Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A09
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: 81831061
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 3560000 characters in sequence are not A, C, G, or T
File 88 of 259
Found at i:28681767 original size:21 final size:20
Alignment explanation
Indices: 28681739--28681777 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
28681729 GCATGTATTT
28681739 TGAAGCTTCTTGATAGATTA
1 TGAAGCTTCTTGATAGATTA
*
28681759 TGAATGCTTGTTGATAGAT
1 TGAA-GCTTCTTGATAGAT
28681778 ATACAAGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.28, C:0.08, G:0.23, T:0.41
Consensus pattern (20 bp):
TGAAGCTTCTTGATAGATTA
Found at i:28681844 original size:28 final size:29
Alignment explanation
Indices: 28681811--28681866 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
28681801 TTAATGAAAA
28681811 TGTAAA-TTAGGGG-CTAAATTGTGAAATG
1 TGTAAATTTAGGGGTCTAAA-TGTGAAATG
*
28681839 TGTAAATTTAGGGGTTTAAATGTGAAAT
1 TGTAAATTTAGGGGTCTAAATGTGAAAT
28681867 AAATGAAAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 6 0.24
29 15 0.60
30 4 0.16
ACGTcount: A:0.36, C:0.02, G:0.27, T:0.36
Consensus pattern (29 bp):
TGTAAATTTAGGGGTCTAAATGTGAAATG
Found at i:28686497 original size:7 final size:7
Alignment explanation
Indices: 28686485--28686524 Score: 53
Period size: 7 Copynumber: 5.7 Consensus size: 7
28686475 CTTTTACTAC
28686485 CTAAATA
1 CTAAATA
28686492 CTAAATA
1 CTAAATA
*
28686499 CTAAAAA
1 CTAAATA
*
28686506 CAAAATA
1 CTAAATA
*
28686513 TTAAATA
1 CTAAATA
28686520 CTAAA
1 CTAAA
28686525 ATTTCTAGAA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.62, C:0.12, G:0.00, T:0.25
Consensus pattern (7 bp):
CTAAATA
Found at i:28686936 original size:47 final size:46
Alignment explanation
Indices: 28686885--28686980 Score: 174
Period size: 46 Copynumber: 2.0 Consensus size: 46
28686875 TAAGGCTCGA
28686885 TTTTTACTTATTTTATATGTTAAAGTTATATTAAAATAATATATATGT
1 TTTTTACTT-TTTTATATGTTAAAGTTAT-TTAAAATAATATATATGT
28686933 TTTTTACTTTTTTATATGTTAAAGTTATTTAAAATAATATATATGT
1 TTTTTACTTTTTTATATGTTAAAGTTATTTAAAATAATATATATGT
28686979 TT
1 TT
28686981 ATTAAACATT
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
46 20 0.42
47 19 0.40
48 9 0.19
ACGTcount: A:0.35, C:0.02, G:0.06, T:0.56
Consensus pattern (46 bp):
TTTTTACTTTTTTATATGTTAAAGTTATTTAAAATAATATATATGT
Found at i:28691844 original size:30 final size:30
Alignment explanation
Indices: 28691810--28691866 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
28691800 TAAACCTCTT
28691810 CACTTT-CCTCCCAAAACTTTTACTCCCTCC
1 CACTTTACC-CCCAAAACTTTTACTCCCTCC
* *
28691840 CACTTTACCCCCATAACTTTTGCTCCC
1 CACTTTACCCCCAAAACTTTTACTCCC
28691867 CTCCTATCCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 22 0.92
31 2 0.08
ACGTcount: A:0.19, C:0.46, G:0.02, T:0.33
Consensus pattern (30 bp):
CACTTTACCCCCAAAACTTTTACTCCCTCC
Found at i:28692092 original size:36 final size:35
Alignment explanation
Indices: 28692050--28692146 Score: 108
Period size: 36 Copynumber: 2.7 Consensus size: 35
28692040 ACCTAAATAA
*
28692050 TAATTTTATTTATATTCACTATTTATATTATTAAAT
1 TAATTTTA-TCATATTCACTATTTATATTATTAAAT
* *
28692086 TAATTTTCA-CATATTCTACTATCTATATTATTGAAT
1 TAATTTT-ATCATATTC-ACTATTTATATTATTAAAT
* *
28692122 T-ATTTTATCATATTGAATATTTATA
1 TAATTTTATCATATTCACTATTTATA
28692147 AATTTATGCT
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
34 9 0.17
35 17 0.33
36 25 0.48
37 1 0.02
ACGTcount: A:0.35, C:0.08, G:0.02, T:0.55
Consensus pattern (35 bp):
TAATTTTATCATATTCACTATTTATATTATTAAAT
Found at i:28692424 original size:19 final size:19
Alignment explanation
Indices: 28692387--28692424 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
28692377 AAAGTTAATA
*
28692387 ACAAATTTGATTAATGTGG
1 ACAAATTTGATTAAGGTGG
*
28692406 ACAAATTTGATTACGGTGG
1 ACAAATTTGATTAAGGTGG
28692425 GTGATAGTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.34, C:0.08, G:0.24, T:0.34
Consensus pattern (19 bp):
ACAAATTTGATTAAGGTGG
Found at i:28694630 original size:18 final size:19
Alignment explanation
Indices: 28694579--28694630 Score: 65
Period size: 18 Copynumber: 2.9 Consensus size: 19
28694569 CTATTAATGA
**
28694579 ATAATTA-ACTGTTACCGG
1 ATAATTAGACTGTTACTAG
28694597 ATAATT-GACTGTTACTAG
1 ATAATTAGACTGTTACTAG
28694615 AT-ATTAGACTGTTACT
1 ATAATTAGACTGTTACT
28694631 GAATAACTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 3 0.10
18 27 0.90
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.38
Consensus pattern (19 bp):
ATAATTAGACTGTTACTAG
Found at i:28694647 original size:18 final size:18
Alignment explanation
Indices: 28694624--28694757 Score: 112
Period size: 18 Copynumber: 7.4 Consensus size: 18
28694614 GATATTAGAC
28694624 TGTTACTGAATAACTGAA
1 TGTTACTGAATAACTGAA
* *
28694642 TATTACTGAATAATTG-A
1 TGTTACTGAATAACTGAA
* *
28694659 TCATTACTGAATAACTGAT
1 T-GTTACTGAATAACTGAA
* *
28694678 TGTCACTGAATGAA-TGAC
1 TGTTACTGAAT-AACTGAA
*
28694696 TGTTACTGAATAACTTAA
1 TGTTACTGAATAACTGAA
*
28694714 TTGTTACTGAATACCTG-A
1 -TGTTACTGAATAACTGAA
* * * *
28694732 TTTTACTAAATAATTGAC
1 TGTTACTGAATAACTGAA
28694750 TGTTACTG
1 TGTTACTG
28694758 GACAACCGAT
Statistics
Matches: 91, Mismatches: 19, Indels: 12
0.75 0.16 0.10
Matches are distributed among these distances:
17 16 0.18
18 58 0.64
19 17 0.19
ACGTcount: A:0.35, C:0.13, G:0.14, T:0.38
Consensus pattern (18 bp):
TGTTACTGAATAACTGAA
Found at i:28694750 original size:54 final size:53
Alignment explanation
Indices: 28694624--28694757 Score: 153
Period size: 54 Copynumber: 2.5 Consensus size: 53
28694614 GATATTAGAC
* * *
28694624 TGTTACTGAATAACTGAATATTACTGAATAATTGATCATTACTGAATAACTGAT
1 TGTTACTGAATAA-TGACTGTTACTGAATAATTAATCATTACTGAATAACTGAT
* ** *
28694678 TGTCACTGAATGAATGACTGTTACTGAATAACTTAATTGTTACTGAATACCTGAT
1 TGTTACTGAAT-AATGACTGTTACTGAATAA-TTAATCATTACTGAATAACTGAT
*
28694733 T-TTACTAAATAATTGACTGTTACTG
1 TGTTACTGAATAA-TGACTGTTACTG
28694758 GACAACCGAT
Statistics
Matches: 68, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
53 2 0.03
54 44 0.65
55 22 0.32
ACGTcount: A:0.35, C:0.13, G:0.14, T:0.38
Consensus pattern (53 bp):
TGTTACTGAATAATGACTGTTACTGAATAATTAATCATTACTGAATAACTGAT
Found at i:28694840 original size:36 final size:36
Alignment explanation
Indices: 28694560--28694855 Score: 179
Period size: 36 Copynumber: 8.0 Consensus size: 36
28694550 AAAGGTATAA
* * * * *
28694560 AATAACTGACTATTAATGAATAATTAACTGTTACCG
1 AATAACTGACTGTTACTGAATAATTGATTGTTACTG
* * *
28694596 GATAATTGACTGTTACT-AGAT-ATTAGACTGTTACTG
1 AATAACTGACTGTTACTGA-ATAATT-GATTGTTACTG
* * **
28694632 AATAACTGAATATTACTGAATAATTGATCATTACTG
1 AATAACTGACTGTTACTGAATAATTGATTGTTACTG
* * *
28694668 AATAACTGATTGTCACTGAATGAA-TGACTGTTACTG
1 AATAACTGACTGTTACTGAAT-AATTGATTGTTACTG
* * ** *
28694704 AATAACTTAATTGTTACTGAATACCTGATT-TTACTA
1 AATAAC-TGACTGTTACTGAATAATTGATTGTTACTG
* * *
28694740 AATAATTGACTGTTACTGGACAACCGATCAATTGATCGATACTG
1 AATAACTGACTGTTACT-G---A---AT-AATTGATTGTTACTG
** * * *
28694784 AATAACTGGTTATTATTGAATAATTGATTGTTACCG
1 AATAACTGACTGTTACTGAATAATTGATTGTTACTG
* *
28694820 AATAACTGACTGTTACTGAATAAATAATTGTT-CTG
1 AATAACTGACTGTTACTGAATAATTGATTGTTACTG
28694855 A
1 A
28694856 TTGTTAATGA
Statistics
Matches: 197, Mismatches: 47, Indels: 33
0.71 0.17 0.12
Matches are distributed among these distances:
35 16 0.08
36 130 0.66
37 25 0.13
39 1 0.01
40 1 0.01
42 2 0.01
43 6 0.03
44 16 0.08
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (36 bp):
AATAACTGACTGTTACTGAATAATTGATTGTTACTG
Found at i:28694851 original size:18 final size:18
Alignment explanation
Indices: 28694624--28694855 Score: 108
Period size: 18 Copynumber: 12.5 Consensus size: 18
28694614 GATATTAGAC
* *
28694624 TGTTACTGAATAACTGAA
1 TGTTACTGAATAAATGAT
* *
28694642 TATTACTGAATAATTGAT
1 TGTTACTGAATAAATGAT
** *
28694660 CATTACTGAATAACTGAT
1 TGTTACTGAATAAATGAT
* * *
28694678 TGTCACTGAATGAATGAC
1 TGTTACTGAATAAATGAT
* *
28694696 TGTTACTGAATAACTTAAT
1 TGTTACTGAATAA-ATGAT
**
28694715 TGTTACTGAATACCTGAT
1 TGTTACTGAATAAATGAT
* * *
28694733 T-TTACTAAATAATTGAC
1 TGTTACTGAATAAATGAT
*
28694750 TGTTACTGGACAACCGATCAATTGAT
1 TGTTACT-G---A---AT-AAATGAT
* * * *
28694776 CGATACTGAATAACTGGT
1 TGTTACTGAATAAATGAT
* * *
28694794 TATTATTGAATAATTGAT
1 TGTTACTGAATAAATGAT
* * *
28694812 TGTTACCGAATAACTGAC
1 TGTTACTGAATAAATGAT
*
28694830 TGTTACTGAATAAATAAT
1 TGTTACTGAATAAATGAT
28694848 TGTT-CTGA
1 TGTTACTGA
28694856 TTGTTAATGA
Statistics
Matches: 160, Mismatches: 44, Indels: 21
0.71 0.20 0.09
Matches are distributed among these distances:
17 17 0.11
18 111 0.69
19 16 0.10
22 2 0.01
25 3 0.02
26 11 0.07
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (18 bp):
TGTTACTGAATAAATGAT
Found at i:28695812 original size:47 final size:46
Alignment explanation
Indices: 28695700--28695829 Score: 154
Period size: 47 Copynumber: 2.8 Consensus size: 46
28695690 TCACTTGTGT
* *
28695700 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGACCACATTACGA
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACATGACGA
* * ***
28695746 GAGCCAGTGTAAGACCATGTTTGGGACATGTCATCGGCGTTGA-GACGA
1 GAGCTAGTGTAAGA-CATGTCTGGGACATG-CATCGGC-CACATGACGA
*
28695794 GTGCTAGTGTAAGACATGTCTGGGACATGCATCGGC
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGC
28695830 ATCGAAACAT
Statistics
Matches: 71, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
46 20 0.28
47 28 0.39
48 22 0.31
49 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.31, T:0.23
Consensus pattern (46 bp):
GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACATGACGA
Found at i:28695850 original size:46 final size:45
Alignment explanation
Indices: 28695705--28695872 Score: 153
Period size: 46 Copynumber: 3.6 Consensus size: 45
28695695 TGTGTGAGCT
* * *
28695705 AGTGTAAGACATGTCTGGGACATGCATCGACCA-C-ATTACGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCG-GCATCGA-AAC-AGAGTC
* * * *
28695751 AGTGTAAGACCATGTTTGGGACATGTCATCGGCGTTGAGAC-GAGTGC
1 AGTGTAAGA-CATGTCTGGGACATG-CATCGGCATCGAAACAGAGT-C
*
28695798 TAGTGTAAGACATGTCTGGGACATGCATCGGCATCGAAACATAAGTC
1 -AGTGTAAGACATGTCTGGGACATGCATCGGCATCGAAACA-GAGTC
* *
28695845 AGTGTAAGACTTGTCTAGGACATGCATC
1 AGTGTAAGACATGTCTGGGACATGCATC
28695873 AGCTACAAGA
Statistics
Matches: 101, Mismatches: 13, Indels: 16
0.78 0.10 0.12
Matches are distributed among these distances:
46 50 0.50
47 31 0.31
48 19 0.19
49 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.28, T:0.24
Consensus pattern (45 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCATCGAAACAGAGTC
Found at i:28702563 original size:18 final size:18
Alignment explanation
Indices: 28702542--28702588 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
28702532 TGTTGTTATT
28702542 ATTAGGCTTGTATAGGGA
1 ATTAGGCTTGTATAGGGA
*
28702560 ATTAGGCATGTATAGGGA
1 ATTAGGCTTGTATAGGGA
28702578 ATTAGGCTTGT
1 ATTAGGCTTGT
28702589 GGTTTGGGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.28, C:0.06, G:0.32, T:0.34
Consensus pattern (18 bp):
ATTAGGCTTGTATAGGGA
Found at i:28712686 original size:53 final size:54
Alignment explanation
Indices: 28712605--28712811 Score: 218
Period size: 53 Copynumber: 3.8 Consensus size: 54
28712595 TTCCTTTTTA
* * * *
28712605 AACTTACCATTGTCATGTCTTGATATGGTCTTACGTGGTATCCTTGCCTTAT-G
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
* * * * * * *
28712658 AACTCACCATTGCCATGCCTTGGCATGGTCTTACATGGGATCTTTGCCTTATCG
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
** * * * * *
28712712 TAGTTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTGTAA
1 -AACTTACCAATGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
* *
28712767 AACTTACCAATGCCATGTCTTGGCATGGTCTTACTTGGTATCCTT
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGGTATCCTT
28712812 AAACCCTAAT
Statistics
Matches: 123, Mismatches: 29, Indels: 3
0.79 0.19 0.02
Matches are distributed among these distances:
53 44 0.36
54 39 0.32
55 40 0.33
ACGTcount: A:0.20, C:0.23, G:0.18, T:0.39
Consensus pattern (54 bp):
AACTTACCAATGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
Found at i:28712744 original size:55 final size:53
Alignment explanation
Indices: 28712618--28712811 Score: 181
Period size: 55 Copynumber: 3.6 Consensus size: 53
28712608 TTACCATTGT
* * * *
28712618 CATGTCTTGATATGGTCTTACGTGGTATCCTTGCCTTATGAACTCACCATTGC
1 CATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTATGAACTCACCAATGC
* * * ** * *
28712671 CATGCCTTGGCATGGTCTTACATGGGATCTTTGCCTTATCGTAGTTTATCAATGC
1 CATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTAT-G-AACTCACCAATGC
*** * * *
28712726 CATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTGTAAAACTTACCAATGC
1 CATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTAT-GAACTCACCAATGC
* * *
28712780 CATGTCTTGGCATGGTCTTACTTGGTATCCTT
1 CATGTCTTGACATGGTCTTACATGGGATCCTT
28712812 AAACCCTAAT
Statistics
Matches: 112, Mismatches: 27, Indels: 3
0.79 0.19 0.02
Matches are distributed among these distances:
53 33 0.29
54 39 0.35
55 40 0.36
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.39
Consensus pattern (53 bp):
CATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTATGAACTCACCAATGC
Found at i:28719411 original size:17 final size:18
Alignment explanation
Indices: 28719377--28719411 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
28719367 TTCCCCGATG
*
28719377 ATAATCTATTACTAACTC
1 ATAATCTATTAATAACTC
28719395 ATAATCT-TTAATAACTC
1 ATAATCTATTAATAACTC
