Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 172 of 198
Found at i:53953428 original size:229 final size:229
Alignment explanation
Indices: 53953009--53953583 Score: 851
Period size: 229 Copynumber: 2.5 Consensus size: 229
53952999 AGCGGCGTTT
* *
53953009 GCAAAAACT-AAACCCAGACGACGTT-GTTTGGAGAAACTTCGGTGACATTAGTGGTGTTTTTCG
1 GCAAAAACTAAAACCCAGACGAC-TTCGTTTGGAGACACTTCGGTGACATTAGTGGCGTTTTTCG
* *
53953072 AATAGCGCCGCTAATAATATGAGTATTAGCGGTGTTTCTGTA-AAAATA--CCGTAAAAACTAAA
65 AATAGCGCCGCTAATAATATGAGTATTAGCGGCGTTT-TGTATAAAA-ACGCCGCAAAAACTAAA
* *
53953134 ACCCAGACGACGTCGTTTGGAGGCACTTCGGTGACATTAGTGGCGTTTTTTGAATAGCGCCGCTA
128 ACCCAGACGACGTCGTTTGGAGACACTTCAGTGACATTAGTGGCGTTTTTTGAATAGCGCCGCTA
53953199 ATAATATGAGTATTAGCGGCGTTTCTACAAAAACGCC
193 ATAATATGAGTATTAGCGGCGTTTCTACAAAAACGCC
* * *
53953236 GGAAAAACTAAAACCCAAACGACTTCGTTTGGAGACACTTCAGTGACATTAGTGGCGTTTTTCGA
1 GCAAAAACTAAAACCCAGACGACTTCGTTTGGAGACACTTCGGTGACATTAGTGGCGTTTTTCGA
*
53953301 GTAGCGCCGCTAATAATATGAGTATTAGCGGCGTTTTGTATAAAAACGCCGCAAAAACTAAAACC
66 ATAGCGCCGCTAATAATATGAGTATTAGCGGCGTTTTGTATAAAAACGCCGCAAAAACTAAAACC
53953366 CAGACGACGTCGTTTGGAGACACTTCAGTGACATTAGTGGCGTTTTTTGAATAGCGCCGCTAATA
131 CAGACGACGTCGTTTGGAGACACTTCAGTGACATTAGTGGCGTTTTTTGAATAGCGCCGCTAATA
* *
53953431 ATATGAGTATTAGCGGCGTTTCTATAAAAATGCC
196 ATATGAGTATTAGCGGCGTTTCTACAAAAACGCC
* * * * *
53953465 GCAAAAACTAAACCCCAGACGACGTCATTTGGAGACACTTCGGTGACTTTAGTGGCGTTTTTAGA
1 GCAAAAACTAAAACCCAGACGACTTCGTTTGGAGACACTTCGGTGACATTAGTGGCGTTTTTCGA
* * * * *
53953530 TTAGTGCCGCAAATAATAT-AGGTTTTAGCGGCGTTTTTGT-T-AAAGCGCCGCAAA
66 ATAGCGCCGCTAATAATATGA-GTATTAGCGGCG-TTTTGTATAAAAACGCCGCAAA
53953584 TGTTCTGGGT
Statistics
Matches: 316, Mismatches: 25, Indels: 13
0.89 0.07 0.04
Matches are distributed among these distances:
227 15 0.05
228 99 0.31
229 196 0.62
230 6 0.02
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (229 bp):
GCAAAAACTAAAACCCAGACGACTTCGTTTGGAGACACTTCGGTGACATTAGTGGCGTTTTTCGA
ATAGCGCCGCTAATAATATGAGTATTAGCGGCGTTTTGTATAAAAACGCCGCAAAAACTAAAACC
CAGACGACGTCGTTTGGAGACACTTCAGTGACATTAGTGGCGTTTTTTGAATAGCGCCGCTAATA
ATATGAGTATTAGCGGCGTTTCTACAAAAACGCC
Found at i:53953580 original size:41 final size:41
Alignment explanation
Indices: 53953535--53953621 Score: 104
Period size: 41 Copynumber: 2.1 Consensus size: 41
53953525 TTAGATTAGT
*
53953535 GCCGCAAATAATATAGGTTTTAGCGGCGTTTTTG-TTAAAGC
1 GCCGCAAATAATATAGGTTTTAGCGGCGTTTCTGCTT-AAGC
** * * *
53953576 GCCGCAAATGTTCTGGGTTTTCGCGGCGTTTCTGCTTAAGC
1 GCCGCAAATAATATAGGTTTTAGCGGCGTTTCTGCTTAAGC
53953617 GCCGC
1 GCCGC
53953622 TAAAAACATT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
41 37 0.95
42 2 0.05
ACGTcount: A:0.18, C:0.22, G:0.28, T:0.32
Consensus pattern (41 bp):
GCCGCAAATAATATAGGTTTTAGCGGCGTTTCTGCTTAAGC
Found at i:53953580 original size:114 final size:114
Alignment explanation
Indices: 53953009--53953583 Score: 823
Period size: 114 Copynumber: 5.0 Consensus size: 114
53952999 AGCGGCGTTT
* * *
53953009 GCAAAAACT-AAACCCAGACGACGTTGTTTGGAGAAACTTCGGTGACATTAGTGGTGTTTTTCGA
1 GCAAAAACTAAAACCCAGACGACGTCGTTTGGAGACACTTCGGTGACATTAGTGGCGTTTTTCGA
* **
53953073 ATAGCGCCGCTAATAATATGAGTATTAGCGGTGTTTCTGTAAAAATACC
66 ATAGCGCCGCTAATAATATGAGTATTAGCGGCGTTTCTGTAAAAACGCC
* * *
53953122 GTAAAAACTAAAACCCAGACGACGTCGTTTGGAGGCACTTCGGTGACATTAGTGGCGTTTTTTGA
1 GCAAAAACTAAAACCCAGACGACGTCGTTTGGAGACACTTCGGTGACATTAGTGGCGTTTTTCGA
**
53953187 ATAGCGCCGCTAATAATATGAGTATTAGCGGCGTTTCTACAAAAACGCC
66 ATAGCGCCGCTAATAATATGAGTATTAGCGGCGTTTCTGTAAAAACGCC
* * * *
53953236 GGAAAAACTAAAACCCAAACGACTTCGTTTGGAGACACTTCAGTGACATTAGTGGCGTTTTTCGA
1 GCAAAAACTAAAACCCAGACGACGTCGTTTGGAGACACTTCGGTGACATTAGTGGCGTTTTTCGA
*
53953301 GTAGCGCCGCTAATAATATGAGTATTAGCGGCGTTT-TGTATAAAAACGCC
66 ATAGCGCCGCTAATAATATGAGTATTAGCGGCGTTTCTG--TAAAAACGCC
* *
53953351 GCAAAAACTAAAACCCAGACGACGTCGTTTGGAGACACTTCAGTGACATTAGTGGCGTTTTTTGA
1 GCAAAAACTAAAACCCAGACGACGTCGTTTGGAGACACTTCGGTGACATTAGTGGCGTTTTTCGA
* *
53953416 ATAGCGCCGCTAATAATATGAGTATTAGCGGCGTTTCTATAAAAATGCC
66 ATAGCGCCGCTAATAATATGAGTATTAGCGGCGTTTCTGTAAAAACGCC
* * * *
53953465 GCAAAAACTAAACCCCAGACGACGTCATTTGGAGACACTTCGGTGACTTTAGTGGCGTTTTTAGA
1 GCAAAAACTAAAACCCAGACGACGTCGTTTGGAGACACTTCGGTGACATTAGTGGCGTTTTTCGA
* * * * * * *
53953530 TTAGTGCCGCAAATAATAT-AGGTTTTAGCGGCGTTTTTGTTAAAGCGCC
66 ATAGCGCCGCTAATAATATGA-GTATTAGCGGCGTTTCTGTAAAAACGCC
53953579 GCAAA
1 GCAAA
53953584 TGTTCTGGGT
Statistics
Matches: 416, Mismatches: 41, Indels: 9
0.89 0.09 0.02
Matches are distributed among these distances:
113 10 0.02
114 300 0.72
115 105 0.25
116 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (114 bp):
GCAAAAACTAAAACCCAGACGACGTCGTTTGGAGACACTTCGGTGACATTAGTGGCGTTTTTCGA
ATAGCGCCGCTAATAATATGAGTATTAGCGGCGTTTCTGTAAAAACGCC
Found at i:53954353 original size:14 final size:15
Alignment explanation
Indices: 53954327--53954357 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
53954317 ACTATATATA
53954327 TATGGATTTAGGGAT
1 TATGGATTTAGGGAT
53954342 TATGGA-TTAGGGAT
1 TATGGATTTAGGGAT
53954356 TA
1 TA
53954358 AGGGTTGGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.29, C:0.00, G:0.32, T:0.39
Consensus pattern (15 bp):
TATGGATTTAGGGAT
Found at i:53954507 original size:320 final size:320
Alignment explanation
Indices: 53954093--53954832 Score: 1385
Period size: 320 Copynumber: 2.3 Consensus size: 320
53954083 GGGGGTAGAT
53954093 GTTAG-GGTTAAGAGTTAGGGATTTAGGGTATAAGGTTCCAAGGGTCGGGTTAGGGTTTTGGGTT
1 GTTAGTGGTTAAGAGTTAGGGATTTAGGGTATAAGGTTCCAAGGGTCGGGTTAGGGTTTTGGGTT
53954157 TAGATTATTATTTATTTATTTATATTTTAAATACGTTATTATGTAGTTGTAAAAGATAATAATAA
66 TAGATTATTATTTATTTATTTATATTTTAAATACGTTATTATGTAGTTGTAAAAGATAATAATAA
53954222 AATTGTTTAGAGTTTTTAATTAGTTTAGGGTATATGATAAATTTAAAATTTAACGCCGGTTTAGG
131 AATTGTTTAGAGTTTTTAATTAGTTTAGGGTATATGATAAATTTAAAATTTAACGCCGGTTTAGG
53954287 AGTTCATATTTAAATTAAGGTTTAGGGAGTACTATATATATATGGATTTAGGGATTATGGATTAG
196 AGTTCATATTTAAATTAAGGTTTAGGGAGTACTATATATATATGGATTTAGGGATTATGGATTAG
53954352 GGATTAAGGGTTGGTCGGGATTTATGGTTTAGGTGTTAGGGGTTTAATAAGGGGTTGCAC
261 GGATTAAGGGTTGGTCGGGATTTATGGTTTAGGTGTTAGGGGTTTAATAAGGGGTTGCAC
53954412 GTTAGTGGTTAAGAGTTAGGGATTTAGGGTATAAGGTTCCAAGGGTCGGGTTAGGGTTTTGGGTT
1 GTTAGTGGTTAAGAGTTAGGGATTTAGGGTATAAGGTTCCAAGGGTCGGGTTAGGGTTTTGGGTT
53954477 TAGATTATTATTTATTTATTTATATTTTAAATACGTTATTATGTAGTTGTAAAAGATAATAATAA
66 TAGATTATTATTTATTTATTTATATTTTAAATACGTTATTATGTAGTTGTAAAAGATAATAATAA
53954542 AATTGTTTAGAGTTTTTAATTAGTTTAGGGTATATGATAAATTTAAAATTTAACGCCGGTTTAGG
131 AATTGTTTAGAGTTTTTAATTAGTTTAGGGTATATGATAAATTTAAAATTTAACGCCGGTTTAGG
53954607 AGTTCATATTTAAATTAAGGTTTAGGGAGTACTATATATATATGGATTTAGGGATTATGGATTAG
196 AGTTCATATTTAAATTAAGGTTTAGGGAGTACTATATATATATGGATTTAGGGATTATGGATTAG
53954672 GGATTAAGGGTTGGTCGGGATTTATGGTTTAGGTGTTAGGGGTTTAATAAGGGGTTGCAC
261 GGATTAAGGGTTGGTCGGGATTTATGGTTTAGGTGTTAGGGGTTTAATAAGGGGTTGCAC
* * ** *
53954732 GTTAGTGGTTAAGAGTTAGGGATTTAAGAGGTTTAGGGTTTTAAGAGGGTCGGGTTAGAGTTTTG
1 GTTAGTGGTTAAGAGTTAGGGATTT-AG-GGTATAAGG-TTCCA-AGGGTCGGGTTAGGGTTTTG
53954797 GGTTTAGATTATTA-TTATTTATTTATATTTTAAATA
62 GGTTTAGATTATTATTTATTTATTTATATTTTAAATA
53954833 TATGTTCTTA
Statistics
Matches: 411, Mismatches: 5, Indels: 6
0.97 0.01 0.01
Matches are distributed among these distances:
319 5 0.01
320 339 0.82
321 2 0.00
322 7 0.02
323 25 0.06
324 33 0.08
ACGTcount: A:0.29, C:0.03, G:0.26, T:0.41
Consensus pattern (320 bp):
GTTAGTGGTTAAGAGTTAGGGATTTAGGGTATAAGGTTCCAAGGGTCGGGTTAGGGTTTTGGGTT
TAGATTATTATTTATTTATTTATATTTTAAATACGTTATTATGTAGTTGTAAAAGATAATAATAA
AATTGTTTAGAGTTTTTAATTAGTTTAGGGTATATGATAAATTTAAAATTTAACGCCGGTTTAGG
AGTTCATATTTAAATTAAGGTTTAGGGAGTACTATATATATATGGATTTAGGGATTATGGATTAG
GGATTAAGGGTTGGTCGGGATTTATGGTTTAGGTGTTAGGGGTTTAATAAGGGGTTGCAC
Found at i:53954673 original size:14 final size:15
Alignment explanation
Indices: 53954647--53954677 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
53954637 ACTATATATA
53954647 TATGGATTTAGGGAT
1 TATGGATTTAGGGAT
53954662 TATGGA-TTAGGGAT
1 TATGGATTTAGGGAT
53954676 TA
1 TA
53954678 AGGGTTGGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.29, C:0.00, G:0.32, T:0.39
Consensus pattern (15 bp):
TATGGATTTAGGGAT
Found at i:53954760 original size:15 final size:16
Alignment explanation
Indices: 53954740--53954778 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
53954730 ACGTTAGTGG
53954740 TTAAGAG-TTAGGGAT
1 TTAAGAGTTTAGGGAT
*
53954755 TTAAGAGGTTTAGGGTT
1 TTAAGA-GTTTAGGGAT
53954772 TTAAGAG
1 TTAAGAG
53954779 GGTCGGGTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 6 0.29
16 2 0.10
17 13 0.62
ACGTcount: A:0.31, C:0.00, G:0.33, T:0.36
Consensus pattern (16 bp):
TTAAGAGTTTAGGGAT
Found at i:53954769 original size:17 final size:17
Alignment explanation
Indices: 53954747--53954779 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
53954737 TGGTTAAGAG
53954747 TTAGGGATTTAAGAGGT
1 TTAGGGATTTAAGAGGT
*
53954764 TTAGGGTTTTAAGAGG
1 TTAGGGATTTAAGAGG
53954780 GTCGGGTTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.36, T:0.36
Consensus pattern (17 bp):
TTAGGGATTTAAGAGGT
Found at i:53955149 original size:20 final size:20
Alignment explanation
Indices: 53955120--53955172 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
53955110 AAATAAAATT
*
53955120 AAAATTAAAATTAAA-ATACA
1 AAAATCAAAATTAAATATA-A
*
53955140 AAAATCAAAATGAAATATAA
1 AAAATCAAAATTAAATATAA
*
53955160 AAACTCTAAAATT
1 AAAATC-AAAATT
53955173 TTTAATTTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 19 0.70
21 8 0.30
ACGTcount: A:0.66, C:0.08, G:0.02, T:0.25
Consensus pattern (20 bp):
AAAATCAAAATTAAATATAA
Found at i:53955684 original size:84 final size:83
Alignment explanation
Indices: 53955467--53955738 Score: 251
Period size: 84 Copynumber: 3.2 Consensus size: 83
53955457 AATTTTATCA
* * * * * ** * **
53955467 TTTTTGTAAACAAAATGGTGTCGTTTTGCCTGGCATATTAACGGCATTAGTGGCATTACGCCGAA
1 TTTTT-TAAACAAAACGGTGTCATTTTCCCTGGCACATTAACGACATTAGTGGCGCTATGGTGAA
**
53955532 AACGCTGCAAA-TTGTCGGGG
65 AACGCCACAAAGTT-TC-GGG
* ** * * ** * * * *
53955552 TTTTTTTTAATGAAATGGTGTCGTTTTAACTAGCACATTAAGGGCATTAGTGGTGCTATGGT-AA
1 -TTTTTTAAACAAAACGGTGTCATTTTCCCTGGCACATTAACGACATTAGTGGCGCTATGGTGAA
*
53955616 AAGCGCCGCAAAGTTTTCGGG
65 AA-CGCCACAAAG-TTTCGGG
*
53955637 TTTTTTAAACCAAACGGTGTCATTTTCCCTGGCACATTAACGACATTAGTGGCGCTATGGTGAAA
1 TTTTTTAAACAAAACGGTGTCATTTTCCCTGGCACATTAACGACATTAGTGGCGCTATGGTGAAA
53955702 ACGCCACAAAGTTTCGGG
66 ACGCCACAAAGTTTCGGG
53955720 TTTTTTAAACAAAACGGTG
1 TTTTTTAAACAAAACGGTG
