Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr7
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: 55462051
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2780933 characters in sequence are not A, C, G, or T
File 89 of 163
Found at i:28758959 original size:26 final size:23
Alignment explanation
Indices: 28758930--28758980 Score: 75
Period size: 26 Copynumber: 2.1 Consensus size: 23
28758920 ATTTTTAAAA
28758930 TATTTTTAAAATATTCTTTATTTTTT
1 TATTTTTAAAATA--CTTT-TTTTTT
28758956 TATTTTTAAAATACTTTTTTTTT
1 TATTTTTAAAATACTTTTTTTTT
28758979 TA
1 TA
28758981 AAAAATTTGG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
23 8 0.32
24 4 0.16
26 13 0.52
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (23 bp):
TATTTTTAAAATACTTTTTTTTT
Found at i:28759586 original size:2 final size:2
Alignment explanation
Indices: 28759581--28759607 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
28759571 TTTTTTTTGT
28759581 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
28759608 CACTACACCA
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:28760010 original size:40 final size:41
Alignment explanation
Indices: 28759843--28760137 Score: 217
Period size: 41 Copynumber: 7.2 Consensus size: 41
28759833 TTTACATAAT
* * * * *
28759843 CGCCGCTAATGCTGCGGTCTTTCGCGGCG-TTTTCAAATATG
1 CGCCGCTAATGCTACGGTCTTTAGCAGCGTTTTTTAAA-AAG
* * * * * *
28759884 CACCGCTAATGCTGA-GGTCTTTAGCGGCGATTCTGACAAAG
1 CGCCGCTAATGCT-ACGGTCTTTAGCAGCGTTTTTTAAAAAG
* * * * * * * *
28759925 TGCCGCGAAGGATACAGTCTTTAGCGGCATTTTTTACTAAA-
1 CGCCGCTAATGCTACGGTCTTTAGCAGCGTTTTTTA-AAAAG
* *
28759966 CGCCGCTAATGCT-CAGGTC-TTAGCAGCGATTGTTAAAAAG
1 CGCCGCTAATGCTAC-GGTCTTTAGCAGCGTTTTTTAAAAAG
**
28760006 CGCCGCTAATGCTACGGTCTTTAGCAGCGTTTTTTATGAAG
1 CGCCGCTAATGCTACGGTCTTTAGCAGCGTTTTTTAAAAAG
* **
28760047 CGTCG-TAAATGCTACGGTCTTTAGCAGCGTTTTTTACGAAG
1 CGCCGCT-AATGCTACGGTCTTTAGCAGCGTTTTTTAAAAAG
* * * *
28760088 TGCCGCTAATGCT-CAGGTATTTAGCGGCGTTTCTTAAAAAG
1 CGCCGCTAATGCTAC-GGTCTTTAGCAGCGTTTTTTAAAAAG
28760129 CGCCGCTAA
1 CGCCGCTAA
28760138 AAACAGCAGC
Statistics
Matches: 201, Mismatches: 42, Indels: 22
0.76 0.16 0.08
Matches are distributed among these distances:
39 3 0.01
40 33 0.16
41 156 0.78
42 9 0.04
ACGTcount: A:0.23, C:0.23, G:0.25, T:0.30
Consensus pattern (41 bp):
CGCCGCTAATGCTACGGTCTTTAGCAGCGTTTTTTAAAAAG
Found at i:28760153 original size:41 final size:41
Alignment explanation
Indices: 28760108--28760201 Score: 120
Period size: 41 Copynumber: 2.3 Consensus size: 41
28760098 GCTCAGGTAT
*
28760108 TTAGCGGCGTTTCTTA-AAAAGCGCCGCTAAA-AACAGCAGCA
1 TTAGCGGCGTTTATTAGAAAA-CGCCGCTAAAGAACAG-AGCA
** *
28760149 TTAGCGGCGCATATTAGAAAACGCCGCTAAAGACCAGAGCA
1 TTAGCGGCGTTTATTAGAAAACGCCGCTAAAGAACAGAGCA
28760190 TTAGCGGCGTTT
1 TTAGCGGCGTTT
28760202 TGTAGCTAGC
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
41 37 0.82
42 8 0.18
ACGTcount: A:0.32, C:0.23, G:0.24, T:0.20
Consensus pattern (41 bp):
TTAGCGGCGTTTATTAGAAAACGCCGCTAAAGAACAGAGCA
Found at i:28761097 original size:74 final size:73
Alignment explanation
Indices: 28760932--28761251 Score: 532
Period size: 74 Copynumber: 4.4 Consensus size: 73
28760922 GCACGAATTT
* * * *
28760932 GCGGCGTTTATTGTAAAAACGCCACAAAAGTTTAACCAAAAGGACTTCGTTTTTATACTGTTTAT
1 GCGGCGTTTCTGGTAAAAACGCCGCAAAAGTTTAACCAAAACGACTTCGTTTTTATACTGTTTAT
28760997 TGGTATTA
66 TGGTATTA
28761005 GCGGCGTTTCTGGTAAAAACGCCGCAAAAGTTTAACCAAAACGACTTCGTTTTGTATACTGTTTA
1 GCGGCGTTTCTGGTAAAAACGCCGCAAAAGTTTAACCAAAACGACTTCGTTTT-TATACTGTTTA
28761070 TTGGTATTA
65 TTGGTATTA
* *
28761079 GCGGCGTTTCTGGTAAAAACGCCGCAAAAGTTTAACCAAAACGACTTTGTTTTTATGCTGTTTAT
1 GCGGCGTTTCTGGTAAAAACGCCGCAAAAGTTTAACCAAAACGACTTCGTTTTTATACTGTTTAT
*
28761144 TAGTATTA
66 TGGTATTA
* *
28761152 GCGGCGTTTCTGGTACAAACGCCGCAAAAGTTTAACCAAAATGACTTCGTTTTTTATACTGTTTA
1 GCGGCGTTTCTGGTAAAAACGCCGCAAAAGTTTAACCAAAACGACTTCG-TTTTTATACTGTTTA
28761217 TTGGTATTA
65 TTGGTATTA
*
28761226 GCGGCGTTTCTGGTACAAACGCCGCA
1 GCGGCGTTTCTGGTAAAAACGCCGCA
28761252 TATGATAGTT
Statistics
Matches: 233, Mismatches: 12, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
73 113 0.48
74 120 0.52
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (73 bp):
GCGGCGTTTCTGGTAAAAACGCCGCAAAAGTTTAACCAAAACGACTTCGTTTTTATACTGTTTAT
TGGTATTA
Found at i:28761249 original size:147 final size:147
Alignment explanation
Indices: 28760932--28761251 Score: 541
Period size: 147 Copynumber: 2.2 Consensus size: 147
28760922 GCACGAATTT
* * * *
28760932 GCGGCGTTTATTGTAAAAACGCCACAAAAGTTTAACCAAAAGGACTTCGTTTTTATACTGTTTAT
1 GCGGCGTTTCTGGTAAAAACGCCGCAAAAGTTTAACCAAAACGACTTCGTTTTTATACTGTTTAT
*
28760997 TGGTATTAGCGGCGTTTCTGGTAAAAACGCCGCAAAAGTTTAACCAAAACGACTTCGTTTTGTAT
66 TAGTATTAGCGGCGTTTCTGGTAAAAACGCCGCAAAAGTTTAACCAAAACGACTTCGTTTTGTAT
28761062 ACTGTTTATTGGTATTA
131 ACTGTTTATTGGTATTA
* *
28761079 GCGGCGTTTCTGGTAAAAACGCCGCAAAAGTTTAACCAAAACGACTTTGTTTTTATGCTGTTTAT
1 GCGGCGTTTCTGGTAAAAACGCCGCAAAAGTTTAACCAAAACGACTTCGTTTTTATACTGTTTAT
* * *
28761144 TAGTATTAGCGGCGTTTCTGGTACAAACGCCGCAAAAGTTTAACCAAAATGACTTCGTTTTTTAT
66 TAGTATTAGCGGCGTTTCTGGTAAAAACGCCGCAAAAGTTTAACCAAAACGACTTCGTTTTGTAT
28761209 ACTGTTTATTGGTATTA
131 ACTGTTTATTGGTATTA
*
28761226 GCGGCGTTTCTGGTACAAACGCCGCA
1 GCGGCGTTTCTGGTAAAAACGCCGCA
28761252 TATGATAGTT
Statistics
Matches: 162, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
147 162 1.00
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (147 bp):
GCGGCGTTTCTGGTAAAAACGCCGCAAAAGTTTAACCAAAACGACTTCGTTTTTATACTGTTTAT
TAGTATTAGCGGCGTTTCTGGTAAAAACGCCGCAAAAGTTTAACCAAAACGACTTCGTTTTGTAT
ACTGTTTATTGGTATTA
Found at i:28761985 original size:74 final size:74
Alignment explanation
Indices: 28761827--28762061 Score: 384
Period size: 74 Copynumber: 3.2 Consensus size: 74
28761817 GCATATATTG
*
28761827 GGTACGAAACGCCGCAAAAGTTTAACCAAAACAACTTCG-TTTTTATACTGTTTATTGGTATTAG
1 GGTAC-AAACGCCGCAAAAGTTTAACCAAAACGACTTCGTTTTTTATACTGTTTATTGGTATTAG
28761891 CGGCGTTTCT
65 CGGCGTTTCT
*
28761901 GGTAAAAACGCCGCAAAAGTTTAACCAAAACGACTTCGTTTTTTCA-ACTGTTTATTGGTATTAG
1 GGTACAAACGCCGCAAAAGTTTAACCAAAACGACTTCGTTTTTT-ATACTGTTTATTGGTATTAG
*
28761965 CGGCGTTTTT
65 CGGCGTTTCT
** *
28761975 ATTACAAACGCCGCAAAAGTTTAACCAAAACGACTTCGTTTTTTATACTGTTTATTGGAATTAGC
1 GGTACAAACGCCGCAAAAGTTTAACCAAAACGACTTCGTTTTTTATACTGTTTATTGGTATTAGC
28762040 GGCGTTTCT
66 GGCGTTTCT
28762049 GGTACAAACGCCG
1 GGTACAAACGCCG
28762062 TAAATGATAG
Statistics
Matches: 148, Mismatches: 10, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
73 33 0.22
74 114 0.77
75 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (74 bp):
GGTACAAACGCCGCAAAAGTTTAACCAAAACGACTTCGTTTTTTATACTGTTTATTGGTATTAGC
GGCGTTTCT
Found at i:28762423 original size:811 final size:813
Alignment explanation
Indices: 28761021--28762546 Score: 2772
Period size: 811 Copynumber: 1.9 Consensus size: 813
28761011 TTTCTGGTAA
*
28761021 AAACGCCGCAAAAGTTTAACCAAAACGACTTCGTTTTGTATACTGTTTATTGGTATTAGCGGCGT
1 AAACGCCGCAAAAGTTTAACCAAAACAACTTCGTTTTGTATACTGTTTATTGGTATTAGCGGCGT
* *
28761086 TTCTGGTAAAAACGCCGCAAAAGTTTAACCAAAACGACTTTGTTTTTATGCTGTTTATTAGTATT
66 TTCTGGTAAAAACGCCGCAAAAGTTTAACCAAAACGACTTCGTTTTTATACTGTTTATTAGTATT
* *
28761151 AGCGGCGTTTCTGGTACAAACGCCGCAAAAGTTTAACCAAAATGACTTCGTTTTTTATACTGTTT
131 AGCGGCGTTTCTAGTACAAACGCCGCAAAAGTTTAACCAAAACGACTTCGTTTTTTATACTGTTT
* *
28761216 ATTGGTATTAGCGGCGTTTCTGGTACAAACGCCGCATATGATAGTTATGTATTTTAGGGTATCAA
196 ATTGGAATTAGCGGCGTTTCTGGTACAAACGCCGCAAATGATAGTTATGTATTTTAGGGTATCAA
28761281 AATTAATATTTAAGTTTTGTCGTATACAGTTTGGGGTTTTAGGGTTCGATACATAATATTTATTA
261 AATTAATATTTAAGTTTTGTCGTATACAGTTTGGGGTTTTAGGGTTCGATACATAATATTTATTA
* *
28761346 ATTTAGGATTACAGTTTTGAGTTTAGGGTTTTGGGTTTAGGTTTACGATCGACTTGGGGATTGGG
326 ATTTAAGATTACAGTTTTGAGTTTAGGGTTTTGGGTTTAGGTTTACGATCGACTTGGGGATTAGG
28761411 GTACGTAGTTTAGGGTTTGAGTTTACATGTTAGTTTTAATGTGAGGTTAATTAGTGTTTACGTAC
391 GTACGTAGTTTAGGGTTTGAGTTTACATGTTAGTTTTAATGTGAGGTTAATTAGTGTTTACGTAC
* *
28761476 GGCTTATAAGATAATGATCAAATTTACTGTTTTACGGCTTGATGTTTATGGTTTATGGTTTAGCC
456 GACTTATAAGATAATGATCAAATTTACTATTTTACGGCTTGATGTTTATGGTTTATGGTTTAGCC
28761541 TTATTGATTTGAATGTTACAATGCATGGTTTTTACGTTTCGGATTTGCATGAAGAATACGAGTTA
521 TTATTGATTTGAATGTTACAATGCATGGTTTTTACGTTTCGGATTTGCATGAAGAATACGAGTTA
28761606 GGGTTTAGGCTTTAATTTTAAAATTTACGGGTTATAGGGATTAATAGCTTTGGGTTTTAGGGTTT
586 GGGTTTAGGCTTTAATTTTAAAATTTACGGGTTATAGGGATTAATAGCTTTGGGTTTTAGGGTTT
*
28761671 AATTAATAACCTATCTAAAACAAAAG-GAAAAAAAAATTATTTGTATTTTTTACTTATTATAATA
651 AATTAATAACCTATCTAAAACAAAAGAAAAAAAAAAATTATTTGTATTTTTTACTTATTATAATA
28761735 TATATATGTTATATATATATTATGAAACATATTAATATTGTGTTAGTTACGTACATTCGTTTGTT
716 TATATATGTTATATATATATTATGAAACATATTAATATTGTGTTAGTTACGTACATTCGTTTGTT
28761800 TGATATTTTAAAATAGAGCATATATTGGGTACG
781 TGATATTTTAAAATAGAGCATATATTGGGTACG
28761833 AAACGCCGCAAAAGTTTAACCAAAACAACTTCGTTTT-TATACTGTTTATTGGTATTAGCGGCGT
1 AAACGCCGCAAAAGTTTAACCAAAACAACTTCGTTTTGTATACTGTTTATTGGTATTAGCGGCGT
*
28761897 TTCTGGTAAAAACGCCGCAAAAGTTTAACCAAAACGACTTCGTTTTT-TCAACTGTTTATTGGTA
66 TTCTGGTAAAAACGCCGCAAAAGTTTAACCAAAACGACTTCGTTTTTAT--ACTGTTTATTAGTA
* *
28761961 TTAGCGGCGTTTTTATTACAAACGCCGCAAAAGTTTAACCAAAACGACTTCGTTTTTTATACTGT
129 TTAGCGGCGTTTCTAGTACAAACGCCGCAAAAGTTTAACCAAAACGACTTCGTTTTTTATACTGT
*
28762026 TTATTGGAATTAGCGGCGTTTCTGGTACAAACGCCGTAAATGATAGTTATGTATTTTAGGGTATC
194 TTATTGGAATTAGCGGCGTTTCTGGTACAAACGCCGCAAATGATAGTTATGTATTTTAGGGTATC
* * *
28762091 AGAATTAATATTTAAGTTTTGTCGTATACGGTTTGGGG-TTTAGGGTTCGATACATAATGTTTAT
259 AAAATTAATATTTAAGTTTTGTCGTATACAGTTTGGGGTTTTAGGGTTCGATACATAATATTTAT
28762155 TAATTTAAGATTACAGTTTTGAGTTTAGGGTTTTGGGTTTAGGTTTACGATCGACTTGGGGATTA
324 TAATTTAAGATTACAGTTTTGAGTTTAGGGTTTTGGGTTTAGGTTTACGATCGACTTGGGGATTA
*
28762220 GGGTACGTAGTTTAGGGTTTGTGTTTACATGTTAGTTTTAATGTGAGGTTAATTAGTGTTTACGT
389 GGGTACGTAGTTTAGGGTTTGAGTTTACATGTTAGTTTTAATGTGAGGTTAATTAGTGTTTACGT
28762285 ACGACTTATAAGATAATGATCAAATTTACTATTTTACGGCTTGATGTTTATGGTTTATGGTTTAG
454 ACGACTTATAAGATAATGATCAAATTTACTATTTTACGGCTTGATGTTTATGGTTTATGGTTTAG
*
28762350 CCTTATTGATTTGAATGTTACAATGCATGGTTTTTGCGTTTCGGATTTGCATGAAGAATACGAGT
519 CCTTATTGATTTGAATGTTACAATGCATGGTTTTTACGTTTCGGATTTGCATGAAGAATACGAGT
*
28762415 TAGGGTTTAGGCTTTAATTTTAAAATTTACGGGTTATAGGGATTAATAGTTTTGGGTTTTAGGGT
584 TAGGGTTTAGGCTTTAATTTTAAAATTTACGGGTTATAGGGATTAATAGCTTTGGGTTTTAGGGT
* * *
28762480 TTAATTAATTACCTATCTAAAACAAAAGCAAAAAAAAAAATTATTTGTGTTTTTTACTTCTTATA
649 TTAATTAATAACCTATCTAAAACAAAAG-AAAAAAAAAAATTATTTGTATTTTTTACTTATTATA
28762545 AT
713 AT
28762547 TATGTCATTA
Statistics
Matches: 685, Mismatches: 25, Indels: 7
0.96 0.03 0.01
Matches are distributed among these distances:
810 1 0.00
811 443 0.65
812 207 0.30
813 34 0.05
ACGTcount: A:0.29, C:0.11, G:0.21, T:0.40
Consensus pattern (813 bp):
AAACGCCGCAAAAGTTTAACCAAAACAACTTCGTTTTGTATACTGTTTATTGGTATTAGCGGCGT
TTCTGGTAAAAACGCCGCAAAAGTTTAACCAAAACGACTTCGTTTTTATACTGTTTATTAGTATT
AGCGGCGTTTCTAGTACAAACGCCGCAAAAGTTTAACCAAAACGACTTCGTTTTTTATACTGTTT
ATTGGAATTAGCGGCGTTTCTGGTACAAACGCCGCAAATGATAGTTATGTATTTTAGGGTATCAA
AATTAATATTTAAGTTTTGTCGTATACAGTTTGGGGTTTTAGGGTTCGATACATAATATTTATTA
ATTTAAGATTACAGTTTTGAGTTTAGGGTTTTGGGTTTAGGTTTACGATCGACTTGGGGATTAGG
GTACGTAGTTTAGGGTTTGAGTTTACATGTTAGTTTTAATGTGAGGTTAATTAGTGTTTACGTAC
GACTTATAAGATAATGATCAAATTTACTATTTTACGGCTTGATGTTTATGGTTTATGGTTTAGCC
TTATTGATTTGAATGTTACAATGCATGGTTTTTACGTTTCGGATTTGCATGAAGAATACGAGTTA
GGGTTTAGGCTTTAATTTTAAAATTTACGGGTTATAGGGATTAATAGCTTTGGGTTTTAGGGTTT
AATTAATAACCTATCTAAAACAAAAGAAAAAAAAAAATTATTTGTATTTTTTACTTATTATAATA
TATATATGTTATATATATATTATGAAACATATTAATATTGTGTTAGTTACGTACATTCGTTTGTT
TGATATTTTAAAATAGAGCATATATTGGGTACG
Found at i:28766305 original size:9 final size:9
Alignment explanation
Indices: 28766291--28766344 Score: 55
Period size: 9 Copynumber: 6.6 Consensus size: 9
28766281 ATAAATGATG
28766291 CATAACTTA
1 CATAACTTA
28766300 CATAACTTA
1 CATAACTTA
*
28766309 -TTAA--TA
1 CATAACTTA
28766315 CATAACTTA
1 CATAACTTA
*
28766324 TATAA--TA
1 CATAACTTA
28766331 CATAACTTA
1 CATAACTTA
28766340 CATAA
1 CATAA
28766345 TACGACATAA
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
6 2 0.06
7 9 0.25
8 3 0.08
9 22 0.61
ACGTcount: A:0.48, C:0.17, G:0.00, T:0.35
Consensus pattern (9 bp):
CATAACTTA
Found at i:28766331 original size:16 final size:16
Alignment explanation
Indices: 28766298--28766440 Score: 101
Period size: 16 Copynumber: 8.2 Consensus size: 16
28766288 ATGCATAACT
28766298 TACATAACTTAT-TAA
1 TACATAACTTATATAA
28766313 TACATAACTTATATAA
1 TACATAACTTATATAA
*
28766329 TACATAACTTACATAA
1 TACATAACTTATATAA
28766345 TACGACATAACTTATTAATATA
1 T---ACATAACTTA-T-ATA-A
* * *
28766367 TTTATGGATAAATGATGCATAA
1 --TA--CATAACTTAT--ATAA
28766389 CTTACATAACTTAT-TAA
1 --TACATAACTTATATAA
28766406 TACATAACTTATATAA
1 TACATAACTTATATAA
*
28766422 TACATAACTTACATAA
1 TACATAACTTATATAA
28766438 TAC
1 TAC
28766441 GACATAACTT
Statistics
Matches: 104, Mismatches: 11, Indels: 25
0.74 0.08 0.18
Matches are distributed among these distances:
15 24 0.23
16 40 0.38
17 3 0.03
19 10 0.10
20 7 0.07
21 4 0.04
22 6 0.06
23 9 0.09
24 1 0.01
ACGTcount: A:0.46, C:0.14, G:0.03, T:0.36
Consensus pattern (16 bp):
TACATAACTTATATAA
Found at i:28766336 original size:31 final size:31
Alignment explanation
Indices: 28766298--28766432 Score: 102
Period size: 31 Copynumber: 4.4 Consensus size: 31
28766288 ATGCATAACT
28766298 TACATAACTTATTAATACATAACTTATATAA
1 TACATAACTTATTAATACATAACTTATATAA
*
28766329 TACATAACTTACATAATACGACATAACTTAT-TAA