28719412 GAGCTATCTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (18 bp):
ATAATCTATTAATAACTC
Found at i:28725231 original size:116 final size:118
Alignment explanation
Indices: 28725074--28725361 Score: 395
Period size: 116 Copynumber: 2.4 Consensus size: 118
28725064 CCGGATTAAG
* *
28725074 ATCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTAT
1 ATCCGAAGG-CATTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTAT
* *
28725139 TAAATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAAT-C-GGTTA-
65 TAAATCCGGATTAAG-TCCCGAAGGCATTCGTGCGAGATACTAAATCCGGGTTAT
*
28725190 ATCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTAT
1 ATCCGAAGGCATT-GTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTAT
* * *
28725255 TAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAT
65 TAAATCCGGATTAAGTCCCGAAGGCATTCGTGCGAGATACTAAATCCGGGTTAT
* * * * *
28725309 GTCCCGAAGGCATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT
1 AT-CCGAAGGCATTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATT
28725362 TGAACGAGGA
Statistics
Matches: 152, Mismatches: 14, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
115 4 0.03
116 96 0.63
117 1 0.01
118 5 0.03
119 35 0.23
120 11 0.07
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.27
Consensus pattern (118 bp):
ATCCGAAGGCATTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATT
AAATCCGGATTAAGTCCCGAAGGCATTCGTGCGAGATACTAAATCCGGGTTAT
Found at i:28725304 original size:40 final size:40
Alignment explanation
Indices: 28725023--28725361 Score: 397
Period size: 40 Copynumber: 8.6 Consensus size: 40
28725013 TTGAATGCTG
* * * * * *
28725023 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* * * * *
28725063 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
28725103 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * * * *
28725143 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
28725183 T-C-GGTTAA-T-CCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
28725219 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
28725259 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
28725299 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
28725338 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
28725362 TGAACGAGGA
Statistics
Matches: 264, Mismatches: 27, Indels: 17
0.86 0.09 0.06
Matches are distributed among these distances:
36 25 0.09
37 1 0.00
38 11 0.04
39 38 0.14
40 180 0.68
41 9 0.03
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:28733213 original size:82 final size:80
Alignment explanation
Indices: 28733048--28733348 Score: 380
Period size: 82 Copynumber: 3.8 Consensus size: 80
28733038 TTGAATGCTG
* * * * * * *
28733048 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGATTAAGATCCGAAGGCCTT
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAATCCGGATTAAGATCCGAAGGCATT
* * *
28733112 TGTGCGAGATACTAAA
65 CGTGCGAGTTATTAAA
28733128 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGATTTAAGATCCCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGA-TTAAGAT-CCGAAGGCAT
28733193 TCGTGCGAGTTATTAAA
64 TCGTGCGAGTTATTAAA
*
28733210 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAG-TCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGATTAAGATCCGAAGGCATTC
28733274 GTGCGAGTTATTAAA
66 GTGCGAGTTATTAAA
* * * ** *
28733289 T-CGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA-CCGGGCTATG-TCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGATTAAGATCCGAAGGCATT
28733349 TGAACGAGGA
Statistics
Matches: 202, Mismatches: 16, Indels: 10
0.89 0.07 0.04
Matches are distributed among these distances:
76 20 0.10
77 13 0.06
78 21 0.10
79 28 0.14
80 34 0.17
81 18 0.09
82 68 0.34
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.28
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGATTAAGATCCGAAGGCATTC
GTGCGAGTTATTAAA
Found at i:28733277 original size:39 final size:40
Alignment explanation
Indices: 28733048--28733348 Score: 364
Period size: 40 Copynumber: 7.6 Consensus size: 40
28733038 TTGAATGCTG
* * * * * *
28733048 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* * * * *
28733088 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
28733128 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
28733168 TCCGGATTTAAGATCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGG-GTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
28733210 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
28733250 TCCGGGTTAAGT-CCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
28733289 T-CGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* *
28733327 -CCGGGCTATGT-CCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
28733349 TGAACGAGGA
Statistics
Matches: 236, Mismatches: 18, Indels: 17
0.87 0.07 0.06
Matches are distributed among these distances:
37 11 0.05
38 31 0.13
39 40 0.17
40 102 0.43
41 18 0.08
42 34 0.14
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.28
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:28733372 original size:76 final size:78
Alignment explanation
Indices: 28733122--28733383 Score: 269
Period size: 82 Copynumber: 3.3 Consensus size: 78
28733112 TGTGCGAGAT
* **
28733122 ACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGATTTAAGATCCCGA
1 ACTAAATCC-GGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAATCCGG-GCTAAG-T-CCGA
** *
28733187 AGGCATTCGTGCGAGTT
62 AGGCATTCGAACGAGTG
* * *
28733204 ATTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCGAAGG
1 ACTAAATCC-GGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAATCCGGGCTAAGTCCGAAGG
** *
28733269 CATTCGTGCGAGTT
65 CATTCGAACGAGTG
* * * * *
28733283 ATTAAATCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA-CCGGGCTATGTCCGAAGGC
1 ACTAAATCCGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAATCCGGGCTAAGTCCGAAGGC
*
28733346 ATTTGAACGAG-G
66 ATTCGAACGAGTG
* *
28733358 AGCTATATCCGGTTAAATCCCGAAGG
1 A-CTAAATCCGGTTAAGTCCCGAAGG
28733384 TACGTGATTT
Statistics
Matches: 162, Mismatches: 17, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
75 1 0.01
76 44 0.27
77 13 0.08
78 19 0.12
79 29 0.18
80 1 0.01
81 5 0.03
82 50 0.31
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.27
Consensus pattern (78 bp):
ACTAAATCCGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAATCCGGGCTAAGTCCGAAGGC
ATTCGAACGAGTG
Found at i:28746250 original size:11 final size:11
Alignment explanation
Indices: 28746234--28746262 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
28746224 GCCTGGACTG
28746234 ATAATCCTGAT
1 ATAATCCTGAT
28746245 ATAATCCTGAT
1 ATAATCCTGAT
28746256 ATAATCC
1 ATAATCC
28746263 CTCTCGAGCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.38, C:0.21, G:0.07, T:0.34
Consensus pattern (11 bp):
ATAATCCTGAT
Found at i:28750825 original size:40 final size:40
Alignment explanation
Indices: 28750778--28750872 Score: 127
Period size: 40 Copynumber: 2.4 Consensus size: 40
28750768 CAGCTATTTG
*
28750778 TGGCACTTAGTTTGCGATTTGACATAGCTTCGGCTATATA
1 TGGCACTTAGTGTGCGATTTGACATAGCTTCGGCTATATA
* * *
28750818 TGGCACTTAGTGTGTGATTTGAGATAGCTTCGGCTATGTA
1 TGGCACTTAGTGTGCGATTTGACATAGCTTCGGCTATATA
* * *
28750858 CGACACTTAATGTGC
1 TGGCACTTAGTGTGC
28750873 AAGATATCGA
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 47 1.00
ACGTcount: A:0.22, C:0.17, G:0.25, T:0.36
Consensus pattern (40 bp):
TGGCACTTAGTGTGCGATTTGACATAGCTTCGGCTATATA
Found at i:28757891 original size:47 final size:47
Alignment explanation
Indices: 28757813--28757980 Score: 264
Period size: 47 Copynumber: 3.6 Consensus size: 47
28757803 CCCTTCGGGA
* * * * * *
28757813 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
28757860 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28757907 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28757954 CTTATCACATATATACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
28757981 ACCAACCCTT
Statistics
Matches: 111, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 111 1.00
ACGTcount: A:0.28, C:0.31, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:28758242 original size:40 final size:39
Alignment explanation
Indices: 28758205--28758296 Score: 132
Period size: 39 Copynumber: 2.3 Consensus size: 39
28758195 GCTACTCGTT
*
28758205 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGG-CATAGCCCGGAAT-TAGTAACTCGCA
* *
28758245 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCATAGCCCGGAATTAGTAACTCGCA
28758284 CAAATGCCTTCGG
1 CAAATGCCTTCGG
28758297 ATCTTAGTCC
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
39 33 0.69
40 15 0.31
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (39 bp):
CAAATGCCTTCGGGCATAGCCCGGAATTAGTAACTCGCA
Found at i:28758276 original size:39 final size:40
Alignment explanation
Indices: 28758186--28758346 Score: 170
Period size: 40 Copynumber: 4.0 Consensus size: 40
28758176 CGGAATTTAA
** *
28758186 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
*
28758226 CCGGTTATAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
28758265 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
28758305 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
28758345 CC
1 CC
28758347 AGACATCATT
Statistics
Matches: 102, Mismatches: 12, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
38 3 0.03
39 32 0.31
40 55 0.54
41 12 0.12
ACGTcount: A:0.24, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:28763960 original size:38 final size:39
Alignment explanation
Indices: 28763905--28764031 Score: 175
Period size: 39 Copynumber: 3.3 Consensus size: 39
28763895 TATGAGATTG
* *
28763905 AAAATATTCGGACATGAGGTCCGCAGGCTATATGCTGGA
1 AAAATATCCGGACATGAGGTCTGCAGGCTATATGCTGGA
* *
28763944 AAAATATCCGGA-ATGAGATCTGCAGGCTATATGCTAGA
1 AAAATATCCGGACATGAGGTCTGCAGGCTATATGCTGGA
* * **
28763982 AATATATCCGGACTTGAGGTCTGCAGGCTACGTGCTGGA
1 AAAATATCCGGACATGAGGTCTGCAGGCTATATGCTGGA
28764021 AAAATATCCGG
1 AAAATATCCGG
28764032 GTTAAAGACC
Statistics
Matches: 76, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
38 34 0.45
39 42 0.55
ACGTcount: A:0.31, C:0.18, G:0.27, T:0.24
Consensus pattern (39 bp):
AAAATATCCGGACATGAGGTCTGCAGGCTATATGCTGGA
Found at i:28764057 original size:77 final size:76
Alignment explanation
Indices: 28763904--28764057 Score: 184
Period size: 77 Copynumber: 2.0 Consensus size: 76
28763894 GTATGAGATT
* * * * *
28763904 GAAAATATTCGGACATGAGGTCCGCAGGCTATATGCTGGAAAAATATCCGGAATGAGATCTGCAG
1 GAAAATATCCGGACATGAGGTCCGCAGGCTACATGCTGGAAAAATATCCGGAATAAGACCCGCAG
*
28763969 GCTATATGCTA
66 GCTATACGCTA
* * * **
28763980 GAAATATATCCGGACTTGAGGTCTGCAGGCTACGTGCTGGAAAAATATCCGGGTTAAAGACCCGC
1 GAAA-ATATCCGGACATGAGGTCCGCAGGCTACATGCTGGAAAAATATCCGGAAT-AAGACCCGC
28764045 AGGCT-TACGCTA
64 AGGCTATACGCTA
28764057 G
1 G
28764058 TAATGTATTC
Statistics
Matches: 65, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
76 4 0.06
77 50 0.77
78 11 0.17
ACGTcount: A:0.31, C:0.19, G:0.27, T:0.23
Consensus pattern (76 bp):
GAAAATATCCGGACATGAGGTCCGCAGGCTACATGCTGGAAAAATATCCGGAATAAGACCCGCAG
GCTATACGCTA
Found at i:28771631 original size:42 final size:42
Alignment explanation
Indices: 28771584--28771747 Score: 172
Period size: 42 Copynumber: 3.9 Consensus size: 42
28771574 TTAGGGTTAC
*
28771584 TGAGACTATGTGTAAGACCATATCTAGGATATGGCATCGATA
1 TGAGACTATGTGTAAGACCATATCTGGGATATGGCATCGATA
*
28771626 TGAGACT-TCGTGTAAGACCGTATCTGGGATATGGCATCGATGA
1 TGAGACTAT-GTGTAAGACCATATCTGGGATATGGCATCGAT-A
* * * * * *
28771669 -GAGATTTTGTGTAAGATCGTAGCTGGGCTATTGGCATCGATA
1 TGAGACTATGTGTAAGACCATATCTGGGATA-TGGCATCGATA
* **
28771711 CGAGA-TGACATGTAAGACCATATCTGGGATATGGCAT
1 TGAGACT-ATGTGTAAGACCATATCTGGGATATGGCAT
28771748 TGGTATGGTA
Statistics
Matches: 103, Mismatches: 13, Indels: 12
0.80 0.10 0.09
Matches are distributed among these distances:
41 1 0.01
42 69 0.67
43 33 0.32
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.29
Consensus pattern (42 bp):
TGAGACTATGTGTAAGACCATATCTGGGATATGGCATCGATA
Found at i:28779173 original size:42 final size:42
Alignment explanation
Indices: 28779126--28779288 Score: 170
Period size: 42 Copynumber: 3.9 Consensus size: 42
28779116 TTAGGGTTAC
* * *
28779126 TGAGACTATGTGTAAGACCATATTTGGGATATGGCATCCAAA
1 TGAGACTATGTGTAAGACCATATCTGGGATATGGCATCGATA
* * *
28779168 TGAGACT-TCGTGTAAGATCGTATCTGGGATATGGCATCGATG
1 TGAGACTAT-GTGTAAGACCATATCTGGGATATGGCATCGATA
* * * * *
28779210 TGAGATTTTGTGTAAGAACAT-TCTGGGCTATTGGCATTGATA
1 TGAGACTATGTGTAAGACCATATCTGGGATA-TGGCATCGATA
*
28779252 TGAGA-TGATATGTAAGACCATATCTGGGATATGGCAT
1 TGAGACT-ATGTGTAAGACCATATCTGGGATATGGCAT
28779289 TGGTATGGTA
Statistics
Matches: 100, Mismatches: 16, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
41 10 0.10
42 81 0.81
43 9 0.09
ACGTcount: A:0.29, C:0.12, G:0.27, T:0.32
Consensus pattern (42 bp):
TGAGACTATGTGTAAGACCATATCTGGGATATGGCATCGATA
Found at i:28782957 original size:27 final size:27
Alignment explanation
Indices: 28782927--28783067 Score: 151
Period size: 27 Copynumber: 5.2 Consensus size: 27
28782917 GGGCAAAATG
* * *
28782927 GTAATTTTACCCCAT-GAGGGTATCTCA
1 GTAATTCTACCCTATAG-GGGTATTTCA
* *
28782954 GTAATTCTACCTTATAGGGGTATTTAA
1 GTAATTCTACCCTATAGGGGTATTTCA
*
28782981 GTAATTCTACCTTATAGGGGTATTTCA
1 GTAATTCTACCCTATAGGGGTATTTCA
*
28783008 GTAATTCTACCCTATAAGGGTATTTC-
1 GTAATTCTACCCTATAGGGGTATTTCA
* * * *
28783034 GTTAATTCTGCCGTAAAGGGGTATTTTA
1 G-TAATTCTACCCTATAGGGGTATTTCA
28783062 GTAATT
1 GTAATT
28783068 TTACAAATTA
Statistics
Matches: 98, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
