAATCGGGA
1 AGC-TCCAAAGAGCCATTAATTGGGA
28921341 AGCTC
1 AGCTC
28921346 ATGAAGAGCC
Statistics
Matches: 78, Mismatches: 20, Indels: 12
0.71 0.18 0.11
Matches are distributed among these distances:
23 13 0.17
24 10 0.13
25 36 0.46
26 19 0.24
ACGTcount: A:0.34, C:0.20, G:0.24, T:0.22
Consensus pattern (25 bp):
AGCTCCAAAGAGCCATTAATTGGGA
Found at i:28924664 original size:18 final size:18
Alignment explanation
Indices: 28924643--28924688 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
28924633 TTTAAATCAA
* *
28924643 TAAAAATTTTAAAAATAT
1 TAAAAATATAAAAAATAT
28924661 TAAAAATATAAAAAATAT
1 TAAAAATATAAAAAATAT
*
28924679 TAAAATTATA
1 TAAAAATATA
28924689 GAAATTATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
TAAAAATATAAAAAATAT
Found at i:28924697 original size:18 final size:17
Alignment explanation
Indices: 28924645--28924693 Score: 62
Period size: 18 Copynumber: 2.8 Consensus size: 17
28924635 TAAATCAATA
*
28924645 AAAATTTTAAAAATATT
1 AAAATTATAAAAATATT
*
28924662 AAAAATATAAAAAATATT
1 AAAATTAT-AAAAATATT
*
28924680 AAAATTATAGAAAT
1 AAAATTATAAAAAT
28924694 TATTTTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
17 11 0.41
18 16 0.59
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (17 bp):
AAAATTATAAAAATATT
Found at i:28924914 original size:10 final size:9
Alignment explanation
Indices: 28924893--28925029 Score: 76
Period size: 9 Copynumber: 14.0 Consensus size: 9
28924883 ATAAAAGGTG
28924893 ATAAAAATT
1 ATAAAAATT
28924902 ATAAAAATAT
1 ATAAAAAT-T
*
28924912 ATAGGAAAAAT
1 ATA--AAAATT
* *
28924923 GTATAAATT
1 ATAAAAATT
**
28924932 ATTAAATTTTT
1 A-TAAA-AATT
28924943 ATACAAAATT
1 ATA-AAAATT
*
28924953 ATTTAAAATTTT
1 A--TAAAA-ATT
*
28924965 AGAAAAAATT
1 ATAA-AAATT
*
28924975 ATAAAAGTT
1 ATAAAAATT
*
28924984 ATAAAAAAT
1 ATAAAAATT
28924993 ATAATAAATT
1 ATAA-AAATT
* *
28925003 ATTAAAAGT
1 ATAAAAATT
28925012 ATAAAAATT
1 ATAAAAATT
28925021 ATAAAAATT
1 ATAAAAATT
28925030 TATGTCAAAG
Statistics
Matches: 95, Mismatches: 22, Indels: 22
0.68 0.16 0.16
Matches are distributed among these distances:
9 47 0.49
10 26 0.27
11 13 0.14
12 9 0.09
ACGTcount: A:0.59, C:0.01, G:0.04, T:0.36
Consensus pattern (9 bp):
ATAAAAATT
Found at i:28924964 original size:22 final size:22
Alignment explanation
Indices: 28924927--28924976 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
28924917 AAAAATGTAT
* * *
28924927 AAATTA-TTAAATTTTTATACA
1 AAATTATTTAAAATTTTAGAAA
28924948 AAATTATTTAAAATTTTAGAAA
1 AAATTATTTAAAATTTTAGAAA
28924970 AAATTAT
1 AAATTAT
28924977 AAAAGTTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 6 0.24
22 19 0.76
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (22 bp):
AAATTATTTAAAATTTTAGAAA
Found at i:28924991 original size:19 final size:19
Alignment explanation
Indices: 28924967--28925032 Score: 73
Period size: 19 Copynumber: 3.5 Consensus size: 19
28924957 AAAATTTTAG
*
28924967 AAAAAATTATAAAAGTTAT
1 AAAAAATTATAAAAATTAT
28924986 AAAAAA-TATAATAAATTAT
1 AAAAAATTATAA-AAATTAT
* *
28925005 -TAAAAGTATAAAAATTAT
1 AAAAAATTATAAAAATTAT
*
28925023 AAAAATTTAT
1 AAAAAATTAT
28925033 GTCAAAGTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
18 16 0.41
19 23 0.59
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (19 bp):
AAAAAATTATAAAAATTAT
Found at i:28925032 original size:28 final size:28
Alignment explanation
Indices: 28924968--28925029 Score: 92
Period size: 28 Copynumber: 2.2 Consensus size: 28
28924958 AAATTTTAGA
28924968 AAAAATTA-TAAAAGTTATAAAAAATAT
1 AAAAATTATTAAAAGTTATAAAAAATAT
*
28924995 AATAAATTATTAAAAG-TATAAAAATTAT
1 AA-AAATTATTAAAAGTTATAAAAAATAT
28925023 AAAAATT
1 AAAAATT
28925030 TATGTCAAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
27 7 0.22
28 19 0.59
29 6 0.19
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (28 bp):
AAAAATTATTAAAAGTTATAAAAAATAT
Found at i:28925283 original size:49 final size:47
Alignment explanation
Indices: 28925212--28925305 Score: 118
Period size: 49 Copynumber: 2.0 Consensus size: 47
28925202 TATATAACAT
**
28925212 TTTTTTAACATTTTTCTAAATTTTTG-ATATTTTTATATTTTTCTGTA
1 TTTTTTAACATTTTTCTAAATTTAAGTAT-TTTTTATATTTTTCTGTA
* *
28925259 TTTTTTAACATTTTTTTATTAATTTAAGTATTTTTTATCTTTTTCTG
1 TTTTTTAACATTTTTCTA--AATTTAAGTATTTTTTATATTTTTCTG
28925306 CCACATGTCA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
47 17 0.43
49 21 0.52
50 2 0.05
ACGTcount: A:0.22, C:0.06, G:0.04, T:0.67
Consensus pattern (47 bp):
