Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr8
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: 70076365
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3341059 characters in sequence are not A, C, G, or T
File 17 of 210
Found at i:5699806 original size:43 final size:42
Alignment explanation
Indices: 5699723--5700217 Score: 381
Period size: 42 Copynumber: 11.7 Consensus size: 42
5699713 CAAAATTAGC
* * * *** *
5699723 GGCGTTTATTGGATAAGCGCCACTAAAGAACCCGCCTCTAGT
1 GGCGTTTTTTGTATAAGCGCCGCTAAAGAACCAATCTATAGT
* * * *
5699765 GGCGTTTTATGCATAAGCGCCGCTAAAGCCACCAATCTCTAGT
1 GGCGTTTTTTGTATAAGCGCCGCTAAAG-AACCAATCTATAGT
* *
5699808 GGCGTTTTGTGTATAAGCGCCGC-AAAAAACTCCAATCTATAGT
1 GGCGTTTTTTGTATAAGCGCCGCTAAAGAA--CCAATCTATAGT
* * * * *
5699851 GGCGTTTTTTGCATAAGCGCCGATACAGAGCCATATCTGTAGT
1 GGCGTTTTTTGTATAAGCGCCGCTAAAGAACCA-ATCTATAGT
* *
5699894 GGCGTTTCTT-TATAAGCGCCAG-TAAAGAAACATATCTATAGT
1 GGCGTTTTTTGTATAAGCGCC-GCTAAAGAACCA-ATCTATAGT
* * * *
5699936 GGCGTTTTTTGTATAAGCGCCGCTATAGAACCGAGCTATCGT
1 GGCGTTTTTTGTATAAGCGCCGCTAAAGAACCAATCTATAGT
* * *
5699978 GGCGTTTTTTGTATAAGCGCCGCTATAGAACCGAGCTATAGT
1 GGCGTTTTTTGTATAAGCGCCGCTAAAGAACCAATCTATAGT
* * * * *
5700020 GGCGTTTTTTGTATAAGTGCCGCTATAGACCCGAGCTATAGT
1 GGCGTTTTTTGTATAAGCGCCGCTAAAGAACCAATCTATAGT
* * * * * *
5700062 GCCGTTTTTTGTATAAGCGCCGGTAGAGCA-GATATCTATTGT
1 GGCGTTTTTTGTATAAGCGCCGCTAAAGAACCA-ATCTATAGT
* * * * * * *
5700104 GGCATTTTCTGTACAAACGCCGGTAAAGAAACCCGATCTGTAGT
1 GGCGTTTTTTGTATAAGCGCCGCTAAAG-AA-CCAATCTATAGT
* * * * * *
5700148 GGCGTTTTTTGCATAAGCGCTGCGAAAGACTCCCACCTATAGT
1 GGCGTTTTTTGTATAAGCGCCGCTAAAGA-ACCAATCTATAGT
* *
5700191 GGCG--TTTTGTGTAAGCGCTGCTAAAGA
1 GGCGTTTTTTGTATAAGCGCCGCTAAAGA
5700218 CGGTATTCTA
Statistics
Matches: 369, Mismatches: 71, Indels: 27
0.79 0.15 0.06
Matches are distributed among these distances:
41 21 0.06
42 206 0.56
43 112 0.30
44 30 0.08
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.29
Consensus pattern (42 bp):
GGCGTTTTTTGTATAAGCGCCGCTAAAGAACCAATCTATAGT
Found at i:5710361 original size:18 final size:18
Alignment explanation
Indices: 5710338--5710372 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
5710328 ATTCTCAATC
*
5710338 CGTTCAATCTGATCTTGT
1 CGTTCAATCTAATCTTGT
5710356 CGTTCAATCTAATCTTG
1 CGTTCAATCTAATCTTG
5710373 CTCAAGTAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.23, G:0.14, T:0.43
Consensus pattern (18 bp):
CGTTCAATCTAATCTTGT
Found at i:5715957 original size:3 final size:3
Alignment explanation
Indices: 5715949--5715985 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
5715939 ATATAGGATT
5715949 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
5715986 NNNNNNNNNN
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:5717340 original size:16 final size:16
Alignment explanation
Indices: 5717320--5717374 Score: 56
Period size: 16 Copynumber: 3.3 Consensus size: 16
5717310 TTGTGTATTT
5717320 CATGTTTTTATATATA
1 CATGTTTTTATATATA
* *
5717336 TATGTATACTTATATATA
1 CATGT-T-TTTATATATA
* *
5717354 CATGTTTTAATATATT
1 CATGTTTTTATATATA
5717370 CATGT
1 CATGT
5717375 ACATATTTTC
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
16 16 0.52
17 2 0.06
18 13 0.42
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.53
Consensus pattern (16 bp):
CATGTTTTTATATATA
Found at i:5718993 original size:86 final size:87
Alignment explanation
Indices: 5718849--5719022 Score: 341
Period size: 86 Copynumber: 2.0 Consensus size: 87
5718839 TATTTAAATT
5718849 AAAATTTTAATCTTTATATTTTAATTGTTAACATAATTCGGTCCTATATTTACATATTATTATTA
1 AAAATTTTAATCTTTATATTTTAATTGTTAACATAATTCGGTCCTATATTTACATATTATTATTA
5718914 CTTAGTTCAAATAGTTAATATA
66 CTTAGTTCAAATAGTTAATATA
5718936 AAAATTTTAA-CTTTATATTTTAATTGTTAACATAATTCGGTCCTATATTTACATATTATTATTA
1 AAAATTTTAATCTTTATATTTTAATTGTTAACATAATTCGGTCCTATATTTACATATTATTATTA
5719000 CTTAGTTCAAATAGTTAATATA
66 CTTAGTTCAAATAGTTAATATA
5719022 A
1 A
5719023 TTAAAATGTT
Statistics
Matches: 87, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
86 77 0.89
87 10 0.11
ACGTcount: A:0.37, C:0.09, G:0.06, T:0.48
Consensus pattern (87 bp):
AAAATTTTAATCTTTATATTTTAATTGTTAACATAATTCGGTCCTATATTTACATATTATTATTA
CTTAGTTCAAATAGTTAATATA
Found at i:5720229 original size:37 final size:37
Alignment explanation
Indices: 5720187--5720262 Score: 143
Period size: 37 Copynumber: 2.1 Consensus size: 37
5720177 AAACATACCC
*
5720187 AATACAATAACTCACTATTTTAGACATTGAAAACCAT
1 AATACAACAACTCACTATTTTAGACATTGAAAACCAT
5720224 AATACAACAACTCACTATTTTAGACATTGAAAACCAT
1 AATACAACAACTCACTATTTTAGACATTGAAAACCAT
5720261 AA
1 AA
5720263 ACATACTTGA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.47, C:0.20, G:0.05, T:0.28
Consensus pattern (37 bp):
AATACAACAACTCACTATTTTAGACATTGAAAACCAT
Found at i:5721108 original size:79 final size:79
Alignment explanation
Indices: 5720970--5721115 Score: 215
Period size: 79 Copynumber: 1.8 Consensus size: 79
5720960 ACATTTATAA
* *
5720970 GTGTTCTATCATATAGCCTATACCCTCCATGCTCTCAAACGCTAGTTAGACCCAGTGATGTTCAA
1 GTGTTCTATCAGATAGCCTATACCATCCATGCTCTCAAACGCTAGTTAGACCCAGTGATGTTCAA
5721035 TGTAGTGTATGTGT
66 TGTAGTGTATGTGT
* * *
5721049 GTGTTCTATCAGATA-CCTTATACCATCCATGTTCTCAAATGCTAGTTAG-GCCAGCTGATGTTC
1 GTGTTCTATCAGATAGCC-TATACCATCCATGCTCTCAAACGCTAGTTAGACCCAG-TGATGTTC
5721112 AATG
64 AATG
5721116 CAGTATGTAT
Statistics
Matches: 60, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
78 6 0.10
79 54 0.90
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.34
Consensus pattern (79 bp):
GTGTTCTATCAGATAGCCTATACCATCCATGCTCTCAAACGCTAGTTAGACCCAGTGATGTTCAA
TGTAGTGTATGTGT
Found at i:5721436 original size:18 final size:18
Alignment explanation
Indices: 5721405--5721444 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
5721395 TTTAGCAATG
*
5721405 GTTTTTTTCTC-AAAAGT
1 GTTTTTTTCCCAAAAAGT
5721422 GTTTTTTGTCCCAAAAAGT
1 GTTTTTT-TCCCAAAAAGT
5721441 GTTT
1 GTTT
5721445 CTAAGAAGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 7 0.35
18 3 0.15
19 10 0.50
ACGTcount: A:0.23, C:0.12, G:0.15, T:0.50
Consensus pattern (18 bp):
GTTTTTTTCCCAAAAAGT
Found at i:5726712 original size:102 final size:102
Alignment explanation
Indices: 5726534--5726942 Score: 728
Period size: 102 Copynumber: 4.0 Consensus size: 102
5726524 GGGTCCCTTG
*
5726534 TTTGTTCCTGAAAAATTAATTTAGAAAGTCAAATTGGAGATTTAGATCATGAAAGCAAGCTTTGG
1 TTTGTTCCTGAAAAATCAATTTAGAAAGTCAAATTGGAGATTTAGATCATGAAAGCAAGCTTTGG
*
5726599 AGATATAGAACATGAGAGCAAACTTAGTAATTAAATT
66 AGATATAGAACATGACAGCAAACTTAGTAATTAAATT
*
5726636 TTTGTTCCTGAAAAATCAATTTAGAAAGTCAAATTGGAGATTTAGATCATGAAAGCAAGCTTTTG
1 TTTGTTCCTGAAAAATCAATTTAGAAAGTCAAATTGGAGATTTAGATCATGAAAGCAAGCTTTGG
*
5726701 AGATATTGAACATGACAGCAAACTTAGTAATTAAATT
66 AGATATAGAACATGACAGCAAACTTAGTAATTAAATT
* *
5726738 TTTGTTACTGAAAAATCAATTTAGAAAGTTAAATTGGAGATTTAGATCATGAAAGCAAGCTTTGG
1 TTTGTTCCTGAAAAATCAATTTAGAAAGTCAAATTGGAGATTTAGATCATGAAAGCAAGCTTTGG
*
5726803 AGATATTGAACATGACAGCAAACTTAGTAATTAAATT
66 AGATATAGAACATGACAGCAAACTTAGTAATTAAATT
*
5726840 TTTGTTCCTGAAAAATCAATTTAGAAAGTTAAATTGGAGATTTAGATCATGAAAGCAAGCTTTGG
1 TTTGTTCCTGAAAAATCAATTTAGAAAGTCAAATTGGAGATTTAGATCATGAAAGCAAGCTTTGG
* *
5726905 AGATATAGAACATAAGAGCAAACTTAGTAATTAAATT
66 AGATATAGAACATGACAGCAAACTTAGTAATTAAATT
5726942 T
1 T
5726943 GTAATCATTG
Statistics
Matches: 296, Mismatches: 11, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
102 296 1.00
ACGTcount: A:0.41, C:0.09, G:0.18, T:0.32
Consensus pattern (102 bp):
TTTGTTCCTGAAAAATCAATTTAGAAAGTCAAATTGGAGATTTAGATCATGAAAGCAAGCTTTGG
AGATATAGAACATGACAGCAAACTTAGTAATTAAATT
Found at i:5733422 original size:23 final size:23
Alignment explanation
Indices: 5733379--5733422 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
5733369 AAATTGAAGC
*
5733379 AAACTCAAACTGACCTGAACTCA
1 AAACTCAAACTGACCTAAACTCA
*
5733402 AAACTCAAGAC-GATCTAAACT
1 AAACTCAA-ACTGACCTAAACT
5733423 TGAAACAACC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 16 0.89
24 2 0.11
ACGTcount: A:0.45, C:0.27, G:0.09, T:0.18
Consensus pattern (23 bp):
AAACTCAAACTGACCTAAACTCA
Found at i:5736555 original size:14 final size:14
Alignment explanation
Indices: 5736536--5736566 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
5736526 AAGTCGGGTG
*
5736536 ACACTAAAGGGCGA
1 ACACTAAAGGACGA
5736550 ACACTAAAGGACGA
1 ACACTAAAGGACGA
5736564 ACA
1 ACA
5736567 TGATTTTCTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.48, C:0.23, G:0.23, T:0.06
Consensus pattern (14 bp):
ACACTAAAGGACGA
Found at i:5739982 original size:14 final size:14
Alignment explanation
Indices: 5739963--5739989 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5739953 TTATTAATAT
5739963 AATTATTTATTTAA
1 AATTATTTATTTAA
5739977 AATTATTTATTTA
1 AATTATTTATTTA
5739990 TATATTGTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
AATTATTTATTTAA
Found at i:5741523 original size:40 final size:40
Alignment explanation
Indices: 5741479--5741558 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
5741469 ATCCACTTGA
5741479 ATGATTACCATTTTGTCCTTCCTCATCTTTCATATTTTGT
1 ATGATTACCATTTTGTCCTTCCTCATCTTTCATATTTTGT
5741519 ATGATTACCATTTTGTCCTTCCTCATCTTTCATATTTTGT
1 ATGATTACCATTTTGTCCTTCCTCATCTTTCATATTTTGT
5741559 GATATGACTC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.17, C:0.23, G:0.07, T:0.53
Consensus pattern (40 bp):
ATGATTACCATTTTGTCCTTCCTCATCTTTCATATTTTGT
Found at i:5744641 original size:20 final size:21
Alignment explanation
Indices: 5744618--5744661 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
5744608 GTATAAATAA
5744618 TATTTAAAA-GTTGTAAAAAT
1 TATTTAAAATGTTGTAAAAAT
* *
