Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001465.1 Hibiscus syriacus cultivar Beakdansim tig00002840_pilon, whole genome shotgun sequence
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: 11160956
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 55
Found at i:2512733 original size:30 final size:30
Alignment explanation
Indices: 2512697--2512756 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
2512687 TAATAAGGTT
* *
2512697 ATTTATTTTAAAATAATTTATTATAAAATA
1 ATTTATTTTAAAATAAATTATAATAAAATA
*
2512727 ATTTATTTTAAAGTAAATTATAATAAAATA
1 ATTTATTTTAAAATAAATTATAATAAAATA
2512757 TGGATTGATT
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:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (30 bp):
ATTTATTTTAAAATAAATTATAATAAAATA
Found at i:2512747 original size:15 final size:15
Alignment explanation
Indices: 2512697--2512738 Score: 75
Period size: 15 Copynumber: 2.8 Consensus size: 15
2512687 TAATAAGGTT
2512697 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
2512712 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
2512727 ATTTATTTTAAA
1 ATTTATTTTAAA
2512739 GTAAATTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:2512853 original size:80 final size:80
Alignment explanation
Indices: 2512755--2512904 Score: 255
Period size: 80 Copynumber: 1.9 Consensus size: 80
2512745 TATAATAAAA
2512755 TATGGATTGATTTATTTTAAATAATTTATCAGTATAAATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATCAGTATAAATTGATTTATTTTAAAATATGGATTGAT
2512820 TTATTATTGTAGTTG
66 TTATTATTGTAGTTG
* * ** *
2512835 TATGTATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGTATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATCAGTATAAATTGATTTATTTTAAAATATGGATTGAT
2512900 TTATT
66 TTATT
2512905 TTAAATAATT
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
80 65 1.00
ACGTcount: A:0.33, C:0.01, G:0.13, T:0.53
Consensus pattern (80 bp):
TATGGATTGATTTATTTTAAATAATTTATCAGTATAAATTGATTTATTTTAAAATATGGATTGAT
TTATTATTGTAGTTG
Found at i:2512876 original size:32 final size:32
Alignment explanation
Indices: 2512834--2512941 Score: 128
Period size: 32 Copynumber: 3.7 Consensus size: 32
2512824 TATTGTAGTT
2512834 GTATGTATTGATTTATTTTAAATAATTTATTA
1 GTATGTATTGATTTATTTTAAATAATTTATTA
*
2512866 GTATGGATTGATTTA-TTT---TAA---A--A
1 GTATGTATTGATTTATTTTAAATAATTTATTA
2512889 -TATGTATTGATTTATTTTAAATAATTTATTA
1 GTATGTATTGATTTATTTTAAATAATTTATTA
*
2512920 GTATATATTGATTTATTTTAAA
1 GTATGTATTGATTTATTTTAAA
2512942 ATATGGATTG
Statistics
Matches: 63, Mismatches: 3, Indels: 20
0.73 0.03 0.23
Matches are distributed among these distances:
22 13 0.21
23 4 0.06
25 1 0.02
26 3 0.05
28 3 0.05
29 1 0.02
31 4 0.06
32 34 0.54
ACGTcount: A:0.35, C:0.00, G:0.10, T:0.55
Consensus pattern (32 bp):
GTATGTATTGATTTATTTTAAATAATTTATTA
Found at i:2512909 original size:54 final size:54
Alignment explanation
Indices: 2512835--2513133 Score: 269
Period size: 54 Copynumber: 5.6 Consensus size: 54
2512825 ATTGTAGTTG
2512835 TATGTATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
1 TATGTATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
**
2512889 TATGTATTGATTTATTTTAAATAATTTATTAGTATATATTGATTTATTTTAAAA
1 TATGTATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
* *
2512943 TATGGATTGATTTA--TT--AT--TGTAGTT-GTATGGATTGATTTATTTT-AAA
1 TATGTATTGATTTATTTTAAATAATTTA-TTAGTATGGATTGATTTATTTTAAAA
* * ** * * * * * * **
2512990 TAATTTATT-AGTATAGATTGATTTATTT-TAAAATATAGATTGATTTATTATTATAGTTG
1 T-ATGTATTGA-TTTATTTTAAATAATTTAT-TAGTATGGATTGATTTATT-TTA-A--AA
*
2513049 TATGTATTGATTTATTTTAAA-ATATTTATTAGTATGAATTGATTTATTTTAAAA
1 TATGTATTGATTTATTTTAAATA-ATTTATTAGTATGGATTGATTTATTTTAAAA
* *
2513103 TATGAATTAATTTATTTTAAATAATTTATTA
1 TATGTATTGATTTATTTTAAATAATTTATTA
2513134 TTGTAGCTGT
Statistics
Matches: 194, Mismatches: 31, Indels: 40
0.73 0.12 0.15
Matches are distributed among these distances:
47 5 0.03
48 28 0.14
49 2 0.01
50 4 0.02
52 4 0.02
54 109 0.56
55 3 0.02
56 1 0.01
57 4 0.02
58 31 0.16
59 3 0.02
ACGTcount: A:0.35, C:0.00, G:0.11, T:0.54
Consensus pattern (54 bp):
TATGTATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
Found at i:2512918 original size:22 final size:22
Alignment explanation
Indices: 2512867--2512909 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
2512857 AATTTATTAG
*
2512867 TATGGATTGATTTATTTTAAAA
1 TATGTATTGATTTATTTTAAAA
2512889 TATGTATTGATTTATTTTAAA
1 TATGTATTGATTTATTTTAAA
2512910 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (22 bp):
TATGTATTGATTTATTTTAAAA
Found at i:2512924 original size:134 final size:133
Alignment explanation
Indices: 2512750--2513038 Score: 515
Period size: 134 Copynumber: 2.2 Consensus size: 133
2512740 TAAATTATAA
2512750 TAAAATATGGATTGATTTATTTTAAATAATTTATCAGTATAAATTGATTTATTTTAAAATATGGA
1 TAAAATAT-GATTGATTTATTTTAAATAATTTATCAGTATAAATTGATTTATTTTAAAATATGGA
* *
2512815 TTGATTTATTATTGTAGTTGTATGTATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTT
65 TTGATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTT
2512880 ATTT
130 ATTT
* *
2512884 TAAAATATGTATTGATTTATTTTAAATAATTTATTAGTATATATTGATTTATTTTAAAATATGGA
1 TAAAATATG-ATTGATTTATTTTAAATAATTTATCAGTATAAATTGATTTATTTTAAAATATGGA
2512949 TTGATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTT
65 TTGATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTT
2513014 ATTT
130 ATTT
2513018 TAAAATATAGATTGATTTATT
1 TAAAATAT-GATTGATTTATT
2513039 ATTATAGTTG
Statistics
Matches: 149, Mismatches: 4, Indels: 4
0.95 0.03 0.03
Matches are distributed among these distances:
133 1 0.01
134 147 0.99
135 1 0.01
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (133 bp):
TAAAATATGATTGATTTATTTTAAATAATTTATCAGTATAAATTGATTTATTTTAAAATATGGAT
TGATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTA
TTT
Found at i:2512983 original size:80 final size:79
Alignment explanation
Indices: 2512889--2513118 Score: 372
Period size: 80 Copynumber: 2.9 Consensus size: 79
2512879 TATTTTAAAA
2512889 TATGTATTGATTTATTTTAAATAATTTATTAGTATATATTGATTTATTTTAAAATATGGATTGAT
1 TATGTATTGATTTATTTTAAATAATTTATTAGTATA-ATTGATTTATTTTAAAATATGGATTGAT
*
2512954 TTATTATTGTAGTTG
65 TTATTATTATAGTTG
* *
2512969 TATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATAGATTGAT
1 TATGTATTGATTTATTTTAAATAATTTATTAGTATA-ATTGATTTATTTTAAAATATGGATTGAT
2513034 TTATTATTATAGTTG
65 TTATTATTATAGTTG
* *
2513049 TATGTATTGATTTATTTTAAA-ATATTTATTAGTATGAATTGATTTATTTTAAAATATGAATTAA
1 TATGTATTGATTTATTTTAAATA-ATTTATTAGTAT-AATTGATTTATTTTAAAATATGGATTGA
2513113 TTTATT
64 TTTATT
2513119 TTAAATAATT
Statistics
Matches: 140, Mismatches: 8, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
79 1 0.01
80 138 0.99
81 1 0.01
ACGTcount: A:0.35, C:0.00, G:0.11, T:0.54
Consensus pattern (79 bp):
TATGTATTGATTTATTTTAAATAATTTATTAGTATAATTGATTTATTTTAAAATATGGATTGATT
TATTATTATAGTTG
Found at i:2513015 original size:18 final size:18
Alignment explanation
Indices: 2512992--2513045 Score: 54
Period size: 22 Copynumber: 2.8 Consensus size: 18
2512982 ATTTTAAATA
*
2512992 ATTTATTAGTATAGATTG
1 ATTTATTAATATAGATTG
2513010 ATTTATTTTAAAATATAGATTG
1 ATTTA--TT--AATATAGATTG
*
2513032 ATTTATTATTATAG
1 ATTTATTAATATAG
2513046 TTGTATGTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
18 11 0.37
20 4 0.13
22 15 0.50
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.52
Consensus pattern (18 bp):
ATTTATTAATATAGATTG
Found at i:2513026 original size:22 final size:22
Alignment explanation
Indices: 2513001--2513073 Score: 83
Period size: 22 Copynumber: 3.1 Consensus size: 22
2512991 AATTTATTAG
2513001 TATAGATTGATTTATTTTAAAA
1 TATAGATTGATTTATTTTAAAA
**
2513023 TATAGATTGATTTATTATTATAGT
1 TATAGATTGATTTATT-TTA-AAA
*
2513047 TGTATGTATTGATTTATTTTAAAA
1 TATA-G-ATTGATTTATTTTAAAA
2513071 TAT
1 TAT
2513074 TTATTAGTAT
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
22 16 0.39
23 3 0.07
24 7 0.17
25 4 0.10
26 11 0.27
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.53
Consensus pattern (22 bp):
TATAGATTGATTTATTTTAAAA
Found at i:2513036 original size:40 final size:40
Alignment explanation
Indices: 2512910--2513118 Score: 121
Period size: 40 Copynumber: 5.2 Consensus size: 40
2512900 TTATTTTAAA
* *
2512910 TAATTTATTAGTATATATTGATTTATTTTAAAATATGGAT
1 TAATTTATTAGTATAGATTGATTTATTTTAAAATATAGAT
* * * * * * *
2512950 TGATTTATTATTGTAGTTGTATGGATTGA-TTT--ATTTTA-AA
1 TAATTTATTA--GTA-TAG-ATTGATTTATTTTAAAATATAGAT
2512990 TAATTTATTAGTATAGATTGATTTATTTTAAAATATAGAT
1 TAATTTATTAGTATAGATTGATTTATTTTAAAATATAGAT
* * * * * * * *
2513030 TGATTTATTATTATAG-TTGTATGTATTGATT-TATTTTAAAA
1 TAATTTATTAGTATAGATTG-ATTTATT--TTAAAATATAGAT
2513071 T-ATTTATTAGTAT-GAATTGATTTATTTTAAAATAT-GAAT
1 TAATTTATTAGTATAG-ATTGATTTATTTTAAAATATAG-AT
2513110 TAATTTATT
1 TAATTTATT
2513119 TTAAATAATT
Statistics
Matches: 122, Mismatches: 31, Indels: 32
0.66 0.17 0.17
Matches are distributed among these distances:
36 7 0.06
37 5 0.04
38 5 0.04
39 13 0.11
40 64 0.52
41 12 0.10
42 5 0.04
43 4 0.03
44 7 0.06
ACGTcount: A:0.35, C:0.00, G:0.11, T:0.54
Consensus pattern (40 bp):
TAATTTATTAGTATAGATTGATTTATTTTAAAATATAGAT
Found at i:2513116 original size:134 final size:131
Alignment explanation
Indices: 2512750--2513133 Score: 429
Period size: 134 Copynumber: 2.9 Consensus size: 131
2512740 TAAATTATAA
* * *
2512750 TAAAATATGGATTGATTTATTTTAAATAATTTATCAGTATAAATTGATTTATTTTAAAATATGGA
1 TAAAATATGTATTGATTTATTTT-AATAA--TATTAGTATATATTGATTTATTTTAAAATATGGA
*** * *
2512815 TTGATTTATTATTGTAGTTGTATGTATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTT
63 TTGATTTATTATTGTAGAAATATGAATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTT
2512880 ATTT
128 ATTT
2512884 TAAAATATGTATTGATTTATTTTAAATAATTTATTAGTATATATTGATTTATTTTAAAATATGGA
1 TAAAATATGTATTGATTTATTTT-AATAA--TATTAGTATATATTGATTTATTTTAAAATATGGA
*** *
2512949 TTGATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTT
63 TTGATTTATTATTGTAGAAATATGAATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTT
2513014 ATTT
128 ATTT
* * **
2513018 TAAAATATAG-ATTGATTTATTATT-AT-A-GTT-GTATGTATTGATTTATTTTAAAATATTTAT
1 TAAAATAT-GTATTGATTTATT-TTAATAATATTAGTATATATTGATTTATTTTAAAATATGGAT
* *
2513078 TAGTATGAATTGATTTATTTTA-AAATATGAATTAATTTATTTTAAATAATTTATTA
64 T-G-AT---TT-A-TTATTGTAGAAATATGAATTGATTTATTTTAAATAATTTATTA
2513134 TTGTAGCTGT
Statistics
Matches: 226, Mismatches: 15, Indels: 18
0.87 0.06 0.07
Matches are distributed among these distances:
128 28 0.12
129 3 0.01
130 2 0.01
132 1 0.00
