Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007926.1 Hibiscus syriacus cultivar Beakdansim tig00110332_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: 10075380
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 28 of 42
Found at i:5804438 original size:183 final size:183
Alignment explanation
Indices: 5804085--5804417 Score: 436
Period size: 183 Copynumber: 1.8 Consensus size: 183
5804075 GACTTTTCGC
* *
5804085 AACGAATTTGGAAAATCGCAACGATAACTGTAGACTATCGCAACGAATTTGGAAAATCGCAATGA
1 AACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCGCAACGAATTTGGAAAATCGCAACGA
* * ** * * *
5804150 CAACTGTAGATTATCGCAACGCGATTTTCAACTATCGCAACCCGAAATGAAAAATCGCAACGCGA
66 CAACTGTAGACTATCACAACGCGAACTGCAACAATCGCAACCCGAAATCAAAAATCGCAACGCGA
** * * *
5804215 TTTTCAACTATCCCAACGCGAACTGGAAAATCGCAACGCGAAATGGAAAATCG
131 AATGCAACAATCCCAACGCGAACTGCAAAATCGCAACGCGAAATGGAAAATCG
5804268 AACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCGCAACGAATTTGGAAAATCGCAACGA
1 AACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCGCAACGAATTTGGAAAATCGCAACGA
* * * ** **
5804333 CAACTGTAGACTATCACAACGTGAACTGGAA-AATCGCAACGCGATTTTCAACTATCGCAACGCG
66 CAACTGTAGACTATCACAACGCGAACTGCAACAATCGCAACCCGA-AATCAAAAATCGCAACGCG
* *
5804397 AAATGGAA-AATCGCAACGCGA
130 AAATGCAACAATCCCAACGCGA
5804418 TTTTCAACTA
Statistics
Matches: 127, Mismatches: 22, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
182 22 0.17
183 105 0.83
ACGTcount: A:0.39, C:0.23, G:0.19, T:0.19
Consensus pattern (183 bp):
AACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCGCAACGAATTTGGAAAATCGCAACGA
CAACTGTAGACTATCACAACGCGAACTGCAACAATCGCAACCCGAAATCAAAAATCGCAACGCGA
AATGCAACAATCCCAACGCGAACTGCAAAATCGCAACGCGAAATGGAAAATCG
Found at i:5812185 original size:30 final size:30
Alignment explanation
Indices: 5812149--5812250 Score: 159
Period size: 30 Copynumber: 3.4 Consensus size: 30
5812139 TATAATGTTA
5812149 TTAATAATGCGCATGATGGGGCCATATCTT
1 TTAATAATGCGCATGATGGGGCCATATCTT
** *
5812179 TTAATAATGCGCATGATGGGGTTATATCCT
1 TTAATAATGCGCATGATGGGGCCATATCTT
* *
5812209 TTAATAATGCGCATGATGGAGCCATACCTT
1 TTAATAATGCGCATGATGGGGCCATATCTT
5812239 TTAATAATGCGC
1 TTAATAATGCGC
5812251 CTCTGGACCA
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 64 1.00
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (30 bp):
TTAATAATGCGCATGATGGGGCCATATCTT
Found at i:5815273 original size:12 final size:12
Alignment explanation
Indices: 5815240--5815267 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
5815230 GAATTAAGTT
5815240 TTTTAATAAATA
1 TTTTAATAAATA
5815252 TTTTAATAAATA
1 TTTTAATAAATA
5815264 TTTT
1 TTTT
5815268 TCTAAAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (12 bp):
TTTTAATAAATA
Found at i:5821046 original size:31 final size:30
Alignment explanation
Indices: 5820998--5821066 Score: 95
Period size: 31 Copynumber: 2.3 Consensus size: 30
5820988 TAAACTACGA
5820998 TTTAGTA-TAAATGATCAATTTTGATTCAT
1 TTTAGTACTAAATGATCAATTTTGATTCAT
* * *
5821027 TTTAGTACCTAAATTATCAATTTTGGTTCGT
1 TTTAGTA-CTAAATGATCAATTTTGATTCAT
5821058 TTTAGTACT
1 TTTAGTACT
5821067 TAAACTTCTA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
29 7 0.20
30 2 0.06
31 26 0.74
ACGTcount: A:0.29, C:0.10, G:0.12, T:0.49
Consensus pattern (30 bp):
TTTAGTACTAAATGATCAATTTTGATTCAT
Found at i:5828080 original size:25 final size:25
Alignment explanation
Indices: 5828052--5828128 Score: 61
Period size: 25 Copynumber: 3.2 Consensus size: 25
5828042 CTTCATTATC
5828052 ATTTTATAAATGTAAACGTATGAAG
1 ATTTTATAAATGTAAACGTATGAAG
* * * * * **
5828077 A--TT-TAATTGTTAGCTTCATTATC
1 ATTTTATAAATGTAAACGT-ATGAAG
5828100 ATTTTATAAATGTAAACGTATGAAG
1 ATTTTATAAATGTAAACGTATGAAG
5828125 ATTT
1 ATTT
5828129 AATATTTATT
Statistics
Matches: 34, Mismatches: 14, Indels: 8
0.61 0.25 0.14
Matches are distributed among these distances:
22 9 0.26
23 6 0.18
25 10 0.29
26 9 0.26
ACGTcount: A:0.38, C:0.06, G:0.13, T:0.43
Consensus pattern (25 bp):
ATTTTATAAATGTAAACGTATGAAG
Found at i:5828087 original size:48 final size:48
Alignment explanation
Indices: 5828025--5828131 Score: 205
Period size: 48 Copynumber: 2.2 Consensus size: 48
5828015 AAACAAGTAC
5828025 GAAGATTTAATTGTTAACTTCATTATCATTTTATAAATGTAAACGTAT
1 GAAGATTTAATTGTTAACTTCATTATCATTTTATAAATGTAAACGTAT
*
5828073 GAAGATTTAATTGTTAGCTTCATTATCATTTTATAAATGTAAACGTAT
1 GAAGATTTAATTGTTAACTTCATTATCATTTTATAAATGTAAACGTAT
5828121 GAAGATTTAAT
1 GAAGATTTAAT
5828132 ATTTATTTAC
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 58 1.00
ACGTcount: A:0.37, C:0.07, G:0.12, T:0.43
Consensus pattern (48 bp):
GAAGATTTAATTGTTAACTTCATTATCATTTTATAAATGTAAACGTAT
Found at i:5829159 original size:17 final size:18
Alignment explanation
Indices: 5829122--5829162 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
5829112 ATATTATGTA
*
5829122 TTTAATTTATTTAAGTAT
1 TTTACTTTATTTAAGTAT
5829140 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGTAT
5829157 TTTACT
1 TTTACT
5829163 AATATAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTACTTTATTTAAGTAT
Found at i:5835442 original size:20 final size:20
Alignment explanation
Indices: 5835419--5835458 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
5835409 ACCGAGATGA
*
5835419 CAACCAAGGAGCATCAACTC
1 CAACCAAGGAACATCAACTC
*
5835439 CAACCAAGGAATATCAACTC
1 CAACCAAGGAACATCAACTC
5835459 TAACATAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.42, C:0.33, G:0.12, T:0.12
Consensus pattern (20 bp):
CAACCAAGGAACATCAACTC
Found at i:5836329 original size:23 final size:24
Alignment explanation
Indices: 5836288--5836332 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
5836278 TATTCATTAT
*
5836288 TTTTTTATTATATTGTATTTTTAA
1 TTTTTTAATATATTGTATTTTTAA
*
5836312 TTTTTTAATA-ATTTTATTTTT
1 TTTTTTAATATATTGTATTTTT
5836333 GATATATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (24 bp):
TTTTTTAATATATTGTATTTTTAA
Found at i:5837232 original size:15 final size:16
Alignment explanation
Indices: 5837202--5837235 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
5837192 GAAAAATATT
*
5837202 TTTATTATTTATTTAA
1 TTTATTATTAATTTAA
5837218 TTTATTA-TAATTTAA
1 TTTATTATTAATTTAA
5837233 TTT
1 TTT
5837236 TAAAAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTATTATTAATTTAA
Found at i:5837237 original size:16 final size:17
Alignment explanation
Indices: 5837201--5837237 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
5837191 AGAAAAATAT
*
5837201 TTTTATTATTTATTTAA
1 TTTTATTATTAATTTAA
5837218 -TTTATTA-TAATTTAA
1 TTTTATTATTAATTTAA
5837233 TTTTA
1 TTTTA
5837238 AAAAATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTTATTATTAATTTAA
Found at i:5837482 original size:21 final size:21
Alignment explanation
Indices: 5837456--5837503 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
5837446 GTTTCCAGAT
5837456 TCGCAACGCGAACATCGACTA
1 TCGCAACGCGAACATCGACTA
*
5837477 TCGCAACGCGAACTTCGACTA
1 TCGCAACGCGAACATCGACTA
5837498 TCGCAA
1 TCGCAA
5837504 ATCAGTTTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.31, C:0.33, G:0.19, T:0.17
Consensus pattern (21 bp):
TCGCAACGCGAACATCGACTA
Found at i:5837872 original size:21 final size:21
Alignment explanation
Indices: 5837848--5837961 Score: 101
Period size: 21 Copynumber: 5.4 Consensus size: 21
5837838 ATTTTGGACT
*
5837848 ATCGCAACGAATTTAGAATAA
1 ATCGCAACGAATTTGGAATAA
* *
5837869 ATCGCAACGCGAACTTGGACT--
1 ATCGCAA--CGAATTTGGAATAA
*
5837890 ATCGCAACGAATTTGTAATAA
1 ATCGCAACGAATTTGGAATAA
* *
5837911 ATCGCAACGCGAACTTGGACT--
1 ATCGCAA--CGAATTTGGAATAA
*
5837932 ATCGCAACAAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
5837953 ATCGCAACG
1 ATCGCAACG
5837962 CGAACTTCGA
Statistics
Matches: 72, Mismatches: 13, Indels: 16
0.71 0.13 0.16
Matches are distributed among these distances:
19 18 0.25
21 36 0.50
23 18 0.25
ACGTcount: A:0.39, C:0.21, G:0.18, T:0.22
Consensus pattern (21 bp):
ATCGCAACGAATTTGGAATAA
Found at i:5837900 original size:42 final size:41
Alignment explanation
Indices: 5837841--5837982 Score: 239
Period size: 42 Copynumber: 3.4 Consensus size: 41
5837831 CGTTGCGATT
5837841 TTGGACTATCGCAACGAATTTAGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAATTT-GAATAAATCGCAACGCGAAC
5837883 TTGGACTATCGCAACGAATTTGTAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAATTTG-AATAAATCGCAACGCGAAC
*
5837925 TTGGACTATCGCAACAAATTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAATTT-GAATAAATCGCAACGCGAAC
*
5837967 TTCGACTATCGCAACG
1 TTGGACTATCGCAACG
5837983 TGAACTTGGA
Statistics
Matches: 95, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
41 1 0.01
42 93 0.98
43 1 0.01
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.23
Consensus pattern (41 bp):
TTGGACTATCGCAACGAATTTGAATAAATCGCAACGCGAAC
Found at i:5837977 original size:21 final size:21
Alignment explanation
Indices: 5837869--5838007 Score: 133
Period size: 21 Copynumber: 6.6 Consensus size: 21
5837859 TTTAGAATAA
