Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D03
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: 50986338
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 218898 characters in sequence are not A, C, G, or T
File 41 of 170
Found at i:11619618 original size:14 final size:13
Alignment explanation
Indices: 11619601--11619631 Score: 53
Period size: 13 Copynumber: 2.3 Consensus size: 13
11619591 AAGAAAGTGA
11619601 AAAATGAAAAAATG
1 AAAATG-AAAAATG
11619615 AAAATGAAAAATG
1 AAAATGAAAAATG
11619628 AAAA
1 AAAA
11619632 ATGGAGAAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.65
14 6 0.35
ACGTcount: A:0.74, C:0.00, G:0.13, T:0.13
Consensus pattern (13 bp):
AAAATGAAAAATG
Found at i:11621074 original size:128 final size:128
Alignment explanation
Indices: 11620846--11621801 Score: 1264
Period size: 128 Copynumber: 7.5 Consensus size: 128
11620836 GATGAAGATT
** * * *
11620846 ACAAGTCCTATATCTTTGCTCAGCAGTGGAGTAGGTTGGAAATTACAGATCTTGTCTCCCTAAGT
1 ACAAGTCCTATATCCCTGGTCAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAGC
* * * * *
11620911 AGTAGCGGAGTAGATCGAAGACGGCTAATTTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCC
66 AGTAGCGGAGCAGATCAAAAACGGCAAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCC
* * * *
11620974 ACAAGTCCTATCTCACTGGTCAGCAGTGGAGTAGGTTGGAAATTACAGATCTTGTCTCCCTAAAC
1 ACAAGTCCTATATCCCTGGTCAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAGC
* *
11621039 AGTAGCGGAGCAGATCAAAAATGGCAAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCC
66 AGTAGCGGAGCAGATCAAAAACGGCAAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCC
* * * * * *
11621102 ACAAGTCTTATGTCCCTGGTTAGTAGTGGAATAGGTTAGAGATTACAGATCTTGTCTCCCTAAGC
1 ACAAGTCCTATATCCCTGGTCAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAGC
* * *
11621167 AGTAGCGGAGCAGATCAAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGTAGATTTAAGCC
66 AGTAGCGGAGCAGATCAAAAACGGCAAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCC
* * * * * * *
11621230 ACAAGTCTTATGTCCCTAGTTAACAGTGGAATAGGTTAGAAATTACAGATCTGGTCTCCCTAAGC
1 ACAAGTCCTATATCCCTGGTCAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAGC
* * * ** *
11621295 AATAGCAGG-GCAGATTAAAGACGGCGGATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCC
66 AGTAGC-GGAGCAGATCAAAAACGGCAAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCC
* * * *
11621358 ACAAGTCCTATTTTCCTGGTCAGCAGTGGAATAGGTTGAAAATTACAAATCTTGTCTCCCTAAGC
1 ACAAGTCCTATATCCCTGGTCAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAGC
* * ** *
11621423 AATAGCGGAGCAGATCAAAGACTGG-GGATCTTATCTTCAAGTGTAAGGAAGCAAATTTAAGCC
66 AGTAGCGGAGCAGATCAAAAAC-GGCAAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCC
* ** *
11621486 ACAAGT-CTAATGTCCCTGGTCAGCAGTGGAATAGGTTTCAAAATTACAGATCTTATCTCCCTAA
1 ACAAGTCCT-ATATCCCTGGTCAGCAGTGGAATAGG-TTGGAAATTACAGATCTTGTCTCCCTAA
* * *
11621550 GCAGTAGC---G--GATCGAAAGCGGCAAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCC
64 GCAGTAGCGGAGCAGATCAAAAACGGCAAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCC
* *
11621610 ACAAGTCGTATATCCCTAGTCAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAGC
1 ACAAGTCCTATATCCCTGGTCAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAGC
*
11621675 AATAGCGGAGCAGATCAAAAACGG-AGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCC
66 AGTAGCGGAGCAGATCAAAAACGGCA-AATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCC
* *
11621738 ACAAGTCCTATATCCCTGGTCAGCAGTGGAATAGGTTGGGAAATTACAGATCCTATCTCCCTAA
1 ACAAGTCCTATATCCCTGGTCAGCAGTGGAATAGGTT-GGAAATTACAGATCTTGTCTCCCTAA
11621802 AGTTGTAGTG
Statistics
Matches: 737, Mismatches: 77, Indels: 27
0.88 0.09 0.03
Matches are distributed among these distances:
123 34 0.05
124 71 0.10
125 1 0.00
126 2 0.00
127 5 0.01
128 564 0.77
129 60 0.08
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (128 bp):
ACAAGTCCTATATCCCTGGTCAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAGC
AGTAGCGGAGCAGATCAAAAACGGCAAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCC
Found at i:11622198 original size:44 final size:43
Alignment explanation
Indices: 11622131--11622257 Score: 148
Period size: 44 Copynumber: 2.9 Consensus size: 43
11622121 AAAAAATTTC
11622131 AAATCTTATCTCTCTGA-AGTTACAGTGGAGCAGATTAAAGCCAG
1 AAATCTTATCTCT-TGAGA-TTACAGTGGAGCAGATTAAAGCCAG
* *
11622175 AAATCTTATCTCATTGAGATTACAGCGGAGCAGATTGAAGCCAG
1 AAATCTTATCTC-TTGAGATTACAGTGGAGCAGATTAAAGCCAG
* * * * *
11622219 TAATCCTATTTCCCTGAGATTACAGTGGAGCGGATTAAA
1 AAATCTTATCT-CTTGAGATTACAGTGGAGCAGATTAAA
11622258 ATAAAGGATC
Statistics
Matches: 71, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
44 68 0.96
45 3 0.04
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (43 bp):
AAATCTTATCTCTTGAGATTACAGTGGAGCAGATTAAAGCCAG
Found at i:11622490 original size:220 final size:218
Alignment explanation
Indices: 11621957--11622610 Score: 981
Period size: 219 Copynumber: 3.0 Consensus size: 218
11621947 TCGAAAATGG
*
11621957 AATCTTATCTCCCTGAGATTACAGCGAAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTA
1 AATCTTATCTCCCTGAGATTACAGCG-AGCAGATTGAAGCTAGTAATCCTATTTCCCTGAGATTA
* * *
11622022 TAGTGGAGCGGATTAAAATAAAAGATCTTATCTCTCTGAAATTACAGTAGAATAGATCGCATCAG
65 CAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAATTACAGTAGAGTAGATCGCATCAG
* * *
11622087 GTCTTATCTCCCTTGGATTACAGTGGAATATACCAAAAAATTTCAAATCTTATCTCTCTGAAGTT
130 GTCTTATCTCCCTGGGATTACAGTGGAATAGACCAAAAAATTTCAAATCTTATCTCCCTGAAGTT
11622152 ACAGTGGAGCAGATTAAAGCCAGA
195 ACAGTGGAGCAGATTAAAGCCAGA
** *
11622176 AATCTTATCTCATTGAGATTACAGCGGAGCAGATTGAAGCCAGTAATCCTATTTCCCTGAGATTA
1 AATCTTATCTCCCTGAGATTACAGC-GAGCAGATTGAAGCTAGTAATCCTATTTCCCTGAGATTA
*
11622241 CAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAATTATAGTAGAGTAGATCGCATCAG
65 CAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAATTACAGTAGAGTAGATCGCATCAG
* * * *
11622306 GTCTTATCTCCCTGGGATTATAGTGGAATAGACCGAAAAATTTCATATCTTATCTCCCTGAGGTT
130 GTCTTATCTCCCTGGGATTACAGTGGAATAGACCAAAAAATTTCAAATCTTATCTCCCTGAAGTT
11622371 ACAGTGGAGCAGATTGAACA-CCAGA
195 ACAGTGGAGCAGATT-AA-AGCCAGA
*
11622396 AATCTTATCTCCCTGAGATTACAGCTGAGCAGATTGAAGCTAGTAATCCTATTTCCCTAAGATTA
1 AATCTTATCTCCCTGAGATTACAGC-GAGCAGATTGAAGCTAGTAATCCTATTTCCCTGAGATTA
* *
11622461 CAGTGGAGCGAATTAAAATAAAGGATCTTATCTCTTTGAAATTACAGTAGAGTAGATCGCATCAG
65 CAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAATTACAGTAGAGTAGATCGCATCAG
* * * * **
11622526 GTCTTATCTCCCTGAGATTACAGGGGAATAGA-CATAAGAATTTCAAATATTA-CTTCCCTGGCG
130 GTCTTATCTCCCTGGGATTACAGTGGAATAGACCA-AAAAATTTCAAATCTTATC-TCCCTGAAG
* * *
11622589 GTGCAGTGGAACAGATTAAAGC
193 TTACAGTGGAGCAGATTAAAGC
11622611 TACAATAACG
Statistics
Matches: 394, Mismatches: 35, Indels: 12
0.89 0.08 0.03
Matches are distributed among these distances:
218 1 0.00
219 198 0.50
220 194 0.49
221 1 0.00
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (218 bp):
AATCTTATCTCCCTGAGATTACAGCGAGCAGATTGAAGCTAGTAATCCTATTTCCCTGAGATTAC
AGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAATTACAGTAGAGTAGATCGCATCAGG
TCTTATCTCCCTGGGATTACAGTGGAATAGACCAAAAAATTTCAAATCTTATCTCCCTGAAGTTA
CAGTGGAGCAGATTAAAGCCAGA
Found at i:11622991 original size:16 final size:16
Alignment explanation
Indices: 11622967--11623006 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
11622957 CCCAAAATTA
11622967 TAACCCAAACCCAAT-
1 TAACCCAAACCCAATC
*
11622982 TAAGCCCAAACCTAATC
1 TAA-CCCAAACCCAATC
11622999 TAACCCAA
1 TAACCCAA
11623007 TACTAAACCC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 3 0.14
16 16 0.73
17 3 0.14
ACGTcount: A:0.45, C:0.38, G:0.03, T:0.15
Consensus pattern (16 bp):
TAACCCAAACCCAATC
Found at i:11627252 original size:18 final size:18
Alignment explanation
Indices: 11627214--11627249 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
11627204 TTATTATTTT
*
11627214 TAAAATTTACTATTAAAA
1 TAAAATTTAATATTAAAA
11627232 TAAAATTTAAATATTAAA
1 TAAAATTT-AATATTAAA
11627250 TAATTTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (18 bp):
TAAAATTTAATATTAAAA
Found at i:11627267 original size:16 final size:19
Alignment explanation
Indices: 11627238--11627297 Score: 56
Period size: 18 Copynumber: 3.2 Consensus size: 19
11627228 AAAATAAAAT
11627238 TTAA-ATATTAAATAATTTA
1 TTAATATATT-AATAATTTA
11627257 TTAA-A-A-TAATAAATTATA
1 TTAATATATTAAT-AATT-TA
11627275 TTAATTATATTAATAATTTA
1 TTAA-TATATTAATAATTTA
11627295 TTA
1 TTA
11627298 TATGACTAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
16 3 0.09
17 5 0.14
18 7 0.20
19 5 0.14
20 6 0.17
21 5 0.14
22 4 0.11
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
TTAATATATTAATAATTTA
Found at i:11639579 original size:16 final size:16
Alignment explanation
Indices: 11639558--11639600 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
11639548 CTCTCAACAT
11639558 TTAATTAAATTTGATA
1 TTAATTAAATTTGATA
* * *
11639574 TTAATTTAGTTTGATT
1 TTAATTAAATTTGATA
11639590 TTAATTTAAAT
1 TTAA-TTAAAT
11639601 GAAAATTAAA
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
16 17 0.81
17 4 0.19
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (16 bp):
TTAATTAAATTTGATA
Found at i:11640423 original size:25 final size:25
Alignment explanation
Indices: 11640376--11640424 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
11640366 AAACATCAAT
* * *
11640376 TTATTTTTATATTCGATAAATAAAA
1 TTATTTATATATGCAATAAATAAAA
*
11640401 TTATTTATATATGCAATATATAAA
1 TTATTTATATATGCAATAAATAAA
11640425 CATAAAATGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (25 bp):
TTATTTATATATGCAATAAATAAAA
Found at i:11641931 original size:23 final size:24
Alignment explanation
Indices: 11641889--11641937 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
11641879 ATATTTTTTA
* *
11641889 TTTTTATTTTTAAGAATTTAATTT
1 TTTTTAATTTTAAGAATTTAAGTT
11641913 TTTTTAATTTTAA-AATTTAAGTT
1 TTTTTAATTTTAAGAATTTAAGTT
11641936 TT
1 TT
11641938 ACTATTATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 11 0.48
24 12 0.52
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (24 bp):
TTTTTAATTTTAAGAATTTAAGTT
Found at i:11646709 original size:30 final size:30
Alignment explanation
Indices: 11646675--11646735 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
11646665 AGTTGCTCCG
11646675 AACTCTGATACAGCAACCTCATAAGTTTCC
1 AACTCTGATACAGCAACCTCATAAGTTTCC
11646705 AACTCTGATACAGCAACCTCATAAGTTTCC
1 AACTCTGATACAGCAACCTCATAAGTTTCC
11646735 A
1 A
11646736 TCAATTTCCC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.34, C:0.30, G:0.10, T:0.26
Consensus pattern (30 bp):
AACTCTGATACAGCAACCTCATAAGTTTCC
Found at i:11662353 original size:18 final size:19
Alignment explanation
Indices: 11662330--11662369 Score: 73
Period size: 18 Copynumber: 2.2 Consensus size: 19
11662320 ATGACTTATT
11662330 TTATATTAATTTGAATA-A
1 TTATATTAATTTGAATATA
11662348 TTATATTAATTTGAATATA
1 TTATATTAATTTGAATATA
11662367 TTA
1 TTA
11662370 CAAAACCGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 17 0.81
19 4 0.19
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (19 bp):
TTATATTAATTTGAATATA
Found at i:11683824 original size:16 final size:16
Alignment explanation
Indices: 11683771--11683830 Score: 61
Period size: 16 Copynumber: 3.7 Consensus size: 16
11683761 AATACGATTT
11683771 TCCCTAATGCAAATTA
1 TCCCTAATGCAAATTA
* *
11683787 T-CCTAAGTATGC-AGTGA
1 TCCCT-A--ATGCAAATTA
11683804 TCCCTAATGCAAATTA
1 TCCCTAATGCAAATTA
11683820 TCCCTAATGCA
1 TCCCTAATGCA
11683831 TTAGAATACT
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
15 7 0.20
16 16 0.46
17 5 0.14
18 7 0.20
ACGTcount: A:0.33, C:0.25, G:0.12, T:0.30
Consensus pattern (16 bp):
TCCCTAATGCAAATTA
