Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold74
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: 4633657
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 25 characters in sequence are not A, C, G, or T
File 15 of 24
Found at i:3070975 original size:20 final size:20
Alignment explanation
Indices: 3070928--3071002 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
3070918 AAAAAGACAT
*
3070928 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
3070947 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
3070968 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
3070988 AATGTATCGATACAT
1 AATGTATCGATACAT
3071003 CAGGGTATGA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:3070996 original size:40 final size:39
Alignment explanation
Indices: 3070925--3071002 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
3070915 GGTAAAAAGA
* *
3070925 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
3070964 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
3071003 CAGGGTATGA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:3071420 original size:2 final size:2
Alignment explanation
Indices: 3071413--3071443 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3071403 AAATCTCTTA
3071413 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3071444 GAGAGAGAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3071448 original size:2 final size:2
Alignment explanation
Indices: 3071443--3071469 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3071433 ATATATATAT
3071443 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
3071470 ACGAAGGCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3076956 original size:2 final size:2
Alignment explanation
Indices: 3076949--3076977 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3076939 GAGACATTGT
3076949 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
3076978 TATATCCCTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:3078656 original size:31 final size:31
Alignment explanation
Indices: 3078620--3078697 Score: 99
Period size: 31 Copynumber: 2.5 Consensus size: 31
3078610 AAAAAATATA
*
3078620 AAAATATAA-AGATAAAGATTTAATA-TGAAAT
1 AAAATATAATA-ATAAA-ATTAAATATTGAAAT
3078651 AAAATATAATAATAAAATTAAATATTGAAAT
1 AAAATATAATAATAAAATTAAATATTGAAAT
3078682 AAAA-ATTAATAATAAA
1 AAAATA-TAATAATAAA
3078698 TTTTATTATA
Statistics
Matches: 43, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
30 8 0.19
31 34 0.79
32 1 0.02
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.29
Consensus pattern (31 bp):
AAAATATAATAATAAAATTAAATATTGAAAT
Found at i:3078668 original size:18 final size:17
Alignment explanation
Indices: 3078622--3078675 Score: 54
Period size: 18 Copynumber: 3.0 Consensus size: 17
3078612 AAAATATAAA
*
3078622 AATATAAAGATAAAGATTT
1 AATATAAA-ATAAA-ATAT
*
3078641 AATATGAAATAAAATAT
1 AATATAAAATAAAATAT
*
3078658 AATAATAAAATTAAATAT
1 AAT-ATAAAATAAAATAT
3078676 TGAAATAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
17 6 0.20
18 17 0.57
19 7 0.23
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (17 bp):
AATATAAAATAAAATAT
Found at i:3079364 original size:12 final size:12
Alignment explanation
Indices: 3079347--3079371 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3079337 ATATTATAAA
3079347 TTTATTTAAATT
1 TTTATTTAAATT
3079359 TTTATTTAAATT
1 TTTATTTAAATT
3079371 T
1 T
3079372 ATTAAATGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTATTTAAATT
Found at i:3085396 original size:17 final size:16
Alignment explanation
Indices: 3085374--3085409 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
3085364 TTTTATTTTA
*
3085374 TTTTTTTAAATTCAAAC
1 TTTTTTT-AACTCAAAC
3085391 TTTTTTTAACTCAAAC
1 TTTTTTTAACTCAAAC
3085407 TTT
1 TTT
3085410 CAGACTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.31, C:0.14, G:0.00, T:0.56
Consensus pattern (16 bp):
TTTTTTTAACTCAAAC
Found at i:3088557 original size:2 final size:2
Alignment explanation
Indices: 3088550--3088584 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
3088540 TCAGTCAGAC
*
3088550 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GG GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
3088585 GGAAAAAGTG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.54, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3089380 original size:2 final size:2
Alignment explanation
Indices: 3089373--3089415 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
3089363 CACTCCCTCC
* *
3089373 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CG CC CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
3089415 C
1 C
3089416 GCTCGCTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.53, G:0.02, T:0.44
Consensus pattern (2 bp):
CT
Found at i:3089936 original size:46 final size:45
Alignment explanation
Indices: 3089886--3090002 Score: 101
Period size: 50 Copynumber: 2.5 Consensus size: 45
3089876 GATTTTTATG
* ** * *
3089886 TTTTTAATTAATTAAATTAAATTATTTATTTATATAATAACTAAATT
1 TTTTTAATTAATTAAATTAAATTATTAATAAAAATAAT-A-TAAATC
* *
3089933 TTTTTATATAAATTTAAATTATAAATATTAATAAAAATAATATAAA-C
1 TTTTTA-ATTAA-TTAAATTA-AATTATTAATAAAAATAATATAAATC
*
3089980 TTTTAAATTAATCTAAATTAAAT
1 TTTTTAATTAAT-TAAATTAAAT
3090003 AAAACTCAAA
Statistics
Matches: 56, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
45 3 0.05
46 11 0.20
47 11 0.20
48 8 0.14
49 9 0.16
50 14 0.25
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.48
Consensus pattern (45 bp):
TTTTTAATTAATTAAATTAAATTATTAATAAAAATAATATAAATC
Found at i:3094754 original size:23 final size:23
Alignment explanation
Indices: 3094727--3094793 Score: 73
Period size: 23 Copynumber: 2.9 Consensus size: 23
3094717 TTTTATATAA
3094727 ATTTTATTATTTTAATAATTTAT
1 ATTTTATTATTTTAATAATTTAT
* *
3094750 ATTTTATAAATTTTAA-AATATAT
1 ATTTTAT-TATTTTAATAATTTAT
* *
3094773 ATTTATATTATATAAATAATT
1 ATTT-TATTATTTTAATAATT
3094794 AATACTATAC
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
23 22 0.63
24 13 0.37
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
ATTTTATTATTTTAATAATTTAT
Found at i:3094761 original size:15 final size:15
Alignment explanation
Indices: 3094719--3094789 Score: 56
Period size: 15 Copynumber: 4.7 Consensus size: 15
3094709 ATATTTGATT
3094719 TTATATAAATTT-TA
1 TTATATAAATTTATA
*
3094733 TTATTTTAATAATTTATA
1 TTA-TAT-A-AATTTATA
*
3094751 TTTTATAAATTT-TA
1 TTATATAAATTTATA
** *
3094765 AAATATATATTTATA
1 TTATATAAATTTATA
3094780 TTATATAAAT
1 TTATATAAAT
3094790 AATTAATACT
Statistics
Matches: 42, Mismatches: 10, Indels: 9
0.69 0.16 0.15
Matches are distributed among these distances:
14 13 0.31
15 16 0.38
16 2 0.05
17 7 0.17
18 4 0.10
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TTATATAAATTTATA
Found at i:3094784 original size:13 final size:13
Alignment explanation
Indices: 3094768--3094832 Score: 50
Period size: 13 Copynumber: 5.3 Consensus size: 13
3094758 AATTTTAAAA
3094768 TATATATTTATAT
1 TATATATTTATAT
**
3094781 TATATAAATA-AT
1 TATATATTTATAT
*
3094793 TA-ATA-CTATA-
1 TATATATTTATAT
*
3094803 CATATATTT-TAT
1 TATATATTTATAT
3094815 TCATATATTTATAT
1 T-ATATATTTATAT
3094829 TATA
1 TATA
3094833 GGGTCTTTCA
Statistics
Matches: 40, Mismatches: 6, Indels: 12
0.69 0.10 0.21
Matches are distributed among these distances:
10 3 0.08
11 9 0.22
12 5 0.12
13 19 0.47
14 4 0.10
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (13 bp):
TATATATTTATAT
Found at i:3094786 original size:29 final size:30
Alignment explanation
Indices: 3094707--3094789 Score: 87
Period size: 32 Copynumber: 2.7 Consensus size: 30
3094697 ATCATATTCA
* * *
3094707 ATATATTTGATTTTATATAAATTTTATTATT
1 ATATATTT-ATATTATATAAATTTTATAAAT
* *
3094738 TTAATAATTTATATTTTATAAATTTTA-AAAT
1 AT-AT-ATTTATATTATATAAATTTTATAAAT
3094769 ATATATTTATATTATATAAAT
1 ATATATTTATATTATATAAAT
3094790 AATTAATACT
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
29 16 0.37
30 2 0.05
31 4 0.09