5837869 ATCGCAACGCGAACTTGGACT
1 ATCGCAACGCGAACTTGGACT
* * *
5837890 ATCGCAA--CGAATTTGTAAT
1 ATCGCAACGCGAACTTGGACT
5837909 AAATCGCAACGCGAACTTGGACT
1 --ATCGCAACGCGAACTTGGACT
* * *
5837932 ATCGCAA--CAAATTTGGAAT
1 ATCGCAACGCGAACTTGGACT
*
5837951 AAATCGCAACGCGAACTTCGACT
1 --ATCGCAACGCGAACTTGGACT
*
5837974 ATCGCAACGTGAACTTGGACT
1 ATCGCAACGCGAACTTGGACT
*
5837995 ATCGCAATGCGAA
1 ATCGCAACGCGAA
5838008 TCGCAACGCG
Statistics
Matches: 93, Mismatches: 17, Indels: 16
0.74 0.13 0.13
Matches are distributed among these distances:
19 18 0.19
21 58 0.62
23 17 0.18
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.22
Consensus pattern (21 bp):
ATCGCAACGCGAACTTGGACT
Found at i:5837999 original size:42 final size:42
Alignment explanation
Indices: 5837841--5838007 Score: 189
Period size: 42 Copynumber: 4.0 Consensus size: 42
5837831 CGTTGCGATT
* *
5837841 TTGGACTATCGCAAC-GAATTTAGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGGAACTTGGAAT-AATCGCAACGCGAAC
* *
5837883 TTGGACTATCGCAAC-GAATTTGTAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGGAACTTGGAAT-AATCGCAACGCGAAC
* *
5837925 TTGGACTATCGCAAC-AAATTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGGAACTTGGAAT-AATCGCAACGCGAAC
* * *
5837967 TTCGACTATCGCAACGTGAACTTGGACT-ATCGCAATGCGAA
1 TTGGACTATCGCAACG-GAACTTGGAATAATCGCAACGCGAA
5838008 TCGCAACGCG
Statistics
Matches: 114, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
42 106 0.93
44 8 0.07
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.23
Consensus pattern (42 bp):
TTGGACTATCGCAACGGAACTTGGAATAATCGCAACGCGAAC
Found at i:5837999 original size:84 final size:83
Alignment explanation
Indices: 5837841--5838007 Score: 237
Period size: 84 Copynumber: 2.0 Consensus size: 83
5837831 CGTTGCGATT
* * * *
5837841 TTGGACTATCGCAACGAATTTAGAATAAATCGCAACGCGAACTTGGACTATCGCAACGAATTTGT
1 TTGGACTATCGCAACAAATTTAGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGG
5837906 AATAAATCGCAACGCGAAC
66 AAT-AATCGCAACGCGAAC
*
5837925 TTGGACTATCGCAACAAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGTGAACTT
1 TTGGACTATCGCAACAAATTTAGAATAAATCGCAACGCGAACTTCGACTATCGCAAC--GAACTT
* *
5837990 GGACT-ATCGCAATGCGAA
64 GGAATAATCGCAACGCGAA
5838008 TCGCAACGCG
Statistics
Matches: 74, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
84 66 0.89
86 8 0.11
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.23
Consensus pattern (83 bp):
TTGGACTATCGCAACAAATTTAGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGG
AATAATCGCAACGCGAAC
Found at i:5838021 original size:33 final size:33
Alignment explanation
Indices: 5837974--5838040 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
5837964 AACTTCGACT
* * *
5837974 ATCGCAACGTGAACTTGGACTATCGCAATGCGA
1 ATCGCAACGCGAACTTCGACTATCGCAACGCGA
5838007 ATCGCAACGCGAACTTCGACTATCGCAACGCGA
1 ATCGCAACGCGAACTTCGACTATCGCAACGCGA
5838040 A
1 A
5838041 CTTGGACTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.31, C:0.28, G:0.22, T:0.18
Consensus pattern (33 bp):
ATCGCAACGCGAACTTCGACTATCGCAACGCGA
Found at i:5838033 original size:21 final size:21
Alignment explanation
Indices: 5838007--5838051 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
5837997 CGCAATGCGA
5838007 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
*
5838028 ATCGCAACGCGAACTTGGACT
1 ATCGCAACGCGAACTTCGACT
5838049 ATC
1 ATC
5838052 ACAATGTGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.29, C:0.31, G:0.20, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAACTTCGACT
Found at i:5838034 original size:54 final size:54
Alignment explanation
Indices: 5837952--5838062 Score: 195
Period size: 54 Copynumber: 2.1 Consensus size: 54
5837942 ATTTGGAATA
* *
5837952 AATCGCAACGCGAACTTCGACTATCGCAACGTGAACTTGGACTATCGCAATGCG
1 AATCGCAACGCGAACTTCGACTATCGCAACGCGAACTTGGACTATCACAATGCG
*
5838006 AATCGCAACGCGAACTTCGACTATCGCAACGCGAACTTGGACTATCACAATGTG
1 AATCGCAACGCGAACTTCGACTATCGCAACGCGAACTTGGACTATCACAATGCG
5838060 AAT
1 AAT
5838063 ATGTAAATCG
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.32, C:0.27, G:0.21, T:0.21
Consensus pattern (54 bp):
AATCGCAACGCGAACTTCGACTATCGCAACGCGAACTTGGACTATCACAATGCG
Found at i:5841477 original size:60 final size:60
Alignment explanation
Indices: 5841384--5841503 Score: 240
Period size: 60 Copynumber: 2.0 Consensus size: 60
5841374 AAAAAGACAA
5841384 GATGGTCTTAAAGATGTTAATATGAAAGGAGGGACAAAGGTTAAACAAGCTTCAGCAGTT
1 GATGGTCTTAAAGATGTTAATATGAAAGGAGGGACAAAGGTTAAACAAGCTTCAGCAGTT
5841444 GATGGTCTTAAAGATGTTAATATGAAAGGAGGGACAAAGGTTAAACAAGCTTCAGCAGTT
1 GATGGTCTTAAAGATGTTAATATGAAAGGAGGGACAAAGGTTAAACAAGCTTCAGCAGTT
5841504 TGCACAAGCA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.38, C:0.10, G:0.27, T:0.25
Consensus pattern (60 bp):
GATGGTCTTAAAGATGTTAATATGAAAGGAGGGACAAAGGTTAAACAAGCTTCAGCAGTT
Found at i:5846283 original size:19 final size:19
Alignment explanation
Indices: 5846259--5846295 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
5846249 CATCGAATGC
5846259 AAGTAGTGCATCGATGCAT
1 AAGTAGTGCATCGATGCAT
5846278 AAGTAGTGCATCGATGCA
1 AAGTAGTGCATCGATGCA
5846296 CCCCCTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.16, G:0.27, T:0.24
Consensus pattern (19 bp):
AAGTAGTGCATCGATGCAT
Found at i:5847682 original size:23 final size:23
Alignment explanation
Indices: 5847650--5847714 Score: 103
Period size: 23 Copynumber: 2.8 Consensus size: 23
5847640 CAGCTCGTAT
* * *
5847650 AATTGAACCGGAGTGCCGTGTAG
1 AATTGCACCGTAGTGCCATGTAG
5847673 AATTGCACCGTAGTGCCATGTAG
1 AATTGCACCGTAGTGCCATGTAG
5847696 AATTGCACCGTAGTGCCAT
1 AATTGCACCGTAGTGCCAT
5847715 ATAATAATGT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (23 bp):
AATTGCACCGTAGTGCCATGTAG
Found at i:5847900 original size:103 final size:103
Alignment explanation
Indices: 5847732--5847943 Score: 379
Period size: 103 Copynumber: 2.1 Consensus size: 103
5847722 TGTCCATAAG
* * * *
5847732 GACCACATATCATTCCTTAAGAATCATATACATGTACTAGGGATCAAGTATGTGTTTCACCAGAC
1 GACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGAC
5847797 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAA
66 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAA
*
5847835 GACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGAC
1 GACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGAC
5847900 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAA
66 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAA
5847938 GACCAC
1 GACCAC
5847944 GTAGACCCTC
Statistics
Matches: 104, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 104 1.00
ACGTcount: A:0.36, C:0.24, G:0.13, T:0.26
Consensus pattern (103 bp):
GACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGAC
TTCACACATGTTCCAAAGAATACATATATGTCCCGAAA
Found at i:5852876 original size:23 final size:23
Alignment explanation
Indices: 5852850--5852941 Score: 139
Period size: 23 Copynumber: 4.0 Consensus size: 23
5852840 CACCACAGCT
* *
5852850 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGGAGTGCCA
*
5852873 CGTAGAATTGCACCGGAGTACCA
1 CGTAGAATTGCACCGGAGTGCCA
*
5852896 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGGAGTGCCA
*
5852919 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGGAGTGCCA
5852942 TATAATAATG
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 62 1.00
ACGTcount: A:0.27, C:0.26, G:0.27, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGGAGTGCCA
Found at i:5853128 original size:103 final size:103
Alignment explanation
Indices: 5852960--5853169 Score: 359
Period size: 103 Copynumber: 2.0 Consensus size: 103
5852950 TGTCCATAAG
*
5852960 GACCACATATCATTCCTTAAGAATCATATACATATACTAGGAATCAAGTATGTGTCTCACCAGAC
1 GACCACATATCATTCCTTAAGAATCATATACATATACAAGGAATCAAGTATGTGTCTCACCAGAC
5853025 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAA
66 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAA
* *
5853063 GACCACATATCATTCTTTAAGAATCATATACATATGCCAAGG-ATCAAGTATGTGTCTCACCAGA
1 GACCACATATCATTCCTTAAGAATCATATACATAT-ACAAGGAATCAAGTATGTGTCTCACCAGA
* *
5853127 CTTCACACATGTTCCAAATAATACATATATGTCCCGAAG
65 CTTCACACATGTTCCAAAGAATACATATATGTCCCGAAA
5853166 GACC
1 GACC
5853170 GCGTAGACCC
Statistics
Matches: 101, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
103 97 0.96
104 4 0.04
ACGTcount: A:0.37, C:0.24, G:0.12, T:0.27
Consensus pattern (103 bp):
GACCACATATCATTCCTTAAGAATCATATACATATACAAGGAATCAAGTATGTGTCTCACCAGAC
TTCACACATGTTCCAAAGAATACATATATGTCCCGAAA
Found at i:5856357 original size:23 final size:23
Alignment explanation
Indices: 5856331--5856420 Score: 108
Period size: 23 Copynumber: 3.9 Consensus size: 23
5856321 ACATTATATA
5856331 GCACTACGGTGCATTTCTACGCG
1 GCACTACGGTGCATTTCTACGCG
* * ***
5856354 GCACTTCGGTGCAATTCTATATG
1 GCACTACGGTGCATTTCTACGCG
*
5856377 GCACTACGGTGCATTTCTATGCG
1 GCACTACGGTGCATTTCTACGCG
* *
5856400 GCACTTCGGTGCATTTATACG
1 GCACTACGGTGCATTTCTACG
5856421 AGCTGTGGAG
Statistics
Matches: 55, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 55 1.00