1 TACATAACTTA-TTAAT---ACATAACTTATATAA
* ** * * * *
28766363 T--AT-ATTTATGGATAAATGA-TGCATA-ACT
1 TACATAACTTATTAATACATAACT-TATATA-A
28766391 TACATAACTTATTAATACATAACTTATATAA
1 TACATAACTTATTAATACATAACTTATATAA
28766422 TACATAACTTA
1 TACATAACTTA
28766433 CATAATACGA
Statistics
Matches: 76, Mismatches: 16, Indels: 24
0.66 0.14 0.21
Matches are distributed among these distances:
26 1 0.01
27 7 0.09
28 1 0.01
30 4 0.05
31 40 0.53
32 8 0.11
34 4 0.05
35 11 0.14
ACGTcount: A:0.46, C:0.13, G:0.04, T:0.37
Consensus pattern (31 bp):
TACATAACTTATTAATACATAACTTATATAA
Found at i:28766396 original size:43 final size:43
Alignment explanation
Indices: 28766349--28766500 Score: 164
Period size: 43 Copynumber: 3.4 Consensus size: 43
28766339 ACATAATACG
28766349 ACATAACTTATTAATATATTTATGGATAAATGATGCATAACTT
1 ACATAACTTATTAATATATTTATGGATAAATGATGCATAACTT
* * * * *
28766392 ACATAACTTATTAATACATAACTTATAT-AATACATAACTTACATAA-TACG
1 ACATAACTTATTAAT--AT-A-TT-TATGGATAAATGA--TGCATAACT--T
28766442 ACATAACTTATTAATATATTTATGGATAAATGATGCATAACTT
1 ACATAACTTATTAATATATTTATGGATAAATGATGCATAACTT
28766485 ACATAACTTATTAATA
1 ACATAACTTATTAATA
28766501 CATAACATTT
Statistics
Matches: 88, Mismatches: 10, Indels: 22
0.73 0.08 0.18
Matches are distributed among these distances:
43 31 0.35
44 6 0.07
45 6 0.07
46 9 0.10
47 9 0.10
48 6 0.07
49 6 0.07
50 15 0.17
ACGTcount: A:0.45, C:0.12, G:0.06, T:0.38
Consensus pattern (43 bp):
ACATAACTTATTAATATATTTATGGATAAATGATGCATAACTT
Found at i:28766398 original size:9 final size:9
Alignment explanation
Indices: 28766384--28766437 Score: 55
Period size: 9 Copynumber: 6.6 Consensus size: 9
28766374 ATAAATGATG
28766384 CATAACTTA
1 CATAACTTA
28766393 CATAACTTA
1 CATAACTTA
*
28766402 -TTAA--TA
1 CATAACTTA
28766408 CATAACTTA
1 CATAACTTA
*
28766417 TATAA--TA
1 CATAACTTA
28766424 CATAACTTA
1 CATAACTTA
28766433 CATAA
1 CATAA
28766438 TACGACATAA
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
6 2 0.06
7 9 0.25
8 3 0.08
9 22 0.61
ACGTcount: A:0.48, C:0.17, G:0.00, T:0.35
Consensus pattern (9 bp):
CATAACTTA
Found at i:28766415 original size:93 final size:93
Alignment explanation
Indices: 28766256--28766540 Score: 545
Period size: 93 Copynumber: 3.1 Consensus size: 93
28766246 TACATACATT
28766256 ACATAACTTATTAATATATTTATGGATAAATGATGCATAACTTACATAACTTATTAATACATAAC
1 ACATAACTTATTAATATATTTATGGATAAATGATGCATAACTTACATAACTTATTAATACATAAC
28766321 TTATATAATACATAACTTACATAATACG
66 TTATATAATACATAACTTACATAATACG
28766349 ACATAACTTATTAATATATTTATGGATAAATGATGCATAACTTACATAACTTATTAATACATAAC
1 ACATAACTTATTAATATATTTATGGATAAATGATGCATAACTTACATAACTTATTAATACATAAC
28766414 TTATATAATACATAACTTACATAATACG
66 TTATATAATACATAACTTACATAATACG
28766442 ACATAACTTATTAATATATTTATGGATAAATGATGCATAACTTACATAACTTATTAATACATAAC
1 ACATAACTTATTAATATATTTATGGATAAATGATGCATAACTTACATAACTTATTAATACATAAC
*
28766507 ATT-TTTAATACATAACTTACATAATACG
66 -TTATATAATACATAACTTACATAATACG
28766535 ACATAA
1 ACATAA
28766541 TAACATAAAT
Statistics
Matches: 190, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
93 188 0.99
94 2 0.01
ACGTcount: A:0.45, C:0.13, G:0.05, T:0.36
Consensus pattern (93 bp):
ACATAACTTATTAATATATTTATGGATAAATGATGCATAACTTACATAACTTATTAATACATAAC
TTATATAATACATAACTTACATAATACG
Found at i:28766533 original size:16 final size:15
Alignment explanation
Indices: 28766298--28766525 Score: 98
Period size: 16 Copynumber: 14.7 Consensus size: 15
28766288 ATGCATAACT
28766298 TACATAACTTATTAA
1 TACATAACTTATTAA
28766313 TACATAACTTATATAA
1 TACATAACTTAT-TAA
*
28766329 TACATAACTTACATAA
1 TACATAACTTA-TTAA
28766345 TACGACATAACTTATTAA
1 T---ACATAACTTATTAA
* **
28766363 T--AT-ATTTATGGA
1 TACATAACTTATTAA
* * *
28766375 TAAATGA-TGCA-TAA
1 TACATAACT-TATTAA
28766389 CTTACATAACTTATTAA
1 --TACATAACTTATTAA
28766406 TACATAACTTATATAA
1 TACATAACTTAT-TAA
*
28766422 TACATAACTTACATAA
1 TACATAACTTA-TTAA
28766438 TACGACATAACTTATTAA
1 T---ACATAACTTATTAA
* **
28766456 T--AT-ATTTATGGA
1 TACATAACTTATTAA
* * *
28766468 TAAATGA-TGCA-TAA
1 TACATAACT-TATTAA
28766482 CTTACATAACTTATTAA
1 --TACATAACTTATTAA
*
28766499 TACATAACATTTTTAA
1 TACATAAC-TTATTAA
28766515 TACATAACTTA
1 TACATAACTTA
28766526 CATAATACGA
Statistics
Matches: 162, Mismatches: 24, Indels: 54
0.68 0.10 0.22
Matches are distributed among these distances:
12 14 0.09
13 4 0.02
14 8 0.05
15 38 0.23
16 62 0.38
17 8 0.05
18 8 0.05
19 20 0.12
ACGTcount: A:0.45, C:0.13, G:0.04, T:0.37
Consensus pattern (15 bp):
TACATAACTTATTAA
Found at i:28771979 original size:21 final size:21
Alignment explanation
Indices: 28771953--28772003 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
28771943 CTACAACTTA
* *
28771953 AAGCAGATGCGGCAGCGAGAG
1 AAGCAGAGGCAGCAGCGAGAG
28771974 AAGCAGAGGCAGCAGCGAGAG
1 AAGCAGAGGCAGCAGCGAGAG
*
28771995 AAGCTGAGG
1 AAGCAGAGG
28772004 TTCAACGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.35, C:0.18, G:0.43, T:0.04
Consensus pattern (21 bp):
AAGCAGAGGCAGCAGCGAGAG
Found at i:28771998 original size:87 final size:87
Alignment explanation
Indices: 28771887--28772084 Score: 283
Period size: 87 Copynumber: 2.3 Consensus size: 87
28771877 ACACAACTTA
* * *
28771887 AAGCGGAGGCAACATCGAGAGAAGCTGAGGTTCAA-AAAAGATATGAAGAACTCCAGCTA-CAAC
1 AAGCAGAGGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAG-TATGAAGAACTCCAGC-AGCAAC
*
28771950 TTAAAGCAGATGCGGCAGCGAGAG
64 TTAAAGCAAATGCGGCAGCGAGAG
* *
28771974 AAGCAGAGGCAGCAGCGAGAGAAGCTGAGGTTCAACGAAAGTATGAAGAACTCCAGCAGCAGCTT
1 AAGCAGAGGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAGTATGAAGAACTCCAGCAGCAACTT
*
28772039 AAAGCAAATGCTGCAGCGAGAG
66 AAAGCAAATGCGGCAGCGAGAG
* *
28772061 AAGCAGAGGCTGCAGCGAGGGAAG
1 AAGCAGAGGCAGCAGCGAGAGAAG
28772085 TAGAGGCTGT
Statistics
Matches: 100, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
86 1 0.01
87 95 0.95
88 4 0.04
ACGTcount: A:0.38, C:0.19, G:0.32, T:0.11
Consensus pattern (87 bp):
AAGCAGAGGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAGTATGAAGAACTCCAGCAGCAACTT
AAAGCAAATGCGGCAGCGAGAG
Found at i:28772065 original size:21 final size:21
Alignment explanation
Indices: 28772040--28772109 Score: 86
Period size: 21 Copynumber: 3.3 Consensus size: 21
28772030 CAGCAGCTTA
* *
28772040 AAGCAAATGCTGCAGCGAGAG
1 AAGCAAAGGCTGCAGCGAGGG
*
28772061 AAGCAGAGGCTGCAGCGAGGG
1 AAGCAAAGGCTGCAGCGAGGG
* * *
28772082 AAGTAGAGGCTGTAGCGAGGG
1 AAGCAAAGGCTGCAGCGAGGG
28772103 AAGCAAA
1 AAGCAAA
28772110 ACAGCTTAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.36, C:0.16, G:0.40, T:0.09
Consensus pattern (21 bp):
AAGCAAAGGCTGCAGCGAGGG
Found at i:28772472 original size:43 final size:43
Alignment explanation
Indices: 28772411--28772760 Score: 495
Period size: 43 Copynumber: 8.1 Consensus size: 43
28772401 CAAAATTAGC
* *
28772411 GGCGTTTTTTGGATAAGCGCCGCTAAAGACCATGGTTTATAGT
1 GGCGTTTTTTGGCTAAGCGCCGCTAAAGACCATGGTCTATAGT
*
28772454 GGCGTTTTTCGGCTAAGCGCCGCTAAAGACCATGGTCTATAGT
1 GGCGTTTTTTGGCTAAGCGCCGCTAAAGACCATGGTCTATAGT
*** *
28772497 GGCGTTTTTCAACTAGGCGCCGCTAAAGACCATGGTCTATAGT
1 GGCGTTTTTTGGCTAAGCGCCGCTAAAGACCATGGTCTATAGT
*
28772540 GGCGTTTTTTGGCTAGGCGCCGCTAAAGACCATGGTCTATAGT
1 GGCGTTTTTTGGCTAAGCGCCGCTAAAGACCATGGTCTATAGT
* * *
28772583 GGCGTTTTTTGGCTAAGTGCTGTTAAAGACCATGGTCTATAGT
1 GGCGTTTTTTGGCTAAGCGCCGCTAAAGACCATGGTCTATAGT
* * *
28772626 GGCGTTTGTTGGCTAAGCGCTGCTAAAGACCATGGTCTATAGC
1 GGCGTTTTTTGGCTAAGCGCCGCTAAAGACCATGGTCTATAGT
** * * *
28772669 GATGTTTGTTGGGTAAGCGCCGCTAAAGACCATGGTCTATAGC
1 GGCGTTTTTTGGCTAAGCGCCGCTAAAGACCATGGTCTATAGT
* *
28772712 GGCGTTTTTTGTG-TAAGCGCCGCTAAAGACCATGGTCTACAGC
1 GGCGTTTTTTG-GCTAAGCGCCGCTAAAGACCATGGTCTATAGT
28772755 GGCGTT
1 GGCGTT
28772761 GTAAAGAAAA
Statistics
Matches: 281, Mismatches: 25, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
43 280 1.00
44 1 0.00
ACGTcount: A:0.21, C:0.20, G:0.29, T:0.30
Consensus pattern (43 bp):
GGCGTTTTTTGGCTAAGCGCCGCTAAAGACCATGGTCTATAGT
Found at i:28772816 original size:129 final size:127
Alignment explanation
Indices: 28772407--28772825 Score: 457
Period size: 129 Copynumber: 3.2 Consensus size: 127
28772397 CTGCCAAAAT
* *
28772407 TAGCGGCGTTTTTTGGATAAGCGCCGCTAAAGACCATGGTTTATAGTGGCGTTTTTCGGCTAAGC
1 TAGCGGCGTTTTTT-GATAAGCGCCGCTAAAGACCATGGTCTATAGTGGCGTTTTTTGGCTAAGC
* * * *
28772472 GCCGCTAAAGACCATGGTCTATAGTGGCGTTTTTCAACTAGGCGCCGCTAAAGACCATGGTCTA
65 GCCGCTAAAGACCATGGTCTATAGTGGCGTTTGT-AAGTAAGCGCAGCTAAAGACCATGGTCTA
* * * *
28772536 TAGTGGCGTTTTTTGGCTAGGCGCCGCTAAAGACCATGGTCTATAGTGGCGTTTTTTGGCTAAGT
1 TAGCGGCGTTTTTT-GATAAGCGCCGCTAAAGACCATGGTCTATAGTGGCGTTTTTTGGCTAAGC
* * ** *
28772601 GCTGTTAAAGACCATGGTCTATAGTGGCGTTTGTTGGCTAAGCGCTGCTAAAGACCATGGTCTA
65 GCCGCTAAAGACCATGGTCTATAGTGGCGTTTGTAAG-TAAGCGCAGCTAAAGACCATGGTCTA
** * * *
28772665 TAGCGATGTTTGTTGGGTAAGCGCCGCTAAAGACCATGGTCTATAGCGGCGTTTTTTGTG-TAAG
1 TAGCGGCGTTT-TTTGATAAGCGCCGCTAAAGACCATGGTCTATAGTGGCGTTTTTTG-GCTAAG
* * * * * **
28772729 CGCCGCTAAAGACCATGGTCTACAGCGGCG-TTGTAAAGAAAACGCAGCTAAAGGTCC-TAATCT
64 CGCCGCTAAAGACCATGGTCTATAGTGGCGTTTGT-AAGTAAGCGCAGCTAAA-GACCATGGTCT
*
28772792 T
127 A
* *
28772793 TAGCGGCGTTTATTATAAAAAGCGCCGCTAAAG
1 TAGCGGCGTTT-TT-TGATAAGCGCCGCTAAAG
28772826 TTACCGACAC
Statistics
Matches: 242, Mismatches: 42, Indels: 12
0.82 0.14 0.04
Matches are distributed among these distances:
128 30 0.12
129 209 0.86
130 3 0.01
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.29
Consensus pattern (127 bp):
TAGCGGCGTTTTTTGATAAGCGCCGCTAAAGACCATGGTCTATAGTGGCGTTTTTTGGCTAAGCG
CCGCTAAAGACCATGGTCTATAGTGGCGTTTGTAAGTAAGCGCAGCTAAAGACCATGGTCTA
Found at i:28776168 original size:19 final size:20
Alignment explanation
Indices: 28776146--28776183 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
28776136 AATTAACTTT
28776146 TTTAATT-ATTTTTAAAGAG
1 TTTAATTGATTTTTAAAGAG
*
28776165 TTTACTTGATTTTTAAAGA
1 TTTAATTGATTTTTAAAGA
28776184 TTATATAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.34, C:0.03, G:0.11, T:0.53
Consensus pattern (20 bp):
TTTAATTGATTTTTAAAGAG
Found at i:28777752 original size:87 final size:87
Alignment explanation
Indices: 28777564--28777936 Score: 541
Period size: 87 Copynumber: 4.3 Consensus size: 87
28777554 AGATCAGTGA
* * *
28777564 AAATCGAAAACAAAGCCTTGCCTCCATAGGTTACAGTGGAGCTGGTTAAAGA-AGCAGATATTGC
1 AAATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
*
28777628 CTTCCTGCGTTAACAACGAAGC
66 CTTCCTGCGTTAACAGCGAAGC
* *
28777650 AGATCGAAAACAAAGCGTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
1 AAATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
28777715 CTTCCTGCGTTAACAGCGAAGC
66 CTTCCTGCGTTAACAGCGAAGC
* * * * * *
28777737 AAATCGAAAATAAAGCCTTGCCTCCATCAGTTGTACTGGAGTTGGTTAAAGATAGCAAATCTTGC
1 AAATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
28777802 CTTCCTGCGTTAACAGCGAAGC
66 CTTCCTGCGTTAACAGCGAAGC
* * *
28777824 AGATCGAAAATAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGTAGATCTTGC
1 AAATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
* * * *
28777889 CTTCCTGCATTGACAGTGAAGT
66 CTTCCTGCGTTAACAGCGAAGC
* *
28777911 AGATCGAAGACACAAGCCTTGCCTCC
1 AAATCGAAAACA-AAGCCTTGCCTCC
28777937 CTAAGCGGTA
Statistics
Matches: 258, Mismatches: 27, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
86 48 0.19
87 197 0.76
88 13 0.05
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.24
Consensus pattern (87 bp):
AAATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
CTTCCTGCGTTAACAGCGAAGC
Found at i:28777846 original size:43 final size:43
Alignment explanation
Indices: 28777624--28777846 Score: 104
Period size: 43 Copynumber: 5.1 Consensus size: 43
28777614 GAAGCAGATA
* * *
28777624 TTGCCTTCCTGCGTTAACAACGAAGCAGATCGAAAACAAAGCG
1 TTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAATAAAGCC
* * * * * * * *
28777667 TTGCC-TCCAT-CGGTT-GCAGTGGAGCTGGT-TAAAGATAGCAGATC
1 TTGCCTTCC-TGC-GTTAACAGCGAAGCAGATCGAAA-ATA-AAG-CC
*
28777711 TTGCCTTCCTGCGTTAACAGCGAAGCAAATCGAAAATAAAGCC
1 TTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAATAAAGCC
* * ** * * **
28777754 TTGCC-TCCAT-CAGTTGTACTG-G-AGTTGGT-TAAAGATAGCAAATC
1 TTGCCTTCC-TGC-GTT-AACAGCGAAGCAGATCGAAA-ATA--AAGCC
28777798 TTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAATAAAGCC
1 TTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAATAAAGCC
28777841 TTGCCT
1 TTGCCT
28777847 CCATCGGTTG
Statistics
Matches: 123, Mismatches: 37, Indels: 40
0.62 0.19 0.20
Matches are distributed among these distances:
41 6 0.05
42 24 0.20
43 34 0.28
44 27 0.22
45 26 0.21
46 6 0.05
ACGTcount: A:0.30, C:0.23, G:0.22, T:0.25
Consensus pattern (43 bp):
TTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAATAAAGCC
Found at i:28778262 original size:98 final size:99
Alignment explanation
Indices: 28778145--28778482 Score: 448
Period size: 99 Copynumber: 3.4 Consensus size: 99
28778135 CTAAAACCAC
*
28778145 GAATCTTGCCTCTCTGACATTGCGGTTAAAAAGATTAAAGCTACTA-CAGCGAATCTTATCTCCC
1 GAATCTTGCCTCCCTGACATTGCGGTTAAAAAGATTAAAGCTAC-AGCAGCGAATCTTATCTCCC
* *
28778209 AGGCAGTGCAGT-AATAGATTAAAGCCACAACGGT
65 AGGCGGTGCAGTGAAAAGATTAAAGCCACAACGGT
* * *
28778243 GAATCTTGCCTCTCTGACATCGCGGTTAAAAAGATTAAAGCTACAGCAGCGAATTTTATCTCCCA
1 GAATCTTGCCTCCCTGACATTGCGGTTAAAAAGATTAAAGCTACAGCAGCGAATCTTATCTCCCA
* *
28778308 GGCGGTGCAGTAAAAAGATTAAAGCCACGACGGT
66 GGCGGTGCAGTGAAAAGATTAAAGCCACAACGGT
* * *
28778342 GAATCTTGCCTCCCTGACATTGCGATTAAAAAAATTAAAGCTACAGCAGCGAATCTTACCTCCCA
1 GAATCTTGCCTCCCTGACATTGCGGTTAAAAAGATTAAAGCTACAGCAGCGAATCTTATCTCCCA
