Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A11
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: 114316535
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4920000 characters in sequence are not A, C, G, or T
File 8 of 356
Found at i:2774233 original size:18 final size:20
Alignment explanation
Indices: 2774194--2774237 Score: 58
Period size: 18 Copynumber: 2.3 Consensus size: 20
2774184 AAATATGCAT
2774194 AAATATATGTAAGTGTATAA
1 AAATATATGTAAGTGTATAA
2774214 AAAT-TATG-AAGTGTGA-AA
1 AAATATATGTAAGTGT-ATAA
2774232 AAATAT
1 AAATAT
2774238 GTTTAAATAG
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
18 12 0.55
19 6 0.27
20 4 0.18
ACGTcount: A:0.52, C:0.00, G:0.16, T:0.32
Consensus pattern (20 bp):
AAATATATGTAAGTGTATAA
Found at i:2781143 original size:31 final size:31
Alignment explanation
Indices: 2781108--2781169 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
2781098 TCTAACTACA
**
2781108 CTTGCTTAAAA-ATTACTCCCTTTGCCACATG
1 CTTGC-TAAAATATTACTCAATTTGCCACATG
2781139 CTTGCTAAAATATTACTCAATTTGCCACATG
1 CTTGCTAAAATATTACTCAATTTGCCACATG
2781170 TATCTATTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 5 0.18
31 23 0.82
ACGTcount: A:0.29, C:0.26, G:0.10, T:0.35
Consensus pattern (31 bp):
CTTGCTAAAATATTACTCAATTTGCCACATG
Found at i:2781834 original size:5 final size:5
Alignment explanation
Indices: 2781821--2781872 Score: 65
Period size: 5 Copynumber: 11.0 Consensus size: 5
2781811 AGTATTAATA
* *
2781821 TATAA TATAT TATAT TATAT TATA- T-TAT TATAT TATAT TATA- TATAA
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
2781868 TATAT
1 TATAT
2781873 AAAACATAAG
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
3 2 0.05
4 6 0.14
5 34 0.81
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (5 bp):
TATAT
Found at i:2781873 original size:7 final size:7
Alignment explanation
Indices: 2781776--2781874 Score: 62
Period size: 7 Copynumber: 14.3 Consensus size: 7
2781766 TTTATATAAA
2781776 AATATAT
1 AATATAT
*
2781783 ATTATAT
1 AATATAT
*
2781790 ATTATATT
1 AATATA-T
*
2781798 AA-CT-T
1 AATATAT
*
2781803 AATATTT
1 AATATAT
2781810 AAGTAT-T
1 AA-TATAT
2781817 AATATAT
1 AATATAT
2781824 AATATAT
1 AATATAT
*
2781831 TATATTAT
1 AATA-TAT
*
2781839 ATTATAT
1 AATATAT
*
2781846 TAT-TAT
1 AATATAT
*
2781852 ATTATAT
1 AATATAT
*
2781859 TATATAT
1 AATATAT
2781866 AATATAT
1 AATATAT
2781873 AA
1 AA
2781875 AACATAAGAA
Statistics
Matches: 71, Mismatches: 14, Indels: 14
0.72 0.14 0.14
Matches are distributed among these distances:
5 3 0.04
6 8 0.11
7 50 0.70
8 10 0.14
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (7 bp):
AATATAT
Found at i:2783078 original size:22 final size:22
Alignment explanation
Indices: 2783050--2783104 Score: 85
Period size: 22 Copynumber: 2.5 Consensus size: 22
2783040 GCACGTTAAA
2783050 TGCTCTCTGTTTAGCACATTT-G
1 TGCTCTCTGTTTAGCAC-TTTAG
*
2783072 TGCTCTCTGTATAGCACTTTAG
1 TGCTCTCTGTTTAGCACTTTAG
2783094 TGCTCTCTGTT
1 TGCTCTCTGTT
2783105 CGTTTGTGCA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 3 0.10
22 27 0.90
ACGTcount: A:0.13, C:0.24, G:0.18, T:0.45
Consensus pattern (22 bp):
TGCTCTCTGTTTAGCACTTTAG
Found at i:2784858 original size:19 final size:18
Alignment explanation
Indices: 2784830--2784868 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
2784820 ATTTTTATTT
2784830 TAAAAAATTAAAATTAAA
1 TAAAAAATTAAAATTAAA
*
2784848 TAAAAATATTAAAATTTAA
1 TAAAAA-ATTAAAATTAAA
2784867 TA
1 TA
2784869 TGAAATTACT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
TAAAAAATTAAAATTAAA
Found at i:2784883 original size:19 final size:19
Alignment explanation
Indices: 2784861--2784900 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
2784851 AAATATTAAA
2784861 ATTTAATATGAAATTACTG
1 ATTTAATATGAAATTACTG
* *
2784880 ATTTAATATTAAATTATTG
1 ATTTAATATGAAATTACTG
2784899 AT
1 AT
2784901 AATAAATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.03, G:0.07, T:0.47
Consensus pattern (19 bp):
ATTTAATATGAAATTACTG
Found at i:2798932 original size:23 final size:23
Alignment explanation
Indices: 2798878--2798934 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
2798868 TTTTAAATAT
**
2798878 TTTTTAAAGTAATTATTTTATTTTA
1 TTTTT-AA-TAATTATTTTATTAAA
* *
2798903 GTATTAATAATTATTTTATTAAA
1 TTTTTAATAATTATTTTATTAAA
2798926 TTTTTAATA
1 TTTTTAATA
2798935 TAATTATCTT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
23 21 0.81
24 2 0.08
25 3 0.12
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.60
Consensus pattern (23 bp):
TTTTTAATAATTATTTTATTAAA
Found at i:2801229 original size:13 final size:13
Alignment explanation
Indices: 2801213--2801237 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2801203 AAAGAACAAA
2801213 TATAATAAAATTT
1 TATAATAAAATTT
2801226 TATAATAAAATT
1 TATAATAAAATT
2801238 AATGTTGAAA
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
TATAATAAAATTT
Found at i:2805637 original size:31 final size:30
Alignment explanation
Indices: 2805602--2805670 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 30
2805592 TTGTCCCCTT
2805602 TATTAAAAAAAAGAGTAAATTAGTCATTATA
1 TATTAAAAAAAA-AGTAAATTAGTCATTATA
* * * *
2805633 TATTAAATCAAAAAGTAATTTGGTCATTTTA
1 TATTAAA-AAAAAAGTAAATTAGTCATTATA
2805664 -ATTAAAA
1 TATTAAAA
2805671 TTTTCATTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
30 6 0.19
31 22 0.69
32 4 0.12
ACGTcount: A:0.51, C:0.04, G:0.09, T:0.36
Consensus pattern (30 bp):
TATTAAAAAAAAAGTAAATTAGTCATTATA
Found at i:2817777 original size:21 final size:21
Alignment explanation
Indices: 2817751--2817791 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2817741 ATCTGCTCAA
* *
2817751 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
2817772 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
2817792 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:2821153 original size:96 final size:98
Alignment explanation
Indices: 2821027--2821209 Score: 275
Period size: 98 Copynumber: 1.9 Consensus size: 98
2821017 CTTGTTTTTC
*
2821027 TTTATTTTCCATTCTACTCTAC-T-TCTCTCTCTGTTTTCC-CCTATTTTCCATTTCTTTTAATA
1 TTTATTTTCCATTCTACTCTACTTCTCTCTCTCTGTTCTCCTCC-ATTTTCCATTTCTTTTAATA
* *
2821089 CAGTTTTTTTATGTTTTCCATTTATTAAAATTAG
65 CAATTTTTCTATGTTTTCCATTTATTAAAATTAG
* *
2821123 TTTATTTTCCATTC-CCTTCTACTTCTCTCTCTCTGTTCTCCTCCATTTTCCATTTCTTTTAATT
1 TTTATTTTCCATTCTAC-TCTACTTCTCTCTCTCTGTTCTCCTCCATTTTCCATTTCTTTTAATA
2821187 CAATTTTTCTATGTTTTCCATTT
65 CAATTTTTCTATGTTTTCCATTT
2821210 GTTAGGGAGA
Statistics
Matches: 78, Mismatches: 5, Indels: 6
0.88 0.06 0.07
Matches are distributed among these distances:
95 1 0.01
96 19 0.24
97 1 0.01
98 55 0.71
99 2 0.03
ACGTcount: A:0.16, C:0.24, G:0.03, T:0.57
Consensus pattern (98 bp):
TTTATTTTCCATTCTACTCTACTTCTCTCTCTCTGTTCTCCTCCATTTTCCATTTCTTTTAATAC
AATTTTTCTATGTTTTCCATTTATTAAAATTAG
Found at i:2822694 original size:17 final size:19
Alignment explanation
Indices: 2822658--2822694 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 19
2822648 AATACATCTC
*
2822658 AAAAATGAATTTACAGAAG
1 AAAAATGAAATTACAGAAG
2822677 AAAAA-GAAATTA-AGAAG
1 AAAAATGAAATTACAGAAG
2822694 A
1 A
2822695 GAGCTAACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 6 0.35
18 6 0.35
19 5 0.29
ACGTcount: A:0.65, C:0.03, G:0.16, T:0.16
Consensus pattern (19 bp):
AAAAATGAAATTACAGAAG
Found at i:2833664 original size:3 final size:3
Alignment explanation
Indices: 2833656--2833693 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
2833646 ATTCTCCTCT
2833656 TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TG
1 TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TG
2833694 TTCCTTTCTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.00, C:0.32, G:0.34, T:0.34
Consensus pattern (3 bp):
TGC
Found at i:2840701 original size:18 final size:18
Alignment explanation
Indices: 2840660--2840701 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
2840650 AACTGATAAT
*
2840660 AATTAATTCGAATAATTA
1 AATTAATTAGAATAATTA
**
2840678 TCTTAATTAGAATAATTA
1 AATTAATTAGAATAATTA
2840696 AATTAA
1 AATTAA
2840702 CAAAAAAATA
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.40
Consensus pattern (18 bp):
AATTAATTAGAATAATTA
Found at i:2846551 original size:18 final size:18
Alignment explanation
Indices: 2846530--2846565 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2846520 TAATTTTAAA
2846530 AAAATATATATAAATATT
1 AAAATATATATAAATATT
* *
2846548 AAAATTTTTATAAATATT
1 AAAATATATATAAATATT
2846566 TTGAAATTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
AAAATATATATAAATATT
Found at i:2851066 original size:41 final size:40
Alignment explanation
Indices: 2851021--2851126 Score: 119
Period size: 39 Copynumber: 2.6 Consensus size: 40
2851011 AAAAAGGTTT
2851021 TTAGCGGCGTTTTGAATAAAAACGCCACTAAAGAGT-GAGCA
1 TTAGCGGCGTTTT-AATAAAAACGCCACTAAAGA-TCGAGCA
* * *
2851062 TTAGCGGCGTTTCT-A-AAAAACGCCGCTAAAGATCGATCT
1 TTAGCGGCGTTT-TAATAAAAACGCCACTAAAGATCGAGCA
*
2851101 TTAGCGGCGTTTTTAATAAAAGCGCC
1 TTAGCGGCG-TTTTAATAAAAACGCC
2851127 TCTATAGGTT
Statistics
Matches: 56, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
38 1 0.02
39 29 0.52
40 5 0.09
41 20 0.36
42 1 0.02
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.25
Consensus pattern (40 bp):
TTAGCGGCGTTTTAATAAAAACGCCACTAAAGATCGAGCA
Found at i:2851886 original size:21 final size:22
Alignment explanation
Indices: 2851860--2851900 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
2851850 GGTACTTTAC
*
2851860 GGTTTAGGGTATATG-GTTAAG
1 GGTTTAAGGTATATGAGTTAAG
*
2851881 GGTTTAAGGTTTATGAGTTA
1 GGTTTAAGGTATATGAGTTA
2851901 TTATTTTAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.24, C:0.00, G:0.34, T:0.41
Consensus pattern (22 bp):
GGTTTAAGGTATATGAGTTAAG
Found at i:2852563 original size:13 final size:14
Alignment explanation
Indices: 2852539--2852573 Score: 63
Period size: 13 Copynumber: 2.6 Consensus size: 14
2852529 GAAAAAAATG
2852539 AAATTATTTAGATT
1 AAATTATTTAGATT
2852553 AAATT-TTTAGATT
1 AAATTATTTAGATT
2852566 AAATTATT
1 AAATTATT
2852574 GAAGAGATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 13 0.65
14 7 0.35
