Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 113035596
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: 113035596
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 271 characters in sequence are not A, C, G, or T
File 103 of 378
Found at i:28279979 original size:43 final size:43
Alignment explanation
Indices: 28279903--28280011 Score: 112
Period size: 43 Copynumber: 2.5 Consensus size: 43
28279893 ATTCTGTTAC
* * * ** *
28279903 CTGATACTGATTTTGATTTTGATTCTATTACCTGATACTAATT
1 CTGATTCTGATTCTGATTCTGATTCTACCACCTGATACTAACT
* * * *
28279946 CTGCTTCTGATTCTGATTCTGATTCTGCCACCTGATTCTGACT
1 CTGATTCTGATTCTGATTCTGATTCTACCACCTGATACTAACT
28279989 CTGATTCTGATTCT-AGTTCTGAT
1 CTGATTCTGATTCTGA-TTCTGAT
28280012 AATGTTTCTT
Statistics
Matches: 54, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
42 1 0.02
43 53 0.98
ACGTcount: A:0.19, C:0.20, G:0.15, T:0.46
Consensus pattern (43 bp):
CTGATTCTGATTCTGATTCTGATTCTACCACCTGATACTAACT
Found at i:28279984 original size:37 final size:37
Alignment explanation
Indices: 28279878--28280012 Score: 125
Period size: 37 Copynumber: 3.6 Consensus size: 37
28279868 TTACCTGATA
* * * *
28279878 CTGATTCTGATTTTGATTCTGTTACCTGATACTGATT
1 CTGATTCTGATTCTGATTCTGATACCTGATTCTGCTT
* * *
28279915 TTGATTTTGATTCT-ATTACCTGATA-CTAATTCTGCTT
1 CTGATTCTGATTCTGATT--CTGATACCTGATTCTGCTT
**
28279952 CTGATTCTGATTCTGATTCTGCCACCTGATTCTGAC-T
1 CTGATTCTGATTCTGATTCTGATACCTGATTCTG-CTT
28279989 CTGATTCTGATTCT-AGTTCTGATA
1 CTGATTCTGATTCTGA-TTCTGATA
28280013 ATGTTTCTTA
Statistics
Matches: 78, Mismatches: 14, Indels: 12
0.75 0.13 0.12
Matches are distributed among these distances:
36 8 0.10
37 61 0.78
38 9 0.12
ACGTcount: A:0.19, C:0.19, G:0.15, T:0.47
Consensus pattern (37 bp):
CTGATTCTGATTCTGATTCTGATACCTGATTCTGCTT
Found at i:28286026 original size:19 final size:19
Alignment explanation
Indices: 28286002--28286038 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
28285992 TCACATGGCC
28286002 GTGTCAAGCACGCACGGCT
1 GTGTCAAGCACGCACGGCT
* *
28286021 GTGTCATGCACGTACGGC
1 GTGTCAAGCACGCACGGC
28286039 CTGGCTCGTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.19, C:0.30, G:0.32, T:0.19
Consensus pattern (19 bp):
GTGTCAAGCACGCACGGCT
Found at i:28287272 original size:33 final size:33
Alignment explanation
Indices: 28287223--28287291 Score: 88
Period size: 33 Copynumber: 2.1 Consensus size: 33
28287213 AATTAGAAAT
* *
28287223 AGTGTGGGCCTGAGCCCATTTCAGTAA-CAGTATC
1 AGTGTGGGCCTAAGCCCATTACAG-AATCAGTA-C
28287257 AGTG-GGGCCTAAGCCCATTACAGAATCAGTAC
1 AGTGTGGGCCTAAGCCCATTACAGAATCAGTAC
28287289 AGT
1 AGT
28287292 ATGCAATCAG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
32 6 0.19
33 22 0.69
34 4 0.12
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.23
Consensus pattern (33 bp):
AGTGTGGGCCTAAGCCCATTACAGAATCAGTAC
Found at i:28293310 original size:40 final size:40
Alignment explanation
Indices: 28293254--28293352 Score: 126
Period size: 40 Copynumber: 2.5 Consensus size: 40
28293244 GGATATAGCG
* * *
28293254 ACTCGCTCAAAAGCCTTCGGGACATAGCCCGGTTATAATA
1 ACTCGCACAAATGCCTTCGGGACATAACCCGGTTATAATA
* * * **
28293294 GCTCGCACAAATGCCTTCGGGACTTAACCCGGTTTTGGTA
1 ACTCGCACAAATGCCTTCGGGACATAACCCGGTTATAATA
28293334 ACTCGCACAAATGCCTTCG
1 ACTCGCACAAATGCCTTCG
28293353 AGAATTGACC
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 50 1.00
ACGTcount: A:0.25, C:0.29, G:0.21, T:0.24
Consensus pattern (40 bp):
ACTCGCACAAATGCCTTCGGGACATAACCCGGTTATAATA
Found at i:28293364 original size:40 final size:40
Alignment explanation
Indices: 28293295--28293408 Score: 120
Period size: 40 Copynumber: 2.8 Consensus size: 40
28293285 GTTATAATAG
* * * *
28293295 CTCGCACAAATGCCTTCGGGACTTAACCCGGTTTTGGTAA
1 CTCGCACAAATGCCTTCGAGAATTAACCCGGATTTAGTAA
* *
28293335 CTCGCACAAATGCCTTCGAGAATTGACCCGGATTTAGTCA
1 CTCGCACAAATGCCTTCGAGAATTAACCCGGATTTAGTAA
* * * * *
28293375 CTTAGCACAAAAGCCTTCGGGACTTAGCCCGGAT
1 C-TCGCACAAATGCCTTCGAGAATTAACCCGGAT
28293409 ACCATTCGAA
Statistics
Matches: 61, Mismatches: 12, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
40 35 0.57
41 26 0.43
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CTCGCACAAATGCCTTCGAGAATTAACCCGGATTTAGTAA
Found at i:28300244 original size:25 final size:25
Alignment explanation
Indices: 28300208--28300258 Score: 61
Period size: 25 Copynumber: 2.0 Consensus size: 25
28300198 TTATCTTGAT
28300208 AAATATTAAATTAAAT-TTAATATTA
1 AAATATTAAATTAAATATT-ATATTA
*
28300233 AAATAATT-AATTTAATATTATATTA
1 AAAT-ATTAAATTAAATATTATATTA
28300258 A
1 A
28300259 TAAAATACTC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
25 18 0.78
26 5 0.22
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (25 bp):
AAATATTAAATTAAATATTATATTA
Found at i:28300259 original size:20 final size:21
Alignment explanation
Indices: 28300210--28300264 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 21
28300200 ATCTTGATAA
28300210 ATATTAAATTAAATTTAATATT
1 ATATT-AATTAAATTTAATATT
* *
28300232 AAAATAATT-AATTTAATATT
1 ATATTAATTAAATTTAATATT
*
28300252 ATATTAATAAAAT
1 ATATTAATTAAAT
28300265 ACTCTTAAGA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
20 17 0.63
21 7 0.26
22 3 0.11
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
ATATTAATTAAATTTAATATT
Found at i:28304154 original size:24 final size:24
Alignment explanation
Indices: 28304127--28304178 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
28304117 ATGTCAACTA
*
28304127 AGATTCTTTTCACTTAGAATAAGG
1 AGATTCTTTTCACTTAAAATAAGG
28304151 AGATTCTTTTCACTTAAAATAAGG
1 AGATTCTTTTCACTTAAAATAAGG
28304175 AGAT
1 AGAT
28304179 GATAGCTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.37
Consensus pattern (24 bp):
AGATTCTTTTCACTTAAAATAAGG
Found at i:28309019 original size:29 final size:29
Alignment explanation
Indices: 28308986--28309068 Score: 139
Period size: 29 Copynumber: 2.9 Consensus size: 29
28308976 GTGTCGAGAT
28308986 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
*
28309015 TGGCACTAAGTGTGCGTGCTGGAAATATT
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
**
28309044 TGGCACTAAGTGTGCAAGCTGGAAA
1 TGGCACTAAGTGTGCGTGCTGGAAA
28309069 AAAAATACGG
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 51 1.00
ACGTcount: A:0.28, C:0.14, G:0.31, T:0.27
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGTGCTGGAAATATA
Found at i:28316238 original size:29 final size:29
Alignment explanation
Indices: 28316205--28316287 Score: 139
Period size: 29 Copynumber: 2.9 Consensus size: 29
28316195 GTGTCGAGAT
28316205 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
*
28316234 TGGCACTAAGTGTGCGTGCTGGAAATATT
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
**
28316263 TGGCACTAAGTGTGCAAGCTGGAAA
1 TGGCACTAAGTGTGCGTGCTGGAAA
28316288 AAAATACGGC
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 51 1.00
ACGTcount: A:0.28, C:0.14, G:0.31, T:0.27
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGTGCTGGAAATATA
Found at i:28329971 original size:17 final size:17
Alignment explanation
Indices: 28329949--28329983 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
28329939 GCTTCTCGAG
*
28329949 AGGCAACCCGAGCACTA
1 AGGCAACCCAAGCACTA
28329966 AGGCAACCCAAGCACTA
1 AGGCAACCCAAGCACTA
28329983 A
1 A
28329984 CATATTTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.40, C:0.34, G:0.20, T:0.06
Consensus pattern (17 bp):
AGGCAACCCAAGCACTA
Found at i:28331000 original size:6 final size:7
Alignment explanation
Indices: 28330984--28331013 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
28330974 TTCAAACTAC
28330984 TTTTTAT
1 TTTTTAT
28330991 TTTTTAT
1 TTTTTAT
28330998 TTTTTA-
1 TTTTTAT
28331004 TTTTTAT
1 TTTTTAT
28331011 TTT
1 TTT
28331014 AGCAGATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (7 bp):
TTTTTAT
Found at i:28331007 original size:13 final size:14
Alignment explanation
Indices: 28330984--28331013 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
28330974 TTCAAACTAC
28330984 TTTTTATTTTTTAT
1 TTTTTATTTTTTAT
28330998 TTTTTA-TTTTTAT
1 TTTTTATTTTTTAT
28331011 TTT
1 TTT
28331014 AGCAGATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (14 bp):
TTTTTATTTTTTAT
Found at i:28335722 original size:40 final size:40
Alignment explanation
Indices: 28335677--28335844 Score: 198
Period size: 40 Copynumber: 4.2 Consensus size: 40
28335667 CGGAATACAA
*
28335677 CCGGATATAACCACACGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACACGCACGAATGCCTTCGGGTATTAGC
* * *
28335717 CCGGATATAACGACTCGCACAAATGCCTTCGGGTATTAGC
1 CCGGATATAACCACACGCACGAATGCCTTCGGGTATTAGC
* **
28335757 CCGGATATAACAACTTGCACGAATGCCTTCGGGTATTAGC
1 CCGGATATAACCACACGCACGAATGCCTTCGGGTATTAGC
* * *
28335797 CCGGATA-AAGTCACTA-GCAC-AATTGCCTTCGGGTCTTAAC
1 CCGGATATAA-CCAC-ACGCACGAA-TGCCTTCGGGTATTAGC
28335837 CCGGATAT
1 CCGGATAT
28335845 CATTCAATTG
Statistics
Matches: 112, Mismatches: 12, Indels: 7
0.85 0.09 0.05
Matches are distributed among these distances:
39 4 0.04
40 108 0.96
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (40 bp):
CCGGATATAACCACACGCACGAATGCCTTCGGGTATTAGC
Found at i:28335817 original size:80 final size:80
Alignment explanation
Indices: 28335677--28335844 Score: 232
Period size: 80 Copynumber: 2.1 Consensus size: 80
28335667 CGGAATACAA
* * *
28335677 CCGGATATAACCACACGCACGAATGCCTTCGGGTCTTAGCCCGGATATAACGACTCGCACAAATG
1 CCGGATATAACAACACGCACGAATGCCTTCGGGTATTAGCCCGGATATAACGACTAGCACAAATG
*
28335742 CCTTCGGGTATTAGC
66 CCTTCGGGTATTAAC
** *
28335757 CCGGATATAACAACTTGCACGAATGCCTTCGGGTATTAGCCCGGATA-AA-GTCACTAGCACAAT
1 CCGGATATAACAACACGCACGAATGCCTTCGGGTATTAGCCCGGATATAACG--ACTAGCACAAA
*
28335820 TGCCTTCGGGTCTTAAC
64 TGCCTTCGGGTATTAAC
28335837 CCGGATAT
1 CCGGATAT
28335845 CATTCAATTG
Statistics
Matches: 78, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
78 1 0.01
79 2 0.03
80 75 0.96
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (80 bp):
CCGGATATAACAACACGCACGAATGCCTTCGGGTATTAGCCCGGATATAACGACTAGCACAAATG
CCTTCGGGTATTAAC
Found at i:28343733 original size:40 final size:40
Alignment explanation
Indices: 28343688--28343855 Score: 198
Period size: 40 Copynumber: 4.2 Consensus size: 40
28343678 CGGAATACAA
*
28343688 CCGGATATAACCACACGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACACGCACGAATGCCTTCGGGTATTAGC
* * *