133 4 0.02
134 178 0.79
135 10 0.04
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.53
Consensus pattern (131 bp):
TAAAATATGTATTGATTTATTTTAATAATATTAGTATATATTGATTTATTTTAAAATATGGATTG
ATTTATTATTGTAGAAATATGAATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATT
T
Found at i:2513133 original size:22 final size:22
Alignment explanation
Indices: 2513081--2513123 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
2513071 TATTTATTAG
*
2513081 TATGAATTGATTTATTTTAAAA
1 TATGAATTAATTTATTTTAAAA
2513103 TATGAATTAATTTATTTTAAA
1 TATGAATTAATTTATTTTAAA
2513124 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (22 bp):
TATGAATTAATTTATTTTAAAA
Found at i:2517743 original size:14 final size:14
Alignment explanation
Indices: 2517724--2517781 Score: 61
Period size: 14 Copynumber: 4.4 Consensus size: 14
2517714 CGTTCGGTAA
*
2517724 TATGTTCGTTCATT
1 TATGTTCATTCATT
*
2517738 TATGTTCATTCGTT
1 TATGTTCATTCATT
*
2517752 TATG-T-A-T-GTT
1 TATGTTCATTCATT
2517762 TATGTTCATTCATT
1 TATGTTCATTCATT
2517776 TATGTT
1 TATGTT
2517782 TAGCCTAATT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
10 7 0.19
11 2 0.05
12 2 0.05
13 2 0.05
14 24 0.65
ACGTcount: A:0.17, C:0.10, G:0.14, T:0.59
Consensus pattern (14 bp):
TATGTTCATTCATT
Found at i:2518374 original size:16 final size:16
Alignment explanation
Indices: 2518353--2518392 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
2518343 AAGATTTTTT
2518353 TGTTCGTTTATATTCA
1 TGTTCGTTTATATTCA
2518369 TGTTCGTTTATATTCA
1 TGTTCGTTTATATTCA
2518385 TGTTCGTT
1 TGTTCGTT
2518393 CATTTGTTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.15, C:0.12, G:0.15, T:0.57
Consensus pattern (16 bp):
TGTTCGTTTATATTCA
Found at i:2519845 original size:7 final size:7
Alignment explanation
Indices: 2519835--2519867 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
2519825 AACCAAAAAG
2519835 GAGAGTT
1 GAGAGTT
2519842 GAGAGTT
1 GAGAGTT
2519849 GAGAGTT
1 GAGAGTT
2519856 GAGAGTT
1 GAGAGTT
2519863 GAGAG
1 GAGAG
2519868 AGATGGCGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.30, C:0.00, G:0.45, T:0.24
Consensus pattern (7 bp):
GAGAGTT
Found at i:2523436 original size:80 final size:83
Alignment explanation
Indices: 2523332--2523503 Score: 185
Period size: 80 Copynumber: 2.1 Consensus size: 83
2523322 AAATTTAAGC
*
2523332 ATGTAGCGGCGTTTACAATCCAAACGTCACAAAAT-GA-TACTTTA-GCGGCGTTTTTT-AATAA
1 ATGTAGCGGCGTTTACAATCCAAACG-C-CAAAATAGAGTACTTTATGCGGCGTTTTTTCAACAA
*
2523393 A-CGCCGCAATAGAGTGGTA
64 AGCGCCGCAATAGAGTAGTA
* * * ** *
2523412 ATGTAGCGGCGTTTA-TAGCTCAAACGCCAGAATAGAGTTGTTTATGTGGCGTTTTTTCAACAAA
1 ATGTAGCGGCGTTTACAATC-CAAACGCCAAAATAGAGTACTTTATGCGGCGTTTTTTCAACAAA
*
2523476 GCGCCGCATTAGAGTAGTA
65 GCGCCGCAATAGAGTAGTA
*
2523495 ATTTAGCGG
1 ATGTAGCGG
2523504 AAACGCCGTA
Statistics
Matches: 76, Mismatches: 10, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
78 5 0.07
79 5 0.07
80 26 0.34
81 11 0.14
82 5 0.07
83 24 0.32
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.29
Consensus pattern (83 bp):
ATGTAGCGGCGTTTACAATCCAAACGCCAAAATAGAGTACTTTATGCGGCGTTTTTTCAACAAAG
CGCCGCAATAGAGTAGTA
Found at i:2524151 original size:22 final size:22
Alignment explanation
Indices: 2524123--2524171 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
2524113 GTGTTTTTCT
2524123 GCTTTCGAACAGAAAAATAATA
1 GCTTTCGAACAGAAAAATAATA
* *
2524145 GCTTTCGAATAGGAAAATAATA
1 GCTTTCGAACAGAAAAATAATA
2524167 GCTTT
1 GCTTT
2524172 TGAAAACGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.43, C:0.12, G:0.16, T:0.29
Consensus pattern (22 bp):
GCTTTCGAACAGAAAAATAATA
Found at i:2527905 original size:24 final size:24
Alignment explanation
Indices: 2527861--2527910 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
2527851 ATAAAGAACC
*
2527861 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
2527885 AAAATAAAGTTCAAACA-ACCATTA
1 AAAATAAACTT-AAACATACCATTA
2527909 AA
1 AA
2527911 TCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.60, C:0.14, G:0.02, T:0.24
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:2534417 original size:24 final size:24
Alignment explanation
Indices: 2534373--2534422 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
2534363 ATAAAGAACC
*
2534373 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
2534397 AAAATAAAGTTCAAACA-ACCATTA
1 AAAATAAACTT-AAACATACCATTA
2534421 AA
1 AA
2534423 TCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.60, C:0.14, G:0.02, T:0.24
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:2542054 original size:21 final size:21
Alignment explanation
Indices: 2542030--2542086 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
2542020 TGAAGTAATG
*
2542030 GAAGCAGAGAGAGCAGCAGTA
1 GAAGCAGAGAGAGCAGCAGAA
2542051 GAAGCAGAGAGAGCAGCAGAA
1 GAAGCAGAGAGAGCAGCAGAA
*
2542072 GAAGCAGTGAGAGCA
1 GAAGCAGAGAGAGCA
2542087 ACAACGGAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.44, C:0.14, G:0.39, T:0.04
Consensus pattern (21 bp):
GAAGCAGAGAGAGCAGCAGAA
Found at i:2542056 original size:12 final size:11
Alignment explanation
Indices: 2542032--2542078 Score: 53
Period size: 12 Copynumber: 4.2 Consensus size: 11
2542022 AAGTAATGGA
2542032 AGCAGAGAGAGC
1 AGCAGAGA-AGC
2542044 AGCAGTAGAAGC
1 AGCAG-AGAAGC
2542056 AG-AGAG-AGC
1 AGCAGAGAAGC
2542065 AGCAGAAGAAGC
1 AGCAG-AGAAGC
2542077 AG
1 AG
2542079 TGAGAGCAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
9 5 0.16
10 4 0.13
11 4 0.13
12 15 0.48
13 3 0.10
ACGTcount: A:0.45, C:0.15, G:0.38, T:0.02
Consensus pattern (11 bp):
AGCAGAGAAGC
Found at i:2542678 original size:43 final size:43
Alignment explanation
Indices: 2542584--2542847 Score: 278
Period size: 43 Copynumber: 6.1 Consensus size: 43
2542574 TATTTTACAA
* ** * *
2542584 CGTTTGTGAGGAAAACGCCGCTAAATCCCAAACACCTATTGCGA
1 CGTTTGTGAGAAAAACGCCGCTAAATGTCACA-ACCTATTGCGG
** * *
2542628 TATTTGTGAGACAAACGCCGTTAAATGTCACAACCTATTGCGG
1 CGTTTGTGAGAAAAACGCCGCTAAATGTCACAACCTATTGCGG
* * * *
2542671 CGTTTGTGAGAAAAACACCTCTAAATGTCACAACCTATTACAG
1 CGTTTGTGAGAAAAACGCCGCTAAATGTCACAACCTATTGCGG
* *
2542714 CGTTTGTGAGAAAAACGCCACAAAATGTCACAACCTATTGCGG
1 CGTTTGTGAGAAAAACGCCGCTAAATGTCACAACCTATTGCGG
* * * **
2542757 CGTTTATGAGAAAAACGTCGCTAAATGTCACAACCTATTACAT
1 CGTTTGTGAGAAAAACGCCGCTAAATGTCACAACCTATTGCGG
* * * * *
2542800 CGTTTGTGAGAAAAATGCTGCTATATCTCA-ACACTTATTGCGG
1 CGTTTGTGAGAAAAACGCCGCTAAATGTCACA-ACCTATTGCGG
2542843 CGTTT
1 CGTTT
2542848 TTTTGGAAAA
Statistics
Matches: 180, Mismatches: 39, Indels: 3
0.81 0.18 0.01
Matches are distributed among these distances:
42 1 0.01
43 155 0.86
44 24 0.13
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.27
Consensus pattern (43 bp):
CGTTTGTGAGAAAAACGCCGCTAAATGTCACAACCTATTGCGG
Found at i:2542767 original size:129 final size:130
Alignment explanation
Indices: 2542578--2542814 Score: 314
Period size: 129 Copynumber: 1.8 Consensus size: 130
2542568 CATACGTATT
* * * * * *
2542578 TTACAACGTTTGTGAGGAAAACGCCGCTAAATCCCAAACACCTATTGCGATATTTGTGAGACAAA
1 TTACAACGTTTGTGAGAAAAACGCCACAAAATCCCAAACACCTATTGCGACATTTATGAGAAAAA
* * *
2542643 CGCCGTTAAATGTCACAACCTATTGCGGCGTTTGTGAGAAAAACACCTCTAAATGTCACAACCTA
66 CGCCGCTAAATGTCACAACCTATTACAGCGTTTGTGAGAAAAACACCTCTAAATGTCACAACCTA
* ** * * *
2542708 TTACAGCGTTTGTGAGAAAAACGCCACAAAATGTCACA-ACCTATTGCGGCGTTTATGAGAAAAA
1 TTACAACGTTTGTGAGAAAAACGCCACAAAATCCCAAACACCTATTGCGACATTTATGAGAAAAA
* *
2542772 CGTCGCTAAATGTCACAACCTATTACATCGTTTGTGAGAAAAA
66 CGCCGCTAAATGTCACAACCTATTACAGCGTTTGTGAGAAAAA
2542815 TGCTGCTATA
Statistics
Matches: 90, Mismatches: 17, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
129 59 0.66
130 31 0.34
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.25
Consensus pattern (130 bp):
TTACAACGTTTGTGAGAAAAACGCCACAAAATCCCAAACACCTATTGCGACATTTATGAGAAAAA
CGCCGCTAAATGTCACAACCTATTACAGCGTTTGTGAGAAAAACACCTCTAAATGTCACAACCTA
Found at i:2553881 original size:137 final size:139
Alignment explanation
Indices: 2553518--2553886 Score: 372
Period size: 139 Copynumber: 2.7 Consensus size: 139
2553508 ATACAGCTAA
* * * * * *
2553518 ACGTCCTCAACACA-AAAGAAA-ATTTTCA-CCGTCCGACCAGATTTTCTCAACGCAAAGGAGTA
1 ACGTCCTCAACACACGAAGAAACAATTTCATCC-ACCAACCAGATCTCCTCAACGCAAAGGAGTA
* * * *
2553580 ATGTCATCCTCAGACAATCATATTTTCTCAACACGAAGGAACCATGTTATCTACAAATTATCCAA
65 GTGTCATCCTCAGACAATCATACTTCCTCAACACGAAGGAACCATATTATCTACAAATTATCCAA
* * *
2553645 CTATGGCTAG
130 ATACGGATAG
* * * * *
2553655 ACGTCCTCAACACACGAGGGAACAATTTCATCCACCAACCAGATCTCCTAAACGCAAAAGAGCAG
1 ACGTCCTCAACACACGAAGAAACAATTTCATCCACCAACCAGATCTCCTCAACGCAAAGGAGTAG
* * * * * * *
2553720 TGTCATCCTTAGACAATCAGACTTCCTCAACATGAATGAACCGTATTGTCTCCAAATTATCCAAA
66 TGTCATCCTCAGACAATCATACTTCCTCAACACGAAGGAACCATATTATCTACAAATTATCCAAA
*
2553785 TACGTATAG
131 TACGGATAG
*** * * **
2553794 ACGTCCTC-A-ATGTGAAGAAACAATGTT-ATCTACCGATTAGATCTCCTCAACGCAAAGGAGTA
1 ACGTCCTCAACACACGAAGAAACAAT-TTCATCCACCAACCAGATCTCCTCAACGCAAAGGAGTA
*
2553856 GTGTCATACTCAGACAATCATACTTCCTCAA
65 GTGTCATCCTCAGACAATCATACTTCCTCAA
2553887 TGAGAAGGAA
Statistics
Matches: 187, Mismatches: 41, Indels: 8
0.79 0.17 0.03
Matches are distributed among these distances:
137 80 0.43
138 7 0.04
139 98 0.52
140 2 0.01
ACGTcount: A:0.36, C:0.26, G:0.14, T:0.24
Consensus pattern (139 bp):
ACGTCCTCAACACACGAAGAAACAATTTCATCCACCAACCAGATCTCCTCAACGCAAAGGAGTAG
TGTCATCCTCAGACAATCATACTTCCTCAACACGAAGGAACCATATTATCTACAAATTATCCAAA
TACGGATAG
Found at i:2553914 original size:137 final size:139
Alignment explanation
Indices: 2553518--2553919 Score: 386
Period size: 137 Copynumber: 2.9 Consensus size: 139
2553508 ATACAGCTAA
* * * * * *
2553518 ACGTCCTCAACACA-AAAGAAA-ATTTTCA-CCGTCCGACCAGATTTTCTCAACGCAAAGGAGTA
1 ACGTCCTCAACACACGAAGAAACAATTTCATCC-ACCAACCAGATCTCCTCAACGCAAAGGAGTA
* * * *
2553580 ATGTCATCCTCAGACAATCATATTTTCTCAACACGAAGGAACCATGTTATCTACAAATTATCCAA
65 GTGTCATCCTCAGACAATCATACTTCCTCAACACGAAGGAACCGTGTTATCTACAAATTATCCAA
* * *
2553645 CTATGGCTAG
130 ATACGGATAG
* * * * *
2553655 ACGTCCTCAACACACGAGGGAACAATTTCATCCACCAACCAGATCTCCTAAACGCAAAAGAGCAG
1 ACGTCCTCAACACACGAAGAAACAATTTCATCCACCAACCAGATCTCCTCAACGCAAAGGAGTAG
* * * * * * *
2553720 TGTCATCCTTAGACAATCAGACTTCCTCAACATGAATGAACCGTATTGTCTCCAAATTATCCAAA
66 TGTCATCCTCAGACAATCATACTTCCTCAACACGAAGGAACCGTGTTATCTACAAATTATCCAAA
*
2553785 TACGTATAG
131 TACGGATAG
*** * * **
2553794 ACGTCCTC-A-ATGTGAAGAAACAATGTT-ATCTACCGATTAGATCTCCTCAACGCAAAGGAGTA
1 ACGTCCTCAACACACGAAGAAACAAT-TTCATCCACCAACCAGATCTCCTCAACGCAAAGGAGTA
* * * **
