Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr11
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: 61124829
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1263459 characters in sequence are not A, C, G, or T
File 8 of 205
Found at i:2153018 original size:68 final size:67
Alignment explanation
Indices: 2152901--2153031 Score: 192
Period size: 68 Copynumber: 1.9 Consensus size: 67
2152891 TAAAAAATGA
* * * *
2152901 TATGATATATTAGTGTATGTTATATGTTATGATATATTAGTGTGTATATTATGTATGTTATGTAT
1 TATGATATATTAGTGTATGTTATATGTTATGATATACTAGTATGGATATTATGTATGGTATGTAT
2152966 TG
66 TG
*
2152968 TATGATATATTA-TGTATGTTATGTATTTTATGATATACTAGTATGGATATTATGTATGGTATGT
1 TATGATATATTAGTGTATGTTA--TATGTTATGATATACTAGTATGGATATTATGTATGGTATGT
2153032 GTCAGACCCT
Statistics
Matches: 57, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
66 9 0.16
67 12 0.21
68 36 0.63
ACGTcount: A:0.29, C:0.01, G:0.19, T:0.51
Consensus pattern (67 bp):
TATGATATATTAGTGTATGTTATATGTTATGATATACTAGTATGGATATTATGTATGGTATGTAT
TG
Found at i:2155662 original size:25 final size:25
Alignment explanation
Indices: 2155632--2155701 Score: 95
Period size: 25 Copynumber: 2.8 Consensus size: 25
2155622 TTTCCCGATT
*
2155632 ATGGCTCTCATGAGCTTCCCGTTAC
1 ATGGCTCACATGAGCTTCCCGTTAC
* *
2155657 ATGGCTCACATGAGCTTCACGTTAT
1 ATGGCTCACATGAGCTTCCCGTTAC
* *
2155682 ATAGCTCAAATGAGCTTCCC
1 ATGGCTCACATGAGCTTCCC
2155702 CTTTATGTGC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.23, C:0.29, G:0.19, T:0.30
Consensus pattern (25 bp):
ATGGCTCACATGAGCTTCCCGTTAC
Found at i:2155713 original size:25 final size:25
Alignment explanation
Indices: 2155623--2155701 Score: 88
Period size: 25 Copynumber: 3.2 Consensus size: 25
2155613 TCGCTTTAAT
* **
2155623 TTCCCGAT-TATGGCTCTCATGAGC
1 TTCCCGTTATATGGCTCAAATGAGC
* *
2155647 TTCCCGTTACATGGCTCACATGAGC
1 TTCCCGTTATATGGCTCAAATGAGC
* *
2155672 TTCACGTTATATAGCTCAAATGAGC
1 TTCCCGTTATATGGCTCAAATGAGC
2155697 TTCCC
1 TTCCC
2155702 CTTTATGTGC
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
24 7 0.15
25 39 0.85
ACGTcount: A:0.22, C:0.29, G:0.18, T:0.32
Consensus pattern (25 bp):
TTCCCGTTATATGGCTCAAATGAGC
Found at i:2162887 original size:35 final size:34
Alignment explanation
Indices: 2162848--2163116 Score: 334
Period size: 35 Copynumber: 8.0 Consensus size: 34
2162838 TTGTCTTTTC
* *
2162848 TTGCAGGGAATATTTCCTGTTCACGCATTATTCTG
1 TTGCAGGGAATCTCTCCTGTTCACGCATTATT-TG
* * *
2162883 TTGCAGGGAATCTTTCCTGTTCA--CATCATTTC
1 TTGCAGGGAATCTCTCCTGTTCACGCATTATTTG
2162915 TTGCAGGGAATCTCTCCTGTTCACGCATTATTTTG
1 TTGCAGGGAATCTCTCCTGTTCACGCATTA-TTTG
*
2162950 TTGCAGGGAATCTCTCCTGTTCACACATTATTTTG
1 TTGCAGGGAATCTCTCCTGTTCACGCATTA-TTTG
* * *
2162985 TTGCAGGGAATCTTTCCTGTTCA--CATCATTTC
1 TTGCAGGGAATCTCTCCTGTTCACGCATTATTTG
*
2163017 TTGCAGGGAATCTCTCCTGTTCACGGATTATTTTG
1 TTGCAGGGAATCTCTCCTGTTCACGCATTA-TTTG
* *
2163052 TTGCAGGGAATCTCTCCTGTTCA--CATCATTTC
1 TTGCAGGGAATCTCTCCTGTTCACGCATTATTTG
* *
2163084 TTGCAGGGAATCTCTCCTGTTCATGTATTATTT
1 TTGCAGGGAATCTCTCCTGTTCACGCATTATTT
2163117 CTTTTTGGAC
Statistics
Matches: 207, Mismatches: 19, Indels: 17
0.85 0.08 0.07
Matches are distributed among these distances:
32 74 0.36
33 13 0.06
34 13 0.06
35 107 0.52
ACGTcount: A:0.19, C:0.23, G:0.18, T:0.41
Consensus pattern (34 bp):
TTGCAGGGAATCTCTCCTGTTCACGCATTATTTG
Found at i:2163024 original size:102 final size:102
Alignment explanation
Indices: 2162843--2163106 Score: 426
Period size: 102 Copynumber: 2.6 Consensus size: 102
2162833 TTCACTTGTC
* * * * *
2162843 TTTTCTTGCAGGGAATATTTCCTGTTCACGCATTATTCTGTTGCAGGGAATCTTTCCTGTTCACA
1 TTTTGTTGCAGGGAATCTCTCCTGTTCACACATTATTTTGTTGCAGGGAATCTTTCCTGTTCACA
2162908 TCATTTCTTGCAGGGAATCTCTCCTGTTCACGCATTA
66 TCATTTCTTGCAGGGAATCTCTCCTGTTCACGCATTA
2162945 TTTTGTTGCAGGGAATCTCTCCTGTTCACACATTATTTTGTTGCAGGGAATCTTTCCTGTTCACA
1 TTTTGTTGCAGGGAATCTCTCCTGTTCACACATTATTTTGTTGCAGGGAATCTTTCCTGTTCACA
*
2163010 TCATTTCTTGCAGGGAATCTCTCCTGTTCACGGATTA
66 TCATTTCTTGCAGGGAATCTCTCCTGTTCACGCATTA
* * *
2163047 TTTTGTTGCAGGGAATCTCTCCTGTT--CACATCA-TTTCTTGCAGGGAATCTCTCCTGTTCA
1 TTTTGTTGCAGGGAATCTCTCCTGTTCACACATTATTTTGTTGCAGGGAATCTTTCCTGTTCA
2163107 TGTATTATTT
Statistics
Matches: 153, Mismatches: 9, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
99 25 0.16
100 6 0.04
102 122 0.80
ACGTcount: A:0.18, C:0.23, G:0.18, T:0.40
Consensus pattern (102 bp):
TTTTGTTGCAGGGAATCTCTCCTGTTCACACATTATTTTGTTGCAGGGAATCTTTCCTGTTCACA
TCATTTCTTGCAGGGAATCTCTCCTGTTCACGCATTA
Found at i:2163114 original size:67 final size:68
Alignment explanation
Indices: 2162843--2163116 Score: 342
Period size: 67 Copynumber: 4.0 Consensus size: 68
2162833 TTCACTTGTC
* * * * *
2162843 TTTTCTTGCAGGGAATATTTCCTGTTCACGCATTATTCTGTTGCAGGGAATCTTTCCTGTTCA--
1 TTTTCTTGCAGGGAATCTCTCCTGTTCAC-CATCATT-TCTTGCAGGGAATCTCTCCTGTTCACG
*
2162906 CATCA
64 CATTA
* * *
2162911 -TTTCTTGCAGGGAATCTCTCCTGTTCACGCATTATTTTGTTGCAGGGAATCTCTCCTGTTCACA
1 TTTTCTTGCAGGGAATCTCTCCTGTTCAC-CATCA-TTTCTTGCAGGGAATCTCTCCTGTTCACG
2162975 CATTA
64 CATTA
* * *
2162980 TTTTGTTGCAGGGAATCTTTCCTGTTCA-CATCATTTCTTGCAGGGAATCTCTCCTGTTCACGGA
1 TTTTCTTGCAGGGAATCTCTCCTGTTCACCATCATTTCTTGCAGGGAATCTCTCCTGTTCACGCA
2163044 TTA
66 TTA
* * *
2163047 TTTTGTTGCAGGGAATCTCTCCTGTTCA-CATCATTTCTTGCAGGGAATCTCTCCTGTTCATGTA
1 TTTTCTTGCAGGGAATCTCTCCTGTTCACCATCATTTCTTGCAGGGAATCTCTCCTGTTCACGCA
2163111 TTA
66 TTA
2163114 TTT
1 TTT
2163117 CTTTTTGGAC
Statistics
Matches: 189, Mismatches: 13, Indels: 9
0.90 0.06 0.04
Matches are distributed among these distances:
67 154 0.81
68 6 0.03
69 4 0.02
70 25 0.13
ACGTcount: A:0.18, C:0.23, G:0.18, T:0.41
Consensus pattern (68 bp):
TTTTCTTGCAGGGAATCTCTCCTGTTCACCATCATTTCTTGCAGGGAATCTCTCCTGTTCACGCA
TTA
Found at i:2165947 original size:21 final size:22
Alignment explanation
Indices: 2165917--2165961 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
2165907 GAGCAAATTG
2165917 TTGATTCTATTTCCTTTTTG-AT
1 TTGATTCTA-TTCCTTTTTGTAT
*
2165939 TTGA-TCTATTCTTTTTTGTAT
1 TTGATTCTATTCCTTTTTGTAT
2165960 TT
1 TT
2165962 CTCTTTTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 9 0.43
21 8 0.38
22 4 0.19
ACGTcount: A:0.13, C:0.11, G:0.09, T:0.67
Consensus pattern (22 bp):
TTGATTCTATTCCTTTTTGTAT
Found at i:2168656 original size:24 final size:25
Alignment explanation
Indices: 2168629--2168676 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 25
2168619 AAGCTCGAAA
*
2168629 GAGCATCCTGTTA-TTAGCTCTCAT
1 GAGCATCCTGATATTTAGCTCTCAT
2168653 GAGCATCCTGATATTTAGCTCTCA
1 GAGCATCCTGATATTTAGCTCTCA
2168677 CAAGCTTCCC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 12 0.55
25 10 0.45
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.35
Consensus pattern (25 bp):
GAGCATCCTGATATTTAGCTCTCAT
Found at i:2168928 original size:25 final size:25
Alignment explanation
Indices: 2168898--2168967 Score: 70
Period size: 25 Copynumber: 2.8 Consensus size: 25
2168888 CTTCCTGATT
* * *
2168898 ATGGCTCTCATAAGTTTCCCGTTAC
1 ATGGCTCACATAAGCTTCCCATTAC
* *
2168923 ATGGCTCACATGAGCTTCCCATTAT
1 ATGGCTCACATAAGCTTCCCATTAC
*
2168948 ATGGCTCGA-ATGAGCTTCCC
1 ATGGCTC-ACATAAGCTTCCC
2168968 GTTTATGTGC
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
25 38 0.97
26 1 0.03
ACGTcount: A:0.21, C:0.29, G:0.19, T:0.31
Consensus pattern (25 bp):
ATGGCTCACATAAGCTTCCCATTAC
Found at i:2168992 original size:26 final size:25
Alignment explanation
Indices: 2168913--2168992 Score: 83
Period size: 25 Copynumber: 3.2 Consensus size: 25
2168903 TCTCATAAGT
* *
2168913 TTCCCGTTACATGGCTC-ACATGAGC
1 TTCCCATTATATGGCTCGA-ATGAGC
2168938 TTCCCATTATATGGCTCGAATGAGC
1 TTCCCATTATATGGCTCGAATGAGC
* *
2168963 TTCCCGTT-TATGTGCTCGTATGAGC
1 TTCCCATTATATG-GCTCGAATGAGC
2168988 ATTCC
1 -TTCC
2168993 TGAATATGAA
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
24 4 0.08
25 39 0.81
26 5 0.10
ACGTcount: A:0.19, C:0.28, G:0.20, T:0.34
Consensus pattern (25 bp):
TTCCCATTATATGGCTCGAATGAGC
Found at i:2169000 original size:26 final size:24
Alignment explanation
Indices: 2168923--2169000 Score: 61
Period size: 25 Copynumber: 3.1 Consensus size: 24
2168913 TTCCCGTTAC
2168923 ATGGCTC-ACATGAGCTTCCC-ATTAT
1 ATGGCTCGA-ATGAGCTTCCCGA--AT
**
2168948 ATGGCTCGAATGAGCTTCCCGTTT
1 ATGGCTCGAATGAGCTTCCCGAAT
* *
2168972 ATGTGCTCGTATGAGCATTCCTGAAT
1 ATG-GCTCGAATGAGC-TTCCCGAAT
2168998 ATG
1 ATG
2169001 AATTGACGGA
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
24 4 0.09
25 29 0.67
26 10 0.23
ACGTcount: A:0.22, C:0.23, G:0.22, T:0.33
Consensus pattern (24 bp):
ATGGCTCGAATGAGCTTCCCGAAT
Found at i:2174569 original size:41 final size:40
Alignment explanation
Indices: 2174511--2174637 Score: 125
Period size: 41 Copynumber: 3.1 Consensus size: 40
2174501 ATAGGGATTT
*
2174511 CTTCGACTTAGAGTCGATGAGACATTGGGTGTCAATTTACTA
1 CTTCGAGTTA-AGTCGATGAGACATTGGGTGTCAATTTA-TA
* * * * *
2174553 CTTCGGGTTAATTCGATGAGGCACTGGGTGCCAATTT-T-
1 CTTCGAGTTAAGTCGATGAGACATTGGGTGTCAATTTATA
* *
2174591 CTTC-AGTTTAGCCGATGAGACATTGGGTGTCAAATTTATTA
1 CTTCGAGTTAAGTCGATGAGACATTGGGTGTC-AATTTA-TA
2174632 CTTCGA
1 CTTCGA
2174638 ATTATCCGAT
Statistics
Matches: 67, Mismatches: 13, Indels: 10
0.74 0.14 0.11
Matches are distributed among these distances:
37 20 0.30
38 9 0.13
39 1 0.01
40 1 0.01
41 27 0.40
42 9 0.13
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.35
Consensus pattern (40 bp):
CTTCGAGTTAAGTCGATGAGACATTGGGTGTCAATTTATA
Found at i:2186796 original size:16 final size:17
Alignment explanation
Indices: 2186772--2186805 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
2186762 TTCTCAGAAA
2186772 TAACCCTCTC-CATCCC
1 TAACCCTCTCACATCCC
*
2186788 TAACTCTCTCACATCCC
1 TAACCCTCTCACATCCC
2186805 T
1 T
2186806 CTTTCCTTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.21, C:0.50, G:0.00, T:0.29
Consensus pattern (17 bp):
TAACCCTCTCACATCCC
Found at i:2187093 original size:43 final size:43
Alignment explanation
Indices: 2187032--2187119 Score: 176
Period size: 43 Copynumber: 2.0 Consensus size: 43
2187022 ATGTTATAGG
2187032 AAATTTCAGATTTCAAACAGCTAAAATAAAGGAACAGCCACAA
1 AAATTTCAGATTTCAAACAGCTAAAATAAAGGAACAGCCACAA
2187075 AAATTTCAGATTTCAAACAGCTAAAATAAAGGAACAGCCACAA
1 AAATTTCAGATTTCAAACAGCTAAAATAAAGGAACAGCCACAA
2187118 AA
1 AA
2187120 GAGAAACGCT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.52, C:0.18, G:0.11, T:0.18
Consensus pattern (43 bp):
AAATTTCAGATTTCAAACAGCTAAAATAAAGGAACAGCCACAA
Found at i:2191106 original size:22 final size:21
Alignment explanation
Indices: 2191071--2191124 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 21
2191061 TTTTTAAAAT
*
2191071 TTAAAATA-TTCTAAGAAGTTA
1 TTAAAATATTTCTAA-AAATTA
2191092 -TAAAATTATTTCTAAAAATTA
1 TTAAAA-TATTTCTAAAAATTA
2191113 TTAAAAATATTT
1 TT-AAAATATTT
2191125 TTATTTTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
20 5 0.18
21 7 0.25
22 12 0.43
23 4 0.14
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.43
Consensus pattern (21 bp):
TTAAAATATTTCTAAAAATTA
Found at i:2191652 original size:52 final size:51
Alignment explanation
Indices: 2191594--2191703 Score: 166
Period size: 52 Copynumber: 2.1 Consensus size: 51
2191584 AAATGGTATG
* * * *
2191594 TTTTTTTAATCGCGTCTATCTGACAGGCGCGAATCAATTTTTTATATTAAAT
1 TTTTTTTAATCGCGCCTATCAGACAGGCACGAATCAATTTTGTATATT-AAT
*
2191646 TTTTTTTAATCGCGCCTATCAGATAGGCACGAATCAATTTTGTATATTAAT