28343728 CCGGATATAACGACTCGCACAAATGCCTTCGGGTATTAGC
1 CCGGATATAACCACACGCACGAATGCCTTCGGGTATTAGC
* **
28343768 CCGGATATAACAACTTGCACGAATGCCTTCGGGTATTAGC
1 CCGGATATAACCACACGCACGAATGCCTTCGGGTATTAGC
* * *
28343808 CCGGATA-AAGTCACTA-GCAC-AATTGCCTTCGGGTCTTAAC
1 CCGGATATAA-CCAC-ACGCACGAA-TGCCTTCGGGTATTAGC
28343848 CCGGATAT
1 CCGGATAT
28343856 CATTCAATTG
Statistics
Matches: 112, Mismatches: 12, Indels: 7
0.85 0.09 0.05
Matches are distributed among these distances:
39 4 0.04
40 108 0.96
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (40 bp):
CCGGATATAACCACACGCACGAATGCCTTCGGGTATTAGC
Found at i:28343828 original size:80 final size:80
Alignment explanation
Indices: 28343688--28343855 Score: 232
Period size: 80 Copynumber: 2.1 Consensus size: 80
28343678 CGGAATACAA
* * *
28343688 CCGGATATAACCACACGCACGAATGCCTTCGGGTCTTAGCCCGGATATAACGACTCGCACAAATG
1 CCGGATATAACAACACGCACGAATGCCTTCGGGTATTAGCCCGGATATAACGACTAGCACAAATG
*
28343753 CCTTCGGGTATTAGC
66 CCTTCGGGTATTAAC
** *
28343768 CCGGATATAACAACTTGCACGAATGCCTTCGGGTATTAGCCCGGATA-AA-GTCACTAGCACAAT
1 CCGGATATAACAACACGCACGAATGCCTTCGGGTATTAGCCCGGATATAACG--ACTAGCACAAA
*
28343831 TGCCTTCGGGTCTTAAC
64 TGCCTTCGGGTATTAAC
28343848 CCGGATAT
1 CCGGATAT
28343856 CATTCAATTG
Statistics
Matches: 78, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
78 1 0.01
79 2 0.03
80 75 0.96
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (80 bp):
CCGGATATAACAACACGCACGAATGCCTTCGGGTATTAGCCCGGATATAACGACTAGCACAAATG
CCTTCGGGTATTAAC
Found at i:28347514 original size:41 final size:42
Alignment explanation
Indices: 28347411--28347526 Score: 128
Period size: 43 Copynumber: 2.8 Consensus size: 42
28347401 CTATACCAAT
* * * * * *
28347411 GCCATATCCCAGATATGTTCTTACATG-GGATCTCGTATCGAT
1 GCCATATCCCAGATATGGTCTTACACGAAG-TCCCATATCGAC
* *
28347453 GCCAATAGCCCAGCTATGGTCTTACACGAAGTCCCATATCG-C
1 GCC-ATATCCCAGATATGGTCTTACACGAAGTCCCATATCGAC
28347495 GCCATATCCCAGATATGGTCTTACACGAAGTC
1 GCCATATCCCAGATATGGTCTTACACGAAGTC
28347527 TCACATCTGT
Statistics
Matches: 62, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
41 27 0.44
42 6 0.10
43 28 0.45
44 1 0.02
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.27
Consensus pattern (42 bp):
GCCATATCCCAGATATGGTCTTACACGAAGTCCCATATCGAC
Found at i:28350321 original size:30 final size:30
Alignment explanation
Indices: 28350287--28350352 Score: 75
Period size: 28 Copynumber: 2.3 Consensus size: 30
28350277 TCCTTCCATG
* *
28350287 CATTTTTATATTTTTTGTTTTTATTAAT-AT
1 CATTTTTACATTTTTT-TCTTTATTAATAAT
*
28350317 CA--TTTACATTTTTTTCTTTATTAGTAAT
1 CATTTTTACATTTTTTTCTTTATTAATAAT
28350345 CATTTTTA
1 CATTTTTA
28350353 AAAATATATA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
27 9 0.30
28 15 0.50
30 6 0.20
ACGTcount: A:0.24, C:0.08, G:0.03, T:0.65
Consensus pattern (30 bp):
CATTTTTACATTTTTTTCTTTATTAATAAT
Found at i:28350336 original size:27 final size:29
Alignment explanation
Indices: 28350291--28350349 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 29
28350281 TCCATGCATT
* *
28350291 TTTATATTTTTTGTTTTTATTAAT-ATCA
1 TTTACATTTTTTGTCTTTATTAATAATCA
*
28350319 TTTACATTTTTT-TCTTTATTAGTAATCA
1 TTTACATTTTTTGTCTTTATTAATAATCA
28350347 TTT
1 TTT
28350350 TTAAAAATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 9 0.33
28 18 0.67
ACGTcount: A:0.24, C:0.07, G:0.03, T:0.66
Consensus pattern (29 bp):
TTTACATTTTTTGTCTTTATTAATAATCA
Found at i:28350660 original size:15 final size:17
Alignment explanation
Indices: 28350642--28350673 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
28350632 GGACAAAAAC
28350642 TATAAT-TAAAC-TTAT
1 TATAATGTAAACATTAT
28350657 TATAATGTAAACATTAT
1 TATAATGTAAACATTAT
28350674 AAATAAGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 5 0.33
17 4 0.27
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (17 bp):
TATAATGTAAACATTAT
Found at i:28355217 original size:56 final size:56
Alignment explanation
Indices: 28355101--28355213 Score: 219
Period size: 55 Copynumber: 2.0 Consensus size: 56
28355091 TTATATATTA
28355101 TTCATCCTAAAAAAAATACTTTCTATATCTACTATTCCGATTTAAGGTCACATATC
1 TTCATCCTAAAAAAAATACTTTCTATATCTACTATTCCGATTTAAGGTCACATATC
28355157 TTCATCCT-AAAAAAATACTTTCTATATCTACTATTCCGATTTAAGGTCACATATC
1 TTCATCCTAAAAAAAATACTTTCTATATCTACTATTCCGATTTAAGGTCACATATC
28355212 TT
1 TT
28355214 TCATTCCAAT
Statistics
Matches: 57, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
55 49 0.86
56 8 0.14
ACGTcount: A:0.35, C:0.21, G:0.05, T:0.39
Consensus pattern (56 bp):
TTCATCCTAAAAAAAATACTTTCTATATCTACTATTCCGATTTAAGGTCACATATC
Found at i:28359817 original size:50 final size:49
Alignment explanation
Indices: 28359707--28359833 Score: 175
Period size: 50 Copynumber: 2.6 Consensus size: 49
28359697 GTACGCATAA
* * **
28359707 TAGCCTGCACTTAGTACTACACATGCGACCAACAGTCTGGTACACGTAG
1 TAGCCTGCACTTAGTACTACACACGTGACCAACAGTCTAATACACGTAG
* *
28359756 TAGCCTACACTTAGTACTACACACGTGACCTCACCA-TCTAATACACGTAG
1 TAGCCTGCACTTAGTACTACACACGTGA-C-CAACAGTCTAATACACGTAG
28359806 TAGCCTGCACTTAGTACTACACACGTGA
1 TAGCCTGCACTTAGTACTACACACGTGA
28359834 TCACAGTTTT
Statistics
Matches: 69, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
49 25 0.36
50 40 0.58
51 4 0.06
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.24
Consensus pattern (49 bp):
TAGCCTGCACTTAGTACTACACACGTGACCAACAGTCTAATACACGTAG
Found at i:28362071 original size:15 final size:15
Alignment explanation
Indices: 28362015--28362079 Score: 64
Period size: 15 Copynumber: 4.4 Consensus size: 15
28362005 TAAAGATAAC
*
28362015 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
28362029 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
* *
28362044 GAA-TAACCCAGAATA
1 -AAGAAATCCAGAATA
28362059 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
28362074 AAGAAA
1 AAGAAA
28362080 CCCAAGATAC
Statistics
Matches: 41, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
14 11 0.27
15 27 0.66
16 3 0.07
ACGTcount: A:0.62, C:0.14, G:0.14, T:0.11
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:28362082 original size:30 final size:31
Alignment explanation
Indices: 28362015--28362083 Score: 83
Period size: 30 Copynumber: 2.3 Consensus size: 31
28362005 TAAAGATAAC
*
28362015 AAGAAAACC-GAATAAAGAAATCCAAGATAG
1 AAGAAACCCAGAATAAAGAAATCCAAGATAG
*
28362045 AA-TAACCCAGAATAAAGAAATCC-AGAATA-
1 AAGAAACCCAGAATAAAGAAATCCAAG-ATAG
28362074 AAGAAACCCA
1 AAGAAACCCA
28362084 AGATACGATA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
29 8 0.24
30 25 0.76
ACGTcount: A:0.59, C:0.17, G:0.13, T:0.10
Consensus pattern (31 bp):
AAGAAACCCAGAATAAAGAAATCCAAGATAG
Found at i:28377906 original size:40 final size:39
Alignment explanation
Indices: 28377741--28377924 Score: 138
Period size: 40 Copynumber: 4.6 Consensus size: 39
28377731 AAATTGAATG
* * *
28377741 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAAT--T
1 ATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATCGT
* * * * * *
28377781 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-T
* * * * *
28377821 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATC-GT
*
28377861 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
* * *
28377900 GATATCCGGGTTAAGTCCCGTAGGC
1 -ATATCCGGGCTAAGACCCGAAGGC
28377925 CTTGGTGCGG
Statistics
Matches: 113, Mismatches: 26, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
37 4 0.04
38 2 0.02
39 3 0.03
40 104 0.92
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
Found at i:28377949 original size:80 final size:81
Alignment explanation
Indices: 28377781--28377969 Score: 186
Period size: 80 Copynumber: 2.4 Consensus size: 81
28377771 GCTGGAAATT
* * * *
28377781 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTACATCCGGGCTAAGACCCGAAGGCA
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
*
28377846 TTCGTGCGAGTCATTC
66 TTCGTGCGAGTCATCC
* * * * * *
28377862 -TATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-TGATATCCGGGTTAAGTCCCGTAGGC
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCT-ACATCCGGGCTAAGACCCGAAGGC
* * * *
28377925 CTTGGTGCGGGTTA-CC
65 ATTCGTGCGAGTCATCC
* * *
28377941 ATAACCGGGCTATGTCCCGAAGGCGATTG
1 ATAACCGGGCTAAGACCCGAAGGCAATTG
28377970 ATCGAGTAGC
Statistics
Matches: 86, Mismatches: 20, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
79 2 0.02
80 84 0.98
ACGTcount: A:0.23, C:0.24, G:0.30, T:0.23
Consensus pattern (81 bp):
ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
TTCGTGCGAGTCATCC
Found at i:28386023 original size:40 final size:39
Alignment explanation
Indices: 28385858--28386041 Score: 138
Period size: 40 Copynumber: 4.6 Consensus size: 39
28385848 AAATTGAATG
* * *
28385858 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAAT--T
1 ATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATCGT
* * * * * *
28385898 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-T
* * * * *
28385938 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATC-GT
*
28385978 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
* * *
28386017 GATATCCGGGTTAAGTCCCGTAGGC
1 -ATATCCGGGCTAAGACCCGAAGGC
28386042 CTTGGTGCGG
Statistics
Matches: 113, Mismatches: 26, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
37 4 0.04
38 2 0.02
39 3 0.03
40 104 0.92
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
Found at i:28386066 original size:80 final size:81
Alignment explanation
Indices: 28385898--28386086 Score: 186
Period size: 80 Copynumber: 2.4 Consensus size: 81
28385888 GCTGGAAATT
* * * *
28385898 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTACATCCGGGCTAAGACCCGAAGGCA
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
*
28385963 TTCGTGCGAGTCATTC
66 TTCGTGCGAGTCATCC
* * * * * *
28385979 -TATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-TGATATCCGGGTTAAGTCCCGTAGGC
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCT-ACATCCGGGCTAAGACCCGAAGGC
* * * *
28386042 CTTGGTGCGGGTTA-CC
65 ATTCGTGCGAGTCATCC
* * *
28386058 ATAACCGGGCTATGTCCCGAAGGCGATTG
1 ATAACCGGGCTAAGACCCGAAGGCAATTG
28386087 ATCGAGTAGC
Statistics
Matches: 86, Mismatches: 20, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
79 2 0.02
80 84 0.98
ACGTcount: A:0.23, C:0.24, G:0.30, T:0.23
Consensus pattern (81 bp):
ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