26 1 0.01
27 95 0.97
28 2 0.02
ACGTcount: A:0.27, C:0.15, G:0.19, T:0.39
Consensus pattern (27 bp):
GTAATTCTACCCTATAGGGGTATTTCA
Found at i:28783083 original size:27 final size:27
Alignment explanation
Indices: 28783050--28783338 Score: 318
Period size: 27 Copynumber: 10.7 Consensus size: 27
28783040 TCTGCCGTAA
* *
28783050 AGGGGTATTTTAGTAATTTTACAAATT
1 AGGGGTATTTTGGTAATTTTACAAACT
* *
28783077 AGAGGTATTTTGGTAATTTTACAAACC
1 AGGGGTATTTTGGTAATTTTACAAACT
* *
28783104 AGGGGTATTTTTGTAATTTTACTAA-T
1 AGGGGTATTTTGGTAATTTTACAAACT
* * *
28783130 TGAGGGTATTTTGGTAATTTCACAAATT
1 AG-GGGTATTTTGGTAATTTTACAAACT
28783158 AGGGGTATTTTGGTAATTTTACAAACT
1 AGGGGTATTTTGGTAATTTTACAAACT
* *
28783185 AGGGGGATTTTGGTAA-TTTAGCAAACA
1 AGGGGTATTTTGGTAATTTTA-CAAACT
*
28783212 AGGGGTATTTTGGTAATTTTACAAACA
1 AGGGGTATTTTGGTAATTTTACAAACT
*
28783239 AGGGGTATTTTAGTAATTTTACAAACT
1 AGGGGTATTTTGGTAATTTTACAAACT
* *
28783266 AGGGGTATTTTTGGTAATTTTGCTAA-T
1 AGGGGTA-TTTTGGTAATTTTACAAACT
* * * *
28783293 CAAGGGCA-TTTGGTAATTTTTCCAA-T
1 -AGGGGTATTTTGGTAATTTTACAAACT
*
28783319 CGAGGGTATTTTGGTAATTT
1 AG-GGGTATTTTGGTAATTT
28783339 GGTAAACTAA
Statistics
Matches: 224, Mismatches: 30, Indels: 16
0.83 0.11 0.06
Matches are distributed among these distances:
26 25 0.11
27 173 0.77
28 26 0.12
ACGTcount: A:0.29, C:0.07, G:0.22, T:0.41
Consensus pattern (27 bp):
AGGGGTATTTTGGTAATTTTACAAACT
Found at i:28783093 original size:81 final size:81
Alignment explanation
Indices: 28782925--28783094 Score: 182
Period size: 81 Copynumber: 2.1 Consensus size: 81
28782915 AGGGGCAAAA
* * * *
28782925 TGGTAATTTTACCCCATGAGGGTATCTCAGTAATTCTACCTTATAGGGGTATTTAAGTAATTCTA
1 TGGTAATTCTACCCCATAAGGGTATCTCAGTAATTCTACCGTAAAGGGGTATTTAAGTAATTCTA
** *
28782990 CCTTATAGGGGTATTT
66 CAATATAGAGGTATTT
** * * * * *
28783006 CAGTAATTCTACCCTATAAGGGTATTTC-GTTAATTCTGCCGTAAAGGGGTATTTTAGTAATTTT
1 TGGTAATTCTACCCCATAAGGGTATCTCAG-TAATTCTACCGTAAAGGGGTATTTAAGTAATTCT
28783070 ACAA-ATTAGAGGTATTT
65 ACAATA-TAGAGGTATTT
28783087 TGGTAATT
1 TGGTAATT
28783095 TTACAAACCA
Statistics
Matches: 71, Mismatches: 16, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
80 2 0.03
81 69 0.97
ACGTcount: A:0.28, C:0.13, G:0.19, T:0.40
Consensus pattern (81 bp):
TGGTAATTCTACCCCATAAGGGTATCTCAGTAATTCTACCGTAAAGGGGTATTTAAGTAATTCTA
CAATATAGAGGTATTT
Found at i:28787501 original size:21 final size:20
Alignment explanation
Indices: 28787462--28787501 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
28787452 TAAGCATGTA
*
28787462 TTTTGATGTTTGATGATAGG
1 TTTTGATGCTTGATGATAGG
*
28787482 TTTTGAATGCTTGTTGATAG
1 TTTTG-ATGCTTGATGATAG
28787502 ATATACAAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.20, C:0.03, G:0.28, T:0.50
Consensus pattern (20 bp):
TTTTGATGCTTGATGATAGG
Found at i:28787796 original size:141 final size:141
Alignment explanation
Indices: 28787542--28787848 Score: 587
Period size: 141 Copynumber: 2.2 Consensus size: 141
28787532 GAAAATGTAA
28787542 AATAAGGATTAAATTGAGAAATGTTAAAATTGTGGTTGAAATGTAAATTAAATGAATGAAAAATA
1 AATAAGGATTAAATTGAGAAATGTTAAAATTGTGGTTGAAATGTAAATTAAATGAATGAAAAATA
28787607 TGGGCTGCTAGGGGCATATTCATAATTCGGCTAAGCATGGGTGTCTTGAAATTTACATGAATTTG
66 TGGGCTGCTAGGGGCATATTCATAATTCGGCTAAGCATGGGTGTCTTGAAATTTACATGAATTTG
28787672 TGATTTTATGT
131 TGATTTTATGT
28787683 AATAAGGATTAAATTGAGAAATGTTAAAATTGTGGTTGAAATGTAAATTAAATGAATGAAAAATA
1 AATAAGGATTAAATTGAGAAATGTTAAAATTGTGGTTGAAATGTAAATTAAATGAATGAAAAATA
28787748 TGGGCTGCTAGGGGCATATTCATAATTCGGCTAAGCATGGGTGTCTTGAAATTTACATGAATTTG
66 TGGGCTGCTAGGGGCATATTCATAATTCGGCTAAGCATGGGTGTCTTGAAATTTACATGAATTTG
28787813 TGATTTTATGT
131 TGATTTTATGT
* *
28787824 AATAAGGACTAAATTGTAAAAATGT
1 AATAAGGATTAAATTG-AGAAATGT
28787849 GAAAGTTTAG
Statistics
Matches: 163, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
141 156 0.96
142 7 0.04
ACGTcount: A:0.37, C:0.06, G:0.22, T:0.34
Consensus pattern (141 bp):
AATAAGGATTAAATTGAGAAATGTTAAAATTGTGGTTGAAATGTAAATTAAATGAATGAAAAATA
TGGGCTGCTAGGGGCATATTCATAATTCGGCTAAGCATGGGTGTCTTGAAATTTACATGAATTTG
TGATTTTATGT
Found at i:28789960 original size:42 final size:42
Alignment explanation
Indices: 28789913--28790076 Score: 181
Period size: 42 Copynumber: 3.9 Consensus size: 42
28789903 TTAGGGTTAC
*
28789913 TGAGACTATGTGTAAGACCATATCTAGGATATGGCATCGATA
1 TGAGACTATGTGTAAGACCATATCTGGGATATGGCATCGATA
*
28789955 TGAGACT-TCGTGTAAGACCGTATCTGGGATATGGCATCGATGA
1 TGAGACTAT-GTGTAAGACCATATCTGGGATATGGCATCGAT-A
* * * * *
28789998 -GAGATTTTGTGTAAGACCGTAGCTGGGTTATTGGCATCGATA
1 TGAGACTATGTGTAAGACCATATCTGGGATA-TGGCATCGATA
* **
28790040 CGAGA-TGACATGTAAGACCATATCTGGGATATGGCAT
1 TGAGACT-ATGTGTAAGACCATATCTGGGATATGGCAT
28790077 TGGTATGGTA
Statistics
Matches: 105, Mismatches: 11, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
41 1 0.01
42 70 0.67
43 34 0.32
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.29
Consensus pattern (42 bp):
TGAGACTATGTGTAAGACCATATCTGGGATATGGCATCGATA
Found at i:28790038 original size:85 final size:84
Alignment explanation
Indices: 28789921--28790076 Score: 215
Period size: 85 Copynumber: 1.8 Consensus size: 84
28789911 ACTGAGACTA
* * * * *
28789921 TGTGTAAGACCATATCTAGGATATGGCATCGATATGAGACT-TCGTGTAAGACCGTATCTGGGAT
1 TGTGTAAGACCATAGCTAGGATATGGCATCGATACGAGA-TGACATGTAAGACCATATCTGGGAT
28789985 ATGGCATCGATGAGAGATTT
65 ATGGCATCGATGAGAGATTT
* * *
28790005 TGTGTAAGACCGTAGCTGGGTTATTGGCATCGATACGAGATGACATGTAAGACCATATCTGGGAT
1 TGTGTAAGACCATAGCTAGGATA-TGGCATCGATACGAGATGACATGTAAGACCATATCTGGGAT
28790070 ATGGCAT
65 ATGGCAT
28790077 TGGTATGGTA
Statistics
Matches: 62, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
84 20 0.32
85 42 0.68
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.29
Consensus pattern (84 bp):
TGTGTAAGACCATAGCTAGGATATGGCATCGATACGAGATGACATGTAAGACCATATCTGGGATA
TGGCATCGATGAGAGATTT
Found at i:28794297 original size:40 final size:40
Alignment explanation
Indices: 28794260--28794444 Score: 225
Period size: 40 Copynumber: 4.7 Consensus size: 40
28794250 GCTACTCGTT
*
28794260 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
28794300 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
28794340 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * * *
28794379 CAAATGCCTT-TGGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
28794420 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
28794445 CATCATTCAA
Statistics
Matches: 125, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
38 2 0.02
39 32 0.26
40 78 0.62
41 13 0.10
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:28794371 original size:79 final size:82
Alignment explanation
Indices: 28794260--28794444 Score: 229
Period size: 79 Copynumber: 2.3 Consensus size: 82
28794250 GCTACTCGTT
* *
28794260 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTT-GGGATCTTAACCC
* *
28794323 GGATTTAGTAAC-TCGCA
65 GGATATAGTAACTTAGCA
* * **
28794340 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTTGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTGGGATCTTAACCCG
* *
28794403 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
28794420 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
28794445 CATCATTCAA
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 3 0.03
79 54 0.59
80 34 0.37
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTGGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:28813990 original size:40 final size:40
Alignment explanation
Indices: 28813906--28814130 Score: 269
Period size: 40 Copynumber: 5.7 Consensus size: 40
28813896 TTGAATGATG
* * * *
28813906 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
28813946 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
28813986 TCCGGGCTAAG-CCCGAAGGCATTGGTGCAAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
28814025 TCCAGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
28814065 TCCGGGTTAAGTCCCGAAGGCATTTGTGTGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
28814106 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
28814131 AACGAGGAGC
Statistics
Matches: 160, Mismatches: 20, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
39 32 0.20
40 118 0.74
41 10 0.06
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:28814152 original size:119 final size:119
Alignment explanation
Indices: 28813913--28814163 Score: 260
Period size: 119 Copynumber: 2.1 Consensus size: 119
28813903 ATGTCCGGGC
*
28813913 TAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTTGTGCGAG
1 TAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTTGTGCGAG
* ** *
28813978 ATACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCAAGTTACTAAATCCAGGT
66 ATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACAAGTGACTAAATCCAGGT
* * * ** *
28814032 TAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCATTTGTGTG
1 TAAGTCCCGAAGGC-TTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCATTTGTGCG
* * * * *
28814095 AGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTATATCC-GGT
64 AGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACAAGTGA-CTAAATCCAGGT
* *
28814151 TAAATTCCGAAGG
1 TAAGTCCCGAAGG
28814164 TACGTGATTT
Statistics
Matches: 109, Mismatches: 18, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
118 3 0.03
119 76 0.70
120 30 0.28
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (119 bp):
TAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTTGTGCGAG
ATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACAAGTGACTAAATCCAGGT
Found at i:28819526 original size:27 final size:27
Alignment explanation
Indices: 28819507--28819797 Score: 413
Period size: 27 Copynumber: 10.8 Consensus size: 27
28819497 ATTACCAAAG
*
28819507 TACCCTCGATTTACAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCATTT
*
28819534 TACCCTCGATTTATAGAATTACCATTT
1 TACCCTCGATTTACAGAATTACCATTT
* * *
28819561 TACCTTCGATTTATAGAATTATCATTT
1 TACCCTCGATTTACAGAATTACCATTT
* *
28819588 TACCCTCGATTTATAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCATTT
* *
28819615 TACCCTCGATTTACAAAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCATTT
28819642 TACCCTCGATTTACAGAATTACCATTT
1 TACCCTCGATTTACAGAATTACCATTT
**
28819669 TACCCTCGATTTATGGAATTACCA-TT
1 TACCCTCGATTTACAGAATTACCATTT
*
28819695 TACCCTCGATTTATAGAATTACCATTT
1 TACCCTCGATTTACAGAATTACCATTT
* * *
28819722 TACCCTCAACTTACAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCATTT
* *
28819749 TACCCTCGATTTACAAAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCATTT
*
28819776 TACCCTCGATTTACAAAATTAC
1 TACCCTCGATTTACAGAATTAC
28819798 TGAAATACCA
Statistics
Matches: 242, Mismatches: 21, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
26 25 0.10
27 217 0.90
ACGTcount: A:0.29, C:0.24, G:0.08, T:0.38
Consensus pattern (27 bp):
TACCCTCGATTTACAGAATTACCATTT
Found at i:28819806 original size:27 final size:27
Alignment explanation
Indices: 28819468--28820104 Score: 359
Period size: 27 Copynumber: 23.6 Consensus size: 27
28819458 TTAGTTTACC
** * * *
28819468 AAATTACTGAAATACCCTCAAATTGTA
1 AAATTACCAAAATACCCTCGATTTATA
* *
28819495 AAATTACCAAAGTACCCTCGATTTACA
1 AAATTACCAAAATACCCTCGATTTATA
* ****
28819522 GAATTACCGTTTTACCCTCGATTTATA
1 AAATTACCAAAATACCCTCGATTTATA
* *** *
28819549 GAATTACCATTTTACCTTCGATTTATA
1 AAATTACCAAAATACCCTCGATTTATA
* * ***
28819576 GAATTATCATTTTACCCTCGATTTATA
1 AAATTACCAAAATACCCTCGATTTATA
* **** *
28819603 GAATTACCGTTTTACCCTCGATTTACA
1 AAATTACCAAAATACCCTCGATTTATA
**** *
28819630 AAATTACCGTTTTACCCTCGATTTACA
1 AAATTACCAAAATACCCTCGATTTATA
* *** *
28819657 GAATTACCATTTTACCCTCGATTTATG
1 AAATTACCAAAATACCCTCGATTTATA
* **
28819684 GAATTACC-ATTTACCCTCGATTTATA
1 AAATTACCAAAATACCCTCGATTTATA
* *** * * *
28819710 GAATTACCATTTTACCCTCAACTTACA
1 AAATTACCAAAATACCCTCGATTTATA
* **** *
28819737 GAATTACCGTTTTACCCTCGATTTACA
1 AAATTACCAAAATACCCTCGATTTATA
**** *
28819764 AAATTACCGTTTTACCCTCGATTTACA
1 AAATTACCAAAATACCCTCGATTTATA
** * * *
28819791 AAATTACTGAAATACCATTGATTTACA
1 AAATTACCAAAATACCCTCGATTTATA
*
28819818 AAATTACCAAAATACCCTCGA-TCAGTA
1 AAATTACCAAAATACCCTCGATTTA-TA
* *
28819845 AAATTACCAAAATACCC-CTAGTTTGTA
1 AAATTACCAAAATACCCTCGA-TTTATA
* * *
28819872 AAATTACTAAAATACCC-CTGGTTTGTA
1 AAATTACCAAAATACCCTC-GATTTATA
* * * *
28819899 AAATTACTAAAATACACTTGGTTTATA
1 AAATTACCAAAATACCCTCGATTTATA
* *
28819926 AAATTACCAAAATACCC-CTAGTTTGTA
1 AAATTACCAAAATACCCTCGA-TTTATA
* * * *
28819953 AAATTACCAAAATACCTTTGGTTTACA
1 AAATTACCAAAATACCCTCGATTTATA
* *
28819980 AAATTACCAAAATA-CCTCTGGTTTGTA
1 AAATTACCAAAATACCCTC-GATTTATA
* * *
28820007 AAATTACCAAAATACCCTTGGTTTACA
1 AAATTACCAAAATACCCTCGATTTATA
* * * *
28820034 AAATTACCAAAATACCATTGGTTTGTA
1 AAATTACCAAAATACCCTCGATTTATA
* * *
28820061 AAATTACCAAAATACCCTTGGTTTACA
1 AAATTACCAAAATACCCTCGATTTATA
28820088 AAATTACCAAAATACCC
1 AAATTACCAAAATACCC
28820105 CTGATTTGTG
Statistics
Matches: 519, Mismatches: 81, Indels: 20
0.84 0.13 0.03
Matches are distributed among these distances:
26 30 0.06
27 485 0.93
28 4 0.01
ACGTcount: A:0.36, C:0.22, G:0.08, T:0.34
Consensus pattern (27 bp):
AAATTACCAAAATACCCTCGATTTATA
Found at i:28819834 original size:54 final size:54
Alignment explanation
Indices: 28819749--28820134 Score: 411
Period size: 54 Copynumber: 7.1 Consensus size: 54
28819739 ATTACCGTTT
* * **** ** **
28819749 TACCCTCGATTTACAAAATTACCGTTTTACCCTCGATTTACAAAATTACTGAAA
1 TACCCTTGGTTTACAAAATTACCAAAATACCCTCGATTTGTAAAATTACCAAAA
* * **
28819803 TACCATTGATTTACAAAATTACCAAAATACCCTCGATCAGTAAAATTACCAAAA
