Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 129486693
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: 129486693
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Warning! 305 characters in sequence are not A, C, G, or T
File 199 of 444
Found at i:55681456 original size:27 final size:27
Alignment explanation
Indices: 55681419--55681566 Score: 122
Period size: 27 Copynumber: 5.5 Consensus size: 27
55681409 ATATCCTCAG
*
55681419 TTGTAAAATTA-CCAAAGTACCCTCGGT
1 TTGTAAAATTATCCAAA-TACCCTCGAT
* * * *
55681446 TTATAAAATTACCCAAATATCCTCAAT
1 TTGTAAAATTATCCAAATACCCTCGAT
*
55681473 TTGTAAAATTATCGAAATACCCTC-AGT
1 TTGTAAAATTATCCAAATACCCTCGA-T
* ** *
55681500 TTGCAAAATTATTGAAATACCCTCGAC
1 TTGTAAAATTATCCAAATACCCTCGAT
* *
55681527 ATGTAAAATTAT-CAAAGTACCCTCGAC
1 TTGTAAAATTATCCAAA-TACCCTCGAT
**
55681554 TTACAAAATTATC
1 TTGTAAAATTATC
55681567 ATTTTACCCT
Statistics
Matches: 99, Mismatches: 17, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
26 4 0.04
27 89 0.90
28 6 0.06
ACGTcount: A:0.39, C:0.21, G:0.09, T:0.31
Consensus pattern (27 bp):
TTGTAAAATTATCCAAATACCCTCGAT
Found at i:55681508 original size:54 final size:53
Alignment explanation
Indices: 55681390--55681564 Score: 158
Period size: 54 Copynumber: 3.3 Consensus size: 53
55681380 AGAATACTTT
* * * *
55681390 AGTTTACCAAATTACTGC-AATATCCTCAGTTGTAAAATTACCAAAGTACCCTC
1 AGTTTACAAAATTAC-CCAAATATCCTCACTTGTAAAATTATCAAAGTACCCTC
* * *
55681443 GGTTTATAAAATTACCCAAATATCCTCAATTTGTAAAATTATCGAAA-TACCCTC
1 AGTTTACAAAATTACCCAAATATCCTC-ACTTGTAAAATTATC-AAAGTACCCTC
* *** * *
55681497 AGTTTGCAAAATTATTGAAATACCCTCGACATGTAAAATTATCAAAGTACCCTC
1 AGTTTACAAAATTACCCAAATATCCTC-ACTTGTAAAATTATCAAAGTACCCTC
*
55681551 -GACTTACAAAATTA
1 AG-TTTACAAAATTA
55681565 TCATTTTACC
Statistics
Matches: 99, Mismatches: 18, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
52 1 0.01
53 25 0.25
54 70 0.71
55 3 0.03
ACGTcount: A:0.39, C:0.21, G:0.09, T:0.31
Consensus pattern (53 bp):
AGTTTACAAAATTACCCAAATATCCTCACTTGTAAAATTATCAAAGTACCCTC
Found at i:55681567 original size:27 final size:26
Alignment explanation
Indices: 55681423--55681618 Score: 108
Period size: 27 Copynumber: 7.3 Consensus size: 26
55681413 CCTCAGTTGT
* * *
55681423 AAAATTACCAAAGTACCCTCGGTTTAT
1 AAAATTATCAAA-TACCCTCGATTTAC
* * * **
55681450 AAAATTACCCAAATATCCTCAATTTGT
1 AAAATTA-TCAAATACCCTCGATTTAC
*
55681477 AAAATTATCGAAATACCCTC-AGTTTGC
1 AAAATTATC-AAATACCCTCGA-TTTAC
* ** **
55681504 AAAATTATTGAAATACCCTCGACATGT
1 AAAATTA-TCAAATACCCTCGATTTAC
*
55681531 AAAATTATCAAAGTACCCTCGACTTAC
1 AAAATTATCAAA-TACCCTCGATTTAC
**
55681558 AAAATTATCATTTTACCCTCGATTTAC
1 AAAATTATCA-AATACCCTCGATTTAC
* ** *
55681585 AGAATTA-CTATTTTACCTTCGATTTAC
1 AAAATTATC-A-AATACCCTCGATTTAC
55681612 AAAATTA
1 AAAATTA
55681619 CTATTTTACC
Statistics
Matches: 140, Mismatches: 21, Indels: 16
0.79 0.12 0.09
Matches are distributed among these distances:
26 7 0.05
27 126 0.90
28 7 0.05
ACGTcount: A:0.38, C:0.21, G:0.08, T:0.33
Consensus pattern (26 bp):
AAAATTATCAAATACCCTCGATTTAC
Found at i:55681619 original size:27 final size:27
Alignment explanation
Indices: 55681544--55681783 Score: 311
Period size: 27 Copynumber: 8.9 Consensus size: 27
55681534 ATTATCAAAG
* *
55681544 TACCCTCGACTTACAAAATTA-TCATTT
1 TACCCTCGATTTACAGAATTACT-ATTT
55681571 TACCCTCGATTTACAGAATTACTATTT
1 TACCCTCGATTTACAGAATTACTATTT
* *
55681598 TACCTTCGATTTACAAAATTACTATTT
1 TACCCTCGATTTACAGAATTACTATTT
*
55681625 TACCCTCGATTTACAGAGTTACTATTT
1 TACCCTCGATTTACAGAATTACTATTT
* * *
55681652 TACCCTTGAATTACAAAATTACTATTT
1 TACCCTCGATTTACAGAATTACTATTT
** *
55681679 TACCCTCGATTTACAGAATTACCGTTC
1 TACCCTCGATTTACAGAATTACTATTT
* *
55681706 TACCCTCGATTTATAGAATTACCATTT
1 TACCCTCGATTTACAGAATTACTATTT
* *
55681733 TACCCTCGATTTAGAGAATTACCATTT
1 TACCCTCGATTTACAGAATTACTATTT
* *
55681760 TACCCTCGATTTAGAAAATTACTA
1 TACCCTCGATTTACAGAATTACTA
55681784 AAATACCCCT
Statistics
Matches: 189, Mismatches: 23, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
27 188 0.99
28 1 0.01
ACGTcount: A:0.31, C:0.23, G:0.07, T:0.39
Consensus pattern (27 bp):
TACCCTCGATTTACAGAATTACTATTT
Found at i:55681806 original size:27 final size:27
Alignment explanation
Indices: 55681784--55682104 Score: 484
Period size: 27 Copynumber: 12.0 Consensus size: 27
55681774 AAAATTACTA
* *
55681784 AAATACCCCTATAAGGTAGAATTACCG
1 AAATACCCCTGTAGGGTAGAATTACCG
55681811 -AATACCCCTGTAGGGTAGAATTACCG
1 AAATACCCCTGTAGGGTAGAATTACCG
*
55681837 AAATACCCCTGTAAGGTAGAATTACCG
1 AAATACCCCTGTAGGGTAGAATTACCG
*
55681864 AAATACCCCTGTAGGGTAGAATTACTG
1 AAATACCCCTGTAGGGTAGAATTACCG
55681891 AAATACCCCTGTAGGGTAGAATTACCG
1 AAATACCCCTGTAGGGTAGAATTACCG
*
55681918 AAATACCCCTGTAGGGTAGAATTACTG
1 AAATACCCCTGTAGGGTAGAATTACCG
55681945 AAATACCCCTGTAGGGTAGAATTACCG
1 AAATACCCCTGTAGGGTAGAATTACCG
*
55681972 AAATACCCCTGTAGGGTAGAATTATCG
1 AAATACCCCTGTAGGGTAGAATTACCG
* *
55681999 CAATACCCCTATAGGGTAGAATTACCG
1 AAATACCCCTGTAGGGTAGAATTACCG
* **
55682026 AAATATCCCTGTAGGGTAGAATTACTA
1 AAATACCCCTGTAGGGTAGAATTACCG
*
55682053 AAATACCCCTGTAGGGTGGAATTACCG
1 AAATACCCCTGTAGGGTAGAATTACCG
* * * *
55682080 AGATA-CCTTGTGGGGTAAAATTACC
1 AAATACCCCTGTAGGGTAGAATTACC
55682105 ATTTTGCCCC
Statistics
Matches: 267, Mismatches: 26, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
26 40 0.15
27 227 0.85
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (27 bp):
AAATACCCCTGTAGGGTAGAATTACCG
Found at i:55682341 original size:27 final size:26
Alignment explanation
Indices: 55682303--55682385 Score: 94
Period size: 27 Copynumber: 3.1 Consensus size: 26
55682293 CGAAGGAAGC
55682303 GTTCTGGTGGCTATGCCACAAATATCT
1 GTTCTGGTGGCTATGCCAC-AATATCT
*
55682330 GTTCTGGTGGCTCTGCCACAATATCT
1 GTTCTGGTGGCTATGCCACAATATCT
* * * * *
55682356 GTATTTGGTGACTCTGTCATAATATCT
1 GT-TCTGGTGGCTATGCCACAATATCT
55682383 GTT
1 GTT
55682386 GACCGATCGA
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
26 10 0.20
27 40 0.80
ACGTcount: A:0.19, C:0.20, G:0.22, T:0.39
Consensus pattern (26 bp):
GTTCTGGTGGCTATGCCACAATATCT
Found at i:55682896 original size:6 final size:6
Alignment explanation
Indices: 55682887--55683049 Score: 152
Period size: 6 Copynumber: 26.5 Consensus size: 6
55682877 TTGCATTCAC
* *
55682887 ATTCTG ATTCTG ATTCTG -TTACTTG ATACTG ATTCTG ATTCTG GTTCTG
1 ATTCTG ATTCTG ATTCTG ATT-C-TG ATTCTG ATTCTG ATTCTG ATTCTG
* * *
55682936 ATTCTG ATTCTG TTATCTG ATACTG ATTCTG ATTCTG -TTACCTA ATTCTG
1 ATTCTG ATTCTG AT-TCTG ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG
* * * *
55682986 ATTCTG GTTCTG ATTTTG ATTCTG -TCACCTG ATTCTG ATTCTG ATTCTA
1 ATTCTG ATTCTG ATTCTG ATTCTG AT--TCTG ATTCTG ATTCTG ATTCTG
*
55683035 ATTATG ATTCTG ATT
1 ATTCTG ATTCTG ATT
55683050 ATAGTTATGA
Statistics
Matches: 127, Mismatches: 20, Indels: 20
0.76 0.12 0.12
Matches are distributed among these distances:
5 5 0.04
6 105 0.83
7 13 0.10
8 4 0.03
ACGTcount: A:0.18, C:0.17, G:0.16, T:0.49
Consensus pattern (6 bp):
ATTCTG
Found at i:55682918 original size:25 final size:24
Alignment explanation
Indices: 55682890--55682975 Score: 103
Period size: 25 Copynumber: 3.8 Consensus size: 24
55682880 CATTCACATT
55682890 CTGATTCTGATTCTGTTACTTGATA
1 CTGATTCTGATTCTGTTA-TTGATA
*
55682915 CTGATTCTGATTCTG-----G-TT
1 CTGATTCTGATTCTGTTATTGATA
55682933 CTGATTCTGATTCTGTTATCTGATA
1 CTGATTCTGATTCTGTTAT-TGATA
55682958 CTGATTCTGATTCTGTTA
1 CTGATTCTGATTCTGTTA
55682976 CCTAATTCTG
Statistics
Matches: 52, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
18 16 0.31
19 1 0.02
24 1 0.02
25 34 0.65
ACGTcount: A:0.17, C:0.16, G:0.17, T:0.49
Consensus pattern (24 bp):
CTGATTCTGATTCTGTTATTGATA
Found at i:55682937 original size:37 final size:37
Alignment explanation
Indices: 55682887--55683046 Score: 172
Period size: 37 Copynumber: 4.5 Consensus size: 37
55682877 TTGCATTCAC
* *
55682887 ATTCTGATTCTGATTCTGTTACTTGATACTGATTCTG
1 ATTCTGATTCTGATTCTGTTACCTGATTCTGATTCTG
*
55682924 ATTCTGGTTCTGATTCTGATT--CTG--T-T-A-TCTG
1 ATTCTGATTCTGATTCTG-TTACCTGATTCTGATTCTG
* *
55682955 ATACTGATTCTGATTCTGTTACCTAATTCTGATTCTG
1 ATTCTGATTCTGATTCTGTTACCTGATTCTGATTCTG
* * *
55682992 GTTCTGATTTTGATTCTGTCACCTGATTCTGATTCTG
1 ATTCTGATTCTGATTCTGTTACCTGATTCTGATTCTG
* *
55683029 ATTCTAATTATGATTCTG
1 ATTCTGATTCTGATTCTG
55683047 ATTATAGTTA
Statistics
Matches: 101, Mismatches: 14, Indels: 16
0.77 0.11 0.12
Matches are distributed among these distances:
30 2 0.02
31 20 0.20
32 3 0.03
33 1 0.01
34 1 0.01
35 1 0.01
36 3 0.03
37 68 0.67
38 2 0.02
ACGTcount: A:0.18, C:0.17, G:0.16, T:0.49
Consensus pattern (37 bp):
ATTCTGATTCTGATTCTGTTACCTGATTCTGATTCTG
Found at i:55682986 original size:25 final size:25
Alignment explanation
Indices: 55682931--55682997 Score: 98
Period size: 25 Copynumber: 2.7 Consensus size: 25
55682921 CTGATTCTGG
* *
55682931 TTCTGATTCTGATTCTGTTATCTGA
1 TTCTGATTCTGATTCTGTTACCTAA
*
55682956 TACTGATTCTGATTCTGTTACCTAA
1 TTCTGATTCTGATTCTGTTACCTAA
*
55682981 TTCTGATTCTGGTTCTG
1 TTCTGATTCTGATTCTG
55682998 ATTTTGATTC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.16, C:0.18, G:0.16, T:0.49
Consensus pattern (25 bp):
TTCTGATTCTGATTCTGTTACCTAA
Found at i:55694650 original size:56 final size:56
Alignment explanation
Indices: 55694564--55694672 Score: 182
Period size: 56 Copynumber: 1.9 Consensus size: 56
55694554 ATGGCATCAA
*
55694564 TATATGTGTACGAGCAAGACCACATTTAATACATTGGCATCGATATGTGATTTTGG
1 TATATGTGTACGAGCAAAACCACATTTAATACATTGGCATCGATATGTGATTTTGG
* * *
55694620 TATATGTGTGCGGGTAAAACCACATTTAATACATTGGCATCGATATGTGATTT
1 TATATGTGTACGAGCAAAACCACATTTAATACATTGGCATCGATATGTGATTT
55694673 CAATTTATGT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
56 49 1.00
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (56 bp):
TATATGTGTACGAGCAAAACCACATTTAATACATTGGCATCGATATGTGATTTTGG
Found at i:55696033 original size:47 final size:47
Alignment explanation
Indices: 55695964--55696084 Score: 172
Period size: 47 Copynumber: 2.6 Consensus size: 47
55695954 TTCGGAGAAA
* *
55695964 TGTGATATGTGCTTCCGTATAAGACCATATCCGGGATATGGCATCGG
1 TGTGATATGTGCTACCGTATAAGACCATATCCGGGATATGGCATCAG
* * *
55696011 TGTGATATGTGCTACTGTATAAGACCATGTCTGGGATATGGCATCAG
1 TGTGATATGTGCTACCGTATAAGACCATATCCGGGATATGGCATCAG
* *
55696058 TGTGATATGTGAT-CCGTGTAAGACCAT
1 TGTGATATGTGCTACCGTATAAGACCAT
55696085 GGCTGGGCTA
Statistics
Matches: 66, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
46 12 0.18
47 54 0.82
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.31
Consensus pattern (47 bp):
TGTGATATGTGCTACCGTATAAGACCATATCCGGGATATGGCATCAG
Found at i:55699661 original size:15 final size:15
Alignment explanation
Indices: 55699641--55699720 Score: 90
Period size: 15 Copynumber: 5.4 Consensus size: 15
55699631 GTATCTTGGG
55699641 TTTCTTTATCCTGGA
1 TTTCTTTATCCTGGA
* *
55699656 TCTCTTTATTCTGGA
1 TTTCTTTATCCTGGA
* *
55699671 TTTCTTTATTCTGGG
1 TTTCTTTATCCTGGA
* *
55699686 TTTCTCTATCTTGGA
1 TTTCTTTATCCTGGA
*
55699701 TTTCTTTATCC-GGT
1 TTTCTTTATCCTGGA
55699715 TTTCTT
1 TTTCTT
55699721 CTTATCTTTG
Statistics
Matches: 54, Mismatches: 11, Indels: 1
0.82 0.17 0.02
Matches are distributed among these distances:
14 8 0.15
15 46 0.85
ACGTcount: A:0.10, C:0.19, G:0.14, T:0.57
Consensus pattern (15 bp):
TTTCTTTATCCTGGA
Found at i:55699677 original size:30 final size:30
Alignment explanation
Indices: 55699632--55699711 Score: 99
Period size: 30 Copynumber: 2.7 Consensus size: 30
55699622 CATAGTATCG
* *
55699632 TATCTTGGGTTTCTTTATCCTGGATCTCTT
1 TATCTTGGATTTCTTTATCCTGGATCTCTC
* * *
55699662 TAT-TCTGGATTTCTTTATTCTGGGTTTCTC
1 TATCT-TGGATTTCTTTATCCTGGATCTCTC
55699692 TATCTTGGATTTCTTTATCC
1 TATCTTGGATTTCTTTATCC
55699712 GGTTTTCTTC
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
29 1 0.02
30 40 0.95
31 1 0.02
ACGTcount: A:0.11, C:0.19, G:0.15, T:0.55
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATCCTGGATCTCTC
Found at i:55701650 original size:52 final size:48
Alignment explanation
Indices: 55701588--55701762 Score: 194
Period size: 47 Copynumber: 3.6 Consensus size: 48
55701578 GAAATGTGAT
* *
55701588 TTCCGTATAAGACCATAGCTGGGCTATGGCTTCGGAGAAATGTGATATGTGC
1 TTCCGTATAAGACCATAGCTGGGATATGGCATC-GAG---TGTGATATGTGC
* *
55701640 TTCCGTATAAGACCATATCCGGGATATGGCATCG-GTGTGATATGTGC
1 TTCCGTATAAGACCATAGCTGGGATATGGCATCGAGTGTGATATGTGC
* * *