1 TTTTTTTAATCGCGCCTATCAGACAGGCACGAATCAATTTTGTATATTAAT
2191697 TTTTTTT
1 TTTTTTT
2191704 CGTTTAATAA
Statistics
Matches: 53, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
51 10 0.19
52 43 0.81
ACGTcount: A:0.26, C:0.15, G:0.13, T:0.46
Consensus pattern (51 bp):
TTTTTTTAATCGCGCCTATCAGACAGGCACGAATCAATTTTGTATATTAAT
Found at i:2191806 original size:27 final size:27
Alignment explanation
Indices: 2191764--2191852 Score: 115
Period size: 27 Copynumber: 3.3 Consensus size: 27
2191754 TATAGATACG
*
2191764 AGGCGCGACTAGTTGAGCCTATCTGAT
1 AGGCGCGACTAGTTGAGCCTATCTGAC
* *
2191791 AGGCGCAACTAATTGAGCCTATCTGAC
1 AGGCGCGACTAGTTGAGCCTATCTGAC
* * * *
2191818 AGGCGCGACTAGTTGTGCCTAACTCAG
1 AGGCGCGACTAGTTGAGCCTATCTGAC
2191845 AGGCGCGA
1 AGGCGCGA
2191853 ATGGTGGGGC
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 53 1.00
ACGTcount: A:0.25, C:0.25, G:0.29, T:0.21
Consensus pattern (27 bp):
AGGCGCGACTAGTTGAGCCTATCTGAC
Found at i:2195552 original size:6 final size:6
Alignment explanation
Indices: 2195543--2195591 Score: 71
Period size: 6 Copynumber: 7.8 Consensus size: 6
2195533 CTCTGCCTCT
*
2195543 GGCTCC GGCTCC GGCTCC GGCTCC GGCTCC GGCTCTC TGGCTCT GGCTC
1 GGCTCC GGCTCC GGCTCC GGCTCC GGCTCC GGCTC-C -GGCTCC GGCTC
2195592 TGGTGCATGA
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
6 34 0.85
7 1 0.03
8 5 0.12
ACGTcount: A:0.00, C:0.45, G:0.33, T:0.22
Consensus pattern (6 bp):
GGCTCC
Found at i:2195566 original size:18 final size:20
Alignment explanation
Indices: 2195539--2195591 Score: 83
Period size: 18 Copynumber: 2.8 Consensus size: 20
2195529 CTGTCTCTGC
2195539 CTCTGGCTCCGGCTCCGGCT
1 CTCTGGCTCCGGCTCCGGCT
2195559 C-C-GGCTCCGGCTCCGGCT
1 CTCTGGCTCCGGCTCCGGCT
*
2195577 CTCTGGCTCTGGCTC
1 CTCTGGCTCCGGCTC
2195592 TGGTGCATGA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
18 17 0.57
19 2 0.07
20 11 0.37
ACGTcount: A:0.00, C:0.45, G:0.30, T:0.25
Consensus pattern (20 bp):
CTCTGGCTCCGGCTCCGGCT
Found at i:2195592 original size:6 final size:6
Alignment explanation
Indices: 2195528--2195594 Score: 53
Period size: 6 Copynumber: 10.8 Consensus size: 6
2195518 AGAATGTAGT
* * * * * * *
2195528 TCTGTC TCTGCC TCTGGC TCCGGC TCCGGC TCCGGC TCCGGC TCCGGCTC
1 TCTGGC TCTGGC TCTGGC TCTGGC TCTGGC TCTGGC TCTGGC TCTGG--C
2195578 TCTGGC TCTGGC TCTGG
1 TCTGGC TCTGGC TCTGG
2195595 TGCATGATGC
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
6 50 0.91
8 5 0.09
ACGTcount: A:0.00, C:0.42, G:0.30, T:0.28
Consensus pattern (6 bp):
TCTGGC
Found at i:2195592 original size:12 final size:12
Alignment explanation
Indices: 2195539--2195594 Score: 67
Period size: 12 Copynumber: 4.5 Consensus size: 12
2195529 CTGTCTCTGC
2195539 CTCTGGCTCCGG
1 CTCTGGCTCCGG
*
2195551 CTCCGGCTCCGG
1 CTCTGGCTCCGG
*
2195563 CTCCGGCTCCGG
1 CTCTGGCTCCGG
*
2195575 CTCTCTGGCTCTGG
1 --CTCTGGCTCCGG
2195589 CTCTGG
1 CTCTGG
2195595 TGCATGATGC
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
12 29 0.74
14 10 0.26
ACGTcount: A:0.00, C:0.43, G:0.32, T:0.25
Consensus pattern (12 bp):
CTCTGGCTCCGG
Found at i:2197829 original size:88 final size:88
Alignment explanation
Indices: 2197731--2197931 Score: 402
Period size: 88 Copynumber: 2.3 Consensus size: 88
2197721 TAAATTTATG
2197731 AAAAGAGTCAGTTATGATTAAACTTGGACAGATTGATATCCAAGTTGATATAAAAAAAATTAAAT
1 AAAAGAGTCAGTTATGATTAAACTTGGACAGATTGATATCCAAGTTGATATAAAAAAAATTAAAT
2197796 GAGTTAACAGTAACTATATGATT
66 GAGTTAACAGTAACTATATGATT
2197819 AAAAGAGTCAGTTATGATTAAACTTGGACAGATTGATATCCAAGTTGATATAAAAAAAATTAAAT
1 AAAAGAGTCAGTTATGATTAAACTTGGACAGATTGATATCCAAGTTGATATAAAAAAAATTAAAT
2197884 GAGTTAACAGTAACTATATGATT
66 GAGTTAACAGTAACTATATGATT
2197907 AAAAGAGTCAGTTATGATTAAACTT
1 AAAAGAGTCAGTTATGATTAAACTT
2197932 TTAATGAAAT
Statistics
Matches: 113, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
88 113 1.00
ACGTcount: A:0.45, C:0.08, G:0.16, T:0.31
Consensus pattern (88 bp):
AAAAGAGTCAGTTATGATTAAACTTGGACAGATTGATATCCAAGTTGATATAAAAAAAATTAAAT
GAGTTAACAGTAACTATATGATT
Found at i:2198071 original size:60 final size:61
Alignment explanation
Indices: 2197999--2198119 Score: 199
Period size: 60 Copynumber: 2.0 Consensus size: 61
2197989 ACAGAACAAT
* * *
2197999 TTATAACTTAATCCTAAATTACTAATAAATTAATTTTAAAATAATTACAAACA-CAAAAAA
1 TTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTACAAAAAGCAAAAAA
*
2198059 TTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTATAAAAAGCAAAAAA
1 TTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTACAAAAAGCAAAAAA
2198120 AAATTACATT
Statistics
Matches: 56, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
60 49 0.88
61 7 0.12
ACGTcount: A:0.56, C:0.11, G:0.01, T:0.32
Consensus pattern (61 bp):
TTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTACAAAAAGCAAAAAA
Found at i:2198283 original size:20 final size:20
Alignment explanation
Indices: 2198258--2198318 Score: 95
Period size: 20 Copynumber: 3.0 Consensus size: 20
2198248 TCTTCTCATT
* *
2198258 GAAGGGAGAGCAGCCTGGTG
1 GAAGGGACAGCAGCATGGTG
*
2198278 GAAGGGACAACAGCATGGTG
1 GAAGGGACAGCAGCATGGTG
2198298 GAAGGGACAGCAGCATGGTG
1 GAAGGGACAGCAGCATGGTG
2198318 G
1 G
2198319 TGCAACAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.30, C:0.15, G:0.46, T:0.10
Consensus pattern (20 bp):
GAAGGGACAGCAGCATGGTG
Found at i:2198514 original size:19 final size:19
Alignment explanation
Indices: 2198462--2198514 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 19
2198452 ATTTATATTT
* *
2198462 AAATATTTTAATAAAAATAA
1 AAATA-TTTAATATAAACAA
*
2198482 AAA-ATTT-ATTTAAACAA
1 AAATATTTAATATAAACAA
2198499 AAATATTTAATATAAA
1 AAATATTTAATATAAA
2198515 AAATTGATTC
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
17 10 0.37
18 7 0.26
19 7 0.26
20 3 0.11
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (19 bp):
AAATATTTAATATAAACAA
Found at i:2210826 original size:30 final size:30
Alignment explanation
Indices: 2210792--2210857 Score: 123
Period size: 30 Copynumber: 2.2 Consensus size: 30
2210782 ATGTAGAAGC
2210792 TGCAAGCAACTTGGCCACATTGAGAAAGTT
1 TGCAAGCAACTTGGCCACATTGAGAAAGTT
*
2210822 TGCAAGCAACTTGGCCACATTGAGGAAGTT
1 TGCAAGCAACTTGGCCACATTGAGAAAGTT
2210852 TGCAAG
1 TGCAAG
2210858 AACAAGGCAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.32, C:0.20, G:0.26, T:0.23
Consensus pattern (30 bp):
TGCAAGCAACTTGGCCACATTGAGAAAGTT
Found at i:2219527 original size:3 final size:3
Alignment explanation
Indices: 2219519--2219559 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
2219509 ATCACATGTT
2219519 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2219560 TGGGTGTAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2219642 original size:73 final size:73
Alignment explanation
Indices: 2219564--2219891 Score: 647
Period size: 73 Copynumber: 4.5 Consensus size: 73
2219554 ATTATTTGGG
*
2219564 TGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTTATTT
1 TGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTTATTT
2219629 TAAGTGGA
66 TAAGTGGA
2219637 TGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTTATTT
1 TGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTTATTT
2219702 TAAGTGGA
66 TAAGTGGA
2219710 TGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTTATTT
1 TGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTTATTT
2219775 TAAGTGGA
66 TAAGTGGA
2219783 TGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTTATTT
1 TGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTTATTT
2219848 TAAGTGGA
66 TAAGTGGA
2219856 TGTAATGATGAAACTTAGTTGTATTCCAACTAAGTT
1 TGTAATGATGAAACTTAGTTGTATTCCAACTAAGTT
2219892 GTCAAGTTGT
Statistics
Matches: 254, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 254 1.00
ACGTcount: A:0.28, C:0.06, G:0.25, T:0.41
Consensus pattern (73 bp):
TGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTTATTT
TAAGTGGA
Found at i:2223934 original size:15 final size:13
Alignment explanation
Indices: 2223910--2223949 Score: 53
Period size: 15 Copynumber: 2.9 Consensus size: 13
2223900 TGATTGTAAT
2223910 AGTTAGTAGTTAA
1 AGTTAGTAGTTAA
2223923 CAGTTAAGTAGTTAA
1 -AGTT-AGTAGTTAA
*
2223938 ATTTAGTAGTTA
1 AGTTAGTAGTTA
2223950 GTAGTTTATG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
13 8 0.33
14 7 0.29
15 9 0.38
ACGTcount: A:0.38, C:0.03, G:0.20, T:0.40
Consensus pattern (13 bp):
AGTTAGTAGTTAA
Found at i:2228523 original size:29 final size:30
Alignment explanation
Indices: 2228490--2228550 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 30
2228480 AAAACGGTTG
2228490 TAACAATTAGTAGTTAACAGTT-ATGTAGT
1 TAACAATTAGTAGTTAACAGTTGATGTAGT
* **
2228519 TAACAGTTAGTAGTTAGTAGTTGATGTAGT
1 TAACAATTAGTAGTTAACAGTTGATGTAGT
2228549 TA
1 TA
2228551 GTCAACAGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 19 0.68
30 9 0.32
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.39
Consensus pattern (30 bp):
TAACAATTAGTAGTTAACAGTTGATGTAGT
Found at i:2228533 original size:7 final size:7
Alignment explanation
Indices: 2228496--2228552 Score: 51
Period size: 7 Copynumber: 7.7 Consensus size: 7
2228486 GTTGTAACAA
2228496 TTAGTAG
1 TTAGTAG
**
2228503 TTAACAG
1 TTAGTAG
2228510 TTATGTAG
1 TTA-GTAG
**
2228518 TTAACAG
1 TTAGTAG
2228525 TTAGTAG
1 TTAGTAG
2228532 TTAGTAG
1 TTAGTAG
2228539 TTGATGTAG
1 TT-A-GTAG
2228548 TTAGT
1 TTAGT
2228553 CAACAGTTAG
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
7 26 0.67
8 7 0.18
9 6 0.15
ACGTcount: A:0.30, C:0.04, G:0.25, T:0.42
Consensus pattern (7 bp):
TTAGTAG
Found at i:2229301 original size:18 final size:18
Alignment explanation
Indices: 2229278--2229315 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
2229268 ACACAATTAA
*
2229278 ATAATAGTTTATATATAT
1 ATAATAATTTATATATAT
*
2229296 ATAATAATTTTTATATAT
1 ATAATAATTTATATATAT
2229314 AT
1 AT
2229316 TATTTTTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (18 bp):
ATAATAATTTATATATAT
Found at i:2229312 original size:16 final size:15
Alignment explanation
Indices: 2229291--2229324 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
2229281 ATAGTTTATA
2229291 TATATATAATAATTTT
1 TATATAT-ATAATTTT
*
2229307 TATATATATTATTTT
1 TATATATATAATTTT
2229322 TAT
1 TAT
2229325 TGAAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TATATATATAATTTT
Found at i:2239536 original size:24 final size:24
Alignment explanation
Indices: 2239509--2239562 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
2239499 ATTATGATTA
* *
2239509 TTATTATTACTAATATTAATATTC
1 TTATTATGACTAATATTAATATCC
* *
2239533 TTATTATGACTATTATTATTATCC
1 TTATTATGACTAATATTAATATCC
2239557 TTATTA
1 TTATTA
2239563 ACACTTTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.33, C:0.09, G:0.02, T:0.56
Consensus pattern (24 bp):
TTATTATGACTAATATTAATATCC
Found at i:2239692 original size:10 final size:9
Alignment explanation
Indices: 2239657--2239721 Score: 53
Period size: 9 Copynumber: 7.2 Consensus size: 9
2239647 TAAGTTTCCT
2239657 TTTTTACTTA
1 TTTTTA-TTA
* *
2239667 TTCTCATTA
1 TTTTTATTA
*
2239676 TTCTTATT-
1 TTTTTATTA
*
2239684 TATTT-TTA
1 TTTTTATTA
*
2239692 TTTTTATCA
1 TTTTTATTA
2239701 TTTTTATTA
1 TTTTTATTA
2239710 TTTTTACTTA
1 TTTTTA-TTA
2239720 TT
1 TT
2239722 ATTCTCCTCT
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
7 2 0.05
8 7 0.16
9 26 0.59
10 9 0.20
ACGTcount: A:0.20, C:0.09, G:0.00, T:0.71
Consensus pattern (9 bp):
TTTTTATTA