ACGTcount: A:0.19, C:0.26, G:0.24, T:0.31
Consensus pattern (23 bp):
GCACTACGGTGCATTTCTACGCG
Found at i:5856381 original size:46 final size:46
Alignment explanation
Indices: 5856325--5856412 Score: 158
Period size: 46 Copynumber: 1.9 Consensus size: 46
5856315 TTATGGACAT
5856325 TATATAGCACTACGGTGCATTTCTACGCGGCACTTCGGTGCAATTC
1 TATATAGCACTACGGTGCATTTCTACGCGGCACTTCGGTGCAATTC
* *
5856371 TATATGGCACTACGGTGCATTTCTATGCGGCACTTCGGTGCA
1 TATATAGCACTACGGTGCATTTCTACGCGGCACTTCGGTGCA
5856413 TTTATACGAG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 40 1.00
ACGTcount: A:0.20, C:0.25, G:0.24, T:0.31
Consensus pattern (46 bp):
TATATAGCACTACGGTGCATTTCTACGCGGCACTTCGGTGCAATTC
Found at i:5859890 original size:19 final size:19
Alignment explanation
Indices: 5859866--5859902 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
5859856 CATCGAATGC
5859866 AAGTAGTGCATCGATGCAT
1 AAGTAGTGCATCGATGCAT
5859885 AAGTAGTGCATCGATGCA
1 AAGTAGTGCATCGATGCA
5859903 CCCCCTTACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.16, G:0.27, T:0.24
Consensus pattern (19 bp):
AAGTAGTGCATCGATGCAT
Found at i:5861477 original size:23 final size:23
Alignment explanation
Indices: 5861451--5861534 Score: 105
Period size: 23 Copynumber: 3.7 Consensus size: 23
5861441 TATAGCACTA
5861451 CGGTGCATTTCTACGCGGTACTT
1 CGGTGCATTTCTACGCGGTACTT
* * * *
5861474 CGGTGCAATTCTATGTGGTACTA
1 CGGTGCATTTCTACGCGGTACTT
* *
5861497 CGGTGCATTTCTACGCAGCACTT
1 CGGTGCATTTCTACGCGGTACTT
*
5861520 CGGTGCATTTATACG
1 CGGTGCATTTCTACG
5861535 AGCTGTGGTG
Statistics
Matches: 50, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 50 1.00
ACGTcount: A:0.18, C:0.24, G:0.25, T:0.33
Consensus pattern (23 bp):
CGGTGCATTTCTACGCGGTACTT
Found at i:5863554 original size:16 final size:17
Alignment explanation
Indices: 5863523--5863555 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
5863513 TCCCAGACCC
*
5863523 TCAATATCTTAAACTCT
1 TCAATATCTAAAACTCT
5863540 TCAAT-TCTAAAACTCT
1 TCAATATCTAAAACTCT
5863556 GTATCTTTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.36, C:0.24, G:0.00, T:0.39
Consensus pattern (17 bp):
TCAATATCTAAAACTCT
Found at i:5863591 original size:16 final size:16
Alignment explanation
Indices: 5863570--5863616 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
5863560 CTTTGAAATC
5863570 TCAAACTCTCAAA-TGT
1 TCAAACTCTCAAACT-T
* *
5863586 TCAAACTTTAAAACTT
1 TCAAACTCTCAAACTT
*
5863602 TGAAACTCTCAAACT
1 TCAAACTCTCAAACT
5863617 AAAAAAATAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
16 24 0.96
17 1 0.04
ACGTcount: A:0.40, C:0.23, G:0.04, T:0.32
Consensus pattern (16 bp):
TCAAACTCTCAAACTT
Found at i:5866250 original size:22 final size:22
Alignment explanation
Indices: 5866222--5866268 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
5866212 TATGATGAAC
5866222 TTCTACTTCAAAGTCTACCTGA
1 TTCTACTTCAAAGTCTACCTGA
5866244 TTCTACTTCAAAGTCTACCTGA
1 TTCTACTTCAAAGTCTACCTGA
5866266 TTC
1 TTC
5866269 GTATGATCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.26, C:0.28, G:0.09, T:0.38
Consensus pattern (22 bp):
TTCTACTTCAAAGTCTACCTGA
Found at i:5870735 original size:2 final size:2
Alignment explanation
Indices: 5870730--5870758 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5870720 TAGCTTTCTT
5870730 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5870759 TAATATTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5873934 original size:17 final size:17
Alignment explanation
Indices: 5873909--5873942 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
5873899 CCGGTTTCGG
5873909 TTTTAAAAAAACCGGTT
1 TTTTAAAAAAACCGGTT
*
5873926 TTTTTAAAAAACCGGTT
1 TTTTAAAAAAACCGGTT
5873943 ATAAAAAACC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (17 bp):
TTTTAAAAAAACCGGTT
Found at i:5874378 original size:13 final size:13
Alignment explanation
Indices: 5874357--5874411 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
5874347 AAGTTCGATA
*
5874357 AATTCAAATACTT
1 AATTGAAATACTT
5874370 AATTGAAATACTT
1 AATTGAAATACTT
* *
5874383 AATT-AACTCAACAT
1 AATTGAAAT--ACTT
5874397 AATTGAAATACTT
1 AATTGAAATACTT
5874410 AA
1 AA
5874412 ATACTTCCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.35
Consensus pattern (13 bp):
AATTGAAATACTT
Found at i:5874493 original size:32 final size:33
Alignment explanation
Indices: 5874397--5874495 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
5874387 AACTCAACAT
* * *
5874397 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
5874430 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
5874463 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
5874495 A
1 A
5874496 TTGAAACAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 12 0.19
33 51 0.81
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.32
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:5874514 original size:21 final size:21
Alignment explanation
Indices: 5874490--5874529 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
5874480 ACTTCAAGTT
5874490 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
5874511 CGATAATTGAAATAAAGTT
1 CGATAATTGAAACAAAGTT
5874530 ATAAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.30
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:5876836 original size:12 final size:12
Alignment explanation
Indices: 5876819--5876864 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
5876809 TTCGGATAAA
5876819 AACCGGTTTTTT
1 AACCGGTTTTTT
5876831 AACCGGTTTTTTT
1 AACCGG-TTTTTT
5876844 CAAACCGGTTTTTT
1 --AACCGGTTTTTT
*
5876858 ATCCGGT
1 AACCGGT
5876865 AAAAAAACCG
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
12 12 0.40
13 6 0.20
14 6 0.20
15 6 0.20
ACGTcount: A:0.17, C:0.20, G:0.17, T:0.46
Consensus pattern (12 bp):
AACCGGTTTTTT
Found at i:5876849 original size:15 final size:14
Alignment explanation
Indices: 5876818--5876857 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
5876808 TTTCGGATAA
5876818 AAACCGG-TTTTTT
1 AAACCGGTTTTTTT
5876831 -AACCGGTTTTTTT
1 AAACCGGTTTTTTT
5876844 CAAACCGGTTTTTT
1 -AAACCGGTTTTTT
5876858 ATCCGGTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 6 0.25
13 6 0.25
15 12 0.50
ACGTcount: A:0.20, C:0.17, G:0.15, T:0.47
Consensus pattern (14 bp):
AAACCGGTTTTTTT
Found at i:5878665 original size:21 final size:21
Alignment explanation
Indices: 5878639--5878681 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
5878629 AGAACATGGA
5878639 TATGTACAGAACGCATATACT
1 TATGTACAGAACGCATATACT
5878660 TATGTACAGAACGCATATACT
1 TATGTACAGAACGCATATACT
5878681 T
1 T
5878682 GGATTAGGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.19, G:0.14, T:0.30
Consensus pattern (21 bp):
TATGTACAGAACGCATATACT
Found at i:5883032 original size:24 final size:24
Alignment explanation
Indices: 5882985--5883032 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
5882975 TCCTTTTGAT
* * *
5882985 AAAAGTATAAAAAAGGCAACAATG
1 AAAAGAATAAAAAAGGAAAAAATG
*
5883009 AAAAGAATAAAAAATGAAAAAATG
1 AAAAGAATAAAAAAGGAAAAAATG
5883033 GAATTTTGAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.69, C:0.04, G:0.15, T:0.12
Consensus pattern (24 bp):
AAAAGAATAAAAAAGGAAAAAATG
Found at i:5884050 original size:11 final size:11
Alignment explanation
Indices: 5884016--5884053 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
5884006 TCAAGACTCG
5884016 AGCTCGATTCA
1 AGCTCGATTCA
* *
5884027 AACTTGATTCA
1 AGCTCGATTCA
5884038 AGCTCGATTCA
1 AGCTCGATTCA
5884049 AGCTC
1 AGCTC
5884054 AAGTGCTCAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (11 bp):
AGCTCGATTCA
Found at i:5886237 original size:14 final size:14
Alignment explanation
Indices: 5886216--5886249 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
5886206 CACATAATCA
*
5886216 GATTTAGGTTTTAG
1 GATTTAGGGTTTAG
*
5886230 GGTTTAGGGTTTAG
1 GATTTAGGGTTTAG
5886244 GATTTA
1 GATTTA
5886250 TTGCAAAGAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.21, C:0.00, G:0.32, T:0.47
Consensus pattern (14 bp):
GATTTAGGGTTTAG
Found at i:5886457 original size:25 final size:25
Alignment explanation
Indices: 5886410--5886457 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
5886400 TATAATTATC
* * * *
5886410 AATAGTGTATTTTTAATATATTTTT
1 AATAATGTAATTTTAAAAAATTTTT
5886435 AATAATGTAATTTTAAAAAATTT
1 AATAATGTAATTTTAAAAAATTT
5886458 AAAATTATAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (25 bp):
AATAATGTAATTTTAAAAAATTTTT
Found at i:5895871 original size:2 final size:2
Alignment explanation
Indices: 5895864--5895897 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
5895854 CATCCTTTGG
5895864 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5895898 GATAATGATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5896257 original size:3 final size:3
Alignment explanation
Indices: 5896239--5896282 Score: 70
Period size: 3 Copynumber: 14.3 Consensus size: 3
5896229 CTAATATAGA