TTCGTGCGAGTCATCC
Found at i:28394209 original size:14 final size:15
Alignment explanation
Indices: 28394175--28394211 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
28394165 AGATAAGTCG
28394175 TTTC-TTCTTCTTCT
1 TTTCTTTCTTCTTCT
28394189 TTT-TTTCTT-TTCT
1 TTTCTTTCTTCTTCT
28394202 TTTCTTTCTT
1 TTTCTTTCTT
28394212 GATTTTCCCT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
13 7 0.33
14 14 0.67
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTCTTTCTTCTTCT
Found at i:28394964 original size:22 final size:22
Alignment explanation
Indices: 28394939--28394987 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
28394929 AGAATTTTAA
28394939 AAATTGATAATCTAAATAATTC
1 AAATTGATAATCTAAATAATTC
*
28394961 AAATTGATAATCTAAATAATTG
1 AAATTGATAATCTAAATAATTC
28394983 AAATT
1 AAATT
28394988 AGATTTAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.51, C:0.06, G:0.06, T:0.37
Consensus pattern (22 bp):
AAATTGATAATCTAAATAATTC
Found at i:28395324 original size:17 final size:17
Alignment explanation
Indices: 28395284--28395316 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
28395274 AATTGTTTAC
28395284 TTAA-ATTTAAAAATAA
1 TTAATATTTAAAAATAA
28395300 TTAATATTTCAAAAATA
1 TTAATATTT-AAAAATA
28395317 TTATTATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 4 0.27
18 7 0.47
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (17 bp):
TTAATATTTAAAAATAA
Found at i:28398149 original size:13 final size:13
Alignment explanation
Indices: 28398131--28398155 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28398121 AAAATAGTTA
28398131 TTTTTATATTTTC
1 TTTTTATATTTTC
28398144 TTTTTATATTTT
1 TTTTTATATTTT
28398156 ATATAAAGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.04, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTTATATTTTC
Found at i:28399010 original size:9 final size:9
Alignment explanation
Indices: 28398998--28399142 Score: 70
Period size: 9 Copynumber: 16.0 Consensus size: 9
28398988 ATTATTTTAG
28398998 AAATTTTTT
1 AAATTTTTT
28399007 AAATTTTTT
1 AAATTTTTT
*
28399016 AAA-ATTTT
1 AAATTTTTT
*
28399024 AACTTTTTT
1 AAATTTTTT
*
28399033 ATATTTTTTT
1 A-AATTTTTT
28399043 AGAA-TTTTT
1 A-AATTTTTT
*
28399052 ATATTTTTTT
1 A-AATTTTTT
* *
28399062 AAA--ATAT
1 AAATTTTTT
*
28399069 AAA-TTTTG
1 AAATTTTTT
28399077 AAATTTTTAT
1 AAATTTTT-T
28399087 AAATATTTTT
1 AAAT-TTTTT
**
28399097 -AATTTTAA
1 AAATTTTTT
28399105 AAATTATTTT
1 AAATT-TTTT
* *
28399115 GAATTTTTGA
1 AAATTTTT-T
28399125 AAATTATTTT
1 AAATT-TTTT
28399135 -AATTTTTT
1 AAATTTTTT
28399143 TGTAATTTTT
Statistics
Matches: 102, Mismatches: 23, Indels: 23
0.69 0.16 0.16
Matches are distributed among these distances:
7 5 0.05
8 17 0.17
9 43 0.42
10 30 0.29
11 7 0.07
ACGTcount: A:0.36, C:0.01, G:0.03, T:0.61
Consensus pattern (9 bp):
AAATTTTTT
Found at i:28399020 original size:19 final size:18
Alignment explanation
Indices: 28398992--28399141 Score: 80
Period size: 19 Copynumber: 8.2 Consensus size: 18
28398982 AAAATTATTA
28398992 TTTTAGAAATTTTTTAAATT
1 TTTTA-AAATTTTTTAAA-T
*
28399012 TTTTAAAA--TTTTAACTT
1 TTTTAAAATTTTTTAA-AT
* *
28399029 TTTTATATTTTTTTAGAAT
1 TTTTAAAATTTTTTA-AAT
* *
28399048 TTTTATATTTTTTTAAA-
1 TTTTAAAATTTTTTAAAT
* * *
28399065 ATAT-AAA-TTTTGAAAT
1 TTTTAAAATTTTTTAAAT
28399081 TTTTATAAATATTTTT-AAT
1 TTTTA-AAAT-TTTTTAAAT
* *
28399100 TTTAAAAATTATTTTGAAT
1 TTTTAAAATT-TTTTAAAT
28399119 TTTTGAAAATTATTTT-AAT
1 TTTT-AAAATT-TTTTAAAT
28399138 TTTT
1 TTTT
28399142 TTGTAATTTT
Statistics
Matches: 104, Mismatches: 14, Indels: 25
0.73 0.10 0.17
Matches are distributed among these distances:
15 7 0.07
16 3 0.03
17 16 0.15
18 13 0.12
19 44 0.42
20 21 0.20
ACGTcount: A:0.35, C:0.01, G:0.03, T:0.61
Consensus pattern (18 bp):
TTTTAAAATTTTTTAAAT
Found at i:28399127 original size:20 final size:19
Alignment explanation
Indices: 28399057--28399141 Score: 84
Period size: 19 Copynumber: 4.3 Consensus size: 19
28399047 TTTTTATATT
28399057 TTTTTAAAATATAAATTTTGAAA
1 TTTTTAAAAT-T--ATTTTG-AA
*
28399080 TTTTTATAAA-TATTTTTAA
1 TTTTTA-AAATTATTTTGAA
*
28399099 TTTTAAAAATTATTTTGAA
1 TTTTTAAAATTATTTTGAA
28399118 TTTTTGAAAATTATTTT-AA
1 TTTTT-AAAATTATTTTGAA
28399137 TTTTT
1 TTTTT
28399142 TTGTAATTTT
Statistics
Matches: 55, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
18 3 0.05
19 26 0.47
20 16 0.29
22 1 0.02
23 6 0.11
24 3 0.05
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
TTTTTAAAATTATTTTGAA
Found at i:28399142 original size:20 final size:20
Alignment explanation
Indices: 28399057--28399141 Score: 86
Period size: 20 Copynumber: 4.2 Consensus size: 20
28399047 TTTTTATATT
*
28399057 TTTTTAAAATATAAATTTTGAAA
1 TTTTTAAAA-AT-TATTTTG-AA
* *
28399080 TTTTTATAAA-TATTTTTAA
1 TTTTTAAAAATTATTTTGAA
28399099 -TTTTAAAAATTATTTTGAA
1 TTTTTAAAAATTATTTTGAA
*
28399118 TTTTTGAAAATTATTTT-AA
1 TTTTTAAAAATTATTTTGAA
28399137 TTTTT
1 TTTTT
28399142 TTGTAATTTT
Statistics
Matches: 54, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
18 8 0.15
19 17 0.31
20 20 0.37
22 1 0.02
23 8 0.15
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.58
Consensus pattern (20 bp):
TTTTTAAAAATTATTTTGAA
Found at i:28403447 original size:50 final size:50
Alignment explanation
Indices: 28403393--28403545 Score: 168
Period size: 50 Copynumber: 3.1 Consensus size: 50
28403383 CTTTCCATAC
28403393 AACACGCCATAAAGACTTTTCA-GATAATTTGCCATAAAGGCTTTACAGAT
1 AACACGCCATAAAGACTTTT-ATGATAATTTGCCATAAAGGCTTTACAGAT
* * ** *
28403443 AACACGCCACAAAGGCTTTTATGATAATTCACCACAAAGGCTTTACAGAT
1 AACACGCCATAAAGACTTTTATGATAATTTGCCATAAAGGCTTTACAGAT
* * * * *
28403493 AACTA-GTCATAAAGGA-TTTTATGATAGTATGTCATAAAGGCTTTATAGAT
1 AAC-ACGCCATAAA-GACTTTTATGATAATTTGCCATAAAGGCTTTACAGAT
28403543 AAC
1 AAC
28403546 TCGTCATAGA
Statistics
Matches: 85, Mismatches: 15, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
49 1 0.01
50 82 0.96
51 2 0.02
ACGTcount: A:0.39, C:0.18, G:0.15, T:0.29
Consensus pattern (50 bp):
AACACGCCATAAAGACTTTTATGATAATTTGCCATAAAGGCTTTACAGAT
Found at i:28403585 original size:25 final size:25
Alignment explanation
Indices: 28403398--28403586 Score: 127
Period size: 25 Copynumber: 7.6 Consensus size: 25
28403388 CATACAACAC
* * * *
28403398 GCCATAAAGACTTTTCAGATAATTT
1 GCCATAAAGGCTTTACAGATAACTA
28403423 GCCATAAAGGCTTTACAGATAAC-A
1 GCCATAAAGGCTTTACAGATAACTA
* * *
28403447 CGCCACAAAGGCTTTTA-TGATAATTCA
1 -GCCATAAAGGC-TTTACAGATAACT-A
*
28403474 -CCACAAAGGCTTTACAGATAACTA
1 GCCATAAAGGCTTTACAGATAACTA
* * * *
28403498 GTCATAAAGGATTTTA-TGAT-AGTA
1 GCCATAAAGG-CTTTACAGATAACTA
* * *
28403522 TGTCATAAAGGCTTTATAGATAACTC
1 -GCCATAAAGGCTTTACAGATAACTA
* *
28403548 GTCATAGAGGCTTTACAGATAACTA
1 GCCATAAAGGCTTTACAGATAACTA
* *
28403573 GCCACAAAAGCTTT
1 GCCATAAAGGCTTT
28403587 TTTTATAATT
Statistics
Matches: 129, Mismatches: 25, Indels: 20
0.74 0.14 0.11
Matches are distributed among these distances:
24 12 0.09
25 106 0.82
26 10 0.08
27 1 0.01
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.29
Consensus pattern (25 bp):
GCCATAAAGGCTTTACAGATAACTA
Found at i:28404177 original size:4 final size:4
Alignment explanation
Indices: 28404170--28404318 Score: 273
Period size: 4 Copynumber: 37.5 Consensus size: 4
28404160 CACACACAAC
*
28404170 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CTTA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
28404218 CATA CATA CATA CATA CATA CATA CATA CATA CA-A CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
28404265 CATA CATA CATA CATA CATA CATA CATA CATA TATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
28404313 CATA CA
1 CATA CA
28404319 ACCATATCTC
Statistics
Matches: 140, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
3 3 0.02
4 137 0.98
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.26
Consensus pattern (4 bp):
CATA
Found at i:28408480 original size:22 final size:22
Alignment explanation
Indices: 28408446--28408487 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
28408436 GGATAAAAAT
28408446 TTTTAAACAATTTAATAATTATC
1 TTTTAAACAATTTAA-AATTATC
*
28408469 TTTT-AACTATTTAAAATTA
1 TTTTAAACAATTTAAAATTA
28408488 AATTAATAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 9 0.50
23 4 0.22
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (22 bp):
TTTTAAACAATTTAAAATTATC
Found at i:28408696 original size:17 final size:17
Alignment explanation
Indices: 28408683--28408730 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 17
28408673 CATAAAATTA
*
28408683 TAAAAAAT-TAAAAACT
1 TAAAAAATATAAAAAAT
* * *
28408699 TGAAAATTATAGAAAAT
1 TAAAAAATATAAAAAAT
28408716 TAAAAAATATAAAAA
1 TAAAAAATATAAAAA
28408731 CACAAAATTA
Statistics
Matches: 24, Mismatches: 7, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
16 6 0.25
17 18 0.75
ACGTcount: A:0.69, C:0.02, G:0.04, T:0.25
Consensus pattern (17 bp):
TAAAAAATATAAAAAAT
Found at i:28408704 original size:25 final size:25
Alignment explanation
Indices: 28408657--28408729 Score: 94
Period size: 25 Copynumber: 2.8 Consensus size: 25
28408647 AAGTTTGAAA
28408657 AAAAATATTAAAAACTCATAAAATTAT
1 AAAAA-ATTAAAAACT-ATAAAATTAT
28408684 AAAAAATTAAAAACT-TGAAAATTAT
1 AAAAAATTAAAAACTAT-AAAATTAT
* *
28408709 AGAAAATTAAAAAATATAAAA
1 AAAAAATTAAAAACTATAAAA
28408730 ACACAAAATT
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
24 1 0.02
25 25 0.60
26 11 0.26
27 5 0.12
ACGTcount: A:0.67, C:0.04, G:0.03, T:0.26
Consensus pattern (25 bp):
AAAAAATTAAAAACTATAAAATTAT
Found at i:28408738 original size:33 final size:33
Alignment explanation
Indices: 28408683--28408747 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
28408673 CATAAAATTA
**
28408683 TAAAAAATTAAAAACTTGAAAATTATAGAAAAT
1 TAAAAAATTAAAAACTACAAAATTATAGAAAAT
*
28408716 TAAAAAATATAAAAAC-ACAAAATTATATAAAA
1 TAAAAAAT-TAAAAACTACAAAATTATAGAAAA
28408748 AAATTATAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 21 0.75
34 7 0.25
ACGTcount: A:0.68, C:0.05, G:0.03, T:0.25
Consensus pattern (33 bp):
TAAAAAATTAAAAACTACAAAATTATAGAAAAT
Found at i:28420264 original size:32 final size:32
Alignment explanation
Indices: 28420228--28420322 Score: 78
Period size: 32 Copynumber: 3.2 Consensus size: 32
28420218 ACATTTTGTA
28420228 AATACTTGCGAACTTAGTGAGTTTTAATACAG
1 AATACTTGCGAACTTAGTGAGTTTTAATACAG
** * ** *
28420260 AATACCTTAAG-TCTTTCT-AG-TTT-GT--A-
