Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007850.1 Hibiscus syriacus cultivar Beakdansim tig00110209_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: 1775394
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 9
Found at i:410056 original size:40 final size:42
Alignment explanation
Indices: 410001--410078 Score: 133
Period size: 40 Copynumber: 1.9 Consensus size: 42
409991 AGGTTTTATA
*
410001 TTTAATTTTATATTATAGATA-TTAATTTTA-ATATTAATTT
1 TTTAATATTATATTATAGATATTTAATTTTATATATTAATTT
410041 TTTAATATTATATTATAGATATTTAATTTTATATATTA
1 TTTAATATTATATTATAGATATTTAATTTTATATATTA
410079 TTAAAATTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
40 20 0.57
41 9 0.26
42 6 0.17
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (42 bp):
TTTAATATTATATTATAGATATTTAATTTTATATATTAATTT
Found at i:410062 original size:14 final size:13
Alignment explanation
Indices: 409996--410063 Score: 59
Period size: 14 Copynumber: 5.2 Consensus size: 13
409986 CAAAGAGGTT
*
409996 TTATATT-TAATT
1 TTATATTATAATA
410008 TTATATTATAGATA
1 TTATATTATA-ATA
*
410022 TTA-ATTTTAATA
1 TTATATTATAATA
* *
410034 TTAATTTTTTAATA
1 TT-ATATTATAATA
410048 TTATATTATAGATA
1 TTATATTATA-ATA
410062 TT
1 TT
410064 TAATTTTATA
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
12 12 0.26
13 14 0.30
14 20 0.43
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (13 bp):
TTATATTATAATA
Found at i:410771 original size:31 final size:31
Alignment explanation
Indices: 410720--410779 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
410710 TAGTTGTATG
* * *
410720 AATTATTTAAATTTTAGTATTGTAAAACTAA
1 AATTATTTAAATCTCAGTATTGCAAAACTAA
*
410751 AATTATTTAAATCTCGGTATTGCAAAACT
1 AATTATTTAAATCTCAGTATTGCAAAACT
410780 CTTTTAAGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.42
Consensus pattern (31 bp):
AATTATTTAAATCTCAGTATTGCAAAACTAA
Found at i:411471 original size:2 final size:2
Alignment explanation
Indices: 411464--411502 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
411454 GTTTTATGAT
411464 TA TA 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 TA TA T
411503 TCTTATGTGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:411923 original size:2 final size:2
Alignment explanation
Indices: 411918--411942 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
411908 TTTTCTCTTG
411918 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
411943 CCATTGAAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:413659 original size:2 final size:2
Alignment explanation
Indices: 413654--413684 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
413644 GTCCAAAATG
413654 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
413685 CAAACACACG
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:416117 original size:16 final size:15
Alignment explanation
Indices: 416092--416123 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
416082 TTGCCTGCTG
416092 GCCGCTGCCGCCGCC
1 GCCGCTGCCGCCGCC
416107 GCCGTCTGCCGCCGCC
1 GCCG-CTGCCGCCGCC
416123 G
1 G
416124 TCAGCCGTCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.00, C:0.56, G:0.34, T:0.09
Consensus pattern (15 bp):
GCCGCTGCCGCCGCC
Found at i:416119 original size:13 final size:13
Alignment explanation
Indices: 416101--416137 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
416091 GGCCGCTGCC
*
416101 GCCGCCGCCGTCT
1 GCCGCCGCCGTCA
416114 GCCGCCGCCGTCA
1 GCCGCCGCCGTCA
416127 GCCGTCCGCCG
1 GCCG-CCGCCG
416138 CCACACTCTG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 16 0.73
14 6 0.27
ACGTcount: A:0.03, C:0.54, G:0.32, T:0.11
Consensus pattern (13 bp):
GCCGCCGCCGTCA
Found at i:416132 original size:20 final size:19
Alignment explanation
Indices: 416093--416139 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
416083 TGCCTGCTGG
* *
416093 CCGCTGCCGCCGCCGCCGT
1 CCGCCGCCGCCGCAGCCGT
*
416112 CTGCCGCCGCCGTCAGCCGT
1 CCGCCGCCGCCG-CAGCCGT
416132 CCGCCGCC
1 CCGCCGCC
416140 ACACTCTGAC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
19 10 0.43
20 13 0.57
ACGTcount: A:0.02, C:0.57, G:0.30, T:0.11
Consensus pattern (19 bp):
CCGCCGCCGCCGCAGCCGT
Found at i:424627 original size:55 final size:54
Alignment explanation
Indices: 424563--424805 Score: 236
Period size: 51 Copynumber: 4.6 Consensus size: 54
424553 TGACGAGTCC
* *
424563 GCTCCCTATTCGTTCAGGGAGTATAAGACTCGAACAATATTC-CGTAAACGTGTCT
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATATTCACG--AACGTGTCT
* * * *
424618 GCTCTCTATTCCTTTAGAGAGTAT-AGAACTCGAACAATCTTCAACGAACTTGTCT
1 GCTCCCTATTCCTTCAGAGAGTATAAG-ACTCGAACAATATTC-ACGAACGTGTCT
* * * *
424673 GCTCCCTATTCCTTCAGAGAGTATAGGACT----CAATCTTCAACGAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATATTC-ACGAACGTGTCT
* * * *
424724 GCTCCCTATTCCTTCAGAGAGTATAGGACT----CAATCTTCAACGAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATATTC-ACGAACGTGTCT
424775 GCTCCCTATTCCTTCAGAGAGTATAAGACTC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTC
424806 AATCTTCAAC
Statistics
Matches: 172, Mismatches: 11, Indels: 13
0.88 0.06 0.07
Matches are distributed among these distances:
51 100 0.58
54 2 0.01
55 67 0.39
56 1 0.01
57 2 0.01
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.30
Consensus pattern (54 bp):
GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATATTCACGAACGTGTCT
Found at i:424728 original size:51 final size:51
Alignment explanation
Indices: 424613--424815 Score: 316
Period size: 51 Copynumber: 3.9 Consensus size: 51
424603 TCCGTAAACG
* * * *
424613 TGTCTGCTCTCTATTCCTTTAGAGAGTATAGAACTCGAACAATCTTCAACGAACT
1 TGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACT----CAATCTTCAACGAACT
*
424668 TGTCTGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACT
1 TGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACT
424719 TGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACT
1 TGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACT
*
424770 TGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTCAATCTTCAAC
1 TGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAAC
424816 AAACGAGTTT
Statistics
Matches: 143, Mismatches: 5, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
51 111 0.78
55 32 0.22
ACGTcount: A:0.27, C:0.28, G:0.15, T:0.31