Found at i:2239692 original size:25 final size:24
Alignment explanation
Indices: 2239664--2239715 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 24
2239654 CCTTTTTTAC
*
2239664 TTATTCTCATTATTCTTATTTATTT
1 TTATTCTCATCATTCTTA-TTATTT
* * *
2239689 TTATTTTTATCATTTTTATTATTT
1 TTATTCTCATCATTCTTATTATTT
2239713 TTA
1 TTA
2239716 CTTATTATTC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
24 9 0.39
25 14 0.61
ACGTcount: A:0.21, C:0.08, G:0.00, T:0.71
Consensus pattern (24 bp):
TTATTCTCATCATTCTTATTATTT
Found at i:2239723 original size:25 final size:29
Alignment explanation
Indices: 2239657--2239723 Score: 81
Period size: 24 Copynumber: 2.5 Consensus size: 29
2239647 TAAGTTTCCT
*
2239657 TTTTTACTTATTCTCATTATTCTTATTTA
1 TTTTTACTTATTATCATTATTCTTATTTA
*
2239686 TTTTTA-TTTTTATCA-T-TT-TTA-TTA
1 TTTTTACTTATTATCATTATTCTTATTTA
2239710 TTTTTACTTATTAT
1 TTTTTACTTATTAT
2239724 TCTCCTCTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
24 9 0.26
25 9 0.26
26 2 0.06
27 1 0.03
28 7 0.21
29 6 0.18
ACGTcount: A:0.21, C:0.09, G:0.00, T:0.70
Consensus pattern (29 bp):
TTTTTACTTATTATCATTATTCTTATTTA
Found at i:2249113 original size:21 final size:21
Alignment explanation
Indices: 2249087--2249137 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
2249077 CAATAAGTCA
2249087 AATTTGAAAATTTAAATCGCC
1 AATTTGAAAATTTAAATCGCC
2249108 AATTTGAAAATTTAAATCGCC
1 AATTTGAAAATTTAAATCGCC
2249129 AATTTGAAA
1 AATTTGAAA
2249138 GCAATAAAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.45, C:0.12, G:0.10, T:0.33
Consensus pattern (21 bp):
AATTTGAAAATTTAAATCGCC
Found at i:2251965 original size:32 final size:33
Alignment explanation
Indices: 2251911--2251985 Score: 102
Period size: 32 Copynumber: 2.3 Consensus size: 33
2251901 AATTAATCTA
*
2251911 AATCCT-AAACCCTAACCCGACCCTAAATCCCT
1 AATCCTCAAACCCTAACCCGACCCCAAATCCCT
*
2251943 AATCCTCAAACCCTAA-CTGACCCCAAATCCCT
1 AATCCTCAAACCCTAACCCGACCCCAAATCCCT
2251975 AA-CCTCTAAAC
1 AATCCTC-AAAC
2251986 ATTATTTAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
31 4 0.10
32 26 0.67
33 9 0.23
ACGTcount: A:0.36, C:0.43, G:0.03, T:0.19
Consensus pattern (33 bp):
AATCCTCAAACCCTAACCCGACCCCAAATCCCT
Found at i:2252855 original size:41 final size:41
Alignment explanation
Indices: 2252798--2253078 Score: 422
Period size: 41 Copynumber: 6.9 Consensus size: 41
2252788 ATTTATTATT
2252798 ATTAGCGGCGCATT-TTCAAAAACGCCGCTAAAGGCCTGAGC
1 ATTAGCGGCGC-TTCTTCAAAAACGCCGCTAAAGGCCTGAGC
* *
2252839 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCGGAGC
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCTGAGC
2252880 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCTGAGC
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCTGAGC
* * *
2252921 ATTAGCGGCGCTACATAAAAAACGCCGCTAAAGGCCTGAGC
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCTGAGC
* * *
2252962 ATTAGCGGCGCTTCTCCAAAAATGCCGCTGAAGGCCTGAGC
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCTGAGC
* **
2253003 ATTAGGGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCAAGC
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCTGAGC
* *
2253044 ATTAGCGACGCTTTTTCAAAAA-GCCGCTAAAGGCC
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCC
2253079 CCCAAAACTC
Statistics
Matches: 218, Mismatches: 21, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
40 15 0.07
41 203 0.93
ACGTcount: A:0.29, C:0.28, G:0.25, T:0.19
Consensus pattern (41 bp):
ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCTGAGC
Found at i:2253245 original size:40 final size:38
Alignment explanation
Indices: 2253115--2253249 Score: 130
Period size: 40 Copynumber: 3.4 Consensus size: 38
2253105 GGGCTTAGGC
2253115 TTTTTATGGCGCTTTTTGAAAAA-CGCCGCTAATGCTT-A
1 TTTTTATGGCG-TTTTT-AAAAAGCGCCGCTAATGCTTGA
* * *
2253153 TTTTTAGCGGCGTTTTCCAAAAAGCGCCGCTAATGCTCGA
1 TTTTTA-TGGCGTTTT-TAAAAAGCGCCGCTAATGCTTGA
** * *
2253193 CCTTTATCGGCGTTTTTATAAAAGTGCCGCTAATACTTGA
1 TTTTTAT-GGCGTTTTTA-AAAAGCGCCGCTAATGCTTGA
2253233 TTTTTAGTGGCGTTTTT
1 TTTTTA-TGGCGTTTTT
2253250 TATCCAAGCG
Statistics
Matches: 78, Mismatches: 12, Indels: 12
0.76 0.12 0.12
Matches are distributed among these distances:
38 15 0.19
39 18 0.23
40 44 0.56
41 1 0.01
ACGTcount: A:0.21, C:0.19, G:0.20, T:0.39
Consensus pattern (38 bp):
TTTTTATGGCGTTTTTAAAAAGCGCCGCTAATGCTTGA
Found at i:2254786 original size:20 final size:19
Alignment explanation
Indices: 2254763--2254805 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
2254753 TTAGGTTTTT
*
2254763 TTTTGCAGTTTTTAATGAAA
1 TTTTACAGTTTTTAA-GAAA
* *
2254783 TTTTATATTTTTTAAGAAA
1 TTTTACAGTTTTTAAGAAA
2254802 TTTT
1 TTTT
2254806 TACATTAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.30, C:0.02, G:0.09, T:0.58
Consensus pattern (19 bp):
TTTTACAGTTTTTAAGAAA
Found at i:2254836 original size:16 final size:17
Alignment explanation
Indices: 2254810--2254844 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
2254800 AATTTTTACA
*
2254810 TTAATTTTTTTACTAAT
1 TTAATTTTTTTAATAAT
2254827 TTAA-TTTTTTAATAAT
1 TTAATTTTTTTAATAAT
2254843 TT
1 TT
2254845 CATAATAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (17 bp):
TTAATTTTTTTAATAAT
Found at i:2254892 original size:17 final size:17
Alignment explanation
Indices: 2254854--2254900 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
2254844 TCATAATAGA
*
2254854 TTATGAATTTGTTAGTTG
1 TTAT-AATTTTTTAGTTG
2254872 TTATAATTTTTTAAGTT-
1 TTATAATTTTTT-AGTTG
*
2254889 TTATGATTTTTT
1 TTATAATTTTTT
2254901 GAAGGATTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
17 18 0.69
18 8 0.31
ACGTcount: A:0.23, C:0.00, G:0.13, T:0.64
Consensus pattern (17 bp):
TTATAATTTTTTAGTTG
Found at i:2256279 original size:246 final size:247
Alignment explanation
Indices: 2255830--2256319 Score: 732
Period size: 246 Copynumber: 2.0 Consensus size: 247
2255820 AATGGCAAAC
* * *
2255830 CTCTCATCTATGTCAAGTAAGTGGTTTTGATTGTTCAAGCTTGTAAGATCTTAGGCTCTCAAGTG
1 CTCTCACCTATGTCAAGTAAGTGGTTTTGATCGTTCAAGCTTGTAAGATCTCAGGCTCTCAAGTG
* * * * * * *
2255895 TCTTAGCTCATAGCGTGATCTTGGTCAAAAAAGCTAACTAGCAAGGCATGAGCTTGCAAGGTGGC
66 TCTTAGCTCACAACATAATCTTGGTCAAAAAAGCTAACCAACAAGGCATGAGCTCGCAAGGTGGC
* * *
2255960 TCACAATTGTAACAACTCAATTTTTAGTAGTACTGAAAAAGGATATTTTTGAACCTTATTTCTGT
131 TCACAATTGTAACAACTCAATTTTTAGTAGTACTGAAAAAGGAGATTTTGGAACCTCATTTCTGT
*
2256025 AACCGAGTCCGTAAATATTAAATATGAATATTTACGAGGTTAATATAAAGAT
196 AACCGAGTCCATAAATATTAAATATGAATATTTACGAGGTTAATATAAAGAT
*
2256077 CTCTCACCTATGTCAAGTAAGTGGTTTTGATCGTTCAAGCTTGTAAGATCTCGGGCTCTCAAGTG
1 CTCTCACCTATGTCAAGTAAGTGGTTTTGATCGTTCAAGCTTGTAAGATCTCAGGCTCTCAAGTG
* * *
2256142 TCTTAGCTTACAACATAATCTTGGT-AAAAGAGCTAACCAACAAGGTATGAGCTCGCAAGGTGGC
66 TCTTAGCTCACAACATAATCTTGGTCAAAAAAGCTAACCAACAAGGCATGAGCTCGCAAGGTGGC
* * * * *
2256206 TCACAATTGTAACAGCTCGATTTTTAGTAGTACCT-AAAAAGGCGGTTTTGGAACCTCATTTTTG
131 TCACAATTGTAACAACTCAATTTTTAGTAGTA-CTGAAAAAGGAGATTTTGGAACCTCATTTCTG
* *
2256270 TAACCGAGTCCATAAATATTAAATATGAATATTTATGGGGTTAATATAAA
195 TAACCGAGTCCATAAATATTAAATATGAATATTTACGAGGTTAATATAAA
2256320 TGTATATAGA
Statistics
Matches: 217, Mismatches: 25, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
246 134 0.62
247 83 0.38
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (247 bp):
CTCTCACCTATGTCAAGTAAGTGGTTTTGATCGTTCAAGCTTGTAAGATCTCAGGCTCTCAAGTG
TCTTAGCTCACAACATAATCTTGGTCAAAAAAGCTAACCAACAAGGCATGAGCTCGCAAGGTGGC
TCACAATTGTAACAACTCAATTTTTAGTAGTACTGAAAAAGGAGATTTTGGAACCTCATTTCTGT
AACCGAGTCCATAAATATTAAATATGAATATTTACGAGGTTAATATAAAGAT
Found at i:2262331 original size:57 final size:57
Alignment explanation
Indices: 2262216--2262327 Score: 201
Period size: 55 Copynumber: 2.0 Consensus size: 57
2262206 TCTTTCGTAC
2262216 ACCAAACCTTTCTCTCTTCAAAATCTCATTCCATTTCTTCATCTTCTCTCTCTCTCT
1 ACCAAACCTTTCTCTCTTCAAAATCTCATTCCATTTCTTCATCTTCTCTCTCTCTCT
*
2262273 ACCAAACC-TT-TCTCTTCAAACTCTCATTCCATTTCTTCATCTTCTCTCTCTCTCT
1 ACCAAACCTTTCTCTCTTCAAAATCTCATTCCATTTCTTCATCTTCTCTCTCTCTCT
2262328 CTACACAAGT
Statistics
Matches: 54, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
55 44 0.81
56 2 0.04
57 8 0.15
ACGTcount: A:0.19, C:0.38, G:0.00, T:0.44
Consensus pattern (57 bp):
ACCAAACCTTTCTCTCTTCAAAATCTCATTCCATTTCTTCATCTTCTCTCTCTCTCT
Found at i:2264163 original size:27 final size:25
Alignment explanation
Indices: 2264112--2264163 Score: 59
Period size: 26 Copynumber: 2.0 Consensus size: 25
2264102 GAACCAACGA
*
2264112 ATTTTATAAAAACAATACCATTATT
1 ATTTTATAAAAACAATACCACTATT
* *
2264137 ATTTTATACAAAAGAATATCACCTATT
1 ATTTTATA-AAAACAATACCA-CTATT
2264164 TTATTTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 8 0.36
26 10 0.45
27 4 0.18
ACGTcount: A:0.46, C:0.13, G:0.02, T:0.38
Consensus pattern (25 bp):
ATTTTATAAAAACAATACCACTATT
Found at i:2267657 original size:63 final size:63
Alignment explanation
Indices: 2267590--2267795 Score: 157
Period size: 63 Copynumber: 3.1 Consensus size: 63
2267580 AAATCTTGCT
2267590 AATTTACGATCAAGGCTTCAGTTAATTGATTTACGATCATAAAAACTTCATTAAGAGTTCGCC
1 AATTTACGATCAAGGCTTCAGTTAATTGATTTACGATCATAAAAACTTCATTAAGAGTTCGCC
* * * * * * *
2267653 AATTTACGATTGCAA--CTCCACTTAAATAATTCACTGATTTACTACCACAACTATCATTTTCAA
1 AATTTACGA-T-CAAGGCTTCAGTTAATTGATTTAC-GA-TCA-TA--AAAACT-TCA--TT-AA
* *
2267716 -AGCTCGCT
55 GAGTTCGCC
* * ** * *
2267724 AATTTACAATCACGGCTTCAGTTCTTTGATTTACGATCATAAACACTTCATTAAGAGTTCACC
1 AATTTACGATCAAGGCTTCAGTTAATTGATTTACGATCATAAAAACTTCATTAAGAGTTCGCC
2267787 AATTTACGA
1 AATTTACGA
2267796 GCACAACTCC
Statistics
Matches: 104, Mismatches: 25, Indels: 28
0.66 0.16 0.18
Matches are distributed among these distances:
62 2 0.02
63 38 0.37
64 3 0.03
65 8 0.08
66 6 0.06
68 7 0.07
69 7 0.07
70 3 0.03
71 28 0.27
72 2 0.02
ACGTcount: A:0.34, C:0.21, G:0.11, T:0.34
Consensus pattern (63 bp):
AATTTACGATCAAGGCTTCAGTTAATTGATTTACGATCATAAAAACTTCATTAAGAGTTCGCC
Found at i:2267658 original size:134 final size:134
Alignment explanation
Indices: 2267410--2267906 Score: 557
Period size: 134 Copynumber: 3.7 Consensus size: 134
2267400 TACAAATCTC
* * ** * *
2267410 ACAGTTCGCTGATTTACGATCACAATTGTCATTTTTTAAGCTCGCCGATTTACGAACACGGCTTA
1 ACAGTTCGCTGATTTACGATCACAACTGTCATTTTTAAAGCTCGCTAATTTACGATCACGGCTTC
* * * * *
2267475 AGTTCATTGATTTACGATCATAAACAGTACATTAAGAGTTTGTCGATTTACGGTCGCAACTCCAC
66 AGTTCATTGATTTACGATCATAAACACTTCATTAAGAGTTCGCCAATTTACGGTCGCAACTCCAC
2267540 TTAA
131 TTAA
* * * * *
2267544 ACAGGTCGCTGATTTACGATCACAATTGTCATTTTTAAATCTTGCTAATTTACGATCAAGGCTTC
1 ACAGTTCGCTGATTTACGATCACAACTGTCATTTTTAAAGCTCGCTAATTTACGATCACGGCTTC
* * * *
2267609 AGTTAATTGATTTACGATCATAAAAACTTCATTAAGAGTTCGCCAATTTACGATTGCAACTCCAC
66 AGTTCATTGATTTACGATCATAAACACTTCATTAAGAGTTCGCCAATTTACGGTCGCAACTCCAC
2267674 TTAA
131 TTAA
* * * * * * * *
2267678 ATAATTCACTGATTTACTACCACAACTATCATTTTCAAAGCTCGCTAATTTACAATCACGGCTTC
1 ACAGTTCGCTGATTTACGATCACAACTGTCATTTTTAAAGCTCGCTAATTTACGATCACGGCTTC
* * *
2267743 AGTTCTTTGATTTACGATCATAAACACTTCATTAAGAGTTCACCAATTTACGAG-CACAACTCCG
66 AGTTCATTGATTTACGATCATAAACACTTCATTAAGAGTTCGCCAATTTACG-GTCGCAACTCC-
*
2267807 A-TTAG
129 ACTTAA
* * * * * * * * * *
2267812 ATAGTTCGTTGATTTACGATCACAACTGTCATTTGTAAAACTCGTTGATTTCCAATCACGACTTT
1 ACAGTTCGCTGATTTACGATCACAACTGTCATTTTTAAAGCTCGCTAATTTACGATCACGGCTTC
* * *
2267877 AGTTCATTGATTTATGATCTTGAACACTTC
66 AGTTCATTGATTTACGATCATAAACACTTC
2267907 TTAGTTCATA
Statistics
Matches: 304, Mismatches: 57, Indels: 4