1 TACCCTTGGTTTACAAAATTACCAAAATACCCTCGATTTGTAAAATTACCAAAA
* * ** * * *
28819857 TACCCCTAGTTTGTAAAATTACTAAAATACCC-CTGGTTTGTAAAATTACTAAAA
1 TACCCTTGGTTTACAAAATTACCAAAATACCCTC-GATTTGTAAAATTACCAAAA
* * *
28819911 TACACTTGGTTTATAAAATTACCAAAATACCC-CTAGTTTGTAAAATTACCAAAA
1 TACCCTTGGTTTACAAAATTACCAAAATACCCTCGA-TTTGTAAAATTACCAAAA
* *
28819965 TACCTTTGGTTTACAAAATTACCAAAATA-CCTCTGGTTTGTAAAATTACCAAAA
1 TACCCTTGGTTTACAAAATTACCAAAATACCCTC-GATTTGTAAAATTACCAAAA
* * *
28820019 TACCCTTGGTTTACAAAATTACCAAAATACCATTGGTTTGTAAAATTACCAAAA
1 TACCCTTGGTTTACAAAATTACCAAAATACCCTCGATTTGTAAAATTACCAAAA
* ***
28820073 TACCCTTGGTTTACAAAATTACCAAAATACCC-CTGATTTGTGAAATTATTGAAA
1 TACCCTTGGTTTACAAAATTACCAAAATACCCTC-GATTTGTAAAATTACCAAAA
28820127 TACCCTTG
1 TACCCTTG
28820135 TAGGGTAGAA
Statistics
Matches: 280, Mismatches: 46, Indels: 12
0.83 0.14 0.04
Matches are distributed among these distances:
53 3 0.01
54 275 0.98
55 2 0.01
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.32
Consensus pattern (54 bp):
TACCCTTGGTTTACAAAATTACCAAAATACCCTCGATTTGTAAAATTACCAAAA
Found at i:28820118 original size:27 final size:27
Alignment explanation
Indices: 28819817--28820120 Score: 367
Period size: 27 Copynumber: 11.3 Consensus size: 27
28819807 ATTGATTTAC
* **
28819817 AAAATTACCAAAATA-CCCTCGATCAGT
1 AAAATTACCAAAATACCCCT-GGTTTGT
*
28819844 AAAATTACCAAAATACCCCTAGTTTGT
1 AAAATTACCAAAATACCCCTGGTTTGT
*
28819871 AAAATTACTAAAATACCCCTGGTTTGT
1 AAAATTACCAAAATACCCCTGGTTTGT
* * * *
28819898 AAAATTACTAAAATACACTTGGTTTAT
1 AAAATTACCAAAATACCCCTGGTTTGT
*
28819925 AAAATTACCAAAATACCCCTAGTTTGT
1 AAAATTACCAAAATACCCCTGGTTTGT
** **
28819952 AAAATTACCAAAATACCTTTGGTTTAC
1 AAAATTACCAAAATACCCCTGGTTTGT
*
28819979 AAAATTACCAAAATACCTCTGGTTTGT
1 AAAATTACCAAAATACCCCTGGTTTGT
* **
28820006 AAAATTACCAAAATACCCTTGGTTTAC
1 AAAATTACCAAAATACCCCTGGTTTGT
**
28820033 AAAATTACCAAAATACCATTGGTTTGT
1 AAAATTACCAAAATACCCCTGGTTTGT
* **
28820060 AAAATTACCAAAATACCCTTGGTTTAC
1 AAAATTACCAAAATACCCCTGGTTTGT
*
28820087 AAAATTACCAAAATACCCCTGATTTGT
1 AAAATTACCAAAATACCCCTGGTTTGT
*
28820114 GAAATTA
1 AAAATTA
28820121 TTGAAATACC
Statistics
Matches: 239, Mismatches: 37, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
27 235 0.98
28 4 0.02
ACGTcount: A:0.41, C:0.19, G:0.09, T:0.31
Consensus pattern (27 bp):
AAAATTACCAAAATACCCCTGGTTTGT
Found at i:28820128 original size:81 final size:81
Alignment explanation
Indices: 28819790--28820130 Score: 409
Period size: 81 Copynumber: 4.2 Consensus size: 81
28819780 CTCGATTTAC
* * * * *
28819790 AAAATTACTGAAATACCATTGATTTACAAAATTACCAAAATACCC-TCGATCAGTAAAATTACCA
1 AAAATTACTAAAATACCATTGGTTTACAAAATTACCAAAATACCCTTGGTTTA-TAAAATTACCA
28819854 AAATACCCCTAGTTTGT
65 AAATACCCCTAGTTTGT
** ** * *
28819871 AAAATTACTAAAATACCCCTGGTTTGTAAAATTACTAAAATACACTTGGTTTATAAAATTACCAA
1 AAAATTACTAAAATACCATTGGTTTACAAAATTACCAAAATACCCTTGGTTTATAAAATTACCAA
28819936 AATACCCCTAGTTTGT
66 AATACCCCTAGTTTGT
* * *
28819952 AAAATTACCAAAATACCTTTGGTTTACAAAATTACCAAAATA-CCTCTGGTTTGTAAAATTACCA
1 AAAATTACTAAAATACCATTGGTTTACAAAATTACCAAAATACCCT-TGGTTTATAAAATTACCA
* * **
28820016 AAATACCCTTGGTTTAC
65 AAATACCCCTAGTTTGT
* ** *
28820033 AAAATTACCAAAATACCATTGGTTTGTAAAATTACCAAAATACCCTTGGTTTACAAAATTACCAA
1 AAAATTACTAAAATACCATTGGTTTACAAAATTACCAAAATACCCTTGGTTTATAAAATTACCAA
28820098 AATACCCCT-GATTTGT
66 AATACCCCTAG-TTTGT
* * *
28820114 GAAATTATTGAAATACC
1 AAAATTACTAAAATACC
28820131 CTTGTAGGGT
Statistics
Matches: 221, Mismatches: 35, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
80 3 0.01
81 211 0.95
82 7 0.03
ACGTcount: A:0.41, C:0.19, G:0.09, T:0.31
Consensus pattern (81 bp):
AAAATTACTAAAATACCATTGGTTTACAAAATTACCAAAATACCCTTGGTTTATAAAATTACCAA
AATACCCCTAGTTTGT
Found at i:28820153 original size:27 final size:28
Alignment explanation
Indices: 28820114--28820171 Score: 91
Period size: 27 Copynumber: 2.1 Consensus size: 28
28820104 CCTGATTTGT
* *
28820114 GAAATTATTGAAATACCCTTGTAGGGTA
1 GAAATTATCGAAATACCCCTGTAGGGTA
28820142 GAAA-TATCGAAATACCCCTGTAGGGTA
1 GAAATTATCGAAATACCCCTGTAGGGTA
28820169 GAA
1 GAA
28820172 TTACCATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
27 24 0.86
28 4 0.14
ACGTcount: A:0.38, C:0.14, G:0.22, T:0.26
Consensus pattern (28 bp):
GAAATTATCGAAATACCCCTGTAGGGTA
Found at i:28820450 original size:25 final size:25
Alignment explanation
Indices: 28820381--28820443 Score: 117
Period size: 25 Copynumber: 2.5 Consensus size: 25
28820371 AGGAAGTGCT
*
28820381 AAAAGGGCTTTGCCCTAGTTTACCG
1 AAAAGGGCTTTGCCCTAGTTTACCA
28820406 AAAAGGGCTTTGCCCTAGTTTACCA
1 AAAAGGGCTTTGCCCTAGTTTACCA
28820431 AAAAGGGCTTTGC
1 AAAAGGGCTTTGC
28820444 TCCAGTTATT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCTAGTTTACCA
Found at i:28822662 original size:27 final size:27
Alignment explanation
Indices: 28822631--28823270 Score: 345
Period size: 27 Copynumber: 23.7 Consensus size: 27
28822621 CCTTAAATTG
*
28822631 TAAAATTACCAAAGTACCCTCGATTTA
1 TAAAATTACCAAAATACCCTCGATTTA
* *****
28822658 CAAAATTACTGTTTTACCCTCGATTTA
1 TAAAATTACCAAAATACCCTCGATTTA
* **** *
28822685 TAGAATTACCGTTTTACCCTCAATTTA
1 TAAAATTACCAAAATACCCTCGATTTA
* * ***
28822712 CAGAATTACCATTTTACCCTCGATTTA
1 TAAAATTACCAAAATACCCTCGATTTA
* *** **
28822739 TAGAATTACCATTTTACCCTTAATTTA
1 TAAAATTACCAAAATACCCTCGATTTA
* **** *
28822766 TAGAATTACCGTTTTACCCTAGATTTA
1 TAAAATTACCAAAATACCCTCGATTTA
* **** * *
28822793 CAAAATTACCGTTTTACACTCAATTTA
1 TAAAATTACCAAAATACCCTCGATTTA
* * ***
28822820 CAGAATTACCATTTTACCCTCGATTTA
1 TAAAATTACCAAAATACCCTCGATTTA
* *** *
28822847 TAGAATTACCATTTTACCCTCAATTTA
1 TAAAATTACCAAAATACCCTCGATTTA
* * ***
28822874 TAGAATTACTATTTTACCCTCGATTTA
1 TAAAATTACCAAAATACCCTCGATTTA
* *** *
28822901 TAGAATTACCATTTTACCCTCGACTTA
1 TAAAATTACCAAAATACCCTCGATTTA
* * * ****
28822928 CAGAATAACCGTTTTACCCTCGATTTA
1 TAAAATTACCAAAATACCCTCGATTTA
* * * *
28822955 CAGAATTACTAAAATACCCTTGATTTA
1 TAAAATTACCAAAATACCCTCGATTTA
* *
28822982 CAAAATTACCAAAATACCCTCGA-TCA
1 TAAAATTACCAAAATACCCTCGATTTA
* *
28823008 GTAAAATTACCAAAATA-CCTCTGGTTTG
1 -TAAAATTACCAAAATACCCTC-GATTTA
* * * *
28823036 TAAAGTTACTAAAATACCC-CTGGTTTG
1 TAAAATTACCAAAATACCCTC-GATTTA
* * * *
28823063 TAAAATTACTAAAATACCTTTGGTTTA
1 TAAAATTACCAAAATACCCTCGATTTA
* *
28823090 TAAAATTACCAAAATACCC-CTAGTTTG
1 TAAAATTACCAAAATACCCTCGA-TTTA
*
28823117 TAAAATTACCAAAATACCCTTGATTTA
1 TAAAATTACCAAAATACCCTCGATTTA
* * *
28823144 CAAAATTACCAAAATACCC-CTAGTTTG
1 TAAAATTACCAAAATACCCTCGA-TTTA
* *
28823171 TAAAATTACCAAAATACCCTTGGTTTA
1 TAAAATTACCAAAATACCCTCGATTTA
* * * *
28823198 CAAAATTACCAAAATACCCTTGGTTTG
1 TAAAATTACCAAAATACCCTCGATTTA
* * *
28823225 GAAAATTACCAAAATACCCTTGGTTTA
1 TAAAATTACCAAAATACCCTCGATTTA
28823252 TAAAATTACCAAAATACCC
1 TAAAATTACCAAAATACCC
28823271 CTAATTTGTG
Statistics
Matches: 522, Mismatches: 82, Indels: 18
0.84 0.13 0.03
Matches are distributed among these distances:
26 7 0.01
27 511 0.98
28 4 0.01
ACGTcount: A:0.36, C:0.22, G:0.08, T:0.35
Consensus pattern (27 bp):
TAAAATTACCAAAATACCCTCGATTTA
Found at i:28822983 original size:54 final size:54
Alignment explanation
Indices: 28822645--28822963 Score: 458
Period size: 54 Copynumber: 5.9 Consensus size: 54
28822635 ATTACCAAAG
* * ** *
28822645 TACCCTCGATTTACAAAATTACTGTTTTACCCTCGATTTATAGAATTACCGTTT
1 TACCCTCAATTTACAGAATTACCATTTTACCCTCGATTTATAGAATTACCATTT
28822699 TACCCTCAATTTACAGAATTACCATTTTACCCTCGATTTATAGAATTACCATTT
1 TACCCTCAATTTACAGAATTACCATTTTACCCTCGATTTATAGAATTACCATTT
* * * * * * *
28822753 TACCCTTAATTTATAGAATTACCGTTTTACCCTAGATTTACAAAATTACCGTTT
1 TACCCTCAATTTACAGAATTACCATTTTACCCTCGATTTATAGAATTACCATTT
*
28822807 TACACTCAATTTACAGAATTACCATTTTACCCTCGATTTATAGAATTACCATTT
1 TACCCTCAATTTACAGAATTACCATTTTACCCTCGATTTATAGAATTACCATTT
* *
28822861 TACCCTCAATTTATAGAATTACTATTTTACCCTCGATTTATAGAATTACCATTT
1 TACCCTCAATTTACAGAATTACCATTTTACCCTCGATTTATAGAATTACCATTT
* * * * *
28822915 TACCCTCGACTTACAGAATAACCGTTTTACCCTCGATTTACAGAATTAC
1 TACCCTCAATTTACAGAATTACCATTTTACCCTCGATTTATAGAATTAC
28822964 TAAAATACCC
Statistics
Matches: 235, Mismatches: 30, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 235 1.00
ACGTcount: A:0.31, C:0.23, G:0.07, T:0.39
Consensus pattern (54 bp):
TACCCTCAATTTACAGAATTACCATTTTACCCTCGATTTATAGAATTACCATTT
Found at i:28823004 original size:81 final size:81
Alignment explanation
Indices: 28822645--28822992 Score: 464
Period size: 81 Copynumber: 4.3 Consensus size: 81
28822635 ATTACCAAAG
* **
28822645 TACCCTCGATTTACAAAATTACTGTTTTACCCTCGATTTATAGAATTACCGTTTTACCCTCAATT
1 TACCCTCGATTTACAGAATTACCATTTTACCCTCGATTTATAGAATTACCGTTTTACCCTCAATT
28822710 TACAGAATTACCATTT
66 TACAGAATTACCATTT
* **
28822726 TACCCTCGATTTATAGAATTACCATTTTACCCTTAATTTATAGAATTACCGTTTTACCCT-AGAT
1 TACCCTCGATTTACAGAATTACCATTTTACCCTCGATTTATAGAATTACCGTTTTACCCTCA-AT
* *
28822790 TTACAAAATTACCGTTT
65 TTACAGAATTACCATTT
* * *
28822807 TACACTCAATTTACAGAATTACCATTTTACCCTCGATTTATAGAATTACCATTTTACCCTCAATT
1 TACCCTCGATTTACAGAATTACCATTTTACCCTCGATTTATAGAATTACCGTTTTACCCTCAATT
* *
28822872 TATAGAATTACTATTT
66 TACAGAATTACCATTT
* * * * *
28822888 TACCCTCGATTTATAGAATTACCATTTTACCCTCGACTTACAGAATAACCGTTTTACCCTCGATT
1 TACCCTCGATTTACAGAATTACCATTTTACCCTCGATTTATAGAATTACCGTTTTACCCTCAATT
* ***
28822953 TACAGAATTACTAAAA
66 TACAGAATTACCATTT
* *
28822969 TACCCTTGATTTACAAAATTACCA
1 TACCCTCGATTTACAGAATTACCA
28822993 AAATACCCTC
Statistics
Matches: 232, Mismatches: 33, Indels: 4
0.86 0.12 0.01
Matches are distributed among these distances:
80 1 0.00
81 230 0.99
82 1 0.00
ACGTcount: A:0.32, C:0.23, G:0.07, T:0.38
Consensus pattern (81 bp):
TACCCTCGATTTACAGAATTACCATTTTACCCTCGATTTATAGAATTACCGTTTTACCCTCAATT
TACAGAATTACCATTT
Found at i:28823284 original size:27 final size:27
Alignment explanation
Indices: 28822958--28823287 Score: 365
Period size: 27 Copynumber: 12.2 Consensus size: 27
28822948 CGATTTACAG
* * * **
28822958 AATTACTAAAATACCCTTGATTTACAA
1 AATTACCAAAATACCCCTGGTTTGTAA
* **
28822985 AATTACCAAAATA-CCCTCGATCAGTAA
1 AATTACCAAAATACCCCT-GGTTTGTAA
*
28823012 AATTACCAAAATACCTCTGGTTTGTAA
1 AATTACCAAAATACCCCTGGTTTGTAA
* *
28823039 AGTTACTAAAATACCCCTGGTTTGTAA
1 AATTACCAAAATACCCCTGGTTTGTAA
* ** *
28823066 AATTACTAAAATACCTTTGGTTTATAA
1 AATTACCAAAATACCCCTGGTTTGTAA
*
28823093 AATTACCAAAATACCCCTAGTTTGTAA
1 AATTACCAAAATACCCCTGGTTTGTAA
* * **
28823120 AATTACCAAAATACCCTTGATTTACAA
1 AATTACCAAAATACCCCTGGTTTGTAA
*
28823147 AATTACCAAAATACCCCTAGTTTGTAA
1 AATTACCAAAATACCCCTGGTTTGTAA
* **
28823174 AATTACCAAAATACCCTTGGTTTACAA
1 AATTACCAAAATACCCCTGGTTTGTAA
* *
28823201 AATTACCAAAATACCCTTGGTTTGGAA
1 AATTACCAAAATACCCCTGGTTTGTAA
* *
28823228 AATTACCAAAATACCCTTGGTTTATAA
1 AATTACCAAAATACCCCTGGTTTGTAA
** *
28823255 AATTACCAAAATACCCCTAATTTGTGA
1 AATTACCAAAATACCCCTGGTTTGTAA
28823282 AATTAC
1 AATTAC
28823288 TGAAATACAC
Statistics
Matches: 256, Mismatches: 45, Indels: 4
0.84 0.15 0.01
Matches are distributed among these distances:
26 3 0.01
27 250 0.98
28 3 0.01
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.31
Consensus pattern (27 bp):
AATTACCAAAATACCCCTGGTTTGTAA
Found at i:28823295 original size:54 final size:54
Alignment explanation
Indices: 28822958--28823287 Score: 448
Period size: 54 Copynumber: 6.1 Consensus size: 54
28822948 CGATTTACAG
* * * **
28822958 AATTACTAAAATACCCTTGATTTACAAAATTACCAAAATA-CCCTCGATCAGTAA
1 AATTACCAAAATACCCTTGGTTTACAAAATTACCAAAATACCCCTAG-TTTGTAA
** * * *
28823012 AATTACCAAAATA-CCTCTGGTTTGTAAAGTTACTAAAATACCCCTGGTTTGTAA
1 AATTACCAAAATACCCT-TGGTTTACAAAATTACCAAAATACCCCTAGTTTGTAA
* * *
28823066 AATTACTAAAATACCTTTGGTTTATAAAATTACCAAAATACCCCTAGTTTGTAA
1 AATTACCAAAATACCCTTGGTTTACAAAATTACCAAAATACCCCTAGTTTGTAA
*
28823120 AATTACCAAAATACCCTTGATTTACAAAATTACCAAAATACCCCTAGTTTGTAA
1 AATTACCAAAATACCCTTGGTTTACAAAATTACCAAAATACCCCTAGTTTGTAA
* * *
28823174 AATTACCAAAATACCCTTGGTTTACAAAATTACCAAAATACCCTTGGTTTGGAA
1 AATTACCAAAATACCCTTGGTTTACAAAATTACCAAAATACCCCTAGTTTGTAA
* * *
28823228 AATTACCAAAATACCCTTGGTTTATAAAATTACCAAAATACCCCTAATTTGTGA
1 AATTACCAAAATACCCTTGGTTTACAAAATTACCAAAATACCCCTAGTTTGTAA
28823282 AATTAC
1 AATTAC
28823288 TGAAATACAC
Statistics
Matches: 244, Mismatches: 29, Indels: 6
0.87 0.10 0.02
Matches are distributed among these distances:
53 3 0.01
54 234 0.96
55 7 0.03
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.31
Consensus pattern (54 bp):
AATTACCAAAATACCCTTGGTTTACAAAATTACCAAAATACCCCTAGTTTGTAA
Found at i:28826542 original size:27 final size:27
Alignment explanation
Indices: 28826365--28826842 Score: 211
Period size: 27 Copynumber: 17.7 Consensus size: 27
28826355 TTAGTTTACC
* * * * *
28826365 AAATTACTGAAATGCCCTCAAATTGTA
1 AAATTACTAAAATACCCTCGATTTATA
*
28826392 AAATTAC-AAAAGTACCCTCAATTTATA
1 AAATTACTAAAA-TACCCTCGATTTATA
* *****
28826419 GAATTACCGTTTTACCCTCGATTTATA
1 AAATTACTAAAATACCCTCGATTTATA
* ***** *
28826446 GAATTACCGTTTTACCCTCGATTTACA
1 AAATTACTAAAATACCCTCGATTTATA
* * ***
28826473 GAATTACCATTTTACCCTCGATTTATA
1 AAATTACTAAAATACCCTCGATTTATA
* **** *
28826500 GAATTACTGTTTTACCCTCGATTTACA
1 AAATTACTAAAATACCCTCGATTTATA
* * *
28826527 AAATTACTAAAATACCCTTGGTTTACA
1 AAATTACTAAAATACCCTCGATTTATA
* *
28826554 AAATTACCAAAATACCCTCGA-TCAGTA
1 AAATTACTAAAATACCCTCGATTTA-TA
* * * *
28826581 AAATTACCAAAATACCCTAG-TCTGTA
1 AAATTACTAAAATACCCTCGATTTATA
* * *
28826607 AAATTGCTAAAATACCC-CTGGTTTGTA
1 AAATTACTAAAATACCCTC-GATTTATA
* *
28826634 AAATTA-TAGAAATACCCTCAATTTGTA
1 AAATTACTA-AAATACCCTCGATTTATA
* *
28826661 AAATTACTAAAATACCC-CTAGTTTGTA
1 AAATTACTAAAATACCCTCGA-TTTATA
* * *