5744638 TA-TTAAAATTTTGTGAAAAT
1 TATTTAAAATGTTGTAAAAAT
5744658 TATT
1 TATT
5744662 AATTTTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
19 6 0.30
20 13 0.65
21 1 0.05
ACGTcount: A:0.45, C:0.00, G:0.09, T:0.45
Consensus pattern (21 bp):
TATTTAAAATGTTGTAAAAAT
Found at i:5747874 original size:18 final size:18
Alignment explanation
Indices: 5747821--5747883 Score: 65
Period size: 18 Copynumber: 3.5 Consensus size: 18
5747811 TTTTAAATGA
*
5747821 TTAAAAATTATAAAAATT
1 TTAAAAATTATGAAAATT
* *
5747839 ATAAGAA-TATTGAAAATT
1 TTAAAAATTA-TGAAAATT
*
5747857 TTAAAAATTATGATAATT
1 TTAAAAATTATGAAAATT
*
5747875 TTTAAAATT
1 TTAAAAATT
5747884 TTAATAAAAC
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
17 2 0.06
18 32 0.89
19 2 0.06
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (18 bp):
TTAAAAATTATGAAAATT
Found at i:5747881 original size:27 final size:27
Alignment explanation
Indices: 5747824--5747887 Score: 83
Period size: 27 Copynumber: 2.4 Consensus size: 27
5747814 TAAATGATTA
*
5747824 AAAATTATAAAAATTATAAGAATATTG
1 AAAATTTTAAAAATTATAAGAATATTG
* * * *
5747851 AAAATTTTAAAAATTATGATAATTTTT
1 AAAATTTTAAAAATTATAAGAATATTG
5747878 AAAATTTTAA
1 AAAATTTTAA
5747888 TAAAACATAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.41
Consensus pattern (27 bp):
AAAATTTTAAAAATTATAAGAATATTG
Found at i:5747883 original size:9 final size:9
Alignment explanation
Indices: 5747821--5747887 Score: 53
Period size: 9 Copynumber: 7.4 Consensus size: 9
5747811 TTTTAAATGA
5747821 TTAAAAATT
1 TTAAAAATT
*
5747830 ATAAAAATT
1 TTAAAAATT
* * *
5747839 ATAAGAATA
1 TTAAAAATT
*
5747848 TTGAAAATT
1 TTAAAAATT
5747857 TTAAAAATT
1 TTAAAAATT
* * *
5747866 ATGATAATT
1 TTAAAAATT
*
5747875 TTTAAAATT
1 TTAAAAATT
5747884 TTAA
1 TTAA
5747888 TAAAACATAA
Statistics
Matches: 43, Mismatches: 15, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
9 43 1.00
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (9 bp):
TTAAAAATT
Found at i:5750333 original size:96 final size:96
Alignment explanation
Indices: 5750164--5750543 Score: 543
Period size: 96 Copynumber: 4.0 Consensus size: 96
5750154 TTCTGTTGAT
* * * *
5750164 CATCTTGTACAGATCTGGGAAATTTAACACAGATCAGATGATGAATCAAAAACAATCCAATCGAA
1 CATCCTGTACAGATCTGGGAAATTTAACTCAGATCAGATGATGAATAAAAAACAATCGAATCGAA
*
5750229 AACATAAAGAACAAGTAAATTAACGACACCA
66 AACATAAAGAACAAGTAAATCAACGACACCA
* * *
5750260 CATCCTGTACAGATCTGGGAAATTAAACTCAGATCAGATGATGAATCAAAAACAATTGAATCGAA
1 CATCCTGTACAGATCTGGGAAATTTAACTCAGATCAGATGATGAATAAAAAACAATCGAATCGAA
*
5750325 AACATAAAGAACAAGTAAATCATCGACACCA
66 AACATAAAGAACAAGTAAATCAACGACACCA
* * * *
5750356 CGTCTTGAACAGATCTGGGAAATTTAACTTAGATCAGAT-ATGAATAAAAAACAATCGAATCGAA
1 CATCCTGTACAGATCTGGGAAATTTAACTCAGATCAGATGATGAATAAAAAACAATCGAATCGAA
5750420 AACATAAAGAACAAGTAAATC-A-GACACCA
66 AACATAAAGAACAAGTAAATCAACGACACCA
* * * * * *
5750449 CAT-CTCGTACAGATCTGGGAATTTTAACTCAGATCAGATGGTGACTAAAAAATAATCAAATCAA
1 CATCCT-GTACAGATCTGGGAAATTTAACTCAGATCAGATGATGAATAAAAAACAATCGAATCGA
*
5750513 AAACATAAAGAGCAAGTAAATCAACGACACC
65 AAACATAAAGAACAAGTAAATCAACGACACC
5750544 GAAACGTTAT
Statistics
Matches: 254, Mismatches: 26, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
92 1 0.00
93 39 0.15
94 40 0.16
95 45 0.18
96 129 0.51
ACGTcount: A:0.47, C:0.18, G:0.14, T:0.20
Consensus pattern (96 bp):
CATCCTGTACAGATCTGGGAAATTTAACTCAGATCAGATGATGAATAAAAAACAATCGAATCGAA
AACATAAAGAACAAGTAAATCAACGACACCA
Found at i:5750518 original size:189 final size:192
Alignment explanation
Indices: 5750166--5750543 Score: 566
Period size: 189 Copynumber: 2.0 Consensus size: 192
5750156 CTGTTGATCA
* *
5750166 TCTTGTACAGATCTGGGAAATTTAACACAGATCAGATGATGAATCAAAAACAATCCAATCGAAAA
1 TCTTGAACAGATCTGGGAAATTTAACACAGATCAGATGATGAATAAAAAACAATCCAATCGAAAA
5750231 CATAAAGAACAAGTAAATTAACGACACCACATCCTGTACAGATCTGGGAAATTAAACTCAGATCA
66 CATAAAGAACAAGTAAATTAACGACACCACATCCTGTACAGATCTGGGAAATTAAACTCAGATCA
* ** * *
5750296 GATGATGAATCAAAAACAATTGAATCGAAAACATAAAGAACAAGTAAATCATCGACACCACG
131 GATGATGAATAAAAAACAATCAAATCAAAAACATAAAGAACAAGTAAATCAACGACACCACG
** *
5750358 TCTTGAACAGATCTGGGAAATTTAACTTAGATCAGAT-ATGAATAAAAAACAATCGAATCGAAAA
1 TCTTGAACAGATCTGGGAAATTTAACACAGATCAGATGATGAATAAAAAACAATCCAATCGAAAA
* * *
5750422 CATAAAGAACAAGTAAA-TCA-GACACCACAT-CTCGTACAGATCTGGGAATTTTAACTCAGATC
66 CATAAAGAACAAGTAAATTAACGACACCACATCCT-GTACAGATCTGGGAAATTAAACTCAGATC
* * * *
5750484 AGATGGTGACTAAAAAATAATCAAATCAAAAACATAAAGAGCAAGTAAATCAACGACACC
130 AGATGATGAATAAAAAACAATCAAATCAAAAACATAAAGAACAAGTAAATCAACGACACC
5750544 GAAACGTTAT
Statistics
Matches: 168, Mismatches: 17, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
188 2 0.01
189 88 0.52
190 2 0.01
191 42 0.25
192 34 0.20
ACGTcount: A:0.47, C:0.18, G:0.15, T:0.20
Consensus pattern (192 bp):
TCTTGAACAGATCTGGGAAATTTAACACAGATCAGATGATGAATAAAAAACAATCCAATCGAAAA
CATAAAGAACAAGTAAATTAACGACACCACATCCTGTACAGATCTGGGAAATTAAACTCAGATCA
GATGATGAATAAAAAACAATCAAATCAAAAACATAAAGAACAAGTAAATCAACGACACCACG
Found at i:5751089 original size:19 final size:19
Alignment explanation
Indices: 5751067--5751156 Score: 53
Period size: 19 Copynumber: 4.7 Consensus size: 19
5751057 TAAAATTTAT
5751067 TAAAAATTATAAATATATA
1 TAAAAATTATAAATATATA
*
5751086 T-AAACTCT-TAATATATATA
1 TAAAAAT-TATAA-ATATATA
* * *
5751105 TATGAAATAATTAA-ATATA
1 TA-AAAATTATAAATATATA
* *
5751124 TAAAAATTCAGAAAGGA-ATA
1 TAAAAATT-ATAAA-TATATA
5751144 TAAAAATTATAAA
1 TAAAAATTATAAA
5751157 ATTTAATTTT
Statistics
Matches: 53, Mismatches: 10, Indels: 16
0.67 0.13 0.20
Matches are distributed among these distances:
18 11 0.21
19 24 0.45
20 12 0.23
21 6 0.11
ACGTcount: A:0.59, C:0.03, G:0.04, T:0.33
Consensus pattern (19 bp):
TAAAAATTATAAATATATA
Found at i:5752901 original size:12 final size:12
Alignment explanation
Indices: 5752884--5752947 Score: 83
Period size: 12 Copynumber: 5.2 Consensus size: 12
5752874 AAGAGTTTAT
5752884 ATGTTTAAAAAA
1 ATGTTTAAAAAA
5752896 ATGTTTAAAAAA
1 ATGTTTAAAAAA
*
5752908 TATTTTTAAAAAA
1 -ATGTTTAAAAAA
*
5752921 ATGTTTATAAAAT
1 ATGTTTA-AAAAA
*
5752934 ATTTTTAAAAAA
1 ATGTTTAAAAAA
5752946 AT
1 AT
5752948 TGATTATAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
12 24 0.53
13 21 0.47
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.41
Consensus pattern (12 bp):
ATGTTTAAAAAA
Found at i:5752962 original size:25 final size:25
Alignment explanation
Indices: 5752882--5752962 Score: 119
Period size: 25 Copynumber: 3.2 Consensus size: 25
5752872 ATAAGAGTTT
* *
5752882 ATATGTTTAAAAAAATGTTTAAAAA
1 ATATTTTTAAAAAAATGTTTATAAA
5752907 ATATTTTTAAAAAAATGTTTATAAA
1 ATATTTTTAAAAAAATGTTTATAAA
*
5752932 ATATTTTTAAAAAAATTGATTATAAA
1 ATATTTTTAAAAAAA-TGTTTATAAA
5752958 A-ATTT
1 ATATTT
5752963 ATATGTTTTA
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
25 42 0.81
26 10 0.19
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (25 bp):
ATATTTTTAAAAAAATGTTTATAAA
Found at i:5757789 original size:152 final size:153
Alignment explanation
Indices: 5757502--5757806 Score: 603
Period size: 152 Copynumber: 2.0 Consensus size: 153
5757492 TCATCGATAA
5757502 AAAAGGTTCTCCGGCACTGCTTCTTTGTGACTCGTCCTTCAGCTACGGACAAGCGACAGGGGACT
1 AAAAGGTTCTCCGGCACTGCTTCTTTGTGACTCGTCCTTCAGCTACGGACAAGCGACAGGGGACT
5757567 AATTCAAGGTCTCTTTTCATGCCCAAGTTAGCCTGATTACCATCGACCGAAAACAGCAGTCCATT
66 AATTCAAGGTCTCTTTTCATGCCCAAGTTAGCCTGATTACCATCGACCGAAAACAGCAGTCCATT
5757632 GGCGCCATCTTTTACTTGAGGTG
131 GGCGCCATCTTTTACTTGAGGTG
5757655 AAAAGGTTCT-CGGCACTGCTTCTTTGTGACTCGTCCTTCAGCTACGGACAAGCGACAGGGGACT
1 AAAAGGTTCTCCGGCACTGCTTCTTTGTGACTCGTCCTTCAGCTACGGACAAGCGACAGGGGACT
5757719 AATTCAAGGTCTCTTTTCATGCCCAAGTTAGCCTGATTACCATCGACCGAAAACAGCAGTCCATT
66 AATTCAAGGTCTCTTTTCATGCCCAAGTTAGCCTGATTACCATCGACCGAAAACAGCAGTCCATT
5757784 GGCGCCATCTTTTACTTGAGGTG
131 GGCGCCATCTTTTACTTGAGGTG
5757807 TCGCCCTCCC
Statistics
Matches: 152, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
152 142 0.93
153 10 0.07
ACGTcount: A:0.24, C:0.27, G:0.22, T:0.28
Consensus pattern (153 bp):
AAAAGGTTCTCCGGCACTGCTTCTTTGTGACTCGTCCTTCAGCTACGGACAAGCGACAGGGGACT
AATTCAAGGTCTCTTTTCATGCCCAAGTTAGCCTGATTACCATCGACCGAAAACAGCAGTCCATT
GGCGCCATCTTTTACTTGAGGTG
Found at i:5757915 original size:84 final size:84
Alignment explanation
Indices: 5757770--5757950 Score: 247
Period size: 84 Copynumber: 2.2 Consensus size: 84
5757760 ATCGACCGAA
* * * * * *
5757770 AACAGCAGTCCATT-GGCGCCATCTTTTACTTGAGGTGTCGCCCTCCCAAGCTGTAGAAGGTTTC
1 AACAGCAGTCCGTTCGTC-CCACCTTGTACTTCAGGCGTCGCCCTCCCAAGCTGTAGAAGGTTTC
5757834 CTGTAGATTCAAGGCTGGAC
65 CTGTAGATTCAAGGCTGGAC
* * * *
5757854 AACGGCAGTCCGTTCGTCCCACCTTGTACTTCAGGCGTCGCCCTCCCAGGCTGTCGAAGGTTTCT
1 AACAGCAGTCCGTTCGTCCCACCTTGTACTTCAGGCGTCGCCCTCCCAAGCTGTAGAAGGTTTCC
*
5757919 TGTAGATTCCAGGCTGGAC
66 TGTAGATTCAAGGCTGGAC
5757938 AACAGCAGTCCGT
1 AACAGCAGTCCGT
5757951 CCGCGCTAGT
Statistics
Matches: 84, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
84 82 0.98
85 2 0.02
ACGTcount: A:0.19, C:0.29, G:0.25, T:0.26
Consensus pattern (84 bp):
AACAGCAGTCCGTTCGTCCCACCTTGTACTTCAGGCGTCGCCCTCCCAAGCTGTAGAAGGTTTCC
TGTAGATTCAAGGCTGGAC
Found at i:5765449 original size:84 final size:84
Alignment explanation
Indices: 5765304--5765484 Score: 238
Period size: 84 Copynumber: 2.2 Consensus size: 84
5765294 ATCGACCGAA
* * * * * *
5765304 AACAGCAGTCCATT-GGCGCCATCTTTTACTTGAGGTGTCGCCCTCCCAAGCTGTCGAAGGTTTC
1 AACAGCAGTCCGTTCGTC-CCACCTTGTACTTCAGGCGTCGCCCTCCCAAGCTGTCGAAGGTTTC
*
5765368 CTGTATAATCAAGGCTGGAC
65 CTGTAGAATCAAGGCTGGAC
* * *
5765388 AACGGCAGTCCGTTCGTCCCACCTTGTACTTCAGGCGTCGCCCTCCCAGGCTGTCGAAGGTTTCT
1 AACAGCAGTCCGTTCGTCCCACCTTGTACTTCAGGCGTCGCCCTCCCAAGCTGTCGAAGGTTTCC
* *