53955739 CCGTTTTGCC
Statistics
Matches: 154, Mismatches: 28, Indels: 11
0.80 0.15 0.06
Matches are distributed among these distances:
83 25 0.16
84 63 0.41
85 57 0.37
86 7 0.05
87 2 0.01
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.32
Consensus pattern (83 bp):
TTTTTTAAACAAAACGGTGTCATTTTCCCTGGCACATTAACGACATTAGTGGCGCTATGGTGAAA
ACGCCACAAAGTTTCGGG
Found at i:53958241 original size:31 final size:31
Alignment explanation
Indices: 53958205--53958359 Score: 173
Period size: 31 Copynumber: 5.1 Consensus size: 31
53958195 TACATATCAT
53958205 TTAATTAATTAATATACATAAATTACATAAC
1 TTAATTAATTAATATACATAAATTACATAAC
53958236 TTAATTAATTAATATACATAAATTACATAAC
1 TTAATTAATTAATATACATAAATTACATAAC
53958267 -TAATTACATTAATATTATACATAAATTACATAAC
1 TTAATTA-ATT-A-A-TATACATAAATTACATAAC
**
53958301 TTTGTTAATTAATAT---T--A-TACATAAC
1 TTAATTAATTAATATACATAAATTACATAAC
* *
53958326 TTACATTAA-TATTATACATAACTTACATAAC
1 TTA-ATTAATTAATATACATAAATTACATAAC
53958357 TTA
1 TTA
53958360 CAACTTACAT
Statistics
Matches: 106, Mismatches: 6, Indels: 24
0.78 0.04 0.18
Matches are distributed among these distances:
25 15 0.14
26 5 0.05
28 2 0.02
30 6 0.06
31 48 0.45
32 2 0.02
33 2 0.02
34 22 0.21
35 4 0.04
ACGTcount: A:0.48, C:0.11, G:0.01, T:0.41
Consensus pattern (31 bp):
TTAATTAATTAATATACATAAATTACATAAC
Found at i:53958254 original size:22 final size:22
Alignment explanation
Indices: 53958228--53958350 Score: 69
Period size: 22 Copynumber: 5.5 Consensus size: 22
53958218 ATACATAAAT
53958228 TACATAACTTAATTAATTAATA
1 TACATAACTTAATTAATTAATA
* *
53958250 TACATAAATTACA-TAACTAAT-
1 TACATAACTTA-ATTAATTAATA
* *
53958271 TACATTAA--TATTATACATAAAT-
1 TACA-TAACTTAAT-TA-ATTAATA
**
53958293 TACATAACTTTGTTAATTAATATTA
1 TACATAACTTAATTAATT-A-A-TA
*
53958318 TACATAACTTACATTAA-TATTA
1 TACATAACTTA-ATTAATTAATA
53958340 TACATAACTTA
1 TACATAACTTA
53958351 CATAACTTAC
Statistics
Matches: 78, Mismatches: 11, Indels: 24
0.69 0.10 0.21
Matches are distributed among these distances:
20 2 0.03
21 11 0.14
22 44 0.56
23 4 0.05
24 2 0.03
25 11 0.14
26 4 0.05
ACGTcount: A:0.47, C:0.11, G:0.01, T:0.41
Consensus pattern (22 bp):
TACATAACTTAATTAATTAATA
Found at i:53958291 original size:34 final size:34
Alignment explanation
Indices: 53958205--53958331 Score: 172
Period size: 34 Copynumber: 3.8 Consensus size: 34
53958195 TACATATCAT
*
53958205 TTAATTAATTAATATACATAAATTACATAACTTAA
1 TTAATTAA-TATTATACATAAATTACATAACTTAA
53958240 TTAATT-A-A-TATACATAAATTACATAAC-TAA
1 TTAATTAATATTATACATAAATTACATAACTTAA
**
53958270 TTACATTAATATTATACATAAATTACATAACTTTG
1 TTA-ATTAATATTATACATAAATTACATAACTTAA
*
53958305 TTAATTAATATTATACATAACTTACAT
1 TTAATTAATATTATACATAAATTACAT
53958332 TAATATTATA
Statistics
Matches: 84, Mismatches: 3, Indels: 11
0.86 0.03 0.11
Matches are distributed among these distances:
30 6 0.07
31 22 0.26
32 2 0.02
33 1 0.01
34 43 0.51
35 10 0.12
ACGTcount: A:0.48, C:0.10, G:0.01, T:0.41
Consensus pattern (34 bp):
TTAATTAATATTATACATAAATTACATAACTTAA
Found at i:53958321 original size:25 final size:24
Alignment explanation
Indices: 53958293--53958349 Score: 75
Period size: 22 Copynumber: 2.4 Consensus size: 24
53958283 ATACATAAAT
53958293 TACATAACTTTGTTA-ATTAATATTA
1 TACATAAC-TT-TTACATTAATATTA
53958318 TACATAAC--TTACATTAATATTA
1 TACATAACTTTTACATTAATATTA
53958340 TACATAACTT
1 TACATAACTT
53958350 ACATAACTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
21 3 0.10
22 18 0.62
25 8 0.28
ACGTcount: A:0.42, C:0.12, G:0.02, T:0.44
Consensus pattern (24 bp):
TACATAACTTTTACATTAATATTA
Found at i:53958351 original size:22 final size:22
Alignment explanation
Indices: 53958308--53958353 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
53958298 AACTTTGTTA
53958308 ATTAATATTATACATAACTTAC
1 ATTAATATTATACATAACTTAC
53958330 ATTAATATTATACATAACTTAC
1 ATTAATATTATACATAACTTAC
53958352 AT
1 AT
53958354 AACTTACAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.41
Consensus pattern (22 bp):
ATTAATATTATACATAACTTAC
Found at i:53958354 original size:9 final size:9
Alignment explanation
Indices: 53958340--53958490 Score: 113
Period size: 9 Copynumber: 17.7 Consensus size: 9
53958330 ATTAATATTA
53958340 TACATAACT
1 TACATAACT
53958349 TACATAACT
1 TACATAACT
53958358 TAC--AACT
1 TACATAACT
53958365 TACATAACT
1 TACATAACT
***
53958374 TACATTTTTT
1 TACA-TAACT
*
53958384 TA-ATTA-T
1 TACATAACT
* *
53958391 T-CGTAAAT
1 TACATAACT
*
53958399 TACATCACT
1 TACATAACT
* *
53958408 TACTTAATT
1 TACATAACT
*
53958417 TTCATAA--
1 TACATAACT
*
53958424 TAAATAACT
1 TACATAACT
53958433 TACATAACT
1 TACATAACT
53958442 TACATAACT
1 TACATAACT
53958451 TAC--AACT
1 TACATAACT
53958458 TACATAACT
1 TACATAACT
* *
53958467 TATATGACT
1 TACATAACT
53958476 TACATAACT
1 TACATAACT
53958485 TACATA
1 TACATA
53958491 GCATAATTTT
Statistics
Matches: 111, Mismatches: 21, Indels: 20
0.73 0.14 0.13
Matches are distributed among these distances:
7 23 0.21
8 4 0.04
9 80 0.72
10 4 0.04
ACGTcount: A:0.41, C:0.19, G:0.01, T:0.39
Consensus pattern (9 bp):
TACATAACT
Found at i:53958366 original size:16 final size:16
Alignment explanation
Indices: 53958345--53958377 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
53958335 TATTATACAT
53958345 AACTTACATAACTTAC
1 AACTTACATAACTTAC
53958361 AACTTACATAACTTAC
1 AACTTACATAACTTAC
53958377 A
1 A
53958378 TTTTTTTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.45, C:0.24, G:0.00, T:0.30
Consensus pattern (16 bp):
AACTTACATAACTTAC
Found at i:53958378 original size:56 final size:58
Alignment explanation
Indices: 53958195--53958378 Score: 146
Period size: 56 Copynumber: 3.1 Consensus size: 58
53958185 CATAAGCTTG
* * * *
53958195 TACATATCATTTA-ATTAATTAATATACATAAATTACATAACTTAATTAATTAATATACATAAAT
1 TACATAACA-TTACATTAA-TATTATACATAAATTACATAAC-T--TTGA-CAAT-TACATAAAT
** *
53958259 TACATAACTAATTACATTAATATTATACATAAATTACATAACTTTGTTAATTA-AT-ATT
1 TACATAAC--ATTACATTAATATTATACATAAATTACATAACTTTGACAATTACATAAAT
* *
53958317 ATACATAAC-TTACATTAATATTATACATAACTTACATAAC-TT-ACAACTTACATAACT
1 -TACATAACATTACATTAATATTATACATAAATTACATAACTTTGACAA-TTACATAAAT
53958374 TACAT
1 TACAT
53958379 TTTTTTAATT
Statistics
Matches: 104, Mismatches: 9, Indels: 22
0.77 0.07 0.16
Matches are distributed among these distances:
54 2 0.02
55 5 0.05
56 37 0.36
57 2 0.02
58 2 0.02
59 10 0.10
60 2 0.02
61 4 0.04
62 2 0.02
64 8 0.08
65 24 0.23
66 6 0.06
ACGTcount: A:0.47, C:0.13, G:0.01, T:0.40
Consensus pattern (58 bp):
TACATAACATTACATTAATATTATACATAAATTACATAACTTTGACAATTACATAAAT
Found at i:53958521 original size:25 final size:25
Alignment explanation
Indices: 53958492--53958547 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
53958482 ACTTACATAG
* *
53958492 CATAATTTTCATAATACACAACTTA
1 CATAATTTGCATAATAAACAACTTA
** *
53958517 CATAATTTGGGTAATAAATAACTTA
1 CATAATTTGCATAATAAACAACTTA
53958542 CATAAT
1 CATAAT
53958548 ACATAACTTA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.45, C:0.14, G:0.05, T:0.36
Consensus pattern (25 bp):
CATAATTTGCATAATAAACAACTTA
Found at i:53958547 original size:16 final size:16
Alignment explanation
Indices: 53958528--53958561 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
53958518 ATAATTTGGG
53958528 TAATAAATAACTTACA
1 TAATAAATAACTTACA
*
53958544 TAATACATAACTTACA
1 TAATAAATAACTTACA
53958560 TA
1 TA
53958562 GCTTAACTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.53, C:0.15, G:0.00, T:0.32
Consensus pattern (16 bp):
TAATAAATAACTTACA
Found at i:53964146 original size:66 final size:66
Alignment explanation
Indices: 53964063--53964209 Score: 199
Period size: 66 Copynumber: 2.2 Consensus size: 66
53964053 GAGACAACAT
*
53964063 CGAGAGAAGCTGAGGTTCAA-AAAAGATATGAAGAACTCCAGCTA-CAACTGAAAGCAGATGCAG
1 CGAGAGAAGTTGAGGTTCAACAAAAG-TATGAAGAACTCCAGC-AGCAACTGAAAGCAGATGCAG
53964126 CAG
64 CAG
* * * *
53964129 CGAGAGAAGTTGAGGTTCAACGAAAGTATGAAGAACTCCAGCAGCAGCTTAAAGCAGATGCGGCA
1 CGAGAGAAGTTGAGGTTCAACAAAAGTATGAAGAACTCCAGCAGCAACTGAAAGCAGATGCAGCA
53964194 G
66 G
* *
53964195 CAAGAGAAGTAGAGG
1 CGAGAGAAGTTGAGG
53964210 CGGCAGCAAG
Statistics
Matches: 72, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
65 1 0.01
66 67 0.93
67 4 0.06
ACGTcount: A:0.40, C:0.17, G:0.29, T:0.14
Consensus pattern (66 bp):
CGAGAGAAGTTGAGGTTCAACAAAAGTATGAAGAACTCCAGCAGCAACTGAAAGCAGATGCAGCA
G
Found at i:53964245 original size:21 final size:21
Alignment explanation
Indices: 53964191--53964258 Score: 82
Period size: 21 Copynumber: 3.2 Consensus size: 21
53964181 AGCAGATGCG
* *
53964191 GCAGCAAGAGAAGTAGAGGCG
1 GCAGCAAGAGAAGTAAAGGCT
*
53964212 GCAGCAAGAGAAGTACAGGCT
1 GCAGCAAGAGAAGTAAAGGCT
* * *
53964233 GCAGCGAGGGAAGCAAAGGCT
1 GCAGCAAGAGAAGTAAAGGCT
53964254 GCAGC
1 GCAGC
53964259 GAGGGAAGCA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.35, C:0.19, G:0.40, T:0.06
Consensus pattern (21 bp):
GCAGCAAGAGAAGTAAAGGCT
Found at i:53964259 original size:21 final size:21
Alignment explanation
Indices: 53964228--53964268 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
53964218 AGAGAAGTAC
53964228 AGGCTGCAGCGAGGGAAGCAA
1 AGGCTGCAGCGAGGGAAGCAA
53964249 AGGCTGCAGCGAGGGAAGCA
1 AGGCTGCAGCGAGGGAAGCA
53964269 GAGCAGCGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.32, C:0.20, G:0.44, T:0.05
Consensus pattern (21 bp):
AGGCTGCAGCGAGGGAAGCAA
Found at i:53964669 original size:43 final size:43
Alignment explanation
Indices: 53964622--53964976 Score: 259
Period size: 43 Copynumber: 8.3 Consensus size: 43
53964612 AGGTGTTGGC
* * * *
53964622 CTTTAGTGGCGTTTTTGGTCAAAGCACCGCTAAAGATAAGGGT
1 CTTTAGCGGCGTTTGTGGTCAAAGCGCCGCTAAAGATCAGGGT
** * *
53964665 CTTTAGCGGCGTTTGTGGAAAAAGCGCCACTAAAGATCATGGT
1 CTTTAGCGGCGTTTGTGGTCAAAGCGCCGCTAAAGATCAGGGT
** * * *
53964708 CTTTAGCGGCGTTTGTGGGGAAAGCGCCGGTAAAGATTAGGTT
1 CTTTAGCGGCGTTTGTGGTCAAAGCGCCGCTAAAGATCAGGGT
* * * * *
53964751 CTTTAGTGACGTTTGTGGTCGAAGCGCAGCTATAGATCAGGGT
1 CTTTAGCGGCGTTTGTGGTCAAAGCGCCGCTAAAGATCAGGGT
** ** * *
53964794 CTATT-GCGGCGTTTAAGGGGAAAGCGCCGCTAAAGATTAGGTT
1 CT-TTAGCGGCGTTTGTGGTCAAAGCGCCGCTAAAGATCAGGGT
* * * ** *
53964837 CTTTCGTGGCATTTGTGGTTGAAGCGCCGCTATAGATCAGGGT
1 CTTTAGCGGCGTTTGTGGTCAAAGCGCCGCTAAAGATCAGGGT
* * * ** *
53964880 CTATT-GCGGCGTTTGAGAG-AAAAGCGCCGCTAAAGACCCTGAT
1 CT-TTAGCGGCGTTTGTG-GTCAAAGCGCCGCTAAAGATCAGGGT
* * * ** * *
53964923 CTTTAGCCGCGCTTCT-CCCAAAAACGCCGCTAAAGATCAAGGT
1 CTTTAGCGGCGTTTGTGGTC-AAAGCGCCGCTAAAGATCAGGGT
53964966 CTTTAGCGGCG
1 CTTTAGCGGCG