* * * * *
28778407 GGTGGTGCAGTGGAACAGATTAAAGCCATATCGAT
66 GGCGGTGCAGT-GAAAAGATTAAAGCCACAACGGT
* * * *
28778442 GCATCTTGCTTCCCCT-ACATTGCAGTTGAAAAGATTAAAGC
1 GAATCTTGCCT-CCCTGACATTGCGGTTAAAAAGATTAAAGC
28778483 CACATCGGTG
Statistics
Matches: 212, Mismatches: 24, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
97 1 0.00
98 71 0.33
99 89 0.42
100 47 0.22
101 4 0.02
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.25
Consensus pattern (99 bp):
GAATCTTGCCTCCCTGACATTGCGGTTAAAAAGATTAAAGCTACAGCAGCGAATCTTATCTCCCA
GGCGGTGCAGTGAAAAGATTAAAGCCACAACGGT
Found at i:28778281 original size:50 final size:49
Alignment explanation
Indices: 28778144--28778405 Score: 197
Period size: 50 Copynumber: 5.3 Consensus size: 49
28778134 ACTAAAACCA
* * *
28778144 CGAATCTTGCCTCTCTGACATTGCGGTTAAAAAGATTAAAGCTACTACAG
1 CGAATCTTGCCTCCCTGACA-TGCGGTTAAAAAGATTAAAGCCACAACAG
** * * * * *
28778194 CGAATCTTATCTCCCAGGCAGTGCAG-T-AATAGATTAAAGCCACAACGG
1 CGAATCTTGCCTCCCTGACA-TGCGGTTAAAAAGATTAAAGCCACAACAG
* * * *
28778242 TGAATCTTGCCTCTCTGACATCGCGGTTAAAAAGATTAAAGCTACAGCAG
1 CGAATCTTGCCTCCCTGACAT-GCGGTTAAAAAGATTAAAGCCACAACAG
* ** * * * * * *
28778292 CGAATTTTATCTCCCAGGCGGTGCAG-TAAAAAGATTAAAGCCACGACGG
1 CGAATCTTGCCTCCCTGAC-ATGCGGTTAAAAAGATTAAAGCCACAACAG
* * * * *
28778341 TGAATCTTGCCTCCCTGACATTGCGATTAAAAAAATTAAAGCTACAGCAG
1 CGAATCTTGCCTCCCTGACA-TGCGGTTAAAAAGATTAAAGCCACAACAG
*
28778391 CGAATCTTACCTCCC
1 CGAATCTTGCCTCCC
28778406 AGGTGGTGCA
Statistics
Matches: 155, Mismatches: 51, Indels: 12
0.71 0.23 0.06
Matches are distributed among these distances:
47 1 0.01
48 34 0.22
49 37 0.24
50 82 0.53
51 1 0.01
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.24
Consensus pattern (49 bp):
CGAATCTTGCCTCCCTGACATGCGGTTAAAAAGATTAAAGCCACAACAG
Found at i:28778429 original size:50 final size:49
Alignment explanation
Indices: 28778171--28778432 Score: 190
Period size: 50 Copynumber: 5.3 Consensus size: 49
28778161 ACATTGCGGT
* *
28778171 TAAAAAGATTAAAGCTACTA-CAGCGAATCTTATCTCCCAGGCAGTGCAG
1 TAAAAAGATTAAAGCTAC-AGCAGCGAATCTTACCTCCCAGGCGGTGCAG
* * * * * * * * * * *
28778220 T-AATAGATTAAAGCCACAACGGTGAATCTTGCCTCTCTGAC-ATCGCGG
1 TAAAAAGATTAAAGCTACAGCAGCGAATCTTACCTCCCAGGCGGT-GCAG
* *
28778268 TTAAAAAGATTAAAGCTACAGCAGCGAATTTTATCTCCCAGGCGGTGCAG
1 -TAAAAAGATTAAAGCTACAGCAGCGAATCTTACCTCCCAGGCGGTGCAG
* * * * * * ** *
28778318 TAAAAAGATTAAAGCCAC-GACGGTGAATCTTGCCTCCCTGACATTGCGAT
1 TAAAAAGATTAAAGCTACAG-CAGCGAATCTTACCTCCCAGGCGGTGC-AG
* *
28778368 TAAAAAAATTAAAGCTACAGCAGCGAATCTTACCTCCCAGGTGGTGCAG
1 TAAAAAGATTAAAGCTACAGCAGCGAATCTTACCTCCCAGGCGGTGCAG
* *
28778417 TGGAACAGATTAAAGC
1 T-AAAAAGATTAAAGC
28778433 CATATCGATG
Statistics
Matches: 155, Mismatches: 49, Indels: 17
0.70 0.22 0.08
Matches are distributed among these distances:
47 2 0.01
48 33 0.21
49 39 0.25
50 79 0.51
51 2 0.01
ACGTcount: A:0.34, C:0.22, G:0.21, T:0.23
Consensus pattern (49 bp):
TAAAAAGATTAAAGCTACAGCAGCGAATCTTACCTCCCAGGCGGTGCAG
Found at i:28778502 original size:25 final size:25
Alignment explanation
Indices: 28778474--28778523 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
28778464 CAGTTGAAAA
* *
28778474 GATTAAAGCCACATCGGTGAATCTT
1 GATTAAAGCCACAACGGCGAATCTT
*
28778499 GATTAAAGCTACAACGGCGAATCTT
1 GATTAAAGCCACAACGGCGAATCTT
28778524 ACTTCCCAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26
Consensus pattern (25 bp):
GATTAAAGCCACAACGGCGAATCTT
Found at i:28778599 original size:125 final size:126
Alignment explanation
Indices: 28778375--28778612 Score: 334
Period size: 125 Copynumber: 1.9 Consensus size: 126
28778365 GATTAAAAAA
* * * * *
28778375 ATTAAAGCTACAGCAGCGAATCTTACCTCCCAGGTGGTGCAGTGGAACAGATTAAAGCCATATCG
1 ATTAAAGCTACAACAGCGAATCTTACCTCCCAAGCGATGCAGTGGAACAGATTAAAGCCAAATCG
* * *
28778440 ATGCATCTTGCTTCCCCTACATTGCAGTTGAAAAGATT-AAAGCCACATCGGTGAATCTTG
66 ATGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTAAAAGCCACATCGGTGAATCTTG
* * * *
28778500 ATTAAAGCTACAACGGCGAATCTTACTTCCCAAGCGATGCAGTGGAATAGATTAAAGCCAAATTG
1 ATTAAAGCTACAACAGCGAATCTTACCTCCCAAGCGATGCAGTGGAACAGATTAAAGCCAAATCG
* * *
28778565 GTGAATCTTGTTTCTCCGACATTGCAGTTAAAAAGATTAAAAGCCACA
66 ATGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTAAAAGCCACA
28778613 ATGGCGAATC
Statistics
Matches: 97, Mismatches: 15, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
125 88 0.91
126 9 0.09
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.26
Consensus pattern (126 bp):
ATTAAAGCTACAACAGCGAATCTTACCTCCCAAGCGATGCAGTGGAACAGATTAAAGCCAAATCG
ATGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTAAAAGCCACATCGGTGAATCTTG
Found at i:28778755 original size:41 final size:41
Alignment explanation
Indices: 28778693--28779079 Score: 171
Period size: 44 Copynumber: 8.9 Consensus size: 41
28778683 TAAATTAAAG
* * *
28778693 GGTCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCATCA
1 GGTCTTATCTCCCTGAGGTTACAGCAGAGTAGATCGAATCA
** *
28778734 GGTCTTATCTCCCTGAGGTTACAATAGAGTAGACCGAAGAATTTCA
1 GGTCTTATCTCCCTGAGGTTACAGCAGAGTAGATC---GAA--TCA
* * ** * * *
28778780 GATCTTATCTTCCTGAGGTTACAGTGGAGCAGATTGAAGCCA
1 GGTCTTATCTCCCTGAGGTTACAGCAGAGTAGATCGAA-TCA
* * * *
28778822 GAGATCTTATCTCCCTGAGATTACAGCGGAGTAGATTGAAGCTA
1 G-G-TCTTATCTCCCTGAGGTTACAGCAGAGTAGATCGAATC-A
* * * * ** * ** *
28778866 GTAATCCTATCTCTCTGAAGTTACAGTGGAGTGGATTAAAATAAA
1 G--GTCTTATCTCCCTGAGGTTACAGCAGAGTAGA-TCGAAT-CA
* * * * *
28778911 TGTCTTATCTCTCTGAAGTTACAGCAGAGTAAATCGTATCA
1 GGTCTTATCTCCCTGAGGTTACAGCAGAGTAGATCGAATCA
* ** * *
28778952 GGTCTTATCTCCCTGAGGTTACGGTGGAGTAGACCGAAGAATGTAA
1 GGTCTTATCTCCCTGAGGTTACAGCAGAGTAGATC---GAA--TCA
* ** * * *
28778998 GATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCA
1 GGTCTTATCTCCCTGAGGTTACAGCAGAGTAGATCGAA-TCA
* * *
28779040 GAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAA
1 G-G-TCTTATCTCCCTGAGGTTACAGCAGAGTAGATCGAA
28779080 GACACTATCC
Statistics
Matches: 264, Mismatches: 64, Indels: 33
0.73 0.18 0.09
Matches are distributed among these distances:
41 58 0.22
42 9 0.03
43 33 0.12
44 96 0.36
45 5 0.02
46 63 0.24
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (41 bp):
GGTCTTATCTCCCTGAGGTTACAGCAGAGTAGATCGAATCA
Found at i:28778839 original size:44 final size:44
Alignment explanation
Indices: 28778779--28779119 Score: 239
Period size: 44 Copynumber: 7.8 Consensus size: 44
28778769 GAAGAATTTC
*
28778779 AGATCTTATCTTCCTGAGGTTACAGTGGAGCAGATTGAAGCCAG
1 AGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAG
* * * *
28778823 AGATCTTATCTCCCTGAGATTACAGCGGAGTAGATTGAAGCTAG
1 AGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAG
* * * ** *** *
28778867 TA-ATCCTATCTCTCTGAAGTTACAGTGGAGTGGATT-AAAATAA
1 -AGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAG
* * ** * * * * *
28778910 ATG-TCTTATCTCTCTGAAGTTACAGCAGAGTAAATCGTA-TCAG
1 A-GATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAG
* * ** *
28778953 -G-TCTTATCTCCCTGAGGTTACGGTGGAGTAGACCGAAG-AATG
1 AGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCA-G
28778995 TAAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAG
1 --AGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAG
* * * *
28779041 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACA-
1 AGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAG
** * * * *
28779084 CTATCCTATCTCCCTGAAGTTATAGTGGAGCGGATT
1 AGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATT
28779120 AAAACTGATT
Statistics
Matches: 235, Mismatches: 51, Indels: 23
0.76 0.17 0.07
Matches are distributed among these distances:
41 30 0.13
42 2 0.01
43 59 0.25
44 107 0.46
45 2 0.01
46 34 0.14
47 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (44 bp):
AGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAG
Found at i:28779025 original size:46 final size:45
Alignment explanation
Indices: 28778736--28779081 Score: 232
Period size: 44 Copynumber: 7.8 Consensus size: 45
28778726 TCGCATCAGG
* * * *
28778736 TCTTATCTCCCTGAGGTTACAATAGAGTAGACCGAAGAATTTCAGA
1 TCTTATCTCCCTGAGGTTACAGTGGAGTAGATCGAAGAATGT-AGA
* * * *
28778782 TCTTATCTTCCTGAGGTTACAGTGGAGCAGATTGAAGCCA-G-AGA
1 TCTTATCTCCCTGAGGTTACAGTGGAGTAGATCGAAG-AATGTAGA
* * * *
28778826 TCTTATCTCCCTGAGATTACAGCGGAGTAGATTGAAG-CTAGTA-A
1 TCTTATCTCCCTGAGGTTACAGTGGAGTAGATCGAAGAAT-GTAGA
* * * * * **
28778870 TCCTATCTCTCTGAAGTTACAGTGGAGTGGAT-TAA-AATAAATG-
1 TCTTATCTCCCTGAGGTTACAGTGGAGTAGATCGAAGAATGTA-GA
* * ** * * * *
28778913 TCTTATCTCTCTGAAGTTACAGCAGAGTAAATC---GTAT-CAGG
1 TCTTATCTCCCTGAGGTTACAGTGGAGTAGATCGAAGAATGTAGA
* *
28778954 TCTTATCTCCCTGAGGTTACGGTGGAGTAGACCGAAGAATGTAAGA
1 TCTTATCTCCCTGAGGTTACAGTGGAGTAGATCGAAGAATGT-AGA
* * *
28779000 TCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCA-G-AGA
1 TCTTATCTCCCTGAGGTTACAGTGGAGTAGATCGAAG-AATGTAGA
* * *
28779044 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGA
1 TCTTATCTCCCTGAGGTTACAGTGGAGTAGATCGAAGA
28779082 CACTATCCTA
Statistics
Matches: 235, Mismatches: 49, Indels: 35
0.74 0.15 0.11
Matches are distributed among these distances:
40 1 0.00
41 27 0.11
42 3 0.01
43 30 0.13
44 104 0.44
45 1 0.00
46 67 0.29
47 2 0.01
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (45 bp):
TCTTATCTCCCTGAGGTTACAGTGGAGTAGATCGAAGAATGTAGA
Found at i:28779030 original size:218 final size:218
Alignment explanation
Indices: 28778651--28779123 Score: 761
Period size: 218 Copynumber: 2.2 Consensus size: 218
28778641 GAGTTACAAG
* *
28778651 TCCTATCTCCCTTAAGTTACAGTGGAGCGGATTAAATTAAAGGGTCTTATCTCTCTGAAGTTACA
1 TCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAAAGGGTCTTATCTCTCTGAAGTTACA
* * *
28778716 GCAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGGTTACAATAGAGTAGACCGAAGAATTTCAG
66 GCAGAGTAAATCGCATCAGGTCTTATCTCCCTGAGGTTACAATAGAGTAGACCGAAGAATGTAAG
*
28778781 ATCTTATCTTCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCCCTGAGATTAC
131 ATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCCCTGAGATTAC
* * *
28778846 AGCGGAGTAGATTGAAG-CTAGTAA
196 AGCGGAGCAGATCGAAGAC-ACT-A
* * *
28778870 TCCTATCTCTCTGAAGTTACAGTGGAGTGGATTAAAATAAA-TGTCTTATCTCTCTGAAGTTACA
1 TCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAAAGGGTCTTATCTCTCTGAAGTTACA
* ** *
28778934 GCAGAGTAAATCGTATCAGGTCTTATCTCCCTGAGGTTACGGTGGAGTAGACCGAAGAATGTAAG
66 GCAGAGTAAATCGCATCAGGTCTTATCTCCCTGAGGTTACAATAGAGTAGACCGAAGAATGTAAG
28778999 ATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCCCTGAGATTAC
131 ATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCCCTGAGATTAC
28779064 AGCGGAGCAGATCGAAGACACTA
196 AGCGGAGCAGATCGAAGACACTA
*
28779087 TCCTATCTCCCTGAAGTTATAGTGGAGCGGATTAAAA
1 TCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAA
28779124 CTGATTTTAT
Statistics
Matches: 234, Mismatches: 19, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
217 35 0.15
218 161 0.69
219 38 0.16
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.28
Consensus pattern (218 bp):
TCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAAAGGGTCTTATCTCTCTGAAGTTACA
GCAGAGTAAATCGCATCAGGTCTTATCTCCCTGAGGTTACAATAGAGTAGACCGAAGAATGTAAG
ATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCCCTGAGATTAC
AGCGGAGCAGATCGAAGACACTA
Found at i:28779174 original size:40 final size:42
Alignment explanation
Indices: 28779130--28779324 Score: 184
Period size: 44 Copynumber: 4.6 Consensus size: 42
28779120 AAAACTGATT
* *
28779130 TTATCTCCCTAAGCAGTAATGGAGCAAACCG-CACCA-AG-TC
1 TTATCTCCCTAAGCAGTAGTGGAGCAAA-CGAAACCACAGATC
*
28779170 TTATCTCCCTAAGCAGTAGCGGAGCAAACGAAACCACAGATC
1 TTATCTCCCTAAGCAGTAGTGGAGCAAACGAAACCACAGATC
* **
28779212 TTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGC-GAATC
1 TTATCTCCCTAAGCAGTAGTGGAGCA-AACGAA-ACCACAG-ATC
* * *** *
28779256 TTATCTTCCTAAGCAGTAGTGAAGCAGATTTAAGCCACCAG-TC
1 TTATCTCCCTAAGCAGTAGTGGAGCA-AACGAAACCA-CAGATC
*
28779299 CTATCTCCCTAAGCAGTAGTGGAGCA
1 TTATCTCCCTAAGCAGTAGTGGAGCA
28779325 GGTCGAGGAT
Statistics
Matches: 130, Mismatches: 17, Indels: 13
0.81 0.11 0.08
Matches are distributed among these distances:
39 2 0.02
40 30 0.23
41 2 0.02
42 27 0.21
43 32 0.25
44 36 0.28
45 1 0.01
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.22
Consensus pattern (42 bp):
TTATCTCCCTAAGCAGTAGTGGAGCAAACGAAACCACAGATC
Found at i:28779272 original size:44 final size:45
Alignment explanation
Indices: 28779168--28779589 Score: 339
Period size: 44 Copynumber: 9.8 Consensus size: 45
28779158 CCGCACCAAG
* * **
28779168 TCTTATCTCCCTAAGCAGTAGCGGAGCA-AACGAA-ACCAC-AGA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCTAGA
*
28779210 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGA-A
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCTAGA
* * ** ** *
28779254 TCTTATCTTCCTAAGCAGTAGTGAAGCAGATTTAAG-CCACCAG-
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCTAGA
* * * *
28779297 TCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCGAGGATGG-TAGA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCTAGA
* * * * *
28779341 TCATATCTCCCTAAGCAGTAGTGGAGTAGGTCGAGGATGG-TAGA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCTAGA
* * * *
28779385 TCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAGATGG-TAGA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCTAGA
* *
28779429 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAGGACGGC-GGA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCTAGA
* * * * *
28779473 TTTTACCTCCCTGAG-ATTACAGTGGAGC--ATTGAAG-C--C----
