Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007882.1 Hibiscus syriacus cultivar Beakdansim tig00110260_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: 1274288
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 5
Found at i:338316 original size:35 final size:35
Alignment explanation
Indices: 338270--338350 Score: 98
Period size: 35 Copynumber: 2.3 Consensus size: 35
338260 AAAAAACTAA
338270 AAAGAA-AAAAAGAA-AAAGAAG-AAGAA-AGAAGAAG
1 AAAGAACAAAAAGAACAAA-AAGAAAGAACA-AA-AAG
338304 AAAGAACAAAAAGAACAAAAAGAAAGAACAAAAAG
1 AAAGAACAAAAAGAACAAAAAGAAAGAACAAAAAG
*
338339 AAGGAACAAAAA
1 AAAGAACAAAAA
338351 AAGGAAAACA
Statistics
Matches: 42, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
34 6 0.14
35 25 0.60
36 10 0.24
37 1 0.02
ACGTcount: A:0.77, C:0.05, G:0.19, T:0.00
Consensus pattern (35 bp):
AAAGAACAAAAAGAACAAAAAGAAAGAACAAAAAG
Found at i:338349 original size:12 final size:13
Alignment explanation
Indices: 338282--338356 Score: 68
Period size: 13 Copynumber: 5.9 Consensus size: 13
338272 AGAAAAAAAG
*
338282 AAAAAGAA-GAAG
1 AAAAAGAAGGAAC
* *
338294 AAAGAAGAAGAAAG
1 AAA-AAGAAGGAAC
338308 AACAAA-AA-GAAC
1 AA-AAAGAAGGAAC
*
338320 AAAAAGAAAGAAC
1 AAAAAGAAGGAAC
338333 AAAAAGAAGGAAC
1 AAAAAGAAGGAAC
338346 AAAAA-AAGGAA
1 AAAAAGAAGGAA
338357 AACAGAAAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
11 3 0.06
12 15 0.28
13 28 0.52
14 7 0.13
15 1 0.02
ACGTcount: A:0.75, C:0.05, G:0.20, T:0.00
Consensus pattern (13 bp):
AAAAAGAAGGAAC
Found at i:339399 original size:30 final size:30
Alignment explanation
Indices: 339364--339427 Score: 94
Period size: 30 Copynumber: 2.1 Consensus size: 30
339354 AATGGATTTA
* *
339364 TTTAGTGACCAAATTATAAA-TTTAGTAAAG
1 TTTAGTGACCAAAGTATAAACTTT-GAAAAG
339394 TTTAGTGACCAAAGTATAAACTTTGAAAAG
1 TTTAGTGACCAAAGTATAAACTTTGAAAAG
339424 TTTA
1 TTTA
339428 TGGAACAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 28 0.90
31 3 0.10
ACGTcount: A:0.42, C:0.08, G:0.14, T:0.36
Consensus pattern (30 bp):
TTTAGTGACCAAAGTATAAACTTTGAAAAG
Found at i:340589 original size:18 final size:18
Alignment explanation
Indices: 340562--340629 Score: 82
Period size: 18 Copynumber: 3.8 Consensus size: 18
340552 TCAGTATTGA
*
340562 AATTTTTGGAATTTCTTG
1 AATTTATGGAATTTCTTG
340580 AATTTATGGAATTTCTTG
1 AATTTATGGAATTTCTTG
* * * *
340598 AAATTATGGAAATTATGG
1 AATTTATGGAATTTCTTG
*
340616 AATTTCTGGAATTT
1 AATTTATGGAATTT
340630 TTGGTATTTG
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 42 1.00
ACGTcount: A:0.31, C:0.04, G:0.18, T:0.47
Consensus pattern (18 bp):
AATTTATGGAATTTCTTG
Found at i:340593 original size:27 final size:27
Alignment explanation
Indices: 340562--340629 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 27
340552 TCAGTATTGA
* * *
340562 AATTTTTGGAATTTCTTGAATTTATGG
1 AATTTTTGGAATTTATGGAAATTATGG
*
340589 AATTTCTT-GAAATTATGGAAATTATGG
1 AATTT-TTGGAATTTATGGAAATTATGG
*
340616 AATTTCTGGAATTT
1 AATTTTTGGAATTT
340630 TTGGTATTTG
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
26 1 0.03
27 30 0.91
28 2 0.06
ACGTcount: A:0.31, C:0.04, G:0.18, T:0.47
Consensus pattern (27 bp):
AATTTTTGGAATTTATGGAAATTATGG
Found at i:340625 original size:9 final size:9
Alignment explanation
Indices: 340562--340629 Score: 64
Period size: 9 Copynumber: 7.6 Consensus size: 9
340552 TCAGTATTGA
*
340562 AATTTTTGG
1 AATTTATGG
* *
340571 AATTTCTTG
1 AATTTATGG
340580 AATTTATGG
1 AATTTATGG
* *
340589 AATTTCTTG
1 AATTTATGG
*
340598 AAATTATGG
1 AATTTATGG
*
340607 AAATTATGG
1 AATTTATGG
*
340616 AATTTCTGG
1 AATTTATGG
340625 AATTT
1 AATTT
340630 TTGGTATTTG
Statistics
Matches: 48, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
9 48 1.00
ACGTcount: A:0.31, C:0.04, G:0.18, T:0.47
Consensus pattern (9 bp):
AATTTATGG
Found at i:341741 original size:38 final size:38
Alignment explanation
Indices: 341687--341807 Score: 179
Period size: 38 Copynumber: 3.2 Consensus size: 38
341677 ACATATGTCC
* * *
341687 TTCGGGACACATATTACATCTTTCAGGATGACAGGTCA
1 TTCGGGACACAAATTACATCCTTCAGGATGATAGGTCA
*
341725 TTCGGGACACAAATTACATCCTTCAGGATGATAGGTCC
1 TTCGGGACACAAATTACATCCTTCAGGATGATAGGTCA
* * *
341763 TTCGGGACACAGATTACATCCTTCGGGATGATAGGTCT
1 TTCGGGACACAAATTACATCCTTCAGGATGATAGGTCA
341801 TTCGGGA
1 TTCGGGA
341808 TATTTATACG
Statistics
Matches: 76, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 76 1.00
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.28
Consensus pattern (38 bp):
TTCGGGACACAAATTACATCCTTCAGGATGATAGGTCA
Found at i:341915 original size:30 final size:30
Alignment explanation
Indices: 341879--341968 Score: 126
Period size: 30 Copynumber: 3.0 Consensus size: 30
341869 GAGTTCTCAG
341879 TAATGTACATGGGCTTATAAAAGATATCAA
1 TAATGTACATGGGCTTATAAAAGATATCAA
* *
341909 TAATGTACATTGGCTTATAAAAGATATCAT
1 TAATGTACATGGGCTTATAAAAGATATCAA
* * * *
341939 TACTGTATATGGGCCTAAAAAAGATATCAA
1 TAATGTACATGGGCTTATAAAAGATATCAA
341969 AAGTATACAT
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 52 1.00
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.31
Consensus pattern (30 bp):
TAATGTACATGGGCTTATAAAAGATATCAA
Found at i:342446 original size:9 final size:9
Alignment explanation
Indices: 342434--342474 Score: 55
Period size: 9 Copynumber: 4.6 Consensus size: 9
342424 CAAATACCAA
342434 AAATTCCAT
1 AAATTCCAT
342443 AAATTCCAT
1 AAATTCCAT
* *
342452 AAATTCAAG
1 AAATTCCAT
*
342461 AAATTCCAA
1 AAATTCCAT
342470 AAATT
1 AAATT
342475 TCAATACTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.51, C:0.17, G:0.02, T:0.29
Consensus pattern (9 bp):
AAATTCCAT
Found at i:342455 original size:18 final size:18
Alignment explanation
Indices: 342425--342474 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
342415 CTTAAATTTC
* * *
342425 AAATACCAAAAATTCCAT
1 AAATTCCAAAAATTCAAG
*
342443 AAATTCCATAAATTCAAG
1 AAATTCCAAAAATTCAAG
342461 AAATTCCAAAAATT
1 AAATTCCAAAAATT
342475 TCAATACTGA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.54, C:0.18, G:0.02, T:0.26
Consensus pattern (18 bp):
AAATTCCAAAAATTCAAG
Found at i:342739 original size:30 final size:30
Alignment explanation
Indices: 342678--342747 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 30
342668 TACAACCATT
* * *
342678 CCTAACTTTTCCAAAATTACCTAATTAGTCC
1 CCTAACTTTTCAAAAATTACCAAAATAGT-C
*
342709 CCTAACTTTTCAAAAATTA-CAAAATGGTC
1 CCTAACTTTTCAAAAATTACCAAAATAGTC
*
342738 CCTAAATTTT
1 CCTAACTTTT
342748 GATAAGGCCT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
29 10 0.29
30 6 0.18
31 18 0.53
ACGTcount: A:0.36, C:0.24, G:0.04, T:0.36
Consensus pattern (30 bp):
CCTAACTTTTCAAAAATTACCAAAATAGTC
Found at i:343722 original size:30 final size:30
Alignment explanation
Indices: 343686--343744 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
343676 TTTGATCCAT
* *
343686 AAACTTT-TCAAAGTTTATACTTTGGTCACC
1 AAACTTTACCAAA-TTTATAATTTGGTCACC
343716 AAACTTTACCAAATTTATAATTTGGTCAC
1 AAACTTTACCAAATTTATAATTTGGTCAC
343745 TAAATAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.34, C:0.19, G:0.08, T:0.39
Consensus pattern (30 bp):
AAACTTTACCAAATTTATAATTTGGTCACC
Found at i:351900 original size:21 final size:20
Alignment explanation
Indices: 351876--351932 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 20
351866 AAGTGAAATA
351876 TTTTTTTCTCATTTCTCATTT
1 TTTTTTTCT-ATTTCTCATTT
* *
351897 TTTTCTTTTTTTTTCTCATTT
1 TTTT-TTTCTATTTCTCATTT
351918 TCTCTTTTTCTATTT
1 T-T-TTTTTCTATTT
351933 GTTTTTTTCT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
21 15 0.52
22 12 0.41
23 2 0.07
ACGTcount: A:0.07, C:0.18, G:0.00, T:0.75
Consensus pattern (20 bp):
TTTTTTTCTATTTCTCATTT
Found at i:351907 original size:8 final size:8
Alignment explanation
Indices: 351894--351972 Score: 51
Period size: 8 Copynumber: 9.9 Consensus size: 8
351884 TCATTTCTCA
351894 TTTTTTTC
1 TTTTTTTC
351902 TTTTTTT-
1 TTTTTTTC
351909 TTCTCATTTTC
1 TT-T--TTTTC
*
351920 TCTTTTTC
1 TTTTTTTC
* *
351928 --TATTTG
1 TTTTTTTC
351934 TTTTTTTC
1 TTTTTTTC
351942 TTTGTTTTC
1 TTT-TTTTC
351951 --TTTTTC
1 TTTTTTTC
351957 TTTTTTTC
1 TTTTTTTC
351965 TGTTTTTT
1 T-TTTTTT
351973 TTCCTTATAT
Statistics
Matches: 56, Mismatches: 5, Indels: 19
0.70 0.06 0.24
Matches are distributed among these distances:
6 9 0.16
7 3 0.05
8 27 0.48
9 11 0.20
10 5 0.09
11 1 0.02
ACGTcount: A:0.03, C:0.13, G:0.04, T:0.81
Consensus pattern (8 bp):
TTTTTTTC
Found at i:351937 original size:28 final size:26
Alignment explanation
Indices: 351876--351963 Score: 95
Period size: 28 Copynumber: 3.2 Consensus size: 26
351866 AAGTGAAATA
*
351876 TTTTTTTCTCATTTCTCATTTTTTTCTT
1 TTTTTTTCTCATTT-TC-TCTTTTTCTT
351904 TTTTTTTCTCATTTTCTCTTTTTCTAT
1 TTTTTTTCTCATTTTCTCTTTTTCT-T
* * *
351931 TTGTTTTTTTCTTTGTTTTCTTTTTCTT
1 TT-TTTTTCTCATT-TTCTCTTTTTCTT
351959 TTTTT
1 TTTTT
351964 CTGTTTTTTT
Statistics
Matches: 53, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
26 8 0.15
27 8 0.15
28 26 0.49
29 11 0.21
ACGTcount: A:0.05, C:0.15, G:0.02, T:0.78
Consensus pattern (26 bp):
TTTTTTTCTCATTTTCTCTTTTTCTT
Found at i:351956 original size:37 final size:38
Alignment explanation
Indices: 351894--351974 Score: 103
Period size: 37 Copynumber: 2.1 Consensus size: 38
351884 TCATTTCTCA
*
351894 TTTTTTTCTTTTTTTTTCTCATTTTCTCTTTTTCTATTT
1 TTTTTTTCTTTTGTTTTCT-ATTTTCTCTTTTTCTATTT
* *
351933 GTTTTTTTC-TTTGTTTTCT-TTTTCTTTTTTTCTGTTT
1 -TTTTTTTCTTTTGTTTTCTATTTTCTCTTTTTCTATTT
351970 TTTTT
1 TTTTT
351975 CCTTATATTA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
36 5 0.13
37 16 0.42
39 9 0.24
40 8 0.21
ACGTcount: A:0.02, C:0.12, G:0.04, T:0.81
Consensus pattern (38 bp):
TTTTTTTCTTTTGTTTTCTATTTTCTCTTTTTCTATTT
Found at i:351970 original size:15 final size:14
Alignment explanation
Indices: 351896--351974 Score: 67
Period size: 14 Copynumber: 5.7 Consensus size: 14
351886 ATTTCTCATT
351896 TTTTTC-TTTTTT-
1 TTTTTCTTTTTTTC
* * *
351908 TTTCTCATTTTCTC
1 TTTTTCTTTTTTTC
*
351922 TTTTTCTATTTGTT-
1 TTTTTCT-TTTTTTC
351936 TTTTTCTTTGTTTTC
1 TTTTTCTTT-TTTTC
351951 TTTTTCTTTTTTTC
1 TTTTTCTTTTTTTC
351965 TGTTTT-TTTT
1 T-TTTTCTTTT
351975 CCTTATATTA
Statistics
Matches: 54, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
12 5 0.09
13 7 0.13
14 25 0.46
15 17 0.31
ACGTcount: A:0.03, C:0.13, G:0.04, T:0.81
Consensus pattern (14 bp):
TTTTTCTTTTTTTC
Found at i:354723 original size:45 final size:45
Alignment explanation