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (14 bp):
AAATTATTTAGATT
Found at i:2856371 original size:13 final size:14
Alignment explanation
Indices: 2856355--2856383 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2856345 TTCTAAATAT
2856355 TTATAA-TGTTTAA
1 TTATAATTGTTTAA
2856368 TTATAATTGTTTAA
1 TTATAATTGTTTAA
2856382 TT
1 TT
2856384 CAATTCATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (14 bp):
TTATAATTGTTTAA
Found at i:2856827 original size:21 final size:21
Alignment explanation
Indices: 2856801--2856894 Score: 120
Period size: 21 Copynumber: 4.5 Consensus size: 21
2856791 TAGAGTGGAG
*
2856801 GCAGCAGGGAGGGAGGCAGCA
1 GCAGCAGCGAGGGAGGCAGCA
*
2856822 GCAGCAGCGAGGGAGGCAGCG
1 GCAGCAGCGAGGGAGGCAGCA
*
2856843 GCAGCAGCGAGGGAGGCAGAA
1 GCAGCAGCGAGGGAGGCAGCA
*
2856864 GCA-CGAACGAGGGAGGCAG-A
1 GCAGC-AGCGAGGGAGGCAGCA
2856884 GGCAGCAGCGA
1 -GCAGCAGCGA
2856895 TGGCAGCAGA
Statistics
Matches: 64, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
20 2 0.03
21 61 0.95
22 1 0.02
ACGTcount: A:0.30, C:0.21, G:0.49, T:0.00
Consensus pattern (21 bp):
GCAGCAGCGAGGGAGGCAGCA
Found at i:2856846 original size:42 final size:42
Alignment explanation
Indices: 2856798--2856894 Score: 142
Period size: 42 Copynumber: 2.3 Consensus size: 42
2856788 ACTTAGAGTG
* * *
2856798 GAGGCAGCAGGGAGGGAGGCAGCAGCA-GCAGCGAGGGAGGCA
1 GAGGCAGCAGCGAGGGAGGCAGAAGCACG-AACGAGGGAGGCA
*
2856840 GCGGCAGCAGCGAGGGAGGCAGAAGCACGAACGAGGGAGGCA
1 GAGGCAGCAGCGAGGGAGGCAGAAGCACGAACGAGGGAGGCA
2856882 GAGGCAGCAGCGA
1 GAGGCAGCAGCGA
2856895 TGGCAGCAGA
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
42 48 0.98
43 1 0.02
ACGTcount: A:0.30, C:0.21, G:0.49, T:0.00
Consensus pattern (42 bp):
GAGGCAGCAGCGAGGGAGGCAGAAGCACGAACGAGGGAGGCA
Found at i:2857330 original size:43 final size:42
Alignment explanation
Indices: 2857257--2857405 Score: 147
Period size: 43 Copynumber: 3.5 Consensus size: 42
2857247 CAAATATGCT
**
2857257 ATGGCTTTTAGCGGAACTTTTCCCACAAACGCCACTAAAAG-C
1 ATGGCTTTTAGCGGCGC-TTTCCCACAAACGCCACTAAAAGCC
* *
2857299 AGTGGCTTTTAGCGGCGCTTTCCCAATAAACGCCGCTAAAAGCC
1 A-TGGCTTTTAGCGGCGCTTTCCC-ACAAACGCCACTAAAAGCC
* * *** *
2857343 ATGACTTTCAGCGGCGCTTTTTTTACAAACGCCGCTAAAAGCC
1 ATGGCTTTTAGCGGCGC-TTTCCCACAAACGCCACTAAAAGCC
* *
2857386 ATGACTTTCAGCGGCGCTTT
1 ATGGCTTTTAGCGGCGCTTT
2857406 TTTAAATAAA
Statistics
Matches: 93, Mismatches: 10, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
42 10 0.11
43 78 0.84
44 5 0.05
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.26
Consensus pattern (42 bp):
ATGGCTTTTAGCGGCGCTTTCCCACAAACGCCACTAAAAGCC
Found at i:2857406 original size:43 final size:43
Alignment explanation
Indices: 2857281--2857410 Score: 172
Period size: 43 Copynumber: 3.0 Consensus size: 43
2857271 AACTTTTCCC
* * * ***
2857281 ACAAACGCCACTAAAAG-CAGTGGCTTTTAGCGGCGCTTTCCCA
1 ACAAACGCCGCTAAAAGCCA-TGACTTTCAGCGGCGCTTTTTTA
* *
2857324 ATAAACGCCGCTAAAAGCCATGACTTTCAGCGGCGCTTTTTTT
1 ACAAACGCCGCTAAAAGCCATGACTTTCAGCGGCGCTTTTTTA
2857367 ACAAACGCCGCTAAAAGCCATGACTTTCAGCGGCGCTTTTTTA
1 ACAAACGCCGCTAAAAGCCATGACTTTCAGCGGCGCTTTTTTA
2857410 A
1 A
2857411 ATAAATGCCA
Statistics
Matches: 76, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
43 74 0.97
44 2 0.03
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (43 bp):
ACAAACGCCGCTAAAAGCCATGACTTTCAGCGGCGCTTTTTTA
Found at i:2859136 original size:23 final size:23
Alignment explanation
Indices: 2859104--2859147 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
2859094 ACTACCGTTT
2859104 TCTAAATAAAATAATAATAAATA
1 TCTAAATAAAATAATAATAAATA
* *
2859127 TCTAAGTAAAATATTAATAAA
1 TCTAAATAAAATAATAATAAA
2859148 ATAATATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (23 bp):
TCTAAATAAAATAATAATAAATA
Found at i:2859140 original size:13 final size:11
Alignment explanation
Indices: 2859108--2859150 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
2859098 CCGTTTTCTA
*
2859108 AATAAAATAAT
1 AATAAAATATT
2859119 AAT-AAATATCT
1 AATAAAATAT-T
2859130 AAGTAAAATATT
1 AA-TAAAATATT
2859142 AATAAAATA
1 AATAAAATA
2859151 ATATTTAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
10 5 0.18
11 13 0.46
12 4 0.14
13 6 0.21
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (11 bp):
AATAAAATATT
Found at i:2861806 original size:22 final size:24
Alignment explanation
Indices: 2861752--2861806 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 24
2861742 TATATAACTG
2861752 ATAATAT-TA-AAATATATACATA
1 ATAATATATATAAATATATACATA
* *
2861774 ATATTATATATAAAT-TATTCAT-
1 ATAATATATATAAATATATACATA
2861796 ATAATATATAT
1 ATAATATATAT
2861807 TAAAAAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
22 16 0.57
23 8 0.29
24 4 0.14
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.44
Consensus pattern (24 bp):
ATAATATATATAAATATATACATA
Found at i:2861991 original size:3 final size:3
Alignment explanation
Indices: 2861983--2862204 Score: 98
Period size: 3 Copynumber: 71.0 Consensus size: 3
2861973 AAGGATATAT
2861983 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * ** * * * *
2862031 TTGA A-A CACA A-A AGCC ATT ATA ATA AGA ATA TTA A-A ATA A-A GTA
1 AT-A ATA -ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * *
2862075 ATA GA-A ACA TTA CTA CAT- ATA TATA CATA CATGA AGA TATA CACTA
1 ATA -ATA ATA ATA ATA -ATA ATA -ATA -ATA -AT-A ATA -ATA -A-TA
* *
2862121 ATGT ACA ATA ATA ACT- ATA ATA ATA ATA ATA ATA ATA ATA ATAA ATA
1 AT-A ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA
* * *
2862168 TTA ATA ATA ATA ATAA ATA TTA ATA ATA TTA ATA ATA
1 ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA
2862205 TGAAAATAAC
Statistics
Matches: 169, Mismatches: 30, Indels: 40
0.71 0.13 0.17
Matches are distributed among these distances:
2 10 0.06
3 129 0.76
4 27 0.16
5 3 0.02
ACGTcount: A:0.59, C:0.06, G:0.04, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:2863093 original size:35 final size:35
Alignment explanation
Indices: 2863047--2863115 Score: 138
Period size: 35 Copynumber: 2.0 Consensus size: 35
2863037 GGGTGTGTGA
2863047 TGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGAG
1 TGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGAG
2863082 TGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGA
1 TGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGA
2863116 AGAGGCAAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.20, C:0.12, G:0.51, T:0.17
Consensus pattern (35 bp):
TGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGAG
Found at i:2864031 original size:148 final size:146
Alignment explanation
Indices: 2863717--2864219 Score: 598
Period size: 148 Copynumber: 3.4 Consensus size: 146
2863707 CTCAACCCAT
* * * *
2863717 TCAGCGTGTCCTGAGGCTCAATTCACCTCTCGCAATATGAGTTGATTTTTGAAACATACAAAAAA
1 TCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTGAAA-AT---AGAAA
* * *
2863782 TTGACAATACCT-AA-GTATGTCTTGAGGCTCAACTCGCCTCTCGCAATACGAGTTGATTTTTTT
62 TTGAAAATACCTCAACG--TGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTT
* * * *
2863845 GACAACACAAATTGAAATTACC
125 GAAAATAGAAATTAAAATTACC
**
2863867 TCAGCATGTGAACCGAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTGAAAATAGAAATT
1 TCAGC--GTGTCCCGAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTGAAAATAGAAATT
* * * * **
2863932 GAAAATACCTCAACGTGTCTTGAGGCTCAATTAATCTCTCGCGATATGAGTTGATTTTTTAAAAA
64 GAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT--TGA
2863997 AAATAGAAATTAAAATTACC
127 AAATAGAAATTAAAATTACC
* * *
2864017 TCAGCGTGTCCCGAGGCTCAATTCATCTCTCGCAATATGAGTTGATTTTTTTGAAAATAGAAATT
1 TCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATAAGTTGA--TTTTTGAAAATAGAAATT
* **
2864082 -AAAATTACCTCATCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAA
64 GAAAA-TACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAA
2864146 AATAGAAATTAAAATTACC
128 AATAGAAATTAAAATTACC
* * ** *
2864165 TCAGCATGTCCCGAGGCTCAACCCATTTCTCGCAATATAAGTTGAATTTTGAAAA
1 TCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTGAAAA
2864220 CGGAAGTAAC
Statistics
Matches: 305, Mismatches: 39, Indels: 22
0.83 0.11 0.06
Matches are distributed among these distances:
146 9 0.03
148 150 0.49
149 6 0.02
150 94 0.31
151 2 0.01
152 44 0.14
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (146 bp):
TCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTGAAAATAGAAATTGA
AAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAT
AGAAATTAAAATTACC
Found at i:2864107 original size:74 final size:74
Alignment explanation
Indices: 2863717--2864214 Score: 540
Period size: 74 Copynumber: 6.7 Consensus size: 74
2863707 CTCAACCCAT
* * *
2863717 TCAGCGTGTCCTGAGGCTCAATTCACCTCTCGCAATATGAGTTGA--TTTTTGAAACATACAAAA
1 TCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAA-AT---AGA
*
2863780 AATTGACAA-TACC
62 AATT-AAAATTACC
* ** ** * * * * *
2863793 TAAGTATGTCTTGAGGCTCAACTCGCCTCTCGCAATACGAGTTGATTTTTTTGACAACACAAATT
1 TCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAATAGAAATT
*
2863858 GAAATTACC
66 AAAATTACC
** *
2863867 TCAGCATGTGAACCGAGGCTCAACTCACCTCTCGCAATATAAGTTGA--TTTTTGAAAATAGAAA
1 TCAGC--GTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAATAGAAA
2863930 TTGAAAA-TACC
64 TT-AAAATTACC
* ** * * * * **
2863941 TCAACGTGTCTTGAGGCTCAATTAATCTCTCGCGATATGAGTTGATTTTTTAAAAAAAATAGAAA
1 TCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT--TGAAAATAGAAA
2864006 TTAAAATTACC
64 TTAAAATTACC
* *
2864017 TCAGCGTGTCCCGAGGCTCAATTCATCTCTCGCAATATGAGTTGATTTTTTTGAAAATAGAAATT
1 TCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAATAGAAATT
2864082 AAAATTACC
66 AAAATTACC
*
2864091 TCATCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAATAGAAATT
1 TCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAATAGAAATT
2864156 AAAATTACC
66 AAAATTACC
* * ** * *
2864165 TCAGCATGTCCCGAGGCTCAACCCATTTCTCGCAATATAAGTTGAATTTT
1 TCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
2864215 GAAAACGGAA
Statistics
Matches: 356, Mismatches: 55, Indels: 24
0.82 0.13 0.06
Matches are distributed among these distances:
72 31 0.09
73 2 0.01
74 175 0.49
75 7 0.02
76 132 0.37
77 1 0.00
78 8 0.02