55701687 TACTGTATAAGACCATATCTGGGATATGGCATC-AGTGTGATATGTG-
1 TTCCGTATAAGACCATAGCTGGGATATGGCATCGAGTGTGATATGTGC
* * * *
55701733 ATCCGTGTAAGACCATGGCTGGGCTATGGC
1 TTCCGTATAAGACCATAGCTGGGATATGGC
55701763 CTCGGTATGT
Statistics
Matches: 108, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
46 23 0.21
47 54 0.50
50 1 0.01
51 1 0.01
52 29 0.27
ACGTcount: A:0.25, C:0.18, G:0.29, T:0.29
Consensus pattern (48 bp):
TTCCGTATAAGACCATAGCTGGGATATGGCATCGAGTGTGATATGTGC
Found at i:55705317 original size:15 final size:15
Alignment explanation
Indices: 55705297--55705376 Score: 90
Period size: 15 Copynumber: 5.4 Consensus size: 15
55705287 GTATCTTGGG
55705297 TTTCTTTATCCTGGA
1 TTTCTTTATCCTGGA
* *
55705312 TCTCTTTATTCTGGA
1 TTTCTTTATCCTGGA
* *
55705327 TTTCTTTATTCTGGG
1 TTTCTTTATCCTGGA
* *
55705342 TTTCTCTATCTTGGA
1 TTTCTTTATCCTGGA
*
55705357 TTTCTTTATCC-GGT
1 TTTCTTTATCCTGGA
55705371 TTTCTT
1 TTTCTT
55705377 CTTATCTTTG
Statistics
Matches: 54, Mismatches: 11, Indels: 1
0.82 0.17 0.02
Matches are distributed among these distances:
14 8 0.15
15 46 0.85
ACGTcount: A:0.10, C:0.19, G:0.14, T:0.57
Consensus pattern (15 bp):
TTTCTTTATCCTGGA
Found at i:55705333 original size:30 final size:30
Alignment explanation
Indices: 55705288--55705367 Score: 99
Period size: 30 Copynumber: 2.7 Consensus size: 30
55705278 CATAGTATCG
* *
55705288 TATCTTGGGTTTCTTTATCCTGGATCTCTT
1 TATCTTGGATTTCTTTATCCTGGATCTCTC
* * *
55705318 TAT-TCTGGATTTCTTTATTCTGGGTTTCTC
1 TATCT-TGGATTTCTTTATCCTGGATCTCTC
55705348 TATCTTGGATTTCTTTATCC
1 TATCTTGGATTTCTTTATCC
55705368 GGTTTTCTTC
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
29 1 0.02
30 40 0.95
31 1 0.02
ACGTcount: A:0.11, C:0.19, G:0.15, T:0.55
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATCCTGGATCTCTC
Found at i:55707297 original size:52 final size:48
Alignment explanation
Indices: 55707235--55707409 Score: 194
Period size: 47 Copynumber: 3.6 Consensus size: 48
55707225 GAAATGTGAT
* *
55707235 TTCCGTATAAGACCATAGCTGGGCTATGGCTTCGGAGAAATGTGATATGTGC
1 TTCCGTATAAGACCATAGCTGGGATATGGCATC-GAG---TGTGATATGTGC
* *
55707287 TTCCGTATAAGACCATATCCGGGATATGGCATCG-GTGTGATATGTGC
1 TTCCGTATAAGACCATAGCTGGGATATGGCATCGAGTGTGATATGTGC
* * *
55707334 TACTGTATAAGACCATATCTGGGATATGGCATC-AGTGTGATATGTG-
1 TTCCGTATAAGACCATAGCTGGGATATGGCATCGAGTGTGATATGTGC
* * * *
55707380 ATCCGTGTAAGACCATGGCTGGGCTATGGC
1 TTCCGTATAAGACCATAGCTGGGATATGGC
55707410 CTCGGTATGT
Statistics
Matches: 108, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
46 23 0.21
47 54 0.50
50 1 0.01
51 1 0.01
52 29 0.27
ACGTcount: A:0.25, C:0.18, G:0.29, T:0.29
Consensus pattern (48 bp):
TTCCGTATAAGACCATAGCTGGGATATGGCATCGAGTGTGATATGTGC
Found at i:55712127 original size:17 final size:18
Alignment explanation
Indices: 55712085--55712133 Score: 50
Period size: 17 Copynumber: 2.8 Consensus size: 18
55712075 AGTTGAAAAG
55712085 GAGCATGATTGTCATACTT
1 GAGCATGA-TGTCATACTT
*
55712104 G-GCCATGATG-CATTCTT
1 GAG-CATGATGTCATACTT
55712121 GAGCATGAT-TCAT
1 GAGCATGATGTCAT
55712134 GCTTCTTGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
17 16 0.62
18 4 0.15
19 6 0.23
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.35
Consensus pattern (18 bp):
GAGCATGATGTCATACTT
Found at i:55713022 original size:40 final size:40
Alignment explanation
Indices: 55712956--55713122 Score: 169
Period size: 40 Copynumber: 4.2 Consensus size: 40
55712946 AAATTGAATG
* * *
55712956 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * **
55712995 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* *
55713035 ATATCCGGGCTAAGGCCCGAAGGC-ATTCGTGC-GAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
* * ** *
55713075 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
55713115 ATATCCGG
1 ATATCCGG
55713123 TTATATTCCG
Statistics
Matches: 105, Mismatches: 18, Indels: 9
0.80 0.14 0.07
Matches are distributed among these distances:
39 16 0.15
40 87 0.83
41 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
Found at i:55720125 original size:17 final size:18
Alignment explanation
Indices: 55720083--55720131 Score: 50
Period size: 17 Copynumber: 2.8 Consensus size: 18
55720073 AGTTGAAAAG
55720083 GAGCATGATTGTCATACTT
1 GAGCATGA-TGTCATACTT
*
55720102 G-GCCATGATG-CATTCTT
1 GAG-CATGATGTCATACTT
55720119 GAGCATGAT-TCAT
1 GAGCATGATGTCAT
55720132 GCTTCTTGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
17 16 0.62
18 4 0.15
19 6 0.23
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.35
Consensus pattern (18 bp):
GAGCATGATGTCATACTT
Found at i:55721019 original size:40 final size:40
Alignment explanation
Indices: 55720953--55721119 Score: 169
Period size: 40 Copynumber: 4.2 Consensus size: 40
55720943 AAATTGAATG
* * *
55720953 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * **
55720992 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* *
55721032 ATATCCGGGCTAAGGCCCGAAGGC-ATTCGTGC-GAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
* * ** *
55721072 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
55721112 ATATCCGG
1 ATATCCGG
55721120 TTATATTCCG
Statistics
Matches: 105, Mismatches: 18, Indels: 9
0.80 0.14 0.07
Matches are distributed among these distances:
39 16 0.15
40 87 0.83
41 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
Found at i:55743675 original size:49 final size:49
Alignment explanation
Indices: 55743601--55743955 Score: 626
Period size: 49 Copynumber: 7.3 Consensus size: 49
55743591 CCCTTCGGGA
* * * * *
55743601 CTTATCACAT-T-TACACACTTCCACATCCATCACGTTGGCCACTAGGC
1 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
55743648 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
55743697 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATT-GGC
1 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
55743745 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
*
55743794 CTTATCACATATATACACACTTTCTCATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
55743843 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
*
55743892 CTTATCACATATATACACACTTTCTCATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
55743941 CTTATCACATATATA
1 CTTATCACATATATA
55743956 TATCTCATAC
Statistics
Matches: 297, Mismatches: 8, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
47 10 0.03
48 49 0.16
49 238 0.80
ACGTcount: A:0.30, C:0.31, G:0.08, T:0.31
Consensus pattern (49 bp):
CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:55746741 original size:40 final size:40
Alignment explanation
Indices: 55746646--55746827 Score: 138
Period size: 40 Copynumber: 4.5 Consensus size: 40
55746636 GAATCACGTA
* * ** * *
55746646 CCTTCGGGATTTA-ACCGGATATAGCGACTCGCTCGATTG
1 CCTTCGGGAATTAGCCCGGATATAGTAACTCGCACAATTG
* * *
55746685 TCTTCGGGACA-TAGCCCGG-TCATAGTGATTCGCACAATTG
1 CCTTCGGGA-ATTAGCCCGGAT-ATAGTAACTCGCACAATTG
* *
55746725 CCTTCGGGAATTAGCCCGGATTTAGTAACTCGCACAAATG
1 CCTTCGGGAATTAGCCCGGATATAGTAACTCGCACAATTG
* * * * **
55746765 CCTTCGGGAATT-GACCCGGATTTAGTCACTTAGTACAAAAG
1 CCTTCGGGAATTAG-CCCGGATATAGTAAC-TCGCACAATTG
*
55746806 CCTTCGGGACTTAGCCCGGATA
1 CCTTCGGGAATTAGCCCGGATA
55746828 CCATTCGAAT
Statistics
Matches: 117, Mismatches: 18, Indels: 14
0.79 0.12 0.09
Matches are distributed among these distances:
39 13 0.11
40 76 0.65
41 27 0.23
42 1 0.01
ACGTcount: A:0.24, C:0.25, G:0.24, T:0.26
Consensus pattern (40 bp):
CCTTCGGGAATTAGCCCGGATATAGTAACTCGCACAATTG
Found at i:55747612 original size:40 final size:40
Alignment explanation
Indices: 55747555--55747872 Score: 506
Period size: 40 Copynumber: 8.1 Consensus size: 40
55747545 CGAATACACG
* * * * *
55747555 TCACTAGCATGATTGCTCTTCGGGACCTAGCCCGGATACA
1 TCACTAGCACGAATGCTCTTCGGAACTTAGTCCGGATACA
*
55747595 TCACTAGCACGAATGCTCTTTGGAACTTAGTCCGGATACA
1 TCACTAGCACGAATGCTCTTCGGAACTTAGTCCGGATACA
55747635 TCACTAGCACGAATGCTCTTCGGAACTTAGTCCGGATACA
1 TCACTAGCACGAATGCTCTTCGGAACTTAGTCCGGATACA
* *
55747675 TCACTAGCACGAATGCTCCTCGGAACTTAGTCCGGATACG
1 TCACTAGCACGAATGCTCTTCGGAACTTAGTCCGGATACA
55747715 TCACTAGCACGAATGCTCTTCGGAACTTAGTCCGGATACA
1 TCACTAGCACGAATGCTCTTCGGAACTTAGTCCGGATACA
55747755 TCACTAGCACGAATGCTCTTCGGAACTTAGTCCGGATACA
1 TCACTAGCACGAATGCTCTTCGGAACTTAGTCCGGATACA
55747795 TCACT-----G--TGCTCTTCGGAACTTAGTCCGGATACA
1 TCACTAGCACGAATGCTCTTCGGAACTTAGTCCGGATACA
*
55747828 TCACTAGCACGAATGCTCTTCGGAACTTAGTCCGGATATA
1 TCACTAGCACGAATGCTCTTCGGAACTTAGTCCGGATACA
55747868 TCACT
1 TCACT
55747873 CTCAATTCTC
Statistics
Matches: 259, Mismatches: 12, Indels: 14
0.91 0.04 0.05
Matches are distributed among these distances:
33 32 0.12
35 1 0.00
38 1 0.00
40 225 0.87
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.26
Consensus pattern (40 bp):
TCACTAGCACGAATGCTCTTCGGAACTTAGTCCGGATACA
Found at i:55747847 original size:73 final size:73
Alignment explanation
Indices: 55747728--55747872 Score: 281
Period size: 73 Copynumber: 2.0 Consensus size: 73
55747718 CTAGCACGAA
55747728 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAATGCTCTTCGGAACTTAGTCCGGATA
1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAATGCTCTTCGGAACTTAGTCCGGATA
55747793 CATCACTG
66 CATCACTG
55747801 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAATGCTCTTCGGAACTTAGTCCGGATA
1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAATGCTCTTCGGAACTTAGTCCGGATA
*
55747866 TATCACT
66 CATCACT
55747873 CTCAATTCTC
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 71 1.00
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.28
Consensus pattern (73 bp):
TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAATGCTCTTCGGAACTTAGTCCGGATA
CATCACTG
Found at i:55750042 original size:49 final size:49
Alignment explanation
Indices: 55749968--55750420 Score: 804
Period size: 49 Copynumber: 9.3 Consensus size: 49
55749958 CCCTTCGGGA
* * * * *
55749968 CTTATCACAT-T-TACACACTTCCACATCCATCACGTTGGCCACTAGGC
1 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
55750015 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
55750064 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
*
55750113 CTTATCACATATATACACACTTTCAAATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
*
55750162 CTTATCACATATATACACACTTTCACATTCATCACATTGGCCATT-GGC
1 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
55750210 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
*
55750259 CTTATCACATATATACACACTTTCACATTTATCACATCGGCCATTAGGC
1 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
55750308 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
*
55750357 CTTATCACATATATACACACTTTCTCATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
55750406 CTTATCACATATATA
1 CTTATCACATATATA
55750421 TATCTCATAC
Statistics
Matches: 391, Mismatches: 12, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
47 10 0.03
48 48 0.12
49 333 0.85
ACGTcount: A:0.30, C:0.30, G:0.08, T:0.31
Consensus pattern (49 bp):
CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:55750408 original size:244 final size:242
Alignment explanation
Indices: 55749968--55750420 Score: 816
Period size: 244 Copynumber: 1.9 Consensus size: 242
55749958 CCCTTCGGGA
* *
55749968 CTTATCACATTTACACACTTCCACATCCATCACGTTGGCCACTAGGCCTTATCACATATATACAC
1 CTTATCACATTTACACACTTCCACATCCATCACATCGGCCACTAGGCCTTATCACATATATACAC
55750033 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACACTTTCACATTCATCA
66 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACACTTTCACATTCATCA
55750098 CATCGGCCATTAGGCCTTATCACATATATACACACTTTCAAATTCATCACATCGGCCATTAGGCC
131 CATCGGCCATTAGGCCTTATCACATATATACACACTTTCAAATTCATCACATCGGCCATTAGGCC
55750163 TTATCACATATATACACACTTTCACATTCATCACATTGGCCATTGGC
196 TTATCACATATATACACACTTTCACATTCATCACATTGGCCATTGGC
* * *
55750210 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 CTTATCACAT-T-TACACACTTCCACATCCATCACATCGGCCACTAGGCCTTATCACATATATAC
*
55750275 ACACTTTCACATTTATCACATCGGCCATTAGGCCTTATCACATATATACACACTTTCACATTCAT
64 ACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACACTTTCACATTCAT
**
55750340 CACATCGGCCATTAGGCCTTATCACATATATACACACTTTCTCATTCATCACATCGGCCATTAGG
129 CACATCGGCCATTAGGCCTTATCACATATATACACACTTTCAAATTCATCACATCGGCCATTAGG
55750405 CCTTATCACATATATA
194 CCTTATCACATATATA
55750421 TATCTCATAC
Statistics
Matches: 201, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
242 10 0.05
243 1 0.00
244 190 0.95