28826688 AAATTACCAAAATACCACT-GGTTTGTA
1 AAATTACTAAAATACC-CTCGATTTATA
** * *
28826715 AAATTACCGAAATACCCTCAATTTGTA
1 AAATTACTAAAATACCCTCGATTTATA
* *
28826742 AAATTACCAAAATACCC-CTGATTTACA
1 AAATTACTAAAATACCCTC-GATTTATA
* * *
28826769 AAGTTAC-AGAAATACCCTTGACTTTCTAA
1 AAATTACTA-AAATACCCTCGA-TTTAT-A
* * * * *
28826798 AAATTA-TGGAAATACCATTGGTTTACA
1 AAATTACT-AAAATACCCTCGATTTATA
*
28826825 AAATTACTGAAATACCCT
1 AAATTACTAAAATACCCT
28826843 TGGTTTGTAG
Statistics
Matches: 369, Mismatches: 61, Indels: 42
0.78 0.13 0.09
Matches are distributed among these distances:
26 31 0.08
27 311 0.84
28 11 0.03
29 16 0.04
ACGTcount: A:0.38, C:0.21, G:0.09, T:0.32
Consensus pattern (27 bp):
AAATTACTAAAATACCCTCGATTTATA
Found at i:28826597 original size:81 final size:80
Alignment explanation
Indices: 28826512--28826788 Score: 292
Period size: 81 Copynumber: 3.4 Consensus size: 80
28826502 ATTACTGTTT
** * *
28826512 TACCCTCGATTTACAAAATTACTAAAATACCCTTGGTTTACAAAATTACCAAAATACCCTCGATC
1 TACCC-CGATTTACAAAATTACTAAAATACCCTTGGTTTGTAAAATTACCAAAATACCCTCAATT
*
28826577 AGTAAAATTACCAAAA
65 TGTAAAATTACCAAAA
* * ** * * *
28826593 TA-CCCTAGTCTGTAAAATTGCTAAAATACCCCTGGTTTGTAAAATTA-TAGAAATACCCTCAAT
1 TACCCCGA-TTTACAAAATTACTAAAATACCCTTGGTTTGTAAAATTACCA-AAATACCCTCAAT
*
28826656 TTGTAAAATTACTAAAA
64 TTGTAAAATTACCAAAA
* ** * *
28826673 TACCCCTAGTTTGTAAAATTACCAAAATACCAC-TGGTTTGTAAAATTACCGAAATACCCTCAAT
1 TACCCCGA-TTTACAAAATTACTAAAATACC-CTTGGTTTGTAAAATTACCAAAATACCCTCAAT
28826737 TTGTAAAATTACCAAAA
64 TTGTAAAATTACCAAAA
*
28826754 TACCCCTGATTTACAAAGTTAC-AGAAATACCCTTG
1 TACCCC-GATTTACAAAATTACTA-AAATACCCTTG
28826789 ACTTTCTAAA
Statistics
Matches: 165, Mismatches: 23, Indels: 16
0.81 0.11 0.08
Matches are distributed among these distances:
79 3 0.02
80 64 0.39
81 96 0.58
82 2 0.01
ACGTcount: A:0.40, C:0.21, G:0.09, T:0.30
Consensus pattern (80 bp):
TACCCCGATTTACAAAATTACTAAAATACCCTTGGTTTGTAAAATTACCAAAATACCCTCAATTT
GTAAAATTACCAAAA
Found at i:28826845 original size:27 final size:27
Alignment explanation
Indices: 28826526--28826871 Score: 243
Period size: 27 Copynumber: 12.8 Consensus size: 27
28826516 CTCGATTTAC
**
28826526 AAAATTACTAAAATACCCTTGGTTTAC
1 AAAATTACTAAAATACCCTTGGTTTGT
* * * **
28826553 AAAATTACCAAAATACCCTCGATCAGT
1 AAAATTACTAAAATACCCTTGGTTTGT
* * *
28826580 AAAATTACCAAAATACCC-TAGTCTGT
1 AAAATTACTAAAATACCCTTGGTTTGT
* *
28826606 AAAATTGCTAAAATACCCCTGGTTTGT
1 AAAATTACTAAAATACCCTTGGTTTGT
***
28826633 AAAATTA-TAGAAATACCCTCAATTTGT
1 AAAATTACTA-AAATACCCTTGGTTTGT
* *
28826660 AAAATTACTAAAATACCCCTAGTTTGT
1 AAAATTACTAAAATACCCTTGGTTTGT
*
28826687 AAAATTACCAAAATACCAC-TGGTTTGT
1 AAAATTACTAAAATACC-CTTGGTTTGT
** ***
28826714 AAAATTACCGAAATACCCTCAATTTGT
1 AAAATTACTAAAATACCCTTGGTTTGT
* * * **
28826741 AAAATTACCAAAATACCCCTGATTTAC
1 AAAATTACTAAAATACCCTTGGTTTGT
* * *
28826768 AAAGTTAC-AGAAATACCCTTGACTTTCT
1 AAAATTACTA-AAATACCCTTG-GTTTGT
* * **
28826796 AAAAATTA-TGGAAATACCATTGGTTTAC
1 -AAAATTACT-AAAATACCCTTGGTTTGT
*
28826824 AAAATTACTGAAATACCCTTGGTTTGT
1 AAAATTACTAAAATACCCTTGGTTTGT
* * * *
28826851 AGATTTACCAAAACACCCTTG
1 AAAATTACTAAAATACCCTTG
28826872 TAGGATGAAA
Statistics
Matches: 254, Mismatches: 54, Indels: 22
0.77 0.16 0.07
Matches are distributed among these distances:
26 24 0.09
27 204 0.80
28 10 0.04
29 16 0.06
ACGTcount: A:0.40, C:0.20, G:0.10, T:0.30
Consensus pattern (27 bp):
AAAATTACTAAAATACCCTTGGTTTGT
Found at i:28826923 original size:27 final size:27
Alignment explanation
Indices: 28826893--28826989 Score: 88
Period size: 27 Copynumber: 3.6 Consensus size: 27
28826883 GACTAAAATA
** *
28826893 CCCCTATTTGGTAAAAAGATCGTAAAG
1 CCCCTATAGGGTAAAAAGACCGTAAAG
* * *
28826920 CCCCTGTAGGGTAAAGAGACCGTAAAT
1 CCCCTATAGGGTAAAAAGACCGTAAAG
* **
28826947 CCCCTGTAGGGTAAAGTGACCGTAATA-
1 CCCCTATAGGGTAAAAAGACCGTAA-AG
*
28826974 CCCCTATATGGTAAAA
1 CCCCTATAGGGTAAAA
28826990 TGGAAAATAT
Statistics
Matches: 59, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
27 58 0.98
28 1 0.02
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.23
Consensus pattern (27 bp):
CCCCTATAGGGTAAAAAGACCGTAAAG
Found at i:28827855 original size:25 final size:26
Alignment explanation
Indices: 28827794--28827939 Score: 208
Period size: 26 Copynumber: 5.7 Consensus size: 26
28827784 GAGGAAGTCC
28827794 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
*
28827820 AAAAGGGCTTATGCCCCAGTTTAGTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
* **
28827846 -AAAGGGCTTATGCCCTAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTG
28827871 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
***
28827897 AAAAGGGCTT-TGCCCCAGTTTACCA
1 AAAAGGGCTTATGCCCCAGTTTATTG
28827922 AAAAGGGCTT-TGCCCCAG
1 AAAAGGGCTTATGCCCCAG
28827940 ATATTAAAGA
Statistics
Matches: 109, Mismatches: 10, Indels: 3
0.89 0.08 0.02
Matches are distributed among these distances:
25 52 0.48
26 57 0.52
ACGTcount: A:0.27, C:0.23, G:0.24, T:0.27
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTATTG
Found at i:28827874 original size:51 final size:52
Alignment explanation
Indices: 28827794--28827939 Score: 226
Period size: 51 Copynumber: 2.9 Consensus size: 52
28827784 GAGGAAGTCC
**
28827794 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATGCCCCAGTTTAGTG
1 AAAAGGGCTTATGCCCCAGTTTACCGAAAAGGGCTTATGCCCCAGTTTAGTG
* *
28827846 -AAAGGGCTTATGCCCTAGTTTACCGAAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCGAAAAGGGCTTATGCCCCAGTTTAGTG
*
28827897 AAAAGGGCTT-TGCCCCAGTTTACCAAAAAGGGCTT-TGCCCCAG
1 AAAAGGGCTTATGCCCCAGTTTACCGAAAAGGGCTTATGCCCCAG
28827940 ATATTAAAGA
Statistics
Matches: 87, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
50 8 0.09
51 70 0.80
52 9 0.10
ACGTcount: A:0.27, C:0.23, G:0.24, T:0.27
Consensus pattern (52 bp):
AAAAGGGCTTATGCCCCAGTTTACCGAAAAGGGCTTATGCCCCAGTTTAGTG
Found at i:28828151 original size:42 final size:42
Alignment explanation
Indices: 28828086--28828177 Score: 130
Period size: 42 Copynumber: 2.2 Consensus size: 42
28828076 TAGTCTCCCC
* * ** *
28828086 AAATGGGCTTGCATACATTCATTGGTATTTCATGTGATATTG
1 AAATAGGCTTGCATACATCCATTGACATTACATGTGATATTG
*
28828128 AAATAGGCTTGTATACATCCATTGACATTACATGTGATATTG
1 AAATAGGCTTGCATACATCCATTGACATTACATGTGATATTG
28828170 AAATAGGC
1 AAATAGGC
28828178 CTAAGGGCCA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.32, C:0.13, G:0.20, T:0.36
Consensus pattern (42 bp):
AAATAGGCTTGCATACATCCATTGACATTACATGTGATATTG
Found at i:28828278 original size:31 final size:31
Alignment explanation
Indices: 28828201--28828279 Score: 115
Period size: 31 Copynumber: 2.5 Consensus size: 31
28828191 CGTTTACAGT
* *
28828201 AAAGGCTTCGGCCTAATGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
28828232 AAAGGCTTCGGCCCAGTGATATGAGTTT-TGA
1 AAAGGCTTCGGCCCAGTGATATGA-TTTATGA
*
28828263 AAAGGCTTCAGCCCAGT
1 AAAGGCTTCGGCCCAGT
28828280 AACCATTAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
31 41 0.93
32 3 0.07
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATGATTTATGA
Found at i:28829512 original size:43 final size:43
Alignment explanation
Indices: 28829356--28829521 Score: 192
Period size: 43 Copynumber: 3.9 Consensus size: 43
28829346 ATTATCAAGA
* * *
28829356 TGTGATTACATGTAAGACCATGTCTGAGACATTGACATGGTAT
1 TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATCGTAT
* *
28829399 TGTGATTACGTGTAAGACCATGTCTGGAACATTGGCATCGTAT
1 TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATCGTAT
* * * * *
28829442 TATGATTTCGTGTAAGACCTTGTCTGGGACAGTGGCATCG-AT
1 TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATCGTAT
* * *
28829484 ATGTGATAACATGTAAGACCATATCTGGGATA-TGGCAT
1 -TGTGATTACATGTAAGACCATGTCTGGGACATTGGCAT
28829522 TGTGTGAGCT
Statistics
Matches: 105, Mismatches: 17, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
42 8 0.08
43 97 0.92
ACGTcount: A:0.28, C:0.15, G:0.25, T:0.32
Consensus pattern (43 bp):
TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATCGTAT
Found at i:28835119 original size:32 final size:32
Alignment explanation
Indices: 28835083--28835148 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
28835073 CTAATTAGAG
28835083 AGACTAAAGAAAAAGTGAAAGTGATCCGCGAT
1 AGACTAAAGAAAAAGTGAAAGTGATCCGCGAT
*
28835115 AGACTGAAGAAAAAGTGAAAGTGATCCGCGAT
1 AGACTAAAGAAAAAGTGAAAGTGATCCGCGAT
28835147 AG
1 AG
28835149 TTTGAAAGCA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.45, C:0.12, G:0.27, T:0.15
Consensus pattern (32 bp):
AGACTAAAGAAAAAGTGAAAGTGATCCGCGAT
Found at i:28843781 original size:43 final size:43
Alignment explanation
Indices: 28843733--28843825 Score: 141
Period size: 43 Copynumber: 2.2 Consensus size: 43
28843723 ATTATCGAGA
* *
28843733 TGTGATTACATGTAAAACCATGTCTGGGACATTGGCATTGTAT
1 TGTGATTACATGTAAAACCATGTCTAGGACATTGACATTGTAT
* *
28843776 TGTGATTACATGTAAGACCATGTCTAGGACATTGATATTGTAT
1 TGTGATTACATGTAAAACCATGTCTAGGACATTGACATTGTAT
*
28843819 TATGATT
1 TGTGATT
28843826 TCGAGTAAGA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.29, C:0.12, G:0.22, T:0.38
Consensus pattern (43 bp):
TGTGATTACATGTAAAACCATGTCTAGGACATTGACATTGTAT
Found at i:28843834 original size:43 final size:43
Alignment explanation
Indices: 28843735--28843843 Score: 139
Period size: 43 Copynumber: 2.5 Consensus size: 43
28843725 TATCGAGATG
* * * *
28843735 TGATTACATGTAAAACCATGTCTGGGACATTGGCATTGTATTG
1 TGATTACATGTAAGACCATGTCTAGGACATTGACATTGTATTA
*
28843778 TGATTACATGTAAGACCATGTCTAGGACATTGATATTGTATTA
1 TGATTACATGTAAGACCATGTCTAGGACATTGACATTGTATTA
* *
28843821 TGATTTCGA-GTAAGACCCTGTCT
1 TGATTAC-ATGTAAGACCATGTCT
28843844 GTAACACCCC
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
43 57 0.98
44 1 0.02
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (43 bp):
TGATTACATGTAAGACCATGTCTAGGACATTGACATTGTATTA
Found at i:28845870 original size:585 final size:585
Alignment explanation
Indices: 28844760--28845932 Score: 2301
Period size: 585 Copynumber: 2.0 Consensus size: 585
28844750 ACCGAACTTA
28844760 TAAGCATTTATACTCATGCATAACCTTAACCAAATTATACTCAAGTATAATTAAAATTATTTACC
1 TAAGCATTTATACTCATGCATAACCTTAACCAAATTATACTCAAGTATAATTAAAATTATTTACC
28844825 AATTCTGGCATATATTAACTACCACATTTACTATGCATCTTAGTAAATAGCTTAATAAATAGGAT
66 AATTCTGGCATATATTAACTACCACATTTACTATGCATCTTAGTAAATAGCTTAATAAATAGGAT
*
28844890 ATACATAATCCATAAGCAAAATGACTAAAATTTCGAACATGAAGTTAAGGCATTTTCAATGCATA
131 ATACATAATCCATAAGCAAAATGACAAAAATTTCGAACATGAAGTTAAGGCATTTTCAATGCATA
*
28844955 AAACTCTTACCACAAGTCATTCATGCATAATACTGGGCACTTTAAACTAACGAATTTCGAGTACA
196 AAACTCTTACCACAAGTCATTCATGCATAATACTGGGCACTTTAAACTAACGAATTTCAAGTACA
28845020 GTAAAGCATAACCGAGTTATCAATACCAAGCTTACTAAACTTTGTAACCAAGCACACATAAAACC
261 GTAAAGCATAACCGAGTTATCAATACCAAGCTTACTAAACTTTGTAACCAAGCACACATAAAACC
28845085 AAATCTAAACATAAATAGCAAGCCATTTTCGCATGGCTTAAATACATAACCAAAATCAATATCTC
326 AAATCTAAACATAAATAGCAAGCCATTTTCGCATGGCTTAAATACATAACCAAAATCAATATCTC
28845150 AAAAGTATGTTCCAGCCTATACATGCCATAATACGAGTTTGATTATCTAAATACCGAAGCTGTAG
391 AAAAGTATGTTCCAGCCTATACATGCCATAATACGAGTTTGATTATCTAAATACCGAAGCTGTAG
*
28845215 ATAGTGTGCTGGGCTTGGCTGATAGTTCCCGAGCTTGTAGCTTGACTTCAAAATCTATAAAACAG
456 ATAGTGTGCTGAGCTTGGCTGATAGTTCCCGAGCTTGTAGCTTGACTTCAAAATCTATAAAACAG
28845280 AGTAAGCATAGCACACAAAGTAAGCTATCAAGGCGTAGTAAGTCATAAGCAAATAAACAACTCAT
521 AGTAAGCATAGCACACAAAGTAAGCTATCAAGGCGTAGTAAGTCATAAGCAAATAAACAACTCAT
28845345 TAAGCATTTATACTCATGCATAACCTTAACCAAATTATACTCAAGTATAATTAAAATTATTTACC
1 TAAGCATTTATACTCATGCATAACCTTAACCAAATTATACTCAAGTATAATTAAAATTATTTACC
*
28845410 AATTCTGGCATATATTAACTACCACATTTACTATGCATCTTAGTACATAGCTTAATAAATAGGAT
66 AATTCTGGCATATATTAACTACCACATTTACTATGCATCTTAGTAAATAGCTTAATAAATAGGAT
28845475 ATACATAATCCATAAGCAAAATGACAAAAATTTCGAACATGAAGTTAAGGCATTTTCAATGCATA
131 ATACATAATCCATAAGCAAAATGACAAAAATTTCGAACATGAAGTTAAGGCATTTTCAATGCATA
*
28845540 AAACTCTTACCACAAGTCATTCATGCATAATACTGGGCACTTTAAATTAACGAATTTCAAGTACA
196 AAACTCTTACCACAAGTCATTCATGCATAATACTGGGCACTTTAAACTAACGAATTTCAAGTACA
28845605 GTAAAGCATAACCGAGTTATCAATACCAAGCTTACTAAACTTTGTAACCAAGCACACATAAAACC
261 GTAAAGCATAACCGAGTTATCAATACCAAGCTTACTAAACTTTGTAACCAAGCACACATAAAACC
28845670 AAATCTAAACATAAATAGCAAGCCATTTTCGCATGGCTTAAATACATAACCAAAATCAATATCTC
326 AAATCTAAACATAAATAGCAAGCCATTTTCGCATGGCTTAAATACATAACCAAAATCAATATCTC
28845735 AAAAGTATGTTCCAGCCTATACATGCCATAATACGAGTTTGATTATCTAAATACCGAAGCTGTAG
391 AAAAGTATGTTCCAGCCTATACATGCCATAATACGAGTTTGATTATCTAAATACCGAAGCTGTAG
28845800 ATAGTGTGCTGAGCTTGGCTGATAGTTCCCGAGCTTGTAGCTTGACTTCAAAATCTATAAAACAG
456 ATAGTGTGCTGAGCTTGGCTGATAGTTCCCGAGCTTGTAGCTTGACTTCAAAATCTATAAAACAG
28845865 AGTAAGCATAGCACACAAAGTAAGCTATCAAGGCGTAGTAAGTCATAAGCAAATAAACAACTCAT
521 AGTAAGCATAGCACACAAAGTAAGCTATCAAGGCGTAGTAAGTCATAAGCAAATAAACAACTCAT
28845930 TAA
1 TAA
28845933 TATAATTGAC
Statistics
Matches: 583, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
585 583 1.00
ACGTcount: A:0.40, C:0.19, G:0.13, T:0.28
Consensus pattern (585 bp):
TAAGCATTTATACTCATGCATAACCTTAACCAAATTATACTCAAGTATAATTAAAATTATTTACC
AATTCTGGCATATATTAACTACCACATTTACTATGCATCTTAGTAAATAGCTTAATAAATAGGAT
ATACATAATCCATAAGCAAAATGACAAAAATTTCGAACATGAAGTTAAGGCATTTTCAATGCATA
AAACTCTTACCACAAGTCATTCATGCATAATACTGGGCACTTTAAACTAACGAATTTCAAGTACA
GTAAAGCATAACCGAGTTATCAATACCAAGCTTACTAAACTTTGTAACCAAGCACACATAAAACC
AAATCTAAACATAAATAGCAAGCCATTTTCGCATGGCTTAAATACATAACCAAAATCAATATCTC
AAAAGTATGTTCCAGCCTATACATGCCATAATACGAGTTTGATTATCTAAATACCGAAGCTGTAG
ATAGTGTGCTGAGCTTGGCTGATAGTTCCCGAGCTTGTAGCTTGACTTCAAAATCTATAAAACAG
AGTAAGCATAGCACACAAAGTAAGCTATCAAGGCGTAGTAAGTCATAAGCAAATAAACAACTCAT
Found at i:28849674 original size:47 final size:46