1 TCTTATCTCCCTAAGCAGT--AGTGGAGCAGATCGAAGACGGCTAGA
* * *
28779510 -CCTATCTCCCTAAGCAGTAGTGGAGCAGGTCGAAGATGG-TAGA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCTAGA
* *
28779553 TCCTATCTCACTAAGCAGTAGTGGAGCAGATCGAAGA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGA
28779590 TGGCGGATTT
Statistics
Matches: 310, Mismatches: 50, Indels: 38
0.78 0.13 0.10
Matches are distributed among these distances:
35 8 0.03
36 10 0.03
37 7 0.02
40 1 0.00
42 28 0.09
43 46 0.15
44 201 0.65
45 9 0.03
ACGTcount: A:0.29, C:0.22, G:0.27, T:0.23
Consensus pattern (45 bp):
TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCTAGA
Found at i:28779549 original size:124 final size:125
Alignment explanation
Indices: 28779386--28779635 Score: 439
Period size: 124 Copynumber: 2.0 Consensus size: 125
28779376 GATGGTAGAT
* *
28779386 CCTATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAGATGGTAGATCTTATCTCCCTAAGCAGTAGT
1 CCTATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAGATGGTAGATCCTATCTCACTAAGCAGTAGT
*
28779451 GGAGCAGATCGAGGACGGCGGATTTTACCTCCCTGAGATTACAGTGGAG-CATTGAAGCC
66 GGAGCAGATCGAAGACGGCGGATTTTACCTCCCTGAGATTACAGTGGAGACATTGAAGCC
*
28779510 CCTATCTCCCTAAGCAGTAGTGGAGCAGGTCGAAGATGGTAGATCCTATCTCACTAAGCAGTAGT
1 CCTATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAGATGGTAGATCCTATCTCACTAAGCAGTAGT
*
28779575 GGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGAGATTACAGTGGAGTACATTGAAGCC
66 GGAGCAGATCGAAGACGGCGGATTTTACCTCCCTGAGATTACAGTGGAG-ACATTGAAGCC
28779636 AGTTAAGACT
Statistics
Matches: 119, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
124 109 0.92
126 10 0.08
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.24
Consensus pattern (125 bp):
CCTATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAGATGGTAGATCCTATCTCACTAAGCAGTAGT
GGAGCAGATCGAAGACGGCGGATTTTACCTCCCTGAGATTACAGTGGAGACATTGAAGCC
Found at i:28781062 original size:3 final size:3
Alignment explanation
Indices: 28781054--28781118 Score: 121
Period size: 3 Copynumber: 21.3 Consensus size: 3
28781044 TAATGTGTGC
28781054 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
28781102 TAT TAT TAT TAT GTAT T
1 TAT TAT TAT TAT -TAT T
28781119 CTTGTTACAC
Statistics
Matches: 61, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
3 58 0.95
4 3 0.05
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:28781659 original size:3 final size:3
Alignment explanation
Indices: 28781651--28781715 Score: 121
Period size: 3 Copynumber: 21.3 Consensus size: 3
28781641 TAATGTGTGC
28781651 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
28781699 TAT TAT TAT TAT GTAT T
1 TAT TAT TAT TAT -TAT T
28781716 CTTGTTACAC
Statistics
Matches: 61, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
3 58 0.95
4 3 0.05
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:28782082 original size:597 final size:597
Alignment explanation
Indices: 28780949--28782141 Score: 2386
Period size: 597 Copynumber: 2.0 Consensus size: 597
28780939 TTTCGATTTA
28780949 ATCCCTTCCGTTTTATTTTATTTTATTTCTCCTTAATTATTAATTTTTGTTTGTTTATATTTTCA
1 ATCCCTTCCGTTTTATTTTATTTTATTTCTCCTTAATTATTAATTTTTGTTTGTTTATATTTTCA
28781014 TTTATCTTATATATATGTGCTACGTTATTTTAATGTGTGCTATTATTATTATTATTATTATTATT
66 TTTATCTTATATATATGTGCTACGTTATTTTAATGTGTGCTATTATTATTATTATTATTATTATT
28781079 ATTATTATTATTATTATTATTATTATTATTATTATGTATTCTTGTTACACCTTTTGGTTCCACGT
131 ATTATTATTATTATTATTATTATTATTATTATTATGTATTCTTGTTACACCTTTTGGTTCCACGT
28781144 TTACTATATATACACACATATATTTTTGTAATGTACTTAAATGCATGCACATGTTTTACAGTCCG
196 TTACTATATATACACACATATATTTTTGTAATGTACTTAAATGCATGCACATGTTTTACAGTCCG
28781209 TATATATACGTATATATATCCTTTATGTTTTATAATTTTAAGATTGACATGTACATACGTATGTT
261 TATATATACGTATATATATCCTTTATGTTTTATAATTTTAAGATTGACATGTACATACGTATGTT
28781274 TTATATATATGTTAAAATATATATGCATACATTTTTAAAATACATGTACGCACATAGATGCTTTT
326 TTATATATATGTTAAAATATATATGCATACATTTTTAAAATACATGTACGCACATAGATGCTTTT
28781339 TATTCTATATATATATACACACTTATATATTATTTATGCTTTATACTTTATACCTTATATGTACA
391 TATTCTATATATATATACACACTTATATATTATTTATGCTTTATACTTTATACCTTATATGTACA
28781404 TATATATACACATATACATACATATTTTTATTTATACATATACATATACATATATATCCCTTCAC
456 TATATATACACATATACATACATATTTTTATTTATACATATACATATACATATATATCCCTTCAC
28781469 ATTTTTAACCTTATTCATTTTCTTTATTGCTATTTACATGCTCGTTATTATTTTAAAAGAATGTT
521 ATTTTTAACCTTATTCATTTTCTTTATTGCTATTTACATGCTCGTTATTATTTTAAAAGAATGTT
28781534 TTGATTTTATTC
586 TTGATTTTATTC
28781546 ATCCCTTCCGTTTTATTTTATTTTATTTCTCCTTAATTATTAATTTTTGTTTGTTTATATTTTCA
1 ATCCCTTCCGTTTTATTTTATTTTATTTCTCCTTAATTATTAATTTTTGTTTGTTTATATTTTCA
28781611 TTTATCTTATATATATGTGCTACGTTATTTTAATGTGTGCTATTATTATTATTATTATTATTATT
66 TTTATCTTATATATATGTGCTACGTTATTTTAATGTGTGCTATTATTATTATTATTATTATTATT
28781676 ATTATTATTATTATTATTATTATTATTATTATTATGTATTCTTGTTACACCTTTTGGTTCCACGT
131 ATTATTATTATTATTATTATTATTATTATTATTATGTATTCTTGTTACACCTTTTGGTTCCACGT
28781741 TTACTATATATACACACATATATTTTTGTAATGTACTTAAATGCATGCACATGTTTTACAGTCCG
196 TTACTATATATACACACATATATTTTTGTAATGTACTTAAATGCATGCACATGTTTTACAGTCCG
28781806 TATATATACGTATATATATCCTTTATGTTTTATAATTTTAAGATTGACATGTACATACGTATGTT
261 TATATATACGTATATATATCCTTTATGTTTTATAATTTTAAGATTGACATGTACATACGTATGTT
28781871 TTATATATATGTTAAAATATATATGCATACATTTTTAAAATACATGTACGCACATAGATGCTTTT
326 TTATATATATGTTAAAATATATATGCATACATTTTTAAAATACATGTACGCACATAGATGCTTTT
28781936 TATTCTATATATATATACACACTTATATATTATTTATGCTTTATACTTTATACCTTATATGTACA
391 TATTCTATATATATATACACACTTATATATTATTTATGCTTTATACTTTATACCTTATATGTACA
28782001 TATATATACACATATACATACATATTTTTATTTATACATATACATATACATATATATCCCTTCAC
456 TATATATACACATATACATACATATTTTTATTTATACATATACATATACATATATATCCCTTCAC
28782066 ATTTTTAACCTTATTCATTTTCTTTATTGCTATTTACATGCTCGTTATTATTTTAAAAGAATGTT
521 ATTTTTAACCTTATTCATTTTCTTTATTGCTATTTACATGCTCGTTATTATTTTAAAAGAATGTT
28782131 TTGATTTTATT
586 TTGATTTTATT
28782142 TGTTTATTTA
Statistics
Matches: 596, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
597 596 1.00
ACGTcount: A:0.30, C:0.12, G:0.07, T:0.51
Consensus pattern (597 bp):
ATCCCTTCCGTTTTATTTTATTTTATTTCTCCTTAATTATTAATTTTTGTTTGTTTATATTTTCA
TTTATCTTATATATATGTGCTACGTTATTTTAATGTGTGCTATTATTATTATTATTATTATTATT
ATTATTATTATTATTATTATTATTATTATTATTATGTATTCTTGTTACACCTTTTGGTTCCACGT
TTACTATATATACACACATATATTTTTGTAATGTACTTAAATGCATGCACATGTTTTACAGTCCG
TATATATACGTATATATATCCTTTATGTTTTATAATTTTAAGATTGACATGTACATACGTATGTT
TTATATATATGTTAAAATATATATGCATACATTTTTAAAATACATGTACGCACATAGATGCTTTT
TATTCTATATATATATACACACTTATATATTATTTATGCTTTATACTTTATACCTTATATGTACA
TATATATACACATATACATACATATTTTTATTTATACATATACATATACATATATATCCCTTCAC
ATTTTTAACCTTATTCATTTTCTTTATTGCTATTTACATGCTCGTTATTATTTTAAAAGAATGTT
TTGATTTTATTC
Found at i:28782640 original size:109 final size:109
Alignment explanation
Indices: 28782369--28782724 Score: 554
Period size: 109 Copynumber: 3.3 Consensus size: 109
28782359 TTGAGAAAGT
* * *
28782369 CGTGCCCTAACT-TACTGGGTTTTCGATTTTTCTCGTTCAACCAAATGGCTTAATATCCTTTTAA
1 CGTGCCCTAA-TGTGCTGGG-TGTCGATTTTTCTCGTTCAACCAAATGGCTAAATATCCTTTTAA
28782433 AAATTTTAAAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAA
64 AAATTTTAAAATAAGGCAATGTTTTGCGTTT-GGAAATTCGAGAAAA
* * * *
28782480 CATGCCCTAAGGTGCTGGGTGTCAATTTTTCTCGTTCAACCAAATGACTAAATATCCTTTTAAAA
1 CGTGCCCTAATGTGCTGGGTGTCGATTTTTCTCGTTCAACCAAATGGCTAAATATCCTTTTAAAA
28782545 ATTTTAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAA
66 ATTTTAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAA
* *
28782589 CGTGCCCTAATGTGCTGGGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTGTAAAA
1 CGTGCCCTAATGTGCTGGGTGTCGATTTTTCTCGTTCAACCAAATGGCTAAATATCCTTTTAAAA
* * *
28782654 ATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAG-GAG
66 ATTTTAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAA
*
28782697 CGTGCCCTAATGTGCTGGGTTTCGATTT
1 CGTGCCCTAATGTGCTGGGTGTCGATTT
28782725 CTCGATTGAC
Statistics
Matches: 227, Mismatches: 17, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
108 28 0.12
109 113 0.50
110 71 0.31
111 15 0.07
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (109 bp):
CGTGCCCTAATGTGCTGGGTGTCGATTTTTCTCGTTCAACCAAATGGCTAAATATCCTTTTAAAA
ATTTTAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAA
Found at i:28783503 original size:40 final size:38
Alignment explanation
Indices: 28783419--28783507 Score: 103
Period size: 40 Copynumber: 2.3 Consensus size: 38
28783409 ATTTTTTGAA
28783419 ATTTTTCTA-GATTTTTATAACATTTAATAATATTTAT
1 ATTTTTCTATGATTTTTATAACATTTAATAATATTTAT
*
28783456 ATTTTTTCATATGATTTTTA-AATATCTT-ATAATATTTTAAT
1 A-TTTTTC-TATGATTTTTATAACAT-TTAATAATA-TTT-AT
28783497 ATTTTTCTATG
1 ATTTTTCTATG
28783508 TCAAATGCCA
Statistics
Matches: 45, Mismatches: 1, Indels: 10
0.80 0.02 0.18
Matches are distributed among these distances:
37 1 0.02
38 6 0.13
39 16 0.36
40 19 0.42
41 3 0.07
ACGTcount: A:0.33, C:0.06, G:0.03, T:0.58
Consensus pattern (38 bp):
ATTTTTCTATGATTTTTATAACATTTAATAATATTTAT
Found at i:28788266 original size:20 final size:20
Alignment explanation
Indices: 28788241--28788280 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
28788231 TTTGTGTAGG
28788241 GCTATAGTTCCTTTTCACAT
1 GCTATAGTTCCTTTTCACAT
28788261 GCTATAGTTCCTTTTCACAT
1 GCTATAGTTCCTTTTCACAT
28788281 TGATTAGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.25, G:0.10, T:0.45
Consensus pattern (20 bp):
GCTATAGTTCCTTTTCACAT
Found at i:28789021 original size:20 final size:20
Alignment explanation
Indices: 28788996--28789035 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
28788986 TTTGTGTAGG
28788996 GCTATAGTTCCTTTTCACAT
1 GCTATAGTTCCTTTTCACAT
28789016 GCTATAGTTCCTTTTCACAT
1 GCTATAGTTCCTTTTCACAT
28789036 TGATTAGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.25, G:0.10, T:0.45
Consensus pattern (20 bp):
GCTATAGTTCCTTTTCACAT
Found at i:28789345 original size:755 final size:755
Alignment explanation
Indices: 28787889--28789405 Score: 3025
Period size: 755 Copynumber: 2.0 Consensus size: 755
28787879 GTCAATTACG
28787889 AAAATAATTGTGTACTTAAGGTGGAAATGCAGATTTAATTTTTACAAAATTAATTTTGTAAAGGT
1 AAAAT-ATTGTGTACTTAAGGTGGAAATGCAGATTTAATTTTTACAAAATTAATTTTGTAAAGGT
28787954 TAAAGTGTAGACTACTAGTGAATATTGAAATTTGTCATTATACATTGTTTTCATTTATATTTATC
65 TAAAGTGTAGACTACTAGTGAATATTGAAATTTGTCATTATACATTGTTTTCATTTATATTTATC
28788019 ATTATATTTTAAAATTATGAGTAAATTTACCATTCAACTCTTATGTGATTGAACTTTACCATTAA
130 ATTATATTTTAAAATTATGAGTAAATTTACCATTCAACTCTTATGTGATTGAACTTTACCATTAA
28788084 ACTTTGAATTTTAATAAATTTTGCCACCAACTTTGTTTTTTAATTAAAATTTACCATTCAATATT
195 ACTTTGAATTTTAATAAATTTTGCCACCAACTTTGTTTTTTAATTAAAATTTACCATTCAATATT
28788149 AATTTTGATGATTTAAAATTGTTAAATTTGTGTGGCTCGAATCTTTGTTAAAGAAATAAAATACA
260 AATTTTGATGATTTAAAATTGTTAAATTTGTGTGGCTCGAATCTTTGTTAAAGAAATAAAATACA
28788214 ATGGCAAAACAAAGGGATTTGTGTAGGGCTATAGTTCCTTTTCACATGCTATAGTTCCTTTTCAC
325 ATGGCAAAACAAAGGGATTTGTGTAGGGCTATAGTTCCTTTTCACATGCTATAGTTCCTTTTCAC
28788279 ATTGATTAGAATAGAGTTTTTCAACAGTTAAATAGACGTAGTCAAAACTTCTTTTGTATGATTCA
390 ATTGATTAGAATAGAGTTTTTCAACAGTTAAATAGACGTAGTCAAAACTTCTTTTGTATGATTCA
28788344 GTTTTCAACATTAATGAATTTCTTCTCATTTGCTTGTGATTTTTCCTGAAAAAGTTTTTCATGTA
455 GTTTTCAACATTAATGAATTTCTTCTCATTTGCTTGTGATTTTTCCTGAAAAAGTTTTTCATGTA
28788409 AAATCTGTGTATTTTATTTTTCTTTTCTTTTTTGATTCGCAACCATGTCTATTGTCATTATCGAC
520 AAATCTGTGTATTTTATTTTTCTTTTCTTTTTTGATTCGCAACCATGTCTATTGTCATTATCGAC
28788474 GTTAATTTTAACAAAAACATATTTTGATAAAAAAAAATCCTTTCAAATATTGTATTTTAATAGGT
585 GTTAATTTTAACAAAAACATATTTTGATAAAAAAAAATCCTTTCAAATATTGTATTTTAATAGGT
28788539 AGCAATAATTTAACTTATAAATATTAAAAAATAATAAGCTCAATTGAAAATTCTAATTAATGAAA
650 AGCAATAATTTAACTTATAAATATTAAAAAATAATAAGCTCAATTGAAAATTCTAATTAATGAAA
28788604 TAAAAACAAGAAAAATGGAATACATATATTGCAAAAGAAAA
715 TAAAAACAAGAAAAATGGAATACATATATTGCAAAAGAAAA
28788645 AAAATATTGTGTACTTAAGGTGGAAATGCAGATTTAATTTTTACAAAATTAATTTTGTAAAGGTT
1 AAAATATTGTGTACTTAAGGTGGAAATGCAGATTTAATTTTTACAAAATTAATTTTGTAAAGGTT
28788710 AAAGTGTAGACTACTAGTGAATATTGAAATTTGTCATTATACATTGTTTTCATTTATATTTATCA
66 AAAGTGTAGACTACTAGTGAATATTGAAATTTGTCATTATACATTGTTTTCATTTATATTTATCA
28788775 TTATATTTTAAAATTATGAGTAAATTTACCATTCAACTCTTATGTGATTGAACTTTACCATTAAA
131 TTATATTTTAAAATTATGAGTAAATTTACCATTCAACTCTTATGTGATTGAACTTTACCATTAAA
28788840 CTTTGAATTTTAATAAATTTTGCCACCAACTTTGTTTTTTAATTAAAATTTACCATTCAATATTA
196 CTTTGAATTTTAATAAATTTTGCCACCAACTTTGTTTTTTAATTAAAATTTACCATTCAATATTA
28788905 ATTTTGATGATTTAAAATTGTTAAATTTGTGTGGCTCGAATCTTTGTTAAAGAAATAAAATACAA
261 ATTTTGATGATTTAAAATTGTTAAATTTGTGTGGCTCGAATCTTTGTTAAAGAAATAAAATACAA
28788970 TGGCAAAACAAAGGGATTTGTGTAGGGCTATAGTTCCTTTTCACATGCTATAGTTCCTTTTCACA
326 TGGCAAAACAAAGGGATTTGTGTAGGGCTATAGTTCCTTTTCACATGCTATAGTTCCTTTTCACA
28789035 TTGATTAGAATAGAGTTTTTCAACAGTTAAATAGACGTAGTCAAAACTTCTTTTGTATGATTCAG
391 TTGATTAGAATAGAGTTTTTCAACAGTTAAATAGACGTAGTCAAAACTTCTTTTGTATGATTCAG
28789100 TTTTCAACATTAATGAATTTCTTCTCATTTGCTTGTGATTTTTCCTGAAAAAGTTTTTCATGTAA
456 TTTTCAACATTAATGAATTTCTTCTCATTTGCTTGTGATTTTTCCTGAAAAAGTTTTTCATGTAA
28789165 AATCTGTGTATTTTATTTTTCTTTTCTTTTTTGATTCGCAACCATGTCTATTGTCATTATCGACG
521 AATCTGTGTATTTTATTTTTCTTTTCTTTTTTGATTCGCAACCATGTCTATTGTCATTATCGACG
28789230 TTAATTTTAACAAAAACATATTTTGATAAAAAAAAATCCTTTCAAATATTGTATTTTAATAGGTA
586 TTAATTTTAACAAAAACATATTTTGATAAAAAAAAATCCTTTCAAATATTGTATTTTAATAGGTA
28789295 GCAATAATTTAACTTATAAATATTAAAAAATAATAAGCTCAATTGAAAATTCTAATTAATGAAAT
651 GCAATAATTTAACTTATAAATATTAAAAAATAATAAGCTCAATTGAAAATTCTAATTAATGAAAT
28789360 AAAAACAAGAAAAATGGAATACATATATTGCAAAAGAAAA
716 AAAAACAAGAAAAATGGAATACATATATTGCAAAAGAAAA
28789400 AAAATA