ACGTcount: A:0.30, C:0.30, G:0.08, T:0.31
Consensus pattern (242 bp):
CTTATCACATTTACACACTTCCACATCCATCACATCGGCCACTAGGCCTTATCACATATATACAC
ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACACTTTCACATTCATCA
CATCGGCCATTAGGCCTTATCACATATATACACACTTTCAAATTCATCACATCGGCCATTAGGCC
TTATCACATATATACACACTTTCACATTCATCACATTGGCCATTGGC
Found at i:55757652 original size:10 final size:11
Alignment explanation
Indices: 55757634--55757708 Score: 57
Period size: 10 Copynumber: 7.1 Consensus size: 11
55757624 ATATTGTTAT
55757634 ACATGATATG-
1 ACATGATATGC
*
55757644 ACATAATATGC
1 ACATGATATGC
55757655 ACATGATATG-
1 ACATGATATGC
** *
55757665 TTATGAGATGC
1 ACATGATATGC
55757676 ACATGATATGC
1 ACATGATATGC
* *
55757687 -TATGATATAC
1 ACATGATATGC
* *
55757697 TCATTATATGC
1 ACATGATATGC
55757708 A
1 A
55757709 TGGTTTGGGT
Statistics
Matches: 48, Mismatches: 14, Indels: 5
0.72 0.21 0.07
Matches are distributed among these distances:
10 24 0.50
11 24 0.50
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.33
Consensus pattern (11 bp):
ACATGATATGC
Found at i:55757690 original size:21 final size:21
Alignment explanation
Indices: 55757634--55757691 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
55757624 ATATTGTTAT
* *
55757634 ACATGATATGAC-ATAATATGC
1 ACATGATATG-CTATGAGATGC
*
55757655 ACATGATATGTTATGAGATGC
1 ACATGATATGCTATGAGATGC
55757676 ACATGATATGCTATGA
1 ACATGATATGCTATGA
55757692 TATACTCATT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (21 bp):
ACATGATATGCTATGAGATGC
Found at i:55761895 original size:79 final size:81
Alignment explanation
Indices: 55761766--55761949 Score: 209
Period size: 79 Copynumber: 2.3 Consensus size: 81
55761756 ACGACTCGCT
** * *
55761766 CAAATGCCTTCGGGACGAAGCCCGG-TTATAGTGACTCGCCGAATGCCTTCGGGA-CTTAACCCG
1 CAAATGCCTTCGGGACTTAGCCCGGATTATAGTAACTCGCCGAATGCCTTC-GGATCCTAACCCG
* *
55761829 GGTTTAGTAACTT-GCA
65 GATATAGTAACTTAGCA
* * **
55761845 CAAATGCCTTCGGG-CTTAGCCCGGATT-TATTAACTCGCATGAATGCCTTCGGATCCTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGATTATAGTAACTCGC-CGAATGCCTTCGGATCCTAACCCG
*
55761908 GATATAGTCACTTAGCA
65 GATATAGTAACTTAGCA
55761925 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
55761950 CATCATTCGA
Statistics
Matches: 89, Mismatches: 11, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
78 20 0.22
79 51 0.57
80 18 0.20
ACGTcount: A:0.23, C:0.27, G:0.24, T:0.25
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTATAGTAACTCGCCGAATGCCTTCGGATCCTAACCCGG
ATATAGTAACTTAGCA
Found at i:55761949 original size:40 final size:39
Alignment explanation
Indices: 55761759--55761949 Score: 145
Period size: 39 Copynumber: 4.8 Consensus size: 39
55761749 GGATATAACG
* ** * *
55761759 ACTCGCTCAAATGCCTTCGGGACGAAGCCCGGTTATAGTG
1 ACTCGCACAAA-GCCTTCGGGACTTAGCCCGGATATAGTA
* * * *
55761799 ACTCGC-CGAATGCCTTCGGGACTTAACCCGGGTTTAGTA
1 ACTCGCAC-AAAGCCTTCGGGACTTAGCCCGGATATAGTA
* * *
55761838 ACTTGCACAAATGCCTTCGGG-CTTAGCCCGGATTTATTA
1 ACTCGCACAAA-GCCTTCGGGACTTAGCCCGGATATAGTA
* * * * *
55761877 ACTCGCATGAATGCCTTC-GGATCCTAGTCCGGATATAGTC
1 ACTCGCA-CAAAGCCTTCGGGA-CTTAGCCCGGATATAGTA
*
55761917 ACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
1 AC-TCGCACAAAGCCTTCGGGACTTAGCCCGGA
55761950 CATCATTCGA
Statistics
Matches: 118, Mismatches: 25, Indels: 16
0.74 0.16 0.10
Matches are distributed among these distances:
38 2 0.02
39 57 0.48
40 52 0.44
41 7 0.06
ACGTcount: A:0.23, C:0.28, G:0.24, T:0.25
Consensus pattern (39 bp):
ACTCGCACAAAGCCTTCGGGACTTAGCCCGGATATAGTA
Found at i:55766381 original size:47 final size:49
Alignment explanation
Indices: 55766115--55766466 Score: 547
Period size: 49 Copynumber: 7.3 Consensus size: 49
55766105 GTATGAGATA
55766115 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
55766164 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
55766213 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
*
55766262 TATATATGTGGTAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
55766311 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTG-AAG-GTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
* * *
55766358 TATATATGTGATAAGGCCGAATGGCCAATATGATGAATGTGAAA--GTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
* * * * * *
55766405 TATATATGTGAT-AGGGCTGAGTGGCCAACGTGATGGATGTGGAA--GTG
1 TATATATGTGATAAGGCCT-AATGGCCGATGTGATGAATGTGAAAGTGTG
*
55766452 TATAAATGTGATAAG
1 TATATATGTGATAAG
55766467 TCCCGAAGGG
Statistics
Matches: 287, Mismatches: 13, Indels: 7
0.93 0.04 0.02
Matches are distributed among these distances:
46 4 0.01
47 90 0.31
48 7 0.02
49 186 0.65
ACGTcount: A:0.31, C:0.08, G:0.31, T:0.30
Consensus pattern (49 bp):
TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
Found at i:55773890 original size:24 final size:24
Alignment explanation
Indices: 55773833--55773904 Score: 67
Period size: 25 Copynumber: 3.0 Consensus size: 24
55773823 AGGAAGTGCG
*
55773833 AAAAG-GGCTTTGCCCCAGTTTACC
1 AAAAGAGGCTTTGCCCCAG-TTATC
*
55773857 AAAA-AGGGCTTTGCCCCAGTTATT
1 AAAAGA-GGCTTTGCCCCAGTTATC
**
55773881 AAAAGAGGCTAGGCCTCCAGTTAT
1 AAAAGAGGCTTTGCC-CCAGTTAT
55773905 ATGATAAAGC
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
24 18 0.45
25 22 0.55
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.25
Consensus pattern (24 bp):
AAAAGAGGCTTTGCCCCAGTTATC
Found at i:55776805 original size:2 final size:2
Alignment explanation
Indices: 55776800--55776837 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
55776790 TCTTGCACAC
55776800 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
55776838 GTTTGCACAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55777716 original size:40 final size:39
Alignment explanation
Indices: 55777662--55777896 Score: 217
Period size: 40 Copynumber: 5.9 Consensus size: 39
55777652 AACCGGGTTG
* *
55777662 AGTCCCG-AGAGCATTTGAGCTAGTGGCTA-ATTCCGGGCTA
1 AGTCCCGAAG-GCATTTGAGCAAGT-ACTATA-TCCGGGCTA
* *
55777702 AGTCCCGAAGGCA-TTCATGCAAGCTACTATATCAGGGCTA
1 AGTCCCGAAGGCATTTGA-GCAAG-TACTATATCCGGGCTA
* * *
55777742 AGTCCCGAAGGCATTCGTGCGAGCTACTATATCCGGGCTA
1 AGTCCCGAAGGCATTTGAGCAAG-TACTATATCCGGGCTA
* * * *
55777782 AGTCCCGAAGGCGTTTGTGCGAGTTATTATA-CCGGGCTA
1 AGTCCCGAAGGCATTTGAGCAAG-TACTATATCCGGGCTA
* *
55777821 AGTCCCGAAGGCATTTGTGCAAGTTACTATAACCGGGCTA
1 AGTCCCGAAGGCATTTGAGCAAG-TACTATATCCGGGCTA
* * *
55777861 TGTCCCGAAGGCATTTGAACTAGTAGCTATATCCGG
1 AGTCCCGAAGGCATTTGAGCAAGTA-CTATATCCGG
55777897 TTAAATTCCG
Statistics
Matches: 167, Mismatches: 21, Indels: 14
0.83 0.10 0.07
Matches are distributed among these distances:
39 41 0.25
40 121 0.72
41 5 0.03
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (39 bp):
AGTCCCGAAGGCATTTGAGCAAGTACTATATCCGGGCTA
Found at i:55777849 original size:79 final size:80
Alignment explanation
Indices: 55777693--55777877 Score: 255
Period size: 79 Copynumber: 2.3 Consensus size: 80
55777683 AGTGGCTAAT
**
55777693 TCCGGGCTAAGTCCCGAAGGCATTCATGCAAGCTACTATATCAGGGCTAAGTCCCGAAGGCATTC
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGCTACTATATCAGGGCTAAGTCCCGAAGGCATTC
*
55777758 GTGCGAGCTACTATA
66 GTGCAAGCTACTATA
* * * * * *
55777773 TCCGGGCTAAGTCCCGAAGGCGTTTGTGCGAGTTATTATA-CCGGGCTAAGTCCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGCTACTATATCAGGGCTAAGTCCCGAAGGCATTC
*
55777837 GTGCAAGTTACTATA
66 GTGCAAGCTACTATA
* *
55777852 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
55777878 AACTAGTAGC
Statistics
Matches: 92, Mismatches: 13, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
79 58 0.63
80 34 0.37
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.25
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGCTACTATATCAGGGCTAAGTCCCGAAGGCATTC
GTGCAAGCTACTATA
Found at i:55777908 original size:79 final size:79
Alignment explanation
Indices: 55777694--55777910 Score: 208
Period size: 79 Copynumber: 2.7 Consensus size: 79
55777684 GTGGCTAATT
* * * *
55777694 CCGGGCTAAGTCCCGAAGGCATTCATG--CAAGCTACTATATCAGGGCTAAGTCCCGAAGGCATT
1 CCGGGCTAAGTCCCGAAGGCATT--TGAACGAGTTACTATA-CCGGGCTAAATCCCGAAGGCATT
* *
55777757 CGTGCGAGCTACTATAT
63 CGTGCAAGCTACTATAA
* ** * * *
55777774 CCGGGCTAAGTCCCGAAGGCGTTTGTGCGAGTTATTATACCGGGCTAAGTCCCGAAGGCATTTGT
1 CCGGGCTAAGTCCCGAAGGCATTTGAACGAGTTACTATACCGGGCTAAATCCCGAAGGCATTCGT
*
55777839 GCAAGTTACTATAA
66 GCAAGCTACTATAA
* * * *
55777853 CCGGGCTATGTCCCGAAGGCATTTGAACTAG-TAGCTATATCC-GGTTAAATTCCGAAGG
1 CCGGGCTAAGTCCCGAAGGCATTTGAACGAGTTA-CTATA-CCGGGCTAAATCCCGAAGG
55777911 TACGTGATTT
Statistics
Matches: 115, Mismatches: 18, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
78 4 0.03
79 78 0.68
80 33 0.29
ACGTcount: A:0.25, C:0.24, G:0.26, T:0.25
Consensus pattern (79 bp):
CCGGGCTAAGTCCCGAAGGCATTTGAACGAGTTACTATACCGGGCTAAATCCCGAAGGCATTCGT
GCAAGCTACTATAA
Found at i:55785757 original size:40 final size:39
Alignment explanation
Indices: 55785695--55785937 Score: 233
Period size: 40 Copynumber: 6.1 Consensus size: 39
55785685 CGGATGATAA
* *
55785695 CCGGGCTAAGTCCCG-AGAGCATTTGAGCTAGTGGCTA-ATT
1 CCGGGCTAAGTCCCGAAG-GCATTTGAGCGAGT-ACTATA-T
*
55785735 CCGGGCTAAGTCCCGAAGGCA-TTCATGCGAGCTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGA-GCGAG-TACTATAT
* * * *
55785775 CCGGGCTTAGTCCCGAACGCATTCGTGCGAGCTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGAGCGAG-TACTATAT
* * *
55785815 CCGGGCTAAGTCCCGAAGGCGTTTGTGCGAGTTATTATA-
1 CCGGGCTAAGTCCCGAAGGCATTTGAGCGAG-TACTATAT
* * *
55785854 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGAGCGAG-TACTATAT
* * *
55785894 CCGGGCTATGTCCCGAAGGCATTTGAACAAGTAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGAGCGAGTA-CTATAT
55785934 CCGG
1 CCGG
55785938 TTAAATTCCG
Statistics
Matches: 175, Mismatches: 21, Indels: 14
0.83 0.10 0.07
Matches are distributed among these distances:
39 41 0.23
40 129 0.74
41 5 0.03
ACGTcount: A:0.23, C:0.25, G:0.27, T:0.25
Consensus pattern (39 bp):
CCGGGCTAAGTCCCGAAGGCATTTGAGCGAGTACTATAT
Found at i:55785949 original size:79 final size:79
Alignment explanation
Indices: 55785735--55785951 Score: 199
Period size: 79 Copynumber: 2.7 Consensus size: 79
55785725 GTGGCTAATT
* * * * *
55785735 CCGGGCTAAGTCCCGAAGGCATTCATG--CGAGCTACTATATCCGGGCTTAGTCCCGAACGCATT
1 CCGGGCTAAGTCCCGAAGGCATT--TGAACAAGTTACTATA-CCGGGCTAAATCCCGAAGGCATT
* *
55785798 CGTGCGAGCTACTATAT
63 CGTGCAAGCTACTATAA
* ** * * * *
55785815 CCGGGCTAAGTCCCGAAGGCGTTTGTGCGAGTTATTATACCGGGCTAAGTCCCGAAGGCATTTGT
1 CCGGGCTAAGTCCCGAAGGCATTTGAACAAGTTACTATACCGGGCTAAATCCCGAAGGCATTCGT
*
55785880 GCAAGTTACTATAA
66 GCAAGCTACTATAA
* * *
55785894 CCGGGCTATGTCCCGAAGGCATTTGAACAAG-TAGCTATATCC-GGTTAAATTCCGAAGG
1 CCGGGCTAAGTCCCGAAGGCATTTGAACAAGTTA-CTATA-CCGGGCTAAATCCCGAAGG
55785952 TACGTGATTT
Statistics
Matches: 115, Mismatches: 18, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
78 4 0.03
79 77 0.67
80 34 0.30
ACGTcount: A:0.24, C:0.24, G:0.26, T:0.25
Consensus pattern (79 bp):
CCGGGCTAAGTCCCGAAGGCATTTGAACAAGTTACTATACCGGGCTAAATCCCGAAGGCATTCGT
GCAAGCTACTATAA
Found at i:55793170 original size:77 final size:78
Alignment explanation
Indices: 55793053--55793201 Score: 246
Period size: 77 Copynumber: 1.9 Consensus size: 78
55793043 TGGTAACCCG
55793053 CACAAATGCCTTCGGGACTTAACCCGGATATCACAACTCGCACAATTGCCTTCGGGCTTAGCCCG
1 CACAAATGCCTTCGGGACTTAACCCGGATATCACAACTCGCACAATTGCCTTCGGGCTTAGCCCG
*
55793118 GGTATCATAGCTC
66 GATATCATAGCTC
* * * *
55793131 CACAATTGCCTTCGGG-CTTAGCCCGGATATCATAGCTCGCACAATTGCCTTCGGGCTTAGCCCG
1 CACAAATGCCTTCGGGACTTAACCCGGATATCACAACTCGCACAATTGCCTTCGGGCTTAGCCCG
55793195 GATATCA
66 GATATCA
55793202 CTCGAACATT
Statistics
Matches: 66, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
77 51 0.77
78 15 0.23
ACGTcount: A:0.23, C:0.32, G:0.21, T:0.24
Consensus pattern (78 bp):
CACAAATGCCTTCGGGACTTAACCCGGATATCACAACTCGCACAATTGCCTTCGGGCTTAGCCCG
GATATCATAGCTC
Found at i:55793185 original size:39 final size:39
Alignment explanation
Indices: 55793051--55793201 Score: 241
Period size: 39 Copynumber: 3.9 Consensus size: 39
55793041 TATGGTAACC
* * * *
55793051 CGCACAAATGCCTTCGGGACTTAACCCGGATATCACAACT
1 CGCACAATTGCCTTCGGG-CTTAGCCCGGATATCATAGCT
*
55793091 CGCACAATTGCCTTCGGGCTTAGCCCGGGTATCATAGCT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCT
55793130 C-CACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCT
55793168 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCA
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCA
55793202 CTCGAACATT
Statistics
Matches: 104, Mismatches: 6, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
38 37 0.36
39 50 0.48
40 17 0.16
ACGTcount: A:0.23, C:0.32, G:0.22, T:0.24
Consensus pattern (39 bp):
CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCT
Found at i:55799773 original size:40 final size:39
Alignment explanation
Indices: 55799729--55799910 Score: 247
Period size: 39 Copynumber: 4.6 Consensus size: 39
55799719 GTTCAAAACA
* * ** * *
55799729 CCTTCGGGACATAGCCCGGTTATGGTAACCCGCACAAATG
1 CCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATTG
* *
55799769 CCTTCGGGACTTAACCCGGATATCACAACTCGCACAATTG
1 CCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATTG
* *
55799809 CCTTCGGGCTTAGCCCGGGTATCATAGCTCGCACAATTG
1 CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
*
55799848 CCTTCGGGCTTAGCCCGGATATCATAGCTCGCACAATTG
1 CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
55799887 CCTTCGGGCTTAGCCCGGATATCA
1 CCTTCGGGCTTAGCCCGGATATCA
55799911 CTCGAACATT
Statistics
Matches: 129, Mismatches: 13, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
39 89 0.69
40 40 0.31
ACGTcount: A:0.22, C:0.31, G:0.23, T:0.24
Consensus pattern (39 bp):
CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
Found at i:55799840 original size:39 final size:39
Alignment explanation
Indices: 55799759--55799910 Score: 250
Period size: 39 Copynumber: 3.9 Consensus size: 39
55799749 TATGGTAACC
* * * *
55799759 CGCACAAATGCCTTCGGGACTTAACCCGGATATCACAACT
1 CGCACAATTGCCTTCGGG-CTTAGCCCGGATATCATAGCT
*
55799799 CGCACAATTGCCTTCGGGCTTAGCCCGGGTATCATAGCT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCT
55799838 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCT
55799877 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCA
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCA
55799911 CTCGAACATT
Statistics
Matches: 106, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
39 89 0.84
40 17 0.16
ACGTcount: A:0.22, C:0.32, G:0.22, T:0.24
Consensus pattern (39 bp):
CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCT
Found at i:55800555 original size:24 final size:24
Alignment explanation
Indices: 55800527--55800576 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
55800517 CATGATCAAC
55800527 TAGTCATCACACATTTCCCCATCA
1 TAGTCATCACACATTTCCCCATCA
55800551 TAGTCATCACACATTTCCCCATCA
1 TAGTCATCACACATTTCCCCATCA
55800575 TA
1 TA
55800577 CTTTCAAAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.30, C:0.36, G:0.04, T:0.30
Consensus pattern (24 bp):
TAGTCATCACACATTTCCCCATCA
Found at i:55802957 original size:40 final size:39
Alignment explanation
Indices: 55802891--55803097 Score: 213
Period size: 40 Copynumber: 5.2 Consensus size: 39
55802881 TGTTCGGATG
* * *
55802891 ATAACCGGGCTAAGTCCCG-AGAGCATTTGAGCTAGTGGCT
1 ATAACCGGGCTAAGTCCCGAAG-GCATTTGTGCGAGT-ACT
* *
55802931 A-ATTCCGGGCTAAGTCCCGAAGGCATTCGTGCGAGCTACT
1 ATA-ACCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TACT
* * *
55802971 ATATCCGGGCTAAGTCCCGAAGGCGTTTGTGCGAGTTATT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TACT
*
55803011 AT-ACCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TACT
* **
55803050 ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAGTAGCT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTA-CT
*
55803090 ATATCCGG
1 ATAACCGG
55803098 TTAAATTCCG
Statistics
Matches: 143, Mismatches: 18, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
39 38 0.27
40 101 0.71
41 4 0.03
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (39 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTACT
Found at i:55803029 original size:39 final size:39
Alignment explanation
Indices: 55802894--55803078 Score: 228
Period size: 40 Copynumber: 4.7 Consensus size: 39
55802884 TCGGATGATA
* * **
55802894 ACCGGGCTAAGTCCCG-AGAGCATTTGAGCTAGTGGCTAAT
1 ACCGGGCTAAGTCCCGAAG-GCATTTGTGCGAGTTACT-AT
* * *
55802934 TCCGGGCTAAGTCCCGAAGGCATTCGTGCGAGCTACTAT
1 ACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAT
* *
55802973 ATCCGGGCTAAGTCCCGAAGGCGTTTGTGCGAGTTATTAT
1 A-CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAT
*
55803013 ACCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTAT
1 ACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAT
*
55803052 AACCGGGCTATGTCCCGAAGGCATTTG
1 -ACCGGGCTAAGTCCCGAAGGCATTTG
55803079 AACGAGTAGC
Statistics
Matches: 126, Mismatches: 16, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
39 37 0.29
40 87 0.69
41 2 0.02
ACGTcount: A:0.23, C:0.24, G:0.29, T:0.25
Consensus pattern (39 bp):
ACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAT
Found at i:55803111 original size:79 final size:80
Alignment explanation
Indices: 55802891--55803097 Score: 260
Period size: 79 Copynumber: 2.6 Consensus size: 80
55802881 TGTTCGGATG
* *
55802891 ATAACCGGGCTAAGTCCCG-AGAGCATTTGAGCTAGTGGCTA-ATTCCGGGCTAAGTCCCGAAGG
1 ATAACCGGGCTAAGTCCCGAAG-GCATTTGAGCGAGTAGCTATA-TCCGGGCTAAGTCCCGAAGG
*
55802954 CATTCGTGCGAGCTACT
64 CATTCGTGCAAGCTACT
* * * *
55802971 ATATCCGGGCTAAGTCCCGAAGGCGTTTGTGCGAGTTA-TTATA-CCGGGCTAAGTCCCGAAGGC
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGAGCGAG-TAGCTATATCCGGGCTAAGTCCCGAAGGC
* *
55803034 ATTTGTGCAAGTTACT
65 ATTCGTGCAAGCTACT
* *
55803050 ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAGTAGCTATATCCGG
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGAGCGAGTAGCTATATCCGG
55803098 TTAAATTCCG
Statistics
Matches: 107, Mismatches: 15, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
78 2 0.02
79 67 0.63
80 34 0.32
81 4 0.04
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (80 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGAGCGAGTAGCTATATCCGGGCTAAGTCCCGAAGGCA
TTCGTGCAAGCTACT
Found at i:55805138 original size:62 final size:62
Alignment explanation
Indices: 55805062--55805178 Score: 191
Period size: 62 Copynumber: 1.9 Consensus size: 62
55805052 CAGGTTCATC
*
55805062 TTTTACATGCCCGTTGAACCATTTTGAATAATAAT-ATATACACGAAAAGCTCACAATTAGTG
1 TTTTACATGCCCGTTGAACCATTTAGAATAAT-ATCATATACACGAAAAGCTCACAATTAGTG
**
55805124 TTTTACATGCCCGTTGAACCATTTAGAATAATATCATATACACGGGAAGCTCACA
1 TTTTACATGCCCGTTGAACCATTTAGAATAATATCATATACACGAAAAGCTCACA
55805179 CCTAGTGTGC
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
61 2 0.04
62 49 0.96
ACGTcount: A:0.36, C:0.20, G:0.14, T:0.31
Consensus pattern (62 bp):
TTTTACATGCCCGTTGAACCATTTAGAATAATATCATATACACGAAAAGCTCACAATTAGTG
Found at i:55810682 original size:38 final size:38
Alignment explanation
Indices: 55810640--55810717 Score: 138
Period size: 38 Copynumber: 2.1 Consensus size: 38
55810630 TATGTTTGGA
*
55810640 TCATTTCTAATTCTCTCCATTTCCCTTAACTATTTTCT
1 TCATTTCTAATCCTCTCCATTTCCCTTAACTATTTTCT
*
55810678 TCATTTCTAATCCTCTCCATTTCCCTTAACTCTTTTCT
1 TCATTTCTAATCCTCTCCATTTCCCTTAACTATTTTCT
55810716 TC
1 TC
55810718 TCTGCCTTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.17, C:0.32, G:0.00, T:0.51
Consensus pattern (38 bp):
TCATTTCTAATCCTCTCCATTTCCCTTAACTATTTTCT
Found at i:55812031 original size:19 final size:19
Alignment explanation
Indices: 55811986--55812032 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
55811976 TAAATATTAA
*
55811986 AATAAAAATAAAAATATAG
1 AATAAAAATAAAAATAAAG
* *
55812005 AATCAAAACT-AAAATAAAT
1 AAT-AAAAATAAAAATAAAG
55812024 AATAAAAAT
1 AATAAAAAT
55812033 TAGATTAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 5 0.22
19 13 0.57
20 5 0.22
ACGTcount: A:0.72, C:0.04, G:0.02, T:0.21
Consensus pattern (19 bp):
AATAAAAATAAAAATAAAG
Found at i:55813245 original size:28 final size:28
Alignment explanation
Indices: 55813205--55813261 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
55813195 ATTGTTCAAG
55813205 ATTGTTCAAGATTGGAGACAGATGTCTT
1 ATTGTTCAAGATTGGAGACAGATGTCTT
55813233 ATTGTTCAAGATTGGAGACAGATGTCTT
1 ATTGTTCAAGATTGGAGACAGATGTCTT
55813261 A
1 A
55813262 ATTCTGAAAA
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:0.30, C:0.11, G:0.25, T:0.35
Consensus pattern (28 bp):
ATTGTTCAAGATTGGAGACAGATGTCTT
Found at i:55813546 original size:2 final size:2
Alignment explanation
Indices: 55813541--55813575 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
55813531 AAAACAACAC
55813541 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
55813576 AAAACCAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:55816311 original size:93 final size:93
Alignment explanation
Indices: 55816182--55816354 Score: 283
Period size: 93 Copynumber: 1.9 Consensus size: 93
55816172 CGCCCATAAG
** * *
55816182 TGAACTCGGACTCAACTCAATGAGCTCGGGCGTTCGCATCCATAAGTGAACTCAGACTCAACTCA
1 TGAACTCGGACTCAACTCAACAAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCA
55816247 ACGAGCTCGGATGCCTAGTTACATCTCA
66 ACGAGCTCGGATGCCTAGTTACATCTCA
* *
55816275 TGAACTCGGACTCAACTCAACAAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 TGAACTCGGACTCAACTCAACAAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCA
*
55816340 ACGAGTTCGGATGCC
66 ACGAGCTCGGATGCC
55816355 CAAATATCCC
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (93 bp):
TGAACTCGGACTCAACTCAACAAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCA
ACGAGCTCGGATGCCTAGTTACATCTCA
Found at i:55816350 original size:46 final size:46
Alignment explanation
Indices: 55816175--55816350 Score: 198
Period size: 46 Copynumber: 3.8 Consensus size: 46
55816165 TGAAACCCGC
* * *
55816175 CCATAAGTGAACTCGGACTCAACTCAATGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
* *
55816221 CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA---C-A-TTCGCAT
* * *
55816271 -C-TCA-TGAACTCGGACTCAACTCAACAAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
55816314 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
55816351 TGCCCAAATA
Statistics
Matches: 109, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 63 0.58
47 27 0.25
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
Found at i:55818310 original size:30 final size:30
Alignment explanation
Indices: 55818266--55818353 Score: 92
Period size: 30 Copynumber: 3.0 Consensus size: 30
55818256 CAAAGATAAC
55818266 AAGAAAACC-GAATAAAGAAATCCAAGATA
1 AAGAAAACCGGAATAAAGAAATCCAAGATA
* *
55818295 GAGAAACCCGGAATAAAGAAATCC-AGAATA
1 AAGAAAACCGGAATAAAGAAATCCAAG-ATA
* * * *
55818325 AAGAGATCAGG-ATAAAGAAACCCAAGATA
1 AAGAAAACCGGAATAAAGAAATCCAAGATA
55818354 CGATACTATG
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
29 23 0.47
30 26 0.53
ACGTcount: A:0.57, C:0.15, G:0.18, T:0.10
Consensus pattern (30 bp):
AAGAAAACCGGAATAAAGAAATCCAAGATA
Found at i:55818341 original size:14 final size:15
Alignment explanation
Indices: 55818266--55818344 Score: 74
Period size: 15 Copynumber: 5.4 Consensus size: 15
55818256 CAAAGATAAC
*
55818266 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
55818280 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
* * *
55818295 GAGAAACCCGGAATA
1 AAGAAATCCAGAATA
55818310 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
* *
55818325 AAGAGAT-CAGGATA
1 AAGAAATCCAGAATA
55818339 AAGAAA
1 AAGAAA
55818345 CCCAAGATAC
Statistics
Matches: 52, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
14 20 0.38
15 31 0.60
16 1 0.02
ACGTcount: A:0.58, C:0.13, G:0.19, T:0.10
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:55821376 original size:93 final size:93
Alignment explanation
Indices: 55821264--55821434 Score: 281
Period size: 93 Copynumber: 1.8 Consensus size: 93
55821254 CCCATAAGTG
*
55821264 AACTCGGACTCAACTCAACGAGCTCAGG-CGTTCGCATCCATAAGTGAAATCAGACTCAACTCAA
1 AACTCGGACTCAACTCAACGAGCTC-GGACATTCGCATCCATAAGTGAAATCAGACTCAACTCAA
55821328 CGAGCTCGGATGCCTAGTTACATCTCACA
65 CGAGCTCGGATGCCTAGTTACATCTCACA
* * *
55821357 AACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
1 AACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAAATCAGACTCAACTCAAC
*
55821422 GAGTTCGGATGCC
66 GAGCTCGGATGCC
55821435 CAAATATCCC
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
92 2 0.03
93 70 0.97
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.20
Consensus pattern (93 bp):
AACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAAATCAGACTCAACTCAAC
GAGCTCGGATGCCTAGTTACATCTCACA
Found at i:55821423 original size:46 final size:46