5765453 TGTAGATTCCAGGCTGGAC
66 TGTAGAATCAAGGCTGGAC
5765472 AACAGCAGTCCGT
1 AACAGCAGTCCGT
5765485 CCGCGTTAGT
Statistics
Matches: 83, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
84 81 0.98
85 2 0.02
ACGTcount: A:0.19, C:0.30, G:0.25, T:0.26
Consensus pattern (84 bp):
AACAGCAGTCCGTTCGTCCCACCTTGTACTTCAGGCGTCGCCCTCCCAAGCTGTCGAAGGTTTCC
TGTAGAATCAAGGCTGGAC
Found at i:5768968 original size:27 final size:27
Alignment explanation
Indices: 5768938--5768991 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
5768928 TCCACTTGAT
*
5768938 CCATTGAATAATAAAGGGACTAATTTA
1 CCATTGAATAATAAAAGGACTAATTTA
*
5768965 CCATTGAATAATAAAAGGACTAGTTTA
1 CCATTGAATAATAAAAGGACTAATTTA
5768992 ATTAAATTCC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.44, C:0.11, G:0.15, T:0.30
Consensus pattern (27 bp):
CCATTGAATAATAAAAGGACTAATTTA
Found at i:5769642 original size:13 final size:13
Alignment explanation
Indices: 5769626--5769651 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5769616 GAAATTTTTA
5769626 ACTTTTCAAAAAT
1 ACTTTTCAAAAAT
5769639 ACTTTTCAAAAAT
1 ACTTTTCAAAAAT
5769652 TCTTCTGAGA
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:0.46, C:0.15, G:0.00, T:0.38
Consensus pattern (13 bp):
ACTTTTCAAAAAT
Found at i:5769926 original size:26 final size:25
Alignment explanation
Indices: 5769897--5769983 Score: 93
Period size: 26 Copynumber: 3.4 Consensus size: 25
5769887 TAAACTAAAC
*
5769897 TTTTCAAAAACACTTCTCAAAAATAA
1 TTTTC-AAAACACTTTTCAAAAATAA
* *
5769923 TTTTGCACAACACTTTTCAAAAGTAA
1 TTTT-CAAAACACTTTTCAAAAATAA
* * *
5769949 TTTTTCACAACACTTTTCAAAGATAT
1 -TTTTCAAAACACTTTTCAAAAATAA
5769975 TTTTCAAAA
1 TTTTCAAAA
5769984 GCAAGGAAGA
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
25 8 0.15
26 39 0.75
27 5 0.10
ACGTcount: A:0.41, C:0.18, G:0.03, T:0.37
Consensus pattern (25 bp):
TTTTCAAAACACTTTTCAAAAATAA
Found at i:5769976 original size:25 final size:25
Alignment explanation
Indices: 5769905--5769980 Score: 100
Period size: 26 Copynumber: 3.0 Consensus size: 25
5769895 ACTTTTCAAA
* *
5769905 AACACTTCTCAAAAATAATTTTGCAC
1 AACACTTTTC-AAAATAATTTTTCAC
5769931 AACACTTTTCAAAAGTAATTTTTCAC
1 AACACTTTTCAAAA-TAATTTTTCAC
5769957 AACACTTTTCAAAGAT-ATTTTTCA
1 AACACTTTTCAAA-ATAATTTTTCA
5769981 AAAGCAAGGA
Statistics
Matches: 46, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
25 12 0.26
26 33 0.72
27 1 0.02
ACGTcount: A:0.39, C:0.20, G:0.04, T:0.37
Consensus pattern (25 bp):
AACACTTTTCAAAATAATTTTTCAC
Found at i:5783334 original size:13 final size:13
Alignment explanation
Indices: 5783316--5783344 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
5783306 ATTTTATTTC
5783316 TTACAAATAAAAT
1 TTACAAATAAAAT
5783329 TTACAAATAAAAT
1 TTACAAATAAAAT
5783342 TTA
1 TTA
5783345 TCGAATTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (13 bp):
TTACAAATAAAAT
Found at i:5787129 original size:22 final size:22
Alignment explanation
Indices: 5787101--5787169 Score: 129
Period size: 22 Copynumber: 3.1 Consensus size: 22
5787091 TTAAAAAGTT
5787101 GGATCGAGAGAAAGAACACCAG
1 GGATCGAGAGAAAGAACACCAG
5787123 GGATCGAGAGAAAGAACACCAG
1 GGATCGAGAGAAAGAACACCAG
*
5787145 GGATCAAGAGAAAGAACACCAG
1 GGATCGAGAGAAAGAACACCAG
5787167 GGA
1 GGA
5787170 AGTGTCACAT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 46 1.00
ACGTcount: A:0.46, C:0.17, G:0.32, T:0.04
Consensus pattern (22 bp):
GGATCGAGAGAAAGAACACCAG
Found at i:5791616 original size:2 final size:2
Alignment explanation
Indices: 5791609--5791633 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5791599 CAATTTCATT
5791609 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 T
5791634 GCCATACCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5794931 original size:29 final size:29
Alignment explanation
Indices: 5794889--5794957 Score: 138
Period size: 29 Copynumber: 2.4 Consensus size: 29
5794879 CACAAAATAA
5794889 AAAACACGATTTATATAATGTATGTTTAG
1 AAAACACGATTTATATAATGTATGTTTAG
5794918 AAAACACGATTTATATAATGTATGTTTAG
1 AAAACACGATTTATATAATGTATGTTTAG
5794947 AAAACACGATT
1 AAAACACGATT
5794958 ACACGAAATT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.43, C:0.09, G:0.13, T:0.35
Consensus pattern (29 bp):
AAAACACGATTTATATAATGTATGTTTAG
Found at i:5795584 original size:29 final size:31
Alignment explanation
Indices: 5795539--5795598 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 31
5795529 GGAAAAGTCG
5795539 AAATTAAATTATAATTTTTACT-ATTTTAAA
1 AAATTAAATTATAATTTTTACTAATTTTAAA
*
5795569 AAATTAAATTA-AATTTTTATTAATTTTAAA
1 AAATTAAATTATAATTTTTACTAATTTTAAA
5795599 GATAACTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 9 0.32
30 19 0.68
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (31 bp):
AAATTAAATTATAATTTTTACTAATTTTAAA
Found at i:5800697 original size:5 final size:5
Alignment explanation
Indices: 5800687--5800716 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
5800677 ATTATACATT
5800687 TCATC TCATC TCATC TCATC TCATC TCATC
1 TCATC TCATC TCATC TCATC TCATC TCATC
5800717 ATATGTTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.20, C:0.40, G:0.00, T:0.40
Consensus pattern (5 bp):
TCATC
Found at i:5802430 original size:20 final size:20
Alignment explanation
Indices: 5802405--5802444 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
5802395 CGTAAAATGA
*
5802405 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
5802425 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
5802445 GGAAATATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:5802558 original size:20 final size:20
Alignment explanation
Indices: 5802533--5802584 Score: 56
Period size: 18 Copynumber: 2.7 Consensus size: 20
5802523 GGAAAAGTTG
5802533 TTTTTACATATATT-AATAAA
1 TTTTTACATATATTAAAT-AA
* *
5802553 TTTTT--ATATTTTAAATTA
1 TTTTTACATATATTAAATAA
5802571 TTTTTACATATATT
1 TTTTTACATATATT
5802585 GCAATGATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
18 12 0.46
19 3 0.12
20 11 0.42
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTTTACATATATTAAATAA
Found at i:5810125 original size:31 final size:29
Alignment explanation
Indices: 5810090--5810156 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 29
5810080 AAAGTACAGG
*
5810090 GACTAAATTTAACTAATTTTAAAAGTATAAA
1 GACTAAATTTAACTAA-ATTAAAA-TATAAA
*
5810121 GACTAAATTTAATTAAATTAAAATATAAA
1 GACTAAATTTAACTAAATTAAAATATAAA
*
5810150 AACTAAA
1 GACTAAA
5810157 GCAGCAACTT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 12 0.36
30 6 0.18
31 15 0.45
ACGTcount: A:0.57, C:0.06, G:0.04, T:0.33
Consensus pattern (29 bp):
GACTAAATTTAACTAAATTAAAATATAAA
Found at i:5813045 original size:13 final size:13
Alignment explanation
Indices: 5813027--5813051 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5813017 AACTCATAAT
5813027 AAAATTATAAAAA
1 AAAATTATAAAAA
5813040 AAAATTATAAAA
1 AAAATTATAAAA
5813052 TAATAATAAT
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:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
AAAATTATAAAAA
Found at i:5813076 original size:3 final size:3
Alignment explanation
Indices: 5813070--5813100 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
5813060 ATAATAATAA
5813070 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
5813101 TTGATAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:5816651 original size:11 final size:11
Alignment explanation
Indices: 5816625--5816665 Score: 66
Period size: 11 Copynumber: 3.8 Consensus size: 11
5816615 AAAATTTTAA
*
5816625 ATTATTAAAA-
1 ATTATAAAAAC
5816635 ATTATAAAAAC
1 ATTATAAAAAC
5816646 ATTATAAAAAC
1 ATTATAAAAAC
5816657 ATTATAAAA
1 ATTATAAAA
5816666 TTATAAATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
10 9 0.31
11 20 0.69
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (11 bp):
ATTATAAAAAC
Found at i:5816663 original size:22 final size:21
Alignment explanation
Indices: 5816625--5816665 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
5816615 AAAATTTTAA
*
5816625 ATTATTAAAAATTATAAAAAC
1 ATTATAAAAAATTATAAAAAC
5816646 ATTATAAAAACATTATAAAA
1 ATTATAAAAA-ATTATAAAA
5816666 TTATAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (21 bp):
ATTATAAAAAATTATAAAAAC
Found at i:5816749 original size:23 final size:23
Alignment explanation
Indices: 5816695--5816749 Score: 101
Period size: 23 Copynumber: 2.4 Consensus size: 23
5816685 AAAATAACAA
*
5816695 TACCTTATGAAGGCATATTTGAT
1 TACCTTATTAAGGCATATTTGAT
5816718 TACCTTATTAAGGCATATTTGAT
1 TACCTTATTAAGGCATATTTGAT
5816741 TACCTTATT
1 TACCTTATT
5816750 TACCACATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.29, C:0.15, G:0.13, T:0.44
Consensus pattern (23 bp):
TACCTTATTAAGGCATATTTGAT
Found at i:5816762 original size:23 final size:23
Alignment explanation
Indices: 5816708--5816760 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
5816698 CTTATGAAGG
**
5816708 CATATTTGATTACCTTATTAAGG
1 CATATTTGATTACCTTATTAACA
*
5816731 CATATTTGATTACCTTATTTACCA
1 CATATTTGATTACCTTA-TTAACA
5816755 CATATT
1 CATATT
5816761 GAACATAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 17 0.65
24 9 0.35
ACGTcount: A:0.30, C:0.17, G:0.08, T:0.45
Consensus pattern (23 bp):
CATATTTGATTACCTTATTAACA
Found at i:5816874 original size:21 final size:20
Alignment explanation
Indices: 5816850--5816895 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
5816840 CAATTAATGC
*
5816850 TATTTAAGTTAAAAATTTTGT
1 TATTTAAGGT-AAAATTTTGT
* *
5816871 TATTTTAGGTAAATTTTTGT
1 TATTTAAGGTAAAATTTTGT
5816891 TATTT
1 TATTT
5816896 TGTTATTTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.59
Consensus pattern (20 bp):
TATTTAAGGTAAAATTTTGT