1 AAAATA
28789406 AGTAATAACC
Statistics
Matches: 761, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
755 756 0.99
756 5 0.01
ACGTcount: A:0.37, C:0.11, G:0.12, T:0.41
Consensus pattern (755 bp):
AAAATATTGTGTACTTAAGGTGGAAATGCAGATTTAATTTTTACAAAATTAATTTTGTAAAGGTT
AAAGTGTAGACTACTAGTGAATATTGAAATTTGTCATTATACATTGTTTTCATTTATATTTATCA
TTATATTTTAAAATTATGAGTAAATTTACCATTCAACTCTTATGTGATTGAACTTTACCATTAAA
CTTTGAATTTTAATAAATTTTGCCACCAACTTTGTTTTTTAATTAAAATTTACCATTCAATATTA
ATTTTGATGATTTAAAATTGTTAAATTTGTGTGGCTCGAATCTTTGTTAAAGAAATAAAATACAA
TGGCAAAACAAAGGGATTTGTGTAGGGCTATAGTTCCTTTTCACATGCTATAGTTCCTTTTCACA
TTGATTAGAATAGAGTTTTTCAACAGTTAAATAGACGTAGTCAAAACTTCTTTTGTATGATTCAG
TTTTCAACATTAATGAATTTCTTCTCATTTGCTTGTGATTTTTCCTGAAAAAGTTTTTCATGTAA
AATCTGTGTATTTTATTTTTCTTTTCTTTTTTGATTCGCAACCATGTCTATTGTCATTATCGACG
TTAATTTTAACAAAAACATATTTTGATAAAAAAAAATCCTTTCAAATATTGTATTTTAATAGGTA
GCAATAATTTAACTTATAAATATTAAAAAATAATAAGCTCAATTGAAAATTCTAATTAATGAAAT
AAAAACAAGAAAAATGGAATACATATATTGCAAAAGAAAA
Found at i:28789537 original size:13 final size:13
Alignment explanation
Indices: 28789519--28789543 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28789509 TCTTTCAAAT
28789519 TAAAATTGAATAG
1 TAAAATTGAATAG
28789532 TAAAATTGAATA
1 TAAAATTGAATA
28789544 AAAACAATTT
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:0.56, C:0.00, G:0.12, T:0.32
Consensus pattern (13 bp):
TAAAATTGAATAG
Found at i:28800544 original size:20 final size:20
Alignment explanation
Indices: 28800519--28800558 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
28800509 TTTGTGTAGG
28800519 GCTATAGTTCCTTTTCACAT
1 GCTATAGTTCCTTTTCACAT
28800539 GCTATAGTTCCTTTTCACAT
1 GCTATAGTTCCTTTTCACAT
28800559 TGATTAGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.25, G:0.10, T:0.45
Consensus pattern (20 bp):
GCTATAGTTCCTTTTCACAT
Found at i:28801060 original size:13 final size:13
Alignment explanation
Indices: 28801042--28801066 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28801032 TCTTTCAAAT
28801042 TAAAATTGAATAG
1 TAAAATTGAATAG
28801055 TAAAATTGAATA
1 TAAAATTGAATA
28801067 AAAACAATTT
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:0.56, C:0.00, G:0.12, T:0.32
Consensus pattern (13 bp):
TAAAATTGAATAG
Found at i:28817097 original size:46 final size:46
Alignment explanation
Indices: 28817024--28817162 Score: 206
Period size: 46 Copynumber: 3.0 Consensus size: 46
28817014 ACAATACTAT
* * * *
28817024 AACTCTGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTTACTGAAATACCATACCTACGTTCCAC
* *
28817070 GATTCAGTATGGTTTTCTTTACTGAAATACCATACCTACGTTCCAC
1 AACTCAGTATGGTTTTCTTTACTGAAATACCATACCTACGTTCCAC
* *
28817116 AACTCAGTATGGTTTTCTTTATTGAAATACCATACCTACATTCCAC
1 AACTCAGTATGGTTTTCTTTACTGAAATACCATACCTACGTTCCAC
28817162 A
1 A
28817163 CTTTGTCATG
Statistics
Matches: 83, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 83 1.00
ACGTcount: A:0.28, C:0.24, G:0.10, T:0.37
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTTACTGAAATACCATACCTACGTTCCAC
Found at i:28819225 original size:21 final size:20
Alignment explanation
Indices: 28819167--28819231 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 20
28819157 TTTTATAATC
28819167 TATA-ATTTATTTCTATTTTAT
1 TATATATTTATTT-TATTTT-T
**
28819188 TATATATTT-TTGAATTTTT
1 TATATATTTATTTTATTTTT
*
28819207 TATATATTTAATTTTATTTTC
1 TATATATTT-ATTTTATTTTT
28819228 TATA
1 TATA
28819232 AGTTTTAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
19 10 0.28
20 5 0.14
21 17 0.47
22 4 0.11
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.66
Consensus pattern (20 bp):
TATATATTTATTTTATTTTT
Found at i:28824633 original size:40 final size:40
Alignment explanation
Indices: 28824584--28824665 Score: 110
Period size: 40 Copynumber: 2.0 Consensus size: 40
28824574 TAAAATATTT
* * *
28824584 TTGAAATATTTATTATATTCTACTAATTATAAATGAAAAG
1 TTGAAATATTTATAATATTATAATAATTATAAATGAAAAG
* * *
28824624 TTGAAATATTTATAATGTTATAATATTTATAAGTGAAAAG
1 TTGAAATATTTATAATATTATAATAATTATAAATGAAAAG
28824664 TT
1 TT
28824666 AAAAGCAATA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.44, C:0.02, G:0.10, T:0.44
Consensus pattern (40 bp):
TTGAAATATTTATAATATTATAATAATTATAAATGAAAAG
Found at i:28825952 original size:21 final size:20
Alignment explanation
Indices: 28825894--28825958 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 20
28825884 TTTTATAATC
*
28825894 TATA-ATTTATTTCGATTTTAT
1 TATATATTTA-TTCTATTTT-T
28825915 TATATATTT-TT-TAATTTTT
1 TATATATTTATTCT-ATTTTT
*
28825934 TATATATTTAATTCTATTTTC
1 TATATATTT-ATTCTATTTTT
28825955 TATA
1 TATA
28825959 AGTTTTAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
19 10 0.27
20 7 0.19
21 15 0.41
22 5 0.14
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.65
Consensus pattern (20 bp):
TATATATTTATTCTATTTTT
Found at i:28827555 original size:16 final size:18
Alignment explanation
Indices: 28827535--28827573 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
28827525 TTGATTAAAT
28827535 TATTTAAT-ATAAAAACA
1 TATTTAATAATAAAAACA
*
28827552 -ATTTAATAATAGAAACA
1 TATTTAATAATAAAAACA
28827569 TATTT
1 TATTT
28827574 TGAAAAGGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
16 7 0.37
17 8 0.42
18 4 0.21
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.38
Consensus pattern (18 bp):
TATTTAATAATAAAAACA
Found at i:28828224 original size:97 final size:90
Alignment explanation
Indices: 28827974--28828230 Score: 286
Period size: 88 Copynumber: 2.8 Consensus size: 90
28827964 AAACTTTTTC
* * * * *
28827974 AAAAAAAGCAATTAGGCCCCTACTTTTTTTTGCACTCAATTGTGAACTTGAACTTTCAAAATGCA
1 AAAAAAAGCAATTAAGCCCCTATTTTTTTTTGCACTCAATTGGGTACTTGAACTATCAAAATGCA
**
28828039 TAAAAAAATGCCCTCAAACTTAAAA
66 TAAAAAAAAACCCTCAAACTTAAAA
* * *
28828064 AAAAAAA--AATTAAACCCCTACTTTTTTTTT-CACTCAATTGGGTATTTGAACTACCAAAATGC
1 AAAAAAAGCAATTAAGCCCCTA-TTTTTTTTTGCACTCAATTGGGTACTTGAACTATCAAAATGC
28828126 ATAAAAAAAAACCCTCAAACTTTTTCAAAA
65 ATAAAAAAAAACCCTCAAAC---TT-AAAA
* * * *
28828156 AAAAAAAGCAATTAAGCCCTTATTTTTTCTTTTTGCACTCAATTGGGTACTTAAACTGTCAAACT
1 AAAAAAAGCAATTAAGCCCCTA--TTTT-TTTTTGCACTCAATTGGGTACTTGAACTATCAAAAT
*
28828221 GCATCAAAAA
63 GCATAAAAAA
28828231 GGTTAGGGGT
Statistics
Matches: 138, Mismatches: 19, Indels: 13
0.81 0.11 0.08
Matches are distributed among these distances:
88 56 0.41
89 8 0.06
90 7 0.05
91 2 0.01
92 11 0.08
94 11 0.08
95 4 0.03
96 5 0.04
97 34 0.25
ACGTcount: A:0.41, C:0.19, G:0.09, T:0.31
Consensus pattern (90 bp):
AAAAAAAGCAATTAAGCCCCTATTTTTTTTTGCACTCAATTGGGTACTTGAACTATCAAAATGCA
TAAAAAAAAACCCTCAAACTTAAAA
Found at i:28828713 original size:19 final size:19
Alignment explanation
Indices: 28828642--28828745 Score: 66
Period size: 20 Copynumber: 5.3 Consensus size: 19
28828632 TTCTTACGAC
28828642 TTTATAAAATTTTATAATT
1 TTTATAAAATTTTATAATT
* * *
28828661 TTTTTCTATATTTCTAT-ATAT
1 TTTAT-AAAATTT-TATAAT-T
* ** *
28828682 TTGATAATTTTTTATGATT
1 TTTATAAAATTTTATAATT
*
28828701 TTTATAAAATTTTACAATT
1 TTTATAAAATTTTATAATT
* **
28828720 CTTTATAAATTTTTACGATT
1 -TTTATAAAATTTTATAATT
28828740 TTTATA
1 TTTATA
28828746 TTTTTTTCTA
Statistics
Matches: 66, Mismatches: 14, Indels: 10
0.73 0.16 0.11
Matches are distributed among these distances:
19 28 0.42
20 31 0.47
21 7 0.11
ACGTcount: A:0.33, C:0.05, G:0.03, T:0.60
Consensus pattern (19 bp):
TTTATAAAATTTTATAATT
Found at i:28828724 original size:20 final size:19
Alignment explanation
Indices: 28828698--28828745 Score: 69
Period size: 20 Copynumber: 2.5 Consensus size: 19
28828688 ATTTTTTATG
28828698 ATTTTTATAAAATTTTACA
1 ATTTTTATAAAATTTTACA
* *
28828717 ATTCTTTATAAATTTTTACG
1 ATT-TTTATAAAATTTTACA
28828737 ATTTTTATA
1 ATTTTTATA
28828746 TTTTTTTCTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 9 0.35
20 17 0.65
ACGTcount: A:0.35, C:0.06, G:0.02, T:0.56
Consensus pattern (19 bp):
ATTTTTATAAAATTTTACA
Found at i:28828752 original size:19 final size:19
Alignment explanation
Indices: 28828583--28828751 Score: 82
Period size: 19 Copynumber: 8.8 Consensus size: 19
28828573 TGGTACGTTT
28828583 ATTTTTAT-ATTTTTCTACG
1 ATTTTTATAATTTTT-TACG
* *
28828602 AATTTAAT-ATTTTTTAC-
1 ATTTTTATAATTTTTTACG
28828619 ATTTTTCATAATTTTCTTACG
1 ATTTTT-ATAATTTT-TTACG
* * *
28828640 ACTTTATAAAATTTTATA--
1 A-TTTTTATAATTTTTTACG
* * * *
28828658 ATTTTTTTCTATATTTCTA-T
1 ATTTTTAT-AAT-TTTTTACG
* *
28828678 ATATTTGATAATTTTTTATG
1 AT-TTTTATAATTTTTTACG
** *
28828698 ATTTTTATAAAATTTTACA
1 ATTTTTATAATTTTTTACG
*
28828717 ATTCTTTATAAATTTTTACG
1 ATT-TTTATAATTTTTTACG
28828737 ATTTTTAT-ATTTTTT
1 ATTTTTATAATTTTTT
28828752 TCTAATTTTA
Statistics
Matches: 114, Mismatches: 25, Indels: 23
0.70 0.15 0.14
Matches are distributed among these distances:
17 8 0.07
18 14 0.12
19 47 0.41
20 29 0.25
21 12 0.11
22 4 0.04
ACGTcount: A:0.30, C:0.07, G:0.03, T:0.60
Consensus pattern (19 bp):
ATTTTTATAATTTTTTACG
Found at i:28849396 original size:42 final size:42
Alignment explanation
Indices: 28849326--28849426 Score: 121
Period size: 42 Copynumber: 2.4 Consensus size: 42
28849316 CGTGTCCTTA
*** *
28849326 CCCGTGTAACTCACTGAGTAGGGTCACACGACCATGTGCCAG
1 CCCGTGTAACTCACTGAGTAGCCACACACGACCATATGCCAG
* * *
28849368 CCCGTGTAACTCTCTGAGTTGCCACACACGACCATATGCTAG
1 CCCGTGTAACTCACTGAGTAGCCACACACGACCATATGCCAG
**
28849410 GTCGTGTAACTCACTGA
1 CCCGTGTAACTCACTGA
28849427 CTTAAAACAC
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.24, C:0.31, G:0.23, T:0.23
Consensus pattern (42 bp):
CCCGTGTAACTCACTGAGTAGCCACACACGACCATATGCCAG
Found at i:28852129 original size:16 final size:17
Alignment explanation
Indices: 28852097--28852130 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
28852087 CAATTCAGTC
28852097 CAAAATTCATACTTTTG
1 CAAAATTCATACTTTTG
*
28852114 CAAAATT-ATGCTTTTG
1 CAAAATTCATACTTTTG
28852130 C
1 C
28852131 CCCTATTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.32, C:0.18, G:0.09, T:0.41
Consensus pattern (17 bp):
CAAAATTCATACTTTTG
Found at i:28862938 original size:18 final size:18
Alignment explanation
Indices: 28862917--28862952 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
28862907 ATTTGTGTAA
*
28862917 AAATTATAATTTTTTTAT
1 AAATTATAAATTTTTTAT
*
28862935 AAATTTTAAATTTTTTAT
1 AAATTATAAATTTTTTAT
28862953 TTTTTATCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
AAATTATAAATTTTTTAT
Found at i:28872463 original size:23 final size:23
Alignment explanation
Indices: 28872437--28872480 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
28872427 GCCAATGAAT
28872437 TAAAAAAT-ATTAAATTTTTTTAA
1 TAAAAAATAATT-AATTTTTTTAA
*
28872460 TAAAATATAATTAATTTTTTT
1 TAAAAAATAATTAATTTTTTT
28872481 CTCGGGTCAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
TAAAAAATAATTAATTTTTTTAA
Found at i:28872553 original size:27 final size:27
Alignment explanation
Indices: 28872517--28872599 Score: 114
Period size: 27 Copynumber: 3.1 Consensus size: 27
28872507 ATACAAAGTA
*
28872517 GTGGTGCCTATCTCAGAGGCGCCAATG
1 GTGGTGCCTATCTGAGAGGCGCCAATG
* *
28872544 GTGGTGCCTATCTGAGAGGCGCCATTA
1 GTGGTGCCTATCTGAGAGGCGCCAATG
*
28872571 GTGGTGCC-ATGTTGAGAGGCGCCAATG
1 GTGGTGCCTAT-CTGAGAGGCGCCAATG
28872598 GT
1 GT
28872600 CTTATTTTTC
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
26 2 0.04
27 47 0.96
ACGTcount: A:0.18, C:0.22, G:0.36, T:0.24
Consensus pattern (27 bp):
GTGGTGCCTATCTGAGAGGCGCCAATG
Found at i:28881314 original size:15 final size:16
Alignment explanation
Indices: 28881294--28881330 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
28881284 ACAAAATCAA
*
28881294 ATAAAA-TTACATTGT
1 ATAAAAGTTACATTAT
28881309 ATAAAAGTTACATTAT
1 ATAAAAGTTACATTAT
28881325 ATAAAA
1 ATAAAA
28881331 ATTAAATGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.35
Consensus pattern (16 bp):
ATAAAAGTTACATTAT
Found at i:28881524 original size:60 final size:60
Alignment explanation
Indices: 28881450--28881571 Score: 192
Period size: 60 Copynumber: 2.0 Consensus size: 60
28881440 ATACTAAACT
* * * *
28881450 AAACACAACAATTTATAACTTAATCCTAAATTACTAATAAATTAAATT-TTAAATAATTAC
1 AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATT-AATTATAAAATAATTAC
28881510 AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTATAAAATAATTAC
1 AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTATAAAATAATTAC
28881570 AA
1 AA
28881572 TATTCATACA
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
59 4 0.07
60 53 0.93
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (60 bp):
AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTATAAAATAATTAC
Found at i:28881654 original size:19 final size:19
Alignment explanation
Indices: 28881594--28881654 Score: 77
Period size: 19 Copynumber: 3.1 Consensus size: 19
28881584 AAATTACGAT
* *
28881594 ATTACAATAGTCATACAAA
1 ATTACAATATTCATAAAAA
28881613 ATTACAATATTCATACAAAAAA
1 ATTACAATATTCAT---AAAAA
28881635 ATTACAATATTCATAAAAA
1 ATTACAATATTCATAAAAA
28881654 A
1 A
28881655 ACTAATCCAA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
19 19 0.51
22 18 0.49
ACGTcount: A:0.57, C:0.13, G:0.02, T:0.28
Consensus pattern (19 bp):
ATTACAATATTCATAAAAA
Found at i:28881655 original size:22 final size:22
Alignment explanation
Indices: 28881610--28881655 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
28881600 ATAGTCATAC
*
28881610 AAAATTACAATATTCATACAAA
1 AAAATTACAATATTCATAAAAA
28881632 AAAATTACAATATTCATAAAAA
1 AAAATTACAATATTCATAAAAA
28881654 AA
1 AA