Indices: 354654--354912 Score: 378
Period size: 45 Copynumber: 5.8 Consensus size: 45
354644 ATATAAATTT
* * *
354654 CTTATCATTTAT-CCTATAAGCTCGTAAGCTTATTATACCAATATA
1 CTTACCATTTATACC-ATAAGCTCGTAAGCTTATTTTACCCATATA
* *
354699 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTTATACCATAAGCTCGTAAGCTTATTTTACCCATATA
* *
354744 CTTACCATTTGTACCATAAGCTTGTAAGCTTATTTTACCCATATA
1 CTTACCATTTATACCATAAGCTCGTAAGCTTATTTTACCCATATA
* * *
354789 CTTATCATTTGTACCATAAGCTCGTAAGCTTATTTTACCCATATG
1 CTTACCATTTATACCATAAGCTCGTAAGCTTATTTTACCCATATA
*
354834 CTTACCATTTGTACCATAAGCTCGTAAGCTTATTTTACCCATATA
1 CTTACCATTTATACCATAAGCTCGTAAGCTTATTTTACCCATATA
* *
354879 CTTGCCA-TTATTCCATAAGCTCGTAAGCTTATTT
1 CTTACCATTTATACCATAAGCTCGTAAGCTTATTT
354913 GCATGGTTAC
Statistics
Matches: 199, Mismatches: 14, Indels: 3
0.92 0.06 0.01
Matches are distributed among these distances:
44 25 0.13
45 172 0.86
46 2 0.01
ACGTcount: A:0.29, C:0.22, G:0.09, T:0.40
Consensus pattern (45 bp):
CTTACCATTTATACCATAAGCTCGTAAGCTTATTTTACCCATATA
Found at i:354785 original size:25 final size:25
Alignment explanation
Indices: 354757--354876 Score: 77
Period size: 25 Copynumber: 5.2 Consensus size: 25
354747 ACCATTTGTA
354757 CCATAAGCTTGTAAGCTTATTTTAC
1 CCATAAGCTTGTAAGCTTATTTTAC
*
354782 CCATATA-C-T-T-A--TCATTTGTA-
1 CCATA-AGCTTGTAAGCTTATTT-TAC
*
354802 CCATAAGCTCGTAAGCTTATTTTAC
1 CCATAAGCTTGTAAGCTTATTTTAC
* *
354827 CCATATGC-T-T-A-C-CATTTGTA-
1 CCATAAGCTTGTAAGCTTATTT-TAC
*
354847 CCATAAGCTCGTAAGCTTATTTTAC
1 CCATAAGCTTGTAAGCTTATTTTAC
354872 CCATA
1 CCATA
354877 TACTTGCCAT
Statistics
Matches: 70, Mismatches: 9, Indels: 32
0.63 0.08 0.29
Matches are distributed among these distances:
19 1 0.01
20 22 0.31
21 5 0.07
22 4 0.06
23 4 0.06
24 6 0.09
25 27 0.39
26 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.10, T:0.38
Consensus pattern (25 bp):
CCATAAGCTTGTAAGCTTATTTTAC
Found at i:355061 original size:40 final size:40
Alignment explanation
Indices: 355017--355098 Score: 137
Period size: 40 Copynumber: 2.0 Consensus size: 40
355007 ACCGTAGTGC
* *
355017 TACACATAAGGTCGTGCTCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
*
355057 TACACATAAGGTCGTGCCCATCATATACACCAAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
355097 TA
1 TA
355099 TAAACGTACA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.26
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
Found at i:361360 original size:27 final size:28
Alignment explanation
Indices: 361322--361379 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 28
361312 CATGTGACTT
361322 ACACAGTAAAG-ATTCTATTAT-GATGTG
1 ACACAGTAAAGAATTC-ATTATAGATGTG
*
361349 ACACTGTAAAGAATTCATTATAAGATGTG
1 ACACAGTAAAGAATTCATTAT-AGATGTG
361378 AC
1 AC
361380 TTTCTCGACT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
27 15 0.56
28 4 0.15
29 8 0.30
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.31
Consensus pattern (28 bp):
ACACAGTAAAGAATTCATTATAGATGTG
Found at i:362168 original size:131 final size:130
Alignment explanation
Indices: 361934--362409 Score: 686
Period size: 131 Copynumber: 3.6 Consensus size: 130
361924 CACGCAAAAT
* * * *
361934 GTATCGATACACATATATAAAGTATTGGTACTTATAATTTCGAAAACTATTACTTTAAAGTAATA
1 GTATCGATACTCATATATAAAGTATCGATACTTATAATTT-AAAAACTATTACTTTAAAGTAATA
* *
361999 GGTAAATTAACAATGTACACGGTAAACGCTTCTACCGGTATAATGAAAATAGGCGTAAATGTCCA
65 GGTAAATTAACAATGTACACGATAAACGTTTCTACCGGTATAATGAAAATAGGCGTAAATGTCCA
362064 A
130 A
*
362065 GTATCGATACTCATATACAAAGTATCGATACTTATAATTTAAAAATCTATTACTTTAAAGTAATA
1 GTATCGATACTCATATATAAAGTATCGATACTTATAATTTAAAAA-CTATTACTTTAAAGTAATA
* *
362130 AGTAAATTAACAATGTACACGTTAAACGTTTCTACCGGTATAATGAAAATAGGCGTAAATGTCCA
65 GGTAAATTAACAATGTACACGATAAACGTTTCTACCGGTATAATGAAAATAGGCGTAAATGTCCA
362195 A
130 A
* * ** *
362196 GTATTGATACTCATATATAAAGTATCAATACTTATAATTTTGAAACTTATTATTTTAAAGTAATA
1 GTATCGATACTCATATATAAAGTATCGATACTTATAATTTAAAAAC-TATTACTTTAAAGTAATA
* * *
362261 GGTAAATTAACAATGTACACGATAAACATTTCTATCGGTATAATGAAAATAGGCGTAAATGTACA
65 GGTAAATTAACAATGTACACGATAAACGTTTCTACCGGTATAATGAAAATAGGCGTAAATGTCCA
362326 A
130 A
* * * * *
362327 ATATCGATACT-GTCATAT-AAGTATCGATACTTATAATTTCGAAACCTATAACTTTAAAGTAAT
1 GTATCGATACTCAT-ATATAAAGTATCGATACTTATAATTT-AAAAACTATTACTTTAAAGTAAT
*
362390 AGGTAGATTAACAATGTACA
64 AGGTAAATTAACAATGTACA
362410 TGGTAATATG
Statistics
Matches: 312, Mismatches: 29, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
130 60 0.19
131 252 0.81
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.33
Consensus pattern (130 bp):
GTATCGATACTCATATATAAAGTATCGATACTTATAATTTAAAAACTATTACTTTAAAGTAATAG
GTAAATTAACAATGTACACGATAAACGTTTCTACCGGTATAATGAAAATAGGCGTAAATGTCCAA
Found at i:368088 original size:27 final size:27
Alignment explanation
Indices: 368050--368149 Score: 166
Period size: 27 Copynumber: 3.7 Consensus size: 27
368040 TTTAAAGTTT
* *
368050 TCGAGTTCGAGTCGAGCTCAGCAATAC
1 TCGAGTTCGACTCGAGCTCAACAATAC
*
368077 TCGAGTTCGAGTCGAGCTCAACAATAC
1 TCGAGTTCGACTCGAGCTCAACAATAC
368104 TCGAGTTCGACTCGAGCTCAACAATAC
1 TCGAGTTCGACTCGAGCTCAACAATAC
368131 TCGAGTTCGACTCG-GCTCA
1 TCGAGTTCGACTCGAGCTCA
368150 TTTAACAAAC
Statistics
Matches: 71, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
26 5 0.07
27 66 0.93
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (27 bp):
TCGAGTTCGACTCGAGCTCAACAATAC
Found at i:368264 original size:19 final size:18
Alignment explanation
Indices: 368215--368278 Score: 62
Period size: 19 Copynumber: 3.5 Consensus size: 18
368205 TGGTTTTCAA
368215 CCGGTTCACGG-TCCAGT
1 CCGGTTCACGGTTCCAGT
368232 CCGGTTCAAACGGTTCACAGT
1 CCGGTTC--ACGGTTC-CAGT
*
368253 -CGGTTCAGCGGTTCC-TT
1 CCGGTTCA-CGGTTCCAGT
368270 CCGGTTCAC
1 CCGGTTCAC
368279 TAGTAGCGGT
Statistics
Matches: 40, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
17 9 0.22
18 9 0.22
19 10 0.25
20 8 0.20
21 4 0.10
ACGTcount: A:0.14, C:0.33, G:0.27, T:0.27
Consensus pattern (18 bp):
CCGGTTCACGGTTCCAGT
Found at i:369544 original size:24 final size:24
Alignment explanation
Indices: 369512--369560 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
369502 GAAAAATGAC
369512 GAGTTTGCAACATATGAATAATCT
1 GAGTTTGCAACATATGAATAATCT
369536 GAGTTTGCAACATATGAATAATCT
1 GAGTTTGCAACATATGAATAATCT
369560 G
1 G
369561 GTGATCATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (24 bp):
GAGTTTGCAACATATGAATAATCT
Found at i:384183 original size:16 final size:16
Alignment explanation
Indices: 384155--384197 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
384145 AAAATATCCC
*
384155 AAAAAATAAAAAATAA
1 AAAAAATACAAAATAA
*
384171 AATAAATACAAAATAA
1 AAAAAATACAAAATAA
384187 AAAAAAT-CAAA
1 AAAAAATACAAA
384198 TATGTTAACT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
15 4 0.17
16 20 0.83
ACGTcount: A:0.81, C:0.05, G:0.00, T:0.14
Consensus pattern (16 bp):
AAAAAATACAAAATAA
Found at i:384279 original size:9 final size:9
Alignment explanation
Indices: 384265--384316 Score: 52
Period size: 9 Copynumber: 5.8 Consensus size: 9
384255 ATAAACAAAG
384265 CAAAAAAAA
1 CAAAAAAAA
384274 CAAAAAAAA
1 CAAAAAAAA
* *
384283 CAAGTATAAA
1 CAA-AAAAAA
384293 CAAAAAAAA
1 CAAAAAAAA
*
384302 -ATAAAAAA
1 CAAAAAAAA
*
384310 TAAAAAA
1 CAAAAAA
384317 TATATAAATG
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
8 7 0.20
9 21 0.60
10 7 0.20
ACGTcount: A:0.83, C:0.08, G:0.02, T:0.08
Consensus pattern (9 bp):
CAAAAAAAA
Found at i:384314 original size:14 final size:14
Alignment explanation
Indices: 384226--384318 Score: 50
Period size: 14 Copynumber: 6.4 Consensus size: 14
384216 GAAATAAATC
*
384226 AAATAAA-ATAAAAG
1 AAATAAACA-AAAAA
*
384240 AAATAAA-AAAATA
1 AAATAAACAAAAAA
*
384253 ATATAAACAAAGCAAA
1 AAATAAACAAA--AAA
*
384269 AAA-AACAAAAAAAA
1 AAATAA-ACAAAAAA
384283 CAAGTATAAACAAAAAA
1 -AA--ATAAACAAAAAA
384300 AAATAAA-AAATAAA
1 AAATAAACAAA-AAA
384314 AAATA
1 AAATA
384319 TATAAATGTT
Statistics
Matches: 63, Mismatches: 7, Indels: 18
0.72 0.08 0.20
Matches are distributed among these distances:
13 12 0.19
14 27 0.43
15 4 0.06
16 10 0.16
17 8 0.13
18 2 0.03
ACGTcount: A:0.80, C:0.05, G:0.03, T:0.12
Consensus pattern (14 bp):
AAATAAACAAAAAA
Found at i:384315 original size:33 final size:35
Alignment explanation
Indices: 384230--384324 Score: 94
Period size: 32 Copynumber: 2.8 Consensus size: 35
384220 TAAATCAAAT
384230 AAAATAAAAGAAATAAAAAAATAATATAAACAAAGCAA
1 AAAAT-AAA-AAATAAAAAAATAATATAAACAAA-CAA
* * *
384268 AAAA-AACAAA-AAAAACA-AGTATAAACAAA-AA
1 AAAATAAAAAATAAAAAAATAATATAAACAAACAA
384299 AAAATAAAAAAT-AAAAAAT-ATATAAA
1 AAAATAAAAAATAAAAAAATAATATAAA
384325 TGTTAGGTAA
Statistics
Matches: 48, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
31 6 0.12
32 16 0.33
33 11 0.23
34 6 0.12
35 3 0.06
36 2 0.04
38 4 0.08
ACGTcount: A:0.79, C:0.05, G:0.03, T:0.13
Consensus pattern (35 bp):
AAAATAAAAAATAAAAAAATAATATAAACAAACAA
Found at i:384391 original size:15 final size:15
Alignment explanation
Indices: 384368--384406 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
384358 AGAAGAAACC
*
384368 AAAAAAAAAAATAAT
1 AAAAAAAAAAATAAA
*
384383 AAAACAAAAAATAAA
1 AAAAAAAAAAATAAA
384398 AAAATAAAA
1 AAAA-AAAA
384407 TACCTAATAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 17 0.85
16 3 0.15
ACGTcount: A:0.87, C:0.03, G:0.00, T:0.10
Consensus pattern (15 bp):
AAAAAAAAAAATAAA
Found at i:384392 original size:20 final size:20
Alignment explanation
Indices: 384367--384406 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
384357 GAGAAGAAAC
384367 CAAAAAA-AAAAATAATAAAA
1 CAAAAAATAAAAA-AATAAAA
384387 CAAAAAATAAAAAAATAAAA
1 CAAAAAATAAAAAAATAAAA
384407 TACCTAATAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.85, C:0.05, G:0.00, T:0.10
Consensus pattern (20 bp):
CAAAAAATAAAAAAATAAAA
Found at i:384516 original size:2 final size:2
Alignment explanation
Indices: 384509--384594 Score: 83
Period size: 2 Copynumber: 45.5 Consensus size: 2
384499 ATGTGGGGTA
384509 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * * *
384550 AT TT A- AT AA AT A- AA AT AA AT AA AC A- 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
384589 A- AT AT A
1 AT AT AT A
384595 AACATATAAA
Statistics
Matches: 70, Mismatches: 9, Indels: 10
0.79 0.10 0.11
Matches are distributed among these distances:
1 5 0.07
2 65 0.93
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (2 bp):
AT
Found at i:384556 original size:7 final size:7