2553856 GTGTCATACTCAGACAATCATACTTCCTCAATGA-GAAGGAACTGTGTTATCTTTAAATTATCCA
65 GTGTCATCCTCAGACAATCATACTTCCTCAA-CACGAAGGAACCGTGTTATCTACAAATTATCCA
2553920 TATTAACTCG
Statistics
Matches: 212, Mismatches: 48, Indels: 10
0.79 0.18 0.04
Matches are distributed among these distances:
137 104 0.49
138 8 0.04
139 98 0.46
140 2 0.01
ACGTcount: A:0.35, C:0.25, G:0.14, T:0.25
Consensus pattern (139 bp):
ACGTCCTCAACACACGAAGAAACAATTTCATCCACCAACCAGATCTCCTCAACGCAAAGGAGTAG
TGTCATCCTCAGACAATCATACTTCCTCAACACGAAGGAACCGTGTTATCTACAAATTATCCAAA
TACGGATAG
Found at i:2554189 original size:20 final size:20
Alignment explanation
Indices: 2554164--2554205 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
2554154 CTAAGAGCCT
*
2554164 ATTTAGGATCATATAGATGC
1 ATTTAGGAGCATATAGATGC
*
2554184 ATTTAGGAGCATATAGTTGC
1 ATTTAGGAGCATATAGATGC
2554204 AT
1 AT
2554206 GTGGTGGACT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.10, G:0.21, T:0.36
Consensus pattern (20 bp):
ATTTAGGAGCATATAGATGC
Found at i:2554601 original size:23 final size:23
Alignment explanation
Indices: 2554573--2554633 Score: 113
Period size: 23 Copynumber: 2.7 Consensus size: 23
2554563 CACCCAGGCT
*
2554573 GGACCACTGCCAGCTGCCGGAGG
1 GGACCACTGCCAGCTGCCCGAGG
2554596 GGACCACTGCCAGCTGCCCGAGG
1 GGACCACTGCCAGCTGCCCGAGG
2554619 GGACCACTGCCAGCT
1 GGACCACTGCCAGCT
2554634 CTGCCAACCC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.18, C:0.38, G:0.34, T:0.10
Consensus pattern (23 bp):
GGACCACTGCCAGCTGCCCGAGG
Found at i:2558876 original size:11 final size:12
Alignment explanation
Indices: 2558836--2558880 Score: 65
Period size: 12 Copynumber: 3.8 Consensus size: 12
2558826 TATTTAAACG
*
2558836 GGTATTGGGCCA
1 GGTATTGGGTCA
*
2558848 GGTATTGGGTCG
1 GGTATTGGGTCA
2558860 GGTATTGGGTC-
1 GGTATTGGGTCA
2558871 GGTATTGGGT
1 GGTATTGGGT
2558881 TGGGAATCGG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
11 10 0.32
12 21 0.68
ACGTcount: A:0.11, C:0.09, G:0.47, T:0.33
Consensus pattern (12 bp):
GGTATTGGGTCA
Found at i:2558878 original size:23 final size:24
Alignment explanation
Indices: 2558834--2558899 Score: 80
Period size: 23 Copynumber: 2.8 Consensus size: 24
2558824 ATTATTTAAA
2558834 CGGGTATTGGGCCAGGTATTGGGT
1 CGGGTATTGGGCCAGGTATTGGGT
*
2558858 CGGGTATTGGGTC-GGTATTGGGT
1 CGGGTATTGGGCCAGGTATTGGGT
* * * *
2558881 TGGGAATCGGGCCGGGTAT
1 CGGGTATTGGGCCAGGTAT
2558900 ATATATATAT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
23 19 0.53
24 17 0.47
ACGTcount: A:0.12, C:0.12, G:0.47, T:0.29
Consensus pattern (24 bp):
CGGGTATTGGGCCAGGTATTGGGT
Found at i:2558957 original size:24 final size:25
Alignment explanation
Indices: 2558897--2558989 Score: 72
Period size: 24 Copynumber: 3.8 Consensus size: 25
2558887 TCGGGCCGGG
2558897 TATATA-TATA-TATTTAAATTAAA
1 TATATATTATATTATTTAAATTAAA
*
2558920 TATATATT-TTTTATTTAAATTAAA
1 TATATATTATATTATTTAAATTAAA
* * *
2558944 T-T-TATTAATATTATATATA-TATA
1 TATATATT-ATATTATTTAAATTAAA
*
2558967 TATATATATATATATATATAAAT
1 TATATAT-TATAT-TATTTAAAT
2558990 AATTATTTTT
Statistics
Matches: 55, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
22 4 0.07
23 12 0.22
24 24 0.44
25 7 0.13
26 8 0.15
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (25 bp):
TATATATTATATTATTTAAATTAAA
Found at i:2558962 original size:2 final size:2
Alignment explanation
Indices: 2558951--2558986 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
2558941 AAATTTATTA
2558951 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2558987 AATAATTATT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2559063 original size:13 final size:13
Alignment explanation
Indices: 2559007--2559050 Score: 72
Period size: 13 Copynumber: 3.5 Consensus size: 13
2558997 TTTAATATTT
*
2559007 ATCGGGTCGGGT-
1 ATCGGGGCGGGTA
2559019 ATCGGGGCGGGTA
1 ATCGGGGCGGGTA
2559032 ATCGGGGCGGGTA
1 ATCGGGGCGGGTA
2559045 ATCGGG
1 ATCGGG
2559051 TAATCGGGGC
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
12 11 0.37
13 19 0.63
ACGTcount: A:0.14, C:0.16, G:0.52, T:0.18
Consensus pattern (13 bp):
ATCGGGGCGGGTA
Found at i:2560080 original size:24 final size:24
Alignment explanation
Indices: 2560024--2560092 Score: 93
Period size: 24 Copynumber: 2.9 Consensus size: 24
2560014 CTAACGATGC
2560024 TCACCAGCCAGCCAATGAAGAGGT
1 TCACCAGCCAGCCAATGAAGAGGT
** **
2560048 TCATTAGCCCTCCAATGAAGAGGT
1 TCACCAGCCAGCCAATGAAGAGGT
*
2560072 TCACCAGCCAGCCGATGAAGA
1 TCACCAGCCAGCCAATGAAGA
2560093 AGAACCAACT
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.32, C:0.29, G:0.23, T:0.16
Consensus pattern (24 bp):
TCACCAGCCAGCCAATGAAGAGGT
Found at i:2560386 original size:18 final size:18
Alignment explanation
Indices: 2560363--2560404 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
2560353 ACTCTAGCCC
*
2560363 TACACAACTGCGAAAGCG
1 TACACAACTACGAAAGCG
2560381 TACACAACTACGAAAGCG
1 TACACAACTACGAAAGCG
2560399 TACACA
1 TACACA
2560405 TCGCACGACT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.43, C:0.29, G:0.17, T:0.12
Consensus pattern (18 bp):
TACACAACTACGAAAGCG
Found at i:2561472 original size:20 final size:20
Alignment explanation
Indices: 2561447--2561489 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
2561437 TCTAAGAGCC
*
2561447 CATTTAGGATCATATAGATG
1 CATTTAGGAGCATATAGATG
*
2561467 CATTTAGGAGCATATAGTTG
1 CATTTAGGAGCATATAGATG
2561487 CAT
1 CAT
2561490 ATGGTGGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.35
Consensus pattern (20 bp):
CATTTAGGAGCATATAGATG
Found at i:2562964 original size:20 final size:22
Alignment explanation
Indices: 2562939--2562979 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
2562929 TTGCTACCAT
2562939 CATTTCAT-TT-CCACAACATC
1 CATTTCATCTTGCCACAACATC
2562959 CATTTCATCTTGCCACAACAT
1 CATTTCATCTTGCCACAACAT
2562980 TATCATATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.42
21 2 0.11
22 9 0.47
ACGTcount: A:0.29, C:0.34, G:0.02, T:0.34
Consensus pattern (22 bp):
CATTTCATCTTGCCACAACATC
Found at i:2563713 original size:14 final size:14
Alignment explanation
Indices: 2563688--2563726 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
2563678 TTGTTTTTAT
*
2563688 TTATTATTATTATTA
1 TTATT-TTATTAATA
2563703 TTATTTTATTAATA
1 TTATTTTATTAATA
*
2563717 ATATTTTATT
1 TTATTTTATT
2563727 TTACATTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 17 0.77
15 5 0.23
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TTATTTTATTAATA
Found at i:2564169 original size:22 final size:22
Alignment explanation
Indices: 2564126--2564169 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
2564116 TCAGGACGAA
* *
2564126 CAGTGAAAAAATACAACCAAAT
1 CAGTAAAAAAATACAACAAAAT
* *
2564148 CAGTAAAAAAATCCAAGAAAAT
1 CAGTAAAAAAATACAACAAAAT
2564170 AAAAACCCAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.61, C:0.16, G:0.09, T:0.14
Consensus pattern (22 bp):
CAGTAAAAAAATACAACAAAAT
Found at i:2581337 original size:28 final size:28
Alignment explanation
Indices: 2581305--2581362 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
2581295 GACACATGAA
*
2581305 TCTACTGAAGTAGATTTTGTATCTTGTG
1 TCTACTGAAGCAGATTTTGTATCTTGTG
2581333 TCTACTGAAGCAGATTTTGTATCTTGTG
1 TCTACTGAAGCAGATTTTGTATCTTGTG
2581361 TC
1 TC
2581363 GAAACGGTCC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.21, C:0.14, G:0.21, T:0.45
Consensus pattern (28 bp):
TCTACTGAAGCAGATTTTGTATCTTGTG
Found at i:2581533 original size:14 final size:14
Alignment explanation
Indices: 2581514--2581540 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2581504 AATACATTTT
2581514 AAAATAATTTTAAG
1 AAAATAATTTTAAG
2581528 AAAATAATTTTAA
1 AAAATAATTTTAA
2581541 AAGATAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (14 bp):
AAAATAATTTTAAG
Found at i:2583620 original size:3 final size:3
Alignment explanation
Indices: 2583614--2583691 Score: 54
Period size: 3 Copynumber: 25.7 Consensus size: 3
2583604 AAAAGAAAAA
* *
2583614 AAT AAT AAT -AT AAAT AAT AAA AAT -AT AAAT AAT AAA AAT -AT AAAT
1 AAT AAT AAT AAT -AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT -AAT
* * *
2583659 AAT AAT AAT AAT AGT ATT AAAT ATT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AA
2583692 CCCGGACAAA
Statistics
Matches: 59, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
2 6 0.10
3 45 0.76
4 8 0.14
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2583638 original size:15 final size:15
Alignment explanation
Indices: 2583614--2583668 Score: 92
Period size: 15 Copynumber: 3.7 Consensus size: 15
2583604 AAAAGAAAAA
*
2583614 AATAATAATATAAAT
1 AATAAAAATATAAAT
2583629 AATAAAAATATAAAT
1 AATAAAAATATAAAT
2583644 AATAAAAATATAAAT
1 AATAAAAATATAAAT
*
2583659 AATAATAATA
1 AATAAAAATA
2583669 ATAGTATTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 38 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
AATAAAAATATAAAT
Found at i:2584131 original size:42 final size:41
Alignment explanation
Indices: 2584038--2584138 Score: 112
Period size: 42 Copynumber: 2.4 Consensus size: 41
2584028 AAGCCTTACG
* * *
2584038 GATGGCCCGAAGGACTTATCATCTTGCTCGAATGACTTATA
1 GATGGCCCGAAGGACTTAGCATCATGCTCGAAAGACTTATA
** * * *
2584079 GATGAACCGAAGGAGTTGAGCATCATGCTTGAAAGACTTATT
1 GATGGCCCGAAGGACTT-AGCATCATGCTCGAAAGACTTATA
*
2584121 GATGGCCCGAATGACTTA
1 GATGGCCCGAAGGACTTA
2584139 CAAGTTTTGG
Statistics
Matches: 47, Mismatches: 12, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
41 15 0.32
42 32 0.68
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.27
Consensus pattern (41 bp):
GATGGCCCGAAGGACTTAGCATCATGCTCGAAAGACTTATA
Found at i:2584335 original size:41 final size:42
Alignment explanation
Indices: 2584290--2584392 Score: 118
Period size: 42 Copynumber: 2.5 Consensus size: 42
2584280 ACCCGAAGGT
* * * *
2584290 CTTACGGATGGCCCGAAGGATTT-ATCATCTTTCTATAAAGA
1 CTTACAGATGGCCCGAAGGATTTAATCATCATGCTAGAAAGA
* * * *
2584331 CTTACAGATGACCCAAAAGATTTAATCATCATGCTCGAAAGA
1 CTTACAGATGGCCCGAAGGATTTAATCATCATGCTAGAAAGA
*
2584373 CTTACTGATGGCCCGAAGGA
1 CTTACAGATGGCCCGAAGGA
2584393 CTTACAAATT
Statistics
Matches: 49, Mismatches: 12, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
41 19 0.39
42 30 0.61
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.26
Consensus pattern (42 bp):
CTTACAGATGGCCCGAAGGATTTAATCATCATGCTAGAAAGA
Found at i:2584398 original size:258 final size:257
Alignment explanation
Indices: 2583834--2584570 Score: 1084
Period size: 257 Copynumber: 2.9 Consensus size: 257
2583824 TAACTCGAAT
* ** *