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (74 bp):
TCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAATAGAAATT
AAAATTACC
Found at i:2864144 original size:224 final size:223
Alignment explanation
Indices: 2863721--2864218 Score: 592
Period size: 224 Copynumber: 2.2 Consensus size: 223
2863711 ACCCATTCAG
* *
2863721 CGTGTCCTGAGGCTCAATTCACCTCTCGCAATATGAGTTGATTTTTGAAACATACAAAAAATTGA
1 CGTGTCCTGAGGCTCAATTAACCTCTCGCAATATGAGTTGATTTTTGAAACATAAAAAAAATTGA
* * ** * *
2863786 CAATACCTAAGTATGTCTTGAGGCTCAACTCGCCTCTCGCAATACGAGTTGATTTTTTTGACAAC
66 AAATACCTAAGCATGTCCCGAGGCTCAACTCACCTCTCGCAATACGAGTTGATTTTTTTGAAAAC
*
2863851 ACAAATTGAAATTACCTCAGCATGTGAACCGAGGCTCAACTCACCTCTCGCAATATAAGTTGATT
131 ACAAATTAAAATTACCTCAGCA-GTGAACCGAGGCTCAACTCACCTCTCGCAATATAAGTTGATT
2863916 TTTGAAAATAGAAATTGAAAA-TACCTCAA
195 TTTGAAAATAGAAATT-AAAATTACCTCAA
* * * *
2863945 CGTGTCTTGAGGCTCAATTAATCTCTCGCGATATGAGTTGATTTTTTAAA-A-AAAATAGAAATT
1 CGTGTCCTGAGGCTCAATTAACCTCTCGCAATATGAGTTGATTTTTGAAACATAAAA-A-AAATT
* * * * *
2864008 -AAAATTACCTCAGCGTGTCCCGAGGCTCAATTCATCTCTCGCAATATGAGTTGATTTTTTTGAA
64 GAAAA-TACCTAAGCATGTCCCGAGGCTCAACTCACCTCTCGCAATACGAGTTGATTTTTTTGAA
* * * ** *
2864072 AATAGAAATTAAAATTACCTCATC-GTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
128 AACACAAATTAAAATTACCTCAGCAGTGAACCGAGGCTCAACTCACCTCTCGCAATATAAGTTGA
*
2864136 TTTTTTTGAAAATAGAAATTAAAATTACCTCAG
193 --TTTTTGAAAATAGAAATTAAAATTACCTCAA
* * *** ** * *
2864169 CATGTCCCGAGGCTCAACCCATTTCTCGCAATATAAGTTGAATTTTGAAA
1 CGTGTCCTGAGGCTCAATTAACCTCTCGCAATATGAGTTGATTTTTGAAA
2864219 ACGGAAGTAA
Statistics
Matches: 232, Mismatches: 36, Indels: 12
0.83 0.13 0.04
Matches are distributed among these distances:
222 40 0.17
223 9 0.04
224 183 0.79
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (223 bp):
CGTGTCCTGAGGCTCAATTAACCTCTCGCAATATGAGTTGATTTTTGAAACATAAAAAAAATTGA
AAATACCTAAGCATGTCCCGAGGCTCAACTCACCTCTCGCAATACGAGTTGATTTTTTTGAAAAC
ACAAATTAAAATTACCTCAGCAGTGAACCGAGGCTCAACTCACCTCTCGCAATATAAGTTGATTT
TTGAAAATAGAAATTAAAATTACCTCAA
Found at i:2887221 original size:231 final size:231
Alignment explanation
Indices: 2886532--2887228 Score: 1344
Period size: 231 Copynumber: 3.0 Consensus size: 231
2886522 TTGATAACTT
* * *
2886532 TTGCTAGTCCTCTTTCCTTACGTAAAGGAAGCTGATTTTCTTTATGACTACGTTTTCTTTTCTTG
1 TTGCTAGTCCTCTTTCCTTTCGCAAAGGAAGCTGATTTTCTTTATGACTACGTTTTCCTTTCTTG
2886597 TGACTTTTTTCTTGTATTATCGTCGGTGCTGGACCTGCTGGTTGTGTAGTCCTTGCATTTAGTGG
66 TGACTTTTTTCTTGTATTATCGTCGGTGCTGGACCTGCTGGTTGTGTAGTCCTTGCATTTAGTGG
2886662 ATAGCAGTATAAG-TGAACTACTTTTATATCTGTGTACCGCCATTTCCTTTAATCTTGATGTAGA
131 ATAGCAGTATAAGTTG-ACTACTTTTATATCTGTGTACCGCCATTTCCTTTAATCTTGATGTAGA
2886726 TTAATTGTGTCCGTTTAATATGGCAAATGTACTATAA
195 TTAATTGTGTCCGTTTAATATGGCAAATGTACTATAA
2886763 TTGCTAGTCCTCTTTCCTTTCGCAAAGGAAGCTGATTTTCTTTATGACTACGTTTTCCTTTCTTG
1 TTGCTAGTCCTCTTTCCTTTCGCAAAGGAAGCTGATTTTCTTTATGACTACGTTTTCCTTTCTTG
2886828 TGAC-TTTTTCTTGTATTATCGTCGGTGCTGGACCTGCTGGTTGTGTAGTCCTTGCATTTAGTGG
66 TGACTTTTTTCTTGTATTATCGTCGGTGCTGGACCTGCTGGTTGTGTAGTCCTTGCATTTAGTGG
2886892 ATAGCAGTATAAGTTGACTACTTTTATATCTGTGTACCGCCATTTCCTTTAATCTTGATGTAGAT
131 ATAGCAGTATAAGTTGACTACTTTTATATCTGTGTACCGCCATTTCCTTTAATCTTGATGTAGAT
2886957 TAATTGTGTCCGTTTAATATGGCAAATGTACTATAA
196 TAATTGTGTCCGTTTAATATGGCAAATGTACTATAA
2886993 TTGCTAGTCCTCTTTCCTTTCGCAAAGGAAGCTGATTTTCTTTATGACTACGTTTTCCTTTCTTG
1 TTGCTAGTCCTCTTTCCTTTCGCAAAGGAAGCTGATTTTCTTTATGACTACGTTTTCCTTTCTTG
2887058 TGACTTTTTTCTTGTATTATCGTCGGTGCTGGACCTGCTGGTTGTGTAGTCCTTGCATTTAGTGG
66 TGACTTTTTTCTTGTATTATCGTCGGTGCTGGACCTGCTGGTTGTGTAGTCCTTGCATTTAGTGG
2887123 ATAGCAGTATAAGTTGACTACTTTTATATCTGTGTACCGCCATTTCCTTTAATCTTGATGTAGAT
131 ATAGCAGTATAAGTTGACTACTTTTATATCTGTGTACCGCCATTTCCTTTAATCTTGATGTAGAT
2887188 TAATTGTGTCCGTTTAATATGGCAAATGTACTATAA
196 TAATTGTGTCCGTTTAATATGGCAAATGTACTATAA
2887224 TTGCT
1 TTGCT
2887229 CTATGGATAT
Statistics
Matches: 461, Mismatches: 3, Indels: 4
0.99 0.01 0.01
Matches are distributed among these distances:
230 227 0.49
231 234 0.51
ACGTcount: A:0.20, C:0.18, G:0.19, T:0.43
Consensus pattern (231 bp):
TTGCTAGTCCTCTTTCCTTTCGCAAAGGAAGCTGATTTTCTTTATGACTACGTTTTCCTTTCTTG
TGACTTTTTTCTTGTATTATCGTCGGTGCTGGACCTGCTGGTTGTGTAGTCCTTGCATTTAGTGG
ATAGCAGTATAAGTTGACTACTTTTATATCTGTGTACCGCCATTTCCTTTAATCTTGATGTAGAT
TAATTGTGTCCGTTTAATATGGCAAATGTACTATAA
Found at i:2889440 original size:30 final size:30
Alignment explanation
Indices: 2889394--2889487 Score: 152
Period size: 30 Copynumber: 3.1 Consensus size: 30
2889384 TTTTATTATG
*
2889394 CCAATATCTCGATACCCATATCTTTGACTTT
1 CCAATAT-TTGATACCCATATCTTTGACTTT
2889425 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
* *
2889455 CCATTATTTGATACCCATATCTTTGATTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
2889485 CCA
1 CCA
2889488 TAAATATGGA
Statistics
Matches: 60, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
30 53 0.88
31 7 0.12
ACGTcount: A:0.26, C:0.26, G:0.06, T:0.43
Consensus pattern (30 bp):
CCAATATTTGATACCCATATCTTTGACTTT
Found at i:2889449 original size:15 final size:15
Alignment explanation
Indices: 2889404--2889481 Score: 70
Period size: 15 Copynumber: 5.2 Consensus size: 15
2889394 CCAATATCTC
2889404 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
2889419 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
2889434 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
2889449 GACTTTCCAT-TATTT
1 GA-TACCCATATCTTT
2889464 GATACCCATATCTTT
1 GATACCCATATCTTT
2889479 GAT
1 GAT
2889482 TTTCCATAAA
Statistics
Matches: 47, Mismatches: 12, Indels: 8
0.70 0.18 0.12
Matches are distributed among these distances:
14 9 0.19
15 29 0.62
16 9 0.19
ACGTcount: A:0.26, C:0.23, G:0.08, T:0.44
Consensus pattern (15 bp):
GATACCCATATCTTT
Found at i:2894113 original size:15 final size:15
Alignment explanation
Indices: 2894068--2894175 Score: 87
Period size: 15 Copynumber: 7.2 Consensus size: 15
2894058 CCAATATCTC
2894068 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
2894083 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
2894098 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
2894113 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
2894128 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
2894143 GACTTTCCAT-TATTT
1 GA-TACCCATATCTTT
2894158 GATACCCATATCTTT
1 GATACCCATATCTTT
2894173 GAT
1 GAT
2894176 TTTCCATAAA
Statistics
Matches: 69, Mismatches: 18, Indels: 12
0.70 0.18 0.12
Matches are distributed among these distances:
14 13 0.19
15 43 0.62
16 13 0.19
ACGTcount: A:0.26, C:0.23, G:0.07, T:0.44
Consensus pattern (15 bp):
GATACCCATATCTTT
Found at i:2894182 original size:30 final size:30
Alignment explanation
Indices: 2894058--2894181 Score: 212
Period size: 30 Copynumber: 4.1 Consensus size: 30
2894048 TTTTATTATG
*
2894058 CCAATATCTCGATACCCATATCTTTGACTTT
1 CCAATAT-TTGATACCCATATCTTTGACTTT
2894089 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
2894119 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
* *
2894149 CCATTATTTGATACCCATATCTTTGATTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
2894179 CCA
1 CCA
2894182 TAAATATGGA
Statistics
Matches: 90, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
30 83 0.92
31 7 0.08
ACGTcount: A:0.26, C:0.25, G:0.06, T:0.43
Consensus pattern (30 bp):
CCAATATTTGATACCCATATCTTTGACTTT
Found at i:2898330 original size:31 final size:31
Alignment explanation
Indices: 2898294--2898360 Score: 125
Period size: 31 Copynumber: 2.2 Consensus size: 31
2898284 TAATAATAAT
2898294 AATAATAACTCACTTTGATGACAATTAGTTC
1 AATAATAACTCACTTTGATGACAATTAGTTC
2898325 AATAATAACTCACTTTGATGACAATTAGTTC
1 AATAATAACTCACTTTGATGACAATTAGTTC
*
2898356 CATAA
1 AATAA
2898361 AACGAGAAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.40, C:0.16, G:0.09, T:0.34
Consensus pattern (31 bp):
AATAATAACTCACTTTGATGACAATTAGTTC
Found at i:2901364 original size:3 final size:3
Alignment explanation
Indices: 2901356--2901381 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2901346 AGTTGAAGGT
2901356 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
2901382 TCAACTTAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:2906733 original size:15 final size:15
Alignment explanation
Indices: 2906715--2906744 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2906705 TCTATCTCTC
2906715 ATCTATCTATTTTTT
1 ATCTATCTATTTTTT
2906730 ATCTATCTATTTTTT
1 ATCTATCTATTTTTT
2906745 CTTTAGTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.13, G:0.00, T:0.67
Consensus pattern (15 bp):
ATCTATCTATTTTTT
Found at i:2908680 original size:18 final size:19
Alignment explanation
Indices: 2908634--2908680 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 19
2908624 GTAGGGATTT
*
2908634 TTATTTTATTTAATATTAA
1 TTATTATATTTAATATTAA
* *
2908653 -TATAAAATTTAA-ATTAA
1 TTATTATATTTAATATTAA
2908670 TTATTATATTT
1 TTATTATATTT
2908681 TTGAATTTTT
Statistics
Matches: 22, Mismatches: 5, Indels: 3
0.73 0.17 0.10
Matches are distributed among these distances:
17 5 0.23
18 17 0.77
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TTATTATATTTAATATTAA
Found at i:2908702 original size:10 final size:10
Alignment explanation
Indices: 2908689--2908713 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
2908679 TTTTGAATTT
2908689 TTTTTATGTA
1 TTTTTATGTA
2908699 TTTTTATGTA
1 TTTTTATGTA
2908709 TTTTT
1 TTTTT
2908714 TTTGAATTTA
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:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (10 bp):
TTTTTATGTA
Found at i:2911304 original size:18 final size:18
Alignment explanation
Indices: 2911263--2911306 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
2911253 CGCAACCGTG
* *
2911263 ATAGGGAACGTGATCGAG
1 ATAGGGAACGGGATCGAC
* *
2911281 ACAGGGATCGGGATCGAC
1 ATAGGGAACGGGATCGAC
2911299 ATAGGGAA
1 ATAGGGAA
2911307 GACAAAGACA
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.34, C:0.14, G:0.39, T:0.14
Consensus pattern (18 bp):
ATAGGGAACGGGATCGAC
Found at i:2920577 original size:16 final size:16
Alignment explanation
Indices: 2920548--2920593 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