Alignment explanation
Indices: 384507--384603 Score: 81
Period size: 8 Copynumber: 13.4 Consensus size: 7
384497 GAATGTGGGG
384507 TAATATA
1 TAATATA
384514 TATATATA
1 TA-ATATA
384522 TATATATA
1 TA-ATATA
384530 TATATATA
1 TA-ATATA
384538 TATATATA
1 TA-ATATA
*
384546 TAATATT
1 TAATATA
*
384553 TAATAAA
1 TAATATA
*
384560 TAAAATA
1 TAATATA
*
384567 -AATAAA
1 TAATATA
*
384573 CAATATA
1 TAATATA
384580 TATATATA
1 TA-ATATA
384588 TAATATA
1 TAATATA
*
384595 -AACATA
1 TAATATA
384601 TAA
1 TAA
384604 AAACAAAAAA
Statistics
Matches: 76, Mismatches: 10, Indels: 8
0.81 0.11 0.09
Matches are distributed among these distances:
6 9 0.12
7 29 0.38
8 38 0.50
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (7 bp):
TAATATA
Found at i:384624 original size:66 final size:66
Alignment explanation
Indices: 384554--384705 Score: 159
Period size: 66 Copynumber: 2.3 Consensus size: 66
384544 TATAATATTT
* * *
384554 AATAAATAAAAT-AAATAAA-C-AATATATATATATATAATATAAACATATAAAAACAAAAAAAC
1 AATAAATAAAATGAAATAAATCAAATAAAAATATATAT-ATATAAA-ATAAAAAAACAAAAAAA-
384616 TAAG
63 TAAG
* * *
384620 AATAAAT-AAATGGAATAAATGAAATAAAAATATATATATATAAAATAAAAAAATAAAAAAATAA
1 AATAAATAAAATGAAATAAATCAAATAAAAATATATATATATAAAATAAAAAAACAAAAAAATAA
*
384684 T
66 G
* *
384685 ATATACATAAAATGGAATAAA
1 A-ATAAATAAAATGAAATAAA
384706 ATAAAAAAAT
Statistics
Matches: 73, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
65 8 0.11
66 33 0.45
67 19 0.26
68 13 0.18
ACGTcount: A:0.68, C:0.03, G:0.04, T:0.24
Consensus pattern (66 bp):
AATAAATAAAATGAAATAAATCAAATAAAAATATATATATATAAAATAAAAAAACAAAAAAATAA
G
Found at i:384663 original size:34 final size:34
Alignment explanation
Indices: 384625--384717 Score: 102
Period size: 34 Copynumber: 2.7 Consensus size: 34
384615 CTAAGAATAA
* *
384625 ATAAATGGAATAAATGAAATAAA-AATATATATAT
1 ATAAATGGAATAAAT-AAAAAAATAATATATACAT
* *
384659 ATAAAAT-AAAAAAATAAAAAAATAATATATACAT
1 AT-AAATGGAATAAATAAAAAAATAATATATACAT
384693 A-AAATGGAATAAAATAAAAAAATAA
1 ATAAATGGAAT-AAATAAAAAAATAA
384718 AAACATGGAA
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
32 4 0.08
33 8 0.16
34 33 0.67
35 4 0.08
ACGTcount: A:0.70, C:0.01, G:0.05, T:0.24
Consensus pattern (34 bp):
ATAAATGGAATAAATAAAAAAATAATATATACAT
Found at i:384672 original size:8 final size:8
Alignment explanation
Indices: 384661--384720 Score: 50
Period size: 8 Copynumber: 7.2 Consensus size: 8
384651 ATATATATAT
384661 AAAATAAA
1 AAAATAAA
384669 AAAATAAA
1 AAAATAAA
384677 AAAAT-AA
1 AAAATAAA
* * *
384684 TATATACAT
1 AAAATA-AA
*
384693 AAAATGGAAT
1 AAAAT--AAA
384703 AAAATAAA
1 AAAATAAA
384711 AAAATAAA
1 AAAATAAA
384719 AA
1 AA
384721 CATGGAAACA
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
7 5 0.12
8 25 0.60
9 4 0.10
10 7 0.17
11 1 0.02
ACGTcount: A:0.77, C:0.02, G:0.03, T:0.18
Consensus pattern (8 bp):
AAAATAAA
Found at i:384695 original size:32 final size:33
Alignment explanation
Indices: 384645--384717 Score: 105
Period size: 34 Copynumber: 2.2 Consensus size: 33
384635 TAAATGAAAT
*
384645 AAAAAT-ATATATATATAAAAT-AAAAAAATAA
1 AAAAATAATATATACATAAAATGAAAAAAATAA
*
384676 AAAAATAATATATACATAAAATGGAATAAAATAA
1 AAAAATAATATATACATAAAAT-GAAAAAAATAA
384710 AAAAATAA
1 AAAAATAA
384718 AAACATGGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
31 6 0.16
32 14 0.38
34 17 0.46
ACGTcount: A:0.73, C:0.01, G:0.03, T:0.23
Consensus pattern (33 bp):
AAAAATAATATATACATAAAATGAAAAAAATAA
Found at i:385709 original size:2 final size:2
Alignment explanation
Indices: 385702--385730 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
385692 AATGAGAATA
385702 AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
385731 GGTTAGAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:386782 original size:86 final size:85
Alignment explanation
Indices: 386616--387227 Score: 664
Period size: 85 Copynumber: 7.2 Consensus size: 85
386606 GAGATAGCTT
* * * * * * *
386616 TTCTCGACTTAAGCTATGTTGTAAATCTGATATGCCATTGAGCTGAATGGAATCGAACTCGAAGG
1 TTCTCGCCTTGAGCTATGCTATAAATTTGATATGCCTTTGAGCTGAATGTAATCGAACTCGAAGG
* *
386681 TATTTGTTGACAGATAGCCC
66 TCTTTGTTGACAGATAACCC
* ** *
386701 TTATTACCTTGAGCTATGCTATAAATTTGATATGCCTTTTGAGCTAAATGTAATCGAACTCGAAG
1 TTCTCGCCTTGAGCTATGCTATAAATTTGATATGCC-TTTGAGCTGAATGTAATCGAACTCGAAG
* * *
386766 GTCTTTGCTAATAGATAACCC
65 GTCTTTGTTGACAGATAACCC
* * *
386787 TTCTCGCCTTGAGTTATGCTGT--A----ATATGCCTTTGAGCTGAATGTAATCAAACTCGAAGG
1 TTCTCGCCTTGAGCTATGCTATAAATTTGATATGCCTTTGAGCTGAATGTAATCGAACTCGAAGG
* *
386846 TCTTTAGGTGACAAATAACCC
66 TCTTT-GTTGACAGATAACCC
* * * * * *
386867 TTATCGCCTTTAGTTATGC-AGTAAATTGGATATGCCTTTGAGCAGAATGTAATCGAACTCAAAG
1 TTCTCGCCTTGAGCTATGCTA-TAAATTTGATATGCCTTTGAGCTGAATGTAATCGAACTCGAAG
* * *
386931 GTCTTTTGTTGACAGTTAGCCT
65 GTC-TTTGTTGACAGATAACCC
* * * * *
386953 TTCTCGCCTTGAGCTATGATGTAAATTTGATGTGCCTTTCAGCTGAGTGTAATCGAACTCGAAGG
1 TTCTCGCCTTGAGCTATGCTATAAATTTGATATGCCTTTGAGCTGAATGTAATCGAACTCGAAGG
* * **
387018 -CATTGGTTGACAAATAGGCC
66 TC-TTTGTTGACAGATAACCC
* * * *
387038 TTCTCGCCTTGAGCTATGCTATAAATTTGATGTGCCTTTGAGCTGAGTGTAATTGAACTTGAAGG
1 TTCTCGCCTTGAGCTATGCTATAAATTTGATATGCCTTTGAGCTGAATGTAATCGAACTCGAAGG
* *
387103 TCTTTGCTGTCAGATAACCC
66 TCTTTGTTGACAGATAACCC
* * * *
387123 ATCTCGCCTTGAGTTATGCTATAAATTGGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGG
1 TTCTCGCCTTGAGCTATGCTATAAATTTGATATGCCTTTGAGCTGAATGTAATCGAACTCGAAGG
* *
387188 TCTTGGTTGATAGATAACCC
66 TCTTTGTTGACAGATAACCC
387208 TTCTCGCCTTGAGCTATGCT
1 TTCTCGCCTTGAGCTATGCT
387228 GCCAATATTT
Statistics
Matches: 437, Mismatches: 78, Indels: 24
0.81 0.14 0.04
Matches are distributed among these distances:
79 32 0.07
80 36 0.08
82 1 0.00
84 1 0.00
85 207 0.47
86 157 0.36
87 3 0.01
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.34
Consensus pattern (85 bp):
TTCTCGCCTTGAGCTATGCTATAAATTTGATATGCCTTTGAGCTGAATGTAATCGAACTCGAAGG
TCTTTGTTGACAGATAACCC
Found at i:391566 original size:21 final size:18
Alignment explanation
Indices: 391535--391581 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 18
391525 GAAACAAATC
391535 AAATAAAATAAATACAAAA
1 AAATAAAAT-AATACAAAA
*
391554 ACAATAGAAATAATGCAAAA
1 A-AATA-AAATAATACAAAA
391574 AAATAAAA
1 AAATAAAA
391582 GAAAACAAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 3 0.12
19 5 0.20
20 13 0.52
21 4 0.16
ACGTcount: A:0.74, C:0.06, G:0.04, T:0.15
Consensus pattern (18 bp):
AAATAAAATAATACAAAA
Found at i:391677 original size:8 final size:8
Alignment explanation
Indices: 391666--391700 Score: 54
Period size: 8 Copynumber: 4.4 Consensus size: 8
391656 ATATAAAGAG
391666 AAAAAATA
1 AAAAAATA
391674 AAAAAA-A
1 AAAAAATA
391681 TAAAAAATA
1 -AAAAAATA
391690 AAAAAATA
1 AAAAAATA
391698 AAA
1 AAA
391701 TACGTAATAC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
7 1 0.04
8 23 0.92
9 1 0.04
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (8 bp):
AAAAAATA
Found at i:391687 original size:16 final size:15
Alignment explanation
Indices: 391666--391700 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
391656 ATATAAAGAG
391666 AAAAAATAAAAAAAAT
1 AAAAAAT-AAAAAAAT
391682 AAAAAATAAAAAAAT
1 AAAAAATAAAAAAAT
391697 AAAA
1 AAAA
391701 TACGTAATAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 12 0.63
16 7 0.37
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (15 bp):
AAAAAATAAAAAAAT
Found at i:391810 original size:2 final size:2
Alignment explanation
Indices: 391803--391880 Score: 58
Period size: 2 Copynumber: 41.5 Consensus size: 2
391793 ATGTGGGGTA
* *
391803 AT AT AT AT AT GT AT AT AT AT AT AT AT A- AT AT A- AT AT TT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * *
391842 AT AA AT A- AA AT AA AT AA AC A- 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
391881 AACATATAAA
Statistics
Matches: 60, Mismatches: 11, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
1 5 0.08
2 55 0.92
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.41
Consensus pattern (2 bp):
AT
Found at i:392027 original size:13 final size:13
Alignment explanation
Indices: 392011--392066 Score: 50
Period size: 13 Copynumber: 4.5 Consensus size: 13
392001 GAAATAAAGA
392011 AAAAATAAATC-AT
1 AAAAATAAA-CAAT
392024 AAAAATAAACAAT
1 AAAAATAAACAAT
392037 --AAA-AAACAA-
1 AAAAATAAACAAT
*
392046 AACAAATAAAAAAT
1 AA-AAATAAACAAT
392060 AAAAATA
1 AAAAATA
392067 GTACTTAAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 12
0.73 0.02 0.24
Matches are distributed among these distances:
10 6 0.17
11 3 0.08
12 4 0.11
13 21 0.58
14 2 0.06
ACGTcount: A:0.79, C:0.07, G:0.00, T:0.14
Consensus pattern (13 bp):
AAAAATAAACAAT
Found at i:392055 original size:16 final size:15
Alignment explanation
Indices: 392030--392063 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
392020 TCATAAAAAT
392030 AAACAATAAAAAACA
1 AAACAATAAAAAACA
*
392045 AAACAAATAAAAAATA
1 AAAC-AATAAAAAACA
392061 AAA
1 AAA
392064 ATAGTACTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.82, C:0.09, G:0.00, T:0.09
Consensus pattern (15 bp):
AAACAATAAAAAACA
Found at i:392312 original size:33 final size:34
Alignment explanation
Indices: 392257--392338 Score: 96
Period size: 34 Copynumber: 2.4 Consensus size: 34
392247 GGAATAAATG
* *
392257 AAATAAATAAATATATATATATATATATAAT-GAA-A
1 AAATAAA-AAA-ATA-ATATATACATAAAATGGAATA
392292 AAATGAAAAAAATAATATATACATAAAATGGAATA
1 AAAT-AAAAAAATAATATATACATAAAATGGAATA
392327 AAATAAAAAAAT
1 AAATAAAAAAAT
392339 TAAAACGTGG
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
33 13 0.31
34 14 0.33
35 12 0.29
36 3 0.07
ACGTcount: A:0.67, C:0.01, G:0.05, T:0.27
Consensus pattern (34 bp):
AAATAAAAAAATAATATATACATAAAATGGAATA
Found at i:395008 original size:50 final size:49
Alignment explanation
Indices: 394880--395008 Score: 143
Period size: 50 Copynumber: 2.6 Consensus size: 49
394870 TATAGCAATT
* * * *
394880 AACACATATTTACATCGATGTAAGTCTTTACATCTCTCAACCTAAAAATA
1 AACACATATTTACACCGA-GTAAATATGTACATCTCTCAACCTAAAAATA
* * * *
394930 AACATATACTTACACCG-GTATAAGTATGTATATCTCTCAACTTAAAAATA
1 AACACATATTTACACCGAGTA-AA-TATGTACATCTCTCAACCTAAAAATA
394980 AACACATATTTACACCGACGTAAATATGT
1 AACACATATTTACACCGA-GTAAATATGT
395009 TTTAATATAT
Statistics
Matches: 65, Mismatches: 10, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
48 3 0.05
49 1 0.02
50 56 0.86
51 2 0.03
52 3 0.05
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.31