1 AATA-CTTGCGAACTTAGTGAGTTTTAATACAG
28420286 AATACTTGCGAACTTAGTGAGTTTTAATACAG
1 AATACTTGCGAACTTAGTGAGTTTTAATACAG
28420318 AATAC
1 AATAC
28420323 CTTAAGTCTT
Statistics
Matches: 43, Mismatches: 12, Indels: 16
0.61 0.17 0.23
Matches are distributed among these distances:
25 4 0.09
26 8 0.19
27 3 0.07
28 3 0.07
29 2 0.05
30 3 0.07
31 3 0.07
32 13 0.30
33 4 0.09
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.37
Consensus pattern (32 bp):
AATACTTGCGAACTTAGTGAGTTTTAATACAG
Found at i:28420312 original size:58 final size:58
Alignment explanation
Indices: 28420222--28420339 Score: 236
Period size: 58 Copynumber: 2.0 Consensus size: 58
28420212 GAACAAACAT
28420222 TTTGTAAATACTTGCGAACTTAGTGAGTTTTAATACAGAATACCTTAAGTCTTTCTAG
1 TTTGTAAATACTTGCGAACTTAGTGAGTTTTAATACAGAATACCTTAAGTCTTTCTAG
28420280 TTTGTAAATACTTGCGAACTTAGTGAGTTTTAATACAGAATACCTTAAGTCTTTCTAG
1 TTTGTAAATACTTGCGAACTTAGTGAGTTTTAATACAGAATACCTTAAGTCTTTCTAG
28420338 TT
1 TT
28420340 AAGTTCCTTA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 60 1.00
ACGTcount: A:0.31, C:0.14, G:0.15, T:0.41
Consensus pattern (58 bp):
TTTGTAAATACTTGCGAACTTAGTGAGTTTTAATACAGAATACCTTAAGTCTTTCTAG
Found at i:28421490 original size:23 final size:23
Alignment explanation
Indices: 28421459--28421512 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
28421449 AACATCACTG
* * *
28421459 AATACGCCACATAGGCATTACAA
1 AATATGCCACAGAGGCAATACAA
*
28421482 AATTTGCCACAGAGGCAATACAA
1 AATATGCCACAGAGGCAATACAA
28421505 AATATGCC
1 AATATGCC
28421513 TAAAAAACTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.43, C:0.24, G:0.15, T:0.19
Consensus pattern (23 bp):
AATATGCCACAGAGGCAATACAA
Found at i:28438122 original size:2 final size:2
Alignment explanation
Indices: 28438115--28438150 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
28438105 TGGTAAGAAG
28438115 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28438151 GAAGAATGAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28438878 original size:35 final size:35
Alignment explanation
Indices: 28438839--28438910 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
28438829 TGCCATGAGG
28438839 TGAGTGTAAGTATGTGAGTGTTTAAGGGTGACAAA
1 TGAGTGTAAGTATGTGAGTGTTTAAGGGTGACAAA
28438874 TGAGTGTAAGTATGTGAGTGTTTAAGGGTGACAAA
1 TGAGTGTAAGTATGTGAGTGTTTAAGGGTGACAAA
28438909 TG
1 TG
28438911 GCTCGGAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.31, C:0.03, G:0.35, T:0.32
Consensus pattern (35 bp):
TGAGTGTAAGTATGTGAGTGTTTAAGGGTGACAAA
Found at i:28444731 original size:42 final size:42
Alignment explanation
Indices: 28444679--28444773 Score: 120
Period size: 42 Copynumber: 2.3 Consensus size: 42
28444669 TGAGACTTCA
* * * * *
28444679 TGTAAGACCATGTCT-AGGACATGGCTTTGATATGATATTTCG
1 TGTAAGACCATGTCTGA-GACATGGCATCGATACGAGATTCCG
*
28444721 TGTAATACCATGTCTGAGACATGGCATCGATACGAGATTCCG
1 TGTAAGACCATGTCTGAGACATGGCATCGATACGAGATTCCG
28444763 TGTAAGACCAT
1 TGTAAGACCAT
28444774 AGTTGGGCTA
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
42 44 0.98
43 1 0.02
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.31
Consensus pattern (42 bp):
TGTAAGACCATGTCTGAGACATGGCATCGATACGAGATTCCG
Found at i:28447207 original size:37 final size:37
Alignment explanation
Indices: 28447166--28447236 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
28447156 CTATAGTGCA
28447166 AAGTATATGGTTATTTGATATGTGAACGAAAATGAAT
1 AAGTATATGGTTATTTGATATGTGAACGAAAATGAAT
*
28447203 AAGTATATGGTTATTTGATATGTGTACGAAAATG
1 AAGTATATGGTTATTTGATATGTGAACGAAAATG
28447237 TTCAAAAGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.38, C:0.03, G:0.23, T:0.37
Consensus pattern (37 bp):
AAGTATATGGTTATTTGATATGTGAACGAAAATGAAT
Found at i:28456618 original size:46 final size:45
Alignment explanation
Indices: 28456467--28456634 Score: 182
Period size: 46 Copynumber: 3.7 Consensus size: 45
28456457 TTTGTGTGCT
**
28456467 AGTGTAAGACATGTCTGGGACATG---CGGCCATATTATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCC-TAAGATGAGAGCC
* * * ** *
28456510 AGTGTAAGACCATGTCTGGGACATGGCATTGGCATTGAGACAAGAGCT
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGC-CTAAGATGAGAGCC
28456558 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCAAGATGTA-AGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCT-AAGATG-AGAGCC
28456604 AGTGTAAGACATGTCTGGGACATGCATCGGC
1 AGTGTAAGACATGTCTGGGACATGCATCGGC
28456635 TACAAAATGT
Statistics
Matches: 103, Mismatches: 14, Indels: 13
0.79 0.11 0.10
Matches are distributed among these distances:
43 9 0.09
44 14 0.14
45 2 0.02
46 44 0.43
47 15 0.15
48 19 0.18
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.23
Consensus pattern (45 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCTAAGATGAGAGCC
Found at i:28464254 original size:86 final size:86
Alignment explanation
Indices: 28464109--28464278 Score: 295
Period size: 86 Copynumber: 2.0 Consensus size: 86
28464099 CTCGACATGA
* *
28464109 AAATTTTCTCCACAAAGGTTATCCTAACTCTGAAAGATCTTTCCATATCATCTCCATTTTATAGG
1 AAATTTTCTCCACAAAGGTTATCCTAACTCCGAAAAATCTTTCCATATCATCTCCATTTTATAGG
*
28464174 AAACATCTACCACCAATATGC
66 AAACATCAACCACCAATATGC
* *
28464195 AAATTTTCTCCACAAAGGTTATCTTAACTCCGAAAAATCTTTTCATATCATCTCCATTTTATAGG
1 AAATTTTCTCCACAAAGGTTATCCTAACTCCGAAAAATCTTTCCATATCATCTCCATTTTATAGG
28464260 AAACATCAACCACCAATAT
66 AAACATCAACCACCAATAT
28464279 AAAACATGAT
Statistics
Matches: 79, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
86 79 1.00
ACGTcount: A:0.35, C:0.25, G:0.07, T:0.33
Consensus pattern (86 bp):
AAATTTTCTCCACAAAGGTTATCCTAACTCCGAAAAATCTTTCCATATCATCTCCATTTTATAGG
AAACATCAACCACCAATATGC
Found at i:28471971 original size:11 final size:11
Alignment explanation
Indices: 28471952--28472004 Score: 65
Period size: 11 Copynumber: 5.0 Consensus size: 11
28471942 GTATTTCATA
28471952 GCATATCATGT
1 GCATATCATGT
* *
28471963 GCATCTCAT-A
1 GCATATCATGT
*
28471973 ACATATCATGT
1 GCATATCATGT
28471984 GCATATCATGT
1 GCATATCATGT
28471995 -CATATCATGT
1 GCATATCATGT
28472005 ATAACAATAT
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
10 17 0.49
11 18 0.51
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.36
Consensus pattern (11 bp):
GCATATCATGT
Found at i:28471971 original size:21 final size:21
Alignment explanation
Indices: 28471947--28472004 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
28471937 AATGAGTATT
*
28471947 TCATAGCATATCATGTGCATC
1 TCATAGCATATCATGTGCATA
*
28471968 TCATAACATATCATGTGCATA
1 TCATAGCATATCATGTGCATA
28471989 TCAT-GTCATATCATGT
1 TCATAG-CATATCATGT
28472005 ATAACAATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.36
Consensus pattern (21 bp):
TCATAGCATATCATGTGCATA
Found at i:28480683 original size:104 final size:104
Alignment explanation
Indices: 28480503--28480713 Score: 386
Period size: 104 Copynumber: 2.0 Consensus size: 104
28480493 TTCTGATCTT
*
28480503 TTAAAATTTTATTTATTCATATAATAATAAAATGAATAGGTATAAATAAAACATATGTTAAACAT
1 TTAAAATTTTATTTATTCATATAATAATAAAATGAATAGGTATAAATAAAACATATATTAAACAT
*
28480568 AACAAATAATAAATTCATGCTACTAATATATCATTATGG
66 AACAAATAATAAATTCATGCTACTAATAAATCATTATGG
*
28480607 TTAAAATTTTATTTATTCATATAATAATAAAATGAATAGGTATAAATAAAACATATATTAAATAT
1 TTAAAATTTTATTTATTCATATAATAATAAAATGAATAGGTATAAATAAAACATATATTAAACAT
*
28480672 AACAAATAATAAATTCATGTTACTAATAAATCATTATGG
66 AACAAATAATAAATTCATGCTACTAATAAATCATTATGG
28480711 TTA
1 TTA
28480714 GATAACATTT
Statistics
Matches: 103, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
104 103 1.00
ACGTcount: A:0.50, C:0.07, G:0.06, T:0.37
Consensus pattern (104 bp):
TTAAAATTTTATTTATTCATATAATAATAAAATGAATAGGTATAAATAAAACATATATTAAACAT
AACAAATAATAAATTCATGCTACTAATAAATCATTATGG
Found at i:28483044 original size:37 final size:35
Alignment explanation
Indices: 28483003--28483157 Score: 114
Period size: 37 Copynumber: 4.2 Consensus size: 35
28482993 TTCTACTCAT
* *
28483003 TTGAGCTTCACTCAGTATAATAGTAGAATTTTCTTGA
1 TTGAGCTTCATTCAGTATAA-AGTA-AATTTGCTTGA
* *
28483040 TTGAGCATCATTCAATATAACAGTAAGATTTGCTT-A
1 TTGAGCTTCATTCAGTATAA-AGTAA-ATTTGCTTGA
* * * *
28483076 GTTAAGCTCCATTCAGTATAACGATATAATTTGCTCGA
1 -TTGAGCTTCATTCAGTATAAAG-TA-AATTTGCTTGA
* * *
28483114 TTGAGCTTCATTTAGTATAACGGTAAAATTTGGCTCGA
1 TTGAGCTTCATTCAGTATAA-AGT-AAATTT-GCTTGA
28483152 TTGAGC
1 TTGAGC
28483158 GTACTTCTAG
Statistics
Matches: 95, Mismatches: 15, Indels: 15
0.76 0.12 0.12
Matches are distributed among these distances:
36 3 0.03
37 76 0.80
38 16 0.17
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.37
Consensus pattern (35 bp):
TTGAGCTTCATTCAGTATAAAGTAAATTTGCTTGA
Found at i:28483999 original size:21 final size:22
Alignment explanation
Indices: 28483961--28484001 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
28483951 AACTTTCTTA
*
28483961 ATTAAGCCTTACTTAATCTAAG
1 ATTAAGCCTTAATTAATCTAAG
28483983 ATTAAGCC-TAATTAATCTA
1 ATTAAGCCTTAATTAATCTA
28484002 TTTCCACTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.39, C:0.17, G:0.07, T:0.37
Consensus pattern (22 bp):
ATTAAGCCTTAATTAATCTAAG
Found at i:28487374 original size:6 final size:6
Alignment explanation
Indices: 28487365--28487394 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
28487355 TTTAAACCAC
*
28487365 TAATTT TAATTT TAATTT TAATTT TTATTT
1 TAATTT TAATTT TAATTT TAATTT TAATTT
28487395 CTTAGAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (6 bp):
TAATTT
Found at i:28491328 original size:47 final size:47
Alignment explanation
Indices: 28491251--28491381 Score: 163
Period size: 47 Copynumber: 2.8 Consensus size: 47
28491241 CACAATCGAT
* * * *
28491251 AAGTACCTATACCATGGCCCATAGCTAAATCAAGGTAACTTATCCCG
1 AAGTACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTCATCCCA
* * * **
28491298 GAGTACCTATACCATGGCCCGTAGCCAAATCAAGGTATCTCCTCTTA
1 AAGTACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTCATCCCA
* *
28491345 AAATACCTATATCATGGCCCGTAGCCAAATCAAGGTA
1 AAGTACCTATACCATGGCCCGTAGCCAAATCAAGGTA
28491382 TTATTCACAC
Statistics
Matches: 72, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
47 72 1.00
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.24
Consensus pattern (47 bp):
AAGTACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTCATCCCA
Found at i:28494438 original size:26 final size:29
Alignment explanation