32 17 0.40
33 4 0.09
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (30 bp):
ATATATTTATATTATATAAATTTTATAAAT
Found at i:3094969 original size:21 final size:21
Alignment explanation
Indices: 3094922--3094980 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 21
3094912 AACTTTAAAG
*
3094922 TAAATTTAAA--TAAATTTTTT
1 TAAATTTAAATTTAAA-TTATT
3094942 TATAATTTAAATTTAAATTATT
1 TA-AATTTAAATTTAAATTATT
3094964 TAAATTT-AATTATAAAT
1 TAAATTTAAATT-TAAAT
3094981 ATTAATATAA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
20 6 0.18
21 18 0.53
22 6 0.18
23 4 0.12
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TAAATTTAAATTTAAATTATT
Found at i:3094976 original size:14 final size:15
Alignment explanation
Indices: 3094946--3094976 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
3094936 TTTTTTTATA
3094946 ATTTAAATTTAAATT
1 ATTTAAATTTAAATT
3094961 ATTTAAATTT-AATT
1 ATTTAAATTTAAATT
3094975 AT
1 AT
3094977 AAATATTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
ATTTAAATTTAAATT
Found at i:3095059 original size:31 final size:32
Alignment explanation
Indices: 3095003--3095062 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 32
3094993 TTATTTTTAT
**
3095003 TTTTAAATTAAAATTAAAAGTAATTAAATATA
1 TTTTAAATTAAAATTAAAAAAAATTAAATATA
*
3095035 TTTTAAATTTAAA-TAAAAAAAATTAAAT
1 TTTTAAATTAAAATTAAAAAAAATTAAAT
3095063 CTCAATTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 13 0.52
32 12 0.48
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (32 bp):
TTTTAAATTAAAATTAAAAAAAATTAAATATA
Found at i:3095072 original size:32 final size:32
Alignment explanation
Indices: 3095004--3095072 Score: 77
Period size: 32 Copynumber: 2.2 Consensus size: 32
3094994 TATTTTTATT
** *
3095004 TTTAAATTAAAATTAAAAGTAATTAAATATAT
1 TTTAAATTAAAATTAAAAAAAATTAAATATAA
* *
3095036 TTTAAATTTAAA-TAAAAAAAATTAAATCTCAA
1 TTTAAATTAAAATTAAAAAAAATTAAATAT-AA
3095068 TTTAA
1 TTTAA
3095073 TTATTCATTA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
31 14 0.45
32 17 0.55
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (32 bp):
TTTAAATTAAAATTAAAAAAAATTAAATATAA
Found at i:3095265 original size:21 final size:21
Alignment explanation
Indices: 3095239--3095282 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
3095229 ATATTTTTAA
*
3095239 AATTATAAAAATTTAAATTTT
1 AATTATAAAAATTAAAATTTT
*
3095260 AATTATTAAAATTAAAATTTT
1 AATTATAAAAATTAAAATTTT
3095281 AA
1 AA
3095283 CGGCTAATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
AATTATAAAAATTAAAATTTT
Found at i:3095668 original size:2 final size:2
Alignment explanation
Indices: 3095661--3095694 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
3095651 CTCTAGAGGC
*
3095661 AT AT AT AT AT AA AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3095695 CAATTTATAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3095754 original size:31 final size:32
Alignment explanation
Indices: 3095718--3095777 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 32
3095708 TTTAAAATTT
*
3095718 TTAATTAAATTAATA-TTACAAAATAAATAAA
1 TTAATTAAATTAAAATTTACAAAATAAATAAA
* *
3095749 TTAATTTAATTAAAATTTATAAAATAAAT
1 TTAATTAAATTAAAATTTACAAAATAAAT
3095778 TCAAATAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 13 0.52
32 12 0.48
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (32 bp):
TTAATTAAATTAAAATTTACAAAATAAATAAA
Found at i:3097044 original size:20 final size:21
Alignment explanation
Indices: 3097014--3097059 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
3097004 ATAATAAAAT
*
3097014 ATAATAAAATTTAAATTTTTA
1 ATAATAAAATTAAAATTTTTA
3097035 ATAA-AAAATTAAAA-TTTTA
1 ATAATAAAATTAAAATTTTTA
3097054 A-AATAA
1 ATAATAA
3097060 TTTTATATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 2 0.09
19 8 0.35
20 9 0.39
21 4 0.17
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
ATAATAAAATTAAAATTTTTA
Found at i:3097046 original size:19 final size:18
Alignment explanation
Indices: 3097015--3097054 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
3097005 TAATAAAATA
* *
3097015 TAATAAAATTTAAATTTT
1 TAATAAAAATTAAAATTT
3097033 TAATAAAAAATTAAAATTT
1 TAAT-AAAAATTAAAATTT
3097052 TAA
1 TAA
3097055 AATAATTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
TAATAAAAATTAAAATTT
Found at i:3097640 original size:19 final size:19
Alignment explanation
Indices: 3097616--3097678 Score: 101
Period size: 19 Copynumber: 3.4 Consensus size: 19
3097606 ATATTAATAT
3097616 TTAAAATAATAATAATAAA
1 TTAAAATAATAATAATAAA
3097635 TTAAAATAATAATAATAAA
1 TTAAAATAATAATAATAAA
* *
3097654 TTAAAATAATATTTAT-AA
1 TTAAAATAATAATAATAAA
3097672 TTAAAAT
1 TTAAAAT
3097679 TAAATAAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
18 9 0.21
19 33 0.79
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
TTAAAATAATAATAATAAA
Found at i:3097682 original size:29 final size:28
Alignment explanation
Indices: 3097650--3097713 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 28
3097640 ATAATAATAA
*
3097650 TAAATTAAAATAATATTTATAATTAAAAT
1 TAAATAAAAATAAT-TTTATAATTAAAAT
**
3097679 TAAATAAAAATAATTTTATTTTTAAAAT
1 TAAATAAAAATAATTTTATAATTAAAAT
3097707 TATAATA
1 TA-AATA
3097714 TAATTTAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
28 14 0.45
29 17 0.55
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (28 bp):
TAAATAAAAATAATTTTATAATTAAAAT
Found at i:3098310 original size:3 final size:3
Alignment explanation
Indices: 3098302--3098338 Score: 56
Period size: 3 Copynumber: 11.7 Consensus size: 3
3098292 CCATTTTTAT
3098302 TAA TAA TAA TAA TAA TAA TAA TAA TAGA TTAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA-A -TAA TAA TA
3098339 GGCAACATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
3 28 0.88
4 2 0.06
5 2 0.06
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:3100007 original size:2 final size:2
Alignment explanation
Indices: 3100000--3100031 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
3099990 ATGGTTAGTG
*
3100000 TA TA TA TA TA TA TA TA TG TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3100032 ATAGTGAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3100217 original size:3 final size:3
Alignment explanation
Indices: 3100209--3100235 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
3100199 GGTAGAATGA
3100209 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
3100236 CTTACACAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:3100646 original size:24 final size:22
Alignment explanation
Indices: 3100617--3100665 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 22
3100607 GCTGTGAAGG
* *
3100617 AAATGAAGAGAAAAAATAAAAGAA
1 AAATGAA-A-AAAAAAAAAAAAAA
3100641 AAATGAAAAAAAAAAAAAAAAA
1 AAATGAAAAAAAAAAAAAAAAA
3100663 AAA
1 AAA
3100666 GCTGGCGTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 15 0.65
23 1 0.04
24 7 0.30
ACGTcount: A:0.84, C:0.00, G:0.10, T:0.06
Consensus pattern (22 bp):
AAATGAAAAAAAAAAAAAAAAA
Found at i:3100661 original size:19 final size:19
Alignment explanation
Indices: 3100626--3100662 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
3100616 GAAATGAAGA
* *
3100626 GAAAAAATAAAAGAAAAAT
1 GAAAAAAAAAAAAAAAAAT
3100645 GAAAAAAAAAAAAAAAAA
1 GAAAAAAAAAAAAAAAAA
3100663 AAAGCTGGCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.86, C:0.00, G:0.08, T:0.05
Consensus pattern (19 bp):
GAAAAAAAAAAAAAAAAAT
Found at i:3100664 original size:11 final size:11
Alignment explanation
Indices: 3100627--3100665 Score: 53
Period size: 10 Copynumber: 3.5 Consensus size: 11
3100617 AAATGAAGAG
3100627 AAAAAATAAAA
1 AAAAAATAAAA
*
3100638 GAAAAATGAAAA
1 AAAAAAT-AAAA
3100650 AAAAAA-AAAA
1 AAAAAATAAAA
3100660 AAAAAA
1 AAAAAA
3100666 GCTGGCGTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
10 10 0.40
11 6 0.24
12 9 0.36
ACGTcount: A:0.90, C:0.00, G:0.05, T:0.05
Consensus pattern (11 bp):
AAAAAATAAAA
Found at i:3101842 original size:12 final size:12
Alignment explanation