TTTTTTAACATTTTTCTAAATTTAAGTATTTTTTATATTTTTCTGTA
Found at i:28926030 original size:26 final size:26
Alignment explanation
Indices: 28926001--28926055 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
28925991 TGAAAAATAA
28926001 GTAAATTTTTGTGTAATTAGATATTT
1 GTAAATTTTTGTGTAATTAGATATTT
*
28926027 GTAAATTTTTGTGTATTTAGATATTT
1 GTAAATTTTTGTGTAATTAGATATTT
28926053 GTA
1 GTA
28926056 TGTCAAAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.29, C:0.00, G:0.16, T:0.55
Consensus pattern (26 bp):
GTAAATTTTTGTGTAATTAGATATTT
Found at i:28926236 original size:2 final size:2
Alignment explanation
Indices: 28926229--28926255 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
28926219 CTTTAAGTGT
28926229 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
28926256 TACCAACTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:28926576 original size:43 final size:43
Alignment explanation
Indices: 28926529--28926714 Score: 122
Period size: 43 Copynumber: 4.3 Consensus size: 43
28926519 CTTTTCCCTA
*
28926529 AAACGCCGCAAAAGACCCTGATCCATAACGGCGC-TTCGACCAC
1 AAACGCCGCTAAAGACCCTGATCCATAACGGCGCTTTC-ACCAC
* * * ** * *
28926572 AAACGCCACTAAAGAACCTAATCTTTAGCGGCGCTTTCCCCAC
1 AAACGCCGCTAAAGACCCTGATCCATAACGGCGCTTTCACCAC
* ** ** ** **
28926615 AAACGCCGCTAAAGACCATGATCTTTAGGGGCGCTTTTTCTGC
1 AAACGCCGCTAAAGACCCTGATCCATAACGGCGCTTTCACCAC
* * ** * * * *
28926658 AAACGCCGCGAAAGACCCTTATCTTTAGCGGTGCTTTTACCAA
1 AAACGCCGCTAAAGACCCTGATCCATAACGGCGCTTTCACCAC
*
28926701 AAACGCCACTAAAG
1 AAACGCCGCTAAAG
28926715 GCCAACACCT
Statistics
Matches: 114, Mismatches: 28, Indels: 2
0.79 0.19 0.01
Matches are distributed among these distances:
43 111 0.97
44 3 0.03
ACGTcount: A:0.30, C:0.31, G:0.18, T:0.20
Consensus pattern (43 bp):
AAACGCCGCTAAAGACCCTGATCCATAACGGCGCTTTCACCAC
Found at i:28926648 original size:86 final size:85
Alignment explanation
Indices: 28926507--28926714 Score: 200
Period size: 86 Copynumber: 2.4 Consensus size: 85
28926497 AAGATTAGGG
* * * *
28926507 TCTTTAGTGGCGCTTTTCCCTAAAACGCCGCAAAAGACCCTGATCCATAACGGCGCTTCGACCAC
1 TCTTTAGCGGCGC-TTTCCCCAAAACGCCGCTAAAGACCATGATCCATAACGGCGCTTCGACCAC
*
28926572 AAACGCCACTAAAGAACCTAA
65 AAACGCCACGAAAGAACCTAA
** ** *** **
28926593 TCTTTAGCGGCGCTTTCCCCACAAACGCCGCTAAAGACCATGATCTTTAGGGGCGCTTTTTCTGC
1 TCTTTAGCGGCGCTTTCCCCA-AAACGCCGCTAAAGACCATGATCCATAACGGCGCTTCGACCAC
* * *
28926658 AAACGCCGCGAAAGACCCTTA
65 AAACGCCACGAAAGAACCTAA
* * * *
28926679 TCTTTAGCGGTGCTTTTACCAAAAACGCCACTAAAG
1 TCTTTAGCGGCGC-TTTCCCCAAAACGCCGCTAAAG
28926715 GCCAACACCT
Statistics
Matches: 99, Mismatches: 21, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
85 7 0.07
86 86 0.87
87 6 0.06
ACGTcount: A:0.28, C:0.31, G:0.18, T:0.23
Consensus pattern (85 bp):
TCTTTAGCGGCGCTTTCCCCAAAACGCCGCTAAAGACCATGATCCATAACGGCGCTTCGACCACA
AACGCCACGAAAGAACCTAA
Found at i:28926727 original size:86 final size:86
Alignment explanation
Indices: 28926571--28926739 Score: 203
Period size: 86 Copynumber: 2.0 Consensus size: 86
28926561 GCTTCGACCA
* * * * **
28926571 CAAACGCCACTAAAGAACCTAATCTTTAGCGGCGCTTTCCCCACAAACGCCGCTAAAGACCATGA
1 CAAACGCCACGAAAGAACCTAATCTTTAGCGGCGCTTTCACCAAAAACGCCACTAAAGACCAACA
*
28926636 TCTTTAGGGGCGCTTTTTCTG
66 CCTTTAGGGGCGCTTTTTCTG
* * * * * *
28926657 CAAACGCCGCGAAAGACCCTTATCTTTAGCGGTGCTTTTACCAAAAACGCCACTAAAGGCCAACA
1 CAAACGCCACGAAAGAACCTAATCTTTAGCGGCGCTTTCACCAAAAACGCCACTAAAGACCAACA
* *
28926722 CCTTTAGTGGCGTTTTTT
66 CCTTTAGGGGCGCTTTTT
28926740 TTTGAAAAAC
Statistics
Matches: 68, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
86 68 1.00
ACGTcount: A:0.27, C:0.29, G:0.18, T:0.25
Consensus pattern (86 bp):
CAAACGCCACGAAAGAACCTAATCTTTAGCGGCGCTTTCACCAAAAACGCCACTAAAGACCAACA
CCTTTAGGGGCGCTTTTTCTG
Found at i:28926727 original size:129 final size:129
Alignment explanation
Indices: 28926489--28926733 Score: 278
Period size: 129 Copynumber: 1.9 Consensus size: 129
28926479 TTAGTGGAAG
** * *
28926489 CGCCGCTAAAGATTAGGGTCTTTAGTGGCGCTTTTCCCTAAAACGCCGCAAAAGACCCTGATCCA
1 CGCCGCTAAAGACCAGGATCTTTAGGGGCGCTTTTCCCTAAAACGCCGCAAAAGACCCTGATCCA
* * *
28926554 TAACGGCGCTTCGACCACAAACGCCACTAAAGAACCTAATCTTTAGCGGCGCTTTCCCCACAAA
66 TAACGGCGCTTCGACCAAAAACGCCACTAAAGAACCAAACCTTTAGCGGCGCTTTCCCCACAAA
* * * * * *
28926618 CGCCGCTAAAGACCATGATCTTTAGGGGCGCTTTT-TCTGCAAACGCCGCGAAAGACCCTTATCT
1 CGCCGCTAAAGACCAGGATCTTTAGGGGCGCTTTTCCCT-AAAACGCCGCAAAAGACCCTGATCC
* * * ** * *
28926682 TTAGCGGTGCTTTTACCAAAAACGCCACTAAAG-GCCAACACCTTTAGTGGCG