Consensus pattern (51 bp):
TGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACT
Found at i:424805 original size:102 final size:104
Alignment explanation
Indices: 424559--424820 Score: 327
Period size: 102 Copynumber: 2.5 Consensus size: 104
424549 CGAATGACGA
* * * *
424559 GTCCGCTCCCTATTCGTTCAGGGAGTATAAGACTCGAACAATATTC--CGTAAACGTGTCTGCTC
1 GTCCGCTCCCTATTCCTTCAGAGAGTATAAGACT----CAATCTTCAACG-AAACGTGTCCGCTC
* *
424622 TCTATTCCTTTAGAGAGTATAGAACTCGAACAATCTTCAACGAACTT
61 CCTATTCCTTCAGAGAGTATAGAACT---ACAATCTTCAACGAACTT
* * *
424669 GTCTGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACG-AACTTGTCCGCTCCCTAT
1 GTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTCAATCTTCAACGAAACGTGTCCGCTCCCTAT
*
424733 TCCTTCAGAGAGTATAGGACT-CAATCTTCAACGAACTT
66 TCCTTCAGAGAGTATAGAACTACAATCTTCAACGAACTT
424771 GTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTCAATCTTCAAC-AAACG
1 GTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTCAATCTTCAACGAAACG
424821 AGTTTGCTTC
Statistics
Matches: 136, Mismatches: 13, Indels: 14
0.83 0.08 0.09
Matches are distributed among these distances:
102 63 0.46
106 41 0.30
108 2 0.01
110 30 0.22
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.29
Consensus pattern (104 bp):
GTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTCAATCTTCAACGAAACGTGTCCGCTCCCTAT
TCCTTCAGAGAGTATAGAACTACAATCTTCAACGAACTT
Found at i:426248 original size:11 final size:10
Alignment explanation
Indices: 426168--426375 Score: 55
Period size: 10 Copynumber: 19.1 Consensus size: 10
426158 TGAAACCTCC
*
426168 TTTTATTTCT
1 TTTTTTTTCT
426178 TTTTTTTT-T
1 TTTTTTTTCT
* *
426187 CATTTTTCTCT
1 -TTTTTTTTCT
426198 TTTTGTTGTTCT
1 TTTT-TT-TTCT
426210 CTTTCATTTTTCT
1 -TTT--TTTTTCT
***
426223 TCCATTTTCT
1 TTTTTTTTCT
* *
426233 ATTTTTTCCT
1 TTTTTTTTCT
426243 TTTTTTTTCTT
1 TTTTTTTTC-T
*
426254 TTCATTTTTTCCA
1 TT--TTTTTT-CT
**
426267 TCATTTTTC-
1 TTTTTTTTCT
*
426276 TTTTTTCTCAT
1 TTTTTTTTC-T
426287 TTTTCTTTTC-
1 TTTT-TTTTCT
*
426297 TTCTTTTTCT
1 TTTTTTTTCT
*
426307 TTTTCTTCTCAT
1 TTTT-TTTTC-T
*
426319 TTTTATTATTAT
1 TTTT-TT-TTCT
426331 TATTTTTTTCT
1 T-TTTTTTTCT
426342 TTTTTTCATT-T
1 TTTTTT--TTCT
426353 TTTCTTTTTCT
1 TTT-TTTTTCT
*
426364 CTTTTATTTCT
1 -TTTTTTTTCT
426375 T
1 T
426376 CTTCAAGCGA
Statistics
Matches: 144, Mismatches: 30, Indels: 48
0.65 0.14 0.22
Matches are distributed among these distances:
9 12 0.08
10 49 0.34
11 34 0.24
12 27 0.19
13 18 0.12
14 3 0.02
15 1 0.01
ACGTcount: A:0.08, C:0.16, G:0.01, T:0.75
Consensus pattern (10 bp):
TTTTTTTTCT
Found at i:426273 original size:43 final size:43
Alignment explanation
Indices: 426189--426298 Score: 109
Period size: 44 Copynumber: 2.5 Consensus size: 43
426179 TTTTTTTTCA
* *
426189 TTTTTCTCTTTTTGTTGTTCTCTTTCATTTTTCTTCCA-TTTTCTAT
1 TTTTTC-CTTTTTCTT-TTCT-TTTCATTTTTCATCCATTTTTCT-T
426235 TTTTTCCTTTTT-TTTTCTTTTCATTTTTTCCAT-CATTTTTCTT
1 TTTTTCCTTTTTCTTTTCTTTTCA-TTTTT-CATCCATTTTTCTT
*
426278 TTTTCTCATTTTTCTTTTCTT
1 TTTT-TCCTTTTTCTTTTCTT
426299 CTTTTTCTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
42 5 0.09
43 16 0.28
44 17 0.30
45 13 0.23
46 6 0.11
ACGTcount: A:0.06, C:0.19, G:0.02, T:0.73
Consensus pattern (43 bp):
TTTTTCCTTTTTCTTTTCTTTTCATTTTTCATCCATTTTTCTT
Found at i:426280 original size:25 final size:25
Alignment explanation
Indices: 426227--426279 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 25
426217 TTTTCTTCCA
* **
426227 TTTTCTATTTTTTCCTTTTTTTTTC
1 TTTTCTATTTTTTCCATCATTTTTC
426252 TTTTC-ATTTTTTCCATCATTTTTC
1 TTTTCTATTTTTTCCATCATTTTTC
426276 TTTT
1 TTTT
426280 TTCTCATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 20 0.80
25 5 0.20
ACGTcount: A:0.08, C:0.17, G:0.00, T:0.75
Consensus pattern (25 bp):
TTTTCTATTTTTTCCATCATTTTTC
Found at i:426353 original size:14 final size:16
Alignment explanation
Indices: 426252--426361 Score: 84
Period size: 16 Copynumber: 6.6 Consensus size: 16
426242 TTTTTTTTTC
426252 TTTTCATTTTTTCCATCAT
1 TTTTC-TTTTTT-C-TCAT
426271 TTTTCTTTTTTCTCAT
1 TTTTCTTTTTTCTCAT
*
426287 TTTTCTTTTCT-TC-T
1 TTTTCTTTTTTCTCAT
426301 TTTTCTTTTTCTTCTCAT
1 TTTTC-TTTT-TTCTCAT
* * *
426319 TTTTATTATTATTAT-TT
1 TTTTCTT-TT-TTCTCAT
426336 TTTTCTTTTTT-TCATT
1 TTTTCTTTTTTCTCA-T
426352 TTTTCTTTTT
1 TTTTCTTTTT
426362 CTCTTTTATT
Statistics
Matches: 76, Mismatches: 8, Indels: 17
0.75 0.08 0.17
Matches are distributed among these distances:
14 7 0.09
15 8 0.11
16 28 0.37
17 12 0.16
18 16 0.21
19 5 0.07
ACGTcount: A:0.09, C:0.15, G:0.00, T:0.75
Consensus pattern (16 bp):
TTTTCTTTTTTCTCAT
Found at i:444912 original size:19 final size:19
Alignment explanation
Indices: 444885--444922 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
444875 TCTCACACAC
444885 ACACACACACACATCGCAT
1 ACACACACACACATCGCAT
*
444904 ACACGCACACACATCGCAT
1 ACACACACACACATCGCAT
444923 TCTTATGTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.39, C:0.42, G:0.08, T:0.11
Consensus pattern (19 bp):
ACACACACACACATCGCAT
Found at i:450722 original size:29 final size:31
Alignment explanation
Indices: 450680--450742 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 31
450670 ACAAGGTAAG
*
450680 TGACTACATTTTAAT-AAATAAAAA-CAAACA
1 TGACTACATCTTAATGAAATAAAAACCAAA-A
450710 TGAC-ACATCTTAATGAAATAAAAACCAAAA
1 TGACTACATCTTAATGAAATAAAAACCAAAA
450740 TGA
1 TGA
450743 TCAAATATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 9 0.30
30 17 0.57
31 4 0.13
ACGTcount: A:0.56, C:0.14, G:0.06, T:0.24
Consensus pattern (31 bp):
TGACTACATCTTAATGAAATAAAAACCAAAA
Found at i:451754 original size:20 final size:20
Alignment explanation
Indices: 451725--451764 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
451715 TTTAAAATTT
*
451725 TTATTTTTAAAAAATAAAAA
1 TTATTATTAAAAAATAAAAA
*
451745 TTATTATTAAATAATAAAAA
1 TTATTATTAAAAAATAAAAA
451765 AACCTTTCCC
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
TTATTATTAAAAAATAAAAA
Found at i:457359 original size:26 final size:24
Alignment explanation
Indices: 457321--457385 Score: 71
Period size: 25 Copynumber: 2.6 Consensus size: 24
457311 CTTTTGCCAA
457321 TTAT-TAATATATTTTT-ATAAGTAAT
1 TTATATAAT-TATTTTTGATAA--AAT
457346 TTAATATAATTATTTTTTGATAAAAT
1 TT-ATATAATTA-TTTTTGATAAAAT
457372 TTATATAATTATTT