Indices: 3101827--3101852 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3101817 TTTTTAAACC
3101827 TTTTTTTCTTTT
1 TTTTTTTCTTTT
3101839 TTTTTTTCTTTT
1 TTTTTTTCTTTT
3101851 TT
1 TT
3101853 CAAAGATTTC
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:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (12 bp):
TTTTTTTCTTTT
Found at i:3114554 original size:226 final size:226
Alignment explanation
Indices: 3114160--3114612 Score: 789
Period size: 226 Copynumber: 2.0 Consensus size: 226
3114150 GGCCGTACTG
* *
3114160 ATCCAAGAAAGACACGGCTGCTTTTCTACAGAAACTCCTCAAGAACTCTTTTCCTAGTTGTTGTA
1 ATCCAAGAAAGACACGGCTGCTTTTCTACAAAAACTCCTCAAAAACTCTTTTCCTAGTTGTTGTA
3114225 CACTGAACAGCTCATCGAATACATCATCATCTTCATCTATATCAGGATTTTAAATAACGATCGCG
66 CACTGAACAGCTCATCGAATACATCATCATCTTCATCTATATCAGGATTTTAAATAACGATCGCG
* * ** *
3114290 TCGCAGAATAATTATCGTTATTTTATGATATTAACCACTTTTATCATCCATATCAATTATTATTC
131 TCACAAAATAATTATCACTATGTTATGATATTAACCACTTTTATCATCCATATCAATTATTATTC
* *
3114355 ACATATGAATAAAGATTTACGTTAATAACAA
196 ACATATAAATAAAAATTTACGTTAATAACAA
3114386 ATCCAAGAAAGACACGGCTGCTTTTCTACAAAAACTCCTCAAAAACTCTTTTCCTAGTTGTTGTA
1 ATCCAAGAAAGACACGGCTGCTTTTCTACAAAAACTCCTCAAAAACTCTTTTCCTAGTTGTTGTA
* * *
3114451 CACTGAACAGCTCATCGAATACATCATCATCTTCATCTATATCAGGATTTTAAATACCGGTTGCG
66 CACTGAACAGCTCATCGAATACATCATCATCTTCATCTATATCAGGATTTTAAATAACGATCGCG
*
3114516 TCACAAAATAATTATCACTATGTTATGATATTAACCACTTTTATCATCGATATCAATTATTATTC
131 TCACAAAATAATTATCACTATGTTATGATATTAACCACTTTTATCATCCATATCAATTATTATTC
3114581 ACATATAAATAAAAATTTACGTTAATAACAA
196 ACATATAAATAAAAATTTACGTTAATAACAA
3114612 A
1 A
3114613 AGTTTACTGT
Statistics
Matches: 214, Mismatches: 13, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
226 214 1.00
ACGTcount: A:0.36, C:0.20, G:0.10, T:0.34
Consensus pattern (226 bp):
ATCCAAGAAAGACACGGCTGCTTTTCTACAAAAACTCCTCAAAAACTCTTTTCCTAGTTGTTGTA
CACTGAACAGCTCATCGAATACATCATCATCTTCATCTATATCAGGATTTTAAATAACGATCGCG
TCACAAAATAATTATCACTATGTTATGATATTAACCACTTTTATCATCCATATCAATTATTATTC
ACATATAAATAAAAATTTACGTTAATAACAA
Found at i:3116244 original size:25 final size:27
Alignment explanation
Indices: 3116203--3116276 Score: 80
Period size: 26 Copynumber: 2.7 Consensus size: 27
3116193 TTTATTTATT
*
3116203 TTTATAAAAAAATTATAAATAT-TAAA
1 TTTATTAAAAAATTATAAATATATAAA
**
3116229 TTTATTAAAAAA-TATATTTATATAAA
1 TTTATTAAAAAATTATAAATATATAAA
*
3116255 TTAATTAAATTAAATTATAAAT
1 TTTATTAAA--AAATTATAAAT
3116277 TTTATTATTA
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
25 7 0.18
26 23 0.61
28 3 0.08
29 5 0.13
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (27 bp):
TTTATTAAAAAATTATAAATATATAAA
Found at i:3116688 original size:21 final size:22
Alignment explanation
Indices: 3116621--3116696 Score: 70
Period size: 21 Copynumber: 3.5 Consensus size: 22
3116611 TTATAACATA
* * *
3116621 ATTTAAAATTTTTAATATTTTT
1 ATTTAAAATTTATAAAAATTTT
*
3116643 ATTT-AAATTTA-AATTAAA-TTA
1 ATTTAAAATTTATAA--AAATTTT
3116664 ATTT-AAATTTATAAAAATTTT
1 ATTTAAAATTTATAAAAATTTT
3116685 ATTTAAAATTTA
1 ATTTAAAATTTA
3116697 ATTTATATAA
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
20 5 0.11
21 25 0.57
22 14 0.32
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
ATTTAAAATTTATAAAAATTTT
Found at i:3116696 original size:11 final size:10
Alignment explanation
Indices: 3116640--3116701 Score: 52
Period size: 11 Copynumber: 5.8 Consensus size: 10
3116630 TTTTAATATT
3116640 TTTATTTAAA
1 TTTATTTAAA
*
3116650 TTTAAATTAAA
1 TTT-ATTTAAA
*
3116661 TTAATTTAAA
1 TTTATTTAAA
**
3116671 TTTATAAAAA
1 TTTATTTAAA
3116681 TTTTATTTAAAA
1 -TTTATTT-AAA
3116693 TTTAATTTA
1 TTT-ATTTA
3116702 TATAAATTAA
Statistics
Matches: 40, Mismatches: 8, Indels: 7
0.73 0.15 0.13
Matches are distributed among these distances:
10 16 0.40
11 17 0.43
12 7 0.17
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (10 bp):
TTTATTTAAA
Found at i:3116721 original size:27 final size:28
Alignment explanation
Indices: 3116640--3116726 Score: 79
Period size: 27 Copynumber: 3.1 Consensus size: 28
3116630 TTTTAATATT
*
3116640 TTTATTTAAATTTAAATTAAATTAATTTAAA
1 TTTATATAAATTTAAA-TAAA-TAATTT-AA
* * * *
3116671 TTTATAAAAATTTTATTTAA-AATTTAA
1 TTTATATAAATTTAAATAAATAATTTAA
*
3116698 TTTATATAAA-TTAAATAAATAATTCAA
1 TTTATATAAATTTAAATAAATAATTTAA
3116725 TT
1 TT
3116727 ATTCAACGAG
Statistics
Matches: 45, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
26 6 0.13
27 19 0.42
28 5 0.11
30 3 0.07
31 12 0.27
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (28 bp):
TTTATATAAATTTAAATAAATAATTTAA
Found at i:3121812 original size:18 final size:17
Alignment explanation
Indices: 3121785--3121820 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
3121775 TAATATAAAT
*
3121785 TAAAATTGAATTGAAAA
1 TAAAATTGAATTAAAAA
3121802 TAAAATCTGAATTAAAAA
1 TAAAAT-TGAATTAAAAA
3121820 T
1 T
3121821 GAGATCATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.58, C:0.03, G:0.08, T:0.31
Consensus pattern (17 bp):
TAAAATTGAATTAAAAA
Found at i:3125343 original size:11 final size:11
Alignment explanation
Indices: 3125307--3125366 Score: 58
Period size: 10 Copynumber: 5.7 Consensus size: 11
3125297 AGTTAATAAT
3125307 TTATATTT-TA
1 TTATATTTATA
3125317 -TATATGTTA-A
1 TTATAT-TTATA
3125327 -TATATTTATA
1 TTATATTTATA
*
3125337 TTATATTTATT
1 TTATATTTATA
3125348 TTATA-TTATA
1 TTATATTTATA
3125358 TTATTATTT
1 TTA-TATTT
3125367 TTTAATTATA
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
9 8 0.19
10 16 0.38
11 16 0.38
12 2 0.05
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (11 bp):
TTATATTTATA
Found at i:3125350 original size:16 final size:16
Alignment explanation
Indices: 3125331--3125379 Score: 62
Period size: 16 Copynumber: 2.9 Consensus size: 16
3125321 TGTTAATATA
3125331 TTTATATTATATTTAT
1 TTTATATTATATTTAT
3125347 TTTATATTATATTATTAT
1 TTTATATTATA-T-TTAT
*
3125365 TTTTTAATTATATTT
1 TTTAT-ATTATATTT
3125380 TCATATTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
16 11 0.38
17 3 0.10
18 9 0.31
19 6 0.21
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
TTTATATTATATTTAT
Found at i:3125368 original size:19 final size:19
Alignment explanation
Indices: 3125307--3125405 Score: 68
Period size: 19 Copynumber: 5.3 Consensus size: 19
3125297 AGTTAATAAT
*
3125307 TTATATTTTATA-TATGTTA
1 TTAT-TTTTATATTATATTA
* *
3125326 ATATATTTATATTATA-T-
1 TTATTTTTATATTATATTA
3125343 TTA-TTTTATATTATATTA
1 TTATTTTTATATTATATTA
3125361 TTATTTTT-TAATTATATT-
1 TTATTTTTAT-ATTATATTA
*
3125379 TTCATATTTTATAATCATATTA
1 TT-AT-TTTTAT-ATTATATTA
3125401 -TATTT
1 TTATTT
3125406 AAAATTATTA
Statistics
Matches: 65, Mismatches: 6, Indels: 18
0.73 0.07 0.20
Matches are distributed among these distances:
16 11 0.17
17 3 0.05
18 13 0.20
19 22 0.34
20 6 0.09
21 10 0.15
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64
Consensus pattern (19 bp):
TTATTTTTATATTATATTA
Found at i:3125388 original size:21 final size:19
Alignment explanation
Indices: 3125332--3125405 Score: 64
Period size: 21 Copynumber: 3.7 Consensus size: 19
3125322 GTTAATATAT
3125332 TTATATTA-TATTTATTTTATA
1 TTATATTATTA-TT-TTTTA-A
3125353 TTATATTATTATTTTTTAA
1 TTATATTATTATTTTTTAA
3125372 TTATATT-TTCATATTTTATAA
1 TTATATTATT-AT-TTTT-TAA
*
3125393 TCATATTA-TATTT
1 TTATATTATTATTT
3125406 AAAATTATTA
Statistics
Matches: 47, Mismatches: 1, Indels: 12
0.78 0.02 0.20
Matches are distributed among these distances:
18 2 0.04
19 12 0.26
20 11 0.23
21 20 0.43
22 2 0.04
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (19 bp):
TTATATTATTATTTTTTAA
Found at i:3127529 original size:68 final size:68
Alignment explanation
Indices: 3127420--3127556 Score: 256
Period size: 68 Copynumber: 2.0 Consensus size: 68
3127410 AATTCCGGAT
3127420 GTTCAAGTTTAGATCAGCCTTATCAGATACTGAACCAGACTTAAAGCTCAGCTCACATGGAAGAT
1 GTTCAAGTTTAGATCAGCCTTATCAGATACTGAACCAGACTTAAAGCTCAGCTCACATGGAAGAT
3127485 AAA
66 AAA
* *
3127488 GTTCAAGTTTAGATCAGCGTTATCAGATACTGAACCAGACTTAAAGCTCAGCTCCCATGGAAGAT