Indices: 28494404--28494456 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 29
28494394 GTCTCAAATG
28494404 CAGATCTTTCTATG-TCA-T-TAGATATTT
1 CAGATCTTT-TATGATCAGTATAGATATTT
28494431 CAGA-CTTTTATGATCAGTATAGATAT
1 CAGATCTTTTATGATCAGTATAGATAT
28494457 GACATTTCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
25 4 0.17
26 7 0.30
27 5 0.22
28 7 0.30
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.43
Consensus pattern (29 bp):
CAGATCTTTTATGATCAGTATAGATATTT
Found at i:28503807 original size:79 final size:81
Alignment explanation
Indices: 28503706--28503890 Score: 227
Period size: 79 Copynumber: 2.3 Consensus size: 81
28503696 ACGACTCGCT
** * *
28503706 CAAATGCCTTCGGGACGAAGCCCGG-TTATAGTGACTCGCACGAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCACGAATGCCTTC-GGATCCTAACCC
* *
28503769 GGGTTTAGTAACTT-GCA
64 GGATATAGTAACTTAGCA
* **
28503786 CAAATGCCTTCGGG-CTTAGCCCGGATTTATTAACTCGCACGAATGCCTTCGGATCCTAGTCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACGAATGCCTTCGGATCCTAACCCGG
*
28503850 ATATAGTCACTTAGCA
66 ATATAGTAACTTAGCA
28503866 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
28503891 CATCATTCGA
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 3 0.03
79 54 0.59
80 34 0.37
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.24
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACGAATGCCTTCGGATCCTAACCCGG
ATATAGTAACTTAGCA
Found at i:28503890 original size:40 final size:39
Alignment explanation
Indices: 28503699--28503890 Score: 163
Period size: 40 Copynumber: 4.8 Consensus size: 39
28503689 GGATATAACG
* ** * *
28503699 ACTCGCTCAAATGCCTTCGGGACGAAGCCCGGTTATAGTG
1 ACTCGCACAAA-GCCTTCGGGACTTAGCCCGGATATAGTA
* * * *
28503739 ACTCGCACGAATGCCTTCGGGACTTAACCCGGGTTTAGTA
1 ACTCGCAC-AAAGCCTTCGGGACTTAGCCCGGATATAGTA
* * *
28503779 ACTTGCACAAATGCCTTCGGG-CTTAGCCCGGATTTATTA
1 ACTCGCACAAA-GCCTTCGGGACTTAGCCCGGATATAGTA
* * * *
28503818 ACTCGCACGAATGCCTTC-GGATCCTAGTCCGGATATAGTC
1 ACTCGCAC-AAAGCCTTCGGGA-CTTAGCCCGGATATAGTA
*
28503858 ACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
1 AC-TCGCACAAAGCCTTCGGGACTTAGCCCGGA
28503891 CATCATTCGA
Statistics
Matches: 121, Mismatches: 24, Indels: 14
0.76 0.15 0.09
Matches are distributed among these distances:
38 2 0.02
39 30 0.25
40 79 0.65
41 10 0.08
ACGTcount: A:0.23, C:0.28, G:0.24, T:0.24
Consensus pattern (39 bp):
ACTCGCACAAAGCCTTCGGGACTTAGCCCGGATATAGTA
Found at i:28505987 original size:40 final size:40
Alignment explanation
Indices: 28505938--28506085 Score: 212
Period size: 40 Copynumber: 3.7 Consensus size: 40
28505928 ATCACGATTT
*
28505938 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGACTC
1 GCACGAATGCCTTCGGGTCTTAGCCCGGATAGAATGACTC
28505978 GCACGAATGCCTTCGGGTCTTAGCCCGGATAGAATGACTC
1 GCACGAATGCCTTCGGGTCTTAGCCCGGATAGAATGACTC
* *
28506018 GCACGAATGCCTTCGGGTCTTAGCCCGGAT-GTA-GCCACTA
1 GCACGAATGCCTTCGGGTCTTAGCCCGGATAGAATG--ACTC
*
28506058 GCAC-AATTGCCTTCGGGTCTTAACCCGG
1 GCACGAA-TGCCTTCGGGTCTTAGCCCGG
28506086 TTATAATTTC
Statistics
Matches: 101, Mismatches: 4, Indels: 6
0.91 0.04 0.05
Matches are distributed among these distances:
38 1 0.01
39 4 0.04
40 96 0.95
ACGTcount: A:0.22, C:0.29, G:0.26, T:0.23
Consensus pattern (40 bp):
GCACGAATGCCTTCGGGTCTTAGCCCGGATAGAATGACTC
Found at i:28506069 original size:80 final size:80
Alignment explanation
Indices: 28505906--28506085 Score: 213
Period size: 80 Copynumber: 2.2 Consensus size: 80
28505896 CCGCACCAAG
* * ** * * *
28505906 GCCTACGGGACTTAACCCGGATATCACGATTTGCACAAATGCCTTCGGGTCTTAGCCCGGATAGA
1 GCCTTCGGGTCTTAACCCGGATAGAATGACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATAGA
*
28505971 ATGACTCGCACGAAT
66 ATGACTAGCACGAAT
* * *
28505986 GCCTTCGGGTCTTAGCCCGGATAGAATGACTCGCACGAATGCCTTCGGGTCTTAGCCCGGAT-GT
1 GCCTTCGGGTCTTAACCCGGATAGAATGACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATAGA
28506050 A-GCCACTAGCAC-AATT
66 ATG--ACTAGCACGAA-T
28506066 GCCTTCGGGTCTTAACCCGG
1 GCCTTCGGGTCTTAACCCGG
28506086 TTATAATTTC
Statistics
Matches: 85, Mismatches: 12, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
78 1 0.01
79 4 0.05
80 80 0.94
ACGTcount: A:0.22, C:0.29, G:0.26, T:0.23
Consensus pattern (80 bp):
GCCTTCGGGTCTTAACCCGGATAGAATGACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATAGA
ATGACTAGCACGAAT
Found at i:28514090 original size:40 final size:40
Alignment explanation
Indices: 28514041--28514188 Score: 212
Period size: 40 Copynumber: 3.7 Consensus size: 40
28514031 ATCACGATTT
*
28514041 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGACTC
1 GCACGAATGCCTTCGGGTCTTAGCCCGGATAGAATGACTC
28514081 GCACGAATGCCTTCGGGTCTTAGCCCGGATAGAATGACTC
1 GCACGAATGCCTTCGGGTCTTAGCCCGGATAGAATGACTC
* *
28514121 GCACGAATGCCTTCGGGTCTTAGCCCGGAT-GTA-GCCACTA
1 GCACGAATGCCTTCGGGTCTTAGCCCGGATAGAATG--ACTC
*
28514161 GCAC-AATTGCCTTCGGGTCTTAACCCGG
1 GCACGAA-TGCCTTCGGGTCTTAGCCCGG
28514189 TTATAATTTC
Statistics
Matches: 101, Mismatches: 4, Indels: 6
0.91 0.04 0.05
Matches are distributed among these distances:
38 1 0.01
39 4 0.04
40 96 0.95
ACGTcount: A:0.22, C:0.29, G:0.26, T:0.23
Consensus pattern (40 bp):
GCACGAATGCCTTCGGGTCTTAGCCCGGATAGAATGACTC
Found at i:28514172 original size:80 final size:80
Alignment explanation
Indices: 28514009--28514188 Score: 213
Period size: 80 Copynumber: 2.2 Consensus size: 80
28513999 CCGCACCAAG
* * ** * * *
28514009 GCCTACGGGACTTAACCCGGATATCACGATTTGCACAAATGCCTTCGGGTCTTAGCCCGGATAGA
1 GCCTTCGGGTCTTAACCCGGATAGAATGACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATAGA
*
28514074 ATGACTCGCACGAAT
66 ATGACTAGCACGAAT
* * *
28514089 GCCTTCGGGTCTTAGCCCGGATAGAATGACTCGCACGAATGCCTTCGGGTCTTAGCCCGGAT-GT
1 GCCTTCGGGTCTTAACCCGGATAGAATGACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATAGA
28514153 A-GCCACTAGCAC-AATT
66 ATG--ACTAGCACGAA-T
28514169 GCCTTCGGGTCTTAACCCGG
1 GCCTTCGGGTCTTAACCCGG
28514189 TTATAATTTC
Statistics
Matches: 85, Mismatches: 12, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
78 1 0.01
79 4 0.05
80 80 0.94
ACGTcount: A:0.22, C:0.29, G:0.26, T:0.23
Consensus pattern (80 bp):
GCCTTCGGGTCTTAACCCGGATAGAATGACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATAGA
ATGACTAGCACGAAT
Found at i:28527507 original size:46 final size:47
Alignment explanation
Indices: 28527456--28527719 Score: 224
Period size: 47 Copynumber: 5.6 Consensus size: 47
28527446 TGTGTGTGCT
*
28527456 AGTGTAAGA-CATGTCTGGGACAT-GCATTGGCATTGAGATGAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGC-TTGAGATGAGAGCC
* * * *
28527502 AGTGTAAGA-CATGTCTGGGACAT-GCATTGGCTATGACAT--GTGTC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCT-TGAGATGAGAGCC
* * * ** * *
28527546 AGTATAAGACCACGTCTAGGACATGGCATCGGCACGGATATGTGAGAGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGC-TTGAGA--TGAGAGCC
*
28527596 AGTGTAAGACCATGTCTGGGACATGGCATCGACTT--GATGGATGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCTTGAGAT-GA-GAGCC
* * *
28527643 AGTGTTAGACCATGTTTGGGACATGGCATCGACTT--GATGGATGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCTTGAGAT-GA-GAGCC
*
28527690 AGTGTTAGACCATGTCTGGGACATGGCATC
1 AGTGTAAGACCATGTCTGGGACATGGCATC
28527720 AACATTATAC
Statistics
Matches: 184, Mismatches: 24, Indels: 19
0.81 0.11 0.08
Matches are distributed among these distances:
44 11 0.06
45 14 0.08
46 48 0.26
47 79 0.43
48 1 0.01
50 31 0.17
ACGTcount: A:0.26, C:0.18, G:0.31, T:0.25
Consensus pattern (47 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGCTTGAGATGAGAGCC
Found at i:28527657 original size:47 final size:47
Alignment explanation
Indices: 28527591--28527719 Score: 231
Period size: 47 Copynumber: 2.7 Consensus size: 47
28527581 GGATATGTGA
* *
28527591 GAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGACTTGATGGAT
1 GAGCCAGTGTTAGACCATGTCTGGGACATGGCATCGACTTGATGGAT
*
28527638 GAGCCAGTGTTAGACCATGTTTGGGACATGGCATCGACTTGATGGAT
1 GAGCCAGTGTTAGACCATGTCTGGGACATGGCATCGACTTGATGGAT
28527685 GAGCCAGTGTTAGACCATGTCTGGGACATGGCATC
1 GAGCCAGTGTTAGACCATGTCTGGGACATGGCATC
28527720 AACATTATAC
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 78 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.26
Consensus pattern (47 bp):
GAGCCAGTGTTAGACCATGTCTGGGACATGGCATCGACTTGATGGAT
Found at i:28530972 original size:31 final size:31
Alignment explanation
Indices: 28530937--28530995 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
28530927 CACAAAGACA
28530937 TATCATAGAA-AGCTCGCATAGGGAGCTTACT
1 TATCATA-AAGAGCTCGCATAGGGAGCTTACT
* *
28530968 TATCATAAAGAGTTCGCATAGGTAGCTT
1 TATCATAAAGAGCTCGCATAGGGAGCTT
28530996 TGCTTGAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 2 0.08
31 23 0.92
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.29
Consensus pattern (31 bp):
TATCATAAAGAGCTCGCATAGGGAGCTTACT
Found at i:28533831 original size:15 final size:16
Alignment explanation
Indices: 28533811--28533853 Score: 63
Period size: 15 Copynumber: 2.8 Consensus size: 16
28533801 TTTATTTTTT
28533811 ATTTAAAATATATA-A
1 ATTTAAAATATATATA
*
28533826 ATTTAAAATATATATT
1 ATTTAAAATATATATA
28533842 ATTTAAAA-ATAT
1 ATTTAAAATATAT
28533854 TTAAAATGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
15 18 0.69
16 8 0.31
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
ATTTAAAATATATATA
Found at i:28533840 original size:17 final size:16
Alignment explanation
Indices: 28533811--28533858 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 16
28533801 TTTATTTTTT
28533811 ATTT-AAAATATATAA
1 ATTTAAAAATATATAA
*
28533826 ATTT-AAAATATATATT
1 ATTTAAAAATATATA-A
*
28533842 ATTTAAAAATATTTAA
1 ATTTAAAAATATATAA
28533858 A
1 A
28533859 ATGAAGTCAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 14 0.50
16 5 0.18
17 9 0.32
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
ATTTAAAAATATATAA
Found at i:28535208 original size:22 final size:22
Alignment explanation
Indices: 28535169--28535227 Score: 70
Period size: 21 Copynumber: 2.8 Consensus size: 22
28535159 GTTTTAAGAA
*
28535169 TTGTTTTAGTA-TTATTTTTAT
1 TTGTTTTAATATTTATTTTTAT
28535190 TTGTTTTAATATTTATTTTTAT
1 TTGTTTTAATATTTATTTTTAT
* *
28535212 GT-TTTTAA-ATATATTT
1 TTGTTTTAATATTTATTT
28535228 GATTTATTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 7 0.21
21 16 0.47
22 11 0.32
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (22 bp):