65 ATAACGGCGCTTCGACCAAAAACGCCACTAAAGAACCAA-ACCTTTAGCGGCG
28926734 TTTTTTTTTG
Statistics
Matches: 94, Mismatches: 20, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
128 5 0.05
129 89 0.95
ACGTcount: A:0.27, C:0.30, G:0.20, T:0.22
Consensus pattern (129 bp):
CGCCGCTAAAGACCAGGATCTTTAGGGGCGCTTTTCCCTAAAACGCCGCAAAAGACCCTGATCCA
TAACGGCGCTTCGACCAAAAACGCCACTAAAGAACCAAACCTTTAGCGGCGCTTTCCCCACAAA
Found at i:28927062 original size:21 final size:21
Alignment explanation
Indices: 28927036--28927127 Score: 103
Period size: 21 Copynumber: 4.4 Consensus size: 21
28927026 TCTAAAGCTA
*
28927036 CTCTGCTTCCCTCGCTGTAGC
1 CTCTGCTTCCCTCGCTGCAGC
28927057 CTCTGCTTCCCTCGCTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
* * * *
28927078 CTATACTTCTCTCGCTGCCGC
1 CTCTGCTTCCCTCGCTGCAGC
* * *
28927099 CTCTGCTTCTCTTGCTGCCGC
1 CTCTGCTTCCCTCGCTGCAGC
*
28927120 ATCTGCTT
1 CTCTGCTT
28927128 TAAGCTGCTG
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 62 1.00
ACGTcount: A:0.05, C:0.42, G:0.17, T:0.35
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCAGC
Found at i:28927175 original size:66 final size:66
Alignment explanation
Indices: 28927098--28927238 Score: 205
Period size: 66 Copynumber: 2.1 Consensus size: 66
28927088 CTCGCTGCCG
* *
28927098 CCTCTGCTTCTCTTGCTGCCGCATCTGCTTTAAGCTGCT-GCTGGAGTTCTTCATA-CTTTCGTT
1 CCTCAGCTTCTCTCGCTGCCGCATCTGCTTTAAGCTG-TAGCTGGAGTTCTTCATATCTTT-GTT
28927161 GAA
64 GAA
* * *
28927164 CCTCAGCTTCTCTCGCTGCTGCATCTGCTTTAAGTTGTAGCTGGAGTTCTTCATATCTTTTTTGA
1 CCTCAGCTTCTCTCGCTGCCGCATCTGCTTTAAGCTGTAGCTGGAGTTCTTCATATCTTTGTTGA
28927229 A
66 A
28927230 CCTCAGCTT
1 CCTCAGCTT
28927239 GCCTCCGCTT
Statistics
Matches: 68, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
65 1 0.01
66 63 0.93
67 4 0.06
ACGTcount: A:0.13, C:0.28, G:0.18, T:0.40
Consensus pattern (66 bp):
CCTCAGCTTCTCTCGCTGCCGCATCTGCTTTAAGCTGTAGCTGGAGTTCTTCATATCTTTGTTGA
A
Found at i:28929218 original size:9 final size:9
Alignment explanation
Indices: 28929201--28929497 Score: 150
Period size: 9 Copynumber: 34.2 Consensus size: 9
28929191 TAAGTATAAT
*
28929201 TAAGCTATG
1 TAAGTTATG
28929210 TAAGTTATG
1 TAAGTTATG
28929219 T-A-TTATG
1 TAAGTTATG
28929226 TAAGTTAT-
1 TAAGTTATG
*
28929234 TTA-TTATG
1 TAAGTTATG
* *
28929242 AAAATTATG
1 TAAGTTATG
*
28929251 TAAGTTGTG
1 TAAGTTATG
28929260 T-A-TTATG
1 TAAGTTATG
* *
28929267 AAAATTATG
1 TAAGTTATG
28929276 CT-A-TATATG
1 -TAAGT-TATG
28929285 TAAGTTATG
1 TAAGTTATG
* *
28929294 TAAGTCATA
1 TAAGTTATG
28929303 TAAGTTATG
1 TAAGTTATG
28929312 T-A-TTATG
1 TAAGTTATG
*
28929319 TAAATTATG
1 TAAGTTATG
28929328 TAAGTTAT-
1 TAAGTTATG
*
28929336 TTA-TTATG
1 TAAGTTATG
* *
28929344 AAAATTAATG
1 TAAGTT-ATG
28929354 TAAGTTATG
1 TAAGTTATG
*
28929363 TAATTTATG
1 TAAGTTATG
*
28929372 -AA-TAAT-
1 TAAGTTATG
*** *
28929378 TAAAAAAAAG
1 T-AAGTTATG
28929388 TAAGTTATG
1 TAAGTTATG
28929397 TAAG-T-TG
1 TAAGTTATG
28929404 TAAGTTATG
1 TAAGTTATG
28929413 TAAGTTATG
1 TAAGTTATG
28929422 TAAGTTATG
1 TAAGTTATG
*
28929431 TATA-ATAT-
1 TA-AGTTATG
28929439 TAA-TTAAT-
1 TAAGTT-ATG
28929447 TAAGTTATG
1 TAAGTTATG
*
28929456 TAATTTATG
1 TAAGTTATG
*
28929465 TATTGCATTAATG
1 TA-AG--TT-ATG
28929478 TAAGTTATG
1 TAAGTTATG
*
28929487 TAACTTATG
1 TAAGTTATG
28929496 TA
1 TA
28929498 TAATATTAAT
Statistics
Matches: 224, Mismatches: 35, Indels: 58
0.71 0.11 0.18
Matches are distributed among these distances:
7 35 0.16
8 29 0.13
9 140 0.62
10 12 0.05
12 3 0.01
13 5 0.02
ACGTcount: A:0.38, C:0.02, G:0.15, T:0.44
Consensus pattern (9 bp):
TAAGTTATG
Found at i:28929227 original size:16 final size:16
Alignment explanation
Indices: 28929206--28929329 Score: 100
Period size: 16 Copynumber: 7.9 Consensus size: 16
28929196 ATAATTAAGC
28929206 TATGTAAGTTATGTAT
1 TATGTAAGTTATGTAT
*
28929222 TATGTAAGTTATTTAT
1 TATGTAAGTTATGTAT
28929238 TATG-AA---A---AT
1 TATGTAAGTTATGTAT
*
28929247 TATGTAAGTTGTGTAT
1 TATGTAAGTTATGTAT
* *
28929263 TATGAAAATTATGCTAT
1 TATGTAAGTTATG-TAT
28929280 ATATGTAAGTTATGTAAGT
1 -TATGTAAGTTATGT-A-T
* *
28929299 CATATAAGTTATGTAT
1 TATGTAAGTTATGTAT
*
28929315 TATGTAAATTATGTA
1 TATGTAAGTTATGTA
28929330 AGTTATTTAT
Statistics
Matches: 85, Mismatches: 12, Indels: 22
0.71 0.10 0.18
Matches are distributed among these distances:
9 6 0.07
10 2 0.02
12 1 0.01
15 2 0.02
16 44 0.52
17 5 0.06
18 24 0.28
19 1 0.01
ACGTcount: A:0.36, C:0.02, G:0.16, T:0.46
Consensus pattern (16 bp):
TATGTAAGTTATGTAT