*
5896239 TAT TAG TAT TATT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
5896283 TAAATCATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 35 0.92
4 3 0.08
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:5896371 original size:25 final size:28
Alignment explanation
Indices: 5896342--5896405 Score: 71
Period size: 28 Copynumber: 2.4 Consensus size: 28
5896332 TCTAAATAAA
* *
5896342 ATTAATAAAA-AAATAA-AATAT-CAAT
1 ATTAATAAAAGAAAAAATAATATAAAAT
5896367 ATTAATTAAAAGAAAAAATAATATAAAAT
1 ATTAA-TAAAAGAAAAAATAATATAAAAT
*
5896396 TTTAATAAAA
1 ATTAATAAAA
5896406 TATATATATT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
25 5 0.16
26 5 0.16
27 5 0.16
28 10 0.31
29 7 0.22
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (28 bp):
ATTAATAAAAGAAAAAATAATATAAAAT
Found at i:5896404 original size:28 final size:30
Alignment explanation
Indices: 5896341--5896405 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 30
5896331 GTCTAAATAA
* *
5896341 AATTAATA-AAAAAATAAAATATCAATATT
1 AATTAAAAGAAAAAATAAAATATAAATATT
* *
5896370 AATTAAAAGAAAAAATAATATA-AAATTTT
1 AATTAAAAGAAAAAATAAAATATAAATATT
5896399 AA-TAAAA
1 AATTAAAA
5896406 TATATATATT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
28 5 0.16
29 14 0.45
30 12 0.39
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.29
Consensus pattern (30 bp):
AATTAAAAGAAAAAATAAAATATAAATATT
Found at i:5899587 original size:21 final size:21
Alignment explanation
Indices: 5899548--5899587 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
5899538 ATTCTAATTT
* *
5899548 TAATTTTTTTTAAATCAAATC
1 TAATTTTATTTAAACCAAATC
*
5899569 TAATTTTATTTAACCCAAA
1 TAATTTTATTTAAACCAAA
5899588 AATAGATAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.47
Consensus pattern (21 bp):
TAATTTTATTTAAACCAAATC
Found at i:5899922 original size:2 final size:2
Alignment explanation
Indices: 5899885--5899910 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5899875 TATTTATTTC
5899885 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
5899911 GTTATTTATA
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:5900057 original size:17 final size:18
Alignment explanation
Indices: 5900020--5900059 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
5900010 TTATTATAAT
*
5900020 TTTAATAGTTAAAGATTA
1 TTTAATAATTAAAGATTA
*
5900038 TTTAATAATTAAA-TTTA
1 TTTAATAATTAAAGATTA
5900055 TTTAA
1 TTTAA
5900060 ATAGAATACT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (18 bp):
TTTAATAATTAAAGATTA
Found at i:5903503 original size:36 final size:36
Alignment explanation
Indices: 5903463--5903534 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
5903453 GAATGTTTAG
*
5903463 TTCTCTTTTTACACGTCACAATTATCTGTTTCATTT
1 TTCTCTTTTTACAAGTCACAATTATCTGTTTCATTT
5903499 TTCTCTTTTTACAAGTCACAATTATCTGTTTCATTT
1 TTCTCTTTTTACAAGTCACAATTATCTGTTTCATTT
5903535 GAGTTTTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.21, C:0.21, G:0.06, T:0.53
Consensus pattern (36 bp):
TTCTCTTTTTACAAGTCACAATTATCTGTTTCATTT
Found at i:5903781 original size:21 final size:22
Alignment explanation
Indices: 5903751--5903898 Score: 114
Period size: 21 Copynumber: 7.0 Consensus size: 22
5903741 GATTTACATA
*
5903751 TTCGCATTGCGA-TAGTCCAAG
1 TTCGCGTTGCGATTAGTCCAAG
* *
5903772 TTCGCGTTGCAATTTATTCCAAG
1 TTCGCGTTGCGA-TTAGTCCAAG
**
5903795 TT--CGTTGCGA-TAGTAGAAG
1 TTCGCGTTGCGATTAGTCCAAG
* *
5903814 TTCGCGTTGCGATTCATTCCAAA
1 TTCGCGTTGCGATT-AGTCCAAG
* *
5903837 TT--CGTTGC-ACTAGTCGAAG
1 TTCGCGTTGCGATTAGTCCAAG
* *
5903856 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA-TTAGTCCAAG
5903879 TTCGCGTTGCGA-TAGTCCAA
1 TTCGCGTTGCGATTAGTCCAA
5903899 AATCGCAACG
Statistics
Matches: 97, Mismatches: 20, Indels: 20
0.71 0.15 0.15
Matches are distributed among these distances:
19 15 0.15
20 2 0.02
21 44 0.45
22 2 0.02
23 34 0.35
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.34
Consensus pattern (22 bp):
TTCGCGTTGCGATTAGTCCAAG
Found at i:5903796 original size:23 final size:23
Alignment explanation
Indices: 5903766--5903891 Score: 106
Period size: 23 Copynumber: 5.8 Consensus size: 23
5903756 ATTGCGATAG
*
5903766 TCCAAGTTCGCGTTGCAATTTAT
1 TCCAAGTTCGCGTTGCGATTTAT
*
5903789 TCCAAGTT--CGTTGCGA--TAG
1 TCCAAGTTCGCGTTGCGATTTAT
** *
5903808 TAGAAGTTCGCGTTGCGATTCAT
1 TCCAAGTTCGCGTTGCGATTTAT
* * *
5903831 TCCAAATT--CGTTGC-A-CTAG
1 TCCAAGTTCGCGTTGCGATTTAT
*
5903850 TCGAAGTTCGCGTTGCGATTTAT
1 TCCAAGTTCGCGTTGCGATTTAT
*
5903873 TCCAAATTCGCGTTGCGAT
1 TCCAAGTTCGCGTTGCGAT
5903892 AGTCCAAAAT
Statistics
Matches: 77, Mismatches: 18, Indels: 16
0.69 0.16 0.14
Matches are distributed among these distances:
19 15 0.19
20 1 0.01
21 27 0.35
22 1 0.01
23 33 0.43
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.35
Consensus pattern (23 bp):
TCCAAGTTCGCGTTGCGATTTAT
Found at i:5903804 original size:42 final size:42
Alignment explanation
Indices: 5903757--5903898 Score: 196
Period size: 42 Copynumber: 3.3 Consensus size: 42
5903747 CATATTCGCA
* *
5903757 TTGCGATAGTCCAAGTTCGCGTTGCAATTTATTCCAAGTTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
** *
5903799 TTGCGATAGTAGAAGTTCGCGTTGCGATTCATTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
*
5903841 TTGC-ACTAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGCG
1 TTGCGA-TAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT--CG
5903885 TTGCGATAGTCCAA
1 TTGCGATAGTCCAA
5903899 AATCGCAACG
Statistics
Matches: 88, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
41 1 0.01
42 73 0.83
44 13 0.15
45 1 0.01
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.34
Consensus pattern (42 bp):
TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
Found at i:5908214 original size:18 final size:18
Alignment explanation
Indices: 5908191--5908225 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
5908181 TTTTCAATAA
*
5908191 TATTTTATTATAAAAATG
1 TATTTTAATATAAAAATG
5908209 TATTTTAATATAAAAAT
1 TATTTTAATATAAAAAT
5908226 TAATTACCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (18 bp):
TATTTTAATATAAAAATG
Found at i:5910971 original size:3 final size:3
Alignment explanation
Indices: 5910963--5910996 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
5910953 TGCCAACTTG
5910963 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
5910997 TTTGGATAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:5912391 original size:67 final size:67
Alignment explanation
Indices: 5912283--5912417 Score: 270
Period size: 67 Copynumber: 2.0 Consensus size: 67
5912273 AAGGCTCAAT
5912283 AGCTCATAGAACTTATCTAAAGTGAATTGCACTCCCAACATAGCACCCAAAGAGCCATGACAAAA
1 AGCTCATAGAACTTATCTAAAGTGAATTGCACTCCCAACATAGCACCCAAAGAGCCATGACAAAA
5912348 AA
66 AA
5912350 AGCTCATAGAACTTATCTAAAGTGAATTGCACTCCCAACATAGCACCCAAAGAGCCATGACAAAA
1 AGCTCATAGAACTTATCTAAAGTGAATTGCACTCCCAACATAGCACCCAAAGAGCCATGACAAAA
5912415 AA
66 AA
5912417 A
1 A
5912418 CCAACAGATC
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 68 1.00
ACGTcount: A:0.44, C:0.25, G:0.13, T:0.18
Consensus pattern (67 bp):
AGCTCATAGAACTTATCTAAAGTGAATTGCACTCCCAACATAGCACCCAAAGAGCCATGACAAAA
AA
Found at i:5913672 original size:20 final size:18
Alignment explanation
Indices: 5913625--5913697 Score: 74
Period size: 18 Copynumber: 3.9 Consensus size: 18
5913615 ACTGAATATT
* *
5913625 TGTCCCGAAAGACCACTA
1 TGTCTCGAAGGACCACTA
5913643 TGTCTCGAAGGACCACTGA
1 TGTCTCGAAGGACCACT-A
* *
5913662 TTGTTTCGAAGAACCACTA
1 -TGTCTCGAAGGACCACTA
* *
5913681 TATCCCGAAGGACCACT
1 TGTCTCGAAGGACCACT
5913698 CCTTAAGAAC
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
18 28 0.62
19 2 0.04
20 15 0.33
ACGTcount: A:0.30, C:0.29, G:0.19, T:0.22
Consensus pattern (18 bp):
TGTCTCGAAGGACCACTA
Found at i:5914500 original size:19 final size:19
Alignment explanation
Indices: 5914432--5914501 Score: 99
Period size: 19 Copynumber: 3.7 Consensus size: 19
5914422 TTTAAGTAGG
5914432 TGCATCGATGCAC-CCTTA
1 TGCATCGATGCACTCCTTA
* *
5914450 TGCACCGATGCA-TTCTTCA
1 TGCATCGATGCACTCCTT-A
5914469 TGCATCGATGCACTCCTTA
1 TGCATCGATGCACTCCTTA
5914488 TGCATCGATGCACT
1 TGCATCGATGCACT
5914502 AATTGCATTT
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
18 14 0.31
19 27 0.60
20 4 0.09
ACGTcount: A:0.21, C:0.31, G:0.17, T:0.30
Consensus pattern (19 bp):
TGCATCGATGCACTCCTTA
Found at i:5914670 original size:20 final size:20
Alignment explanation
Indices: 5914645--5914691 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
5914635 TATCATGTCA
5914645 TTAAACCCAACCATCATTAC
1 TTAAACCCAACCATCATTAC
5914665 TTAAACCCAACCATCATTAC
1 TTAAACCCAACCATCATTAC
5914685 TTAAACC
1 TTAAACC
5914692 AACTTATATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.40, C:0.34, G:0.00, T:0.26
Consensus pattern (20 bp):
TTAAACCCAACCATCATTAC
Found at i:5918099 original size:3 final size:3
Alignment explanation
Indices: 5918093--5918118 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
5918083 TTATTATTAT