53964977 CTTCCACTAA
Statistics
Matches: 237, Mismatches: 68, Indels: 14
0.74 0.21 0.04
Matches are distributed among these distances:
42 4 0.02
43 228 0.96
44 5 0.02
ACGTcount: A:0.24, C:0.20, G:0.30, T:0.27
Consensus pattern (43 bp):
CTTTAGCGGCGTTTGTGGTCAAAGCGCCGCTAAAGATCAGGGT
Found at i:53964865 original size:129 final size:129
Alignment explanation
Indices: 53964622--53964854 Score: 290
Period size: 129 Copynumber: 1.8 Consensus size: 129
53964612 AGGTGTTGGC
* * * **
53964622 CTTTAGTGGCGTTTTTGGTCAAAGCACCGCTAAAGATAAGGGTCTTTAGCGGCGTTTGTGGAAAA
1 CTTTAGTGACGTTTGTGGTCAAAGCACAGCTAAAGATAAGGGTCTTTAGCGGCGTTTAAGGAAAA
*
53964687 AGCGCCACTAAAGATCATGGTCTTTAGCGGCGTTTGTGGGGAAAGCGCCGGTAAAGATTAGGTT
66 AGCGCCACTAAAGATCATGGTCTTTAGCGGCATTTGTGGGGAAAGCGCCGGTAAAGATTAGGTT
* * * * **
53964751 CTTTAGTGACGTTTGTGGTCGAAGCGCAGCTATAGATCAGGGTCTATT-GCGGCGTTTAAGGGGA
1 CTTTAGTGACGTTTGTGGTCAAAGCACAGCTAAAGATAAGGGTCT-TTAGCGGCGTTTAAGGAAA
* * * *
53964815 AAGCGCCGCTAAAGATTA-GGTTCTTTCGTGGCATTTGTGG
65 AAGCGCCACTAAAGATCATGG-TCTTTAGCGGCATTTGTGG
53964855 TTGAAGCGCC
Statistics
Matches: 86, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
128 2 0.02
129 82 0.95
130 2 0.02
ACGTcount: A:0.23, C:0.16, G:0.32, T:0.29
Consensus pattern (129 bp):
CTTTAGTGACGTTTGTGGTCAAAGCACAGCTAAAGATAAGGGTCTTTAGCGGCGTTTAAGGAAAA
AGCGCCACTAAAGATCATGGTCTTTAGCGGCATTTGTGGGGAAAGCGCCGGTAAAGATTAGGTT
Found at i:53964926 original size:86 final size:86
Alignment explanation
Indices: 53964642--53964915 Score: 334
Period size: 86 Copynumber: 3.2 Consensus size: 86
53964632 GTTTTTGGTC
* * * * * * *** * * *
53964642 AAAGCACCGCTAAAGATAAGGGTCTTTAGCGGCGTTTGTGGAAAAAGCGCCACTAAAGATCATGG
1 AAAGCGCCGCTAAAGATTAGGTTCTTTAGTGACATTTGTGGTCGAAGCGCCGCTATAGATCAGGG
*
53964707 TCT-TTAGCGGCGTTTGTGGGG
66 TCTATT-GCGGCGTTTGAGGGG
* * *
53964728 AAAGCGCCGGTAAAGATTAGGTTCTTTAGTGACGTTTGTGGTCGAAGCGCAGCTATAGATCAGGG
1 AAAGCGCCGCTAAAGATTAGGTTCTTTAGTGACATTTGTGGTCGAAGCGCCGCTATAGATCAGGG
*
53964793 TCTATTGCGGCGTTTAAGGGG
66 TCTATTGCGGCGTTTGAGGGG
* * *
53964814 AAAGCGCCGCTAAAGATTAGGTTCTTTCGTGGCATTTGTGGTTGAAGCGCCGCTATAGATCAGGG
1 AAAGCGCCGCTAAAGATTAGGTTCTTTAGTGACATTTGTGGTCGAAGCGCCGCTATAGATCAGGG
* *
53964879 TCTATTGCGGCGTTTGAGAGA
66 TCTATTGCGGCGTTTGAGGGG
53964900 AAAGCGCCGCTAAAGA
1 AAAGCGCCGCTAAAGA
53964916 CCCTGATCTT
Statistics
Matches: 163, Mismatches: 24, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
86 161 0.99
87 2 0.01
ACGTcount: A:0.25, C:0.17, G:0.32, T:0.26
Consensus pattern (86 bp):
AAAGCGCCGCTAAAGATTAGGTTCTTTAGTGACATTTGTGGTCGAAGCGCCGCTATAGATCAGGG
TCTATTGCGGCGTTTGAGGGG
Found at i:53964978 original size:43 final size:43
Alignment explanation
Indices: 53964899--53965043 Score: 130
Period size: 43 Copynumber: 3.4 Consensus size: 43
53964889 CGTTTGAGAG
* ** *
53964899 AAAAGCGCCGCTAAAGACCCTGATCTTTAGCCGCGCTTCTCCC
1 AAAAACGCCGCTAAAGACCAAGATCTTTAGCGGCGCTTCTCCC
* * *
53964942 AAAAACGCCGCTAAAGATCAAGGTCTTTAGCGGCGCTTC-CAC
1 AAAAACGCCGCTAAAGACCAAGATCTTTAGCGGCGCTTCTCCC
* * * * * * * * *
53964984 TAAAGCGCCGCTATAGACCAACACCTTTAGCGGCGTTTATTTCT
1 AAAAACGCCGCTAAAGACCAAGATCTTTAGCGGCGCTT-CTCCC
53965028 AAAAACGCCGCTAAAG
1 AAAAACGCCGCTAAAG
53965044 TTAGCGGCGC
Statistics
Matches: 78, Mismatches: 22, Indels: 3
0.76 0.21 0.03
Matches are distributed among these distances:
42 32 0.41
43 33 0.42
44 13 0.17
ACGTcount: A:0.29, C:0.30, G:0.19, T:0.21
Consensus pattern (43 bp):
AAAAACGCCGCTAAAGACCAAGATCTTTAGCGGCGCTTCTCCC
Found at i:53968841 original size:16 final size:17
Alignment explanation
Indices: 53968820--53968851 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
53968810 TTTTATTTAA
53968820 TTATTTAAA-TAAAATT
1 TTATTTAAATTAAAATT
53968836 TTATTTAAATTAAAAT
1 TTATTTAAATTAAAAT
53968852 GATAAAGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TTATTTAAATTAAAATT
Found at i:53978805 original size:50 final size:50
Alignment explanation
Indices: 53978724--53978821 Score: 117
Period size: 50 Copynumber: 2.0 Consensus size: 50
53978714 ACCTTATTCT
* * *
53978724 AATCAATGTCAAATAGAAAGAGAGAAGTTCTATACAGATTCTACTTGTAC
1 AATCAATATCAAATAGAAAGAGAGAACTTCTATACAGATTCCACTTGTAC
* * **
53978774 AATCAATATCAAATAG-AAGAAGTGTACTTCTATATGGATTCCACTTGT
1 AATCAATATCAAATAGAAAG-AGAGAACTTCTATACAGATTCCACTTGT
53978822 GTAGCCTGTA
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
49 3 0.08
50 37 0.93
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.31
Consensus pattern (50 bp):
AATCAATATCAAATAGAAAGAGAGAACTTCTATACAGATTCCACTTGTAC
Found at i:53985050 original size:17 final size:17
Alignment explanation
Indices: 53985025--53985074 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
53985015 AACTATGTTG
* * *
53985025 ATAATTAAAATATTACA
1 ATAAATAAAATAATAAA
53985042 ATAAATAAAA-AATAAA
1 ATAAATAAAATAATAAA
53985058 ATAAAATAAAATAATAA
1 AT-AAATAAAATAATAA
53985075 TAAAATTCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 6 0.21
17 17 0.61
18 5 0.18
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (17 bp):
ATAAATAAAATAATAAA
Found at i:53985060 original size:5 final size:5
Alignment explanation
Indices: 53985050--53985080 Score: 53
Period size: 5 Copynumber: 6.0 Consensus size: 5
53985040 CAATAAATAA
53985050 AAAAT AAAAT AAAAT AAAAT AATAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AA-AAT AAAAT
53985081 TCTTATTACA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 20 0.80
6 5 0.20
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (5 bp):
AAAAT
Found at i:53985062 original size:16 final size:16
Alignment explanation
Indices: 53985041--53985079 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
53985031 AAAATATTAC
53985041 AATAAATAAAAAATAA-
1 AATAAA-AAAAAATAAT
*
53985057 AATAAAATAAAATAAT
1 AATAAAAAAAAATAAT
53985073 AATAAAA
1 AATAAAA
53985080 TTCTTATTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (16 bp):
AATAAAAAAAAATAAT
Found at i:53990334 original size:31 final size:31
Alignment explanation
Indices: 53990296--53990396 Score: 107
Period size: 31 Copynumber: 3.3 Consensus size: 31
53990286 TAATCACATT
*
53990296 AATATTAAATTAATAAAATATTATCTAGATA
1 AATATTAAATTAATAAAATAATATCTAGATA
** * *
53990327 AATATTAAATT-A-AATTTAATATCTCATATT
1 AATATTAAATTAATAAAATAATATCT-AGATA
* * *
53990357 GATATTAAATTAATAAAATACTATGTAGATA
1 AATATTAAATTAATAAAATAATATCTAGATA
53990388 AATATTAAA
1 AATATTAAA
53990397 ATTATGAGAT
Statistics
Matches: 54, Mismatches: 13, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
29 9 0.17
30 14 0.26
31 23 0.43
32 8 0.15
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.40
Consensus pattern (31 bp):
AATATTAAATTAATAAAATAATATCTAGATA
Found at i:53990842 original size:85 final size:85
Alignment explanation
Indices: 53990699--53990868 Score: 313
Period size: 85 Copynumber: 2.0 Consensus size: 85
53990689 ATACACTTGG
**
53990699 CCCGGTTCAACCAGTTTTGGGTCTCGATTTTGGTTTTTGATTCTCAGGTCCAATCTTCGATCTCG
1 CCCGGTTCAACCAGTTTTGGGTCTCGATTTCAGTTTTTGATTCTCAGGTCCAATCTTCGATCTCG
*
53990764 GGTCCAATTTTTAAGTTCAA
66 AGTCCAATTTTTAAGTTCAA
53990784 CCCGGTTCAACCAGTTTTGGGTCTCGATTTCAGTTTTTGATTCTCAGGTCCAATCTTCGATCTCG
1 CCCGGTTCAACCAGTTTTGGGTCTCGATTTCAGTTTTTGATTCTCAGGTCCAATCTTCGATCTCG
53990849 AGTCCAATTTTTAAGTTCAA
66 AGTCCAATTTTTAAGTTCAA
53990869 TTACCCATTA
Statistics
Matches: 82, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
85 82 1.00
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.39
Consensus pattern (85 bp):
CCCGGTTCAACCAGTTTTGGGTCTCGATTTCAGTTTTTGATTCTCAGGTCCAATCTTCGATCTCG
AGTCCAATTTTTAAGTTCAA
Found at i:53991989 original size:22 final size:22
Alignment explanation
Indices: 53991964--53992008 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
53991954 AAGATTATGG
53991964 ACTCGTTTAGATTATCTACTGA
1 ACTCGTTTAGATTATCTACTGA
53991986 ACTCGTTTAGATTATCTACTGA
1 ACTCGTTTAGATTATCTACTGA
53992008 A
1 A
53992009 GTAAGTTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.40
Consensus pattern (22 bp):
ACTCGTTTAGATTATCTACTGA
Found at i:53992481 original size:17 final size:18
Alignment explanation
Indices: 53992459--53992493 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
53992449 TGGTAGGGAT
53992459 TAAA-TTGAAGGCAAAAA
1 TAAATTTGAAGGCAAAAA
*
53992476 TAAATTTGAGGGCAAAAA
1 TAAATTTGAAGGCAAAAA
53992494 GCGTGAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.54, C:0.06, G:0.20, T:0.20
Consensus pattern (18 bp):
TAAATTTGAAGGCAAAAA
Found at i:53993473 original size:13 final size:14
Alignment explanation
Indices: 53993445--53993473 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
53993435 TCCCTCCATA
53993445 TTTTTAATTTTGTT
1 TTTTTAATTTTGTT
53993459 TTTTTAATTTT-TT
1 TTTTTAATTTTGTT
53993472 TT
1 TT
53993474 CCAAGTACAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.27
14 11 0.73
ACGTcount: A:0.14, C:0.00, G:0.03, T:0.83
Consensus pattern (14 bp):
TTTTTAATTTTGTT
Found at i:53994915 original size:41 final size:39
Alignment explanation
Indices: 53994793--53994928 Score: 125
Period size: 40 Copynumber: 3.5 Consensus size: 39
53994783 ATCAGTTTGG
* * * *
53994793 CACCCAGTGCCTCATCGGATAATTCAAAGGAATAATTTGA
1 CACCCAGTGCCTCATCGAATAATCCGAA-GAATAAATTGA
* * ** * *
53994833 CACCCAATGTCTCATCGGCTAAACCGAAG--TAAATTGG
1 CACCCAGTGCCTCATCGAATAATCCGAAGAATAAATTGA
53994870 CACCCAGTGCCTCATCGAATTAATCCGAAGTAATAAATTGA
1 CACCCAGTGCCTCATCGAA-TAATCCGAAG-AATAAATTGA
53994911 CACCCAGTGTCC-CATCGA
1 CACCCAGTG-CCTCATCGA
53994929 CTCAAAGTCT
Statistics
Matches: 77, Mismatches: 14, Indels: 9
0.77 0.14 0.09
Matches are distributed among these distances:
37 21 0.27
38 9 0.12
39 1 0.01
40 22 0.29
41 22 0.29
42 2 0.03
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (39 bp):
CACCCAGTGCCTCATCGAATAATCCGAAGAATAAATTGA
Found at i:53995903 original size:3 final size:3
Alignment explanation
Indices: 53995895--53995926 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
53995885 TGTTTTGTTT
53995895 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
53995927 TATTTACTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:53997777 original size:27 final size:27
Alignment explanation
Indices: 53997758--53998014 Score: 271
Period size: 27 Copynumber: 9.5 Consensus size: 27
53997748 GGGTATAACA
53997758 GTCATTTTACCCTATGGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
*
53997785 GTCATTTTACCTTATGGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* * *
53997812 GTTATTCTACCCTATGGGGGTACTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* ** *