Found at i:28929248 original size:25 final size:25
Alignment explanation
Indices: 28929220--28929379 Score: 144
Period size: 25 Copynumber: 6.2 Consensus size: 25
28929210 TAAGTTATGT
28929220 ATTATGTAAGTTATTTATTATGAAA
1 ATTATGTAAGTTATTTATTATGAAA
* *
28929245 ATTATGTAAGTTGTGTATTATGAAA
1 ATTATGTAAGTTATTTATTATGAAA
* *
28929270 ATTATGCT-A-TATATGTAAGTTATGTAA
1 ATTATG-TAAGT-TAT-TTA-TTATGAAA
* * * * *
28929297 GTCATATAAGTTATGTATTATGTAA
1 ATTATGTAAGTTATTTATTATGAAA
28929322 ATTATGTAAGTTATTTATTATGAAA
1 ATTATGTAAGTTATTTATTATGAAA
*
28929347 ATTAATGTAAGTTATGTAATTTATGAATA
1 ATT-ATGTAAGTTAT-TTA-TTATGAA-A
28929376 ATTA
1 ATTA
28929380 AAAAAAAGTA
Statistics
Matches: 108, Mismatches: 17, Indels: 17
0.76 0.12 0.12
Matches are distributed among these distances:
24 1 0.01
25 63 0.58
26 15 0.14
27 16 0.15
28 9 0.08
29 4 0.04
ACGTcount: A:0.39, C:0.01, G:0.14, T:0.46
Consensus pattern (25 bp):
ATTATGTAAGTTATTTATTATGAAA
Found at i:28929425 original size:34 final size:33
Alignment explanation
Indices: 28929206--28929531 Score: 124
Period size: 34 Copynumber: 9.7 Consensus size: 33
28929196 ATAATTAAGC
* *
28929206 TATGTAAGTTATGT-A-TTATGTAAGTTATTTAT
1 TATGTAAGTTATGTAAGTTATGTAAGTT-GTAAT
* * * * *
28929238 TATGAAAATTATGTAAGTTGTGT-ATTATGAAAAT
1 TATGTAAGTTATGTAAGTTATGTAAGT-TG-TAAT
*
28929272 TATGCT-A-TATATGTAAGTTATGTAAGTCATATAAGT
1 TATG-TAAGT-TATGTAAGTTATGTAAGT--TGTAA-T
* * *
28929308 TATGT-A-TTATGTAAATTATGTAAGTTATTTAT
1 TATGTAAGTTATGTAAGTTATGTAAGTT-GTAAT
* * * *
28929340 TATGAAAATTAATGTAAGTTATGTAATTTATGAAT
1 TATGTAAGTT-ATGTAAGTTATGTAAGTTGT-AAT
* *** *
28929375 AAT-TAAAAAAAAGTAAGTTATGTAAGTTGTAAGT
1 TATGT-AAGTTATGTAAGTTATGTAAGTTGTAA-T
*
28929409 TATGTAAGTTATGTAAGTTATGTATAATAT-TAAT
1 TATGTAAGTTATGTAAGTTATGTA-AGT-TGTAAT
* *
28929443 TAAT-TAAGTTATGTAATTTATGT-A-TTG-CAT
1 T-ATGTAAGTTATGTAAGTTATGTAAGTTGTAAT
* *
28929473 TAATGTAAGTTATGTAACTTATGTATAATAT-TAAT
1 T-ATGTAAGTTATGTAAGTTATGTA-AGT-TGTAAT
* *
28929508 TAAT-TAAGTCATGTAATTTATGTA
1 T-ATGTAAGTTATGTAAGTTATGTA
28929532 TAATATTAAT
Statistics
Matches: 228, Mismatches: 39, Indels: 52
0.71 0.12 0.16
Matches are distributed among these distances:
30 7 0.03
31 19 0.08
32 19 0.08
33 10 0.04
34 120 0.53
35 45 0.20
36 8 0.04
ACGTcount: A:0.39, C:0.02, G:0.15, T:0.45
Consensus pattern (33 bp):
TATGTAAGTTATGTAAGTTATGTAAGTTGTAAT
Found at i:28929485 original size:31 final size:30
Alignment explanation
Indices: 28929413--28929561 Score: 138
Period size: 31 Copynumber: 4.6 Consensus size: 30
28929403 GTAAGTTATG
*
28929413 TAAGTTATGTAAGTTATGTATAATATTAATTAAT
1 TAAGTTATGTAATTTATGTAT--TA--AATTAAT
**
28929447 TAAGTTATGTAATTTATGTATTGCATTAAT
1 TAAGTTATGTAATTTATGTATTAAATTAAT
*
28929477 GTAAGTTATGTAACTTATGTATAATATTAATTAAT
1 -TAAGTTATGTAATTTATGTAT--TA--AATTAAT
*
28929512 TAAGTCATGTAATTTATGTA-TAATATTAAT
1 TAAGTTATGTAATTTATGTATTAA-ATTAAT
*
28929542 GCAAGTTATGTAATTTATGT
1 -TAAGTTATGTAATTTATGT
28929562 TTTTGGCAAA
Statistics
Matches: 98, Mismatches: 10, Indels: 17
0.78 0.08 0.14
Matches are distributed among these distances:
29 1 0.01
30 12 0.12
31 39 0.40
32 1 0.01
33 1 0.01
34 38 0.39
35 6 0.06
ACGTcount: A:0.38, C:0.03, G:0.13, T:0.47
Consensus pattern (30 bp):
TAAGTTATGTAATTTATGTATTAAATTAAT
Found at i:28929488 original size:65 final size:65
Alignment explanation
Indices: 28929410--28929561 Score: 241
Period size: 65 Copynumber: 2.3 Consensus size: 65
28929400 GTTGTAAGTT
* * **
28929410 ATGTAAGTTATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATTGCATTA
1 ATGTAAGTTATGTAACTTATGTATAATATTAATTAATTAAGTCATGTAATTTATGTATAACATTA
*
28929475 ATGTAAGTTATGTAACTTATGTATAATATTAATTAATTAAGTCATGTAATTTATGTATAATATTA
1 ATGTAAGTTATGTAACTTATGTATAATATTAATTAATTAAGTCATGTAATTTATGTATAACATTA
* *
28929540 ATGCAAGTTATGTAATTTATGT
1 ATGTAAGTTATGTAACTTATGT
28929562 TTTTGGCAAA
Statistics
Matches: 80, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
65 80 1.00
ACGTcount: A:0.38, C:0.03, G:0.13, T:0.47
Consensus pattern (65 bp):
ATGTAAGTTATGTAACTTATGTATAATATTAATTAATTAAGTCATGTAATTTATGTATAACATTA
Found at i:28929532 original size:34 final size:34
Alignment explanation
Indices: 28929413--28929561 Score: 177
Period size: 34 Copynumber: 4.6 Consensus size: 34
28929403 GTAAGTTATG
*
28929413 TAAGTTATGTAAGTTATGTATAATATTAATTAAT
1 TAAGTTATGTAATTTATGTATAATATTAATTAAT
**
28929447 TAAGTTATGTAATTTATG--T-AT-TGCATTAAT
1 TAAGTTATGTAATTTATGTATAATATTAATTAAT
*
28929477 GTAAGTTATGTAACTTATGTATAATATTAATTAAT
1 -TAAGTTATGTAATTTATGTATAATATTAATTAAT