Alignment explanation
Indices: 55821255--55821430 Score: 184
Period size: 46 Copynumber: 3.8 Consensus size: 46
55821245 TCAAATCCGC
*
55821255 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCAGG-CGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTC-GGACATTCGCAT
* * *
55821301 CCATAAGTGAAATCAGACTCAACTCAACGAGCTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA---C-A-TTCGCAT
* *
55821351 CTCA-CA---AACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 C-CATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
55821394 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
55821431 TGCCCAAATA
Statistics
Matches: 108, Mismatches: 10, Indels: 24
0.76 0.07 0.17
Matches are distributed among these distances:
42 4 0.04
43 6 0.06
44 1 0.01
45 2 0.02
46 60 0.56
47 25 0.23
49 1 0.01
50 5 0.05
51 4 0.04
ACGTcount: A:0.31, C:0.29, G:0.19, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
Found at i:55823624 original size:16 final size:14
Alignment explanation
Indices: 55823592--55823644 Score: 56
Period size: 14 Copynumber: 3.7 Consensus size: 14
55823582 ATTGATACCT
55823592 TTTGCATTCATGCA
1 TTTGCATTCATGCA
55823606 TTTGCATCTCATAGCA
1 TTTGCAT-TCAT-GCA
*
55823622 TTT-CATTGCAT-TA
1 TTTGCATT-CATGCA
55823635 TTTGCATTCA
1 TTTGCATTCA
55823645 AGATTATAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
13 6 0.18
14 12 0.35
15 10 0.29
16 6 0.18
ACGTcount: A:0.23, C:0.21, G:0.11, T:0.45
Consensus pattern (14 bp):
TTTGCATTCATGCA
Found at i:55824754 original size:10 final size:10
Alignment explanation
Indices: 55824739--55824763 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
55824729 CATCCATTTC
55824739 AAAAAAAATA
1 AAAAAAAATA
55824749 AAAAAAAATA
1 AAAAAAAATA
55824759 AAAAA
1 AAAAA
55824764 TAAAAAGAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (10 bp):
AAAAAAAATA
Found at i:55826265 original size:19 final size:19
Alignment explanation
Indices: 55826241--55826315 Score: 98
Period size: 19 Copynumber: 3.9 Consensus size: 19
55826231 CTATTTCAAA
55826241 AAAAAGGAAAAAAGAAATG
1 AAAAAGGAAAAAAGAAATG
*
55826260 AAAAAGGGAAAAAGAAATG
1 AAAAAGGAAAAAAGAAATG
* *
55826279 AAAAA-AAAAAAAGAAAAAG
1 AAAAAGGAAAAAAG-AAATG
55826298 AAAAAGAGAAAAAAGAAA
1 AAAAAG-GAAAAAAGAAA
55826316 AAAGGAAACT
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
18 6 0.12
19 32 0.67
20 3 0.06
21 7 0.15
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.03
Consensus pattern (19 bp):
AAAAAGGAAAAAAGAAATG
Found at i:55826285 original size:14 final size:12
Alignment explanation
Indices: 55826248--55826317 Score: 50
Period size: 12 Copynumber: 5.5 Consensus size: 12
55826238 AAAAAAAAGG
**
55826248 AAAAAAGAAATG
1 AAAAAAGAAAAA
* *
55826260 AAAAAGGGAAAA
1 AAAAAAGAAAAA
* *
55826272 AGAAATGAAAAAA
1 AAAAAAG-AAAAA
55826285 AAAAAAGAAAAA
1 AAAAAAGAAAAA
55826297 GAAAAAGAGAAAAA
1 -AAAAA-AGAAAAA
55826311 AGAAAAA
1 A-AAAAA
55826318 AGGAAACTAG
Statistics
Matches: 45, Mismatches: 9, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
12 18 0.40
13 16 0.36
14 11 0.24
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (12 bp):
AAAAAAGAAAAA
Found at i:55826301 original size:15 final size:15
Alignment explanation
Indices: 55826267--55826317 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
55826257 ATGAAAAAGG
55826267 GAAAAAGAAATGAAAAA
1 GAAAAAGAAA--AAAAA
*
55826284 -AAAAA-AAGAAAAA
1 GAAAAAGAAAAAAAA
*
55826297 GAAAAAGAGAAAAAA
1 GAAAAAGAAAAAAAA
55826312 GAAAAA
1 GAAAAA
55826318 AGGAAACTAG
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
13 5 0.17
14 5 0.17
15 14 0.48
16 5 0.17
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (15 bp):
GAAAAAGAAAAAAAA
Found at i:55827367 original size:44 final size:44
Alignment explanation
Indices: 55827215--55827842 Score: 373
Period size: 44 Copynumber: 14.3 Consensus size: 44
55827205 GAAACAAGAT
55827215 TTGGCATCCCTGTGTTTATAGGGAAC-AGATCGAAGATAGCAGA
1 TTGGCATCCCTGTGTTTATAGGGAACAAGATCGAAGATAGCAGA
* * * * * * * **
55827258 TCTGACA-CTCTTATGCTTACAGCGAAGC-AGATCAAAGATTTCAGCA
1 T-TGGCATC-CCTGTGTTTATAGGGAA-CAAGATCGAAGATAGCAG-A
55827304 -TGGCATCCCTGTGTTTATAGGGAACAAG-TCG-AGAATAGCAGA
1 TTGGCATCCCTGTGTTTATAGGGAACAAGATCGAAG-ATAGCAGA
*
55827346 TTTGGCATCCCTGTGTTTATAGGGAACAA-ATCAAAGATAGCAGA
1 -TTGGCATCCCTGTGTTTATAGGGAACAAGATCGAAGATAGCAGA
* * * * * * ** ***
55827390 TCTGACATTCCTATGCTTACAGTGAAGTAGATCGAAGATTTTAGCA
1 T-TGGCATCCCTGTGTTTATAGGGAACAAGATCGAAGATAGCAG-A
* *
55827436 -TGGCATCCCTATGTTTATAGGGAAC-AGATCAAAGATAGCAGA
1 TTGGCATCCCTGTGTTTATAGGGAACAAGATCGAAGATAGCAGA
* * * * * ** **
55827478 TCTGACATTCATGTGCTTACAGCAAAGC-AGATCGAAGATTTCAGCA
1 T-TGGCATCCCTGTGTTTATAGGGAA-CAAGATCGAAGATAGCAG-A
* *
55827524 -TGGCATCCCTGAGTTTATAGGGAACAAG-TTGAAGATAGCAGA
1 TTGGCATCCCTGTGTTTATAGGGAACAAGATCGAAGATAGCAGA
* *
55827566 TTTGGCATCCCTGTGTTTATAGGGAA-TAGATC-AAAATAGCAGA
1 -TTGGCATCCCTGTGTTTATAGGGAACAAGATCGAAGATAGCAGA
* * * * * * * **
55827609 TCTGACATTCCTATGCTTACAGCGAAGC-AGATTGAAGATTTCAGCA
1 T-TGGCATCCCTGTGTTTATAGGGAA-CAAGATCGAAGATAGCAG-A
*
55827655 -TGGCATCCCTGTGTTTATAGGGAACAAG-TTGAAGATAGCAGA
1 TTGGCATCCCTGTGTTTATAGGGAACAAGATCGAAGATAGCAGA
* * *
55827697 TTTGGCATCCCTATGTTTATAGGGAAC-AGATTGAAGATAACAGA
1 -TTGGCATCCCTGTGTTTATAGGGAACAAGATCGAAGATAGCAGA
* * * *** * **
55827741 TCTGACA-CTCCTGTGCTTACAATAAAGC-AGATCGAGGATTTCAGCA
1 T-TGGCATC-CCTGTGTTTATAGGGAA-CAAGATCGAAGATAGCAG-A
*
55827787 -TGGCATCCCTGTGTTTATAGGGAACAAG-TTGAAGATAGCAGA
1 TTGGCATCCCTGTGTTTATAGGGAACAAGATCGAAGATAGCAGA
*
55827829 TTTGGCATCTCTGT
1 -TTGGCATCCCTGT
55827843 ATTGTCAGAG
Statistics
Matches: 437, Mismatches: 109, Indels: 77
0.70 0.17 0.12
Matches are distributed among these distances:
42 8 0.02
43 90 0.21
44 272 0.62
45 62 0.14
46 5 0.01
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (44 bp):
TTGGCATCCCTGTGTTTATAGGGAACAAGATCGAAGATAGCAGA
Found at i:55827451 original size:132 final size:132
Alignment explanation
Indices: 55827211--55827461 Score: 421
Period size: 132 Copynumber: 1.9 Consensus size: 132
55827201 CAAAGAAACA
* * *
55827211 AGATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGACACTCTTATGCTT
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCAAAGATAGCAGATCTGACACTCCTATGCTT
*
55827276 ACAGCGAAGCAGATCAAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTCGAGAATA
66 ACAGCGAAGCAGATCAAAGATTTCAGCATGGCATCCCTATGTTTATAGGGAACAAGTCGAGAATA
55827341 GC
131 GC
*
55827343 AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCAAAGATAGCAGATCTGACATTCCTATGCTT
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCAAAGATAGCAGATCTGACACTCCTATGCTT
* * * *
55827408 ACAGTGAAGTAGATCGAAGATTTTAGCATGGCATCCCTATGTTTATAGGGAACA
66 ACAGCGAAGCAGATCAAAGATTTCAGCATGGCATCCCTATGTTTATAGGGAACA
55827462 GATCAAAGAT
Statistics
Matches: 110, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
132 110 1.00
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.27
Consensus pattern (132 bp):
AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCAAAGATAGCAGATCTGACACTCCTATGCTT
ACAGCGAAGCAGATCAAAGATTTCAGCATGGCATCCCTATGTTTATAGGGAACAAGTCGAGAATA
GC
Found at i:55827474 original size:132 final size:132
Alignment explanation
Indices: 55827197--55827478 Score: 417
Period size: 132 Copynumber: 2.1 Consensus size: 132
55827187 GGGACAATGT
* * *
55827197 AGATCAAAGA-AACAAGATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCT
1 AGATCAAAGATAGC-AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCAAAGATAGCAGATCT
* *
55827261 GACACTCTTATGCTTACAGCGAAGCAGATCAAAGATTTCAGCATGGCATCCCTGTGTTTATAGGG
65 GACACTCCTATGCTTACAGCGAAGCAGATCAAAGATTTCAGCATGGCATCCCTATGTTTATAGGG
55827326 AAC
130 AAC
*
55827329 A-AGTC-GAGAATAGCAGATTTGGCATCCCTGTGTTTATAGGGAACAAATCAAAGATAGCAGATC
1 AGA-TCAAAG-ATAGCAGATTTGGCATCCCTGTGTTTATAGGGAACAAATCAAAGATAGCAGATC
* * * * *
55827392 TGACATTCCTATGCTTACAGTGAAGTAGATCGAAGATTTTAGCATGGCATCCCTATGTTTATAGG
64 TGACACTCCTATGCTTACAGCGAAGCAGATCAAAGATTTCAGCATGGCATCCCTATGTTTATAGG
55827457 GAAC
129 GAAC
55827461 AGATCAAAGATAGCAGAT
1 AGATCAAAGATAGCAGAT
55827479 CTGACATTCA
Statistics
Matches: 133, Mismatches: 12, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
131 3 0.02
132 125 0.94
133 5 0.04
ACGTcount: A:0.34, C:0.17, G:0.23, T:0.26
Consensus pattern (132 bp):
AGATCAAAGATAGCAGATTTGGCATCCCTGTGTTTATAGGGAACAAATCAAAGATAGCAGATCTG
ACACTCCTATGCTTACAGCGAAGCAGATCAAAGATTTCAGCATGGCATCCCTATGTTTATAGGGA
AC
Found at i:55827572 original size:132 final size:132
Alignment explanation
Indices: 55827436--55827837 Score: 671
Period size: 132 Copynumber: 3.1 Consensus size: 132
55827426 GATTTTAGCA
*
55827436 TGGCATCCCTATGTTTATAGGGAACAGATCAAAGATAGCAGATCTGACATTCATGTGCTTACAGC
1 TGGCATCCCTATGTTTATAGGGAACAGATCAAAGATAGCAGATCTGACATTCCTGTGCTTACAGC
*
55827501 AAAGCAGATCGAAGATTTCAGCATGGCATCCCTGAGTTTATAGGGAACAAGTTGAAGATAGCAGA
66 AAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGA
55827566 TT
131 TT
* * *
55827568 TGGCATCCCTGTGTTTATAGGGAATAGATCAAA-ATAGCAGATCTGACATTCCTATGCTTACAGC
1 TGGCATCCCTATGTTTATAGGGAACAGATCAAAGATAGCAGATCTGACATTCCTGTGCTTACAGC
* *
55827632 GAAGCAGATTGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGA
66 AAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGA
55827697 TT
131 TT
** * * **
55827699 TGGCATCCCTATGTTTATAGGGAACAGATTGAAGATAACAGATCTGACACTCCTGTGCTTACAAT
1 TGGCATCCCTATGTTTATAGGGAACAGATCAAAGATAGCAGATCTGACATTCCTGTGCTTACAGC
*
55827764 AAAGCAGATCGAGGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGA
66 AAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGA
55827829 TT
131 TT
55827831 TGGCATC
1 TGGCATC
55827838 TCTGTATTGT
Statistics
Matches: 250, Mismatches: 19, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
131 122 0.49
132 128 0.51
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (132 bp):
TGGCATCCCTATGTTTATAGGGAACAGATCAAAGATAGCAGATCTGACATTCCTGTGCTTACAGC
AAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGA
TT
Found at i:55827673 original size:87 final size:87
Alignment explanation
Indices: 55827568--55827734 Score: 228
Period size: 87 Copynumber: 1.9 Consensus size: 87
55827558 ATAGCAGATT
* *
55827568 TGGCATCCCTGTGTTTATAGGGAA-TAGATCAAAATAGCAGATCTGACATTCCTATGCTTACAGC
1 TGGCATCCCTGTGTTTATAGGGAACAAGATCAAAATAGCAGATCTGACATCCCTATGCTTACAGC
55827632 GAAGCAGATTGAAGATTTCAGCA
66 GAA-CAGATTGAAGATTTCAGCA
* * * * * * * *
55827655 TGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATTTGGCATCCCTATGTTTATAGG
1 TGGCATCCCTGTGTTTATAGGGAACAAGATCAAAATAGCAGATCTGACATCCCTATGCTTACAGC
55827720 GAACAGATTGAAGAT
66 GAACAGATTGAAGAT
55827735 AACAGATCTG
Statistics
Matches: 69, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
87 36 0.52
88 33 0.48
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29
Consensus pattern (87 bp):
TGGCATCCCTGTGTTTATAGGGAACAAGATCAAAATAGCAGATCTGACATCCCTATGCTTACAGC
GAACAGATTGAAGATTTCAGCA
Found at i:55827793 original size:219 final size:219
Alignment explanation
Indices: 55827216--55827829 Score: 634
Period size: 220 Copynumber: 2.8 Consensus size: 219
55827206 AAACAAGATT
* * *
55827216 TGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGACA-CTCTTATGCTTACAG
1 TGGCATCCCTATGTTTATAGGGAACAGATCAAAGATAGCAGATCTGACATC-CATATGCTTACAG
* * ** * * * * * *
55827280 CGAAGCAGATCAAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTCG-AGAATAGCA
65 CAAAGCAGATCGAAGATAACAGCATGACATCCCTGAGCTTACAAGAAACAAGTCGAAG-ATAGCA
55827344 GATTTGGCATCCCTGTGTTTATAGGGAACAAATCAAAGATAGCAGATCTGACATTCCTATGCTTA
129 GA-TTGGCATCCCTGTGTTTATAGGGAACAAATCAAAGATAGCAGATCTGACATTCCTATGCTTA
* * *
55827409 CAGTGAAGTAGATCGAAGATTTTAGCA
193 CAGCGAAGCAGATCGAAGATTTCAGCA
* *
55827436 TGGCATCCCTATGTTTATAGGGAACAGATCAAAGATAGCAGATCTGACATTCATGTGCTTACAGC
1 TGGCATCCCTATGTTTATAGGGAACAGATCAAAGATAGCAGATCTGACATCCATATGCTTACAGC
** * * * * * *
55827501 AAAGCAGATCGAAGATTTCAGCATGGCATCCCTGAGTTTATAGGGAACAAGTTGAAGATAGCAGA
66 AAAGCAGATCGAAGATAACAGCATGACATCCCTGAGCTTACAAGAAACAAGTCGAAGATAGCAGA
* *
55827566 TTTGGCATCCCTGTGTTTATAGGGAATAGATCAAA-ATAGCAGATCTGACATTCCTATGCTTACA
131 -TTGGCATCCCTGTGTTTATAGGGAACAAATCAAAGATAGCAGATCTGACATTCCTATGCTTACA
*
55827630 GCGAAGCAGATTGAAGATTTCAGCA
195 GCGAAGCAGATCGAAGATTTCAGCA
* ** * * * * *
55827655 TGGCATCCCTGTGTTTATAGGGAACA-AGTTGAAGATAGCAGATTTGGCATCCCTATGTTTATAG
1 TGGCATCCCTATGTTTATAGGGAACAGA-TCAAAGATAGCAGATCTGACATCCATATGCTTACAG