0.83 0.16 0.01
Matches are distributed among these distances:
134 303 1.00
135 1 0.00
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.35
Consensus pattern (134 bp):
ACAGTTCGCTGATTTACGATCACAACTGTCATTTTTAAAGCTCGCTAATTTACGATCACGGCTTC
AGTTCATTGATTTACGATCATAAACACTTCATTAAGAGTTCGCCAATTTACGGTCGCAACTCCAC
TTAA
Found at i:2269087 original size:134 final size:134
Alignment explanation
Indices: 2268806--2269105 Score: 313
Period size: 134 Copynumber: 2.2 Consensus size: 134
2268796 TAATCAAAGA
* * * *
2268806 TTTAGTTCATTGATTTACAATCATGAAAACTTTATTATGAGTTCACTGATTTACGATCACAACTC
1 TTTAGTTCATTGATTTACGATCATGAAAACTTTATTAAGAGTTCACTGATTTACAATCACAACGC
* ** *
2268871 CATTTAAACACTTCGTTGATTTACGATCACAACTTTCATTTTCAAAGCTCGATAATTTACAATAA
66 CATTTAAACAATTCACTGATTTACAATCACAACTTTCATTTTCAAAGCTCGATAATTTACAATAA
*
2268936 CGGC
131 CGAC
* * * * * * *
2268940 TTCAATTCTTTGATTTACGATCATGAATATTTTATTAAGAGTTC-GTCGATTTACAATCGCAACG
1 TTTAGTTCATTGATTTACGATCATGAAAACTTTATTAAGAGTTCACT-GATTTACAATCACAACG
* * *
2269004 CCGA-TTAAACAATTCACTGATTTACAATCACAA-TTGTCATCTTT-AAAGCT-TACTGATTTCC
65 CC-ATTTAAACAATTCACTGATTTACAATCACAACTT-TCAT-TTTCAAAGCTCGA-TAATTTAC
* *
2269065 AATCATGAC
126 AATAACGAC
* *
2269074 TTTAGTTCATTGATTTACGATCTTGAACACTT
1 TTTAGTTCATTGATTTACGATCATGAAAACTT
2269106 CTTGTTTCAC
Statistics
Matches: 134, Mismatches: 27, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
133 4 0.03
134 126 0.94
135 4 0.03
ACGTcount: A:0.32, C:0.19, G:0.11, T:0.38
Consensus pattern (134 bp):
TTTAGTTCATTGATTTACGATCATGAAAACTTTATTAAGAGTTCACTGATTTACAATCACAACGC
CATTTAAACAATTCACTGATTTACAATCACAACTTTCATTTTCAAAGCTCGATAATTTACAATAA
CGAC
Found at i:2269216 original size:16 final size:18
Alignment explanation
Indices: 2269180--2269245 Score: 55
Period size: 18 Copynumber: 3.5 Consensus size: 18
2269170 TAAAATGTTT
*
2269180 TTTAAAAAATATATTATAA
1 TTTAAAAAATATA-TAAAA
2269199 -TTAAAAAATATA-AAAA
1 TTTAAAAAATATATAAAA
*
2269215 TTTAAAATAAATATGTAAAAA
1 TTT-AAA-AAATATAT-AAAA
2269236 TTTATAAAAA
1 TTTA-AAAAA
2269246 AAATTTTTGA
Statistics
Matches: 39, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
16 3 0.08
17 2 0.05
18 15 0.38
19 6 0.15
20 4 0.10
21 9 0.23
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.35
Consensus pattern (18 bp):
TTTAAAAAATATATAAAA
Found at i:2270120 original size:18 final size:18
Alignment explanation
Indices: 2270084--2270117 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2270074 GTGTTTTAAT
*
2270084 ATAATTTTTAATATTTTA
1 ATAATTTATAATATTTTA
2270102 ATAATTTAT-ATATTTT
1 ATAATTTATAATATTTT
2270118 TAAAGATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
ATAATTTATAATATTTTA
Found at i:2277137 original size:44 final size:46
Alignment explanation
Indices: 2277072--2277200 Score: 138
Period size: 49 Copynumber: 2.7 Consensus size: 46
2277062 ATGCACTAAT
* * *
2277072 GAACAGAGAGCACTAAAGTGCTATA-CAGAGAGCA-CAGATGTGCTA
1 GAACAGAGAGCACTAACGTGCTAAATCAGAGAGCACCA-ACGTGCTA
*
2277117 -AACAGAGAGCACTGACGTGCTAAAATCAGAGAGCACCAACGTGCTA
1 GAACAGAGAGCACTAACGTGCT-AAATCAGAGAGCACCAACGTGCTA
*
2277163 GTAGTCAGAGAGCACTAACGTGCTAATAATCAGAGAGC
1 G-A-ACAGAGAGCACTAACGTGCT-A-AATCAGAGAGC
2277201 GCGCTAAAGT
Statistics
Matches: 71, Mismatches: 6, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
44 19 0.27
45 2 0.03
46 16 0.23
47 2 0.03
48 1 0.01
49 20 0.28
50 11 0.15
ACGTcount: A:0.39, C:0.20, G:0.26, T:0.16
Consensus pattern (46 bp):
GAACAGAGAGCACTAACGTGCTAAATCAGAGAGCACCAACGTGCTA
Found at i:2277176 original size:25 final size:24
Alignment explanation
Indices: 2277075--2277200 Score: 136
Period size: 22 Copynumber: 5.3 Consensus size: 24
2277065 CACTAATGAA
*
2277075 CAGAGAGCACTAAAGTGCTAT-A-
1 CAGAGAGCACTAACGTGCTATAAT
*
2277097 CAGAGAGCAC-AGATGTGCTA-AA-
1 CAGAGAGCACTA-ACGTGCTATAAT
* *
2277119 CAGAGAGCACTGACGTGCTAAAAT
1 CAGAGAGCACTAACGTGCTATAAT
* *
2277143 CAGAGAGCACCAACGTGCTAGTAGT
1 CAGAGAGCACTAACGTGCTA-TAAT
2277168 CAGAGAGCACTAACGTGCTAATAAT
1 CAGAGAGCACTAACGTGCT-ATAAT
2277193 CAGAGAGC
1 CAGAGAGC
2277201 GCGCTAAAGT
Statistics
Matches: 88, Mismatches: 9, Indels: 11
0.81 0.08 0.10
Matches are distributed among these distances:
21 1 0.01
22 35 0.40
23 2 0.02
24 18 0.20
25 31 0.35
26 1 0.01
ACGTcount: A:0.38, C:0.21, G:0.25, T:0.16
Consensus pattern (24 bp):
CAGAGAGCACTAACGTGCTATAAT
Found at i:2277567 original size:15 final size:15
Alignment explanation
Indices: 2277547--2277576 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2277537 AATATAAGCA
*
2277547 TTTAAATAAAATAAT
1 TTTAAAAAAAATAAT
2277562 TTTAAAAAAAATAAT
1 TTTAAAAAAAATAAT
2277577 CTTGTAGTAC
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:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
TTTAAAAAAAATAAT
Found at i:2281476 original size:42 final size:42
Alignment explanation
Indices: 2281416--2281822 Score: 444
Period size: 42 Copynumber: 9.7 Consensus size: 42
2281406 TCGAAAGCTG
* * * *
2281416 AACAGAAGCTCATGAGAGCTAAACAGAAAC-CTATAA-AGGTTG
1 AACAGAAGCTCATAAGAGCTGAACGGAAACTC-ATAAGA-GTTA
* * * * *
2281458 AACAGAAGCTCTTAAGAGCTTAACGGAAACCCATAAGGGCTA
1 AACAGAAGCTCATAAGAGCTGAACGGAAACTCATAAGAGTTA
* * *
2281500 AACAGAAGCTCAAAAGAGCTGAACGGAAATTCATATGAGTTA
1 AACAGAAGCTCATAAGAGCTGAACGGAAACTCATAAGAGTTA
* * *
2281542 AACAGAAGCTCATAAGAGATGAACAGAAACTCATAAGAGTTG
1 AACAGAAGCTCATAAGAGCTGAACGGAAACTCATAAGAGTTA
* * * *
2281584 AACAGAAGCTCATGAGAGCTAAACAGAAAC-CTATAA-AGGTTG
1 AACAGAAGCTCATAAGAGCTGAACGGAAACTC-ATAAGA-GTTA
* * * * *
2281626 AACAGAAGCTCTTAAGAGCTTAACGGAAACCCATAAGGGCTA
1 AACAGAAGCTCATAAGAGCTGAACGGAAACTCATAAGAGTTA
* *
2281668 AACAGAAGCTCAAAAGAGCTGAACGGAAACTCATATGAGTTA
1 AACAGAAGCTCATAAGAGCTGAACGGAAACTCATAAGAGTTA
* * *
2281710 AACAGAAGCTCATAAGAGATGAACAGAAACTCATAAGAGTTG
1 AACAGAAGCTCATAAGAGCTGAACGGAAACTCATAAGAGTTA
* * *
2281752 AACAGAAGCTCAAAAGAGCTGAATGGAAACTCATATGAGTTA
1 AACAGAAGCTCATAAGAGCTGAACGGAAACTCATAAGAGTTA
* *
2281794 AACAGAAGCTCGTAAGAGCTAAACGGAAA
1 AACAGAAGCTCATAAGAGCTGAACGGAAA
2281823 GTAAAACACG
Statistics
Matches: 306, Mismatches: 53, Indels: 12
0.82 0.14 0.03
Matches are distributed among these distances:
41 2 0.01
42 302 0.99
43 2 0.01
ACGTcount: A:0.45, C:0.17, G:0.22, T:0.17
Consensus pattern (42 bp):
AACAGAAGCTCATAAGAGCTGAACGGAAACTCATAAGAGTTA
Found at i:2281692 original size:168 final size:168
Alignment explanation
Indices: 2281414--2281822 Score: 696
Period size: 168 Copynumber: 2.4 Consensus size: 168
2281404 GCTCGAAAGC
2281414 TGAACAGAAGCTCATGAGAGCTAAACAGAAACCTATAAAGGTTGAACAGAAGCTCTTAAGAGCTT
1 TGAACAGAAGCTCATGAGAGCTAAACAGAAACCTATAAAGGTTGAACAGAAGCTCTTAAGAGCTT
*
2281479 AACGGAAACCCATAAGGGCTAAACAGAAGCTCAAAAGAGCTGAACGGAAATTCATATGAGTTAAA
66 AACGGAAACCCATAAGGGCTAAACAGAAGCTCAAAAGAGCTGAACGGAAACTCATATGAGTTAAA
2281544 CAGAAGCTCATAAGAGATGAACAGAAACTCATAAGAGT
131 CAGAAGCTCATAAGAGATGAACAGAAACTCATAAGAGT
2281582 TGAACAGAAGCTCATGAGAGCTAAACAGAAACCTATAAAGGTTGAACAGAAGCTCTTAAGAGCTT
1 TGAACAGAAGCTCATGAGAGCTAAACAGAAACCTATAAAGGTTGAACAGAAGCTCTTAAGAGCTT
2281647 AACGGAAACCCATAAGGGCTAAACAGAAGCTCAAAAGAGCTGAACGGAAACTCATATGAGTTAAA
66 AACGGAAACCCATAAGGGCTAAACAGAAGCTCAAAAGAGCTGAACGGAAACTCATATGAGTTAAA
2281712 CAGAAGCTCATAAGAGATGAACAGAAACTCATAAGAGT
131 CAGAAGCTCATAAGAGATGAACAGAAACTCATAAGAGT
** * ** * * *
2281750 TGAACAGAAGCTCAAAAGAGCTGAATGGAAA-CTCAT-ATGAGTTAAACAGAAGCTCGTAAGAGC
1 TGAACAGAAGCTCATGAGAGCTAAACAGAAACCT-ATAAAG-GTTGAACAGAAGCTCTTAAGAGC
*
2281813 TAAACGGAAA
64 TTAACGGAAA
2281823 GTAAAACACG
Statistics
Matches: 229, Mismatches: 10, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
167 4 0.02
168 225 0.98
ACGTcount: A:0.45, C:0.17, G:0.22, T:0.17
Consensus pattern (168 bp):
TGAACAGAAGCTCATGAGAGCTAAACAGAAACCTATAAAGGTTGAACAGAAGCTCTTAAGAGCTT
AACGGAAACCCATAAGGGCTAAACAGAAGCTCAAAAGAGCTGAACGGAAACTCATATGAGTTAAA
CAGAAGCTCATAAGAGATGAACAGAAACTCATAAGAGT
Found at i:2286226 original size:17 final size:16
Alignment explanation
Indices: 2286206--2286260 Score: 56
Period size: 17 Copynumber: 3.3 Consensus size: 16
2286196 AGAGAGAAGC
*
2286206 AAAAGAGAATAAAAAG
1 AAAAAAGAATAAAAAG
*
2286222 AAAAAAAGAAAAAAAAG
1 -AAAAAAGAATAAAAAG
**
2286239 TTAAAAGAATATAAAAG
1 AAAAAAGAATA-AAAAG
2286256 AAAAA
1 AAAAA
2286261 TTTTAAATTG
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
16 8 0.27
17 22 0.73
ACGTcount: A:0.78, C:0.00, G:0.13, T:0.09
Consensus pattern (16 bp):
AAAAAAGAATAAAAAG
Found at i:2298920 original size:60 final size:61
Alignment explanation
Indices: 2298846--2298971 Score: 152
Period size: 60 Copynumber: 2.1 Consensus size: 61
2298836 AATCAAATTC
*
2298846 AGGTATCAATTTGAACC-AAGAAGCCAAGTTC-AGATACCTAATTGGACCAAA-ATAAACT-TT
1 AGGTATCAAATTGAACCTAA-AAGCCAAGTTCAAG-TACCTAATTGGACCAAAGA-AAACTCTT
* * * *
2298906 AGGTATTAAATTGAACCTTAAAGTCAAGTTCAAGTACCTAATTGGACTAAAGAAAACTCTT
1 AGGTATCAAATTGAACCTAAAAGCCAAGTTCAAGTACCTAATTGGACCAAAGAAAACTCTT
2298967 AGGTA
1 AGGTA
2298972 CCAATATGCA
Statistics
Matches: 57, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
60 46 0.81
61 11 0.19
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.27
Consensus pattern (61 bp):
AGGTATCAAATTGAACCTAAAAGCCAAGTTCAAGTACCTAATTGGACCAAAGAAAACTCTT
Found at i:2300967 original size:12 final size:11
Alignment explanation
Indices: 2300946--2301002 Score: 53
Period size: 12 Copynumber: 4.7 Consensus size: 11
2300936 CACAAAATGT
2300946 TTTTTATTTTA
1 TTTTTATTTTA
2300957 TTTTTATTTTTA
1 TTTTTA-TTTTA
2300969 TCGTTATTATTTTA
1 T--TT-TTATTTTA
2300983 TTTTTAATTTT-
1 TTTTT-ATTTTA
2300994 TTTATTATT
1 TTT-TTATT
2301003 CTCGTTGTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
11 14 0.35
12 15 0.38
14 8 0.20
15 3 0.08
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.77
Consensus pattern (11 bp):
TTTTTATTTTA
Found at i:2301001 original size:26 final size:26
Alignment explanation
Indices: 2300949--2301002 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
2300939 AAAATGTTTT
*
2300949 TTATTTTATTTTTATTTTTATCGTTA
1 TTATTTTATTTTTATTTTTATCATTA
*
2300975 TTATTTTATTTTTAATTTTT-TTATTA
1 TTATTTTATTTTT-ATTTTTATCATTA
2301001 TT
1 TT
2301003 CTCGTTGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 19 0.76
27 6 0.24
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (26 bp):
TTATTTTATTTTTATTTTTATCATTA
Found at i:2303542 original size:18 final size:17
Alignment explanation
Indices: 2303517--2303559 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
2303507 AGTGCTTTAA
*
2303517 ATTT-TTTTATTTGTTT
1 ATTTCTTTTATTTGTTG
2303533 ATTTACTTTTATTTGTTG
1 ATTT-CTTTTATTTGTTG
2303551 ATTTCTTTT
1 ATTTCTTTT
2303560 CATTATATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 4 0.17
17 5 0.21
18 15 0.62
ACGTcount: A:0.14, C:0.05, G:0.07, T:0.74
Consensus pattern (17 bp):
ATTTCTTTTATTTGTTG
Found at i:2304053 original size:219 final size:218
Alignment explanation
Indices: 2303669--2304149 Score: 809
Period size: 219 Copynumber: 2.2 Consensus size: 218
2303659 TCAAAAACGA
* * *
2303669 AAAAATTTTCAAATAAGGCAATGTTTTGCGTTTGAAAATTCGAGAAAATATGCCCTAAGGTGCTG
1 AAAAATTTTAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTG
* * * * *
2303734 GGTGTCGATTTTTCTCGTTCAACCAAATGACTTAATATCCTTTTAGAAATTTTAAAATAAGGTAA
66 GGTGTCAATTTTTCTCGTTCAACCAAATGACTAAATATCCTTTAAAAAATTTTAAAATAAGGCAA
*
2303799 TGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCTCGTTCA
131 TGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCTCATTCA
*