2920538 TGGCTTTGGC
*
2920548 AAAA-AAAAA-AAAAA
1 AAAAGAAAAAGAAAAG
2920562 AAAAGAGAAAAGAAAAG
1 AAAAGA-AAAAGAAAAG
2920579 AAAAGAAAAAGAAAA
1 AAAAGAAAAAGAAAA
2920594 TGCAAAACAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
14 4 0.14
15 1 0.04
16 13 0.46
17 10 0.36
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (16 bp):
AAAAGAAAAAGAAAAG
Found at i:2924748 original size:33 final size:33
Alignment explanation
Indices: 2924711--2924864 Score: 218
Period size: 33 Copynumber: 4.7 Consensus size: 33
2924701 AGGGCCAGGA
2924711 GCTCCTCCTCCAGGAGGTGGTGGCGGAGGTGGT
1 GCTCCTCCTCCAGGAGGTGGTGGCGGAGGTGGT
*
2924744 GCTCCTCCACCAGGAGGTGGTGGCGGAGGTGGT
1 GCTCCTCCTCCAGGAGGTGGTGGCGGAGGTGGT
2924777 GCTCCTCCTCCAGGAGGTGGTGGCGGAGGTGGT
1 GCTCCTCCTCCAGGAGGTGGTGGCGGAGGTGGT
* * * * *
2924810 GCTCCTCCCCCTGGAGGTAGTGGTGGCGGTGGT
1 GCTCCTCCTCCAGGAGGTGGTGGCGGAGGTGGT
* ** *
2924843 GGTCCAACTCCAAGAGGTGGTG
1 GCTCCTCCTCCAGGAGGTGGTG
2924865 CTGGAAGTGG
Statistics
Matches: 107, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 107 1.00
ACGTcount: A:0.11, C:0.25, G:0.44, T:0.21
Consensus pattern (33 bp):
GCTCCTCCTCCAGGAGGTGGTGGCGGAGGTGGT
Found at i:2925368 original size:39 final size:39
Alignment explanation
Indices: 2925317--2925449 Score: 115
Period size: 39 Copynumber: 3.3 Consensus size: 39
2925307 TGGTGGAGAT
2925317 GGAGAAGGTGGGGCACTAGTTGTCAAAGTGGTTGTTGAA
1 GGAGAAGGTGGGGCACTAGTTGTCAAAGTGGTTGTTGAA
* ** * ** * * *
2925356 GGAGGAGGTGGGGTGCTAGATAT-TGATGGGGGTGGTGGAGA
1 GGAGAAGGTGGGGCACTAG-T-TGTCAAAGTGGTTGTTGA-A
*
2925397 TGGAGAAGGTGGGGCACTAGTCGTCAAAGTGGTTGTTGAA
1 -GGAGAAGGTGGGGCACTAGTTGTCAAAGTGGTTGTTGAA
* *
2925437 AGAGGAGGTGGGG
1 GGAGAAGGTGGGG
2925450 TGCTAGATAT
Statistics
Matches: 68, Mismatches: 21, Indels: 10
0.69 0.21 0.10
Matches are distributed among these distances:
39 27 0.40
40 12 0.18
41 13 0.19
42 16 0.24
ACGTcount: A:0.23, C:0.06, G:0.48, T:0.23
Consensus pattern (39 bp):
GGAGAAGGTGGGGCACTAGTTGTCAAAGTGGTTGTTGAA
Found at i:2925376 original size:81 final size:81
Alignment explanation
Indices: 2925275--2925489 Score: 385
Period size: 81 Copynumber: 2.7 Consensus size: 81
2925265 CATCGATGGG
* * *
2925275 GGAGGAGGTGGGGTGTTAGATGTTGATGGGGGTGGTGGAGATGGAGAAGGTGGGGCACTAGTTGT
1 GGAGGAGGTGGGGTGCTAGATATTGATGGGGGTGGTGGAGATGGAGAAGGTGGGGCACTAGTCGT
2925340 CAAAGTGGTTGTTGAA
66 CAAAGTGGTTGTTGAA
2925356 GGAGGAGGTGGGGTGCTAGATATTGATGGGGGTGGTGGAGATGGAGAAGGTGGGGCACTAGTCGT
1 GGAGGAGGTGGGGTGCTAGATATTGATGGGGGTGGTGGAGATGGAGAAGGTGGGGCACTAGTCGT
2925421 CAAAGTGGTTGTTGAA
66 CAAAGTGGTTGTTGAA
* *
2925437 AGAGGAGGTGGGGTGCTAGATATTGATGGGGGTGGTGGAGATGGTGAAGGTGG
1 GGAGGAGGTGGGGTGCTAGATATTGATGGGGGTGGTGGAGATGGAGAAGGTGG
2925490 AGGAGGTAGG
Statistics
Matches: 129, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
81 129 1.00
ACGTcount: A:0.21, C:0.04, G:0.50, T:0.24
Consensus pattern (81 bp):
GGAGGAGGTGGGGTGCTAGATATTGATGGGGGTGGTGGAGATGGAGAAGGTGGGGCACTAGTCGT
CAAAGTGGTTGTTGAA
Found at i:2925408 original size:42 final size:42
Alignment explanation
Indices: 2925275--2925489 Score: 147
Period size: 42 Copynumber: 5.3 Consensus size: 42
2925265 CATCGATGGG
* * *
2925275 GGAGGAGGTGGGGTGTTAGATGTTGATGGGGGTGGTGGAGAT
1 GGAGAAGGTGGGGTGCTAGATATTGATGGGGGTGGTGGAGAT
** * ** * * *
2925317 GGAGAAGGTGGGGCACTAG-T-TGTCAAAGTGGTTGTTGA-A-
1 GGAGAAGGTGGGGTGCTAGATAT-TGATGGGGGTGGTGGAGAT
*
2925356 GGAGGAGGTGGGGTGCTAGATATTGATGGGGGTGGTGGAGAT
1 GGAGAAGGTGGGGTGCTAGATATTGATGGGGGTGGTGGAGAT
** ** * ** * * *
2925398 GGAGAAGGTGGGGCACTAG-TCGTCAAAGTGGTTGTTGA-A-
1 GGAGAAGGTGGGGTGCTAGATATTGATGGGGGTGGTGGAGAT
* *
2925437 AGAGGAGGTGGGGTGCTAGATATTGATGGGGGTGGTGGAGAT
1 GGAGAAGGTGGGGTGCTAGATATTGATGGGGGTGGTGGAGAT
*
2925479 GGTGAAGGTGG
1 GGAGAAGGTGG
2925490 AGGAGGTAGG
Statistics
Matches: 120, Mismatches: 45, Indels: 16
0.66 0.25 0.09
Matches are distributed among these distances:
39 31 0.26
40 25 0.21
41 25 0.21
42 39 0.32
ACGTcount: A:0.21, C:0.04, G:0.50, T:0.24
Consensus pattern (42 bp):
GGAGAAGGTGGGGTGCTAGATATTGATGGGGGTGGTGGAGAT
Found at i:2925641 original size:42 final size:41
Alignment explanation
Indices: 2925563--2925722 Score: 119
Period size: 42 Copynumber: 3.9 Consensus size: 41
2925553 CATAGATGAG
* * * * * *
2925563 GGAGAAGGTGGGGTGCTAGATATTGATGGGGGTGGTGGAGAT
1 GGAGGAGGTGGGGTACTAG-TATCGAAGTGGTTGGTGGAGAT
*
2925605 GAAGGAGGTGGGGTACTAGTCATCGAAGTGGTTGGT-GA-A-
1 GGAGGAGGTGGGGTACTAGT-ATCGAAGTGGTTGGTGGAGAT
* * * * *
2925644 GGAGGAGGTGGGGTGCTAGATATTGACGGGGGTGGTGGAGAT
1 GGAGGAGGTGGGGTACTAG-TATCGAAGTGGTTGGTGGAGAT
* * * *
2925686 GGAGGAGGTAGGGCACTAGTTGTCAAAGTGGTTGGTG
1 GGAGGAGGTGGGGTACTAG-TATCGAAGTGGTTGGTG
2925723 AAGAAGAACA
Statistics
Matches: 90, Mismatches: 23, Indels: 10
0.73 0.19 0.08
Matches are distributed among these distances:
39 28 0.31
40 4 0.04
41 4 0.04
42 54 0.60
ACGTcount: A:0.22, C:0.06, G:0.49, T:0.23
Consensus pattern (41 bp):
GGAGGAGGTGGGGTACTAGTATCGAAGTGGTTGGTGGAGAT
Found at i:2925661 original size:81 final size:81
Alignment explanation
Indices: 2925563--2925730 Score: 255
Period size: 81 Copynumber: 2.1 Consensus size: 81
2925553 CATAGATGAG
* * *
2925563 GGAGAAGGTGGGGTGCTAGATATTGATGGGGGTGGTGGAGATGAAGGAGGTGGGGTACTAGTCAT
1 GGAGAAGGTGGGGTGCTAGATATTGACGGGGGTGGTGGAGATGAAGGAGGTAGGGCACTAGTCAT
*
2925628 CGAAGTGGTTGGTGAA
66 CAAAGTGGTTGGTGAA
* * **
2925644 GGAGGAGGTGGGGTGCTAGATATTGACGGGGGTGGTGGAGATGGAGGAGGTAGGGCACTAGTTGT
1 GGAGAAGGTGGGGTGCTAGATATTGACGGGGGTGGTGGAGATGAAGGAGGTAGGGCACTAGTCAT
2925709 CAAAGTGGTTGGTGAA
66 CAAAGTGGTTGGTGAA
*
2925725 GAAGAA
1 GGAGAA
2925731 CAAGGAATTA
Statistics
Matches: 77, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
81 77 1.00
ACGTcount: A:0.24, C:0.05, G:0.48, T:0.22
Consensus pattern (81 bp):
GGAGAAGGTGGGGTGCTAGATATTGACGGGGGTGGTGGAGATGAAGGAGGTAGGGCACTAGTCAT
CAAAGTGGTTGGTGAA
Found at i:2925680 original size:39 final size:42
Alignment explanation
Indices: 2925563--2925694 Score: 155
Period size: 42 Copynumber: 3.2 Consensus size: 42
2925553 CATAGATGAG
* *
2925563 GGAGAAGGTGGGGTGCTAGATATTGATGGGGGTGGTGGAGAT
1 GGAGGAGGTGGGGTGCTAGATATTGAAGGGGGTGGTGGAGAT
* * * * *
2925605 GAAGGAGGTGGGGTACTAG-TCATCGAAGTGGTTGGT-GA-A-
1 GGAGGAGGTGGGGTGCTAGAT-ATTGAAGGGGGTGGTGGAGAT
*
2925644 GGAGGAGGTGGGGTGCTAGATATTGACGGGGGTGGTGGAGAT
1 GGAGGAGGTGGGGTGCTAGATATTGAAGGGGGTGGTGGAGAT
2925686 GGAGGAGGT
1 GGAGGAGGT
2925695 AGGGCACTAG
Statistics
Matches: 72, Mismatches: 13, Indels: 10
0.76 0.14 0.11
Matches are distributed among these distances:
39 28 0.39
40 4 0.06
41 4 0.06
42 36 0.50
ACGTcount: A:0.22, C:0.05, G:0.52, T:0.22
Consensus pattern (42 bp):
GGAGGAGGTGGGGTGCTAGATATTGAAGGGGGTGGTGGAGAT
Found at i:2925813 original size:198 final size:201
Alignment explanation
Indices: 2925360--2925823 Score: 587
Period size: 198 Copynumber: 2.3 Consensus size: 201
2925350 GTTGAAGGAG
*** *
2925360 GAGGTGGGGTGCTAGATATTGATGGGGGTGGTGGAGATGGAGAAGGTGGGGCACTAGTCGTCAAA
1 GAGGTGGGGTGCTAGATATTGATGGGGGTGGTGGAGAAAAAG-AGGTGGGGCACTAGTCATCAAA
* *
2925425 GTGGTTGTTGAAAGAGGAGGTGGGGTGCTAGATATTGATGGGGGTGGTGGAGATGGTGAAGGTGG
65 GTGGTTGGTGAAAGAGGAGGTGGGGTGCTAGATATTGACGGGGGTGGTGGAGA--G-GAA-GTGG
* ** ** * *
2925490 AGGAGGTAGGGCACTAGTCATCAAAGTATTTGGTGAAGGTGAAGGAGGAATTGAAGCATTAGACA
126 AGGAGGTAGGGCACTAGTCATCAAAGTAGTTGGTGAAGAAGAACAAGGAATTAAAGCAGTAGACA
2925555 TAGATGAGGGA
191 TAGATGAGGGA
* * * *
2925566 GAAGGTGGGGTGCTAGATATTGATGGGGGTGGTGGAGATGAAGGAGGTGGGGTACTAGTCATCGA
1 G-AGGTGGGGTGCTAGATATTGATGGGGGTGGTGGAGA-AAAAGAGGTGGGGCACTAGTCATCAA
*
2925631 AGTGGTTGGTGAAGGAGGAGGTGGGGTGCTAGATATTGACGGGGGTGGT-G-GA-G-A-TGGAGG
64 AGTGGTTGGTGAAAGAGGAGGTGGGGTGCTAGATATTGACGGGGGTGGTGGAGAGGAAGTGGAGG
** * *
2925691 AGGTAGGGCACTAGTTGTCAAAGTGGTTGGTGAAGAAGAACAAGGAATTAAAGCAGTAGACATCG
129 AGGTAGGGCACTAGTCATCAAAGTAGTTGGTGAAGAAGAACAAGGAATTAAAGCAGTAGACATAG
2925756 ATGAGGGAA
194 ATGAGGG-A
* * *
2925765 GAGGTTGGATGCTAGATATTGATAGGGGTGGTGGAGACAAAAGAGGTGGGGCACTAGTC
1 GAGGTGGGGTGCTAGATATTGATGGGGGTGGTGGAGA-AAAAGAGGTGGGGCACTAGTC
2925824 GTTGCAGAGG
Statistics
Matches: 227, Mismatches: 28, Indels: 14
0.84 0.10 0.05
Matches are distributed among these distances:
198 118 0.52
199 2 0.01
200 1 0.00
201 1 0.00
205 2 0.01
206 2 0.01
207 100 0.44
208 1 0.00
ACGTcount: A:0.27, C:0.06, G:0.44, T:0.22
Consensus pattern (201 bp):
GAGGTGGGGTGCTAGATATTGATGGGGGTGGTGGAGAAAAAGAGGTGGGGCACTAGTCATCAAAG
TGGTTGGTGAAAGAGGAGGTGGGGTGCTAGATATTGACGGGGGTGGTGGAGAGGAAGTGGAGGAG
GTAGGGCACTAGTCATCAAAGTAGTTGGTGAAGAAGAACAAGGAATTAAAGCAGTAGACATAGAT
GAGGGA
Found at i:2926066 original size:216 final size:216
Alignment explanation
Indices: 2925688--2926137 Score: 532
Period size: 216 Copynumber: 2.1 Consensus size: 216
2925678 GTGGAGATGG
** *
2925688 AGGAGGTAGGGCACTAGTTGTCAAAGTGGTTGGTGAAGAAGAACAAGGAATTAAAGCAGTAGACA
1 AGGAGGTAGGGCACTAGTCATCAAAGTGGTTGGTGAAGAAGAACAAGGAAGTAAAGCAGTAGACA
* * *
2925753 TCGATGAGGGAAGAGGTTGGATGCTAGATATTGATAGGGGTGGTGGAGACAAAAGAGGTGGGGCA
66 CCGATGAGGGAAGAGGTGGGATGCTAGATATTGATAGGGGTAGTGGAGACAAAAGAGGTGGGGCA
* * ** * **
2925818 CTAGTCGTTGCAGAGGGTGGTGAAGGTGGAGGAGGAAGTGGGGCAGTAGACATCAATGTGGGAGG
131 CTAGTCGATGCAGAGGGTGGTGAAGATGGAGGAGGAAACGAGGCAGTAGACATCAATAAGGGAGG
2925883 TGAAGATGGTAGTGAAGGTGA
196 TGAAGATGGTAGTGAAGGTGA
* ** **
2925904 AGGAGGT-GGGCCACTAGTCATCAAAGTGGTTTGTGAAGGTGAA-AGAGGAAGTGGAGCAGTAGA
1 AGGAGGTAGGG-CACTAGTCATCAAAGTGGTTGGTGAAGAAGAACA-AGGAAGTAAAGCAGTAGA
* * * * * *** *
2925967 TACCGATGGGGGAGGAGGTGGGGTGCTAGATATTGATGGGGGTAGTGGAGATGGAGGAGGTGGGG
64 CACCGATGAGGGAAGAGGTGGGATGCTAGATATTGATAGGGGTAGTGGAGACAAAAGAGGTGGGG
2926032 CACTAGTC-AT-CAAGGAGGGTGGTGAAGATGGAGGAGGAAACGAGGCAGTAGACATCAATAAGG
129 CACTAGTCGATGC-A-GAGGGTGGTGAAGATGGAGGAGGAAACGAGGCAGTAGACATCAATAAGG
* * *
2926095 GAGGTGGAGATGGTGGTGGAA-TTGA
192 GAGGTGAAGATGGTAGT-GAAGGTGA
* *
2926120 AAGAGGTAAGGCACTAGT
1 AGGAGGTAGGGCACTAGT
2926138 AACCGAAGCG
Statistics
Matches: 196, Mismatches: 32, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
214 1 0.01
215 6 0.03
216 184 0.94
217 5 0.03
ACGTcount: A:0.30, C:0.08, G:0.43, T:0.19
Consensus pattern (216 bp):
AGGAGGTAGGGCACTAGTCATCAAAGTGGTTGGTGAAGAAGAACAAGGAAGTAAAGCAGTAGACA
CCGATGAGGGAAGAGGTGGGATGCTAGATATTGATAGGGGTAGTGGAGACAAAAGAGGTGGGGCA