28881656 CTAATCCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.63, C:0.11, G:0.00, T:0.26
Consensus pattern (22 bp):
AAAATTACAATATTCATAAAAA
Found at i:28881806 original size:19 final size:19
Alignment explanation
Indices: 28881782--28881842 Score: 95
Period size: 19 Copynumber: 3.1 Consensus size: 19
28881772 AATACATTAC
28881782 ATTACAATATTCATACAAA
1 ATTACAATATTCATACAAA
28881801 ATTACAATATTCATACAAAAA
1 ATTACAATATTCATAC--AAA
*
28881822 ATTAGAATATTCATACAAA
1 ATTACAATATTCATACAAA
28881841 AT
1 AT
28881843 ACTAATCCAA
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
19 21 0.54
21 18 0.46
ACGTcount: A:0.54, C:0.13, G:0.02, T:0.31
Consensus pattern (19 bp):
ATTACAATATTCATACAAA
Found at i:28881898 original size:188 final size:187
Alignment explanation
Indices: 28881594--28881968 Score: 698
Period size: 188 Copynumber: 2.0 Consensus size: 187
28881584 AAATTACGAT
28881594 ATTACAATAGTCATACAAAATTACAATATTCATACAAAAAAATTACAATATTCATAAAAAAACTA
1 ATTACAATAGTCATACAAAATTACAATATTCATACAAAAAAATTACAATATTCATAAAAAAACTA
28881659 ATCCAAACTATAAACACTAAACATAAATAATTTATAATTAATAATTAATAACAAAAAATTCACAA
66 ATCCAAACTATAAACACTAAACATAAATAATTTATAATTAATAATTAATAACAAAAAATTCACAA
28881724 TATCTTAATTAAACTCTTTAAATTATAAACAAAATTATTTACTAAAATAATACATTAC
131 TATCTTAATTAAACTCTTTAAATTATAAA-AAAATTATTTACTAAAATAATACATTAC
* * *
28881782 ATTACAATATTCATACAAAATTACAATATTCATAC-AAAAAATTAGAATATTCATACAAAATACT
1 ATTACAATAGTCATACAAAATTACAATATTCATACAAAAAAATTACAATATTCATA-AAAAAACT
28881846 AATCCAAACTATAAACACTAAACATAAATAATTTATAATTAATAATTAATAACAAAAAATTCACA
65 AATCCAAACTATAAACACTAAACATAAATAATTTATAATTAATAATTAATAACAAAAAATTCACA
28881911 ATATCTTAATTAAACTCTTTAAATTATAAAAAAATTATTTACTAAAATAATACATTAC
130 ATATCTTAATTAAACTCTTTAAATTATAAAAAAATTATTTACTAAAATAATACATTAC
28881969 CTTTTTCTTT
Statistics
Matches: 183, Mismatches: 3, Indels: 3
0.97 0.02 0.02
Matches are distributed among these distances:
187 47 0.26
188 136 0.74
ACGTcount: A:0.54, C:0.13, G:0.01, T:0.32
Consensus pattern (187 bp):
ATTACAATAGTCATACAAAATTACAATATTCATACAAAAAAATTACAATATTCATAAAAAAACTA
ATCCAAACTATAAACACTAAACATAAATAATTTATAATTAATAATTAATAACAAAAAATTCACAA
TATCTTAATTAAACTCTTTAAATTATAAAAAAATTATTTACTAAAATAATACATTAC
Found at i:28882203 original size:27 final size:27
Alignment explanation
Indices: 28882146--28882207 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
28882136 GGTCACCCAT
***
28882146 TGGCGCCTCCCTATGAGGCATTTTTAA
1 TGGCGCCTCCCTATGAGGCACAATTAA
* *
28882173 TGGCGCCTCTCTATGAGGCACAATTAG
1 TGGCGCCTCCCTATGAGGCACAATTAA
28882200 TGGCGCCT
1 TGGCGCCT
28882208 ACCTGACAGG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.18, C:0.27, G:0.26, T:0.29
Consensus pattern (27 bp):
TGGCGCCTCCCTATGAGGCACAATTAA
Found at i:28882914 original size:27 final size:27
Alignment explanation
Indices: 28882873--28882934 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
28882863 CTCTCAACAT
* *
28882873 GGCACCACTAATGGCGCCTGTCAGATA
1 GGCACCACCAATGGCGCCTCTCAGATA
* *
28882900 GGCACCACCATTGGCGCCTCTGAGATA
1 GGCACCACCAATGGCGCCTCTCAGATA
*
28882927 GGCGCCAC
1 GGCACCAC
28882935 TACTTTGTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.23, C:0.34, G:0.27, T:0.16
Consensus pattern (27 bp):
GGCACCACCAATGGCGCCTCTCAGATA
Found at i:28885935 original size:29 final size:30
Alignment explanation
Indices: 28885893--28885967 Score: 107
Period size: 30 Copynumber: 2.5 Consensus size: 30
28885883 ACAAACGTAT
**
28885893 GAAAGATTAAAACCTTTTG-TTCAAAAAAA
1 GAAAGATTAAAACCTTTTGAAACAAAAAAA
*
28885922 GAAAGATTAAAACCTTTTGAAAGAAAAAAA
1 GAAAGATTAAAACCTTTTGAAACAAAAAAA
*
28885952 GAAAGATTGAAACCTT
1 GAAAGATTAAAACCTT
28885968 GAATTTATTC
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 19 0.46
30 22 0.54
ACGTcount: A:0.53, C:0.09, G:0.13, T:0.24
Consensus pattern (30 bp):
GAAAGATTAAAACCTTTTGAAACAAAAAAA
Found at i:28886919 original size:27 final size:25
Alignment explanation
Indices: 28886862--28886932 Score: 81
Period size: 26 Copynumber: 2.8 Consensus size: 25
28886852 TAAAATTAAT
*
28886862 TTTTTAAAAATTT-AAAAATAAAAAC
1 TTTTT-AAAATTTAAAAAATAAAAAA
*
28886887 TCTTTAAAATTATAAAAAATAAAAAGA
1 TTTTTAAAATT-TAAAAAATAAAAA-A
*
28886914 TTTTTAAAATCTAAAAAAT
1 TTTTTAAAATTTAAAAAAT
28886933 TTCAAAATTC
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
24 6 0.15
25 5 0.13
26 19 0.49
27 9 0.23
ACGTcount: A:0.59, C:0.04, G:0.01, T:0.35
Consensus pattern (25 bp):
TTTTTAAAATTTAAAAAATAAAAAA
Found at i:28887054 original size:19 final size:21
Alignment explanation
Indices: 28887030--28887074 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
28887020 ATTGACCCAC
*
28887030 GAACCGG-TATAAAA-TGGTT
1 GAACCGGATATAAAACTAGTT
28887049 GAACCGGACTATAAAACTAGTT
1 GAACCGGA-TATAAAACTAGTT
28887071 GAAC
1 GAAC
28887075 TACAGTTGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 7 0.32
21 7 0.32
22 8 0.36
ACGTcount: A:0.40, C:0.16, G:0.22, T:0.22
Consensus pattern (21 bp):
GAACCGGATATAAAACTAGTT
Found at i:28887110 original size:17 final size:16
Alignment explanation
Indices: 28887087--28887126 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
28887077 CAGTTGAACT
*
28887087 AATTTTTATATTTTTA
1 AATTTTTATAATTTTA
28887103 ATATTTTT-TAATTTTA
1 A-ATTTTTATAATTTTA
28887119 AATTTTTA
1 AATTTTTA
28887127 ATAACTTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 6 0.29
16 9 0.43
17 6 0.29
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
AATTTTTATAATTTTA
Found at i:28890500 original size:18 final size:18
Alignment explanation
Indices: 28890468--28890502 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
28890458 TAAAAAAAAC
*
28890468 TAGAATAATAGTACATAA
1 TAGAATAAAAGTACATAA
*
28890486 TAGAATAAAATTACATA
1 TAGAATAAAAGTACATA
28890503 TAAAAAATTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.57, C:0.06, G:0.09, T:0.29
Consensus pattern (18 bp):
TAGAATAAAAGTACATAA
Found at i:28890585 original size:3 final size:3
Alignment explanation
Indices: 28890579--28890607 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
28890569 CAACAACAAC
28890579 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
28890608 GATTAATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:28891607 original size:25 final size:25
Alignment explanation
Indices: 28891554--28891613 Score: 79
Period size: 25 Copynumber: 2.4 Consensus size: 25
28891544 AAGAAAATCC
*
28891554 AAAAGAATGAAAGAATAATTACTCG
1 AAAAGAATGAAAGAATAATTACTCA
*
28891579 AAAAGAATGAAAGAAT-ATTGGCTCA
1 AAAAGAATGAAAGAATAATT-ACTCA
28891604 AAAA-AATGAA
1 AAAAGAATGAA
28891614 TGAGAAAATG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
24 9 0.28
25 23 0.72
ACGTcount: A:0.58, C:0.07, G:0.17, T:0.18
Consensus pattern (25 bp):
AAAAGAATGAAAGAATAATTACTCA
Found at i:28893944 original size:388 final size:390
Alignment explanation
Indices: 28893186--28893972 Score: 1463
Period size: 388 Copynumber: 2.0 Consensus size: 390
28893176 AATTCCAGGG
28893186 GACCTTTTTGCTATCCTTATATGAGAAATTTGATGGTTTCTGAATTACGATCTTTGGTGTCACCT
1 GACCTTTTTGCTATCCTTATATGAGAAATTTGATGGTTTCTGAATTACGATCTTTGGTGTCACCT
*
28893251 GTGCCCCTACCTCGTTAATATTAGGGCGCGAGATGATAATCACAGGATGATTTACTTTCAGAATT
66 GTGCCCCTACCTCGTTAATATTAGGGCACGAGATGATAATCACAGGATGATTTACTTTCAGAATT
28893316 CTCATCATTGACTCCGACGCGCATATGCTTCCTTTTTCCTCTACTTCTTCATAAAACTCTATTTC
131 CTCATCATTGACTCCGACGCGCATATGCTTCCTTTTTCCTCTACTTCTTCATAAAACTCTATTTC
* *
28893381 TTTATTATCCATCATGCTCTGGACCAGAACTCTGAATTCTTCACATCTTTGGATTTCGTGCCCCA
196 TTTATTATCCATCATGCTCCGGACCAGAACTCTGAATTCTTCACATCTTTGCATTTCGTGCCCCA
28893446 CCTCATGATGGAACTCACAATAATTTTTGGTCTCACCACCTTCCTCTAAATCCAAAATGATTAAC
261 CCTCATGATGGAACTCACAATAATTTTTGGTCTCACCACCTTCCTCTAAATCCAAAATGATTAAC
28893511 CCTCTTCTTGCCATCTCTTCCCAAACCCATTTCAAAGGGGTTTTCACTTCAGCAATATTTGCCTT
326 CCTCTTCTTGCCATCTCTTCCCAAACCCATTTCAAAGGGGTTTTCACTTCAGCAATATTTGCCTT
*
28893576 GACCTTTTTGTTATCCTTATATGAGAAATTT-ACTGGTTT-T-AATTACGATCTTTGGTGTCACC
1 GACCTTTTTGCTATCCTTATATGAGAAATTTGA-TGGTTTCTGAATTACGATCTTTGGTGTCACC
*
28893638 TGTGCCCCTACCTCGTTAATATTAGGGCACGATATGATAATCACAGGATGATTTACTTTCAGAAT
65 TGTGCCCCTACCTCGTTAATATTAGGGCACGAGATGATAATCACAGGATGATTTACTTTCAGAAT
* *
28893703 TCTCATCATTGACTCCGACGCGCATATGCTTCTTTTTTCCTCTGCTTCTTCATAAAACTCTATTT
130 TCTCATCATTGACTCCGACGCGCATATGCTTCCTTTTTCCTCTACTTCTTCATAAAACTCTATTT
28893768 CTTTATTATCCATCATGCTCCGGACCAGAACTCTGAATTCTTCACATCTTTGCATTTCGTGCCCC
195 CTTTATTATCCATCATGCTCCGGACCAGAACTCTGAATTCTTCACATCTTTGCATTTCGTGCCCC
*
28893833 ACCTCATGATGGAACTCACTATAATTTTTGGTCTCACCACCTTCCTCTAAATCCAAAATGATTAA
260 ACCTCATGATGGAACTCACAATAATTTTTGGTCTCACCACCTTCCTCTAAATCCAAAATGATTAA
28893898 CCCTCTTCTTGCCATCTCTTCCCAAACCCATTTCAAAGGGGTTTTCACTTCAGCAATATTTGCCT
325 CCCTCTTCTTGCCATCTCTTCCCAAACCCATTTCAAAGGGGTTTTCACTTCAGCAATATTTGCCT
28893963 T
390 T
28893964 GACTCTTTT
1 GAC-CTTTT
28893973 CCCTATATTT
Statistics
Matches: 387, Mismatches: 8, Indels: 5
0.97 0.02 0.01
Matches are distributed among these distances:
388 344 0.89
389 7 0.02
390 36 0.09
ACGTcount: A:0.24, C:0.26, G:0.13, T:0.37
Consensus pattern (390 bp):
GACCTTTTTGCTATCCTTATATGAGAAATTTGATGGTTTCTGAATTACGATCTTTGGTGTCACCT
GTGCCCCTACCTCGTTAATATTAGGGCACGAGATGATAATCACAGGATGATTTACTTTCAGAATT
CTCATCATTGACTCCGACGCGCATATGCTTCCTTTTTCCTCTACTTCTTCATAAAACTCTATTTC
TTTATTATCCATCATGCTCCGGACCAGAACTCTGAATTCTTCACATCTTTGCATTTCGTGCCCCA
CCTCATGATGGAACTCACAATAATTTTTGGTCTCACCACCTTCCTCTAAATCCAAAATGATTAAC
CCTCTTCTTGCCATCTCTTCCCAAACCCATTTCAAAGGGGTTTTCACTTCAGCAATATTTGCCTT
Found at i:28895240 original size:28 final size:28
Alignment explanation
Indices: 28895163--28895242 Score: 80
Period size: 28 Copynumber: 3.0 Consensus size: 28
28895153 TATTGGATTT
28895163 TAAAAAAAATAA-AATAGTACAT--T-A
1 TAAAAAAAATAATAATAGTACATAATAA
* *
28895187 TAAAATTAAATAATAATA-TATGATAATAA
1 TAAAA-AAAATAATAATAGTA-CATAATAA
*
28895216 TAAAAAAAAGAATAATAGTACATAATA
1 TAAAAAAAATAATAATAGTACATAATA
28895243 GAATAAAATT
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
24 5 0.11
25 8 0.18
26 6 0.14
28 17 0.39
29 8 0.18
ACGTcount: A:0.65, C:0.03, G:0.05, T:0.28
Consensus pattern (28 bp):
TAAAAAAAATAATAATAGTACATAATAA
Found at i:28895255 original size:18 final size:18
Alignment explanation
Indices: 28895224--28895273 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
28895214 AATAAAAAAA
* *
28895224 AGAATAATAGTACATAAT
1 AGAATAAAATTACATAAT
28895242 AGAATAAAATTACAT-AT
1 AGAATAAAATTACATAAT
*
28895259 A-AA-AAAATTAGATAA
1 AGAATAAAATTACATAA
28895274 ATTGCCATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
15 9 0.32
16 3 0.11
17 3 0.11
18 13 0.46
ACGTcount: A:0.62, C:0.04, G:0.08, T:0.26
Consensus pattern (18 bp):
AGAATAAAATTACATAAT
Found at i:28895305 original size:15 final size:15
Alignment explanation
Indices: 28895293--28895322 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
28895283 ACAATAATGC
*
28895293 TAACGATAATAATAA
1 TAACAATAATAATAA
28895308 TAACAATAATAATAA
1 TAACAATAATAATAA
28895323 GATTAATTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.07, G:0.03, T:0.27
Consensus pattern (15 bp):
TAACAATAATAATAA
Found at i:28898073 original size:162 final size:163
Alignment explanation
Indices: 28897806--28898133 Score: 649
Period size: 162 Copynumber: 2.0 Consensus size: 163
28897796 AAATTTGACC
28897806 CTTAACCTTTTAAAAAGAGTCAATTTTGACATCAACCTTTTGAAAACTAGTCAACATAATTTTTT
1 CTTAACCTTTTAAAAAGAGTCAATTTTGACATCAACCTTTTGAAAACTAGTCAACATAATTTTTT
28897871 ATAACGAGAATGTCAACTAAAATGTTAATTTTTAAAATACGGCAACCTACATGACAATCCACATG
66 ATAACGAGAATGTCAACTAAAATGTTAATTTTTAAAATACGGCAACCTACATGACAATCCACATG
28897936 CACTCCATGCTAATTTTTTTGAA-TTTTATGAA
131 CACTCCATGCTAATTTTTTTGAATTTTTATGAA
28897968 CTTAACCTTTTAAAAAGAGTCAATTTTGACATCAACCTTTTGAAAACTAGTCAACATAATTTTTT
1 CTTAACCTTTTAAAAAGAGTCAATTTTGACATCAACCTTTTGAAAACTAGTCAACATAATTTTTT
28898033 ATAACGAGAATGTCAACTAAAATGTTAATTTTTAAAATACGGCAACCTACATGACAATCCACATG
66 ATAACGAGAATGTCAACTAAAATGTTAATTTTTAAAATACGGCAACCTACATGACAATCCACATG
28898098 CACTCCATGCTAATTTTTTTGAATTTTTATGAA
131 CACTCCATGCTAATTTTTTTGAATTTTTATGAA
28898131 CTT
1 CTT
28898134 TTTATATTTT
Statistics
Matches: 165, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
162 153 0.93
163 12 0.07
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.36
Consensus pattern (163 bp):
CTTAACCTTTTAAAAAGAGTCAATTTTGACATCAACCTTTTGAAAACTAGTCAACATAATTTTTT
ATAACGAGAATGTCAACTAAAATGTTAATTTTTAAAATACGGCAACCTACATGACAATCCACATG
CACTCCATGCTAATTTTTTTGAATTTTTATGAA
Found at i:28898160 original size:5 final size:5
Alignment explanation
Indices: 28898150--28898177 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
28898140 TTTTTTAAAT
28898150 TTTAA TTTAA TTTAA TTTAA TTTAA TTT
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTT
28898178 TATAATTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (5 bp):
TTTAA
Found at i:28903169 original size:18 final size:20
Alignment explanation
Indices: 28903132--28903176 Score: 58
Period size: 18 Copynumber: 2.3 Consensus size: 20
28903122 TCTTTTCACG
28903132 TTCTTTTTCTTTGGGTTTTCC
1 TTCTTTTTCTTT-GGTTTTCC
*
28903153 TTCTTTTT-TTT-GTTTTCT
1 TTCTTTTTCTTTGGTTTTCC
28903171 TTCTTT
1 TTCTTT
28903177 GTTTACTTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 12 0.52
20 3 0.13
21 8 0.35
ACGTcount: A:0.00, C:0.16, G:0.09, T:0.76
Consensus pattern (20 bp):
TTCTTTTTCTTTGGTTTTCC
Found at i:28904023 original size:16 final size:16
Alignment explanation
Indices: 28904004--28904061 Score: 55
Period size: 16 Copynumber: 3.7 Consensus size: 16
28903994 ATTATATTTT
28904004 TATATTTGTATATCTG