* *
28929512 TAAGTCATGTAATTTATGTATAATATTAA-T--G
1 TAAGTTATGTAATTTATGTATAATATTAATTAAT
*
28929543 CAAGTTATGTAATTTATGT
1 TAAGTTATGTAATTTATGT
28929562 TTTTGGCAAA
Statistics
Matches: 99, Mismatches: 11, Indels: 13
0.80 0.09 0.11
Matches are distributed among these distances:
30 7 0.07
31 36 0.36
32 1 0.01
33 2 0.02
34 46 0.46
35 7 0.07
ACGTcount: A:0.38, C:0.03, G:0.13, T:0.47
Consensus pattern (34 bp):
TAAGTTATGTAATTTATGTATAATATTAATTAAT
Found at i:28929744 original size:22 final size:22
Alignment explanation
Indices: 28929703--28929756 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 22
28929693 TTATATTTTC
* *
28929703 ATTAAAATTTTTAGTAAATAATT
1 ATTAAAGTTTTAAGTAAAT-ATT
28929726 ATTAAAGTTTTAAGT-AATATT
1 ATTAAAGTTTTAAGTAAATATT
*
28929747 -TAAAAGTTTT
1 ATTAAAGTTTT
28929757 TGATAAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 9 0.32
21 3 0.11
22 3 0.11
23 13 0.46
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.48
Consensus pattern (22 bp):
ATTAAAGTTTTAAGTAAATATT
Found at i:28929771 original size:21 final size:21
Alignment explanation
Indices: 28929705--28929771 Score: 50
Period size: 20 Copynumber: 3.2 Consensus size: 21
28929695 ATATTTTCAT
*
28929705 TAAAA-TTTTTAGTAAATAATTA
1 TAAAAGTTTTAAGT-AA-AATTA
* *
28929727 TTAAAGTTTTAAGTAATATT-
1 TAAAAGTTTTAAGTAAAATTA
*
28929747 TAAAAGTTTT-TGATAAAATTA
1 TAAAAGTTTTAAG-TAAAATTA
28929768 TAAA
1 TAAA
28929772 TTTTAGTTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
19 1 0.03
20 15 0.42
21 7 0.19
22 6 0.17
23 7 0.19
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (21 bp):
TAAAAGTTTTAAGTAAAATTA
Found at i:28929806 original size:22 final size:22
Alignment explanation
Indices: 28929778--28929824 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 22
28929768 TAAATTTTAG
28929778 TTTTTTTATTTCCTTT-TTATATT
1 TTTTTTTATTT--TTTCTTATATT
28929801 TTTTTTTATTTTTTCTTATATT
1 TTTTTTTATTTTTTCTTATATT
28929823 TT
1 TT
28929825 GGTCCTGTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 3 0.13
22 9 0.39
23 11 0.48
ACGTcount: A:0.13, C:0.06, G:0.00, T:0.81
Consensus pattern (22 bp):
TTTTTTTATTTTTTCTTATATT
Found at i:28930141 original size:89 final size:88
Alignment explanation
Indices: 28930016--28930252 Score: 411
Period size: 89 Copynumber: 2.7 Consensus size: 88
28930006 CCAAACCCCT
*
28930016 ACCCCTAAACCCTAAACATTATCTAATATATAAATTAAAAAACACTAATTAATCTAAATCCTAAA
1 ACCCCT-AACCCTAAACATTATTTAATATATAAATTAAAAAACACTAATTAATCTAAATCCTAAA
* *
28930081 CCCTAACTCGATCCCGAATCACTA
65 CCCTAAATCGACCCCGAATCACTA
28930105 ACCCCTAACCCTTAAACATTATTTAATATATAAATTAAAAAACACTAATTAATCTAAATCCTAAA
1 ACCCCTAACCC-TAAACATTATTTAATATATAAATTAAAAAACACTAATTAATCTAAATCCTAAA
*
28930170 CCCTAAATTGACCCCGAATCACTA
65 CCCTAAATCGACCCCGAATCACTA
28930194 ACCCCTAACCCCTAAACATTATTTAATATATAAATTAAAAAACACTAATTAATCTAAAT
1 ACCCCTAA-CCCTAAACATTATTTAATATATAAATTAAAAAACACTAATTAATCTAAAT
28930253 TAATTCTAAA
Statistics
Matches: 142, Mismatches: 4, Indels: 4
0.95 0.03 0.03
Matches are distributed among these distances:
88 5 0.04
89 134 0.94
90 3 0.02
ACGTcount: A:0.46, C:0.24, G:0.02, T:0.28
Consensus pattern (88 bp):
ACCCCTAACCCTAAACATTATTTAATATATAAATTAAAAAACACTAATTAATCTAAATCCTAAAC
CCTAAATCGACCCCGAATCACTA
Found at i:28930282 original size:14 final size:14
Alignment explanation
Indices: 28930258--28930291 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
28930248 TAAATTAATT
28930258 CTAAACCCTAA-CC
1 CTAAACCCTAACCC
28930271 CTAAATCCCTAACCC
1 CTAAA-CCCTAACCC
28930286 CTAAAC
1 CTAAAC
28930292 ATTATTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 5 0.26
14 7 0.37
15 7 0.37
ACGTcount: A:0.38, C:0.44, G:0.00, T:0.18
Consensus pattern (14 bp):
CTAAACCCTAACCC
Found at i:28930928 original size:41 final size:41
Alignment explanation
Indices: 28930874--28931057 Score: 248
Period size: 41 Copynumber: 4.5 Consensus size: 41
28930864 GCGCTTCCTC
*
28930874 AAAAAACGCCGCTAAAGGTA-C-GAGCACTAGCGGCGCTTATT
1 AAAAAACGCCGCTAAA-G-ACCTGAGCATTAGCGGCGCTTATT
* *
28930915 AAAAAACGCCGCTAAAGACTTGAGAATTAGCGGCGCTTATT
1 AAAAAACGCCGCTAAAGACCTGAGCATTAGCGGCGCTTATT
* *
28930956 AAAAAACGCCGCTAAAGACCTGAACATTAGTGGCGCTTATT
1 AAAAAACGCCGCTAAAGACCTGAGCATTAGCGGCGCTTATT
*
28930997 TAAAAACGCCGCTAAAGACCTGAGCATTAGCGGCGCTT-TT
1 AAAAAACGCCGCTAAAGACCTGAGCATTAGCGGCGCTTATT
* *
28931037 CAGAAAATGCCGCTAAAGACC
1 -AAAAAACGCCGCTAAAGACC
28931058 CCAAAAAACT
Statistics
Matches: 127, Mismatches: 13, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