Found at i:5816898 original size:8 final size:8
Alignment explanation
Indices: 5816885--5816932 Score: 51
Period size: 8 Copynumber: 5.5 Consensus size: 8
5816875 TTAGGTAAAT
5816885 TTTTGTTA
1 TTTTGTTA
5816893 TTTTGTTA
1 TTTTGTTA
*
5816901 TTTTAGGTAAA
1 TTTT--GT-TA
5816912 TTTTTGTTA
1 -TTTTGTTA
5816921 TTTTGTTA
1 TTTTGTTA
5816929 TTTT
1 TTTT
5816933 AGGTAAAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
8 24 0.71
9 1 0.03
10 4 0.12
11 1 0.03
12 4 0.12
ACGTcount: A:0.17, C:0.00, G:0.12, T:0.71
Consensus pattern (8 bp):
TTTTGTTA
Found at i:5816904 original size:28 final size:28
Alignment explanation
Indices: 5816864--5816944 Score: 153
Period size: 28 Copynumber: 2.9 Consensus size: 28
5816854 TAAGTTAAAA
5816864 ATTTTGTTATTTTAGGTAAATTTTTGTT
1 ATTTTGTTATTTTAGGTAAATTTTTGTT
5816892 ATTTTGTTATTTTAGGTAAATTTTTGTT
1 ATTTTGTTATTTTAGGTAAATTTTTGTT
*
5816920 ATTTTGTTATTTTAGGTAAAATTTT
1 ATTTTGTTATTTTAGGTAAATTTTT
5816945 ATTTATGGAA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 52 1.00
ACGTcount: A:0.23, C:0.00, G:0.14, T:0.63
Consensus pattern (28 bp):
ATTTTGTTATTTTAGGTAAATTTTTGTT
Found at i:5819424 original size:2 final size:2
Alignment explanation
Indices: 5819417--5819441 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5819407 CATTTCAGTC
5819417 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 T
5819442 TATTTAACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5824996 original size:28 final size:28
Alignment explanation
Indices: 5824965--5825023 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
5824955 AATTTTATTT
5824965 AGATAAGTAATCCAAATTACATCACTGA
1 AGATAAGTAATCCAAATTACATCACTGA
5824993 AGATAAGTAATCCAAATTACATCACTGA
1 AGATAAGTAATCCAAATTACATCACTGA
5825021 AGA
1 AGA
5825024 CTTAACAACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.47, C:0.17, G:0.12, T:0.24
Consensus pattern (28 bp):
AGATAAGTAATCCAAATTACATCACTGA
Found at i:5829616 original size:295 final size:295
Alignment explanation
Indices: 5829086--5829676 Score: 1110
Period size: 295 Copynumber: 2.0 Consensus size: 295
5829076 ATGATGCTGT
*
5829086 ATTCTTTGCTTTCTTTGCAGGAGAAGATCCAATTTCTTTTGATGGTGCATATCAAGAAGAAATAT
1 ATTCTTTGCTTTCTTTGCAAGAGAAGATCCAATTTCTTTTGATGGTGCATATCAAGAAGAAATAT
*
5829151 GAAGGAAAGCCATGAAAGAAGAGATTTGCTCAATTGAAAACAATGATACATGGGAACTCACAGAT
66 GAAGGAAAGCCATGAAAGAAGAGATTTGCTCAATTGAAAACAATGATACACGGGAACTCACAGAT
*
5829216 TTACCACCGCACAAGAATTCAATTGGAGTCAAATGGGTGTACAAGATAAAGATGAATCTGAATGG
131 TTACCACCGCACAAGAATTCAATTGGAGTCAAATGGGTGTACAAGACAAAGATGAATCTGAATGG
*
5829281 CTCTATCAACAAGTACAAGGCAAGACTGGTTGCAAAAGGATACAAGTAAAAGGAAAGGGAAGATT
196 CTCTATCAACAAGTACAAGGCAAGACTGGTTGCAAAAGGATACAAGCAAAAGGAAAGGGAAGATT
5829346 TTACAGAGGTATTTGCTCCAGTTTCAAGACTTGAG
261 TTACAGAGGTATTTGCTCCAGTTTCAAGACTTGAG
*
5829381 ATTCTTTGCTTTCTTTGTAAGAGAAGATCCAATTTCTTTTGATGGTGCATATCAAGAAGAAATAT
1 ATTCTTTGCTTTCTTTGCAAGAGAAGATCCAATTTCTTTTGATGGTGCATATCAAGAAGAAATAT
5829446 GAAGGAAAGCCATGAAAGAAGAGATTTGCTCAATTGAAAACAATGATACACGGGAACTCACAGAT
66 GAAGGAAAGCCATGAAAGAAGAGATTTGCTCAATTGAAAACAATGATACACGGGAACTCACAGAT
*
5829511 TTACCGCCGCACAAGAATTCAATTGGAGTCAAATGGGTGTACAAGACAAAGATGAATCTGAATGG
131 TTACCACCGCACAAGAATTCAATTGGAGTCAAATGGGTGTACAAGACAAAGATGAATCTGAATGG
*
5829576 CTCTATCAACAAGTACAAGGCAAGACTGGTTGCAAAAGGATACAAGCAAAAGGAAGGGGAAGATT
196 CTCTATCAACAAGTACAAGGCAAGACTGGTTGCAAAAGGATACAAGCAAAAGGAAAGGGAAGATT
*
5829641 TTACAGATGTATTTGCTCCAGTTTCAAGACTTGAG
261 TTACAGAGGTATTTGCTCCAGTTTCAAGACTTGAG
5829676 A
1 A
5829677 CAGTTCAGTT
Statistics
Matches: 288, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
295 288 1.00
ACGTcount: A:0.38, C:0.15, G:0.22, T:0.25
Consensus pattern (295 bp):
ATTCTTTGCTTTCTTTGCAAGAGAAGATCCAATTTCTTTTGATGGTGCATATCAAGAAGAAATAT
GAAGGAAAGCCATGAAAGAAGAGATTTGCTCAATTGAAAACAATGATACACGGGAACTCACAGAT
TTACCACCGCACAAGAATTCAATTGGAGTCAAATGGGTGTACAAGACAAAGATGAATCTGAATGG
CTCTATCAACAAGTACAAGGCAAGACTGGTTGCAAAAGGATACAAGCAAAAGGAAAGGGAAGATT
TTACAGAGGTATTTGCTCCAGTTTCAAGACTTGAG
Found at i:5831030 original size:23 final size:23
Alignment explanation
Indices: 5831004--5831094 Score: 100
Period size: 23 Copynumber: 4.1 Consensus size: 23
5830994 TGAAAAGTTA
5831004 GAAGAGTGAAGAGACTTGAATAT
1 GAAGAGTGAAGAGACTTGAATAT
*
5831027 GAAGAGTGAAGAGACTTGAAGAT
1 GAAGAGTGAAGAGACTTGAATAT
* * * * *
5831050 GAAAAGT-TACACAC---ATTAT
1 GAAGAGTGAAGAGACTTGAATAT
5831069 GAAGAGTGAAGAGACTTGAATAT
1 GAAGAGTGAAGAGACTTGAATAT
5831092 GAA
1 GAA
5831095 AAGTTACACA
Statistics
Matches: 52, Mismatches: 12, Indels: 8
0.72 0.17 0.11
Matches are distributed among these distances:
19 9 0.17
20 4 0.08
22 4 0.08
23 35 0.67
ACGTcount: A:0.45, C:0.07, G:0.27, T:0.21
Consensus pattern (23 bp):
GAAGAGTGAAGAGACTTGAATAT
Found at i:5831071 original size:42 final size:42
Alignment explanation
Indices: 5831024--5831107 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
5831014 GAGACTTGAA
5831024 TATGAAGAGTGAAGAGACTTGAAGATGAAAAGTTACACACAT
1 TATGAAGAGTGAAGAGACTTGAAGATGAAAAGTTACACACAT
*
5831066 TATGAAGAGTGAAGAGACTTGAATATGAAAAGTTACACACAT
1 TATGAAGAGTGAAGAGACTTGAAGATGAAAAGTTACACACAT
5831108 GCATGGATAG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.45, C:0.10, G:0.23, T:0.23
Consensus pattern (42 bp):
TATGAAGAGTGAAGAGACTTGAAGATGAAAAGTTACACACAT
Found at i:5832691 original size:26 final size:26
Alignment explanation
Indices: 5832653--5832706 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
5832643 TGATGCTCAT
*
5832653 ATGGTATTTGGTATTTAAACTCAGTGA
1 ATGGTATTGGGTATTTAAACTC-GTGA
*
5832680 ATGG-ATTGGGTATTTCAACTCGTGA
1 ATGGTATTGGGTATTTAAACTCGTGA
5832705 AT
1 AT
5832707 TTGTATGGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 6 0.24
26 15 0.60
27 4 0.16
ACGTcount: A:0.28, C:0.09, G:0.24, T:0.39
Consensus pattern (26 bp):
ATGGTATTGGGTATTTAAACTCGTGA
Found at i:5836298 original size:41 final size:42
Alignment explanation
Indices: 5836241--5836323 Score: 132
Period size: 41 Copynumber: 2.0 Consensus size: 42
5836231 GAGACTTGAA
*
5836241 TATGAAGAGTGAAGAGACTT-AAGATGAAAAGTTATACACAT
1 TATGAAGAGTGAAGAGACTTGAAGATGAAAAGTTACACACAT
**
5836282 TATGAAGAGTGAAGAGACTTGAATTTGAAAAGTTACACACAT
1 TATGAAGAGTGAAGAGACTTGAAGATGAAAAGTTACACACAT
5836324 GCATGGATAG
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
41 20 0.53
42 18 0.47
ACGTcount: A:0.45, C:0.08, G:0.22, T:0.25
Consensus pattern (42 bp):
TATGAAGAGTGAAGAGACTTGAAGATGAAAAGTTACACACAT
Found at i:5841838 original size:23 final size:23
Alignment explanation
Indices: 5841812--5841902 Score: 91
Period size: 23 Copynumber: 4.1 Consensus size: 23
5841802 TGAAAAGTTA
5841812 GAAGAGTGAAGAGACTTGAATAT
1 GAAGAGTGAAGAGACTTGAATAT
* *
5841835 GAAGAGGGAAGAGACTTGAAGAT
1 GAAGAGTGAAGAGACTTGAATAT
* * * * *
5841858 GAAAAGT-TACACAC---ATTAT
1 GAAGAGTGAAGAGACTTGAATAT
5841877 GAAGAGTGAAGAGACTTGAATAT
1 GAAGAGTGAAGAGACTTGAATAT
5841900 GAA
1 GAA
5841903 AAGTTACACA
Statistics
Matches: 50, Mismatches: 14, Indels: 8
0.69 0.19 0.11
Matches are distributed among these distances:
19 9 0.18
20 4 0.08
22 4 0.08
23 33 0.66
ACGTcount: A:0.45, C:0.07, G:0.29, T:0.20
Consensus pattern (23 bp):
GAAGAGTGAAGAGACTTGAATAT
Found at i:5841879 original size:42 final size:42
Alignment explanation
Indices: 5841832--5841915 Score: 150
Period size: 42 Copynumber: 2.0 Consensus size: 42
5841822 GAGACTTGAA
5841832 TATGAAGAGGGAAGAGACTTGAAGATGAAAAGTTACACACAT
1 TATGAAGAGGGAAGAGACTTGAAGATGAAAAGTTACACACAT
* *
5841874 TATGAAGAGTGAAGAGACTTGAATATGAAAAGTTACACACAT
1 TATGAAGAGGGAAGAGACTTGAAGATGAAAAGTTACACACAT
5841916 GCATGGATAG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.45, C:0.10, G:0.24, T:0.21
Consensus pattern (42 bp):
TATGAAGAGGGAAGAGACTTGAAGATGAAAAGTTACACACAT
Found at i:5843500 original size:25 final size:26
Alignment explanation
Indices: 5843471--5843519 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
5843461 TCATATGGTA
5843471 TTTGG-TATTTAAACTCAGTGAATGG
1 TTTGGATATTTAAACTCAGTGAATGG
* *
5843496 TTTGGATATTTCAACTCGGTGAAT
1 TTTGGATATTTAAACTCAGTGAAT
5843520 TTGTATAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 5 0.24
26 16 0.76
ACGTcount: A:0.27, C:0.10, G:0.22, T:0.41
Consensus pattern (26 bp):
TTTGGATATTTAAACTCAGTGAATGG
Found at i:5845938 original size:19 final size:19
Alignment explanation
Indices: 5845903--5845940 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
5845893 TTAAATTATG
**
5845903 TATATATTATTTCCCTTAA
1 TATATATTATTAACCTTAA
5845922 TATATATTATTAACCTTAA
1 TATATATTATTAACCTTAA
5845941 GCTTAATTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.37, C:0.13, G:0.00, T:0.50
Consensus pattern (19 bp):
TATATATTATTAACCTTAA
Found at i:5848332 original size:18 final size:18
Alignment explanation
Indices: 5848248--5848334 Score: 66
Period size: 19 Copynumber: 4.4 Consensus size: 18
5848238 CTAAAAAATT
*
5848248 ATTTTAAAATTTTAAAAA
1 ATTTAAAAATTTTAAAAA
5848266 ATTTAAAATATATATTTTAAAAAA
1 ATTT--AA-A-A-ATTTT-AAAAA
* **
5848290 ATTTTAAAATTAAAAAAA
1 ATTTAAAAATTTTAAAAA
5848308 ATTTTAAAAATTTTAAAAA
1 A-TTTAAAAATTTTAAAAA
*
5848327 AGTTAAAA
1 ATTTAAAA
5848335 GGCCCGTTTT
Statistics
Matches: 54, Mismatches: 8, Indels: 14
0.71 0.11 0.18
Matches are distributed among these distances:
18 16 0.30
19 18 0.33
20 2 0.04
21 2 0.04
22 2 0.04
23 5 0.09
24 9 0.17
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (18 bp):
ATTTAAAAATTTTAAAAA
Found at i:5848692 original size:17 final size:17
Alignment explanation
Indices: 5848670--5848702 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
5848660 TAGAAAAAAT
5848670 ATAATTT-TATTCTTTAA
1 ATAATTTATATT-TTTAA
5848687 ATAATTTATATTTTTA
1 ATAATTTATATTTTTA
