Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr14
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: 244914714
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.31
Warning! 4503000 characters in sequence are not A, C, G, or T
File 137 of 770
Found at i:40297282 original size:13 final size:14
Alignment explanation
Indices: 40297254--40297285 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
40297244 TACTTATTTA
40297254 TTATTTTATGTTTT
1 TTATTTTATGTTTT
40297268 TTATTTTAT-TTTT
1 TTATTTTATGTTTT
40297281 TTATT
1 TTATT
40297286 ATTAAAACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.16, C:0.00, G:0.03, T:0.81
Consensus pattern (14 bp):
TTATTTTATGTTTT
Found at i:40303435 original size:49 final size:49
Alignment explanation
Indices: 40303364--40303662 Score: 472
Period size: 49 Copynumber: 5.9 Consensus size: 49
40303354 GTACATAATA
* *
40303364 ATATATGTATATAAGGCTTAATGGCCGATGTGATGAATGTGAAAATGTAT
1 ATATATGT-GATAAGGCCTAATGGCCGATGTGATGAATGTGAAAATGTAT
40303414 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAATGTAT
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAATGTAT
*
40303463 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAACGTGAAAATGTAT
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAATGTAT
40303512 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAATGTATATATATATAT
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAATG----------TAT
40303571 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAATGTAT
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAATGTAT
40303620 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
40303663 GCGTATATCT
Statistics
Matches: 235, Mismatches: 4, Indels: 21
0.90 0.02 0.08
Matches are distributed among these distances:
49 178 0.76
50 8 0.03
59 49 0.21
ACGTcount: A:0.35, C:0.08, G:0.25, T:0.31
Consensus pattern (49 bp):
ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAATGTAT
Found at i:40303580 original size:59 final size:58
Alignment explanation
Indices: 40303509--40303678 Score: 241
Period size: 59 Copynumber: 3.1 Consensus size: 58
40303499 CGTGAAAATG
40303509 TATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAATGTATATATATA
1 TATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAATGTATAT-TATA
40303568 TATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAATG---------
1 TATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAATGTATATTATA
**
40303617 TATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGCGTATATCTATA
1 TATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAATGTATAT-TATA
40303676 TAT
1 TAT
40303679 GTGGTAAAGC
Statistics
Matches: 99, Mismatches: 2, Indels: 20
0.82 0.02 0.17
Matches are distributed among these distances:
49 47 0.47
59 52 0.53
ACGTcount: A:0.35, C:0.08, G:0.24, T:0.33
Consensus pattern (58 bp):
TATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAATGTATATTATA
Found at i:40303586 original size:108 final size:108
Alignment explanation
Indices: 40303460--40303678 Score: 402
Period size: 108 Copynumber: 2.0 Consensus size: 108
40303450 TGTGAAAATG
40303460 TATATATATGTGATAAGGCCTAATGGCCGATGTGATGAACGTGAAAATGTATATATATGTGATAA
1 TATATATATGTGATAAGGCCTAATGGCCGATGTGATGAACGTGAAAATGTATATATATGTGATAA
*
40303525 GGCCTAATGGCCGATGTGATGAATGTGAAAATGTATATATATA
66 GGCCTAATGGCCGATGTGATGAATGTGAAAACGTATATATATA
*
40303568 TATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAATGTATATATATGTGATAA
1 TATATATATGTGATAAGGCCTAATGGCCGATGTGATGAACGTGAAAATGTATATATATGTGATAA
* *
40303633 GGCCTAATGGCCGATGTGATGAATGTGAAAGCGTATATCTATA
66 GGCCTAATGGCCGATGTGATGAATGTGAAAACGTATATATATA
40303676 TAT
1 TAT
40303679 GTGGTAAAGC
Statistics
Matches: 107, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
108 107 1.00
ACGTcount: A:0.35, C:0.09, G:0.24, T:0.32
Consensus pattern (108 bp):
TATATATATGTGATAAGGCCTAATGGCCGATGTGATGAACGTGAAAATGTATATATATGTGATAA
GGCCTAATGGCCGATGTGATGAATGTGAAAACGTATATATATA
Found at i:40303704 original size:53 final size:50
Alignment explanation
Indices: 40303364--40303696 Score: 422
Period size: 49 Copynumber: 6.5 Consensus size: 50
40303354 GTACATAATA
* * *
40303364 ATATATGTATATAAGGCTTAATGGCCGATGTGATGAATGTGAAA-ATGTAT
1 ATATATGT-GATAAGGCCTAATGGCCGATGTGATGAATGTGAAATATATAT
*
40303414 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA-ATGTAT
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAATATATAT
* *
40303463 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAACGTGAAA-ATGTAT
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAATATATAT
40303512 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAATGTATATATATATAT
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAA--TG----TG-A-A-ATATATAT
*
40303571 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA-ATGTAT
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAATATATAT
*
40303620 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGCGTATATCT
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA---TATATAT
* * *
40303673 ATATATGTGGTAAAGCCGAATGGC
1 ATATATGTGATAAGGCCTAATGGC
40303697 TAATGTGAAT
Statistics
Matches: 258, Mismatches: 11, Indels: 25
0.88 0.04 0.09
Matches are distributed among these distances:
49 171 0.66
50 9 0.03
51 2 0.01
52 1 0.00
53 27 0.10
55 2 0.01
56 1 0.00
57 3 0.01
58 1 0.00
59 41 0.16
ACGTcount: A:0.35, C:0.09, G:0.26, T:0.31
Consensus pattern (50 bp):
ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAATATATAT
Found at i:40303800 original size:37 final size:36
Alignment explanation
Indices: 40303745--40303831 Score: 147
Period size: 37 Copynumber: 2.3 Consensus size: 36
40303735 AATTTGGAAA
40303745 TATGTTCCGGGTGAGACCCGATGACTACGTGTGGAGAT
1 TATG-TCCGGGT-AGACCCGATGACTACGTGTGGAGAT
40303783 TATGTCCGGGTACGACCCGATGACTACGTGTGGAGAT
1 TATGTCCGGGTA-GACCCGATGACTACGTGTGGAGAT
40303820 TATGTCCGGGTA
1 TATGTCCGGGTA
40303832 AGACTTCGTA
Statistics
Matches: 48, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
36 1 0.02
37 43 0.90
38 4 0.08
ACGTcount: A:0.21, C:0.20, G:0.33, T:0.26
Consensus pattern (36 bp):
TATGTCCGGGTAGACCCGATGACTACGTGTGGAGAT
Found at i:40306716 original size:20 final size:20
Alignment explanation
Indices: 40306673--40306716 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
40306663 TACAAATTCT
* *
40306673 ATTTATATAGATGAAGTATT
1 ATTTATATAGATCAAGTATG
40306693 ATTTATATAGA-CAAGTTATG
1 ATTTATATAGATCAAG-TATG
40306713 ATTT
1 ATTT
40306717 TCAAACGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 3 0.14
20 18 0.86
ACGTcount: A:0.39, C:0.02, G:0.14, T:0.45
Consensus pattern (20 bp):
ATTTATATAGATCAAGTATG
Found at i:40311101 original size:74 final size:75
Alignment explanation
Indices: 40310979--40311129 Score: 259
Period size: 74 Copynumber: 2.0 Consensus size: 75
40310969 GGTGTTACAA
40310979 TTCTTGCTCCCTATCCTTTTAATTTTGTTGTTGTTAATATGAACAAGTATATAAACATTTGTGAT
1 TTCTTGCTCCCTATCCTTTTAATTTTGTTGTTGTTAATATGAACAAGTATATAAACATTTGTGAT
40311044 GTTGATATGT
66 GTTGATATGT
* * * *
40311054 TTCTTGTTCCCTATCC-TTTAATTTTGTTGTTGTTATTATGAACAAGTATATGAATATTTGTGAT
1 TTCTTGCTCCCTATCCTTTTAATTTTGTTGTTGTTAATATGAACAAGTATATAAACATTTGTGAT
40311118 GTTGATATGT
66 GTTGATATGT
40311128 TT
1 TT
40311130 AATTTAATTA
Statistics
Matches: 72, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
74 57 0.79
75 15 0.21
ACGTcount: A:0.24, C:0.11, G:0.15, T:0.50
Consensus pattern (75 bp):
TTCTTGCTCCCTATCCTTTTAATTTTGTTGTTGTTAATATGAACAAGTATATAAACATTTGTGAT
GTTGATATGT
Found at i:40315701 original size:40 final size:40
Alignment explanation
Indices: 40315642--40315721 Score: 142
Period size: 40 Copynumber: 2.0 Consensus size: 40
40315632 GATGTTAGTT
* *
40315642 AATCTGTATGTTTGTATGTCTAATTCTGCTGGGTTACACA
1 AATCTGTATGTTTGCATGTCTAATTCTACTGGGTTACACA
40315682 AATCTGTATGTTTGCATGTCTAATTCTACTGGGTTACACA
1 AATCTGTATGTTTGCATGTCTAATTCTACTGGGTTACACA
40315722 CTGAGTTTAC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.24, C:0.16, G:0.19, T:0.41
Consensus pattern (40 bp):
AATCTGTATGTTTGCATGTCTAATTCTACTGGGTTACACA
Found at i:40324754 original size:33 final size:33
Alignment explanation
Indices: 40324714--40324791 Score: 95
Period size: 33 Copynumber: 2.4 Consensus size: 33
40324704 ATATGTATAC
* * *
40324714 GTGTAAGACCATAGCTGGGCTATGGCATCCTGA
1 GTGTAAGACCATAACTAGGCTATGGCATCATGA
* *
40324747 -TGATAAGACCATAACTAGGTTATGGCATTATGA
1 GTG-TAAGACCATAACTAGGCTATGGCATCATGA
40324780 GTGTAAGACCAT
1 GTGTAAGACCAT
40324792 GGCAGGACCA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
32 2 0.05
33 34 0.89
34 2 0.05
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.27
Consensus pattern (33 bp):
GTGTAAGACCATAACTAGGCTATGGCATCATGA
Found at i:40324769 original size:105 final size:101
Alignment explanation
Indices: 40324476--40324808 Score: 402
Period size: 101 Copynumber: 3.3 Consensus size: 101
40324466 AATTGATGGA
* * *
40324476 TAAGACCATGGTTGGACCATGGCAATGTTTGAATGCAAGACCATAGCTGCGCCATGGTATTTTAA
1 TAAGACCATGGTTGGACCATGGCAATGTTTGAATGTAAGACCATAGCTGGGCTATGGTATTTTAA
* * *
40324541 TGAAAAAACCATAACTGGGTTATGGCACCTTGAACG
66 TGAAAAGACCATAACTAGGTTATGGCACCTTAAACG
* *
40324577 TAAGACCATGGTTAGACCATGGCAATGTTTGAATGTAAGACCATAGTTGGGCTATGGTATTTTAA
1 TAAGACCATGGTTGGACCATGGCAATGTTTGAATGTAAGACCATAGCTGGGCTATGGTATTTTAA
*
40324642 TGAAAAGACCATAACTTGGTTATGGCACCTTAAACG
66 TGAAAAGACCATAACTAGGTTATGGCACCTTAAACG
* * *
40324678 TAAGACCATGGTTGGACCATGGCAGAATATGTAT-ACGTGTAAGACCATAGCTGGGCTATGGCAT
1 TAAGACCATGGTTGGACCATGGC---A-ATGTTTGA-ATGTAAGACCATAGCTGGGCTATGGTAT
** * * **
40324742 CCTGATGATAAGACCATAACTAGGTTATGGCA--TTATGAGTG
61 TTTAATGAAAAGACCATAACTAGGTTATGGCACCTTA--AACG
**
40324783 TAAGACCATGGCAGGACCATGGCAAT
1 TAAGACCATGGTTGGACCATGGCAAT
40324809 TGTGTAAGAC
Statistics
Matches: 203, Mismatches: 22, Indels: 14
0.85 0.09 0.06
Matches are distributed among these distances:
101 117 0.58
102 1 0.00
103 3 0.01
104 2 0.01
105 80 0.39
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.26
Consensus pattern (101 bp):
TAAGACCATGGTTGGACCATGGCAATGTTTGAATGTAAGACCATAGCTGGGCTATGGTATTTTAA
TGAAAAGACCATAACTAGGTTATGGCACCTTAAACG
Found at i:40327246 original size:9 final size:9
Alignment explanation
Indices: 40327232--40327265 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
40327222 TGGGTCATAT
40327232 TGAATTTTG
1 TGAATTTTG
40327241 TGAATTTTG
1 TGAATTTTG
40327250 TGAATTTTG
1 TGAATTTTG
*
40327259 TGTATTT
1 TGAATTT
40327266 ATGAAATAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.21, C:0.00, G:0.21, T:0.59
Consensus pattern (9 bp):
TGAATTTTG
Found at i:40333091 original size:30 final size:29
Alignment explanation
Indices: 40333029--40333102 Score: 78
Period size: 30 Copynumber: 2.5 Consensus size: 29
40333019 TATGATATGG
*
40333029 TATCTTGGATTTCTGTACCTTGGATATCTT
1 TATCTTGGATTTCTGTA-CTTGGATATATT
*
40333059 TATCTTGGATTCCTCTGT-CTTGGATTTATT
1 TATCTTGGATT--TCTGTACTTGGATATATT
* *
40333089 TATTTTGGTTTTCT
1 TATCTTGGATTTCT
40333103 TGTTATCTTC
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
28 3 0.08
30 30 0.79
32 5 0.13
ACGTcount: A:0.14, C:0.15, G:0.16, T:0.55
Consensus pattern (29 bp):
TATCTTGGATTTCTGTACTTGGATATATT
Found at i:40342429 original size:40 final size:39
Alignment explanation
Indices: 40342384--40342510 Score: 130
Period size: 40 Copynumber: 3.2 Consensus size: 39
40342374 CGGAACATAA
40342384 CCGGATATAACCATGTGCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAT-TGCACAAATGCCTTCGGGTCTTAGC
* * * *
40342424 CCGGATAGAATGTC-TCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAA--CCATTGCACAAATGCCTTCGGGTCTTAGC
* * * * *
40342464 CCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCA-TTGCACAAATGCCTTCGGGTCTTAGC
40342504 CCGGATA
1 CCGGATA
40342511 AAATTTCCAG
Statistics
Matches: 70, Mismatches: 13, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