CTAGTCGATGCAGAGGGTGGTGAAGATGGAGGAGGAAACGAGGCAGTAGACATCAATAAGGGAGG
TGAAGATGGTAGTGAAGGTGA
Found at i:2926267 original size:84 final size:84
Alignment explanation
Indices: 2926147--2926422 Score: 283
Period size: 84 Copynumber: 3.3 Consensus size: 84
2926137 TAACCGAAGC
* * * * * * * * *
2926147 GGGTGATGAAGGTCGAAGAAGT-GAGGCACTAGACATTGATGGGAGTTGTGGAGCTAGAGGAGA-
1 GGGTGGTGAAGGTGGAGGAAGTGGA-GTACTACACATTGGTGGGAGTGGTAGAGATAGAGGAGAC
** *
2926210 TGGGACAATATTAG-TCAAAGA
65 AAGG-CAATAGTAGTTCAAA-A
* *
2926231 GGGTGGTGAAGGTGGAGGAAGTGGAGTACTACACATTGGTGGGGGTGGTAGAGATGGAGGAGACA
1 GGGTGGTGAAGGTGGAGGAAGTGGAGTACTACACATTGGTGGGAGTGGTAGAGATAGAGGAGACA
*
2926296 AGGCAATAGTAGTTGAAAA
66 AGGCAATAGTAGTTCAAAA
** * *
2926315 GGGTGGTGAAAATGGAGGAAGTGGAGTACTACACATTGGTGGGGGTGGT-GAAGATGGAGGAGAC
1 GGGTGGTGAAGGTGGAGGAAGTGGAGTACTACACATTGGTGGGAGTGGTAG-AGATAGAGGAGAC
*
2926379 AAGGCAATAGTAGTTGAAAA
65 AAGGCAATAGTAGTTCAAAA
*
2926399 AGGTGGTG-AGGTTGGAGGAAGTGG
1 GGGTGGTGAAGG-TGGAGGAAGTGG
2926423 GGTAGTAGTC
Statistics
Matches: 167, Mismatches: 20, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
83 2 0.01
84 157 0.94
85 8 0.05
ACGTcount: A:0.32, C:0.06, G:0.43, T:0.20
Consensus pattern (84 bp):
GGGTGGTGAAGGTGGAGGAAGTGGAGTACTACACATTGGTGGGAGTGGTAGAGATAGAGGAGACA
AGGCAATAGTAGTTCAAAA
Found at i:2926278 original size:42 final size:42
Alignment explanation
Indices: 2926231--2926375 Score: 127
Period size: 42 Copynumber: 3.5 Consensus size: 42
2926221 TAGTCAAAGA
*
2926231 GGGTGGTGAAGGTGGAGGAAGTGGAGTACTACACATTGGTGG
1 GGGTGGTGAAGATGGAGGAAGTGGAGTACTACACATTGGTGG
** * * * ****
2926273 GGGTGGT-AGAGATGGAGGAGACAAGGCAATAGT--A-GTTGAAAA
1 GGGTGGTGA-AGATGGAGGA-A-GTGG-AGTACTACACATTGGTGG
*
2926315 GGGTGGTGAAAATGGAGGAAGTGGAGTACTACACATTGGTGG
1 GGGTGGTGAAGATGGAGGAAGTGGAGTACTACACATTGGTGG
2926357 GGGTGGTGAAGATGGAGGA
1 GGGTGGTGAAGATGGAGGA
2926376 GACAAGGCAA
Statistics
Matches: 74, Mismatches: 21, Indels: 16
0.67 0.19 0.14
Matches are distributed among these distances:
39 4 0.05
40 2 0.03
41 3 0.04
42 56 0.76
43 3 0.04
44 2 0.03
45 4 0.05
ACGTcount: A:0.30, C:0.06, G:0.46, T:0.19
Consensus pattern (42 bp):
GGGTGGTGAAGATGGAGGAAGTGGAGTACTACACATTGGTGG
Found at i:2926437 original size:42 final size:44
Alignment explanation
Indices: 2926381--2926537 Score: 151
Period size: 45 Copynumber: 3.6 Consensus size: 44
2926371 GAGGAGACAA
* * *
2926381 GGCAATAGTAGTTGAAAAAGGTGGTG-AGGTTGGAGGA-A-GTGG
1 GGCAGTAGTAGTTGAAGAGGGTGGTGAAGG-TGGAGGAGATGTGG
* *
2926423 GGTAGTAGTCGTTGAAGAGGGTGGTGAAGGTGGAGGAGGATGTGG
1 GGCAGTAGTAGTTGAAGAGGGTGGTGAAGGTGGAGGA-GATGTGG
* * *
2926468 GGCAGTAGTTGCTGAAGAGGGTGGTGAAGGTGGAGGAGGAAGTGG
1 GGCAGTAGTAGTTGAAGAGGGTGGTGAAGGTGGAGGA-GATGTGG
* * *
2926513 GACACTAGCT-GTTGAAGAGGATGGT
1 GGCAGTAG-TAGTTGAAGAGGGTGGT
2926538 AAAGACGGAG
Statistics
Matches: 97, Mismatches: 13, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
42 28 0.29
43 3 0.03
44 1 0.01
45 64 0.66
46 1 0.01
ACGTcount: A:0.26, C:0.04, G:0.48, T:0.21
Consensus pattern (44 bp):
GGCAGTAGTAGTTGAAGAGGGTGGTGAAGGTGGAGGAGATGTGG
Found at i:2926445 original size:84 final size:84
Alignment explanation
Indices: 2926232--2926460 Score: 280
Period size: 84 Copynumber: 2.7 Consensus size: 84
2926222 AGTCAAAGAG
** ** *
2926232 GGTGGTGAAGGTGGAGGAAGTGGAGTACTACACATTGGTGGGGGTGGT-AGAGATGGAGGAGACA
1 GGTGGTGAAAATGGAGGAAGTGGAGTACTACACATTGAAGAGGGTGGTGA-AGATGGAGGAGACA
*
2926296 AGGCAATAGTAGTTGAAAAG
65 AGGCAATAGTAGTTGAAAAA
** *
2926316 GGTGGTGAAAATGGAGGAAGTGGAGTACTACACATTGGTGGGGGTGGTGAAGATGGAGGAGACAA
1 GGTGGTGAAAATGGAGGAAGTGGAGTACTACACATTGAAGAGGGTGGTGAAGATGGAGGAGACAA
2926381 GGCAATAGTAGTTGAAAAA
66 GGCAATAGTAGTTGAAAAA
*** * * ** * *
2926400 GGTGGTGAGGTTGGAGGAAGTGGGGTAGTAGTCGTTGAAGAGGGTGGTGAAGGTGGAGGAG
1 GGTGGTGAAAATGGAGGAAGTGGAGTACTACACATTGAAGAGGGTGGTGAAGATGGAGGAG
2926461 GATGTGGGGC
Statistics
Matches: 129, Mismatches: 15, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
84 128 0.99
85 1 0.01
ACGTcount: A:0.30, C:0.05, G:0.46, T:0.20
Consensus pattern (84 bp):
GGTGGTGAAAATGGAGGAAGTGGAGTACTACACATTGAAGAGGGTGGTGAAGATGGAGGAGACAA
GGCAATAGTAGTTGAAAAA
Found at i:2926476 original size:45 final size:45
Alignment explanation
Indices: 2926412--2926537 Score: 173
Period size: 45 Copynumber: 2.8 Consensus size: 45
2926402 TGGTGAGGTT
*
2926412 GGAGGAAGTGGGGTAGTAGTCGTTGAAGAGGGTGGTGAAGGTGGA
1 GGAGGAAGTGGGGCAGTAGTCGTTGAAGAGGGTGGTGAAGGTGGA
* * *
2926457 GGAGGATGTGGGGCAGTAGTTGCTGAAGAGGGTGGTGAAGGTGGA
1 GGAGGAAGTGGGGCAGTAGTCGTTGAAGAGGGTGGTGAAGGTGGA
* * *
2926502 GGAGGAAGTGGGACACTAG-CTGTTGAAGAGGATGGT
1 GGAGGAAGTGGGGCAGTAGTC-GTTGAAGAGGGTGGT
2926538 AAAGACGGAG
Statistics
Matches: 70, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
45 70 1.00
ACGTcount: A:0.25, C:0.05, G:0.51, T:0.20
Consensus pattern (45 bp):
GGAGGAAGTGGGGCAGTAGTCGTTGAAGAGGGTGGTGAAGGTGGA
Found at i:2926564 original size:45 final size:45
Alignment explanation
Indices: 2926480--2926565 Score: 102
Period size: 45 Copynumber: 1.9 Consensus size: 45
2926470 CAGTAGTTGC
* * ** * *
2926480 TGAAGAGGGTGGTGAAGGTGGAGGAGGAAGTGGGACACTAGCTGT
1 TGAAGAGGATGGTAAAGACGGAGAAGGAACTGGGACACTAGCTGT
2926525 TGAAGAGGATGGTAAAGACGGAGAAGGAACTAGGG-CACTAG
1 TGAAGAGGATGGTAAAGACGGAGAAGGAACT-GGGACACTAG
2926566 ATGTCAATGG
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
45 31 0.91
46 3 0.09
ACGTcount: A:0.33, C:0.08, G:0.44, T:0.15
Consensus pattern (45 bp):
TGAAGAGGATGGTAAAGACGGAGAAGGAACTGGGACACTAGCTGT
Found at i:2928123 original size:54 final size:54
Alignment explanation
Indices: 2928036--2928147 Score: 152
Period size: 54 Copynumber: 2.1 Consensus size: 54
2928026 TTGGATAGTC
* * *
2928036 TGAAGGCTTTGTAAGGTCAACCTTTTGACCTTTTTGCTCAGATGAAAAATCCTT
1 TGAAGGCTTTGTAACGTCAACCTTCTGAACTTTTTGCTCAGATGAAAAATCCTT
* * ** *
2928090 TGAAGTCTTTGTATCGTCAACCTTCTGAACTTTTTGCTTGGATGAAACATCCTT
1 TGAAGGCTTTGTAACGTCAACCTTCTGAACTTTTTGCTCAGATGAAAAATCCTT
2928144 TGAA
1 TGAA
2928148 ATCACAGCTC
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
54 50 1.00
ACGTcount: A:0.25, C:0.19, G:0.18, T:0.38
Consensus pattern (54 bp):
TGAAGGCTTTGTAACGTCAACCTTCTGAACTTTTTGCTCAGATGAAAAATCCTT
Found at i:2928919 original size:93 final size:92
Alignment explanation
Indices: 2928788--2929066 Score: 409
Period size: 93 Copynumber: 3.0 Consensus size: 92
2928778 TGAATTCTAA
*
2928788 GGGGATCTACATCTTCCCTCAAGATATCTTTCTGCTCTGGCTTGTTTTCATGAACTATCTGACTG
1 GGGGATCTACATC-TCCCTCAGGATATCTTTCTGCTCTGGCTTGTTTTCATGAACTATCTGACTG
* *
2928853 TCATAATCCACCTTTCCATCCAGTGCAT
65 TCGTAATCCACCTTTCCATCCAGCGCAT
* *
2928881 GGGGATCTACATACTCCCTCAGGATATCTTTCTGCTCTGGCTTGTTTTGATGACCTATCTGACTG
1 GGGGATCTACAT-CTCCCTCAGGATATCTTTCTGCTCTGGCTTGTTTTCATGAACTATCTGACT-
*
2928946 GT-GTAATCCACCTTTCCATCCAGCACAT
64 GTCGTAATCCACCTTTCCATCCAGCGCAT
* * *
2928974 GGGAATCTACATCCTCTCTC-GAGATATCTTTCTGCTCTGGCTTGATTTCATGAACTATCTGACT
1 GGGGATCTACAT-CTCCCTCAG-GATATCTTTCTGCTCTGGCTTGTTTTCATGAACTATCTGACT
*
2929038 GCCGTAATCCACCTTTCCATCCAGCGCAT
64 GTCGTAATCCACCTTTCCATCCAGCGCAT
2929067 CGACTTTTCC
Statistics
Matches: 168, Mismatches: 14, Indels: 8
0.88 0.07 0.04
Matches are distributed among these distances:
92 2 0.01
93 163 0.97
94 3 0.02
ACGTcount: A:0.20, C:0.29, G:0.16, T:0.35
Consensus pattern (92 bp):
GGGGATCTACATCTCCCTCAGGATATCTTTCTGCTCTGGCTTGTTTTCATGAACTATCTGACTGT
CGTAATCCACCTTTCCATCCAGCGCAT
Found at i:2929075 original size:21 final size:21
Alignment explanation
Indices: 2929048--2929112 Score: 94
Period size: 21 Copynumber: 3.1 Consensus size: 21
2929038 GCCGTAATCC
*
2929048 ACCTTTCCATCCAGCGCATCG
1 ACCTTTCCATCCAGCGCATCA
* *
2929069 ACTTTTCCATCCAGCACATCA
1 ACCTTTCCATCCAGCGCATCA
*
2929090 ACCTTTCCCTCCAGCGCATCA
1 ACCTTTCCATCCAGCGCATCA
2929111 AC
1 AC
2929113 TGCATTGCTG
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.23, C:0.43, G:0.09, T:0.25
Consensus pattern (21 bp):
ACCTTTCCATCCAGCGCATCA
Found at i:2939108 original size:28 final size:28
Alignment explanation
Indices: 2939053--2939119 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 28
2939043 ATTTAGAAAT
* *** *
2939053 ATAATAATATATGATCTTACTTTCAAAA
1 ATAATAATATATGATATTAAAATAAAAA
2939081 ATAATAATATATGATATTAAAATAAAAA
1 ATAATAATATATGATATTAAAATAAAAA
*
2939109 TTAAT-ATATAT
1 ATAATAATATAT
2939120 TAAGTTTGAT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
27 6 0.18
28 27 0.82
ACGTcount: A:0.54, C:0.04, G:0.03, T:0.39
Consensus pattern (28 bp):
ATAATAATATATGATATTAAAATAAAAA
Found at i:2939499 original size:169 final size:169
Alignment explanation
Indices: 2939211--2939519 Score: 471
Period size: 169 Copynumber: 1.8 Consensus size: 169
2939201 TTTTCTGATG
*
2939211 TTTGTTTGGCTGAAAATAATTTCTCACGATAAAACCTTTTACAAAACACGGGAAAATAAACGTTT
1 TTTGTTTGGCTGAAAATAATTCCTCACGATAAAACCTTTTACAAAACACGGGAAAATAAACGTTT
* * * *
2939276 ATTTTAGGAAAATGTCTTACAAATTTTATTTTAATAAGACGTTTTCTAAAA-TTTTTCTTTTCAC
66 ATTTTAAGAAAATGTCTTAAAAATTTTATTTTAATAAGACATTTTCTAAAATTTTTTCTCTTCAC
2939340 CAATAAACTTAGGCTGTGTTTGTTTACTTGTAAAAGCTT
131 CAATAAACTTAGGCTGTGTTTGTTTACTTGTAAAAGCTT
* * *
2939379 TTTGTTTGGCTGAAAATAATTGCCT-ACGATAAAATCTTTTTTCAAAACATGGGAAAATAAACGT
1 TTTGTTTGGCTGAAAATAATT-CCTCACGATAAAA-CCTTTTACAAAACACGGGAAAATAAACGT
** *
2939443 TTATTTTAAGAAAATGTCTTAAAAATTTTATTTTGGTAAGACATATTT-TCAAATTTTTTCTCTT
64 TTATTTTAAGAAAATGTCTTAAAAATTTTATTTTAATAAGACAT-TTTCTAAAATTTTTTCTCTT
2939507 CACCAATAAACTT
128 CACCAATAAACTT
2939520 TTAAGTTATA
Statistics
Matches: 126, Mismatches: 11, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
168 30 0.24
169 71 0.56
170 25 0.20
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.41
Consensus pattern (169 bp):
TTTGTTTGGCTGAAAATAATTCCTCACGATAAAACCTTTTACAAAACACGGGAAAATAAACGTTT
ATTTTAAGAAAATGTCTTAAAAATTTTATTTTAATAAGACATTTTCTAAAATTTTTTCTCTTCAC
CAATAAACTTAGGCTGTGTTTGTTTACTTGTAAAAGCTT
Found at i:2942259 original size:12 final size:13
Alignment explanation
Indices: 2942227--2942259 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
2942217 TAAAAATTTT
*
2942227 ATTAGAAAAAATA
1 ATTATAAAAAATA
2942240 ATTATAAAAAATA
1 ATTATAAAAAATA
2942253 ATT-TAAA
1 ATTATAAA
2942260 TTTTAAAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (13 bp):