1 TTATATAATTATTT
457386 AAATTTAGCA
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
24 3 0.08
25 11 0.31
26 9 0.25
27 9 0.25
28 4 0.11
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (24 bp):
TTATATAATTATTTTTGATAAAAT
Found at i:458188 original size:19 final size:19
Alignment explanation
Indices: 458164--458216 Score: 97
Period size: 19 Copynumber: 2.8 Consensus size: 19
458154 AATGACCAAC
458164 AAAATCGCAATGCGAAATA
1 AAAATCGCAATGCGAAATA
458183 AAAATCGCAATGCGAAATA
1 AAAATCGCAATGCGAAATA
*
458202 AAAATCGCAACGCGA
1 AAAATCGCAATGCGA
458217 TCTCCAGAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.51, C:0.19, G:0.17, T:0.13
Consensus pattern (19 bp):
AAAATCGCAATGCGAAATA
Found at i:458248 original size:21 final size:20
Alignment explanation
Indices: 458166--458250 Score: 66
Period size: 19 Copynumber: 4.3 Consensus size: 20
458156 TGACCAACAA
* * *
458166 AATCGCAATGCGAAAT-AAA
1 AATCGCAACGCGATATCAAG
* * *
458185 AATCGCAATGCGAAAT-AAA
1 AATCGCAACGCGATATCAAG
* *
458204 AATCGCAACGCGATCTCCAG
1 AATCGCAACGCGATATCAAG
*
458224 AATCGCAACGCGATTATGAAG
1 AATCGCAACGCGA-TATCAAG
458245 AATCGC
1 AATCGC
458251 GCAAATTAGC
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
19 32 0.57
20 14 0.25
21 10 0.18
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.16
Consensus pattern (20 bp):
AATCGCAACGCGATATCAAG
Found at i:458301 original size:20 final size:20
Alignment explanation
Indices: 458276--458528 Score: 147
Period size: 20 Copynumber: 12.5 Consensus size: 20
458266 GATTTTCCAG
*
458276 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATACGAA
* *
458296 AATCGCAACGCGAACA-TATA
1 AATCGCAACGCGAATACGA-A
* *
458316 AATCGCAACGCG-ATTCTGAC
1 AATCGCAACGCGAATAC-GAA
* * * *
458336 TATCGCAACGAGTATCCGTAA
1 AATCGCAACGCGAATACG-AA
** * * *
458357 AATCATAACGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
458377 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATACG-AA
* * *
458398 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
* *
458418 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATACGAA
* *
458438 AATCGCAACGCGTAT-CTGTA
1 AATCGCAACGCGAATAC-GAA
* *
458458 AATCGCAACGTGAATACGTA
1 AATCGCAACGCGAATACGAA
* * * *
458478 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
*
458498 AATCGCAACGAC-AATACATAA
1 AATCGCAACG-CGAATAC-GAA
458519 AATCGCAACG
1 AATCGCAACG
458529 TGATTTTTAA
Statistics
Matches: 182, Mismatches: 39, Indels: 23
0.75 0.16 0.09
Matches are distributed among these distances:
19 3 0.02
20 131 0.72
21 48 0.26
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAATACGAA
Found at i:458359 original size:61 final size:61
Alignment explanation
Indices: 458294--458528 Score: 187
Period size: 61 Copynumber: 3.9 Consensus size: 61
458284 CGCGAATATG
** * **
458294 AAAATCGCAACGCGAACATATAAATCGCAACGCGATTC-TGACTATCGCAACGAGTATCCGT
1 AAAATCGCAACGCGAACACGTAAATCGCAACGCGATACGT-AAAATCGCAACGAGTATCCGT
** * * *
458355 AAAATCATAACGCGTATC-CGTAAATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGT
1 AAAATCGCAACGCG-AACACGTAAATCGCAACG-CGATACGTAAAATCGCAACGAGTATCCGT
* * * * *
458417 -AAATCGCAACGAGAATACGTAAATCGCAACGCG-TATCTGT-AAATCGCAACGTGAATACGT
1 AAAATCGCAACGCGAACACGTAAATCGCAACGCGATA-C-GTAAAATCGCAACGAGTATCCGT
* * * *
458477 -AAATCGCAATGCGTATC-CGTAAATCGCAACGACAATACATAAAATCGCAACG
1 AAAATCGCAACGCG-AACACGTAAATCGCAACG-CGATACGTAAAATCGCAACG
458529 TGATTTTTAA
Statistics
Matches: 139, Mismatches: 25, Indels: 20
0.76 0.14 0.11
Matches are distributed among these distances:
59 2 0.01
60 46 0.33
61 64 0.46
62 26 0.19
63 1 0.01
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (61 bp):
AAAATCGCAACGCGAACACGTAAATCGCAACGCGATACGTAAAATCGCAACGAGTATCCGT
Found at i:458371 original size:21 final size:21
Alignment explanation
Indices: 458337--458507 Score: 167
Period size: 20 Copynumber: 8.4 Consensus size: 21
458327 GATTCTGACT
*
458337 ATCGCAACGAGTATCCGTAAA
1 ATCGCAACGCGTATCCGTAAA
**
458358 ATCATAACGCGTATCCGT-AA
1 ATCGCAACGCGTATCCGTAAA
* *
458378 ATCGCAACGAC-AATACGTAAA
1 ATCGCAACG-CGTATCCGTAAA
458399 ATCGCAACGCGTATCCGT-AA
1 ATCGCAACGCGTATCCGTAAA
* * *
458419 ATCGCAACGAGAATACGT-AA
1 ATCGCAACGCGTATCCGTAAA
*
458439 ATCGCAACGCGTATCTGT-AA
1 ATCGCAACGCGTATCCGTAAA
* * *
458459 ATCGCAACGTGAATACGT-AA
1 ATCGCAACGCGTATCCGTAAA
*
458479 ATCGCAATGCGTATCCGT-AA
1 ATCGCAACGCGTATCCGTAAA
458499 ATCGCAACG
1 ATCGCAACG
458508 ACAATACATA
Statistics
Matches: 122, Mismatches: 25, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
20 90 0.74
21 32 0.26
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGTATCCGTAAA
Found at i:458382 original size:41 final size:40
Alignment explanation
Indices: 458276--458528 Score: 267
Period size: 40 Copynumber: 6.2 Consensus size: 40
458266 GATTTTCCAG
* ** * * * **
458276 AATCGCAACGCGAATATGAAAATCGCAACGCGAACATATA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTA
* * * *
458316 AATCGCAACGCG-ATTC-TGACTATCGCAACGAGTATCCGTAA
1 AATCGCAACGCGTATCCGT-A-AATCGCAACGAGAATACGT-A
** *
458357 AATCATAACGCGTATCCGTAAATCGCAACGACAATACGTAA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGT-A
458398 AATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTA
* *
458438 AATCGCAACGCGTATCTGTAAATCGCAACGTGAATACGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTA
* * *
458478 AATCGCAATGCGTATCCGTAAATCGCAACGACAATACATAA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGT-A
458519 AATCGCAACG
1 AATCGCAACG
458529 TGATTTTTAA
Statistics
Matches: 179, Mismatches: 28, Indels: 11
0.82 0.13 0.05
Matches are distributed among these distances:
39 3 0.02
40 97 0.54
41 74 0.41
42 4 0.02
43 1 0.01
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.19
Consensus pattern (40 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTA
Found at i:458452 original size:40 final size:41
Alignment explanation
Indices: 458337--458528 Score: 280
Period size: 40 Copynumber: 4.7 Consensus size: 41
458327 GATTCTGACT
* * **
458337 ATCGCAACGAGTATCCGTAAAATCATAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
*
458378 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
*
458419 ATCGCAACGAGAATACGT-AAATCGCAACGCGTATCTGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* *