38 1 0.01
40 67 0.96
41 1 0.01
42 1 0.01
ACGTcount: A:0.23, C:0.28, G:0.24, T:0.24
Consensus pattern (39 bp):
CCGGATATAACCATTGCACAAATGCCTTCGGGTCTTAGC
Found at i:40342528 original size:40 final size:40
Alignment explanation
Indices: 40342400--40342550 Score: 137
Period size: 40 Copynumber: 3.8 Consensus size: 40
40342390 ATAACCATGT
* * *
40342400 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGTCTC-
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATAAAATCTC-CA
** ** * *
40342440 GCACGAA-TGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATTGCCTTCGGGTCTTAGCCCGGATAAAATCTCCA
* *
40342480 GCACAATTGCCTTCGGGTCTTAACCCGGATAAAATTTCCA
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATAAAATCTCCA
* *
40342520 GCATAATTGTCTTCGGGAT-TTAGCCCGGATA
1 GCACAATTGCCTTCGGG-TCTTAGCCCGGATA
40342551 TCATTCATTT
Statistics
Matches: 89, Mismatches: 18, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
39 2 0.02
40 84 0.94
41 3 0.03
ACGTcount: A:0.23, C:0.26, G:0.24, T:0.26
Consensus pattern (40 bp):
GCACAATTGCCTTCGGGTCTTAGCCCGGATAAAATCTCCA
Found at i:40342534 original size:80 final size:80
Alignment explanation
Indices: 40342400--40342549 Score: 198
Period size: 80 Copynumber: 1.9 Consensus size: 80
40342390 ATAACCATGT
* *
40342400 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGTCTCGCACGAATGCCTTCGGG-TCTTAGC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAAAATGTCTCGCACGAATGCCTTCGGGAT-TTAGC
40342464 CCGGATGTAGCCACTA
65 CCGGATGTAGCCACTA
* * * *
40342480 GCACAATTGCCTTCGGGTCTTAACCCGGATAAAATTTC-CAGCA-TAATTGTCTTCGGGATTTAG
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAAAATGTCTC-GCACGAA-TGCCTTCGGGATTTAG
40342543 CCCGGAT
64 CCCGGAT
40342550 ATCATTCATT
Statistics
Matches: 61, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
79 3 0.05
80 57 0.93
81 1 0.02
ACGTcount: A:0.23, C:0.27, G:0.24, T:0.27
Consensus pattern (80 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATAAAATGTCTCGCACGAATGCCTTCGGGATTTAGCC
CGGATGTAGCCACTA
Found at i:40350431 original size:40 final size:39
Alignment explanation
Indices: 40350386--40350512 Score: 130
Period size: 40 Copynumber: 3.2 Consensus size: 39
40350376 CGGAATATAA
40350386 CCGGATATAACCATGTGCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAT-TGCACAAATGCCTTCGGGTCTTAGC
* * * *
40350426 CCGGATAGAATGTC-TCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAA--CCATTGCACAAATGCCTTCGGGTCTTAGC
* * * * *
40350466 CCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCA-TTGCACAAATGCCTTCGGGTCTTAGC
40350506 CCGGATA
1 CCGGATA
40350513 AATTTCCAGC
Statistics
Matches: 70, Mismatches: 13, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
38 1 0.01
40 67 0.96
41 1 0.01
42 1 0.01
ACGTcount: A:0.23, C:0.28, G:0.24, T:0.24
Consensus pattern (39 bp):
CCGGATATAACCATTGCACAAATGCCTTCGGGTCTTAGC
Found at i:40357505 original size:41 final size:41
Alignment explanation
Indices: 40357427--40357686 Score: 310
Period size: 41 Copynumber: 6.4 Consensus size: 41
40357417 CGTTTTACCA
* * * **
40357427 AAAACGTCGCTAAAAA-CAGAGCAATAGCGGCATTTTTGGT
1 AAAACGCCACTAAAAACCAGAGCATTAGCGGCGCTTTTGGT
* * * *
40357467 AAAACACCGCTAAAAGCCAGAGCATTAGTGGCGCTTTTGGT
1 AAAACGCCACTAAAAACCAGAGCATTAGCGGCGCTTTTGGT
* * * *
40357508 AAAACGCCACTAAAAACCAAAGAATTAACAGCGC-TTTGCGT
1 AAAACGCCACTAAAAACCAGAGCATTAGCGGCGCTTTTG-GT
*
40357549 AAAACGCCACTAAAAACCAGAGCATTAGTGGCGCTTTTGGT
1 AAAACGCCACTAAAAACCAGAGCATTAGCGGCGCTTTTGGT
* * *
40357590 AAAACGCCACTAAAAACCAAAGAATTAGCAGCGC-TTTGCGT
1 AAAACGCCACTAAAAACCAGAGCATTAGCGGCGCTTTTG-GT
*
40357631 AAAACGCCACTAAAAACCAGAGCATTAGCGGCGTTTTTGGT
1 AAAACGCCACTAAAAACCAGAGCATTAGCGGCGCTTTTGGT
*
40357672 AAAACGCCGCTAAAA
1 AAAACGCCACTAAAA
40357687 GTCATTTAAC
Statistics
Matches: 186, Mismatches: 29, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
40 21 0.11
41 157 0.84
42 8 0.04
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.20
Consensus pattern (41 bp):
AAAACGCCACTAAAAACCAGAGCATTAGCGGCGCTTTTGGT
Found at i:40357571 original size:82 final size:82
Alignment explanation
Indices: 40357461--40357686 Score: 382
Period size: 82 Copynumber: 2.8 Consensus size: 82
40357451 TAGCGGCATT
* * *
40357461 TTTG-GTAAAACACCGCTAAAAGCCAGAGCATTAGTGGCGCTTTTGGTAAAACGCCACTAAAAAC
1 TTTGCGTAAAACGCCACTAAAAACCAGAGCATTAGTGGCGCTTTTGGTAAAACGCCACTAAAAAC
40357525 CAAAGAATTAACAGCGC
66 CAAAGAATTAACAGCGC
40357542 TTTGCGTAAAACGCCACTAAAAACCAGAGCATTAGTGGCGCTTTTGGTAAAACGCCACTAAAAAC
1 TTTGCGTAAAACGCCACTAAAAACCAGAGCATTAGTGGCGCTTTTGGTAAAACGCCACTAAAAAC
*
40357607 CAAAGAATTAGCAGCGC
66 CAAAGAATTAACAGCGC
* * *
40357624 TTTGCGTAAAACGCCACTAAAAACCAGAGCATTAGCGGCGTTTTTGGTAAAACGCCGCTAAAA
1 TTTGCGTAAAACGCCACTAAAAACCAGAGCATTAGTGGCGCTTTTGGTAAAACGCCACTAAAA
40357687 GTCATTTAAC
Statistics
Matches: 137, Mismatches: 7, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
81 4 0.03
82 133 0.97
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.20
Consensus pattern (82 bp):
TTTGCGTAAAACGCCACTAAAAACCAGAGCATTAGTGGCGCTTTTGGTAAAACGCCACTAAAAAC
CAAAGAATTAACAGCGC
Found at i:40357737 original size:44 final size:44
Alignment explanation
Indices: 40357678--40357766 Score: 169
Period size: 44 Copynumber: 2.0 Consensus size: 44
40357668 TGGTAAAACG
40357678 CCGCTAAAAGTCATTTAACCCCTAAAACCCTAAACCCCAAAAAA
1 CCGCTAAAAGTCATTTAACCCCTAAAACCCTAAACCCCAAAAAA
*
40357722 CCGCTAAAAGTCATTTAACCCCTAAAACCCTAAACCCTAAAAAA
1 CCGCTAAAAGTCATTTAACCCCTAAAACCCTAAACCCCAAAAAA
40357766 C
1 C
40357767 ACAAACACTA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.45, C:0.34, G:0.04, T:0.17
Consensus pattern (44 bp):
CCGCTAAAAGTCATTTAACCCCTAAAACCCTAAACCCCAAAAAA
Found at i:40357811 original size:15 final size:16
Alignment explanation
Indices: 40357783--40357816 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
40357773 ACTAATCTAT
40357783 AACCCCTAAAACACTA
1 AACCCCTAAAACACTA
40357799 AACCCCT-AAACACTA
1 AACCCCTAAAACACTA
40357814 AAC
1 AAC
40357817 ACTAAACTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.50, C:0.38, G:0.00, T:0.12
Consensus pattern (16 bp):
AACCCCTAAAACACTA
Found at i:40357838 original size:22 final size:22
Alignment explanation
Indices: 40357769--40357830 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
40357759 TAAAAAACAC
* *
40357769 AAACACTAATCTATAACCCCTA
1 AAACACTAAACTATAACCACTA
** *
40357791 AAACACTAAACCCCTAAACACT-
1 AAACACTAAA-CTATAACCACTA
40357813 AAACACTAAACTATAACC
1 AAACACTAAACTATAACC
40357831 TTTAAAACCC
Statistics
Matches: 31, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
21 5 0.16
22 19 0.61
23 7 0.23
ACGTcount: A:0.50, C:0.32, G:0.00, T:0.18
Consensus pattern (22 bp):
AAACACTAAACTATAACCACTA
Found at i:40358838 original size:114 final size:114
Alignment explanation
Indices: 40358694--40359210 Score: 478
Period size: 114 Copynumber: 4.5 Consensus size: 114
40358684 CCGTTTTCTT
* * *
40358694 TGGATTTTTAGTGGCGTTTTAGGTTAAAACGCCACAATAGGGTTGATTTAGCGGCGC-AAGGTTA
1 TGGATTTTTAGTGGCGTTTTAGGTTAAAACGCCGCAATAGGTTTGCTTTAGCGGCGCTAAGG-TA
* * * * *
40358758 TAAACGCCACTAAGGGTTATTTTGTTTAGATCAAAACGGTGTAGTTTTTA
65 TAAACACCACTAAAGGTTATTCTGTTTATATCAAAACGATGTAGTTTTTA
* * * * * *
40358808 TGGATTTTTAGTGGCGTTTTTGGTTCAAACGCCACAATACGTTTGATTTAGTGGCGCTAAGGTAT
1 TGGATTTTTAGTGGCGTTTTAGGTTAAAACGCCGCAATAGGTTTGCTTTAGCGGCGCTAAGGTAT
*
40358873 AAACACCACTAATGGTTAATT-TGTTTATATCAAAACGATGTAG-TTTTA
66 AAACACCACTAAAGGTT-ATTCTGTTTATATCAAAACGATGTAGTTTTTA
* * * * * * *
40358921 TTCGATTATTATTGGCATTTTAGGGTAAAACGCCGGAATA-GTTTCGCCTTTAGCGGCGCT-TGG
1 -TGGATTTTTAGTGGCGTTTTAGGTTAAAACGCCGCAATAGGTTT-G-CTTTAGCGGCGCTAAGG
* * * * * *
40358984 TGATAAAACGCCACTAAATGTTATTCTGTTCATATGAAAAC-ATCGTCGTTTTTTT
63 T-AT-AAACACCACTAAAGGTTATTCTGTTTATATCAAAACGAT-GTAG-TTTTTA
* * * * *
40359039 TGGATTTTTAGTGGCGTTTTAGGGTGAAACGCCGCAATTGATTTGCTTTAGCGGCACTACA-G-A
1 TGGATTTTTAGTGGCGTTTTAGGTTAAAACGCCGCAATAGGTTTGCTTTAGCGGCGCTA-AGGTA
* * * *
40359102 AAAACACCACTAAAGTTTATTCTGTTTATATCAAAACGGTGTCGTTTTGT-
65 TAAACACCACTAAAGGTTATTCTGTTTATATCAAAACGATGTAGTTTT-TA
*** * *
40359152 TTTTTTTTTAGTGGCG-TTTATGTTAAAACGCCGCAATTGGTTTGCCTTTAGCGGCGCTA
1 TGGATTTTTAGTGGCGTTTTAGGTTAAAACGCCGCAATAGGTTTG-CTTTAGCGGCGCTA
40359211 GCGCCGCAAA
Statistics
Matches: 333, Mismatches: 53, Indels: 35
0.79 0.13 0.08
Matches are distributed among these distances:
112 24 0.07
113 39 0.12
114 160 0.48
115 27 0.08
116 42 0.13
117 34 0.10
118 7 0.02
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.37
Consensus pattern (114 bp):
TGGATTTTTAGTGGCGTTTTAGGTTAAAACGCCGCAATAGGTTTGCTTTAGCGGCGCTAAGGTAT
AAACACCACTAAAGGTTATTCTGTTTATATCAAAACGATGTAGTTTTTA
Found at i:40359351 original size:59 final size:59
Alignment explanation
Indices: 40359284--40359412 Score: 163
Period size: 58 Copynumber: 2.2 Consensus size: 59
40359274 ACACCGAGTT
* * ** *
40359284 CCCCCTTCTCCCTGGTTTATTTCCC-CTATTTTCCCTTCTTCGAATCCCTAAAATAATCA
1 CCCCCTTCTCCCTAGTTTA-TTCCCTCCATTTTCCCTAATTCGAAACCCTAAAATAATCA
* *
40359343 CCCCCTTCT-CCTAGTTTATTCCCTCCATTTTCCCTAATTTGAAACCCTAAAATAATTA
1 CCCCCTTCTCCCTAGTTTATTCCCTCCATTTTCCCTAATTCGAAACCCTAAAATAATCA
*
40359401 CCCCTTTCTCCC
1 CCCCCTTCTCCC
40359413 CAATTTGAAA
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
57 5 0.08
58 44 0.73
59 11 0.18
ACGTcount: A:0.20, C:0.38, G:0.04, T:0.38
Consensus pattern (59 bp):
CCCCCTTCTCCCTAGTTTATTCCCTCCATTTTCCCTAATTCGAAACCCTAAAATAATCA
Found at i:40361649 original size:25 final size:24
Alignment explanation
Indices: 40361621--40361694 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 24
40361611 TTTATTTTGG
40361621 ATTAATCAGGACACAATTTTTTTAA
1 ATTAATCA-GACACAATTTTTTTAA
**
40361646 ATT-A-C-GACAC-ATATTTTGCAA
1 ATTAATCAGACACAAT-TTTTTTAA
*
40361667 TTTAATCACGACACAA-TTTTTTAA
1 ATTAATCA-GACACAATTTTTTTAA
40361691 ATTA
1 ATTA
40361695 CATATTTTGG
Statistics
Matches: 37, Mismatches: 6, Indels: 13
0.66 0.11 0.23
Matches are distributed among these distances:
20 2 0.05
21 13 0.35
22 1 0.03
23 2 0.05
24 10 0.27
25 8 0.22
26 1 0.03
ACGTcount: A:0.39, C:0.15, G:0.07, T:0.39
Consensus pattern (24 bp):
ATTAATCAGACACAATTTTTTTAA
Found at i:40361771 original size:9 final size:9
Alignment explanation
Indices: 40361759--40361832 Score: 55
Period size: 9 Copynumber: 8.4 Consensus size: 9
40361749 ATATCATATA
40361759 ATAACTTAC
1 ATAACTTAC
40361768 ATAACTTAC
1 ATAACTTAC
*
40361777 AAAACTTAC
1 ATAACTTAC
40361786 ATAA--TAC
1 ATAACTTAC
* *
40361793 ATAA-ATAT
1 ATAACTTAC
* *
40361801 ATATCATATC
1 ATAACTTA-C
40361811 ATAACTTAC
1 ATAACTTAC
* *
40361820 ACAACTAAC
1 ATAACTTAC
40361829 ATAA
1 ATAA
40361833 TACATAAATA
Statistics
Matches: 52, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
7 7 0.13
8 5 0.10
9 34 0.65
10 6 0.12
ACGTcount: A:0.51, C:0.19, G:0.00, T:0.30
Consensus pattern (9 bp):
ATAACTTAC
Found at i:40361815 original size:43 final size:43
Alignment explanation
Indices: 40361767--40361851 Score: 143
Period size: 43 Copynumber: 2.0 Consensus size: 43
40361757 TAATAACTTA
*
40361767 CATAACTTACAAAACTTACATAATACATAAATATATATCATAT
1 CATAACTTACAAAACTAACATAATACATAAATATATATCATAT
* *
40361810 CATAACTTACACAACTAACATAATACATAAATATATTTCATA
1 CATAACTTACAAAACTAACATAATACATAAATATATATCATA
40361852 AATATGTATC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.51, C:0.18, G:0.00, T:0.32
Consensus pattern (43 bp):
CATAACTTACAAAACTAACATAATACATAAATATATATCATAT
Found at i:40361933 original size:113 final size:108
Alignment explanation
Indices: 40361750--40361964 Score: 322
Period size: 113 Copynumber: 1.9 Consensus size: 108
40361740 TTTATTTATA
* * *
40361750 TATCATATAATAACTTACATAACTTACAAAACTTACATAATACATAAATATATATCATATCATAA
1 TATCATATAATAACTTACACAACTTACAAAACTCAAATAATACATAAATATATATCATATCATAA
*
40361815 CTTACACAACTAACATAATACATAAATATATTTCATAAATATG
66 CTTACACAACTAACATAATACATAAATATATATCATAAATATG
* *