2583834 GATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCAAAGGACTTACAAATTTTTAAAATAAT
1 GATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACAAATTTTGGAAATAGT
2583899 TTACTGGGTAAGAAACTTTGGAAATCGT-TTTCTTACTTTTCAAAAATTTCATTTTCT-AAAAAT
66 TTACTGGGTAAGAAACTTTGGAAATC-TCTTTCTTACTTTTCAAAAATTTCATTTTCTGAAAAA-
2583962 ACTAAATGAGAAACTTTGGAAATCGTTTTCTCATTTTTCAAATTCATGTGAAAACATCCTACCCG
129 ACTAAATGAGAAACTTTGGAAATCGTTTTCTCATTTTTCAAATTCATGTGAAAACATCCTACCCG
* * * * * * * *
2584027 AAAGCCTTACGGATGGCCCGAAGGACTTATCATCTTGCTCGAATGACTTATAGATGAACCGAAG
194 AAGGTCTTACGGATGGCCCGAAGGATTTATCATCTTGCTAGAAAGACTTACAGATGAACCAAAA
* * * * * * *
2584091 GAGTTGAGCATCATGCTTGAAAGACTTATTGATGGCCCGAATGACTTACAAGTTTTGGAAATAGT
1 GATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACAAATTTTGGAAATAGT
* * *
2584156 TTACTGGGTAAGAAACTTTGAAAATCTCTTTCTTACTTTTCAAAAATTTTATTTTCTGAAAAAAT
66 TTACTGGGTAAGAAACTTTGGAAATCTCTTTCTTACTTTTCAAAAATTTCATTTTCTGAAAAAAC
* * * *
2584221 TAAATGAAAAACTTTGGAAATCGTTTTCTCATTTTTCGAAAATCATGTGGAAACATCTTACCCGA
131 TAAATGAGAAACTTTGGAAATCGTTTTCTCATTTTTC-AAATTCATGTGAAAACATCCTACCCGA
* * *
2584286 AGGTCTTACGGATGGCCCGAAGGATTTATCATCTTTCTATAAAGACTTACAGATGACCCAAAA
195 AGGTCTTACGGATGGCCCGAAGGATTTATCATCTTGCTAGAAAGACTTACAGATGAACCAAAA
2584349 GATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACAAATTTTGGGAAATAG
1 GATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACAAATTTT-GGAAATAG
* * * * *
2584414 TTTACTAGGTAAAAAACTTTGGAAATCGCTTTCTTACTTTTTAAAAATTTCATTTTCTGAAAATA
65 TTTACTGGGTAAGAAACTTTGGAAATCTCTTTCTTACTTTTCAAAAATTTCATTTTCTGAAAAAA
* *
2584479 CTAAATGAGAAACTTTGGAAATCGCTTTCCCA-TTTTCAAATTCATGTGAAAACATCCTACCCGA
130 CTAAATGAGAAACTTTGGAAATCGTTTTCTCATTTTTCAAATTCATGTGAAAACATCCTACCCGA
*
2584543 AGGTCTTACGGATGGCCTGAAGGATTTA
195 AGGTCTTACGGATGGCCCGAAGGATTTA
2584571 AGCATCATGC
Statistics
Matches: 425, Mismatches: 51, Indels: 8
0.88 0.11 0.02
Matches are distributed among these distances:
256 1 0.00
257 195 0.46
258 135 0.32
259 94 0.22
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (257 bp):
GATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACAAATTTTGGAAATAGT
TTACTGGGTAAGAAACTTTGGAAATCTCTTTCTTACTTTTCAAAAATTTCATTTTCTGAAAAAAC
TAAATGAGAAACTTTGGAAATCGTTTTCTCATTTTTCAAATTCATGTGAAAACATCCTACCCGAA
GGTCTTACGGATGGCCCGAAGGATTTATCATCTTGCTAGAAAGACTTACAGATGAACCAAAA
Found at i:2584724 original size:215 final size:217
Alignment explanation
Indices: 2584331--2584808 Score: 712
Period size: 216 Copynumber: 2.2 Consensus size: 217
2584321 TCTATAAAGA
* * * * * * *
2584331 CTTACAGATGACCCAAAAGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTT
1 CTTACAGATGGCCCGAAGGATTTAAGCATCATGCTCAAAAGACTTACTCATGGCCCAAAGGACTT
*
2584396 ACAAATTTTGGGAAATAGTTTACTAGGTAAAAAACTTTGGAAATCGCTTTCTTACTTTTTAAAAA
66 ACAAATTTTGGGAAATAGTTTACTAGGTAAAAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAA
* *
2584461 TTTCATTTTCTGAAAATACTAAATGAGAAACTTTGGAAATCGCTTTCCCA-TTTTCAAATTCATG
131 TTTAATTTTCTGAAAATACTAAATGAGAAACTTTGGAAATCACTTTCCCATTTTTCAAATTCATG
*
2584525 TGAAAACATCCTACCCGAAGGT
196 TGAAAACATCATACCCGAAGGT
* * *
2584547 CTTACGGATGGCCTGAAGGATTTAAGCATCATGCTCAAAATACTTACTCATGGCCCAAAGGACTT
1 CTTACAGATGGCCCGAAGGATTTAAGCATCATGCTCAAAAGACTTACTCATGGCCCAAAGGACTT
* * *
2584612 ACAAATTTT-GGAAATAGTTTACTGGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCACAAA
66 ACAAATTTTGGGAAATAGTTTACTAGGTAAAAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAA
2584676 TTTAATTTTCT-AGAAATACTAAATGAGAAACTTTGGAAATCACTTTCCCATTTTTCAAATTCAT
131 TTTAATTTTCTGA-AAATACTAAATGAGAAACTTTGGAAATCACTTTCCCATTTTTCAAATTCAT
2584740 GTGAAAACATCATACCCGAAGGT
195 GTGAAAACATCATACCCGAAGGT
* * * * * *
2584763 CTTATAGATGGCCCGAAGGACTT-ATCATCTTGCTCGAAAGGCTTAC
1 CTTACAGATGGCCCGAAGGATTTAAGCATCATGCTCAAAAGACTTAC
2584809 AGATGACCCG
Statistics
Matches: 234, Mismatches: 26, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
214 1 0.00
215 115 0.49
216 118 0.50
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.32
Consensus pattern (217 bp):
CTTACAGATGGCCCGAAGGATTTAAGCATCATGCTCAAAAGACTTACTCATGGCCCAAAGGACTT
ACAAATTTTGGGAAATAGTTTACTAGGTAAAAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAA
TTTAATTTTCTGAAAATACTAAATGAGAAACTTTGGAAATCACTTTCCCATTTTTCAAATTCATG
TGAAAACATCATACCCGAAGGT
Found at i:2584861 original size:42 final size:41
Alignment explanation
Indices: 2584763--2584869 Score: 124
Period size: 42 Copynumber: 2.6 Consensus size: 41
2584753 ACCCGAAGGT
* * * *
2584763 CTTATAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGG
1 CTTATAGATGGCCCGAAGGACTTAACATCATGCTCAAAAGA
* * * *
2584804 CTTACAGATGACCCGAATGAGTTAAACATCATGCTCAAAAGA
1 CTTATAGATGGCCCGAAGGACTT-AACATCATGCTCAAAAGA
*
2584846 CTTATTGATGGCCCGAAGGACTTA
1 CTTATAGATGGCCCGAAGGACTTA
2584870 CAAGTTTTGG
Statistics
Matches: 52, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
41 20 0.38
42 32 0.62
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.25
Consensus pattern (41 bp):
CTTATAGATGGCCCGAAGGACTTAACATCATGCTCAAAAGA
Found at i:2584990 original size:473 final size:474
Alignment explanation
Indices: 2584087--2584993 Score: 1352
Period size: 474 Copynumber: 1.9 Consensus size: 474
2584077 TAGATGAACC
* ** * * * * *
2584087 GAAGGAGTTGAGCATCATGCTTGAAAGACTTATTGATGGCCCGAATGACTTACAAGTTTTGGAAA
1 GAAGGAGTTAAGCATCATGCTCAAAAGACTTACTCATGGCCCAAAGGACTTACAAATTTTGGAAA
* *
2584152 TAGTTTACTGGGTAAGAAACTTTGAAAATCTCTTTCTTACTTTTCAAAAATTTTATTTTCTGAAA
66 TAGTTTACTGGGTAAGAAACTTTGAAAATCGCTTTCTTACTTTTCAAAAATTTAATTTTCTGAAA
* ** * * *
2584217 AAATTAAATGAAAAACTTTGGAAATCGTTTTCTCATTTTTCGAAAATCATGTGGAAACATCTTAC
131 AAACTAAATGAAAAACTTTGGAAATCACTTTCCCATTTTTCGAAAATCATGTGAAAACATCATAC
* * * *
2584282 CCGAAGGTCTTACGGATGGCCCGAAGGATTTATCATCTTTCTATAAAGACTTACAGATGACCCAA
196 CCGAAGGTCTTACAGATGGCCCGAAGGACTTATCATCTTGCTAGAAAGACTTACAGATGACCCAA
* * *
2584347 AAGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACAAATTTTGGGAAAT
261 AAGAGTTAAACATCATGCTCAAAAGACTTACTGATGGCCCGAAGGACTTACAAATTTTGGGAAAT
** *
2584412 AGTTTACTAGGTAAAAAACTTTGGAAATCGCTTTCTTACTTTTTAAAAATTTCATTTTCTGAAAA
326 AGTTTACTAGGTAAAAAACTTTGGAAATAACTTTCTTACTTTTCAAAAATTTCATTTTCTGAAAA
2584477 TACTAAATGAGAAACTTTGGAAATCGCTTTCCCATTTTCAAATTCATGTGAAAACATCCTACCCG
391 TACTAAATGAGAAACTTTGGAAATCGCTTTCCCATTTTCAAATTCATGTGAAAACATCCTACCCG
2584542 AAGGTCTTACGGATGGCCT
456 AAGGTCTTACGGATGGCCT
* *
2584561 GAAGGATTTAAGCATCATGCTCAAAATACTTACTCATGGCCCAAAGGACTTACAAATTTTGGAAA
1 GAAGGAGTTAAGCATCATGCTCAAAAGACTTACTCATGGCCCAAAGGACTTACAAATTTTGGAAA
* *
2584626 TAGTTTACTGGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCACAAATTTAATTTTCT-AGA
66 TAGTTTACTGGGTAAGAAACTTTGAAAATCGCTTTCTTACTTTTCAAAAATTTAATTTTCTGA-A
* * *
2584690 AATACTAAATGAGAAACTTTGGAAATCACTTTCCCATTTTTC-AAATTCATGTGAAAACATCATA
130 AAAACTAAATGAAAAACTTTGGAAATCACTTTCCCATTTTTCGAAAATCATGTGAAAACATCATA
* * * *
2584754 CCCGAAGGTCTTATAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGGCTTACAGATGACCCG
195 CCCGAAGGTCTTACAGATGGCCCGAAGGACTTATCATCTTGCTAGAAAGACTTACAGATGACCCA
* * *
2584819 AATGAGTTAAACATCATGCTCAAAAGACTTATTGATGGCCCGAAGGACTTACAAGTTTT-GGAAA
260 AAAGAGTTAAACATCATGCTCAAAAGACTTACTGATGGCCCGAAGGACTTACAAATTTTGGGAAA
* * * *
2584883 TAGTTTACTGGGTAAGAAACTTTGGAAATAACTTTTTTACTTTTCAAAAATTTTATTTTCTGAAA
325 TAGTTTACTAGGTAAAAAACTTTGGAAATAACTTTCTTACTTTTCAAAAATTTCATTTTCTGAAA
* **
2584948 ATATTAAATGAGAAACTTTGGAAATCGCTTTCTTATTTTTCAAATT
390 ATACTAAATGAGAAACTTTGGAAATCGCTTTCCCA-TTTTCAAATT
2584994 TAATGGTTGG
Statistics
Matches: 384, Mismatches: 47, Indels: 5
0.88 0.11 0.01
Matches are distributed among these distances:
472 95 0.25
473 140 0.36
474 149 0.39
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Consensus pattern (474 bp):
GAAGGAGTTAAGCATCATGCTCAAAAGACTTACTCATGGCCCAAAGGACTTACAAATTTTGGAAA
TAGTTTACTGGGTAAGAAACTTTGAAAATCGCTTTCTTACTTTTCAAAAATTTAATTTTCTGAAA
AAACTAAATGAAAAACTTTGGAAATCACTTTCCCATTTTTCGAAAATCATGTGAAAACATCATAC
CCGAAGGTCTTACAGATGGCCCGAAGGACTTATCATCTTGCTAGAAAGACTTACAGATGACCCAA
AAGAGTTAAACATCATGCTCAAAAGACTTACTGATGGCCCGAAGGACTTACAAATTTTGGGAAAT
AGTTTACTAGGTAAAAAACTTTGGAAATAACTTTCTTACTTTTCAAAAATTTCATTTTCTGAAAA
TACTAAATGAGAAACTTTGGAAATCGCTTTCCCATTTTCAAATTCATGTGAAAACATCCTACCCG
AAGGTCTTACGGATGGCCT
Found at i:2590664 original size:3 final size:3
Alignment explanation
Indices: 2590658--2590711 Score: 56
Period size: 3 Copynumber: 17.7 Consensus size: 3
2590648 AAAAGAAAAA
* * *
2590658 AAT AAT AAT -AT AAAT AAT AAT GAT AAT AAT AAT AAT ATT AAAT ATT
1 AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT
2590704 AAT AAT AA
1 AAT AAT AA
2590712 CCCGGACAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
2 2 0.05
3 36 0.86
4 4 0.10
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:2590674 original size:12 final size:12
Alignment explanation
Indices: 2590657--2590707 Score: 57
Period size: 13 Copynumber: 3.9 Consensus size: 12
2590647 GAAAAGAAAA
2590657 AAATAATAATAT
1 AAATAATAATAT
2590669 AAATAATAATGAT
1 AAATAATAAT-AT
2590682 AATAATAATAATATT
1 -A-AATAATAATA-T
*
2590697 AAATATTAATA
1 AAATAATAATA
2590708 ATAACCCGGA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
12 10 0.29
13 11 0.32
14 3 0.09
15 10 0.29
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (12 bp):
AAATAATAATAT
Found at i:2592337 original size:18 final size:18
Alignment explanation
Indices: 2592314--2592392 Score: 113
Period size: 18 Copynumber: 4.4 Consensus size: 18
2592304 ACCGGTCACA
2592314 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
* *
2592332 ACCCGATCTGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
2592350 ACCCGACCCGACCCGCTG
1 ACCCGACCCGACCCGTTG
**
2592368 ACCCGACCCGATTCGTTG
1 ACCCGACCCGACCCGTTG
2592386 ACCCGAC
1 ACCCGAC
2592393 TCGTTGACCA
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 53 1.00
ACGTcount: A:0.18, C:0.47, G:0.22, T:0.14
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:2592388 original size:13 final size:13
Alignment explanation
Indices: 2592372--2592401 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2592362 CCGCTGACCC
*
2592372 GACCCGATTCGTT
1 GACCCGACTCGTT
2592385 GACCCGACTCGTT
1 GACCCGACTCGTT
2592398 GACC
1 GACC
2592402 ATTGACCGGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.37, G:0.23, T:0.23
Consensus pattern (13 bp):
GACCCGACTCGTT
Found at i:2594921 original size:48 final size:48
Alignment explanation
Indices: 2594861--2594992 Score: 158
Period size: 48 Copynumber: 2.8 Consensus size: 48
2594851 TTGATTTGAT
*
2594861 TTCTGATCTGATACTTGACATGGATTCTGATTTGATA-TCTGACATGGA