5918093 TAG TAG TAG TAG TAG TAG TAG TAG TA
1 TAG TAG TAG TAG TAG TAG TAG TAG TA
5918119 TTATCATTAT
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:0.35, C:0.00, G:0.31, T:0.35
Consensus pattern (3 bp):
TAG
Found at i:5922513 original size:37 final size:37
Alignment explanation
Indices: 5922467--5922538 Score: 117
Period size: 37 Copynumber: 1.9 Consensus size: 37
5922457 TCCTCAACGC
* *
5922467 TAATATAACATAATTTAGTCTCTTTACTTTTATAAGT
1 TAATATAACATAATTTAGTCCCTCTACTTTTATAAGT
*
5922504 TAATGTAACATAATTTAGTCCCTCTACTTTTATAA
1 TAATATAACATAATTTAGTCCCTCTACTTTTATAA
5922539 TGTAATTAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.35, C:0.14, G:0.06, T:0.46
Consensus pattern (37 bp):
TAATATAACATAATTTAGTCCCTCTACTTTTATAAGT
Found at i:5944312 original size:16 final size:16
Alignment explanation
Indices: 5944288--5944321 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
5944278 TATCGCCGAC
*
5944288 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
5944304 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
5944320 CG
1 CG
5944322 TGAATAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.32
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:5947792 original size:2 final size:2
Alignment explanation
Indices: 5947785--5947821 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
5947775 TTTCACATAA
5947785 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5947822 GAAAATGAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:5948003 original size:30 final size:31
Alignment explanation
Indices: 5947959--5948034 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 31
5947949 TTTTCATTAA
* * *
5947959 AACAAATTAATCACTAATATTATCGATTTGT
1 AACAAAATGATCACTAACATTATCGATTTGT
* * *
5947990 AACAAAA-GATCACTAGCGTTATCGATTTTT
1 AACAAAATGATCACTAACATTATCGATTTGT
*
5948020 AATAAAATGATCACT
1 AACAAAATGATCACT
5948035 CCATTAGTAT
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
30 24 0.65
31 13 0.35
ACGTcount: A:0.42, C:0.14, G:0.09, T:0.34
Consensus pattern (31 bp):
AACAAAATGATCACTAACATTATCGATTTGT
Found at i:5948280 original size:17 final size:17
Alignment explanation
Indices: 5948234--5948282 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
5948224 AAAAAATATA
*
5948234 TAAAAATATTAAAAATG
1 TAAAAAAATTAAAAATG
* *
5948251 TGAAAAAGTTAAAAAT-
1 TAAAAAAATTAAAAATG
5948267 TAAAAAAATCTAAAAA
1 TAAAAAAAT-TAAAAA
5948283 ATACTAAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
16 7 0.27
17 19 0.73
ACGTcount: A:0.67, C:0.02, G:0.06, T:0.24
Consensus pattern (17 bp):
TAAAAAAATTAAAAATG
Found at i:5953101 original size:29 final size:29
Alignment explanation
Indices: 5953059--5953118 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
5953049 CAACCAATCA
5953059 TATTCATCCACTAATAAAAGTTGACTGTT
1 TATTCATCCACTAATAAAAGTTGACTGTT
5953088 TATTCATCCACTAATAAAAGTTGACTGTT
1 TATTCATCCACTAATAAAAGTTGACTGTT
5953117 TA
1 TA
5953119 AAGTTGTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.38
Consensus pattern (29 bp):
TATTCATCCACTAATAAAAGTTGACTGTT
Found at i:5954285 original size:15 final size:17
Alignment explanation
Indices: 5954246--5954286 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
5954236 ATATTAAAAT
5954246 AATTTATTTATTATTAA
1 AATTTATTTATTATTAA
*
5954263 AATATTATTTTTTA-T-A
1 AAT-TTATTTATTATTAA
5954279 AATTTATT
1 AATTTATT
5954287 AATAAAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 5 0.23
16 4 0.18
17 4 0.18
18 9 0.41
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
AATTTATTTATTATTAA
Found at i:5955694 original size:25 final size:25
Alignment explanation
Indices: 5955623--5955694 Score: 65
Period size: 30 Copynumber: 2.7 Consensus size: 25
5955613 CATCGAATCG
*
5955623 AATATATTTTAA-CTTAATTTACTA
1 AATATATTTTAATCTTAAATTACTA
* *
5955647 AATATATTATATTATTATTTTAAATTATTA
1 AATATA-T-T-TTA--ATCTTAAATTACTA
5955677 AATATATTTTAATCTTAA
1 AATATATTTTAATCTTAA
5955695 CTTCAAAATA
Statistics
Matches: 38, Mismatches: 4, Indels: 11
0.72 0.08 0.21
Matches are distributed among these distances:
24 6 0.16
25 7 0.18
26 1 0.03
27 6 0.16
28 1 0.03
29 2 0.05
30 15 0.39
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (25 bp):
AATATATTTTAATCTTAAATTACTA
Found at i:5955773 original size:25 final size:26
Alignment explanation
Indices: 5955711--5955774 Score: 78
Period size: 25 Copynumber: 2.5 Consensus size: 26
5955701 AATATAAATG
*
5955711 AAATAGTTTTAAATTAAGTTAATAATA
1 AAATA-TTTTTAATTAAGTTAATAATA
*
5955738 AAATATATTTAA-TAAGTTAAT-ATAA
1 AAATATTTTTAATTAAGTTAATAAT-A
5955763 AAATATTTTTAA
1 AAATATTTTTAA
5955775 AGTAAATATA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
24 2 0.06
25 21 0.64
26 5 0.15
27 5 0.15
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (26 bp):
AAATATTTTTAATTAAGTTAATAATA
Found at i:5955777 original size:23 final size:26
Alignment explanation
Indices: 5955725--5955795 Score: 80
Period size: 25 Copynumber: 2.9 Consensus size: 26
5955715 AGTTTTAAAT
5955725 TAAGTTAATA-ATAAAATATATTTAA
1 TAAGTTAATATATAAAATATATTTAA
*
5955750 TAAGTTAATATA-AAAATAT-TTTTA
1 TAAGTTAATATATAAAATATATTTAA
*
5955774 -AAGTAAATATATATAAA-ATATT
1 TAAGTTAATATATA-AAATATATT
5955796 ATGAATTTAC
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
23 10 0.25
24 7 0.17
25 22 0.55
26 1 0.03
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (26 bp):
TAAGTTAATATATAAAATATATTTAA
Found at i:5956094 original size:10 final size:10
Alignment explanation
Indices: 5956079--5956117 Score: 69
Period size: 10 Copynumber: 3.9 Consensus size: 10
5956069 GAGGACTAAA
5956079 TTTATTTAAT
1 TTTATTTAAT
*
5956089 TTTATTTAAG
1 TTTATTTAAT
5956099 TTTATTTAAT
1 TTTATTTAAT
5956109 TTTATTTAA
1 TTTATTTAA
5956118 GTATGACTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (10 bp):
TTTATTTAAT
Found at i:5956104 original size:20 final size:20
Alignment explanation
Indices: 5956079--5956119 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
5956069 GAGGACTAAA
5956079 TTTATTTAATTTTATTTAAG
1 TTTATTTAATTTTATTTAAG
5956099 TTTATTTAATTTTATTTAAG
1 TTTATTTAATTTTATTTAAG
5956119 T
1 T
5956120 ATGACTAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (20 bp):
TTTATTTAATTTTATTTAAG
Found at i:5962962 original size:25 final size:25
Alignment explanation
Indices: 5962920--5962967 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
5962910 GTTCGCAATC
* * *
5962920 TTAAAATTTCAAGTTCGACTTGAAA
1 TTAAAAATTAAAGCTCGACTTGAAA
*
5962945 TTAAAAATTAAAGCTCGATTTGA
1 TTAAAAATTAAAGCTCGACTTGA
5962968 GCTCAAAAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.35
Consensus pattern (25 bp):
TTAAAAATTAAAGCTCGACTTGAAA
Found at i:5963398 original size:12 final size:12
Alignment explanation
Indices: 5963381--5963405 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5963371 TTATGTGGTG
5963381 CGTCAAACTAGT
1 CGTCAAACTAGT
5963393 CGTCAAACTAGT
1 CGTCAAACTAGT
5963405 C
1 C
5963406 ACCTGTGACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.24
Consensus pattern (12 bp):
CGTCAAACTAGT
Found at i:5964824 original size:2 final size:2
Alignment explanation
Indices: 5964819--5964859 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
5964809 ATGTAGAGGG
5964819 AT AT AT AT AT 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 AT AT A
5964860 AACAGAATTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5983920 original size:31 final size:31
Alignment explanation
Indices: 5983885--5983972 Score: 131
Period size: 31 Copynumber: 2.8 Consensus size: 31
5983875 ATCCCCTAAC
* *
5983885 ATTTAATCCGTTTACAATATGGTCCCTCAAT
1 ATTTAGTCCGTTTGCAATATGGTCCCTCAAT
* * *
5983916 ATTTAGTTCATTTGCAATATGATCCCTCAAT
1 ATTTAGTCCGTTTGCAATATGGTCCCTCAAT
5983947 ATTTAGTCCGTTTGCAATATGGTCCC
1 ATTTAGTCCGTTTGCAATATGGTCCC
5983973 CGACGTAACT
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 49 1.00
ACGTcount: A:0.26, C:0.22, G:0.12, T:0.40
Consensus pattern (31 bp):
ATTTAGTCCGTTTGCAATATGGTCCCTCAAT
Found at i:5984411 original size:21 final size:21
Alignment explanation
Indices: 5984382--5984426 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
5984372 ACTTAAGGCG
5984382 TTTACTACCTAAACTATCAGT
1 TTTACTACCTAAACTATCAGT
* * *
5984403 TTTAGTACCTAAACTTTCATT
1 TTTACTACCTAAACTATCAGT
5984424 TTT
1 TTT
5984427 TTCTTCAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.20, G:0.04, T:0.47
Consensus pattern (21 bp):
TTTACTACCTAAACTATCAGT
Found at i:5985007 original size:21 final size:21
Alignment explanation
Indices: 5984978--5985035 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
5984968 ATCTCCGGTA
* *
5984978 TCGCATTGCGATAGTCCAAGT
1 TCGCGTTGCGATAGTCCAAAT
*
5984999 TCGCGTTGCGATTTATTCCAAAT
1 TCGCGTTGCGA--TAGTCCAAAT
5985022 T--CGTTGCGATAGTC
1 TCGCGTTGCGATAGTC
5985036 AGAATTGTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
19 4 0.13
21 18 0.58
23 9 0.29
ACGTcount: A:0.21, C:0.22, G:0.22, T:0.34
Consensus pattern (21 bp):
TCGCGTTGCGATAGTCCAAAT