TTGTTTTAATATTTATTTTTAT
Found at i:28535244 original size:26 final size:24
Alignment explanation
Indices: 28535198--28535257 Score: 75
Period size: 26 Copynumber: 2.4 Consensus size: 24
28535188 ATTTGTTTTA
*
28535198 ATATTTATTTTTATGTTTTTAAAT
1 ATATTTATTTTTATATTTTTAAAT
28535222 ATATTTGATTTATTATATTTTTAAAT
1 ATATTT-ATTT-TTATATTTTTAAAT
* *
28535248 TTTTTTATTT
1 ATATTTATTT
28535258 AATAAAATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 6 0.19
25 8 0.26
26 17 0.55
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.68
Consensus pattern (24 bp):
ATATTTATTTTTATATTTTTAAAT
Found at i:28541955 original size:3 final size:3
Alignment explanation
Indices: 28541947--28541986 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
28541937 ACAAAATCCT
28541947 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
28541987 TTCACCATTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.35
Consensus pattern (3 bp):
TCA
Found at i:28543845 original size:20 final size:20
Alignment explanation
Indices: 28543820--28543859 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
28543810 CCAGCAATAG
28543820 ATAGTCCTTAGTGGACTATC
1 ATAGTCCTTAGTGGACTATC
28543840 ATAGTCCTTAGTGGACTATC
1 ATAGTCCTTAGTGGACTATC
28543860 TTCTCATTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.35
Consensus pattern (20 bp):
ATAGTCCTTAGTGGACTATC
Found at i:28545001 original size:26 final size:26
Alignment explanation
Indices: 28544947--28545003 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
28544937 TCTCAACCCT
*
28544947 ATTTTACCTCTAGCAAAATTTTGATG
1 ATTTTACCTCTAGCAAAATTTTGACG
* *
28544973 ATTTTACC-CTTAGTAAAATTTTGGCG
1 ATTTTACCTC-TAGCAAAATTTTGACG
28544999 ATTTT
1 ATTTT
28545004 GCCACTGTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 1 0.04
26 26 0.96
ACGTcount: A:0.28, C:0.14, G:0.12, T:0.46
Consensus pattern (26 bp):
ATTTTACCTCTAGCAAAATTTTGACG
Found at i:28548072 original size:29 final size:29
Alignment explanation
Indices: 28548039--28548098 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
28548029 AGCACTTCGG
28548039 TGCATATTGGATGATGTGGCTTCGGGCCA
1 TGCATATTGGATGATGTGGCTTCGGGCCA
28548068 TGCATATTGGATGATGTGGCTTCGGGCCA
1 TGCATATTGGATGATGTGGCTTCGGGCCA
28548097 TG
1 TG
28548099 ATAATAGTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.17, C:0.17, G:0.35, T:0.32
Consensus pattern (29 bp):
TGCATATTGGATGATGTGGCTTCGGGCCA
Found at i:28561702 original size:46 final size:46
Alignment explanation
Indices: 28561634--28561724 Score: 146
Period size: 46 Copynumber: 2.0 Consensus size: 46
28561624 TATATATACA
* *
28561634 CATCTCATACATATCTCACATTAGCCATTTGGCTTTACCACATATC
1 CATCTCATACACATCTCACATTAGCCATTCGGCTTTACCACATATC
* *
28561680 CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCACATAT
1 CATCTCATACACATCTCACATTAGCCATTCGGCTTTACCACATAT
28561725 ATATACACTT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.27, C:0.31, G:0.08, T:0.34
Consensus pattern (46 bp):
CATCTCATACACATCTCACATTAGCCATTCGGCTTTACCACATATC
Found at i:28561771 original size:22 final size:22
Alignment explanation
Indices: 28561743--28561864 Score: 67
Period size: 22 Copynumber: 5.3 Consensus size: 22
28561733 TTCCACGTTC
28561743 ATCACATTGGCCATTCTGCCTT
1 ATCACATTGGCCATTCTGCCTT
*
28561765 ATCACATATATG-CATGT-T-CACATTT
1 ATCACAT-T-GGCCAT-TCTGC-C--TT
*
28561790 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCTGCCTT
28561812 ATCACATATGTG-CATGT-T-CACATTT
1 ATCACAT-TG-GCCAT-TCTGC-C--TT
*
28561837 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCTGCCTT
28561859 ATCACA
1 ATCACA
28561865 CATATGTGCA
Statistics
Matches: 77, Mismatches: 5, Indels: 36
0.65 0.04 0.31
Matches are distributed among these distances:
22 26 0.34
23 16 0.21
24 15 0.19
25 20 0.26
ACGTcount: A:0.25, C:0.27, G:0.13, T:0.35
Consensus pattern (22 bp):
ATCACATTGGCCATTCTGCCTT
Found at i:28561775 original size:49 final size:48
Alignment explanation
Indices: 28561698--28561940 Score: 323
Period size: 47 Copynumber: 5.1 Consensus size: 48
28561688 ACACATTTCG
* * * * * *
28561698 CATTAGCCATTCGGCTTTACCACATATATATACACT-TCCACGTTCATCA
1 CATTGGCCATTCGGCCTTATCACA-ATATATGCA-TGTTCACATTCATCA
* *
28561747 CATTGGCCATTCTGCCTTATCAC-ATATATGCATGTTCACATTTATCA
1 CATTGGCCATTCGGCCTTATCACAATATATGCATGTTCACATTCATCA
* *
28561794 CATTGGCCATTCGGCCTTATCAC-ATATGTGCATGTTCACATTTATCA
1 CATTGGCCATTCGGCCTTATCACAATATATGCATGTTCACATTCATCA
*
28561841 CATTGGCCATTCGGCCTTATCACACATATGTGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACA-ATATATGCATGTTCACATTCATCA
*
28561890 CATTGGCCATTCGGCCTTATCAC-ACATATGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACAATATATGCATGTTCACATTCATCA
28561937 CATT
1 CATT
28561941 TGCCTTGGCT
Statistics
Matches: 178, Mismatches: 13, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
46 1 0.01
47 112 0.63
49 65 0.37
ACGTcount: A:0.26, C:0.28, G:0.12, T:0.35
Consensus pattern (48 bp):
CATTGGCCATTCGGCCTTATCACAATATATGCATGTTCACATTCATCA
Found at i:28561796 original size:47 final size:47
Alignment explanation
Indices: 28561740--28561940 Score: 330
Period size: 47 Copynumber: 4.2 Consensus size: 47
28561730 CACTTCCACG
*
28561740 TTCATCACATTGGCCATTCTGCCTTATCACATATATGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACA
* *
28561787 TTTATCACATTGGCCATTCGGCCTTATCACATATGTGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACA
* *
28561834 TTTATCACATTGGCCATTCGGCCTTATCACACATATGTGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTAT--CACATATATGCATGTTCACA
*
28561883 TTCATCACATTGGCCATTCGGCCTTATCACACATATGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACA
28561930 TTCATCACATT
1 TTCATCACATT
28561941 TGCCTTGGCT
Statistics
Matches: 146, Mismatches: 6, Indels: 4
0.94 0.04 0.03
Matches are distributed among these distances:
47 100 0.68
49 46 0.32
ACGTcount: A:0.25, C:0.27, G:0.12, T:0.35
Consensus pattern (47 bp):
TTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACA
Found at i:28561818 original size:96 final size:96
Alignment explanation
Indices: 28561698--28561940 Score: 305
Period size: 96 Copynumber: 2.5 Consensus size: 96
28561688 ACACATTTCG
* * * * *
28561698 CATTAGCCATTCGGCTTTACCACATATATATACACT-TCCACGTTCATCACATTGGCCATTCTGC
1 CATTGGCCATTCGGCCTTATCACA-ATATATACA-TGTCCACATTCATCACATTGGCCATTCGGC
*
28561762 CTTAT-CACATATATGCATGTTCACATTTATCA
64 CTTATACACATATATGCATGTTCACATTCATCA
* * * *
28561794 CATTGGCCATTCGGCCTTATCAC-ATATGTGCATGTTCACATTTATCACATTGGCCATTCGGCCT
1 CATTGGCCATTCGGCCTTATCACAATATATACATGTCCACATTCATCACATTGGCCATTCGGCCT
*
28561858 TATCACACATATGTGCATGTTCACATTCATCA
66 TAT-ACACATATATGCATGTTCACATTCATCA
* * *
28561890 CATTGGCCATTCGGCCTTATCAC-ACATATGCATGTTCACATTCATCACATT
1 CATTGGCCATTCGGCCTTATCACAATATATACATGTCCACATTCATCACATT
28561941 TGCCTTGGCT
Statistics
Matches: 130, Mismatches: 14, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
93 1 0.01
94 36 0.28
96 93 0.72
ACGTcount: A:0.26, C:0.28, G:0.12, T:0.35
Consensus pattern (96 bp):
CATTGGCCATTCGGCCTTATCACAATATATACATGTCCACATTCATCACATTGGCCATTCGGCCT
TATACACATATATGCATGTTCACATTCATCA
Found at i:28564814 original size:28 final size:28
Alignment explanation
Indices: 28564783--28564840 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 28
28564773 TATTTTGTGA
*
28564783 TTAGAGTTTTGAGTTTAGGGTTTATGGT
1 TTAGAGTTTGGAGTTTAGGGTTTATGGT
* * *
28564811 TTAGAGTTTGGTGTTTGGGGTTTATTGT
1 TTAGAGTTTGGAGTTTAGGGTTTATGGT
28564839 TT
1 TT
28564841 TATAGTTAGG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.14, C:0.00, G:0.33, T:0.53
Consensus pattern (28 bp):
TTAGAGTTTGGAGTTTAGGGTTTATGGT
Found at i:28565028 original size:21 final size:21
Alignment explanation
Indices: 28564999--28565050 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
28564989 GTAATATATA
*
28564999 TTTAGGGTTTAGGATGTA-AG
1 TTTATGGTTTAGGATGTAGAG
* *
28565019 TTTTATGGTTTATGATTTAGAG
1 -TTTATGGTTTAGGATGTAGAG
28565041 TTTATGGTTT
1 TTTATGGTTT
28565051 GAGTTTTTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 25 0.93
22 2 0.07
ACGTcount: A:0.21, C:0.00, G:0.27, T:0.52
Consensus pattern (21 bp):
TTTATGGTTTAGGATGTAGAG
Found at i:28565326 original size:35 final size:34
Alignment explanation
Indices: 28565280--28565355 Score: 134
Period size: 35 Copynumber: 2.2 Consensus size: 34
28565270 TGATATAACA
28565280 TAATTTTATATTTATATATTGCATACATAAATATT
1 TAATTTTATATTTATATATTGCATA-ATAAATATT
28565315 TAATTTTATATTTATATATTGCATAATAAATATT
1 TAATTTTATATTTATATATTGCATAATAAATATT
28565349 TATATTT
1 TA-ATTT
28565356 ATTCAATATA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
34 11 0.28
35 29 0.73
ACGTcount: A:0.39, C:0.04, G:0.03, T:0.54
Consensus pattern (34 bp):
TAATTTTATATTTATATATTGCATAATAAATATT
Found at i:28565450 original size:31 final size:31
Alignment explanation
Indices: 28565406--28565466 Score: 72
Period size: 31 Copynumber: 2.0 Consensus size: 31
28565396 ATGTGTATGA
*
28565406 TTAAATCAAAATTA-AAGTTTCAAC-TATACAT
1 TTAAACCAAAATTAGAA-TTTC-ACGTATACAT
*
28565437 TTAAACCATAATTAGAATTTCACGTATACA
1 TTAAACCAAAATTAGAATTTCACGTATACA
28565467 ATTACACATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
30 2 0.08
31 22 0.85
32 2 0.08
ACGTcount: A:0.46, C:0.15, G:0.05, T:0.34
Consensus pattern (31 bp):
TTAAACCAAAATTAGAATTTCACGTATACAT
Found at i:28565634 original size:7 final size:7
Alignment explanation
Indices: 28565621--28565677 Score: 69
Period size: 8 Copynumber: 7.6 Consensus size: 7
28565611 AAATCTTCAA
28565621 AAAAATT
1 AAAAATT
*
28565628 GAAAATTT
1 -AAAAATT
28565636 AAAAATT
1 AAAAATT
28565643 AAAAAATT
1 -AAAAATT
28565651 AAAAATT
1 AAAAATT
28565658 AAAAACTT
1 AAAAA-TT
28565666 AAAAACTT
1 AAAAA-TT
28565674 AAAA
1 AAAA
28565678 TTTTAATATT
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
7 18 0.40
8 27 0.60
ACGTcount: A:0.68, C:0.04, G:0.02, T:0.26
Consensus pattern (7 bp):
AAAAATT
Found at i:28565640 original size:8 final size:8
Alignment explanation
Indices: 28565595--28565683 Score: 65
Period size: 8 Copynumber: 10.9 Consensus size: 8
28565585 TTTATATGTT
28565595 AATTTAAA
1 AATTTAAA
*
28565603 AATGATAAA
1 AAT-TTAAA
28565612 AATCTTCAAAA
1 AAT-TT--AAA
* *
28565623 AAATTGAA
1 AATTTAAA
28565631 AATTTAAA
1 AATTTAAA
28565639 AA-TTAAA
1 AATTTAAA
*
28565646 AAATTAAA
1 AATTTAAA
28565654 AA-TTAAA
1 AATTTAAA
*
28565661 AACTTAAA
1 AATTTAAA
*
28565669 AACTTAAA