53997839 GTCATTTTATCCTATGCAGGTAATTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
** * **
53997866 GTCATTTTACCCCGTGAGGGTATTTTA
1 GTCATTTTACCCTATGGGGGTATTTCG
* *
53997893 GTCATTCTACCTTATGGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* * *
53997920 GTCATTCTACCCTATGAGGGTATTTCA
1 GTCATTTTACCCTATGGGGGTATTTCG
* * *
53997947 GTCATTTAACCCTATGAGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCG
* * * * *
53997974 ATCATTCTATCTTATGGGGGTATTTCA
1 GTCATTTTACCCTATGGGGGTATTTCG
*
53998001 GTCATTTTATCCTA
1 GTCATTTTACCCTA
53998015 ATGAGGTATT
Statistics
Matches: 186, Mismatches: 44, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 186 1.00
ACGTcount: A:0.19, C:0.18, G:0.22, T:0.41
Consensus pattern (27 bp):
GTCATTTTACCCTATGGGGGTATTTCG
Found at i:53997887 original size:81 final size:80
Alignment explanation
Indices: 53997758--53998025 Score: 329
Period size: 81 Copynumber: 3.3 Consensus size: 80
53997748 GGGTATAACA
* * * * *
53997758 GTCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCTTATGGGGGTATTTCGGTTATTCTACC
1 GTCATTTTACCCTAT-GAGGTATTTCGGTCATTTTACCCTATGAGGGTATTTTGGTCATTCTACC
* *
53997823 CTATGGGGGTACTTCG
65 TTATGGGGGTATTTCG
* * ** *
53997839 GTCATTTTATCCTATGCAGGTAATTCGGTCATTTTACCCCGTGAGGGTATTTTAGTCATTCTACC
1 GTCATTTTACCCTATG-AGGTATTTCGGTCATTTTACCCTATGAGGGTATTTTGGTCATTCTACC
53997904 TTATGGGGGTATTTCG
65 TTATGGGGGTATTTCG
* * * * *
53997920 GTCATTCTACCCTATGAGGGTATTTCAGTCATTTAACCCTATGAGGGTATTTTGATCATTCTATC
1 GTCATTTTACCCTATGA-GGTATTTCGGTCATTTTACCCTATGAGGGTATTTTGGTCATTCTACC
*
53997985 TTATGGGGGTATTTCA
65 TTATGGGGGTATTTCG
*
53998001 GTCATTTTATCCTAATGAGGTATTT
1 GTCATTTTACCCT-ATGAGGTATTT
53998026 TGTTCATAAC
Statistics
Matches: 159, Mismatches: 25, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
80 2 0.01
81 153 0.96
82 4 0.03
ACGTcount: A:0.19, C:0.18, G:0.22, T:0.41
Consensus pattern (80 bp):
GTCATTTTACCCTATGAGGTATTTCGGTCATTTTACCCTATGAGGGTATTTTGGTCATTCTACCT
TATGGGGGTATTTCG
Found at i:53998665 original size:24 final size:24
Alignment explanation
Indices: 53998640--53998686 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
53998630 CCAAAACCCC
53998640 AATATTCTCTCATCAAATCTCTCCA
1 AATA-TCTCTCATCAAATCTCTCCA
* *
53998665 AATATCTCTCCTCAATTCTCTC
1 AATATCTCTCATCAAATCTCTC
53998687 TATGACCAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.28, C:0.34, G:0.00, T:0.38
Consensus pattern (24 bp):
AATATCTCTCATCAAATCTCTCCA
Found at i:54000973 original size:27 final size:26
Alignment explanation
Indices: 54000941--54001195 Score: 260
Period size: 27 Copynumber: 9.5 Consensus size: 26
54000931 TCTTCACTTA
**
54000941 GGGGTATAATAGTCATTTTACCCTAT
1 GGGGTATTTTAGTCATTTTACCCTAT
*
54000967 GGAGGTATTTTGGTCATTTTACCCTAT
1 GG-GGTATTTTAGTCATTTTACCCTAT
* *
54000994 GGGGTTATTTCAGTCATTTTACCTTAT
1 GGGG-TATTTTAGTCATTTTACCCTAT
* * *
54001021 AGGGGTATTTTGGTCATTCTACACTAT
1 -GGGGTATTTTAGTCATTTTACCCTAT
* *
54001048 AGGGGTATTTCGAG-CATTCTACCCTAT
1 -GGGGTATTT-TAGTCATTTTACCCTAT
54001075 AGGGGTATTTTAGTCATTTTACCCTATT
1 -GGGGTATTTTAGTCATTTTACCCTA-T
*
54001103 GGGGTATTTCAGTCATTTTACCCTAT
1 GGGGTATTTTAGTCATTTTACCCTAT
* * *
54001129 GGGGTATTTCAGTCATTCTACCCAAT
1 GGGGTATTTTAGTCATTTTACCCTAT
* ** *
54001155 AGGGATATTTCGGTTATTTTACCCTAT
1 -GGGGTATTTTAGTCATTTTACCCTAT
54001182 GGAGGTATTTTAGT
1 GG-GGTATTTTAGT
54001196 ATAACAGTGT
Statistics
Matches: 194, Mismatches: 27, Indels: 15
0.82 0.11 0.06
Matches are distributed among these distances:
26 33 0.17
27 155 0.80
28 6 0.03
ACGTcount: A:0.22, C:0.16, G:0.21, T:0.42
Consensus pattern (26 bp):
GGGGTATTTTAGTCATTTTACCCTAT
Found at i:54001009 original size:54 final size:52
Alignment explanation
Indices: 54000951--54001195 Score: 294
Period size: 54 Copynumber: 4.6 Consensus size: 52
54000941 GGGGTATAAT
* *
54000951 AGTCATTTTACCCTATGGAGGTATTTTGGTCATTTTACCCTATGGGGTTATTTC
1 AGTCATTTTACCCTATGG-GGTATTTTAGTCATTCTACCCTATGGGG-TATTTC
* * *
54001005 AGTCATTTTACCTTATAGGGGTATTTTGGTCATTCTACACTATAGGGGTATTTC
1 AGTCATTTTACCCTAT-GGGGTATTTTAGTCATTCTACCCTAT-GGGGTATTTC
* *
54001059 GAG-CATTCTACCCTATAGGGGTATTTTAGTCATTTTACCCTATTGGGGTATTTC
1 -AGTCATTTTACCCTAT-GGGGTATTTTAGTCATTCTACCCTA-TGGGGTATTTC
* * *
54001113 AGTCATTTTACCCTATGGGGTATTTCAGTCATTCTACCCAATAGGGATATTTC
1 AGTCATTTTACCCTATGGGGTATTTTAGTCATTCTACCCTAT-GGGGTATTTC
* *
54001166 GGTTATTTTACCCTATGGAGGTATTTTAGT
1 AGTCATTTTACCCTATGG-GGTATTTTAGT
54001196 ATAACAGTGT
Statistics
Matches: 168, Mismatches: 16, Indels: 14
0.85 0.08 0.07
Matches are distributed among these distances:
52 1 0.01
53 49 0.29
54 109 0.65
55 9 0.05
ACGTcount: A:0.21, C:0.17, G:0.20, T:0.42
Consensus pattern (52 bp):
AGTCATTTTACCCTATGGGGTATTTTAGTCATTCTACCCTATGGGGTATTTC
Found at i:54005969 original size:34 final size:35
Alignment explanation
Indices: 54005925--54005991 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
54005915 CAGTAAAATA
*
54005925 TTTTCCGTAAAATGATTT-CGGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
* *
54005959 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTT
54005992 CTAGTGTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.31, C:0.09, G:0.15, T:0.45
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
Found at i:54007287 original size:46 final size:46
Alignment explanation
Indices: 54007214--54007302 Score: 124
Period size: 46 Copynumber: 1.9 Consensus size: 46
54007204 TTACTGTATG
* * * *
54007214 ATATCGGTTGTATTGGTTGATATGTATAAGTTCTAAACCAATATCA
1 ATATCGATTGTATTAGTTGACAAGTATAAGTTCTAAACCAATATCA
* *
54007260 ATATCGATTGTATTAGTTGGCAAGTATAAGTTCTAAATCAATA
1 ATATCGATTGTATTAGTTGACAAGTATAAGTTCTAAACCAATA
54007303 CTAAGTAGTC
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
46 37 1.00
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.38
Consensus pattern (46 bp):
ATATCGATTGTATTAGTTGACAAGTATAAGTTCTAAACCAATATCA
Found at i:54015356 original size:24 final size:24
Alignment explanation
Indices: 54015291--54015369 Score: 72
Period size: 24 Copynumber: 3.2 Consensus size: 24
54015281 GCCATGTAAC
*
54015291 GGGAAGCT-TATGTGAGCCATATAAT
1 GGGAAGCTCTA-GAGAGCCA-ATAAT
* *
54015316 AGGAAGCTCTAGAGAGCCACTAAT
1 GGGAAGCTCTAGAGAGCCAATAAT
* *
54015340 GGGAAGCTCATA-CGAGCCAATAAC
1 GGGAAGCTC-TAGAGAGCCAATAAT
54015364 GGGAAG
1 GGGAAG
54015370 GTTCAAGTGA
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
24 27 0.60
25 16 0.36
26 2 0.04
ACGTcount: A:0.35, C:0.18, G:0.29, T:0.18
Consensus pattern (24 bp):
GGGAAGCTCTAGAGAGCCAATAAT
Found at i:54017739 original size:16 final size:17
Alignment explanation
Indices: 54017704--54017741 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
54017694 AATAAACATT
*
54017704 TTAAAATAATTTCCCAAA
1 TTAAAAAAATTT-CCAAA
54017722 TTAAAAAAATTT-CAAA
1 TTAAAAAAATTTCCAAA
54017738 TTAA
1 TTAA
54017742 TTCTAATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 8 0.42
18 11 0.58
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.34
Consensus pattern (17 bp):
TTAAAAAAATTTCCAAA
Found at i:54024558 original size:27 final size:27
Alignment explanation
Indices: 54024494--54024566 Score: 78
Period size: 27 Copynumber: 2.7 Consensus size: 27
54024484 TTTTTTGAGG
54024494 GGGAAGTAAAAGTTTTAGGAGAAAGTAAA
1 GGGAAGTAAAAGTTTT-GG-GAAAGTAAA
* **
54024523 AGGAA--AAAAGTTTTGGGAATTTAAA
1 GGGAAGTAAAAGTTTTGGGAAAGTAAA
*
54024548 GGGAAGTAAAATTTTTGGG
1 GGGAAGTAAAAGTTTTGGG
54024567 GGGAAAGTAA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
25 11 0.30
26 2 0.05
27 20 0.54
29 4 0.11
ACGTcount: A:0.44, C:0.00, G:0.30, T:0.26
Consensus pattern (27 bp):
GGGAAGTAAAAGTTTTGGGAAAGTAAA
Found at i:54024563 original size:74 final size:73
Alignment explanation
Indices: 54024420--54024579 Score: 207
Period size: 74 Copynumber: 2.2 Consensus size: 73
54024410 GAGGTTTGGA
* ** * *
54024420 GGAAGTAAAAGTTTTGGGAAGAAAGTAAAAGGAAAAAAGTTTTGGGGGTTTGGAAATAAATAAAT
1 GGAAGTAAAAGTTTTAGGAAGAAAGTAAAAGGAAAAAAGTTTTGGGAATTT-GAAAGAAATAAAA
54024485 TTTTTGAGGG
65 TTTTTG-GGG
*
54024495 GGAAGTAAAAGTTTTAGG-AGAAAGTAAAAGGAAAAAAGTTTTGGGAATTT-AAAGGGAAGTAAA
1 GGAAGTAAAAGTTTTAGGAAGAAAGTAAAAGGAAAAAAGTTTTGGGAATTTGAAA--GAAATAAA
54024558 ATTTTTGGGG
64 ATTTTTGGGG
54024568 GGAAAGTAAAAG
1 GG-AAGTAAAAG
54024580 AGTTTGAGGG
Statistics
Matches: 76, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
72 3 0.04
73 5 0.07
74 51 0.67
75 17 0.22
ACGTcount: A:0.44, C:0.00, G:0.31, T:0.26
Consensus pattern (73 bp):
GGAAGTAAAAGTTTTAGGAAGAAAGTAAAAGGAAAAAAGTTTTGGGAATTTGAAAGAAATAAAAT
TTTTGGGG
Found at i:54026785 original size:43 final size:43
Alignment explanation
Indices: 54026737--54026987 Score: 378
Period size: 43 Copynumber: 5.8 Consensus size: 43
54026727 GATTTTACAA
* * *
54026737 AAACGCCGCTAAAGGTCATTACCTTTAGCGGCGCTTCTCCCAC
1 AAACGCCGCTATAGATCATGACCTTTAGCGGCGCTTCTCCCAC
*
54026780 AAACGCCGCTATAGATCATGACCTTTAGCGGCGCTTCTTCCAC
1 AAACGCCGCTATAGATCATGACCTTTAGCGGCGCTTCTCCCAC
*
54026823 AAACGCCGCTATAGATCATGA-CTTGTAGTGGCGCTTCTCCCAC
1 AAACGCCGCTATAGATCATGACCTT-TAGCGGCGCTTCTCCCAC
* * * *
54026866 AAACGCTGCTATAGATCATGACTTTTAGCGGCCCTTCTCCTAC
1 AAACGCCGCTATAGATCATGACCTTTAGCGGCGCTTCTCCCAC
* * *
54026909 AAATGCCGCTACAGATCATGACTTTTAGCGGCGCTTCTCCCAC
1 AAACGCCGCTATAGATCATGACCTTTAGCGGCGCTTCTCCCAC
54026952 AAACGCCGCTATAGATCATGACCTTTAGCGGCGCTT
1 AAACGCCGCTATAGATCATGACCTTTAGCGGCGCTT
54026988 TTTTTTATAA
Statistics
Matches: 187, Mismatches: 19, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
42 3 0.02
43 182 0.97
44 2 0.01
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.26
Consensus pattern (43 bp):
AAACGCCGCTATAGATCATGACCTTTAGCGGCGCTTCTCCCAC
Found at i:54027042 original size:129 final size:129
Alignment explanation
Indices: 54026737--54027044 Score: 289
Period size: 129 Copynumber: 2.4 Consensus size: 129
54026727 GATTTTACAA
* ** * * * ** * * *
54026737 AAACGCCGCTAAAGGTCATTACCTTTAGCGGCGCTTCTCCCACAAACGCCGCTATAGATCATGAC
1 AAACGCCGCTAAAGATCACGACGTTTAGCGACCCTTCTCAAAAAAATGCCGCTACAGATCATGAC
* *
54026802 CTTTAGCGGCGCTTCTTCCACAAACGCCGCTATAGATCATGACTTGTAGTGGCGCTTCTCCCAC
66 CTTTAGCGGCGCTTCTCCCACAAACGCCGCTATAGATCATGACTTGTAGCGGCGCTTCTCCCAC
* * * * * ** *
54026866 AAACGCTGCTATAGATCATGACTTTTAGCGGCCCTTCTCCTACAAATGCCGCTACAGATCATGAC
1 AAACGCCGCTAAAGATCACGACGTTTAGCGACCCTTCTCAAAAAAATGCCGCTACAGATCATGAC
* * ***
54026931 TTTTAGCGGCGCTTCTCCCACAAACGCCGCTATAGATCATGACCTT-TAGCGGCGCTTTTTTTTA
66 CTTTAGCGGCGCTTCTCCCACAAACGCCGCTATAGATCATGA-CTTGTAGCGGCGC-TTCTCCCA
*
54026995 T
129 C
** * *
54026996 AAACGCCGCTAAAGAAT-ACGA-GTTTAGCGACGTTTTTTAAAAAAATGCC