458459 ATCGCAACGTGAATACGT-AAATCGCAATGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* *
458499 ATCGCAACGACAATACATAAAATCGCAACG
1 ATCGCAACGAGAATACGTAAAATCGCAACG
458529 TGATTTTTAA
Statistics
Matches: 136, Mismatches: 14, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
40 73 0.54
41 63 0.46
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.19
Consensus pattern (41 bp):
ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
Found at i:459149 original size:21 final size:20
Alignment explanation
Indices: 459088--459167 Score: 92
Period size: 20 Copynumber: 4.0 Consensus size: 20
459078 TTCTAAACTT
459088 AAAATCGCAAC-ATGAAAATG
1 AAAATCGCAACGA-GAAAATG
459108 AAAATCGCAAC-ACGAAAATG
1 AAAATCGCAACGA-GAAAATG
**
459128 ACTATCGCAACGAGAGAAATG
1 AAAATCGCAACGAGA-AAATG
*
459149 AAAATCACAACGAGAAAAT
1 AAAATCGCAACGAGAAAAT
459168 CGCAACGCGA
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
20 34 0.65
21 18 0.35
ACGTcount: A:0.54, C:0.17, G:0.16, T:0.12
Consensus pattern (20 bp):
AAAATCGCAACGAGAAAATG
Found at i:459151 original size:41 final size:40
Alignment explanation
Indices: 459091--459167 Score: 104
Period size: 41 Copynumber: 1.9 Consensus size: 40
459081 TAAACTTAAA
*
459091 ATCGCAACATGAAAATGAAAATCGCAAC-ACGAAAATGACT
1 ATCGCAACATGAAAATGAAAATCACAACGA-GAAAATGACT
459131 ATCGCAACGA-GAGAAATGAAAATCACAACGAGAAAAT
1 ATCGCAAC-ATGA-AAATGAAAATCACAACGAGAAAAT
459168 CGCAACGCGA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
40 10 0.30
41 22 0.67
42 1 0.03
ACGTcount: A:0.52, C:0.18, G:0.17, T:0.13
Consensus pattern (40 bp):
ATCGCAACATGAAAATGAAAATCACAACGAGAAAATGACT
Found at i:459210 original size:14 final size:14
Alignment explanation
Indices: 459191--459244 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
459181 CAAAATCGCA
459191 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
459205 TTGCGATTTTCATTTCGCG
1 TTGCGA--TTC---TCTCG
459224 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
459238 TTGCGAT
1 TTGCGAT
459245 AGTCATTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 17 0.52
16 3 0.09
17 3 0.09
19 10 0.30
ACGTcount: A:0.09, C:0.24, G:0.22, T:0.44
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:459233 original size:33 final size:33
Alignment explanation
Indices: 459186--459293 Score: 126
Period size: 33 Copynumber: 3.1 Consensus size: 33
459176 GAAACCAAAA
*
459186 TCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTCTCTCGTTGCGATTTTCATT
**
459219 TCGCGTTGCGATTCTCTCGTTGCGATAGTCATTT
1 TCGCGTTGCGATTCTCTCGTTGCGATTTTCA-TT
459253 TCGCGTTGCGATAGTCATTCTCTCGTTGCGATTTTCATT
1 TCGCGTTGC----G--ATTCTCTCGTTGCGATTTTCATT
459292 TC
1 TC
459294 AACCAAAAGA
Statistics
Matches: 63, Mismatches: 5, Indels: 8
0.83 0.07 0.11
Matches are distributed among these distances:
33 28 0.44
34 11 0.17
38 1 0.02
39 4 0.06
40 19 0.30
ACGTcount: A:0.12, C:0.24, G:0.20, T:0.44
Consensus pattern (33 bp):
TCGCGTTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:459291 original size:20 final size:20
Alignment explanation
Indices: 459229--459284 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
459219 TCGCGTTGCG
459229 ATTCTCTCGTTGCGATAGTC
1 ATTCTCTCGTTGCGATAGTC
* *
459249 ATTTTCGCGTTGCGATAGTC
1 ATTCTCTCGTTGCGATAGTC
459269 ATTCTCTCGTTGCGAT
1 ATTCTCTCGTTGCGAT
459285 TTTCATTTCA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.14, C:0.23, G:0.21, T:0.41
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATAGTC
Found at i:461150 original size:94 final size:94
Alignment explanation
Indices: 460989--461368 Score: 638
Period size: 94 Copynumber: 4.1 Consensus size: 94
460979 TAGATTGCTT
* *
460989 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACTGTTTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
461054 ATTTGTCTTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGAA
461083 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
461148 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* * * *
461177 AGTAAATTTGTTCGGTTGTTGTCAATTCTGCTAAACTGTATATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
461242 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* ** * *
461271 AGTAAATTTGTTCGGAAGCTGCCAATTCTGCTAAACTGTGTATTCTTTAATACTATGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
461336 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
461364 AGTAA
1 AGTAA
461369 TGCAATCCAT
Statistics
Matches: 272, Mismatches: 13, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
93 26 0.10
94 246 0.90
ACGTcount: A:0.22, C:0.12, G:0.19, T:0.47
Consensus pattern (94 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:461531 original size:19 final size:19
Alignment explanation
Indices: 461416--461533 Score: 84
Period size: 19 Copynumber: 6.2 Consensus size: 19
461406 TAGTTTACTT
*
461416 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-TAAAA
* *
461436 GCGCAACGTGAAA--AAGACTA
1 TCGCAACGCGAAACTAA-A--A
* *
461456 TCGCAACGTGAAA-T-GAA
1 TCGCAACGCGAAACTAAAA
*
461473 TCGCGACGCGAAA-TGAAAA
1 TCGCAACGCGAAACT-AAAA
*
461492 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACTAAAA
*
461511 TCGCAACGCGAAACTATAA
1 TCGCAACGCGAAACTAAAA
461530 TCGC
1 TCGC
461534 GTTGCGATTT
Statistics
Matches: 79, Mismatches: 12, Indels: 15
0.75 0.11 0.14
Matches are distributed among these distances:
17 15 0.19
18 1 0.01
19 40 0.51
20 23 0.29
ACGTcount: A:0.43, C:0.25, G:0.19, T:0.13
Consensus pattern (19 bp):
TCGCAACGCGAAACTAAAA
Found at i:461552 original size:19 final size:19
Alignment explanation
Indices: 461530--461617 Score: 87
Period size: 19 Copynumber: 4.8 Consensus size: 19
461520 GAAACTATAA
461530 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
461549 TCGCGTTGCGATTCTC--T
1 TCGCGTTGCGATTTTCATT
461566 T---GTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
461582 TCGCGTTGCGATAGTCATTTT
1 TCGCGTTGCGATTTTCA--TT
*
461603 TCACGTTGCGATTTT
1 TCGCGTTGCGATTTT
461618 AAGTTCCAGA
Statistics
Matches: 55, Mismatches: 7, Indels: 12
0.74 0.09 0.16
Matches are distributed among these distances:
14 11 0.20
16 2 0.04
17 2 0.04
19 26 0.47
21 14 0.25
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:462094 original size:21 final size:21
Alignment explanation
Indices: 462070--462136 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