Alignment explanation
Indices: 28849610--28849773 Score: 188
Period size: 47 Copynumber: 3.5 Consensus size: 46
28849600 ATCCATAAGT
28849610 GAACTCGGACTCAACTCAACGAGCTCAGATGCCTAGTTACATCTCTC
1 GAACTCGGACTCAACTCAACGAG-TCAGATGCCTAGTTACATCTCTC
* * * * * * ***
28849657 GAACTCAGACTCAACTCAACGAGTTCGGACG-CTCGCATCCATAAGT-
1 GAACTCGGACTCAACTCAACGAG-TCAGATGCCTAG-TTACATCTCTC
*
28849703 GAACTCGGACTCAACTCAACGAGTCCAGATGCCTAGTTACATCTCAC
1 GAACTCGGACTCAACTCAACGAGT-CAGATGCCTAGTTACATCTCTC
28849750 GAACTCGGACTCAACTCAACGAGT
1 GAACTCGGACTCAACTCAACGAGT
28849774 TCGGACATTC
Statistics
Matches: 93, Mismatches: 20, Indels: 8
0.77 0.17 0.07
Matches are distributed among these distances:
45 1 0.01
46 33 0.35
47 59 0.63
ACGTcount: A:0.30, C:0.31, G:0.18, T:0.21
Consensus pattern (46 bp):
GAACTCGGACTCAACTCAACGAGTCAGATGCCTAGTTACATCTCTC
Found at i:28849820 original size:46 final size:46
Alignment explanation
Indices: 28849556--28849820 Score: 206
Period size: 46 Copynumber: 5.7 Consensus size: 46
28849546 AGTAACCCGC
* * * * *
28849556 CCATAAGTGAACTCGGGCTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCACAT
* *
28849602 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCAGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTC-G--GAC-A-TTCACAT
* * ** *
28849652 CTC-T---CGAACTCAGACTCAACTCAACGAGTTCGGACGCTCGCAT
1 C-CATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCACAT
* *
28849695 CCATAAGTGAACTCGGACTCAACTCAACGAGTCCAGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTC-G--GAC-A-TTCACAT
* *
28849745 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCACAT
* *
28849788 CCATAAGTGAACTCGAACTCAACTCAATGAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTT
28849821 TGGATGCTCA
Statistics
Matches: 173, Mismatches: 26, Indels: 40
0.72 0.11 0.17
Matches are distributed among these distances:
42 4 0.02
43 10 0.06
44 5 0.03
45 2 0.01
46 82 0.47
47 51 0.29
48 2 0.01
49 5 0.03
50 8 0.05
51 4 0.02
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCACAT
Found at i:28849827 original size:93 final size:93
Alignment explanation
Indices: 28849564--28849820 Score: 406
Period size: 93 Copynumber: 2.8 Consensus size: 93
28849554 GCCCATAAGT
* * *
28849564 GAACTCGGGCTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
* *
28849629 CGAGCTCAGATGCCTAGTTACATCTCTC
66 CGAGTTCAGATGCCTAGTTACATCTCAC
* *
28849657 GAACTCAGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
28849722 CGAGTCCAGATGCCTAGTTACATCTCAC
66 CGAGTTCAGATGCCTAGTTACATCTCAC
* * *
28849750 GAACTCGGACTCAACTCAACGAGTTCGGACATTCACATCCATAAGTGAACTCGAACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
28849815 TGAGTT
66 CGAGTT
28849821 TGGATGCTCA
Statistics
Matches: 149, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 149 1.00
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCAGATGCCTAGTTACATCTCAC
Found at i:28852251 original size:30 final size:30
Alignment explanation
Indices: 28852207--28852295 Score: 94
Period size: 30 Copynumber: 3.0 Consensus size: 30
28852197 CAAAGATAAC
*
28852207 AAGAAAACC-GAATAAAGAAATCCAAGATA
1 AAGAAACCCGGAATAAAGAAATCCAAGATA
*
28852236 GAGAAACCCGGAATAAAGAAATCCATA-ATA
1 AAGAAACCCGGAATAAAGAAATCCA-AGATA
* * *
28852266 AAGAGATCCAGG-ATAAAGAAACCCAAGATA
1 AAGA-AACCCGGAATAAAGAAATCCAAGATA
28852296 CGATACTATG
Statistics
Matches: 50, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
29 8 0.16
30 36 0.72
31 6 0.12
ACGTcount: A:0.56, C:0.16, G:0.17, T:0.11
Consensus pattern (30 bp):
AAGAAACCCGGAATAAAGAAATCCAAGATA
Found at i:28852295 original size:15 final size:15
Alignment explanation
Indices: 28852218--28852295 Score: 70
Period size: 15 Copynumber: 5.2 Consensus size: 15
28852208 AGAAAACCGA
28852218 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* **
28852233 ATAGAGAAA-CCCGG
1 ATAAAGAAATCCAAG
28852247 AATAAAGAAATCCATA-
1 -ATAAAGAAATCCA-AG
* *
28852263 ATAAAGAGATCCAGG
1 ATAAAGAAATCCAAG
*
28852278 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
28852293 ATA
1 ATA
28852296 CGATACTATG
Statistics
Matches: 48, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
14 3 0.06
15 43 0.90
16 2 0.04
ACGTcount: A:0.55, C:0.15, G:0.17, T:0.13
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:28853154 original size:45 final size:45
Alignment explanation
Indices: 28853090--28853181 Score: 166
Period size: 45 Copynumber: 2.0 Consensus size: 45
28853080 ACCACTTTGG
* *
28853090 TAAGGGGGAGGGGTTGTAGGACCTCTGACTCGACTTTCTTATACA
1 TAAGGGGGAAGGGTTGTAGGACCTCCGACTCGACTTTCTTATACA
28853135 TAAGGGGGAAGGGTTGTAGGACCTCCGACTCGACTTTCTTATACA
1 TAAGGGGGAAGGGTTGTAGGACCTCCGACTCGACTTTCTTATACA
28853180 TA
1 TA
28853182 CACATATGAC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.28
Consensus pattern (45 bp):
TAAGGGGGAAGGGTTGTAGGACCTCCGACTCGACTTTCTTATACA
Found at i:28855319 original size:46 final size:47
Alignment explanation
Indices: 28855252--28855523 Score: 234
Period size: 46 Copynumber: 5.7 Consensus size: 47
28855242 TGTAACCCGC
*
28855252 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGAG-CGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGAGACGTTCGCAT
* * * * *
28855298 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCG-GATGCCTAG-TT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGAGACG-TTCGCAT
* *** *
28855344 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTCG-GACGCTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGTTCGAGACGTTCGCAT
* * *
28855391 CCATAAGTGAACTCAGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTC-GA-GAC--GTTCGCAT
* * * * * *
28855441 CTAACGAACTCAGACTC-AACTCAACTCAACGAGTTCG-GACATTCGCAT
1 C-CA-TAAGTGA-ACTCGGACTCAACTCAACGAGTTCGAGACGTTCGCAT
28855489 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCG
28855524 GATGCTCAAC
Statistics
Matches: 179, Mismatches: 33, Indels: 28
0.75 0.14 0.12
Matches are distributed among these distances:
45 5 0.03
46 92 0.51
47 40 0.22
48 4 0.02
49 4 0.02
50 4 0.02
51 4 0.02
52 22 0.12
53 4 0.02
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.21
Consensus pattern (47 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGAGACGTTCGCAT
Found at i:28855372 original size:93 final size:93
Alignment explanation
Indices: 28855260--28855528 Score: 405
Period size: 93 Copynumber: 2.8 Consensus size: 93
28855250 GCCCATAAGT
*
28855260 GAACTCGGACTCAACTCAACGAGCTC-GAGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 GAACTCGGACTCAACTCAACGAGTTCGGA-CGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
* **
28855324 ACGAGCTCGGATGCCTAGTTACATCTCTC
65 ACGAGTTCGGATGCCTAGTTACATCTAAC
* *
28855353 GAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGTGAACTCAGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
28855418 CGAGTTCGGATGCCTAGTTACATCTAAC
66 CGAGTTCGGATGCCTAGTTACATCTAAC
* *
28855446 GAACTCAGACTCAACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAA
1 GAACTC-G----GACTCAACTCAACGAGTTCGGACGTTCGCATCCATAAGTGAACTCGGACTCAA
28855511 CTCAACGAGTTCGGATGC
61 CTCAACGAGTTCGGATGC
28855529 TCAACCATCC
Statistics
Matches: 160, Mismatches: 10, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
93 90 0.56
94 3 0.02
98 67 0.42
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTAAC
Found at i:28855375 original size:47 final size:47
Alignment explanation
Indices: 28855306--28855465 Score: 191
Period size: 47 Copynumber: 3.4 Consensus size: 47
28855296 ATCCATAAGT
* * *
28855306 GAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCTC
1 GAACTCAGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTATC
* * * * * *
28855353 GAACTCGGACTCAACTCAACGAGTTCGGACG-CTCGCATCCAT-AAGT-
1 GAACTCAGACTCAACTCAACGAGTTCGGATGCCTAG-TTACATCTA-TC
*
28855399 GAACTCAGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTAAC
1 GAACTCAGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTATC
28855446 GAACTCAGACTCAACTCAAC
1 GAACTCAGACTCAACTCAAC
28855466 TCAACGAGTT
Statistics
Matches: 94, Mismatches: 14, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
46 36 0.38
47 58 0.62
ACGTcount: A:0.30, C:0.31, G:0.18, T:0.21
Consensus pattern (47 bp):
GAACTCAGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTATC
Found at i:28860031 original size:32 final size:32
Alignment explanation
Indices: 28859995--28860060 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
28859985 AGCTTATGTT
28859995 TCTTGGCAGTTAAAGCCACATGAAAAGAATAA
1 TCTTGGCAGTTAAAGCCACATGAAAAGAATAA
28860027 TCTTGGCAGTTAAAGCCACATGAAAAGAATAA
1 TCTTGGCAGTTAAAGCCACATGAAAAGAATAA
28860059 TC
1 TC
28860061 ATACTCATGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.42, C:0.17, G:0.18, T:0.23
Consensus pattern (32 bp):
TCTTGGCAGTTAAAGCCACATGAAAAGAATAA
Found at i:28864824 original size:31 final size:31
Alignment explanation
Indices: 28864789--28864851 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
28864779 CATAGTTCGT
28864789 AGAAACCAAAGAGAAATAAGGCGAAGCTTAA
1 AGAAACCAAAGAGAAATAAGGCGAAGCTTAA
28864820 AGAAACCAAAGAGAAATAAGGCGAAGCTTAA
1 AGAAACCAAAGAGAAATAAGGCGAAGCTTAA
28864851 A
1 A
28864852 ATACACAGAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.56, C:0.13, G:0.22, T:0.10
Consensus pattern (31 bp):
AGAAACCAAAGAGAAATAAGGCGAAGCTTAA
Found at i:28871882 original size:39 final size:39
Alignment explanation
Indices: 28871685--28871900 Score: 184
Period size: 40 Copynumber: 5.4 Consensus size: 39
28871675 TTGTCTGGGC
* * * * * **
28871685 TAAGTCCCGAAGGCTTTGTGCTAAGTGAATATATCCGGAC
1 TAAGTCCCGAAGGCATTGTGC-GAGTTACTAAATCCGGGT
* *
28871725 TAAGAT-CCGAAGGCTTTTGTGCGAGATAC-AAATTCCGGGT
1 TAAG-TCCCGAAGGC-ATTGTGCGAGTTACTAAA-TCCGGGT
* * *
28871765 TAAGCCCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGT
1 TAAGTCCCGAAGG-CATTGTGCGAGTTACTAAATCCGGGT
* **
28871805 TAAGTCCCGAAGACATTCGTGCGAGTTGTTAAATCCGGGT
1 TAAGTCCCGAAGGCATT-GTGCGAGTTACTAAATCCGGGT
* * * *
28871845 TATGTCCCGAAGGCATTGTGTGAGTTACTAAAACCGGGC
1 TAAGTCCCGAAGGCATTGTGCGAGTTACTAAATCCGGGT
*
28871884 TATGTCCCGAAGGCATT
1 TAAGTCCCGAAGGCATT
28871901 TGAACGAGGA
Statistics
Matches: 148, Mismatches: 21, Indels: 15
0.80 0.11 0.08
Matches are distributed among these distances:
39 39 0.26
40 97 0.66
41 12 0.08
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (39 bp):
TAAGTCCCGAAGGCATTGTGCGAGTTACTAAATCCGGGT
Found at i:28871920 original size:79 final size:80
Alignment explanation
Indices: 28871758--28871935 Score: 189
Period size: 79 Copynumber: 2.2 Consensus size: 80
28871748 AGATACAAAT
* * * *
28871758 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGACATTC
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGACATTC
** ** *
28871823 GTGCGAGTTGTTAAA
66 GAACGAGGAGCTAAA
* * * * * *
28871838 TCCGGGTTATGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGACATTC
*
28871902 GAACGAGGAGCTATA
66 GAACGAGGAGCTAAA
*
28871917 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
28871936 TACGTGATTT
Statistics
Matches: 80, Mismatches: 18, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
78 14 0.17
79 48 0.60
80 18 0.22
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGACATTC
GAACGAGGAGCTAAA
Found at i:28879156 original size:80 final size:79
Alignment explanation
Indices: 28879072--28879243 Score: 193
Period size: 79 Copynumber: 2.2 Consensus size: 79
28879062 GGACTAAGAT
* *
28879072 CCGAAGGCTTTTGTGCGAGAT-ACAAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACT
1 CCGAAGGCATTTGTGCGAGATGACAAA-TCCGGGTTAAGCCCCGAAGG-CATTGTGCGAGATACT
* *
28879136 AAATCCGGGTTAAGTC
64 AAAACCGGGCTAAGTC
* * * ** * * * *
28879152 CCGAAGACATTCGTGCGAGTTGTTAAATCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATGACAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAA
*
28879217 AACCGGGCTATGTC
66 AACCGGGCTAAGTC
28879231 CCGAAGGCATTTG
1 CCGAAGGCATTTG
28879244 AACGAGGAGC
Statistics
Matches: 75, Mismatches: 16, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
79 37 0.49
80 35 0.47
81 3 0.04
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATGACAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAA
AACCGGGCTAAGTC
Found at i:28879223 original size:39 final size:39
Alignment explanation
Indices: 28879019--28879241 Score: 189
Period size: 40 Copynumber: 5.6 Consensus size: 39
28879009 TTGAATGCTG
* * * * * *
28879019 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGC-GAGTTACTAAA
** * *
28879059 TCCGGACTAAGAT-CCGAAGGCTTTTGTGCGAGATAC-AAA
1 TCCGGGTTAAG-TCCCGAAGGC-ATTGTGCGAGTTACTAAA
* * *
28879098 TTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
1 -TCCGGGTTAAGTCCCGAAGG-CATTGTGCGAGTTACTAAA
* **
28879139 TCCGGGTTAAGTCCCGAAGACATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTACTAAA
* *
28879179 TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
* * *
28879218 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
28879242 TGAACGAGGA
Statistics
Matches: 154, Mismatches: 22, Indels: 15
0.81 0.12 0.08
Matches are distributed among these distances:
39 39 0.25
40 103 0.67
41 12 0.08
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
Found at i:28879261 original size:79 final size:80
Alignment explanation
Indices: 28879099--28879276 Score: 189
Period size: 79 Copynumber: 2.2 Consensus size: 80
28879089 AGATACAAAT
* * * *
28879099 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGACATTC
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGACATTC
** ** *
28879164 GTGCGAGTTGTTAAA
66 GAACGAGGAGCTAAA
* * * * * *
28879179 TCCGGGTTATGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGACATTC
*
28879243 GAACGAGGAGCTATA
66 GAACGAGGAGCTAAA
*
28879258 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
28879277 TACGTGATTT
Statistics
Matches: 80, Mismatches: 18, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
78 14 0.17
79 48 0.60
80 18 0.22
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGACATTC
GAACGAGGAGCTAAA
Found at i:28891115 original size:12 final size:12
Alignment explanation
Indices: 28891098--28891123 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
28891088 TACACTTGAA
28891098 GTGTACAAATCT
1 GTGTACAAATCT
28891110 GTGTACAAATCT
1 GTGTACAAATCT
28891122 GT
1 GT
28891124 AAACCGTCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35
Consensus pattern (12 bp):
GTGTACAAATCT
Found at i:28891390 original size:25 final size:24
Alignment explanation
Indices: 28891352--28891404 Score: 70
Period size: 25 Copynumber: 2.2 Consensus size: 24
28891342 ATGTTCAAGC
*
28891352 GAGCCATATTAGGAAGCTCAAAAA
1 GAGCCATATCAGGAAGCTCAAAAA
* *
28891376 GAGCCTATATCAGGACGCTCATAAA
1 GAGCC-ATATCAGGAAGCTCAAAAA
28891401 GAGC
1 GAGC
28891405 TACGTTTGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 5 0.20
25 20 0.80
ACGTcount: A:0.40, C:0.21, G:0.23, T:0.17
Consensus pattern (24 bp):
GAGCCATATCAGGAAGCTCAAAAA
Found at i:28891911 original size:21 final size:20
Alignment explanation
Indices: 28891881--28891925 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
28891871 AATGAAGTTA
28891881 ACATTAATTTAATAAAATTC
1 ACATTAATTTAATAAAATTC
* **
28891901 ACATTCAATTTCATTCAATTC
1 ACATT-AATTTAATAAAATTC
28891922 ACAT
1 ACAT
28891926 CTTAGGAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.42, C:0.18, G:0.00, T:0.40
Consensus pattern (20 bp):
ACATTAATTTAATAAAATTC
Found at i:28894078 original size:21 final size:23
Alignment explanation
Indices: 28894053--28894094 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
28894043 TTGTATAATA
*
28894053 TCTTCTATACA-A-ATTTTGAAT
1 TCTTCGATACACATATTTTGAAT
28894074 TCTTCGATACACATATTTTGA
1 TCTTCGATACACATATTTTGA
28894095 CTCTGAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 10 0.56
22 1 0.06
23 7 0.39
ACGTcount: A:0.31, C:0.17, G:0.07, T:0.45
Consensus pattern (23 bp):
TCTTCGATACACATATTTTGAAT
Found at i:28899068 original size:157 final size:158
Alignment explanation
Indices: 28898845--28899155 Score: 543
Period size: 157 Copynumber: 2.0 Consensus size: 158
28898835 GCGATTTCAT
*
28898845 GGTCTAAGGCCGATTTGGACCATGATGGCTCGAAATGGGCCATGTGGGCCCCCCGAGCTCGTGGG
1 GGTCTAAGGCCGATTTGGACCATGATGGCTCGAAATGGGCCATGTGGGCCCCACGAGCTCGTGGG
* *
28898910 CCCCACACGAGTAAACCACACGAGCATGTGGAGATTGTTGGGCAGGCTGTGTAAACTACGCGGCC
66 CCCCACACGAGTAAACCACACGAACATGTGGAGATTGTTGGGCAGGCTGTGTAAACCACGCGGCC
28898975 AAGGCTATTTTTGGCCTTGTGGGCACGA
131 AAGGCTATTTTTGGCCTTGTGGGCACGA
* * *
28899003 GGTCTAAGGCTGATTTGGGCCATGATGGCTCG-AATGGGCCGTGTGGGCCCCACGAGCTCGTGGG
1 GGTCTAAGGCCGATTTGGACCATGATGGCTCGAAATGGGCCATGTGGGCCCCACGAGCTCGTGGG
*
28899067 CCCCACACGGGTAAACCACACGAACATGTGGAGATTGTTGGGCAGGCTGTGTAAACCACGCGGCC
66 CCCCACACGAGTAAACCACACGAACATGTGGAGATTGTTGGGCAGGCTGTGTAAACCACGCGGCC
*
28899132 AAGGCTATTTTTGGCCTTTTGGGC
131 AAGGCTATTTTTGGCCTTGTGGGC
28899156 CACATAAGTT
Statistics
Matches: 145, Mismatches: 8, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
157 115 0.79
158 30 0.21
ACGTcount: A:0.20, C:0.25, G:0.33, T:0.22
Consensus pattern (158 bp):
GGTCTAAGGCCGATTTGGACCATGATGGCTCGAAATGGGCCATGTGGGCCCCACGAGCTCGTGGG
CCCCACACGAGTAAACCACACGAACATGTGGAGATTGTTGGGCAGGCTGTGTAAACCACGCGGCC
AAGGCTATTTTTGGCCTTGTGGGCACGA
Found at i:28908498 original size:42 final size:42
Alignment explanation
Indices: 28908428--28908516 Score: 124
Period size: 42 Copynumber: 2.1 Consensus size: 42
28908418 TGCTGGGAAA
* * * *
28908428 ACACGGCCACACCACATGTTCGTACACATGGCCGTGTGTCAC
1 ACACGACCAAACCACACGTCCGTACACATGGCCGTGTGTCAC
* *
28908470 ACACGACCAAACCACACGTCCGTGCACATGGTCGTGTGTCAC
1 ACACGACCAAACCACACGTCCGTACACATGGCCGTGTGTCAC
28908512 ACACG
1 ACACG
28908517 GTTGAGACAC
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.26, C:0.36, G:0.21, T:0.17
Consensus pattern (42 bp):
ACACGACCAAACCACACGTCCGTACACATGGCCGTGTGTCAC
Found at i:28913428 original size:47 final size:47
Alignment explanation
Indices: 28913368--28913497 Score: 172
Period size: 47 Copynumber: 2.8 Consensus size: 47
28913358 GTGTGAATAA
* * * *
28913368 TACCTAGATTTGGCTACGGGCCATGGTATAGGT-TTTTAGAGAGGAGT
1 TACCTTGATTTGGCTACGGGCCATGGTATAGGTACTCT-GAGAGAAGT
* * *
28913415 TACCTTGATTTGGCTACGGGCCATGGTATAGATACTCTGGGATAAGT
1 TACCTTGATTTGGCTACGGGCCATGGTATAGGTACTCTGAGAGAAGT
*
28913462 TACCTTGATTTGGCTACGGGCCATTGTATAGGTACT
1 TACCTTGATTTGGCTACGGGCCATGGTATAGGTACT
28913498 ATAAAACAGA
Statistics
Matches: 73, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
47 71 0.97
48 2 0.03
ACGTcount: A:0.22, C:0.16, G:0.28, T:0.33
Consensus pattern (47 bp):
TACCTTGATTTGGCTACGGGCCATGGTATAGGTACTCTGAGAGAAGT
Found at i:28932395 original size:21 final size:20
Alignment explanation
Indices: 28932366--28932410 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
28932356 AACAAATTTA
28932366 ACATTAATTTAATAAAATTC
1 ACATTAATTTAATAAAATTC
* **
28932386 ACATTCAATTTCATTCAATTC
1 ACATT-AATTTAATAAAATTC
28932407 ACAT
1 ACAT
28932411 CTTAGGAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.42, C:0.18, G:0.00, T:0.40
Consensus pattern (20 bp):
ACATTAATTTAATAAAATTC
Found at i:28932855 original size:20 final size:18
Alignment explanation
Indices: 28932815--28932858 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 18
28932805 TGTGGGTAGA
*
28932815 CCGTGTGATTACACACAC
1 CCGTGTGATTAAACACAC
*
28932833 CCGTGTGACTTCAAACACGC
1 CCGTGTGA-TT-AAACACAC
28932853 CCGTGT
1 CCGTGT
28932859 CCTCAACCTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 8 0.36
19 2 0.09
20 12 0.55
ACGTcount: A:0.23, C:0.34, G:0.20, T:0.23
Consensus pattern (18 bp):
CCGTGTGATTAAACACAC
Found at i:28936167 original size:29 final size:29
Alignment explanation
Indices: 28936104--28936213 Score: 109
Period size: 29 Copynumber: 3.9 Consensus size: 29
28936094 ACATACATGT
*
28936104 ATATGGCCCACTT-GGCCC--ATCTCATTC
1 ATATGGCCCA-TTAGGCCCAAATCACATTC
* * *
28936131 ATATGGCCCATCAGGCCCAATTCATATTC
1 ATATGGCCCATTAGGCCCAAATCACATTC
* * * *
28936160 ATATGGCCTATTAGTCCCAAATCACCTTT
1 ATATGGCCCATTAGGCCCAAATCACATTC
*
28936189 ATATGGCCCGTTAGGCCCAAATCAC
1 ATATGGCCCATTAGGCCCAAATCAC
28936214 CTTATATTCA
Statistics
Matches: 66, Mismatches: 14, Indels: 4
0.79 0.17 0.05
Matches are distributed among these distances:
26 1 0.02
27 15 0.23
29 50 0.76
ACGTcount: A:0.25, C:0.32, G:0.15, T:0.28
Consensus pattern (29 bp):
ATATGGCCCATTAGGCCCAAATCACATTC
Found at i:28937727 original size:16 final size:16
Alignment explanation
Indices: 28937702--28937734 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
28937692 AAAAATTTAA
*
28937702 GATTTTGGGATTTTTG
1 GATTTCGGGATTTTTG
28937718 GATTTCGGGATTTTTG
1 GATTTCGGGATTTTTG
28937734 G
1 G
28937735 GGTGTTACAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.03, G:0.33, T:0.52
Consensus pattern (16 bp):
GATTTCGGGATTTTTG
Found at i:28949066 original size:21 final size:20
Alignment explanation
Indices: 28949038--28949076 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
28949028 ACCTTAAAAT
*
28949038 AGGGAACACGTCCGTGTGGA
1 AGGGAACACGCCCGTGTGGA
*
28949058 AGGGTAACATGCCCGTGTG
1 AGGG-AACACGCCCGTGTG
28949077 ACCATTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.23, C:0.21, G:0.38, T:0.18
Consensus pattern (20 bp):
AGGGAACACGCCCGTGTGGA
Found at i:28950239 original size:49 final size:48
Alignment explanation
Indices: 28950181--28950493 Score: 167
Period size: 46 Copynumber: 6.6 Consensus size: 48
28950171 GTAAAGTGTC
* *
28950181 GATGGCATGTCCCAGACATGGTCTCACACTGGCTATCATCTTCGAGGCT
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTATCATCTTCGA-GCT
* * * * *
28950230 GATGCCATGTCCCAGGCATGGTCTTACACTAGCTTTCA-CATAAC-ATTGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTATCATC-T-TCGA--GCT
28950280 GATGCCATGTCCCAGACATGGTCTTACACTGGC-A-CATC-TCGTAGCT
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTATCATCTTCG-AGCT
** * * * *
28950326 GATG-CATGTCCCAGACA-CCTATTATACTGGCT-TACGTC-CCGAGGCT
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTAT-CATCTTCGA-GCT
*** * * *
28950372 GATG-CATGTTTTAGACAT-GTCTTATACTAGC-ACTCATC-TCAATG-T
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTA-TCATCTTCGA-GCT
* * * * *
28950417 CGATGCCATGTCCGAGACATGGTCTTACACTGGGTCTCATAATGT-G-GCC
1 -GATGCCATGTCCCAGACATGGTCTTACACTGGCTATCAT-CT-TCGAGCT
28950466 GATG-CATGTCCCAGACAT-GTCTTACACT
1 GATGCCATGTCCCAGACATGGTCTTACACT
28950494 AGCTCACACA
Statistics
Matches: 203, Mismatches: 40, Indels: 45
0.70 0.14 0.16
Matches are distributed among these distances:
44 10 0.05
45 15 0.07
46 59 0.29
47 25 0.12
48 23 0.11
49 36 0.18
50 34 0.17
51 1 0.00
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (48 bp):
GATGCCATGTCCCAGACATGGTCTTACACTGGCTATCATCTTCGAGCT
Found at i:28954167 original size:34 final size:35
Alignment explanation
Indices: 28954079--28954168 Score: 119
Period size: 35 Copynumber: 2.6 Consensus size: 35
28954069 CATAATAGCC
* *
28954079 AGTCCAACCAAAACACACCAATGCTCAAAAGGGCT
1 AGTCCAACCAAAACACACCAATACTCAAAAGAGCT
** *
28954114 AGTCCTTCCGAAACACACCAATACTCAAAAGAGCT
1 AGTCCAACCAAAACACACCAATACTCAAAAGAGCT
*
28954149 AGTCC-ACTAAAACACACCAA
1 AGTCCAACCAAAACACACCAA
28954169 ACAAAGAGTA
Statistics
Matches: 47, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
34 12 0.26
35 35 0.74
ACGTcount: A:0.43, C:0.32, G:0.11, T:0.13
Consensus pattern (35 bp):
AGTCCAACCAAAACACACCAATACTCAAAAGAGCT
Found at i:28954886 original size:46 final size:46
Alignment explanation
Indices: 28954818--28954908 Score: 128
Period size: 46 Copynumber: 2.0 Consensus size: 46
28954808 TATATATACA
* * *
28954818 CATCTCATACATATCTCACATTAGCCATTTGGCTTTACCACATATC
1 CATCTCATACACATCTCACATTAGCCATTCGACTTTACCACATATC
* * *
28954864 CATCTCATACGCATTTCGCATTAGCCATTCGACTTTACCACATAT
1 CATCTCATACACATCTCACATTAGCCATTCGACTTTACCACATAT
28954909 ATACACTTCC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.27, C:0.31, G:0.08, T:0.34
Consensus pattern (46 bp):
CATCTCATACACATCTCACATTAGCCATTCGACTTTACCACATATC
Found at i:28954953 original size:47 final size:47
Alignment explanation
Indices: 28954922--28955355 Score: 742
Period size: 47 Copynumber: 9.2 Consensus size: 47
28954912 CACTTCCACG
28954922 TTCATCACATTGGCCATTCGGCCTTATCACATATGTGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATGTGCATGTTCACA
* *
28954969 TTCATCACATTGGCCATTCGGCCTTATCACACATATGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATGTGCATGTTCACA
*
28955016 TTTATCACATTGGCCATTCGGCCTTATCACATATGTGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATGTGCATGTTCACA
* * * *
28955063 TTCATCACATTGGCCATTCGGTCTTATCACACATATTCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATGTGCATGTTCACA
*
28955110 TTCGTCACATTGGCCATTCGGCCTTATCACATATGTGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATGTGCATGTTCACA
*
28955157 TTTATCACATTGGCCATTCGGCCTTATCACATATGTGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATGTGCATGTTCACA
* *
28955204 TTCGTCACATTGGACATTCGGCCTTATCACATATGTGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATGTGCATGTTCACA
*
28955251 TTCGTCACATTGGCCATTCGGCCTTATCACATATGTGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATGTGCATGTTCACA
* *
28955298 TTCGTCACATTGGCCATTCAGCCTTATCACATATGTGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATGTGCATGTTCACA
28955345 TTCATCACATT
1 TTCATCACATT
28955356 AAATCCTAAA
Statistics
Matches: 364, Mismatches: 23, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 364 1.00
ACGTcount: A:0.24, C:0.27, G:0.15, T:0.35
Consensus pattern (47 bp):
TTCATCACATTGGCCATTCGGCCTTATCACATATGTGCATGTTCACA
Found at i:28960353 original size:49 final size:50
Alignment explanation
Indices: 28960271--28960503 Score: 247
Period size: 49 Copynumber: 4.7 Consensus size: 50
28960261 ATCTATTGTG
* * *
28960271 AGGTCACGTGTGTAGTACTAAGTGTAGGATACTACGTGTACCGGATAATT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
* * * *
28960321 -GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGATAACTT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAA-TT
* * * * * * **
28960371 CGATCACGTGTGTAGTACTAAGTTCAGGCTACTACATGTATCAGG-TGGTT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTA-CCGGATAATT
* * *
28960421 AGGTCACGTGTGTAGTACTAAGTGCAAGCTACTACGTGTACTGGATAATT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
* *
28960471 -GGTCGCATGTGTAGTACTAAGTGCGGGCTACTA
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTA
28960504 TGCGTACCAG
Statistics
Matches: 149, Mismatches: 30, Indels: 9
0.79 0.16 0.05
Matches are distributed among these distances:
49 72 0.48
50 42 0.28
51 33 0.22
52 2 0.01
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (50 bp):
AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
Found at i:28960452 original size:101 final size:98
Alignment explanation
Indices: 28960274--28960503 Score: 248
Period size: 101 Copynumber: 2.3 Consensus size: 98
28960264 TATTGTGAGG
* * * *
28960274 TCACGTGTGTAGTACTAAGTGT-AGGATACTACGTGTACCGGATAATTGGTCGCATGTGTAGTAC
1 TCACGTGTGTAGTACTAAGT-TCAGGCTACTACATGTACAGGATAATTGGTCACATGTGTAGTAC
* *
28960338 TAAGTGCAGGCTACTATGCGTACCCGATAACTTCGA
65 TAAGTGCAAGCTACTACGCGTACCCGATAA-TT-GA
** *
28960374 TCACGTGTGTAGTACTAAGTTCAGGCTACTACATGTATCAGG-TGGTTAGGTCACGTGTGTAGTA