1 AAACGCCGCTAAAG-ATCACGACGTTTAGCGACCCTTCTCAAAAAAATGCC
54027045 ACTAATTTTG
Statistics
Matches: 147, Mismatches: 29, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
129 123 0.84
130 22 0.15
131 2 0.01
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.27
Consensus pattern (129 bp):
AAACGCCGCTAAAGATCACGACGTTTAGCGACCCTTCTCAAAAAAATGCCGCTACAGATCATGAC
CTTTAGCGGCGCTTCTCCCACAAACGCCGCTATAGATCATGACTTGTAGCGGCGCTTCTCCCAC
Found at i:54027376 original size:21 final size:21
Alignment explanation
Indices: 54027331--54027376 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
54027321 CCTCTGCTCT
* *
54027331 GCTTCTCTCGCTGCAGCCTCT
1 GCTTCTCTCGCTGCAGCATCA
*
54027352 GCTTCTCTCGCTGCTGCATCA
1 GCTTCTCTCGCTGCAGCATCA
54027373 GCTT
1 GCTT
54027377 TAAGTTGTAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.07, C:0.39, G:0.20, T:0.35
Consensus pattern (21 bp):
GCTTCTCTCGCTGCAGCATCA
Found at i:54027449 original size:87 final size:87
Alignment explanation
Indices: 54027331--54027524 Score: 289
Period size: 87 Copynumber: 2.2 Consensus size: 87
54027321 CCTCTGCTCT
* * * *
54027331 GCTTCTCTCGCTGCAGCCTCTGCTTCTCTCGCTGCTGCATCAGCTTTAAGTTGTAGCTGGAGTTC
1 GCTTCTCTCGATGCTGCCTCTACTTCCCTCGCTGCTGCATCAGCTTTAAGTTGTAGCTGGAGTTC
*
54027396 TTCATAATTTCTTTGAACTTCA
66 TTCATAATTTCTTTGAACCTCA
* * *
54027418 GCTTCTCTCGATGCTGCCTCTACTTCCCTCGCTGTTGCATCTGCTTTAAGTTGTAGTTGGAGTTC
1 GCTTCTCTCGATGCTGCCTCTACTTCCCTCGCTGCTGCATCAGCTTTAAGTTGTAGCTGGAGTTC
* *
54027483 TTCATATTTTCTTTGGACCTCA
66 TTCATAATTTCTTTGAACCTCA
*
54027505 GCTTTTCTCGATGCTGCCTC
1 GCTTCTCTCGATGCTGCCTC
54027525 CGCTTTAAGT
Statistics
Matches: 96, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
87 96 1.00
ACGTcount: A:0.13, C:0.28, G:0.19, T:0.41
Consensus pattern (87 bp):
GCTTCTCTCGATGCTGCCTCTACTTCCCTCGCTGCTGCATCAGCTTTAAGTTGTAGCTGGAGTTC
TTCATAATTTCTTTGAACCTCA
Found at i:54028330 original size:19 final size:19
Alignment explanation
Indices: 54028306--54028343 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
54028296 AGTTTGAAAG
*
54028306 TACGTAATACCTCTCCTTT
1 TACGTAATACATCTCCTTT
54028325 TACGTAATACATCTCCTTT
1 TACGTAATACATCTCCTTT
54028344 CTTTGAATTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.24, C:0.29, G:0.05, T:0.42
Consensus pattern (19 bp):
TACGTAATACATCTCCTTT
Found at i:54031439 original size:27 final size:27
Alignment explanation
Indices: 54031388--54031439 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
54031378 GTTACTAAAA
* *
54031388 TTCTCTTTGAGTTTTCTTTTTAAGAAT
1 TTCTCTTTGAGTTTTATTTTGAAGAAT
54031415 TTCTC-TTGAGTTTTATTTTAGAAGA
1 TTCTCTTTGAGTTTTATTTT-GAAGA
54031440 GTTTTAACAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 13 0.59
27 9 0.41
ACGTcount: A:0.21, C:0.10, G:0.13, T:0.56
Consensus pattern (27 bp):
TTCTCTTTGAGTTTTATTTTGAAGAAT
Found at i:54035474 original size:40 final size:38
Alignment explanation
Indices: 54035381--54035518 Score: 114
Period size: 40 Copynumber: 3.5 Consensus size: 38
54035371 CGTTTGGACA
* * *
54035381 AAAAACGCGGGTAAAAATCGAGCATTAGCGGCGCTTTATG
1 AAAAACGCCGCTAAAAA-CGAGCATTAGCGGCG-TTTTTG
* ** *
54035421 GAAATTGCTGCTAAAGAACGAGCATTAGCGGCGTTTTCTG
1 AAAAACGCCGCTAAA-AACGAGCATTAGCGGCGTTTT-TG
* * *
54035461 AAAAACGCCGCTAAAAATGAGCATTCGCGACAGTTTTTAG
1 AAAAACGCCGCTAAAAACGAGCATTAGCGGC-GTTTTT-G
* *
54035501 AAAAATGCCGCAAAAAAC
1 AAAAACGCCGCTAAAAAC
54035519 CTAAGCCCAA
Statistics
Matches: 78, Mismatches: 16, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
39 17 0.22
40 59 0.76
41 2 0.03
ACGTcount: A:0.37, C:0.19, G:0.23, T:0.21
Consensus pattern (38 bp):
AAAAACGCCGCTAAAAACGAGCATTAGCGGCGTTTTTG
Found at i:54035611 original size:41 final size:41
Alignment explanation
Indices: 54035552--54035706 Score: 238
Period size: 41 Copynumber: 3.8 Consensus size: 41
54035542 TGACATTTTA
*
54035552 GGGTTTTAGCGGCATTTTTGAAAAAGCGCCGCTAATGCTCG
1 GGGTTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCG
* *
54035593 GGGTTTTAGCGGCGTTTTTGAAAAAGCGCAGCGAATGCTCG
1 GGGTTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCG
* *
54035634 GGGTTTTTGCGGCGTTTTTGAAAAAGCGCTGCTAATGCTCG
1 GGGTTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCG
* * *
54035675 AGGCTTTAGCGGCGTTTTTGAAAAAGCACCGC
1 GGGTTTTAGCGGCGTTTTTGAAAAAGCGCCGC
54035707 AAAAAACATT
Statistics
Matches: 103, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 103 1.00
ACGTcount: A:0.21, C:0.19, G:0.31, T:0.29
Consensus pattern (41 bp):
GGGTTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCG
Found at i:54036077 original size:14 final size:15
Alignment explanation
Indices: 54036051--54036088 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
54036041 GTTTAGGGGG
54036051 TATGGATTTAGGGAC
1 TATGGATTTAGGGAC
*
54036066 TATGGA-TTAGGGAT
1 TATGGATTTAGGGAC
54036080 TATGG-TTTA
1 TATGGATTTA
54036089 AGGGTTGGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.26, C:0.03, G:0.32, T:0.39
Consensus pattern (15 bp):
TATGGATTTAGGGAC
Found at i:54037754 original size:9 final size:9
Alignment explanation
Indices: 54037740--54037769 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
54037730 TTTTTTCTCC
54037740 AAAATCCTA
1 AAAATCCTA
54037749 AAAATCCTA
1 AAAATCCTA
*
54037758 AAAACCCTA
1 AAAATCCTA
54037767 AAA
1 AAA
54037770 CCCTAAACCC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.60, C:0.23, G:0.00, T:0.17
Consensus pattern (9 bp):
AAAATCCTA
Found at i:54039978 original size:5 final size:5
Alignment explanation
Indices: 54039968--54039993 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
54039958 CTCGAAAATT
54039968 TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA T
54039994 CGAATGCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:54040653 original size:16 final size:17
Alignment explanation
Indices: 54040626--54040658 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
54040616 TCTACATCAC
*
54040626 TAGTTAAAGAAACTAAA
1 TAGTTAAAGAAAATAAA
54040643 TAGTT-AAGAAAATAAA
1 TAGTTAAAGAAAATAAA
54040659 ACAGTAAAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.61, C:0.03, G:0.12, T:0.24
Consensus pattern (17 bp):
TAGTTAAAGAAAATAAA
Found at i:54041355 original size:76 final size:76
Alignment explanation
Indices: 54041229--54041380 Score: 295
Period size: 76 Copynumber: 2.0 Consensus size: 76
54041219 AATGCTTTTA
*
54041229 AAACGTGAAGATTTGATATCTCAAATGAAAGTTGTCTAGCTATATACCATTTGCAAGTTATATTA
1 AAACGTGAAGATTTGATATCTCAAATCAAAGTTGTCTAGCTATATACCATTTGCAAGTTATATTA
54041294 AAGAACTTGTC
66 AAGAACTTGTC
54041305 AAACGTGAAGATTTGATATCTCAAATCAAAGTTGTCTAGCTATATACCATTTGCAAGTTATATTA
1 AAACGTGAAGATTTGATATCTCAAATCAAAGTTGTCTAGCTATATACCATTTGCAAGTTATATTA
54041370 AAGAACTTGTC
66 AAGAACTTGTC
54041381 TTCACTATTG
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
76 75 1.00
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.34
Consensus pattern (76 bp):
AAACGTGAAGATTTGATATCTCAAATCAAAGTTGTCTAGCTATATACCATTTGCAAGTTATATTA
AAGAACTTGTC
Found at i:54043738 original size:43 final size:43
Alignment explanation
Indices: 54043684--54043785 Score: 150
Period size: 43 Copynumber: 2.4 Consensus size: 43
54043674 TTTTCATGAC
* * * *
54043684 CTTTAACGGCGTTTTTGGGGAAAGCGTCGTTAAAGGTCATGTT
1 CTTTAGCGGCGTTTTTGGGAAAAGCGCCGCTAAAGGTCATGTT
* *
54043727 CTTTAGCGGCGTTTGTGGGAAAAGTGCCGCTAAAGGTCATGTT
1 CTTTAGCGGCGTTTTTGGGAAAAGCGCCGCTAAAGGTCATGTT
54043770 CTTTAGCGGCGTTTTT
1 CTTTAGCGGCGTTTTT
54043786 TTGCATAAAC
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 52 1.00
ACGTcount: A:0.19, C:0.16, G:0.30, T:0.35
Consensus pattern (43 bp):
CTTTAGCGGCGTTTTTGGGAAAAGCGCCGCTAAAGGTCATGTT
Found at i:54046646 original size:26 final size:24
Alignment explanation
Indices: 54046599--54046646 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 24
54046589 ATTAAAATTG
**
54046599 TAAATATATTGATTTTTGCCTCCT
1 TAAATATATTGATTTTAACCTCCT
54046623 TAAATATATTGATTAATTAACCTC
1 TAAATATATTGATT--TTAACCTC
54046647 AAAAATTTGG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 14 0.70
26 6 0.30
ACGTcount: A:0.33, C:0.15, G:0.06, T:0.46
Consensus pattern (24 bp):
TAAATATATTGATTTTAACCTCCT
Found at i:54050417 original size:13 final size:13
Alignment explanation
Indices: 54050401--54050454 Score: 81
Period size: 13 Copynumber: 4.2 Consensus size: 13
54050391 TACTTTTAAA
54050401 AAGTGCTTTTCAG
1 AAGTGCTTTTCAG
*
54050414 AAGTGCTTGTCAG
1 AAGTGCTTTTCAG
54050427 AAGTGCTTTTCAG
1 AAGTGCTTTTCAG
* *
54050440 AAGTACTTTTGAG
1 AAGTGCTTTTCAG
54050453 AA
1 AA
54050455 ATTTGAGTGT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 37 1.00
ACGTcount: A:0.28, C:0.13, G:0.24, T:0.35
Consensus pattern (13 bp):
AAGTGCTTTTCAG
Found at i:54050454 original size:26 final size:26
Alignment explanation
Indices: 54050391--54050454 Score: 83
Period size: 26 Copynumber: 2.5 Consensus size: 26
54050381 AGTTCTTTAT
*
54050391 TACTTTTAAAAAGTGCTTTTCAGAAG
1 TACTTTTAAGAAGTGCTTTTCAGAAG
* * *
54050417 TGCTTGTCAGAAGTGCTTTTCAGAAG
1 TACTTTTAAGAAGTGCTTTTCAGAAG
*
54050443 TACTTTTGAGAA
1 TACTTTTAAGAA
54050455 ATTTGAGTGT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.30, C:0.12, G:0.20, T:0.38
Consensus pattern (26 bp):
TACTTTTAAGAAGTGCTTTTCAGAAG
Found at i:54053681 original size:19 final size:19
Alignment explanation
Indices: 54053635--54053683 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
54053625 AACAACTTCA
* * *
54053635 AAATATTAAACTGAAGAGG
1 AAATATAAAACAGAAGAAG
*
54053654 AACTAATAAAACAGAAGAAG
1 AAAT-ATAAAACAGAAGAAG
54053674 AAATATAAAA
1 AAATATAAAA
54053684 GAAACTTTCA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.63, C:0.06, G:0.14, T:0.16
Consensus pattern (19 bp):
AAATATAAAACAGAAGAAG
Found at i:54055329 original size:23 final size:23
Alignment explanation
Indices: 54055303--54055348 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
54055293 TGTTGAAGAT
54055303 AGTGAATATTTTTCATTGAACTA
1 AGTGAATATTTTTCATTGAACTA
54055326 AGTGAATATTTTTCATTGAACTA
1 AGTGAATATTTTTCATTGAACTA
54055349 GGCTTCGCGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.09, G:0.13, T:0.43
Consensus pattern (23 bp):
AGTGAATATTTTTCATTGAACTA
Found at i:54059076 original size:30 final size:31
Alignment explanation
Indices: 54059042--54059103 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
54059032 GTTCCAAAAT
* * *
54059042 AATCATTAAATTATTC-AAAAGTTTTATTTA
1 AATCACTAAACTATTCAAAAAATTTTATTTA
*
54059072 AATCACTGAACTATTCAAAAAATTTTATTTA
1 AATCACTAAACTATTCAAAAAATTTTATTTA