1 TTCTGATCTGATACTTGACATGGATTATGATTTGATACT-TGACATGGA
* * * *
2594909 TTCTGATCTGATACTTGACTTGGATTTTGATCTGATACTTGACTTGGA
1 TTCTGATCTGATACTTGACATGGATTATGATTTGATACTTGACATGGA
* * * * *
2594957 TTTTGATATGATACTTTACGTGAATTATGATTTGAT
1 TTCTGATCTGATACTTGACATGGATTATGATTTGAT
2594993 TTTTGATATA
Statistics
Matches: 72, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
48 71 0.99
49 1 0.01
ACGTcount: A:0.24, C:0.12, G:0.20, T:0.44
Consensus pattern (48 bp):
TTCTGATCTGATACTTGACATGGATTATGATTTGATACTTGACATGGA
Found at i:2594992 original size:24 final size:24
Alignment explanation
Indices: 2594858--2594972 Score: 151
Period size: 24 Copynumber: 4.8 Consensus size: 24
2594848 TTTTTGATTT
*
2594858 GATTTCTGATCTGATACTTGACATG
1 GATTT-TGATCTGATACTTGACTTG
* * *
2594883 GATTCTGATTTGATA-TCTGACATG
1 GATTTTGATCTGATACT-TGACTTG
*
2594907 GATTCTGATCTGATACTTGACTTG
1 GATTTTGATCTGATACTTGACTTG
2594931 GATTTTGATCTGATACTTGACTTG
1 GATTTTGATCTGATACTTGACTTG
*
2594955 GATTTTGATATGATACTT
1 GATTTTGATCTGATACTT
2594973 TACGTGAATT
Statistics
Matches: 82, Mismatches: 6, Indels: 5
0.88 0.06 0.05
Matches are distributed among these distances:
23 1 0.01
24 76 0.93
25 5 0.06
ACGTcount: A:0.23, C:0.13, G:0.20, T:0.43
Consensus pattern (24 bp):
GATTTTGATCTGATACTTGACTTG
Found at i:2596646 original size:30 final size:30
Alignment explanation
Indices: 2596574--2596647 Score: 76
Period size: 30 Copynumber: 2.4 Consensus size: 30
2596564 ACTTTTCAGC
** *
2596574 CCTTTTTAATTTTTGTTTTTGCTATTTTAGA
1 CCTTTTT-ATTTTTACTTTAGCTATTTTAGA
* ** *
2596605 CCTGTAAATTTTTACTTTAGCTATTTTAGT
1 CCTTTTTATTTTTACTTTAGCTATTTTAGA
2596635 CCTTTTTATTTTT
1 CCTTTTTATTTTT
2596648 GATTTTATTT
Statistics
Matches: 33, Mismatches: 10, Indels: 1
0.75 0.23 0.02
Matches are distributed among these distances:
30 29 0.88
31 4 0.12
ACGTcount: A:0.18, C:0.12, G:0.08, T:0.62
Consensus pattern (30 bp):
CCTTTTTATTTTTACTTTAGCTATTTTAGA
Found at i:2596721 original size:27 final size:25
Alignment explanation
Indices: 2596684--2596734 Score: 59
Period size: 27 Copynumber: 2.0 Consensus size: 25
2596674 TTTTAATTTA
*
2596684 TTTTTTCTATT-TTCTTTTTTTCTTT
1 TTTTTTCTATTAAT-TTTTTTTCTTT
2596709 TTTTATTCTTATTAATTTTTTTTCTT
1 TTTT-TTC-TATTAATTTTTTTTCTT
2596735 GGTTAACTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
25 4 0.18
26 3 0.14
27 14 0.64
28 1 0.05
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.80
Consensus pattern (25 bp):
TTTTTTCTATTAATTTTTTTTCTTT
Found at i:2596795 original size:5 final size:5
Alignment explanation
Indices: 2596748--2596788 Score: 55
Period size: 5 Copynumber: 7.8 Consensus size: 5
2596738 TAACTAACAT
*
2596748 TTTTA TTATTA TTTTA TTTTA TTTTA TGTTA TTATTA TTTT
1 TTTTA TT-TTA TTTTA TTTTA TTTTA TTTTA TT-TTA TTTT
2596789 TTATTTTCTA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 22 0.69
6 10 0.31
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (5 bp):
TTTTA
Found at i:2596800 original size:17 final size:18
Alignment explanation
Indices: 2596780--2596813 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2596770 TTTATGTTAT
2596780 TATTAT-TTTTTATTTTC
1 TATTATCTTTTTATTTTC
*
2596797 TATTATCTTTTTCTTTT
1 TATTATCTTTTTATTTT
2596814 TTTACTAACT
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:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (18 bp):
TATTATCTTTTTATTTTC
Found at i:2596802 original size:23 final size:22
Alignment explanation
Indices: 2596746--2596802 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 22
2596736 GTTAACTAAC
2596746 ATTTTTATTATTATTTTATTTT
1 ATTTTTATTATTATTTTATTTT
*
2596768 ATTTTATGTTATTATTATT-TTTT
1 ATTTT-TATTATTATT-TTATTTT
2596791 ATTTTCTATTAT
1 ATTTT-TATTAT
2596803 CTTTTTCTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
22 5 0.17
23 23 0.77
24 2 0.07
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.74
Consensus pattern (22 bp):
ATTTTTATTATTATTTTATTTT
Found at i:2598243 original size:30 final size:30
Alignment explanation
Indices: 2598209--2598268 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
2598199 CTGAGATAAT
*
2598209 TACATTGATTTTGTGCCATATTGCAGTTAA
1 TACATTGATTTTGTACCATATTGCAGTTAA
2598239 TACATTGATTTTGTACCATATTGCAGTTAA
1 TACATTGATTTTGTACCATATTGCAGTTAA
2598269 CATATTCTAC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.43
Consensus pattern (30 bp):
TACATTGATTTTGTACCATATTGCAGTTAA
Found at i:2612199 original size:16 final size:17
Alignment explanation
Indices: 2612162--2612201 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
2612152 TTAGACCCTT
2612162 AATTTTTAATTTTGTAA
1 AATTTTTAATTTTGTAA
*
2612179 AATTTTTAGTTTT-TAA
1 AATTTTTAATTTTGTAA
*
2612195 TATTTTT
1 AATTTTT
2612202 TCCATTTATC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 9 0.43
17 12 0.57
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (17 bp):
AATTTTTAATTTTGTAA
Found at i:2612703 original size:2 final size:2
Alignment explanation
Indices: 2612696--2612721 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2612686 TTCATTTAGC
2612696 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
2612722 AAAGAAGGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2617604 original size:22 final size:22
Alignment explanation
Indices: 2617576--2617623 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
2617566 CGTACTGAAT
*
2617576 CGCGATTTTGGAACGACCAGAA
1 CGCGATTTTAGAACGACCAGAA
**
2617598 CGCGATTTTAGAACGACTGGAA
1 CGCGATTTTAGAACGACCAGAA
2617620 CGCG
1 CGCG
2617624 TTCGTACCGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.29, C:0.23, G:0.29, T:0.19
Consensus pattern (22 bp):
CGCGATTTTAGAACGACCAGAA
Found at i:2618637 original size:27 final size:27
Alignment explanation
Indices: 2618599--2618666 Score: 127
Period size: 27 Copynumber: 2.5 Consensus size: 27
2618589 GGATTGTAGA
*
2618599 ATATTTACAGAATCCCTTAATTAAAGG
1 ATATTTACAGAATCCCTTAAGTAAAGG
2618626 ATATTTACAGAATCCCTTAAGTAAAGG
1 ATATTTACAGAATCCCTTAAGTAAAGG
2618653 ATATTTACAGAATC
1 ATATTTACAGAATC
2618667 ATATATTTCT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.41, C:0.15, G:0.12, T:0.32
Consensus pattern (27 bp):
ATATTTACAGAATCCCTTAAGTAAAGG
Found at i:2633042 original size:20 final size:20
Alignment explanation
Indices: 2633017--2633056 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
2633007 TGTTTAAAAA
2633017 ATTACTTTA-GTATCGATACC
1 ATTAC-TTAGGTATCGATACC
2633037 ATTACTTAGGGTATCGATAC
1 ATTACTTA-GGTATCGATAC
2633057 TCCCTTGAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 3 0.17
20 5 0.28
21 10 0.56
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (20 bp):
ATTACTTAGGTATCGATACC
Found at i:2634513 original size:21 final size:21
Alignment explanation
Indices: 2634489--2634528 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2634479 TGTTATGGGC
* *
2634489 AATGGGTATCGATGCCCTATG
1 AATGGGTACCGATACCCTATG
2634510 AATGGGTACCGATACCCTA
1 AATGGGTACCGATACCCTA
2634529 AGACCATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.25
Consensus pattern (21 bp):
AATGGGTACCGATACCCTATG
Found at i:2635896 original size:23 final size:23
Alignment explanation
Indices: 2635869--2635938 Score: 95
Period size: 23 Copynumber: 3.0 Consensus size: 23
2635859 GTCACCACAG
* * *
2635869 CTCATATAAATGCACCGAAGTGC
1 CTCATAGAATTGCACCGTAGTGC
2635892 CTCATAGAATTGCACCGTAGTGC
1 CTCATAGAATTGCACCGTAGTGC
* *
2635915 CGCGTAGAATTGCACCGTAGTGC
1 CTCATAGAATTGCACCGTAGTGC
2635938 C
1 C
2635939 ATATAATAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.27, C:0.27, G:0.23, T:0.23
Consensus pattern (23 bp):
CTCATAGAATTGCACCGTAGTGC
Found at i:2636126 original size:103 final size:103
Alignment explanation
Indices: 2635955--2636275 Score: 588
Period size: 103 Copynumber: 3.1 Consensus size: 103
2635945 TAATGTCCAT
* * *
2635955 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
2636020 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
2636058 AAGGACCACATATCATTCCTTAAGAATCATATATATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
*
2636123 GACTTCACACATGTTCCAAAGAATATATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
2636161 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCACACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
2636226 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
2636264 AAGGACCACATA
1 AAGGACCACATA
2636276 GACCCTCGAC
Statistics
Matches: 210, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 210 1.00
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:2641394 original size:23 final size:23
Alignment explanation
Indices: 2641367--2641436 Score: 95
Period size: 23 Copynumber: 3.0 Consensus size: 23
2641357 GTCACCACAG
* * *
2641367 CTCATATAAATGCACCGAAGTGC
1 CTCATAGAATTGCACCGTAGTGC
2641390 CTCATAGAATTGCACCGTAGTGC
1 CTCATAGAATTGCACCGTAGTGC
* *
2641413 CGCGTAGAATTGCACCGTAGTGC
1 CTCATAGAATTGCACCGTAGTGC
2641436 C
1 C
2641437 ATATAATAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.27, C:0.27, G:0.23, T:0.23
Consensus pattern (23 bp):
CTCATAGAATTGCACCGTAGTGC
Found at i:2641632 original size:103 final size:103
Alignment explanation
Indices: 2641453--2641773 Score: 579
Period size: 103 Copynumber: 3.1 Consensus size: 103
2641443 TAATGTCCAT
* * *
2641453 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
* *
2641518 GACTTCACACATGTTCCAAAGAATACATATATCTCCTG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
2641556 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGCGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
2641621 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
2641659 AAGGACCACATATCATTCATTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
2641724 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
2641762 AAGGACCACATA
1 AAGGACCACATA
2641774 GACCCTCGAC
Statistics
Matches: 210, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 210 1.00
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:2643848 original size:23 final size:23
Alignment explanation
Indices: 2643821--2643888 Score: 73
Period size: 23 Copynumber: 3.0 Consensus size: 23
2643811 CATTTTATAT
*
2643821 GGCACTTCAGTGCATTTCTACGC
1 GGCACTTCGGTGCATTTCTACGC
** * *
2643844 GGCACTTCGGTATAATTCTACGT
1 GGCACTTCGGTGCATTTCTACGC
* *
2643867 TGCACTTCGGTGCATTTATACG
1 GGCACTTCGGTGCATTTCTACG
2643889 AACTGTAGTG
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.19, C:0.25, G:0.22, T:0.34
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:2646010 original size:21 final size:20