40361858 TATCATATCATAACTTACACAACTTACATAATACTCCAAATATATATCATAAATATATATCTTAT
1 TATCATATAATAACTTACACAACTTACA-AA-ACT-CAAATA-ATA-CATAAATATATATCATAT
*
40361923 CATAACTTACACAACTTACATAATACATAAATATATATCATA
61 CATAACTTACACAACTAACATAATACATAAATATATATCATA
40361965 TCATAACTTA
Statistics
Matches: 95, Mismatches: 7, Indels: 5
0.89 0.07 0.05
Matches are distributed among these distances:
108 26 0.27
109 2 0.02
110 3 0.03
111 4 0.04
112 3 0.03
113 57 0.60
ACGTcount: A:0.48, C:0.17, G:0.00, T:0.34
Consensus pattern (108 bp):
TATCATATAATAACTTACACAACTTACAAAACTCAAATAATACATAAATATATATCATATCATAA
CTTACACAACTAACATAATACATAAATATATATCATAAATATG
Found at i:40362015 original size:9 final size:9
Alignment explanation
Indices: 40361918--40362038 Score: 63
Period size: 9 Copynumber: 13.6 Consensus size: 9
40361908 AAATATATAT
40361918 CTTATCATAA
1 CTTA-CATAA
*
40361928 CTTACACAA
1 CTTACATAA
40361937 CTTACATAA
1 CTTACATAA
40361946 --TACATAA
1 CTTACATAA
* * *
40361953 -ATATATAT
1 CTTACATAA
*
40361961 CATATCATAA
1 CTTA-CATAA
**
40361971 CTTACATGC
1 CTTACATAA
40361980 CTTACATAA
1 CTTACATAA
* * *
40361989 ATGTATATCA
1 CT-TACATAA
*
40361999 -TAACATAA
1 CTTACATAA
40362007 CTTACATAA
1 CTTACATAA
40362016 CTTACA-AA
1 CTTACATAA
*
40362024 GCTTACTTAA
1 -CTTACATAA
40362034 CTTAC
1 CTTAC
40362039 GTAATATATA
Statistics
Matches: 85, Mismatches: 19, Indels: 15
0.71 0.16 0.13
Matches are distributed among these distances:
7 7 0.08
8 11 0.13
9 50 0.59
10 17 0.20
ACGTcount: A:0.43, C:0.21, G:0.02, T:0.34
Consensus pattern (9 bp):
CTTACATAA
Found at i:40362020 original size:36 final size:36
Alignment explanation
Indices: 40361935--40362021 Score: 124
Period size: 36 Copynumber: 2.5 Consensus size: 36
40361925 TAACTTACAC
*
40361935 AACTTACATAA--TACATAAATATATATCATATCAT
1 AACTTACATAACTTACATAAATATATATCATAACAT
** *
40361969 AACTTACATGCCTTACATAAATGTATATCATAACAT
1 AACTTACATAACTTACATAAATATATATCATAACAT
40362005 AACTTACATAACTTACA
1 AACTTACATAACTTACA
40362022 AAGCTTACTT
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
34 9 0.20
36 36 0.80
ACGTcount: A:0.46, C:0.18, G:0.02, T:0.33
Consensus pattern (36 bp):
AACTTACATAACTTACATAAATATATATCATAACAT
Found at i:40367616 original size:21 final size:21
Alignment explanation
Indices: 40367591--40367661 Score: 94
Period size: 21 Copynumber: 3.4 Consensus size: 21
40367581 AACTTAGAGC
40367591 GGAGGCAGCAGCAGCAGCGAG
1 GGAGGCAGCAGCAGCAGCGAG
40367612 GGAGGCAGC-GACAGCAGCGAG
1 GGAGGCAGCAG-CAGCAGCGAG
40367633 GGAGGCAG-AGGCA-CGAGCGAG
1 GGAGGCAGCA-GCAGC-AGCGAG
40367654 GGAGGCAG
1 GGAGGCAG
40367662 AGGACGATGA
Statistics
Matches: 46, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
20 2 0.04
21 43 0.93
22 1 0.02
ACGTcount: A:0.28, C:0.21, G:0.51, T:0.00
Consensus pattern (21 bp):
GGAGGCAGCAGCAGCAGCGAG
Found at i:40367662 original size:21 final size:21
Alignment explanation
Indices: 40367606--40367668 Score: 85
Period size: 21 Copynumber: 3.0 Consensus size: 21
40367596 CAGCAGCAGC
* *
40367606 AGCGAGGGAGGCAGCGACA-G
1 AGCGAGGGAGGCAGAGGCACG
40367626 CAGCGAGGGAGGCAGAGGCACG
1 -AGCGAGGGAGGCAGAGGCACG
40367648 AGCGAGGGAGGCAGAGG-ACG
1 AGCGAGGGAGGCAGAGGCACG
40367668 A
1 A
40367669 TGACCTCCAG
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
20 4 0.10
21 34 0.87
22 1 0.03
ACGTcount: A:0.30, C:0.19, G:0.51, T:0.00
Consensus pattern (21 bp):
AGCGAGGGAGGCAGAGGCACG
Found at i:40368161 original size:43 final size:43
Alignment explanation
Indices: 40368026--40368143 Score: 227
Period size: 43 Copynumber: 2.7 Consensus size: 43
40368016 TTTGCCATAA
*
40368026 AAACACCGCTAAAGGCCATGGCTTTTAGCGGCGCTTTTCCAAC
1 AAACGCCGCTAAAGGCCATGGCTTTTAGCGGCGCTTTTCCAAC
40368069 AAACGCCGCTAAAGGCCATGGCTTTTAGCGGCGCTTTTCCAAC
1 AAACGCCGCTAAAGGCCATGGCTTTTAGCGGCGCTTTTCCAAC
40368112 AAACGCCGCTAAAGGCCATGGCTTTTAGCGGC
1 AAACGCCGCTAAAGGCCATGGCTTTTAGCGGC
40368144 ATTTTTTAAA
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
43 74 1.00
ACGTcount: A:0.25, C:0.30, G:0.24, T:0.22
Consensus pattern (43 bp):
AAACGCCGCTAAAGGCCATGGCTTTTAGCGGCGCTTTTCCAAC
Found at i:40371029 original size:7 final size:7
Alignment explanation
Indices: 40371014--40371051 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
40371004 ACCTCATTTG
40371014 ATCCCTC
1 ATCCCTC
*
40371021 ATCCATC
1 ATCCCTC
*
40371028 ATCCATC
1 ATCCCTC
40371035 ATCCCTC
1 ATCCCTC
40371042 ATCCCTC
1 ATCCCTC
40371049 ATC
1 ATC
40371052 ATTCTCTCTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.21, C:0.50, G:0.00, T:0.29
Consensus pattern (7 bp):
ATCCCTC
Found at i:40373145 original size:53 final size:53
Alignment explanation
Indices: 40373032--40373146 Score: 124
Period size: 53 Copynumber: 2.2 Consensus size: 53
40373022 ACGATAAGGC
* * * * * *
40373032 AAAGATCCCATGTAAGACCATGCCAAGGCATGACAATGGTGAGTTCATAAGGC
1 AAAGATACCACGTAAGACCATGCCAAGACATGACAATGGTGAGTTCAAAAAGA
* * * *
40373085 AAGGATACCACGTAAGACCATGTCAAGACATGGCAATGGT-ATGTTTAAAAAGA
1 AAAGATACCACGTAAGACCATGCCAAGACATGACAATGGTGA-GTTCAAAAAGA
40373138 AAAGATACC
1 AAAGATACC
40373147 CGTGTATCCT
Statistics
Matches: 50, Mismatches: 11, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
52 1 0.02
53 49 0.98
ACGTcount: A:0.40, C:0.18, G:0.23, T:0.19
Consensus pattern (53 bp):
AAAGATACCACGTAAGACCATGCCAAGACATGACAATGGTGAGTTCAAAAAGA
Found at i:40375477 original size:25 final size:25
Alignment explanation
Indices: 40375449--40375518 Score: 122
Period size: 25 Copynumber: 2.8 Consensus size: 25
40375439 CTCTTTTAAT
40375449 AACTGGGGCAAAGCCCTTTTCGGTA
1 AACTGGGGCAAAGCCCTTTTCGGTA
* *
40375474 AACTGGGGCAGAGCCCTTTTTGGTA
1 AACTGGGGCAAAGCCCTTTTCGGTA
40375499 AACTGGGGCAAAGCCCTTTT
1 AACTGGGGCAAAGCCCTTTT
40375519 GCACTTCCTC
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 42 1.00
ACGTcount: A:0.23, C:0.23, G:0.29, T:0.26
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTCGGTA
Found at i:40375577 original size:10 final size:10
Alignment explanation
Indices: 40375564--40375598 Score: 61
Period size: 10 Copynumber: 3.4 Consensus size: 10
40375554 ATATATGTAT
40375564 ATATCATGGC
1 ATATCATGGC
40375574 ATATCATGTGC
1 ATATCATG-GC
40375585 ATATCATGGC
1 ATATCATGGC
40375595 ATAT
1 ATAT
40375599 TATGTACAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 14 0.58
11 10 0.42
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Consensus pattern (10 bp):
ATATCATGGC
Found at i:40375611 original size:21 final size:21
Alignment explanation
Indices: 40375552--40375611 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 21
40375542 CCCAACCCAT
*
40375552 GCATA-TATGTATATATCATG
1 GCATATTATGTACATATCATG
* *
40375572 GCATATCATGTGCATATCATG
1 GCATATTATGTACATATCATG
*
40375593 GCATATTATGTACAAATCA
1 GCATATTATGTACATATCA
40375612 ATATCACATG
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 5 0.15
21 28 0.85
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (21 bp):
GCATATTATGTACATATCATG
Found at i:40376127 original size:8 final size:8
Alignment explanation
Indices: 40376114--40376139 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
40376104 GAATGCCAAA
40376114 ATTTCGGC
1 ATTTCGGC
40376122 ATTTCGGC
1 ATTTCGGC
40376130 ATTTCGGC
1 ATTTCGGC
40376138 AT
1 AT
40376140 ATATTGATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.15, C:0.23, G:0.23, T:0.38
Consensus pattern (8 bp):
ATTTCGGC
Found at i:40383449 original size:53 final size:53
Alignment explanation
Indices: 40383266--40383472 Score: 209
Period size: 53 Copynumber: 3.8 Consensus size: 53
40383256 ATTAGGGTTT
* * * *
40383266 AAGGATACCAAGTAAGACCATGCCAAGGCATGGCATTGGTAAGTTTTACAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAG-TTCATAAGGC
* * * * *
40383320 AAGG-TAATCATGTAAGACCATGTCAAGACATGGCATTGATAAACTACGATAAGGC
1 AAGGAT-ACCATGTAAGACCATGCCAAGACATGGCATTGGT-AAGTTC-ATAAGGC
* * * * *
40383375 AAGGATCCCATATAAGACCATGCCAAGGCATGGCAATGGTGAGTTCATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTCATAAGGC
* * * *
40383428 AAGGATACCACGTAAGGCCATGTCAAGACATGGCAGTGGTAAGTT
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTT
40383473 TAAAAAGGAA
Statistics
Matches: 122, Mismatches: 27, Indels: 9
0.77 0.17 0.06
Matches are distributed among these distances:
53 45 0.37
54 37 0.30
55 39 0.32
56 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.26, T:0.20
Consensus pattern (53 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTCATAAGGC
Found at i:40386736 original size:47 final size:47
Alignment explanation
Indices: 40386678--40386799 Score: 190
Period size: 47 Copynumber: 2.6 Consensus size: 47
40386668 ACATTGGCAC
* * *
40386678 TAAGACAAGGATACCATTTAAGACCATGTTTGGAACATGGCATTTGG
1 TAAGAAAAGGATACCATGTAAGACCATGTTTGGAACATGGAATTTGG
*
40386725 TAAGAAAAGGATACCATGTAAGACCATGTTTGGAATATGGAATTTGG
1 TAAGAAAAGGATACCATGTAAGACCATGTTTGGAACATGGAATTTGG
* *
40386772 TAAGATAAGGATATCATGTAAGACCATG
1 TAAGAAAAGGATACCATGTAAGACCATG
40386800 CCAGGGCATG
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 69 1.00
ACGTcount: A:0.38, C:0.11, G:0.24, T:0.27
Consensus pattern (47 bp):
TAAGAAAAGGATACCATGTAAGACCATGTTTGGAACATGGAATTTGG
Found at i:40386907 original size:55 final size:54
Alignment explanation
Indices: 40386778--40386973 Score: 261
Period size: 55 Copynumber: 3.6 Consensus size: 54
40386768 TTGGTAAGAT
* * * *
40386778 AAGGATATCATGTAAGACCATGCCAGGGCATGGCATTGATAAGTTCTATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATGAGTTCTATAAGGC
* * *
40386832 AAGGAAATCATGTAAGACCATGTCAAGACATGGCATTGATGAGTTACTATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATGAGTT-CTATAAGGC
* * *
40386887 AAAGG-TCCCATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTC-ATAAGGC
1 -AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATGAGTTCTATAAGGC
*
40386940 AAGGATACCATGTAAGACCATGTCAAGACATGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGC
40386974 TGTAACACCC
Statistics
Matches: 125, Mismatches: 14, Indels: 7
0.86 0.10 0.05
Matches are distributed among these distances:
52 4 0.03
53 33 0.26
54 41 0.33
55 43 0.34
56 4 0.03
ACGTcount: A:0.35, C:0.18, G:0.26, T:0.22
Consensus pattern (54 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATGAGTTCTATAAGGC
Found at i:40388400 original size:40 final size:40
Alignment explanation
Indices: 40388350--40388517 Score: 182
Period size: 40 Copynumber: 4.2 Consensus size: 40
40388340 CGGAATACAA
* * *
40388350 CCGGACATAACCACACGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACAACACGCACGAATGCCTTCGGGTATTAGC
* *
40388390 CCGGATATAACAACTCGCACAAATGCCTTCGGGTATTAGC
1 CCGGATATAACAACACGCACGAATGCCTTCGGGTATTAGC
**
40388430 CCGGATATAACAACTTGCACGAATGCCTTCGGGTATTAGC
1 CCGGATATAACAACACGCACGAATGCCTTCGGGTATTAGC
* * *
40388470 CTGGATA-AAGTC-ACTA-GCAC-AATTGCCTTCGGGTCTTAAC
1 CCGGATATAA--CAAC-ACGCACGAA-TGCCTTCGGGTATTAGC
40388510 CCGGATAT
1 CCGGATAT
40388518 CATTCAATTG
Statistics
Matches: 111, Mismatches: 12, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
39 4 0.04
40 106 0.95
41 1 0.01
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.23
Consensus pattern (40 bp):
CCGGATATAACAACACGCACGAATGCCTTCGGGTATTAGC
Found at i:40388490 original size:80 final size:80
Alignment explanation
Indices: 40388366--40388517 Score: 218
Period size: 80 Copynumber: 1.9 Consensus size: 80
40388356 ATAACCACAC
* * *
40388366 GCACGAATGCCTTCGGGTCTTAGCCCGGATATAACAACTCGCACAAATGCCTTCGGGTATTAGCC
1 GCACGAATGCCTTCGGGTATTAGCCCGGATATAACAACTAGCACAAATGCCTTCGGGTATTAACC
40388431 CGGATATAACAACTT
66 CGGATATAACAACTT
* * *
40388446 GCACGAATGCCTTCGGGTATTAGCCTGGATA-AAGTC-ACTAGCACAATTGCCTTCGGGTCTTAA
1 GCACGAATGCCTTCGGGTATTAGCCCGGATATAA--CAACTAGCACAAATGCCTTCGGGTATTAA
40388509 CCCGGATAT
64 CCCGGATAT
40388518 CATTCAATTG
Statistics
Matches: 64, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
79 2 0.03
80 61 0.95
81 1 0.02