** * * * *
55827719 GGAA-CAGATTGAAGATAACAG-ATCTGACA-CTCCTGTGCTTACAATAAAGC-AGATCGAGGAT
65 CAAAGCAGATCGAAGATAACAGCA--TGACATC-CCTGAGCTTACAAGAAA-CAAG-TCGAAGAT
** * **
55827780 TTCAGCA-TGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGAT
125 AGCAG-ATTGGCATCCCTGTGTTTATAGGGAACAAATCAAAGATAGCAGAT
55827830 TTGGCATCTC
Statistics
Matches: 338, Mismatches: 46, Indels: 20
0.84 0.11 0.05
Matches are distributed among these distances:
217 1 0.00
218 16 0.05
219 149 0.44
220 169 0.50
221 3 0.01
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (219 bp):
TGGCATCCCTATGTTTATAGGGAACAGATCAAAGATAGCAGATCTGACATCCATATGCTTACAGC
AAAGCAGATCGAAGATAACAGCATGACATCCCTGAGCTTACAAGAAACAAGTCGAAGATAGCAGA
TTGGCATCCCTGTGTTTATAGGGAACAAATCAAAGATAGCAGATCTGACATTCCTATGCTTACAG
CGAAGCAGATCGAAGATTTCAGCA
Found at i:55827992 original size:131 final size:131
Alignment explanation
Indices: 55827827--55828122 Score: 439
Period size: 131 Copynumber: 2.3 Consensus size: 131
55827817 GAAGATAGCA
* * *
55827827 GATTTGGCATCTCTGTATTGTCAGAGAGTAGATCGAAGATACCAGATTTGACATCTCTGTATTGG
1 GATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATAACAGATTTGACATCTCTGTATTGG
* *
55827892 TGGAGAGCATATCAAAGACATAGCTGATTTGGCTTTCACGTGTTTACATTAAAGCAAATCTAAGA
66 AGGAGAGCAGATCAAAGACATAGCTGATTTGGCTTTCACGTGTTTACATTAAAGCAAATCTAAGA
55827957 T
131 T
* * * * * *
55827958 GATTTGGCGTCTCTGTATTGGCGGAGCGCAGATCGAAGATAACATATTTGGCATCTTTGTATTGG
1 GATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATAACAGATTTGACATCTCTGTATTGG
* * * *
55828023 AGGAGAGCAGATCGAAGCCATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAATCTAAGA
66 AGGAGAGCAGATCAAAGACATAGCTGATTTGGCTTTCACGTGTTTACATTAAAGCAAATCTAAGA
55828088 T
131 T
* *
55828089 GATTTGGCATCTCTGTATTAGTAGAGAGCAGATC
1 GATTTGGCATCTCTGTATTGGCAGAGAGCAGATC
55828123 AAAAATACTA
Statistics
Matches: 145, Mismatches: 20, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
131 145 1.00
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (131 bp):
GATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATAACAGATTTGACATCTCTGTATTGG
AGGAGAGCAGATCAAAGACATAGCTGATTTGGCTTTCACGTGTTTACATTAAAGCAAATCTAAGA
T
Found at i:55828463 original size:28 final size:28
Alignment explanation
Indices: 55828432--55828498 Score: 66
Period size: 28 Copynumber: 2.4 Consensus size: 28
55828422 GCCTGACAAA
*
55828432 ACCCAAATACCTAAAACCCAGCTAAATT
1 ACCCAAATACCTAAAACCCAGCTAAACT
* ***
55828460 ACCC-ATTAACCCGTAACCCAGCTAAACT
1 ACCCAAAT-ACCTAAAACCCAGCTAAACT
55828488 ACCCAAA-ACCT
1 ACCCAAATACCT
55828499 GGTACCCATT
Statistics
Matches: 30, Mismatches: 7, Indels: 5
0.71 0.17 0.12
Matches are distributed among these distances:
27 5 0.17
28 24 0.80
29 1 0.03
ACGTcount: A:0.42, C:0.37, G:0.04, T:0.16
Consensus pattern (28 bp):
ACCCAAATACCTAAAACCCAGCTAAACT
Found at i:55829695 original size:26 final size:27
Alignment explanation
Indices: 55829632--55829697 Score: 77
Period size: 26 Copynumber: 2.5 Consensus size: 27
55829622 TTGTTATATG
*
55829632 TATTTCATTATATTATTTATTTGTATA
1 TATTTCATTATATAATTTATTTGTATA
55829659 T-TTT-ATCTATA-AATTATATTT-TATA
1 TATTTCAT-TATATAATT-TATTTGTATA
55829684 TATTTCATTATATA
1 TATTTCATTATATA
55829698 TTTCCTTATA
Statistics
Matches: 33, Mismatches: 1, Indels: 10
0.75 0.02 0.23
Matches are distributed among these distances:
25 10 0.30
26 19 0.58
27 4 0.12
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.61
Consensus pattern (27 bp):
TATTTCATTATATAATTTATTTGTATA
Found at i:55829696 original size:12 final size:12
Alignment explanation
Indices: 55829679--55829713 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
55829669 AAATTATATT
55829679 TTATATATTTCA
1 TTATATATTTCA
*
55829691 TTATATATTTCC
1 TTATATATTTCA
55829703 TTATATTATTT
1 TTATA-TATTT
55829714 TTGTGTATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 16 0.76
13 5 0.24
ACGTcount: A:0.29, C:0.09, G:0.00, T:0.63
Consensus pattern (12 bp):
TTATATATTTCA
Found at i:55829915 original size:21 final size:21
Alignment explanation
Indices: 55829896--55829953 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 21
55829886 ATACTTTATC
*
55829896 TATAATACAATTTATATTATTA
1 TATATTAC-ATTTATATTATTA
*
55829918 TATATTACATTTATA-AATT-
1 TATATTACATTTATATTATTA
55829937 T-TATTACATATTATATT
1 TATATTACAT-TTATATT
55829954 TTACCATGCA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
18 8 0.26
19 6 0.19
20 3 0.10
21 7 0.23
22 7 0.23
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.53
Consensus pattern (21 bp):
TATATTACATTTATATTATTA
Found at i:55834668 original size:7 final size:7
Alignment explanation
Indices: 55834651--55834687 Score: 65
Period size: 7 Copynumber: 5.1 Consensus size: 7
55834641 AAATATGGAC
55834651 TAAATTAT
1 TAAA-TAT
55834659 TAAATAT
1 TAAATAT
55834666 TAAATAT
1 TAAATAT
55834673 TAAATAT
1 TAAATAT
55834680 TAAATAT
1 TAAATAT
55834687 T
1 T
55834688 TAAGTTTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
7 25 0.86
8 4 0.14
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (7 bp):
TAAATAT
Found at i:55835048 original size:14 final size:14
Alignment explanation
Indices: 55835025--55835066 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
55835015 CCCTAAAAAT
*
55835025 CTAACACTTAACCC
1 CTAACCCTTAACCC
55835039 CTAACCCTTAACCC
1 CTAACCCTTAACCC
*
55835053 TTAAACCC-TAACCC
1 CT-AACCCTTAACCC
55835067 TTAAACCGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 20 0.80
15 5 0.20
ACGTcount: A:0.33, C:0.45, G:0.00, T:0.21
Consensus pattern (14 bp):
CTAACCCTTAACCC
Found at i:55835050 original size:21 final size:21
Alignment explanation
Indices: 55835026--55835070 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
55835016 CCTAAAAATC
*
55835026 TAACACTTAACCCCTAACCCT
1 TAACACTTAAACCCTAACCCT
*
55835047 TAACCCTTAAACCCTAACCCT
1 TAACACTTAAACCCTAACCCT
55835068 TAA
1 TAA
55835071 ACCGTAATCC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.36, C:0.40, G:0.00, T:0.24
Consensus pattern (21 bp):
TAACACTTAAACCCTAACCCT
Found at i:55835067 original size:14 final size:14
Alignment explanation
Indices: 55835041--55835114 Score: 58
Period size: 14 Copynumber: 5.1 Consensus size: 14
55835031 CTTAACCCCT
55835041 AACCCTTAACCCTTA
1 AACCC-TAACCCTTA
55835056 AACCCTAACCCTTA
1 AACCCTAACCCTTA
* * *
55835070 AACCGTAATCCATA
1 AACCCTAACCCTTA
* *
55835084 ATCCCTAAACCCATA
1 AACCCT-AACCCTTA
* * *
55835099 ATCCATAAACCTTA
1 AACCCTAACCCTTA
55835113 AA
1 AA
55835115 ATAGTAACTC
Statistics
Matches: 48, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
14 31 0.65
15 17 0.35
ACGTcount: A:0.41, C:0.35, G:0.01, T:0.23
Consensus pattern (14 bp):
AACCCTAACCCTTA
Found at i:55835099 original size:15 final size:15
Alignment explanation
Indices: 55835079--55835109 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
55835069 AAACCGTAAT
*
55835079 CCATAATCCCTAAAC
1 CCATAATCCATAAAC
55835094 CCATAATCCATAAAC
1 CCATAATCCATAAAC
55835109 C
1 C
55835110 TTAAAATAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.39, G:0.00, T:0.19
Consensus pattern (15 bp):
CCATAATCCATAAAC
Found at i:55835114 original size:22 final size:21
Alignment explanation
Indices: 55835065--55835114 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
55835055 AAACCCTAAC
* *
55835065 CCTTAAACCGTAATCCATAAT
1 CCTTAAACCATAATCCATAAA
*
55835086 CCCTAAACCCATAATCCATAAA
1 CCTTAAA-CCATAATCCATAAA
55835108 CCTTAAA
1 CCTTAAA
55835115 ATAGTAACTC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 6 0.25
22 18 0.75
ACGTcount: A:0.42, C:0.32, G:0.02, T:0.24
Consensus pattern (21 bp):
CCTTAAACCATAATCCATAAA
Found at i:55835310 original size:14 final size:14
Alignment explanation
Indices: 55835288--55835338 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
55835278 TTAATCCTTA
55835288 AACCCTAAACCATG
1 AACCCTAAACCATG
* * *
55835302 AATCCTAAAACATA
1 AACCCTAAACCATG
*
55835316 AACCCTGAACCATG
1 AACCCTAAACCATG
55835330 AACCACTAA
1 AACC-CTAA
55835339 CCCTTAACCC
Statistics
Matches: 28, Mismatches: 8, Indels: 1
0.76 0.22 0.03
Matches are distributed among these distances:
14 25 0.89
15 3 0.11
ACGTcount: A:0.47, C:0.31, G:0.06, T:0.16
Consensus pattern (14 bp):
AACCCTAAACCATG
Found at i:55835359 original size:21 final size:21
Alignment explanation
Indices: 55835316--55835390 Score: 62
Period size: 21 Copynumber: 3.4 Consensus size: 21
55835306 CTAAAACATA
* * * *
55835316 AACCCTGAACCATGAACCACT
1 AACCCTTAACCCTTAACCCCT
55835337 AACCCTTAACCCTTAACCCCT
1 AACCCTTAACCCTTAACCCCT
*
55835358 AACACCTAAACGACCTTAAACCCC-
1 AAC-CCTTAAC--CCTT-AACCCCT
55835382 AACCCTTAA
1 AACCCTTAA
55835391 ACCACCCTTA
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
21 20 0.45
22 6 0.14
23 5 0.11
24 7 0.16
25 6 0.14
ACGTcount: A:0.37, C:0.41, G:0.04, T:0.17
Consensus pattern (21 bp):
AACCCTTAACCCTTAACCCCT
Found at i:55835399 original size:25 final size:26
Alignment explanation
Indices: 55835345--55835404 Score: 74
Period size: 25 Copynumber: 2.4 Consensus size: 26
55835335 CTAACCCTTA
*
55835345 ACCCTT-AACCCCTAACACCTAAACG
1 ACCCTTAAACCCCTAACACCTAAACC
55835370 A-CCTTAAACCCC-AAC-CCTTAAACC
1 ACCCTTAAACCCCTAACACC-TAAACC
55835394 ACCCTTAAACC
1 ACCCTTAAACC
55835405 ATAATCCATA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
23 2 0.06
24 13 0.42
25 16 0.52
ACGTcount: A:0.37, C:0.45, G:0.02, T:0.17
Consensus pattern (26 bp):
ACCCTTAAACCCCTAACACCTAAACC
Found at i:55835914 original size:12 final size:12
Alignment explanation
Indices: 55835897--55835924 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
55835887 TTTTTCATTC
55835897 AAACGCCGCTAA
1 AAACGCCGCTAA
55835909 AAACGCCGCTAA
1 AAACGCCGCTAA
55835921 AAAC
1 AAAC
55835925 CTGTTTTGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.46, C:0.32, G:0.14, T:0.07
Consensus pattern (12 bp):
AAACGCCGCTAA
Found at i:55837847 original size:41 final size:40
Alignment explanation
Indices: 55837783--55837862 Score: 115
Period size: 41 Copynumber: 2.0 Consensus size: 40
55837773 GGGGGAAGAA
*
55837783 ATTGAGGACACAAGGTTGATTGACGACCGTGGATCCACCG
1 ATTGAGGACACAAGGTTGATTGACAACCGTGGATCCACCG
* * *
55837823 ATTGAGGATCGCATGGTTGGTTGACAACCGTGGATCCACC
1 ATTGAGGA-CACAAGGTTGATTGACAACCGTGGATCCACC
55837863 AGTGGCTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
40 8 0.23
41 27 0.77
ACGTcount: A:0.25, C:0.23, G:0.30, T:0.23
Consensus pattern (40 bp):
ATTGAGGACACAAGGTTGATTGACAACCGTGGATCCACCG
Found at i:55838057 original size:22 final size:22
Alignment explanation
Indices: 55838005--55838058 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
55837995 GCCAATTATT
* *
55838005 CTGATTATGGCTTTGCGCCAAC
1 CTGATTATGGCTCTACGCCAAC
* *
55838027 CT-ACATATGGCTCTATGCCAAC
1 CTGA-TTATGGCTCTACGCCAAC
55838049 CTGATTATGG
1 CTGATTATGG
55838059 TTGTGTGCCA
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
21 1 0.04
22 23 0.92
23 1 0.04
ACGTcount: A:0.22, C:0.26, G:0.20, T:0.31
Consensus pattern (22 bp):
CTGATTATGGCTCTACGCCAAC
Found at i:55840963 original size:27 final size:27
Alignment explanation
Indices: 55840933--55841039 Score: 135
Period size: 27 Copynumber: 4.0 Consensus size: 27
55840923 CTCATATCTA
* *
55840933 TAGGCTAGTATTACTGAAATACCCTTG
1 TAGGGTAGAATTACTGAAATACCCTTG
* * *
55840960 TAGGGTA-AGTTACTGAAATGCCCCTG
1 TAGGGTAGAATTACTGAAATACCCTTG
* * *
55840986 TAGGATTGAATTACTGAAATGCCCTTG
1 TAGGGTAGAATTACTGAAATACCCTTG
55841013 TAGGGTAGAATTACTGAAATACCCTTG
1 TAGGGTAGAATTACTGAAATACCCTTG
55841040 GTTTACAAAA
Statistics
Matches: 67, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
26 20 0.30
27 47 0.70
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Consensus pattern (27 bp):
TAGGGTAGAATTACTGAAATACCCTTG
Found at i:55841051 original size:27 final size:27
Alignment explanation
Indices: 55840994--55841369 Score: 260
Period size: 27 Copynumber: 14.0 Consensus size: 27
55840984 TGTAGGATTG
* ** *
55840994 AATTACTGAAATGCCCTTG-TAGGGTAG
1 AATTACTGAAATACCCTTGAT-TTGTAA
* **
55841021 AATTACTGAAATACCCTTGGTTTACAA
1 AATTACTGAAATACCCTTGATTTGTAA
** **
55841048 AATTGTTG-AATACCCTTTG-TTTACAA
1 AATTACTGAAATACCC-TTGATTTGTAA
** * *
55841074 AATTACCAAAATA-CCTCGATTAGTAA
1 AATTACTGAAATACCCTTGATTTGTAA
** * * *
55841100 AATTACCAAAATACCCCTAATTTGTGA
1 AATTACTGAAATACCCTTGATTTGTAA
* * *
55841127 AATTATTGAAATACCCTCGACTTGTAA
1 AATTACTGAAATACCCTTGATTTGTAA
*
55841154 AATTACTGAAATA-CCTTCGAATTGTAA
1 AATTACTGAAATACCCTT-GATTTGTAA