Found at i:11689199 original size:24 final size:24
Alignment explanation
Indices: 11689149--11689200 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
11689139 AATCAAAGTC
* *
11689149 AAATATATTATGCTAATAAATGCT
1 AAATATATTATACTAATAAATACT
*
11689173 AAATATATTATACTAATAAATATT
1 AAATATATTATACTAATAAATACT
11689197 AAAT
1 AAAT
11689201 CTTTTAGAAA
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:0.52, C:0.06, G:0.04, T:0.38
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Found at i:11692058 original size:35 final size:35
Alignment explanation
Indices: 11691993--11692219 Score: 267
Period size: 35 Copynumber: 6.3 Consensus size: 35
11691983 ACGTGTTTAC
* *
11691993 CCCAACC-TTTTAAGGTTACCGTAGACGGGTCTAT
1 CCCAACCTTTTTAAGGTTACCTTAGACAGGTCTAT
* * **
11692027 CCCAGCCTTTTTAAGGTTGCCTTAGATGGGTCTAT
1 CCCAACCTTTTTAAGGTTACCTTAGACAGGTCTAT
* * *
11692062 CCCAACTTTTTTTAAAGGTTGCCTTAGAAAAGGTCTAT
1 CCCAAC-CTTTTT-AAGGTTACCTTAG-ACAGGTCTAT
*
11692100 CCCAACCTTTTTAAGGTTACCTTAGACAGCTCTAT
1 CCCAACCTTTTTAAGGTTACCTTAGACAGGTCTAT
* * *
11692135 ACCAACCTTTTTTAAAGGTTGCCTCAGACAAGGTCTAT
1 CCCAACC-TTTTT-AAGGTTACCTTAGAC-AGGTCTAT
11692173 CCCAACCTTTTTAAGGTTACCTTAGACAGGTCTAT
1 CCCAACCTTTTTAAGGTTACCTTAGACAGGTCTAT
*
11692208 CCCAACATTTTT
1 CCCAACCTTTTT
11692220 TAAAGGTATG
Statistics
Matches: 166, Mismatches: 20, Indels: 13
0.83 0.10 0.07
Matches are distributed among these distances:
34 6 0.04
35 62 0.37
36 35 0.21
37 36 0.22
38 27 0.16
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.34
Consensus pattern (35 bp):
CCCAACCTTTTTAAGGTTACCTTAGACAGGTCTAT
Found at i:11692109 original size:73 final size:73
Alignment explanation
Indices: 11692020--11692233 Score: 329
Period size: 73 Copynumber: 2.9 Consensus size: 73
11692010 ACCGTAGACG
* * ** *
11692020 GGTCTATCCCAGCCTTTTTAAGGTTGCCTTAGATGGGTCTATCCCAACTTTTTTTAAAGGTTGCC
1 GGTCTATCCCAACCTTTTTAAGGTTACCTTAGACAGGTCTATCCCAACATTTTTTAAAGGTTGCC
11692085 TTAGAAAA
66 TTAGAAAA
* * *
11692093 GGTCTATCCCAACCTTTTTAAGGTTACCTTAGACAGCTCTATACCAACCTTTTTTAAAGGTTGCC
1 GGTCTATCCCAACCTTTTTAAGGTTACCTTAGACAGGTCTATCCCAACATTTTTTAAAGGTTGCC
* *
11692158 TCAGACAA
66 TTAGAAAA
11692166 GGTCTATCCCAACCTTTTTAAGGTTACCTTAGACAGGTCTATCCCAACATTTTTTAAAGGTATGC
1 GGTCTATCCCAACCTTTTTAAGGTTACCTTAGACAGGTCTATCCCAACATTTTTTAAAGGT-TGC
11692231 CTT
65 CTT
11692234 GACTAAGTCT
Statistics
Matches: 127, Mismatches: 13, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
73 122 0.96
74 5 0.04
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (73 bp):
GGTCTATCCCAACCTTTTTAAGGTTACCTTAGACAGGTCTATCCCAACATTTTTTAAAGGTTGCC
TTAGAAAA
Found at i:11699658 original size:19 final size:21
Alignment explanation
Indices: 11699636--11699678 Score: 63
Period size: 19 Copynumber: 2.1 Consensus size: 21
11699626 ATAAAAGACC
11699636 ATAAAAATA-TAGAAA-TTAT
1 ATAAAAATATTAGAAATTTAT
*
11699655 ATAAAATTATTAGAAATTTAT
1 ATAAAAATATTAGAAATTTAT
11699676 ATA
1 ATA
11699679 TATTTGAGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 8 0.38
20 6 0.29
21 7 0.33
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (21 bp):
ATAAAAATATTAGAAATTTAT
Found at i:11699663 original size:10 final size:11
Alignment explanation
Indices: 11699642--11699678 Score: 51
Period size: 10 Copynumber: 3.5 Consensus size: 11
11699632 GACCATAAAA
11699642 ATATAGAAATT
1 ATATAGAAATT
11699653 ATATA-AAATT
1 ATATAGAAATT
11699663 AT-TAGAAATTT
1 ATATAGAAA-TT
11699674 ATATA
1 ATATA
11699679 TATTTGAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
9 2 0.09
10 10 0.43
11 9 0.39
12 2 0.09
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (11 bp):
ATATAGAAATT
Found at i:11699739 original size:22 final size:20
Alignment explanation
Indices: 11699689--11699751 Score: 83
Period size: 22 Copynumber: 3.1 Consensus size: 20
11699679 TATTTGAGTT
11699689 TTATTAAAAA-ATAGAAAAA
1 TTATTAAAAATATAGAAAAA
*
11699708 CTATTAAAAATATAGAAAAA
1 TTATTAAAAATATAGAAAAA
*
11699728 TTATCTTAAAAATATAGGAAAA
1 TTA--TTAAAAATATAGAAAAA
11699750 TT
1 TT
11699752 TAAAAAAATA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
19 9 0.24
20 11 0.29
22 18 0.47
ACGTcount: A:0.60, C:0.03, G:0.06, T:0.30
Consensus pattern (20 bp):
TTATTAAAAATATAGAAAAA
Found at i:11699860 original size:20 final size:20
Alignment explanation
Indices: 11699831--11699868 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
11699821 TGACAACATG
*
11699831 ATAAAAAATAATTAAAATCA
1 ATAAAAAATAATAAAAATCA
*
11699851 ATAAATAATAATAAAAAT
1 ATAAAAAATAATAAAAAT
11699869 ATTTTGAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (20 bp):
ATAAAAAATAATAAAAATCA
Found at i:11710361 original size:19 final size:20
Alignment explanation
Indices: 11710328--11710368 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
11710318 ATAAACACAG
*
11710328 AAAAGAAAACCGAAAGAAAA
1 AAAAGAAAACAGAAAGAAAA
11710348 AAAAGAAAA-AGAAAGAAAA
1 AAAAGAAAACAGAAAGAAAA
11710367 AA
1 AA
11710369 GAAAACCAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.80, C:0.05, G:0.15, T:0.00
Consensus pattern (20 bp):
AAAAGAAAACAGAAAGAAAA
Found at i:11710369 original size:11 final size:10
Alignment explanation
Indices: 11710329--11710372 Score: 54
Period size: 11 Copynumber: 4.3 Consensus size: 10
11710319 TAAACACAGA
*
11710329 AAAGAAAACCG
1 AAAGAAAA-AG
11710340 AAAGAAAAA-
1 AAAGAAAAAG
11710349 AAAGAAAAAG
1 AAAGAAAAAG
11710359 AAAGAAAAAAG
1 AAAG-AAAAAG
11710370 AAA
1 AAA
11710373 ACCAGGAAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
9 9 0.30
10 4 0.13
11 17 0.57
ACGTcount: A:0.80, C:0.05, G:0.16, T:0.00
Consensus pattern (10 bp):
AAAGAAAAAG
Found at i:11710381 original size:20 final size:19
Alignment explanation
Indices: 11710328--11710383 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 19
11710318 ATAAACACAG
11710328 AAAAGAAAACC-GAAAGAAAA
1 AAAAGAAAACCAGAAAG--AA
11710348 AAAAGAAAA--AGAAAGAA
1 AAAAGAAAACCAGAAAGAA
11710365 AAAAGAAAACCAGGAAAGA
1 AAAAGAAAACCA-GAAAGA
11710384 TTTAAAACCA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
17 11 0.34
19 6 0.19
20 15 0.47
ACGTcount: A:0.75, C:0.07, G:0.18, T:0.00
Consensus pattern (19 bp):
AAAAGAAAACCAGAAAGAA
Found at i:11711307 original size:101 final size:101
Alignment explanation
Indices: 11711130--11711311 Score: 247
Period size: 101 Copynumber: 1.8 Consensus size: 101
11711120 TAAGATTCGC
* * * * * * *
11711130 CATTGTGGCTTTAATCTTTTTAGCTGGAATGTCGAAAAAGTAAGATTCATCGTTGTGGCTTTAAC
1 CATTGTGACTTTAATCCTTTTAACTGCAAAGTCGAAAAAGCAAGATTCACCGTTGTGGCTTTAAC
*
11711195 CTGCTCTACTGCACTGGATGAGAGAGTGAGATTCAT
66 CTGCTCCACTGCACTGGATGAGAGAGTGAGATTCAT
** * *
11711231 CATTGTGACTTTAATCCTTTTAACTGCAAAGTCGGGAAAGCAATATTCACCGTTGTGGCTTTAAT
1 CATTGTGACTTTAATCCTTTTAACTGCAAAGTCGAAAAAGCAAGATTCACCGTTGTGGCTTTAAC
*
11711296 CTGTTCCACTGCACTG
66 CTGCTCCACTGCACTG
11711312 CTTGGGAAGA
Statistics
Matches: 68, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
101 68 1.00
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (101 bp):
CATTGTGACTTTAATCCTTTTAACTGCAAAGTCGAAAAAGCAAGATTCACCGTTGTGGCTTTAAC
CTGCTCCACTGCACTGGATGAGAGAGTGAGATTCAT
Found at i:11711453 original size:44 final size:44
Alignment explanation
Indices: 11711347--11711596 Score: 111
Period size: 44 Copynumber: 5.5 Consensus size: 44
11711337 TTCGATCTAT
* * * * *
11711347 TCCACTGTAATCTCAGGGAGATAAGA-CC--TAATATGATCTAC
1 TCCACTGTAATCTCAAGGAGATAAGATCCTTTATTTTAATCCAC
* ** *
11711388 TCTACTGTAA-CTTTAGAGAGATAAGATCCTTTATTTTAATCCGC
1 TCCACTGTAATCTCAAG-GAGATAAGATCCTTTATTTTAATCCAC
* * * * **
11711432 TCCACTGTAATCTCAAGGAGATAGGAT--TACTAGCTTCAATCTGC
1 TCCACTGTAATCTCAAGGAGATAAGATCCT-TTA-TTTTAATCCAC
* * * * *
11711476 TCCGCTGTAATCTCAGGGAGATAAGATTTCTGGCTTCAATCTGATACGATCTAC
1 TCCACTGTAATCTCAAGGAGATAAGA--TC---CTT-TAT-T-TTA--ATCCAC
*
11711530 TCTACTGTAA-CTTC-AGAGAGATAAGATCCTTTATTTTAATCCAC
1 TCCACTGTAATC-TCAAG-GAGATAAGATCCTTTATTTTAATCCAC
*
11711574 TCCACTGTAATCTCAGGGAGATA
1 TCCACTGTAATCTCAAGGAGATA
11711597 GGATTACTAG
Statistics
Matches: 152, Mismatches: 34, Indels: 43
0.66 0.15 0.19
Matches are distributed among these distances:
40 3 0.02
41 18 0.12
42 3 0.02
43 2 0.01
44 79 0.52
45 6 0.04
46 3 0.02
47 1 0.01
48 2 0.01
49 3 0.02
51 3 0.02
52 3 0.02
53 2 0.01
54 24 0.16
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (44 bp):
TCCACTGTAATCTCAAGGAGATAAGATCCTTTATTTTAATCCAC
Found at i:11711556 original size:142 final size:142
Alignment explanation
Indices: 11711381--11711703 Score: 574
Period size: 142 Copynumber: 2.3 Consensus size: 142
11711371 GACCTAATAT
* *
11711381 GATCTACTCTACTGTAACTTTAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTC
1 GATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCACTCCACTGTAATCTC
*
11711446 AAGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTTCTGGCT
66 AAGGAGATAGGATTACTAGCTTCAATCTACTCCGCTGTAATCTCAGGGAGATAAGATTTCTGGCT
11711511 TCAATCTGATAC
131 TCAATCTGATAC
11711523 GATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCACTCCACTGTAATCTC
1 GATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCACTCCACTGTAATCTC
* *
11711588 AGGGAGATAGGATTACTAGCTTCAATCTACTCCGCTGTAATCTCAGGGAGATAATATTTCTGGCT
66 AAGGAGATAGGATTACTAGCTTCAATCTACTCCGCTGTAATCTCAGGGAGATAAGATTTCTGGCT
* *
11711653 TCAATCTGCTGC
131 TCAATCTGATAC
*
11711665 GATCTACTCTACCGTAACTTCAGAGAGATAAGATCCTTT
1 GATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTT
11711704 CTCAGTCTCC
Statistics
Matches: 173, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
142 173 1.00
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (142 bp):
GATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCACTCCACTGTAATCTC
AAGGAGATAGGATTACTAGCTTCAATCTACTCCGCTGTAATCTCAGGGAGATAAGATTTCTGGCT
TCAATCTGATAC
Found at i:11711620 original size:44 final size:44
Alignment explanation
Indices: 11711567--11711659 Score: 132
Period size: 44 Copynumber: 2.1 Consensus size: 44
11711557 CCTTTATTTT
* *
11711567 AATCCACTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTC
1 AATCTACTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTC
* * * *
11711611 AATCTACTCCGCTGTAATCTCAGGGAGATAATATTTCTGGCTTC
1 AATCTACTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTC
11711655 AATCT
1 AATCT
11711660 GCTGCGATCT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (44 bp):
AATCTACTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTC
Found at i:11712066 original size:87 final size:87
Alignment explanation
Indices: 11711944--11712535 Score: 889
Period size: 87 Copynumber: 6.8 Consensus size: 87
11711934 CTGTCGACAT
* * **
11711944 AGGAGGGCAAGATCTGCTATCTTCAACCAGCTCCACTAAAACCGATGGAGGCAAGGCTTTGTTTT
1 AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTT
11712009 CGATCTGCTTCGCCGTTAACGC
66 CGATCTGCTTCGCCGTTAACGC
*
11712031 AGGAAGGTAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTT
1 AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTT
* * *
11712096 TGATCTGCTTCACCGTTAATGC
66 CGATCTGCTTCGCCGTTAACGC
*
11712118 AGGAAGGCAAGATCTGCTATCTTTAACTAGCTCCA-TGCAACCGATGGAGGCAAGGCTTTGTTTT
1 AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTT
*
11712182 CGATCTGCTTCACCGTTAACGC
66 CGATCTGCTTCGCCGTTAACGC
* *
11712204 AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCTACTGCAACCGATGGAGGCAAGGCTTTTTTTT
1 AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTT
* *
11712269 CGATCTGTTTCGCTGTTAACGC
66 CGATCTGCTTCGCCGTTAACGC
* * * * *
11712291 AGAAAGACAAGATCTGCTATCTTTAACCAACTCCACTACAACCAATGGAGGCAAGGCTTTGTTTT
1 AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTT
* * *
11712356 TGATCTGCTTCGCTGTTAATGC
66 CGATCTGCTTCGCCGTTAACGC
* * * * *
11712378 AGGAAGGCAAGATCTACTATCTTTAACCAGCTTCACTGTAACTGATGGAGGCAAGACTTTGTTTT