ATTATAAAAAATA
Found at i:2944501 original size:13 final size:13
Alignment explanation
Indices: 2944483--2944521 Score: 55
Period size: 12 Copynumber: 3.2 Consensus size: 13
2944473 ATAGATGTAA
2944483 TTTTTATTATTAT
1 TTTTTATTATTAT
*
2944496 TTTTTATTA-TAG
1 TTTTTATTATTAT
2944508 TTTTTATT-TTAT
1 TTTTTATTATTAT
2944520 TT
1 TT
2944522 ATTTTTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
12 14 0.61
13 9 0.39
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.77
Consensus pattern (13 bp):
TTTTTATTATTAT
Found at i:2944980 original size:6 final size:6
Alignment explanation
Indices: 2944960--2944991 Score: 55
Period size: 6 Copynumber: 5.2 Consensus size: 6
2944950 GAAAAACTCT
2944960 TAAAAA TATAAAA TAAAAA TAAAAA TAAAAA T
1 TAAAAA TA-AAAA TAAAAA TAAAAA TAAAAA T
2944992 TAATTAAATC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 19 0.76
7 6 0.24
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (6 bp):
TAAAAA
Found at i:2945275 original size:45 final size:44
Alignment explanation
Indices: 2945196--2945282 Score: 106
Period size: 45 Copynumber: 1.9 Consensus size: 44
2945186 ATTAAAAATA
* *
2945196 TAAAATATAAAAAAATCATCAAAAAATATAAAATTTATTAAATGT
1 TAAAATATAAAAAAA-CATAAAAAAATATAAAATTTAATAAATGT
2945241 TAAAATATAATAAAAA-ATAAAAATTAATAT-AAATTTAATAAA
1 TAAAATATAA-AAAAACATAAAAA--AATATAAAATTTAATAAA
2945283 ACATATTTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
44 6 0.16
45 21 0.57
46 10 0.27
ACGTcount: A:0.66, C:0.02, G:0.01, T:0.31
Consensus pattern (44 bp):
TAAAATATAAAAAAACATAAAAAAATATAAAATTTAATAAATGT
Found at i:2945313 original size:21 final size:22
Alignment explanation
Indices: 2945280--2945326 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
2945270 TAAATTTAAT
* *
2945280 AAAACATATTTAAATTTTTATA
1 AAAACATATTTAAAATTCTATA
*
2945302 AAAACGTA-TTAAAATTCTATA
1 AAAACATATTTAAAATTCTATA
2945323 AAAA
1 AAAA
2945327 TAATAAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.55, C:0.06, G:0.02, T:0.36
Consensus pattern (22 bp):
AAAACATATTTAAAATTCTATA
Found at i:2946989 original size:39 final size:40
Alignment explanation
Indices: 2946942--2947017 Score: 127
Period size: 40 Copynumber: 1.9 Consensus size: 40
2946932 GTAGTACAAA
* *
2946942 AAAAAT-AAAAAAATTCAAAATAATATAATCCAAAAAACT
1 AAAAATAAAAAAAATCCAAAATAATATAATACAAAAAACT
2946981 AAAAATAAAAAAAATCCAAAATAATATAATACAAAAA
1 AAAAATAAAAAAAATCCAAAATAATATAATACAAAAA
2947018 CTATGTACCA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
39 6 0.18
40 28 0.82
ACGTcount: A:0.72, C:0.09, G:0.00, T:0.18
Consensus pattern (40 bp):
AAAAATAAAAAAAATCCAAAATAATATAATACAAAAAACT
Found at i:2947839 original size:13 final size:13
Alignment explanation
Indices: 2947821--2947852 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
2947811 ATAGTTTAAT
2947821 AATAAAATAAAGA
1 AATAAAATAAAGA
*
2947834 AATAAAATAACGA
1 AATAAAATAAAGA
2947847 AATAAA
1 AATAAA
2947853 TGAAATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.75, C:0.03, G:0.06, T:0.16
Consensus pattern (13 bp):
AATAAAATAAAGA
Found at i:2949155 original size:15 final size:15
Alignment explanation
Indices: 2949132--2949179 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
2949122 TATCAAATTT
2949132 ATATTGATTGAAATC
1 ATATTGATTGAAATC
* * *
2949147 ATTTTGATTGAATTT
1 ATATTGATTGAAATC
2949162 ATATTGATTGAAAT-
1 ATATTGATTGAAATC
2949176 ATAT
1 ATAT
2949180 ATTATATATA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
14 4 0.14
15 24 0.86
ACGTcount: A:0.38, C:0.02, G:0.12, T:0.48
Consensus pattern (15 bp):
ATATTGATTGAAATC
Found at i:2949835 original size:18 final size:19
Alignment explanation
Indices: 2949814--2949854 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
2949804 AATGACATGA
2949814 GAAATTGA-AT-TGAGAATT
1 GAAATTGAGATATGAG-ATT
2949832 GAAATTGAGATATGAGATT
1 GAAATTGAGATATGAGATT
2949851 GAAA
1 GAAA
2949855 ACATGAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.29
Consensus pattern (19 bp):
GAAATTGAGATATGAGATT
Found at i:2950776 original size:12 final size:11
Alignment explanation
Indices: 2950756--2950787 Score: 55
Period size: 12 Copynumber: 2.8 Consensus size: 11
2950746 TTGTATAAAA
2950756 ATTATTTTATT
1 ATTATTTTATT
2950767 ATTAATTTTATT
1 ATT-ATTTTATT
2950779 ATTATTTTA
1 ATTATTTTA
2950788 AAGGCATTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 9 0.45
12 11 0.55
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
ATTATTTTATT
Found at i:2950804 original size:30 final size:30
Alignment explanation
Indices: 2950768--2950827 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
2950758 TATTTTATTA
2950768 TTAATTTTATTATTATTTTAAAGGCATTTG
1 TTAATTTTATTATTATTTTAAAGGCATTTG
* * *
2950798 TTAATTTTGTTATTATTTTAGAGGTATTTG
1 TTAATTTTATTATTATTTTAAAGGCATTTG
2950828 CTTGTTAAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.27, C:0.02, G:0.13, T:0.58
Consensus pattern (30 bp):
TTAATTTTATTATTATTTTAAAGGCATTTG
Found at i:2953990 original size:36 final size:36
Alignment explanation
Indices: 2953950--2954022 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
2953940 CTAATTATTA
2953950 TTACGATGTAAAGCAATTTATATTAATGATTCAACC
1 TTACGATGTAAAGCAATTTATATTAATGATTCAACC
2953986 TTACGATGTAAAGCAATTTATATTAATGATTCAACC
1 TTACGATGTAAAGCAATTTATATTAATGATTCAACC
2954022 T
1 T
2954023 GATAAAAGAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.37
Consensus pattern (36 bp):
TTACGATGTAAAGCAATTTATATTAATGATTCAACC
Found at i:2954503 original size:13 final size:13
Alignment explanation
Indices: 2954485--2954525 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
2954475 TCATACAACC
2954485 ATCATTAAGTAAA
1 ATCATTAAGTAAA
2954498 ATCATTAAGTAAA
1 ATCATTAAGTAAA
*
2954511 ATGATTCAAG-AAA
1 ATCATT-AAGTAAA
2954524 AT
1 AT
2954526 AAAAGATTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
13 23 0.88
14 3 0.12
ACGTcount: A:0.54, C:0.07, G:0.10, T:0.29
Consensus pattern (13 bp):
ATCATTAAGTAAA
Found at i:2955040 original size:21 final size:22
Alignment explanation
Indices: 2955016--2955076 Score: 63
Period size: 21 Copynumber: 2.8 Consensus size: 22
2955006 AAAAACTTGC
**
2955016 TATTTTGCTACTATTTTTTTA-
1 TATTTTGCTACTATTTTACTAT
*
2955037 TATTTTGTTA-TCATTTTACTAT
1 TATTTTGCTACT-ATTTTACTAT
*
2955059 TATGTTGCTACTATTTTA
1 TATTTTGCTACTATTTTA
2955077 ATGTTAATGT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
20 1 0.03
21 16 0.50
22 14 0.44
23 1 0.03
ACGTcount: A:0.21, C:0.10, G:0.07, T:0.62
Consensus pattern (22 bp):
TATTTTGCTACTATTTTACTAT
Found at i:2963595 original size:19 final size:17
Alignment explanation
Indices: 2963548--2963582 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
2963538 AGTAGGCTCC
2963548 TATAAATTTTAATCATA
1 TATAAATTTTAATCATA
2963565 TATAAATTTTAATCATA
1 TATAAATTTTAATCATA
2963582 T
1 T
2963583 CAATTCATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.49
Consensus pattern (17 bp):
TATAAATTTTAATCATA
Found at i:2964513 original size:9 final size:9
Alignment explanation
Indices: 2964499--2964568 Score: 104
Period size: 9 Copynumber: 7.8 Consensus size: 9
2964489 TTTGGTTAAA
2964499 AATTACCCG
1 AATTACCCG
2964508 AATTACCCG
1 AATTACCCG
2964517 AATTACCCG
1 AATTACCCG
*
2964526 AATTACCCA
1 AATTACCCG
*
2964535 AATTAACCG
1 AATTACCCG
*
2964544 AATTAACCG
1 AATTACCCG
*
2964553 AATTAACCG
1 AATTACCCG
2964562 AATTACC
1 AATTACC
2964569 GAAAAATACC
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 57 1.00
ACGTcount: A:0.40, C:0.29, G:0.09, T:0.23
Consensus pattern (9 bp):
AATTACCCG
Found at i:2965176 original size:23 final size:21
Alignment explanation
Indices: 2965130--2965169 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
2965120 TATTTTAATT
2965130 TTTTTCAAAAGAAAATCTTAA
1 TTTTTCAAAAGAAAATCTTAA
2965151 TTTTTCAAGAA-AAAATCTT
1 TTTTTCAA-AAGAAAATCTT
2965170 CAAATTTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.45, C:0.10, G:0.05, T:0.40
Consensus pattern (21 bp):
TTTTTCAAAAGAAAATCTTAA
Found at i:2976644 original size:25 final size:23
Alignment explanation
Indices: 2976615--2976686 Score: 74
Period size: 22 Copynumber: 3.1 Consensus size: 23
2976605 AAATTTAATT
2976615 TAATTTTTAAAAATTATAAAAATA
1 TAATTTTT-AAAATTATAAAAATA
* * *
2976639 TGAATTATTAAAATGATAAAATTA
1 T-AATTTTTAAAATTATAAAAATA
**
2976663 T-ATTTTTATTATTATAAAAATA
1 TAATTTTTAAAATTATAAAAATA
2976685 TA
1 TA
2976687 TAATTTAATT
Statistics
Matches: 38, Mismatches: 8, Indels: 5
0.75 0.16 0.10
Matches are distributed among these distances:
22 17 0.45
24 15 0.39
25 6 0.16
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (23 bp):
TAATTTTTAAAATTATAAAAATA
Found at i:2981443 original size:21 final size:21
Alignment explanation
Indices: 2981413--2981459 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
2981403 TGAGATAGGT
2981413 AATTTAGGGTATCCTTTTAAC
1 AATTTAGGGTATCCTTTTAAC
*
2981434 AATTTGGGGTATCCTTTTAAC
1 AATTTAGGGTATCCTTTTAAC
2981455 AATTT
1 AATTT
2981460 TGTATTATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.45
Consensus pattern (21 bp):
AATTTAGGGTATCCTTTTAAC
Found at i:2982872 original size:29 final size:28
Alignment explanation
Indices: 2982814--2982872 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
2982804 TTTTTATAAT
* * *
2982814 TTTTAAATGGTTAAATTAAAATTTATTA
1 TTTTAAAAGGTTAAAATAAAATTTAGTA
*
2982842 TTTTAAAAGGTTAAAATATAATCTTAGTA
1 TTTTAAAAGGTTAAAATAAAAT-TTAGTA
2982871 TT
1 TT
2982873 ACTAATTTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
28 19 0.73
29 7 0.27
ACGTcount: A:0.42, C:0.02, G:0.08, T:0.47
Consensus pattern (28 bp):
TTTTAAAAGGTTAAAATAAAATTTAGTA
Found at i:2984111 original size:24 final size:23
Alignment explanation
Indices: 2984078--2984131 Score: 72
Period size: 24 Copynumber: 2.3 Consensus size: 23
2984068 GCTTCACTTT
*
2984078 TTTAAATACACAACATAAATAAA
1 TTTAAATACACAACAAAAATAAA
* *
2984101 TTTAACATACACTAGAAAAATAAA
1 TTTAA-ATACACAACAAAAATAAA
2984125 TTTAAAT
1 TTTAAAT
2984132 TATACAGGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 7 0.26
24 20 0.74
ACGTcount: A:0.57, C:0.11, G:0.02, T:0.30
Consensus pattern (23 bp):
TTTAAATACACAACAAAAATAAA