39 1 0.01
40 3 0.02
41 123 0.97
ACGTcount: A:0.35, C:0.23, G:0.22, T:0.20
Consensus pattern (41 bp):
AAAAAACGCCGCTAAAGACCTGAGCATTAGCGGCGCTTATT
Found at i:28931519 original size:14 final size:15
Alignment explanation
Indices: 28931500--28931530 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
28931490 ATGTGAGTTT
28931500 TAAATATATTT-TTA
1 TAAATATATTTGTTA
28931514 TAAATATATTTGTTA
1 TAAATATATTTGTTA
28931529 TA
1 TA
28931531 TAAAATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (15 bp):
TAAATATATTTGTTA
Found at i:28932071 original size:27 final size:27
Alignment explanation
Indices: 28932022--28932088 Score: 118
Period size: 27 Copynumber: 2.5 Consensus size: 27
28932012 GATGAAGCCA
*
28932022 AAATTTTTTTAG-GAAAGTTAAATTAT
1 AAATTTTATTAGAGAAAGTTAAATTAT
28932048 AAATTTTATTAGAGAAAGTTAAATTAT
1 AAATTTTATTAGAGAAAGTTAAATTAT
28932075 AAATTTTATTAGAG
1 AAATTTTATTAGAG
28932089 GTATAATGTA
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
26 11 0.28
27 28 0.72
ACGTcount: A:0.45, C:0.00, G:0.12, T:0.43
Consensus pattern (27 bp):
AAATTTTATTAGAGAAAGTTAAATTAT
Found at i:28938163 original size:26 final size:26
Alignment explanation
Indices: 28938134--28938183 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
28938124 CAGTGGCTGG
28938134 TTTGACCAACTGATTCTATTAACTAA
1 TTTGACCAACTGATTCTATTAACTAA
*
28938160 TTTGACCAACTGATTTTATTAACT
1 TTTGACCAACTGATTCTATTAACT
28938184 GTTTATTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.32, C:0.18, G:0.08, T:0.42
Consensus pattern (26 bp):
TTTGACCAACTGATTCTATTAACTAA
Found at i:28938281 original size:115 final size:115
Alignment explanation
Indices: 28938150--28938380 Score: 453
Period size: 115 Copynumber: 2.0 Consensus size: 115
28938140 CAACTGATTC
*
28938150 TATTAACTAATTTGACCAACTGATTTTATTAACTGTTTATTTAAAAGTGTTTGATAAATCTTAAT
1 TATTAACTAATTTGACCAACTGATTTTATTAACTGTTTATTTAAAAGTGTTTGATAAAACTTAAT
28938215 TGATAGATAAAAGCTGATATGTGTAAAATGACAAATACGGGTATGCCACA
66 TGATAGATAAAAGCTGATATGTGTAAAATGACAAATACGGGTATGCCACA
28938265 TATTAACTAATTTGACCAACTGATTTTATTAACTGTTTATTTAAAAGTGTTTGATAAAACTTAAT
1 TATTAACTAATTTGACCAACTGATTTTATTAACTGTTTATTTAAAAGTGTTTGATAAAACTTAAT
28938330 TGATAGATAAAAGCTGATATGTGTAAAATGACAAATACGGGTATGCCACA
66 TGATAGATAAAAGCTGATATGTGTAAAATGACAAATACGGGTATGCCACA
28938380 T
1 T
28938381 TCTATTGTTA
Statistics
Matches: 115, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
115 115 1.00
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (115 bp):
TATTAACTAATTTGACCAACTGATTTTATTAACTGTTTATTTAAAAGTGTTTGATAAAACTTAAT
TGATAGATAAAAGCTGATATGTGTAAAATGACAAATACGGGTATGCCACA
Found at i:28940382 original size:9 final size:9
Alignment explanation
Indices: 28940368--28940435 Score: 50
Period size: 9 Copynumber: 7.3 Consensus size: 9
28940358 CTCTCTCACA
28940368 ATAAAAATT
1 ATAAAAATT
28940377 ATAAAAAATT
1 AT-AAAAATT
*
28940387 AAAATAAATT
1 ATAA-AAATT
28940397 -TAAAAAATT
1 AT-AAAAATT
28940406 CA-AAAAATT
1 -ATAAAAATT
*
28940415 ATAGAAATT
1 ATAAAAATT
* *
28940424 CTAAAATTT
1 ATAAAAATT
28940433 ATA
1 ATA
28940436 TTTTTAAAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
8 1 0.02
9 30 0.65
10 15 0.33
ACGTcount: A:0.63, C:0.03, G:0.01, T:0.32
Consensus pattern (9 bp):
ATAAAAATT
Found at i:28940385 original size:10 final size:10
Alignment explanation
Indices: 28940370--28940417 Score: 57
Period size: 10 Copynumber: 5.0 Consensus size: 10
28940360 CTCTCACAAT
28940370 AAAAATTATA
1 AAAAATTATA
28940380 AAAAATTA-A
1 AAAAATTATA
28940389 AATAAATT-TA
1 AA-AAATTATA
*
28940399 AAAAATT-CA
1 AAAAATTATA
28940408 AAAAATTATA
1 AAAAATTATA
28940418 GAAATTCTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
9 16 0.48
10 17 0.52
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (10 bp):
AAAAATTATA
Found at i:28940402 original size:19 final size:19
Alignment explanation
Indices: 28940370--28940417 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 19
28940360 CTCTCACAAT
28940370 AAAAATTATAAAAAATTAA
1 AAAAATTATAAAAAATTAA
*
28940389 AATAAATT-TAAAAAATTCA
1 AA-AAATTATAAAAAATTAA
28940408 AAAAATTATA
1 AAAAATTATA
28940418 GAAATTCTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
18 5 0.19
19 16 0.62
20 5 0.19
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (19 bp):
AAAAATTATAAAAAATTAA
Found at i:28940422 original size:18 final size:19
Alignment explanation
Indices: 28940370--28940435 Score: 73
Period size: 18 Copynumber: 3.5 Consensus size: 19