Alignment explanation
Indices: 2645972--2646011 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
2645962 TAACATTATA
2645972 AAAATATTTATTTAATTTTT
1 AAAATATTTATTTAATTTTT
2645992 AAAATCATATTATTT-ATTTT
1 AAAAT-AT-TTATTTAATTTT
2646012 ATTTTAAGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.28
21 7 0.39
22 6 0.33
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (20 bp):
AAAATATTTATTTAATTTTT
Found at i:2646048 original size:23 final size:24
Alignment explanation
Indices: 2645993--2646050 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 24
2645983 TTAATTTTTA
* * *
2645993 AAATCATATTATTTATTTTATTTT
1 AAATAATATTAATTATTTTATTTG
* *
2646017 AAGTGATATTAATTA-TTTATTTG
1 AAATAATATTAATTATTTTATTTG
2646040 AAATAATATTA
1 AAATAATATTA
2646051 TTTTTAAATT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
23 16 0.57
24 12 0.43
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (24 bp):
AAATAATATTAATTATTTTATTTG
Found at i:2647466 original size:23 final size:21
Alignment explanation
Indices: 2647415--2647468 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
2647405 ATTCAAGGTA
2647415 TAAAT-TATTTTTTATCATTT
1 TAAATATATTTTTTATCATTT
*
2647435 T-AATATATTTATTTATCTTTT
1 TAAATATATTT-TTTATCATTT
2647456 TAAAATATATTTT
1 T-AAATATATTTT
2647469 AATGACTAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
19 3 0.10
20 6 0.21
21 10 0.34
22 1 0.03
23 9 0.31
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (21 bp):
TAAATATATTTTTTATCATTT
Found at i:2650785 original size:23 final size:23
Alignment explanation
Indices: 2650751--2650855 Score: 113
Period size: 23 Copynumber: 4.6 Consensus size: 23
2650741 ATAAATTGCA
*
2650751 CCGAAGTG-CCACGTAGAAATGTC
1 CCGAAG-GACCACATAGAAATGTC
*
2650774 CCGAAGGACCACATAGACATGTC
1 CCGAAGGACCACATAGAAATGTC
* * *
2650797 TCGAAGGACCACATAGTATTGTC
1 CCGAAGGACCACATAGAAATGTC
* * *
2650820 CCAAAGGACCGCGTAGAAATGTC
1 CCGAAGGACCACATAGAAATGTC
*
2650843 TCGAAGGACCACA
1 CCGAAGGACCACA
2650856 CGTAGAACCC
Statistics
Matches: 65, Mismatches: 16, Indels: 2
0.78 0.19 0.02
Matches are distributed among these distances:
22 1 0.02
23 64 0.98
ACGTcount: A:0.33, C:0.27, G:0.24, T:0.16
Consensus pattern (23 bp):
CCGAAGGACCACATAGAAATGTC
Found at i:2658281 original size:19 final size:20
Alignment explanation
Indices: 2658241--2658278 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2658231 TAAATGACTA
2658241 GGGGTATCAGTACCCATAAG
1 GGGGTATCAGTACCCATAAG
*
2658261 GGGGTATCGGTACCCATA
1 GGGGTATCAGTACCCATA
2658279 GGGCATTCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.21, G:0.32, T:0.21
Consensus pattern (20 bp):
GGGGTATCAGTACCCATAAG
Found at i:2660205 original size:12 final size:12
Alignment explanation
Indices: 2660188--2660213 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2660178 TTGTTGAATA
2660188 GGAGGTGGATTT
1 GGAGGTGGATTT
2660200 GGAGGTGGATTT
1 GGAGGTGGATTT
2660212 GG
1 GG
2660214 TGGTCGGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.00, G:0.54, T:0.31
Consensus pattern (12 bp):
GGAGGTGGATTT
Found at i:2660418 original size:13 final size:13
Alignment explanation
Indices: 2660389--2660434 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
2660379 ATGGGCAAAC
* *
2660389 TTTGAAAACTATG
1 TTTGAAAACAATA
*
2660402 TTTGACAACAATA
1 TTTGAAAACAATA
*
2660415 TTTGAAAACAATG
1 TTTGAAAACAATA
2660428 TTTGAAA
1 TTTGAAA
2660435 TCAAAATGTA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.43, C:0.09, G:0.13, T:0.35
Consensus pattern (13 bp):
TTTGAAAACAATA
Found at i:2666751 original size:19 final size:20
Alignment explanation
Indices: 2666694--2666748 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
2666684 ATGACTAGGA
2666694 GTATCGGTACCCATAAGGGG
1 GTATCGGTACCCATAAGGGG
2666714 GTATCGGTACCCATAAGGGG
1 GTATCGGTACCCATAAGGGG
*
2666734 GTATCGTTACCCATA
1 GTATCGGTACCCATA
2666749 GGGCATTCTA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.25, C:0.22, G:0.29, T:0.24
Consensus pattern (20 bp):
GTATCGGTACCCATAAGGGG
Found at i:2670640 original size:50 final size:50
Alignment explanation
Indices: 2670565--2670664 Score: 173
Period size: 50 Copynumber: 2.0 Consensus size: 50
2670555 GATTGGTGTT
* * *
2670565 GAGGTTGTGGGAAAACCAGTGATTTGGTGTGATAACTCCTCCACTATGTC
1 GAGGTTGTGAGAAAACAAGTGATTTGGTGTGATAACTCCACCACTATGTC
2670615 GAGGTTGTGAGAAAACAAGTGATTTGGTGTGATAACTCCACCACTATGTC
1 GAGGTTGTGAGAAAACAAGTGATTTGGTGTGATAACTCCACCACTATGTC
2670665 CATGCCGGCT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.29
Consensus pattern (50 bp):
GAGGTTGTGAGAAAACAAGTGATTTGGTGTGATAACTCCACCACTATGTC
Found at i:2683240 original size:17 final size:17
Alignment explanation
Indices: 2683218--2683271 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
2683208 AATGTTAATA
2683218 TTTAAATTTATTTTTAT
1 TTTAAATTTATTTTTAT
* * * *
2683235 TTTAAAGTTATTATGAA
1 TTTAAATTTATTTTTAT
* *
2683252 TTTATATTAATTTTTAT
1 TTTAAATTTATTTTTAT
2683269 TTT
1 TTT
2683272 TTATAATGTA
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
TTTAAATTTATTTTTAT
Found at i:2689567 original size:18 final size:19
Alignment explanation
Indices: 2689546--2689581 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
2689536 ATATTGATCG
2689546 ATTTAAATTTAA-ATATTT
1 ATTTAAATTTAATATATTT
*
2689564 ATTTAATTTTAATATATT
1 ATTTAAATTTAATATATT
2689582 ATTATATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
ATTTAAATTTAATATATTT
Found at i:2689577 original size:17 final size:19
Alignment explanation
Indices: 2689546--2689584 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
2689536 ATATTGATCG
2689546 ATTTAAATTTAAATAT-TT
1 ATTTAAATTTAAATATATT
*
2689564 ATTT-AATTTTAATATATT
1 ATTTAAATTTAAATATATT
2689582 ATT
1 ATT
2689585 ATATTTAGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
ATTTAAATTTAAATATATT
Found at i:2697964 original size:35 final size:35
Alignment explanation
Indices: 2697892--2697981 Score: 119
Period size: 36 Copynumber: 2.5 Consensus size: 35
2697882 TGAGGGTGTT
*
2697892 TTTTCTAAAAACAAAGTTTTTTCTCACTTGAAACAA
1 TTTTCTAAAAACAAA-TTTTGTCTCACTTGAAACAA
* *
2697928 TTTTCTAAAAACAAATTTTGTCTCGCTTGAGACAA
1 TTTTCTAAAAACAAATTTTGTCTCACTTGAAACAA
2697963 -TTTCTCACAAAACAAATTT
1 TTTTCT-A-AAAACAAATTT
2697982 CATCTCATTG
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
34 5 0.10
35 18 0.37
36 26 0.53
ACGTcount: A:0.38, C:0.18, G:0.07, T:0.38
Consensus pattern (35 bp):
TTTTCTAAAAACAAATTTTGTCTCACTTGAAACAA
Found at i:2698240 original size:163 final size:164
Alignment explanation
Indices: 2698012--2698308 Score: 454
Period size: 163 Copynumber: 1.8 Consensus size: 164
2698002 TTCTTTAAAA
*
2698012 CAAATTCTGAAATTGTTTAACTGAAAACAAAATTTATAATCTTTGAGTCTGTTTCTCTAGAAACA
1 CAAATTCTGAAATTGTTTAACTGAAAACAAAA--TATAATCTTTGAGTCTGTCTCTCTAGAAACA
2698077 AAGTTTTGTCTCTTGAGACAATCTCTTTTGAAAAAAAAATCTTTGAGTCTGTTTCCTCTGAAACA
64 AAGTTTTGTCTCTTGAGACAATCTCTTTTGAAAAAAAAATCTTTGAGTCTGTTTCCTCTGAAACA
2698142 AAGTCGTCTCACTTGAGACAACTTTCCTTAAAACAC
129 AAGTCGTCTCACTTGAGACAACTTTCCTTAAAACAC
* * * * *
2698178 CAAATTCTGAAATTGTTTCACTTG-AAACAAAA-ATCATTTTTGAGTCTGTCTCTTTGGAAACAA
1 CAAATTCTGAAATTGTTTAAC-TGAAAACAAAATATAATCTTTGAGTCTGTCTCTCTAGAAACAA
* * * * *
2698241 AGTTTTGTCTTTTGAGACAATTTCTTTTGAGAAAAAAATCTTTGAGTTTGTTTCCTTTGAAACAA
65 AGTTTTGTCTCTTGAGACAATCTCTTTTGAAAAAAAAATCTTTGAGTCTGTTTCCTCTGAAACAA
2698306 AGT
130 AGT
2698309 TAGTCTCTTT
Statistics
Matches: 119, Mismatches: 11, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
163 89 0.75
166 28 0.24
167 2 0.02
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.38
Consensus pattern (164 bp):
CAAATTCTGAAATTGTTTAACTGAAAACAAAATATAATCTTTGAGTCTGTCTCTCTAGAAACAAA
GTTTTGTCTCTTGAGACAATCTCTTTTGAAAAAAAAATCTTTGAGTCTGTTTCCTCTGAAACAAA
GTCGTCTCACTTGAGACAACTTTCCTTAAAACAC
Found at i:2698299 original size:66 final size:66
Alignment explanation
Indices: 2698193--2698372 Score: 186
Period size: 66 Copynumber: 2.7 Consensus size: 66
2698183 TCTGAAATTG
* * * *
2698193 TTTCACTTGAAACAAAAATCATTTTTGAGTCTGTCT-CTTTGGAAACAAAGTT-TTGTCTTTTGA
1 TTTCTCTTGAAACAAAAATC---TTTGAGTCTGTTTCCTTT-GAAACAAAGTTAGTCTCTTTTGA
2698256 GACAA
62 GACAA
* * *
2698261 TTTCTTTTGAGAA-AAAAATCTTTGAGTTTGTTTCCTTTGAAACAAAGTTAGTCTCTTTTGAGAT
1 TTTCTCTTGA-AACAAAAATCTTTGAGTCTGTTTCCTTTGAAACAAAGTTAGTCTCTTTTGAGAC
*
2698325 AG
65 AA
*** *
2698327 TTTCTCTTGAAACACCCATCTTTGAGTCTGTTTCCCTTGAAACAAA
1 TTTCTCTTGAAACAAAAATCTTTGAGTCTGTTTCCTTTGAAACAAA
2698373 AGAAACATCT
Statistics
Matches: 94, Mismatches: 14, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
65 24 0.26
66 53 0.56
68 15 0.16
69 2 0.02
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41
Consensus pattern (66 bp):
TTTCTCTTGAAACAAAAATCTTTGAGTCTGTTTCCTTTGAAACAAAGTTAGTCTCTTTTGAGACA
A
Found at i:2698384 original size:66 final size:64
Alignment explanation
Indices: 2698278--2698404 Score: 150
Period size: 66 Copynumber: 1.9 Consensus size: 64
2698268 TGAGAAAAAA
* * **
2698278 ATCTTTGAGTTTGTTTCCTTTGAAACAAAGTTAGTCTCTTTTGAGAT-AGTTTCTCTTGAAACAC
1 ATCTTTGAGTCTGTTTCCCTTGAAACAAAG-TAAACTC-TTTGAGATCAGTTTC-CTTGAAACAC
2698342 CC
63 CC
*
2698344 ATCTTTGAGTCTGTTTCCCTTGAAACAAAAG-AAACATCTTTGAGATCATTTTCCTTGAAAC
1 ATCTTTGAGTCTGTTTCCCTTGAAAC-AAAGTAAAC-TCTTTGAGATCAGTTTCCTTGAAAC
2698405 TAATTTTGTC
Statistics
Matches: 53, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
65 18 0.34
66 31 0.58
67 4 0.08
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (64 bp):
ATCTTTGAGTCTGTTTCCCTTGAAACAAAGTAAACTCTTTGAGATCAGTTTCCTTGAAACACCC
Found at i:2698888 original size:3 final size:3
Alignment explanation
Indices: 2698880--2698911 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
2698870 TATACAAAAA
2698880 TAT TAT TAT TAT TA- TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2698912 GTTTACATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:2698898 original size:14 final size:14
Alignment explanation
Indices: 2698879--2698908 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
2698869 TTATACAAAA
2698879 ATATTATTATTATT
1 ATATTATTATTATT
2698893 ATATTATTATTATT
1 ATATTATTATTATT
2698907 AT
1 AT
2698909 TATGTTTACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
ATATTATTATTATT
Found at i:2700537 original size:64 final size:63
Alignment explanation
Indices: 2700464--2700647 Score: 210
Period size: 64 Copynumber: 2.9 Consensus size: 63
2700454 TAAAATAAAA
**
2700464 AATAA-AAACATCGAATGCAATTCATGCATCGATGCATAAGTAGTGCATCGATGCATCCCATT
1 AATAATAAACATCGAATGCAATTCATGCATCGATGCATAAGTAGTGCATCGATGCATCCCAGC