1 AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTT
* *
11712443 CGATCTGCTTCGCTGTTAATGC
66 CGATCTGCTTCGCCGTTAACGC
* * *
11712465 AGGAATGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATAGAGGTAAGGCTTTGTTTT
1 AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTT
11712530 CGATCT
66 CGATCT
11712536 TCACTGATAT
Statistics
Matches: 457, Mismatches: 47, Indels: 2
0.90 0.09 0.00
Matches are distributed among these distances:
86 82 0.18
87 375 0.82
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.29
Consensus pattern (87 bp):
AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTT
CGATCTGCTTCGCCGTTAACGC
Found at i:11712381 original size:260 final size:261
Alignment explanation
Indices: 11711944--11712535 Score: 925
Period size: 260 Copynumber: 2.3 Consensus size: 261
11711934 CTGTCGACAT
* * **
11711944 AGGAGGGCAAGATCTGCTATCTTCAACCAGCTCCACTAAAACCGATGGAGGCAAGGCTTTGTTTT
1 AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTT
* ** * *
11712009 CGATCTGCTTCGCCGTTAACGCAGGAAGGTAAGATCTGCTATCTTTAACCAGCTCCACTGCAACC
66 CGATCTGCTTCGCCGTTAACGCAGAAAGACAAGATCTGCTATCTTTAACCAACTCCACTACAACC
* *
11712074 GATGGAGGCAAGGCTTTGTTTTTGATCTGCTTCACCGTTAATGCAGGAAGGCAAGATCTGCTATC
131 AATGGAGGCAAGGCTTTGTTTTTGATCTGCTTCACCGTTAATGCAGGAAGGCAAGATCTACTATC
* *
11712139 TTTAACTAGCTCCA-TGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGCTTCACCGTTAACG
196 TTTAACCAGCTCCACTGCAACCGATGGAGGCAAGACTTTGTTTTCGATCTGCTTCACCGTTAACG
11712203 C
261 C
* *
11712204 AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCTACTGCAACCGATGGAGGCAAGGCTTTTTTTT
1 AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTT
* *
11712269 CGATCTGTTTCGCTGTTAACGCAGAAAGACAAGATCTGCTATCTTTAACCAACTCCACTACAACC
66 CGATCTGCTTCGCCGTTAACGCAGAAAGACAAGATCTGCTATCTTTAACCAACTCCACTACAACC
* *
11712334 AATGGAGGCAAGGCTTTGTTTTTGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTACTATC
131 AATGGAGGCAAGGCTTTGTTTTTGATCTGCTTCACCGTTAATGCAGGAAGGCAAGATCTACTATC
* * * * * *
11712399 TTTAACCAGCTTCACTGTAACTGATGGAGGCAAGACTTTGTTTTCGATCTGCTTCGCTGTTAATG
196 TTTAACCAGCTCCACTGCAACCGATGGAGGCAAGACTTTGTTTTCGATCTGCTTCACCGTTAACG
11712464 C
261 C
* * *
11712465 AGGAATGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATAGAGGTAAGGCTTTGTTTT
1 AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTT
11712530 CGATCT
66 CGATCT
11712536 TCACTGATAT
Statistics
Matches: 301, Mismatches: 30, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
260 190 0.63
261 111 0.37
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.29
Consensus pattern (261 bp):
AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTT
CGATCTGCTTCGCCGTTAACGCAGAAAGACAAGATCTGCTATCTTTAACCAACTCCACTACAACC
AATGGAGGCAAGGCTTTGTTTTTGATCTGCTTCACCGTTAATGCAGGAAGGCAAGATCTACTATC
TTTAACCAGCTCCACTGCAACCGATGGAGGCAAGACTTTGTTTTCGATCTGCTTCACCGTTAACG
C
Found at i:11713771 original size:20 final size:20
Alignment explanation
Indices: 11713743--11713800 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
11713733 CCCCTTAGCC
11713743 TCTCTATTTTTCATTTTTCAT
1 TCTC-ATTTTTCATTTTTCAT
* * **
11713764 TTTCATTTTTTACATTTCAT
1 TCTCATTTTTCATTTTTCAT
11713784 TCTCATTTTTCATTTTT
1 TCTCATTTTTCATTTTT
11713801 TTTCATTTTT
Statistics
Matches: 29, Mismatches: 8, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
20 26 0.90
21 3 0.10
ACGTcount: A:0.16, C:0.17, G:0.00, T:0.67
Consensus pattern (20 bp):
TCTCATTTTTCATTTTTCAT
Found at i:11713804 original size:10 final size:10
Alignment explanation
Indices: 11713789--11713813 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
11713779 TTCATTCTCA
11713789 TTTTTCATTT
1 TTTTTCATTT
11713799 TTTTTCATTT
1 TTTTTCATTT
11713809 TTTTT
1 TTTTT
11713814 GAAATCCATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.84
Consensus pattern (10 bp):
TTTTTCATTT
Found at i:11713810 original size:7 final size:7
Alignment explanation
Indices: 11713748--11713800 Score: 56
Period size: 7 Copynumber: 7.9 Consensus size: 7
11713738 TAGCCTCTCT
11713748 ATTTTTC
1 ATTTTTC
11713755 ATTTTTC
1 ATTTTTC
11713762 A-TTTTC
1 ATTTTTC
*
11713768 ATTTTTT
1 ATTTTTC
**
11713775 ACATTTC
1 ATTTTTC
*
11713782 A-TTCTC
1 ATTTTTC
11713788 ATTTTTC
1 ATTTTTC
11713795 ATTTTT
1 ATTTTT
11713801 TTTCATTTTT
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
6 10 0.27
7 27 0.73
ACGTcount: A:0.17, C:0.15, G:0.00, T:0.68
Consensus pattern (7 bp):
ATTTTTC
Found at i:11714233 original size:27 final size:27
Alignment explanation
Indices: 11714203--11714254 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
11714193 TTTGACTTTG
*
11714203 ATTGA-TTTCTCTTTTTTTGTTTTTGAC
1 ATTGATTTTCTCTTTTCTT-TTTTTGAC
*
11714230 ATTGATTTTTTCTTTTCTTTTTTTG
1 ATTGATTTTCTCTTTTCTTTTTTTG
11714255 TTTTTGATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 11 0.50
28 11 0.50
ACGTcount: A:0.10, C:0.10, G:0.10, T:0.71
Consensus pattern (27 bp):
ATTGATTTTCTCTTTTCTTTTTTTGAC
Found at i:11714271 original size:33 final size:33
Alignment explanation
Indices: 11714207--11714278 Score: 99
Period size: 33 Copynumber: 2.2 Consensus size: 33
11714197 ACTTTGATTG
11714207 ATTTCTCTTTTTTTGTTTTTGACATTGATTTTTT
1 ATTT-TCTTTTTTTGTTTTTGACATTGATTTTTT
* ** *
11714241 CTTTTCTTTTTTTGTTTTTGATTTTTATTTTTT
1 ATTTTCTTTTTTTGTTTTTGACATTGATTTTTT
11714274 ATTTT
1 ATTTT
11714279 GAATCTGAAC
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
33 30 0.91
34 3 0.09
ACGTcount: A:0.10, C:0.07, G:0.07, T:0.76
Consensus pattern (33 bp):
ATTTTCTTTTTTTGTTTTTGACATTGATTTTTT
Found at i:11720093 original size:11 final size:11
Alignment explanation
Indices: 11720065--11720113 Score: 66
Period size: 11 Copynumber: 4.5 Consensus size: 11
11720055 AAATAAACAC
11720065 AGAAAAGAAAA
1 AGAAAAGAAAA
*
11720076 CCG-AAAGAAAA
1 -AGAAAAGAAAA
11720087 AGAAAAGAAAA
1 AGAAAAGAAAA
11720098 AGAAAA-AAAA
1 AGAAAAGAAAA
11720108 AGAAAA
1 AGAAAA
11720114 CCAGGAAAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
10 11 0.32
11 22 0.65
12 1 0.03
ACGTcount: A:0.80, C:0.04, G:0.16, T:0.00
Consensus pattern (11 bp):
AGAAAAGAAAA
Found at i:11720799 original size:18 final size:19
Alignment explanation
Indices: 11720763--11720807 Score: 74
Period size: 18 Copynumber: 2.4 Consensus size: 19
11720753 ATAACTTTAA
11720763 AATTTTTATATTTTATAAT
1 AATTTTTATATTTTATAAT
*
11720782 AATTTTTATA-TTTCTAAT
1 AATTTTTATATTTTATAAT
11720800 AATTTTTA
1 AATTTTTA
11720808 AAAAATTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 15 0.60
19 10 0.40
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (19 bp):
AATTTTTATATTTTATAAT
Found at i:11728910 original size:141 final size:143
Alignment explanation
Indices: 11728647--11728930 Score: 545
Period size: 141 Copynumber: 2.0 Consensus size: 143
11728637 ACTAAATCAG
11728647 AAAAGTATAGAATTTTTTTCAAACTGTAGAGATCACACAGCTGAGACACATGCCCCTGTCTTAGG
1 AAAAGTATAGAATTTTTTTCAAACTGTAGAGATCACACAGCTGAGACACATGCCCCTGTCTTAGG
11728712 CCATGTGGACATTCGAAGTAGGGACAGACGGCCGTGTCCCAGCCCGTGTCCGTGCCCGTGTAACT
66 CCATGTGGACATTCGAAGTAGGGACAGACGGCCGTGTCCCAGCCCGTGTCCGTGCCCGTGTAACT
*
11728777 CTCTGACTTGGGT
131 CTCTAACTTGGGT
11728790 AAAAGT-T-GAATTTTTTTCAAACTGTAGAGATCACACAGCTGAGACACATGCCCCTGTCTTAGG
1 AAAAGTATAGAATTTTTTTCAAACTGTAGAGATCACACAGCTGAGACACATGCCCCTGTCTTAGG
11728853 CCATGTGGACATTCGAAGTAGGGACAGACGGCCGTGTCCCAGCCCGTGTCCGTGCCCGTGTAACT
66 CCATGTGGACATTCGAAGTAGGGACAGACGGCCGTGTCCCAGCCCGTGTCCGTGCCCGTGTAACT
11728918 CTCTAACTTGGGT
131 CTCTAACTTGGGT
11728931 CACACGGCCA
Statistics
Matches: 140, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
141 133 0.95
142 1 0.01
143 6 0.04
ACGTcount: A:0.24, C:0.25, G:0.25, T:0.25
Consensus pattern (143 bp):
AAAAGTATAGAATTTTTTTCAAACTGTAGAGATCACACAGCTGAGACACATGCCCCTGTCTTAGG
CCATGTGGACATTCGAAGTAGGGACAGACGGCCGTGTCCCAGCCCGTGTCCGTGCCCGTGTAACT
CTCTAACTTGGGT
Found at i:11729210 original size:23 final size:23
Alignment explanation
Indices: 11729175--11729225 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 23
11729165 AAGCATCCAA
11729175 TGTAATATGCCGAAAATTACTAC
1 TGTAATATGCCGAAAATTACTAC
11729198 TGTAATACT-CCGAAAATTACTAC
1 TGTAATA-TGCCGAAAATTACTAC
*
11729221 AGTAA
1 TGTAA
11729226 GAAAGTAGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 25 0.96
24 1 0.04
ACGTcount: A:0.41, C:0.18, G:0.12, T:0.29
Consensus pattern (23 bp):
TGTAATATGCCGAAAATTACTAC
Found at i:11754509 original size:23 final size:24
Alignment explanation
Indices: 11754483--11754535 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
11754473 ATAGGTGTAG
11754483 TTATCAGGGGTGCATA-AGCACGA
1 TTATCAGGGGTGCATATAGCACGA
* * *
11754506 TTATCATGGGTGTATATAGCATGA
1 TTATCAGGGGTGCATATAGCACGA
*
11754530 ATATCA
1 TTATCA
11754536 AGGGCACCAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
23 14 0.56
24 11 0.44
ACGTcount: A:0.32, C:0.13, G:0.25, T:0.30
Consensus pattern (24 bp):
TTATCAGGGGTGCATATAGCACGA
Found at i:11762523 original size:40 final size:41
Alignment explanation
Indices: 11762479--11762583 Score: 135
Period size: 40 Copynumber: 2.6 Consensus size: 41
11762469 GCCTGCTAAT
* *
11762479 TACACCGGCACTAAGCCTGTAAGGCAA-TAAGCCAAATAGA
1 TACACCGGCACAAAGCCTGTTAGGCAACTAAGCCAAATAGA
*
11762519 TACACCGGCACAAAGCCT-TCTAGG-AACTAAGCCCAATAGA
1 TACACCGGCACAAAGCCTGT-TAGGCAACTAAGCCAAATAGA
* *
11762559 TACACCGACACAAACCCTGTTAGGC
1 TACACCGGCACAAAGCCTGTTAGGC
11762584 TCAAGGTTTG
Statistics
Matches: 56, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
39 3 0.05
40 52 0.93
41 1 0.02
ACGTcount: A:0.37, C:0.30, G:0.18, T:0.15
Consensus pattern (41 bp):
TACACCGGCACAAAGCCTGTTAGGCAACTAAGCCAAATAGA
Found at i:11765493 original size:34 final size:35
Alignment explanation
Indices: 11765418--11765493 Score: 136
Period size: 35 Copynumber: 2.2 Consensus size: 35
11765408 TCATTGGGAT
11765418 TTAGCCCTTTTCAATATCAGTGACAGTCTTGGGCC
1 TTAGCCCTTTTCAATATCAGTGACAGTCTTGGGCC
*
11765453 TAAGCCCTTTTCAATATCAGTGACAGT-TTGGGCC
1 TTAGCCCTTTTCAATATCAGTGACAGTCTTGGGCC
11765487 TTAGCCC
1 TTAGCCC
11765494 ATCTCAGTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
34 13 0.33
35 26 0.67
ACGTcount: A:0.21, C:0.26, G:0.20, T:0.33
Consensus pattern (35 bp):
TTAGCCCTTTTCAATATCAGTGACAGTCTTGGGCC
Found at i:11772510 original size:26 final size:26
Alignment explanation
Indices: 11772451--11772512 Score: 88
Period size: 26 Copynumber: 2.4 Consensus size: 26
11772441 TACCTACAGT
* *
11772451 AGTTTCAAAATATCTTAACATATATC
1 AGTTTCAGAATATCATAACATATATC
* *
11772477 AGTTTCAGAATATCATAGCATGTATC
1 AGTTTCAGAATATCATAACATATATC
11772503 AGTTTCAGAA
1 AGTTTCAGAA
11772513 CACTTACAGG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.39, C:0.15, G:0.11, T:0.35
Consensus pattern (26 bp):
AGTTTCAGAATATCATAACATATATC
Found at i:11773268 original size:34 final size:34
Alignment explanation
Indices: 11773221--11773288 Score: 84
Period size: 34 Copynumber: 2.0 Consensus size: 34
11773211 TCATAGTTGA
* * *
11773221 ACAGTCTTTGGCCTAAGCCCTTTTCAGTATCAGTG
1 ACAGTCTTGGGCCTAAGACCATTTCAGTA-CAGTG
*
11773256 ACAGT-TTGGGCCTTAGACCATTTCAGTACAGTG
1 ACAGTCTTGGGCCTAAGACCATTTCAGTACAGTG
11773289 TCAAAAATGC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
33 5 0.17
34 19 0.66
35 5 0.17
ACGTcount: A:0.22, C:0.24, G:0.22, T:0.32
Consensus pattern (34 bp):
ACAGTCTTGGGCCTAAGACCATTTCAGTACAGTG
Found at i:11780742 original size:19 final size:19
Alignment explanation
Indices: 11780718--11780757 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
11780708 GAACCACTAA
11780718 TATATGTAAAATATTTATT
1 TATATGTAAAATATTTATT
11780737 TATATGTAAAATATTTATT
1 TATATGTAAAATATTTATT
11780756 TA
1 TA
11780758 ATAAATATTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (19 bp):