5848703 TAATTTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (17 bp):
ATAATTTATATTTTTAA
Found at i:5850188 original size:26 final size:25
Alignment explanation
Indices: 5850158--5850206 Score: 80
Period size: 26 Copynumber: 1.9 Consensus size: 25
5850148 AACCATACTA
5850158 ATTCACCGAGTTGAAATATCCAAACC
1 ATTCACCGAGTTGAAATA-CCAAACC
*
5850184 ATTCACCGAGTTTAAATACCAAA
1 ATTCACCGAGTTGAAATACCAAA
5850207 TACCATATGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 5 0.23
26 17 0.77
ACGTcount: A:0.41, C:0.24, G:0.10, T:0.24
Consensus pattern (25 bp):
ATTCACCGAGTTGAAATACCAAACC
Found at i:5854503 original size:21 final size:21
Alignment explanation
Indices: 5854479--5854545 Score: 116
Period size: 21 Copynumber: 3.2 Consensus size: 21
5854469 ATTAGTAAGA
5854479 GTTGGCGTACCTCTGATTGTT
1 GTTGGCGTACCTCTGATTGTT
5854500 GTTGGCGTACCTCTGATTGTT
1 GTTGGCGTACCTCTGATTGTT
* *
5854521 GCTGGCGTACCTCTGATAGTT
1 GTTGGCGTACCTCTGATTGTT
5854542 GTTG
1 GTTG
5854546 TTTGCATTCC
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.10, C:0.19, G:0.30, T:0.40
Consensus pattern (21 bp):
GTTGGCGTACCTCTGATTGTT
Found at i:5855283 original size:209 final size:207
Alignment explanation
Indices: 5854900--5855289 Score: 577
Period size: 209 Copynumber: 1.9 Consensus size: 207
5854890 CTGTCAACAT
* *
5854900 AAACCTGCATTAAAAGGAAACCATACAAAATCAAAGAAATTAGTGATTCAGTAGCACTCACTCCT
1 AAACCTGCATTAAAAGGAAACCATACAAAATCAAAGAAATCAGTGATTCAATAGCACTCACTCCT
* * *
5854965 ACAGAATTCAGATCAGAAGAAATCATTGAACCAAAAACAGTAAAAAAGCACAAACTAGCTTTTCC
66 ACAGAACTCAGACCAGAAGAAATCATTGAACCAAAAACAGTAAAAAAGAACAAACTAGCTTTTCC
*
5855030 AATTCAGAACAAAAATATCCAAACAACAGACATAAAACTGACAAAAAAGAAATGAAATTTTGGAT
131 AATTCAAAACAAAAATATCCAAACAACAGACATAAAACTGAC-AAAAAGAAATGAAATTTTGGAT
5855095 CAAGCAATTAAAG
195 CAAGCAATTAAAG
* * * *
5855108 AAACCTGCATTAAAAGGGAAACTC-TACAAAATCAAAGTAATCAGTGATTCAATAGCACTGATTG
1 AAACCTGCATTAAAA-GGAAAC-CATACAAAATCAAAGAAATCAGTGATTCAATAGCACTCACTC
* * ** *
5855172 GTACAGAACTCAGACCAGAAGAAATCTTTGAACTGAAAACAGTAAAAAAGAACTAACTAG-TTTT
64 CTACAGAACTCAGACCAGAAGAAATCATTGAACCAAAAACAGTAAAAAAGAACAAACTAGCTTTT
* *
5855236 CCCAATTCAAAACAAAAATATTCAAACAACAGATATAAAACTGACAAAAAGAAA
129 -CCAATTCAAAACAAAAATATCCAAACAACAGACATAAAACTGACAAAAAGAAA
5855290 AAAGAAATGA
Statistics
Matches: 162, Mismatches: 17, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
208 28 0.17
209 133 0.82
210 1 0.01
ACGTcount: A:0.50, C:0.18, G:0.12, T:0.20
Consensus pattern (207 bp):
AAACCTGCATTAAAAGGAAACCATACAAAATCAAAGAAATCAGTGATTCAATAGCACTCACTCCT
ACAGAACTCAGACCAGAAGAAATCATTGAACCAAAAACAGTAAAAAAGAACAAACTAGCTTTTCC
AATTCAAAACAAAAATATCCAAACAACAGACATAAAACTGACAAAAAGAAATGAAATTTTGGATC
AAGCAATTAAAG
Found at i:5856228 original size:14 final size:14
Alignment explanation
Indices: 5856205--5856303 Score: 123
Period size: 14 Copynumber: 7.3 Consensus size: 14
5856195 TAAGGTGCAG
5856205 TATTTATAACAGTA
1 TATTTATAACAGTA
*
5856219 TATTTGTAACAGTA
1 TATTTATAACAGTA
* *
5856233 TA-TTAAAACATTA
1 TATTTATAACAGTA
*
5856246 TA-TTAAAACAGTA
1 TATTTATAACAGTA
5856259 TATTTATAACAGTA
1 TATTTATAACAGTA
*
5856273 TATTTATAACATTA
1 TATTTATAACAGTA
*
5856287 TA-TTAAAACAGTA
1 TATTTATAACAGTA
5856300 TATT
1 TATT
5856304 ACAAATTAAT
Statistics
Matches: 74, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
13 33 0.45
14 41 0.55
ACGTcount: A:0.45, C:0.07, G:0.06, T:0.41
Consensus pattern (14 bp):
TATTTATAACAGTA
Found at i:5856247 original size:27 final size:27
Alignment explanation
Indices: 5856202--5856303 Score: 127
Period size: 27 Copynumber: 3.8 Consensus size: 27
5856192 AATTAAGGTG
* *
5856202 CAGTAT-TTATAACAGTATATTTGTAA
1 CAGTATATTAAAACAGTATATTTATAA
* *
5856228 CAGTATATTAAAACATTATA-TTAAAA
1 CAGTATATTAAAACAGTATATTTATAA
*
5856254 CAGTATATTTATAACAGTATATTTATAA
1 CAGTATA-TTAAAACAGTATATTTATAA
*
5856282 CATTATATTAAAACAGTATATT
1 CAGTATATTAAAACAGTATATT
5856304 ACAAATTAAT
Statistics
Matches: 64, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
26 17 0.27
27 36 0.56
28 11 0.17
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.40
Consensus pattern (27 bp):
CAGTATATTAAAACAGTATATTTATAA
Found at i:5856317 original size:27 final size:27
Alignment explanation
Indices: 5856212--5856315 Score: 99
Period size: 27 Copynumber: 4.0 Consensus size: 27
5856202 CAGTATTTAT
** *
5856212 AACAGTATATTTGTAACAGTATATTAA
1 AACAGTATATTTACAACATTATATTAA
* * * *
5856239 AACATTATA-TTAAAACAGTATATTTAT
1 AACAGTATATTTACAACATTATA-TTAA
*
5856266 AACAGTATATTTATAACATTATATTAA
1 AACAGTATATTTACAACATTATATTAA
5856293 AACAGTATA-TTACAA-ATTA-ATTA
1 AACAGTATATTTACAACATTATATTA
5856316 TTTAGTTAAT
Statistics
Matches: 66, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
24 4 0.06
25 4 0.06
26 16 0.24
27 31 0.47
28 11 0.17
ACGTcount: A:0.48, C:0.08, G:0.06, T:0.38
Consensus pattern (27 bp):
AACAGTATATTTACAACATTATATTAA
Found at i:5856319 original size:41 final size:41
Alignment explanation
Indices: 5856212--5856307 Score: 142
Period size: 40 Copynumber: 2.4 Consensus size: 41
5856202 CAGTATTTAT
** *
5856212 AACAGTATATTTGTAACAGTATA-TTAAAACATTATATTAA
1 AACAGTATATTTACAACAGTATATTTATAACATTATATTAA
*
5856252 AACAGTATATTTATAACAGTATATTTATAACATTATATTAA
1 AACAGTATATTTACAACAGTATATTTATAACATTATATTAA
5856293 AACAGTATA-TTACAA
1 AACAGTATATTTACAA
5856308 ATTAATTATT
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
40 27 0.52
41 25 0.48
ACGTcount: A:0.48, C:0.08, G:0.06, T:0.38
Consensus pattern (41 bp):
AACAGTATATTTACAACAGTATATTTATAACATTATATTAA
Found at i:5857840 original size:83 final size:83
Alignment explanation
Indices: 5857701--5857866 Score: 305
Period size: 83 Copynumber: 2.0 Consensus size: 83
5857691 ACTAAAGATA
*
5857701 AATTCAAGCCATATATCTTTGACCTTTTATAAGATATATAATTGTTTTCAATGCAGCAAATAGCC
1 AATTCAAGCCATATATCTTTGACCTTTTATAAGATATATAACTGTTTTCAATGCAGCAAATAGCC
5857766 AGTTGCTTTTCTCCCACT
66 AGTTGCTTTTCTCCCACT
* *
5857784 AATTCAAGCCGTATATCTTTGACCTTTTATAAGATATATAACTGTTTTCAATGCAGCAAATAGTC
1 AATTCAAGCCATATATCTTTGACCTTTTATAAGATATATAACTGTTTTCAATGCAGCAAATAGCC
5857849 AGTTGCTTTTCTCCCACT
66 AGTTGCTTTTCTCCCACT
5857867 GATCTGTTCA
Statistics
Matches: 80, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
83 80 1.00
ACGTcount: A:0.30, C:0.20, G:0.11, T:0.39
Consensus pattern (83 bp):
AATTCAAGCCATATATCTTTGACCTTTTATAAGATATATAACTGTTTTCAATGCAGCAAATAGCC
AGTTGCTTTTCTCCCACT
Found at i:5865694 original size:2 final size:2
Alignment explanation
Indices: 5865687--5865714 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5865677 GAAATACATC
5865687 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5865715 TCGGGTTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5867260 original size:16 final size:16
Alignment explanation
Indices: 5867239--5867273 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
5867229 ACCCATGATT
5867239 AAAATT-TTAAAATTCA
1 AAAATTATTAAAATT-A
5867255 AAAATTATTAAAATTA
1 AAAATTATTAAAATTA
5867271 AAA
1 AAA
5867274 TTCATCAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (16 bp):
AAAATTATTAAAATTA
Found at i:5867314 original size:16 final size:15
Alignment explanation
Indices: 5867255--5867315 Score: 52
Period size: 15 Copynumber: 3.9 Consensus size: 15
5867245 TTAAAATTCA
* *
5867255 AAAATTATTAAAATT
1 AAAATTATCAAATTT
*
5867270 AAAATTCATCAATTTT
1 AAAATT-ATCAAATTT
*
5867286 AAAAATA-CAAAATTT
1 AAAATTATC-AAATTT
5867301 AAAATTAATCAAATT
1 AAAATT-ATCAAATT
5867316 AAAGCAAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
14 1 0.03
15 17 0.47
16 17 0.47
17 1 0.03
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (15 bp):
AAAATTATCAAATTT
Found at i:5873714 original size:15 final size:17
Alignment explanation
Indices: 5873679--5873715 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
5873669 AATAAACCCA
*
5873679 ATTTTATGATTAGACTT
1 ATTTTATGAATAGACTT
5873696 ATTTTAT-AATAGA-TT
1 ATTTTATGAATAGACTT
5873711 ATTTT
1 ATTTT
5873716 TATAGGTGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 7 0.37
16 5 0.26
17 7 0.37
ACGTcount: A:0.32, C:0.03, G:0.08, T:0.57
Consensus pattern (17 bp):
ATTTTATGAATAGACTT
Found at i:5873927 original size:6 final size:7
Alignment explanation
Indices: 5873900--5873925 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
5873890 ATAAATATAT
5873900 ATTTTTA
1 ATTTTTA
5873907 ATTTTTA
1 ATTTTTA
5873914 ATTTTTA
1 ATTTTTA
5873921 ATTTT
1 ATTTT
5873926 AAAATATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (7 bp):
ATTTTTA
Found at i:5873988 original size:24 final size:24
Alignment explanation
Indices: 5873934--5873988 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
5873924 TTAAAATATT
* * *
5873934 TTAAAAATATTTTTATTTTTTTTT
1 TTAAAAATATTTTTATTGTGTTTA
*
5873958 TTTAAAATATTTTT-TTGGTGTTTA
1 TTAAAAATATTTTTATT-GTGTTTA
5873982 TTAAAAA
1 TTAAAAA
5873989 ATAGGCCAGG
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
23 2 0.08
24 23 0.92
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (24 bp):
TTAAAAATATTTTTATTGTGTTTA
Found at i:5874265 original size:45 final size:46
Alignment explanation
Indices: 5874179--5874273 Score: 138
Period size: 45 Copynumber: 2.1 Consensus size: 46
5874169 ATTTGATTCG
*
5874179 TTTTTCTTTTGTATTTTTTTATATTCGTTTCACTGTGAGTTATTTGA
1 TTTTTCTTTTGTA-TTTTTTATATTCGTTTCACTGTAAGTTATTTGA
* * *
5874226 TTTTTCTTTTGTA-TTTTTATGTTCGTTTTAGTGTAAGTTATTTGA
1 TTTTTCTTTTGTATTTTTTATATTCGTTTCACTGTAAGTTATTTGA
5874271 TTT
1 TTT
5874274 GATGTTCATT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
45 31 0.70
47 13 0.30
ACGTcount: A:0.15, C:0.06, G:0.14, T:0.65
Consensus pattern (46 bp):
TTTTTCTTTTGTATTTTTTATATTCGTTTCACTGTAAGTTATTTGA