* * * *
2700526 AATAGTGAAACATCGAATGCAA-TCGGTGCATCGATGCATAAGGAGTTCATCGATGCATCCCAGC
1 AATAAT-AAACATCGAATGCAATTC-ATGCATCGATGCATAAGTAGTGCATCGATGCATCCCAGC
* * * ** * *
2700590 AATAATACTACATCAAATACCTTTTATGCATCGATGCATCAGTAGTGCATCGATGCAT
1 AATAATA-AACATCGAATGCAATTCATGCATCGATGCATAAGTAGTGCATCGATGCAT
2700648 ACCTTCATTA
Statistics
Matches: 100, Mismatches: 17, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
62 4 0.04
63 3 0.03
64 92 0.92
65 1 0.01
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (63 bp):
AATAATAAACATCGAATGCAATTCATGCATCGATGCATAAGTAGTGCATCGATGCATCCCAGC
Found at i:2701051 original size:28 final size:29
Alignment explanation
Indices: 2700994--2701051 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 29
2700984 TGATATGAAG
* *
2700994 TGACATGAGCTACATGATCACAAGAGAAA
1 TGACATGAGCTACATGAACACAAGAAAAA
* *
2701023 TGACATGAG-TACATGAACATATGAAAAA
1 TGACATGAGCTACATGAACACAAGAAAAA
2701051 T
1 T
2701052 AAGAATAATG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
28 16 0.64
29 9 0.36
ACGTcount: A:0.47, C:0.14, G:0.19, T:0.21
Consensus pattern (29 bp):
TGACATGAGCTACATGAACACAAGAAAAA
Found at i:2702827 original size:30 final size:30
Alignment explanation
Indices: 2702758--2702831 Score: 91
Period size: 30 Copynumber: 2.5 Consensus size: 30
2702748 GTTTTTATTG
*
2702758 TTTAGCCCTTTAAGATTACATGTTTGCTAT
1 TTTAGTCCTTTAAGATTACATGTTTGCTAT
2702788 TTTAGTCCTTTAA-ATTAC-TGTTTGTACTAT
1 TTTAGTCCTTTAAGATTACATGTTTG--CTAT
2702818 TTT-GATCCTTTAAG
1 TTTAG-TCCTTTAAG
2702832 TTGATGTTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
28 6 0.15
29 6 0.15
30 27 0.69
ACGTcount: A:0.23, C:0.15, G:0.12, T:0.50
Consensus pattern (30 bp):
TTTAGTCCTTTAAGATTACATGTTTGCTAT
Found at i:2702840 original size:30 final size:27
Alignment explanation
Indices: 2702758--2702840 Score: 69
Period size: 30 Copynumber: 2.8 Consensus size: 27
2702748 GTTTTTATTG
*
2702758 TTTAGCCCTTTAAGATTACATGTTTGCTAT
1 TTTAGTCCTTTAA-ATT--ATGTTTGCTAT
2702788 TTTAGTCCTTTAAATTACTGTTTGTACTAT
1 TTTAGTCCTTTAAATTA-TGTTTG--CTAT
*
2702818 TTT-GATCCTTTAAGTTGATGTTT
1 TTTAG-TCCTTTAAATT-ATGTTT
2702841 TCCTCATTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
27 1 0.02
28 6 0.13
29 4 0.09
30 34 0.74
31 1 0.02
ACGTcount: A:0.22, C:0.13, G:0.13, T:0.52
Consensus pattern (27 bp):
TTTAGTCCTTTAAATTATGTTTGCTAT
Found at i:2703205 original size:31 final size:32
Alignment explanation
Indices: 2703167--2703231 Score: 82
Period size: 31 Copynumber: 2.1 Consensus size: 32
2703157 TCCACGGTTA
2703167 TTTATTTTG-ATTATTTTCACTGTT-TTTTA-CT
1 TTTATTTTGTATTATTTT-A-TGTTATTTTATCT
*
2703198 TTTATTTTGTTTTATTTTATGTTATTTTATCT
1 TTTATTTTGTATTATTTTATGTTATTTTATCT
2703230 TT
1 TT
2703232 ACAAAAATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
30 4 0.13
31 15 0.50
32 11 0.37
ACGTcount: A:0.15, C:0.06, G:0.06, T:0.72
Consensus pattern (32 bp):
TTTATTTTGTATTATTTTATGTTATTTTATCT
Found at i:2703217 original size:15 final size:15
Alignment explanation
Indices: 2703177--2703232 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
2703167 TTTATTTTGA
2703177 TTATTTTCACTGTT-TT
1 TTATTTT-A-TGTTATT
* *
2703193 TTACTTTTATTTTGTT
1 TTA-TTTTATGTTATT
2703209 TTATTTTATGTTATT
1 TTATTTTATGTTATT
2703224 TTATCTTTA
1 TTAT-TTTA
2703233 CAAAAATTAC
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
15 17 0.50
16 13 0.38
17 4 0.12
ACGTcount: A:0.16, C:0.07, G:0.05, T:0.71
Consensus pattern (15 bp):
TTATTTTATGTTATT
Found at i:2706794 original size:24 final size:24
Alignment explanation
Indices: 2706748--2706804 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
2706738 CACCACAGCT
* *
2706748 CGTATAAATTGCACCGAAGTGCCG
1 CGTAGAAATTGCACCGAAGTGCCA
2706772 CGTAGAAATTGCACCGTAA-TGCCA
1 CGTAGAAATTGCACCG-AAGTGCCA
*
2706796 CATAGAAAT
1 CGTAGAAAT
2706805 ATCCCGAAGG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 27 0.93
25 2 0.07
ACGTcount: A:0.35, C:0.23, G:0.21, T:0.21
Consensus pattern (24 bp):
CGTAGAAATTGCACCGAAGTGCCA
Found at i:2706851 original size:46 final size:46
Alignment explanation
Indices: 2706799--2706894 Score: 120
Period size: 46 Copynumber: 2.1 Consensus size: 46
2706789 AATGCCACAT
*
2706799 AGAAATATCCCGAAGGACAACATAGTATTGTCCCAAAGAACCGCGC
1 AGAAATATCCCGAAGGACAACATAGAATTGTCCCAAAGAACCGCGC
* * * * * * *
2706845 AGAAATATCCCTAAGGACCACGTAGAATTGTCTCGAAGGACCGCGT
1 AGAAATATCCCGAAGGACAACATAGAATTGTCCCAAAGAACCGCGC
2706891 AGAA
1 AGAA
2706895 CCCTCGACTC
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.38, C:0.24, G:0.22, T:0.17
Consensus pattern (46 bp):
AGAAATATCCCGAAGGACAACATAGAATTGTCCCAAAGAACCGCGC
Found at i:2706871 original size:23 final size:23
Alignment explanation
Indices: 2706793--2706894 Score: 69
Period size: 23 Copynumber: 4.4 Consensus size: 23
2706783 CACCGTAATG
*
2706793 CCACATAGAAATATCCCGAAGGA
1 CCACGTAGAAATATCCCGAAGGA
* * * * * * *
2706816 CAACATAGTATTGTCCCAAAGAA
1 CCACGTAGAAATATCCCGAAGGA
* * *
2706839 CCGCGCAGAAATATCCCTAAGGA
1 CCACGTAGAAATATCCCGAAGGA
* * *
2706862 CCACGTAGAATTGTCTCGAAGGA
1 CCACGTAGAAATATCCCGAAGGA
*
2706885 CCGCGTAGAA
1 CCACGTAGAA
2706895 CCCTCGACTC
Statistics
Matches: 57, Mismatches: 22, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
23 57 1.00
ACGTcount: A:0.37, C:0.25, G:0.21, T:0.17
Consensus pattern (23 bp):
CCACGTAGAAATATCCCGAAGGA
Found at i:2707015 original size:31 final size:31
Alignment explanation
Indices: 2706980--2707038 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
2706970 TCACATATTC
* *
2706980 ATATAATCACGTAG-TTCAATATCACATAGAT
1 ATATAAACACATAGATTC-ATATCACATAGAT
*
2707011 ATATAAACACATAGATTCTTATCACATA
1 ATATAAACACATAGATTCATATCACATA
2707039 ACTTATATCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 21 0.88
32 3 0.12
ACGTcount: A:0.44, C:0.17, G:0.07, T:0.32
Consensus pattern (31 bp):
ATATAAACACATAGATTCATATCACATAGAT
Found at i:2707654 original size:19 final size:20
Alignment explanation
Indices: 2707632--2707671 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2707622 GGAATTCATC
2707632 CTTAAA-AATGGTACCGATA
1 CTTAAACAATGGTACCGATA
* *
2707651 CTTAAACATTGGTATCGATA
1 CTTAAACAATGGTACCGATA
2707671 C
1 C
2707672 CCCTAGTATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.30
Consensus pattern (20 bp):
CTTAAACAATGGTACCGATA
Found at i:2707737 original size:36 final size:36
Alignment explanation
Indices: 2707693--2707766 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
2707683 ATGCTACTAC
2707693 TTTGATATCGATACTCTTAAAAGGATTCATCAACTT
1 TTTGATATCGATACTCTTAAAAGGATTCATCAACTT
2707729 TTTGATATCGATACTCTTAAAAGGATTCATCAACTT
1 TTTGATATCGATACTCTTAAAAGGATTCATCAACTT
2707765 TT
1 TT
2707767 AATTTATGGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.41
Consensus pattern (36 bp):
TTTGATATCGATACTCTTAAAAGGATTCATCAACTT
Found at i:2731337 original size:30 final size:31
Alignment explanation
Indices: 2731296--2731378 Score: 89
Period size: 31 Copynumber: 2.7 Consensus size: 31
2731286 ACTCTTGAAT
* *
2731296 TTTAGATAAAATATTAATTT-GGC-CTTAAAA
1 TTTATATAAAATATTAATTTAAGCAC-TAAAA
* * *
2731326 TTTATATAAAATACTAATTTAATCACTAAAT
1 TTTATATAAAATATTAATTTAAGCACTAAAA
*
2731357 TTTATATAAAATATCAATTTAA
1 TTTATATAAAATATTAATTTAA
2731379 TCCATGAATC
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
30 18 0.41
31 25 0.57
32 1 0.02
ACGTcount: A:0.47, C:0.07, G:0.04, T:0.42
Consensus pattern (31 bp):
TTTATATAAAATATTAATTTAAGCACTAAAA
Found at i:2731364 original size:31 final size:31
Alignment explanation
Indices: 2731321--2731380 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 31
2731311 AATTTGGCCT
2731321 TAAAATTTATATAAAATA-CTAATTTAATCAC
1 TAAAATTTATATAAAATATC-AATTTAATCAC
*
2731352 TAAATTTTATATAAAATATCAATTTAATC
1 TAAAATTTATATAAAATATCAATTTAATC
2731381 CATGAATCCA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 26 0.96
32 1 0.04
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (31 bp):
TAAAATTTATATAAAATATCAATTTAATCAC
Found at i:2731680 original size:31 final size:29
Alignment explanation
Indices: 2731645--2731743 Score: 92
Period size: 31 Copynumber: 3.2 Consensus size: 29
2731635 CTGAATTCAT
*
2731645 GGGTTAAATTGATATTTGATATAAAGTTTA
1 GGGTTAAATT-ATATTTGATATAAAATTTA
*
2731675 GGGGTTAAATTAGTATTTTATATAAAATTTA
1 -GGGTTAAATTA-TATTTGATATAAAATTTA
* * *
2731706 AGGTTAAATTAATATTATG-TGTAAAATTCA
1 GGGTTAAATT-ATATT-TGATATAAAATTTA
2731736 GGAGTTAA
1 GG-GTTAA
2731744 GTTAAAATTT
Statistics
Matches: 57, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
30 24 0.42
31 33 0.58
ACGTcount: A:0.39, C:0.01, G:0.18, T:0.41
Consensus pattern (29 bp):
GGGTTAAATTATATTTGATATAAAATTTA
Found at i:2731713 original size:30 final size:31
Alignment explanation
Indices: 2731646--2731721 Score: 93
Period size: 31 Copynumber: 2.5 Consensus size: 31
2731636 TGAATTCATG
* *
2731646 GGTTAAATT-GATATTTGATATAAAGTTTAGG
1 GGTTAAATTAG-TATTTGATATAAAATTTAGA
*
2731677 GGTTAAATTAGTATTTTATATAAAATTTA-A
1 GGTTAAATTAGTATTTGATATAAAATTTAGA
*
2731707 GGTTAAATTAATATT
1 GGTTAAATTAGTATT
2731722 ATGTGTAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
30 14 0.35
31 25 0.62
32 1 0.03
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.45
Consensus pattern (31 bp):
GGTTAAATTAGTATTTGATATAAAATTTAGA
Found at i:2731731 original size:30 final size:30
Alignment explanation
Indices: 2731646--2731733 Score: 88
Period size: 30 Copynumber: 2.9 Consensus size: 30
2731636 TGAATTCATG
* * *
2731646 GGTTAAATTGATATTTGATATAAAGTTTAGG
1 GGTTAAATTAATATTTG-TATAAAATTTAGA
* *
2731677 GGTTAAATTAGTATTTTATATAAAATTTA-A
1 GGTTAAATTAATA-TTTGTATAAAATTTAGA
*
2731707 GGTTAAATTAATATTATGTGTAAAATT
1 GGTTAAATTAATATT-TGTATAAAATT
2731734 CAGGAGTTAA
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
29 2 0.04
30 21 0.45
31 21 0.45
32 3 0.06
ACGTcount: A:0.40, C:0.00, G:0.16, T:0.44
Consensus pattern (30 bp):
GGTTAAATTAATATTTGTATAAAATTTAGA
Found at i:2734514 original size:5 final size:5
Alignment explanation
Indices: 2734504--2734532 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
2734494 ACCACGACCA
2734504 CGAGC CGAGC CGAGC CGAGC CGAGC CGAG
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAG
2734533 ACGGAGGGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.21, C:0.38, G:0.41, T:0.00
Consensus pattern (5 bp):
CGAGC
Found at i:2743027 original size:113 final size:113
Alignment explanation
Indices: 2742471--2743018 Score: 936
Period size: 113 Copynumber: 4.9 Consensus size: 113
2742461 ATAGAGTCAT
* *