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.25
Consensus pattern (80 bp):
GCACGAATGCCTTCGGGTATTAGCCCGGATATAACAACTAGCACAAATGCCTTCGGGTATTAACC
CGGATATAACAACTT
Found at i:40390328 original size:17 final size:16
Alignment explanation
Indices: 40390295--40390328 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
40390285 CTTATTTAAT
*
40390295 ATTGAGATTGTAAGTA
1 ATTGAGATTATAAGTA
40390311 ATTGAGATTATCAAGTA
1 ATTGAGATTAT-AAGTA
40390328 A
1 A
40390329 GTGATGAGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.41, C:0.03, G:0.21, T:0.35
Consensus pattern (16 bp):
ATTGAGATTATAAGTA
Found at i:40390619 original size:28 final size:28
Alignment explanation
Indices: 40390585--40390641 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
40390575 ATTATTTTAC
40390585 ATGTGAACTTACTAAGCTTTATAAGCTT
1 ATGTGAACTTACTAAGCTTTATAAGCTT
40390613 ATGTGAACTTACTAAGCTTTATAAGCTT
1 ATGTGAACTTACTAAGCTTTATAAGCTT
40390641 A
1 A
40390642 CTTCTTTCAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.39
Consensus pattern (28 bp):
ATGTGAACTTACTAAGCTTTATAAGCTT
Found at i:40399213 original size:22 final size:22
Alignment explanation
Indices: 40399188--40399230 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
40399178 GTAAGGCAAA
*
40399188 TAAATTGCTTAAATTTTTAAAT
1 TAAATTGCTCAAATTTTTAAAT
*
40399210 TAAATTTCTCAAATTTTTAAA
1 TAAATTGCTCAAATTTTTAAA
40399231 ATTTTCAAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.42, C:0.07, G:0.02, T:0.49
Consensus pattern (22 bp):
TAAATTGCTCAAATTTTTAAAT
Found at i:40400913 original size:6 final size:6
Alignment explanation
Indices: 40400895--40400991 Score: 65
Period size: 6 Copynumber: 15.8 Consensus size: 6
40400885 AAGAAACATT
* * *
40400895 ATCAGA A-CTAGA ATCAGA ATCAGA ATCAGA ATTAG- GTGACAAA ATCAGA
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA ATCAGA AT--CAGA ATCAGA
* * * *
40400944 ATCAGA ATCAGT ATCAGGTA AT-AGA ATCAAA ATCAAA ATCAGT ATCAG
1 ATCAGA ATCAGA ATCA-G-A ATCAGA ATCAGA ATCAGA ATCAGA ATCAG
40400992 GTAACAGAAT
Statistics
Matches: 72, Mismatches: 11, Indels: 16
0.73 0.11 0.16
Matches are distributed among these distances:
5 5 0.07
6 60 0.83
7 4 0.06
8 3 0.04
ACGTcount: A:0.48, C:0.14, G:0.16, T:0.21
Consensus pattern (6 bp):
ATCAGA
Found at i:40400972 original size:31 final size:31
Alignment explanation
Indices: 40400904--40401003 Score: 137
Period size: 31 Copynumber: 3.2 Consensus size: 31
40400894 TATCAGAACT
* * *
40400904 AGAATCAGAATCAGAATCAGAATTAGGTGAC
1 AGAATCAGAATCAGAATCAGTATCAGGTAAC
* *
40400935 AAAATCAGAATCAGAATCAGTATCAGGTAAT
1 AGAATCAGAATCAGAATCAGTATCAGGTAAC
* *
40400966 AGAATCAAAATCAAAATCAGTATCAGGTAAC
1 AGAATCAGAATCAGAATCAGTATCAGGTAAC
40400997 AGAATCA
1 AGAATCA
40401004 AAAATCAAAA
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 60 1.00
ACGTcount: A:0.49, C:0.14, G:0.17, T:0.20
Consensus pattern (31 bp):
AGAATCAGAATCAGAATCAGTATCAGGTAAC
Found at i:40401193 original size:27 final size:27
Alignment explanation
Indices: 40401151--40401225 Score: 105
Period size: 27 Copynumber: 2.8 Consensus size: 27
40401141 GCTCAGTTAT
* * *
40401151 CAGATATTGTGACAGAGTCACCAGATA
1 CAGATATTGTGGCAGAGCCACCAGAAA
40401178 CAGATATTGTGGCAGAGCCACCAGAAA
1 CAGATATTGTGGCAGAGCCACCAGAAA
* *
40401205 CAGATAATGTGGCAAAGCCAC
1 CAGATATTGTGGCAGAGCCAC
40401226 TTAACAGAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.37, C:0.21, G:0.24, T:0.17
Consensus pattern (27 bp):
CAGATATTGTGGCAGAGCCACCAGAAA
Found at i:40401412 original size:22 final size:22
Alignment explanation
Indices: 40401384--40401470 Score: 113
Period size: 22 Copynumber: 4.0 Consensus size: 22
40401374 GCAAATACGT
*
40401384 TTGGCACACAGCCATAATCAGG
1 TTGGCACAGAGCCATAATCAGG
40401406 TTGGCACAGAGCCATAATCAGG
1 TTGGCACAGAGCCATAATCAGG
* *
40401428 TTGGCATAGAGCCAT-ATGTAGG
1 TTGGCACAGAGCCATAAT-CAGG
* *
40401450 TTGACACAAAGCCATAATCAG
1 TTGGCACAGAGCCATAATCAG
40401471 AAGGCTTTAA
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
21 2 0.04
22 52 0.93
23 2 0.04
ACGTcount: A:0.33, C:0.22, G:0.24, T:0.21
Consensus pattern (22 bp):
TTGGCACAGAGCCATAATCAGG
Found at i:40403457 original size:29 final size:28
Alignment explanation
Indices: 40403422--40403495 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 28
40403412 GTTGTGAGAT
*
40403422 TGGCACTAAGTGTGCGGGCTTGAAATGT-A
1 TGGCACTAAGTGTGCGAG-TTGAAA-GTAA
*
40403451 TGGCACTAAGTGTGCGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGAGTTGAAAGTA-A
40403480 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
40403496 TGGTTGATTA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
27 2 0.05
28 5 0.12
29 34 0.83
ACGTcount: A:0.26, C:0.15, G:0.32, T:0.27
Consensus pattern (28 bp):
TGGCACTAAGTGTGCGAGTTGAAAGTAA
Found at i:40412790 original size:40 final size:40
Alignment explanation
Indices: 40412721--40412834 Score: 131
Period size: 40 Copynumber: 2.8 Consensus size: 40
40412711 CCTTTCATAT
*
40412721 CTGAAGCTATCTTAG-TATCGCATACTAAGTGCCATATATAG
1 CTGAAGCTAT-TTCGAT-TCGCATACTAAGTGCCATATATAG
***
40412762 CTGAAGCTATTTCGATTCGCATACTAAGTGTTTTATATAG
1 CTGAAGCTATTTCGATTCGCATACTAAGTGCCATATATAG
* * * *
40412802 CCGAAGCTATCTCGATACGCACACTAAGTGCCA
1 CTGAAGCTATTTCGATTCGCATACTAAGTGCCA
40412835 AACATAATCA
Statistics
Matches: 61, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
40 50 0.82
41 11 0.18
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.31
Consensus pattern (40 bp):
CTGAAGCTATTTCGATTCGCATACTAAGTGCCATATATAG
Found at i:40421784 original size:20 final size:20
Alignment explanation
Indices: 40421759--40421797 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
40421749 AATTATGGAT
40421759 GTATGCTAATTACTCGGTAA
1 GTATGCTAATTACTCGGTAA
*
40421779 GTATGCTAATTATTCGGTA
1 GTATGCTAATTACTCGGTA
40421798 CGTTTATTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.13, G:0.21, T:0.38
Consensus pattern (20 bp):
GTATGCTAATTACTCGGTAA
Found at i:40424551 original size:29 final size:29
Alignment explanation
Indices: 40424516--40424652 Score: 127
Period size: 29 Copynumber: 4.7 Consensus size: 29
40424506 CTACTCGATT
* *
40424516 TCGCACACTTAGTGCCACGTAATTT-AAGC
1 TCGCACACTTAGTGCCA-ATAATTTCCAGC
** **
40424545 TCGCACACACAGTGCCATATTTTTTTCCAGC
1 TCGCACACTTAGTGCCA-A-TAATTTCCAGC
*
40424576 TTGCACACTTAGTGCCAA-ATATTTCCAGC
1 TCGCACACTTAGTGCCAATA-ATTTCCAGC
*
40424605 ACGCACACTTAGTGCC-ATATATTTCCAGC
1 TCGCACACTTAGTGCCAATA-ATTTCCAGC
*
40424634 ACGCACACTTAGTGCCAAT
1 TCGCACACTTAGTGCCAAT
40424653 CTCGACACCA
Statistics
Matches: 89, Mismatches: 14, Indels: 9
0.79 0.12 0.08
Matches are distributed among these distances:
28 1 0.01
29 64 0.72
30 7 0.08
31 17 0.19
ACGTcount: A:0.27, C:0.30, G:0.15, T:0.28
Consensus pattern (29 bp):
TCGCACACTTAGTGCCAATAATTTCCAGC
Found at i:40424592 original size:60 final size:58
Alignment explanation
Indices: 40424517--40424651 Score: 155
Period size: 60 Copynumber: 2.3 Consensus size: 58
40424507 TACTCGATTT
** * * *
40424517 CGCACACTTAGTGCCACGTAATTT-AAGCTCGCACACACAGTGCCATATTTTTTTCCAGCT
1 CGCACACTTAGTGCCAAAT-ATTTCAAGCACGCACACACAGTGCCATA--TATTTCCAGCA
* * **
40424577 TGCACACTTAGTGCCAAATATTTCCAGCACGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCAAATATTTCAAGCACGCACACACAGTGCCATATATTTCCAGCA
40424635 CGCACACTTAGTGCCAA
1 CGCACACTTAGTGCCAA
40424652 TCTCGACACC
Statistics
Matches: 64, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
58 25 0.39
59 4 0.06
60 35 0.55
ACGTcount: A:0.27, C:0.30, G:0.15, T:0.27
Consensus pattern (58 bp):
CGCACACTTAGTGCCAAATATTTCAAGCACGCACACACAGTGCCATATATTTCCAGCA
Found at i:40432635 original size:29 final size:29
Alignment explanation
Indices: 40432601--40432732 Score: 140
Period size: 29 Copynumber: 4.6 Consensus size: 29
40432591 TACTCGATTT
** * *
40432601 CGCACACTTAGTGCCATGCGATTT-AAGCC
1 CGCACACTTAGTGCCAT-ATATTTCCAGCA
* **** * *
40432630 CGCACACATAGTGCCATGCCCTTCGAGCT
1 CGCACACTTAGTGCCATATATTTCCAGCA
40432659 CGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
*
40432688 TGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
40432717 CGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
40432733 ATCTCGTCAC
Statistics
Matches: 86, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
28 2 0.02
29 84 0.98
ACGTcount: A:0.25, C:0.33, G:0.17, T:0.25
Consensus pattern (29 bp):
CGCACACTTAGTGCCATATATTTCCAGCA
Found at i:40438196 original size:14 final size:14
Alignment explanation
Indices: 40438177--40438203 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
40438167 TATTAAAGCA
40438177 ATAATTAAGAACAC
1 ATAATTAAGAACAC
40438191 ATAATTAAGAACA
1 ATAATTAAGAACA
40438204 AATCAAGTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.11, G:0.07, T:0.22
Consensus pattern (14 bp):
ATAATTAAGAACAC
Found at i:40443014 original size:48 final size:48
Alignment explanation
Indices: 40442933--40443243 Score: 342
Period size: 48 Copynumber: 6.5 Consensus size: 48
40442923 GTACCAATGT
* * *
40442933 CATGTCCCCGACATGGTCTTACA-T-GAATCCACATATCATCGCCGATGC
1 CATGTCCCAGACATGGTCTTACACTGGCA--CACATATCATCACCGATGC
* * *
40442981 CATGTTCCAGACATGGTCTTACACTGGCACACATACCATCATCGATGC
1 CATGTCCCAGACATGGTCTTACACTGGCACACATATCATCACCGATGC
* * ** ** ***
40443029 CATGTCCCAGACATGGTCCTACACAGGTGCATGTATCATCTTTGATGC
1 CATGTCCCAGACATGGTCTTACACTGGCACACATATCATCACCGATGC
* * *
40443077 CAGGTCCTAGACATGGTCTTACACTGGCACATATATCAT-AGCCGATGC
1 CATGTCCCAGACATGGTCTTACACTGGCACACATATCATCA-CCGATGC
* *
40443125 CATGTCCCAGACATGGTCTTACACTAGCACACATATCATCACTGATGC
1 CATGTCCCAGACATGGTCTTACACTGGCACACATATCATCACCGATGC
* * * *
40443173 CATGTCCCGGACATGGTCTTACACAGGCACATATATCATC-CATGATGC
1 CATGTCCCAGACATGGTCTTACACTGGCACACATATCATCAC-CGATGC
40443221 CATGTCCCAGACATGGTCTTACA
1 CATGTCCCAGACATGGTCTTACA
40443244 TAGAATCTCA
Statistics
Matches: 222, Mismatches: 36, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
47 1 0.00
48 217 0.98
49 2 0.01
50 2 0.01
ACGTcount: A:0.26, C:0.30, G:0.18, T:0.26
Consensus pattern (48 bp):
CATGTCCCAGACATGGTCTTACACTGGCACACATATCATCACCGATGC
Found at i:40443210 original size:144 final size:144
Alignment explanation
Indices: 40442965--40443243 Score: 425
Period size: 144 Copynumber: 1.9 Consensus size: 144
40442955 ATGAATCCAC
* * *
40442965 ATATCATCGCCGATGCCATGTTCCAGACATGGTCTTACACTGGCACACATACCATCATCGATGCC
1 ATATCATAGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCACACATACCATCATCGATGCC
** * ** *
40443030 ATGTCCCAGACATGGTCCTACACAGGTGCATGTATCATCTTTGATGCCAGGTCCTAGACATGGTC
66 ATGTCCCAGACATGGTCCTACACAGGCACATATATCATCCATGATGCCAGGTCCCAGACATGGTC
40443095 TTACACTGGCACAT
131 TTACACTGGCACAT
*
40443109 ATATCATAGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCACACATATCATCA-CTGATGC
1 ATATCATAGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCACACATACCATCATC-GATGC
* * *
40443173 CATGTCCCGGACATGGTCTTACACAGGCACATATATCATCCATGATGCCATGTCCCAGACATGGT
65 CATGTCCCAGACATGGTCCTACACAGGCACATATATCATCCATGATGCCAGGTCCCAGACATGGT
40443238 CTTACA
130 CTTACA
40443244 TAGAATCTCA
Statistics
Matches: 121, Mismatches: 13, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
143 1 0.01
144 120 0.99
ACGTcount: A:0.27, C:0.29, G:0.18, T:0.26
Consensus pattern (144 bp):
ATATCATAGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCACACATACCATCATCGATGCC
ATGTCCCAGACATGGTCCTACACAGGCACATATATCATCCATGATGCCAGGTCCCAGACATGGTC
TTACACTGGCACAT
Found at i:40443739 original size:34 final size:34
Alignment explanation
Indices: 40443701--40443767 Score: 125
Period size: 34 Copynumber: 2.0 Consensus size: 34
40443691 AACCCTAGCC
*
40443701 GAATCATTTTCCCTCTTATACGAGCCCATATTTA
1 GAATCATTTTCCCTCTTATACGAACCCATATTTA
40443735 GAATCATTTTCCCTCTTATACGAACCCATATTT
1 GAATCATTTTCCCTCTTATACGAACCCATATTT
40443768 TTCATTCACA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.27, C:0.27, G:0.07, T:0.39
Consensus pattern (34 bp):
GAATCATTTTCCCTCTTATACGAACCCATATTTA