TATATGTAAAATATTTATT
Found at i:11783296 original size:23 final size:23
Alignment explanation
Indices: 11783270--11783315 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
11783260 TAAAAGAAGC
*
11783270 ATAGTTCTATAGGAATTTTACTT
1 ATAGTTCTACAGGAATTTTACTT
* *
11783293 ATAGTTGTACATGAATTTTACTT
1 ATAGTTCTACAGGAATTTTACTT
11783316 GTATTTTATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.30, C:0.09, G:0.13, T:0.48
Consensus pattern (23 bp):
ATAGTTCTACAGGAATTTTACTT
Found at i:11789301 original size:485 final size:485
Alignment explanation
Indices: 11788391--11789364 Score: 1876
Period size: 485 Copynumber: 2.0 Consensus size: 485
11788381 GAAGAGAGAG
* *
11788391 AAATCTAGAAGATAATGATGATGTTGGAGATATTTTATATTAATTAAATAAATATTAGTTTATTA
1 AAATCTAGAAGATAATGATGATGTTAGAGATATTTTAGATTAATTAAATAAATATTAGTTTATTA
*
11788456 ATATTTTAATTTGATTTTTAAATGATATTTTATTATTTTATTATTTAGTATATATAACTGTAAAG
66 ATATTTTAATTTGATTTTTAAATGATATTTTATTATTTTATTATTTAGTATATATAACTGGAAAG
*
11788521 AAAGATGAAAATGAACCAACCCACCATCTTTTCCATGCAATTCATGTTAGAAGAGAAGAGAAGAA
131 AAAGATGAAAATGAACCAACCCACCATCTTTTCCATGCAATTCACGTTAGAAGAGAAGAGAAGAA
11788586 AGAAAGTTTTGCTTTCTTTACAATTTGGTCCTTCCACCAAAAAAATTCACCATTTTCAATTAGAA
196 AGAAAGTTTTGCTTTCTTTACAATTTGGTCCTTCCACCAAAAAAATTCACCATTTTCAATTAGAA
11788651 ATCAAAAGAATTTCCATAGCCATCAAGAGAGAAAGATAACAATGAGACTATGGGGAGCTAGAATA
261 ATCAAAAGAATTTCCATAGCCATCAAGAGAGAAAGATAACAATGAGACTATGGGGAGCTAGAATA
11788716 TCAAGTTGGATTCAAGAAATTGAAGCTGGAGGAGAGAGAAAATTAAGTTAAAGGTTGAAATCAAT
326 TCAAGTTGGATTCAAGAAATTGAAGCTGGAGGAGAGAGAAAATTAAGTTAAAGGTTGAAATCAAT
* * *
11788781 AGGACAAGGTAAGAACATTGAGATTTCAGTATATTTTTAAGTTTTATATTATTGAAATAGCGTGG
391 AGGACAAGGTAAGAACATTGAGATTTCAATATATTTTTAAGTTTGATATTATTGAAATAGCATGG
11788846 AAAAGATGTTATAGTAGAGTTTTCTTATAT
456 AAAAGATGTTATAGTAGAGTTTTCTTATAT
11788876 AAATCTAGAAGATAATGATGATGTTAGAGATATTTTAGATTAATTAAATAAATATTAGTTTATTA
1 AAATCTAGAAGATAATGATGATGTTAGAGATATTTTAGATTAATTAAATAAATATTAGTTTATTA
*
11788941 ATATTTTAATTTGATTTTTAAATGATATTTTATTATTTTATTATTTAGTATATATAAGTGGAAAG
66 ATATTTTAATTTGATTTTTAAATGATATTTTATTATTTTATTATTTAGTATATATAACTGGAAAG
11789006 AAAGATGAAAATGAACCAACCCACCATCTTTTCCATGCAATTCACGTTAGAAGAGAAGAGAAGAA
131 AAAGATGAAAATGAACCAACCCACCATCTTTTCCATGCAATTCACGTTAGAAGAGAAGAGAAGAA
11789071 AGAAAGTTTTGCTTTCTTTACAATTTGGTCCTTCCACCAAAAAAATTCACCATTTTCAATTAGAA
196 AGAAAGTTTTGCTTTCTTTACAATTTGGTCCTTCCACCAAAAAAATTCACCATTTTCAATTAGAA
11789136 ATCAAAAGAATTTCCATAGCCATCAAGAGAGAAAGATAACAATGAGACTATGGGGAGCTAGAATA
261 ATCAAAAGAATTTCCATAGCCATCAAGAGAGAAAGATAACAATGAGACTATGGGGAGCTAGAATA
11789201 TCAAGTTGGATTCAAGAAATTGAAGCTGGAGGAGAGAGAAAATTAAGTTAAAGGTTGAAATCAAT
326 TCAAGTTGGATTCAAGAAATTGAAGCTGGAGGAGAGAGAAAATTAAGTTAAAGGTTGAAATCAAT
11789266 AGGACAAGGTAAGAACATTGAGATTTCAATATATTTTTAAGTTTGATATTATTGAAATAGCATGG
391 AGGACAAGGTAAGAACATTGAGATTTCAATATATTTTTAAGTTTGATATTATTGAAATAGCATGG
11789331 AAAAGATGTTATAGTAGAGTTTTCTTATAT
456 AAAAGATGTTATAGTAGAGTTTTCTTATAT
11789361 AAAT
1 AAAT
11789365 TCATATTTTC
Statistics
Matches: 481, Mismatches: 8, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
485 481 1.00
ACGTcount: A:0.40, C:0.09, G:0.17, T:0.34
Consensus pattern (485 bp):
AAATCTAGAAGATAATGATGATGTTAGAGATATTTTAGATTAATTAAATAAATATTAGTTTATTA
ATATTTTAATTTGATTTTTAAATGATATTTTATTATTTTATTATTTAGTATATATAACTGGAAAG
AAAGATGAAAATGAACCAACCCACCATCTTTTCCATGCAATTCACGTTAGAAGAGAAGAGAAGAA
AGAAAGTTTTGCTTTCTTTACAATTTGGTCCTTCCACCAAAAAAATTCACCATTTTCAATTAGAA
ATCAAAAGAATTTCCATAGCCATCAAGAGAGAAAGATAACAATGAGACTATGGGGAGCTAGAATA
TCAAGTTGGATTCAAGAAATTGAAGCTGGAGGAGAGAGAAAATTAAGTTAAAGGTTGAAATCAAT
AGGACAAGGTAAGAACATTGAGATTTCAATATATTTTTAAGTTTGATATTATTGAAATAGCATGG
AAAAGATGTTATAGTAGAGTTTTCTTATAT
Found at i:11797758 original size:12 final size:12
Alignment explanation
Indices: 11797741--11797774 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
11797731 CAGTTACTGG
*
11797741 CCTAGCGCACGA
1 CCTAGCACACGA
11797753 CCTAGCACACGA
1 CCTAGCACACGA
11797765 CCTAGCACAC
1 CCTAGCACAC
11797775 AAGTGTTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.29, C:0.44, G:0.18, T:0.09
Consensus pattern (12 bp):
CCTAGCACACGA
Found at i:11813460 original size:54 final size:54
Alignment explanation
Indices: 11813392--11813584 Score: 172
Period size: 54 Copynumber: 3.6 Consensus size: 54
11813382 ATTCGTGGGC
* * * * * ** *
11813392 AAATGACTGTAATACCCTTAGAGGGTAAAATAATTGAAATACCGTCGGAGGGTA
1 AAATGACCGAAATACCCTCAAAGGGTAAAATAATCGAAATACCCCCGAAGGGTA
* *
11813446 AAATGACCGAAATACCCTCAAAGGGTGAAATGATCGAAATACCCCCGAAGGGTA
1 AAATGACCGAAATACCCTCAAAGGGTAAAATAATCGAAATACCCCCGAAGGGTA
* * * * * * *
11813500 AATTGATCGAAATACCCCCGAAGGGT-AAATGGATCGAAATACCCTCAAAGGGTA
1 AAATGACCGAAATACCCTCAAAGGGTAAAAT-AATCGAAATACCCCCGAAGGGTA
** * * *
11813554 AAATGACATAAAGACCCACGAAGGGTAAAAT
1 AAATGACCGAAATACCCTCAAAGGGTAAAAT
11813585 GATTGTTATA
Statistics
Matches: 115, Mismatches: 22, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
53 4 0.03
54 107 0.93
55 4 0.03
ACGTcount: A:0.41, C:0.18, G:0.22, T:0.18
Consensus pattern (54 bp):
AAATGACCGAAATACCCTCAAAGGGTAAAATAATCGAAATACCCCCGAAGGGTA
Found at i:11813570 original size:27 final size:27
Alignment explanation
Indices: 11813413--11813587 Score: 183
Period size: 27 Copynumber: 6.5 Consensus size: 27
11813403 ATACCCTTAG
* * ** *
11813413 AGGGTAAAATAATTGAAATACCGTCGG
1 AGGGTAAAATGATCGAAATACCCCCGA
* * *
11813440 AGGGTAAAATGACCGAAATACCCTCAA
1 AGGGTAAAATGATCGAAATACCCCCGA
*
11813467 AGGGTGAAATGATCGAAATACCCCCGA
1 AGGGTAAAATGATCGAAATACCCCCGA
*
11813494 AGGGTAAATTGATCGAAATACCCCCGA
1 AGGGTAAAATGATCGAAATACCCCCGA
* *
11813521 AGGGT-AAATGGATCGAAATACCCTCAA
1 AGGGTAAAAT-GATCGAAATACCCCCGA
* * *
11813548 AGGGTAAAATGA-CATAAAGACCCACGA
1 AGGGTAAAATGATC-GAAATACCCCCGA
11813575 AGGGTAAAATGAT
1 AGGGTAAAATGAT
11813588 TGTTATACCC
Statistics
Matches: 125, Mismatches: 19, Indels: 7
0.83 0.13 0.05
Matches are distributed among these distances:
26 4 0.03
27 117 0.94
28 4 0.03
ACGTcount: A:0.42, C:0.18, G:0.23, T:0.17
Consensus pattern (27 bp):
AGGGTAAAATGATCGAAATACCCCCGA
Found at i:11813596 original size:81 final size:81
Alignment explanation
Indices: 11813413--11813598 Score: 223
Period size: 81 Copynumber: 2.3 Consensus size: 81
11813403 ATACCCTTAG
* ** * *
11813413 AGGGTAAAATAATTGAAATACCGTCGGAGGGTAAAATGACCGAAATACCCTCAAAGGGTGAAATG
1 AGGGTAAAATGATTGAAATACCCCCGAAGGGTAAAATGACCGAAATACCCTCAAAGGGTAAAATG
* *
11813478 ATCGAAATACCCCCGA
66 ATCGAAAGACCCACGA
* * *
11813494 AGGGTAAATTGATCGAAATACCCCCGAAGGGT-AAATGGATCGAAATACCCTCAAAGGGTAAAAT
1 AGGGTAAAATGATTGAAATACCCCCGAAGGGTAAAAT-GACCGAAATACCCTCAAAGGGTAAAAT
*
11813558 GA-CATAAAGACCCACGA
65 GATC-GAAAGACCCACGA
**
11813575 AGGGTAAAATGATTGTTATACCCC
1 AGGGTAAAATGATTGAAATACCCC
11813599 TAGGAGTTCA
Statistics
Matches: 88, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
80 5 0.06
81 83 0.94
ACGTcount: A:0.40, C:0.19, G:0.23, T:0.18
Consensus pattern (81 bp):
AGGGTAAAATGATTGAAATACCCCCGAAGGGTAAAATGACCGAAATACCCTCAAAGGGTAAAATG
ATCGAAAGACCCACGA
Found at i:11813700 original size:20 final size:21
Alignment explanation
Indices: 11813675--11813714 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
11813665 TATGTTCAAA
11813675 TATGATATTTT-ACAT-ACATG
1 TATGAT-TTTTGACATGACATG
11813695 TATGATTTTTGACATGACAT
1 TATGATTTTTGACATGACAT
11813715 ATTGCATGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.22
20 10 0.56
21 4 0.22
ACGTcount: A:0.33, C:0.10, G:0.12, T:0.45
Consensus pattern (21 bp):
TATGATTTTTGACATGACATG
Found at i:11813788 original size:26 final size:26
Alignment explanation
Indices: 11813749--11813824 Score: 73
Period size: 26 Copynumber: 2.9 Consensus size: 26
11813739 ATGGAGGAAG
* *
11813749 TATACTGTTTCTGGCAGCTTTGCTAC
1 TATACTGATACTGGCAGCTTTGCTAC
* *
11813775 TATACTGATACTGGCAGCTCTGCTGC
1 TATACTGATACTGGCAGCTTTGCTAC
* * *
11813801 GATGCT-ACTACTGGCAGTTTTGCT
1 TATACTGA-TACTGGCAGCTTTGCT
11813825 GCGATATTGG
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
25 1 0.02
26 40 0.98
ACGTcount: A:0.17, C:0.24, G:0.22, T:0.37
Consensus pattern (26 bp):
TATACTGATACTGGCAGCTTTGCTAC
Found at i:11815283 original size:20 final size:21
Alignment explanation
Indices: 11815258--11815300 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
11815248 TAATATGCTC
11815258 GAAAAA-AAAAGAGAAAA-AAA
1 GAAAAAGAAAA-AGAAAAGAAA
11815278 GAAAAAGAAAAAGAAAAGAAA
1 GAAAAAGAAAAAGAAAAGAAA
11815299 GA
1 GA
11815301 GCATATGTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (21 bp):
GAAAAAGAAAAAGAAAAGAAA
Found at i:11815318 original size:33 final size:34
Alignment explanation
Indices: 11815280--11815350 Score: 90
Period size: 34 Copynumber: 2.1 Consensus size: 34
11815270 GAAAAAAAGA
*
11815280 AAAAGAAAAAGA-AAAGAAAGAGCATATGTACTC
1 AAAAGAAAAAGATAAACAAAGAGCATATGTACTC
* ** *
11815313 AAAAGAAATAGATGTACAAAGAGCATGTGTACTC
1 AAAAGAAAAAGATAAACAAAGAGCATATGTACTC
11815347 AAAA
1 AAAA
11815351 TGCAAAATGA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
33 11 0.34
34 21 0.66
ACGTcount: A:0.56, C:0.10, G:0.18, T:0.15
Consensus pattern (34 bp):
AAAAGAAAAAGATAAACAAAGAGCATATGTACTC
Found at i:11817467 original size:16 final size:17
Alignment explanation
Indices: 11817446--11817479 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
11817436 ATTAGAATTT
11817446 TTACTT-TTAATTTTTA
1 TTACTTATTAATTTTTA
11817462 TTACTTAGTTAATTTTTA
1 TTACTTA-TTAATTTTTA
11817480 GTTTTTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
18 10 0.62
ACGTcount: A:0.26, C:0.06, G:0.03, T:0.65
Consensus pattern (17 bp):
TTACTTATTAATTTTTA
Found at i:11818612 original size:188 final size:188
Alignment explanation
Indices: 11818299--11818654 Score: 439
Period size: 188 Copynumber: 1.9 Consensus size: 188
11818289 ATATCATAAT
* * * * * *
11818299 AGAATAGCACCAAATTGCGTTATCAAAATAGAGTGGCACCAAAGTGCATTAATAGAACTGAGAGC
1 AGAATAACACCAAATTGCGTTATCAAAACAGAATGGCACCAAAGTGCATTAACAGAAATGAGAGA
* * *** * *
11818364 ACATTGAATGTTTCCTAATGGCATGCCATCTATATCCCTCTACTTTGTATCTTGTCTACTTGGGA
66 ACATTGAATGTTTCCTAATGGCATACCATCTATATCCCACTACTTCACATATTGTCTACTTGAGA
*
11818429 A-AGTATACCAAGACTAGCTTCACATTTACATTTCAAAACCAAAGTGCAATATTGGAAC
131 AGA-TATACCAAAACTAGCTTCACATTTACATTTCAAAACCAAAGTGCAATATTGGAAC
* * *
11818487 AGAATAACACCAAATTGCTTTATCATAACAGAATGGCACTAAAGTGCATTAACA-AAAT-AGAGA
1 AGAATAACACCAAATTGCGTTATCAAAACAGAATGGCACCAAAGTGCATTAACAGAAATGAGAGA
* * * *
11818550 ACGTGTTGAATGTTTCCTAATGGCATACCATCTATATCTCACTAGTTCACATATTTTCTACTTGA
66 AC--ATTGAATGTTTCCTAATGGCATACCATCTATATCCCACTACTTCACATATTGTCTACTTGA
** * *
11818615 GAAGATATATTAAAATTAGCTTTACATTTACATTTCAAAA
129 GAAGATATACCAAAACTAGCTTCACATTTACATTTCAAAA
11818655 TAGAGCTTAT
Statistics
Matches: 140, Mismatches: 25, Indels: 6
0.82 0.15 0.04
Matches are distributed among these distances:
186 6 0.04
187 3 0.02
188 130 0.93
189 1 0.01
ACGTcount: A:0.37, C:0.19, G:0.14, T:0.31
Consensus pattern (188 bp):
AGAATAACACCAAATTGCGTTATCAAAACAGAATGGCACCAAAGTGCATTAACAGAAATGAGAGA
ACATTGAATGTTTCCTAATGGCATACCATCTATATCCCACTACTTCACATATTGTCTACTTGAGA
AGATATACCAAAACTAGCTTCACATTTACATTTCAAAACCAAAGTGCAATATTGGAAC
Found at i:11825694 original size:51 final size:50
Alignment explanation
Indices: 11825575--11825768 Score: 155
Period size: 51 Copynumber: 3.8 Consensus size: 50
11825565 CCAATGATGT
* * * * * * *
11825575 TCGGTTCACATAGTAGTCTACACATAGTACTACACATGTGAC-TATTATC
1 TCGGTACACATAATAGCCTGCACATAGTACTACACACGTGACGAACTATC
* ** * *
11825624 ATTCGATACATGTAGTAGCCTACACATAGTACTACACACGTGATCGAAACTATC
1 --TCGGTACACATAATAGCCTGCACATAGTACTACACACGTGA-CG-AACTATC
* *
11825678 -CGGTACGCATAATAGCCTGCACATAGTACTACACA--T-ACGACCTATC
1 TCGGTACACATAATAGCCTGCACATAGTACTACACACGTGACGAACTATC
*