54059103 A
1 A
54059104 GTTAGACCTG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
30 13 0.48
31 14 0.52
ACGTcount: A:0.45, C:0.10, G:0.03, T:0.42
Consensus pattern (31 bp):
AATCACTAAACTATTCAAAAAATTTTATTTA
Found at i:54059523 original size:16 final size:16
Alignment explanation
Indices: 54059502--54059543 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
54059492 AATAATTTGA
*
54059502 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
54059518 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
54059534 TAGTTTTAAT
1 TAATTTTAAT
54059544 TTTATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:54066441 original size:14 final size:14
Alignment explanation
Indices: 54066424--54066462 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
54066414 ACATATCAAT
54066424 CTTACCATATTAGG
1 CTTACCATATTAGG
54066438 CTTACCATATTAGG
1 CTTACCATATTAGG
*
54066452 CATACCATATT
1 CTTACCATATT
54066463 TCAATCATGC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.31, C:0.23, G:0.10, T:0.36
Consensus pattern (14 bp):
CTTACCATATTAGG
Found at i:54067763 original size:21 final size:21
Alignment explanation
Indices: 54067737--54067798 Score: 88
Period size: 21 Copynumber: 3.0 Consensus size: 21
54067727 TGAACACGCC
* *
54067737 AACAGAAGCTTATAAGAGCTT
1 AACAGAAGCTCATAAGAGCTA
*
54067758 AACAGAAGCTCGTAAGAGCTA
1 AACAGAAGCTCATAAGAGCTA
*
54067779 AACATAAGCTCATAAGAGCT
1 AACAGAAGCTCATAAGAGCT
54067799 GATCCACCCG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.44, C:0.18, G:0.19, T:0.19
Consensus pattern (21 bp):
AACAGAAGCTCATAAGAGCTA
Found at i:54076899 original size:24 final size:24
Alignment explanation
Indices: 54076872--54076923 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
54076862 TTAGTAGGTC
*
54076872 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
54076896 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
54076920 AAAT
1 AAAT
54076924 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:54077448 original size:20 final size:21
Alignment explanation
Indices: 54077425--54077475 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
54077415 ATTTTTGTTC
54077425 ATTTTTATAACTTTTAAATA-
1 ATTTTTATAACTTTTAAATAT
*
54077445 ATTTTTCAT-ACTTTTATATAT
1 ATTTTT-ATAACTTTTAAATAT
*
54077466 TTTTTTATAA
1 ATTTTTATAA
54077476 TTATTTAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 18 0.69
21 8 0.31
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (21 bp):
ATTTTTATAACTTTTAAATAT
Found at i:54082067 original size:26 final size:24
Alignment explanation
Indices: 54082038--54082096 Score: 66
Period size: 23 Copynumber: 2.4 Consensus size: 24
54082028 CTTAGGGGTT
54082038 TTTTTTTTACTTTGGGGTTGTAATAA
1 TTTTTTTT--TTTGGGGTTGTAATAA
* *
54082064 -TTTTTCTTTTGGGTTTGTAATAA
1 TTTTTTTTTTTGGGGTTGTAATAA
*
54082087 TTATTTTTTT
1 TTTTTTTTTT
54082097 ATTTTATTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
23 15 0.54
24 7 0.25
25 6 0.21
ACGTcount: A:0.17, C:0.03, G:0.15, T:0.64
Consensus pattern (24 bp):
TTTTTTTTTTTGGGGTTGTAATAA
Found at i:54082072 original size:22 final size:24
Alignment explanation
Indices: 54082041--54082088 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 24
54082031 AGGGGTTTTT
54082041 TTTTTAC-TTTGGGGTTGTAATAA
1 TTTTTACTTTTGGGGTTGTAATAA
*
54082064 TTTTT-CTTTTGGGTTTGTAATAA
1 TTTTTACTTTTGGGGTTGTAATAA
54082087 TT
1 TT
54082089 ATTTTTTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 1 0.04
23 22 0.96
ACGTcount: A:0.19, C:0.04, G:0.19, T:0.58
Consensus pattern (24 bp):
TTTTTACTTTTGGGGTTGTAATAA
Found at i:54082074 original size:23 final size:23
Alignment explanation
Indices: 54082048--54082096 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
54082038 TTTTTTTTAC
54082048 TTTGGGGTTGTAATAATT-TTTCT
1 TTTGGGGTTGTAATAATTATTT-T
*
54082071 TTTGGGTTTGTAATAATTATTTT
1 TTTGGGGTTGTAATAATTATTTT
54082094 TTT
1 TTT
54082097 ATTTTATTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 21 0.88
24 3 0.12
ACGTcount: A:0.18, C:0.02, G:0.18, T:0.61
Consensus pattern (23 bp):
TTTGGGGTTGTAATAATTATTTT
Found at i:54093580 original size:161 final size:160
Alignment explanation
Indices: 54093296--54093600 Score: 434
Period size: 161 Copynumber: 1.9 Consensus size: 160
54093286 ATAGAAAATT
* * *
54093296 TAACAAAAAGAGATAGAAAAATTTTTAGGATAACAAAAATTGGCAGAGAGGAAACAAAAGGAACA
1 TAACAAAAAGAGACAGAAAAATTTTTAGGATAACAAAAATTAGCAAAGAGGAAACAAAAGGAACA
* * *
54093361 ACAAAAGAGAGAAAAGGTTTACCTAAAGGAGGCTCCGATGAAGGGGAGGAGTGCTAGTGGTCGGA
66 ACAAAAGAGAGAAAAGGTTTACCTAAAGGAAGCTACGATGAAGGGGAGGAGTGCTAGTGGTCAGA
54093426 GGCAAAGGAAGCAAACTCTACTTAAATGGG
131 GGCAAAGGAAGCAAACTCTACTTAAATGGG
* *
54093456 TAACAAAAAGA-AGCAGAAAAATTTTTAGGGTAAGAAAAATTAGCAAAGAGGAAAACGAAAA-GA
1 TAACAAAAAGAGA-CAGAAAAATTTTTAGGATAACAAAAATTAGCAAAGAGG-AAAC-AAAAGGA
** * * * *
54093519 ACAACGGAAGAGAGAAAATGTTTACTTGAAGGAAGCTACGATGAAGGGTAGGAGTGCTAGTGGTC
63 ACAACAAAAGAGAGAAAAGGTTTACCTAAAGGAAGCTACGATGAAGGGGAGGAGTGCTAGTGGTC
*
54093584 AGAGTCAAAGGAAGCAA
128 AGAGGCAAAGGAAGCAA
54093601 GGGAGTGGTT
Statistics
Matches: 127, Mismatches: 15, Indels: 5
0.86 0.10 0.03
Matches are distributed among these distances:
159 1 0.01
160 44 0.35
161 78 0.61
162 4 0.03
ACGTcount: A:0.46, C:0.10, G:0.28, T:0.16
Consensus pattern (160 bp):
TAACAAAAAGAGACAGAAAAATTTTTAGGATAACAAAAATTAGCAAAGAGGAAACAAAAGGAACA
ACAAAAGAGAGAAAAGGTTTACCTAAAGGAAGCTACGATGAAGGGGAGGAGTGCTAGTGGTCAGA
GGCAAAGGAAGCAAACTCTACTTAAATGGG
Found at i:54095237 original size:23 final size:23
Alignment explanation
Indices: 54095210--54095255 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
54095200 TTAACCGAAT
*
54095210 TAATTTGGTTGGGA-GTCGGTTAA
1 TAATTT-GTTGGAAGGTCGGTTAA
*
54095233 TAATTTTTTGGAAGGTCGGTTAA
1 TAATTTGTTGGAAGGTCGGTTAA
54095256 CTGTTAATTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.24, C:0.04, G:0.30, T:0.41
Consensus pattern (23 bp):
TAATTTGTTGGAAGGTCGGTTAA
Found at i:54095951 original size:18 final size:19
Alignment explanation
Indices: 54095909--54095958 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
54095899 ATTACAAAAA
* *
54095909 AAAACTTCAAAATAATTTTT
1 AAAA-TTCAAAATAATCTAT
54095929 AAAATTCAAAAT-ATCTAT
1 AAAATTCAAAATAATCTAT
*
54095947 AAAATTCCAAAT
1 AAAATTCAAAAT
54095959 TTTATATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
18 15 0.56
19 8 0.30
20 4 0.15
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.34
Consensus pattern (19 bp):
AAAATTCAAAATAATCTAT
Found at i:54096260 original size:26 final size:26
Alignment explanation
Indices: 54096228--54096282 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
54096218 ACTCAATTCA
*
54096228 ACTCGACTCAAATTTCATTTCACTTG
1 ACTCGACTCAAATTTCATTTCACTCG
* *
54096254 ACTCGACTTAAATTTTATTTCACTCG
1 ACTCGACTCAAATTTCATTTCACTCG
54096280 ACT
1 ACT
54096283 AAATTCAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.27, C:0.25, G:0.07, T:0.40
Consensus pattern (26 bp):
ACTCGACTCAAATTTCATTTCACTCG
Found at i:54096268 original size:21 final size:20
Alignment explanation
Indices: 54096244--54096287 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
54096234 CTCAAATTTC
*
54096244 ATTTCACTTGACTCGACTTAA
1 ATTTCACTTCACTCGAC-TAA
* *
54096265 ATTTTATTTCACTCGACTAA
1 ATTTCACTTCACTCGACTAA
54096285 ATT
1 ATT
54096288 CAAAAAATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.30, C:0.20, G:0.07, T:0.43
Consensus pattern (20 bp):
ATTTCACTTCACTCGACTAA
Found at i:54096589 original size:25 final size:25
Alignment explanation
Indices: 54096527--54096584 Score: 80
Period size: 25 Copynumber: 2.2 Consensus size: 25
54096517 GATTTTTTAT
*
54096527 TTTATTTAATATTAATGTAATTATA
1 TTTATTTAATATTAATGTAATTAAA
*
54096552 TTTATTTAATATTAATTTAAATTTAAA
1 TTTATTTAATATTAATGT-AA-TTAAA
54096579 TTTATT
1 TTTATT
54096585 ATATTGTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 17 0.59
26 2 0.07
27 10 0.34
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.59
Consensus pattern (25 bp):
TTTATTTAATATTAATGTAATTAAA
Found at i:54096658 original size:20 final size:18
Alignment explanation
Indices: 54096607--54096660 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 18
54096597 AAATATTTAT
54096607 TTTTATGTATTTTTAAAA
1 TTTTATGTATTTTTAAAA
*
54096625 TTCATTAT-TTTTTTTGAAAA
1 TT--TTATGTATTTTT-AAAA
54096645 TATTTATGTATTTTTA
1 T-TTTATGTATTTTTA
54096661 TATATTTCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
18 2 0.07
19 11 0.38
20 15 0.52
21 1 0.03
ACGTcount: A:0.30, C:0.02, G:0.06, T:0.63
Consensus pattern (18 bp):
TTTTATGTATTTTTAAAA
Found at i:54097815 original size:14 final size:14
Alignment explanation
Indices: 54097789--54097822 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
54097779 ATATACAGTA
54097789 AGAAATGAAATAAC
1 AGAAATGAAATAAC
54097803 AGAAA-GAACATAAC
1 AGAAATGAA-ATAAC
54097817 AGAAAT
1 AGAAAT
54097823 ATAACTGCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 3 0.17
14 15 0.83
ACGTcount: A:0.65, C:0.09, G:0.15, T:0.12
Consensus pattern (14 bp):
AGAAATGAAATAAC
Found at i:54102120 original size:14 final size:14
Alignment explanation
Indices: 54102094--54102127 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
54102084 ATATACAGTA
54102094 AGAAATGAAATAAC
1 AGAAATGAAATAAC
54102108 AGAAA-GAACATAAC
1 AGAAATGAA-ATAAC
54102122 AGAAAT
1 AGAAAT
54102128 ATAACTGCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 3 0.17
14 15 0.83
ACGTcount: A:0.65, C:0.09, G:0.15, T:0.12
Consensus pattern (14 bp):
AGAAATGAAATAAC
Found at i:54104615 original size:29 final size:29
Alignment explanation
Indices: 54104557--54104615 Score: 68
Period size: 29 Copynumber: 2.0 Consensus size: 29
54104547 CCCAGCCTGA
**
54104557 AAAATATTAAATATTTTTTTTTTATTTTT
1 AAAATATTAAATATTTTTTTTTTAAGTTT
54104586 AAAATA-T-AATAGTTTTTTATTTTAAGTTT
1 AAAATATTAAATA-TTTTTT-TTTTAAGTTT
54104615 A
1 A
54104616 TTTACTTTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
27 4 0.15
28 7 0.27
29 15 0.58
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.59
Consensus pattern (29 bp):
AAAATATTAAATATTTTTTTTTTAAGTTT
Found at i:54104738 original size:59 final size:59
Alignment explanation
Indices: 54104675--54104853 Score: 250
Period size: 68 Copynumber: 2.9 Consensus size: 59
54104665 TCAAGTTTGT
*
54104675 TTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATACAATTAATAATTTGATAAA
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATTTGATAAA
54104734 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATT---AC-----A-ACAATTAATACAATTAATAATTTGAT
54104799 AAA
57 AAA
* *
54104802 TTTATTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAACAATT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATT
54104854 AATAATTTGA
Statistics
Matches: 108, Mismatches: 3, Indels: 18
0.84 0.02 0.14
Matches are distributed among these distances:
59 47 0.44
60 1 0.01
62 2 0.02
65 2 0.02
67 1 0.01
68 55 0.51
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.41
Consensus pattern (59 bp):
TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATTTGATAAA
Found at i:54104776 original size:9 final size:9
Alignment explanation
Indices: 54104764--54104791 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
54104754 TTTTATTACA
54104764 ACAATTAAT
1 ACAATTAAT
54104773 ACAATTAAT
1 ACAATTAAT
54104782 ACAATTAAT
1 ACAATTAAT
54104791 A
1 A
54104792 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:54104782 original size:68 final size:68
Alignment explanation
Indices: 54104705--54104875 Score: 310
Period size: 68 Copynumber: 2.5 Consensus size: 68
54104695 TTTTGTTACA
54104705 ACAATTAATACAATTAATAATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACAACAATT
1 ACAATTAATACAATTAATAATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACAACAATT
54104770 AAT
66 AAT
*
54104773 ACAATTAATACAATTAATAATTTGATAAATTTATTAATCAAATGTTAGATTTTATTACAACAATT
1 ACAATTAATACAATTAATAATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACAACAATT
54104838 AAT
66 AAT
*
54104841 ACAATT-A-ACAATTAATAATTTGATAATTTTACTAA
1 ACAATTAATACAATTAATAATTTGATAAATTTACTAA
54104876 CAATTAATTT
Statistics
Matches: 100, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
66 26 0.26
67 1 0.01
68 73 0.73
ACGTcount: A:0.47, C:0.08, G:0.04, T:0.40
Consensus pattern (68 bp):
ACAATTAATACAATTAATAATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACAACAATT
AAT
Found at i:54104885 original size:16 final size:16
Alignment explanation
Indices: 54104864--54104905 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
54104854 AATAATTTGA
*
54104864 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
54104880 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
54104896 TAGTTTTAAT
1 TAATTTTAAT
54104906 TTTATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:54104925 original size:21 final size:21
Alignment explanation
Indices: 54104879--54104939 Score: 77
Period size: 22 Copynumber: 2.8 Consensus size: 21
54104869 TTACTAACAA
* * *
54104879 TTAATTTTAATAACAATTAGTT
1 TTAATTTTATTAA-AAATAATT
54104901 TTAATTTTATTAAAAATAATT
1 TTAATTTTATTAAAAATAATT
54104922 TTAATTTTAATTAAAAAT
1 TTAATTTT-ATTAAAAAT
54104940 GGGCCTGGCC
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
21 14 0.40
22 21 0.60
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (21 bp):
TTAATTTTATTAAAAATAATT
Found at i:54106549 original size:13 final size:13
Alignment explanation
Indices: 54106531--54106555 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54106521 CCTGGAGATT
54106531 TAATGAGCAAATG
1 TAATGAGCAAATG
54106544 TAATGAGCAAAT
1 TAATGAGCAAAT
54106556 TTTTATTAGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.20, T:0.24
Consensus pattern (13 bp):
TAATGAGCAAATG
Found at i:54109410 original size:22 final size:22
Alignment explanation
Indices: 54109361--54109410 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
54109351 ATAGTCTAGT
* * *
54109361 TTTTAGTTTATTAAAAAATATA
1 TTTTATTTTAGTAAAAAATAAA
*
54109383 TATTATTTTAGTAAAAAATAAA
1 TTTTATTTTAGTAAAAAATAAA
54109405 TTTTAT
1 TTTTAT
54109411 ATTATATATA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (22 bp):
TTTTATTTTAGTAAAAAATAAA
Found at i:54123985 original size:41 final size:41
Alignment explanation
Indices: 54123929--54124040 Score: 143
Period size: 41 Copynumber: 2.7 Consensus size: 41
54123919 TGATTCGATA
* * *
54123929 CACCGGCTTTTAGCCTGCTAGACCTATAGTCTGAAATATAT
1 CACCGGCATTAAGCCTGCTAGACCTAAAGTCTGAAATATAT
* * *
54123970 CACCGGCATTAAGCCTGCTAGACGTAAAGTCTGAATTATTT
1 CACCGGCATTAAGCCTGCTAGACCTAAAGTCTGAAATATAT
* * *
54124011 CACCGGCATCAAGCCCGCTAGACATAAAGT
1 CACCGGCATTAAGCCTGCTAGACCTAAAGT
54124041 TTGTATTACA
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 62 1.00
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Consensus pattern (41 bp):
CACCGGCATTAAGCCTGCTAGACCTAAAGTCTGAAATATAT
Found at i:54124210 original size:76 final size:75
Alignment explanation
Indices: 54124128--54124270 Score: 182
Period size: 76 Copynumber: 1.9 Consensus size: 75
54124118 TGAATATACA
* * * *
54124128 TACATAATCGAAACTTTCACAT-ACATATATAAAT-TCCATACTTAAATTCATTACAAGAACATA
1 TACATAATC-AAAC-CTCACATAACATATATAAATGTCC-TACCTAAATTCAATAAAAGAACATA
54124191 TACACATAATCTT
63 TACACATAATCTT
* *
54124204 TACATAATCAAACCTCATATAAACTTATATAAATGTCCTACCTAAATTCAATAAAAGAACATATA
1 TACATAATCAAACCTCACAT-AACATATATAAATGTCCTACCTAAATTCAATAAAAGAACATATA
54124269 CA
65 CA
54124271 TATATGTAAG
Statistics
Matches: 58, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
74 5 0.09
75 4 0.07
76 46 0.79
77 3 0.05
ACGTcount: A:0.47, C:0.20, G:0.03, T:0.31
Consensus pattern (75 bp):
TACATAATCAAACCTCACATAACATATATAAATGTCCTACCTAAATTCAATAAAAGAACATATAC
ACATAATCTT
Found at i:54124536 original size:2 final size:2
Alignment explanation
Indices: 54124529--54124596 Score: 59
Period size: 2 Copynumber: 34.5 Consensus size: 2
54124519 CTCAAAAACT
* * * *
54124529 TA TA TA TA TA TA TG TA TA TA TA TA T- TC GA GTA T- TA TA CA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
* *
54124570 CA TA TA TA TA TA TA TA TA TA TA CA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
54124597 CTTTGTCTAA
Statistics
Matches: 52, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
1 2 0.04
2 49 0.94
3 1 0.02
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (2 bp):
TA
Found at i:54131598 original size:2 final size:2
Alignment explanation
Indices: 54131593--54131628 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
54131583 TTTGTGTGTG
54131593 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
54131629 CTCATTATAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:54132125 original size:41 final size:41
Alignment explanation
Indices: 54132069--54132171 Score: 127
Period size: 41 Copynumber: 2.5 Consensus size: 41
54132059 TGATTCGATA
* * * *
54132069 CACCGGCTTTTAGCCTGCTAGACCTATAGTCC-GAAATGTAT
1 CACCGGCATTAAGCCTGCTAGACCTAAAG-CCTGAAATATAT
* * *
54132110 CACCGGCATTAAGCCTGCTAGACGTAAAGCCTGAATTATTT
1 CACCGGCATTAAGCCTGCTAGACCTAAAGCCTGAAATATAT
54132151 CACCGGCATTAAGCCTGCTAG
1 CACCGGCATTAAGCCTGCTAG
54132172 GCACATAGCC
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
40 2 0.04
41 52 0.96
ACGTcount: A:0.26, C:0.27, G:0.20, T:0.26
Consensus pattern (41 bp):
CACCGGCATTAAGCCTGCTAGACCTAAAGCCTGAAATATAT
Found at i:54132182 original size:41 final size:41
Alignment explanation
Indices: 54132109--54132186 Score: 120
Period size: 41 Copynumber: 1.9 Consensus size: 41
54132099 CCGAAATGTA
**
54132109 TCACCGGCATTAAGCCTGCTAGACGTAAAGCCTGAATTATT
1 TCACCGGCATTAAGCCTGCTAGACACAAAGCCTGAATTATT
* *
54132150 TCACCGGCATTAAGCCTGCTAGGCACATAGCCTGAAT
1 TCACCGGCATTAAGCCTGCTAGACACAAAGCCTGAAT
54132187 AACTCAAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (41 bp):
TCACCGGCATTAAGCCTGCTAGACACAAAGCCTGAATTATT
Found at i:54140009 original size:41 final size:41
Alignment explanation
Indices: 54139948--54140027 Score: 124
Period size: 41 Copynumber: 2.0 Consensus size: 41
54139938 ACTGGCTTTT
*
54139948 AGCCTGCTAGACCTACAGTCTGAAATATATCACCGGCATTA
1 AGCCTGCTAGACCTAAAGTCTGAAATATATCACCGGCATTA
* * *
54139989 AGCCTGCTAGACGTAAAGTCTGAATTATTTCACCGGCAT
1 AGCCTGCTAGACCTAAAGTCTGAAATATATCACCGGCAT
54140028 CAATCTTGCT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (41 bp):
AGCCTGCTAGACCTAAAGTCTGAAATATATCACCGGCATTA
Found at i:54140038 original size:41 final size:41
Alignment explanation
Indices: 54139948--54140040 Score: 123
Period size: 41 Copynumber: 2.3 Consensus size: 41
54139938 ACTGGCTTTT
* *
54139948 AGCCTGCTAGACCTACAGTCTGAAATATATCACCGGCATTA
1 AGCCTGCTAGACCTAAAGTCTGAAATATATCACCGGCATCA
* * *
54139989 AGCCTGCTAGACGTAAAGTCTGAATTATTTCACCGGCATCA
1 AGCCTGCTAGACCTAAAGTCTGAAATATATCACCGGCATCA
* *
54140030 ATCTTGCTAGA
1 AGCCTGCTAGA
54140041 AATAAAATCT
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 45 1.00
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (41 bp):
AGCCTGCTAGACCTAAAGTCTGAAATATATCACCGGCATCA
Found at i:54140539 original size:2 final size:2
Alignment explanation
Indices: 54140532--54140564 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
54140522 CTCAAAAACT
*
54140532 TA TA TA TA TA TA TA CA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
54140565 TCGAGTATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:54143226 original size:17 final size:18
Alignment explanation
Indices: 54143199--54143232 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
54143189 TAATTTTGTT
54143199 TAAGTTATGTTAATTAAG
1 TAAGTTATGTTAATTAAG
54143217 TAAG-TATGTTAATTAA
1 TAAGTTATGTTAATTAA
54143233 TTAGTTTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.41, C:0.00, G:0.15, T:0.44
Consensus pattern (18 bp):
TAAGTTATGTTAATTAAG
Found at i:54143668 original size:28 final size:27
Alignment explanation
Indices: 54143637--54143730 Score: 84
Period size: 28 Copynumber: 3.3 Consensus size: 27
54143627 AAATTAGCGC
*
54143637 GCTTATCGTAATTAATTCACACTTCGGT
1 GCTTATCGTAATTAATT-GCACTTCGGT
*
54143665 GCTTATCATTGTAA--AATATGCACTTTGGT
1 GCTTATC---GTAATTAAT-TGCACTTCGGT
* *
54143694 GCTTATTGTAATTATTTTGCACTTCGGT
1 GCTTATCGTAATTA-ATTGCACTTCGGT
54143722 GCTTATCGT
1 GCTTATCGT
54143731 TATTTGCATT
Statistics
Matches: 53, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
26 4 0.08
28 26 0.49
29 18 0.34
30 1 0.02
31 4 0.08
ACGTcount: A:0.22, C:0.17, G:0.17, T:0.44
Consensus pattern (27 bp):
GCTTATCGTAATTAATTGCACTTCGGT
Found at i:54154097 original size:2 final size:2
Alignment explanation
Indices: 54154090--54154115 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
54154080 AAAGTTACAA
54154090 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
54154116 CAGCATATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:54154260 original size:2 final size:2
Alignment explanation
Indices: 54154253--54154288 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
54154243 GCTAGTGTCT
54154253 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