Consensus pattern (49 bp):
AACACATATTTACACCGAGTAAATATGTACATCTCTCAACCTAAAAATA
Found at i:395491 original size:21 final size:21
Alignment explanation
Indices: 395465--395509 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
395455 TTAAAAATGT
*
395465 TAAAAATATTAATATTTTAGA
1 TAAAAATAATAATATTTTAGA
395486 TAAAAATAATAATATTTTAGA
1 TAAAAATAATAATATTTTAGA
395507 TAA
1 TAA
395510 TATTTTATTA
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:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (21 bp):
TAAAAATAATAATATTTTAGA
Found at i:396606 original size:30 final size:30
Alignment explanation
Indices: 396572--396634 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
396562 GCTGTCTGAC
396572 CTTTGTTTTGGCTATTTTATGTCTAAGTTT
1 CTTTGTTTTGGCTATTTTATGTCTAAGTTT
396602 CTTTGTTTTGGCTATTTTATGTCTAAGTTT
1 CTTTGTTTTGGCTATTTTATGTCTAAGTTT
396632 CTT
1 CTT
396635 ATTTTTAGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.13, C:0.11, G:0.16, T:0.60
Consensus pattern (30 bp):
CTTTGTTTTGGCTATTTTATGTCTAAGTTT
Found at i:409758 original size:22 final size:22
Alignment explanation
Indices: 409732--409794 Score: 72
Period size: 28 Copynumber: 2.6 Consensus size: 22
409722 AAATTAAACT
409732 CTTAAAACGAAATACAGAGGAA
1 CTTAAAACGAAATACAGAGGAA
409754 CTTAAAACGAAATGACTATACAGAGGAA
1 CTTAAAACG--A--A--ATACAGAGGAA
409782 CTTAAAACGAAAT
1 CTTAAAACGAAAT
409795 GACTATGGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
22 11 0.31
24 2 0.06
26 2 0.06
28 20 0.57
ACGTcount: A:0.52, C:0.14, G:0.16, T:0.17
Consensus pattern (22 bp):
CTTAAAACGAAATACAGAGGAA
Found at i:409775 original size:28 final size:28
Alignment explanation
Indices: 409743--409800 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
409733 TTAAAACGAA
409743 ATACAGAGGAACTTAAAACGAAATGACT
1 ATACAGAGGAACTTAAAACGAAATGACT
409771 ATACAGAGGAACTTAAAACGAAATGACT
1 ATACAGAGGAACTTAAAACGAAATGACT
409799 AT
1 AT
409801 GGAAATGGCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.50, C:0.14, G:0.17, T:0.19
Consensus pattern (28 bp):
ATACAGAGGAACTTAAAACGAAATGACT
Found at i:410561 original size:17 final size:17
Alignment explanation
Indices: 410521--410561 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
410511 AGCCGACCGT
*
410521 GTTGACCGTTGACCCGC
1 GTTGACTGTTGACCCGC
*
410538 GTTGACTGTTGACCGGC
1 GTTGACTGTTGACCCGC
410555 GTTGACT
1 GTTGACT
410562 TCCGATGAGC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.12, C:0.27, G:0.32, T:0.29
Consensus pattern (17 bp):
GTTGACTGTTGACCCGC
Found at i:412986 original size:21 final size:19
Alignment explanation
Indices: 412948--412993 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
412938 AATTAATCCT
412948 ACTAAGTATTAAAGCTAAGA
1 ACTAA-TATTAAAGCTAAGA
412968 ACTAATATTAAGGAGCTAAGA
1 ACTAATATTAA--AGCTAAGA
412989 A-TAAT
1 ACTAAT
412994 GATTCAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.50, C:0.09, G:0.15, T:0.26
Consensus pattern (19 bp):
ACTAATATTAAAGCTAAGA
Found at i:420798 original size:23 final size:23
Alignment explanation
Indices: 420772--420840 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
420762 CACCATAGCT
*
420772 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* *
420795 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
* *
420818 CGTAGAATTGCGCCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
420841 TATAATAATG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.25, C:0.26, G:0.29, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:421085 original size:30 final size:30
Alignment explanation
Indices: 421050--421118 Score: 104
Period size: 30 Copynumber: 2.3 Consensus size: 30
421040 ACATAATTTG
* *
421050 TATCACGTAGACATATTATTTTCC-TACCTT
1 TATCACATAGACATATCA-TTTCCATACCTT
421080 TATCACATAGACATATCATTTCCATACCTT
1 TATCACATAGACATATCATTTCCATACCTT
421110 TATCACATA
1 TATCACATA
421119 ACTCATATAA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
29 5 0.14
30 31 0.86
ACGTcount: A:0.32, C:0.25, G:0.04, T:0.39
Consensus pattern (30 bp):
TATCACATAGACATATCATTTCCATACCTT
Found at i:421570 original size:63 final size:65
Alignment explanation
Indices: 421463--421604 Score: 175
Period size: 64 Copynumber: 2.2 Consensus size: 65
421453 AATGGAGGTA
* *
421463 TGCATCGATGCACTACACCATGCATCGATGCATAAATCATATTCGATGTTTGTA-TTT-AATGAG
1 TGCATCGATGCACTACACCATGCATCGATGCATAAATCACATTCGATGTTTGTATTTTAAAAGA-
421526 G
65 G
* * * **
421527 TGCATCGATGCACT-C-CTTATGCATTGATGCATCAATGGCATTCGATGTTTGTATTTTAAAAGA
1 TGCATCGATGCACTACAC-CATGCATCGATGCATAAATCACATTCGATGTTTGTATTTTAAAAGA
421590 G
65 G
421591 TGCATCGATGCACT
1 TGCATCGATGCACT
421605 TCATGTGCAT
Statistics
Matches: 68, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
62 1 0.01
63 31 0.46
64 32 0.47
65 4 0.06
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (65 bp):
TGCATCGATGCACTACACCATGCATCGATGCATAAATCACATTCGATGTTTGTATTTTAAAAGAG
Found at i:428015 original size:30 final size:30
Alignment explanation
Indices: 427972--428040 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 30
427962 ATATAATTTG
* *
427972 TATCACGTAGACATATTATTTTCC-TACCTT
1 TATCACATAGACATATCA-TTTCCATACCTT
*
428002 TATCGCATAGACATATCATTTCCATACCTT
1 TATCACATAGACATATCATTTCCATACCTT
428032 TATCACATA
1 TATCACATA
428041 ACTCATATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 5 0.15
30 29 0.85
ACGTcount: A:0.30, C:0.25, G:0.06, T:0.39
Consensus pattern (30 bp):
TATCACATAGACATATCATTTCCATACCTT
Found at i:432096 original size:21 final size:19
Alignment explanation
Indices: 432058--432103 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
432048 AATTAATCCT
432058 ACTAAGTATTAAAGCTAAGA
1 ACTAA-TATTAAAGCTAAGA
432078 ACTAATATTAAGGAGCTAAGA
1 ACTAATATTAA--AGCTAAGA
432099 A-TAAT
1 ACTAAT
432104 GATTCAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.50, C:0.09, G:0.15, T:0.26
Consensus pattern (19 bp):
ACTAATATTAAAGCTAAGA
Found at i:436383 original size:20 final size:20
Alignment explanation
Indices: 436358--436405 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
436348 TTGCATCGTC
*
436358 TTGATCCTTGCTCGGTCGCA
1 TTGATCCTTGCTCGGCCGCA
*
436378 TTGATCCTTGCTTGGCCGCA
1 TTGATCCTTGCTCGGCCGCA
436398 TTGATCCT
1 TTGATCCT
436406 CTCAATCACA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.10, C:0.29, G:0.23, T:0.38
Consensus pattern (20 bp):
TTGATCCTTGCTCGGCCGCA
Found at i:439866 original size:34 final size:34
Alignment explanation
Indices: 439826--439893 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
439816 CATAAACTCA
439826 AAATGTTGAAGAGACTACAAAAGAGTTGTATCTC
1 AAATGTTGAAGAGACTACAAAAGAGTTGTATCTC
* *
439860 AAATGTTGCAGAGACTACAAAAGGGTTGTATCTC
1 AAATGTTGAAGAGACTACAAAAGAGTTGTATCTC
439894 TCCAAAATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.38, C:0.13, G:0.22, T:0.26
Consensus pattern (34 bp):
AAATGTTGAAGAGACTACAAAAGAGTTGTATCTC
Found at i:443788 original size:19 final size:20
Alignment explanation
Indices: 443764--443807 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
443754 TTTTACTAAA
*
443764 CGCATCGGCCCGCATCA-AC
1 CGCATCGGACCGCATCAGAC
*
443783 CGCATCGGATCGCATCAGAC
1 CGCATCGGACCGCATCAGAC
443803 CGCAT
1 CGCAT
443808 TATGTACCCC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.23, C:0.41, G:0.23, T:0.14
Consensus pattern (20 bp):
CGCATCGGACCGCATCAGAC
Found at i:456063 original size:16 final size:15
Alignment explanation
Indices: 456037--456067 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
456027 TCAGTCTCCC
456037 ATGATACAACAATAA
1 ATGATACAACAATAA
456052 ATGATCACAACAATAA
1 ATGAT-ACAACAATAA
456068 GCACAACTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.58, C:0.16, G:0.06, T:0.19
Consensus pattern (15 bp):
ATGATACAACAATAA
Found at i:457720 original size:21 final size:21
Alignment explanation
Indices: 457696--457878 Score: 74
Period size: 21 Copynumber: 9.0 Consensus size: 21
457686 TTGAAACAAC
457696 TATAATATATATATATATATA
1 TATAATATATATATATATATA
* *
457717 TAT-ATATGTATAAACTATAGT-
1 TATAATATATATATA-TATA-TA
*
457738 TAT-ATTTATATTATATATATA
1 TATAATATATA-TATATATATA
*
457759 TATAACTATATAGTTTAT-TA-A
1 TATAA-TATATA-TATATATATA
457780 TATAA-AT-TATATAGT-TAGTA
1 TATAATATATATATA-TATA-TA
457800 TATAAT-TATATATGA-ATTATA
1 TATAATATATATAT-ATA-TATA
* *
457821 TTTAA-ATATATACA-ACT-TA
1 TATAATATATATATATA-TATA
* * *
457840 TAT-TTATATTTATAT-TATG
1 TATAATATATATATATATATA
*
457859 TATAAT-TATAAATATATATA
1 TATAATATATATATATATATA
457879 CTATGTATAA
Statistics
Matches: 121, Mismatches: 21, Indels: 41
0.66 0.11 0.22
Matches are distributed among these distances:
17 3 0.02
18 6 0.05
19 24 0.20
20 24 0.20
21 45 0.37
22 10 0.08
23 9 0.07
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (21 bp):
TATAATATATATATATATATA
Found at i:457753 original size:11 final size:11
Alignment explanation
Indices: 457696--457895 Score: 73
Period size: 11 Copynumber: 17.9 Consensus size: 11
457686 TTGAAACAAC
*
457696 TATAATATATA
1 TATATTATATA
457707 TATATATATATA
1 TATAT-TATATA
*
457719 TATATGTATAAA
1 TATAT-TATATA
*
457731 CTATAGTTATATT
1 -TATA-TTATATA
457744 TATATTATATA
1 TATATTATATA
457755 TATA-TATAACTA
1 TATATTAT-A-TA
457767 TATAGTT-TAT-
1 TATA-TTATATA
*
457777 TA-ATATAAATTA
1 TATAT-TATA-TA
457789 TATAGTTAGTATA
1 TATA-TTA-TATA
457802 TA-ATTATATA
1 TATATTATATA
*
457812 TGA-ATTATATT
1 T-ATATTATATA
*
457823 TA-AATATATA
1 TATATTATATA
* *
457833 CA-ACTTATATT
1 TATA-TTATATA
457844 TATATT-TATA
1 TATATTATATA
457854 T-TATGTATA-A
1 TATAT-TATATA
*
457864 T-TATAAATATA
1 TATAT-TATATA
* *
457875 TATACTATGTA
1 TATATTATATA
*
457886 TAAATTATAT
1 TATATTATAT
457896 TGTTTATTAA
Statistics
Matches: 144, Mismatches: 24, Indels: 42
0.69 0.11 0.20
Matches are distributed among these distances:
8 1 0.01
9 5 0.03
10 33 0.23
11 52 0.36
12 33 0.23
13 16 0.11
14 4 0.03
ACGTcount: A:0.45, C:0.03, G:0.04, T:0.48
Consensus pattern (11 bp):
TATATTATATA
Found at i:457770 original size:2 final size:2
Alignment explanation
Indices: 457696--457762 Score: 68
Period size: 2 Copynumber: 34.0 Consensus size: 2
457686 TTGAAACAAC
* *
457696 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TG TA TA AA CTA TA GT-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA -TA
*
457738 TA TA TT TA TA T- TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
457763 ACTATATAGT
Statistics
Matches: 54, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
1 3 0.06
2 49 0.91