462060 TCATTCCTCG
462070 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
462091 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
462112 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
462133 AGAG
1 AGAG
462137 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:462094 original size:42 final size:42
Alignment explanation
Indices: 462018--462136 Score: 107
Period size: 42 Copynumber: 2.8 Consensus size: 42
462008 GACTCGCCTG
* * * * * * *
462018 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
*
462060 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
* * *
462102 TCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 TCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
462137 CCCGATTCAC
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 4 0.06
42 58 0.91
43 2 0.03
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:463519 original size:14 final size:14
Alignment explanation
Indices: 463486--463522 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
463476 GATTGTTTAA
463486 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
**
463500 AAGATTTGTAAAAG
1 TTGATTTGTAAAAG
463514 TTGATTTGT
1 TTGATTTGT
463523 TTAATTGATG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.35, C:0.00, G:0.22, T:0.43
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:463644 original size:19 final size:19
Alignment explanation
Indices: 463628--463668 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
463618 CAAAATGACT
*
463628 ATCGCAATGCGAAATGAAA
1 ATCGAAATGCGAAATGAAA
463647 ATCGAAATGCGAAATGAAA
1 ATCGAAATGCGAAATGAAA
463666 ATC
1 ATC
463669 ACAACGAGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.49, C:0.15, G:0.20, T:0.17
Consensus pattern (19 bp):
ATCGAAATGCGAAATGAAA
Found at i:463683 original size:33 final size:33
Alignment explanation
Indices: 463644--463740 Score: 115
Period size: 33 Copynumber: 2.9 Consensus size: 33
463634 ATGCGAAATG
*
463644 AAAATCGAAATGCGAAATGAAAATCACAACGAG
1 AAAATCGAAATGCGAAATGAAAATCACAACGAC
* * *
463677 AGAATCGCAATGCGAAATGAAAATCTCAACGAC
1 AAAATCGAAATGCGAAATGAAAATCACAACGAC
* * *
463710 AAAATCGTAACGCGAAACT-AAAATCGCAACG
1 AAAATCGAAATGCGAAA-TGAAAATCACAACG
463741 CGAAACTAAA
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
33 54 0.98
34 1 0.02
ACGTcount: A:0.49, C:0.20, G:0.18, T:0.13
Consensus pattern (33 bp):
AAAATCGAAATGCGAAATGAAAATCACAACGAC
Found at i:463762 original size:19 final size:19
Alignment explanation
Indices: 463710--463755 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
463700 TCTCAACGAC
*
463710 AAAATCGTAACGCGAAACT
1 AAAATCGCAACGCGAAACT
463729 AAAATCGCAACGCGAAACT
1 AAAATCGCAACGCGAAACT
*
463748 AAATTCGC
1 AAAATCGC
463756 GTTGCGATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.46, C:0.24, G:0.15, T:0.15
Consensus pattern (19 bp):
AAAATCGCAACGCGAAACT
Found at i:463773 original size:19 final size:19
Alignment explanation
Indices: 463751--463921 Score: 93
Period size: 19 Copynumber: 9.7 Consensus size: 19
463741 CGAAACTAAA
463751 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
463770 TTCGCTTTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
** *
463785 -TCTAGTTGCAATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* * **
463803 TTCGCATTGCAATAGTCAT
1 TTCGCGTTGCGATTTTCAT
*
463822 TTCCGCGTTGCGATATTCAT
1 TT-CGCGTTGCGATTTTCAT
*
463842 ATCCGCGTTGCGATTTTCA-
1 -TTCGCGTTGCGATTTTCAT
*
463861 ----CGTTGCGATTTTTAT
1 TTCGCGTTGCGATTTTCAT
*
463876 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
463891 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
463909 TTCGCATTGCGAT
1 TTCGCGTTGCGAT
463922 AGACATTAAG
Statistics
Matches: 113, Mismatches: 22, Indels: 34
0.67 0.13 0.20
Matches are distributed among these distances:
14 29 0.26
16 6 0.05
17 5 0.04
19 43 0.38
20 29 0.26
21 1 0.01
ACGTcount: A:0.15, C:0.22, G:0.19, T:0.44
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:463799 original size:33 final size:33
Alignment explanation
Indices: 463756--463921 Score: 154
Period size: 33 Copynumber: 4.8 Consensus size: 33
463746 CTAAATTCGC
*
463756 GTTGCGATTTTCATTTCGCTTTGCGATTCTCTA
1 GTTGCGATTTTCATTTCGCATTGCGATTCTCTA
* * **
463789 GTTGCAATTTTCATTTCGCATTGCAATAGTCATTTCCGC
1 GTTGCGATTTTCATTTCGCATTGCGAT--TC---T-CTA
* * * *
463828 GTTGCGATATTCATATCCGCGTTGCGATTTTC-A
1 GTTGCGATTTTCAT-TTCGCATTGCGATTCTCTA
* *
463861 CGTTGCGATTTTTATTTCGCATTGCGATTCTCTC
1 -GTTGCGATTTTCATTTCGCATTGCGATTCTCTA
463895 GTTGCGATTTTCATTTCGCATTGCGAT
1 GTTGCGATTTTCATTTCGCATTGCGAT
463922 AGACATTAAG
Statistics
Matches: 105, Mismatches: 19, Indels: 18
0.74 0.13 0.13
Matches are distributed among these distances:
33 64 0.61
34 13 0.12
35 3 0.03
38 2 0.02
39 13 0.12
40 10 0.10
ACGTcount: A:0.16, C:0.22, G:0.19, T:0.44
Consensus pattern (33 bp):
GTTGCGATTTTCATTTCGCATTGCGATTCTCTA
Found at i:463841 original size:20 final size:20
Alignment explanation
Indices: 463798--463860 Score: 74
Period size: 20 Copynumber: 3.2 Consensus size: 20
463788 AGTTGCAATT
* *
463798 TTCATTT-CGCATTGCAATA
1 TTCATTTCCGCGTTGCGATA
*
463817 GTCATTTCCGCGTTGCGATA
1 TTCATTTCCGCGTTGCGATA
* *
463837 TTCATATCCGCGTTGCGATT
1 TTCATTTCCGCGTTGCGATA
463857 TTCA
1 TTCA
463861 CGTTGCGATT
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
19 6 0.16
20 31 0.84
ACGTcount: A:0.19, C:0.24, G:0.17, T:0.40
Consensus pattern (20 bp):
TTCATTTCCGCGTTGCGATA
Found at i:466490 original size:24 final size:24
Alignment explanation
Indices: 466423--466482 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
466413 CTGAAAAATC
466423 ATCAAAATTCGAGTATTGACCAAG
1 ATCAAAATTCGAGTATTGACCAAG
* * *
466447 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATTCGAGTATTGACCAAG
*
466471 ATCAAATTTCGA
1 ATCAAAATTCGA
466483 ATACTGACTA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.25
Consensus pattern (24 bp):
ATCAAAATTCGAGTATTGACCAAG
Found at i:467364 original size:20 final size:20
Alignment explanation
Indices: 467339--467550 Score: 178
Period size: 20 Copynumber: 10.5 Consensus size: 20
467329 GTCAGAATCT
*
467339 CGTTGCGATTTACGTATTCG
1 CGTTGCGATTTACGTATACG
* *
467359 CATTGCGATTTACGTATTCG
1 CGTTGCGATTTACGTATACG
* *
467379 CATTGCGATTTACGGATACG
1 CGTTGCGATTTACGTATACG
*