28940360 CTCTCACAAT
*
28940370 AAAAATTATAAAAAATTAA
1 AAAAATTATAAAAAATTCA
28940389 AATAAATT-TAAAAAATTCA
1 AA-AAATTATAAAAAATTCA
* *
28940408 AAAAATTAT-AGAAATTCT
1 AAAAATTATAAAAAATTCA
*
28940426 AAAATTTATA
1 AAAAATTATA
28940436 TTTTTAAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
18 20 0.50
19 15 0.38
20 5 0.12
ACGTcount: A:0.64, C:0.03, G:0.02, T:0.32
Consensus pattern (19 bp):
AAAAATTATAAAAAATTCA
Found at i:28947276 original size:11 final size:11
Alignment explanation
Indices: 28947260--28947285 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
28947250 TTTTTTAATA
28947260 TTATTTAATTT
1 TTATTTAATTT
28947271 TTATTTAATTT
1 TTATTTAATTT
28947282 TTAT
1 TTAT
28947286 AATTTAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (11 bp):
TTATTTAATTT
Found at i:28947296 original size:29 final size:30
Alignment explanation
Indices: 28947244--28947314 Score: 85
Period size: 29 Copynumber: 2.4 Consensus size: 30
28947234 ATAAGGGTTA
* *
28947244 ATTTCATTTTTTAATATTATTTAAT-TTTT
1 ATTTAATTTTTTAATATTAATTAATATTTT
28947273 ATTTAATTTTTATAAT-TTAATTAATATTTT
1 ATTTAATTTTT-TAATATTAATTAATATTTT
28947303 -TTATAATTTTTT
1 ATT-TAATTTTTT
28947315 TTTATAATAG
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
29 21 0.57
30 16 0.43
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.68
Consensus pattern (30 bp):
ATTTAATTTTTTAATATTAATTAATATTTT
Found at i:28947395 original size:41 final size:41
Alignment explanation
Indices: 28947338--28947416 Score: 131
Period size: 41 Copynumber: 1.9 Consensus size: 41
28947328 GTAGATCCAA
* *
28947338 TGTTACAATGTTTTATTCGTAATCTACCTGGTCCTCCAGAG
1 TGTTACAACGTTTTATTCATAATCTACCTGGTCCTCCAGAG
*
28947379 TGTTACAACGTTTTATTCATAATCTATCTGGTCCTCCA
1 TGTTACAACGTTTTATTCATAATCTACCTGGTCCTCCA
28947417 TCACTGTTGA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.23, C:0.23, G:0.14, T:0.41
Consensus pattern (41 bp):
TGTTACAACGTTTTATTCATAATCTACCTGGTCCTCCAGAG
Found at i:28949448 original size:29 final size:29
Alignment explanation
Indices: 28949416--28949495 Score: 99
Period size: 29 Copynumber: 2.8 Consensus size: 29
28949406 AAAACAAAAT
*
28949416 ACATCTTGTCAAAATAATTTTTTCAGAAC
1 ACATCTTGTCAAAATTATTTTTTCAGAAC
** *
28949445 ACATCACGTCAAATTTATTTTTTCAGAAC
1 ACATCTTGTCAAAATTATTTTTTCAGAAC
*
28949474 -CTATCTTGTTAAAATTATTTTT
1 AC-ATCTTGTCAAAATTATTTTT
28949496 CCCATAACAA
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
28 1 0.02
29 41 0.98
ACGTcount: A:0.34, C:0.16, G:0.06, T:0.44
Consensus pattern (29 bp):
ACATCTTGTCAAAATTATTTTTTCAGAAC
Found at i:28958393 original size:13 final size:13
Alignment explanation
Indices: 28958375--28958399 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28958365 CTAAATCGTA
28958375 ATTTTAGTAAAAT
1 ATTTTAGTAAAAT
28958388 ATTTTAGTAAAA
1 ATTTTAGTAAAA
28958400 CCTTTTTGGT
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:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (13 bp):
ATTTTAGTAAAAT
Found at i:28959482 original size:19 final size:19
Alignment explanation
Indices: 28959455--28959519 Score: 53
Period size: 19 Copynumber: 3.4 Consensus size: 19
28959445 AATTTGATAC
*
28959455 TTAACTTAATAGTAATTTG
1 TTAATTTAATAGTAATTTG
**
28959474 TTAATTTAATA-TGAAAGTG
1 TTAATTTAATAGT-AATTTG
*
28959493 ATT-ATCTTAATAGTATTTTG
1 -TTAAT-TTAATAGTAATTTG
28959513 TTAATTT
1 TTAATTT
28959520 TTAAAAGATT
Statistics
Matches: 35, Mismatches: 6, Indels: 10
0.69 0.12 0.20
Matches are distributed among these distances:
18 1 0.03
19 20 0.57
20 13 0.37
21 1 0.03
ACGTcount: A:0.35, C:0.03, G:0.11, T:0.51
Consensus pattern (19 bp):
TTAATTTAATAGTAATTTG
Found at i:28962579 original size:22 final size:23
Alignment explanation
Indices: 28962551--28962657 Score: 85
Period size: 25 Copynumber: 4.4 Consensus size: 23
28962541 CACTGATGAA
*
28962551 CAGAGAGCACAGATGTGC-TAAT
1 CAGAGAGCACAGACGTGCATAAT
*
28962573 CAGAGAGCACTGACGTGCTAGTAAT
1 CAGAGAGCACAGACGTGC-A-TAAT
*
28962598 CAGAGAGCACCA-ACATGCTAATAAT
1 CAGAGAGCA-CAGACGTGC--ATAAT
*
28962623 CAGATAGCACCA-ACGTGCTAATAAT
1 CAGAGAGCA-CAGACGTGC--ATAAT
28962648 CAGAGAGCAC
1 CAGAGAGCAC
28962658 GCTAAAGTTC
Statistics
Matches: 72, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
22 16 0.22
24 1 0.01
25 53 0.74
26 2 0.03
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.17
Consensus pattern (23 bp):
CAGAGAGCACAGACGTGCATAAT
Found at i:28962603 original size:25 final size:25
Alignment explanation