3 2 0.04
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:457793 original size:22 final size:20
Alignment explanation
Indices: 457732--457811 Score: 64
Period size: 19 Copynumber: 4.2 Consensus size: 20
457722 ATGTATAAAC
* *
457732 TATAGTTA-TATTTATATTA
1 TATAGTTAGTATATAAATTA
*
457751 TATA--TA-TATAT-AACTA
1 TATAGTTAGTATATAAATTA
*
457767 TATAGTTTATTAATATAAATTA
1 TATAG-TTAGT-ATATAAATTA
457789 TATAGTTAGTATAT-AATTA
1 TATAGTTAGTATATAAATTA
457808 TATA
1 TATA
457812 TGAATTATAT
Statistics
Matches: 50, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
16 7 0.14
17 6 0.12
19 15 0.30
20 5 0.10
21 8 0.16
22 9 0.18
ACGTcount: A:0.44, C:0.01, G:0.05, T:0.50
Consensus pattern (20 bp):
TATAGTTAGTATATAAATTA
Found at i:457857 original size:49 final size:47
Alignment explanation
Indices: 457737--457868 Score: 119
Period size: 49 Copynumber: 2.7 Consensus size: 47
457727 TAAACTATAG
*
457737 TTATATTTATA-TTATATATATATATAACTATATAGTTTATTAATATAAA
1 TTATATTTATATTTATAT-TATATATAA-T-TATAGTTTAATAATATAAA
*
457786 TTATATAGTTAGTATATA-ATTATATATGAATTATA-TTTAA-ATATATACAA
1 TTATAT--TTA-TATTTATATTATATAT-AATTATAGTTTAATA-ATATA-AA
*
457836 CTTATATTTATATTTATATTATGTATAATTATA
1 -TTATATTTATATTTATATTATATATAATTATA
457869 AATATATATA
Statistics
Matches: 70, Mismatches: 4, Indels: 19
0.75 0.04 0.20
Matches are distributed among these distances:
48 13 0.19
49 26 0.37
50 6 0.09
51 17 0.24
52 6 0.09
53 2 0.03
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (47 bp):
TTATATTTATATTTATATTATATATAATTATAGTTTAATAATATAAA
Found at i:457873 original size:25 final size:26
Alignment explanation
Indices: 457845--457941 Score: 80
Period size: 25 Copynumber: 4.0 Consensus size: 26
457835 ACTTATATTT
* *
457845 ATATTTATATTATGTAT-AATTATAA
1 ATATATATACTATGTATAAATTATAA
457870 ATATATATACTATGTATAAATTAT--
1 ATATATATACTATGTATAAATTATAA
* * * * *
457894 AT-TGTTTATTA-ATATAAACTA-AA
1 ATATATATACTATGTATAAATTATAA
*
457917 ATTTATATACTATGTATAAATTATA
1 ATATATATACTATGTATAAATTATA
457942 TAGTTTATAT
Statistics
Matches: 54, Mismatches: 12, Indels: 11
0.70 0.16 0.14
Matches are distributed among these distances:
22 8 0.15
23 8 0.15
24 8 0.15
25 23 0.43
26 7 0.13
ACGTcount: A:0.45, C:0.03, G:0.04, T:0.47
Consensus pattern (26 bp):
ATATATATACTATGTATAAATTATAA
Found at i:457971 original size:47 final size:48
Alignment explanation
Indices: 457868--458003 Score: 143
Period size: 47 Copynumber: 2.8 Consensus size: 48
457858 GTATAATTAT
* *
457868 AAATATATATACTATGTATAAATTATATTGTTTAT-TAATATAAACTA
1 AAATGTATATACTATGTATAAATTATATAGTTTATATAATATAAACTA
* * *
457915 AAATTTATATACTATGTATAAATTATATAGTTTATATAGTTTAAA-TA
1 AAATGTATATACTATGTATAAATTATATAGTTTATATAATATAAACTA
* * *
457962 TAAA-GTATATAAGTATATATATAAAGTATATAGTTTATATAA
1 -AAATGTATAT-A--CTATGTATAAATTATATAGTTTATATAA
458004 AACCTAAACT
Statistics
Matches: 75, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
47 40 0.53
48 11 0.15
50 24 0.32
ACGTcount: A:0.47, C:0.02, G:0.07, T:0.44
Consensus pattern (48 bp):
AAATGTATATACTATGTATAAATTATATAGTTTATATAATATAAACTA
Found at i:457985 original size:21 final size:20
Alignment explanation
Indices: 457947--458002 Score: 76
Period size: 21 Copynumber: 2.8 Consensus size: 20
457937 TTATATAGTT
* *
457947 TATATAGTTTAAATATAAAG
1 TATATAGTATATATATAAAG
457967 TATATAAGTATATATATAAAG
1 TATAT-AGTATATATATAAAG
*
457988 TATATAGTTTATATA
1 TATATAGTATATATA
458003 AAACCTAAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
20 14 0.44
21 18 0.56
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.43
Consensus pattern (20 bp):
TATATAGTATATATATAAAG
Found at i:458205 original size:20 final size:20
Alignment explanation
Indices: 458182--458227 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
458172 TATAGTACAT
* *
458182 GTATGTACAAACTATGTATA
1 GTATATACAAACTATATATA
*
458202 GTATATATAAACTATATATA
1 GTATATACAAACTATATATA
458222 -TATATA
1 GTATATA
458228 ACCTATATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.46, C:0.07, G:0.09, T:0.39
Consensus pattern (20 bp):
GTATATACAAACTATATATA
Found at i:458225 original size:17 final size:17
Alignment explanation
Indices: 458198--458237 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
458188 ACAAACTATG
458198 TATAGTATATATAAACTA
1 TATA-TATATATAAACTA
*
458216 TATATATATATAACCTA
1 TATATATATATAAACTA
458233 TATAT
1 TATAT
458238 GTAAACCATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.42
Consensus pattern (17 bp):
TATATATATATAAACTA
Found at i:458356 original size:48 final size:48
Alignment explanation
Indices: 458239--458356 Score: 112
Period size: 49 Copynumber: 2.4 Consensus size: 48
458229 CCTATATATG
* * ** **
458239 TAAACCATATAAAGTAAATTATTTATATAGTTTATAGAAACACTATGCA
1 TAAACTATATAAAGT-AATAAAGTATATAGTTTATAGAAACACTAACCA
* * *
458288 TAAACTATATAAAGTAATAAAGTATATAGTTTATATAAACCCTAAACCC
1 TAAACTATATAAAGTAATAAAGTATATAGTTTATAGAAACACT-AACCA
* *
458337 TAAATTATATATAGT-ATAAA
1 TAAACTATATAAAGTAATAAA
458357 CTTTAAACCC
Statistics
Matches: 57, Mismatches: 11, Indels: 3
0.80 0.15 0.04
Matches are distributed among these distances:
48 28 0.49
49 29 0.51
ACGTcount: A:0.49, C:0.10, G:0.07, T:0.34
Consensus pattern (48 bp):
TAAACTATATAAAGTAATAAAGTATATAGTTTATAGAAACACTAACCA
Found at i:458472 original size:37 final size:36
Alignment explanation
Indices: 458396--458466 Score: 90
Period size: 37 Copynumber: 2.0 Consensus size: 36
458386 ATAGTTAATC
* *
458396 TATGTAACCTATAGTATATGTATACATGTAAACTATA
1 TATGTAACCTATAGTACATGTATA-ATATAAACTATA
* *
458433 TATGTAACTTATAGTACATGTAT-GTATAAACTAT
1 TATGTAACCTATAGTACATGTATAATATAAACTAT
458467 GTATATTATA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
35 9 0.30
37 21 0.70
ACGTcount: A:0.39, C:0.10, G:0.11, T:0.39
Consensus pattern (36 bp):
TATGTAACCTATAGTACATGTATAATATAAACTATA
Found at i:458486 original size:20 final size:22
Alignment explanation
Indices: 458450--458526 Score: 81
Period size: 22 Copynumber: 3.6 Consensus size: 22
458440 CTTATAGTAC
*
458450 ATGTATGTATAAACTAT-GTAT
1 ATGTATATATAAACTATGGTAT
*
458471 AT-TATATATAACCTATGGTAT
1 ATGTATATATAAACTATGGTAT
*
458492 ATGTATATATACAATCTAT-TTAT
1 ATGTATATATA-AA-CTATGGTAT
458515 ATGT-TATATAAA
1 ATGTATATATAAA
458527 TTATATATGT
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
20 12 0.25
21 10 0.21
22 14 0.29
23 8 0.17
24 4 0.08
ACGTcount: A:0.40, C:0.06, G:0.09, T:0.44
Consensus pattern (22 bp):
ATGTATATATAAACTATGGTAT
Found at i:458497 original size:42 final size:45
Alignment explanation
Indices: 458431--458525 Score: 108
Period size: 42 Copynumber: 2.2 Consensus size: 45
458421 ATGTAAACTA
* * *
458431 TATATGTAACTTATAGTACATGTATGTATA-AA-CTATGTATAT-
1 TATATATAACCTATAGTACATGTATATATACAATCTATGTATATG
* * *
458473 TATATATAACCTATGGTATATGTATATATACAATCTATTTATATG
1 TATATATAACCTATAGTACATGTATATATACAATCTATGTATATG
458518 T-TATATAA
1 TATATATAA
458526 ATTATATATG
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
42 25 0.57
43 2 0.05
44 16 0.36
45 1 0.02
ACGTcount: A:0.39, C:0.07, G:0.09, T:0.44
Consensus pattern (45 bp):
TATATATAACCTATAGTACATGTATATATACAATCTATGTATATG
Found at i:458623 original size:21 final size:21
Alignment explanation
Indices: 458599--458760 Score: 61
Period size: 21 Copynumber: 7.5 Consensus size: 21
458589 TTGATAACCC
458599 ATAGTATATAATTTATAAACT
1 ATAGTATATAATTTATAAACT
* *
458620 ATAGTTTATATTAATGTTAATTATCT
1 ATAG--TATA-TAAT-TT-ATAAACT
458646 -TA--ACTATAATTTATATTAA-T
1 ATAGTA-TATAATTTATA--AACT
* *
458666 ATAATATATAGTTTATAAACT
1 ATAGTATATAATTTATAAACT
* *
458687 ATAATGTAT-TAA--TATTAATT
1 AT-A-GTATATAATTTATAAACT
* *
458707 ATATTAACTATAATGTATAAACT
1 ATAGT-A-TATAATTTATAAACT
*
458730 ATACTATATAATTTAT-AACAT
1 ATAGTATATAATTTATAAAC-T
*
458751 ATAGTTTATA
1 ATAGTATATA
458761 TTAATATTAA
Statistics
Matches: 105, Mismatches: 16, Indels: 40
0.65 0.10 0.25
Matches are distributed among these distances:
18 1 0.01
19 4 0.04
20 17 0.16
21 36 0.34
22 16 0.15
23 18 0.17
24 4 0.04
25 4 0.04
26 5 0.05
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.46
Consensus pattern (21 bp):
ATAGTATATAATTTATAAACT
Found at i:458655 original size:15 final size:14
Alignment explanation
Indices: 458625--458906 Score: 98
Period size: 15 Copynumber: 18.4 Consensus size: 14
458615 AAACTATAGT
*
458625 TTATATTAATGTTAA
1 TTATATTAAT-ATAA
*
458640 TTATCTTAACTATAA
1 TTATATTAA-TATAA
458655 TTTATATTAATATAA
1 -TTATATTAATATAA
458670 TATATAGTTTATAAACTATAA
1 T-TATA---T-T-AA-TATAA
*
458691 -TGTATTAATATTAA
1 TTATATTAATA-TAA
458705 TTATATTAACTATAA
1 TTATATTAA-TATAA
458720 TGTATAAACTATACTATATAA
1 T-TAT--A-T-TA--ATATAA
* *
458741 TT-TATAACATATAGT
1 TTATATTA-ATATA-A
458756 TTATATTAATATTAA
1 TTATATTAATA-TAA
*
458771 TT-TGA-TAGACTATATT
1 TTAT-ATTA-A-TATA-A
458787 TTATATTAATATTAA
1 TTATATTAATA-TAA
458802 TTATA--AATTATAAA
1 TTATATTAA-TAT-AA
*
458816 TTATA--AACTA-GA
1 TTATATTAA-TATAA
458828 TTATATTAATATAA
1 TTATATTAATATAA
458842 GTTAATATTAATATTAA
1 -TT-ATATTAATA-TAA
458859 TTATATTAATATTAA
1 TTATATTAATA-TAA
*
458874 TTATAAT-ATATAA
1 TTATATTAATATAA
*
458887 TTATTTTAATATTAA
1 TTATATTAATA-TAA
458902 TTATA
1 TTATA
458907 AATAGTTTAT
Statistics
Matches: 209, Mismatches: 19, Indels: 78
0.68 0.06 0.25
Matches are distributed among these distances:
12 6 0.03
13 15 0.07
14 36 0.17
15 79 0.38
16 41 0.20
17 7 0.03
18 2 0.01
19 6 0.03
20 5 0.02
21 11 0.05
22 1 0.00
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.48
Consensus pattern (14 bp):
TTATATTAATATAA
Found at i:458739 original size:14 final size:14
Alignment explanation
Indices: 458679--458740 Score: 54
Period size: 14 Copynumber: 4.4 Consensus size: 14
458669 ATATATAGTT
*
458679 TATAAACTATAATG
1 TATAAACTATAATA
*
458693 TATTAA-TATTAATTA
1 TATAAACTA-TAA-TA
* *
458708 TATTAACTATAATG
1 TATAAACTATAATA
*
458722 TATAAACTATACTA
1 TATAAACTATAATA
458736 TATAA
1 TATAA
458741 TTTATAACAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
13 2 0.05
14 25 0.64
15 10 0.26
16 2 0.05
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.42
Consensus pattern (14 bp):
TATAAACTATAATA
Found at i:458791 original size:31 final size:30
Alignment explanation
Indices: 458738--458807 Score: 99
Period size: 31 Copynumber: 2.3 Consensus size: 30
458728 CTATACTATA
458738 TAATTTATAACATATAGTTTATATTAATAT
1 TAATTTATAACATATAGTTTATATTAATAT
*
458768 TAATTTGATAGAC-TATATTTTATATTAATAT
1 TAATTT-ATA-ACATATAGTTTATATTAATAT
458799 TAA-TTATAA