2742471 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * **
2742535 ATTATGAACTTTCTCTGGCAATGCTTATCCATCAAGTGATGGATTTGA
66 ATTATGAACTTTCTCTGGCAATGCTAATCCATCAAGTGATGAATTAAA
* * *
2742583 GCAAAAGGTTGAACAAGTTCTTCTTATTATAAACTTCCTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
*
2742648 ATTATGAACTTTCTCTGGCAATGCTAATCCATCAGGTGATGAATTAAA
66 ATTATGAACTTTCTCTGGCAATGCTAATCCATCAAGTGATGAATTAAA
* *
2742696 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTTTTCTTCATTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
2742761 ATTATGAACTTTCTCTGGCAATGCTAATCCATCAAGTGATGAATTAAA
66 ATTATGAACTTTCTCTGGCAATGCTAATCCATCAAGTGATGAATTAAA
* *
2742809 GCAAAAGGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTATTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
2742874 ATTATGAACTTTCTCTGGCAATGCTAATCCATCAAGTGATGAATTAAA
66 ATTATGAACTTTCTCTGGCAATGCTAATCCATCAAGTGATGAATTAAA
* *
2742922 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAATTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
*
2742987 ATTATGAACTTTCTCTGGCAATGGTAATCCAT
66 ATTATGAACTTTCTCTGGCAATGCTAATCCAT
2743019 TGGGTGATGG
Statistics
Matches: 410, Mismatches: 25, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
112 40 0.10
113 370 0.90
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (113 bp):
GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACTTTCTCTGGCAATGCTAATCCATCAAGTGATGAATTAAA
Found at i:2744570 original size:11 final size:10
Alignment explanation
Indices: 2744556--2744624 Score: 61
Period size: 10 Copynumber: 6.7 Consensus size: 10
2744546 TTTTTCAACA
*
2744556 TTTTTTCTCTC
1 TTTTTTC-CTT
*
2744567 TTTTTT-CAT
1 TTTTTTCCTT
2744576 TTTTTT-CTT
1 TTTTTTCCTT
*
2744585 CATTTTTTCTTTT
1 --TTTTTTC-CTT
2744598 TTTTTTCCTT
1 TTTTTTCCTT
2744608 TTTTTTCCTT
1 TTTTTTCCTT
2744618 TTTTTTC
1 TTTTTTC
2744625 AATCTTCTTC
Statistics
Matches: 49, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
9 9 0.18
10 19 0.39
11 19 0.39
13 2 0.04
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (10 bp):
TTTTTTCCTT
Found at i:2744576 original size:19 final size:20
Alignment explanation
Indices: 2744556--2744611 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 20
2744546 TTTTTCAACA
2744556 TTTTTTCTCTC-TTTTTTCAT
1 TTTTTTCT-TCATTTTTTCAT
2744576 TTTTTTCTTCATTTTTTC-T
1 TTTTTTCTTCATTTTTTCAT
* *
2744595 TTTTTTTTTCCTTTTTT
1 TTTTTTCTTCATTTTTT
2744612 TTCCTTTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 18 0.55
20 15 0.45
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.80
Consensus pattern (20 bp):
TTTTTTCTTCATTTTTTCAT
Found at i:2744579 original size:20 final size:20
Alignment explanation
Indices: 2744556--2744622 Score: 73
Period size: 20 Copynumber: 3.3 Consensus size: 20
2744546 TTTTTCAACA
2744556 TTTTTTCTCTCTTTTTTCAT
1 TTTTTTCTCTCTTTTTTCAT
*
2744576 TTTTTTCT-TCATTTTTTCTT
1 TTTTTTCTCTC-TTTTTTCAT
* * *
2744596 TTTTTTTTCCTTTTTTTTCCT
1 TTTTTTCT-CTCTTTTTTCAT
2744617 TTTTTT
1 TTTTTT
2744623 TCAATCTTCT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
19 2 0.05
20 23 0.57
21 14 0.35
22 1 0.03
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.81
Consensus pattern (20 bp):
TTTTTTCTCTCTTTTTTCAT
Found at i:2744589 original size:31 final size:31
Alignment explanation
Indices: 2744537--2744612 Score: 93
Period size: 31 Copynumber: 2.5 Consensus size: 31
2744527 CCTGACCCTC
2744537 CTTTTTT-A-TTTTTTCAACATTTTTTCTCT
1 CTTTTTTCATTTTTTTCAACATTTTTTCTCT
** *
2744566 CTTTTTTCATTTTTTTCTTCATTTTTTCTTT
1 CTTTTTTCATTTTTTTCAACATTTTTTCTCT
* *
2744597 TTTTTTTCCTTTTTTT
1 CTTTTTTCATTTTTTT
2744613 TCCTTTTTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
29 7 0.17
30 1 0.03
31 32 0.80
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (31 bp):
CTTTTTTCATTTTTTTCAACATTTTTTCTCT
Found at i:2744600 original size:10 final size:10
Alignment explanation
Indices: 2744556--2744624 Score: 59
Period size: 11 Copynumber: 6.7 Consensus size: 10
2744546 TTTTTCAACA
*
2744556 TTTTTTCTCTC
1 TTTTTTCT-TT
*
2744567 TTTTTTC-AT
1 TTTTTTCTTT
*
2744576 TTTTTTCTTCA
1 TTTTTTCTT-T
2744587 TTTTTTCTTTT
1 TTTTTTC-TTT
*
2744598 TTTTTTCCTT
1 TTTTTTCTTT
*
2744608 TTTTTTCCTT
1 TTTTTTCTTT
2744618 TTTTTTC
1 TTTTTTC
2744625 AATCTTCTTC
Statistics
Matches: 49, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
9 7 0.14
10 19 0.39
11 21 0.43
12 2 0.04
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (10 bp):
TTTTTTCTTT
Found at i:2751964 original size:15 final size:15
Alignment explanation
Indices: 2751940--2751977 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
2751930 AAATAATGCA
*
2751940 ATGCATAATGAATGT
1 ATGCAAAATGAATGT
*
2751955 ATGCAAAATGCATGT
1 ATGCAAAATGAATGT
2751970 ATGCAAAA
1 ATGCAAAA
2751978 GGTATTGATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.45, C:0.11, G:0.18, T:0.26
Consensus pattern (15 bp):
ATGCAAAATGAATGT
Found at i:2756134 original size:38 final size:38
Alignment explanation
Indices: 2756060--2756134 Score: 89
Period size: 39 Copynumber: 2.0 Consensus size: 38
2756050 ATTTCTCATT
* *
2756060 TCTATTTTTAAAATTATTTCACCCTACCATTCTAAATC
1 TCTATTTTTAAAATTATTTCACACTAACATTCTAAATC
* * *
2756098 TCTATTTTTTCAAATTATTTTACATTAACATT-TAAAT
1 TCTA-TTTTTAAAATTATTTCACACTAACATTCTAAAT
2756135 TAATTTTTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
38 9 0.29
39 22 0.71
ACGTcount: A:0.33, C:0.17, G:0.00, T:0.49
Consensus pattern (38 bp):
TCTATTTTTAAAATTATTTCACACTAACATTCTAAATC
Found at i:2756192 original size:13 final size:14
Alignment explanation
Indices: 2756172--2756206 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
2756162 AATTTAGTTG
2756172 TAATTTTAATATTT
1 TAATTTTAATATTT
*
2756186 T-ATTTTATTATTT
1 TAATTTTAATATTT
2756199 TAATTTTA
1 TAATTTTA
2756207 GATTATATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (14 bp):
TAATTTTAATATTT
Found at i:2756219 original size:21 final size:21
Alignment explanation
Indices: 2756172--2756219 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
2756162 AATTTAGTTG
* *
2756172 TAATTTTAATATTTTATTTTA
1 TAATTTTAATATTTGATTATA
*
2756193 TTATTTTAAT-TTTAGATTATA
1 TAATTTTAATATTT-GATTATA
2756214 TAATTT
1 TAATTT
2756220 GGATTCTAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 3 0.14
21 19 0.86
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (21 bp):
TAATTTTAATATTTGATTATA
Found at i:2756465 original size:60 final size:61
Alignment explanation
Indices: 2756401--2756547 Score: 165
Period size: 59 Copynumber: 2.5 Consensus size: 61
2756391 ATGAATTTTG
* ** *
2756401 GGATGAAATTGGAATATTTAAAAGTTTAGA-GACCAATTTAGAAAGAGTGACATAGTTTAA
1 GGATGAAATTGGAATATTCAAAAGTTTAGAGGACCAATTTAGAAAGAAAGACATACTTTAA
* * ** * *
2756461 GGATG-AATTAGAATGTTCAAAAGTTT-GAGGATTAATTTAGAACGAAAGTCATACTTTAA
1 GGATGAAATTGGAATATTCAAAAGTTTAGAGGACCAATTTAGAAAGAAAGACATACTTTAA
* *
2756520 GTATGAAATTGAAATATTCAAAAGTTTA
1 GGATGAAATTGGAATATTCAAAAGTTTA
2756548 AAGAATAATT
Statistics
Matches: 70, Mismatches: 14, Indels: 5
0.79 0.16 0.06
Matches are distributed among these distances:
58 2 0.03
59 45 0.64
60 23 0.33
ACGTcount: A:0.43, C:0.05, G:0.20, T:0.32
Consensus pattern (61 bp):
GGATGAAATTGGAATATTCAAAAGTTTAGAGGACCAATTTAGAAAGAAAGACATACTTTAA
Found at i:2757660 original size:344 final size:341
Alignment explanation
Indices: 2757015--2758054 Score: 1789
Period size: 344 Copynumber: 3.0 Consensus size: 341
2757005 AACTATAATG
*
2757015 GAAATTTATTTTTGTTGTATCAAACTTAATACTTACTTGCACAAACCATGCGACCTCTGTGGTAA
1 GAAATTTATTTTTGTTGTATCAAACTTAATACTTACTTGCACAAACCATGTGACCTCTGTGGTAA
2757080 AGGAATTGTTGTTATTCCCGAGGAGTCGGGTTCGAGCACCATAAATGCCAGGGGTGTGAGCGATC
66 AGGAATTGTTGTTATT-CCGAGGAGTCGGGTTCGAGCACCATAAATGCCAGGGGTGTGAGCGATC
* * *
2757145 AATGTCGAAAAGATTGAGAGTTTATCTTCGAATAGATATCGACTTATATTTACCCCAGATTAATA
130 AATGTCGAAAAGATTGAGAGTTTATCTTCGAATAGATATTGGCTTGTATTTACCCCAGATTAATA
*
2757210 AAAAAAACTTAATACTTACTTATATCATTACTAAATTAAAGAATAATTTTCACTTAATTTCAAAA
195 AAAAAAACTTAATACTTACTTATATCATTACTAAATTAAAGAATAATTTTCACTTTATTTCAAAA
2757275 TAAAAAATAATTAAATAATGATTTATATTATATTTATAAAATTTATATTAAATTATTCTAAAAAG
260 TAAAAAATAATTAAATAATGATTTATATTATATTTATAAAATTTATATTAAATTATTCTAAAAAG
2757340 TATATTTATAATATTAT
325 TATATTTATAATATTAT
* *
2757357 GAAATTTTATTTTTGTTGTATCAAACTTAATACTTACTTGCACAAACCAAGTGACCTATGTGGTA
1 GAAA-TTTATTTTTGTTGTATCAAACTTAATACTTACTTGCACAAACCATGTGACCTCTGTGGTA
* * * * *
2757422 AAGGAATTGTTGTTATTCCTGAAGAGTCGAGTTCGAGGACAATAAATACCAGGGGTGTGAGCGAT
65 AAGGAATTGTTGTTATTCC-GAGGAGTCGGGTTCGAGCACCATAAATGCCAGGGGTGTGAGCGAT
* *
2757487 CAATGTCGAAAAGATTGAGATTTTATCTTCGAATAGATATTGGCTTGTATTTACCCCATATTAAT
129 CAATGTCGAAAAGATTGAGAGTTTATCTTCGAATAGATATTGGCTTGTATTTACCCCAGATTAAT
2757552 AAAAAAAAACTTAATACTTACTTATATCATTACTAAATTAAAGAATAATTTTCACTTTATTTCAA
194 -AAAAAAAACTTAATACTTACTTATATCATTACTAAATTAAAGAATAATTTTCACTTTATTTCAA
2757617 AATAAAAAATAATTAAATAATGATTTATATTATATTTATAAAATTTATATTAAATTATTCTAAAA
258 AATAAAAAATAATTAAATAATGATTTATATTATATTTATAAAATTTATATTAAATTATTCTAAAA
2757682 AGTATATTTATAATATTAT
323 AGTATATTTATAATATTAT
2757701 GAAATTTTATTTTTGTTGTATCAAACTTAATACTTACTTGCACAAACCATGTGACCTCTGTGGTA
1 GAAA-TTTATTTTTGTTGTATCAAACTTAATACTTACTTGCACAAACCATGTGACCTCTGTGGTA
* *
2757766 AAGGAATTGTTGTTATTTCCGAGGAGTCGGGTTCGAGCACCATAAATGCCAGGGGTGTAAGAGAT
65 AAGGAATTGTTGTTA-TTCCGAGGAGTCGGGTTCGAGCACCATAAATGCCAGGGGTGTGAGCGAT
* *
2757831 CAATGTCGAAAAGATTGAGAGTTTATCTTTGAATAGATATTGGCTTGTATTTATCCCAGATTAAT
129 CAATGTCGAAAAGATTGAGAGTTTATCTTCGAATAGATATTGGCTTGTATTTACCCCAGATTAAT
*
2757896 AAAAAAAACTTAATAGTTACTTATATCATTACTAAATTAAAGAATAA-TTTCACTTTATTTCAAA
194 AAAAAAAACTTAATACTTACTTATATCATTACTAAATTAAAGAATAATTTTCACTTTATTTCAAA
* *
2757960 A-AAAATAATAATTAAATAATGATTTATATTATTTTTATAAAATTTAAATTAAATTATTCTAAAA
259 ATAAAA-AATAATTAAATAATGATTTATATTATATTTATAAAATTTATATTAAATTATTCTAAAA
*
2758024 AGGCATATTTATAATATTAT
323 A-GTATATTTATAATATTAT
2758044 G-AATTTATTTT
1 GAAATTTATTTT
2758055 AAAATATTTA
Statistics
Matches: 661, Mismatches: 31, Indels: 13
0.94 0.04 0.02
Matches are distributed among these distances:
341 12 0.02
342 83 0.13
343 238 0.36
344 324 0.49
345 4 0.01
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.38
Consensus pattern (341 bp):
GAAATTTATTTTTGTTGTATCAAACTTAATACTTACTTGCACAAACCATGTGACCTCTGTGGTAA
AGGAATTGTTGTTATTCCGAGGAGTCGGGTTCGAGCACCATAAATGCCAGGGGTGTGAGCGATCA
ATGTCGAAAAGATTGAGAGTTTATCTTCGAATAGATATTGGCTTGTATTTACCCCAGATTAATAA
AAAAAACTTAATACTTACTTATATCATTACTAAATTAAAGAATAATTTTCACTTTATTTCAAAAT
AAAAAATAATTAAATAATGATTTATATTATATTTATAAAATTTATATTAAATTATTCTAAAAAGT
ATATTTATAATATTAT
Done.