467399 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGTATACG
*
467419 CGTTGCGATTTTACGTAT-TG
1 CGTTGCGA-TTTACGTATACG
* *
467439 TTGTTGCGATTTACGAATACG
1 -CGTTGCGATTTACGTATACG
* *
467460 CGTTGCGATTTTACGGATACT
1 CGTTGCGA-TTTACGTATACG
* *
467481 CGTTGCGATAGT-CAGAAT-CG
1 CGTTGCGAT-TTAC-GTATACG
** * *
467501 CGTTGCGATTTATATGTTCG
1 CGTTGCGATTTACGTATACG
* * *
467521 CGTTGCGATTTTCATATTCG
1 CGTTGCGATTTACGTATACG
467541 CGTTGCGATT
1 CGTTGCGATT
467551 CTGGAAAATC
Statistics
Matches: 161, Mismatches: 23, Indels: 16
0.81 0.12 0.08
Matches are distributed among these distances:
19 2 0.01
20 121 0.75
21 38 0.24
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.38
Consensus pattern (20 bp):
CGTTGCGATTTACGTATACG
Found at i:467506 original size:61 final size:60
Alignment explanation
Indices: 467339--467512 Score: 181
Period size: 61 Copynumber: 2.9 Consensus size: 60
467329 GTCAGAATCT
* * * * * * *
467339 CGTTGCGATTTACGTATTCGCATTGCGAT-TTACGTATTCGCATTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACGCGTTGCGATGTCACG-AATCGCGTTGCGATTTACGAATACG
* * * * *
467399 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTTGTTGCGATTTACGAATACG
1 CGTTGCGATTTACGGATACGCGTTGCGATGTCACGAATCG-CGTTGCGATTTACGAATACG
*
467460 CGTTGCGATTTTACGGATACTCGTTGCGATAGTCA-GAATCGCGTTGCGATTTA
1 CGTTGCGA-TTTACGGATACGCGTTGCGAT-GTCACGAATCGCGTTGCGATTTA
467513 TATGTTCGCG
Statistics
Matches: 95, Mismatches: 15, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
60 28 0.29
61 41 0.43
62 24 0.25
63 2 0.02
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.36
Consensus pattern (60 bp):
CGTTGCGATTTACGGATACGCGTTGCGATGTCACGAATCGCGTTGCGATTTACGAATACG
Found at i:467649 original size:20 final size:19
Alignment explanation
Indices: 467600--467653 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
467590 ATTCTTAATA
467600 ATCGCGTTGCGATTCTGGG
1 ATCGCGTTGCGATTCTGGG
* **
467619 AACTGATTTGCGATTCTGGAG
1 ATC-GCGTTGCGATTCTGG-G
467640 ATCGCGTTGCGATT
1 ATCGCGTTGCGATT
467654 TTTATTTCGC
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 3 0.11
ACGTcount: A:0.17, C:0.19, G:0.31, T:0.33
Consensus pattern (19 bp):
ATCGCGTTGCGATTCTGGG
Found at i:470033 original size:20 final size:20
Alignment explanation
Indices: 470008--470055 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
469998 TGAAAATCGT
470008 GTTGCGATTTTCCATTTCGC
1 GTTGCGATTTTCCATTTCGC
470028 GTTGCGATTTTCCATTTCGC
1 GTTGCGATTTTCCATTTCGC
470048 GTTGCGAT
1 GTTGCGAT
470056 AGTCTACAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.10, C:0.23, G:0.23, T:0.44
Consensus pattern (20 bp):
GTTGCGATTTTCCATTTCGC
Found at i:470072 original size:41 final size:41
Alignment explanation
Indices: 470027--470184 Score: 232
Period size: 41 Copynumber: 3.9 Consensus size: 41
470017 TTCCATTTCG
*
470027 CGTTGCGATTTTCC-ATTTCGCGTTGCGATAGTCTACA-ATGT
1 CGTTGCGATTTTCCAAATT--CGTTGCGATAGTCTACAGATGT
* *
470068 CGTTGCGATTTTCCAAATTCGTTGCGATAGTCTATAGTTGT
1 CGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGATGT
* *
470109 CGTTGCGATTTTCCAAATTCGTTGCGAAAGTCTACAGTTGT
1 CGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGATGT
470150 CGTTGCGATTTTCCAAATTCGTTGCGATAGT-TACA
1 CGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACA
470185 AAAAAAGATT
Statistics
Matches: 109, Mismatches: 6, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
40 20 0.18
41 86 0.79
42 3 0.03
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.39
Consensus pattern (41 bp):
CGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGATGT
Found at i:470114 original size:22 final size:21
Alignment explanation
Indices: 470047--470158 Score: 72
Period size: 19 Copynumber: 5.4 Consensus size: 21
470037 TTCCATTTCG
*
470047 CGTTGCGATAGTCTACA-ATGT
1 CGTTGCGATAGTCTA-AGTTGT
** * *
470068 CGTTGCGATTTTCCAA-AT-T
1 CGTTGCGATAGTCTAAGTTGT
470087 CGTTGCGATAGTCTATAGTTGT
1 CGTTGCGATAGTCTA-AGTTGT
** * *
470109 CGTTGCGATTTTCCAA-AT-T
1 CGTTGCGATAGTCTAAGTTGT
*
470128 CGTTGCGAAAGTCTACAGTTGT
1 CGTTGCGATAGTCTA-AGTTGT
470150 CGTTGCGAT
1 CGTTGCGAT
470159 TTTCCAAATT
Statistics
Matches: 68, Mismatches: 17, Indels: 11
0.71 0.18 0.11
Matches are distributed among these distances:
19 25 0.37
20 6 0.09
21 15 0.22
22 22 0.32
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.38
Consensus pattern (21 bp):
CGTTGCGATAGTCTAAGTTGT
Found at i:470268 original size:6 final size:6
Alignment explanation
Indices: 470257--470307 Score: 95
Period size: 6 Copynumber: 8.7 Consensus size: 6
470247 AGACACGTAT
470257 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACC-C
1 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC
470304 GACC
1 GACC
470308 CGAGACGAGA
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 5 0.11
6 40 0.89
ACGTcount: A:0.31, C:0.51, G:0.18, T:0.00
Consensus pattern (6 bp):
GACCAC
Found at i:470841 original size:6 final size:6
Alignment explanation
Indices: 470820--470871 Score: 90
Period size: 6 Copynumber: 9.0 Consensus size: 6
470810 TCTCGTCTCG
470820 GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
470866 GGTCGT
1 GGTCGT
470872 ACGTGTCTTC
Statistics
Matches: 46, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 10 0.22
6 36 0.78
ACGTcount: A:0.00, C:0.17, G:0.52, T:0.31
Consensus pattern (6 bp):
GGTCGT
Found at i:470973 original size:19 final size:19
Alignment explanation
Indices: 470949--471156 Score: 141
Period size: 19 Copynumber: 10.4 Consensus size: 19
470939 TTTTGTAACT
470949 ATCGCAACGAATTTGGAAA
1 ATCGCAACGAATTTGGAAA
470968 ATCGCAACGAATTTGGAAA
1 ATCGCAACGAATTTGGAAA
* * **
470987 ATCGCAACGACAACTGTAGACT
1 ATCGCAACG--AA-TTTGGAAA
*
471009 TTCGCAACGAATTTGGAAA
1 ATCGCAACGAATTTGGAAA
**
471028 ATCGCAATTAATTTGGAAA
1 ATCGCAACGAATTTGGAAA
* * **
471047 ATCGCAACGACAACTGTAGACT
1 ATCGCAACG--AA-TTTGGAAA
*
471069 ATCGTAACGAATTTGGAAA
1 ATCGCAACGAATTTGGAAA
* **
471088 ATCGCAACGACATTGTAGACT
1 ATCGCAACGA-ATT-TGGAAA
*
471109 ATCGCAACGCGAA-ATGGAAA
1 ATCGCAA--CGAATTTGGAAA
*
471129 ATCGCAACGCGAA-ATGGAAA
1 ATCGCAA--CGAATTTGGAAA
471149 ATCGCAAC
1 ATCGCAAC
471157 ACGATTTTTA
Statistics
Matches: 148, Mismatches: 31, Indels: 21
0.74 0.16 0.10
Matches are distributed among these distances:
18 1 0.01
19 68 0.46
20 37 0.25
21 14 0.09
22 25 0.17