1 TAATTTATAA
458808 ATTATAAATT
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
28 1 0.03
29 3 0.08
30 8 0.22
31 23 0.62
32 2 0.05
ACGTcount: A:0.43, C:0.03, G:0.04, T:0.50
Consensus pattern (30 bp):
TAATTTATAACATATAGTTTATATTAATAT
Found at i:458852 original size:6 final size:6
Alignment explanation
Indices: 458830--458902 Score: 50
Period size: 6 Copynumber: 12.3 Consensus size: 6
458820 AAACTAGATT
*
458830 ATATTA ATA-TA A-GTTA ATATTA ATATT- A-ATT- ATATTA ATATTA
1 ATATTA ATATTA ATATTA ATATTA ATATTA ATATTA ATATTA ATATTA
458873 AT-TATA ATATATA ATTATTTTA ATATTA AT
1 ATAT-TA ATAT-TA A-TA--TTA ATATTA AT
458903 TATAAATAGT
Statistics
Matches: 56, Mismatches: 2, Indels: 18
0.74 0.03 0.24
Matches are distributed among these distances:
4 4 0.07
5 11 0.20
6 28 0.50
7 5 0.09
8 4 0.07
9 3 0.05
10 1 0.02
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (6 bp):
ATATTA
Found at i:458896 original size:28 final size:27
Alignment explanation
Indices: 458793--458927 Score: 104
Period size: 28 Copynumber: 5.0 Consensus size: 27
458783 TATTTTATAT
*
458793 TAATATTAATTATA--AATTATAAATTA
1 TAATATTAATTATATTAA-TATTAATTA
*
458819 TAA-ACTAGATTATATTAATA-TAAGTTAATA
1 TAATATTA-ATTATATTAATATTAA--T--TA
458849 TTAATATTAATTATATTAATATTAATTA
1 -TAATATTAATTATATTAATATTAATTA
*
458877 TAATATATAATTATTTTAATATTAATTA
1 TAATAT-TAATTATATTAATATTAATTA
* *
458905 TAA-A-TAGTT-TATTAATATAAATT
1 TAATATTAATTATATTAATATTAATT
458928 TTATAGGAAT
Statistics
Matches: 91, Mismatches: 7, Indels: 24
0.75 0.06 0.20
Matches are distributed among these distances:
24 12 0.13
25 7 0.08
26 11 0.12
27 9 0.10
28 28 0.31
30 3 0.03
31 15 0.16
32 6 0.07
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.48
Consensus pattern (27 bp):
TAATATTAATTATATTAATATTAATTA
Found at i:460901 original size:12 final size:12
Alignment explanation
Indices: 460886--460934 Score: 55
Period size: 12 Copynumber: 3.9 Consensus size: 12
460876 TTCCTTTTAA
460886 TTTTAGTTTATTT
1 TTTTA-TTTATTT
460899 TTTTATTTATTT
1 TTTTATTTATTT
*
460911 GTTTT-TTTCTTAT
1 -TTTTATTTATT-T
460924 TTTTATTTATT
1 TTTTATTTATT
460935 ACCTTTAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
12 16 0.52
13 15 0.48
ACGTcount: A:0.14, C:0.02, G:0.04, T:0.80
Consensus pattern (12 bp):
TTTTATTTATTT
Found at i:460917 original size:41 final size:42
Alignment explanation
Indices: 460815--460919 Score: 117
Period size: 41 Copynumber: 2.5 Consensus size: 42
460805 GCCTTTTAAA
* *
460815 TTTTTAGTTATTCATTTTTTCCCTTTTTAATTTTAGCATTTTT
1 TTTTTAGTTATTTATTTTTTTCCTTTTTAATTTTAG-ATTTTT
* *
460858 ATTTTAGTTATTCA-TTTTTTCC-TTTTAATTTTAG-TTTATT
1 TTTTTAGTTATTTATTTTTTTCCTTTTTAATTTTAGATTT-TT
* *
460898 TTTTTATTTATTTGTTTTTTTC
1 TTTTTAGTTATTTATTTTTTTC
460920 TTATTTTTAT
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
39 3 0.06
40 12 0.22
41 19 0.35
42 7 0.13
43 13 0.24
ACGTcount: A:0.16, C:0.09, G:0.05, T:0.70
Consensus pattern (42 bp):
TTTTTAGTTATTTATTTTTTTCCTTTTTAATTTTAGATTTTT
Found at i:463581 original size:18 final size:17
Alignment explanation
Indices: 463503--463593 Score: 78
Period size: 18 Copynumber: 5.1 Consensus size: 17
463493 AATAAATTTA
*
463503 TAATATAAGAATTATAA-
1 TAATATAAAAATTA-AAT
463520 -AATATAAAGAATTGAAAT
1 TAATATAAA-AATT-AAAT
463538 TAATATAAAAATTAAATTT
1 TAATATAAAAATTAAA--T
*
463557 ATAATATACAAATTATAAT
1 -TAATATAAAAATTA-AAT
*
463576 TAATATAAAAACTAAAT
1 TAATATAAAAATTAAAT
463593 T
1 T
463594 TCAGAAAGTA
Statistics
Matches: 62, Mismatches: 4, Indels: 16
0.76 0.05 0.20
Matches are distributed among these distances:
16 7 0.11
17 13 0.21
18 17 0.27
19 10 0.16
20 13 0.21
21 2 0.03
ACGTcount: A:0.59, C:0.02, G:0.03, T:0.35
Consensus pattern (17 bp):
TAATATAAAAATTAAAT
Found at i:463730 original size:16 final size:18
Alignment explanation
Indices: 463696--463730 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
463686 CAGGACAATA
463696 TCAGATCACTTTAACATG
1 TCAGATCACTTTAACATG
463714 TCAGATCA-TTT-ACATG
1 TCAGATCACTTTAACATG
463730 T
1 T
463731 TGAGTCATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
17 3 0.18
18 8 0.47
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.37
Consensus pattern (18 bp):
TCAGATCACTTTAACATG
Found at i:463753 original size:15 final size:15
Alignment explanation
Indices: 463735--463777 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
463725 ACATGTTGAG
*
463735 TCATTACAGGTCAGT
1 TCATAACAGGTCAGT
463750 TCATAACAGGTCAGGT
1 TCATAACAGGTCA-GT
* *
463766 TGAAAACAGGTC
1 TCATAACAGGTC
463778 GAGTATACCA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
15 12 0.50
16 12 0.50
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.26
Consensus pattern (15 bp):
TCATAACAGGTCAGT
Found at i:463912 original size:22 final size:22
Alignment explanation
Indices: 463870--463912 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
463860 TCGGTTCAAT
* *
463870 TCGGGTTCAGGTCGTTCTCAGG
1 TCGGGTGCAGGTCGGTCTCAGG
463892 TCGGGTGCAGGTCAGGT-TCAG
1 TCGGGTGCAGGTC-GGTCTCAG
463913 ATCCACAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 16 0.89
23 2 0.11
ACGTcount: A:0.12, C:0.21, G:0.40, T:0.28
Consensus pattern (22 bp):
TCGGGTGCAGGTCGGTCTCAGG
Found at i:470666 original size:2 final size:2
Alignment explanation
Indices: 470661--470695 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
470651 ACACACACTT
470661 TA TA TA 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 TA TA TA T
470696 TCGTAAACTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:473099 original size:25 final size:27
Alignment explanation
Indices: 473048--473101 Score: 85
Period size: 25 Copynumber: 2.1 Consensus size: 27
473038 GAGACAGATT
473048 ATGAATTAATTTATTATTAAACAAAAA
1 ATGAATTAATTTATTATTAAACAAAAA
*
473075 ATGAATTATTTTA-TA-TAAACAAAAA
1 ATGAATTAATTTATTATTAAACAAAAA
473100 AT
1 AT
473102 ATGAAAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 12 0.46
26 2 0.08
27 12 0.46
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.37
Consensus pattern (27 bp):
ATGAATTAATTTATTATTAAACAAAAA
Found at i:473105 original size:27 final size:28
Alignment explanation
Indices: 473047--473106 Score: 81
Period size: 27 Copynumber: 2.2 Consensus size: 28
473037 AGAGACAGAT
473047 TATGAATTAATTTATTATTAAACAAAAA
1 TATGAATTAATTTATTATTAAACAAAAA
*
473075 -ATGAATTATTTTA-TA-TAAACAAAAAA
1 TATGAATTAATTTATTATTAAAC-AAAAA
473101 TATGAA
1 TATGAA
473107 AAAAATGAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
25 5 0.17
26 7 0.24
27 17 0.59
ACGTcount: A:0.55, C:0.03, G:0.05, T:0.37
Consensus pattern (28 bp):
TATGAATTAATTTATTATTAAACAAAAA
Found at i:474239 original size:17 final size:17
Alignment explanation
Indices: 474217--474249 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
474207 ATAGTAAACT
*
474217 AATAATTTTTTAAATAG
1 AATAATTTTTAAAATAG
474234 AATAATTTTTAAAATA
1 AATAATTTTTAAAATA
474250 ACTACTAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (17 bp):
AATAATTTTTAAAATAG
Found at i:475589 original size:19 final size:19
Alignment explanation
Indices: 475565--475677 Score: 82
Period size: 22 Copynumber: 5.6 Consensus size: 19
475555 ACCTAATTTT
475565 GGTATCGATACCATATAGG
1 GGTATCGATACCATATAGG
*
475584 GGTATCGATACCATAGTATAGT
1 GGTATCGATACC--A-TATAGG
* *** *
475606 AGTATCGATACTGGATGGG
1 GGTATCGATACCATATAGG
*
475625 GGTATCGATACCAAAGTAGG
1 GGTATCGATACCATA-TAGG
* *
475645 GTAGTATCGATACCATGGTAAG
1 G--GTATCGATACCAT-ATAGG
475667 GGTATCGATAC
1 GGTATCGATAC
475678 TGAAGGGCCA
Statistics
Matches: 72, Mismatches: 15, Indels: 13
0.72 0.15 0.13
Matches are distributed among these distances:
19 26 0.36
20 14 0.19
21 1 0.01
22 31 0.43
ACGTcount: A:0.31, C:0.14, G:0.28, T:0.27
Consensus pattern (19 bp):
GGTATCGATACCATATAGG
Found at i:475616 original size:41 final size:41
Alignment explanation
Indices: 475566--475677 Score: 134
Period size: 41 Copynumber: 2.7 Consensus size: 41
475556 CCTAATTTTG
* *
475566 GTATCGATACCATATAGGGGTATCGATACCATAGTATAGTA
1 GTATCGATACCATATAGGGGTATCGATACCAAAGTAGAGTA
*** * *
475607 GTATCGATACTGGATGGGGGTATCGATACCAAAGTAGGGTA
1 GTATCGATACCATATAGGGGTATCGATACCAAAGTAGAGTA
* *
475648 GTATCGATACCATGGTAAGGGTATCGATAC
1 GTATCGATACCAT-ATAGGGGTATCGATAC
475678 TGAAGGGCCA
Statistics
Matches: 57, Mismatches: 13, Indels: 1
0.80 0.18 0.01
Matches are distributed among these distances:
41 44 0.77
42 13 0.23
ACGTcount: A:0.31, C:0.14, G:0.28, T:0.27
Consensus pattern (41 bp):
GTATCGATACCATATAGGGGTATCGATACCAAAGTAGAGTA
Found at i:476074 original size:59 final size:59
Alignment explanation
Indices: 475999--476231 Score: 317
Period size: 59 Copynumber: 4.0 Consensus size: 59
475989 GAATTACCAA
* * * *
475999 AGGGCACTTTATGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATAAATTTACAAAC
1 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAAAT
* * *
476058 AGGGCACTTTGTGTGCTAAAATGGTAAAGAAATCATACTAAGTGTGTGAATTTCCAGAT
1 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAAAT
** * *
476117 AGGGGGCTTTGTGTGCTAAAATAGTAAGG-AATCATACTAAATGTATGAATTTCCAAAT
1 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAAAT
* * *
476175 AGGGCACTTTGTGTGCTAAAATGATAAGAAAATCATACTAA-TGGTGTGAATTTCCAA
1 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGT-GTATGAATTTCCAA
476232 TTGAATTTAT
Statistics
Matches: 152, Mismatches: 20, Indels: 4
0.86 0.11 0.02
Matches are distributed among these distances:
58 51 0.34
59 101 0.66
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.30
Consensus pattern (59 bp):
AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAAAT
Found at i:476222 original size:117 final size:118
Alignment explanation
Indices: 476005--476230 Score: 350
Period size: 117 Copynumber: 1.9 Consensus size: 118
475995 CCAAAGGGCA
* *
476005 CTTTATGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATAAATTTACAAACAGGGCACTTTGT
1 CTTTATGTGCTAAAATAGTAAGGAAATCATACTAAATGTATAAATTTACAAACAGGGCACTTTGT
*
476070 GTGCTAAAATGGTAAAGAAATCATACTAAGTGTGTGAATTTCCAGATAGGGGG
66 GTGCTAAAATGATAAAGAAATCATACTAAGTGTGTGAATTTCCAGATAGGGGG
* * * *
476123 CTTTGTGTGCTAAAATAGTAAGG-AATCATACTAAATGTATGAATTTCCAAATAGGGCACTTTGT
1 CTTTATGTGCTAAAATAGTAAGGAAATCATACTAAATGTATAAATTTACAAACAGGGCACTTTGT
476187 GTGCTAAAATGAT-AAGAAAATCATACTAA-TGGTGTGAATTTCCA
66 GTGCTAAAATGATAAAG-AAATCATACTAAGT-GTGTGAATTTCCA
476231 ATTGAATTTA
Statistics
Matches: 99, Mismatches: 7, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