11825724 ATTTCGGTACACGTAATAGCCTGCACATAGTACTACACACGTGAC
1 ---TCGGTACACATAATAGCCTGCACATAGTACTACACACGTGAC
11825769 CATCACTTTC
Statistics
Matches: 116, Mismatches: 17, Indels: 18
0.77 0.11 0.12
Matches are distributed among these distances:
46 6 0.05
47 2 0.02
48 1 0.01
49 1 0.01
50 33 0.28
51 64 0.55
52 2 0.02
53 2 0.02
54 5 0.04
ACGTcount: A:0.32, C:0.26, G:0.15, T:0.26
Consensus pattern (50 bp):
TCGGTACACATAATAGCCTGCACATAGTACTACACACGTGACGAACTATC
Found at i:11832930 original size:10 final size:8
Alignment explanation
Indices: 11832908--11832940 Score: 57
Period size: 8 Copynumber: 4.0 Consensus size: 8
11832898 GTACAAACTA
11832908 GTATATAG
1 GTATATAG
11832916 GTATATAG
1 GTATATAG
11832924 GTATATAG
1 GTATATAG
11832932 GTTATATAG
1 G-TATATAG
11832941 ATAAATTTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 17 0.71
9 7 0.29
ACGTcount: A:0.36, C:0.00, G:0.24, T:0.39
Consensus pattern (8 bp):
GTATATAG
Found at i:11839168 original size:9 final size:9
Alignment explanation
Indices: 11839156--11839198 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
11839146 TATTAAAAAC
11839156 GAGAGAGTT
1 GAGAGAGTT
*
11839165 GAGAGACTT
1 GAGAGAGTT
*
11839174 GAGAGGGTTT
1 GAGAGAG-TT
*
11839184 GAAAGAGTT
1 GAGAGAGTT
11839193 GAGAGA
1 GAGAGA
11839199 AGGATGTGAA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
9 20 0.74
10 7 0.26
ACGTcount: A:0.35, C:0.02, G:0.42, T:0.21
Consensus pattern (9 bp):
GAGAGAGTT
Found at i:11840894 original size:7 final size:7
Alignment explanation
Indices: 11840882--11840906 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
11840872 CCCACCCTGC
11840882 CTCTTCA
1 CTCTTCA
11840889 CTCTTCA
1 CTCTTCA
11840896 CTCTTCA
1 CTCTTCA
11840903 CTCT
1 CTCT
11840907 CTCTCTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.44, G:0.00, T:0.44
Consensus pattern (7 bp):
CTCTTCA
Found at i:11843959 original size:41 final size:39
Alignment explanation
Indices: 11843893--11843970 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 39
11843883 GGAGTTTAGA
*
11843893 GTTTGGGTTTGGATTCGAGTTTAAGGTTTATGGTTTATG
1 GTTTGGGTTTGGATTCGAGTTTAAGGTTTAAGGTTTATG
* *
11843932 GTTTGAGGTTTGGGGTTTGAGTTTAAGGTTTAAGGTTTA
1 GTTTG-GGTTT-GGATTCGAGTTTAAGGTTTAAGGTTTA
11843971 AGATTATGGG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
39 5 0.15
40 5 0.15
41 24 0.71
ACGTcount: A:0.17, C:0.01, G:0.35, T:0.47
Consensus pattern (39 bp):
GTTTGGGTTTGGATTCGAGTTTAAGGTTTAAGGTTTATG
Found at i:11843960 original size:20 final size:20
Alignment explanation
Indices: 11843879--11843962 Score: 57
Period size: 20 Copynumber: 4.2 Consensus size: 20
11843869 AAGGCTTCAA
* *
11843879 GTTTGGAGTTTAGAGTTT-GG
1 GTTTGGGGTTT-GAGTTTAAG
* *
11843899 GTTT-GGATTCGAGTTTAAG
1 GTTTGGGGTTTGAGTTTAAG
** *
11843918 GTTTATGGTTT-ATGGTTTGAG
1 GTTTGGGGTTTGA--GTTTAAG
11843939 GTTTGGGGTTTGAGTTTAAG
1 GTTTGGGGTTTGAGTTTAAG
11843959 GTTT
1 GTTT
11843963 AAGGTTTAAG
Statistics
Matches: 48, Mismatches: 11, Indels: 10
0.70 0.16 0.14
Matches are distributed among these distances:
18 6 0.12
19 9 0.19
20 17 0.35
21 15 0.31
22 1 0.02
ACGTcount: A:0.15, C:0.01, G:0.36, T:0.48
Consensus pattern (20 bp):
GTTTGGGGTTTGAGTTTAAG
Found at i:11843970 original size:7 final size:7
Alignment explanation
Indices: 11843911--11843972 Score: 63
Period size: 7 Copynumber: 9.0 Consensus size: 7
11843901 TTGGATTCGA
11843911 GTTTAAG
1 GTTTAAG
*
11843918 GTTTATG
1 GTTTAAG
*
11843925 GTTTATG
1 GTTTAAG
*
11843932 GTTTGAG
1 GTTTAAG
**
11843939 GTTTGGG
1 GTTTAAG
*
11843946 GTTTGA-
1 GTTTAAG
11843952 GTTTAAG
1 GTTTAAG
11843959 GTTTAAG
1 GTTTAAG
11843966 GTTTAAG
1 GTTTAAG
11843973 ATTATGGGTT
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
6 5 0.10
7 43 0.90
ACGTcount: A:0.19, C:0.00, G:0.34, T:0.47
Consensus pattern (7 bp):
GTTTAAG
Found at i:11843982 original size:34 final size:35
Alignment explanation
Indices: 11843916--11843996 Score: 85
Period size: 34 Copynumber: 2.3 Consensus size: 35
11843906 TTCGAGTTTA
* * * * *
11843916 AGGTTTATGGTTTATGGTTTGAGGTTTGGGGTTTG
1 AGGTTTAAGGTTTAAGGTTTAAGATTTGGGGTTCG
11843951 A-GTTTAAGGTTTAAGGTTTAAGATTAT-GGGTTCG
1 AGGTTTAAGGTTTAAGGTTTAAGATT-TGGGGTTCG
*
11843985 AGGTTTAGGGTT
1 AGGTTTAAGGTT
11843997 CTAGTTCGAG
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
34 27 0.71
35 11 0.29
ACGTcount: A:0.19, C:0.01, G:0.36, T:0.44
Consensus pattern (35 bp):
AGGTTTAAGGTTTAAGGTTTAAGATTTGGGGTTCG
Found at i:11843990 original size:41 final size:41
Alignment explanation
Indices: 11843909--11843990 Score: 103
Period size: 41 Copynumber: 2.0 Consensus size: 41
11843899 GTTTGGATTC
* * * * *
11843909 GAGTTTAAGGTTTATGGTTTATGGTTTGAGGTTTGGGGTTT
1 GAGTTTAAGGTTTAAGGTTTAAGATTTGAGGTTCGAGGTTT
11843950 GAGTTTAAGGTTTAAGGTTTAAGATTATG-GGTTCGAGGTTT
1 GAGTTTAAGGTTTAAGGTTTAAGATT-TGAGGTTCGAGGTTT
11843991 AGGGTTCTAG
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
41 33 0.94
42 2 0.06
ACGTcount: A:0.20, C:0.01, G:0.34, T:0.45
Consensus pattern (41 bp):
GAGTTTAAGGTTTAAGGTTTAAGATTTGAGGTTCGAGGTTT
Found at i:11844009 original size:48 final size:48
Alignment explanation
Indices: 11843893--11844015 Score: 121
Period size: 48 Copynumber: 2.6 Consensus size: 48
11843883 GGAGTTTAGA
* * *
11843893 GTTT-GGGTTTG-GATTCGA-GTTTAAGGTTTATGGTTTATGGTTTGAG
1 GTTTAGGGTTTGAG-TTCGAGGTTTAAGGTTTATAGATTATGGTTCGAG
* **
11843939 GTTTGGGGTTTGAGTTTAAGGTTTAAGGTTTA-AGATTATGGGTTCGAG
1 GTTTAGGGTTTGAGTTCGAGGTTTAAGGTTTATAGATTAT-GGTTCGAG
*
11843987 GTTTAGGGTTCT-AGTTCGAGGTTCAAGGT
1 GTTTAGGGTT-TGAGTTCGAGGTTTAAGGT
11844016 AAAAAAATTA
Statistics
Matches: 63, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
46 4 0.06
47 15 0.24
48 43 0.68
49 1 0.02
ACGTcount: A:0.18, C:0.04, G:0.35, T:0.43
Consensus pattern (48 bp):
GTTTAGGGTTTGAGTTCGAGGTTTAAGGTTTATAGATTATGGTTCGAG
Found at i:11847656 original size:14 final size:14
Alignment explanation
Indices: 11847637--11847667 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
11847627 GACATTTTTT
*
11847637 TAATGATATTATTC
1 TAATGATACTATTC
11847651 TAATGATACTATTC
1 TAATGATACTATTC
11847665 TAA
1 TAA
11847668 CATGTAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.39, C:0.10, G:0.06, T:0.45
Consensus pattern (14 bp):
TAATGATACTATTC
Found at i:11848331 original size:12 final size:12
Alignment explanation
Indices: 11848316--11848345 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
11848306 GCGGAGCCAA
11848316 AGCCCGAGCCTG
1 AGCCCGAGCCTG
11848328 AGCCCGAGCCTG
1 AGCCCGAGCCTG
11848340 AGCCCG
1 AGCCCG
11848346 TCAGGCAGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.17, C:0.43, G:0.33, T:0.07
Consensus pattern (12 bp):
AGCCCGAGCCTG
Found at i:11848517 original size:33 final size:33
Alignment explanation
Indices: 11848466--11848560 Score: 120
Period size: 33 Copynumber: 2.9 Consensus size: 33
11848456 TAGTTCAGTA
*
11848466 CCACCGCAGTACAACACTCCTCCTAGC-CTGTAT
1 CCACCGCAGTACAGCACTCCTCCTAGCTC-GTAT
* * * *
11848499 CTACCGCATTACTGCACTCCTCCTAGGTCGTAT
1 CCACCGCAGTACAGCACTCCTCCTAGCTCGTAT
*
11848532 CCACCGCAGTACAGCACTCCTCCTGGCTC
1 CCACCGCAGTACAGCACTCCTCCTAGCTC
11848561 AAGTTCATCG
Statistics
Matches: 51, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
33 50 0.98
34 1 0.02
ACGTcount: A:0.20, C:0.42, G:0.15, T:0.23
Consensus pattern (33 bp):
CCACCGCAGTACAGCACTCCTCCTAGCTCGTAT
Found at i:11848887 original size:14 final size:14
Alignment explanation
Indices: 11848868--11848896 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
11848858 TGGAACAAAC
11848868 TTTGTAATATAAAT
1 TTTGTAATATAAAT
11848882 TTTGTAATATAAAT
1 TTTGTAATATAAAT
11848896 T
1 T
11848897 AAATACATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (14 bp):
TTTGTAATATAAAT
Found at i:11848936 original size:62 final size:62
Alignment explanation
Indices: 11848839--11849068 Score: 424
Period size: 62 Copynumber: 3.7 Consensus size: 62
11848829 CAACATTACA
*
11848839 ACATTACAACATTAAAACTTGGAACAAACTTTGTAATATAAATTTTGTAATATAAATTAAAT
1 ACATTACAACATTAAAACTTGGAACAAACTTTGTAATATAAATTTTGTTATATAAATTAAAT
* *
11848901 ACATTACAATATTAAAACTTGGAACTAACTTTGTAATATAAATTTTGTTATATAAATTAAAT
1 ACATTACAACATTAAAACTTGGAACAAACTTTGTAATATAAATTTTGTTATATAAATTAAAT
*
11848963 ACATTACAACATTAAAAATTGGAACAAACTTTGTAATATAAATTTTGTTATATAAATTAAAT
1 ACATTACAACATTAAAACTTGGAACAAACTTTGTAATATAAATTTTGTTATATAAATTAAAT
11849025 ACATTACAACATTAAAACTTGGAACAAACTTTGTAATATAAATT
1 ACATTACAACATTAAAACTTGGAACAAACTTTGTAATATAAATT
11849069 AGGTACATTG
Statistics
Matches: 161, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
62 161 1.00
ACGTcount: A:0.47, C:0.10, G:0.07, T:0.37
Consensus pattern (62 bp):
ACATTACAACATTAAAACTTGGAACAAACTTTGTAATATAAATTTTGTTATATAAATTAAAT
Found at i:11852517 original size:216 final size:210
Alignment explanation
Indices: 11852086--11852720 Score: 972
Period size: 216 Copynumber: 3.0 Consensus size: 210
11852076 CAATATATAA
*
11852086 AATAACTTTAAAACAAAACATAAAAATAACACAAAACAAACTATATAATACTAACAAAATAATTT
1 AATAACTTTAAAACAAAACATAAAAATAACACAAAACAAACTATATAATACTAACAAAATAAATT
* * *
11852151 TTTCTTATC-ATAACCTATTCTATTTGAGAATAACAA-AAAA-AATAATACCTTTTATTTCTTTC
66 TTTCTTA-CAATAATCTATTCTATTTGAAAATAACAATAAAATAATAATACCTTTTCTTTCTTTC
* * *
11852213 TTCTCTTCTCCCTCTCTTATTCTGCTATTTTTTTAACTGATATTTTAAAATTGAGCTGGATGGGG
130 TTCTCTTCTCCCTCTCTTGTTCTGCTATTTTTTTAACTGATACTTTAAAATTGAGCCGGATGGGG
*
11852278 GAGTGGCCGAGGGGGG
195 GAGCGGCCGAGGGGGG
* *
11852294 AATAACTTTAAAACAAAACATAAAAAAAACACAAAACAAATTATATAATACTAACAAAATAAATT
1 AATAACTTTAAAACAAAACATAAAAATAACACAAAACAAACTATATAATACTAACAAAATAAATT
* *
11852359 TTTCTTACAATAATATATTCTATTTGAAAATAATAATAAAGATAATAATACCTTCTCTTTCTTTC
66 TTTCTTACAATAATCTATTCTATTTGAAAATAACAATAAA-ATAATAATA-C--CT-TTTCTTTC
11852424 TTCTCTTCTCTTCTCCCTCTCTTGTTCTGCTATTTTTTTAACTGATACTTTAAAATTGAGCCGGA
126 TT-TCTTCTCTTCTCCCTCTCTTGTTCTGCTATTTTTTTAACTGATACTTTAAAATTGAGCCGGA
*
11852489 TGGGGGAGCGGCCGGGGGGGG
190 TGGGGGAGCGGCCGAGGGGGG
*
11852510 AATAACTTTAAAACAAAACATAAAAATAACACAAAACAAACTATATAATACTAACAAAATAAAAT
1 AATAACTTTAAAACAAAACATAAAAATAACACAAAACAAACTATATAATACTAACAAAATAAATT
* * * *
11852575 TTTCTTATAGTAATCTATTCTATTTGAAAATAACAATATAAATAATAATACATATTCTTTCTTTC
66 TTTCTTACAATAATCTATTCTATTTGAAAATAACAATA-AAATAATAATACCTTTTCTTTCTTTC
* *
11852640 TTCTCTTCTCCCTCTCTTGTTCTGCTATTTTTTAAAACTGATACTTTAAAATTGAGCCGGAAGGG
130 TTCTCTTCTCCCTCTCTTGTTCTGCTATTTTTT-TAACTGATACTTTAAAATTGAGCCGGATGGG
*
11852705 GGAGCGG-AGAGGGGGG
194 GGAGCGGCCGAGGGGGG
11852721 CGAGGGGAAT
Statistics
Matches: 390, Mismatches: 26, Indels: 19
0.90 0.06 0.04
Matches are distributed among these distances:
207 1 0.00
208 92 0.24
209 3 0.01
210 1 0.00
211 49 0.13
212 46 0.12
213 1 0.00
214 2 0.01
215 10 0.03
216 183 0.47
217 2 0.01
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.34
Consensus pattern (210 bp):
AATAACTTTAAAACAAAACATAAAAATAACACAAAACAAACTATATAATACTAACAAAATAAATT
TTTCTTACAATAATCTATTCTATTTGAAAATAACAATAAAATAATAATACCTTTTCTTTCTTTCT
TCTCTTCTCCCTCTCTTGTTCTGCTATTTTTTTAACTGATACTTTAAAATTGAGCCGGATGGGGG
AGCGGCCGAGGGGGG
Found at i:11856620 original size:30 final size:30
Alignment explanation
Indices: 11856586--11856646 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
11856576 GAATTTTAAG
11856586 TATTGGAGTACTTTATGGCATTTATTTAGT
1 TATTGGAGTACTTTATGGCATTTATTTAGT
11856616 TATTGGAGTACTTTATGGCATTTATTTAGT
1 TATTGGAGTACTTTATGGCATTTATTTAGT
11856646 T
1 T
11856647 TATGTTTCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.23, C:0.07, G:0.20, T:0.51
Consensus pattern (30 bp):
TATTGGAGTACTTTATGGCATTTATTTAGT
Found at i:11857041 original size:22 final size:23
Alignment explanation
Indices: 11857010--11857066 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 23