1 TATATTTGTATATCTG
* ** *
28904020 TATATCTACACATCTG
1 TATATTTGTATATCTG
* *
28904036 TATATTGGTATATCTT
1 TATATTTGTATATCTG
28904052 TAT-TTTGTAT
1 TATATTTGTAT
28904062 CTATATATGG
Statistics
Matches: 31, Mismatches: 11, Indels: 1
0.72 0.26 0.02
Matches are distributed among these distances:
15 6 0.19
16 25 0.81
ACGTcount: A:0.26, C:0.10, G:0.10, T:0.53
Consensus pattern (16 bp):
TATATTTGTATATCTG
Found at i:28904945 original size:12 final size:12
Alignment explanation
Indices: 28904928--28904954 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
28904918 CATACCAAAC
28904928 CATGAATTAGCA
1 CATGAATTAGCA
28904940 CATGAATTAGCA
1 CATGAATTAGCA
28904952 CAT
1 CAT
28904955 TATTAACTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.19, G:0.15, T:0.26
Consensus pattern (12 bp):
CATGAATTAGCA
Found at i:28909794 original size:22 final size:22
Alignment explanation
Indices: 28909766--28909809 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
28909756 CCCACTACGA
**
28909766 TTAACACTCCGTTCATCAGTGT
1 TTAACACTCCACTCATCAGTGT
28909788 TTAACACTCCACTCATCAGTGT
1 TTAACACTCCACTCATCAGTGT
28909810 CTCCCACTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.25, C:0.30, G:0.11, T:0.34
Consensus pattern (22 bp):
TTAACACTCCACTCATCAGTGT
Found at i:28918588 original size:43 final size:43
Alignment explanation
Indices: 28918531--28919039 Score: 687
Period size: 43 Copynumber: 11.8 Consensus size: 43
28918521 TTTTTATAAT
*
28918531 AAACGCCGCTATAGACCATGGTCTTTAGCGGCGCCTATCCATC
1 AAACGCCGCTATAGACCATGGTCTTTAGCGGCGCTTATCCATC
* *
28918574 AAAGGCCGCTATAGACCATGGTCTTTAGCGGCGCTTATCTATC
1 AAACGCCGCTATAGACCATGGTCTTTAGCGGCGCTTATCCATC
* *
28918617 AAATGCCGCTATAGACCATGGTCTTTAGCGGCGCTTATCTATC
1 AAACGCCGCTATAGACCATGGTCTTTAGCGGCGCTTATCCATC
* *
28918660 AAACGCCGCTATAGACCATGGTATTTAGCGGCGCTTATCCATA
1 AAACGCCGCTATAGACCATGGTCTTTAGCGGCGCTTATCCATC
* * *
28918703 AAATGCCGCTATAGACCATGGTCTTTAACGGCGCTTATCCATA
1 AAACGCCGCTATAGACCATGGTCTTTAGCGGCGCTTATCCATC
* *
28918746 AAACGCCGCTATAGACCATGGTCTTTAGCGGCGCTTTTGCATC
1 AAACGCCGCTATAGACCATGGTCTTTAGCGGCGCTTATCCATC
* * * * * **
28918789 AAACGCCGCTATAGACCACGGTCTTTAGAGGTGTTTTTGTATC
1 AAACGCCGCTATAGACCATGGTCTTTAGCGGCGCTTATCCATC
* * * * *
28918832 AAAGGCCACTATAGACCATAGTCTTTAGCGGGGCTTACCCATC
1 AAACGCCGCTATAGACCATGGTCTTTAGCGGCGCTTATCCATC
* * *
28918875 AAACGCCGCTACAGCCCATGGTCTTTAGCGGCGCTTACCCATC
1 AAACGCCGCTATAGACCATGGTCTTTAGCGGCGCTTATCCATC
* *
28918918 AAACGCCGCTATAGACCTTGGTCTTTAGCGGCGCTTACCCATC
1 AAACGCCGCTATAGACCATGGTCTTTAGCGGCGCTTATCCATC
* * * *
28918961 AAACGCCGCTATAGACCTTGGTCTTTAGCGGCGCTTAACAAAC
1 AAACGCCGCTATAGACCATGGTCTTTAGCGGCGCTTATCCATC
* *
28919004 AAACGCCGCTATAG-CTCATGGTTTTTAGCGGTGCTT
1 AAACGCCGCTATAGAC-CATGGTCTTTAGCGGCGCTT
28919040 TTAGAAAAAC
Statistics
Matches: 418, Mismatches: 47, Indels: 2
0.90 0.10 0.00
Matches are distributed among these distances:
42 1 0.00
43 417 1.00
ACGTcount: A:0.24, C:0.28, G:0.22, T:0.27
Consensus pattern (43 bp):
AAACGCCGCTATAGACCATGGTCTTTAGCGGCGCTTATCCATC
Found at i:28919384 original size:21 final size:21
Alignment explanation
Indices: 28919358--28919416 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
28919348 TTTAAGCTGT
28919358 TCTACTTCCCTCGCTGCAGCC
1 TCTACTTCCCTCGCTGCAGCC
** *
28919379 TCTACTTCCCTCATTGTAGCC
1 TCTACTTCCCTCGCTGCAGCC
* *
28919400 TCTGCTTCTCTCGCTGC
1 TCTACTTCCCTCGCTGC
28919417 CACATTTGCT
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.08, C:0.42, G:0.14, T:0.36
Consensus pattern (21 bp):
TCTACTTCCCTCGCTGCAGCC
Found at i:28919493 original size:21 final size:21
Alignment explanation
Indices: 28919464--28919514 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
28919454 TTTCATTGAA
* *
28919464 CCTCAGCTTCTCTCGCTGCTG
1 CCTCTGCTTCTCTCGCTGCCG
28919485 CCTCTGCTTCTCTCGCTGCCG
1 CCTCTGCTTCTCTCGCTGCCG
*
28919506 CATCTGCTT
1 CCTCTGCTT
28919515 TAAGTTGTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.04, C:0.43, G:0.18, T:0.35
Consensus pattern (21 bp):
CCTCTGCTTCTCTCGCTGCCG
Found at i:28929684 original size:16 final size:16
Alignment explanation
Indices: 28929663--28929693 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
28929653 GTAAATGGAG
28929663 TTAGGGATTTCAGAAC
1 TTAGGGATTTCAGAAC
*
28929679 TTAGGGATTTTAGAA
1 TTAGGGATTTCAGAA
28929694 GAGGAAAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.06, G:0.26, T:0.35
Consensus pattern (16 bp):
TTAGGGATTTCAGAAC
Found at i:28930030 original size:78 final size:78
Alignment explanation
Indices: 28929940--28930097 Score: 316
Period size: 78 Copynumber: 2.0 Consensus size: 78
28929930 GTAGGATTAA
28929940 TTTAAATATTAACAACATTAAAATTTATAAATATTAATCCCAATACCCTAAAATACATAACTTTC
1 TTTAAATATTAACAACATTAAAATTTATAAATATTAATCCCAATACCCTAAAATACATAACTTTC
28930005 ATTTGCGGCGTTT
66 ATTTGCGGCGTTT
28930018 TTTAAATATTAACAACATTAAAATTTATAAATATTAATCCCAATACCCTAAAATACATAACTTTC
1 TTTAAATATTAACAACATTAAAATTTATAAATATTAATCCCAATACCCTAAAATACATAACTTTC
28930083 ATTTGCGGCGTTT
66 ATTTGCGGCGTTT
28930096 TT
1 TT
28930098 ACAAAAAACG
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 80 1.00
ACGTcount: A:0.41, C:0.16, G:0.05, T:0.38
Consensus pattern (78 bp):
TTTAAATATTAACAACATTAAAATTTATAAATATTAATCCCAATACCCTAAAATACATAACTTTC
ATTTGCGGCGTTT
Found at i:28930517 original size:23 final size:23
Alignment explanation
Indices: 28930474--28930518 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
28930464 TACTTTTGTA
*
28930474 CCCTAAAACCCGAAGCTATTAAT
1 CCCTAAAACCCGAAACTATTAAT
*
28930497 CCCTATAACCCGTAAAC-ATTAA
1 CCCTAAAACCCG-AAACTATTAA
28930519 AATTAAAGGC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.40, C:0.31, G:0.07, T:0.22
Consensus pattern (23 bp):
CCCTAAAACCCGAAACTATTAAT
Found at i:28931158 original size:23 final size:23
Alignment explanation
Indices: 28931115--28931159 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
28931105 TGCTTTTGTA
*
28931115 CCCTAAAACCCGAAGCTATTAAT
1 CCCTAAAACCCGAAACTATTAAT
*
28931138 CCCTATAACCCGTAAAC-ATTAA
1 CCCTAAAACCCG-AAACTATTAA
28931160 AATTAAAGGC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.40, C:0.31, G:0.07, T:0.22
Consensus pattern (23 bp):
CCCTAAAACCCGAAACTATTAAT
Found at i:28932142 original size:41 final size:41
Alignment explanation
Indices: 28932050--28932142 Score: 134
Period size: 41 Copynumber: 2.3 Consensus size: 41
28932040 TAGATTTTTT
* *
28932050 AATTAGCGGCGTTTTTACACAAACGCCGCTATAGACCGAAG
1 AATTAGCGGCGCTGTTACACAAACGCCGCTATAGACCGAAG
*
28932091 AATTACCGGCGCTGTTACACAAACGCCGCTATAGACCGGAA-
1 AATTAGCGGCGCTGTTACACAAACGCCGCTATAGACC-GAAG
*
28932132 CATTAGCGGCG
1 AATTAGCGGCG
28932143 ATTCTCCATA
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
41 43 0.93
42 3 0.07
ACGTcount: A:0.30, C:0.27, G:0.24, T:0.19
Consensus pattern (41 bp):
AATTAGCGGCGCTGTTACACAAACGCCGCTATAGACCGAAG
Found at i:28932263 original size:40 final size:40
Alignment explanation
Indices: 28932191--28932266 Score: 98
Period size: 40 Copynumber: 1.9 Consensus size: 40
28932181 CGGGGGATTT
* ** ** *
28932191 AAAAACGCCGCTATAGATCGGATTATTTGCGGCGCATAAA
1 AAAAACGCCGCTAAAGATAAGACCATTAGCGGCGCATAAA
28932231 AAAAACGCCGCTAAAGATAAGACCATTAGCGGCGCA
1 AAAAACGCCGCTAAAGATAAGACCATTAGCGGCGCA
28932267 GACACAAAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 30 1.00
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.17
Consensus pattern (40 bp):
AAAAACGCCGCTAAAGATAAGACCATTAGCGGCGCATAAA
Found at i:28932472 original size:38 final size:39
Alignment explanation
Indices: 28932414--28932559 Score: 150
Period size: 40 Copynumber: 3.7 Consensus size: 39
28932404 TTACTCTATT
* * *
28932414 GCGGCGCTTTTTGTAAAACGCCGCTAATGCTTGGTTTTA
1 GCGGCGTTTTTTATAAAACGCCGCTAATGCTTGATTTTA
** * *
28932453 GCGGC-TTTTTTATGTAACGCCGCTAATGCTCGATATTTT
1 GCGGCGTTTTTTATAAAACGCCGCTAATGCTTGAT-TTTA
* *
28932492 GCGGCGTTTTTCATAAAATGCCGCTAATGCTTGATTGTTA
1 GCGGCGTTTTTTATAAAACGCCGCTAATGCTTGATT-TTA
* * *
28932532 GTGGCGTTTTTTGTCCAAACGCCGCTAA
1 GCGGCGTTTTTTAT-AAAACGCCGCTAA
28932560 AAGCGCCGCT
Statistics
Matches: 85, Mismatches: 18, Indels: 6
0.78 0.17 0.06
Matches are distributed among these distances:
38 23 0.27
39 14 0.16
40 37 0.44
41 11 0.13
ACGTcount: A:0.19, C:0.21, G:0.23, T:0.37
Consensus pattern (39 bp):
GCGGCGTTTTTTATAAAACGCCGCTAATGCTTGATTTTA
Found at i:28940501 original size:20 final size:20
Alignment explanation
Indices: 28940464--28940503 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
28940454 GTCAATAAAT
*
28940464 AATTTAAAAGTTATAAAAAA
1 AATTTAAAAGTTAAAAAAAA
28940484 AATTGTAAAA-TTAAAAAAAA
1 AATT-TAAAAGTTAAAAAAAA
28940504 CATGAAGTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.28
Consensus pattern (20 bp):
AATTTAAAAGTTAAAAAAAA
Found at i:28940502 original size:19 final size:20
Alignment explanation
Indices: 28940464--28940503 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
28940454 GTCAATAAAT
28940464 AATTTAAAAGTTATAAAAAA
1 AATTTAAAAGTTATAAAAAA
28940484 AATTGTAAAA-TTA-AAAAAA
1 AATT-TAAAAGTTATAAAAAA
28940503 A
1 A
28940504 CATGAAGTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.37
20 7 0.37
21 5 0.26
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.28
Consensus pattern (20 bp):
AATTTAAAAGTTATAAAAAA
Found at i:28942839 original size:24 final size:24
Alignment explanation
Indices: 28942797--28942848 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
28942787 AATCAAAGTC
** *
28942797 AAATATATTATGTTAATAAATGCT
1 AAATATATTATACTAATAAATACT
*
28942821 AAATATATTATACTCATAAATACT
1 AAATATATTATACTAATAAATACT
28942845 AAAT
1 AAAT
28942849 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.50, C:0.08, G:0.04, T:0.38
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Found at i:28947635 original size:19 final size:21
Alignment explanation
Indices: 28947608--28947657 Score: 59
Period size: 19 Copynumber: 2.4 Consensus size: 21
28947598 TATTTATACT
*
28947608 TATTCTTTATAT-AA-AAATA
1 TATTTTTTATATGAATAAATA
28947627 TATTTTTTATATGAATAAATA
1 TATTTTTTATATGAATAAATA
*
28947648 AAGTTTTTTA
1 TA-TTTTTTA
28947658 AGATCTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 11 0.42
20 2 0.08
21 6 0.23
22 7 0.27
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (21 bp):
TATTTTTTATATGAATAAATA
Found at i:28947654 original size:21 final size:19
Alignment explanation
Indices: 28947613--28947655 Score: 50
Period size: 21 Copynumber: 2.2 Consensus size: 19
28947603 ATACTTATTC
* *
28947613 TTTATATAAAAATATATTT
1 TTTATATAAAAATAAAGTT
28947632 TTTATATGAATAAATAAAGTT
1 TTTATAT-AA-AAATAAAGTT
28947653 TTT
1 TTT
28947656 TAAGATCTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 7 0.35
20 2 0.10
21 11 0.55
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (19 bp):
TTTATATAAAAATAAAGTT
Found at i:28949729 original size:19 final size:21
Alignment explanation
Indices: 28949702--28949751 Score: 59
Period size: 19 Copynumber: 2.4 Consensus size: 21
28949692 TATTTATACT
*
28949702 TATTCTTTATAT-AA-AAATA
1 TATTTTTTATATGAATAAATA
28949721 TATTTTTTATATGAATAAATA
1 TATTTTTTATATGAATAAATA
*
28949742 AAGTTTTTTA
1 TA-TTTTTTA
28949752 AGATCTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 11 0.42
20 2 0.08
21 6 0.23
22 7 0.27
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (21 bp):
TATTTTTTATATGAATAAATA
Found at i:28949748 original size:21 final size:19
Alignment explanation
Indices: 28949707--28949749 Score: 50
Period size: 21 Copynumber: 2.2 Consensus size: 19
28949697 ATACTTATTC
* *
28949707 TTTATATAAAAATATATTT
1 TTTATATAAAAATAAAGTT
28949726 TTTATATGAATAAATAAAGTT
1 TTTATAT-AA-AAATAAAGTT
28949747 TTT
1 TTT
28949750 TAAGATCTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 7 0.35
20 2 0.10
21 11 0.55
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (19 bp):
TTTATATAAAAATAAAGTT
Found at i:28954428 original size:9 final size:9
Alignment explanation
Indices: 28954414--28954444 Score: 62
Period size: 9 Copynumber: 3.4 Consensus size: 9
28954404 TTGGTTATAA
28954414 TTACAGTAT
1 TTACAGTAT
28954423 TTACAGTAT
1 TTACAGTAT
28954432 TTACAGTAT
1 TTACAGTAT
28954441 TTAC
1 TTAC
28954445 TGTTTGAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.32, C:0.13, G:0.10, T:0.45
Consensus pattern (9 bp):
TTACAGTAT
Found at i:28956380 original size:49 final size:49
Alignment explanation
Indices: 28956323--28956426 Score: 163
Period size: 49 Copynumber: 2.1 Consensus size: 49
28956313 TCATGTGTTA
* ** * *
28956323 TAATTTTATAAAGTGTTGAGGTTTTGATTCATGATGTTGAACTTAATTT
1 TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTTAATTT
28956372 TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTTAATTT
1 TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTTAATTT
28956421 TAATTT
1 TAATTT
28956427 ATTTTTTTCT
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.31, C:0.07, G:0.12, T:0.50
Consensus pattern (49 bp):
TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTTAATTT
Found at i:28984875 original size:17 final size:16
Alignment explanation
Indices: 28984846--28984879 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
28984836 TTTGCAATCG
28984846 ATTTTTTTATATTTTT
1 ATTTTTTTATATTTTT
*
28984862 ATTTTTGTTTTATTTTT
1 ATTTTT-TTATATTTTT
28984879 A
1 A
28984880 AACAACGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (16 bp):
ATTTTTTTATATTTTT
Found at i:28991193 original size:16 final size:16
Alignment explanation
Indices: 28991164--28991214 Score: 68