23 3 0.02
ACGTcount: A:0.40, C:0.20, G:0.20, T:0.20
Consensus pattern (19 bp):
ATCGCAACGAATTTGGAAA
Found at i:471043 original size:60 final size:60
Alignment explanation
Indices: 470942--471097 Score: 269
Period size: 60 Copynumber: 2.6 Consensus size: 60
470932 AATCTTTTTT
470942 TGTA-ACTATCGCAACGAATTTGGAAAATCGCAACGAATTTGGAAAATCGCAACGACAAC
1 TGTAGACTATCGCAACGAATTTGGAAAATCGCAACGAATTTGGAAAATCGCAACGACAAC
* **
471001 TGTAGACTTTCGCAACGAATTTGGAAAATCGCAATTAATTTGGAAAATCGCAACGACAAC
1 TGTAGACTATCGCAACGAATTTGGAAAATCGCAACGAATTTGGAAAATCGCAACGACAAC
*
471061 TGTAGACTATCGTAACGAATTTGGAAAATCGCAACGA
1 TGTAGACTATCGCAACGAATTTGGAAAATCGCAACGA
471098 CATTGTAGAC
Statistics
Matches: 89, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
59 4 0.04
60 85 0.96
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.23
Consensus pattern (60 bp):
TGTAGACTATCGCAACGAATTTGGAAAATCGCAACGAATTTGGAAAATCGCAACGACAAC
Found at i:471086 original size:41 final size:41
Alignment explanation
Indices: 471037--471137 Score: 143
Period size: 41 Copynumber: 2.5 Consensus size: 41
471027 AATCGCAATT
*
471037 AATTTGGAAAATCGCAACGACAACTGTAGACTATCGTAA-CG
1 AATTTGGAAAATCGCAACGAC-ACTGTAGACTATCGCAACCG
*
471078 AATTTGGAAAATCGCAACGACATTGTAGACTATCGCAACGCG
1 AATTTGGAAAATCGCAACGACACTGTAGACTATCGCAAC-CG
*
471120 AA-ATGGAAAATCGCAACG
1 AATTTGGAAAATCGCAACG
471138 CGAAATGGAA
Statistics
Matches: 55, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
40 15 0.27
41 36 0.65
42 4 0.07
ACGTcount: A:0.40, C:0.20, G:0.21, T:0.20
Consensus pattern (41 bp):
AATTTGGAAAATCGCAACGACACTGTAGACTATCGCAACCG
Found at i:471134 original size:20 final size:20
Alignment explanation
Indices: 471109--471156 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
471099 ATTGTAGACT
471109 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
471129 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
471149 ATCGCAAC
1 ATCGCAAC
471157 ACGATTTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.44, C:0.23, G:0.23, T:0.10
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:471173 original size:101 final size:101
Alignment explanation
Indices: 470968--471156 Score: 258
Period size: 101 Copynumber: 1.9 Consensus size: 101
470958 AATTTGGAAA
* *
470968 ATCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTTTCGCAACGAATTTGGAAAATCGC
1 ATCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCGCAACGAATATGGAAAATCGC
** *
471033 AATTAATTTGGAAAATCGCAACGACAACTGTAGACT
66 AACGAATATGGAAAATCGCAACGACAACTGTAGACT
* *
471069 ATCGTAACGAATTTGGAAAATCGCAACGAC-ATTGTAGACTATCGCAACGCGAA-ATGGAAAATC
1 ATCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCGCAA--CGAATATGGAAAATC
471132 GCAACGCGAA-ATGGAAAATCGCAAC
64 GCAA--CGAATATGGAAAATCGCAAC
471157 ACGATTTTTA
Statistics
Matches: 77, Mismatches: 7, Indels: 7
0.85 0.08 0.08
Matches are distributed among these distances:
100 15 0.19
101 42 0.55
102 18 0.23
103 2 0.03
ACGTcount: A:0.40, C:0.20, G:0.20, T:0.20
Consensus pattern (101 bp):
ATCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCGCAACGAATATGGAAAATCGC
AACGAATATGGAAAATCGCAACGACAACTGTAGACT
Found at i:473660 original size:43 final size:43
Alignment explanation
Indices: 473591--473676 Score: 115
Period size: 43 Copynumber: 2.0 Consensus size: 43
473581 AAAAATTGAT
*
473591 GAAGAAGTTTTGAAAATGCTTTATGAAAGAATTTT-AAATAATG
1 GAAGAAGTTTTGAAAATGATTTATGAAAGAATTTTGAAA-AATG
473634 GAAGAA-TTTTGAATAAT-ATTTGATGAAAGAATTTTGAAAAATG
1 GAAGAAGTTTTGAA-AATGATTT-ATGAAAGAATTTTGAAAAATG
473677 TTTGATGAAG
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
42 10 0.26
43 26 0.67
44 3 0.08
ACGTcount: A:0.45, C:0.01, G:0.19, T:0.35
Consensus pattern (43 bp):
GAAGAAGTTTTGAAAATGATTTATGAAAGAATTTTGAAAAATG
Found at i:473692 original size:25 final size:25
Alignment explanation
Indices: 473635--473685 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
473625 TAAATAATGG
* *
473635 AAGAATTTTGAATAATATTTGATGA
1 AAGAATTTTGAAAAATGTTTGATGA
473660 AAGAATTTTGAAAAATGTTTGATGA
1 AAGAATTTTGAAAAATGTTTGATGA
473685 A
1 A
473686 GTTATTTGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.45, C:0.00, G:0.18, T:0.37
Consensus pattern (25 bp):
AAGAATTTTGAAAAATGTTTGATGA
Found at i:480216 original size:24 final size:24
Alignment explanation
Indices: 480182--480242 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
480172 GATGATTTGA
*
480182 TTTATATTCTTTAAAATTTTGTAAT
1 TTTATA-TCTTTAAAATTTTATAAT
480207 TTTATATCTTTAAAATTTTATAAT
1 TTTATATCTTTAAAATTTTATAAT
*
480231 ATTAT-T-TTTAAA
1 TTTATATCTTTAAA
480243 GTTTATACTC
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
22 6 0.18
23 1 0.03
24 21 0.62
25 6 0.18
ACGTcount: A:0.36, C:0.03, G:0.02, T:0.59
Consensus pattern (24 bp):
TTTATATCTTTAAAATTTTATAAT
Found at i:482004 original size:159 final size:159
Alignment explanation
Indices: 481715--482030 Score: 623
Period size: 159 Copynumber: 2.0 Consensus size: 159
481705 TGCAAGATTT
481715 ATCTTGCAAGTCTGAAGCGGATATGACCAATTGCTGATGTCAGCTGCCAGCTGTACGACTGACCT
1 ATCTTGCAAGTCTGAAGCGGATATGACCAATTGCTGATGTCAGCTGCCAGCTGTACGACTGACCT
481780 TACGTGCAATCAAGCCCCCAAGATTCTGACCATATCCAACTGCCTTTCCATCAATAGCATGGACA
66 TACGTGCAATCAAGCCCCCAAGATTCTGACCATATCCAACTGCCTTTCCATCAATAGCATGGACA
481845 AGTTAACACGGGTATTTAGGGAATATTAA
131 AGTTAACACGGGTATTTAGGGAATATTAA
481874 ATCTTGCAAGTCTGAAGCGGATATGACCAATTGCTGATGTCAGCTGCCAGCTGTACGACTGACCT
1 ATCTTGCAAGTCTGAAGCGGATATGACCAATTGCTGATGTCAGCTGCCAGCTGTACGACTGACCT
481939 TACGTGCAATCAAGCCCCCAAGATTCTGACCATATCCAACTGCCTTTCCATCAATAGCATGGACA
66 TACGTGCAATCAAGCCCCCAAGATTCTGACCATATCCAACTGCCTTTCCATCAATAGCATGGACA
*
482004 AGTTAACATGGGTATTTAGGGAATATT
131 AGTTAACACGGGTATTTAGGGAATATT
482031 TAATTACGTA
Statistics
Matches: 156, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
159 156 1.00
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.26
Consensus pattern (159 bp):
ATCTTGCAAGTCTGAAGCGGATATGACCAATTGCTGATGTCAGCTGCCAGCTGTACGACTGACCT
TACGTGCAATCAAGCCCCCAAGATTCTGACCATATCCAACTGCCTTTCCATCAATAGCATGGACA
AGTTAACACGGGTATTTAGGGAATATTAA
Found at i:491179 original size:16 final size:18
Alignment explanation
Indices: 491160--491202 Score: 54
Period size: 16 Copynumber: 2.5 Consensus size: 18
491150 AAGCATATTA
491160 ATACATATAA-TCATG-C
1 ATACATATAATTCATGCC