11857000 TCCCTAATGC
* *
11857010 ATGAATAGACAAAAATAAA-AAA
1 ATGAAAAGACAAAAAGAAATAAA
* *
11857032 ATGAAAAGACATATAGAAATAAA
1 ATGAAAAGACAAAAAGAAATAAA
*
11857055 ATGTAAAGACAA
1 ATGAAAAGACAA
11857067 CAATTATGAA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
22 15 0.54
23 13 0.46
ACGTcount: A:0.67, C:0.05, G:0.12, T:0.16
Consensus pattern (23 bp):
ATGAAAAGACAAAAAGAAATAAA
Found at i:11865296 original size:60 final size:60
Alignment explanation
Indices: 11865188--11865311 Score: 187
Period size: 60 Copynumber: 2.1 Consensus size: 60
11865178 CTGGAATATT
* *
11865188 TTCTTCCTCATCTGTTGAAGTTTTATCTTCATCTGAATTATAATTAGTGACTTTTAAGTC
1 TTCTTCCTCATCTGTTGAAGTTTTATCTTCATCAGAATTATAACTAGTGACTTTTAAGTC
* * *
11865248 TTCTTCCTGATCTGTTGAAGTTTTTTCTTCATCAG-ATTAATAACTAGTGACTTTTAAGTT
1 TTCTTCCTCATCTGTTGAAGTTTTATCTTCATCAGAATT-ATAACTAGTGACTTTTAAGTC
11865308 TTCT
1 TTCT
11865312 GTATTTTCAG
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
59 3 0.05
60 55 0.95
ACGTcount: A:0.23, C:0.16, G:0.12, T:0.49
Consensus pattern (60 bp):
TTCTTCCTCATCTGTTGAAGTTTTATCTTCATCAGAATTATAACTAGTGACTTTTAAGTC
Found at i:11865558 original size:18 final size:19
Alignment explanation
Indices: 11865516--11865567 Score: 61
Period size: 18 Copynumber: 2.7 Consensus size: 19
11865506 CTGGAAATAT
*
11865516 TTTTTTTCATATTTTTTTACG
1 TTTTTTT-AT-TTTTTTTACA
11865537 TTTTTTTATTTTTTTTA-A
1 TTTTTTTATTTTTTTTACA
*
11865555 TTTTTATATTTTT
1 TTTTTTTATTTTT
11865568 CATACTAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 12 0.41
19 8 0.28
20 2 0.07
21 7 0.24
ACGTcount: A:0.15, C:0.04, G:0.02, T:0.79
Consensus pattern (19 bp):
TTTTTTTATTTTTTTTACA
Found at i:11867732 original size:76 final size:75
Alignment explanation
Indices: 11867649--11867848 Score: 183
Period size: 78 Copynumber: 2.6 Consensus size: 75
11867639 GAAATTAGGG
* *
11867649 ATGTATATATTAGATTCGAATATATATGAGTATACAAGTATAAGTTCATGTTTTG-ATTATGAGT
1 ATGTATATATTAGATTCGAATATATATGAGTATACATGTATAAGTTCATGTATTGAATTA-GA-T
11867713 ATGTAA-TTATAT
64 ATG-AATTTATAT
* * * * * *
11867725 ATGTATATGA-TAAACTCGAATATATATATAAATATACATGTATAAATTCTTGTATTGAAATTAG
1 ATGTATAT-ATTAGATTCG-A-ATATATATGAGTATACATGTATAAGTTCATGTATTG-AATTAG
11867789 ATATGAATTTATAT
62 ATATGAATTTATAT
* * * * *
11867803 ATGTATATGTGAGGTTCGAATGTGTATG-GTTATACATGTATAAGTT
1 ATGTATATATTAGATTCGAATATATATGAG-TATACATGTATAAGTT
11867849 TTATATTGAA
Statistics
Matches: 98, Mismatches: 18, Indels: 16
0.74 0.14 0.12
Matches are distributed among these distances:
76 35 0.36
77 5 0.05
78 52 0.53
79 2 0.02
80 4 0.04
ACGTcount: A:0.38, C:0.04, G:0.16, T:0.42
Consensus pattern (75 bp):
ATGTATATATTAGATTCGAATATATATGAGTATACATGTATAAGTTCATGTATTGAATTAGATAT
GAATTTATAT
Found at i:11867801 original size:78 final size:78
Alignment explanation
Indices: 11867668--11867811 Score: 186
Period size: 78 Copynumber: 1.8 Consensus size: 78
11867658 TTAGATTCGA
* * * *
11867668 ATATATATGAGTATACAAGTATAAGTTCATGTTTTGATTATGAGTATGTAATTATATATGTATAT
1 ATATATATAAATATACAAGTATAAATTCATGTATTGATTATGAGTATGTAATTATATATGTATAT
11867733 GATAAACTCGAAT
66 GATAAACTCGAAT
* *
11867746 ATATATATAAATATACATGTATAAATTCTTGTATTGAAATTA-GA-TATG-AATTTATATATGTA
1 ATATATATAAATATACAAGTATAAATTCATGTATTG--ATTATGAGTATGTAA-TTATATATGTA
11867808 TATG
63 TATG
11867812 TGAGGTTCGA
Statistics
Matches: 57, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
77 2 0.04
78 49 0.86
79 2 0.04
80 4 0.07
ACGTcount: A:0.40, C:0.04, G:0.13, T:0.42
Consensus pattern (78 bp):
ATATATATAAATATACAAGTATAAATTCATGTATTGATTATGAGTATGTAATTATATATGTATAT
GATAAACTCGAAT
Found at i:11868286 original size:41 final size:41
Alignment explanation
Indices: 11868240--11868460 Score: 352
Period size: 41 Copynumber: 5.4 Consensus size: 41
11868230 CAGGCTTAGC
* *
11868240 GCCTAGCAGGCTAAGTGTCGGTGATCTGAATCAGGCTATAA
1 GCCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAA
* *
11868281 GCCTAGCAGGCTAAGTGCCGGTGAACTGAATTAGGTTATAA
1 GCCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAA
*
11868322 GCCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAA
1 GCCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAA
* *
11868363 GCCTAGCAGGCTAAGTGCCGGTGAACTGAGTCAGGTTATAA
1 GCCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAA
* *
11868404 GCCTAGCAGGCTAAGTGCCAGTGATCTGAATCAGGTTATCA
1 GCCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAA
*
11868445 GCCTAGCAAGCTAAGT
1 GCCTAGCAGGCTAAGT
11868461 ACAGGTGAAT
Statistics
Matches: 165, Mismatches: 15, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 165 1.00
ACGTcount: A:0.28, C:0.20, G:0.29, T:0.23
Consensus pattern (41 bp):
GCCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAA
Found at i:11875774 original size:76 final size:76
Alignment explanation
Indices: 11875679--11875878 Score: 194
Period size: 78 Copynumber: 2.6 Consensus size: 76
11875669 GAAATTAGGG
* * *
11875679 ATGTATAT-ATTAGATTCGAATATGTATGAGTATACAAGTATAAGTTCATGTTTTGATTATAAG-
1 ATGTATATGA-TAGATTCGAATATGTATGAGTATACATGTATAAGTTCATGTATTGA-AATAAGA
11875742 TATGTAA-TTATAT
64 TATG-AATTTATAT
* * * * * * *
11875755 ATGTATATGATAGACTCGAATATATATATAAATATACATGTATAAATTCTTGTATTGAAATTAGA
1 ATGTATATGATAGATTCG-A-ATATGTATGAGTATACATGTATAAGTTCATGTATTGAAATAAGA
11875820 TATGAATTTATAT
64 TATGAATTTATAT
* *
11875833 ATGTATATG-TGAGGTTCGAATGTGTATG-GTTATACATGTATAAGTT
1 ATGTATATGAT-AGATTCGAATATGTATGAG-TATACATGTATAAGTT
11875879 TTATATTGAA
Statistics
Matches: 100, Mismatches: 17, Indels: 14
0.76 0.13 0.11
Matches are distributed among these distances:
76 36 0.36
77 10 0.10
78 54 0.54
ACGTcount: A:0.37, C:0.04, G:0.17, T:0.42
Consensus pattern (76 bp):
ATGTATATGATAGATTCGAATATGTATGAGTATACATGTATAAGTTCATGTATTGAAATAAGATA
TGAATTTATAT
Found at i:11876319 original size:41 final size:41
Alignment explanation
Indices: 11876273--11876496 Score: 274
Period size: 41 Copynumber: 5.5 Consensus size: 41
11876263 CAGGCTTAGC
*
11876273 GCCTAGCAGGCTAAGTGCCGATGATCTGAATCAGGCTATAA
1 GCCTAGCAGGCTAAGTGCCGATGATCTGAATCAGGTTATAA
*
11876314 GCCTAGCAGGCTAAGTGCCGGTGAAT-TGAATCAGGTTATAA
1 GCCTAGCAGGCTAAGTGCCGATG-ATCTGAATCAGGTTATAA
*
11876355 GCCTAGCAGGCTAAGTGCC-AGTGATCTGAATCAGGCTATAA
1 GCCTAGCAGGCTAAGTGCCGA-TGATCTGAATCAGGTTATAA
** * * * **
11876396 TTCTAGCATGCTAAGTGTC-AGTGAACTGAATCATATTATAA
1 GCCTAGCAGGCTAAGTGCCGA-TGATCTGAATCAGGTTATAA
* * * *
11876437 GCCTAGCAAGCTATGTGTCGATGATCTAAATCAGGTTATAA
1 GCCTAGCAGGCTAAGTGCCGATGATCTGAATCAGGTTATAA
11876478 GCCTAGCAGGCTAAGTGCC
1 GCCTAGCAGGCTAAGTGCC
11876497 AGTGAATTTG
Statistics
Matches: 156, Mismatches: 23, Indels: 8
0.83 0.12 0.04
Matches are distributed among these distances:
40 2 0.01
41 151 0.97
42 3 0.02
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (41 bp):
GCCTAGCAGGCTAAGTGCCGATGATCTGAATCAGGTTATAA
Found at i:11876402 original size:82 final size:82
Alignment explanation
Indices: 11876273--11876504 Score: 331
Period size: 82 Copynumber: 2.8 Consensus size: 82
11876263 CAGGCTTAGC
*
11876273 GCCTAGCAGGCTAAGTGCCGATGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGTGA
1 GCCTAGCAGGCTAAGTGCCGATGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCAGTGA
*
11876338 ATTGAATCAGGTTATAA
66 ATTGAATCAGATTATAA
** * *
11876355 GCCTAGCAGGCTAAGTGCC-AGTGATCTGAATCAGGCTATAATTCTAGCATGCTAAGTGTCAGTG
1 GCCTAGCAGGCTAAGTGCCGA-TGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCAGTG
* *
11876419 AACTGAATCATATTATAA
65 AATTGAATCAGATTATAA
* * * * *
11876437 GCCTAGCAAGCTATGTGTCGATGATCTAAATCAGGTTATAAGCCTAGCAGGCTAAGTGCCAGTGA
1 GCCTAGCAGGCTAAGTGCCGATGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCAGTGA
11876502 ATT
66 ATT
11876505 TGTTTAAATT
Statistics
Matches: 130, Mismatches: 18, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
81 1 0.01
82 128 0.98
83 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.26
Consensus pattern (82 bp):
GCCTAGCAGGCTAAGTGCCGATGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCAGTGA
ATTGAATCAGATTATAA
Found at i:11876726 original size:34 final size:35
Alignment explanation
Indices: 11876674--11876747 Score: 87
Period size: 34 Copynumber: 2.1 Consensus size: 35
11876664 AATTGTTGGA
* *
11876674 TATATATGTATGCATTCGGCATATGTGGATGATAAG
1 TATATATG-ATGCATTCGGCACATGTAGATGATAAG
* * *
11876710 TATATATG-TGCCTTCGGCACATGTAGTTTATAAG
1 TATATATGATGCATTCGGCACATGTAGATGATAAG
11876744 TATA
1 TATA
11876748 AATAAATGCT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
34 25 0.76
36 8 0.24
ACGTcount: A:0.30, C:0.11, G:0.22, T:0.38
Consensus pattern (35 bp):
TATATATGATGCATTCGGCACATGTAGATGATAAG
Found at i:11882993 original size:27 final size:27
Alignment explanation
Indices: 11882963--11883016 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
11882953 TTTATTTCTT
* * *
11882963 AGATTTTCTCAACGTTAGAATCAAATA
1 AGATTTTATCAACATAAGAATCAAATA
*
11882990 AGATTTTATTAACATAAGAATCAAATA
1 AGATTTTATCAACATAAGAATCAAATA
11883017 TTTACCAACA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.46, C:0.11, G:0.09, T:0.33
Consensus pattern (27 bp):
AGATTTTATCAACATAAGAATCAAATA
Found at i:11889715 original size:12 final size:12
Alignment explanation
Indices: 11889700--11889731 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
11889690 TTAGAAGTAG
11889700 TTTTCTTCTTGA
1 TTTTCTTCTTGA
11889712 TTTTCTTCTTGA
1 TTTTCTTCTTGA
11889724 TTTTCTTC
1 TTTTCTTC
11889732 AAGGAGTCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.06, C:0.19, G:0.06, T:0.69
Consensus pattern (12 bp):
TTTTCTTCTTGA
Found at i:11905418 original size:21 final size:21
Alignment explanation
Indices: 11905394--11905437 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
11905384 TATTGATAAT
*
11905394 CAATACACAATCTCAAGATAC
1 CAATACACAATCGCAAGATAC
11905415 CAATACACAATCGCAAGATAC
1 CAATACACAATCGCAAGATAC
11905436 CA
1 CA
11905438 TCTTTCCTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.48, C:0.30, G:0.07, T:0.16
Consensus pattern (21 bp):
CAATACACAATCGCAAGATAC
Found at i:11908547 original size:16 final size:16
Alignment explanation
Indices: 11908528--11908561 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
11908518 AGAAAGTGTG
*
11908528 AAAAGAAAGAAAATAA
1 AAAAAAAAGAAAATAA
*
11908544 AAAAAAAAGAAATTAA
1 AAAAAAAAGAAAATAA
11908560 AA
1 AA
11908562 CGTGAGGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.82, C:0.00, G:0.09, T:0.09
Consensus pattern (16 bp):
AAAAAAAAGAAAATAA
Found at i:11911750 original size:20 final size:20
Alignment explanation
Indices: 11911727--11911765 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
11911717 ATTTTGACAA
*
11911727 GTTAAAATAATTTTTACTTT
1 GTTAAAATAATTTTAACTTT
*
11911747 GTTAAAATCATTTTAACTT
1 GTTAAAATAATTTTAACTT
11911766 GATTTTGAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.36, C:0.08, G:0.05, T:0.51
Consensus pattern (20 bp):
GTTAAAATAATTTTAACTTT
Found at i:11928311 original size:17 final size:15
Alignment explanation
Indices: 11928284--11928322 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
11928274 ATATAAGAAC
*
11928284 ATTTTATTATTAAATT
1 ATTTTAATATT-AATT
11928300 ATATTTAATATTAATT
1 AT-TTTAATATTAATT
11928316 ATTTTAA
1 ATTTTAA
11928323 ATTGTATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 5 0.24
16 8 0.38
17 8 0.38
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
ATTTTAATATTAATT
Found at i:11928397 original size:47 final size:46
Alignment explanation
Indices: 11928346--11928487 Score: 134
Period size: 46 Copynumber: 3.1 Consensus size: 46
11928336 ATATGATAAA
*
11928346 ATTTATTATCAAGACTTTTATGAAATTATATATCATTATTAAATTAT
1 ATTTATTATCAAGA-TTTTATGAAATTATATATAATTATTAAATTAT
* * * *
11928393 ATTTAATAT-TA-ATTATT-TTAAATTATATA-AATTCATATAAA--AA