Found at i:40445664 original size:40 final size:40
Alignment explanation
Indices: 40445581--40445733 Score: 143
Period size: 40 Copynumber: 3.8 Consensus size: 40
40445571 TCGAATGATG
* *
40445581 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTGACCAAA
* **
40445621 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTCCCAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTGACCAAA
* **
40445661 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGCT-ATTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TGACCA-AA
* * *
40445702 -CCGGGCTATGTCCCGAAGGCTTTTGAGCGAGT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT
40445734 CGTTATATCC
Statistics
Matches: 94, Mismatches: 14, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
39 2 0.02
40 81 0.86
41 11 0.12
ACGTcount: A:0.23, C:0.24, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACCAAA
Found at i:40453656 original size:40 final size:40
Alignment explanation
Indices: 40453579--40453684 Score: 117
Period size: 40 Copynumber: 2.6 Consensus size: 40
40453569 GATGTCTGGG
* *
40453579 CTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGA
1 CTAAGTCCCGAAGGCATTTGTGC-GAGTGACCAAATCCGGA
** *
40453619 CTAAGAT-CCGAAGGCATTTGTGCGAGTTCCCAAATCCGGG
1 CTAAG-TCCCGAAGGCATTTGTGCGAGTGACCAAATCCGGA
* *
40453659 TTAAGTCCCAAAGGCATTTGTGCGAG
1 CTAAGTCCCGAAGGCATTTGTGCGAG
40453685 CTATTATAAC
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
39 1 0.02
40 47 0.84
41 8 0.14
ACGTcount: A:0.25, C:0.24, G:0.26, T:0.25
Consensus pattern (40 bp):
CTAAGTCCCGAAGGCATTTGTGCGAGTGACCAAATCCGGA
Found at i:40461905 original size:48 final size:48
Alignment explanation
Indices: 40461834--40462148 Score: 305
Period size: 48 Copynumber: 6.6 Consensus size: 48
40461824 ATAAGTACCA
* ***
40461834 ATGCCATGTCCCCGACATGGTCTTACATGAATC-CACATATCATTGTCG
1 ATGCCATGTCCCAGACATGGTCTTACAT-AATCACACATATCATCACCG
* * * *
40461882 ATGCCATGTCCCAAACATGGTCTTACACAATCACACATATCATCTCTG
1 ATGCCATGTCCCAGACATGGTCTTACATAATCACACATATCATCACCG
* * * * * * *
40461930 ATCCCATGTCTCAAACATGGTCTTACATAGGT-ACATATATCATCGCTG
1 ATGCCATGTCCCAGACATGGTCTTACATA-ATCACACATATCATCACCG
* * *** *
40461978 ATGCCATGTCCTAGATATGGTCTTACATTGGCACATATATCATCACCG
1 ATGCCATGTCCCAGACATGGTCTTACATAATCACACATATCATCACCG
*
40462026 ATGCCATGTCCCAGACATGGTCTTACACT-AGCACACATATCATCACCG
1 ATGCCATGTCCCAGACATGGTCTTACA-TAATCACACATATCATCACCG
* * * * *
40462074 ATGCCATGTCCCTGACATGGTCTTACACAAGCACATATATCATCGCC-
1 ATGCCATGTCCCAGACATGGTCTTACATAATCACACATATCATCACCG
* *
40462121 ATTTCCATGTCCCAGACATGGTTTTACA
1 A-TGCCATGTCCCAGACATGGTCTTACA
40462149 CAGAATCTCA
Statistics
Matches: 228, Mismatches: 33, Indels: 12
0.84 0.12 0.04
Matches are distributed among these distances:
47 6 0.03
48 220 0.96
49 2 0.01
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.29
Consensus pattern (48 bp):
ATGCCATGTCCCAGACATGGTCTTACATAATCACACATATCATCACCG
Found at i:40462129 original size:144 final size:144
Alignment explanation
Indices: 40461834--40462148 Score: 375
Period size: 144 Copynumber: 2.2 Consensus size: 144
40461824 ATAAGTACCA
* * * ***
40461834 ATGCCATGTCCCCGACATGGTCTTACA-T-GAATCCACATATCATTGTCGATGCCATGTCCCAAA
1 ATGCCATGTCCCAGACATGGTCTTACATTGGCA--CATATATCATCACCGATGCCATGTCCCAAA
* * * * * * *
40461897 CATGGTCTTACACAATCACACATATCATCTCTGATCCCATGTCTCAAACATGGTCTTACATAGGT
64 CATGGTCTTACACAAGCACACATATCATCACCGATCCCATGTCCCAAACATGGTCTTACACAAGC
*
40461962 ACATATATCATCGCTG
129 ACATATATCATCGCTC
* * *
40461978 ATGCCATGTCCTAGATATGGTCTTACATTGGCACATATATCATCACCGATGCCATGTCCCAGACA
1 ATGCCATGTCCCAGACATGGTCTTACATTGGCACATATATCATCACCGATGCCATGTCCCAAACA
* * **
40462043 TGGTCTTACACTAGCACACATATCATCACCGATGCCATGTCCCTGACATGGTCTTACACAAGCAC
66 TGGTCTTACACAAGCACACATATCATCACCGATCCCATGTCCCAAACATGGTCTTACACAAGCAC
40462108 ATATATCATCGC-C
131 ATATATCATCGCTC
* *
40462121 ATTTCCATGTCCCAGACATGGTTTTACA
1 A-TGCCATGTCCCAGACATGGTCTTACA
40462149 CAGAATCTCA
Statistics
Matches: 143, Mismatches: 25, Indels: 6
0.82 0.14 0.03
Matches are distributed among these distances:
143 1 0.01
144 139 0.97
145 1 0.01
146 2 0.01
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.29
Consensus pattern (144 bp):
ATGCCATGTCCCAGACATGGTCTTACATTGGCACATATATCATCACCGATGCCATGTCCCAAACA
TGGTCTTACACAAGCACACATATCATCACCGATCCCATGTCCCAAACATGGTCTTACACAAGCAC
ATATATCATCGCTC
Found at i:40474416 original size:21 final size:21
Alignment explanation
Indices: 40474390--40474429 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
40474380 GAGTCCGAGT
40474390 TCACTTATGGATGCGAATGCC
1 TCACTTATGGATGCGAATGCC
40474411 TCACTTATGGATGCGAATG
1 TCACTTATGGATGCGAATG
40474430 TCCGAACTCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (21 bp):
TCACTTATGGATGCGAATGCC
Found at i:40483086 original size:49 final size:50
Alignment explanation
Indices: 40482797--40483078 Score: 259
Period size: 49 Copynumber: 5.6 Consensus size: 50
40482787 ATTGTGAGGA
* * *
40482797 CACGTGTGTAGTACTAAGTGGAGGCTACTACGTGTTCCGAATAATT-GGT
1 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTCGGT
* * * * * * *
40482846 CGCATGTGTAGTACTAAGCGCAGGCTACTATGCGTACCCGATAACTTCGAT
1 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAA-TTCGGT
** * * *
40482897 CACGTGTGTAGTACTTGGTCGCATGTG-TAGTAC-TAAGT-GCGGATAACTTCGAT
1 CACGTGTGTAGTACTAAGT-GCA-G-GCTACTACGT--GTACCGGATAA-TTCGGT
* * * ** *
40482950 CACGGGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGTTAGGT
1 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTCGGT
40483000 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT-GGT
1 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTCGGT
* *
40483049 CGCATGTGTAGTACTAAGTGCAGGCTACTA
1 CACGTGTGTAGTACTAAGTGCAGGCTACTA
40483079 TGCGTACCAG
Statistics
Matches: 186, Mismatches: 37, Indels: 20
0.77 0.15 0.08
Matches are distributed among these distances:
49 66 0.35
50 50 0.27
51 26 0.14
52 7 0.04
53 34 0.18
54 3 0.02
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.29
Consensus pattern (50 bp):
CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTCGGT
Found at i:40487254 original size:9 final size:9
Alignment explanation
Indices: 40487240--40487265 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
40487230 AGAAAAATCA
40487240 AAAGTTGGG
1 AAAGTTGGG
40487249 AAAGTTGGG
1 AAAGTTGGG
40487258 AAAGTTGG
1 AAAGTTGG
40487266 TAAGTTCATA
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:0.35, C:0.00, G:0.42, T:0.23
Consensus pattern (9 bp):
AAAGTTGGG
Found at i:40489000 original size:46 final size:46
Alignment explanation
Indices: 40488933--40489061 Score: 222
Period size: 46 Copynumber: 2.8 Consensus size: 46
40488923 TGTAACCCGC
* * * *
40488933 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
40488979 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
40489025 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
40489062 TGCTCAACCA
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 79 1.00
ACGTcount: A:0.29, C:0.29, G:0.22, T:0.19
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:40489080 original size:46 final size:45
Alignment explanation
Indices: 40488941--40489080 Score: 140
Period size: 46 Copynumber: 3.0 Consensus size: 45
40488931 GCCCATAAGC
* ** * *
40488941 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTC-GCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCTCACCATCC-T-AGT
*** *
40488987 GAACTCGGACTCAACTCAACGAGTTCGGACATTC-GCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCTCACCATCC-T-AGT
40489033 GAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCTAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCTC-ACCATCCTAGT
40489079 GA
1 GA
40489081 CATGTCACTT
Statistics
Matches: 85, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
46 79 0.93
47 1 0.01
48 5 0.06
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (45 bp):
GAACTCGGACTCAACTCAACGAGTTCGGATGCTCACCATCCTAGT
Found at i:40491499 original size:46 final size:46
Alignment explanation
Indices: 40491444--40491624 Score: 233
Period size: 46 Copynumber: 3.9 Consensus size: 46
40491434 TAGGATGGTT
40491444 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
1 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
* * *
40491490 GAGCGTCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAAC
1 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG---C
*
40491536 TAGGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
1 GA-GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
* ** *
40491583 GAACGCCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
40491625 GCGGGTTACA
Statistics
Matches: 116, Mismatches: 12, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 4 0.03
45 2 0.02
46 71 0.61
47 33 0.28
48 2 0.02
50 4 0.03
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (46 bp):
GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
Found at i:40491605 original size:93 final size:93
Alignment explanation
Indices: 40491446--40491616 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
40491436 GGATGGTTGA
* *
40491446 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
40491511 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
40491539 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
40491604 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
40491617 ACTTATGGGC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:40494474 original size:15 final size:15
Alignment explanation
Indices: 40494454--40494522 Score: 84
Period size: 15 Copynumber: 4.6 Consensus size: 15
40494444 GTATCTTGGG
40494454 TTTCTTTATCCTGGA
1 TTTCTTTATCCTGGA
* *
40494469 TCTCTTTATTCTGGA
1 TTTCTTTATCCTGGA
* *
40494484 TTTCTTTATTCTGGG
1 TTTCTTTATCCTGGA
* *
40494499 TTTCTCTATCTTGGA
1 TTTCTTTATCCTGGA
40494514 TTTCTTTAT
1 TTTCTTTAT
40494523 TCGGTTTTCT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 45 1.00
ACGTcount: A:0.12, C:0.17, G:0.13, T:0.58
Consensus pattern (15 bp):
TTTCTTTATCCTGGA
Found at i:40494523 original size:30 final size:30
Alignment explanation
Indices: 40494445--40494532 Score: 99
Period size: 30 Copynumber: 3.0 Consensus size: 30
40494435 CATAGTATCG
* * * *
40494445 TATCTTGGGTTTCTTTATCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTCTGGATTTCTC
*
40494475 TAT-TCTGGATTTCTTTATTCTGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCTGGATTTCTC
*
40494505 TATCTTGGATTTCTTTATTC-GGTTTTCT
1 TATCTTGGATTTCTTTATTCTGGATTTCT
40494533 TGTTATCTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
29 8 0.16
30 41 0.82
31 1 0.02
ACGTcount: A:0.10, C:0.17, G:0.16, T:0.57
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATTCTGGATTTCTC
Found at i:40496937 original size:46 final size:46
Alignment explanation
Indices: 40496882--40497062 Score: 233
Period size: 46 Copynumber: 3.9 Consensus size: 46
40496872 TAGGATGGTT
40496882 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
1 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
* * *
40496928 GAGCGTCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAAC
1 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG---C
*
40496974 TAGGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
1 GA-GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
* ** *
40497021 GAACGCCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
40497063 GCGGGTTACA
Statistics
Matches: 116, Mismatches: 12, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 4 0.03
45 2 0.02
46 71 0.61
47 33 0.28
48 2 0.02
50 4 0.03
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (46 bp):
GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
Found at i:40497043 original size:93 final size:93
Alignment explanation
Indices: 40496884--40497054 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
40496874 GGATGGTTGA
* *