Found at i:5985654 original size:6 final size:6
Alignment explanation
Indices: 5985632--5985664 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
5985622 GTCCGTCTCG
*
5985632 GGTCG- GGTCGT GATCGT GGTCGT GGTCGT GGTC
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTC
5985665 AATGAGGTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.03, C:0.18, G:0.48, T:0.30
Consensus pattern (6 bp):
GGTCGT
Found at i:5987326 original size:31 final size:31
Alignment explanation
Indices: 5987286--5987352 Score: 125
Period size: 31 Copynumber: 2.2 Consensus size: 31
5987276 TGTAATACAA
5987286 TCCCCCAACATTTAGTCTGTTTGCAATATGG
1 TCCCCCAACATTTAGTCTGTTTGCAATATGG
*
5987317 TCCCTCAACATTTAGTCTGTTTGCAATATGG
1 TCCCCCAACATTTAGTCTGTTTGCAATATGG
5987348 TCCCC
1 TCCCC
5987353 GACGTAACTG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.21, C:0.28, G:0.15, T:0.36
Consensus pattern (31 bp):
TCCCCCAACATTTAGTCTGTTTGCAATATGG
Found at i:6001810 original size:2 final size:2
Alignment explanation
Indices: 6001803--6001856 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
6001793 AGAAACTTTC
6001803 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6001845 AT AT AT AT AT AT
1 AT AT AT AT AT AT
6001857 TTGACAAATT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6006223 original size:97 final size:96
Alignment explanation
Indices: 6006053--6006253 Score: 296
Period size: 96 Copynumber: 2.1 Consensus size: 96
6006043 AAAGGAAACA
* * *
6006053 GTTAGAAAATAAAAATTCAGGGCAGATGTACTAAACTCTATAGGAAGTCAAGTGTATTCTCATTA
1 GTTAGAAAATAAAAATTCAGGGCAGATGTACTAAACTCCATAGGAAGTCAAATGCATTCTCATTA
*
6006118 TTTTAAAAAATGGTGAAATTTAGTTTAATAT
66 TTTTAAAAAATGATGAAATTTAGTTTAATAT
* * * *
6006149 GTTAGAAAATAAAAATTCAGAGGCGGATGTACTAAATTCCATAGGGAGTCAAATGCA-TCTCCTT
1 GTTAGAAAATAAAAATTCAG-GGCAGATGTACTAAACTCCATAGGAAGTCAAATGCATTCTCATT
*
6006213 GTTTTAAAAAATGATGAAATTTAGTTTAATAT
65 ATTTTAAAAAATGATGAAATTTAGTTTAATAT
*
6006245 GTTAAAAAA
1 GTTAGAAAA
6006254 ATTACATGCC
Statistics
Matches: 94, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
96 64 0.68
97 30 0.32
ACGTcount: A:0.41, C:0.09, G:0.17, T:0.33
Consensus pattern (96 bp):
GTTAGAAAATAAAAATTCAGGGCAGATGTACTAAACTCCATAGGAAGTCAAATGCATTCTCATTA
TTTTAAAAAATGATGAAATTTAGTTTAATAT
Found at i:6008865 original size:331 final size:331
Alignment explanation
Indices: 6008263--6008924 Score: 1315
Period size: 331 Copynumber: 2.0 Consensus size: 331
6008253 ACCCAACAGA
6008263 TATAATGTACATGCCACTAATCAGTCAAAGTTAGGATGACTTACTGATTCTATGAGTAGGTTTGA
1 TATAATGTACATGCCACTAATCAGTCAAAGTTAGGATGACTTACTGATTCTATGAGTAGGTTTGA
6008328 TTTCCATAAAATGTTGGCAAACTCCTTACTTCACGTCCTCTACTTTATTCGACCCTATGCATGAA
66 TTTCCATAAAATGTTGGCAAACTCCTTACTTCACGTCCTCTACTTTATTCGACCCTATGCATGAA
6008393 AATTTTCACGCGTTAAGTAAAACTTAGTAAGACAAGTAAATAAATCAGAGTGAACTATATCAGTA
131 AATTTTCACGCGTTAAGTAAAACTTAGTAAGACAAGTAAATAAATCAGAGTGAACTATATCAGTA
6008458 GAATATCATAAATCTTTAAAAATTCAAACCGAACTTTCCAAGCCATATTTTTCCTCATCAGAAAT
196 GAATATCATAAATCTTTAAAAATTCAAACCGAACTTTCCAAGCCATATTTTTCCTCATCAGAAAT
6008523 TTGAAAATCATGGTCTCGTAATTTTATCAAAATCACAATAACCAACATCAACAATATTATACTTT
261 TTGAAAATCATGGTCTCGTAATTTTATCAAAATCACAATAACCAACATCAACAATATTATACTTT
6008588 GCATAT
326 GCATAT
*
6008594 TATAATGTACATGCTACTAATCAGTCAAAGTTAGGATGACTTACTGATTCTATGAGTAGGTTTGA
1 TATAATGTACATGCCACTAATCAGTCAAAGTTAGGATGACTTACTGATTCTATGAGTAGGTTTGA
6008659 TTTCCATAAAATGTTGGCAAACTCCTTACTTCACGTCCTCTACTTTATTCGACCCTATGCATGAA
66 TTTCCATAAAATGTTGGCAAACTCCTTACTTCACGTCCTCTACTTTATTCGACCCTATGCATGAA
6008724 AATTTTCACGCGTTAAGTAAAACTTAGTAAGACAAGTAAATAAATCAGAGTGAACTATATCAGTA
131 AATTTTCACGCGTTAAGTAAAACTTAGTAAGACAAGTAAATAAATCAGAGTGAACTATATCAGTA
6008789 GAATATCATAAATCTTTAAAAATTCAAACCGAACTTTCCAAGCCATATTTTTCCTCATCAGAAAT
196 GAATATCATAAATCTTTAAAAATTCAAACCGAACTTTCCAAGCCATATTTTTCCTCATCAGAAAT
6008854 TTGAAAATCATGGTCTCGTAATTTTATCAAAATCACAATAACCAACATCAACAATATTATACTTT
261 TTGAAAATCATGGTCTCGTAATTTTATCAAAATCACAATAACCAACATCAACAATATTATACTTT
6008919 GCATAT
326 GCATAT
6008925 ACTTTCAATT
Statistics
Matches: 330, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
331 330 1.00
ACGTcount: A:0.37, C:0.19, G:0.12, T:0.33
Consensus pattern (331 bp):
TATAATGTACATGCCACTAATCAGTCAAAGTTAGGATGACTTACTGATTCTATGAGTAGGTTTGA
TTTCCATAAAATGTTGGCAAACTCCTTACTTCACGTCCTCTACTTTATTCGACCCTATGCATGAA
AATTTTCACGCGTTAAGTAAAACTTAGTAAGACAAGTAAATAAATCAGAGTGAACTATATCAGTA
GAATATCATAAATCTTTAAAAATTCAAACCGAACTTTCCAAGCCATATTTTTCCTCATCAGAAAT
TTGAAAATCATGGTCTCGTAATTTTATCAAAATCACAATAACCAACATCAACAATATTATACTTT
GCATAT
Found at i:6026846 original size:60 final size:60
Alignment explanation
Indices: 6026703--6026891 Score: 188
Period size: 61 Copynumber: 3.2 Consensus size: 60
6026693 GAACAATACA
* * * * * *
6026703 TAAACGAACATGAAA-ACCTT--AAAATAAATAAACAAAGATGAACACGATAGTAATAATT
1 TAAACGAACA-CAAACACCTTAAAAAATAAATAAACAAACATAAACACTATATTAAAAATT
* * * * * *
6026761 GAAACAAATACAAACACATTCAAAAATAAATAAACAAACATAAACACTACATTAAAAATT
1 TAAACGAACACAAACACCTTAAAAAATAAATAAACAAACATAAACACTATATTAAAAATT
* **
6026821 TAAACGAACGCAAAACACCTTAAAAAATAAATAAATGAACATAAACA-TAATATTAAAAATT
1 TAAACGAACAC-AAACACCTTAAAAAATAAATAAACAAACATAAACACT-ATATTAAAAATT
6026882 TAAACGAACA
1 TAAACGAACA
6026892 TGAACATAAT
Statistics
Matches: 105, Mismatches: 21, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
57 3 0.03
58 11 0.10
60 40 0.38
61 51 0.49
ACGTcount: A:0.60, C:0.14, G:0.06, T:0.20
Consensus pattern (60 bp):
TAAACGAACACAAACACCTTAAAAAATAAATAAACAAACATAAACACTATATTAAAAATT
Found at i:6030109 original size:24 final size:25
Alignment explanation
Indices: 6030063--6030110 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
6030053 AAGTTATTTC
*
6030063 TTTTCTTTTCAAGTTTTCATTTTTA
1 TTTTATTTTCAAGTTTTCATTTTTA
6030088 TTTTATTTT-AAGTTTT-ATTTTTA
1 TTTTATTTTCAAGTTTTCATTTTTA
6030111 ATCATGTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 7 0.32
24 7 0.32
25 8 0.36
ACGTcount: A:0.19, C:0.06, G:0.04, T:0.71
Consensus pattern (25 bp):
TTTTATTTTCAAGTTTTCATTTTTA
Found at i:6030111 original size:13 final size:13
Alignment explanation
Indices: 6030063--6030111 Score: 50
Period size: 13 Copynumber: 3.9 Consensus size: 13
6030053 AAGTTATTTC
* *
6030063 TTTTCTTTTCAAG
1 TTTTATTTTTAAG
6030076 TTTTCATTTTT-A-
1 TTTT-ATTTTTAAG
6030088 TTTTA-TTTTAAG
1 TTTTATTTTTAAG
6030100 TTTTATTTTTAA
1 TTTTATTTTTAA
6030112 TCATGTTAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
10 4 0.13
11 2 0.07
12 9 0.30
13 11 0.37
14 4 0.13
ACGTcount: A:0.20, C:0.06, G:0.04, T:0.69
Consensus pattern (13 bp):
TTTTATTTTTAAG
Found at i:6037384 original size:29 final size:29
Alignment explanation
Indices: 6037352--6037411 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
6037342 ATGAATTCGA
* *
6037352 ATCTCGTC-ATTTATTTTAAAAATATAATT
1 ATCTC-TCTATTTAATTAAAAAATATAATT
*
6037381 ATCTCTCTATTTAATTAAAAAATATATTT
1 ATCTCTCTATTTAATTAAAAAATATAATT
6037410 AT
1 AT
6037412 AATAAATAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 2 0.07
29 25 0.93
ACGTcount: A:0.40, C:0.10, G:0.02, T:0.48
Consensus pattern (29 bp):
ATCTCTCTATTTAATTAAAAAATATAATT
Found at i:6039989 original size:29 final size:29
Alignment explanation
Indices: 6039934--6039989 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
6039924 ACTTACTGAT
*
6039934 AAATAGATATCATTTTCTTAGATAATTGA
1 AAATAGATATCATTTTCTAAGATAATTGA
* *
6039963 AAATAGATGTTATTTCTCTAAGA-AATT
1 AAATAGATATCATTT-TCTAAGATAATT
6039990 TCGAGTCTCA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 17 0.74
30 6 0.26
ACGTcount: A:0.41, C:0.07, G:0.11, T:0.41
Consensus pattern (29 bp):
AAATAGATATCATTTTCTAAGATAATTGA
Found at i:6044361 original size:20 final size:20
Alignment explanation
Indices: 6044336--6044374 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
6044326 TTTAGTTTAT
*
6044336 TAATATTATACTTTAACATA
1 TAATATAATACTTTAACATA
*
6044356 TAATATAATATTTTAACAT
1 TAATATAATACTTTAACAT
6044375 TTGGTTGTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (20 bp):
TAATATAATACTTTAACATA
Found at i:6045745 original size:15 final size:14
Alignment explanation
Indices: 6045727--6045756 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
6045717 ATTGTTTTAT
6045727 AAAATATAAATATTA
1 AAAATATAAA-ATTA
6045742 AAAATATAAAATTA
1 AAAATATAAAATTA
6045756 A
1 A
6045757 GAGGGACCGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
AAAATATAAAATTA
Found at i:6057484 original size:15 final size:14
Alignment explanation
Indices: 6057465--6057514 Score: 50
Period size: 13 Copynumber: 3.6 Consensus size: 14
6057455 AAACACTCAA
6057465 AATATTATTATTTT
1 AATATTATTATTTT
* *
6057479 ATATATT-TCATATT
1 A-ATATTATTATTTT
6057493 AATA-TATTATTTT
1 AATATTATTATTTT
*
6057506 AGTATTATT
1 AATATTATT
6057515 TTAATAAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
12 1 0.04
13 11 0.39
14 11 0.39
15 5 0.18
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (14 bp):
AATATTATTATTTT
Found at i:6057527 original size:30 final size:27