1 ATTTATTATCAAGATT-TTATGAAATTATATATAATT-AT-TAAATTAT
* *
11928436 ATTTATTATCACGAATTTTATGAAATTATATATTATTATTAAATTAT
1 ATTTATTATCAAG-ATTTTATGAAATTATATATAATTATTAAATTAT
11928483 ATTTA
1 ATTTA
11928488 ATAATAATTA
Statistics
Matches: 74, Mismatches: 11, Indels: 20
0.70 0.10 0.19
Matches are distributed among these distances:
43 12 0.16
44 15 0.20
45 13 0.18
46 17 0.23
47 17 0.23
ACGTcount: A:0.44, C:0.04, G:0.03, T:0.49
Consensus pattern (46 bp):
ATTTATTATCAAGATTTTATGAAATTATATATAATTATTAAATTAT
Found at i:11928487 original size:90 final size:90
Alignment explanation
Indices: 11928287--11928534 Score: 415
Period size: 90 Copynumber: 2.7 Consensus size: 90
11928277 TAAGAACATT
* *
11928287 TTATTATTAAATTATATTTAATATTAATTATTTTAAATTGTATAAATTCATATGATAAAATTTAT
1 TTATTATTAAATTATATTTAATATTAATTATTTTAAATTATATAAATTCATAT-AAAAAATTTAT
*
11928352 TATCAAGACTTTTATGAAATTATATA
65 TATCAAGAATTTTATGAAATTATATA
*
11928378 TCATTATTAAATTATATTTAATATTAATTATTTTAAATTATATAAATTCATATAAAAAATTTATT
1 TTATTATTAAATTATATTTAATATTAATTATTTTAAATTATATAAATTCATATAAAAAATTTATT
*
11928443 ATCACGAATTTTATGAAATTATATA
66 ATCAAGAATTTTATGAAATTATATA
* *
11928468 TTATTATTAAATTATATTTAATAATAATTATTTTAAATTATACAAATTCATATAAGAAAATTTAT
1 TTATTATTAAATTATATTTAATATTAATTATTTTAAATTATATAAATTCATATAA-AAAATTTAT
11928533 TA
65 TA
11928535 GTTATAATTA
Statistics
Matches: 148, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
90 86 0.58
91 62 0.42
ACGTcount: A:0.45, C:0.04, G:0.03, T:0.48
Consensus pattern (90 bp):
TTATTATTAAATTATATTTAATATTAATTATTTTAAATTATATAAATTCATATAAAAAATTTATT
ATCAAGAATTTTATGAAATTATATA
Found at i:11928675 original size:120 final size:119
Alignment explanation
Indices: 11928550--11928966 Score: 647
Period size: 120 Copynumber: 3.5 Consensus size: 119
11928540 AATTATTTTA
* * * *
11928550 AATTTTATTAAATCATATATTTTAATTAAAATATTTTTAATATTAATTACT-TCAAATTATATTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTA-TGTTAAATTATATTT
* * *
11928614 TATAGTATCATATTTTATGATTTTAGTAAATTCATATAATAATTTTGATTATTAAG
65 TATAGTATCATATATTATGATTTGAGTAAATTCATATAA-AATATTGATTATTAAG
* *
11928670 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATCTTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTT
* *
11928735 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTTTTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAA-AATATTGATTATTAAG
* *
11928790 AATTTTACTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAATTATATTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTT
*
11928855 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGATATTGATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAAATATTGATTATTAAG
* *
11928909 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATTATTATGTTTAAAT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATG-TTAAAT
11928967 ATGATTAAAT
Statistics
Matches: 274, Mismatches: 21, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
119 63 0.23
120 211 0.77
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (119 bp):
AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTT
ATAGTATCATATATTATGATTTGAGTAAATTCATATAAAATATTGATTATTAAG
Found at i:11928699 original size:18 final size:17
Alignment explanation
Indices: 11928671--11928705 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
11928661 ATTATTAAGA
*
11928671 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
11928688 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
11928706 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:11928825 original size:16 final size:16
Alignment explanation
Indices: 11928804--11928850 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
11928794 TTACTAAATT
11928804 ATATATTTTAATTATA
1 ATATATTTTAATTATA
*
11928820 ATATA-TTTAATAATA
1 ATATATTTTAATTATA
*
11928835 AT-TATGTTAAATTATA
1 ATATAT-TTTAATTATA
11928851 TTTTATAGTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 2 0.08
15 11 0.42
16 13 0.50
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (16 bp):
ATATATTTTAATTATA
Found at i:11928830 original size:15 final size:15
Alignment explanation
Indices: 11928800--11928850 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
11928790 AATTTTACTA
11928800 AATTAT-ATAT-TTT
1 AATTATAATATATTT
11928813 AATTATAATATATTT
1 AATTATAATATATTT
*
11928828 AATAATAAT-TATGTT
1 AATTATAATATAT-TT
11928843 AAATTATA
1 -AATTATA
11928851 TTTTATAGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
13 6 0.19
14 7 0.22
15 13 0.41
16 6 0.19
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (15 bp):
AATTATAATATATTT
Found at i:11929199 original size:16 final size:16
Alignment explanation
Indices: 11929178--11929214 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
11929168 CTGATTTGCT
11929178 ATTACGCCTATATTCC
1 ATTACGCCTATATTCC
*
11929194 ATTACGCCTCTATTCC
1 ATTACGCCTATATTCC
11929210 ATTAC
1 ATTAC
11929215 AGCGAACCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.24, C:0.32, G:0.05, T:0.38
Consensus pattern (16 bp):
ATTACGCCTATATTCC
Found at i:11933681 original size:18 final size:17
Alignment explanation
Indices: 11933648--11933686 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
11933638 TTTTATAAAT
11933648 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
11933666 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
11933683 TGTG
1 TGTG
11933687 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:11933946 original size:23 final size:23
Alignment explanation
Indices: 11933912--11934033 Score: 154
Period size: 23 Copynumber: 5.3 Consensus size: 23
11933902 AGTGTTATTG
11933912 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* * * *
11933935 TTCAGTGCTAGCTACGGCTATAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
11933958 ATCAGTGGTAGCTTTGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* * * * *
11933981 TTTAGTGGTAGCTACGACTACGT
1 ATCAGTGGTAGCTTCGGCTACAT
11934004 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
11934027 ATCAGTG
1 ATCAGTG
11934034 TGACACTTAT
Statistics
Matches: 79, Mismatches: 20, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 79 1.00
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.33
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:11933964 original size:46 final size:46
Alignment explanation
Indices: 11933912--11934033 Score: 181
Period size: 46 Copynumber: 2.7 Consensus size: 46
11933902 AGTGTTATTG
* *
11933912 ATCAGTGGTAGCTTCGGCTACATTTCAGTGCTAGCTACGGCTATAT
1 ATCAGTGGTAGCTTCGGCTACATTTCAGTGCTAGCTACGACTACAT
* * * *
11933958 ATCAGTGGTAGCTTTGGCTACATTTTAGTGGTAGCTACGACTACGT
1 ATCAGTGGTAGCTTCGGCTACATTTCAGTGCTAGCTACGACTACAT
*
11934004 ATCAGTGGTAGCTTCGGCTACATATCAGTG
1 ATCAGTGGTAGCTTCGGCTACATTTCAGTG
11934034 TGACACTTAT
Statistics
Matches: 67, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 67 1.00
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.33
Consensus pattern (46 bp):
ATCAGTGGTAGCTTCGGCTACATTTCAGTGCTAGCTACGACTACAT
Found at i:11936825 original size:54 final size:54
Alignment explanation
Indices: 11936714--11936855 Score: 169
Period size: 54 Copynumber: 2.6 Consensus size: 54
11936704 ACAGCCTATA
* **
11936714 ACACGACCGTGTGA-ATCAAGTCAGTGAGTTACACGGTCTAGCACACGACTTGCG
1 ACACGACCGTGTGACA-CAAGTCAGTGAGTTACACGGTCTAGCACACGACCTAAG
* * * * *
11936768 ACACGATCGTGTGACACAAGTCAGAGAGCTACACGGTCTAGCACATGGCCTAAG
1 ACACGACCGTGTGACACAAGTCAGTGAGTTACACGGTCTAGCACACGACCTAAG
* * *
11936822 ACACGGCCCTGTGACCCAAGTCAGTGAGTTACAC
1 ACACGACCGTGTGACACAAGTCAGTGAGTTACAC
11936856 AATTTAAGAC
Statistics
Matches: 73, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
54 72 0.99
55 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.25, T:0.18
Consensus pattern (54 bp):
ACACGACCGTGTGACACAAGTCAGTGAGTTACACGGTCTAGCACACGACCTAAG
Found at i:11959297 original size:33 final size:33
Alignment explanation
Indices: 11959232--11959297 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 33
11959222 AAAATTATAA
* * * *
11959232 TTATTATATGTACTCTAATACTTTATTTATTAT
1 TTATTAGATGTAATCTAATACTTAATTAATTAT
11959265 TTATTAGATGTAATCTAATGA-TTAATTAATTAT
1 TTATTAGATGTAATCTAAT-ACTTAATTAATTAT
11959298 GATTATGATT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 27 0.96
34 1 0.04
ACGTcount: A:0.35, C:0.06, G:0.06, T:0.53
Consensus pattern (33 bp):
TTATTAGATGTAATCTAATACTTAATTAATTAT
Found at i:11965672 original size:16 final size:16
Alignment explanation
Indices: 11965648--11965679 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
11965638 ATGTTATAAA
11965648 GTTTGGACTAGAAGTG
1 GTTTGGACTAGAAGTG
*
11965664 GTTTTGACTAGAAGTG
1 GTTTGGACTAGAAGTG
11965680 AAATAATTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.06, G:0.34, T:0.34
Consensus pattern (16 bp):
GTTTGGACTAGAAGTG
Found at i:11966680 original size:40 final size:39
Alignment explanation
Indices: 11966625--11966736 Score: 111
Period size: 40 Copynumber: 2.9 Consensus size: 39
11966615 GGCGTTTGTA
* *
11966625 TAAAAAACGCTGCTAAAAATCAAGCATTA-CTGGCGCTTT
1 TAAAAAAAGCCGCTAAAAATCAAGCATTAGC-GGCGCTTT
* *
11966664 TAAAAAAATGCCGCTAAAGATCAAGTATTAGCGGCGCTTT
1 TAAAAAAA-GCCGCTAAAAATCAAGCATTAGCGGCGCTTT
** * * *
11966704 TTGAAAAAGCCACTAAAAAT-GAGTATTAGCGGC
1 TAAAAAAAGCCGCTAAAAATCAAGCATTAGCGGC
11966737 ATTTCCCAAA
Statistics
Matches: 62, Mismatches: 9, Indels: 5
0.82 0.12 0.07
Matches are distributed among these distances:
38 12 0.19
39 17 0.27
40 32 0.52
41 1 0.02
ACGTcount: A:0.39, C:0.18, G:0.19, T:0.24
Consensus pattern (39 bp):
TAAAAAAAGCCGCTAAAAATCAAGCATTAGCGGCGCTTT
Found at i:11966869 original size:41 final size:41
Alignment explanation
Indices: 11966819--11966994 Score: 192
Period size: 41 Copynumber: 4.2 Consensus size: 41
11966809 GTTTCTCAAG
* * * *
11966819 AAGCGCCGCTAATGCTCGGGGCTTTAGCGATGTTTTTGGAA
1 AAGCACCGCTAATGCTCTGGTCTTTAGCGACGTTTTTGGAA
** *
11966860 ATTCACCGCTAATGCTTTGGTCTTTAGCGACGTTTTTGGAA
1 AAGCACCGCTAATGCTCTGGTCTTTAGCGACGTTTTTGGAA
* *
11966901 AAGCGCCGCTAATGCTCTGGTCTTTAGCGGCGTTTTTGGAA
1 AAGCACCGCTAATGCTCTGGTCTTTAGCGACGTTTTTGGAA
* * *
11966942 AAGCGCCGCTGCTAATGCTCTGGTCTTTAGC-AGCATTTTTGAAA
1 AAGC-AC-C-GCTAATGCTCTGGTCTTTAGCGA-CGTTTTTGGAA
*
11966986 AAGCTCCGC
1 AAGCACCGC
11966995 AAAAAGTATT
Statistics
Matches: 114, Mismatches: 17, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
41 76 0.67
42 2 0.02
43 2 0.02
44 34 0.30
ACGTcount: A:0.20, C:0.22, G:0.26, T:0.32
Consensus pattern (41 bp):
AAGCACCGCTAATGCTCTGGTCTTTAGCGACGTTTTTGGAA
Found at i:11966951 original size:82 final size:85
Alignment explanation
Indices: 11966819--11966994 Score: 216
Period size: 82 Copynumber: 2.1 Consensus size: 85
11966809 GTTTCTCAAG
* ** *
11966819 AAGCGCCGCTAATGCTCGGGGCTTTAGCGATGTTTTTGGAAATTCA-C-C-GCTAATGCTTTGGT
1 AAGCGCCGCTAATGCTCGGGGCTTTAGCGACGTTTTTGGAAAAGCACCGCTGCTAATGCTCTGGT
* *
11966881 CTTTAGC-GACGTTTTTGGAA
66 CTTTAGCAG-CATTTTTGAAA
* * * *
11966901 AAGCGCCGCTAATGCTCTGGTCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTGCTAATGCTCTGGT
1 AAGCGCCGCTAATGCTCGGGGCTTTAGCGACGTTTTTGGAAAAGCACCGCTGCTAATGCTCTGGT
11966966 CTTTAGCAGCATTTTTGAAA
66 CTTTAGCAGCATTTTTGAAA
*
11966986 AAGCTCCGC
1 AAGCGCCGC
11966995 AAAAAGTATT
Statistics
Matches: 79, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
82 39 0.49
83 1 0.01
84 1 0.01
85 37 0.47
86 1 0.01
ACGTcount: A:0.20, C:0.22, G:0.26, T:0.32
Consensus pattern (85 bp):
AAGCGCCGCTAATGCTCGGGGCTTTAGCGACGTTTTTGGAAAAGCACCGCTGCTAATGCTCTGGT
CTTTAGCAGCATTTTTGAAA
Found at i:11967520 original size:21 final size:22
Alignment explanation
Indices: 11967494--11967556 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 22
11967484 TTAGTAGTAT
*
11967494 TTAAGGGTTAGGGGTTTA-TGA