Found at i:2984677 original size:33 final size:32
Alignment explanation
Indices: 2984618--2984679 Score: 79
Period size: 33 Copynumber: 1.9 Consensus size: 32
2984608 TGTATCTTTG
* * *
2984618 CTATTTAAAAAAAATAATGTTAATATTATTTA
1 CTATTAAAAAAAAAAAATATTAATATTATTTA
*
2984650 CTATTAAAAAAAAGAAAATATTTATATTAT
1 CTATTAAAAAAAA-AAAATATTAATATTAT
2984680 ATTTATTTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
32 12 0.48
33 13 0.52
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.40
Consensus pattern (32 bp):
CTATTAAAAAAAAAAAATATTAATATTATTTA
Found at i:2998844 original size:23 final size:23
Alignment explanation
Indices: 2998795--2998844 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 23
2998785 TTTTAAATTC
**
2998795 ATATTTCGATTGAACATAAATTC
1 ATATTTCGATTGAACATAAATAA
* * *
2998818 ATATTTCGATTGGACTTAAGTAA
1 ATATTTCGATTGAACATAAATAA
2998841 ATAT
1 ATAT
2998845 AAAATGTATT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.40
Consensus pattern (23 bp):
ATATTTCGATTGAACATAAATAA
Found at i:3000945 original size:26 final size:26
Alignment explanation
Indices: 3000916--3000992 Score: 64
Period size: 28 Copynumber: 2.8 Consensus size: 26
3000906 TCCCTTTGAA
* * *
3000916 TCATTCGATATTTTGCACACTAAGTG
1 TCATTCAATATCTCGCACACTAAGTG
3000942 TCATTCTCAATATCTCGCACACTAAGTG
1 TCA-T-TCAATATCTCGCACACTAAGTG
* * *
3000970 CCATTATCAATATTTCGTACACT
1 TCA-T-TCAATATCTCGCACACT
3000993 GAGTACCATA
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
26 3 0.07
27 1 0.02
28 38 0.90
ACGTcount: A:0.29, C:0.25, G:0.10, T:0.36
Consensus pattern (26 bp):
TCATTCAATATCTCGCACACTAAGTG
Found at i:3000961 original size:28 final size:28
Alignment explanation
Indices: 3000930--3001029 Score: 92
Period size: 28 Copynumber: 3.5 Consensus size: 28
3000920 TCGATATTTT
* *
3000930 GCACACTAAGTGTCATTCTCAATATCTC
1 GCACACTAAGTGCCATTATCAATATCTC
*
3000958 GCACACTAAGTGCCATTATCAATATTTC
1 GCACACTAAGTGCCATTATCAATATCTC
* * * * * * * *
3000986 GTACACTGAGTACCATATTTGATTACCCC
1 GCACACTAAGTGCCAT-TATCAATATCTC
3001015 GCACACTAAGTGCCA
1 GCACACTAAGTGCCA
3001030 CATTTTGTCG
Statistics
Matches: 56, Mismatches: 15, Indels: 1
0.78 0.21 0.01
Matches are distributed among these distances:
28 38 0.68
29 18 0.32
ACGTcount: A:0.30, C:0.28, G:0.13, T:0.29
Consensus pattern (28 bp):
GCACACTAAGTGCCATTATCAATATCTC
Found at i:3006010 original size:28 final size:28
Alignment explanation
Indices: 3005973--3006183 Score: 140
Period size: 28 Copynumber: 7.4 Consensus size: 28
3005963 ACCGATCTTA
3005973 CACACACAGTGCTAGGTTACGGAACTCG
1 CACACACAGTGCTAGGTTACGGAACTCG
* *** * * *
3006001 CACACGCAGTGCCTCA-ACAACTGATCTCA
1 CACACACAGTG-CT-AGGTTACGGAACTCG
*
3006030 CACACACAGTGCTCGGTTACGGAACTCG
1 CACACACAGTGCTAGGTTACGGAACTCG
* *** * * *
3006058 CACACAAAGTGCCTCA-ACAACCGATCTCA
1 CACACACAGTG-CT-AGGTTACGGAACTCG
* *
3006087 CACACACAGTGCTCGGTTACGGAAGTCG
1 CACACACAGTGCTAGGTTACGGAACTCG
*** * *
3006115 CACACACAGTGCCTCA-ACAACCGATCTCG
1 CACACACAGTG-CT-AGGTTACGGAACTCG
*
3006144 CACACACAGTGCTCGGTTACGGAACTCG
1 CACACACAGTGCTAGGTTACGGAACTCG
3006172 CACACACAGTGC
1 CACACACAGTGC
3006184 CTCAACAACC
Statistics
Matches: 129, Mismatches: 45, Indels: 18
0.67 0.23 0.09
Matches are distributed among these distances:
28 70 0.54
29 58 0.45
30 1 0.01
ACGTcount: A:0.29, C:0.35, G:0.20, T:0.16
Consensus pattern (28 bp):
CACACACAGTGCTAGGTTACGGAACTCG
Found at i:3006036 original size:57 final size:57
Alignment explanation
Indices: 3005951--3006311 Score: 497
Period size: 57 Copynumber: 6.1 Consensus size: 57
3005941 TCACACATTT
* * * *
3005951 AGTGCCCCAACAACCGATCTTACACACACAGTGCTAGGTTACGGAACTCGCACACGC
1 AGTGCCTCAACAACCGATCTCACACACACAGTGCTCGGTTACGGAACTCGCACACAC
* *
3006008 AGTGCCTCAACAACTGATCTCACACACACAGTGCTCGGTTACGGAACTCGCACACAA
1 AGTGCCTCAACAACCGATCTCACACACACAGTGCTCGGTTACGGAACTCGCACACAC
*
3006065 AGTGCCTCAACAACCGATCTCACACACACAGTGCTCGGTTACGGAAGTCGCACACAC
1 AGTGCCTCAACAACCGATCTCACACACACAGTGCTCGGTTACGGAACTCGCACACAC
*
3006122 AGTGCCTCAACAACCGATCTCGCACACACAGTGCTCGGTTACGGAACTCGCACACAC
1 AGTGCCTCAACAACCGATCTCACACACACAGTGCTCGGTTACGGAACTCGCACACAC
* * *
3006179 AGTGCCTCAACAACCCATCTCGCACACACAGTGCTCGGTTACAGAACTCACCAAGCCACAGTGCC
1 AGTGCCTCAACAACCGATCTCACACACACAGTGCTCGGTTACGGAACT---C--G---CA----C
3006244 ACAC
54 ACAC
* *
3006248 AGTGCCTCAACAACCGATCTCGCACACACAGTGCTCGGTTACGGAACTCACACACAC
1 AGTGCCTCAACAACCGATCTCACACACACAGTGCTCGGTTACGGAACTCGCACACAC
3006305 AGTGCCT
1 AGTGCCT
3006312 ATGTTCACTT
Statistics
Matches: 276, Mismatches: 16, Indels: 24
0.87 0.05 0.08
Matches are distributed among these distances:
57 218 0.79
60 1 0.00
61 2 0.01
62 1 0.00
65 2 0.01
66 1 0.00
69 51 0.18
ACGTcount: A:0.30, C:0.36, G:0.18, T:0.16
Consensus pattern (57 bp):
AGTGCCTCAACAACCGATCTCACACACACAGTGCTCGGTTACGGAACTCGCACACAC
Found at i:3006039 original size:29 final size:29
Alignment explanation
Indices: 3005997--3006212 Score: 186
Period size: 29 Copynumber: 7.6 Consensus size: 29
3005987 GGTTACGGAA
* *
3005997 CTCGCACACGCAGTGCCTCAACAACTGAT
1 CTCGCACACACAGTGCCTCAACAACCGAT
* **** * *
3006026 CTCACACACACAGTG-CTCGGTTACGGAA
1 CTCGCACACACAGTGCCTCAACAACCGAT
*
3006054 CTCGCACACAAAGTGCCTCAACAACCGAT
1 CTCGCACACACAGTGCCTCAACAACCGAT
* **** * *
3006083 CTCACACACACAGTG-CTCGGTTACGGAA
1 CTCGCACACACAGTGCCTCAACAACCGAT
*
3006111 GTCGCACACACAGTGCCTCAACAACCGAT
1 CTCGCACACACAGTGCCTCAACAACCGAT
**** * *
3006140 CTCGCACACACAGTG-CTCGGTTACGGAA
1 CTCGCACACACAGTGCCTCAACAACCGAT
*
3006168 CTCGCACACACAGTGCCTCAACAACCCAT
1 CTCGCACACACAGTGCCTCAACAACCGAT
3006197 CTCGCACACACAGTGC
1 CTCGCACACACAGTGC
3006213 TCGGTTACAG
Statistics
Matches: 138, Mismatches: 46, Indels: 6
0.73 0.24 0.03
Matches are distributed among these distances:
28 62 0.45
29 76 0.55
ACGTcount: A:0.29, C:0.37, G:0.18, T:0.16
Consensus pattern (29 bp):
CTCGCACACACAGTGCCTCAACAACCGAT
Found at i:3008300 original size:28 final size:28
Alignment explanation
Indices: 3008232--3008301 Score: 97
Period size: 28 Copynumber: 2.5 Consensus size: 28
3008222 GAATCATTCG
* *
3008232 ATATTTTGCACACTAAGTGTCATTCTCA
1 ATATTTCGTACACTAAGTGTCATTCTCA
*
3008260 ATATCTC-TCACACTAAGTGTCATTCTCA
1 ATATTTCGT-ACACTAAGTGTCATTCTCA
3008288 ATATTTCGTACACT
1 ATATTTCGTACACT
3008302 GAGTACCATA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
28 35 0.97
29 1 0.03
ACGTcount: A:0.29, C:0.24, G:0.09, T:0.39
Consensus pattern (28 bp):
ATATTTCGTACACTAAGTGTCATTCTCA
Found at i:3011526 original size:34 final size:34
Alignment explanation
Indices: 3011483--3011552 Score: 131
Period size: 34 Copynumber: 2.1 Consensus size: 34
3011473 GAGGGCACTG
*
3011483 ATTTAGTTAAAGAAATATTGGACAGATTTCTTAT
1 ATTTAGTTAAAGAAAGATTGGACAGATTTCTTAT
3011517 ATTTAGTTAAAGAAAGATTGGACAGATTTCTTAT
1 ATTTAGTTAAAGAAAGATTGGACAGATTTCTTAT
3011551 AT
1 AT
3011553 CTGAAGATCT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.39, C:0.06, G:0.16, T:0.40
Consensus pattern (34 bp):
ATTTAGTTAAAGAAAGATTGGACAGATTTCTTAT
Found at i:3016547 original size:21 final size:21
Alignment explanation
Indices: 3016482--3016561 Score: 88
Period size: 21 Copynumber: 3.8 Consensus size: 21
3016472 TCATTTCTGT
* * *
3016482 CATAGCCCCCCCCACCACCTC
1 CATAGCCGCCACCGCCACCTC
* * * *
3016503 CATAGCCACCACTGCCCCCAC
1 CATAGCCGCCACCGCCACCTC
3016524 CATAGCCGCCACCGCCACCTC
1 CATAGCCGCCACCGCCACCTC
*
3016545 CATATCCGCCACCGCCA
1 CATAGCCGCCACCGCCA
3016562 TAACCACTAT
Statistics
Matches: 48, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 48 1.00
ACGTcount: A:0.21, C:0.59, G:0.10, T:0.10
Consensus pattern (21 bp):
CATAGCCGCCACCGCCACCTC
Found at i:3020758 original size:29 final size:30
Alignment explanation
Indices: 3020707--3020771 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 30
3020697 TAGTGTATAT
*
3020707 TTTTATAATTTTTAAAAGATTAAATTAAAA
1 TTTTATAATTTTTAAAAGATTAAAGTAAAA
* * * *
3020737 TTTTATAA-TTTTAGAGGGTTAAAGTATAA
1 TTTTATAATTTTTAAAAGATTAAAGTAAAA
3020766 TTTTAT
1 TTTTAT
3020772 TTTTATTAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 22 0.73
30 8 0.27
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.49
Consensus pattern (30 bp):
TTTTATAATTTTTAAAAGATTAAAGTAAAA
Found at i:3023250 original size:18 final size:19
Alignment explanation
Indices: 3023213--3023250 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
3023203 GACACCGCCT
3023213 GAGAGCCCTAAGGTAGAAGCA
1 GAGAGCCCTAA-G-AGAAGCA
3023234 GAGAGCCCTAA-AGAAGC
1 GAGAGCCCTAAGAGAAGC
3023251 CTCAGAAAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 6 0.35
21 11 0.65
ACGTcount: A:0.39, C:0.21, G:0.32, T:0.08
Consensus pattern (19 bp):
GAGAGCCCTAAGAGAAGCA
Found at i:3027630 original size:50 final size:50
Alignment explanation
Indices: 3027571--3027670 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
3027561 ATATCTCCAC
3027571 AAACAAAAATTTAAAAATATCCATTCCTAAATTTTAGCATATCCACCAAA
1 AAACAAAAATTTAAAAATATCCATTCCTAAATTTTAGCATATCCACCAAA
3027621 AAACAAAAATTTAAAAATATCCATTCCTAAATTTTAGCATATCCACCAAA
1 AAACAAAAATTTAAAAATATCCATTCCTAAATTTTAGCATATCCACCAAA
3027671 GAAGCCATTA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.50, C:0.20, G:0.02, T:0.28
Consensus pattern (50 bp):
AAACAAAAATTTAAAAATATCCATTCCTAAATTTTAGCATATCCACCAAA
Found at i:3033381 original size:26 final size:26
Alignment explanation
Indices: 3033325--3033383 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 26
3033315 TTTTATTCAA
** *
3033325 AAGAAAAAAATTTTAAATATTAAGAT
1 AAGAAAAAAATCATAAATATCAAGAT
*
3033351 GAGAAAAAAATCATAAATATCAA-ATT
1 AAGAAAAAAATCATAAATATCAAGA-T
3033377 AAGAAAA
1 AAGAAAA
3033384 TATACTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
25 1 0.04
26 26 0.96
ACGTcount: A:0.64, C:0.03, G:0.08, T:0.24
Consensus pattern (26 bp):
AAGAAAAAAATCATAAATATCAAGAT
Found at i:3043510 original size:4 final size:4
Alignment explanation
Indices: 3043501--3043581 Score: 83
Period size: 4 Copynumber: 20.2 Consensus size: 4
3043491 ATTTCTTGGT
* * * *
3043501 TGTA TGTA TGTT TGTA TGTA TGTA TGTA TTTA TGTA TG-A CGTA TGCA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
* **
3043548 TGCA TGCG TGTA TGTA TGTA TGTAA TGTA TGTA T
1 TGTA TGTA TGTA TGTA TGTA TGT-A TGTA TGTA T
3043582 AGAAAGAATT