116 4 0.04
117 74 0.75
118 21 0.21
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.31
Consensus pattern (118 bp):
CTTTATGTGCTAAAATAGTAAGGAAATCATACTAAATGTATAAATTTACAAACAGGGCACTTTGT
GTGCTAAAATGATAAAGAAATCATACTAAGTGTGTGAATTTCCAGATAGGGGG
Found at i:481983 original size:22 final size:20
Alignment explanation
Indices: 481952--482005 Score: 72
Period size: 22 Copynumber: 2.6 Consensus size: 20
481942 ATACTGGATG
481952 GGGGTATCGATACCAAAGTA
1 GGGGTATCGATACCAAAGTA
**
481972 GGGTAGTATCGATACCATGGTA
1 GGG--GTATCGATACCAAAGTA
481994 GGGGTATCGATA
1 GGGGTATCGATA
482006 TTGAAGGGCC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 12 0.40
22 18 0.60
ACGTcount: A:0.30, C:0.13, G:0.33, T:0.24
Consensus pattern (20 bp):
GGGGTATCGATACCAAAGTA
Found at i:482404 original size:59 final size:59
Alignment explanation
Indices: 482328--482440 Score: 183
Period size: 59 Copynumber: 1.9 Consensus size: 59
482318 GAATTACCAA
*
482328 AGGGCACTTTGTATGCTAAAATGGTAAGGAAATCATACTAA-GTGTATGAATTTCTAGAT
1 AGGGCACTTTGTATGCTAAAATGATAAGGAAATCATACTAATG-GTATGAATTTCTAGAT
* *
482387 AGGGCACTTTGTTTGCTAAAATGATAAGGAAATCATACTAATGGTGTGAATTTC
1 AGGGCACTTTGTATGCTAAAATGATAAGGAAATCATACTAATGGTATGAATTTC
482441 CAATTGAATT
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
59 49 0.98
60 1 0.02
ACGTcount: A:0.35, C:0.11, G:0.22, T:0.33
Consensus pattern (59 bp):
AGGGCACTTTGTATGCTAAAATGATAAGGAAATCATACTAATGGTATGAATTTCTAGAT
Found at i:501121 original size:36 final size:36
Alignment explanation
Indices: 501075--501147 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
501065 TGGGTATTTC
501075 AGATATTGGTAAGACCTTACCTTGATATTGGGCCCG
1 AGATATTGGTAAGACCTTACCTTGATATTGGGCCCG
501111 AGATATTGGTAAGACCTTACCTTGATATTGGGCCCG
1 AGATATTGGTAAGACCTTACCTTGATATTGGGCCCG
501147 A
1 A
501148 CGGCTACAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30
Consensus pattern (36 bp):
AGATATTGGTAAGACCTTACCTTGATATTGGGCCCG
Found at i:503411 original size:19 final size:19
Alignment explanation
Indices: 503384--503420 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
503374 TCCCCTGGGG
*
503384 AAGAGATTAAGAATTTTAT
1 AAGAAATTAAGAATTTTAT
*
503403 AAGAAATTAAGATTTTTA
1 AAGAAATTAAGAATTTTA
503421 AAACATTAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.49, C:0.00, G:0.14, T:0.38
Consensus pattern (19 bp):
AAGAAATTAAGAATTTTAT
Found at i:505512 original size:24 final size:23
Alignment explanation
Indices: 505472--505516 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
505462 GTCGATCAAT
*
505472 AAATAAAAATTAATAATTAAATCA
1 AAATAAAAAATAATAA-TAAATCA
*
505496 AAATAAAAAATAGTAATAAAT
1 AAATAAAAAATAATAATAAAT
505517 ATAATATAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (23 bp):
AAATAAAAAATAATAATAAATCA
Found at i:507897 original size:21 final size:21
Alignment explanation
Indices: 507873--507915 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
507863 CACTTTTAAC
507873 ATTTGTTCTCTT-AATTTATTT
1 ATTT-TTCTCTTCAATTTATTT
507894 ATTTTTCTCTTCAATTTATTT
1 ATTTTTCTCTTCAATTTATTT
507915 A
1 A
507916 GTATTGTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.21, C:0.12, G:0.02, T:0.65
Consensus pattern (21 bp):
ATTTTTCTCTTCAATTTATTT
Found at i:508899 original size:720 final size:720
Alignment explanation
Indices: 507521--508963 Score: 2733
Period size: 720 Copynumber: 2.0 Consensus size: 720
507511 CTACGAGGAC
*
507521 GTTTGGCTCCGGTCCTCCGACGGAATCAAACTCCATTCTTGGTTCATCAAGCTCTTTCCTGATTG
1 GTTTGGCTCCGATCCTCCGACGGAATCAAACTCCATTCTTGGTTCATCAAGCTCTTTCCTGATTG
*
507586 CCGAGGTCCAACCATCCTATTTTTTTTTCAAGAGAATGCTAGAAACATTGCTCACCGTCTGGAAA
66 CCAAGGTCCAACCATCCTATTTTTTTTTCAAGAGAATGCTAGAAACATTGCTCACCGTCTGGAAA
507651 TGGTTCGTATAATGCTACAAAGGTTACAATGTAATGTCTTCATGCTTCCATATCGAGGTTATGGA
131 TGGTTCGTATAATGCTACAAAGGTTACAATGTAATGTCTTCATGCTTCCATATCGAGGTTATGGA
507716 GCAAGTGATGGTTATCCTTCTCAGCGTGGAATTATTAACGATTGCATCAGACTGACATGGGGGAG
196 GCAAGTGATGGTTATCCTTCTCAGCGTGGAATTATTAACGATTGCATCAGACTGACATGGGGGAG
507781 TAAGTTTTTAAAATGCACGTGGAGATGTGCAGCCATTTATGGCCATGCATTTGAGTATTTATTAA
261 TAAGTTTTTAAAATGCACGTGGAGATGTGCAGCCATTTATGGCCATGCATTTGAGTATTTATTAA
*
507846 GTGTATATTATATTACACACTTTTAACATTTGTTCTCTTAATTTATTTATTTTTCTCTTCAATTT
326 GTGTATATTATATTACACACTTTTAACATTTGTTCTCTTAATTTATTTATTTTTCTCTACAATTT
507911 ATTTAGTATTGTTTTATCTAACATTTTTTACTTTCTTTTTAGGACAATTTTAACTAGTTAAAGGT
391 ATTTAGTATTGTTTTATCTAACATTTTTTACTTTCTTTTTAGGACAATTTTAACTAGTTAAAGGT
507976 AAATGATTTGAATCGAGTATTTTAATTCTAATTTAAATTTTCGCAACTAAGACAACCGGCAAATT
456 AAATGATTTGAATCGAGTATTTTAATTCTAATTTAAATTTTCGCAACTAAGACAACCGGCAAATT
* * *
508041 AATTGGTACCGAAAAGGCGGTTCAAGGGTGCTAATCCTTCCTTGGCTGTAACCGACTCCCGAACC
521 AATTAGTACCGAAAAGGCGGTTCAAGGGTGCTAATCCTTCCATGGCCGTAACCGACTCCCGAACC
* *
508106 CGACACGTTTCTGGTACAACGCAGATCAGGTAAGATGGTGTTCGACCCACCTAAATTCGTTTTAA
586 CGACACATTTCTGGTACAACGCAGATCAGGTAAGATGGTGTCCGACCCACCTAAATTCGTTTTAA
* *
508171 AGTGGTCGGTGGCGACTCCAATCCACATTTTTCAAGTCGAAGCCCAATTTCGGGGCCCAACCGAA
651 AATGGTCGGTGGCGACTCCAATCCACATTTTTCAAGTCGAAGCCCAATTCCGGGGCCCAACCGAA
*
508236 ATACG
716 AGACG
508241 GTTTGGCTCCGATCCTCCGACGGAATCAAACTCCATTCTTGGTTCATCAAGCTCTTTCCTGATTG
1 GTTTGGCTCCGATCCTCCGACGGAATCAAACTCCATTCTTGGTTCATCAAGCTCTTTCCTGATTG
* *
508306 CCAATGTCCAACCATCCTATTTTTTTTTCAAGAGAATGCTGGAAACATTGCTCACCGTCTGGAAA
66 CCAAGGTCCAACCATCCTATTTTTTTTTCAAGAGAATGCTAGAAACATTGCTCACCGTCTGGAAA
*
508371 TGGTTCGTATAATGCTACAAAGGTTACAATGTAATGTCTTCATGCTTTCATATCGAGGTTATGGA
131 TGGTTCGTATAATGCTACAAAGGTTACAATGTAATGTCTTCATGCTTCCATATCGAGGTTATGGA
508436 GCAAGTGATGGTTATCCTTCTCAGCGTGGAATTATTAACGATTGCATCAGACTGACATGGGGGAG
196 GCAAGTGATGGTTATCCTTCTCAGCGTGGAATTATTAACGATTGCATCAGACTGACATGGGGGAG
508501 TAAGTTTTTAAAATGCACGTGGAGATGTGCAGCCATTTATGGCCATGCATTTGAGTATTTATTAA
261 TAAGTTTTTAAAATGCACGTGGAGATGTGCAGCCATTTATGGCCATGCATTTGAGTATTTATTAA
508566 GTGTATATTATATTACACACTTTTAACATTTGTTCTCTTAATTTATTTATTTTTCTCTACAATTT
326 GTGTATATTATATTACACACTTTTAACATTTGTTCTCTTAATTTATTTATTTTTCTCTACAATTT
508631 ATTTAGTATTGTTTTATCTAACATTTTTTACTTTCTTTTTAGGACAATTTTAACTAGTTAAAGGT
391 ATTTAGTATTGTTTTATCTAACATTTTTTACTTTCTTTTTAGGACAATTTTAACTAGTTAAAGGT
508696 AAATGATTTGAATCGAGTATTTTAATTCTAATTTAAATTTTCGCAACTAAGACAACCGGCAAATT
456 AAATGATTTGAATCGAGTATTTTAATTCTAATTTAAATTTTCGCAACTAAGACAACCGGCAAATT
*
508761 AATTAGTACCGAAAGGGCGGTTCAAGGGTGCTAATCCTTCCATGGCCGTAACCGACTCCCGAACC
521 AATTAGTACCGAAAAGGCGGTTCAAGGGTGCTAATCCTTCCATGGCCGTAACCGACTCCCGAACC
508826 CGACACATTTCTGGTACAACGCAGATCAGGTAAGATGGTGTCCGACCCACCTAAATTCGTTTTAA
586 CGACACATTTCTGGTACAACGCAGATCAGGTAAGATGGTGTCCGACCCACCTAAATTCGTTTTAA
* *
508891 AATGGTCGGTGGCGACTCCAATCCATATTTTTCAAGTCGAAGCCCAATTCCGGTGCCCAACCGAA
651 AATGGTCGGTGGCGACTCCAATCCACATTTTTCAAGTCGAAGCCCAATTCCGGGGCCCAACCGAA
508956 AGACG
716 AGACG
508961 GTT
1 GTT
508964 CCGACAGCTT
Statistics
Matches: 706, Mismatches: 17, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
720 706 1.00
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (720 bp):
GTTTGGCTCCGATCCTCCGACGGAATCAAACTCCATTCTTGGTTCATCAAGCTCTTTCCTGATTG
CCAAGGTCCAACCATCCTATTTTTTTTTCAAGAGAATGCTAGAAACATTGCTCACCGTCTGGAAA
TGGTTCGTATAATGCTACAAAGGTTACAATGTAATGTCTTCATGCTTCCATATCGAGGTTATGGA
GCAAGTGATGGTTATCCTTCTCAGCGTGGAATTATTAACGATTGCATCAGACTGACATGGGGGAG
TAAGTTTTTAAAATGCACGTGGAGATGTGCAGCCATTTATGGCCATGCATTTGAGTATTTATTAA
GTGTATATTATATTACACACTTTTAACATTTGTTCTCTTAATTTATTTATTTTTCTCTACAATTT
ATTTAGTATTGTTTTATCTAACATTTTTTACTTTCTTTTTAGGACAATTTTAACTAGTTAAAGGT
AAATGATTTGAATCGAGTATTTTAATTCTAATTTAAATTTTCGCAACTAAGACAACCGGCAAATT
AATTAGTACCGAAAAGGCGGTTCAAGGGTGCTAATCCTTCCATGGCCGTAACCGACTCCCGAACC
CGACACATTTCTGGTACAACGCAGATCAGGTAAGATGGTGTCCGACCCACCTAAATTCGTTTTAA
AATGGTCGGTGGCGACTCCAATCCACATTTTTCAAGTCGAAGCCCAATTCCGGGGCCCAACCGAA
AGACG
Found at i:511725 original size:16 final size:14
Alignment explanation
Indices: 511706--511765 Score: 66
Period size: 16 Copynumber: 3.9 Consensus size: 14
511696 AACAAATAGG
511706 GAAAAAACCAAAAAAA
1 GAAAAAA-C-AAAAAA
511722 GAAAAGAAGCAAAAAA
1 GAAAA-AA-CAAAAAA
511738 GAAGAAAACAAAAAA
1 GAA-AAAACAAAAAA
*
511753 GAAAGAACAAAAA
1 GAAAAAACAAAAA
511766 TCAAAAAGAA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
14 9 0.22
15 10 0.25
16 16 0.40
17 5 0.12
ACGTcount: A:0.78, C:0.08, G:0.13, T:0.00
Consensus pattern (14 bp):
GAAAAAACAAAAAA
Found at i:511742 original size:14 final size:14
Alignment explanation
Indices: 511716--511765 Score: 64
Period size: 15 Copynumber: 3.4 Consensus size: 14
511706 GAAAAAACCA
511716 AAAAAAGAAAAGAAGC
1 AAAAAAG-AAAGAA-C
*
511732 AAAAAAGAAGAAAAC
1 AAAAAAGAA-AGAAC
511747 AAAAAAGAAAGAAC
1 AAAAAAGAAAGAAC
511761 AAAAA
1 AAAAA
511766 TCAAAAAGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
14 9 0.29
15 12 0.39
16 10 0.32
ACGTcount: A:0.80, C:0.06, G:0.14, T:0.00
Consensus pattern (14 bp):
AAAAAAGAAAGAAC
Found at i:512431 original size:21 final size:22
Alignment explanation
Indices: 512386--512439 Score: 92
Period size: 21 Copynumber: 2.5 Consensus size: 22
512376 GCTACCCCGT
*
512386 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATAC
512408 CAAACCTTTGAGCA-CAAATAC
1 CAAACCTTTGAGCATCAAATAC
512429 CAAACCTTTGA
1 CAAACCTTTGA
512440 CCAAACACAA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 17 0.55
22 14 0.45
ACGTcount: A:0.39, C:0.28, G:0.11, T:0.22
Consensus pattern (22 bp):
CAAACCTTTGAGCATCAAATAC
Found at i:513222 original size:106 final size:106
Alignment explanation
Indices: 513037--514436 Score: 2266
Period size: 106 Copynumber: 13.3 Consensus size: 106
513027 TTTAGAGTCA
* *
513037 AATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCATGACGAAGG
1 AATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
*
513102 GACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCC
66 GACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCC
*
513143 AATTTCAACTTCACAGCGAAGGATATTGGCCTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* *
513208 GACCGCTGGTTGTCAACAAATAACTTCTCAATTTCAGAGCC
66 GACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCC
*
513249 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
*
513314 GACTGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCC
66 GACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCC
* * * *
513355 AATTTCAACTTCACAACGAAGAATATTGGACTCGAGACAACGAAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
*
513420 GACCGCTGGTTGTCAACAAACAATTTCCCAATTTC-G-G--
66 GACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCC
* * *
513457 ------AGC-TCACATCGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* *
513515 GACCGCTGGTTGTCAACAAACAATTTTCCAATTTC-GAAGCC
66 GACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAG-AGCC
* *
513556 AATTTCAACTTCACAGCGAAGGATATTGGACTCTAGACAACGCAAGTTCAATTTCACGACGAAGG
1 AATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* * * *
513621 GACCGCTGGTTGTCAATAAACAATTTCCCAATTTCATATCC
66 GACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCC
* * *
513662 AATTTCAACTTCACAACGAATGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* *
513727 GACCGCTGGTTGTCAATAAACAACTTTCCAATTTCAGAGCC
66 GACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCC
513768 AATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* *
513833 GACCGCTGGTTGTCAACAAATAACTTCTCAATTTCAGAGCC
66 GACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCC
*
513874 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* * * *
513939 GACCGCTGGTTGTTAATAAACAACTTCACAATTTCAGAACC
66 GACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCC
*
513980 AAATTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
*
514045 GACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCC
66 GACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCC
*
514086 AATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* * *
514151 GACCACTTGTTGTCAACAAACAACTTCTCAATTTCAGAGCC
66 GACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCC
*
514192 AATTTAAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* *
514257 GACCGCTGGTTGTCAATAAACAACTTCCTAATTTCAGAGCC
66 GACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCC
*
514298 AATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
*
514363 GACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCC
66 GACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCC
* *
514404 AATTTCAACTTCACAGTGGAGGATATTGGACTC
1 AATTTCAACTTCACAGCGAAGGATATTGGACTC
514437 GGAACAATAT
Statistics
Matches: 1204, Mismatches: 78, Indels: 24
0.92 0.06 0.02
Matches are distributed among these distances:
95 85 0.07
96 2 0.00
97 1 0.00
104 1 0.00
105 3 0.00
106 1112 0.92
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
AATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
GACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCC
Found at i:515409 original size:21 final size:21
Alignment explanation
Indices: 515385--515427 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
515375 CACTTTTAAC
515385 ATTTGTTCTCTT-AATTTATTT
1 ATTT-TTCTCTTCAATTTATTT
515406 ATTTTTCTCTTCAATTTATTT
1 ATTTTTCTCTTCAATTTATTT
515427 A
1 A
515428 GTATTGTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.21, C:0.12, G:0.02, T:0.65
Consensus pattern (21 bp):
ATTTTTCTCTTCAATTTATTT
Found at i:516128 original size:21 final size:21
Alignment explanation
Indices: 516104--516146 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
516094 CACTTTTAAC
516104 ATTTGTTCTCTT-AATTTATTT
1 ATTT-TTCTCTTCAATTTATTT
516125 ATTTTTCTCTTCAATTTATTT
1 ATTTTTCTCTTCAATTTATTT
516146 A
1 A
516147 GTATTGTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.21, C:0.12, G:0.02, T:0.65
Consensus pattern (21 bp):
ATTTTTCTCTTCAATTTATTT
Found at i:517585 original size:29 final size:29
Alignment explanation
Indices: 517534--517591 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
517524 CACTAAACTT
* * * *
517534 TTTTAAAACTTTCATTTAGGTCCCCCAAC
1 TTTTAAAACTTACAATAAAGTCCCCCAAC
*
517563 TTTTAAAACTTACAATAAAGTCCTCCAAC
1 TTTTAAAACTTACAATAAAGTCCCCCAAC
517592 ATGTAGTCTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.34, C:0.26, G:0.05, T:0.34
Consensus pattern (29 bp):
TTTTAAAACTTACAATAAAGTCCCCCAAC
Found at i:517630 original size:31 final size:31
Alignment explanation
Indices: 517582--517649 Score: 109
Period size: 31 Copynumber: 2.2 Consensus size: 31
517572 TTACAATAAA
*
517582 GTCCTCCAACATGTAGTCTATTTGCAAAATG
1 GTCCCCCAACATGTAGTCTATTTGCAAAATG
* *
517613 GTCCCCCAACATTTAGTCTATTTGCAATATG
1 GTCCCCCAACATGTAGTCTATTTGCAAAATG
517644 GTCCCC
1 GTCCCC
517650 GACCGTTTGA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.25, C:0.28, G:0.15, T:0.32
Consensus pattern (31 bp):
GTCCCCCAACATGTAGTCTATTTGCAAAATG
Found at i:521986 original size:45 final size:45
Alignment explanation
Indices: 521895--522079 Score: 273
Period size: 45 Copynumber: 4.1 Consensus size: 45
521885 GGTAATCATG
* * * * *
521895 AAAATAAGCTTATGAGCATATGTAAT-AATGGCAAGTATATTAGT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGT
521939 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGT
*
521984 AAAATAAGCTTACGAGCTTATGGAACAAATGGTAAGTATATTGGT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGT
** * *
522029 AAAATAATTTTACGAGCTTATGGATTAAATGGTAAGTATATTGAT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGT
522074 AAAATA
1 AAAATA
522080 TTGGATATGT
Statistics
Matches: 129, Mismatches: 11, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
44 23 0.18
45 106 0.82
ACGTcount: A:0.42, C:0.06, G:0.19, T:0.32
Consensus pattern (45 bp):
AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGT
Found at i:524929 original size:18 final size:17
Alignment explanation
Indices: 524882--524954 Score: 59
Period size: 16 Copynumber: 4.6 Consensus size: 17
524872 AATATAGTAT
*
524882 AAGAAAAGAAGAAAAA-
1 AAGAAAAAAAGAAAAAG
*
524898 AAG--AAGAA-AAAAAG
1 AAGAAAAAAAGAAAAAG
524912 AAGAAAAAATAGAAAAAG
1 AAGAAAAAA-AGAAAAAG
*
524930 AA-AAGAAAAGAAAAA-
1 AAGAAAAAAAGAAAAAG
*
524945 TAGAAAAAAA
1 AAGAAAAAAA
524955 ATGAGAGATT
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
13 5 0.11
14 8 0.17
15 1 0.02
16 19 0.40
17 6 0.13
18 8 0.17
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.03
Consensus pattern (17 bp):
AAGAAAAAAAGAAAAAG
Found at i:524956 original size:11 final size:11
Alignment explanation
Indices: 524885--524954 Score: 83
Period size: 11 Copynumber: 6.4 Consensus size: 11
524875 ATAGTATAAG
524885 AAAAGAAGAAA
1 AAAAGAAGAAA
524896 AAAAGAAGAAA
1 AAAAGAAGAAA
524907 AAAAGAAGAAA
1 AAAAGAAGAAA
524918 AAATAGAA-AAA
1 AAA-AGAAGAAA
524929 GAAAAGAA-AAGA
1 -AAAAGAAGAA-A
*
524941 AAAA-TAGAAA
1 AAAAGAAGAAA
524951 AAAA
1 AAAA
524955 ATGAGAGATT
Statistics
Matches: 54, Mismatches: 1, Indels: 9
0.84 0.02 0.14
Matches are distributed among these distances:
10 6 0.11
11 40 0.74
12 8 0.15
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.03
Consensus pattern (11 bp):
AAAAGAAGAAA
Found at i:527933 original size:45 final size:45
Alignment explanation
Indices: 527846--528030 Score: 246
Period size: 45 Copynumber: 4.1 Consensus size: 45
527836 GGTAATCATG
* ** * * *
527846 AAAATCAGCTTATAAGCATATGTAAT-AATGGCAAGTATATTGGT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGT
527890 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGT
*
527935 AAAATAAGCTTACGAGCTTATGGAACAAATGGTAAGTATATTGGT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGT
*** * * *
527980 TTTATAAGCTTACGAGCTTACGGATTAAATGGTAAGTATATTGAT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGT
528025 AAAATA
1 AAAATA
528031 CTGGATACGT
Statistics
Matches: 123, Mismatches: 17, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
44 21 0.17
45 102 0.83
ACGTcount: A:0.40, C:0.08, G:0.20, T:0.32
Consensus pattern (45 bp):
AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGT
Found at i:530041 original size:14 final size:13
Alignment explanation
Indices: 530022--530068 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 13
530012 AAACATAAAA
530022 AAAAAACAAAGAAG
1 AAAAAA-AAAGAAG
530036 AAAAAAAATAGAAG
1 AAAAAAAA-AGAAG
*
530050 AAGAAAAAAAAAAG
1 AA-AAAAAAAGAAG
530064 AAAAA
1 AAAAA
530069 TAGAAAAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
13 5 0.17
14 19 0.63
15 6 0.20
ACGTcount: A:0.83, C:0.02, G:0.13, T:0.02
Consensus pattern (13 bp):
AAAAAAAAAGAAG
Found at i:530065 original size:17 final size:17
Alignment explanation
Indices: 530018--530065 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
530008 TATAAAACAT
*
530018 AAAAAAAAAACAAAGAAG
1 AAAAAAAAAA-GAAGAAG
*
530036 AAAAAAAATAGAAGAAG
1 AAAAAAAAAAGAAGAAG
530053 AAAAAAAAAAGAA
1 AAAAAAAAAAGAA
530066 AAATAGAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 18 0.67
18 9 0.33
ACGTcount: A:0.83, C:0.02, G:0.12, T:0.02
Consensus pattern (17 bp):
AAAAAAAAAAGAAGAAG
Found at i:533157 original size:45 final size:45
Alignment explanation
Indices: 532928--533149 Score: 356
Period size: 45 Copynumber: 5.0 Consensus size: 45
532918 GATAATCATG
* * * *
532928 AAAATAAACTTATGAGCTTATGTAAT-AATGGCAAGTATATTGGT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGT
* *
532972 AAAATAAGCTTACTAGCTTATGTAATAAATGGTAAGTATATTGGT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGT
*
533017 AAAATAAGCTTACGAGCTTATGGAACAAATGGTAAGTATATTGGT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGT
*
533062 AAAATAAGCTTACGAGCTTATGGATTAAATGGTAAGTATATTGGT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGT
*
533107 AAAATAAGCTTACGAGCTTATGGATTAAATGGTAAGTATATTG
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTG
533150 ATGAAATATT
Statistics
Matches: 168, Mismatches: 9, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
44 23 0.14
45 145 0.86
ACGTcount: A:0.40, C:0.07, G:0.20, T:0.33
Consensus pattern (45 bp):
AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGT
Found at i:535458 original size:24 final size:24
Alignment explanation
Indices: 535381--535458 Score: 86
Period size: 24 Copynumber: 3.2 Consensus size: 24
535371 AACAAATCAT
*
535381 AATTCAGATCAGATATCAGAACAG
1 AATTCATATCAGATATCAGAACAG
* *
535405 AATCCATGTCAGGA-ATCAGAACAG
1 AATTCATATCA-GATATCAGAACAG
* * *
535429 ATTTCATATCAGATGTCAGAACAA
1 AATTCATATCAGATATCAGAACAG
535453 AATTCA
1 AATTCA
535459 AATAGGAAAT
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
23 2 0.05
24 39 0.91
25 2 0.05
ACGTcount: A:0.44, C:0.18, G:0.15, T:0.23
Consensus pattern (24 bp):
AATTCATATCAGATATCAGAACAG
Found at i:537748 original size:14 final size:15
Alignment explanation
Indices: 537729--537758 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
537719 TTGGTCGGAC
537729 CGGGTCAAA-CGGGT
1 CGGGTCAAACCGGGT
537743 CGGGTCAAACCGGGT
1 CGGGTCAAACCGGGT
537758 C
1 C
537759 AACTGCCCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.20, C:0.27, G:0.40, T:0.13
Consensus pattern (15 bp):
CGGGTCAAACCGGGT
Done.