1 AATTTAAA
*
28565677 ATTTTAA
1 AATTTAA
28565684 TATTTAGTAT
Statistics
Matches: 67, Mismatches: 9, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
7 14 0.21
8 38 0.57
9 8 0.12
10 2 0.03
11 5 0.07
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.30
Consensus pattern (8 bp):
AATTTAAA
Found at i:28565641 original size:15 final size:15
Alignment explanation
Indices: 28565621--28565683 Score: 81
Period size: 15 Copynumber: 4.1 Consensus size: 15
28565611 AAATCTTCAA
*
28565621 AAAAATTGAAAATTT
1 AAAAATTAAAAATTT
*
28565636 AAAAATTAAAAAATT
1 AAAAATTAAAAATTT
*
28565651 AAAAATTAAAAACTT
1 AAAAATTAAAAATTT
*
28565666 AAAAACTTAAAATTTT
1 AAAAA-TTAAAAATTT
28565682 AA
1 AA
28565684 TATTTAGTAT
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
15 32 0.76
16 10 0.24
ACGTcount: A:0.65, C:0.03, G:0.02, T:0.30
Consensus pattern (15 bp):
AAAAATTAAAAATTT
Found at i:28565647 original size:23 final size:23
Alignment explanation
Indices: 28565620--28565680 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
28565610 AAAATCTTCA
28565620 AAAAAATTGAAAATTTAAAAA-TT
1 AAAAAATT-AAAATTTAAAAACTT
*
28565643 AAAAAATTAAAAATTAAAAACTT
1 AAAAAATTAAAATTTAAAAACTT
*
28565666 AAAAACTTAAAATTT
1 AAAAAATTAAAATTT
28565681 TAATATTTAG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
22 11 0.32
23 23 0.68
ACGTcount: A:0.66, C:0.03, G:0.02, T:0.30
Consensus pattern (23 bp):
AAAAAATTAAAATTTAAAAACTT
Found at i:28565758 original size:23 final size:24
Alignment explanation
Indices: 28565718--28565763 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
28565708 CATATTTCAA
* * *
28565718 TTAAAAAGATCAATATT-CAAAAT
1 TTAAAAAAATAAAAATTCCAAAAT
28565741 TTAAAAAAATAAAAATTCCAAAA
1 TTAAAAAAATAAAAATTCCAAAA
28565764 AATGATGATC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.63, C:0.09, G:0.02, T:0.26
Consensus pattern (24 bp):
TTAAAAAAATAAAAATTCCAAAAT
Found at i:28568938 original size:30 final size:30
Alignment explanation
Indices: 28568902--28568996 Score: 136
Period size: 30 Copynumber: 3.1 Consensus size: 30
28568892 ATTGTTATTC
28568902 TTTTTTTAATGAATTTAATCTAATGAATTG
1 TTTTTTTAATGAATTTAATCTAATGAATTG
* *
28568932 TTTTTTTAATGAATTTAATCTAACGGATTATTA
1 TTTTTTTAATGAATTTAATCTAA-TGA--ATTG
*
28568965 TTTTTTTAATGAATTTAATCTAATGGATTG
1 TTTTTTTAATGAATTTAATCTAATGAATTG
28568995 TT
1 TT
28568997 ATTCTTTCTT
Statistics
Matches: 57, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
30 28 0.49
31 2 0.04
32 1 0.02
33 26 0.46
ACGTcount: A:0.32, C:0.04, G:0.11, T:0.54
Consensus pattern (30 bp):
TTTTTTTAATGAATTTAATCTAATGAATTG
Found at i:28568974 original size:33 final size:32
Alignment explanation
Indices: 28568896--28568999 Score: 140
Period size: 33 Copynumber: 3.2 Consensus size: 32
28568886 TTATGGATTG
* *
28568896 TTATTCTTTTTTTAATGAATTTAATCTAATGA
1 TTATTATTTTTTTAATGAATTTAATCTAAGGA
*
28568928 --ATTGTTTTTTTAATGAATTTAATCTAACGGA
1 TTATTATTTTTTTAATGAATTTAATCTAA-GGA
28568959 TTATTATTTTTTTAATGAATTTAATCTAATGGA
1 TTATTATTTTTTTAATGAATTTAATCTAA-GGA
*
28568992 TTGTTATT
1 TTATTATT
28569000 CTTTCTTTCT
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
30 26 0.41
31 2 0.03
33 36 0.56
ACGTcount: A:0.31, C:0.05, G:0.10, T:0.55
Consensus pattern (32 bp):
TTATTATTTTTTTAATGAATTTAATCTAAGGA
Found at i:28574272 original size:22 final size:22
Alignment explanation
Indices: 28574244--28574287 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
28574234 TACTGGAGGT
*
28574244 TGAGTTATTTGATGTATGGGGA
1 TGAGTTATTTGATGTAGGGGGA
28574266 TGAGTTATTTGATGTAGGGGGA
1 TGAGTTATTTGATGTAGGGGGA
28574288 ATAGACTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.23, C:0.00, G:0.39, T:0.39
Consensus pattern (22 bp):
TGAGTTATTTGATGTAGGGGGA
Found at i:28581158 original size:17 final size:17
Alignment explanation
Indices: 28581138--28581198 Score: 86
Period size: 17 Copynumber: 3.6 Consensus size: 17
28581128 TTGCTCCAAT
*
28581138 AATAGGGTTGCTTTGGC
1 AATAGGGTTGCTCTGGC
*
28581155 AATAGGGTTGCTCCGGC
1 AATAGGGTTGCTCTGGC
*
28581172 AATAAGGTTGCTCTGGC
1 AATAGGGTTGCTCTGGC
*
28581189 GATAGGGTTG
1 AATAGGGTTG
28581199 TTCCAACGAG
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 38 1.00
ACGTcount: A:0.20, C:0.15, G:0.36, T:0.30
Consensus pattern (17 bp):
AATAGGGTTGCTCTGGC
Found at i:28581160 original size:34 final size:34
Alignment explanation
Indices: 28581122--28581215 Score: 107
Period size: 34 Copynumber: 2.8 Consensus size: 34
28581112 TGTAGCAGCG
* * *
28581122 ATAGGGTTGCTCCAATAATAGGGTTGCTTTGGCA
1 ATAGGGTTGCTCCAACAATAAGGTTGCTCTGGCA
** *
28581156 ATAGGGTTGCTCCGGCAATAAGGTTGCTCTGGCG
1 ATAGGGTTGCTCCAACAATAAGGTTGCTCTGGCA
* * *
28581190 ATAGGGTTGTTCCAACGAGAAGGTTG
1 ATAGGGTTGCTCCAACAATAAGGTTG
28581216 TTGCGATGAT
Statistics
Matches: 49, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
34 49 1.00
ACGTcount: A:0.22, C:0.16, G:0.33, T:0.29
Consensus pattern (34 bp):
ATAGGGTTGCTCCAACAATAAGGTTGCTCTGGCA
Found at i:28595207 original size:35 final size:35
Alignment explanation
Indices: 28595161--28595236 Score: 116
Period size: 35 Copynumber: 2.2 Consensus size: 35
28595151 CGAACTACAA
28595161 TGATCCCGGCACGGTCCAATTTCGCCTAGGAGGAT
1 TGATCCCGGCACGGTCCAATTTCGCCTAGGAGGAT
* * *
28595196 TGATCTCGGCACGGTGCAATTTCGCCTAGGCGGAT
1 TGATCCCGGCACGGTCCAATTTCGCCTAGGAGGAT
*
28595231 TAATCC
1 TGATCC
28595237 GCTAGATAAG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.20, C:0.28, G:0.28, T:0.25
Consensus pattern (35 bp):
TGATCCCGGCACGGTCCAATTTCGCCTAGGAGGAT
Found at i:28608889 original size:40 final size:40
Alignment explanation
Indices: 28608844--28609010 Score: 185
Period size: 40 Copynumber: 4.2 Consensus size: 40
28608834 CGGAATATAA
28608844 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * *
28608884 CCGGATAGAATAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
28608924 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
28608964 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
28609003 CCGGATAT
1 CCGGATAT
28609011 CATTCAATTT
Statistics
Matches: 107, Mismatches: 19, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
39 14 0.13
40 93 0.87
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:28616856 original size:40 final size:38
Alignment explanation
Indices: 28616811--28616937 Score: 119
Period size: 40 Copynumber: 3.2 Consensus size: 38
28616801 CGGAATATAA
*
28616811 CCGGATATAATCACGTGCACAAATGCCTTCGGGCCTTAGC
1 CCGGATATAATAAC-TGCACAAATGCCTTCGGG-CTTAGC
* * *
28616851 CCGGATAGAATAACTCGCACGAATGCCTTCGGGTCTTAAC
1 CCGGATATAATAACT-GCACAAATGCCTTCGGG-CTTAGC
** * * * *
28616891 CCGGATATAATTTCCAGCATAATTGTCTTCGGGCTTAGC
1 CCGGATATAA-TAACTGCACAAATGCCTTCGGGCTTAGC
28616930 CCGGATAT
1 CCGGATAT
28616938 CATTCAATTT
Statistics
Matches: 71, Mismatches: 14, Indels: 5
0.79 0.16 0.06
Matches are distributed among these distances:
39 14 0.20
40 55 0.77
41 2 0.03
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (38 bp):
CCGGATATAATAACTGCACAAATGCCTTCGGGCTTAGC
Found at i:28619457 original size:48 final size:47
Alignment explanation
Indices: 28619362--28619524 Score: 165
Period size: 46 Copynumber: 3.5 Consensus size: 47
28619352 TTTTTGTGCC
* * ** *
28619362 AGTGTAAGACATGTCT-GGACATG-CATCAGCCA-CATTAAGAGAGCT
1 AGTGTAAGACATGTCTGGGACATGACAAC-GGCATCAAGACGAGAGCT
* *
28619407 AGTGTAAGACCATGTCTGGGACATGGCAACGGTATCAAGACGAGAGCT
1 AGTGTAAGA-CATGTCTGGGACATGACAACGGCATCAAGACGAGAGCT
* * * *
28619455 AGTGTAAGACATGTCTGGGACAT-ACATCGGCCTCGAGATGTA-AGCT
1 AGTGTAAGACATGTCTGGGACATGACAACGGCATCAAGACG-AGAGCT
28619501 AGTGTAAGACATGTCTGGGACATG
1 AGTGTAAGACATGTCTGGGACATG
28619525 CATCGGCTAC
Statistics
Matches: 100, Mismatches: 12, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
45 9 0.09
46 45 0.45
47 24 0.24
48 22 0.22
ACGTcount: A:0.31, C:0.18, G:0.29, T:0.22
Consensus pattern (47 bp):
AGTGTAAGACATGTCTGGGACATGACAACGGCATCAAGACGAGAGCT
Found at i:28619512 original size:46 final size:49
Alignment explanation
Indices: 28619403--28619770 Score: 260
Period size: 46 Copynumber: 7.7 Consensus size: 49
28619393 ACATTAAGAG
* * * *
28619403 AGCTAGTGTAAGACCATGTCTGGGACATGGCAACGGTA-TCAAGACG-A
1 AGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCACTCGAGATGTA
*
28619450 GAGCTAGTGTAAGA-CATGTCTGGGACAT-ACATCGGC-CTCGAGATGTA
1 -AGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCACTCGAGATGTA
* *
28619497 AGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCTACTTGATATGT-
1 AGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGC-ACTCGAGATGTA
** *
28619544 --C-AGTGTAAGACCATGTCTGGGACATGGCATCGGCACGTATAGAGGT-
1 AGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCAC-TCGAGATGTA
* * *
28619590 -G-TCAGTGTAAGACCATGTCTGGGACATGACATCGGCAC-GGATATGTGA
1 AGCT-AGTGTAAGACCATGTCTGGGACATGGCATCGGCACTCGAGATGT-A
* * * * *
28619638 GAGCTAGTGTAAGACCATGTCTAGGACTTGGC-GCTGGC-CTCGA-TTTTGA
1 -AGCTAGTGTAAGACCATGTCTGGGACATGGCATC-GGCACTCGAGATGT-A
* *
28619687 TAG-TCAATGTAAGACCATGTCTGGGACATGGCATC-G-ACTTGATGGATG--
1 -AGCT-AGTGTAAGACCATGTCTGGGACATGGCATCGGCACTCGA--GATGTA
* * *
28619735 AGCCAATGTAAGACCATGTCTGGGACATGACATCGG
1 AGCTAGTGTAAGACCATGTCTGGGACATGGCATCGG
28619771 TATTATACCC
Statistics
Matches: 261, Mismatches: 34, Indels: 50
0.76 0.10 0.14
Matches are distributed among these distances:
44 9 0.03
45 17 0.07
46 62 0.24
47 46 0.18
48 62 0.24
49 32 0.12
50 31 0.12
51 2 0.01
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.24
Consensus pattern (49 bp):
AGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCACTCGAGATGTA
Found at i:28619603 original size:48 final size:48
Alignment explanation
Indices: 28619501--28619770 Score: 202
Period size: 48 Copynumber: 5.7 Consensus size: 48
28619491 GATGTAAGCT
**
28619501 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCTAC-T-T-GATATGTC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGC-ACGTATAGAGGTGTC
28619545 AGTGTAAGACCATGTCTGGGACATGGCATCGGCACGTATAGAGGTGTC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCACGTATAGAGGTGTC
* * * *
28619593 AGTGTAAGACCATGTCTGGGACATGACATCGGCACGGATATGTGAGAG-C
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCACGTATA-GAG-GTGTC
* * * * * *
28619642 TAGTGTAAGACCATGTCTAGGACTTGGC-GCTGGCCTCGATTTTGA--TAGTC
1 -AGTGTAAGACCATGTCTGGGACATGGCATC-GG-CACG-TATAGAGGT-GTC
* * * * * *