Indices: 28962569--28962657 Score: 133
Period size: 25 Copynumber: 3.6 Consensus size: 25
28962559 ACAGATGTGC
** *
28962569 TAATCAGAGAGCACTGACGTGCTAG
1 TAATCAGAGAGCACCAACGTGCTAA
*
28962594 TAATCAGAGAGCACCAACATGCTAA
1 TAATCAGAGAGCACCAACGTGCTAA
*
28962619 TAATCAGATAGCACCAACGTGCTAA
1 TAATCAGAGAGCACCAACGTGCTAA
28962644 TAATCAGAGAGCAC
1 TAATCAGAGAGCAC
28962658 GCTAAAGTTC
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 57 1.00
ACGTcount: A:0.39, C:0.22, G:0.20, T:0.18
Consensus pattern (25 bp):
TAATCAGAGAGCACCAACGTGCTAA
Found at i:28963630 original size:5 final size:5
Alignment explanation
Indices: 28963620--28963662 Score: 79
Period size: 5 Copynumber: 8.8 Consensus size: 5
28963610 TTATTTCGTT
28963620 TATAA TATAA TATAA TATAA TATAA TATAA TAT-A TATAA TATA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATA
28963663 TAACTTAACT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
4 4 0.11
5 33 0.89
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
TATAA
Found at i:28970237 original size:6 final size:6
Alignment explanation
Indices: 28970226--28970256 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
28970216 CAGGTAAGGC
28970226 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG T
1 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG T
28970257 GTTGTTTAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (6 bp):
TTTTTG
Found at i:28970914 original size:17 final size:15
Alignment explanation
Indices: 28970875--28970906 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
28970865 TTTAAACATA
*
28970875 ATTATTATTAAATAT
1 ATTATAATTAAATAT
28970890 ATTATAATTAAATAT
1 ATTATAATTAAATAT
28970905 AT
1 AT
28970907 AATTTAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:28970963 original size:54 final size:54
Alignment explanation
Indices: 28970905--28971083 Score: 137
Period size: 60 Copynumber: 3.1 Consensus size: 54
28970895 AATTAAATAT
28970905 ATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATC
1 ATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATC
* * * * * * *
28970959 ATAATATATGATACTATAAAATATAAATTAA-CATAATTATTATTAAAT-ATATTATATTTAAAA
1 ATAAT-T-T-A-A-TA-AAATTCTTAA-TAATC--AA-TATTCTTATATGA-ATT-TA-CTCAAA
*
28971022 TAT
53 T-C
*
28971025 ATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATC
1 ATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATC
28971079 ATAAT
1 ATAAT
28971084 ATATGATACT
Statistics
Matches: 92, Mismatches: 17, Indels: 32
0.65 0.12 0.23
Matches are distributed among these distances:
54 10 0.11
55 6 0.07
56 3 0.03
57 13 0.14
58 4 0.04
59 5 0.05
60 15 0.16
61 5 0.05
62 4 0.04
63 13 0.14
64 3 0.03
65 6 0.07
66 5 0.05
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (54 bp):
ATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATC
Found at i:28971037 original size:59 final size:59
Alignment explanation
Indices: 28970869--28971159 Score: 188
Period size: 59 Copynumber: 4.9 Consensus size: 59
28970859 ATCATATTTA
* *
28970869 AACATAATTATTATTAAATATATTATAATT-AAATATATAATTTAATAAAATTCTTAA-T
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAA-TATAAATT
* * * * * * * *
28970927 AATCA-ATATTCTTATATGAATTTACTCA-AATCATAATATATGATACT-ATAAAATATAAATT
1 AA-CATA-ATTATTAT-TAAATATA-TTATAATTAAAATATATAAT-TTAATAAAATATAAATT
* * *
28970988 AACATAATTATTATTAAATATATTATATTTAAAATATATAATTTAATAAAATTCTTAA-T
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAA-TATAAATT
* * * * * * * * *
28971047 AA-TTAA-TATTCTTATATGA-ATTTACTCAAATCATAATATATGATACT-ATAAAAGATAATTT
1 AACATAATTATTATTAAAT-ATA-TTA-T--AATTAAAATATATAAT-TTAATAAAATATAAATT
*
28971108 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAAT
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAAT
28971160 TCTTAATAAT
Statistics
Matches: 169, Mismatches: 42, Indels: 43
0.67 0.17 0.17
Matches are distributed among these distances:
57 10 0.06
58 14 0.08
59 56 0.33
60 28 0.17
61 43 0.25
62 8 0.05
63 10 0.06
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (59 bp):
AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATATAAATT
Found at i:28971146 original size:18 final size:17
Alignment explanation
Indices: 28971125--28971159 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
28971115 TTATTATTAA
*
28971125 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
28971143 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
28971160 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Done.