40496884 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
40496949 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
40496977 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
40497042 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
40497055 ACTTATGGGC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:40504756 original size:92 final size:92
Alignment explanation
Indices: 40504644--40504813 Score: 288
Period size: 92 Copynumber: 1.8 Consensus size: 92
40504634 CGCCCATAAG
* *
40504644 CGAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTC-GACTCAACTCA
1 CGAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
40504708 ACGAGTTCGGATGCCTAGTTACATCTCT
66 ACGAGTTC-GATGCCTAGTTACATCTCT
* *
40504736 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
40504801 ACGAGTTCGATGC
66 ACGAGTTCGATGC
40504814 TCAACCATCC
Statistics
Matches: 73, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
92 54 0.74
93 19 0.26
ACGTcount: A:0.28, C:0.30, G:0.20, T:0.22
Consensus pattern (92 bp):
CGAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGATGCCTAGTTACATCTCT
Found at i:40504788 original size:46 final size:45
Alignment explanation
Indices: 40504637--40504809 Score: 190
Period size: 46 Copynumber: 3.8 Consensus size: 45
40504627 TGTAACCCGC
* * * *
40504637 CCATAAGCGAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTC-GGCATTCGCAT
*
40504683 CCATAAGTGAACTC-GACTCAACTCAACGAGTTCGG-ATGC-CTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGCATTCGC-A--T
* ***
40504728 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGTTCGG-CATTCGCAT
40504775 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCG
40504810 ATGCTCAACC
Statistics
Matches: 106, Mismatches: 13, Indels: 16
0.79 0.10 0.12
Matches are distributed among these distances:
42 1 0.01
43 3 0.03
44 2 0.02
45 23 0.22
46 46 0.43
47 26 0.25
49 4 0.04
50 1 0.01
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (45 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGCATTCGCAT
Found at i:40512054 original size:79 final size:82
Alignment explanation
Indices: 40511917--40512101 Score: 229
Period size: 79 Copynumber: 2.3 Consensus size: 82
40511907 TCGAATGATG
* *
40511917 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATACCCGGACTAGGATTCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACTAAACCCGGACTAAGATTCGAAGGCATT
*
40511981 CGTACGAGTTAATA-AA
66 CGTACGAGTCAATATAA
* **
40511997 TCCGGGCTAAG-CCCGAAGGCATTTGTGC-AAGTTACTAAACCCGGGTTAAG-TTCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACTAAACCCGGACTAAGATT-CGAAGGCAT
* *
40512059 TCGTGCGAGTCACTATAA
65 TCGTACGAGTCAATATAA
**
40512077 -CCGGGCTTCGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
40512102 AGCGAGTCGT
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 2 0.02
79 55 0.60
80 34 0.37
ACGTcount: A:0.25, C:0.24, G:0.27, T:0.24
Consensus pattern (82 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACTAAACCCGGACTAAGATTCGAAGGCATT
CGTACGAGTCAATATAA
Found at i:40512058 original size:40 final size:40
Alignment explanation
Indices: 40511918--40512101 Score: 160
Period size: 40 Copynumber: 4.6 Consensus size: 40
40511908 CGAATGATGT
* *
40511918 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATAC
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-AAGTTACTAAAC
* * * * * * * *
40511958 CCGGACTAGGAT-TCGAAGGCATTCGTACGAGTTAATAAAT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCAAGTTACTAAAC
40511998 CCGGGCTAAG-CCCGAAGGCATTTGTGCAAGTTACTAAAC
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTAAAC
* * * * *
40512037 CCGGGTTAAGTTCCGAAGGCATTCGTGCGAGTCACTATAA-
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTA-AAC
**
40512077 CCGGGCTTCGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
40512102 AGCGAGTCGT
Statistics
Matches: 111, Mismatches: 28, Indels: 10
0.74 0.19 0.07
Matches are distributed among these distances:
39 31 0.28
40 72 0.65
41 8 0.07
ACGTcount: A:0.25, C:0.24, G:0.27, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTAAAC
Found at i:40523422 original size:27 final size:27
Alignment explanation
Indices: 40523385--40523498 Score: 126
Period size: 27 Copynumber: 4.2 Consensus size: 27
40523375 AGCATGGCTG
** *
40523385 CCAG-AACAGATATTGTGATAGAGTCA
1 CCAGAAACAGATATTGTGGCAGAGCCA
* *
40523411 CCAGATACAGATATTATGGCAGAGCCA
1 CCAGAAACAGATATTGTGGCAGAGCCA
*
40523438 CCA-AAACAGATATTTGTGGCATAGCCA
1 CCAGAAACAGATA-TTGTGGCAGAGCCA
40523465 CCAGAAACAGATATTTGTGGCATG-GCCA
1 CCAGAAACAGATA-TTGTGGCA-GAGCCA
40523493 CCAGAA
1 CCAGAA
40523499 CGCTTCCTCC
Statistics
Matches: 75, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
26 12 0.16
27 35 0.47
28 28 0.37
ACGTcount: A:0.37, C:0.21, G:0.22, T:0.20
Consensus pattern (27 bp):
CCAGAAACAGATATTGTGGCAGAGCCA
Found at i:40523481 original size:28 final size:28
Alignment explanation
Indices: 40523409--40523498 Score: 130
Period size: 28 Copynumber: 3.3 Consensus size: 28
40523399 GTGATAGAGT
* * *
40523409 CACCAGATACAGATA-TTATGGCAGAGC
1 CACCAGAAACAGATATTTGTGGCATAGC
40523436 CACCA-AAACAGATATTTGTGGCATAGC
1 CACCAGAAACAGATATTTGTGGCATAGC
*
40523463 CACCAGAAACAGATATTTGTGGCATGGC
1 CACCAGAAACAGATATTTGTGGCATAGC
40523491 CACCAGAA
1 CACCAGAA
40523499 CGCTTCCTCC
Statistics
Matches: 57, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
26 8 0.14
27 20 0.35
28 29 0.51
ACGTcount: A:0.37, C:0.23, G:0.21, T:0.19
Consensus pattern (28 bp):
CACCAGAAACAGATATTTGTGGCATAGC
Found at i:40524605 original size:9 final size:9
Alignment explanation
Indices: 40524591--40524619 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
40524581 AAAAGAAAAT
40524591 GACAAAAGA
1 GACAAAAGA
40524600 GACAAAAGA
1 GACAAAAGA
40524609 GACAAAAGA
1 GACAAAAGA
40524618 GA
1 GA
40524620 GGAGAGTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.66, C:0.10, G:0.24, T:0.00
Consensus pattern (9 bp):
GACAAAAGA
Found at i:40529671 original size:37 final size:37
Alignment explanation
Indices: 40529599--40529704 Score: 149
Period size: 37 Copynumber: 2.9 Consensus size: 37
40529589 AGCTCAGACG
* * ** *
40529599 AAATCTCCACACGAAGTTATCGAATCTTTCCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
*
40529636 AAATCTCCACACGTAGTCATCGGGTCTTACTCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
*
40529673 TAATCTCCACACGTAGTCATCGGGTCTTACCC
1 AAATCTCCACACGTAGTCATCGGGTCTTACCC
40529705 AGAATATATT
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 61 1.00
ACGTcount: A:0.27, C:0.31, G:0.16, T:0.25
Consensus pattern (37 bp):
AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
Found at i:40529906 original size:48 final size:48
Alignment explanation
Indices: 40529854--40530230 Score: 535
Period size: 48 Copynumber: 7.7 Consensus size: 48
40529844 GCACATCGCC
* *
40529854 TACATATTTCACACTAGCCATTAGGCTTTACCATATATACATATCTCA
1 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCA
40529902 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATA
1 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTC--A
* * *
40529952 TATATATTTCACA-TTGACCATTCGACTTTACCACATATACATATCTCA
1 TACATATTTCACACTAG-CCATTCGGCTTTACCACATATACATATCTCA
40530000 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATA
1 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTC--A
* *
40530050 TATATATTTCACA-TTGACCATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACACTAG-CCATTCGGCTTTACCACATATACATATCTCA
40530098 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATA
1 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTC--A
* * *
40530148 TATATATTTCACA-TTGACCATTCGGCTTTACCACATATGCATATCTCA
1 TACATATTTCACACTAG-CCATTCGGCTTTACCACATATACATATCTCA
* * *
40530196 TACATATTTCACATTAGCAATTCGGCCTTACCACA
1 TACATATTTCACACTAGCCATTCGGCTTTACCACA
40530231 AATATGCATG
Statistics
Matches: 298, Mismatches: 19, Indels: 24
0.87 0.06 0.07
Matches are distributed among these distances:
48 159 0.53
49 12 0.04
50 127 0.43
ACGTcount: A:0.32, C:0.27, G:0.06, T:0.35
Consensus pattern (48 bp):
TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCA
Found at i:40529990 original size:98 final size:98
Alignment explanation
Indices: 40529857--40530230 Score: 660
Period size: 98 Copynumber: 3.8 Consensus size: 98
40529847 CATCGCCTAC
* * *
40529857 ATATTTCACACT-AGCCATTAGGCTTTACCATATATACATATCTCATACATATTTCACACTAGCC
1 ATATTTCACATTGA-CCATTCGGCTTTACCACATATACATATCTCATACATATTTCACACTAGCC
40529921 ATTCGGCTTTACCACATATACATATCTCATATAT
65 ATTCGGCTTTACCACATATACATATCTCATATAT
*
40529955 ATATTTCACATTGACCATTCGACTTTACCACATATACATATCTCATACATATTTCACACTAGCCA
1 ATATTTCACATTGACCATTCGGCTTTACCACATATACATATCTCATACATATTTCACACTAGCCA
40530020 TTCGGCTTTACCACATATACATATCTCATATAT
66 TTCGGCTTTACCACATATACATATCTCATATAT
40530053 ATATTTCACATTGACCATTCGGCTTTACCACATATACATATCTCATACATATTTCACACTAGCCA
1 ATATTTCACATTGACCATTCGGCTTTACCACATATACATATCTCATACATATTTCACACTAGCCA
40530118 TTCGGCTTTACCACATATACATATCTCATATAT
66 TTCGGCTTTACCACATATACATATCTCATATAT
* * *
40530151 ATATTTCACATTGACCATTCGGCTTTACCACATATGCATATCTCATACATATTTCACATTAGCAA
1 ATATTTCACATTGACCATTCGGCTTTACCACATATACATATCTCATACATATTTCACACTAGCCA
*
40530216 TTCGGCCTTACCACA
66 TTCGGCTTTACCACA
40530231 AATATGCATG
Statistics
Matches: 266, Mismatches: 9, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
98 265 1.00
99 1 0.00
ACGTcount: A:0.32, C:0.26, G:0.06, T:0.35
Consensus pattern (98 bp):
ATATTTCACATTGACCATTCGGCTTTACCACATATACATATCTCATACATATTTCACACTAGCCA
TTCGGCTTTACCACATATACATATCTCATATAT
Found at i:40530269 original size:47 final size:47
Alignment explanation
Indices: 40530204--40530443 Score: 356
Period size: 47 Copynumber: 5.1 Consensus size: 47
40530194 CATACATATT
* * * * *
40530204 TCACATTAGCAATTCGGCCTTACCACAAATATGCATGTTCATATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
* *
40530251 TCACATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
*
40530298 TCACATTGGCCATTCGACCTTATCACATATATGCATGTTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
*
40530345 TCACATTGGCCATTC-GCCTTATTACATATATGCATGTTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
* * **
40530391 TCACATTGGCCATTCGGCCTTATCTCATATATACACATTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
40530438 TCACAT
1 TCACAT
40530444 AAAATCCTAA
Statistics
Matches: 176, Mismatches: 16, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
46 44 0.25
47 132 0.75
ACGTcount: A:0.28, C:0.28, G:0.10, T:0.33
Consensus pattern (47 bp):
TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
Found at i:40530324 original size:22 final size:22
Alignment explanation
Indices: 40530250--40530325 Score: 59
Period size: 23 Copynumber: 3.3 Consensus size: 22
40530240 GTTCATATTC
*
40530250 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGACCTT
*
40530272 ATCACACATAT-G-CATGCTC-ACATT
1 AT--CACAT-TGGCCAT--TCGACCTT
40530296 CATCACATTGGCCATTCGACCTT
1 -ATCACATTGGCCATTCGACCTT
40530319 ATCACAT
1 ATCACAT
40530326 ATATGCATGT
Statistics
Matches: 42, Mismatches: 3, Indels: 18
0.67 0.05 0.29
Matches are distributed among these distances:
22 12 0.29
23 13 0.31
24 12 0.29
25 5 0.12
ACGTcount: A:0.26, C:0.32, G:0.12, T:0.30
Consensus pattern (22 bp):
ATCACATTGGCCATTCGACCTT
Found at i:40530412 original size:93 final size:94
Alignment explanation
Indices: 40530156--40530443 Score: 359
Period size: 93 Copynumber: 3.1 Consensus size: 94
40530146 TATATATATT
* * * * * *
40530156 TCACATTGACCATTCGGCTTTA-C-CACATATGCATATCTCATACATAT-TTCACATTAGCAATT
1 TCACATTGGCCATTCGGCCTTATCACACATATGCAT-GCTC--ACAT-TCATCACATTGGCCATT
* * *
40530218 CGGCCTTACCACAAATATGCATGTTCATATTCA
62 CGGCCTTATCACATATATGCATGTTCACATTCA
*
40530251 TCACATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCATCACATTGGCCATTCGAC
1 TCACATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCATCACATTGGCCATTCGGC
40530316 CTTATCACATATATGCATGTTCACATTCA
66 CTTATCACATATATGCATGTTCACATTCA
* * *
40530345 TCACATTGGCCATTC-GCCTTATTACATATATGCATGTTCACATTCATCACATTGGCCATTCGGC
1 TCACATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCATCACATTGGCCATTCGGC
* * **
40530409 CTTATCTCATATATACACATTCACATTCA
66 CTTATCACATATATGCATGTTCACATTCA
40530438 TCACAT
1 TCACAT
40530444 AAAATCCTAA
Statistics
Matches: 172, Mismatches: 18, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
93 77 0.45
94 60 0.35
95 20 0.12
96 4 0.02
97 11 0.06
ACGTcount: A:0.28, C:0.28, G:0.10, T:0.34
Consensus pattern (94 bp):
TCACATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCATCACATTGGCCATTCGGC
CTTATCACATATATGCATGTTCACATTCA
Found at i:40533488 original size:18 final size:18
Alignment explanation
Indices: 40533465--40533499 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
40533455 GATCCTTCTC
40533465 ACAATTCTGTCTTTTAGT
1 ACAATTCTGTCTTTTAGT
40533483 ACAATTCTGTCTTTTAG
1 ACAATTCTGTCTTTTAG
40533500 CAGCGAAGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.23, C:0.17, G:0.11, T:0.49
Consensus pattern (18 bp):
ACAATTCTGTCTTTTAGT
Found at i:40535432 original size:27 final size:26
Alignment explanation
Indices: 40535391--40535504 Score: 138
Period size: 27 Copynumber: 4.2 Consensus size: 26
40535381 AGCATGGCTG
* * * *
40535391 CCAGAATAGATATTGTGACAGAGTCA
1 CCAGAACAGATATTGTGGCATAGCCA
40535417 CCAGATACAGATATTGTGGCATAGCCA
1 CCAGA-ACAGATATTGTGGCATAGCCA
*
40535444 CCAGAACAAATATTTGTGGCATAGCCA
1 CCAGAACAGATA-TTGTGGCATAGCCA
*
40535471 CCAGAAACAGATATTTGTGGCATGGCCA
1 CCAG-AACAGATA-TTGTGGCATAGCCA
40535499 CCAGAA
1 CCAGAA
40535505 TGCTTCCTCC
Statistics
Matches: 78, Mismatches: 7, Indels: 5
0.87 0.08 0.06
Matches are distributed among these distances:
26 11 0.14
27 42 0.54
28 25 0.32
ACGTcount: A:0.36, C:0.21, G:0.22, T:0.21
Consensus pattern (26 bp):
CCAGAACAGATATTGTGGCATAGCCA
Found at i:40537467 original size:27 final size:28
Alignment explanation
Indices: 40537410--40537479 Score: 115
Period size: 27 Copynumber: 2.5 Consensus size: 28
40537400 AAACTTGTAC
*
40537410 AGCACTAAGTGTGCGAGTTTGATCATGT
1 AGCACTAAGTGTGCGAGTTTGATCATAT
*
40537438 AGCACTAAGTGTGCGAG-TTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATCATAT
40537465 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
40537480 GACACACTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
27 23 0.57
28 17 0.43
ACGTcount: A:0.27, C:0.14, G:0.29, T:0.30
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTGATCATAT
Found at i:40547023 original size:56 final size:56
Alignment explanation
Indices: 40546937--40547108 Score: 344
Period size: 56 Copynumber: 3.1 Consensus size: 56
40546927 TAAGTTTAAG
40546937 TTAGGTAATGCCTCATATTCTGACTCGATGTGGGATACAAGTGTAGGGTGTTACAT
1 TTAGGTAATGCCTCATATTCTGACTCGATGTGGGATACAAGTGTAGGGTGTTACAT
40546993 TTAGGTAATGCCTCATATTCTGACTCGATGTGGGATACAAGTGTAGGGTGTTACAT
1 TTAGGTAATGCCTCATATTCTGACTCGATGTGGGATACAAGTGTAGGGTGTTACAT
40547049 TTAGGTAATGCCTCATATTCTGACTCGATGTGGGATACAAGTGTAGGGTGTTACAT
1 TTAGGTAATGCCTCATATTCTGACTCGATGTGGGATACAAGTGTAGGGTGTTACAT
40547105 TTAG
1 TTAG
40547109 TGGTATCAGA
Statistics
Matches: 116, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 116 1.00
ACGTcount: A:0.25, C:0.14, G:0.27, T:0.34
Consensus pattern (56 bp):
TTAGGTAATGCCTCATATTCTGACTCGATGTGGGATACAAGTGTAGGGTGTTACAT
Found at i:40550344 original size:53 final size:53
Alignment explanation
Indices: 40550171--40550374 Score: 213
Period size: 53 Copynumber: 3.8 Consensus size: 53
40550161 ATTAGGGTTT
* *
40550171 AAGGATTCCATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTC-TAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGC-ATTGGTAA-G-TTCATAAGGC
* * * *
40550226 AAGGA-A--AT-CATGACCATGTCAAGACATGGCATTGATAAGTTACTATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTT-C-ATAAGGC
* * *
40550277 AAAGG-TCCCATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTCATAAGGC
1 -AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTCATAAGGC
* *
40550330 AAGGATACCATGTAAGACCATGTCAAGACATGGCAATGGTAAGTT
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTT
40550375 TCAAAAGGAT
Statistics
Matches: 122, Mismatches: 18, Indels: 20
0.76 0.11 0.12
Matches are distributed among these distances:
48 2 0.02
49 2 0.02
50 7 0.06
51 24 0.20
52 10 0.08
53 42 0.34
54 3 0.02
55 32 0.26
ACGTcount: A:0.34, C:0.18, G:0.25, T:0.23
Consensus pattern (53 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTCATAAGGC
Found at i:40550623 original size:26 final size:26
Alignment explanation
Indices: 40550587--40550639 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
40550577 AGGAAAAAGG
40550587 TAAGTAAAATGTATTAATAAATTTGA
1 TAAGTAAAATGTATTAATAAATTTGA
40550613 TAAGTAAAATGTATTAATAAATTTGA
1 TAAGTAAAATGTATTAATAAATTTGA
40550639 T
1 T
40550640 TAAATAAGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.49, C:0.00, G:0.11, T:0.40
Consensus pattern (26 bp):
TAAGTAAAATGTATTAATAAATTTGA
Found at i:40557819 original size:55 final size:54
Alignment explanation
Indices: 40557732--40557986 Score: 278
Period size: 55 Copynumber: 4.8 Consensus size: 54
40557722 ATTAGGGTTT
*
40557732 AAGGATACCATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAA-GTTTCTAAGGC
* * * * *
40557787 AAGGAAATCATGTAAGACCATGTCAAGACATGGC-ATTGATAAGTTACTATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAAGTT--TCTAAGGC
* * *
40557842 AAAGG-TCCCATGTAAGACCATGCCAAGGCATGGC-ATTGGTGAG-TTCATAAGGC
1 -AAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAAGTTTC-TAAGGC
*
40557895 AAGGATACCATGTAAGACCATGTCAAGACATGGCAA-TGGTAAGTTTC-AA---
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAAGTTTCTAAGGC
* * *
40557944 AAGGATACCACGTAAGACCATGACAAGTCATGGCAA-TGGTAAG
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAAG
40557987 GTACCCGTGT
Statistics
Matches: 172, Mismatches: 21, Indels: 20
0.81 0.10 0.09
Matches are distributed among these distances:
49 40 0.23
52 7 0.04
53 41 0.24
54 12 0.07
55 68 0.40
56 4 0.02
ACGTcount: A:0.36, C:0.18, G:0.25, T:0.21
Consensus pattern (54 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAAGTTTCTAAGGC
Found at i:40557938 original size:108 final size:110
Alignment explanation
Indices: 40557739--40557939 Score: 327
Period size: 108 Copynumber: 1.8 Consensus size: 110
40557729 TTTAAGGATA
*
40557739 CCATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGCAAGGAAATCATGTAAGA
1 CCATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGCAAGGAAACCATGTAAGA
*
40557804 CCATGTCAAGACATGGCATTGATAAGTTACTATAAGGCAAAGGTC
66 CCATGTCAAGACATGGCAATGATAAGTTACTATAAGGCAAAGGTC
* *
40557849 CCATGTAAGACCATGCCAAGGCATGGC-ATTGGTGA-G-TTCATAAGGCAAGGATACCATGTAAG
1 CCATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTC-TAAGGCAAGGAAACCATGTAAG
*
40557911 ACCATGTCAAGACATGGCAATGGTAAGTT
65 ACCATGTCAAGACATGGCAATGATAAGTT
40557940 TCAAAAGGAT
Statistics
Matches: 85, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
107 3 0.04
108 48 0.56
109 7 0.08
110 27 0.32
ACGTcount: A:0.34, C:0.18, G:0.25, T:0.22
Consensus pattern (110 bp):
CCATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGCAAGGAAACCATGTAAGA
CCATGTCAAGACATGGCAATGATAAGTTACTATAAGGCAAAGGTC
Found at i:40558199 original size:16 final size:16
Alignment explanation
Indices: 40558178--40558208 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40558168 ATAAATTTGA
40558178 TTAAGTAAGTAAGTAT
1 TTAAGTAAGTAAGTAT
*
40558194 TTAAGTAAGTGAGTA
1 TTAAGTAAGTAAGTA
40558209 AGTGAAGAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.23, T:0.35
Consensus pattern (16 bp):
TTAAGTAAGTAAGTAT
Found at i:40565507 original size:55 final size:54
Alignment explanation
Indices: 40565420--40565674 Score: 278
Period size: 55 Copynumber: 4.8 Consensus size: 54
40565410 ATTAGGGTTT
*
40565420 AAGGATACCATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAA-GTTTCTAAGGC
* * * * *
40565475 AAGGAAATCATGTAAGACCATGTCAAGACATGGC-ATTGATAAGTTACTATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAAGTT--TCTAAGGC
* * *
40565530 AAAGG-TCCCATGTAAGACCATGCCAAGGCATGGC-ATTGGTGAG-TTCATAAGGC
1 -AAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAAGTTTC-TAAGGC
*
40565583 AAGGATACCATGTAAGACCATGTCAAGACATGGCAA-TGGTAAGTTTC-AA---
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAAGTTTCTAAGGC
* * *
40565632 AAGGATACCACGTAAGACCATGACAAGTCATGGCAA-TGGTAAG
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAAG
40565675 GTACCCGTGT
Statistics
Matches: 172, Mismatches: 21, Indels: 20
0.81 0.10 0.09
Matches are distributed among these distances:
49 40 0.23
52 7 0.04
53 41 0.24
54 12 0.07
55 68 0.40
56 4 0.02
ACGTcount: A:0.36, C:0.18, G:0.25, T:0.21
Consensus pattern (54 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAAGTTTCTAAGGC
Found at i:40565626 original size:108 final size:110
Alignment explanation
Indices: 40565427--40565627 Score: 327
Period size: 108 Copynumber: 1.8 Consensus size: 110
40565417 TTTAAGGATA
*
40565427 CCATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGCAAGGAAATCATGTAAGA
1 CCATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGCAAGGAAACCATGTAAGA
*
40565492 CCATGTCAAGACATGGCATTGATAAGTTACTATAAGGCAAAGGTC
66 CCATGTCAAGACATGGCAATGATAAGTTACTATAAGGCAAAGGTC
* *
40565537 CCATGTAAGACCATGCCAAGGCATGGC-ATTGGTGA-G-TTCATAAGGCAAGGATACCATGTAAG
1 CCATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTC-TAAGGCAAGGAAACCATGTAAG
*
40565599 ACCATGTCAAGACATGGCAATGGTAAGTT
65 ACCATGTCAAGACATGGCAATGATAAGTT
40565628 TCAAAAGGAT
Statistics
Matches: 85, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
107 3 0.04
108 48 0.56
109 7 0.08
110 27 0.32
ACGTcount: A:0.34, C:0.18, G:0.25, T:0.22
Consensus pattern (110 bp):
CCATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGCAAGGAAACCATGTAAGA
CCATGTCAAGACATGGCAATGATAAGTTACTATAAGGCAAAGGTC
Found at i:40565769 original size:23 final size:24
Alignment explanation
Indices: 40565743--40565787 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
40565733 AAGGTAAGGT
*
40565743 AAGGTAAGACGAGTT-ATGCTAAA
1 AAGGTAAGACAAGTTCATGCTAAA
40565766 AAGGTAAGACAAGTTCATGCTA
1 AAGGTAAGACAAGTTCATGCTA
40565788 GAAGAGCAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.42, C:0.11, G:0.24, T:0.22
Consensus pattern (24 bp):
AAGGTAAGACAAGTTCATGCTAAA
Found at i:40565886 original size:16 final size:16
Alignment explanation
Indices: 40565867--40565908 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
40565857 TAAATTTGAT
*
40565867 TAAGTAAGTATTTAAG
1 TAAGTGAGTATTTAAG
40565883 TAAGTGAGTATTTAAG
1 TAAGTGAGTATTTAAG
40565899 TAAGTGAGTA
1 TAAGTGAGTA
40565909 AGTGAAGAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.40, C:0.00, G:0.24, T:0.36
Consensus pattern (16 bp):
TAAGTGAGTATTTAAG
Found at i:40572702 original size:92 final size:91
Alignment explanation
Indices: 40572546--40572714 Score: 311
Period size: 92 Copynumber: 1.8 Consensus size: 91
40572536 CGCCCTAAGT
*
40572546 GAACTCGGACTCAACTCAACGAGCTCGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
1 GAACTCGGACTCAACTCAACGAGCTCGGCATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
40572611 GAGTTCGGATGCCTAGTTACATTCAC
66 GAGTTCGGATGCCTAGTTACATTCAC
*
40572637 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGG-CATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
40572702 CGAGTTCGGATGC
65 CGAGTTCGGATGC
40572715 TCAACCATCC
Statistics
Matches: 75, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
91 27 0.36
92 48 0.64
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.21
Consensus pattern (91 bp):
GAACTCGGACTCAACTCAACGAGCTCGGCATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
GAGTTCGGATGCCTAGTTACATTCAC
Found at i:40572711 original size:46 final size:45
Alignment explanation