28619692 AATGTAAGACCATGTCTGGGACATGGCATC-G-ACTTGATGGATGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCACGT-ATAGAGGTGTC
* *
28619739 AATGTAAGACCATGTCTGGGACATGACATCGG
1 AGTGTAAGACCATGTCTGGGACATGGCATCGG
28619771 TATTATACCC
Statistics
Matches: 181, Mismatches: 27, Indels: 32
0.75 0.11 0.13
Matches are distributed among these distances:
44 9 0.05
45 17 0.09
46 13 0.07
47 32 0.18
48 46 0.25
49 29 0.16
50 30 0.17
51 4 0.02
52 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.25
Consensus pattern (48 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGCACGTATAGAGGTGTC
Found at i:28623693 original size:40 final size:40
Alignment explanation
Indices: 28623639--28623719 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
28623629 ATTCAATACA
*
28623639 TATTATTCATATAAACATTTTTGTAATTGTCATTGCATTT
1 TATTATTCATATAAACATTTTCGTAATTGTCATTGCATTT
28623679 TATTATTCATATAAACATTTTCGTAATTGTCATTGCATTT
1 TATTATTCATATAAACATTTTCGTAATTGTCATTGCATTT
28623719 T
1 T
28623720 TACTCTTACA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.30, C:0.11, G:0.07, T:0.52
Consensus pattern (40 bp):
TATTATTCATATAAACATTTTCGTAATTGTCATTGCATTT
Found at i:28624055 original size:15 final size:15
Alignment explanation
Indices: 28624035--28624063 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
28624025 CTTAATTCCA
28624035 TTAGTTTAATTTAAC
1 TTAGTTTAATTTAAC
28624050 TTAGTTTAATTTAA
1 TTAGTTTAATTTAA
28624064 TTTCTACAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.03, G:0.07, T:0.55
Consensus pattern (15 bp):
TTAGTTTAATTTAAC
Found at i:28639151 original size:32 final size:32
Alignment explanation
Indices: 28639110--28639174 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
28639100 AAAAGTTATA
28639110 ATTTATGCCTTTAGACAGGGTCAATTGTCTGT
1 ATTTATGCCTTTAGACAGGGTCAATTGTCTGT
28639142 ATTTATGCCTTTAGACAGGGTCAATTGTCTGT
1 ATTTATGCCTTTAGACAGGGTCAATTGTCTGT
28639174 A
1 A
28639175 CTTTGCATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.23, C:0.15, G:0.22, T:0.40
Consensus pattern (32 bp):
ATTTATGCCTTTAGACAGGGTCAATTGTCTGT
Found at i:28651751 original size:3 final size:3
Alignment explanation
Indices: 28651743--28651874 Score: 228
Period size: 3 Copynumber: 44.0 Consensus size: 3
28651733 CTGTGAAATT
* *
28651743 TTC TTC TTC TTC TTC TTC TTC TTT TTC TTC TTT TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
28651791 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
* *
28651839 TTC TTC TTC TTC TTC TTC TTC TTC TTA ATC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
28651875 AGGATCCTTG
Statistics
Matches: 121, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 121 1.00
ACGTcount: A:0.02, C:0.31, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:28661763 original size:13 final size:13
Alignment explanation
Indices: 28661747--28661772 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
28661737 ACACACAGCT
28661747 AAACTACACGCCC
1 AAACTACACGCCC
28661760 AAACTACACGCCC
1 AAACTACACGCCC
28661773 GTGCGTATGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.46, G:0.08, T:0.08
Consensus pattern (13 bp):
AAACTACACGCCC
Found at i:28662806 original size:45 final size:45
Alignment explanation
Indices: 28662757--28662858 Score: 123
Period size: 45 Copynumber: 2.3 Consensus size: 45
28662747 TTTCAACAAT
* * *
28662757 GGTCTTATTCATCAGATTCATGATGCCATAGCATCTTTCAGCTAA
1 GGTCTTACTCATCAGAATCATGATGCCATAACATCTTTCAGCTAA
* * * * * *
28662802 GGTCTTACTCGTTAGAATCGTGATGCCATAACGTCTTTCAGTTAT
1 GGTCTTACTCATCAGAATCATGATGCCATAACATCTTTCAGCTAA
28662847 GGTCTTACTCAT
1 GGTCTTACTCAT
28662859 TTCCGGTATG
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.24, C:0.22, G:0.18, T:0.37
Consensus pattern (45 bp):
GGTCTTACTCATCAGAATCATGATGCCATAACATCTTTCAGCTAA
Found at i:28663505 original size:25 final size:25
Alignment explanation
Indices: 28663472--28663534 Score: 90
Period size: 25 Copynumber: 2.5 Consensus size: 25
28663462 TAAACGATAC
*
28663472 GCTCATCCGAGCTGAATATCGGTAA
1 GCTCATCCGAGCTAAATATCGGTAA
*
28663497 GCTCTTCCGAGCTAAATATCGGTAA
1 GCTCATCCGAGCTAAATATCGGTAA
* *
28663522 GCTTATGCGAGCT
1 GCTCATCCGAGCT
28663535 GTGGTGAGTC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.27
Consensus pattern (25 bp):
GCTCATCCGAGCTAAATATCGGTAA
Found at i:28668257 original size:93 final size:93
Alignment explanation
Indices: 28668145--28668316 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
28668135 CGCCCATAAG
* *
28668145 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
28668210 ACAAGTTCGGATGCCTAGTTACATCTCT
66 ACAAGTTCGGATGCCTAGTTACATCTCT
* * *
28668238 CGAACTCGGACTCAACTCAATGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
*
28668303 ACGAGTTCGGATGC
66 ACAAGTTCGGATGC
28668317 TCAACCATCC
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACAAGTTCGGATGCCTAGTTACATCTCT
Found at i:28668313 original size:46 final size:46
Alignment explanation
Indices: 28668138--28668313 Score: 189
Period size: 46 Copynumber: 3.8 Consensus size: 46
28668128 TGTAACCCGC
* * * *
28668138 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
* * * *
28668184 CCATAAGTGAACTCGGACTCAACTCAACAAGTTCGGATGCCTAGTTACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-ATTTGCAT
*
28668234 CTC-T---CGAACTCGGACTCAACTCAATGAGTTCGGACATTTGCAT
1 C-CATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
*
28668277 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
28668314 TGCTCAACCA
Statistics
Matches: 106, Mismatches: 15, Indels: 18
0.76 0.11 0.13
Matches are distributed among these distances:
42 1 0.01
43 8 0.08
44 1 0.01
46 61 0.58
47 27 0.25
49 1 0.01
50 6 0.06
51 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.22
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
Found at i:28668332 original size:46 final size:46
Alignment explanation
Indices: 28668146--28668332 Score: 122
Period size: 46 Copynumber: 4.0 Consensus size: 46
28668136 GCCCATAAGC
* ** * *
28668146 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTC--GCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCC-T-AGT
* *
28668192 GAACTCGGACTCAACTCAACAAGTTCGGATGC-CTAGTTA-CATCTCT--C
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCTC-A---ACCATC-CTAGT
* * * *
28668239 GAACTCGGACTCAACTCAATGAGTTCGGACAT-TTGCATCCAT--AAGT
1 GAACTCGGACTCAACTCAACGAGTTCGG--ATGCT-CAACCATCCTAGT
28668285 GAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCTAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCTAGT
28668331 GA
1 GA
28668333 CATGTCACTT
Statistics
Matches: 108, Mismatches: 16, Indels: 34
0.68 0.10 0.22
Matches are distributed among these distances:
44 8 0.07
45 2 0.02
46 59 0.55
47 29 0.27
49 3 0.03
50 6 0.06
51 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.23
Consensus pattern (46 bp):
GAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCTAGT
Found at i:28671005 original size:71 final size:71
Alignment explanation
Indices: 28670889--28671030 Score: 275
Period size: 71 Copynumber: 2.0 Consensus size: 71
28670879 ATATATTTAC
*
28670889 AATGAAACTTATTACATACGAACTTACCTCGGATGTAAAAACGGCTAAATTGATCAATTAGTCGA
1 AATGAAACTTATTACATACGAACTTACCTCGGATGTAAAAACGGCTAAATTGATCAATTAGTCAA
28670954 GAACTT
66 GAACTT
28670960 AATGAAACTTATTACATACGAACTTACCTCGGATGTAAAAACGGCTAAATTGATCAATTAGTCAA
1 AATGAAACTTATTACATACGAACTTACCTCGGATGTAAAAACGGCTAAATTGATCAATTAGTCAA
28671025 GAACTT
66 GAACTT
28671031 TCTCTTTCCC
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 70 1.00
ACGTcount: A:0.40, C:0.17, G:0.15, T:0.28
Consensus pattern (71 bp):
AATGAAACTTATTACATACGAACTTACCTCGGATGTAAAAACGGCTAAATTGATCAATTAGTCAA
GAACTT
Found at i:28672029 original size:45 final size:45
Alignment explanation
Indices: 28671965--28672054 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
28671955 TTTTGACTTC
28671965 AGATTTGTGGTTCCAAAACTACTGTTTCAATTTGACTTAAAAGGG
1 AGATTTGTGGTTCCAAAACTACTGTTTCAATTTGACTTAAAAGGG
28672010 AGATTTGTGGTTCCAAAACTACTGTTTCAATTTGACTTAAAAGGG
1 AGATTTGTGGTTCCAAAACTACTGTTTCAATTTGACTTAAAAGGG
28672055 GCTGTTACAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.31, C:0.13, G:0.20, T:0.36
Consensus pattern (45 bp):
AGATTTGTGGTTCCAAAACTACTGTTTCAATTTGACTTAAAAGGG
Found at i:28683945 original size:18 final size:18
Alignment explanation
Indices: 28683898--28683945 Score: 51
Period size: 22 Copynumber: 2.4 Consensus size: 18
28683888 GTATACGATG
28683898 TAGAATAAAAATAAATAAA
1 TAGAA-AAAAATAAATAAA
28683917 TATTGTAAAAAAAATAAATAAA
1 TA--G--AAAAAAATAAATAAA
28683939 TAGAAAA
1 TAGAAAA
28683946 TAATCACTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 9
0.74 0.00 0.26
Matches are distributed among these distances:
18 4 0.16
19 2 0.08
20 1 0.04
21 1 0.04
22 15 0.60
23 2 0.08
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.23
Consensus pattern (18 bp):
TAGAAAAAAATAAATAAA
Found at i:28684959 original size:15 final size:15
Alignment explanation
Indices: 28684939--28684974 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
28684929 TCATCTATTC
28684939 TCTCAACTATTTTGT
1 TCTCAACTATTTTGT
28684954 TCTCAACTATTTTGT
1 TCTCAACTATTTTGT
28684969 TCTCAA
1 TCTCAA
28684975 TTTTTCTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.22, C:0.22, G:0.06, T:0.50
Consensus pattern (15 bp):
TCTCAACTATTTTGT
Found at i:28685037 original size:22 final size:21
Alignment explanation
Indices: 28685007--28685052 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
28684997 ATTCTTGTTG
*
28685007 TTTTAATTTTATATTTAGTAAT
1 TTTTAATTTGATATTTA-TAAT
* *
28685029 TTTTTATTTGATTTTTATAAT
1 TTTTAATTTGATATTTATAAT
28685050 TTT
1 TTT
28685053 AAAAATGCGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (21 bp):
TTTTAATTTGATATTTATAAT
Found at i:28685632 original size:39 final size:38
Alignment explanation
Indices: 28685589--28685677 Score: 101
Period size: 37 Copynumber: 2.3 Consensus size: 38
28685579 TTAAATTTAA
*
28685589 TATTAAGATAATGATTTTAAAATTAAATTAATA-AAATAC
1 TATTAAGATAATG-TATTAAAATTAAATTAATACAAAT-C
* *
28685628 TATTAAGATAA-GTATTAAATTTAATTTAATACTAAATC
1 TATTAAGATAATGTATTAAAATTAAATTAATAC-AAATC
*
28685666 TATTAAAATAAT
1 TATTAAGATAAT
28685678 ATTATTTTTA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
37 16 0.37
38 12 0.28
39 15 0.35
ACGTcount: A:0.52, C:0.03, G:0.04, T:0.40
Consensus pattern (38 bp):
TATTAAGATAATGTATTAAAATTAAATTAATACAAATC
Done.