1 GTTCAAGTTTAGATCAGCCTTATCAGATACTGAACCAGACTTAAAGCTCAGCTCACATGGAAGAT
3127553 AAA
66 AAA
3127556 G
1 G
3127557 CTATAAAAGT
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
68 67 1.00
ACGTcount: A:0.36, C:0.20, G:0.19, T:0.25
Consensus pattern (68 bp):
GTTCAAGTTTAGATCAGCCTTATCAGATACTGAACCAGACTTAAAGCTCAGCTCACATGGAAGAT
AAA
Found at i:3129636 original size:30 final size:32
Alignment explanation
Indices: 3129587--3129654 Score: 88
Period size: 30 Copynumber: 2.2 Consensus size: 32
3129577 GTCGAGAAAT
*
3129587 AATATTAATTATAATTATAAAAAT-TAATTAAA
1 AATATTAATTATAAATATAAAAATATAA-TAAA
3129619 AATATT-A-TATAAATATAAAAATATAATAAA
1 AATATTAATTATAAATATAAAAATATAATAAA
3129649 ATATAT
1 A-ATAT
3129655 GAATACTGAG
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
30 19 0.58
31 8 0.24
32 6 0.18
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (32 bp):
AATATTAATTATAAATATAAAAATATAATAAA
Found at i:3129659 original size:18 final size:19
Alignment explanation
Indices: 3129615--3129653 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
3129605 AAAAATTAAT
*
3129615 TAAAAATATTATATAAATA
1 TAAAAATATAATATAAATA
3129634 TAAAAATATAATA-AAATA
1 TAAAAATATAATATAAATA
3129652 TA
1 TA
3129654 TGAATACTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
TAAAAATATAATATAAATA
Found at i:3130163 original size:15 final size:14
Alignment explanation
Indices: 3130140--3130169 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
3130130 AGTAATTAAC
3130140 TTAAATTAATTTGA
1 TTAAATTAATTTGA
3130154 TTAAATTTAATTTGA
1 TTAAA-TTAATTTGA
3130169 T
1 T
3130170 GTACTTAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (14 bp):
TTAAATTAATTTGA
Found at i:3130368 original size:24 final size:23
Alignment explanation
Indices: 3130326--3130376 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
3130316 ATTATTGATA
3130326 TTAT-TAAATATTAAAATATAATT
1 TTATATAAATATTAAAATAT-ATT
* * *
3130349 TTATATAAATATTTATATATTTT
1 TTATATAAATATTAAAATATATT
3130372 TTATA
1 TTATA
3130377 ATTAAAATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 11 0.46
24 13 0.54
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
TTATATAAATATTAAAATATATT
Found at i:3130427 original size:20 final size:18
Alignment explanation
Indices: 3130396--3130448 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 18
3130386 AAATAAACAT
3130396 ATTAATTT--ATTTTTAA
1 ATTAATTTAAATTTTTAA
3130412 ATAATAATTTAAATTTAATTAA
1 AT--TAATTTAAATTT--TTAA
3130434 ATTAATTTAAATTTT
1 ATTAATTTAAATTTT
3130449 CATAAAAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
16 2 0.06
18 7 0.23
20 16 0.52
22 6 0.19
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
ATTAATTTAAATTTTTAA
Found at i:3130435 original size:10 final size:11
Alignment explanation
Indices: 3130416--3130447 Score: 50
Period size: 10 Copynumber: 3.1 Consensus size: 11
3130406 TTTTAAATAA
3130416 TAATTTAAATT
1 TAATTTAAATT
3130427 TAA-TTAAA-T
1 TAATTTAAATT
3130436 TAATTTAAATT
1 TAATTTAAATT
3130447 T
1 T
3130448 TCATAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
9 4 0.21
10 10 0.53
11 5 0.26
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
TAATTTAAATT
Found at i:3131028 original size:28 final size:27
Alignment explanation
Indices: 3130987--3131052 Score: 91
Period size: 27 Copynumber: 2.4 Consensus size: 27
3130977 AAAAAAACAA
3130987 TTAAAATATAAT-AAATATATAAATATT
1 TTAAAATATAATAAAATATAT-AATATT
*
3131014 TTAAAATTTATATAAAATATATAATATT
1 TTAAAATATA-ATAAAATATATAATATT
3131042 TT-AAATATAAT
1 TTAAAATATAAT
3131053 TATGAGATAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
26 2 0.06
27 15 0.43
28 10 0.29
29 8 0.23
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (27 bp):
TTAAAATATAATAAAATATATAATATT
Found at i:3131864 original size:18 final size:19
Alignment explanation
Indices: 3131843--3131887 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
3131833 AGTCAATAAA
*
3131843 TTTTATTAATTGAAT-ATT
1 TTTTATTAATTCAATAATT
3131861 TTTTATTAATTCAATAAATT
1 TTTTATTAATTCAAT-AATT
3131881 TTTTATT
1 TTTTATT
3131888 TTAAATTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 14 0.58
20 10 0.42
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (19 bp):
TTTTATTAATTCAATAATT
Found at i:3133359 original size:30 final size:30
Alignment explanation
Indices: 3133323--3133402 Score: 99
Period size: 30 Copynumber: 2.7 Consensus size: 30
3133313 ACTAAGATAA
* *
3133323 TTTTAATTTTTAATTTATATTCAAATATAC
1 TTTTAATTATTAATTTATATTCAAATAAAC
* *
3133353 TTTTAATTATTAATTTATATTTAAATAAAT
1 TTTTAATTATTAATTTATATTCAAATAAAC
* *
3133383 TTTTAA-TATAAATTAATATT
1 TTTTAATTATTAATTTATATT
3133403 TTATTAAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 12 0.27
30 32 0.73
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (30 bp):
TTTTAATTATTAATTTATATTCAAATAAAC
Found at i:3133387 original size:18 final size:19
Alignment explanation
Indices: 3133366--3133415 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 19
3133356 TAATTATTAA
*
3133366 TTTATATTTAAATAAAT-T
1 TTTATATATAAATAAATAT
*
3133384 TTTA-ATATAAATTAATAT
1 TTTATATATAAATAAATAT
*
3133402 TTTAT-TAAAAATAA
1 TTTATATATAAATAA
3133416 GAATTTATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
17 10 0.38
18 16 0.62
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TTTATATATAAATAAATAT
Found at i:3134671 original size:6 final size:7
Alignment explanation
Indices: 3134655--3134685 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
3134645 TATTATTTTT
3134655 AATTAAA
1 AATTAAA
3134662 AATT-AA
1 AATTAAA
3134668 AATTAAA
1 AATTAAA
3134675 AATTAAA
1 AATTAAA
3134682 AATT
1 AATT
3134686 TAAAGACATG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (7 bp):
AATTAAA
Found at i:3134673 original size:13 final size:13
Alignment explanation
Indices: 3134655--3134682 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3134645 TATTATTTTT
3134655 AATTAAAAATTAA
1 AATTAAAAATTAA
3134668 AATTAAAAATTAA
1 AATTAAAAATTAA
3134681 AA
1 AA
3134683 ATTTAAAGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (13 bp):
AATTAAAAATTAA
Found at i:3134782 original size:20 final size:19
Alignment explanation
Indices: 3134712--3134783 Score: 56
Period size: 20 Copynumber: 3.6 Consensus size: 19
3134702 ACTCAAAATT
*
3134712 TTTTAATTATTTTTTACTATA
1 TTTTAATTATTTTTTA--AAA
* * *
3134733 TTATAATTATATTTAAAACA
1 TTTTAATTATTTTTTAAA-A
3134753 TTTT-ATATATTTTTTAAAA
1 TTTTAAT-TATTTTTTAAAA
3134772 TTTTAATATATT
1 TTTTAAT-TATT
3134784 AATAATTTAT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
19 8 0.20
20 20 0.49
21 13 0.32
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (19 bp):
TTTTAATTATTTTTTAAAA
Found at i:3134813 original size:12 final size:12
Alignment explanation
Indices: 3134788--3134840 Score: 61
Period size: 12 Copynumber: 4.2 Consensus size: 12
3134778 TATATTAATA
3134788 ATTTATATTATAT
1 ATTTATA-TATAT
*
3134801 ATTTTTATATAT
1 ATTTATATATAT
*
3134813 ATTTATATATTT
1 ATTTATATATAT
*
3134825 ATATTATATTTAT
1 AT-TTATATATAT
3134838 ATT
1 ATT
3134841 AATTTTTTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
12 18 0.53
13 16 0.47
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
ATTTATATATAT
Found at i:3134821 original size:40 final size:46
Alignment explanation
Indices: 3134755--3134852 Score: 117
Period size: 40 Copynumber: 2.3 Consensus size: 46
3134745 TTAAAACATT
3134755 TTATATATTTTT-TA-AAATTTTAATATA-TTA-A-TA-ATTTATA
1 TTATATATTTTTATATAAATTTTAATATATTTATATTATATTTATA
*
3134795 TTATATATTTTTATATATA-TTT-ATATATTTATATTATATTTATA
1 TTATATATTTTTATATAAATTTTAATATATTTATATTATATTTATA
3134839 TTA-AT-TTTTTATAT
1 TTATATATTTTTATAT
3134853 TTAATGTGAT
Statistics
Matches: 51, Mismatches: 1, Indels: 10
0.82 0.02 0.16
Matches are distributed among these distances:
40 17 0.33
41 8 0.16
42 12 0.24
43 4 0.08
44 10 0.20
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (46 bp):
TTATATATTTTTATATAAATTTTAATATATTTATATTATATTTATA
Found at i:3134825 original size:33 final size:31