Indices: 40572541--40572710 Score: 220
Period size: 46 Copynumber: 3.7 Consensus size: 45
40572531 TAACCCGCCC
* *
40572541 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGCATTCGCATCCA
* *
40572586 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG-ATGC-CTAGTTACA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGCATTCGC-A--TCCA
* *
40572632 TTCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 -TAAGTGAACTCGGACTCAACTCAACGAGTTCGG-CATTCGCATCCA
40572678 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG
40572711 ATGCTCAACC
Statistics
Matches: 107, Mismatches: 10, Indels: 15
0.81 0.08 0.11
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 34 0.32
46 62 0.58
47 2 0.02
48 4 0.04
49 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (45 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGCATTCGCATCCA
Found at i:40572730 original size:46 final size:46
Alignment explanation
Indices: 40572543--40572730 Score: 151
Period size: 46 Copynumber: 4.1 Consensus size: 46
40572533 ACCCGCCCTA
* * * *
40572543 AGTGAACTCGGACTCAACTCAACGAGCTCGG-CGTTC--GCATCCAT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCC-T
*
40572587 AAGTGAACTCGGACTCAACTCAACGAGTTCGGATGC-CTAGTTA-CATTC-
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTC-A---ACCATCCT
* * * * *
40572635 A-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCAT--A
1 AGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGCTCAACCATCCT
40572680 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCT
40572726 AGTGA
1 AGTGA
40572731 CATGTCACTT
Statistics
Matches: 116, Mismatches: 12, Indels: 29
0.74 0.08 0.18
Matches are distributed among these distances:
44 9 0.08
45 32 0.28
46 65 0.56
47 1 0.01
48 4 0.03
49 1 0.01
50 4 0.03
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.22
Consensus pattern (46 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCT
Found at i:40573154 original size:30 final size:30
Alignment explanation
Indices: 40573120--40573179 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
40573110 ATTTAATACG
40573120 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
40573150 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
40573180 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:40580198 original size:93 final size:93
Alignment explanation
Indices: 40580091--40580261 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
40580081 GCCCATAAGT
* *
40580091 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
40580156 CGAGTTCGGATGCCTAGTTACATTTCAC
66 CGAGTTCGGATGCCTAGTTACATTTCAC
*
40580184 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
40580249 CGAGTTCGGATGC
66 CGAGTTCGGATGC
40580262 TCAACCATCC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATTTCAC
Found at i:40580258 original size:46 final size:46
Alignment explanation
Indices: 40580083--40580258 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
40580073 TGTAACCCGC
* * *
40580083 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
40580129 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
* * *
40580179 --TTCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
40580222 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
40580259 TGCTCAACCA
Statistics
Matches: 110, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 1 0.01
45 2 0.02
46 64 0.58
47 29 0.26
48 2 0.02
49 1 0.01
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:40580715 original size:30 final size:30
Alignment explanation
Indices: 40580681--40580740 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
40580671 ATTTAATACG
40580681 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
40580711 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
40580741 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:40584181 original size:16 final size:15
Alignment explanation
Indices: 40584148--40584176 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
40584138 ATTTTCTATG
40584148 TTTATTGTGTGTGAA
1 TTTATTGTGTGTGAA
40584163 TTTA-TGTGTGTGAA
1 TTTATTGTGTGTGAA
40584177 AATTTCGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.21, C:0.00, G:0.28, T:0.52
Consensus pattern (15 bp):
TTTATTGTGTGTGAA
Found at i:40586533 original size:28 final size:28
Alignment explanation
Indices: 40586486--40586601 Score: 112
Period size: 28 Copynumber: 4.2 Consensus size: 28
40586476 GGAGGAAGCA
* ** *
40586486 TTCTGGTGGCTATGAAACAAATATATGT
1 TTCTGGTGGCTCTGCCACAAATATCTGT
**
40586514 TTCTGGTGGCTCTGCCACAAATATCTAA
1 TTCTGGTGGCTCTGCCACAAATATCTGT
* *
40586542 TTCTGGTGGCACTGCCACAAATATTTGT
1 TTCTGGTGGCTCTGCCACAAATATCTGT
* *
40586570 ATT-TGGTGACTCTGTCAC-AATATCTG-
1 -TTCTGGTGGCTCTGCCACAAATATCTGT
40586596 TTCTGG
1 TTCTGG
40586602 CAGCCATGTT
Statistics
Matches: 72, Mismatches: 14, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
25 2 0.03
26 3 0.04
27 7 0.10
28 58 0.81
29 2 0.03
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.36
Consensus pattern (28 bp):
TTCTGGTGGCTCTGCCACAAATATCTGT
Found at i:40586577 original size:56 final size:55
Alignment explanation
Indices: 40586485--40586594 Score: 134
Period size: 56 Copynumber: 2.0 Consensus size: 55
40586475 TGGAGGAAGC
*
40586485 ATTCTGGTGGCTATGAAACAAATATATGTTTCTGGTGGCTCTGCCACAAATATCTA
1 ATTCTGGTGGCTATGAAACAAATATATGTTTCTGGTGACTCTGCCAC-AATATCTA
** * *
40586541 ATTCTGGTGGC-ACTGCCACAAATATTTGTATT-TGGTGACTCTGTCACAATATCT
1 ATTCTGGTGGCTA-TGAAACAAATATATGT-TTCTGGTGACTCTGCCACAATATCT
40586595 GTTCTGGCAG
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
55 8 0.17
56 37 0.79
57 2 0.04
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.35
Consensus pattern (55 bp):
ATTCTGGTGGCTATGAAACAAATATATGTTTCTGGTGACTCTGCCACAATATCTA
Found at i:40591633 original size:26 final size:26
Alignment explanation
Indices: 40591578--40591639 Score: 90
Period size: 26 Copynumber: 2.3 Consensus size: 26
40591568 ATTTACTAAA
40591578 ATACCCCTAAGTATGAAAATTACCACT
1 ATACCCCTAAG-ATGAAAATTACCACT
*
40591605 ATACCCCTAAG-TGCAAAATTACCATT
1 ATACCCCTAAGATG-AAAATTACCACT
40591631 ATACCCCTA
1 ATACCCCTA
40591640 GGGTTAGTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
25 2 0.06
26 20 0.61
27 11 0.33
ACGTcount: A:0.39, C:0.29, G:0.06, T:0.26
Consensus pattern (26 bp):
ATACCCCTAAGATGAAAATTACCACT
Found at i:40591791 original size:28 final size:28
Alignment explanation
Indices: 40591743--40591859 Score: 130
Period size: 28 Copynumber: 4.2 Consensus size: 28
40591733 TGGAGGAAGC
* ** *
40591743 TTTCTGGTGGCTATGAAACAAATATTTG
1 TTTCTGGTGGCTCTGCCACAAATATCTG
40591771 TTTCTGGTGGCTCTGCCACAAATATCTG
1 TTTCTGGTGGCTCTGCCACAAATATCTG
* * *
40591799 ATTCTGGTGGCACTGCCACAAATATTTG
1 TTTCTGGTGGCTCTGCCACAAATATCTG
* * *
40591827 TATCTGGTGACTCTGTCAC-AATATCTG
1 TTTCTGGTGGCTCTGCCACAAATATCTG
40591854 -TTCTGG
1 TTTCTGG
40591860 CAGCCATGCT
Statistics
Matches: 75, Mismatches: 14, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
26 5 0.07
27 7 0.09
28 63 0.84
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.37
Consensus pattern (28 bp):
TTTCTGGTGGCTCTGCCACAAATATCTG
Found at i:40594218 original size:43 final size:43
Alignment explanation
Indices: 40594169--40594413 Score: 350
Period size: 43 Copynumber: 5.7 Consensus size: 43
40594159 TATGTGTGTG
* *
40594169 CGTGTAAGACCATGTCTGGGATGTTGGCATCGATATGTGATTA
1 CGTGTAAGACCACGTCTGGGACGTTGGCATCGATATGTGATTA
* * *
40594212 CGTGTAAGACCATGTTTAGGACGTTGGCATCGATATGTGATTA
1 CGTGTAAGACCACGTCTGGGACGTTGGCATCGATATGTGATTA
*
40594255 CATGTAAGACCACGTCTGGGACGTTGGCATCGATATGTGATTA
1 CGTGTAAGACCACGTCTGGGACGTTGGCATCGATATGTGATTA
* *
40594298 CGTGTAAGACCACGTCTGGGACATTGGCATCAATATGTGATTA
1 CGTGTAAGACCACGTCTGGGACGTTGGCATCGATATGTGATTA
* *
40594341 TGTGTAAGACC-CTGTCTAGGACAG-TGGCATCGATATGTGATTA
1 CGTGTAAGACCAC-GTCTGGGAC-GTTGGCATCGATATGTGATTA
* *
40594384 CATGTAAGACCACGTTTGGGACGTTGGCAT
1 CGTGTAAGACCACGTCTGGGACGTTGGCAT
40594414 TGTACGATAT
Statistics
Matches: 180, Mismatches: 18, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
42 2 0.01
43 177 0.98
44 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (43 bp):
CGTGTAAGACCACGTCTGGGACGTTGGCATCGATATGTGATTA
Found at i:40594388 original size:129 final size:129
Alignment explanation
Indices: 40594169--40594413 Score: 402
Period size: 129 Copynumber: 1.9 Consensus size: 129
40594159 TATGTGTGTG
* ** * *
40594169 CGTGTAAGACCATGTCTGGGATGTTGGCATCGATATGTGATTACGTGTAAGACCATGTTTAGGAC
1 CGTGTAAGACCACGTCTGGGACATTGGCATCAATATGTGATTACGTGTAAGACCATGTCTAGGAC
40594234 GTTGGCATCGATATGTGATTACATGTAAGACCACGTCTGGGACGTTGGCATCGATATGTGATTA
66 GTTGGCATCGATATGTGATTACATGTAAGACCACGTCTGGGACGTTGGCATCGATATGTGATTA
* *
40594298 CGTGTAAGACCACGTCTGGGACATTGGCATCAATATGTGATTATGTGTAAGACCCTGTCTAGGAC
1 CGTGTAAGACCACGTCTGGGACATTGGCATCAATATGTGATTACGTGTAAGACCATGTCTAGGAC
*
40594363 AG-TGGCATCGATATGTGATTACATGTAAGACCACGTTTGGGACGTTGGCAT
66 -GTTGGCATCGATATGTGATTACATGTAAGACCACGTCTGGGACGTTGGCAT
40594414 TGTACGATAT
Statistics
Matches: 107, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
129 106 0.99
130 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (129 bp):
CGTGTAAGACCACGTCTGGGACATTGGCATCAATATGTGATTACGTGTAAGACCATGTCTAGGAC
GTTGGCATCGATATGTGATTACATGTAAGACCACGTCTGGGACGTTGGCATCGATATGTGATTA
Found at i:40597427 original size:12 final size:12
Alignment explanation
Indices: 40597410--40597434 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40597400 TTGTGTGTTC
40597410 TTTATTTTATTT
1 TTTATTTTATTT
40597422 TTTATTTTATTT
1 TTTATTTTATTT
40597434 T
1 T
40597435 ATTTTTCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTATTTTATTT
Found at i:40601868 original size:13 final size:13
Alignment explanation
Indices: 40601850--40601876 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
40601840 TTGTGTGTTC
40601850 TTTATTTTATTTT
1 TTTATTTTATTTT
40601863 TTTATTTTATTTT
1 TTTATTTTATTTT
40601876 T
1 T
40601877 CACATTATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTATTTTATTTT
Found at i:40607290 original size:47 final size:48
Alignment explanation
Indices: 40607236--40607367 Score: 180
Period size: 46 Copynumber: 2.8 Consensus size: 48
40607226 GTAGTTGTAT
*
40607236 TAATTAGAACACATTAAATAAACTTAAGACATATTAAATGGCTGAA-C
1 TAATTAGAACACATTAAATAAACTTAAGACATATTAAATGACTGAATC
* *
40607283 TAATTAGAACACATT-AATTAACTTAAGACATATT-AATTACTGAATC
1 TAATTAGAACACATTAAATAAACTTAAGACATATTAAATGACTGAATC
* * * *
40607329 TAATTAGAACATATTAAATAGACTCAAGACACATTAAAT
1 TAATTAGAACACATTAAATAAACTTAAGACATATTAAAT
40607368 ACTTAAACTA
Statistics
Matches: 74, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
45 8 0.11
46 33 0.45
47 30 0.41
48 3 0.04
ACGTcount: A:0.48, C:0.13, G:0.08, T:0.30
Consensus pattern (48 bp):
TAATTAGAACACATTAAATAAACTTAAGACATATTAAATGACTGAATC
Found at i:40613465 original size:80 final size:81
Alignment explanation
Indices: 40613325--40613530 Score: 247
Period size: 80 Copynumber: 2.6 Consensus size: 81
40613315 CGGAATACAA
* * * *
40613325 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGCCCAGA-TAGAACGACTTGCACAAAT
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATTAGAACGACTAGCACAAAT
*
40613389 GCCTTCGGGTATTAGC
66 GCCTTCGGGTATTAAC
* * *
40613405 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAG-TC-ACTAGCACAAT
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGAT-TAGAACGACTAGCACAAA
*
40613468 TGCCTTCGGGTCTTAAC
65 TGCCTTCGGGTATTAAC
** * * * *
40613485 CCGGATATAATTACTAGCACAAATGTCTTCGGGACTTAGCCCGGAT
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGAT
40613531 ATCATTCAAT
Statistics
Matches: 108, Mismatches: 16, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
80 104 0.96
81 1 0.01
82 3 0.03
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (81 bp):
CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATTAGAACGACTAGCACAAAT
GCCTTCGGGTATTAAC
Done.