Period size: 16 Copynumber: 3.1 Consensus size: 16
28991154 CAGACTCAAA
28991164 AAAAATAAAAAAAAATC
1 AAAAAT-AAAAAAAATC
*
28991181 AAAAA-AATCAAAAATC
1 AAAAATAA-AAAAAATC
28991197 AAAAATAAAAAAAATC
1 AAAAATAAAAAAAATC
28991213 AA
1 AA
28991215 TCAATCAAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
15 2 0.07
16 21 0.70
17 7 0.23
ACGTcount: A:0.80, C:0.08, G:0.00, T:0.12
Consensus pattern (16 bp):
AAAAATAAAAAAAATC
Found at i:28991200 original size:23 final size:24
Alignment explanation
Indices: 28991174--28991223 Score: 75
Period size: 23 Copynumber: 2.1 Consensus size: 24
28991164 AAAAATAAAA
*
28991174 AAAAATCAAAAAAATCAA-AAATC
1 AAAAATAAAAAAAATCAATAAATC
*
28991197 AAAAATAAAAAAAATCAATCAATC
1 AAAAATAAAAAAAATCAATAAATC
28991221 AAA
1 AAA
28991224 GCCAAAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 17 0.71
24 7 0.29
ACGTcount: A:0.74, C:0.12, G:0.00, T:0.14
Consensus pattern (24 bp):
AAAAATAAAAAAAATCAATAAATC
Found at i:28991253 original size:7 final size:6
Alignment explanation
Indices: 28991237--28991273 Score: 56
Period size: 6 Copynumber: 5.8 Consensus size: 6
28991227 AAAAATAGGG
28991237 GAAAAA GAAAGAA GAAAAAA GAAAAA GAAAAA GAAAA
1 GAAAAA GAAA-AA G-AAAAA GAAAAA GAAAAA GAAAA
28991274 GGAGAGGTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
6 20 0.69
7 6 0.21
8 3 0.10
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (6 bp):
GAAAAA
Found at i:28993622 original size:44 final size:44
Alignment explanation
Indices: 28993568--28994057 Score: 250
Period size: 44 Copynumber: 11.3 Consensus size: 44
28993558 GATCGTGTCA
*
28993568 AATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGATAGT
1 AATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGATAGT
* * *
28993612 AATCCTATCTCCCTGAGATTACAGTGGAGCGGATT-AAAATGAAG-
1 AATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGAT--AGT
* * ** * * *
28993656 GATCTTATCTCTCTGA-AGTTACAGCAGAGTAGATCG-CG-TCAG-
1 AATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAAGAT-AGT
* * * * ** *
28993698 -GTCTTATTTCCCTGAGGTTACAGTGGAACAGACCGAAGA-ATTT
1 AATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGATA-GT
* *
28993741 CAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGT
1 -A-ATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGATAGT
* * * * **
28993787 AATCCTATCTCCCTGAGATTACAGTGAAGCGGATT-AAAATAAA
1 AATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGATAGT
** * * * *
28993830 AGATCTTATCTTTCTGA-AGTTACAGTAGAGTAGATCG-TG-TCA--
1 A-ATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAAGAT-AGT
* * *
28993872 AATCTTATCTCCTTGAGATTACAGCGGAGCAGATTGAAGTTAGT
1 AATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGATAGT
* ** * *
28993916 AATCCTATCTCCCTGAGATTACAGTGGAGTGGATT-AAAATA-A
1 AATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGATAGT
* * * * *
28993958 ACGATCTTATCTCTCTGA-AGTTACAGTAGAGAAGATCG--TATCAG-
1 A--ATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAAGAT-AGT
* * **
28994002 -GTCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCCAGT
1 AATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGATAGT
28994045 AAT-TCTATCTCCC
1 AATCT-TATCTCCC
28994058 CGACGTTGCG
Statistics
Matches: 326, Mismatches: 86, Indels: 68
0.68 0.18 0.14
Matches are distributed among these distances:
41 79 0.24
42 11 0.03
43 22 0.07
44 178 0.55
45 3 0.01
46 32 0.10
47 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (44 bp):
AATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGATAGT
Found at i:28993670 original size:129 final size:131
Alignment explanation
Indices: 28993517--28993777 Score: 357
Period size: 129 Copynumber: 2.0 Consensus size: 131
28993507 GTGAAGCTGA
* *
28993517 TAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGTGTCAAATCTTATCTCCCT
1 TAAAATAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCGTCAAATCTTATCTCCCT
* ** * *
28993582 GAGATTACAGCGGAGCAGATTGAAG-ATAGT-A-ATCCTATCTCCCTGAGATTACAGTGGAGCGG
66 GAGATTACAGCGGAACAGACCGAAGAAT-GTCAGATCCTATCTCCCTGAGATTACAGCGGAGCAG
28993644 AT
130 AT
* ** *
28993646 TAAAATGAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCGTCAGGTCTTATTTCCCT
1 TAAAATAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCGTCAAATCTTATCTCCCT
* * * *
28993711 GAGGTTACAGTGGAACAGACCGAAGAATTTCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGA
66 GAGATTACAGCGGAACAGACCGAAGAATGTCAGATCCTATCTCCCTGAGATTACAGCGGAGCAGA
28993776 T
131 T
28993777 T
1 T
28993778 GAAGCTAGTA
Statistics
Matches: 114, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
129 80 0.70
130 3 0.03
131 31 0.27
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (131 bp):
TAAAATAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCGTCAAATCTTATCTCCCT
GAGATTACAGCGGAACAGACCGAAGAATGTCAGATCCTATCTCCCTGAGATTACAGCGGAGCAGA
T
Found at i:28993719 original size:85 final size:84
Alignment explanation
Indices: 28993617--28993906 Score: 260
Period size: 85 Copynumber: 3.4 Consensus size: 84
28993607 ATAGTAATCC
* *
28993617 TATCTCCCTGAGATTACAGTGGAGCGGATTAAAATGAAGGATCTTATCTCTCTGAAGTTACAGCA
1 TATCTCCCTGAGATTACAGTGGAGCAGATTAAAAT-AAAGATCTTATCTCTCTGAAGTTACAGCA
* *
28993682 GAGTAGATCGCGTCAGGTCT
65 GAGTAGATCGAGTCAGATCT
* * * ** ** *
28993702 TATTTCCCTGAGGTTACAGTGGAACAGACCGAAGAATTTCAGATCTTATCTCCCTG-AGATTACA
1 TATCTCCCTGAGATTACAGTGGAGCAGA-TTAA-AA-TAAAGATCTTATCTCTCTGAAG-TTACA
* * * *
28993766 GCGGAGCAGATTGAAG-CTAGTAATCC
62 GCAGAGTAGATCG-AGTC-AG--ATCT
* * * *
28993792 TATCTCCCTGAGATTACAGTGAAGCGGATTAAAATAAAAGATCTTATCTTTCTGAAGTTACAGTA
1 TATCTCCCTGAGATTACAGTGGAGCAGATTAAAAT-AAAGATCTTATCTCTCTGAAGTTACAGCA
* *
28993857 GAGTAGATCGTGTCAAATCT
65 GAGTAGATCGAGTCAGATCT
* *
28993877 TATCTCCTTGAGATTACAGCGGAGCAGATT
1 TATCTCCCTGAGATTACAGTGGAGCAGATT
28993907 GAAGTTAGTA
Statistics
Matches: 156, Mismatches: 38, Indels: 22
0.72 0.18 0.10
Matches are distributed among these distances:
85 53 0.34
86 4 0.03
87 35 0.22
88 35 0.22
89 4 0.03
90 25 0.16
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (84 bp):
TATCTCCCTGAGATTACAGTGGAGCAGATTAAAATAAAGATCTTATCTCTCTGAAGTTACAGCAG
AGTAGATCGAGTCAGATCT
Found at i:28993773 original size:175 final size:175
Alignment explanation
Indices: 28993569--28993904 Score: 546
Period size: 175 Copynumber: 1.9 Consensus size: 175
28993559 ATCGTGTCAA
28993569 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGATAGTAATCCTATCTCCCTGAGATTAC
1 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGATAGTAATCCTATCTCCCTGAGATTAC
* * * **
28993634 AGTGGAGCGGATTAAAATGAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCGTCAGG
66 AGTGAAGCGGATTAAAATAAAAGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCGTCAAA
* * *
28993699 TCTTATTTCCCTGAGGTTACAGTGGAACAGACCGAAGAATTTCAG
131 TCTTATCTCCCTGAGATTACAGCGGAACAGACCGAAGAATTTCAG
*
28993744 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTAC
1 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGATAGTAATCCTATCTCCCTGAGATTAC
* * *
28993809 AGTGAAGCGGATTAAAATAAAAGATCTTATCTTTCTGAAGTTACAGTAGAGTAGATCGTGTCAAA
66 AGTGAAGCGGATTAAAATAAAAGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCGTCAAA
* *
28993874 TCTTATCTCCTTGAGATTACAGCGGAGCAGA
131 TCTTATCTCCCTGAGATTACAGCGGAACAGA
28993905 TTGAAGTTAG
Statistics
Matches: 147, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
175 147 1.00
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (175 bp):
ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGATAGTAATCCTATCTCCCTGAGATTAC
AGTGAAGCGGATTAAAATAAAAGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCGTCAAA
TCTTATCTCCCTGAGATTACAGCGGAACAGACCGAAGAATTTCAG
Found at i:28993897 original size:129 final size:129
Alignment explanation
Indices: 28993744--28994057 Score: 520
Period size: 129 Copynumber: 2.4 Consensus size: 129
28993734 AGAATTTCAG
28993744 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTAC
1 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTAC
* * *
28993809 AGTGAAGCGGATTAAAATAAAAGATCTTATCTTTCTGAAGTTACAGTAGAGTAGATCGTGTCAA
66 AGTGAAGCGGATTAAAATAAAAGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCGTATCAA
* *
28993873 ATCTTATCTCCTTGAGATTACAGCGGAGCAGATTGAAGTTAGTAATCCTATCTCCCTGAGATTAC
1 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTAC
* * * *
28993938 AGTGGAGTGGATTAAAATAAACGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCGTATCAG
66 AGTGAAGCGGATTAAAATAAAAGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCGTATCAA
* * *
28994002 GTCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCCAGTAATTCTATCTCCC
1 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCC
28994058 CGACGTTGCG
Statistics
Matches: 171, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
129 171 1.00
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (129 bp):
ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTAC
AGTGAAGCGGATTAAAATAAAAGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCGTATCAA
Found at i:28994950 original size:17 final size:16
Alignment explanation
Indices: 28994921--28994954 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
28994911 TTTGCAATCG
28994921 ATTTTTTTATATTTTT
1 ATTTTTTTATATTTTT
*
28994937 ATTTTTGTTTTATTTTT
1 ATTTTT-TTATATTTTT
28994954 A
1 A
28994955 AACAACGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (16 bp):
ATTTTTTTATATTTTT
Found at i:28997541 original size:21 final size:21
Alignment explanation
Indices: 28997515--28997567 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
28997505 AGCGGTGGCG
*
28997515 GTGAGATTAGTTACTGTAGCA
1 GTGAGATTAGATACTGTAGCA
* *
28997536 GTGAGATTGGATACTGTAGCG
1 GTGAGATTAGATACTGTAGCA
28997557 GTGAGATTAGA
1 GTGAGATTAGA
28997568 AACAATGGTG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.28, C:0.08, G:0.34, T:0.30
Consensus pattern (21 bp):
GTGAGATTAGATACTGTAGCA
Found at i:28997993 original size:30 final size:31
Alignment explanation
Indices: 28997959--28998017 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
28997949 ATAAATTTTA
* *
28997959 AATTT-ATACACGAATTTTGATCCAATGTGC
1 AATTTAATACACAAACTTTGATCCAATGTGC
* *
28997989 AATTTAATACATAAACTTTGATTCAATGT
1 AATTTAATACACAAACTTTGATCCAATGT
28998018 AATTAAATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 5 0.21
31 19 0.79
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.39
Consensus pattern (31 bp):
AATTTAATACACAAACTTTGATCCAATGTGC
Found at i:29002535 original size:38 final size:40
Alignment explanation
Indices: 29002430--29002535 Score: 117
Period size: 40 Copynumber: 2.7 Consensus size: 40
29002420 AGAGAATTTT
* * * *
29002430 TTTCAATATATTCAGTAGGTATGGCTTGAGAGCACATACG
1 TTTCAGTAGATTCAGTAGGTATGGCTCGAAAGCACATACG
* * *
29002470 TTTCAGTAGATTCAATAGGTAAGGCTCGAAAGCGCATACG
1 TTTCAGTAGATTCAGTAGGTATGGCTCGAAAGCACATACG
* *
29002510 -TT-AGTAGATTTAGTAGGTATCGCTCG
1 TTTCAGTAGATTCAGTAGGTATGGCTCG
29002536 TCTGAGCACC
Statistics
Matches: 55, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
38 20 0.36
39 2 0.04
40 33 0.60
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (40 bp):
TTTCAGTAGATTCAGTAGGTATGGCTCGAAAGCACATACG
Found at i:29012765 original size:55 final size:55
Alignment explanation
Indices: 29012706--29012855 Score: 168
Period size: 52 Copynumber: 2.8 Consensus size: 55
29012696 TTTGGATTTG
*
29012706 AACTGATTGTTATGTTGAAATATTGTTTCTTTTGAATCAATTGTATATATGTTTA
1 AACTGATTGTTATGTTGAAATATTGTTTCTTTTAAATCAATTGTATATATGTTTA
* * * ** *
29012761 AACTGATTGTCATGTTGAAATA---CTACTTTTAAATTGATTGTTTATATGTTTA
1 AACTGATTGTTATGTTGAAATATTGTTTCTTTTAAATCAATTGTATATATGTTTA
29012813 AA-TCGATTGTTATGTT-AGAAT-TCTGTTTCTTTTAAATCAATTG
1 AACT-GATTGTTATGTTGA-AATAT-TGTTTCTTTTAAATCAATTG
29012856 ATACGTAGCA
Statistics
Matches: 77, Mismatches: 12, Indels: 12
0.76 0.12 0.12
Matches are distributed among these distances:
51 2 0.03
52 40 0.52
55 35 0.45
ACGTcount: A:0.29, C:0.07, G:0.14, T:0.49
Consensus pattern (55 bp):
AACTGATTGTTATGTTGAAATATTGTTTCTTTTAAATCAATTGTATATATGTTTA
Found at i:29027423 original size:40 final size:40
Alignment explanation
Indices: 29027379--29027469 Score: 114
Period size: 40 Copynumber: 2.3 Consensus size: 40
29027369 CGTTTGGACA
* **
29027379 AAAAACGTCGCTATAGATCGAGC-ATTAGTGGCGCTTTT-TG
1 AAAAACGCCGCTATAGATCGA-CAATTAGCAGCG-TTTTCTG
*
29027419 AAAAACGCCGCTATAGGTCGACAATTAGCAGCGTTTTCTG
1 AAAAACGCCGCTATAGATCGACAATTAGCAGCGTTTTCTG
29027459 AAAAACGCCGC
1 AAAAACGCCGC
29027470 AAAAACAATT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
39 5 0.11
40 40 0.89
ACGTcount: A:0.31, C:0.22, G:0.23, T:0.24
Consensus pattern (40 bp):
AAAAACGCCGCTATAGATCGACAATTAGCAGCGTTTTCTG
Found at i:29027664 original size:40 final size:40
Alignment explanation
Indices: 29027579--29027728 Score: 135
Period size: 40 Copynumber: 3.8 Consensus size: 40
29027569 AGCTTTAGTG
* * *
29027579 GCATTAGCGGCGCTTTTTGAAAAACACCGCTT-TAGGTCGA
1 GCATTAGCGACGCTTTTTGAAAAACGCCG-TTATAGATCGA
* **
29027619 CCATTAGCGACGCTTTTTGAAAAACGTTGTTATAGATCGA
1 GCATTAGCGACGCTTTTTGAAAAACGCCGTTATAGATCGA
**
29027659 GCATTAGC-AGCGCTTCTTT-AAAAACGCCACTATAGATCGA
1 GCATTAGCGA-CGCTT-TTTGAAAAACGCCGTTATAGATCGA
** * * *
29027699 GCATTAATGGCGCTTTCTAAAAAACGCCGT
1 GCATTAGCGACGCTTTTTGAAAAACGCCGT
29027729 AAAAAATTCA
Statistics
Matches: 88, Mismatches: 17, Indels: 10
0.77 0.15 0.09
Matches are distributed among these distances:
39 5 0.06
40 80 0.91
41 3 0.03
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.28
Consensus pattern (40 bp):
GCATTAGCGACGCTTTTTGAAAAACGCCGTTATAGATCGA
Done.