** *
55841181 AATTTTTGAAATACCCTTAATTTGTAA
1 AATTACTGAAATACCCTTGATTTGTAA
** * *
55841208 AATTACCAAAATACCCCTGATTTGGAA
1 AATTACTGAAATACCCTTGATTTGTAA
** * * *
55841235 AATTACCAAAATACCCCTAATTTGGAA
1 AATTACTGAAATACCCTTGATTTGTAA
* **
55841262 AATTACAGAAATACCCTTGATTTACAA
1 AATTACTGAAATACCCTTGATTTGTAA
* **
55841289 AATTACAGAAATACCCTTGACTTTCAAA
1 AATTACTGAAATACCCTTGA-TTTGTAA
* *
55841317 AATTACAGAAATACCCTTGGTTTGTAA
1 AATTACTGAAATACCCTTGATTTGTAA
*
55841344 AATTA-TCGAAATACCCTTGTTTTGTA
1 AATTACT-GAAATACCCTTGATTTGTA
55841370 GATTTTCCAA
Statistics
Matches: 283, Mismatches: 57, Indels: 18
0.79 0.16 0.05
Matches are distributed among these distances:
25 2 0.01
26 40 0.14
27 212 0.75
28 29 0.10
ACGTcount: A:0.39, C:0.18, G:0.11, T:0.33
Consensus pattern (27 bp):
AATTACTGAAATACCCTTGATTTGTAA
Found at i:55841672 original size:41 final size:41
Alignment explanation
Indices: 55841625--55841749 Score: 187
Period size: 41 Copynumber: 3.0 Consensus size: 41
55841615 GGAGGAAGAA
* *
55841625 ATTGAGGATCACATGGTTGCTTGATGACTGTGGATCCACCG
1 ATTGAGGATCACATGGTTGCTTGACGACCGTGGATCCACCG
** * *
55841666 ATTGAGGATTGCATGGTTTCTTGACGACCGTGGATCCACTG
1 ATTGAGGATCACATGGTTGCTTGACGACCGTGGATCCACCG
*
55841707 ATTAAGGATCACATGGTTGCTTGACGACCGTGGATCCACCG
1 ATTGAGGATCACATGGTTGCTTGACGACCGTGGATCCACCG
55841748 AT
1 AT
55841750 GGCTTTTAAG
Statistics
Matches: 73, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 73 1.00
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (41 bp):
ATTGAGGATCACATGGTTGCTTGACGACCGTGGATCCACCG
Found at i:55844339 original size:48 final size:48
Alignment explanation
Indices: 55844287--55844392 Score: 167
Period size: 48 Copynumber: 2.2 Consensus size: 48
55844277 TCGACACGAT
*
55844287 TTAATAATTAATTCATTAAGTACCTTACAATTATAATGCAAGAATAAC
1 TTAATAATGAATTCATTAAGTACCTTACAATTATAATGCAAGAATAAC
* * *
55844335 TTAATCATGATTTCATTAGGTACCTTACAATTATAATGCAAGAATAAC
1 TTAATAATGAATTCATTAAGTACCTTACAATTATAATGCAAGAATAAC
*
55844383 TTAATCATGA
1 TTAATAATGA
55844393 TTTTACTTAT
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 54 1.00
ACGTcount: A:0.42, C:0.13, G:0.08, T:0.36
Consensus pattern (48 bp):
TTAATAATGAATTCATTAAGTACCTTACAATTATAATGCAAGAATAAC
Found at i:55844393 original size:48 final size:48
Alignment explanation
Indices: 55844298--55844395 Score: 187
Period size: 48 Copynumber: 2.0 Consensus size: 48
55844288 TAATAATTAA
55844298 TTCATTAAGTACCTTACAATTATAATGCAAGAATAACTTAATCATGAT
1 TTCATTAAGTACCTTACAATTATAATGCAAGAATAACTTAATCATGAT
*
55844346 TTCATTAGGTACCTTACAATTATAATGCAAGAATAACTTAATCATGAT
1 TTCATTAAGTACCTTACAATTATAATGCAAGAATAACTTAATCATGAT
55844394 TT
1 TT
55844396 TACTTATTCA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.40, C:0.14, G:0.09, T:0.37
Consensus pattern (48 bp):
TTCATTAAGTACCTTACAATTATAATGCAAGAATAACTTAATCATGAT
Found at i:55846292 original size:38 final size:39
Alignment explanation
Indices: 55846222--55846299 Score: 149
Period size: 38 Copynumber: 2.0 Consensus size: 39
55846212 TTTATGACAA
55846222 CTTAAAGATAATTAAGAGAAAAGTGATGGCTAAAAATTG
1 CTTAAAGATAATTAAGAGAAAAGTGATGGCTAAAAATTG
55846261 CTTAAAGATAATTAAGAG-AAAGTGATGGCTAAAAATTG
1 CTTAAAGATAATTAAGAGAAAAGTGATGGCTAAAAATTG
55846299 C
1 C
55846300 AAAGGTTCAA
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
38 21 0.54
39 18 0.46
ACGTcount: A:0.47, C:0.06, G:0.21, T:0.26
Consensus pattern (39 bp):
CTTAAAGATAATTAAGAGAAAAGTGATGGCTAAAAATTG
Found at i:55849550 original size:68 final size:65
Alignment explanation
Indices: 55849336--55849585 Score: 206
Period size: 68 Copynumber: 3.8 Consensus size: 65
55849326 CATAATTTTG
* * *
55849336 GCTCTCTTGTACACATGGTGTACACATAGTATCACCCATGTGACCTAGCCACT--TTATCTCGTA
1 GCTCTCTTGTACACATGGTGTACACATAGTATCACACATGCGACCTAGCTACTCATTATCTCGTA
** * * * * * *
55849399 GCTCTCTTGTTTACATGGTGTTCTTCACCTGGAACCACACATGCAACCTAGCTA--CATCTATCT
1 GCTCTCTTGTACACATGGTG---TACACATAGTATCACACATGCGACCTAGCTACTCAT-TATCT
*
55849462 CTTA
62 CGTA
* *
55849466 GCTCTCTTGT-CTACATGGTGTACACATAGTATCACCCATGCGACCTAGCTACCTCATAATATAT
1 GCTCTCTTGTAC-ACATGGTGTACACATAGTATCACACATGCGACCTAGCTA-CTCAT--TATCT
55849530 CGTA
62 CGTA
* * * * *
55849534 GCTCTCTTATACACATGGTATACATC-TCGTATTACACATGTGACCTAGCTAC
1 GCTCTCTTGTACACATGGTGTACA-CATAGTATCACACATGCGACCTAGCTAC
55849586 ATACCTTCTA
Statistics
Matches: 145, Mismatches: 29, Indels: 22
0.74 0.15 0.11
Matches are distributed among these distances:
63 18 0.12
64 24 0.17
66 23 0.16
67 30 0.21
68 48 0.33
69 2 0.01
ACGTcount: A:0.25, C:0.28, G:0.14, T:0.32
Consensus pattern (65 bp):
GCTCTCTTGTACACATGGTGTACACATAGTATCACACATGCGACCTAGCTACTCATTATCTCGTA
Found at i:55855105 original size:16 final size:16
Alignment explanation
Indices: 55855086--55855116 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
55855076 CTTCTTCACT
55855086 TACTCACTTACTTAAA
1 TACTCACTTACTTAAA
*
55855102 TACTTACTTACTTAA
1 TACTCACTTACTTAA
55855117 TCAAATTTAT
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:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (16 bp):
TACTCACTTACTTAAA
Found at i:55855122 original size:20 final size:20
Alignment explanation
Indices: 55855083--55855122 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
55855073 AAACTTCTTC
* *
55855083 ACTTACTCACTTACTTAAAT
1 ACTTACTCACTTAATCAAAT
*
55855103 ACTTACTTACTTAATCAAAT
1 ACTTACTCACTTAATCAAAT
55855123 TTATTAATAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.40
Consensus pattern (20 bp):
ACTTACTCACTTAATCAAAT
Found at i:55855506 original size:108 final size:110
Alignment explanation
Indices: 55855354--55855554 Score: 300
Period size: 108 Copynumber: 1.8 Consensus size: 110
55855344 ATTCTTTTGA
* *
55855354 AACTTACCATTGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATG-AACC-AACCAA
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTA-GAAACCTAACCAA
55855417 -TGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATGGT
65 TTGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATGGT
* * * * *
55855462 AACTTATCAATGCCATGTCTTGACATGGTCTTACGTGATTTCCTTTCCTTAGAAACCTTACCAAT
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTAGAAACCTAACCAAT
*
55855527 TGTCATGCCTTGGCATGGTCTTACATGG
66 TGCCATGCCTTGGCATGGTCTTACATGG
55855555 TATCCTTAAA
Statistics
Matches: 82, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
107 1 0.01
108 49 0.60
109 5 0.06
110 27 0.33
ACGTcount: A:0.22, C:0.25, G:0.18, T:0.35
Consensus pattern (110 bp):
AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTAGAAACCTAACCAAT
TGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATGGT
Found at i:55855512 original size:55 final size:52
Alignment explanation
Indices: 55855308--55855561 Score: 196
Period size: 55 Copynumber: 4.8 Consensus size: 52
55855298 ACGCAGGTAC
* * * * * * *
55855308 CTTACCATTGCCATGACTTGTCATGGTCTTACGTGGATTCTTT--TGA--AA
1 CTTACCAATGCCATGTCTTGACATGGTCTTACATGTATCCTTTCCTTATGAA
* *
55855356 CTTACCATTGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAA
1 CTTACCAATGCCATGTCTTGACATGGTCTTACAT-GTATCCTTTCCTTATGAA
** * * *
55855409 CCAACCAATGCCATGCCTTGGCATGGTCTTACATGGGA-CCTTTGCCTTATGGTAA
1 CTTACCAATGCCATGTCTTGACATGGTCTTACAT-GTATCCTTT-CCTTAT-G-AA
* * *
55855464 CTTATCAATGCCATGTCTTGACATGGTCTTACGTGATTTCCTTTCCTTA-GAAA
1 CTTACCAATGCCATGTCTTGACATGGTCTTACATG-TATCCTTTCCTTATG-AA
* * *
55855517 CCTTACCAATTGTCATGCCTTGGCATGGTCTTACATGGTATCCTT
1 -CTTACCAA-TGCCATGTCTTGACATGGTCTTACAT-GTATCCTT
55855562 AAACCCTAAT
Statistics
Matches: 164, Mismatches: 29, Indels: 19
0.77 0.14 0.09
Matches are distributed among these distances:
48 31 0.19
49 6 0.04
51 2 0.01
52 4 0.02
53 43 0.26
54 9 0.05
55 63 0.38
56 6 0.04
ACGTcount: A:0.21, C:0.24, G:0.18, T:0.37
Consensus pattern (52 bp):
CTTACCAATGCCATGTCTTGACATGGTCTTACATGTATCCTTTCCTTATGAA
Found at i:55859634 original size:40 final size:40
Alignment explanation
Indices: 55859589--55859755 Score: 176
Period size: 40 Copynumber: 4.2 Consensus size: 40
55859579 CGGAATATAA
55859589 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * * *
55859629 CCGGATAGAATAACTCGCACGAATGCCTTCGGGCCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
55859669 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
55859709 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
55859748 CCGGATAT
1 CCGGATAT
55859756 CATTCAATTT
Statistics
Matches: 105, Mismatches: 21, Indels: 3
0.81 0.16 0.02
Matches are distributed among these distances:
39 14 0.13
40 91 0.87
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:55859739 original size:80 final size:79
Alignment explanation
Indices: 55859605--55859755 Score: 198
Period size: 80 Copynumber: 1.9 Consensus size: 79
55859595 ATAATCACGT
*
55859605 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATAACTCGCACGAATGCCTTCGGGCCTTAGCC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATGCCTTCGGG-CTTAGCC
55859670 CGGATATAGCCACTA
65 CGGATATAGCCACTA
* * ** * *
55859685 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAATTGTCTTCGGGCTTAGC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTC-GCACGAA-TGCCTTCGGGCTTAGC
55859748 CCGGATAT
64 CCGGATAT
55859756 CATTCAATTT
Statistics
Matches: 62, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
79 17 0.27
80 45 0.73
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.26
Consensus pattern (79 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATGCCTTCGGGCTTAGCCC
GGATATAGCCACTA
Found at i:55867615 original size:40 final size:40
Alignment explanation
Indices: 55867570--55867736 Score: 176
Period size: 40 Copynumber: 4.2 Consensus size: 40
55867560 CGGAATATAA
55867570 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * * *
55867610 CCGGATAGAATAACTCGCACGAATGCCTTCGGGCCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
55867650 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
55867690 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
55867729 CCGGATAT
1 CCGGATAT
55867737 CATTCAATTT
Statistics
Matches: 105, Mismatches: 21, Indels: 3
0.81 0.16 0.02
Matches are distributed among these distances:
39 14 0.13
40 91 0.87
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:55867720 original size:80 final size:79
Alignment explanation
Indices: 55867586--55867736 Score: 198
Period size: 80 Copynumber: 1.9 Consensus size: 79
55867576 ATAATCACGT
*
55867586 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATAACTCGCACGAATGCCTTCGGGCCTTAGCC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATGCCTTCGGG-CTTAGCC
55867651 CGGATATAGCCACTA
65 CGGATATAGCCACTA
* * ** * *
55867666 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAATTGTCTTCGGGCTTAGC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTC-GCACGAA-TGCCTTCGGGCTTAGC
55867729 CCGGATAT
64 CCGGATAT
55867737 CATTCAATTT
Statistics
Matches: 62, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
79 17 0.27
80 45 0.73
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.26
Consensus pattern (79 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATGCCTTCGGGCTTAGCCC
GGATATAGCCACTA
Found at i:55871228 original size:15 final size:16
Alignment explanation
Indices: 55871208--55871240 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
55871198 TTGTGGGCTC
55871208 AGTTCGC-CCCTCGTG
1 AGTTCGCACCCTCGTG
*
55871223 AGTTCGCACGCTCGTG
1 AGTTCGCACCCTCGTG
55871239 AG
1 AG
55871241 GCCTCGAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.12, C:0.33, G:0.30, T:0.24
Consensus pattern (16 bp):
AGTTCGCACCCTCGTG
Found at i:55872184 original size:48 final size:48
Alignment explanation
Indices: 55872095--55872296 Score: 191
Period size: 48 Copynumber: 4.2 Consensus size: 48
55872085 TTCCAAACAT
* * *
55872095 GGTCTTACACTGACT-TCCATATATCAAAGCCGATGCCATGTCCGAGACA
1 GGTCTTACACTGGCTCT-CATATATCAAGGCCGAT-CCATGTCCCAGACA
* *
55872144 GGTCTTACACT-GCTCTCATCTATC-AGTGTCGATACCATGTCCCAGACA
1 GGTCTTACACTGGCTCTCATATATCAAG-GCCGAT-CCATGTCCCAGACA
* * * *
55872192 GGTCTTACACTGGCTCGCATATCTCAAGGCCGATGCATGTCCTAGACA
1 GGTCTTACACTGGCTCTCATATATCAAGGCCGATCCATGTCCCAGACA
* * **
55872240 TGTCTTACACTGGCTCTCA-AAAT-GTGGCCGA-CGCATGTCCCAGACA
1 GGTCTTACACTGGCTCTCATATATCAAGGCCGATC-CATGTCCCAGACA
*
55872286 TGTCTTACACT
1 GGTCTTACACT
55872297 AGCACACATA
Statistics
Matches: 128, Mismatches: 20, Indels: 13
0.80 0.12 0.08
Matches are distributed among these distances:
46 29 0.23
47 3 0.02