2303864 ACCAAATGGCTTAATATCCTTTT
196 ACCAAATGGCTAAATATCCTTTT
* *
2303887 AAAAATTTTAAAATAAGACAATGTTTTGCGTTTGGGAAATTCGAGAAAACATGCTCTAAGGTGCT
1 AAAAATTTTAAAATAAGGCAATGTTTTGCGTTT-GGAAATTCGAGAAAACATGCCCTAAGGTGCT
*
2303952 GGGTGTCAATTTTTCTCGTTCAACCAAATGGCTAAATATCCTTTAAAAAATTTTAAAATAAGGCA
65 GGGTGTCAATTTTTCTCGTTCAACCAAATGACTAAATATCCTTTAAAAAATTTTAAAATAAGGCA
* *
2304017 ATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTGTCGATTTTTCTCATTC
130 ATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCTCATTC
2304082 AACCAAATGGCTAAATATCCTTTT
195 AACCAAATGGCTAAATATCCTTTT
*
2304106 AAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAG
1 AAAAATTTTAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAG
2304150 GAACGTGCCA
Statistics
Matches: 245, Mismatches: 17, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
218 42 0.17
219 203 0.83
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.35
Consensus pattern (218 bp):
AAAAATTTTAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTG
GGTGTCAATTTTTCTCGTTCAACCAAATGACTAAATATCCTTTAAAAAATTTTAAAATAAGGCAA
TGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCTCATTCA
ACCAAATGGCTAAATATCCTTTT
Found at i:2304183 original size:109 final size:109
Alignment explanation
Indices: 2303669--2304182 Score: 814
Period size: 109 Copynumber: 4.7 Consensus size: 109
2303659 TCAAAAACGA
* * *
2303669 AAAAATTTTCAAATAAGGCAATGTTTTGCGTTTGAAAATTCGAGAAAATATGCCCTAAGGTGCTG
1 AAAAATTTTAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTG
* *
2303734 GGTGTCGATTTTTCTCGTTCAACCAAATGACTTAATATCCTTTT
66 GGTGTCGATTTTTCTCGTTCAACCAAATGGCTAAATATCCTTTT
* *
2303778 AGAAATTTTAAAATAAGGTAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTG
1 AAAAATTTTAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTG
*
2303843 GGTGTCGATTTTTCTCGTTCAACCAAATGGCTTAATATCCTTTT
66 GGTGTCGATTTTTCTCGTTCAACCAAATGGCTAAATATCCTTTT
* *
2303887 AAAAATTTTAAAATAAGACAATGTTTTGCGTTTGGGAAATTCGAGAAAACATGCTCTAAGGTGCT
1 AAAAATTTTAAAATAAGGCAATGTTTTGCGTTT-GGAAATTCGAGAAAACATGCCCTAAGGTGCT
* *
2303952 GGGTGTCAATTTTTCTCGTTCAACCAAATGGCTAAATATCCTTTA
65 GGGTGTCGATTTTTCTCGTTCAACCAAATGGCTAAATATCCTTTT
* *
2303997 AAAAATTTTAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTG
1 AAAAATTTTAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTG
*
2304062 GGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTTT
66 GGTGTCGATTTTTCTCGTTCAACCAAATGGCTAAATATCCTTTT
* * * * **
2304106 AAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAG-GAACGTGCCATAATATGCTG
1 AAAAATTTTAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTG
*
2304170 GGTTTCGATTTTT
66 GGTGTCGATTTTT
2304183 TGATTGACCG
Statistics
Matches: 379, Mismatches: 25, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
108 29 0.08
109 246 0.65
110 104 0.27
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35
Consensus pattern (109 bp):
AAAAATTTTAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTG
GGTGTCGATTTTTCTCGTTCAACCAAATGGCTAAATATCCTTTT
Found at i:2305907 original size:24 final size:24
Alignment explanation
Indices: 2305880--2305930 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
2305870 AAAGAGTCTA
*
2305880 TAACGGGTAGCTCCAAAAAGCAAT
1 TAACAGGTAGCTCCAAAAAGCAAT
* *
2305904 TAACAGGTAGCTCTAAAGAGCAAT
1 TAACAGGTAGCTCCAAAAAGCAAT
2305928 TAA
1 TAA
2305931 TATGAAGCAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.43, C:0.18, G:0.20, T:0.20
Consensus pattern (24 bp):
TAACAGGTAGCTCCAAAAAGCAAT
Found at i:2306034 original size:26 final size:26
Alignment explanation
Indices: 2305983--2306041 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 26
2305973 CACTAACGGG
* * * *
2305983 AAGCTCACAAAGAGCCTTTAATCAGA
1 AAGCTCACAAAGAGACATAAAACAGA
2306009 AAGCTCACAAAGAGACATAAAACAGA
1 AAGCTCACAAAGAGACATAAAACAGA
*
2306035 ACGCTCA
1 AAGCTCA
2306042 TAAGAGCTGC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.47, C:0.24, G:0.15, T:0.14
Consensus pattern (26 bp):
AAGCTCACAAAGAGACATAAAACAGA
Found at i:2306385 original size:13 final size:13
Alignment explanation
Indices: 2306367--2306391 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2306357 TAAAGTATTT
2306367 TAAAATTAAAAAA
1 TAAAATTAAAAAA
2306380 TAAAATTAAAAA
1 TAAAATTAAAAA
2306392 TATATATTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
TAAAATTAAAAAA
Found at i:2308082 original size:18 final size:18
Alignment explanation
Indices: 2308059--2308095 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
2308049 TCAATCTAAA
*
2308059 ACCAAACCAAGGCATACC
1 ACCAAACCAACGCATACC
2308077 ACCAAACCAACGCATACC
1 ACCAAACCAACGCATACC
2308095 A
1 A
2308096 AAGTATCATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.46, C:0.41, G:0.08, T:0.05
Consensus pattern (18 bp):
ACCAAACCAACGCATACC
Found at i:2309276 original size:43 final size:42
Alignment explanation
Indices: 2309106--2309312 Score: 215
Period size: 42 Copynumber: 4.9 Consensus size: 42
2309096 AACTCGCACA
* * * * * *
2309106 ATGCC-ATATCCCAGATATGGTCGTACATGCTATCATATATCG
1 ATGCCAATGTCCCAGACATGGTCTTACACG-AATCACATATCG
* *
2309148 ATGCCAATAG--CCAG-CTATGGTCTTACACGAATCTCATATCA
1 ATGCCAAT-GTCCCAGAC-ATGGTCTTACACGAATCACATATCG
***
2309189 ATGCCAATGTCCCAGACATGGTCTTACACGAATCTTGTATCG
1 ATGCCAATGTCCCAGACATGGTCTTACACGAATCACATATCG
* * *
2309231 ATGCCAATGTCCCAGACATGGGTTTTACATGAATCACATAACG
1 ATGCCAATGTCCCAGACAT-GGTCTTACACGAATCACATATCG
2309274 ATGCCAATGTCCCAGACATGGTCTTACACGTAATCACAT
1 ATGCCAATGTCCCAGACATGGTCTTACACG-AATCACAT
2309313 CTCAGTATCC
Statistics
Matches: 138, Mismatches: 19, Indels: 15
0.80 0.11 0.09
Matches are distributed among these distances:
40 1 0.01
41 16 0.12
42 74 0.54
43 47 0.34
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.28
Consensus pattern (42 bp):
ATGCCAATGTCCCAGACATGGTCTTACACGAATCACATATCG
Found at i:2316179 original size:91 final size:91
Alignment explanation
Indices: 2316024--2316207 Score: 332
Period size: 91 Copynumber: 2.0 Consensus size: 91
2316014 TTAATGGAAA
2316024 AATAATATTCAAGTAAAAGGATTTCTGCATATTGCTCTAAAAGGTTTTCTAAATAGTACAAGGAC
1 AATAATATTCAAGTAAAAGGATTTCTGCATATTGCTCTAAAAGGTTTTCTAAATAGTACAAGGAC
2316089 CTAAAACAAGACCACTAGTCAGAACT
66 CTAAAACAAGACCACTAGTCAGAACT
* **
2316115 AATAATATTCAAGTAAAAGGATTTCTGCATATTGCTCTGAAAGGTTTTCTAAATAGTGTAAGGAC
1 AATAATATTCAAGTAAAAGGATTTCTGCATATTGCTCTAAAAGGTTTTCTAAATAGTACAAGGAC
*
2316180 CTGAAACAAGACCACTAGTCAGAACT
66 CTAAAACAAGACCACTAGTCAGAACT
2316206 AA
1 AA
2316208 CCAAATTTAA
Statistics
Matches: 89, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
91 89 1.00
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.28
Consensus pattern (91 bp):
AATAATATTCAAGTAAAAGGATTTCTGCATATTGCTCTAAAAGGTTTTCTAAATAGTACAAGGAC
CTAAAACAAGACCACTAGTCAGAACT
Found at i:2316742 original size:88 final size:85
Alignment explanation
Indices: 2316591--2317178 Score: 243
Period size: 96 Copynumber: 6.4 Consensus size: 85
2316581 CATCGTGGCG
* * * * *
2316591 AATCTTATCTCCCTGAAGTTACAGTAGAGTAGATTAAA-GCCACAAGTCTCATTTCCCTGAAGTT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAATG-C-GAA-TCTTATTTCCCTGAAGTT
*
2316655 ACAGTGAAGCATATTGAAGTTAC
63 GCAGTGAAGCATATTGAAGTTAC
*
2316678 AAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTCAATATGCGAATCTTATTTCCGTGAAGTT
1 AA-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT-AA-ATGCGAATCTTATTTCCCTGAAGTT
* * *
2316743 GTAGTGGAA-CAGATTAAAGCTGCAGGTTAC
63 GCAGT-GAAGC--A-T--A-TTG-AAGTTAC
* * * * * *
2316773 AAATCTTATCTCCCTGAGGTTGTAGTGGAGCAAATTAAAGATAGCGAATCTTATTTTCTTGAAAT
1 -AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT-AA-AT-GCGAATCTTATTTCCCTGAAGT
* * * *
2316838 TGCAGTGGAGCAGATTAAAGATAAC
62 TGCAGTGAAGCATATTGAAG-TTAC
* * * * *
2316863 GAATCTTATTTCCCTGAAGTTGCAATGGAACAGATTAAAGTTACAAGTTACAAATCTTATCTCCC
1 -AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAA--T----G---CGAATCTTATTTCCC
* * * *
2316928 TGAAGTTGAAGTGGAGCAGATTGAAGATAGC
56 TGAAGTTGCAGTGAAGCATATTGAAGTTA-C
* * * * *
2316959 AAATCTTATTTTCCTGAAGTTGCAGTGGAACAGATTAAAGCTACAAGTTACAATTCTTATCTCCC
1 -AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAA--TGC--G----AA-TCTTATTTCCC
* * * * *
2317024 TGAACG-TGCAATGGAGCAGATTAAAG--CC
56 TGAA-GTTGCAGTGAAGCATATTGAAGTTAC
* * * * * *
2317052 AACCTTATCTCCTTGAAGTTGCAGTGGAGCTAG-TTAAAGCTACAAATCTTATCTCCCTAAAGTT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGC-AGATTAAA--TGCGAATCTTATTTCCCTGAAGTT
* * * *
2317116 GTAGTGGAGCAGATTGAAGATAGC
63 GCAGTGAAGCATATTGAAGTTA-C
* * * *
2317140 AAATCTTATTTCCCTAAAGTTACAGTGGAACAGATTAAA
1 -AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAA
2317179 GCTACAAGTT
Statistics
Matches: 393, Mismatches: 68, Indels: 78
0.73 0.13 0.14
Matches are distributed among these distances:
84 1 0.00
85 31 0.08
86 2 0.01
87 2 0.01
88 54 0.14
89 41 0.10
90 37 0.09
91 3 0.01
92 35 0.09
93 6 0.02
94 3 0.01
95 45 0.11
96 132 0.34
97 1 0.00
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (85 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAATGCGAATCTTATTTCCCTGAAGTTGCA
GTGAAGCATATTGAAGTTAC
Found at i:2316786 original size:95 final size:96
Alignment explanation
Indices: 2316673--2316857 Score: 264
Period size: 95 Copynumber: 1.9 Consensus size: 96
2316663 GCATATTGAA
* * * *
2316673 GTTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTCAATAT-GCGAATCTTATTTCCGT
1 GTTACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAGATAGCGAATCTTATTTCCGT
* *
2316737 GAAGTTGTAGTGGAACAGATTAAAGCTGCAG
66 GAAATTGCAGTGGAACAGATTAAAGCTGCAG
* * * *
2316768 GTTACAAATCTTATCTCCCTGAGGTTGTAGTGGAGCAAATTAAAGATAGCGAATCTTATTTTCTT
1 GTTACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAGATAGCGAATCTTATTTCCGT
*
2316833 GAAATTGCAGTGGAGCAGATTAAAG
66 GAAATTGCAGTGGAACAGATTAAAG
2316858 ATAACGAATC
Statistics
Matches: 78, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
95 41 0.53
96 37 0.47
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.31
Consensus pattern (96 bp):
GTTACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAGATAGCGAATCTTATTTCCGT
GAAATTGCAGTGGAACAGATTAAAGCTGCAG
Found at i:2316845 original size:45 final size:45
Alignment explanation
Indices: 2316591--2317448 Score: 449
Period size: 44 Copynumber: 18.6 Consensus size: 45
2316581 CATCGTGGCG
* * * * **
2316591 AATCTTATCTCCCTGAAGTTACAGTAGAGTAGATTAAAGCCA-CA
1 AATCTTATTTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATAGCA
* * * * * * *
2316635 AGTCTCATTTCCCTGAAGTTACAGTGAAGCATATTGAAGTTA-CA
1 AATCTTATTTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATAGCA
* * * * *
2316679 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTCAATAT-GCG
1 AATCTTATTTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATAGCA
* * * *
2316723 AATCTTATTTCCGTGAAGTTGTAGTGGAACAGATTAAAGCTGCAGGTTACA
1 AATCTTATTTCCCTGAAGTTGCAGTGGAGCAGATTAAAGAT--A-G---CA
* * * * *
2316774 AATCTTATCTCCCTGAGGTTGTAGTGGAGCAAATTAAAGATAGCG
1 AATCTTATTTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATAGCA
* * * * *
2316819 AATCTTATTTTCTTGAAATTGCAGTGGAGCAGATTAAAGATAACG
1 AATCTTATTTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATAGCA
* * *
2316864 AATCTTATTTCCCTGAAGTTGCAATGGAACAGATTAAAGTTACAAGTTACA
1 AATCTTATTTCCCTGAAGTTGCAGTGGAGCAGATTAAAG--A-TAG---CA
* * *
2316915 AATCTTATCTCCCTGAAGTTGAAGTGGAGCAGATTGAAGATAGCA
1 AATCTTATTTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATAGCA
* * *