Alignment explanation
Indices: 3134772--3134833 Score: 97
Period size: 33 Copynumber: 1.9 Consensus size: 31
3134762 TTTTTTAAAA
3134772 TTTTAATATATTAATAATTTATATTATATAT
1 TTTTAATATATTAATAATTTATATTATATAT
*
3134803 TTTTATATATATTTATATATTTATATTATAT
1 TTTTA-ATATATTAATA-ATTTATATTATAT
3134834 TTATATTAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
31 5 0.18
32 10 0.36
33 13 0.46
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (31 bp):
TTTTAATATATTAATAATTTATATTATATAT
Found at i:3134850 original size:19 final size:19
Alignment explanation
Indices: 3134778--3134855 Score: 81
Period size: 19 Copynumber: 4.1 Consensus size: 19
3134768 AAAATTTTAA
* *
3134778 TATATTAATAATTTATATT
1 TATATTATTTATTTATATT
*
3134797 ATATATT-TTTATATATATT
1 -TATATTATTTATTTATATT
3134816 TATA-TATTTATATTATATT
1 TATATTATTTAT-TTATATT
3134835 TATATTAATTT-TTTATATT
1 TATATT-ATTTATTTATATT
3134854 TA
1 TA
3134856 ATGTGATATG
Statistics
Matches: 50, Mismatches: 4, Indels: 9
0.79 0.06 0.14
Matches are distributed among these distances:
17 1 0.02
18 9 0.18
19 28 0.56
20 8 0.16
21 4 0.08
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
TATATTATTTATTTATATT
Found at i:3138548 original size:15 final size:15
Alignment explanation
Indices: 3138528--3138557 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3138518 AACATCGAAT
*
3138528 ATATATCATATATAA
1 ATATATCACATATAA
3138543 ATATATCACATATAA
1 ATATATCACATATAA
3138558 TTTAATAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.53, C:0.10, G:0.00, T:0.37
Consensus pattern (15 bp):
ATATATCACATATAA
Found at i:3140131 original size:38 final size:38
Alignment explanation
Indices: 3140089--3140162 Score: 139
Period size: 38 Copynumber: 1.9 Consensus size: 38
3140079 TTTTACAAGA
3140089 TAGAACTCAAATGCAATGATCATCGTCAATTTTCCATT
1 TAGAACTCAAATGCAATGATCATCGTCAATTTTCCATT
*
3140127 TAGAACTCAAATGCGATGATCATCGTCAATTTTCCA
1 TAGAACTCAAATGCAATGATCATCGTCAATTTTCCA
3140163 CTTACCTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.34, C:0.22, G:0.12, T:0.32
Consensus pattern (38 bp):
TAGAACTCAAATGCAATGATCATCGTCAATTTTCCATT
Found at i:3143532 original size:26 final size:26
Alignment explanation
Indices: 3143497--3143565 Score: 70
Period size: 26 Copynumber: 2.6 Consensus size: 26
3143487 ATGATTTGAA
*
3143497 TTAATTTAATTAA-AATTATTATTTAT
1 TTAATATAA-TAATAATTATTATTTAT
*
3143523 TTAATATAATAATAATTTTTATTTAAAT
1 TTAATATAATAATAATTATTATTT--AT
3143551 TTAATTATAA-AATAA
1 TTAA-TATAATAATAA
3143566 AATATTAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
25 3 0.08
26 18 0.49
28 11 0.30
29 5 0.14
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (26 bp):
TTAATATAATAATAATTATTATTTAT
Found at i:3143546 original size:22 final size:21
Alignment explanation
Indices: 3143500--3143548 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
3143490 ATTTGAATTA
*
3143500 ATTTAATTAAAATTATTATTT
1 ATTTAATTAAAATAATTATTT
3143521 ATTTAATATAATAATAATT-TTT
1 ATTTAAT-TAA-AATAATTATTT
3143543 ATTTAA
1 ATTTAA
3143549 ATTTAATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 7 0.28
22 12 0.48
23 6 0.24
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
ATTTAATTAAAATAATTATTT
Found at i:3144578 original size:14 final size:14
Alignment explanation
Indices: 3144559--3144594 Score: 65
Period size: 13 Copynumber: 2.6 Consensus size: 14
3144549 TATTTTTGAA
3144559 AAAAAATAATTTTT
1 AAAAAATAATTTTT
3144573 AAAAAAT-ATTTTT
1 AAAAAATAATTTTT
3144586 AAAAAATAA
1 AAAAAATAA
3144595 ATATAAACTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 13 0.62
14 8 0.38
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
AAAAAATAATTTTT
Found at i:3145147 original size:23 final size:23
Alignment explanation
Indices: 3145119--3145191 Score: 71
Period size: 23 Copynumber: 3.2 Consensus size: 23
3145109 TTGAATTATT
*
3145119 ATTTAATAAAAAAATTTATTTAA
1 ATTTAATTAAAAAATTTATTTAA
* *
3145142 ATTTAATTATAAAA--TATATAA
1 ATTTAATTAAAAAATTTATTTAA
3145163 ATATTAATCTAAAAAATATT-TTTAA
1 AT-TTAAT-TAAAAAAT-TTATTTAA
3145188 ATTT
1 ATTT
3145192 TTATTAATTT
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
21 8 0.20
22 5 0.12
23 18 0.45
24 2 0.05
25 6 0.15
26 1 0.03
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.45
Consensus pattern (23 bp):
ATTTAATTAAAAAATTTATTTAA
Found at i:3145221 original size:16 final size:17
Alignment explanation
Indices: 3145202--3145240 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
3145192 TTATTAATTT
*
3145202 ATAAAT-AATAATTTAA
1 ATAAATAAAAAATTTAA
3145218 ATAAATAAAAAATTTAA
1 ATAAATAAAAAATTTAA
*
3145235 AAAAAT
1 ATAAAT
3145241 TTCAAATCGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
ATAAATAAAAAATTTAA
Found at i:3145615 original size:2 final size:2
Alignment explanation
Indices: 3145599--3145649 Score: 79
Period size: 2 Copynumber: 26.5 Consensus size: 2
3145589 ATTCTTGTGT
*
3145599 TA TA CA TA T- TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3145639 TA TA TA TA TA T
1 TA TA TA TA TA T
3145650 GCAAACACTT
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
1 2 0.04
2 43 0.96
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:3146815 original size:3 final size:3
Alignment explanation
Indices: 3146809--3146837 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
3146799 ACAACAACGC
3146809 CTG CTG CTG CTG CTG CTG CTG CTG CTG CT
1 CTG CTG CTG CTG CTG CTG CTG CTG CTG CT
3146838 TCAGATTTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.34, G:0.31, T:0.34
Consensus pattern (3 bp):
CTG
Found at i:3148214 original size:23 final size:23
Alignment explanation
Indices: 3148184--3148238 Score: 101
Period size: 23 Copynumber: 2.4 Consensus size: 23
3148174 AATAGCTTTA
3148184 ACATGAAACCTGGGTTTCAAGGT
1 ACATGAAACCTGGGTTTCAAGGT
3148207 ACATGAAACCTGGGTTTCAAGGT
1 ACATGAAACCTGGGTTTCAAGGT
*
3148230 ACAAGAAAC
1 ACATGAAAC
3148239 TAGAAGAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.36, C:0.18, G:0.24, T:0.22
Consensus pattern (23 bp):
ACATGAAACCTGGGTTTCAAGGT
Found at i:3161161 original size:3 final size:3
Alignment explanation
Indices: 3161153--3161195 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
3161143 GAAAGTTAAA
*
3161153 AAT AAT AAT AAC AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
3161196 GCATTCTATA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:3165291 original size:101 final size:102
Alignment explanation
Indices: 3165025--3165439 Score: 324
Period size: 100 Copynumber: 4.1 Consensus size: 102
3165015 TTGCTACATA
** * * ** * ** *
3165025 CATGCTTTGATAAGCTGAACCTACAAGATCCAGTGC-AATTGAGCCTGTATTGTA-AGATGTATT
1 CATGCTTTGATTTGCTCAACCTACCAGATCCAGTGCAAACAGAACCTGTATTACATA-ATGCATT
* ** *
3165088 CCGATCTGGTAGAGGCCTTGTAAGCTTTTCC-TAT-AG
65 CCAATCTGGTAGAGGAATTGTGAGCTTTTCCTTATAAG
* ** * * * * * * * * *
3165124 AATGCTTTGATTCACTGATACCTGCCAGATCTAGTGC-AACTGTATCTGCATTGCATGATGCATT
1 CATGCTTTGATTTGCTCA-ACCTACCAGATCCAGTGCAAACAGAACCTGTATTACATAATGCATT
** * *
3165188 CCACCCTCGTAGAGGCATTGTGAGCTTTTCCTTATAAG
65 CCAATCTGGTAGAGGAATTGTGAGCTTTTCCTTATAAG
* * *
3165226 CATGCTTTGATTTGC-CAAGCCTACCTGATCCAGTGC-AACAGAGCCTGTATTATATAATGCATT
1 CATGCTTTGATTTGCTCAA-CCTACCAGATCCAGTGCAAACAGAACCTGTATTACATAATGCATT
* * ** * * * *
3165289 CCAATCTGGTACACGTTTTGCGA-CCTTTGCTTATAAA
65 CCAATCTGGTAGAGGAATTGTGAGCTTTTCCTTATAAG
* * *
3165326 CATGCTTTGATTTGCTGAACCTACCAGATCCAGTGCAAACAGAACCTGTATTGCATAATGCGTTC
1 CATGCTTTGATTTGCTCAACCTACCAGATCCAGTGCAAACAGAACCTGTATTACATAATGCATTC
* *
3165391 CAATCTGGCAGAGGAATTGTGAGCTTTTCCTTATGAG
66 CAATCTGGTAGAGGAATTGTGAGCTTTTCCTTATAAG
*
3165428 CATGCATTGATT
1 CATGCTTTGATT
3165440 CGCTGTGTCG
Statistics
Matches: 244, Mismatches: 64, Indels: 13
0.76 0.20 0.04
Matches are distributed among these distances:
99 14 0.06
100 101 0.41
101 94 0.39
102 35 0.14
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.33
Consensus pattern (102 bp):
CATGCTTTGATTTGCTCAACCTACCAGATCCAGTGCAAACAGAACCTGTATTACATAATGCATTC