Alignment explanation
Indices: 6057463--6057527 Score: 67
Period size: 30 Copynumber: 2.3 Consensus size: 27
6057453 ATAAACACTC
*
6057463 AAAATATTATTATTTTATATATTTCATA
1 AAAATA-TATTATTTTATATATTTAATA
**
6057491 TTAATATATTATTTTAGTATTATTTTAATA
1 AAAATATATTATTTTA-TA-TA-TTTAATA
6057521 AAAATAT
1 AAAATAT
6057528 TTAGTATTAA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
27 10 0.34
28 6 0.21
29 2 0.07
30 11 0.38
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (27 bp):
AAAATATATTATTTTATATATTTAATA
Found at i:6057602 original size:39 final size:39
Alignment explanation
Indices: 6057559--6057853 Score: 102
Period size: 41 Copynumber: 7.5 Consensus size: 39
6057549 CGATAATTTT
6057559 TATAATATAATATAATATAATATTTTTATTTTAATAATA
1 TATAATATAATATAATATAATATTTTTATTTTAATAATA
* * * * *
6057598 TATAATA-AATTATTATTAAAAACTAATTTTA-TTTATTAATT
1 TATAATATAA-TA-TAAT-ATAA-TATTTTTATTTTAATAATA
* * **
6057639 TCATAAAAATAATATTAT-TGAAT-TGTTAAATATTTAA-AATA
1 T-AT-AATATAATATAATAT-AATAT-TTTTAT-TTTAATAATA
** * *
6057680 TATTCCTTAAAATATAATATAATATTCTTATTTTAAT-AT-
1 TA-T-AATATAATATAATATAATATTTTTATTTTAATAATA
* * * *
6057719 TATAAGTTTATTAGT-TTAATAATATTATTATTTTAATAAGTA
1 TATAA-TATAATA-TAAT-ATAATATTTTTATTTTAATAA-TA
*
6057761 -ATTAATATACT-TAATTATATATTATTTTTATTTTAATAA-A
1 TA-TAATATAATATAA-TATA-A-TATTTTTATTTTAATAATA
* *
6057801 TAT--T-TAATATAATTATAATA-TTTTATTTCAA-AAAA
1 TATAATATAATATAA-TATAATATTTTTATTTTAATAATA
6057836 TATAATA-AATATTAATAT
1 TATAATATAATA-TAATAT
6057854 GTTTATTTGA
Statistics
Matches: 187, Mismatches: 36, Indels: 68
0.64 0.12 0.23
Matches are distributed among these distances:
34 2 0.01
35 14 0.07
36 2 0.01
37 12 0.06
38 20 0.11
39 31 0.17
40 21 0.11
41 42 0.22
42 36 0.19
43 5 0.03
44 2 0.01
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (39 bp):
TATAATATAATATAATATAATATTTTTATTTTAATAATA
Found at i:6057808 original size:42 final size:41
Alignment explanation
Indices: 6057692--6057828 Score: 120
Period size: 42 Copynumber: 3.4 Consensus size: 41
6057682 TTCCTTAAAA
* * * * *
6057692 TATAATATAATATTCTTATTTTAATATTATAAGTTTAT-TAGT
1 TATAATATATTATTTTTATTTTAATA-AATAA-TTAATATAAT
* * *
6057734 T-TAATA-A-TATTATTATTTTAATAAGTAATTAATATACT
1 TATAATATATTATTTTTATTTTAATAAATAATTAATATAAT
* *
6057772 TAATTATATATTATTTTTATTTTAATAAATATTTAATATAAT
1 T-ATAATATATTATTTTTATTTTAATAAATAATTAATATAAT
*
6057814 TATAATATTTTATTT
1 TATAATATATTATTT
6057829 CAAAAAATAT
Statistics
Matches: 78, Mismatches: 12, Indels: 11
0.77 0.12 0.11
Matches are distributed among these distances:
37 4 0.05
38 7 0.09
39 15 0.19
40 5 0.06
41 18 0.23
42 29 0.37
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.55
Consensus pattern (41 bp):
TATAATATATTATTTTTATTTTAATAAATAATTAATATAAT
Found at i:6057972 original size:21 final size:22
Alignment explanation
Indices: 6057930--6057972 Score: 52
Period size: 24 Copynumber: 1.9 Consensus size: 22
6057920 ATTTTAATAT
6057930 TTAAAAAATAATATCATTATTTTG
1 TTAAAAAATAATATC--TATTTTG
*
6057954 TTAATAAATAATATC-ATTT
1 TTAAAAAATAATATCTATTT
6057973 ATTACATTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 4 0.22
24 14 0.78
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.47
Consensus pattern (22 bp):
TTAAAAAATAATATCTATTTTG
Found at i:6066590 original size:33 final size:33
Alignment explanation
Indices: 6066548--6066655 Score: 173
Period size: 33 Copynumber: 3.3 Consensus size: 33
6066538 AGTTTACAAT
* *
6066548 AATTGAAATACTTAAATACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
*
6066581 AATTCAAATACTTAAAAACTTCCAAGTTCTATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
6066614 AATTCAAATACTTAAAAACTTCCAAGTTCGAT-
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
*
6066646 AATTGAAATA
1 AATTCAAATA
6066656 AAGTTTACGA
Statistics
Matches: 70, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
32 9 0.13
33 61 0.87
ACGTcount: A:0.45, C:0.16, G:0.06, T:0.32
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:6066667 original size:21 final size:21
Alignment explanation
Indices: 6066642--6066683 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
6066632 CTTCCAAGTT
6066642 CGATAATTGAAATAAAGTTTA
1 CGATAATTGAAATAAAGTTTA
6066663 CGATAATTGAAATAAAGTTTA
1 CGATAATTGAAATAAAGTTTA
6066684 AAAATAAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.48, C:0.05, G:0.14, T:0.33
Consensus pattern (21 bp):
CGATAATTGAAATAAAGTTTA
Found at i:6070981 original size:32 final size:32
Alignment explanation
Indices: 6070937--6071003 Score: 93
Period size: 32 Copynumber: 2.1 Consensus size: 32
6070927 CCCGAGCCGA
*
6070937 AACCGAAATTAACCTGAA-CCAAAAGCAACCCG
1 AACCGAAATTAA-CTCAACCCAAAAGCAACCCG
6070969 AACC-AAATTTAACTCAACCCAAAAGCAACCCG
1 AACCGAAA-TTAACTCAACCCAAAAGCAACCCG
6071001 AAC
1 AAC
6071004 AGATTGAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
31 7 0.22
32 25 0.78
ACGTcount: A:0.48, C:0.33, G:0.09, T:0.10
Consensus pattern (32 bp):
AACCGAAATTAACTCAACCCAAAAGCAACCCG
Found at i:6071231 original size:9 final size:9
Alignment explanation
Indices: 6071219--6071244 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
6071209 AAAAATAATA
6071219 TAAAACAAC
1 TAAAACAAC
6071228 TAAAACAAC
1 TAAAACAAC
6071237 TAAAACAA
1 TAAAACAA
6071245 ATGAAATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.69, C:0.19, G:0.00, T:0.12
Consensus pattern (9 bp):
TAAAACAAC
Found at i:6076069 original size:21 final size:21
Alignment explanation
Indices: 6076045--6076265 Score: 161
Period size: 21 Copynumber: 10.6 Consensus size: 21
6076035 GATTTACATA
* *
6076045 TTCGCATTTCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
6076066 TTCGCGTTGTGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
** *
6076087 TTCGCGTTGCGATTTTCCAAA
1 TTCGCGTTGCGATAGTCCAAG
6076108 TT--CGTTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
6076127 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
* *
6076150 TT--TGTTGAGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
6076169 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
*
6076192 TT--TGTTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
* * *
6076211 TTCGCGTTGCGATTTATTACAAA
1 TTCGCGTTGCGA--TAGTCCAAG
* *
6076234 TT--CGTTGTGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
6076253 TTCGCGTTGCGAT
1 TTCGCGTTGCGAT
6076266 TTATTCCAAA
Statistics
Matches: 151, Mismatches: 35, Indels: 28
0.71 0.16 0.13
Matches are distributed among these distances:
19 41 0.27
21 84 0.56
23 26 0.17
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.37
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCCAAG
Found at i:6076106 original size:42 final size:42
Alignment explanation
Indices: 6076070--6076293 Score: 353
Period size: 42 Copynumber: 5.4 Consensus size: 42
6076060 TCCAAGTTCG
* *
6076070 CGTTGTGATAGTCGAAGTTCGCGTTGCGA-TT-TTCCAAATT
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
6076110 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
* *
6076152 TGTTGAGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
* *
6076194 TGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTACAAATT
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
* *
6076236 CGTTGTGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
*
6076278 CATTGCGATAGTCCAA
1 CGTTGCGATAGTCCAA
6076294 AATCGCAACG
Statistics
Matches: 169, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
40 27 0.16
41 2 0.01
42 140 0.83
ACGTcount: A:0.23, C:0.18, G:0.22, T:0.37
Consensus pattern (42 bp):
CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
Found at i:6077029 original size:5 final size:5
Alignment explanation
Indices: 6077015--6077051 Score: 67
Period size: 5 Copynumber: 7.6 Consensus size: 5
6077005 CCGCCGGCGC
6077015 CGTC- CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGT
1 CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGT
6077052 GGTCGTGGTC
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 4 0.12
5 28 0.88
ACGTcount: A:0.00, C:0.41, G:0.22, T:0.38
Consensus pattern (5 bp):
CGTCT
Found at i:6077208 original size:21 final size:20
Alignment explanation
Indices: 6077182--6077303 Score: 88
Period size: 21 Copynumber: 5.9 Consensus size: 20
6077172 AATTTGAAAA
*
6077182 ATCGCAACGCGAACTTCGACT
1 ATCGCAA-GCGAACTTGGACT
* *
6077203 ATCGCAA-CGAATTTGGAAT
1 ATCGCAAGCGAACTTGGACT
*
6077222 AAATCGCAAAGCGAACTTTGACT
1 --ATCGC-AAGCGAACTTGGACT
* * *
6077245 ATCGCAA-TGAATTTGGAAT
1 ATCGCAAGCGAACTTGGACT
6077264 AAATCGCAAAGCGAACTTGGACT
1 --ATCGC-AAGCGAACTTGGACT
*
6077287 ATCGCAA-CGAATTTGGA
1 ATCGCAAGCGAACTTGGA
6077304 AAATCGCATT
Statistics
Matches: 79, Mismatches: 14, Indels: 18
0.71 0.13 0.16
Matches are distributed among these distances:
19 26 0.33
20 4 0.05
21 27 0.34
22 4 0.05
23 18 0.23
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.23
Consensus pattern (20 bp):
ATCGCAAGCGAACTTGGACT
Found at i:6077237 original size:42 final size:41
Alignment explanation