1 TTAAGGGTTAGGGGTTTAGGGA
* * * *
11967515 TTAAGGTTTAAGGGATAAGGGA
1 TTAAGGGTTAGGGGTTTAGGGA
11967537 -TAAGGGTTAGGGGTTTAGGG
1 TTAAGGGTTAGGGGTTTAGGG
11967557 TTTATATTAA
Statistics
Matches: 32, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.27, C:0.00, G:0.41, T:0.32
Consensus pattern (22 bp):
TTAAGGGTTAGGGGTTTAGGGA
Found at i:11971464 original size:43 final size:43
Alignment explanation
Indices: 11971403--11971489 Score: 120
Period size: 43 Copynumber: 2.0 Consensus size: 43
11971393 CAATGATGTA
* * * *
11971403 CAAGATTTCCTTGATTAAGTAAATGTATTATATCTTTTATTAC
1 CAAGATTTACTTAATTAAGAAAATGCATTATATCTTTTATTAC
* *
11971446 CAAGATTTACTTAATTAAGAAAATGCATTGTATGTTTTATTAC
1 CAAGATTTACTTAATTAAGAAAATGCATTATATCTTTTATTAC
11971489 C
1 C
11971490 TTGCGTATGT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.34, C:0.11, G:0.10, T:0.44
Consensus pattern (43 bp):
CAAGATTTACTTAATTAAGAAAATGCATTATATCTTTTATTAC
Found at i:11971862 original size:43 final size:43
Alignment explanation
Indices: 11971759--11972022 Score: 237
Period size: 43 Copynumber: 6.2 Consensus size: 43
11971749 GATATGTTTT
* * *
11971759 TAGCGGCGTTTGTGTGAAAAGCGCCGCTAAAGGTC-T-ATTCTA
1 TAGCGGCATTTGTGGGAAAAGCGCCGCTAAAAGTCATGA-TCTA
* * * * *
11971801 TAGTGGCGTTTGTGGGAAAAGTGTCGCTAAAAGTGATGATCTA
1 TAGCGGCATTTGTGGGAAAAGCGCCGCTAAAAGTCATGATCTA
* *
11971844 TAGCGGCATTTGTAGGAAAAGCGCCGCTAAAAGTCATGACCTA
1 TAGCGGCATTTGTGGGAAAAGCGCCGCTAAAAGTCATGATCTA
* * * * *
11971887 TAGCGGCGTTTGTGGGAAAAGTGCCGCTAAAAGTCATGTTATT
1 TAGCGGCATTTGTGGGAAAAGCGCCGCTAAAAGTCATGATCTA
* * * * *
11971930 TAGCGGCGA-TTGTTGGAAAAGCGTCGCTAAAGGTCTTGTTCTA
1 TAGCGGC-ATTTGTGGGAAAAGCGCCGCTAAAAGTCATGATCTA
* * * * * * * *
11971973 TAGCAGCGTTTGTGTGAAAAGCACCGCTAAAGGTCTTGTTTTA
1 TAGCGGCATTTGTGGGAAAAGCGCCGCTAAAAGTCATGATCTA
11972016 TAGCGGC
1 TAGCGGC
11972023 GGTGTCAATA
Statistics
Matches: 182, Mismatches: 36, Indels: 7
0.81 0.16 0.03
Matches are distributed among these distances:
42 29 0.16
43 152 0.84
44 1 0.01
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.28
Consensus pattern (43 bp):
TAGCGGCATTTGTGGGAAAAGCGCCGCTAAAAGTCATGATCTA
Found at i:11972018 original size:129 final size:128
Alignment explanation
Indices: 11971752--11972023 Score: 314
Period size: 129 Copynumber: 2.1 Consensus size: 128
11971742 TTTTAAAGAT
* * * * *
11971752 ATGTTTT-TAGCGGCGTTTGTGTGAAAAGCGCCGCTAAAGGTCTATTCTATAGTGGCGTTTGTGG
1 ATGTTTTATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAAGTCTATTATATAGCGGCGATTGTGG
* * * *
11971816 GAAAAGTGTCGCTAAAAGTGATGATCTATAGCGGCATTTGTAGGAAAAGCGCCGCTAAAAGTC
66 GAAAAGCGTCGCTAAAAGTCATGATCTATAGCAGCATTTGTAGGAAAAGCACCGCTAAAAGTC
*** * * * *
11971879 ATGACCTATAGCGGCGTTTGTGGGAAAAGTGCCGCTAAAAGTCATGTTATTTAGCGGCGATTGTT
1 ATGTTTTATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAAGTC-TATTATATAGCGGCGATTGTG
* * * * *
11971944 GGAAAAGCGTCGCTAAAGGTCTTGTTCTATAGCAGCGTTTGT-GTGAAAAGCACCGCTAAAGGTC
65 GGAAAAGCGTCGCTAAAAGTCATGATCTATAGCAGCATTTGTAG-GAAAAGCACCGCTAAAAGTC
*
11972008 TTGTTTTATAGCGGCG
1 ATGTTTTATAGCGGCG
11972024 GTGTCAATAG
Statistics
Matches: 117, Mismatches: 25, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
127 4 0.03
128 33 0.28
129 80 0.68
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.29
Consensus pattern (128 bp):
ATGTTTTATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAAGTCTATTATATAGCGGCGATTGTGG
GAAAAGCGTCGCTAAAAGTCATGATCTATAGCAGCATTTGTAGGAAAAGCACCGCTAAAAGTC
Found at i:11972023 original size:86 final size:84
Alignment explanation
Indices: 11971752--11972023 Score: 305
Period size: 86 Copynumber: 3.2 Consensus size: 84
11971742 TTTTAAAGAT
* * *
11971752 ATGTTTTTAGCGGCGTTTG-TGTGAAAAGCGCCGCTAAAGGTCTATTCTATAGTGGCGTTTGTGG
1 ATGTTTTTAGCGGCGATTGTTG-GAAAAGCGCCGCTAAAGGTCTGTTCTATAGCGGCGTTTGTGG
* *
11971816 GAAAAGTGTCGCTAAAAGTG
65 GAAAAGTGCCGCTAAAAGTC
* * * * **
11971836 ATGATCTATAGCGGC-ATTTGTAGGAAAAGCGCCGCTAAAAGTCATGACCTATAGCGGCGTTTGT
1 ATG-TTTTTAGCGGCGA-TTGTTGGAAAAGCGCCGCTAAAGGTC-TGTTCTATAGCGGCGTTTGT
11971900 GGGAAAAGTGCCGCTAAAAGTC
63 GGGAAAAGTGCCGCTAAAAGTC
* *
11971922 ATGTTATTTAGCGGCGATTGTTGGAAAAGCGTCGCTAAAGGTCTTGTTCTATAGCAGCGTTTGTG
1 ATGTT-TTTAGCGGCGATTGTTGGAAAAGCGCCGCTAAAGGTC-TGTTCTATAGCGGCGTTTGTG
* ** *
11971987 TGAAAAGCACCGCTAAAGGTC
64 GGAAAAGTGCCGCTAAAAGTC
*
11972008 TTGTTTTATAGCGGCG
1 ATGTTTT-TAGCGGCG
11972024 GTGTCAATAG
Statistics
Matches: 156, Mismatches: 25, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
84 3 0.02
85 34 0.22
86 118 0.76
87 1 0.01
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.29
Consensus pattern (84 bp):
ATGTTTTTAGCGGCGATTGTTGGAAAAGCGCCGCTAAAGGTCTGTTCTATAGCGGCGTTTGTGGG
AAAAGTGCCGCTAAAAGTC
Found at i:11990928 original size:27 final size:27
Alignment explanation
Indices: 11990883--11991031 Score: 79
Period size: 27 Copynumber: 5.5 Consensus size: 27
11990873 TAGTCCATCA
* * *
11990883 GGACATCAAACACTG-GATAGTTCGATG
1 GGACATTAAACA-TGAGATAGTCCAATG
** *
11990910 GGATGTTAAGCATGAGATAGTCCAATG
1 GGACATTAAACATGAGATAGTCCAATG
* ***
11990937 GGACATTAAACATGGGATAGTCCGGCG
1 GGACATTAAACATGAGATAGTCCAATG
* * *
11990964 GGACGTTAAACATG-GTATAG-CCTGATA
1 GGACATTAAACATGAG-ATAGTCC-AATG
* ** * * *
11990991 AGACGGTGAACACGAGATAGTCCGATG
1 GGACATTAAACATGAGATAGTCCAATG
11991018 GGACATTAAACATG
1 GGACATTAAACATG
11991032 GAATACTCTA
Statistics
Matches: 90, Mismatches: 27, Indels: 10
0.71 0.21 0.08
Matches are distributed among these distances:
26 5 0.06
27 82 0.91
28 3 0.03
ACGTcount: A:0.34, C:0.16, G:0.29, T:0.21
Consensus pattern (27 bp):
GGACATTAAACATGAGATAGTCCAATG
Found at i:11994427 original size:22 final size:23
Alignment explanation
Indices: 11994397--11994440 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
11994387 CTTCATGGGT
* *
11994397 TCTTCTCTTTTTAATTTTTCTTG
1 TCTTCTCTTTTCAAATTTTCTTG
11994420 TCTT-TCTTTTCAAATTTTCTT
1 TCTTCTCTTTTCAAATTTTCTT
11994441 AAGATCTCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.11, C:0.18, G:0.02, T:0.68
Consensus pattern (23 bp):
TCTTCTCTTTTCAAATTTTCTTG
Found at i:11995145 original size:9 final size:9
Alignment explanation
Indices: 11995131--11995156 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
11995121 TTTTTAAGTT
11995131 TAAATTGAA
1 TAAATTGAA
11995140 TAAATTGAA
1 TAAATTGAA
11995149 TAAATTGA
1 TAAATTGA
11995157 GCTTTTGTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.12, T:0.35
Consensus pattern (9 bp):
TAAATTGAA
Found at i:11997558 original size:27 final size:27
Alignment explanation
Indices: 11997520--11997727 Score: 237
Period size: 27 Copynumber: 7.7 Consensus size: 27
11997510 ACACACCGGA
* *
11997520 GAAATGAAAGCCTTTGTGGCAATATAT
1 GAAATGGAAGCCTTTGTGGCAATCTAT
*
11997547 GACATGGAAGCCTTTGTGGCAATCTAT
1 GAAATGGAAGCCTTTGTGGCAATCTAT
* * *
11997574 GAAATGGAAGTCTTTAT-G--ATGTATCT
1 GAAATGGAAGCCTTTGTGGCAATCTA--T
* * * *
11997600 GAAATAGAAGCCTTTCTGACGTATC--T
1 GAAATGGAAGCCTTTGTGGC-AATCTAT
*
11997626 GAAATAGAAGCCTTTGTGGCAATCTAT
1 GAAATGGAAGCCTTTGTGGCAATCTAT
11997653 GAAATGGAAGCCTTTGTGGCAATCTAT
1 GAAATGGAAGCCTTTGTGGCAATCTAT
11997680 GAAATGGAAGCCTTTGTGGCAATCTAT
1 GAAATGGAAGCCTTTGTGGCAATCTAT
*
11997707 GAAAAGGAAGGCCTTTGTGGC
1 GAAATGGAA-GCCTTTGTGGC
11997728 GTAGTCTAAA
Statistics
Matches: 155, Mismatches: 17, Indels: 17
0.82 0.09 0.09
Matches are distributed among these distances:
24 4 0.03
25 3 0.02
26 35 0.23
27 100 0.65
28 11 0.07
30 2 0.01
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.30
Consensus pattern (27 bp):
GAAATGGAAGCCTTTGTGGCAATCTAT
Found at i:11997609 original size:26 final size:26
Alignment explanation
Indices: 11997573--11997640 Score: 100
Period size: 26 Copynumber: 2.6 Consensus size: 26
11997563 TGGCAATCTA
* * *
11997573 TGAAATGGAAGTCTTTATGATGTATC
1 TGAAATAGAAGCCTTTATGACGTATC
*
11997599 TGAAATAGAAGCCTTTCTGACGTATC
1 TGAAATAGAAGCCTTTATGACGTATC
11997625 TGAAATAGAAGCCTTT
1 TGAAATAGAAGCCTTT
11997641 GTGGCAATCT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.32, C:0.13, G:0.21, T:0.34
Consensus pattern (26 bp):
TGAAATAGAAGCCTTTATGACGTATC
Found at i:11997988 original size:81 final size:81
Alignment explanation
Indices: 11997861--11998081 Score: 277
Period size: 81 Copynumber: 2.7 Consensus size: 81
11997851 GGACTGGATG
* * * ** *
11997861 GTATGGTAAACACTGAAGGAATAGTACATAT-GAAAAATACTAAAGGAATAGTACATATGGTGAA
1 GTATGGCAAACACTAAAGGAATGGTACATATGGCGAAA-ACTGAAGGAATAGTACATATGGTGAA
11997925 CTCTGAAAGAATAGTAC
65 CTCTGAAAGAATAGTAC
* * *
11997942 GTATGGCAAACACTAAAGGAATGGTACATGTGGCGAAAACTGAAGGAATAATACATATAGTGAAC
1 GTATGGCAAACACTAAAGGAATGGTACATATGGCGAAAACTGAAGGAATAGTACATATGGTGAAC
11998007 TCTGAAAGAATAGTAC
66 TCTGAAAGAATAGTAC
* * * * *
11998023 GTAT-GCAAAAACTAAAAGAATGGTACATCTGGCGAACACTGACA-GAATAGTACGTATGG
1 GTATGGCAAACACTAAAGGAATGGTACATATGGCGAAAACTGA-AGGAATAGTACATATGG
11998082 CGAAAATTGA
Statistics
Matches: 122, Mismatches: 16, Indels: 5
0.85 0.11 0.03
Matches are distributed among these distances:
80 46 0.38
81 72 0.59
82 4 0.03
ACGTcount: A:0.43, C:0.12, G:0.23, T:0.22
Consensus pattern (81 bp):
GTATGGCAAACACTAAAGGAATGGTACATATGGCGAAAACTGAAGGAATAGTACATATGGTGAAC
TCTGAAAGAATAGTAC
Found at i:11998083 original size:27 final size:27
Alignment explanation
Indices: 11997869--11998085 Score: 170
Period size: 27 Copynumber: 8.1 Consensus size: 27
11997859 TGGTATGGTA
* ***
11997869 AACACTGAAGGAATAGTACATATGAAA
1 AACACTGAAAGAATAGTACATATGGCG
* *
11997896 AATACT-AAAGGAATAGTACATATGGTG
1 AACACTGAAA-GAATAGTACATATGGCG
* * *
11997923 AACTCTGAAAGAATAGTACGTATGGCA
1 AACACTGAAAGAATAGTACATATGGCG
* *
11997950 AACACT-AAAGGAATGGTACATGTGGCG
1 AACACTGAAA-GAATAGTACATATGGCG
* * * * *
11997977 AAAACTGAAGGAATAATACATATAGTG
1 AACACTGAAAGAATAGTACATATGGCG
* * *
11998004 AACTCTGAAAGAATAGTACGTAT-GCA
1 AACACTGAAAGAATAGTACATATGGCG
* * * *
11998030 AAAACTAAAAGAATGGTACATCTGGCG
1 AACACTGAAAGAATAGTACATATGGCG
* *
11998057 AACACTGACAGAATAGTACGTATGGCG
1 AACACTGAAAGAATAGTACATATGGCG
11998084 AA
1 AA
11998086 AATTGAGAGA
Statistics
Matches: 143, Mismatches: 42, Indels: 10
0.73 0.22 0.05
Matches are distributed among these distances:
26 23 0.16
27 115 0.80
28 5 0.03
ACGTcount: A:0.44, C:0.13, G:0.22, T:0.21
Consensus pattern (27 bp):
AACACTGAAAGAATAGTACATATGGCG
Found at i:12003020 original size:18 final size:18
Alignment explanation
Indices: 12002997--12003040 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
12002987 AATTAAAATA
12002997 TTAAAAATA-TAATTAATT
1 TTAAAAATATTAATT-ATT
*
12003015 TTAAAAATATTTATTATT
1 TTAAAAATATTAATTATT
12003033 TTAAAAAT
1 TTAAAAAT
12003041 TATCTTTTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 20 0.83
19 4 0.17
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
TTAAAAATATTAATTATT
Found at i:12005978 original size:18 final size:17
Alignment explanation
Indices: 12005950--12005984 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
12005940 ATTAATATAA
*
12005950 TTAATATTTTTATTATT
1 TTAATATTTTTAATATT
12005967 TTAATAATTTTTAATATT
1 TTAAT-ATTTTTAATATT
12005985 ATTTTTTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TTAATATTTTTAATATT
Found at i:12005997 original size:28 final size:27
Alignment explanation
Indices: 12005950--12006015 Score: 89
Period size: 28 Copynumber: 2.4 Consensus size: 27
12005940 ATTAATATAA
12005950 TTAATATTTTTATTATTTTAATAATTT
1 TTAATATTTTTATTATTTTAATAATTT
*
12005977 TTAATATTATTTTTTATTTTAATAATAATT
1 TTAATATT-TTTATTATTTTAATAAT--TT
12006007 TTAA-ATTTT
1 TTAATATTTT
12006016 AAAAAATATT
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
27 8 0.23
28 18 0.51
29 3 0.09
30 6 0.17
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (27 bp):
TTAATATTTTTATTATTTTAATAATTT
Done.