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
3 2 0.03
4 59 0.91
5 4 0.06
ACGTcount: A:0.23, C:0.05, G:0.25, T:0.47
Consensus pattern (4 bp):
TGTA
Found at i:3045408 original size:20 final size:20
Alignment explanation
Indices: 3045372--3045409 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3045362 TACCATAATG
*
3045372 TGTTATATATTATATATTAA
1 TGTTATATATTAAATATTAA
3045392 TGTTA-ATATTTAAATATT
1 TGTTATATA-TTAAATATT
3045410 TTAAATTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.55
Consensus pattern (20 bp):
TGTTATATATTAAATATTAA
Found at i:3045417 original size:27 final size:26
Alignment explanation
Indices: 3045378--3045430 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
3045368 AATGTGTTAT
* *
3045378 ATATTATATATTAATGTTAATATTTAA
1 ATATTATAAATTAAT-TTAAAATTTAA
*
3045405 ATATTTTAAATTAATTTAAAATTTAA
1 ATATTATAAATTAATTTAAAATTTAA
3045431 TACATATATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 10 0.43
27 13 0.57
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (26 bp):
ATATTATAAATTAATTTAAAATTTAA
Found at i:3047694 original size:46 final size:46
Alignment explanation
Indices: 3047627--3047748 Score: 165
Period size: 46 Copynumber: 2.6 Consensus size: 46
3047617 GGGGATATAG
3047627 ATCTATTTATTTACCGTATTACTTAGCATGACTAAG-AGATTATTAC
1 ATCTATTTATTTACCGTATTACTTAGCATGA-TAAGAAGATTATTAC
* ** *
3047673 ATCTATTTATTTACCATATTACTTAGCATGATTGGAAGATTATTAG
1 ATCTATTTATTTACCGTATTACTTAGCATGATAAGAAGATTATTAC
* *
3047719 GTCTATTTATTTTTCCGTATTACTTAGCAT
1 ATCTATTTA-TTTACCGTATTACTTAGCAT
3047749 TAGAGGTGCT
Statistics
Matches: 67, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
45 2 0.03
46 47 0.70
47 18 0.27
ACGTcount: A:0.30, C:0.14, G:0.11, T:0.45
Consensus pattern (46 bp):
ATCTATTTATTTACCGTATTACTTAGCATGATAAGAAGATTATTAC
Found at i:3047947 original size:13 final size:11
Alignment explanation
Indices: 3047911--3047941 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
3047901 CCACATGTAT
3047911 TAATTTTTATA
1 TAATTTTTATA
*
3047922 TTATTTTTATA
1 TAATTTTTATA
3047933 TAATTTTTA
1 TAATTTTTA
3047942 AATATATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TAATTTTTATA
Found at i:3048193 original size:11 final size:11
Alignment explanation
Indices: 3048154--3048224 Score: 54
Period size: 11 Copynumber: 6.5 Consensus size: 11
3048144 ATATTTAAAC
*
3048154 AATAACAATAA
1 AATAATAATAA
* * *
3048165 AATAGTGACAA
1 AATAATAATAA
*
3048176 CATAATAATAA
1 AATAATAATAA
*
3048187 AATAATAGTAA
1 AATAATAATAA
3048198 AATAAGTAA-AA
1 AATAA-TAATAA
* *
3048209 AACAATAAGAA
1 AATAATAATAA
3048220 AATAA
1 AATAA
3048225 CATTAAAAAA
Statistics
Matches: 45, Mismatches: 13, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
10 3 0.07
11 40 0.89
12 2 0.04
ACGTcount: A:0.68, C:0.06, G:0.07, T:0.20
Consensus pattern (11 bp):
AATAATAATAA
Found at i:3049528 original size:46 final size:46
Alignment explanation
Indices: 3049341--3049514 Score: 285
Period size: 46 Copynumber: 3.8 Consensus size: 46
3049331 CACAATATAT
* * * * *
3049341 ATATACATCTCATACATATCTCACATTAGCCATTCGGCTTTACTTC
1 ATATCCATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCTC
*
3049387 ATATCCATCTCATACACGTTTCGCATTAGCCATTCGGCTTTACCTC
1 ATATCCATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCTC
*
3049433 ATATCCATCTCATACACGTTTCGCATTAGCCATTCGGCTTTACCTC
1 ATATCCATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCTC
3049479 ATATCCATCTCATACACATTTCGCATTAGCCATTCG
1 ATATCCATCTCATACACATTTCGCATTAGCCATTCG
3049515 ACTTCGCCAC
Statistics
Matches: 121, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 121 1.00
ACGTcount: A:0.25, C:0.31, G:0.09, T:0.35
Consensus pattern (46 bp):
ATATCCATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCTC
Found at i:3049593 original size:47 final size:47
Alignment explanation
Indices: 3049542--3049641 Score: 148
Period size: 47 Copynumber: 2.1 Consensus size: 47
3049532 CACTTCCACG
* *
3049542 TTCATCACATTGGTCATTCT-ACCTTATCACATATATGTATGTTCACA
1 TTCATCACATTGGCCATT-TGACCTTATCACATATATGCATGTTCACA
* *
3049589 TTCATCATATTGGCCATTTGGCCTTATCACATATATGCATGTTCACA
1 TTCATCACATTGGCCATTTGACCTTATCACATATATGCATGTTCACA
3049636 TTCATC
1 TTCATC
3049642 TTATAAAATC
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
46 1 0.02
47 47 0.98
ACGTcount: A:0.26, C:0.24, G:0.10, T:0.40
Consensus pattern (47 bp):
TTCATCACATTGGCCATTTGACCTTATCACATATATGCATGTTCACA
Found at i:3053319 original size:17 final size:16
Alignment explanation
Indices: 3053285--3053322 Score: 58
Period size: 17 Copynumber: 2.3 Consensus size: 16
3053275 TTTATTTATT
3053285 TATTTATTTATAAATA
1 TATTTATTTATAAATA
*
3053301 TATTTATTATATAATTA
1 TATTTATT-TATAAATA
3053318 TATTT
1 TATTT
3053323 TTACTCACAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TATTTATTTATAAATA
Found at i:3078621 original size:3 final size:3
Alignment explanation
Indices: 3078615--3078639 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3078605 TCTTAAAGGA
3078615 ATC ATC ATC ATC ATC ATC ATC ATC A
1 ATC ATC ATC ATC ATC ATC ATC ATC A
3078640 CCATGACCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.32, G:0.00, T:0.32
Consensus pattern (3 bp):
ATC
Found at i:3093035 original size:30 final size:30
Alignment explanation
Indices: 3092978--3093060 Score: 103
Period size: 30 Copynumber: 2.7 Consensus size: 30
3092968 AAAAAAAAGA
*
3092978 TTAGGTACTAAATTAGAAAAAAGTATCAATT
1 TTAGGTACTAAATTA-AAAAAAGTATCAAAT
*
3093009 TTAGGTACTAAATTAAAAAAATTATCAAAT
1 TTAGGTACTAAATTAAAAAAAGTATCAAAT
** *
3093039 TTAAATATTAAATTAAACAAAA
1 TTAGGTACTAAATTAAA-AAAA
3093061 AAATATTTAA
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
30 27 0.59
31 19 0.41
ACGTcount: A:0.54, C:0.06, G:0.07, T:0.33
Consensus pattern (30 bp):
TTAGGTACTAAATTAAAAAAAGTATCAAAT
Found at i:3093073 original size:28 final size:27
Alignment explanation
Indices: 3093037--3093091 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 27
3093027 AAATTATCAA
*
3093037 ATTTAAATATTAAATTAAACAAAAAAAT
1 ATTTAAATATCAAATTAAA-AAAAAAAT
*
3093065 ATTTAAATATCAAATTAGAAAAAAAAT
1 ATTTAAATATCAAATTAAAAAAAAAAT
3093092 CAAGTTCAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 8 0.32
28 17 0.68
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.31
Consensus pattern (27 bp):
ATTTAAATATCAAATTAAAAAAAAAAT
Found at i:3100694 original size:18 final size:20
Alignment explanation
Indices: 3100664--3100716 Score: 65
Period size: 18 Copynumber: 2.8 Consensus size: 20
3100654 AAATAAATTC
*
3100664 TAATAAATATTTTTAATA-A
1 TAATGAATATTTTTAATACA
* *
3100683 TAAT-ATTATTTTTATTACA
1 TAATGAATATTTTTAATACA
3100702 TAATGAATATTTTTA
1 TAATGAATATTTTTA
3100717 TTTAAAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
18 11 0.38
19 9 0.31
20 9 0.31
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (20 bp):
TAATGAATATTTTTAATACA
Found at i:3102721 original size:20 final size:20
Alignment explanation
Indices: 3102693--3102731 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3102683 ACTTTAAACT
*
3102693 AAACATTGATTCATGAATTG
1 AAACATTGAATCATGAATTG
* *
3102713 AAACTTTGAATCTTGAATT
1 AAACATTGAATCATGAATT
3102732 CATAGTTTAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.38
Consensus pattern (20 bp):
AAACATTGAATCATGAATTG
Found at i:3126908 original size:16 final size:17
Alignment explanation
Indices: 3126880--3126916 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
3126870 ATGTAATTGA
*
3126880 AAAAATATAATAAATAT
1 AAAAATATAATAAAAAT
3126897 AAAAATAT-ATAAAAAT
1 AAAAATATAATAAAAAT
3126913 AAAA
1 AAAA
3126917 CACATGATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (17 bp):
AAAAATATAATAAAAAT
Found at i:3127306 original size:17 final size:20
Alignment explanation
Indices: 3127290--3127339 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
3127280 TTCCATATTT
3127290 ATTA-TAATTATATATTTTA
1 ATTAGTAATTATATATTTTA
*
3127309 ATTAGTAATTATTAAATTTATA
1 ATTAGTAATTA-TATATTT-TA
3127331 ATTA-TAATT
1 ATTAGTAATT
3127340 GTACTTGTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
19 4 0.15
20 6 0.22
21 11 0.41
22 6 0.22
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (20 bp):
ATTAGTAATTATATATTTTA
Found at i:3128308 original size:14 final size:15
Alignment explanation
Indices: 3128283--3128312 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
3128273 TTTTATAAAT
3128283 TAATATATATTTTTA
1 TAATATATATTTTTA
3128298 TAATA-ATATTTTTA
1 TAATATATATTTTTA
3128312 T
1 T
3128313 TTTTATATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TAATATATATTTTTA
Found at i:3128322 original size:19 final size:20
Alignment explanation
Indices: 3128290--3128328 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
3128280 AATTAATATA
*
3128290 TATTTTTATAATAATATTTT
1 TATTTTTATAATAAAATTTT
3128310 TATTTTTAT-ATAAAATTTT
1 TATTTTTATAATAAAATTTT
3128329 AAAAATTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
TATTTTTATAATAAAATTTT
Found at i:3139632 original size:18 final size:17
Alignment explanation
Indices: 3139609--3139642 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
3139599 TATCTCTTAA
3139609 ATAATTTAAATTATATTG
1 ATAATTTAAA-TATATTG
*
3139627 ATAATTTTAATATATT
1 ATAATTTAAATATATT
3139643 AAAATAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
ATAATTTAAATATATTG
Found at i:3140239 original size:7 final size:7
Alignment explanation
Indices: 3140229--3140262 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
3140219 CCCTAAACTC
3140229 TAAACCA
1 TAAACCA
*
3140236 TAAAACA
1 TAAACCA
3140243 TAAACCA
1 TAAACCA
3140250 TAAACCA
1 TAAACCA
*
3140257 TTAACC
1 TAAACC
3140263 CCAACCCTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.56, C:0.26, G:0.00, T:0.18
Consensus pattern (7 bp):
TAAACCA
Found at i:3140779 original size:21 final size:21
Alignment explanation
Indices: 3140740--3140780 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3140730 ACCCCAAATC
*
3140740 CTAAACTATAGGCCCTAAACA
1 CTAAACTATAGACCCTAAACA
3140761 CTAAACTATA-ACCCATAAAC
1 CTAAACTATAGACCC-TAAAC
3140781 TAAATTACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.46, C:0.29, G:0.05, T:0.20
Consensus pattern (21 bp):
CTAAACTATAGACCCTAAACA
Done.