Indices: 6077162--6077311 Score: 223
Period size: 42 Copynumber: 3.7 Consensus size: 41
6077152 GATTTTGGAG
* *
6077162 TATCGCAACAAATTT-GAAAAATCGCAACGCGAACTTCGAC
1 TATCGCAACGAATTTGGAAAAATCGCAAAGCGAACTTCGAC
*
6077202 TATCGCAACGAATTTGGAATAAATCGCAAAGCGAACTTTGAC
1 TATCGCAACGAATTTGGAA-AAATCGCAAAGCGAACTTCGAC
* *
6077244 TATCGCAATGAATTTGGAATAAATCGCAAAGCGAACTTGGAC
1 TATCGCAACGAATTTGGAA-AAATCGCAAAGCGAACTTCGAC
6077286 TATCGCAACGAATTTGG-AAAATCGCA
1 TATCGCAACGAATTTGGAAAAATCGCA
6077312 TTGCGATAGT
Statistics
Matches: 102, Mismatches: 6, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
40 22 0.22
41 4 0.04
42 76 0.75
ACGTcount: A:0.39, C:0.20, G:0.19, T:0.23
Consensus pattern (41 bp):
TATCGCAACGAATTTGGAAAAATCGCAAAGCGAACTTCGAC
Found at i:6086077 original size:22 final size:21
Alignment explanation
Indices: 6086033--6086128 Score: 54
Period size: 22 Copynumber: 4.5 Consensus size: 21
6086023 AAATATTAAT
* *
6086033 ATATATATATATAACAATAAA
1 ATATATATATAAAAAAATAAA
*
6086054 ATATAGTATATAAAAAAATCAA
1 ATATA-TATATAAAAAAATAAA
*
6086076 ATGACA-ATA-AATAAAAAT-AA
1 AT-ATATATATAA-AAAAATAAA
* * * * *
6086096 ATAAATAAATAAATATATATAT
1 ATATATATATAAAAAAATA-AA
6086118 ATATATATATA
1 ATATATATATA
6086129 CGTATAATAA
Statistics
Matches: 57, Mismatches: 11, Indels: 13
0.70 0.14 0.16
Matches are distributed among these distances:
19 2 0.04
20 12 0.21
21 16 0.28
22 25 0.44
23 2 0.04
ACGTcount: A:0.64, C:0.03, G:0.02, T:0.31
Consensus pattern (21 bp):
ATATATATATAAAAAAATAAA
Found at i:6086104 original size:18 final size:21
Alignment explanation
Indices: 6086067--6086108 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 21
6086057 TAGTATATAA
6086067 AAAAATCAAATGACAATAAAT
1 AAAAATCAAATGACAATAAAT
6086088 AAAAAT-AAAT-A-AATAAAT
1 AAAAATCAAATGACAATAAAT
6086106 AAA
1 AAA
6086109 TATATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 10 0.48
19 1 0.05
20 4 0.19
21 6 0.29
ACGTcount: A:0.74, C:0.05, G:0.02, T:0.19
Consensus pattern (21 bp):
AAAAATCAAATGACAATAAAT
Found at i:6088113 original size:110 final size:107
Alignment explanation
Indices: 6087845--6088114 Score: 348
Period size: 110 Copynumber: 2.5 Consensus size: 107
6087835 TCCAAGTAAG
* *
6087845 TTGTATTGTTCTGAGTCCAATATCCTTCGTCGTGAAGTTGAAATTGGCTCTG--GAACTGAGAAA
1 TTGTGTTGTCCTGAGTCCAATATCCTTCGT-GTGAAGTTGAAATTGGCTCTGAAGAACTGAGAAA
*
6087908 TTATTTATTGACAGCCAGCCGCCCCTTCGACGTGAAGTTGAGC
65 TTATTTATTGACAACCAGCCGCCCCTTCGACGTGAAGTTGAGC
* * * ** *
6087951 TTGTGTTGTCTTGAGTCCAATATCATTCGTTATGAAGTTGAAATTAACTCTGAATGAAATTGA-A
1 TTGTGTTGTCCTGAGTCCAATATCCTTCG-TGTGAAGTTGAAATTGGCTCTGAA-G-AACTGAGA
* *
6088015 AAGTTATTTATTGACAATCAGCCGCCCCTTCGTCGTGAAGTTGAGC
63 AA-TTATTTATTGACAACCAGCCGCCCCTTCGACGTGAAGTTGAGC
* *
6088061 TTGTGTTGTCCTGGGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGTTCTGAA
1 TTGTGTTGTCCTGAGTCCAATATCCTTCG-TGTGAAGTTGAAATTGGCTCTGAA
6088115 ATTGGGAAGC
Statistics
Matches: 139, Mismatches: 19, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
106 43 0.31
107 1 0.01
109 4 0.03
110 91 0.65
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.35
Consensus pattern (107 bp):
TTGTGTTGTCCTGAGTCCAATATCCTTCGTGTGAAGTTGAAATTGGCTCTGAAGAACTGAGAAAT
TATTTATTGACAACCAGCCGCCCCTTCGACGTGAAGTTGAGC
Found at i:6089264 original size:15 final size:15
Alignment explanation
Indices: 6089242--6089297 Score: 78
Period size: 15 Copynumber: 3.7 Consensus size: 15
6089232 CTTATTTTTC
*
6089242 TTTTCTTTTTTAT-T
1 TTTTCTTTTTTCTCT
6089256 TTGTTCTTTTTTCTCT
1 TT-TTCTTTTTTCTCT
*
6089272 TTTTCTCTTTTCTCT
1 TTTTCTTTTTTCTCT
6089287 TTTTCTTTTTT
1 TTTTCTTTTTT
6089298 TCAATTTAGG
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
14 2 0.05
15 32 0.86
16 3 0.08
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.80
Consensus pattern (15 bp):
TTTTCTTTTTTCTCT
Found at i:6089274 original size:8 final size:7
Alignment explanation
Indices: 6089242--6089297 Score: 67
Period size: 7 Copynumber: 7.6 Consensus size: 7
6089232 CTTATTTTTC
6089242 TTTTCTT
1 TTTTCTT
*
6089249 TTTTATT
1 TTTTCTT
6089256 TTGTTCTT
1 TT-TTCTT
6089264 TTTTCTCT
1 TTTTCT-T
*
6089272 TTTTCTC
1 TTTTCTT
6089279 TTTTCTCT
1 TTTTCT-T
6089287 TTTTCTT
1 TTTTCTT
6089294 TTTT
1 TTTT
6089298 TCAATTTAGG
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
7 23 0.55
8 19 0.45
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.80
Consensus pattern (7 bp):
TTTTCTT
Found at i:6089298 original size:8 final size:8
Alignment explanation
Indices: 6089242--6089299 Score: 50
Period size: 8 Copynumber: 7.6 Consensus size: 8
6089232 CTTATTTTTC
6089242 TTTTC-TT
1 TTTTCTTT
*
6089249 TTTTATTT
1 TTTTCTTT
*
6089257 TGTTC-TT
1 TTTTCTTT
*
6089264 TTTTCTCT
1 TTTTCTTT
*
6089272 TTTTC-TC
1 TTTTCTTT
*
6089279 TTTTCTCT
1 TTTTCTTT
6089287 TTTTCTTT
1 TTTTCTTT
6089295 TTTTC
1 TTTTC
6089300 AATTTAGGGC
Statistics
Matches: 38, Mismatches: 10, Indels: 5
0.72 0.19 0.09
Matches are distributed among these distances:
7 15 0.39
8 23 0.61
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.79
Consensus pattern (8 bp):
TTTTCTTT
Found at i:6099996 original size:22 final size:21
Alignment explanation
Indices: 6099950--6100025 Score: 66
Period size: 22 Copynumber: 3.6 Consensus size: 21
6099940 TAAAATATTG
* *
6099950 AAATATATATATATAACAATA
1 AAATATATATATAAAAAAATA
*
6099971 AAATATAGTATATAAAAAAATC
1 AAATATA-TATATAAAAAAATA
* * *
6099993 AAAT-GACA-ATAAATAAATA
1 AAATATATATATAAAAAAATA
6100012 AATATATATATATA
1 AA-ATATATATATA
6100026 TATATATATA
Statistics
Matches: 42, Mismatches: 9, Indels: 7
0.72 0.16 0.12
Matches are distributed among these distances:
19 11 0.26
20 3 0.07
21 10 0.24
22 18 0.43
ACGTcount: A:0.63, C:0.04, G:0.03, T:0.30
Consensus pattern (21 bp):
AAATATATATATAAAAAAATA
Found at i:6100020 original size:2 final size:2
Alignment explanation
Indices: 6100013--6100043 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
6100003 AAATAAATAA
6100013 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6100044 ATAATATGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6103316 original size:25 final size:25
Alignment explanation
Indices: 6103287--6103351 Score: 71
Period size: 25 Copynumber: 2.6 Consensus size: 25
6103277 TAAATAATTT
6103287 ATATTATTTATTATT-TCATAAAATA
1 ATATTATTTATTATTATCAT-AAATA
* *
6103312 ATATTATTAAATTATTAATCATGAATA
1 ATATTATT-TATTATT-ATCATAAATA
6103339 ATATTATTT-TTAT
1 ATATTATTTATTAT
6103352 ATTTGATATT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
25 12 0.35
26 6 0.18
27 12 0.35
28 4 0.12
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52
Consensus pattern (25 bp):
ATATTATTTATTATTATCATAAATA
Found at i:6103863 original size:31 final size:30
Alignment explanation
Indices: 6103763--6103865 Score: 125
Period size: 31 Copynumber: 3.3 Consensus size: 30
6103753 GTGGAGTAAT
* *
6103763 CATTTTGTTACAAATCGATAACGTTGATAAC
1 CATTTTGTTACAAATCGATAACATTG-TGAC
* *
6103794 CATTTTGTTACAAATCGATAATAATGGTGAC
1 CATTTTGTTACAAATCGATAA-CATTGTGAC
*
6103825 CATTTTGTTACAAATCGATAACATTAGTGAT
1 CATTTTGTTACAAATCGATAACATT-GTGAC
*
6103856 CAATTTGTTA
1 CATTTTGTTA
6103866 TTTTTGAAAC
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
30 2 0.03
31 58 0.94
32 2 0.03
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.38
Consensus pattern (30 bp):
CATTTTGTTACAAATCGATAACATTGTGAC
Found at i:6111927 original size:16 final size:17
Alignment explanation
Indices: 6111906--6111948 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
6111896 AAGTAAAAAT
6111906 AAATATTTAAATTTA-A
1 AAATATTTAAATTTATA
** *
6111922 AAATATGAAAATTTATT
1 AAATATTTAAATTTATA
6111939 AAATATTTAA
1 AAATATTTAA
6111949 TCAAGTAGAG
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (17 bp):
AAATATTTAAATTTATA
Found at i:6127286 original size:20 final size:20
Alignment explanation
Indices: 6127266--6127371 Score: 88
Period size: 20 Copynumber: 5.2 Consensus size: 20
6127256 AAATCGTAAT
*
6127266 GCGATACTGACTATCGCAAT
1 GCGATACTGACTATCGCAAC
* * *
6127286 GCGATACTTACTATCGTAAT
1 GCGATACTGACTATCGCAAC
* *
6127306 GCGATAAT-ACAAAATCGCAAC
1 GCGATACTGAC--TATCGCAAC
* * *
6127327 GAGATACTGACTTTTGCAAC
1 GCGATACTGACTATCGCAAC
* *
6127347 GCGATTCTGACTTTCGCAAC
1 GCGATACTGACTATCGCAAC
6127367 GCGAT
1 GCGAT
6127372 TTACATAGCG
Statistics
Matches: 69, Mismatches: 14, Indels: 6
0.78 0.16 0.07
Matches are distributed among these distances:
19 2 0.03
20 53 0.77
21 12 0.17
22 2 0.03
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (20 bp):
GCGATACTGACTATCGCAAC
Found at i:6127976 original size:19 final size:19
Alignment explanation
Indices: 6127929--6127970 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
6127919 ACGAGATAAT
*
6127929 CGCAACGCGAAATAAAAAG
1 CGCAACGCGAAACAAAAAG
*
6127948 CGCAACGCGAAACAAAAAT
1 CGCAACGCGAAACAAAAAG
6127967 CGCA
1 CGCA
6127971 TTGCGATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.50, C:0.26, G:0.19, T:0.05
Consensus pattern (19 bp):
CGCAACGCGAAACAAAAAG
Done.