CAATCTGGTAGAGGAATTGTGAGCTTTTCCTTATAAG
Found at i:3166311 original size:159 final size:159
Alignment explanation
Indices: 3166022--3166336 Score: 558
Period size: 159 Copynumber: 2.0 Consensus size: 159
3166012 TCCCTCATCT
***
3166022 TACTGCACAAATTCAAGTCCTCGGTCTCCAAAAAATAGCAATCTTTGATCATGGAAGATGCAATT
1 TACTGCACAAATTCAAGTCCTCGGTCTCCAAAAAATAGCAATCTCCAATCATGGAAGATGCAATT
* *
3166087 CCTCTCCACATAGAAGTATCCTCTGTTCTTTATATCTAAAGAGAGATAAAAAACCAGATTCTTAT
66 CCCCTCCACATAGAAGTATCCTCTGTTCTTCATATCTAAAGAGAGATAAAAAACCAGATTCTTAT
*
3166152 GGTCATACTGAAATAATAGGAGCAAGTCC
131 GGTCATACCGAAATAATAGGAGCAAGTCC
*
3166181 TACTGCACAAATTCAAGTCCTCGGTCTCCAAAAAATAGCAATCTCCAATCGTGGAAGATGCAATT
1 TACTGCACAAATTCAAGTCCTCGGTCTCCAAAAAATAGCAATCTCCAATCATGGAAGATGCAATT
*
3166246 CCCCTCCACATAGAAGTATCCTCTGTTCTTCATATCTAAAGAGAGATGAAAAACCAGATTCTTAT
66 CCCCTCCACATAGAAGTATCCTCTGTTCTTCATATCTAAAGAGAGATAAAAAACCAGATTCTTAT
3166311 GGTCATACCGAAATAATAGGAGCAAG
131 GGTCATACCGAAATAATAGGAGCAAG
3166337 ACCTCAACAA
Statistics
Matches: 148, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
159 148 1.00
ACGTcount: A:0.36, C:0.22, G:0.16, T:0.27
Consensus pattern (159 bp):
TACTGCACAAATTCAAGTCCTCGGTCTCCAAAAAATAGCAATCTCCAATCATGGAAGATGCAATT
CCCCTCCACATAGAAGTATCCTCTGTTCTTCATATCTAAAGAGAGATAAAAAACCAGATTCTTAT
GGTCATACCGAAATAATAGGAGCAAGTCC
Found at i:3170973 original size:2 final size:2
Alignment explanation
Indices: 3170966--3171009 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
3170956 ACAACTGGTA
3170966 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
3171008 AG
1 AG
3171010 TACCCAGTAG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3171518 original size:18 final size:18
Alignment explanation
Indices: 3171485--3171519 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3171475 CACCTGGACT
*
3171485 TGACGACGATGGTGGTTC
1 TGACGACGAAGGTGGTTC
*
3171503 TGACGACGAAGTTGGTT
1 TGACGACGAAGGTGGTT
3171520 TCCTGCGAGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.20, C:0.14, G:0.37, T:0.29
Consensus pattern (18 bp):
TGACGACGAAGGTGGTTC
Found at i:3172115 original size:15 final size:15
Alignment explanation
Indices: 3172054--3172114 Score: 58
Period size: 15 Copynumber: 4.2 Consensus size: 15
3172044 AAAGTTCATC
3172054 TTTA-TTAAATTAAAT
1 TTTATTTAAATT-AAT
* *
3172069 TTTAATAAAATT--T
1 TTTATTTAAATTAAT
3172082 TATTATTTAAATTAAT
1 T-TTATTTAAATTAAT
3172098 TTTATTTAAATT-AT
1 TTTATTTAAATTAAT
3172112 TTT
1 TTT
3172115 TTACCTAATT
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
13 2 0.05
14 14 0.36
15 15 0.38
16 8 0.21
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TTTATTTAAATTAAT
Found at i:3172584 original size:17 final size:17
Alignment explanation
Indices: 3172543--3172599 Score: 53
Period size: 17 Copynumber: 3.3 Consensus size: 17
3172533 ATTATTAAAT
*
3172543 ATAATAAATATTTAATA
1 ATAATACATATTTAATA
*
3172560 A-AATTACATATTTAGTA
1 ATAA-TACATATTTAATA
*
3172577 ATAATACAATTTTTAATA
1 ATAATAC-ATATTTAATA
*
3172595 TTAAT
1 ATAAT
3172600 CTGATTAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
16 2 0.06
17 16 0.50
18 14 0.44
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.44
Consensus pattern (17 bp):
ATAATACATATTTAATA
Found at i:3174543 original size:16 final size:16
Alignment explanation
Indices: 3174519--3174550 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3174509 TTTTTATTTA
3174519 ATTTCATCATTAACGT
1 ATTTCATCATTAACGT
*
3174535 ATTTTATCATTAACGT
1 ATTTCATCATTAACGT
3174551 CAGTAAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.31, C:0.16, G:0.06, T:0.47
Consensus pattern (16 bp):
ATTTCATCATTAACGT
Found at i:3184584 original size:30 final size:29
Alignment explanation
Indices: 3184529--3184587 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
3184519 ATAATATTTT
* * *
3184529 AAATATTTTAAAAATTAGATATTAAATAA
1 AAATATTTTAAAAAATAAAAATTAAATAA
3184558 AAATATTTTAAAAAATAAAAATTTAAATAA
1 AAATATTTTAAAAAATAAAAA-TTAAATAA
3184588 TATAGGTATA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 18 0.69
30 8 0.31
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.36
Consensus pattern (29 bp):
AAATATTTTAAAAAATAAAAATTAAATAA
Found at i:3186209 original size:17 final size:17
Alignment explanation
Indices: 3186187--3186242 Score: 59
Period size: 16 Copynumber: 3.5 Consensus size: 17
3186177 ATATATAAAT
3186187 ATATAAAAATTTATATA
1 ATATAAAAATTTATATA
3186204 ATAT--AAA-TTAT-TA
1 ATATAAAAATTTATATA
*
3186217 ATGATTAAAATTTATATA
1 AT-ATAAAAATTTATATA
3186235 A-ATAAAAA
1 ATATAAAAA
3186243 ATTTTAAAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 11
0.73 0.02 0.24
Matches are distributed among these distances:
13 4 0.12
14 6 0.18
15 3 0.09
16 9 0.27
17 8 0.24
18 3 0.09
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (17 bp):
ATATAAAAATTTATATA
Found at i:3186862 original size:2 final size:2
Alignment explanation
Indices: 3186855--3186879 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3186845 GAATACTTAT
3186855 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
3186880 GTTTTATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3187339 original size:16 final size:15
Alignment explanation
Indices: 3187299--3187346 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
3187289 AATATAAATA
3187299 TAAATTTTAATATAT
1 TAAATTTTAATATAT
*
3187314 T-AATTATTTATATTATT
1 TAAATT-TTAATA-TA-T
3187331 TAAATTTTAATATAT
1 TAAATTTTAATATAT
3187346 T
1 T
3187347 TTACATATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
14 4 0.15
15 8 0.30
16 4 0.15
17 7 0.26
18 4 0.15
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TAAATTTTAATATAT
Found at i:3187347 original size:16 final size:16
Alignment explanation
Indices: 3187299--3187347 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
3187289 AATATAAATA
3187299 TAAATTTTAATATA-T
1 TAAATTTTAATATATT
*
3187314 T-AATTATTTATATTATT
1 TAAATT-TTAATA-TATT
3187331 TAAATTTTAATATATT
1 TAAATTTTAATATATT
3187347 T
1 T
3187348 TACATATAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
14 4 0.14
15 6 0.21
16 7 0.25
17 7 0.25
18 4 0.14
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TAAATTTTAATATATT
Found at i:3188756 original size:38 final size:38
Alignment explanation
Indices: 3188714--3188803 Score: 87
Period size: 39 Copynumber: 2.4 Consensus size: 38
3188704 TCATAATAAA
3188714 ATTTTTAATTTTATAAATAAATTAAAAAT-TTATTA-T
1 ATTTTTAATTTTATAAATAAATTAAAAATCTTATTATT
* * * * *
3188750 ATATTTTATTTTTTAATTAATATATTAAAATTCTTGTTATT
1 AT-TTTTA-ATTTT-ATAAATAAATTAAAAATCTTATTATT
3188791 -TTTTTAATTTTAT
1 ATTTTTAATTTTAT
3188804 TTATAAAATT
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
36 2 0.05
37 7 0.16
38 8 0.19
39 19 0.44
40 6 0.14
41 1 0.02
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.60
Consensus pattern (38 bp):
ATTTTTAATTTTATAAATAAATTAAAAATCTTATTATT
Found at i:3189124 original size:18 final size:18
Alignment explanation
Indices: 3189096--3189131 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
3189086 TTTATATATA
3189096 TTTATTAAATAAT-AATT
1 TTTATTAAATAATGAATT
3189113 TTTATGTAAATAATGAATT
1 TTTAT-TAAATAATGAATT
3189132 AATTTATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.29
18 8 0.47
19 4 0.24
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (18 bp):
TTTATTAAATAATGAATT
Found at i:3189829 original size:24 final size:24
Alignment explanation
Indices: 3189801--3189850 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
3189791 AAAATGTTTT
* * *
3189801 AATTAAATTAATTTTTTATTAATA
1 AATTAAATAAATTTATTAATAATA
3189825 AATTAAATAAATTTATTAATAATA
1 AATTAAATAAATTTATTAATAATA
3189849 AA
1 AA
3189851 AAAATAATGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
AATTAAATAAATTTATTAATAATA
Found at i:3191195 original size:22 final size:22
Alignment explanation
Indices: 3191166--3191215 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
3191156 TCATTAAAAA
*
3191166 ATTAAAAATAAATATAAATAATT
1 ATTAAAAATAAAAATAAA-AATT
3191189 -TTAAAAATAAAAATAAAAATT