54154289 ATAACTCAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:54167025 original size:24 final size:26
Alignment explanation
Indices: 54166970--54167025 Score: 73
Period size: 24 Copynumber: 2.2 Consensus size: 26
54166960 AATATATCAT
54166970 AAATTTTTATATTCTTTTAGTTTATA
1 AAATTTTTATATTCTTTTAGTTTATA
*
54166996 ATATTTTTAT-TT-TTTTAGATTT-TA
1 AAATTTTTATATTCTTTTAG-TTTATA
54167020 AAATTT
1 AAATTT
54167026 AAGTCCAGCT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 13 0.48
25 5 0.19
26 9 0.33
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.64
Consensus pattern (26 bp):
AAATTTTTATATTCTTTTAGTTTATA
Found at i:54169436 original size:4 final size:4
Alignment explanation
Indices: 54169429--54169480 Score: 61
Period size: 4 Copynumber: 12.8 Consensus size: 4
54169419 TTAAAACATG
* *
54169429 ATTA ATTA ATTA ATTA ATTA ATTA ATTAA ACTA AGTTA ATTA ACT- ATTA
1 ATTA ATTA ATTA ATTA ATTA ATTA ATT-A ATTA A-TTA ATTA ATTA ATTA
54169478 ATT
1 ATT
54169481 GAAGTATAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
3 2 0.05
4 33 0.80
5 6 0.15
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (4 bp):
ATTA
Found at i:54173200 original size:51 final size:50
Alignment explanation
Indices: 54173136--54173423 Score: 326
Period size: 51 Copynumber: 5.7 Consensus size: 50
54173126 TATCGATGAA
** * *
54173136 CACGTGTGTAGTACTGCGTGAAGGCTACTACGTGAATCGATAAATGATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATAAAT-TTGGT
* * * * * * *
54173187 CACATGTGTAGTACTAAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATAA-ATTTGGT
* * *
54173238 CCCGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATGATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATAAAT-TTGGT
* * * * *
54173289 CACATGTGTAGTACTAAGTGAAGGCTACTATGTGTACCGAAAAACTTTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATAAA-TTTGGT
* * *
54173340 CACGTGTGTAGTACTATGTGAAGGTTACTACGTGAACCG-TAAAACTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGAT-AAATTTGGT
54173390 CACGTGTGTAGTACTATGTGAAGGCTACTACGTG
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTG
54173424 TATCGAATGA
Statistics
Matches: 196, Mismatches: 37, Indels: 9
0.81 0.15 0.04
Matches are distributed among these distances:
50 38 0.19
51 156 0.80
52 2 0.01
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.29
Consensus pattern (50 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATAAATTTGGT
Found at i:54173314 original size:102 final size:102
Alignment explanation
Indices: 54173136--54173417 Score: 431
Period size: 102 Copynumber: 2.8 Consensus size: 102
54173126 TATCGATGAA
**
54173136 CACGTGTGTAGTACTGCGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTAC
* *
54173201 TAAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGT
66 TAAGTGAAGGCTACAATGTGTACCGAAAAACTTTGGT
*
54173238 CCCGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTAC
*
54173303 TAAGTGAAGGCTACTATGTGTACCGAAAAACTTTGGT
66 TAAGTGAAGGCTACAATGTGTACCGAAAAACTTTGGT
* * *** * *
54173340 CACGTGTGTAGTACTATGTGAAGGTTACTACGTGAACCG-TAAAACTTGATCACGTGTGTAGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTAC
*
54173404 TATGTGAAGGCTAC
66 TAAGTGAAGGCTAC
54173418 TACGTGTATC
Statistics
Matches: 165, Mismatches: 15, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
101 33 0.20
102 132 0.80
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.29
Consensus pattern (102 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTAC
TAAGTGAAGGCTACAATGTGTACCGAAAAACTTTGGT
Found at i:54173452 original size:101 final size:102
Alignment explanation
Indices: 54173143--54173462 Score: 293
Period size: 102 Copynumber: 3.1 Consensus size: 102
54173133 GAACACGTGT
** * ** *
54173143 GTAGTACTGCGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTACTAAGTGA
1 GTAGTACTATGTGAAGGCTACTACGTGAACCGATAAAACATGATCACATGTGTAGTACTAAGTGA
* * * * *** ** * *
54173208 AGGCTACAATGTGTACCGAGAAGCTTTGGTCCCGTGT
66 AGGCTACTACGTGTACCGAAAAACTAAAGTAACATGG
* ** *
54173245 GTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTACTAAGTGA
1 GTAGTACTATGTGAAGGCTACTACGTGAACCGATAAAACATGATCACATGTGTAGTACTAAGTGA
* *** * * *
54173310 AGGCTACTATGTGTACCGAAAAACTTTGGTCACGTGT
66 AGGCTACTACGTGTACCGAAAAACTAAAGTAACATGG
* * * *
54173347 GTAGTACTATGTGAAGGTTACTACGTGAACCG-TAAAACTTGATCACGTGTGTAGTACTATGTGA
1 GTAGTACTATGTGAAGGCTACTACGTGAACCGATAAAACATGATCACATGTGTAGTACTAAGTGA
* **
54173411 AGGCTACTACGTGTATCGAATGA-TAAAAGTAACATGG
66 AGGCTACTACGTGTACCGAAAAACT-AAAGTAACATGG
*
54173448 GTAGTACTGTGTGAA
1 GTAGTACTATGTGAA
54173463 AAACCCCAAA
Statistics
Matches: 192, Mismatches: 25, Indels: 3
0.87 0.11 0.01
Matches are distributed among these distances:
100 1 0.01
101 65 0.34
102 126 0.66
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.29
Consensus pattern (102 bp):
GTAGTACTATGTGAAGGCTACTACGTGAACCGATAAAACATGATCACATGTGTAGTACTAAGTGA
AGGCTACTACGTGTACCGAAAAACTAAAGTAACATGG
Found at i:54174551 original size:15 final size:15
Alignment explanation
Indices: 54174531--54174561 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
54174521 TGTATTTGGT
54174531 ATATGATTTGGTATG
1 ATATGATTTGGTATG
54174546 ATATGATTTGGTATG
1 ATATGATTTGGTATG
54174561 A
1 A
54174562 AGTAAGGCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.29, C:0.00, G:0.26, T:0.45
Consensus pattern (15 bp):
ATATGATTTGGTATG
Found at i:54175632 original size:29 final size:28
Alignment explanation
Indices: 54175559--54175634 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 28
54175549 TTTTCACAAA
*
54175559 TTTTTTATTCATTTATTTATTTTAAACCC
1 TTTTTTATT-ATTTATTTATTTTAAAACC
* * **
54175588 TTTTCTCTTATATTATTTATTTTAAAATG
1 TTTTTTATTAT-TTATTTATTTTAAAACC
54175617 TTTTATTATTATTTATTT
1 TTTT-TTATTATTTATTT
54175635 CAAGTTTTCC
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
28 2 0.05
29 31 0.82
30 5 0.13
ACGTcount: A:0.25, C:0.08, G:0.01, T:0.66
Consensus pattern (28 bp):
TTTTTTATTATTTATTTATTTTAAAACC
Found at i:54175748 original size:31 final size:29
Alignment explanation
Indices: 54175686--54175807 Score: 87
Period size: 29 Copynumber: 4.3 Consensus size: 29
54175676 ATTATCCATT
* * * *
54175686 TTTTTATATATATTATTTATTTTGAATTG
1 TTTTTATACATATCATTTATTTTAAACTG
54175715 TTTTTATACATATCATTTATTTTTTAAACTG
1 TTTTTATACATATCATTTA--TTTTAAACTG
*
54175746 TTTTGTAT--AT-T-ATTTATTTGAAA-T-
1 TTTT-TATACATATCATTTATTTTAAACTG
* *
54175770 TTCTTTTTACATATTATTTATTTTAAACT-
1 TT-TTTATACATATCATTTATTTTAAACTG
54175799 TTTTATATA
1 TTTT-TATA
54175808 TTATTTTAAA
Statistics
Matches: 75, Mismatches: 8, Indels: 20
0.73 0.08 0.19
Matches are distributed among these distances:
24 4 0.05
25 3 0.04
26 8 0.11
27 1 0.01
28 18 0.24
29 24 0.32
30 2 0.03
31 12 0.16
32 3 0.04
ACGTcount: A:0.29, C:0.05, G:0.04, T:0.62
Consensus pattern (29 bp):
TTTTTATACATATCATTTATTTTAAACTG
Found at i:54175777 original size:28 final size:25
Alignment explanation
Indices: 54175687--54175813 Score: 92
Period size: 28 Copynumber: 4.6 Consensus size: 25
54175677 TTATCCATTT
**
54175687 TTTTATATATATTATTTATTTTGAATTG
1 TTTT-TATATATTATTTA-TTTGAA-AC
* *
54175715 TTTTTATACATATCATTTATTTTTTAAAC
1 TTTTTAT--ATATTATTTA--TTTGAAAC
*
54175744 TGTTTTGTATATTATTTATTTGAAATTTC
1 T-TTTTATATATTATTTATTTGAAA---C
* *
54175773 TTTTTACATATTATTTATTTTAAAC
1 TTTTTATATATTATTTATTTGAAAC
54175798 TTTTTATATATTATTT
1 TTTTTATATATTATTT
54175814 TAAATTGTCT
Statistics
Matches: 81, Mismatches: 11, Indels: 17
0.74 0.10 0.16
Matches are distributed among these distances:
25 16 0.20
26 6 0.07
27 3 0.04
28 33 0.41
29 12 0.15
30 11 0.14
ACGTcount: A:0.28, C:0.05, G:0.04, T:0.63
Consensus pattern (25 bp):
TTTTTATATATTATTTATTTGAAAC
Found at i:54175789 original size:56 final size:54
Alignment explanation
Indices: 54175687--54175813 Score: 161
Period size: 57 Copynumber: 2.3 Consensus size: 54
54175677 TTATCCATTT
54175687 TTTTATATATATTATTTATTTTGAATTGTTTTTATACATATCATTTATTTTTTAAAC
1 TTTT-TATATATTATTTATTTTGAATTGTTTTTATACATATCATTTA--TTTTAAAC
* *
54175744 TGTTTTGTATATTATTTA-TTTGAAATT-TCTTTT-TACATATTATTTATTTTAAAC
1 T-TTTTATATATTATTTATTTTG-AATTGT-TTTTATACATATCATTTATTTTAAAC
54175798 TTTTTATATATTATTT
1 TTTTTATATATTATTT
54175814 TAAATTGTCT
Statistics
Matches: 64, Mismatches: 3, Indels: 10
0.83 0.04 0.13
Matches are distributed among these distances:
53 14 0.22
54 9 0.14
56 17 0.27
57 21 0.33
58 3 0.05
ACGTcount: A:0.28, C:0.05, G:0.04, T:0.63
Consensus pattern (54 bp):
TTTTTATATATTATTTATTTTGAATTGTTTTTATACATATCATTTATTTTAAAC
Found at i:54175834 original size:75 final size:72
Alignment explanation
Indices: 54175732--54175868 Score: 175
Period size: 75 Copynumber: 1.9 Consensus size: 72
54175722 ACATATCATT
* * * * *
54175732 TATTTTTTAAACTGTTTTGTATATTATTTATTTGAAATTTCTTTTTACATATTATTTATTTTAAA
1 TATTTTTTAAACTGTCTTCTATATTATTTATTTGAAATTGCATTGT--ATATTATTTATTTTAAA
54175797 CTTTTTATA
64 CTTTTTATA
* * *
54175806 TATTATTTTAAATTGTCTTCTATGTTATTTATTTTAAATTGCATTGTATATTATTTATTTTAA
1 TATT-TTTTAAACTGTCTTCTATATTATTTATTTGAAATTGCATTGTATATTATTTATTTTAA
54175869 TTTGTTTTGC
Statistics
Matches: 54, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
73 16 0.30
74 4 0.07
75 34 0.63
ACGTcount: A:0.28, C:0.05, G:0.05, T:0.61
Consensus pattern (72 bp):
TATTTTTTAAACTGTCTTCTATATTATTTATTTGAAATTGCATTGTATATTATTTATTTTAAACT
TTTTATA
Found at i:54175882 original size:26 final size:26
Alignment explanation
Indices: 54175695--54175923 Score: 143
Period size: 26 Copynumber: 8.8 Consensus size: 26
54175685 TTTTTTATAT
* *
54175695 ATATTATTTATTTTGAATTGTTTTTATAC
1 ATATTATTTATTTTAAATTG--TTT-TGC
* * *
54175724 ATATCATTTATTTTTTAAACTGTTTTGT
1 ATATTATTTA--TTTTAAATTGTTTTGC
* * *
54175752 ATATTATTTATTTGAAATTTCTTTTTAC
1 ATATTATTTATTTTAAA-TT-GTTTTGC
*
54175780 ATATTATTTATTTTAAACT-TTTT--
1 ATATTATTTATTTTAAATTGTTTTGC
*
54175803 ATA-TA-TTATTTTAAATTGTCTT-C
1 ATATTATTTATTTTAAATTGTTTTGC
* ** *
54175826 TATGTTATTTATTTTAAATTGCATTGT
1 -ATATTATTTATTTTAAATTGTTTTGC
*
54175853 ATATTATTTATTTTAATTTGTTTTGC
1 ATATTATTTATTTTAAATTGTTTTGC
* *
54175879 ATATTA-TTACTTTGAATTGTTTT--
1 ATATTATTTATTTTAAATTGTTTTGC
* * *
54175902 ATACTATTTACTTCAAATTGTT
1 ATATTATTTATTTTAAATTGTT
54175924 CTATATATTA
Statistics
Matches: 159, Mismatches: 30, Indels: 27
0.74 0.14 0.12
Matches are distributed among these distances:
21 11 0.07
22 5 0.03
23 8 0.05
24 15 0.09
25 20 0.13
26 48 0.30
27 2 0.01
28 30 0.19
29 12 0.08
31 8 0.05
ACGTcount: A:0.28, C:0.06, G:0.06, T:0.60
Consensus pattern (26 bp):
ATATTATTTATTTTAAATTGTTTTGC
Done.