1 TCACGTGTGTAGTACTAAGTTCAGGCTACTACATGTA-CAGGATAATT-GGTCACATGTGTAGTA
* ** *
28960438 CTAAGTGCAAGCTACTACGTGTACTGGATAATTGG
64 CTAAGTGCAAGCTACTACGCGTACCCGATAATTGA
* * * *
28960473 TCGCATGTGTAGTACTAAGTGCGGGCTACTA
1 TCACGTGTGTAGTACTAAGTTCAGGCTACTA
28960504 TGCGTACCAG
Statistics
Matches: 110, Mismatches: 17, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
99 29 0.26
100 38 0.35
101 43 0.39
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (98 bp):
TCACGTGTGTAGTACTAAGTTCAGGCTACTACATGTACAGGATAATTGGTCACATGTGTAGTACT
AAGTGCAAGCTACTACGCGTACCCGATAATTGA
Found at i:28965598 original size:49 final size:49
Alignment explanation
Indices: 28965509--28965731 Score: 223
Period size: 49 Copynumber: 4.5 Consensus size: 49
28965499 TCTATTGTGA
* * * *
28965509 GGTCACGTGTGTAGTACTAAATGTAGGATACTACGTGTACCGGATAATT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
* ** * *
28965558 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTGTGCGTACCCGATAACTTT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAA--TT
* * * * * *
28965609 GATCACGTGTGTAGTCCTAAGTTCAGGCTACTACGTGTATCAGG-TGATT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTA-CCGGATAATT
* * * *
28965658 AGGTCACGTGTGTAGTACTAAGTGCAAGCCACTACGTGTACTGGATAATT
1 -GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
*
28965708 GGTCGCATGTGTAGTACTAAGTGC
1 GGTCACATGTGTAGTACTAAGTGC
28965732 GGATGACTAT
Statistics
Matches: 140, Mismatches: 29, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
49 65 0.46
50 38 0.27
51 35 0.25
52 2 0.01
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (49 bp):
GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
Found at i:28988187 original size:16 final size:15
Alignment explanation
Indices: 28988161--28988190 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
28988151 ATTGGGTTAA
28988161 AAATTATTTAATTAG
1 AAATTATTTAATTAG
28988176 AAATTAATTTAATTA
1 AAATT-ATTTAATTA
28988191 ATTAAAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (15 bp):
AAATTATTTAATTAG
Found at i:28988935 original size:17 final size:18
Alignment explanation
Indices: 28988913--28988947 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
28988903 TCACATTGAA
28988913 GTGTTTT-AGTGAAAATC
1 GTGTTTTCAGTGAAAATC
*
28988930 GTGTTTTCATTGAAAATC
1 GTGTTTTCAGTGAAAATC
28988948 CGTCTTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.29, C:0.09, G:0.20, T:0.43
Consensus pattern (18 bp):
GTGTTTTCAGTGAAAATC
Found at i:28992309 original size:46 final size:46
Alignment explanation
Indices: 28992256--28992431 Score: 191
Period size: 46 Copynumber: 3.8 Consensus size: 46
28992246 TATTTGGGCA
*
28992256 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
* * *
28992302 TCCGAACTCGTTGAGTTGAGTCCGAGTT---TGA-GAGATGTAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATG-GATGCAA--ATG
* * *
28992347 CATCCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCAAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
*
28992395 -CTCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TC-CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
28992432 GCGGGTTACA
Statistics
Matches: 110, Mismatches: 10, Indels: 20
0.79 0.07 0.14
Matches are distributed among these distances:
42 1 0.01
43 7 0.06
45 3 0.03
46 62 0.56
47 26 0.24
48 2 0.02
50 8 0.07
51 1 0.01
ACGTcount: A:0.22, C:0.19, G:0.29, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
Found at i:28992411 original size:93 final size:93
Alignment explanation
Indices: 28992252--28992422 Score: 281
Period size: 93 Copynumber: 1.8 Consensus size: 93
28992242 AGGATATTTG
* *
28992252 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCCGAACTCGTTGAG
28992317 TTGAGTCCGAGTTTGAGAGATGTAACTA
66 TTGAGTCCGAGTTTGAGAGATGTAACTA
* * *
28992345 GGCATCCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCAAACG-CTCGAGCTCGTTGA
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTC-CGAACTCGTTGA
28992409 GTTGAGTCCGAGTT
65 GTTGAGTCCGAGTT
28992423 CACTTATGGG
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
92 1 0.01
93 71 0.99
ACGTcount: A:0.22, C:0.19, G:0.30, T:0.29
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCCGAACTCGTTGAG
TTGAGTCCGAGTTTGAGAGATGTAACTA
Found at i:28999887 original size:43 final size:43
Alignment explanation
Indices: 28999840--28999979 Score: 162
Period size: 43 Copynumber: 3.3 Consensus size: 43
28999830 ATCCTGGATG
*
28999840 TGGTCTTACATGTAAATCAATATCGATGCCGATGTCCCAGACA
1 TGGTCTTACACGTAAATCAATATCGATGCCGATGTCCCAGACA
* *
28999883 TGGTCCTATACG-AAATCAGATA-CGATGCCGATGTCCCAGACA
1 TGGTCTTACACGTAAATCA-ATATCGATGCCGATGTCCCAGACA
* * *
28999925 TGGTCTTATACGTAAATCTCAAT-T-GAGGCCTATGTCCCAGACA
1 TGGTCTTACACGTAAA--TCAATATCGATGCCGATGTCCCAGACA
*
28999968 CGGTCTTACACG
1 TGGTCTTACACG
28999980 ATGTCTCAGA
Statistics
Matches: 84, Mismatches: 8, Indels: 10
0.82 0.08 0.10
Matches are distributed among these distances:
42 37 0.44
43 42 0.50
44 2 0.02
45 3 0.04
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.26
Consensus pattern (43 bp):
TGGTCTTACACGTAAATCAATATCGATGCCGATGTCCCAGACA
Found at i:28999910 original size:42 final size:43
Alignment explanation
Indices: 28999851--28999972 Score: 153
Period size: 42 Copynumber: 2.9 Consensus size: 43
28999841 GGTCTTACAT
28999851 GTAAATCAATATCGATGCCGATGTCCCAGACATGGTCCTATAC
1 GTAAATCAATATCGATGCCGATGTCCCAGACATGGTCCTATAC
*
28999894 G-AAATCAGATA-CGATGCCGATGTCCCAGACATGGTCTTATAC
1 GTAAATCA-ATATCGATGCCGATGTCCCAGACATGGTCCTATAC
* * *
28999936 GTAAATCTCAAT-T-GAGGCCTATGTCCCAGACACGGTC
1 GTAAA--TCAATATCGATGCCGATGTCCCAGACATGGTC
28999973 TTACACGATG
Statistics
Matches: 70, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
42 37 0.53
43 28 0.40
44 2 0.03
45 3 0.04
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (43 bp):
GTAAATCAATATCGATGCCGATGTCCCAGACATGGTCCTATAC
Found at i:29001072 original size:29 final size:29
Alignment explanation
Indices: 29000954--29001100 Score: 104
Period size: 29 Copynumber: 5.1 Consensus size: 29
29000944 ACATACATGC
* *
29000954 ATATGGCCCACTT-GGCCC-AATCTCATTT
1 ATATGGCCCA-TTAGGCCCAAATCACCTTT
* * ** *
29000982 ATATGGTCCATCAGGCCCATTTCACAC-TC
1 ATATGGCCCATTAGGCCCAAATCAC-CTTT
* * * ** *
29001011 ATATGGCTCATCAGGCCCAATTCATATTC
1 ATATGGCCCATTAGGCCCAAATCACCTTT
29001040 ATATGGCCCATTAGGCCCAAATCACCTTT
1 ATATGGCCCATTAGGCCCAAATCACCTTT
* * *
29001069 ATATGGACCGTTAGGCCCAAATTACC-TT
1 ATATGGCCCATTAGGCCCAAATCACCTTT
29001097 ATAT
1 ATAT
29001101 TCATGCTCAC
Statistics
Matches: 94, Mismatches: 21, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
27 1 0.01
28 20 0.21
29 73 0.78
ACGTcount: A:0.27, C:0.29, G:0.14, T:0.30
Consensus pattern (29 bp):
ATATGGCCCATTAGGCCCAAATCACCTTT
Found at i:29001975 original size:26 final size:26
Alignment explanation
Indices: 29001945--29001999 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
29001935 TCAGCTAAGC
29001945 GAAACAAAGAAAATTATGTAGAGAAA
1 GAAACAAAGAAAATTATGTAGAGAAA
29001971 GAAACAAAGAAAATTATGTAGAGAAA
1 GAAACAAAGAAAATTATGTAGAGAAA
29001997 GAA
1 GAA
29002000 TAGAAATCGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.62, C:0.04, G:0.20, T:0.15
Consensus pattern (26 bp):
GAAACAAAGAAAATTATGTAGAGAAA
Found at i:29006249 original size:44 final size:44
Alignment explanation
Indices: 29006200--29006283 Score: 123
Period size: 44 Copynumber: 1.9 Consensus size: 44
29006190 CCAAAACATG
* * *
29006200 TGTCATACATATCACGAACTCAGACACAACTCAATGAGTTTGGA
1 TGTCATACATATCACGAACTCAAACACAACACAATAAGTTTGGA
* *
29006244 TGTCATATATATCATGAACTCAAACACAACACAATAAGTT
1 TGTCATACATATCACGAACTCAAACACAACACAATAAGTT
29006284 CAGATTACAT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 35 1.00
ACGTcount: A:0.40, C:0.21, G:0.12, T:0.26
Consensus pattern (44 bp):
TGTCATACATATCACGAACTCAAACACAACACAATAAGTTTGGA
Found at i:29012288 original size:23 final size:22
Alignment explanation
Indices: 29012250--29012309 Score: 68
Period size: 22 Copynumber: 2.6 Consensus size: 22
29012240 GATTATATGA
29012250 TAATTAACTTTAATTAATTAGTT
1 TAATTAACTTTAATT-ATTAGTT
**
29012273 TAATTAAGCTTT-ATTATTCTTT
1 TAATTAA-CTTTAATTATTAGTT
29012295 TAATTAACTATTAAT
1 TAATTAACT-TTAAT
29012310 CACACTTAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
21 2 0.06
22 14 0.44
23 12 0.38
24 4 0.12
ACGTcount: A:0.37, C:0.07, G:0.03, T:0.53
Consensus pattern (22 bp):
TAATTAACTTTAATTATTAGTT
Found at i:29019455 original size:79 final size:81
Alignment explanation
Indices: 29019319--29019501 Score: 232
Period size: 79 Copynumber: 2.3 Consensus size: 81
29019309 TCGAATGATG
* *
29019319 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
29019383 TGTGCGAGTTACTA-A
66 TGTGCGAGTTACTATA
* * * **
29019398 TTCCGGGCTAAG-CCCGAAGGCATTGGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
29019460 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGTTACTATA
* *
29019478 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
29019502 TGAACGAGTA
Statistics
Matches: 90, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 1 0.01
79 59 0.66
80 30 0.33
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGTTACTATA
Found at i:29019517 original size:40 final size:40
Alignment explanation
Indices: 29019320--29019503 Score: 216
Period size: 40 Copynumber: 4.6 Consensus size: 40
29019310 CGAATGATGT
* * * *
29019320 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* *
29019360 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
*
29019400 CCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
29019438 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
29019479 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
29019504 AACGAGTAGC
Statistics
Matches: 126, Mismatches: 11, Indels: 14
0.83 0.07 0.09
Matches are distributed among these distances:
39 35 0.28
40 81 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:29019525 original size:79 final size:79
Alignment explanation
Indices: 29019372--29019536 Score: 210
Period size: 79 Copynumber: 2.1 Consensus size: 79
29019362 GGACTAAGAT
* **
29019372 CCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
*
29019437 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
29019451 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGTTACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTTA-C
* *
29019514 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
29019530 CCGAAGG
1 CCGAAGG
29019537 TACGTGATTC
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
78 2 0.03
79 49 0.65
80 24 0.32
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:29027483 original size:79 final size:81
Alignment explanation
Indices: 29027347--29027529 Score: 223
Period size: 79 Copynumber: 2.3 Consensus size: 81
29027337 TCGAATGATG
* *
29027347 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
29027411 TGTGCAAGTTACTA-A
66 TGTGCAAGTTACTATA
* * * **
29027426 TTCCGGGCTAAG-CCCGAAGGCATTGGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
29027488 TTTGTGCGAGTTACTATA
64 TTTGTGCAAGTTACTATA
* *
29027506 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
29027530 TGAACGAGTA
Statistics
Matches: 89, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 1 0.01
79 58 0.65
80 30 0.34
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCAAGTTACTATA
Found at i:29027545 original size:40 final size:41
Alignment explanation
Indices: 29027347--29027531 Score: 222
Period size: 40 Copynumber: 4.6 Consensus size: 41
29027337 TCGAATGATG
* * *
29027347 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCAT-A
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
29027387 TCCGGACTAAGAT-CCGAAGGCATTTGTGCAAGTTACTA-AT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATAA
*
29027427 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTA-AA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
29027466 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
29027507 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
29027532 AACGAGTAGC
Statistics
Matches: 127, Mismatches: 12, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
39 34 0.27
40 83 0.65
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (41 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:29030921 original size:26 final size:26
Alignment explanation
Indices: 29030890--29030997 Score: 162
Period size: 26 Copynumber: 4.2 Consensus size: 26
29030880 TGAAATGCCC
*
29030890 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
*
29030916 ATCATGAAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* * *
29030942 ATCATGGAATATTTGCCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
29030968 ATCATGGAACATTTATCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
29030994 ATCA
1 ATCA
29030998 ATTTGTACCA
Statistics
Matches: 72, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 72 1.00
ACGTcount: A:0.36, C:0.23, G:0.07, T:0.33
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:29031976 original size:13 final size:13
Alignment explanation
Indices: 29031955--29032012 Score: 62
Period size: 13 Copynumber: 4.5 Consensus size: 13
29031945 AAATTTTTCC
*
29031955 AAAGCACTTCTTA
1 AAAGCACTTCTCA
*
29031968 AAAGTACTTCTCA
1 AAAGCACTTCTCA
* *
29031981 AAAGCACTTTTCC
1 AAAGCACTTCTCA
* *
29031994 ACAGCACTTTTCA
1 AAAGCACTTCTCA
29032007 AAAGCA
1 AAAGCA
29032013 ATGAAGAACT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 37 1.00
ACGTcount: A:0.38, C:0.26, G:0.09, T:0.28
Consensus pattern (13 bp):
AAAGCACTTCTCA
Done.