1 ATTAAAAATAAAAATAAAAATT
3191210 ATTAAA
1 ATTAAA
3191216 TGATTGGTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 4 0.16
22 21 0.84
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (22 bp):
ATTAAAAATAAAAATAAAAATT
Found at i:3192704 original size:15 final size:15
Alignment explanation
Indices: 3192684--3192721 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
3192674 TTCTCAATTC
3192684 TCCTTTCTTTATC-TT
1 TCCTTTCTTT-TCGTT
*
3192699 TCCTTTCCTTTCGTT
1 TCCTTTCTTTTCGTT
3192714 TCCTTTCT
1 TCCTTTCT
3192722 ATCTCTATCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 2 0.10
15 18 0.90
ACGTcount: A:0.03, C:0.32, G:0.03, T:0.63
Consensus pattern (15 bp):
TCCTTTCTTTTCGTT
Found at i:3192808 original size:77 final size:77
Alignment explanation
Indices: 3192721--3192874 Score: 263
Period size: 77 Copynumber: 2.0 Consensus size: 77
3192711 GTTTCCTTTC
*
3192721 TATCTCTATCTTTACCTCTCATTCTTCATCTGTCTCATAAATAATCTCCAGAGTAGCCGAATACG
1 TATCTCTATCTTTACCTCTCATTCTTCATCGGTCTCATAAATAATCTCCAGAGTAGCCGAATACG
*
3192786 ATACTCTCTATT
66 ATACTCGCTATT
* * *
3192798 TATCTCTATCTTTATCTCTCATTCTTCATCGGTCTCATAAATGATCTCCAGAGTAGCTGAATACG
1 TATCTCTATCTTTACCTCTCATTCTTCATCGGTCTCATAAATAATCTCCAGAGTAGCCGAATACG
3192863 ATACTCGCTATT
66 ATACTCGCTATT
3192875 CGAAGATAAG
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
77 72 1.00
ACGTcount: A:0.25, C:0.26, G:0.10, T:0.39
Consensus pattern (77 bp):
TATCTCTATCTTTACCTCTCATTCTTCATCGGTCTCATAAATAATCTCCAGAGTAGCCGAATACG
ATACTCGCTATT
Found at i:3196107 original size:2 final size:2
Alignment explanation
Indices: 3196102--3196136 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
3196092 TGTACGTGTC
* *
3196102 TA TA TA TA CA TA CA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3196137 TGGAAATATT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:3198478 original size:5 final size:5
Alignment explanation
Indices: 3198449--3198489 Score: 50
Period size: 5 Copynumber: 8.6 Consensus size: 5
3198439 GTTCTAACGT
* *
3198449 CTCCC C-CCC C-CCC CCCCC CTCCC CTCCC CTCCC ATCCC CTC
1 CTCCC CTCCC CTCCC CTCCC CTCCC CTCCC CTCCC CTCCC CTC
3198490 TTAAACAATC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
4 8 0.25
5 24 0.75
ACGTcount: A:0.02, C:0.83, G:0.00, T:0.15
Consensus pattern (5 bp):
CTCCC
Found at i:3199333 original size:2 final size:2
Alignment explanation
Indices: 3199326--3199354 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3199316 TCAAAACGTG
3199326 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3199355 GATTAGACAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3202373 original size:15 final size:16
Alignment explanation
Indices: 3202348--3202381 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
3202338 TTGAACTAGC
3202348 TTTTCTTTTTTCTTCA
1 TTTTCTTTTTTCTTCA
*
3202364 TTTT-TTTTTTTTTCA
1 TTTTCTTTTTTCTTCA
3202379 TTT
1 TTT
3202382 CACAAAAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.06, C:0.12, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTTCTTTTTTCTTCA
Found at i:3205789 original size:21 final size:21
Alignment explanation
Indices: 3205765--3205804 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
3205755 ATTAAAATTT
3205765 TATTTTATT-TTAATATTTATA
1 TATTTTATTATTAA-ATTTATA
3205786 TATTTTATTATTAAATTTA
1 TATTTTATTATTAAATTTA
3205805 AAAATATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (21 bp):
TATTTTATTATTAAATTTATA
Found at i:3205832 original size:21 final size:19
Alignment explanation
Indices: 3205793--3205833 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
3205783 ATATATTTTA
*
3205793 TTATTAAATTTAAAAATAT
1 TTATTAAATTAAAAAATAT
3205812 TTATATAAATTAAATAAATAT
1 TTAT-TAAATTAAA-AAATAT
3205833 T
1 T
3205834 CGAGCTTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 4 0.21
20 8 0.42
21 7 0.37
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
TTATTAAATTAAAAAATAT
Found at i:3206150 original size:21 final size:21
Alignment explanation
Indices: 3206118--3206175 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
3206108 AAAGAGGGTC
**
3206118 ATAAAA-TTATCAAAAATGCT
1 ATAAAAGTTATCAAAAATAAT
*
3206138 ATAAAAGTTATCAAAACTAAT
1 ATAAAAGTTATCAAAAATAAT
*
3206159 ATAAAAGTTAGCAAAAA
1 ATAAAAGTTATCAAAAA
3206176 CATCATAGAA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 6 0.19
21 26 0.81
ACGTcount: A:0.59, C:0.09, G:0.07, T:0.26
Consensus pattern (21 bp):
ATAAAAGTTATCAAAAATAAT
Found at i:3207777 original size:25 final size:26
Alignment explanation
Indices: 3207734--3207790 Score: 73
Period size: 25 Copynumber: 2.2 Consensus size: 26
3207724 AATAAAAATT
3207734 ATAAATATAATTAATATTTATA-AAA
1 ATAAATATAATTAATATTTATACAAA
*
3207759 ATAAATAT-TTTAATCATTTATACAAA
1 ATAAATATAATTAAT-ATTTATACAAA
3207785 AGTAAA
1 A-TAAA
3207791 ACAAAAATAG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
24 5 0.18
25 15 0.54
26 4 0.14
27 4 0.14
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.39
Consensus pattern (26 bp):
ATAAATATAATTAATATTTATACAAA
Found at i:3207797 original size:38 final size:38
Alignment explanation
Indices: 3207755--3207842 Score: 104
Period size: 39 Copynumber: 2.3 Consensus size: 38
3207745 TAATATTTAT
*** *
3207755 AAAAATAAATATTTTAATCATTTATACAAAAGTAAAAC
1 AAAAATAAATAGGCTAAACATTTATACAAAAGTAAAAC
* *
3207793 AAAAATAGATTAGGCTAAACATTTATACAAAAGTAAAGC
1 AAAAATA-AATAGGCTAAACATTTATACAAAAGTAAAAC
*
3207832 GAAAATAAATA
1 AAAAATAAATA
3207843 AGTCGCCCCG
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
38 10 0.24
39 31 0.76
ACGTcount: A:0.58, C:0.08, G:0.08, T:0.26
Consensus pattern (38 bp):
AAAAATAAATAGGCTAAACATTTATACAAAAGTAAAAC
Found at i:3208381 original size:15 final size:15
Alignment explanation
Indices: 3208353--3208386 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
3208343 ATGTTTTTCA
3208353 AAATTTTTTATATAT
1 AAATTTTTTATATAT
3208368 AAATTATTTT-TATAT
1 AAATT-TTTTATATAT
3208383 AAAT
1 AAAT
3208387 AAAATTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
AAATTTTTTATATAT
Found at i:3210675 original size:17 final size:19
Alignment explanation
Indices: 3210655--3210703 Score: 61
Period size: 17 Copynumber: 2.7 Consensus size: 19
3210645 ATTAGAGTAG
3210655 ATTTAATTTAAATT-AA-T
1 ATTTAATTTAAATTAAAGT
3210672 ATTTAA-TT-AATTAAAGT
1 ATTTAATTTAAATTAAAGT
3210689 ATTTATATTTAAATT
1 ATTTA-ATTTAAATT
3210704 TAATTATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
15 4 0.15
16 4 0.15
17 12 0.44
18 1 0.04
19 2 0.07
20 4 0.15
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (19 bp):
ATTTAATTTAAATTAAAGT
Found at i:3210903 original size:2 final size:2
Alignment explanation
Indices: 3210896--3210925 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3210886 TAATCATAGA
3210896 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3210926 TTGACATTGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3216158 original size:17 final size:17
Alignment explanation
Indices: 3216138--3216171 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3216128 ATTATACTAA
3216138 TTTATCAAATATATATT
1 TTTATCAAATATATATT
* *
3216155 TTTATTAAATATTTATT
1 TTTATCAAATATATATT
3216172 ATATTTAATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (17 bp):
TTTATCAAATATATATT
Found at i:3216181 original size:16 final size:16
Alignment explanation
Indices: 3216157--3216187 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3216147 TATATATTTT
3216157 TATTAAATATTTATTA
1 TATTAAATATTTATTA
*
3216173 TATTTAATATTTATT
1 TATTAAATATTTATT
3216188 TAATATAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TATTAAATATTTATTA
Found at i:3217300 original size:23 final size:23
Alignment explanation
Indices: 3217274--3217318 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
3217264 GGGGCTTGTG
*
3217274 GACCCGG-GAAGGCAAGCAGCTTT
1 GACCCGGCG-AGGCAAACAGCTTT
*
3217297 GACCTGGCGAGGCAAACAGCTT
1 GACCCGGCGAGGCAAACAGCTT
3217319 GACAGGTCTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.27, C:0.27, G:0.33, T:0.13