Found at i:5878188 original size:15 final size:15
Alignment explanation
Indices: 5878164--5878226 Score: 51
Period size: 15 Copynumber: 4.1 Consensus size: 15
5878154 AAATATGATT
*
5878164 TTAATTTTTTTAAAA
1 TTAATATTTTTAAAA
*
5878179 TTAATATTTTATTAAA
1 TTAATATTTT-TAAAA
5878195 -TAA-ATTTTT-AAA
1 TTAATATTTTTAAAA
5878207 TTCACATATTTTTAATAA
1 TT-A-ATATTTTTAA-AA
5878225 TT
1 TT
5878227 TCTAATCAGA
Statistics
Matches: 39, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
12 3 0.08
13 2 0.05
14 6 0.15
15 13 0.33
16 10 0.26
17 1 0.03
18 4 0.10
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (15 bp):
TTAATATTTTTAAAA
Found at i:5878195 original size:16 final size:16
Alignment explanation
Indices: 5878164--5878204 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
5878154 AAATATGATT
5878164 TTAATTTTT-TTAAAA
1 TTAATTTTTATTAAAA
5878179 TTAATATTTTATT-AAA
1 TTAAT-TTTTATTAAAA
*
5878195 TAAATTTTTA
1 TTAATTTTTA
5878205 AATTCACATA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 10 0.43
16 11 0.48
17 2 0.09
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TTAATTTTTATTAAAA
Found at i:5891998 original size:27 final size:27
Alignment explanation
Indices: 5891968--5892044 Score: 72
Period size: 27 Copynumber: 2.9 Consensus size: 27
5891958 ATTTTAATGT
5891968 TCAATTTGGTATCTATATTTTTTTTTC
1 TCAATTTGGTATCTATATTTTTTTTTC
5891995 TCAATTTTTGAGT-T-T-TGA-TTTTTTTTC
1 TCAA--TTTG-GTATCTAT-ATTTTTTTTTC
**
5892022 TCAATTAAGTATCTATATTTTTT
1 TCAATTTGGTATCTATATTTTTT
5892045 GGGATAATAT
Statistics
Matches: 40, Mismatches: 2, Indels: 16
0.69 0.03 0.28
Matches are distributed among these distances:
24 2 0.05
25 3 0.08
26 2 0.05
27 24 0.60
28 2 0.05
29 5 0.12
30 2 0.05
ACGTcount: A:0.21, C:0.09, G:0.08, T:0.62
Consensus pattern (27 bp):
TCAATTTGGTATCTATATTTTTTTTTC
Found at i:5892737 original size:24 final size:25
Alignment explanation
Indices: 5892693--5892761 Score: 86
Period size: 25 Copynumber: 2.8 Consensus size: 25
5892683 TATTTAAGCT
* *
5892693 AAACTCAAATGCCAAATTGAG-AAA
1 AAACTCAGATACCAAATTGAGAAAA
* * *
5892717 AAGCTTAGATATCAAATTGAGAAAA
1 AAACTCAGATACCAAATTGAGAAAA
5892742 AAACTCAGATACCAAATTGA
1 AAACTCAGATACCAAATTGA
5892762 ACATTAAAAC
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
24 16 0.44
25 20 0.56
ACGTcount: A:0.52, C:0.14, G:0.13, T:0.20
Consensus pattern (25 bp):
AAACTCAGATACCAAATTGAGAAAA
Found at i:5896874 original size:24 final size:24
Alignment explanation
Indices: 5896774--5896941 Score: 97
Period size: 24 Copynumber: 6.9 Consensus size: 24
5896764 TGAGCACATA
* *
5896774 AACGGGAAGCTCTTTCGAGCCACAT
1 AACGGGAAGCTCATACGAGCCA-AT
* * * *
5896799 AACGGGAAGCTCATATGATCTATGT
1 AACGGGAAGCTCATACGAGCCA-AT
** *
5896824 AACGGGAAGCTCCGGA-GAGCCATT
1 AACGGGAAGCT-CATACGAGCCAAT
*
5896848 AACGGGAAGCTCATACGAGACAAT
1 AACGGGAAGCTCATACGAGCCAAT
* *
5896872 AACGGAAAGTTCA-AGCGAGCCAAT
1 AACGGGAAGCTCATA-CGAGCCAAT
* * ** * *
5896896 ATCGAGAAGCTCCGAAGAGCCATT
1 AACGGGAAGCTCATACGAGCCAAT
* *
5896920 AATCAGGAAGCTCATAAGAGCC
1 AA-CGGGAAGCTCATACGAGCC
5896942 TTTAATCAGG
Statistics
Matches: 107, Mismatches: 31, Indels: 10
0.72 0.21 0.07
Matches are distributed among these distances:
23 3 0.03
24 53 0.50
25 49 0.46
26 2 0.02
ACGTcount: A:0.35, C:0.23, G:0.26, T:0.17
Consensus pattern (24 bp):
AACGGGAAGCTCATACGAGCCAAT
Found at i:5896931 original size:25 final size:25
Alignment explanation
Indices: 5896901--5896953 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
5896891 CCAATATCGA
*
5896901 GAAGCTCCGAAGAGCCATTAATCAG
1 GAAGCTCAGAAGAGCCATTAATCAG
* *
5896926 GAAGCTCATAAGAGCCTTTAATCAG
1 GAAGCTCAGAAGAGCCATTAATCAG
5896951 GAA
1 GAA
5896954 ACTTTGATGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.38, C:0.21, G:0.23, T:0.19
Consensus pattern (25 bp):
GAAGCTCAGAAGAGCCATTAATCAG
Found at i:5897297 original size:19 final size:19
Alignment explanation
Indices: 5897260--5897298 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
5897250 GACAATAATA
*
5897260 CAATTACATACATACAATT
1 CAATTACATACATAAAATT
5897279 CAATTA-ATACATATAAATT
1 CAATTACATACATA-AAATT
5897298 C
1 C
5897299 TCACATTAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.49, C:0.18, G:0.00, T:0.33
Consensus pattern (19 bp):
CAATTACATACATAAAATT
Found at i:5912192 original size:5 final size:5
Alignment explanation
Indices: 5912178--5912231 Score: 56
Period size: 5 Copynumber: 10.8 Consensus size: 5
5912168 TTTAATTTAT
* * * *
5912178 ATTCA ATTCG GTTCG GTTCG ATTCG ATTCG ATTCG ATTC- AGTTCG GTTCG
1 ATTCG ATTCG ATTCG ATTCG ATTCG ATTCG ATTCG ATTCG A-TTCG ATTCG
5912228 ATTC
1 ATTC
5912232 ATTTATTTAT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
4 1 0.02
5 41 0.98
ACGTcount: A:0.17, C:0.20, G:0.22, T:0.41
Consensus pattern (5 bp):
ATTCG
Found at i:5912232 original size:15 final size:15
Alignment explanation
Indices: 5912183--5912232 Score: 66
Period size: 15 Copynumber: 3.3 Consensus size: 15
5912173 TTTATATTCA
*
5912183 ATTCGGTTCGGTTCG
1 ATTCAGTTCGGTTCG
*
5912198 ATTC-GATTCGATTCG
1 ATTCAG-TTCGGTTCG
5912213 ATTCAGTTCGGTTCG
1 ATTCAGTTCGGTTCG
5912228 ATTCA
1 ATTCA
5912233 TTTATTTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
14 1 0.03
15 29 0.94
16 1 0.03
ACGTcount: A:0.16, C:0.20, G:0.24, T:0.40
Consensus pattern (15 bp):
ATTCAGTTCGGTTCG
Found at i:5912565 original size:26 final size:25
Alignment explanation
Indices: 5912534--5912584 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
5912524 AATAATTTCA
5912534 AAATTGTATTTGAGTTTAT-TTATTTT
1 AAATTGTATTT--GTTTATATTATTTT
*
5912560 AAATTGTGTTTGTTTATATTATTTT
1 AAATTGTATTTGTTTATATTATTTT
5912585 GTTTAATGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 6 0.26
25 7 0.30
26 10 0.43
ACGTcount: A:0.25, C:0.00, G:0.12, T:0.63
Consensus pattern (25 bp):
AAATTGTATTTGTTTATATTATTTT
Found at i:5917749 original size:353 final size:354
Alignment explanation
Indices: 5917091--5917798 Score: 1409
Period size: 353 Copynumber: 2.0 Consensus size: 354
5917081 TATAAATTTT
5917091 AAATAAATATATTTGCAATATAATTTTTTTTACTCTTATCGTTATTGATACCCTTATTGTTTTTT
1 AAATAAATATATTTGCAATATAATTTTTTTTACTCTTATCGTTATTGATACCCTTATTGTTTTTT
5917156 ATTTGAAGGTCCATTTTTTTCTTTTCTAGAATAATTTACATCCAAATATTTGATTATGACACATA
66 ATTTGAAGGTCCATTTTTTTCTTTTCTAGAATAATTTACATCCAAATATTTGATTATGACACATA
5917221 TTACGGGTATAATTTTTTTATATTAAAATGTATTTATAGATGAGGTTTTGGTTGAAATGTATTTT
131 TTACGGGTATAATTTTTTTATATTAAAATGTATTTATAGATGAGGTTTTGGTTGAAATGTATTTT
5917286 GGGTTTATAAATTCAATATAAAAAGATAAAAATACTCTTAAAATAAATTTTTATTTCCTTTTAAA
196 GGGTTTATAAATTCAATATAAAAAGATAAAAATACTCTTAAAATAAATTTTTATTTCCTTTTAAA
5917351 TAAACGAGATTTTAGTCATTTTTTAATTGAATTAATATCCGATTGACTTATGATTAGTGACTCAA
261 TAAACGAGATTTTAGTCATTTTTTAATTGAATTAATATCCGATTGACTTATGATTAGTGACTCAA
5917416 AGGCAGAAAGAATGACATGTGATTGTAAG
326 AGGCAGAAAGAATGACATGTGATTGTAAG
5917445 AAATAAATATA-TTGCAATATAATTTTTTTTACTCTTATCGTTATTGATACCCTTATTGTTTTTT
1 AAATAAATATATTTGCAATATAATTTTTTTTACTCTTATCGTTATTGATACCCTTATTGTTTTTT
5917509 ATTTGAAGGTCCATTTTTTTCTTTTCTAGAATAATTTACATCCAAATATTTGATTATGACACATA
66 ATTTGAAGGTCCATTTTTTTCTTTTCTAGAATAATTTACATCCAAATATTTGATTATGACACATA
5917574 TTACGGGTATAATTTTTTTATATTAAAATGTATTTATAGATGAGGTTTTGGTTGAAATGTATTTT
131 TTACGGGTATAATTTTTTTATATTAAAATGTATTTATAGATGAGGTTTTGGTTGAAATGTATTTT
5917639 GGGTTTATAAATTCAATATAAAAAGATAAAAATACTCTTAAAATAAATTTTTATTTCCTTTTAAA
196 GGGTTTATAAATTCAATATAAAAAGATAAAAATACTCTTAAAATAAATTTTTATTTCCTTTTAAA
5917704 TAAACGAGATTTTAGTCATTTTTTAATTGAATTAATATCCGATTGACTTATGATTAGTGACTCAA
261 TAAACGAGATTTTAGTCATTTTTTAATTGAATTAATATCCGATTGACTTATGATTAGTGACTCAA
5917769 AGGCAGAAAGAATGACATGTGATTGTAAG
326 AGGCAGAAAGAATGACATGTGATTGTAAG
5917798 A
1 A
5917799 TCTGTAACAA
Statistics
Matches: 354, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
353 343 0.97
354 11 0.03
ACGTcount: A:0.35, C:0.09, G:0.12, T:0.44
Consensus pattern (354 bp):
AAATAAATATATTTGCAATATAATTTTTTTTACTCTTATCGTTATTGATACCCTTATTGTTTTTT
ATTTGAAGGTCCATTTTTTTCTTTTCTAGAATAATTTACATCCAAATATTTGATTATGACACATA
TTACGGGTATAATTTTTTTATATTAAAATGTATTTATAGATGAGGTTTTGGTTGAAATGTATTTT
GGGTTTATAAATTCAATATAAAAAGATAAAAATACTCTTAAAATAAATTTTTATTTCCTTTTAAA
TAAACGAGATTTTAGTCATTTTTTAATTGAATTAATATCCGATTGACTTATGATTAGTGACTCAA
AGGCAGAAAGAATGACATGTGATTGTAAG
Found at i:5918094 original size:16 final size:16
Alignment explanation
Indices: 5918062--5918093 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
5918052 TATTCATATC
5918062 TCGATTAAATTTAAAA
1 TCGATTAAATTTAAAA
5918078 TCGAGTTAAATTTAAA
1 TCGA-TTAAATTTAAA
5918094 TTTTAAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.47, C:0.06, G:0.09, T:0.38
Consensus pattern (16 bp):
TCGATTAAATTTAAAA
Found at i:5920629 original size:12 final size:12
Alignment explanation
Indices: 5920611--5920650 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
5920601 TACTATTTGA
*
5920611 ATATATATGTGT
1 ATATATATGTAT
*
5920623 GTATATATGTAT
1 ATATATATGTAT
*
5920635 ATATATATATAT
1 ATATATATGTAT
5920647 ATAT
1 ATAT
5920651 TCTTTCTTGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (12 bp):
ATATATATGTAT
Found at i:5924704 original size:24 final size:26
Alignment explanation
Indices: 5924659--5924721 Score: 76
Period size: 24 Copynumber: 2.4 Consensus size: 26
5924649 AGAGTGAAAA
5924659 AAAAGAAAAAAAAAGTTAAAATAACAT
1 AAAAG-AAAAAAAAGTTAAAATAACAT
* *
5924686 AAAAGAAAAAAAA-TT-AAATTACTT
1 AAAAGAAAAAAAAGTTAAAATAACAT
5924710 AAAACGAAAAAA
1 AAAA-GAAAAAA
5924722 TATGGGGACC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
24 11 0.33
25 9 0.27
26 8 0.24
27 5 0.15
ACGTcount: A:0.73, C:0.05, G:0.06, T:0.16
Consensus pattern (26 bp):
AAAAGAAAAAAAAGTTAAAATAACAT