48 67 0.52
49 27 0.21
50 2 0.02
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.27
Consensus pattern (48 bp):
GGTCTTACACTGGCTCTCATATATCAAGGCCGATCCATGTCCCAGACA
Found at i:55872286 original size:46 final size:46
Alignment explanation
Indices: 55872179--55872296 Score: 148
Period size: 46 Copynumber: 2.5 Consensus size: 46
55872169 GTGTCGATAC
* * *
55872179 CATGTCCCAGACAGGTCTTACACTGGCTCGCATATCTCAAGGCCGATG
1 CATGTCCCAGACATGTCTTACACTGGCTCGCAAATCT--AGGCCGACG
* * *
55872227 CATGTCCTAGACATGTCTTACACTGGCTCTCAAAATGT-GGCCGACG
1 CATGTCCCAGACATGTCTTACACTGGCTCGC-AAATCTAGGCCGACG
55872273 CATGTCCCAGACATGTCTTACACT
1 CATGTCCCAGACATGTCTTACACT
55872297 AGCACACATA
Statistics
Matches: 62, Mismatches: 7, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
46 30 0.48
48 28 0.45
49 4 0.06
ACGTcount: A:0.24, C:0.31, G:0.20, T:0.25
Consensus pattern (46 bp):
CATGTCCCAGACATGTCTTACACTGGCTCGCAAATCTAGGCCGACG
Found at i:55872979 original size:20 final size:18
Alignment explanation
Indices: 55872942--55872992 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 18
55872932 CTATAGCAAC
55872942 TCACAATTT-CAATTATT
1 TCACAATTTACAATTATT
55872959 TCACACATTTACAACTTATT
1 TCACA-ATTTACAA-TTATT
*
55872979 TTACAACTTTACAA
1 TCACAA-TTTACAA
55872993 AATAATGCTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
17 5 0.17
18 4 0.14
19 4 0.14
20 16 0.55
ACGTcount: A:0.37, C:0.22, G:0.00, T:0.41
Consensus pattern (18 bp):
TCACAATTTACAATTATT
Found at i:55874969 original size:13 final size:13
Alignment explanation
Indices: 55874951--55874975 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55874941 ACAAACAATA
55874951 AAACTTTCACACG
1 AAACTTTCACACG
55874964 AAACTTTCACAC
1 AAACTTTCACAC
55874976 ATATAAATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.32, G:0.04, T:0.24
Consensus pattern (13 bp):
AAACTTTCACACG
Found at i:55875144 original size:13 final size:13
Alignment explanation
Indices: 55875126--55875150 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55875116 GGAGAGTTTT
55875126 AGGTGGTGGTTGA
1 AGGTGGTGGTTGA
55875139 AGGTGGTGGTTG
1 AGGTGGTGGTTG
55875151 GTTTGTTAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.00, G:0.56, T:0.32
Consensus pattern (13 bp):
AGGTGGTGGTTGA
Found at i:55876954 original size:28 final size:28
Alignment explanation
Indices: 55876885--55876985 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
55876875 GACAAGATTG
* * * *
55876885 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGTTT--GATTATATA
55876915 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
55876943 GCACTAAGTGTGCGAG-TTGAATACATATA
1 GCACTAAGTGTGCGAGTTTG-AT-TATATA
55876972 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
55876986 GATTCACTAT
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 3 0.05
28 24 0.38
29 19 0.30
30 18 0.28
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:55884907 original size:28 final size:28
Alignment explanation
Indices: 55884838--55884938 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
55884828 GACAAGATTG
* * * *
55884838 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGTTT--GATTATATA
55884868 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
55884896 GCACTAAGTGTGCGAG-TTGAATACATATA
1 GCACTAAGTGTGCGAGTTTG-AT-TATATA
55884925 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
55884939 GATTCACTAT
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 3 0.05
28 24 0.38
29 19 0.30
30 18 0.28
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:55907865 original size:40 final size:40
Alignment explanation
Indices: 55907816--55907910 Score: 163
Period size: 40 Copynumber: 2.4 Consensus size: 40
55907806 CGGATGTAAC
*
55907816 AACCAGCACGAATGCCTTCGGGACTTAACCCGATTATAAT
1 AACCCGCACGAATGCCTTCGGGACTTAACCCGATTATAAT
* *
55907856 AACCCGCACGAATTCCTTCGGGACTTAACCCGGTTATAAT
1 AACCCGCACGAATGCCTTCGGGACTTAACCCGATTATAAT
55907896 AACCCGCACGAATGC
1 AACCCGCACGAATGC
55907911 TATGCACATA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 51 1.00
ACGTcount: A:0.31, C:0.31, G:0.18, T:0.21
Consensus pattern (40 bp):
AACCCGCACGAATGCCTTCGGGACTTAACCCGATTATAAT
Found at i:55916323 original size:40 final size:40
Alignment explanation
Indices: 55916260--55916394 Score: 225
Period size: 40 Copynumber: 3.4 Consensus size: 40
55916250 CGGATGTAAC
* *
55916260 AACCAGCACGAATGCCTTAGGGACTTAACCCGGTTATAAT
1 AACCCGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
*
55916300 AACCCGCACGAATGCCTTCGGGACTTAACCCGATTATAAT
1 AACCCGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
*
55916340 AACCCGCACGAATTCCTTCGGGACTTAACCCGGTTATAAT
1 AACCCGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
*
55916380 AACCCGCACAAATGC
1 AACCCGCACGAATGC
55916395 TATGCACATA
Statistics
Matches: 88, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 88 1.00
ACGTcount: A:0.31, C:0.30, G:0.18, T:0.21
Consensus pattern (40 bp):
AACCCGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
Found at i:55917636 original size:31 final size:31
Alignment explanation
Indices: 55917595--55917658 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
55917585 CCTTTTCATA
*
55917595 TTTCATATTTCATAACACTGGGCCGAAGCCT
1 TTTCAAATTTCATAACACTGGGCCGAAGCCT
**
55917626 TTTCAAATTTCATATTACTGGGCCGAAGCCT
1 TTTCAAATTTCATAACACTGGGCCGAAGCCT
55917657 TT
1 TT
55917659 ACTGTAAACG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (31 bp):
TTTCAAATTTCATAACACTGGGCCGAAGCCT
Found at i:55917901 original size:24 final size:24
Alignment explanation
Indices: 55917850--55917992 Score: 209
Period size: 24 Copynumber: 6.0 Consensus size: 24
55917840 GCTTTATCAT
*
55917850 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
* *
55917875 ATAACTGGGGCAAAAGCCCTTTCA
1 ATAACTGGGGCATAAGCCCTTTTA
55917899 ATAACTGGGGCATAAGCCCTTTT-
1 ATAACTGGGGCATAAGCCCTTTTA
*
55917922 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
*
55917946 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
55917970 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
55917993 TCACTTCCTC
Statistics
Matches: 111, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
23 23 0.21
24 76 0.68
25 12 0.11
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:55917929 original size:47 final size:48
Alignment explanation
Indices: 55917850--55917991 Score: 207
Period size: 47 Copynumber: 3.0 Consensus size: 48
55917840 GCTTTATCAT
* *
55917850 ATAACTGGAGGCCT-AGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTCA
1 ATAACTGG-GGCATAAGCC-CTTTTAATAACTGGGGCATAAGCCCTTTCA
**
55917899 ATAACTGGGGCATAAGCCCTTTT-ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTCA
*
55917946 ATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCCTTT
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTT
55917992 TTCACTTCCT
Statistics
Matches: 87, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
47 44 0.51
48 31 0.36
49 12 0.14
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.28
Consensus pattern (48 bp):
ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTCA
Found at i:55917950 original size:71 final size:72
Alignment explanation
Indices: 55917849--55917992 Score: 220
Period size: 71 Copynumber: 2.0 Consensus size: 72
55917839 TGCTTTATCA
*
55917849 TATAACTGGAGGCCTAGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTCAATAACTGGGGCATAA
1 TATAACTGGAGGCATAGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTCAATAACTGGGGCATAA
55917914 GCCCTTT
66 GCCCTTT
* * **
55917921 TATAACTGG-GGCATAAGCC-CTTTTGATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATA
1 TATAACTGGAGGCAT-AGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTCAATAACTGGGGCATA
55917984 AGCCCTTT
65 AGCCCTTT
55917992 T
1 T
55917993 TCACTTCCTC
Statistics
Matches: 66, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
71 53 0.80
72 13 0.20
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.29
Consensus pattern (72 bp):
TATAACTGGAGGCATAGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTCAATAACTGGGGCATAA
GCCCTTT
Found at i:55918067 original size:20 final size:20
Alignment explanation
Indices: 55918042--55918102 Score: 104
Period size: 20 Copynumber: 3.0 Consensus size: 20
55918032 TTATGATTAC
55918042 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
55918062 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
* *
55918082 GTCATGTGCATCTCATACAT
1 ATCATGTGCATATCATACAT
55918102 A
1 A
55918103 CCATATTTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.33, C:0.21, G:0.11, T:0.34
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:55918177 original size:25 final size:25
Alignment explanation
Indices: 55918145--55918192 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
55918135 ATACATAAAC
* * *
55918145 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
55918170 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
55918193 CATGGTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:55919452 original size:27 final size:27
Alignment explanation
Indices: 55919432--55920042 Score: 675
Period size: 27 Copynumber: 22.6 Consensus size: 27
55919422 AGGGTATTTT
*
55919432 AGTAATTTTGTAAATCGAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
*
55919459 AGTAATTCTGTAAATCAAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
* *
55919486 AGTAATTCTATAAATCGAGGGTAAAAT
1 AGTAATTCTGTAAATCGAGGGTAAAAC
* * *
55919513 GGAAATACTGTAAATCGAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
*
55919540 GGTAATTCTGTAAATCGAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
* * *
55919567 -GATAATTATGTAAATCGGGGGTAAAAT
1 AG-TAATTCTGTAAATCGAGGGTAAAAC
* * * *
55919594 GGTAATTATGTAAAT-TAGGGGTAAAAT
1 AGTAATTCTGTAAATCGA-GGGTAAAAC
* * *
55919621 GGTAATTCTATAAATCGAGGGTAAAAT
1 AGTAATTCTGTAAATCGAGGGTAAAAC
55919648 AGTAATTCTGTAAA-CTGAGGGTAAAAC
1 AGTAATTCTGTAAATC-GAGGGTAAAAC
*
55919675 GGTAATTCTGTAAATCGAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
*
55919702 GGTAATT-T-TACAGATCGAGGGTAAAAC
1 AGTAATTCTGTA-A-ATCGAGGGTAAAAC
* *
55919729 -GATAATTCTATAAATCGAGGGTAAAAT
1 AG-TAATTCTGTAAATCGAGGGTAAAAC
* *
55919756 AGTAATTCTGTAAATCAATGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
*
55919783 AATAATTCTGTAAA-CTGAGGGTAAAAC
1 AGTAATTCTGTAAATC-GAGGGTAAAAC
* *
55919810 GGTAATTCTGTAAATCGAGGGTAAAAT
1 AGTAATTCTGTAAATCGAGGGTAAAAC
55919837 AGTAATTCTGTAAA-CTGAGGGTAAAAC
1 AGTAATTCTGTAAATC-GAGGGTAAAAC
* *
55919864 GGTAATTCTGTAAATAGAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
* * **
55919891 GGTAATTTTACAAATCGAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
* *
55919918 GGTAATTCTATAAATCGAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
* * **
55919945 GGTAATTTTACAAATCGAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
*
55919972 AGTAATTCTATAAA-CTGAGGGTAAAAC
1 AGTAATTCTGTAAATC-GAGGGTAAAAC
*
55919999 AGTAATTCTATAAA-CTGAGGGTAAAAC
1 AGTAATTCTGTAAATC-GAGGGTAAAAC
* *
55920026 GGTAAATCTGTAAATCG
1 AGTAATTCTGTAAATCG
55920043 GGAGTACTTT
Statistics
Matches: 513, Mismatches: 53, Indels: 36
0.85 0.09 0.06
Matches are distributed among these distances:
25 2 0.00
26 8 0.02
27 493 0.96
28 8 0.02
29 2 0.00
ACGTcount: A:0.41, C:0.09, G:0.22, T:0.27
Consensus pattern (27 bp):
AGTAATTCTGTAAATCGAGGGTAAAAC
Found at i:55927977 original size:53 final size:53
Alignment explanation
Indices: 55927803--55928005 Score: 203
Period size: 53 Copynumber: 3.8 Consensus size: 53
55927793 ATTAGGATTT
* * *
55927803 AAGGATACCATGTAAGACCATGCCAAGGCATGACAATGGTAAGGTTTC-TAAGGA
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGT-AGG-TTCATAAGGC
* * * * * * * *
55927857 AAGGAAATCACGTAATACCATGTCAAGACATGGCATTGATAAGTTACCATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAGGTT--CATAAGGC
* * * *
55927912 AAAGG-TCCCATGTAAGACCATGCCAAGGCATGGCATTGGTTGGTTCATAAGGC
1 -AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAGGTTCATAAGGC
*
55927965 AAGGATACCATGTAAGACCATGTCAAGACATGGCAATGGTA
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTA
55928006 AGTTTCAAAA
Statistics
Matches: 118, Mismatches: 26, Indels: 11
0.76 0.17 0.07
Matches are distributed among these distances:
52 6 0.05
53 41 0.35
54 32 0.27
55 35 0.30
56 4 0.03
ACGTcount: A:0.36, C:0.18, G:0.25, T:0.21
Consensus pattern (53 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAGGTTCATAAGGC
Done.