Consensus pattern (23 bp):
GACCCGGCGAGGCAAACAGCTTT
Found at i:3220787 original size:3 final size:3
Alignment explanation
Indices: 3220779--3220818 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
3220769 TTTGAATAAC
3220779 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
3220819 CTATACATAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3220945 original size:37 final size:36
Alignment explanation
Indices: 3220904--3221007 Score: 96
Period size: 32 Copynumber: 2.9 Consensus size: 36
3220894 AGAAAGAAAA
3220904 AAAATTATATTTATATTTATATTATTTTTTTATATAT-
1 AAAATTATATTTATATTT-T-TTATTTTTTTATATATG
*
3220941 -AAA--ATA-TTATATTTTTGTATATTTTTATATATG
1 AAAATTATATTTATATTTTT-TATTTTTTTATATATG
3220974 AATAATT-TATTT-TATTTTTTATATATTTTTATAT
1 AA-AATTATATTTATATTTTTTAT-T-TTTTTATAT
3221008 GTATGTATAT
Statistics
Matches: 56, Mismatches: 2, Indels: 18
0.74 0.03 0.24
Matches are distributed among these distances:
31 1 0.02
32 15 0.27
33 8 0.14
34 4 0.07
35 5 0.09
36 12 0.21
37 11 0.20
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (36 bp):
AAAATTATATTTATATTTTTTATTTTTTTATATATG
Found at i:3221889 original size:4 final size:4
Alignment explanation
Indices: 3221880--3221941 Score: 53
Period size: 4 Copynumber: 16.8 Consensus size: 4
3221870 TTCTGTCAAT
* * * *
3221880 AAAG AAAG AAAA AAAG AAAG AAA- AAAG -GAG AAAA AAAG AAA- AAGG
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG
3221925 AAAG AAA- AAA- AAAG AAA
1 AAAG AAAG AAAG AAAG AAA
3221942 AAAATTATGT
Statistics
Matches: 46, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
3 13 0.28
4 33 0.72
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:3221911 original size:22 final size:20
Alignment explanation
Indices: 3221886--3221945 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 20
3221876 CAATAAAGAA
3221886 AGAAAAAAAGAAAGAAAAAAGG
1 AGAAAAAAAGAAA-AAAAAA-G
*
3221908 AGAAAAAAAGAAAAAGGAAAG
1 AGAAAAAAAGAAAAA-AAAAG
*
3221929 AAAAAAAAAGAAAAAAA
1 AGAAAAAAAGAAAAAAA
3221946 TTATGTATTC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
20 1 0.03
21 17 0.50
22 16 0.47
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (20 bp):
AGAAAAAAAGAAAAAAAAAG
Found at i:3221927 original size:29 final size:30
Alignment explanation
Indices: 3221884--3221945 Score: 90
Period size: 29 Copynumber: 2.1 Consensus size: 30
3221874 GTCAATAAAG
**
3221884 AAAGAAAAAAAGAAAGAAAAAAGGAGAAAA
1 AAAGAAAAAAAGAAAGAAAAAAAAAGAAAA
*
3221914 AAAG-AAAAAGGAAAGAAAAAAAAAGAAAA
1 AAAGAAAAAAAGAAAGAAAAAAAAAGAAAA
3221943 AAA
1 AAA
3221946 TTATGTATTC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 25 0.86
30 4 0.14
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (30 bp):
AAAGAAAAAAAGAAAGAAAAAAAAAGAAAA
Found at i:3221945 original size:11 final size:11
Alignment explanation
Indices: 3221880--3221945 Score: 71
Period size: 11 Copynumber: 6.0 Consensus size: 11
3221870 TTCTGTCAAT
3221880 AAAGAAAGAAAA
1 AAAGAAA-AAAA
*
3221892 AAAGAAAGAAA
1 AAAGAAAAAAA
* *
3221903 AAAGGAGAAAA
1 AAAGAAAAAAA
**
3221914 AAAGAAAAAGG
1 AAAGAAAAAAA
3221925 AAAG-AAAAAA
1 AAAGAAAAAAA
3221935 AAAGAAAAAAA
1 AAAGAAAAAAA
3221946 TTATGTATTC
Statistics
Matches: 43, Mismatches: 10, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
10 8 0.19
11 28 0.65
12 7 0.16
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (11 bp):
AAAGAAAAAAA
Found at i:3222804 original size:18 final size:18
Alignment explanation
Indices: 3222777--3222814 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
3222767 TTTATATAAA
*
3222777 TATTTATATATTAATAATT
1 TATTTATATATAAAT-ATT
3222796 TATTT-TATATAAATATT
1 TATTTATATATAAATATT
3222813 TA
1 TA
3222815 CATATTTATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 5 0.28
18 8 0.44
19 5 0.28
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TATTTATATATAAATATT
Found at i:3222878 original size:18 final size:16
Alignment explanation
Indices: 3222839--3222889 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 16
3222829 TCTGCCATGT
*
3222839 TTATATTATTTTTGTA
1 TTATATTATTTTTATA
*
3222855 TCATATTATTTTT-TA
1 TTATATTATTTTTATA
*
3222870 --ATATTATATTTATA
1 TTATATTATTTTTATA
3222884 TTATAT
1 TTATAT
3222890 CTCAATTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
13 10 0.33
14 2 0.07
15 2 0.07
16 16 0.53
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (16 bp):
TTATATTATTTTTATA
Found at i:3222918 original size:22 final size:22
Alignment explanation
Indices: 3222873--3222927 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
3222863 TTTTTTAATA
* *
3222873 TTATATTTATATTATATCTCAAT
1 TTAT-TTTATATTATATATAAAT
*
3222896 TTATTTTATATTTTATATAAAT
1 TTATTTTATATTATATATAAAT
3222918 TT-TTTATATA
1 TTATTT-TATA
3222928 ATTAAATTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 3 0.11
22 21 0.75
23 4 0.14
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.62
Consensus pattern (22 bp):
TTATTTTATATTATATATAAAT
Found at i:3223014 original size:15 final size:15
Alignment explanation
Indices: 3222919--3223021 Score: 58
Period size: 14 Copynumber: 7.0 Consensus size: 15
3222909 TATATAAATT
3222919 TTTTATATAATT-AAA
1 TTTTAT-TAATTAAAA
* *
3222934 TTTTA--ACTTTAAA
1 TTTTATTAATTAAAA
*
3222947 -TTTATTTATT-AAA
1 TTTTATTAATTAAAA
*
3222960 TATTT-TTAAAT-AAA
1 T-TTTATTAATTAAAA
*
3222974 TTTTATTAATTATAA
1 TTTTATTAATTAAAA
3222989 TTTTATTTAATTAAAAA
1 TTTTA-TTAATT-AAAA
*
3223006 TTTTATAATATTAAAA
1 TTTTATTA-ATTAAAA
3223022 CTCGAGTGAA
Statistics
Matches: 69, Mismatches: 9, Indels: 19
0.71 0.09 0.20
Matches are distributed among these distances:
12 7 0.10
13 9 0.13
14 15 0.22
15 15 0.22
16 12 0.17
17 11 0.16
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (15 bp):
TTTTATTAATTAAAA
Found at i:3223331 original size:22 final size:22
Alignment explanation
Indices: 3223305--3223351 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
3223295 TTTAAAATAT
*
3223305 AATATTTTATATATAACTATAA
1 AATATTTTAAATATAACTATAA
*
3223327 AATATTTTAAATATAATTATAA
1 AATATTTTAAATATAACTATAA
3223349 AAT
1 AAT
3223352 CAATATTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (22 bp):
AATATTTTAAATATAACTATAA
Found at i:3225979 original size:99 final size:102
Alignment explanation
Indices: 3225785--3225980 Score: 290
Period size: 99 Copynumber: 1.9 Consensus size: 102
3225775 TAAATTCTAG
* * * * *
3225785 CTTGACTTACTTCAACTTTGTTTAACAACCAAGTACTTAGTAAATTCCCCAACTAATTTCAGCAT
1 CTTGACTTACTTCAACTTTGTTTAACAACCAAGTACATAGAAAATT-CCCAACTAATTCCACCAC
3225850 TTGTTTATTCCCCAGAAATTAAATGAGAGAGAAAGAAA
65 TTGTTTATTCCCCAGAAATTAAATGAGAGAGAAAGAAA
* *
3225888 CTTGAC-TACTTCAACTTTGTTTAATAACCGAGTACATAGAAAATT-CCAACTAA-TCCACCACT
1 CTTGACTTACTTCAACTTTGTTTAACAACCAAGTACATAGAAAATTCCCAACTAATTCCACCACT
*
3225950 TGTTTATTTCCCAGAAATTAAATGAGAGAGA
66 TGTTTATTCCCCAGAAATTAAATGAGAGAGA
3225981 GAGAGAGAGA
Statistics
Matches: 85, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
99 36 0.42
100 8 0.09
102 35 0.41
103 6 0.07
ACGTcount: A:0.37, C:0.20, G:0.12, T:0.32
Consensus pattern (102 bp):
CTTGACTTACTTCAACTTTGTTTAACAACCAAGTACATAGAAAATTCCCAACTAATTCCACCACT
TGTTTATTCCCCAGAAATTAAATGAGAGAGAAAGAAA
Found at i:3225980 original size:2 final size:2
Alignment explanation
Indices: 3225973--3226000 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3225963 GAAATTAAAT
3225973 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
3226001 ATCTGAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3226210 original size:19 final size:20
Alignment explanation
Indices: 3226164--3226211 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
3226154 ATTATTTTAT
*
3226164 TATTTTATTTGTAAAGTAAAA
1 TATTTT-TTAGTAAAGTAAAA
*
3226185 -ATATTTTAGTAAA-TAAAA
1 TATTTTTTAGTAAAGTAAAA
3226203 TATTTTTTA
1 TATTTTTTA
3226212 TTTTATATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
18 5 0.22
19 14 0.61
20 4 0.17
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (20 bp):
TATTTTTTAGTAAAGTAAAA
Done.