Found at i:5928127 original size:299 final size:299
Alignment explanation
Indices: 5927589--5928188 Score: 1191
Period size: 299 Copynumber: 2.0 Consensus size: 299
5927579 AACAGATCGA
5927589 TTCGATTTAAACATTATTTAAGCTTAGTTTGGATGGGCGGTGTGTTTACCTCCAGTGAGATTAAA
1 TTCGATTTAAACATTATTTAAGCTTAGTTTGGATGGGCGGTGTGTTTACCTCCAGTGAGATTAAA
5927654 AACAACAATGGAGTGTATGTTTGGATTCAAAAGCAGCTGTAACGGTATGGTGATAATAAAAAACG
66 AACAACAATGGAGTGTATGTTTGGATTCAAAAGCAGCTGTAACGGTATGGTGATAATAAAAAACG
5927719 ACTATTAAGGACATTAGATTAAAAATGATATATAATAGAAGTTTTTTAAATTATTTTACTTTTAT
131 ACTATTAAGGACATTAGATTAAAAATGATATATAATAGAAGTTTTTTAAATTATTTTACTTTTAT
5927784 GAAATTATTAAAAATATATGAATTTATAAATTCATTTAATAAAATATTAAAATGTATCTTATGAT
196 GAAATTATTAAAAATATATGAATTTATAAATTCATTTAATAAAATATTAAAATGTATCTTATGAT
*
5927849 ATTTTATTATAAATATTTTAATTAATTATATAATTATTT
261 ATTTTATTATAAATATTTTAATTAATTATATAAGTATTT
5927888 TTCGATTTAAACATTATTTAAGCTTAGTTTGGATGGGCGGTGTGTTTACCTCCAGTGAGATTAAA
1 TTCGATTTAAACATTATTTAAGCTTAGTTTGGATGGGCGGTGTGTTTACCTCCAGTGAGATTAAA
5927953 AACAACAATGGAGTGTATGTTTGGATTCAAAAGCAGCTGTAACGGTATGGTGATAATAAAAAACG
66 AACAACAATGGAGTGTATGTTTGGATTCAAAAGCAGCTGTAACGGTATGGTGATAATAAAAAACG
5928018 ACTATTAAGGACATTAGATTAAAAATGATATATAATAGAAGTTTTTTAAATTATTTTACTTTTAT
131 ACTATTAAGGACATTAGATTAAAAATGATATATAATAGAAGTTTTTTAAATTATTTTACTTTTAT
5928083 GAAATTATTAAAAATATATGAATTTATAAATTCATTTAATAAAATATTAAAATGTATCTTATGAT
196 GAAATTATTAAAAATATATGAATTTATAAATTCATTTAATAAAATATTAAAATGTATCTTATGAT
5928148 ATTTTATTATAAATATTTTAATTAATTATATAAGTATTT
261 ATTTTATTATAAATATTTTAATTAATTATATAAGTATTT
5928187 TT
1 TT
5928189 TTTATAAAAA
Statistics
Matches: 300, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
299 300 1.00
ACGTcount: A:0.39, C:0.07, G:0.14, T:0.40
Consensus pattern (299 bp):
TTCGATTTAAACATTATTTAAGCTTAGTTTGGATGGGCGGTGTGTTTACCTCCAGTGAGATTAAA
AACAACAATGGAGTGTATGTTTGGATTCAAAAGCAGCTGTAACGGTATGGTGATAATAAAAAACG
ACTATTAAGGACATTAGATTAAAAATGATATATAATAGAAGTTTTTTAAATTATTTTACTTTTAT
GAAATTATTAAAAATATATGAATTTATAAATTCATTTAATAAAATATTAAAATGTATCTTATGAT
ATTTTATTATAAATATTTTAATTAATTATATAAGTATTT
Found at i:5931616 original size:20 final size:20
Alignment explanation
Indices: 5931591--5931661 Score: 65
Period size: 20 Copynumber: 3.5 Consensus size: 20
5931581 ATGAAAGGTT
*
5931591 AATTTATTAATATTTCTAAG
1 AATTTATTAAAATTTCTAAG
* *
5931611 AATTTACTAAAATTTATAA-
1 AATTTATTAAAATTTCTAAG
* *
5931630 AATTTTATCAAAATATCTTAAG
1 AA-TTTATTAAAATTTC-TAAG
5931652 -ATTTATTAAA
1 AATTTATTAAA
5931662 TTTTTTAATA
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
19 2 0.05
20 34 0.85
21 4 0.10
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.45
Consensus pattern (20 bp):
AATTTATTAAAATTTCTAAG
Found at i:5931696 original size:28 final size:28
Alignment explanation
Indices: 5931673--5931726 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
5931663 TTTTTAATAC
5931673 TTTACTAAAAAATCAAAATATTTAAGAA
1 TTTACTAAAAAATCAAAATATTTAAGAA
*
5931701 TTTACTAAAAAATCAAAATATCTAAG
1 TTTACTAAAAAATCAAAATATTTAAG
5931727 GCTTGAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.56, C:0.09, G:0.04, T:0.31
Consensus pattern (28 bp):
TTTACTAAAAAATCAAAATATTTAAGAA
Found at i:5935148 original size:31 final size:32
Alignment explanation
Indices: 5935107--5935178 Score: 103
Period size: 31 Copynumber: 2.3 Consensus size: 32
5935097 NNNNNNNNAT
* *
5935107 ATTTTTAAAATA-TTTTCTTTAATTTTTTT-TA
1 ATTTTAAAAATACTTTT-TTTAATTTTTTTAAA
5935138 ATTTTAAAAATACTTTTTTTAATTTTTTTAAA
1 ATTTTAAAAATACTTTTTTTAATTTTTTTAAA
5935170 ATTTTAAAA
1 ATTTTAAAA
5935179 TAAAAATGGG
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
31 23 0.62
32 14 0.38
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (32 bp):
ATTTTAAAAATACTTTTTTTAATTTTTTTAAA
Found at i:5935281 original size:11 final size:11
Alignment explanation
Indices: 5935265--5935289 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5935255 ATATTTCGGG
5935265 CCGAACCCGGC
1 CCGAACCCGGC
5935276 CCGAACCCGGC
1 CCGAACCCGGC
5935287 CCG
1 CCG
5935290 GCCCATGAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.56, G:0.28, T:0.00
Consensus pattern (11 bp):
CCGAACCCGGC
Found at i:5940012 original size:20 final size:19
Alignment explanation
Indices: 5939987--5940032 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
5939977 TGTAAAAATA
5939987 ATTAAATAAAAGTATAATTT
1 ATTAAATAAAA-TATAATTT
**
5940007 ATTAAAATGCAATATAATTT
1 ATT-AAATAAAATATAATTT
5940027 ATTAAA
1 ATTAAA
5940033 ATGCAATACA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 3 0.13
20 14 0.61
21 6 0.26
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.39
Consensus pattern (19 bp):
ATTAAATAAAATATAATTT
Found at i:5940033 original size:20 final size:20
Alignment explanation
Indices: 5939999--5940040 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
5939989 TAAATAAAAG
5939999 TATAATTTATTAAAATGCAA
1 TATAATTTATTAAAATGCAA
5940019 TATAATTTATTAAAATGCAA
1 TATAATTTATTAAAATGCAA
5940039 TA
1 TA
5940041 CAATAACAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.40
Consensus pattern (20 bp):
TATAATTTATTAAAATGCAA
Found at i:5948319 original size:2 final size:2
Alignment explanation
Indices: 5948312--5948338 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5948302 CATATAATCC
5948312 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
5948339 CTTTTTTAAC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5948419 original size:92 final size:92
Alignment explanation
Indices: 5948323--5948506 Score: 352
Period size: 92 Copynumber: 2.0 Consensus size: 92
5948313 TATATATATA
5948323 TATATATATATATATAC-TTTTTTAACTTAGACAAAAAAAATACCCTTTACTTTATTAGATTAGT
1 TATATATATATATATACTTTTTTTAACTTA-ACAAAAAAAATACCCTTTACTTTATTAGATTAGT
5948387 ACATTAAAATTAGAGTAGTGTCTTGTTT
65 ACATTAAAATTAGAGTAGTGTCTTGTTT
5948415 TATATATATATATATACTTTTTTTAACTTAACAAAAAAAATACCCTTTACTTTATTAGATTAGTA
1 TATATATATATATATACTTTTTTTAACTTAACAAAAAAAATACCCTTTACTTTATTAGATTAGTA
5948480 CATTAAAATTAGAGTAGTGTCTTGTTT
66 CATTAAAATTAGAGTAGTGTCTTGTTT
5948507 GTTGACTAAG
Statistics
Matches: 91, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
92 79 0.87
93 12 0.13
ACGTcount: A:0.38, C:0.10, G:0.08, T:0.44
Consensus pattern (92 bp):
TATATATATATATATACTTTTTTTAACTTAACAAAAAAAATACCCTTTACTTTATTAGATTAGTA
CATTAAAATTAGAGTAGTGTCTTGTTT
Found at i:5951855 original size:21 final size:21
Alignment explanation
Indices: 5951831--5951878 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
5951821 AGAAGAGCAT
5951831 GAAAAATAAAGAAACA-AAAAG
1 GAAAAATAAAG-AACATAAAAG
**
5951852 GAAAGTTAAAGAACATAAAAG
1 GAAAAATAAAGAACATAAAAG
*
5951873 AAAAAA
1 GAAAAA
5951879 AAATTAAATT
Statistics
Matches: 21, Mismatches: 5, Indels: 2
0.75 0.18 0.07
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.73, C:0.04, G:0.15, T:0.08
Consensus pattern (21 bp):
GAAAAATAAAGAACATAAAAG
Found at i:5956112 original size:47 final size:41
Alignment explanation
Indices: 5955972--5956096 Score: 250
Period size: 41 Copynumber: 3.0 Consensus size: 41
5955962 GGAAATAGTC
5955972 TTCTATAAATTTGAATTTGAGAATTGAAAGCTCGATCGGTT
1 TTCTATAAATTTGAATTTGAGAATTGAAAGCTCGATCGGTT
5956013 TTCTATAAATTTGAATTTGAGAATTGAAAGCTCGATCGGTT
1 TTCTATAAATTTGAATTTGAGAATTGAAAGCTCGATCGGTT
5956054 TTCTATAAATTTGAATTTGAGAATTGAAAGCTCGATCGGTT
1 TTCTATAAATTTGAATTTGAGAATTGAAAGCTCGATCGGTT
5956095 TT
1 TT
5956097 ATCTCTTATC
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 84 1.00
ACGTcount: A:0.31, C:0.10, G:0.19, T:0.40
Consensus pattern (41 bp):
TTCTATAAATTTGAATTTGAGAATTGAAAGCTCGATCGGTT
Found at i:5959042 original size:12 final size:12
Alignment explanation
Indices: 5959021--5959050 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
5959011 CGTTTTGTAA
5959021 TTCTTCATCGTC
1 TTCTTCATCGTC
*
5959033 TTCTTTATCGTC
1 TTCTTCATCGTC
5959045 TTCTTC
1 TTCTTC
5959051 TTGTTATGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.07, C:0.30, G:0.07, T:0.57
Consensus pattern (12 bp):
TTCTTCATCGTC
Found at i:5975071 original size:21 final size:21
Alignment explanation
Indices: 5975045--5975086 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
5975035 AAAATCAGCA
5975045 ATATTTCAAAGTAGTGCCAAT
1 ATATTTCAAAGTAGTGCCAAT
5975066 ATATTTCAAAGTAGTGCCAAT
1 ATATTTCAAAGTAGTGCCAAT
5975087 GGCAGGCAAA
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:0.38, C:0.14, G:0.14, T:0.33
Consensus pattern (21 bp):
ATATTTCAAAGTAGTGCCAAT
Found at i:5977754 original size:21 final size:20
Alignment explanation
Indices: 5977725--5977780 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 20
5977715 ATTATTTTTT
5977725 AAAATTTTAAAAAATTCAAAA
1 AAAATTTTAAAAAATT-AAAA
*
5977746 AATATTTT-AAAAATTAAAA
1 AAAATTTTAAAAAATTAAAA
*
5977765 AAAATTATAAGAAAAT
1 AAAATTTTAA-AAAAT
5977781 ATTTTTTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 10 0.33
20 8 0.27
21 12 0.40
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (20 bp):
AAAATTTTAAAAAATTAAAA
Found at i:5977759 original size:20 final size:20
Alignment explanation
Indices: 5977728--5977780 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
5977718 ATTTTTTAAA
5977728 ATTTTAAAAAATTCAAAAAAT
1 ATTTTAAAAAATT-AAAAAAT
*
5977749 ATTTT-AAAAATTAAAAAAA
1 ATTTTAAAAAATTAAAAAAT
*
5977768 ATTATAAGAAAAT
1 ATTTTAA-AAAAT
5977781 ATTTTTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 10 0.36
20 8 0.29
21 10 0.36
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (20 bp):
ATTTTAAAAAATTAAAAAAT
Found at i:5982058 original size:3 final size:3
Alignment explanation
Indices: 5982050--5982088 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
5982040 AATTTGATTC
* *