2316960 AATCTTATTTTCCTGAAGTTGCAGTGGAACAGATTAAAGCTACAAGTTACA
1 AATCTTATTTCCCTGAAGTTGCAGTGGAGCAGATTAAAG--A-TAG---CA
* * * *
2317011 ATTCTTATCTCCCTGAACG-TGCAATGGAGCAGATT--A-A-AGCC
1 AATCTTATTTCCCTGAA-GTTGCAGTGGAGCAGATTAAAGATAGCA
* * * *
2317052 AACCTTATCTCCTTGAAGTTGCAGTGGAGCTAG-TTAAAGCTA-CA
1 AATCTTATTTCCCTGAAGTTGCAGTGGAGC-AGATTAAAGATAGCA
* * * *
2317096 AATCTTATCTCCCTAAAGTTGTAGTGGAGCAGATTGAAGATAGCA
1 AATCTTATTTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATAGCA
* * * *
2317141 AATCTTATTTCCCTAAAGTTACAGTGGAACAGATTAAAGCTACAAGTTACA
1 AATCTTATTTCCCTGAAGTTGCAGTGGAGCAGATTAAAG--A-TAG---CA
* * * **
2317192 AATCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTGAAGCGA-CA
1 AATCTTATTTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATAGCA
* * * * * * *
2317236 AGTCCTA-TACCTCTGAGGTTGCAGTGGATCGGATTAAGTCTACCATAGCA
1 AATCTTATTTCC-CTGAAGTTGCAGTGGAGCAGATTAA----A-GATAGCA
* * *
2317286 AATCTTATTTCCCTAAAGTTGCAGTGGAATAGACTAAAGTTACAAGCTA-CA
1 AATCTTATTTCCCTGAAGTTGCAGTGG---AG-C-AGA-TTA-AAGATAGCA
* * ** * * * *
2317337 AATCTTATCTCCCTGAAGTTGCAGCGGAATAGGTTGAATATA-CG
1 AATCTTATTTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATAGCA
* * *
2317381 AA---TATCTCCCTGAAGTTGCAGTAGAGTAGATTAAA-ATTA-CA
1 AATCTTATTTCCCTGAAGTTGCAGTGGAGCAGATTAAAGA-TAGCA
* * *
2317422 ATTCTTATATCCCTGAAATTGCAGTGG
1 AATCTTATTTCCCTGAAGTTGCAGTGG
2317449 GTGGGAATGA
Statistics
Matches: 622, Mismatches: 138, Indels: 108
0.72 0.16 0.12
Matches are distributed among these distances:
40 2 0.00
41 59 0.09
42 2 0.00
43 5 0.01
44 190 0.31
45 147 0.24
46 2 0.00
47 3 0.00
48 12 0.02
49 4 0.01
50 20 0.03
51 165 0.27
52 3 0.00
53 2 0.00
54 1 0.00
55 1 0.00
56 3 0.00
57 1 0.00
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (45 bp):
AATCTTATTTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATAGCA
Found at i:2317044 original size:51 final size:51
Alignment explanation
Indices: 2316723--2317359 Score: 277
Period size: 51 Copynumber: 13.5 Consensus size: 51
2316713 TCAATATGCG
* * * * * *
2316723 AATCTTATTTCCGTGAAGTTGTAGTGGAACAGATTAAAGCTGCAGGTTACA
1 AATCTTATCTCCCTGAAGTTGCAATGGAACAGATTAAAGCTACAAGTTACA
* * * * * * *
2316774 AATCTTATCTCCCTGAGGTTGTAGTGGAGCAAATTAAAG--A-TAG---CG
1 AATCTTATCTCCCTGAAGTTGCAATGGAACAGATTAAAGCTACAAGTTACA
* * * * * * * *
2316819 AATCTTATTTTCTTGAAATTGCAGTGGAGCAGATTAAAG-----A-TAACG
1 AATCTTATCTCCCTGAAGTTGCAATGGAACAGATTAAAGCTACAAGTTACA
* *
2316864 AATCTTATTTCCCTGAAGTTGCAATGGAACAGATTAAAGTTACAAGTTACA
1 AATCTTATCTCCCTGAAGTTGCAATGGAACAGATTAAAGCTACAAGTTACA
* * *
2316915 AATCTTATCTCCCTGAAGTTG-AAGTGGAGCAGATTGAAG--A-TAG---CA
1 AATCTTATCTCCCTGAAGTTGCAA-TGGAACAGATTAAAGCTACAAGTTACA
* * *
2316960 AATCTTATTTTCCTGAAGTTGCAGTGGAACAGATTAAAGCTACAAGTTACA
1 AATCTTATCTCCCTGAAGTTGCAATGGAACAGATTAAAGCTACAAGTTACA
* *
2317011 ATTCTTATCTCCCTGAACG-TGCAATGGAGCAGATTAAAGC--C-A---AC-
1 AATCTTATCTCCCTGAA-GTTGCAATGGAACAGATTAAAGCTACAAGTTACA
* * *
2317055 ---CTTATCTCCTTGAAGTTGCAGTGGAGCTAG-TTAAAG---C----TACA
1 AATCTTATCTCCCTGAAGTTGCAATGGAAC-AGATTAAAGCTACAAGTTACA
* * * * * *
2317096 AATCTTATCTCCCTAAAGTTGTAGTGGAGCAGATTGAAG--A-TAG---CA
1 AATCTTATCTCCCTGAAGTTGCAATGGAACAGATTAAAGCTACAAGTTACA
* * * *
2317141 AATCTTATTTCCCTAAAGTTACAGTGGAACAGATTAAAGCTACAAGTTACA
1 AATCTTATCTCCCTGAAGTTGCAATGGAACAGATTAAAGCTACAAGTTACA
* * * * *
2317192 AATCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTGAAGCGACAAG-T-C-
1 AATCTTATCTCCCTGAAGTTGCAATGGAACAGATTAAAGCTACAAGTTACA
* * * * * *
2317240 ---C-TATAC-CTCTGAGGTTGCAGTGGATCGGATT-AAGTCTACCA--TAGCA
1 AATCTTAT-CTCCCTGAAGTTGCAATGGAACAGATTAAAG-CTACAAGTTA-CA
* * * * * * *
2317286 AATCTTATTTCCCTAAAGTTGCAGTGGAATAGACTAAAGTTACAAGCTACA
1 AATCTTATCTCCCTGAAGTTGCAATGGAACAGATTAAAGCTACAAGTTACA
2317337 AATCTTATCTCCCTGAAGTTGCA
1 AATCTTATCTCCCTGAAGTTGCA
2317360 GCGGAATAGG
Statistics
Matches: 461, Mismatches: 76, Indels: 98
0.73 0.12 0.15
Matches are distributed among these distances:
40 4 0.01
41 29 0.06
42 2 0.00
43 7 0.02
44 56 0.12
45 144 0.31
46 1 0.00
47 2 0.00
48 8 0.02
49 4 0.01
50 29 0.06
51 172 0.37
52 3 0.01
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (51 bp):
AATCTTATCTCCCTGAAGTTGCAATGGAACAGATTAAAGCTACAAGTTACA
Found at i:2317124 original size:181 final size:182
Alignment explanation
Indices: 2316901--2317231 Score: 549
Period size: 181 Copynumber: 1.8 Consensus size: 182
2316891 AACAGATTAA
* *
2316901 AGTTACAAGTTACAAATCTTATCTCCCTGAAGTTGAAGTGGAGCAGATTGAAGATAGCAAATCTT
1 AGTTACAAGCTACAAATCTTATCTCCCTAAAGTTGAAGTGGAGCAGATTGAAGATAGCAAATCTT
* * * *
2316966 ATTTTCCTGAAGTTGCAGTGGAACAGATTAAAGCTACAAGTTACAATTCTTATCTCCCTGAACG-
66 ATTTCCCTAAAGTTACAGTGGAACAGATTAAAGCTACAAGTTACAAATCTTATCTCCCTGAA-GT
2317030 TGCAATGGAGCAGATTAAAGCCAACCTTATCTCCTTGAAGTTGCAGTGGAGCT
130 TGCAATGGAGCAGATTAAAGCCAACCTTATCTCCTTGAAGTTGCAGTGGAGCT
*
2317083 AGTTA-AAGCTACAAATCTTATCTCCCTAAAGTTGTAGTGGAGCAGATTGAAGATAGCAAATCTT
1 AGTTACAAGCTACAAATCTTATCTCCCTAAAGTTGAAGTGGAGCAGATTGAAGATAGCAAATCTT
*
2317147 ATTTCCCTAAAGTTACAGTGGAACAGATTAAAGCTACAAGTTACAAATCTTATCTCCTTGAAGTT
66 ATTTCCCTAAAGTTACAGTGGAACAGATTAAAGCTACAAGTTACAAATCTTATCTCCCTGAAGTT
* *
2317212 GCAGTGGAGCAGATTGAAGC
131 GCAATGGAGCAGATTAAAGC
2317232 GACAAGTCCT
Statistics
Matches: 138, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
180 1 0.01
181 132 0.96
182 5 0.04
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (182 bp):
AGTTACAAGCTACAAATCTTATCTCCCTAAAGTTGAAGTGGAGCAGATTGAAGATAGCAAATCTT
ATTTCCCTAAAGTTACAGTGGAACAGATTAAAGCTACAAGTTACAAATCTTATCTCCCTGAAGTT
GCAATGGAGCAGATTAAAGCCAACCTTATCTCCTTGAAGTTGCAGTGGAGCT
Found at i:2317227 original size:96 final size:96
Alignment explanation
Indices: 2316832--2317313 Score: 514
Period size: 96 Copynumber: 5.2 Consensus size: 96
2316822 CTTATTTTCT
* * * * *
2316832 TGAAATTGCAGTGGAGCAGATTAAAGATAACGAATCTTATTTCCCTGAAGTTGCAATGGAACAGA
1 TGAAGTTGCAGTGGAGCAGATTGAAGATAGCAAATCTTATTTCCCTGAAGTTGCAGTGGAACAGA
*
2316897 TTAAAGTTACAAGTTACAAATCTTATCTCCC
66 TTAAAGCTACAAGTTACAAATCTTATCTCCC
* *
2316928 TGAAGTTGAAGTGGAGCAGATTGAAGATAGCAAATCTTATTTTCCTGAAGTTGCAGTGGAACAGA
1 TGAAGTTGCAGTGGAGCAGATTGAAGATAGCAAATCTTATTTCCCTGAAGTTGCAGTGGAACAGA
*
2316993 TTAAAGCTACAAGTTACAATTCTTATCTCCC
66 TTAAAGCTACAAGTTACAAATCTTATCTCCC
* * * * * *
2317024 TGAACG-TGCAATGGAGCAGATT--A-A-AGCCAACCTTATCTCCTTGAAGTTGCAGTGGAGCTA
1 TGAA-GTTGCAGTGGAGCAGATTGAAGATAGCAAATCTTATTTCCCTGAAGTTGCAGTGGAAC-A
2317084 G-TTAAAG---C----TACAAATCTTATCTCCC
64 GATTAAAGCTACAAGTTACAAATCTTATCTCCC
* * * *
2317109 TAAAGTTGTAGTGGAGCAGATTGAAGATAGCAAATCTTATTTCCCTAAAGTTACAGTGGAACAGA
1 TGAAGTTGCAGTGGAGCAGATTGAAGATAGCAAATCTTATTTCCCTGAAGTTGCAGTGGAACAGA
*
2317174 TTAAAGCTACAAGTTACAAATCTTATCTCCT
66 TTAAAGCTACAAGTTACAAATCTTATCTCCC
** * * * * * *
2317205 TGAAGTTGCAGTGGAGCAGATTGAAGCGA-CAAGTCCTA-TACCTCTGAGGTTGCAGTGGATCGG
1 TGAAGTTGCAGTGGAGCAGATTGAAGATAGCAAATCTTATTTCC-CTGAAGTTGCAGTGGAACAG
* *
2317268 ATT-AAGTCTACCA--TAGCAAATCTTATTTCCC
65 ATTAAAG-CTACAAGTTA-CAAATCTTATCTCCC
*
2317299 TAAAGTTGCAGTGGA
1 TGAAGTTGCAGTGGA
2317314 ATAGACTAAA
Statistics
Matches: 323, Mismatches: 45, Indels: 38
0.80 0.11 0.09
Matches are distributed among these distances:
84 1 0.00
85 33 0.10
87 1 0.00
88 3 0.01
89 34 0.11
92 35 0.11
93 5 0.02
94 34 0.11
95 30 0.09
96 146 0.45
97 1 0.00
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.29
Consensus pattern (96 bp):
TGAAGTTGCAGTGGAGCAGATTGAAGATAGCAAATCTTATTTCCCTGAAGTTGCAGTGGAACAGA
TTAAAGCTACAAGTTACAAATCTTATCTCCC
Found at i:2318811 original size:10 final size:10
Alignment explanation
Indices: 2318798--2318822 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
2318788 TTATTTTGTT
2318798 TTATTAATTA
1 TTATTAATTA
2318808 TTATTAATTA
1 TTATTAATTA
2318818 TTATT
1 TTATT
2318823 TACAATTCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (10 bp):
TTATTAATTA
Found at i:2319043 original size:39 final size:39
Alignment explanation
Indices: 2318988--2319066 Score: 115
Period size: 39 Copynumber: 2.0 Consensus size: 39
2318978 TTGTGCATTT
*
2318988 TTATTATTATTGTTATTATCATTATTATT-TTATTTTTAA
1 TTATTATTATTATTATTATCATTATT-TTATTATTTTTAA
* *
2319027 TTATTATTATTATTATTCTCGTTATTTTATTATTTTTAA
1 TTATTATTATTATTATTATCATTATTTTATTATTTTTAA
2319066 T
1 T
2319067 ATCTTCATTT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
38 2 0.06
39 34 0.94
ACGTcount: A:0.27, C:0.04, G:0.03, T:0.67
Consensus pattern (39 bp):
TTATTATTATTATTATTATCATTATTTTATTATTTTTAA
Found at i:2319052 original size:36 final size:35
Alignment explanation
Indices: 2318984--2319057 Score: 96
Period size: 36 Copynumber: 2.1 Consensus size: 35
2318974 TTATTTGTGC
* *
2318984 ATTTTTATTATTATTGTTATTATCATTATTATTTT
1 ATTTTTATTATTATTATTATTATCATCATTATTTT
*
2319019 ATTTTTAATTATTATTATTATTATTC-TCGTTATTTT
1 ATTTTT-ATTATTATTATTATTA-TCATCATTATTTT
2319055 ATT
1 ATT
2319058 ATTTTTAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
35 6 0.18
36 26 0.76
37 2 0.06
ACGTcount: A:0.26, C:0.04, G:0.03, T:0.68
Consensus pattern (35 bp):
ATTTTTATTATTATTATTATTATCATCATTATTTT
Found at i:2319060 original size:3 final size:3
Alignment explanation
Indices: 2318988--2319043 Score: 69
Period size: 3 Copynumber: 18.7 Consensus size: 3
2318978 TTGTGCATTT
* * *
2318988 TTA TTA TTA TTG TTA TTA TCA TTA TTA TT- TTA TTT TTAA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA
2319033 TTA TTA TTA TT
1 TTA TTA TTA TT
2319044 CTCGTTATTT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
2 2 0.04
3 41 0.91
4 2 0.04
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2319202 original size:17 final size:18
Alignment explanation
Indices: 2319179--2319230 Score: 61
Period size: 17 Copynumber: 2.8 Consensus size: 18
2319169 TAATATTGTT
2319179 TTCATTATTATAATTACA
1 TTCATTATTATAATTACA
* *
2319197 -TCATTATTATTATTATA
1 TTCATTATTATAATTACA
2319214 TTCTATTATTTATAATT
1 TTC-ATTA-TTATAATT
2319231 TATCATTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
17 15 0.54
18 2 0.07
19 4 0.14
20 7 0.25
ACGTcount: A:0.35, C:0.08, G:0.00, T:0.58
Consensus pattern (18 bp):
TTCATTATTATAATTACA
Found at i:2322749 original size:3 final size:3
Alignment explanation
Indices: 2322741--2322767 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2322731 CTAAAATTGG
2322741 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
2322768 TATTATTATT
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2322772 original size:3 final size:3
Alignment explanation
Indices: 2322766--2322792 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2322756 AATAATAATA
2322766 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
2322793 CCAATTTTAG
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:2323162 original size:18 final size:16
Alignment explanation
Indices: 2323118--2323163 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 16
2323108 TAATTAGTTA
2323118 AAATATTATGTATAAT
1 AAATATTATGTATAAT
2323134 AATATAGTTATGTATTAAT
1 AA-ATA-TTATGTA-TAAT
2323153 ATAATATTATG
1 A-AATATTATG
2323164 ATAGATATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 2 0.08
17 3 0.12
18 12 0.46
19 8 0.31
20 1 0.04
ACGTcount: A:0.46, C:0.00, G:0.09, T:0.46
Consensus pattern (16 bp):
AAATATTATGTATAAT
Found at i:2331145 original size:49 final size:49
Alignment explanation
Indices: 2331055--2331160 Score: 126
Period size: 49 Copynumber: 2.2 Consensus size: 49
2331045 CCAGTTCATG
* *
2331055 GTGGTTATACGATCACATGTTCAAGTATAACTAGGGTTTCTAGTTGACA
1 GTGGTTATACGATCACATGTTCAAGTATAACTAGAGCTTCTAGTTGACA
* * *
2331104 GTGGTTATACGATCACGA-GTTTAAGTATAATTCA-AGCTTCTAGTTGATA
1 GTGGTTATACGATCAC-ATGTTCAAGTATAACT-AGAGCTTCTAGTTGACA
*
2331153 GTGATTAT
1 GTGGTTAT
2331161 GCGGTTACGG
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
49 47 0.96
50 2 0.04
ACGTcount: A:0.29, C:0.12, G:0.22, T:0.37
Consensus pattern (49 bp):
GTGGTTATACGATCACATGTTCAAGTATAACTAGAGCTTCTAGTTGACA
Found at i:2336832 original size:23 final size:21
Alignment explanation
Indices: 2336802--2336861 Score: 75
Period size: 23 Copynumber: 2.8 Consensus size: 21
2336792 TAGTATGATA
**
2336802 AATTTTTTTAAAATATTCTTTT
1 AATTTTTTTAAAATATT-TCAT
*
2336824 GAATTTTTTTAAAAAATTTCAT
1 -AATTTTTTTAAAATATTTCAT
2336846 AATTTTTTTAAAATAT
1 AATTTTTTTAAAATAT
2336862 AAATTTTAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 15 0.45
22 2 0.06
23 16 0.48
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.57
Consensus pattern (21 bp):
AATTTTTTTAAAATATTTCAT
Found at i:2336877 original size:44 final size:45
Alignment explanation
Indices: 2336802--2336887 Score: 104
Period size: 44 Copynumber: 1.9 Consensus size: 45
2336792 TAGTATGATA
** **
2336802 AATTTTTTTAAAATATTCTTTTGAATTTTTTTA-AAAAATTTCAT
1 AATTTTTTTAAAATATAATTTTGAAAATTTTTATAAAAATTTCAT
*
2336846 AATTTTTTTAAAATATAAATTTT-AAAATTTTTATAAATATTT
1 AATTTTTTTAAAATAT-AATTTTGAAAATTTTTATAAAAATTT
2336888 TGAATTTTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
44 24 0.69
45 11 0.31
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.56
Consensus pattern (45 bp):
AATTTTTTTAAAATATAATTTTGAAAATTTTTATAAAAATTTCAT
Found at i:2336895 original size:19 final size:18
Alignment explanation
Indices: 2336871--2336924 Score: 58
Period size: 18 Copynumber: 3.0 Consensus size: 18
2336861 TAAATTTTAA
2336871 AATTTTTATAAATATTTT
1 AATTTTTATAAATATTTT
*
2336889 GAA-TTTTAAAAATTATTTT
1 -AATTTTTATAAA-TATTTT
*
2336908 AATTTTT-TAAAAATTTT
1 AATTTTTATAAATATTTT
2336925 TGTTGAGTTC
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
17 5 0.17
18 13 0.43
19 12 0.40
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (18 bp):
AATTTTTATAAATATTTT
Found at i:2336917 original size:20 final size:21
Alignment explanation
Indices: 2336805--2336922 Score: 79
Period size: 20 Copynumber: 5.6 Consensus size: 21
2336795 TATGATAAAT
*
2336805 TTTTTTAAAATATTCTTTTGAA
1 TTTTTTAAAA-ATTATTTTGAA
2336827 TTTTTTTAAAAA--ATTTCAT-AA
1 -TTTTTTAAAAATTATTT--TGAA
* *
2336848 TTTTTTTAAAATATAAATTTTAAA
1 -TTTTTTAAAA-AT-TATTTTGAA
* *
2336872 ATTTTTATAAA-TATTTTGAA
1 TTTTTTAAAAATTATTTTGAA
2336892 --TTTTAAAAATTATTTT-AA
1 TTTTTTAAAAATTATTTTGAA
2336910 TTTTTTAAAAATT
1 TTTTTTAAAAATT
2336923 TTTGTTGAGT
Statistics
Matches: 79, Mismatches: 6, Indels: 23
0.73 0.06 0.21
Matches are distributed among these distances:
18 10 0.13
19 6 0.08
20 21 0.27
21 13 0.16
22 4 0.05
23 19 0.24
24 2 0.03
25 4 0.05
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (21 bp):
TTTTTTAAAAATTATTTTGAA
Found at i:2343483 original size:23 final size:23
Alignment explanation
Indices: 2343457--2343547 Score: 100
Period size: 23 Copynumber: 4.1 Consensus size: 23
2343447 TGAAAAGTTA
2343457 GAAGAGTGAAGAGACTTGAATAT
1 GAAGAGTGAAGAGACTTGAATAT
*
2343480 GAAGAGTGAAGAGACTTGAAGAT
1 GAAGAGTGAAGAGACTTGAATAT
* * * * *
2343503 GAAAAGT-TACACAC---ATTAT
1 GAAGAGTGAAGAGACTTGAATAT
2343522 GAAGAGTGAAGAGACTTGAATAT
1 GAAGAGTGAAGAGACTTGAATAT
2343545 GAA
1 GAA
2343548 AGGTTACACA
Statistics
Matches: 52, Mismatches: 12, Indels: 8
0.72 0.17 0.11
Matches are distributed among these distances:
19 9 0.17
20 4 0.08
22 4 0.08
23 35 0.67
ACGTcount: A:0.45, C:0.07, G:0.27, T:0.21
Consensus pattern (23 bp):
GAAGAGTGAAGAGACTTGAATAT
Found at i:2343524 original size:42 final size:42
Alignment explanation
Indices: 2343477--2343560 Score: 150
Period size: 42 Copynumber: 2.0 Consensus size: 42
2343467 GAGACTTGAA
2343477 TATGAAGAGTGAAGAGACTTGAAGATGAAAAGTTACACACAT
1 TATGAAGAGTGAAGAGACTTGAAGATGAAAAGTTACACACAT
* *
2343519 TATGAAGAGTGAAGAGACTTGAATATGAAAGGTTACACACAT
1 TATGAAGAGTGAAGAGACTTGAAGATGAAAAGTTACACACAT
2343561 GCATGAATAG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.44, C:0.10, G:0.24, T:0.23
Consensus pattern (42 bp):
TATGAAGAGTGAAGAGACTTGAAGATGAAAAGTTACACACAT
Found at i:2355181 original size:33 final size:33
Alignment explanation
Indices: 2355106--2355181 Score: 91
Period size: 33 Copynumber: 2.3 Consensus size: 33
2355096 AGTTTGTCAA
* * * *
2355106 ATATCAATATTATTTTATTATTTTTATCTTTTC
1 ATATCATTAATATTTTATTATTTTTATCTATAC
2355139 ATATCATTAATATTTTATTATTATTTATCTATAC
1 ATATCATTAATATTTTATTATT-TTTATCTATAC
*
2355173 -TATTATTAA
1 ATATCATTAA
2355182 ACCTTTCACA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 28 0.76
34 9 0.24
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.59
Consensus pattern (33 bp):
ATATCATTAATATTTTATTATTTTTATCTATAC
Found at i:2358739 original size:9 final size:9
Alignment explanation
Indices: 2358725--2358752 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
2358715 TAAGTTTTCG
2358725 AATTCGAAT
1 AATTCGAAT
2358734 AATTCGAAT
1 AATTCGAAT
2358743 AATTCGAAT
1 AATTCGAAT
2358752 A
1 A
2358753 TTAAACTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (9 bp):
AATTCGAAT
Found at i:2359114 original size:17 final size:16
Alignment explanation
Indices: 2359080--2359110 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2359070 ACTATTTACT
*
2359080 TTCCCTCAAACTTTTA
1 TTCCCCCAAACTTTTA
2359096 TTCCCCCAAACTTTT
1 TTCCCCCAAACTTTT
2359111 TATTTTTCCC
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:0.23, C:0.35, G:0.00, T:0.42
Consensus pattern (16 bp):
TTCCCCCAAACTTTTA
Found at i:2363777 original size:21 final size:21
Alignment explanation
Indices: 2363751--2363792 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
2363741 TTAGCTCAGA
2363751 CGGGTAACCTGATATATTTAT
1 CGGGTAACCTGATATATTTAT
*
2363772 CGGGTAACCTGATGTATTTAT
1 CGGGTAACCTGATATATTTAT
2363793 ACTCTTCTCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.14, G:0.21, T:0.38
Consensus pattern (21 bp):
CGGGTAACCTGATATATTTAT
Found at i:2365268 original size:160 final size:160
Alignment explanation
Indices: 2365004--2365483 Score: 933
Period size: 160 Copynumber: 3.0 Consensus size: 160
2364994 ATGGACACCA
*
2365004 TAGAAGGATTTATCAAAAAAGGCTTACTAGGATAACTTGTAAAGAGGAAACCTAGATAGTAAGAA
1 TAGAAGGATTTATCAGAAAAGGCTTACTAGGATAACTTGTAAAGAGGAAACCTAGATAGTAAGAA
* *
2365069 TATCAAGAAGAAAAGATATCCAAGAGAAGAGAGACAAGTTATAAAGAGTAATTGAAGGGAACTAT
66 TATCGAGAAGAAAAGATATCCAAGAGAAGAGAGACAAGTTATAGAGAGTAATTGAAGGGAACTAT
2365134 TTATGATAGTAAGTGCTAAAAAAGAGTGGG
131 TTATGATAGTAAGTGCTAAAAAAGAGTGGG
2365164 TAGAAGGATTTATCAGAAAAGGCTTACTAGGATAACTTGTAAAGAGGAAACCTAGATAGTAAGAA
1 TAGAAGGATTTATCAGAAAAGGCTTACTAGGATAACTTGTAAAGAGGAAACCTAGATAGTAAGAA
2365229 TATCGAGAAGAAAAGATATCCAAGAGAAGAGAGACAAGTTATAGAGAGTAATTGAAGGGAACTAT
66 TATCGAGAAGAAAAGATATCCAAGAGAAGAGAGACAAGTTATAGAGAGTAATTGAAGGGAACTAT
2365294 TTATGATAGTAAGTGCTAAAAAAGAGTGGG
131 TTATGATAGTAAGTGCTAAAAAAGAGTGGG
2365324 TAGAAGGATTTATCAGAAAAGGCTTACTAGGATAACTTGTAAAGAGGAAACCTAGATAGTAAGAA
1 TAGAAGGATTTATCAGAAAAGGCTTACTAGGATAACTTGTAAAGAGGAAACCTAGATAGTAAGAA
2365389 TATCGAGAAGAAAAGATATCCAAGAGAAGAGAGACAAGTTATAGAGAGTAATTGAAGGGAACTAT
66 TATCGAGAAGAAAAGATATCCAAGAGAAGAGAGACAAGTTATAGAGAGTAATTGAAGGGAACTAT
2365454 TTATGATAGTAAGTGCTAAAAAAGAGTGGG
131 TTATGATAGTAAGTGCTAAAAAAGAGTGGG
2365484 ATACCTTGAA
Statistics
Matches: 317, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
160 317 1.00
ACGTcount: A:0.46, C:0.07, G:0.25, T:0.22
Consensus pattern (160 bp):
TAGAAGGATTTATCAGAAAAGGCTTACTAGGATAACTTGTAAAGAGGAAACCTAGATAGTAAGAA
TATCGAGAAGAAAAGATATCCAAGAGAAGAGAGACAAGTTATAGAGAGTAATTGAAGGGAACTAT
TTATGATAGTAAGTGCTAAAAAAGAGTGGG
Found at i:2366472 original size:29 final size:29
Alignment explanation
Indices: 2366430--2366488 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
2366420 TGTCCTAGAG
*
2366430 ATTGGTTTGGATTTGGATCAAAGGCATCA
1 ATTGGTTTGGATTTGGATCAAAGACATCA
*
2366459 ATTGGTTTGGATTTGGTTCAAAGACATCA
1 ATTGGTTTGGATTTGGATCAAAGACATCA
2366488 A
1 A
2366489 CTTCTCAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.29, C:0.10, G:0.25, T:0.36
Consensus pattern (29 bp):
ATTGGTTTGGATTTGGATCAAAGACATCA
Found at i:2367903 original size:22 final size:22
Alignment explanation
Indices: 2367878--2367920 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
2367868 GTCTTATAAC
2367878 AAATTATTAATATAATAAATAT
1 AAATTATTAATATAATAAATAT
* *
2367900 AAATTATTATTTTAATAAATA
1 AAATTATTAATATAATAAATA
2367921 ATTTAATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
AAATTATTAATATAATAAATAT
Found at i:2367971 original size:30 final size:31
Alignment explanation
Indices: 2367899--2367971 Score: 82
Period size: 30 Copynumber: 2.4 Consensus size: 31
2367889 ATAATAAATA
2367899 TAAATTATTATTTTAATAAATAATTTAATATT
1 TAAATTATTATTTTAATAAATAA-TTAATATT
*
2367931 TCAATT-TTATTTTAA-AAATAA-TAAT-TT
1 TAAATTATTATTTTAATAAATAATTAATATT
2367958 TAAATAATATTATT
1 TAAAT--TATTATT
2367972 CACGTATTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
27 6 0.17
28 4 0.11
29 1 0.03
30 11 0.31
31 9 0.25
32 5 0.14
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (31 bp):
TAAATTATTATTTTAATAAATAATTAATATT
Found at i:2368540 original size:14 final size:14
Alignment explanation
Indices: 2368521--2368555 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
2368511 GAAAAGTAAG
2368521 TCATTTTCCAGAAA
1 TCATTTTCCAGAAA
*
2368535 TCATTTTCCAGAAG
1 TCATTTTCCAGAAA
2368549 TCATTTT
1 TCATTTT
2368556 TAGTGAAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.29, C:0.20, G:0.09, T:0.43
Consensus pattern (14 bp):
TCATTTTCCAGAAA
Found at i:2373971 original size:18 final size:18
Alignment explanation
Indices: 2373944--2373984 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
2373934 TTAAATAATT
* *
2373944 TTTTATTAAGTAAAAATA
1 TTTTAATAAGCAAAAATA
2373962 TTTTAATAAGCAAAAATA
1 TTTTAATAAGCAAAAATA
2373980 TTTTA
1 TTTTA
2373985 TTAATTAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (18 bp):
TTTTAATAAGCAAAAATA
Found at i:2378258 original size:23 final size:23
Alignment explanation
Indices: 2378231--2378352 Score: 183
Period size: 23 Copynumber: 5.3 Consensus size: 23
2378221 AGTGTTATTG
2378231 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
2378254 TTCAGTGGTGGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
2378277 AAT-AGTGGTAGCTTCGGCTACAT
1 -ATCAGTGGTAGCTTCGGCTACAT
* *
2378300 TTCAGTGGTATCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
2378323 AACAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
2378346 ATCAGTG
1 ATCAGTG
2378353 TTGCACTTAT
Statistics
Matches: 87, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
22 1 0.01
23 85 0.98
24 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.26, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:2378287 original size:46 final size:46
Alignment explanation
Indices: 2378233--2378352 Score: 204
Period size: 46 Copynumber: 2.6 Consensus size: 46
2378223 TGTTATTGAT
*
2378233 CAGTGGTAGCTTCGGCTACATTTCAGTGGTGGCTTCGGCTACATAA
1 CAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTTCGGCTACATAA
* *
2378279 TAGTGGTAGCTTCGGCTACATTTCAGTGGTATCTTCGGCTACATAA
1 CAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTTCGGCTACATAA
*
2378325 CAGTGGTAGCTTCGGCTACATATCAGTG