5982050 TGA TGA TGA TTA TGA TGA TGA TGA TTA TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
5982089 GAAGTCACTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.33, C:0.00, G:0.28, T:0.38
Consensus pattern (3 bp):
TGA
Found at i:5982070 original size:15 final size:15
Alignment explanation
Indices: 5982050--5982088 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
5982040 AATTTGATTC
5982050 TGATGATGATTATGA
1 TGATGATGATTATGA
5982065 TGATGATGATTATGA
1 TGATGATGATTATGA
5982080 TGATGATGA
1 TGATGATGA
5982089 GAAGTCACTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.28, T:0.38
Consensus pattern (15 bp):
TGATGATGATTATGA
Found at i:5984564 original size:15 final size:15
Alignment explanation
Indices: 5984540--5984583 Score: 53
Period size: 11 Copynumber: 3.3 Consensus size: 15
5984530 TTATCAAAAT
5984540 ACAA-GTAATTTTCA
1 ACAATGTAATTTTCA
5984554 ACAATGTAA--TT-A
1 ACAATGTAATTTTCA
5984566 A-AATGTAATTTTCA
1 ACAATGTAATTTTCA
5984580 ACAA
1 ACAA
5984584 GGTAGCGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 9
0.74 0.00 0.26
Matches are distributed among these distances:
11 7 0.28
12 2 0.08
13 4 0.16
14 6 0.24
15 6 0.24
ACGTcount: A:0.48, C:0.11, G:0.07, T:0.34
Consensus pattern (15 bp):
ACAATGTAATTTTCA
Found at i:5984757 original size:30 final size:30
Alignment explanation
Indices: 5984694--5984750 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
5984684 CTTAGTGAAG
* *
5984694 ATTTTAAAAAAATTGAGGAGTTTAATTAAA
1 ATTTTAAAAAAATTGAAGAGCTTAATTAAA
5984724 ATTTTCAAAAAAATTGAAG-GCTTAATT
1 ATTTT-AAAAAAATTGAAGAGCTTAATT
5984751 CGAATTTCCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 12 0.50
31 12 0.50
ACGTcount: A:0.47, C:0.04, G:0.12, T:0.37
Consensus pattern (30 bp):
ATTTTAAAAAAATTGAAGAGCTTAATTAAA
Found at i:5989031 original size:18 final size:18
Alignment explanation
Indices: 5989010--5989059 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
5989000 ATTTTCCTTT
5989010 TTTCTTTTTCTTTCTCTG
1 TTTCTTTTTCTTTCTCTG
* *
5989028 TTTCGTTCTAC-TTCTCTG
1 TTTC-TTTTTCTTTCTCTG
5989046 -TTCTTTTTCTTTCT
1 TTTCTTTTTCTTTCT
5989060 TTATTTCCTT
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
16 4 0.15
17 7 0.27
18 11 0.42
19 4 0.15
ACGTcount: A:0.02, C:0.24, G:0.06, T:0.68
Consensus pattern (18 bp):
TTTCTTTTTCTTTCTCTG
Found at i:5995626 original size:28 final size:28
Alignment explanation
Indices: 5995593--5995654 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
5995583 TTAATAAATA
* * *
5995593 TAAAAATTTAAAAAAAGTATACAACTTAT
1 TAAAAGTTT-AAAAAAGTATAAAAATTAT
*
5995622 TAAAAGTTTTAAAAAGTATAAAAATTAT
1 TAAAAGTTTAAAAAAGTATAAAAATTAT
5995650 TAAAA
1 TAAAA
5995655 ACTATTTTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 21 0.72
29 8 0.28
ACGTcount: A:0.60, C:0.03, G:0.05, T:0.32
Consensus pattern (28 bp):
TAAAAGTTTAAAAAAGTATAAAAATTAT
Found at i:5996139 original size:85 final size:85
Alignment explanation
Indices: 5995983--5996151 Score: 191
Period size: 85 Copynumber: 2.0 Consensus size: 85
5995973 TTAAGTTTCT
* * * *
5995983 CTATTTTTTTTACTCAATTGAGCACTTAAATTTTCAAAATATATTAAAAAGTCCTCAAACCTCTT
1 CTATTTTTTTCACTCAATTGAGCACTTAAATTTTCAAAATACATAAAAAAGCCCTCAAACCTCTT
5996048 CAAAAAATA-CAATTAAGCCC
66 CAAAAAA-AGCAATTAAGCCC
* * * * * * *
5996068 CTATTTTTTTCACTCAATTGGGTACTTGAATTTTTAAAATGCATAAAAAAGACCCTCAGAA-TTG
1 CTATTTTTTTCACTCAATTGAGCACTTAAATTTTCAAAATACATAAAAAAG-CCCTCA-AACCTC
5996132 TTC-AAAAAAGCAATTAAGCC
64 TTCAAAAAAAGCAATTAAGCC
5996152 ATACTCTTAT
Statistics
Matches: 70, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
84 1 0.01
85 58 0.83
86 9 0.13
87 2 0.03
ACGTcount: A:0.39, C:0.18, G:0.08, T:0.34
Consensus pattern (85 bp):
CTATTTTTTTCACTCAATTGAGCACTTAAATTTTCAAAATACATAAAAAAGCCCTCAAACCTCTT
CAAAAAAAGCAATTAAGCCC
Found at i:5996576 original size:19 final size:20
Alignment explanation
Indices: 5996522--5996576 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 20
5996512 CTTATGATTT
*
5996522 TTTTATGATTTTTATA-AAA
1 TTTTACGATTTTTATATAAA
* * *
5996541 TTTTACAATTTATATATATA
1 TTTTACGATTTTTATATAAA
5996561 -TTTACGATTTTTATAT
1 TTTTACGATTTTTATAT
5996577 TTTTTTTCTA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
19 27 0.93
20 2 0.07
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.58
Consensus pattern (20 bp):
TTTTACGATTTTTATATAAA
Found at i:5996674 original size:11 final size:12
Alignment explanation
Indices: 5996650--5996675 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
5996640 TTGATTTTAA
5996650 TTTTTAAAATTT
1 TTTTTAAAATTT
5996662 TTTTTAAAATTT
1 TTTTTAAAATTT
5996674 TT
1 TT
5996676 AATAAAAGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TTTTTAAAATTT
Found at i:5996824 original size:88 final size:90
Alignment explanation
Indices: 5996689--5996859 Score: 258
Period size: 88 Copynumber: 1.9 Consensus size: 90
5996679 AAAAGCAGGT
*
5996689 GCTTAATTGATTTTCTTGAAAAAGTTTGAGGGTCTTTTTGATGCATTTTAAAAGTTCAAGTACCC
1 GCTTAATTGATTTTCTTGAAAAAGTTTGAGGGACTTTTTGATGCATTTTAAAAGTTCAAGTACCC
* * *
5996754 AATTGAGTGCAAAGAAAAGTAGAGG
66 AAATGAATGCAAAAAAAAGTAGAGG
* *
5996779 GCTTAATTGCA-TTT-TTGAAAAGGTTTGA-GGACTTTTTGATGCATTTTGAAAGTTCAAGTACC
1 GCTTAATTG-ATTTTCTTGAAAAAGTTTGAGGGACTTTTTGATGCATTTTAAAAGTTCAAGTACC
5996841 CAAATGAATGCAAAAAAAA
65 CAAATGAATGCAAAAAAAA
5996860 AAAAAACAGT
Statistics
Matches: 74, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
88 48 0.65
89 13 0.18
90 12 0.16
91 1 0.01
ACGTcount: A:0.35, C:0.11, G:0.20, T:0.34
Consensus pattern (90 bp):
GCTTAATTGATTTTCTTGAAAAAGTTTGAGGGACTTTTTGATGCATTTTAAAAGTTCAAGTACCC
AAATGAATGCAAAAAAAAGTAGAGG
Found at i:5998654 original size:16 final size:17
Alignment explanation
Indices: 5998630--5998678 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 17
5998620 AATTTTATCA
*
5998630 TTATTAATT-TAAAATT
1 TTATAAATTATAAAATT
5998646 TTATAAATTATAAAA-T
1 TTATAAATTATAAAATT
* *
5998662 GTGTAAATTA-AAAATT
1 TTATAAATTATAAAATT
5998678 T
1 T
5998679 ATCATTTTAG
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
15 4 0.15
16 18 0.67
17 5 0.19
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (17 bp):
TTATAAATTATAAAATT
Found at i:6001567 original size:3 final size:3
Alignment explanation
Indices: 6001559--6001588 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
6001549 AATTTGATTC
*
6001559 TGA TGA TGA AGA TGA TGA TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
6001589 GAAGTCACTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.37, C:0.00, G:0.33, T:0.30
Consensus pattern (3 bp):
TGA
Found at i:6008514 original size:16 final size:14
Alignment explanation
Indices: 6008470--6008515 Score: 60
Period size: 12 Copynumber: 3.3 Consensus size: 14
6008460 ATGTATGTGT
6008470 AAAATAAATATTTA
1 AAAATAAATATTTA
6008484 AAAAT--ATATTTA
1 AAAATAAATATTTA
6008496 AAAATAAAATATCTTA
1 AAAAT-AAATAT-TTA
6008512 AAAA
1 AAAA
6008516 AAAACCAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
12 12 0.43
14 5 0.18
15 4 0.14
16 7 0.25
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (14 bp):
AAAATAAATATTTA
Found at i:6010708 original size:12 final size:12
Alignment explanation
Indices: 6010682--6010715 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
6010672 CCACATATCA
*
6010682 ATTAA-TCCTTT
1 ATTAATTCCTTC
6010693 ATTAATTCCTTC
1 ATTAATTCCTTC
6010705 ATTAATTCCTT
1 ATTAATTCCTT
6010716 TGTTTAAGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 5 0.24
12 16 0.76
ACGTcount: A:0.26, C:0.21, G:0.00, T:0.53
Consensus pattern (12 bp):
ATTAATTCCTTC
Found at i:6012344 original size:225 final size:225
Alignment explanation
Indices: 6012084--6012547 Score: 833
Period size: 225 Copynumber: 2.1 Consensus size: 225
6012074 TCTCCCCATT
6012084 TGGCTTCAACATCTTGTTCAATTGAAAACATTAAAAATTCATAACTGCAATGGATTGAGGTCACT
1 TGGCTTCAACATCTTGTTCAATTGAAAACATTAAAAATTCATAACTGCAATGGATTGAGGTCACT
*
6012149 GCTTTCCTGTGTT-CAACATCTCACTTTCCTTGAA-GAGTTTGAAGTAAAGGACTGCAAGGAGCT
66 GC-TTCCTGTGTTCCAACACCTCACTTTCCTTGAACG-GTTTGAAGTAAAGGACTGCAAGGAGCT
*
6012212 GGAGTTATCTGGAGCTGGCATCCAAATATTCCAAGATCATACAAACCTACGCTCTCTATGGCTGC
129 GGAGTTATCTGGAGCTGGCATCCAAATATTCCAAGATCATACAAACCTACGCTCTCTATCGCTGC
*
6012277 AAAATATTCCAAAGTGTCGGCATCTTCCGGAG
194 AAAATATTCCAAAGTGTCGGCATCTGCCGGAG
* *
6012309 TGGCTTCAACATCTTGTTCAATTGAAAACATTAAAAATTCGTAATTGCAATGGATTGAGGTCACT
1 TGGCTTCAACATCTTGTTCAATTGAAAACATTAAAAATTCATAACTGCAATGGATTGAGGTCACT
*
6012374 GCTTCCTGTGTTCCAACACCTCACTTTCCTTGAACGGTTTGAAGTAGAGGACTGCAAGGAGCTGG
66 GCTTCCTGTGTTCCAACACCTCACTTTCCTTGAACGGTTTGAAGTAAAGGACTGCAAGGAGCTGG
*
6012439 AGTTATCTGGAGCTGGCATCCAAATATTCCAAGATCATACAAGCCTACGCTCTCTATCGCTGCAA
131 AGTTATCTGGAGCTGGCATCCAAATATTCCAAGATCATACAAACCTACGCTCTCTATCGCTGCAA
6012504 AATATTCCAAAGTGTCGGCATCTGCCGGAG
196 AATATTCCAAAGTGTCGGCATCTGCCGGAG
6012534 TGGCTTCAACATCT
1 TGGCTTCAACATCT
6012548 AACAAATCTG
Statistics
Matches: 230, Mismatches: 7, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
224 10 0.04
225 219 0.95
226 1 0.00
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (225 bp):
TGGCTTCAACATCTTGTTCAATTGAAAACATTAAAAATTCATAACTGCAATGGATTGAGGTCACT
GCTTCCTGTGTTCCAACACCTCACTTTCCTTGAACGGTTTGAAGTAAAGGACTGCAAGGAGCTGG
AGTTATCTGGAGCTGGCATCCAAATATTCCAAGATCATACAAACCTACGCTCTCTATCGCTGCAA
AATATTCCAAAGTGTCGGCATCTGCCGGAG
Found at i:6015004 original size:24 final size:24
Alignment explanation
Indices: 6014958--6015004 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
6014948 CAAAACTATG
**
6014958 TTTATATTAAAAAATAATTTATAT
1 TTTATATTAAAAAATAAAATATAT
**
6014982 TTTATATTAAATTATAAAATATA
1 TTTATATTAAAAAATAAAATATA
6015005 CATAAGAATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
TTTATATTAAAAAATAAAATATAT
Done.