1 CAGTGGTAGCTTCGGCTACATTTCAGTG
2378353 TTGCACTTAT
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 69 1.00
ACGTcount: A:0.21, C:0.21, G:0.27, T:0.32
Consensus pattern (46 bp):
CAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTTCGGCTACATAA
Found at i:2385702 original size:23 final size:23
Alignment explanation
Indices: 2385675--2385750 Score: 134
Period size: 23 Copynumber: 3.3 Consensus size: 23
2385665 AGTGTTATTG
2385675 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
2385698 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
2385721 AACAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
2385744 ATCAGTG
1 ATCAGTG
2385751 TTGCACTTAT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 49 1.00
ACGTcount: A:0.22, C:0.21, G:0.26, T:0.30
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:2390626 original size:21 final size:19
Alignment explanation
Indices: 2390583--2390627 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 19
2390573 ACATCGTTTT
* *
2390583 CAGAAGCTCGAAGGCTGAA
1 CAGAAGCTCGAAAGCTAAA
2390602 CAGAAGCTCATGAAAGCTAAA
1 CAGAAGCTC--GAAAGCTAAA
2390623 CAGAA
1 CAGAA
2390628 TACCATCAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 9 0.41
21 13 0.59
ACGTcount: A:0.44, C:0.20, G:0.24, T:0.11
Consensus pattern (19 bp):
CAGAAGCTCGAAAGCTAAA
Found at i:2390857 original size:101 final size:101
Alignment explanation
Indices: 2390669--2390908 Score: 354
Period size: 101 Copynumber: 2.4 Consensus size: 101
2390659 AATTCATCCT
* * * *
2390669 TTACATTCGTAGTGCCATAACCCAGTTATGGTCTTATCATCAGAATGCCACAGCCCAGCTATGGT
1 TTACGTTCATAGTGCCATAACCCAGTTATGGTCTTATCATCAGAATGCCACAGCCCAACTATAGT
* * * **
2390734 CTTACGTATAAACATTGTCATGGTTCAACCATGGTC
66 CTTACATATAAACACTGCCATGGGCCAACCATGGTC
* *
2390770 TTACGTTCATAGTGCCATAACCCAGTTATGGTCTTATCATTAGAATGCCATAGCCCAACTATAGT
1 TTACGTTCATAGTGCCATAACCCAGTTATGGTCTTATCATCAGAATGCCACAGCCCAACTATAGT
*
2390835 CTTACATATAAACACTGCCATGGGCCAACCTTGGTC
66 CTTACATATAAACACTGCCATGGGCCAACCATGGTC
* *
2390871 TTACGTTCATAGTGCCATAACCCAGCTATGGTTTTATC
1 TTACGTTCATAGTGCCATAACCCAGTTATGGTCTTATC
2390909 CGTCAATTCA
Statistics
Matches: 125, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
101 125 1.00
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.31
Consensus pattern (101 bp):
TTACGTTCATAGTGCCATAACCCAGTTATGGTCTTATCATCAGAATGCCACAGCCCAACTATAGT
CTTACATATAAACACTGCCATGGGCCAACCATGGTC
Found at i:2392876 original size:11 final size:11
Alignment explanation
Indices: 2392823--2392880 Score: 62
Period size: 11 Copynumber: 5.1 Consensus size: 11
2392813 TTTTATACTA
2392823 AATAAAATAAT
1 AATAAAATAAT
*
2392834 AACAAAATAAT
1 AATAAAATAAT
*
2392845 AATAAAATATCTT
1 AATAAAATA--AT
* *
2392858 ATTAAAATATT
1 AATAAAATAAT
2392869 AATAAAATAAT
1 AATAAAATAAT
2392880 A
1 A
2392881 TTTATCTAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
11 30 0.77
13 9 0.23
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (11 bp):
AATAAAATAAT
Found at i:2394286 original size:44 final size:44
Alignment explanation
Indices: 2394234--2394377 Score: 252
Period size: 44 Copynumber: 3.3 Consensus size: 44
2394224 TTTTAATTTT
*
2394234 TATTATTAAATGAGATAATTAATTTAGCGTGGATATCTTTTCAA
1 TATTATTAAATGAGATAATTAATTTAGCGTGAATATCTTTTCAA
*
2394278 TACTATTAAATGAGATAATTAATTTAGCGTGAATATCTTTTCAA
1 TATTATTAAATGAGATAATTAATTTAGCGTGAATATCTTTTCAA
* *
2394322 TATTATTAAATGAGATAATTAATTTAGTGTAAATATCTTTTCAA
1 TATTATTAAATGAGATAATTAATTTAGCGTGAATATCTTTTCAA
2394366 TATTATTAAATG
1 TATTATTAAATG
2394378 GGTTGTATGA
Statistics
Matches: 95, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 95 1.00
ACGTcount: A:0.39, C:0.06, G:0.11, T:0.44
Consensus pattern (44 bp):
TATTATTAAATGAGATAATTAATTTAGCGTGAATATCTTTTCAA
Found at i:2394376 original size:21 final size:21
Alignment explanation
Indices: 2394309--2394376 Score: 59
Period size: 21 Copynumber: 3.1 Consensus size: 21
2394299 ATTTAGCGTG
2394309 AATATCTTTTCAATATTATTA
1 AATATCTTTTCAATATTATTA
** *
2394330 AATGAGATAATT-AAT-TTAGTGTA
1 AAT-ATCT-TTTCAATATTA-T-TA
2394353 AATATCTTTTCAATATTATTA
1 AATATCTTTTCAATATTATTA
2394374 AAT
1 AAT
2394377 GGGTTGTATG
Statistics
Matches: 35, Mismatches: 6, Indels: 12
0.66 0.11 0.23
Matches are distributed among these distances:
21 13 0.37
22 12 0.34
23 10 0.29
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.47
Consensus pattern (21 bp):
AATATCTTTTCAATATTATTA
Found at i:2395560 original size:12 final size:12
Alignment explanation
Indices: 2395543--2395567 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2395533 ATTTAGTGTT
2395543 AAAAGAAGAAGA
1 AAAAGAAGAAGA
2395555 AAAAGAAGAAGA
1 AAAAGAAGAAGA
2395567 A
1 A
2395568 GCAGCGGCAA
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:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (12 bp):
AAAAGAAGAAGA
Found at i:2396190 original size:25 final size:25
Alignment explanation
Indices: 2396156--2396211 Score: 112
Period size: 25 Copynumber: 2.2 Consensus size: 25
2396146 TGCCACCTTA
2396156 AATTAAAACTTTCGAATAATTCGAT
1 AATTAAAACTTTCGAATAATTCGAT
2396181 AATTAAAACTTTCGAATAATTCGAT
1 AATTAAAACTTTCGAATAATTCGAT
2396206 AATTAA
1 AATTAA
2396212 TGGTACGGTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.36
Consensus pattern (25 bp):
AATTAAAACTTTCGAATAATTCGAT
Found at i:2400590 original size:87 final size:90
Alignment explanation
Indices: 2400487--2400712 Score: 253
Period size: 87 Copynumber: 2.5 Consensus size: 90
2400477 AGCCTTTATA
* * * * *
2400487 TTTTTTGCACTTAATTGAGTACTTAAACTTTCAAAATGCATCGAAAAGCCCCT-TAAACTTTTCA
1 TTTTTTGCACTCAATTGAGTACTTAAACTTTCAAAATGTATCAAAAAGACCCTCAAAACTTTTCA
*
2400551 A-AATAAGCAATGATG-CCC-CTATT
66 ATAA-AAGCAATGAAGCCCCGCTATT
* * * *
2400574 TTTTTTGCACTCAATTGCGTACTTAAATTTTCAAAATATATCAAAAAGACCCTCAAAATTTTTCA
1 TTTTTTGCACTCAATTGAGTACTTAAACTTTCAAAATGTATCAAAAAGACCCTCAAAACTTTTCA
* *
2400639 ATAAAAGCAATTAAGCCCCTGCTTTT
66 ATAAAAGCAATGAAGCCCC-GCTATT
* * * * *
2400665 TTTTTTACACTCGATTGGGTACTTGAACTGTCAAAATGTATCAAAAAG
1 TTTTTTGCACTCAATTGAGTACTTAAACTTTCAAAATGTATCAAAAAG
2400713 GCATTTTGGT
Statistics
Matches: 115, Mismatches: 19, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
87 46 0.40
88 19 0.17
89 5 0.04
91 45 0.39
ACGTcount: A:0.35, C:0.19, G:0.11, T:0.35
Consensus pattern (90 bp):
TTTTTTGCACTCAATTGAGTACTTAAACTTTCAAAATGTATCAAAAAGACCCTCAAAACTTTTCA
ATAAAAGCAATGAAGCCCCGCTATT
Found at i:2400888 original size:19 final size:19
Alignment explanation
Indices: 2400866--2400924 Score: 59
Period size: 19 Copynumber: 3.0 Consensus size: 19
2400856 ATTATTAAAT
2400866 TTTAATAAAAATGTAAAAA
1 TTTAATAAAAATGTAAAAA
*
2400885 TTTATTAAAAAT-TAGAAAA
1 TTTAATAAAAATGTA-AAAA
2400904 TAATT-ATAAAAATTGTAAAAA
1 T--TTAATAAAAA-TGTAAAAA
2400925 AAATTATAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
18 2 0.06
19 16 0.48
20 6 0.18
21 7 0.21
22 2 0.06
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (19 bp):
TTTAATAAAAATGTAAAAA
Found at i:2400903 original size:20 final size:20
Alignment explanation
Indices: 2400870--2400936 Score: 61
Period size: 21 Copynumber: 3.4 Consensus size: 20
2400860 TTAAATTTTA
2400870 ATAAAAATGTA-AAAAT--TT
1 ATAAAAAT-TAGAAAATAATT
2400888 ATTAAAAATTAGAAAATAATT
1 A-TAAAAATTAGAAAATAATT
*
2400909 ATAAAAATT-GTAAAAAAAATT
1 ATAAAAATTAG--AAAATAATT
2400930 ATAAAAA
1 ATAAAAA
2400937 ATTGTAAAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
18 3 0.07
19 13 0.31
20 8 0.19
21 18 0.43
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (20 bp):
ATAAAAATTAGAAAATAATT
Found at i:2400915 original size:21 final size:20
Alignment explanation
Indices: 2400880--2400953 Score: 69
Period size: 21 Copynumber: 3.6 Consensus size: 20
2400870 ATAAAAATGT
* *
2400880 AAAAATTTATTAAAAATTAGA
1 AAAAAATTATAAAAAATTA-A
* *
2400901 AAATAATTATAAAAATTGTAA
1 AAAAAATTATAAAAAAT-TAA
*
2400922 AAAAAATTATAAAAAATTGTA
1 AAAAAATTATAAAAAATT-AA
2400943 AAAAAA-TATAA
1 AAAAAATTATAA
2400954 TATATATAGA
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
20 6 0.14
21 36 0.82
22 2 0.05
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (20 bp):
AAAAAATTATAAAAAATTAA
Found at i:2400926 original size:12 final size:12
Alignment explanation
Indices: 2400911--2400948 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
2400901 AAATAATTAT
2400911 AAAAATTGTAAA
1 AAAAATTGTAAA
*
2400923 AAAAA-T-TATA
1 AAAAATTGTAAA
2400933 AAAAATTGTAAA
1 AAAAATTGTAAA
2400945 AAAA
1 AAAA
2400949 TATAATATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
10 8 0.36
11 2 0.09
12 12 0.55
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (12 bp):
AAAAATTGTAAA
Found at i:2400935 original size:10 final size:10
Alignment explanation
Indices: 2400814--2401029 Score: 94
Period size: 10 Copynumber: 22.1 Consensus size: 10
2400804 TGACATGTTG
*
2400814 TAAAAAATGA
1 TAAAAAATTA
2400824 TAAAAAA--A
1 TAAAAAATTA
*
2400832 T-AAAAATCA
1 TAAAAAATTA
2400841 -ATAAAAATTA
1 TA-AAAAATTA
2400851 -AAAAAATTA
1 TAAAAAATTA
* *
2400860 T--TAAATTT
1 TAAAAAATTA
* *
2400868 TAATAAAAATG
1 TAA-AAAATTA
*
2400879 TAAAAATTTA
1 TAAAAAATTA
*
2400889 TTAAAAATTA
1 TAAAAAATTA
*
2400899 GAAAATAATTA
1 TAAAA-AATTA
*
2400910 TAAAAATTGTA
1 TAAAAAAT-TA
*
2400921 AAAAAAATTA
1 TAAAAAATTA
*
2400931 TAAAAAATTG
1 TAAAAAATTA
*
2400941 TAAAAAAATA
1 TAAAAAATTA
* *
2400951 TAATATA-TA
1 TAAAAAATTA
*
2400960 T-AGAAATATA
1 TAAAAAAT-TA
*
2400970 GAAAAAATTA
1 TAAAAAATTA
*
2400980 T--AAAATTT
1 TAAAAAATTA
* * *
2400988 TATAAAGTCA
1 TAAAAAATTA
2400998 TAAGAAAATTA
1 TAA-AAAATTA
* *
2401009 TAAAAAAATG
1 TAAAAAATTA
2401019 TAAAAAATTA
1 TAAAAAATTA
2401029 T
1 T
2401030 CAAATTCGTA
Statistics
Matches: 151, Mismatches: 39, Indels: 32
0.68 0.18 0.14
Matches are distributed among these distances:
7 5 0.03
8 18 0.12
9 12 0.08
10 79 0.52
11 37 0.25
ACGTcount: A:0.64, C:0.01, G:0.05, T:0.30
Consensus pattern (10 bp):
TAAAAAATTA
Found at i:2400940 original size:22 final size:21
Alignment explanation
Indices: 2400900--2400948 Score: 80
Period size: 22 Copynumber: 2.3 Consensus size: 21
2400890 TAAAAATTAG
*
2400900 AAAATAATTATAAAAATTGTA
1 AAAAAAATTATAAAAATTGTA
2400921 AAAAAAATTATAAAAAATTGTA
1 AAAAAAATTAT-AAAAATTGTA
2400943 AAAAAA
1 AAAAAA
2400949 TATAATATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
21 10 0.38
22 16 0.62
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (21 bp):
AAAAAAATTATAAAAATTGTA
Found at i:2401040 original size:19 final size:19
Alignment explanation
Indices: 2401018--2401054 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2401008 ATAAAAAAAT
*
2401018 GTAAAAAATTATCAAATTC
1 GTAAAAAATTATAAAATTC
*
2401037 GTAAAAGATTATAAAATT
1 GTAAAAAATTATAAAATT
2401055 TATCGTACCA
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:0.54, C:0.05, G:0.08, T:0.32
Consensus pattern (19 bp):
GTAAAAAATTATAAAATTC
Found at i:2401280 original size:9 final size:9
Alignment explanation
Indices: 2401238--2401287 Score: 57
Period size: 10 Copynumber: 5.4 Consensus size: 9
2401228 GCATTTTATA
2401238 TTTTAT-AT
1 TTTTATAAT
2401246 TTTTATAAT
1 TTTTATAAT
*
2401255 ATTTTAAAAT
1 -TTTTATAAT
*
2401265 ATTTTATGAT
1 -TTTTATAAT
2401275 TTTTATAAT
1 TTTTATAAT
2401284 TTTT
1 TTTT
2401288 TCTATTTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
8 6 0.17
9 14 0.39
10 16 0.44
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (9 bp):
TTTTATAAT
Done.