*
491176 ATACATACAATTCATGCC
1 ATACATATAATTCATGCC
*
491194 ATCCATATA
1 ATACATATA
491203 CATATAATCA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 9 0.41
17 5 0.23
18 8 0.36
ACGTcount: A:0.42, C:0.23, G:0.05, T:0.30
Consensus pattern (18 bp):
ATACATATAATTCATGCC
Found at i:491183 original size:20 final size:22
Alignment explanation
Indices: 491160--491213 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 22
491150 AAGCATATTA
491160 ATACATATAATCATG-CAT-AC
1 ATACATATAATCATGCCATCAC
*
491180 ATACA-AT--TCATGCCATCCAT
1 ATACATATAATCATGCCAT-CAC
491200 ATACATATAATCAT
1 ATACATATAATCAT
491214 ATATTCATGC
Statistics
Matches: 27, Mismatches: 1, Indels: 9
0.73 0.03 0.24
Matches are distributed among these distances:
17 5 0.19
18 3 0.11
19 2 0.07
20 11 0.41
21 2 0.07
23 4 0.15
ACGTcount: A:0.43, C:0.22, G:0.04, T:0.31
Consensus pattern (22 bp):
ATACATATAATCATGCCATCAC
Found at i:491525 original size:20 final size:20
Alignment explanation
Indices: 491497--491534 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
491487 TTCCCCTTAA
491497 AGTGAATCGATACATTCTAC
1 AGTGAATCGATACATTCTAC
* *
491517 AGTGTATCGATGCATTCT
1 AGTGAATCGATACATTCT
491535 TTAACATGTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.34
Consensus pattern (20 bp):
AGTGAATCGATACATTCTAC
Found at i:493816 original size:21 final size:21
Alignment explanation
Indices: 493790--493834 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
493780 GATTTCTGGG
* *
493790 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
493811 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
493832 CAA
1 CAA
493835 ACGAACAACA
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:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:494676 original size:31 final size:31
Alignment explanation
Indices: 494638--494762 Score: 198
Period size: 31 Copynumber: 4.0 Consensus size: 31
494628 AGGGTCGAGG
494638 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
494669 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
494700 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
494731 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
494762 G
1 G
494763 GTCCTTCGGG
Statistics
Matches: 88, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
31 87 0.99
32 1 0.01
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.37
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:497940 original size:21 final size:21
Alignment explanation
Indices: 497914--497958 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
497904 GATTTCTGGG
* *
497914 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
497935 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
497956 CAA
1 CAA
497959 ACGAACAACA
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:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:498800 original size:31 final size:31
Alignment explanation
Indices: 498762--498871 Score: 184
Period size: 31 Copynumber: 3.5 Consensus size: 31
498752 AGGGTCGAGG
498762 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
498793 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
498824 GTTTACCTATGTCCTTCGGGATATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
498855 GATTACCTAGGTTCTTC
1 GTTTACCTATGTTCTTC
498872 AGAATCTATG
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 74 1.00
ACGTcount: A:0.19, C:0.20, G:0.22, T:0.39
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:498882 original size:31 final size:31
Alignment explanation
Indices: 498762--498886 Score: 164
Period size: 31 Copynumber: 4.0 Consensus size: 31
498752 AGGGTCGAGG
498762 GTTTACCTATGTTCTTCGGGA-CATATGGACT
1 GTTTACCTATGTTCTTCGGGATC-TATGGACT
498793 GTTTACCTATGTTCTTCGGGA-CATATGGACT
1 GTTTACCTATGTTCTTCGGGATC-TATGGACT
* *
498824 GTTTACCTATGTCCTTCGGGATATATGGACT
1 GTTTACCTATGTTCTTCGGGATCTATGGACT
* * * *
498855 GATTACCTAGGTTCTTCAGAATCTATGGACT
1 GTTTACCTATGTTCTTCGGGATCTATGGACT
498886 G
1 G
498887 GTCCTTCGGG
Statistics
Matches: 85, Mismatches: 8, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
31 85 1.00
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGATCTATGGACT
Found at i:502036 original size:20 final size:20
Alignment explanation
Indices: 502011--502068 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
502001 TTCCCCTTGA
*
502011 AGTGTATCGATACATTCTAT
1 AGTGTATCGATACATTCTAC
502031 AGTGTATCGATACATTCTAC
1 AGTGTATCGATACATTCTAC
* *
502051 AGTGTATAGATGCATTCT
1 AGTGTATCGATACATTCT
502069 TTAACATGTG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.29, C:0.16, G:0.17, T:0.38
Consensus pattern (20 bp):
AGTGTATCGATACATTCTAC
Found at i:503422 original size:2 final size:2
Alignment explanation
Indices: 503415--503445 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
503405 CCCTAAAGTA
503415 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
503446 TAAATATTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:510045 original size:21 final size:21
Alignment explanation
Indices: 509994--510046 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
509984 AGTATGACTA
*
509994 TCGCAATGCGATTTTTCAATT
1 TCGCAATGCGATTTTCCAATT
**
510015 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
510036 TCGCAATGCGA
1 TCGCAATGCGA
510047 ATAAGTAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 23 0.88
22 3 0.12
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:510079 original size:21 final size:21
Alignment explanation
Indices: 510036--510126 Score: 148
Period size: 21 Copynumber: 4.4 Consensus size: 21
510026 TTTTCCCAAT
** *
510036 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTTGGAAAA
510056 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTTGGAAAA
510077 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTTGGAAAA
510098 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTTGGAAAA
510119 TCGCAATG
1 TCGCAATG
510127 GGATACTGAC
Statistics
Matches: 67, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
20 12 0.18
21 55 0.82
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.23
Consensus pattern (21 bp):
TCGCAATGCGAATTTGGAAAA
Found at i:510087 original size:62 final size:62
Alignment explanation
Indices: 510021--510170 Score: 142
Period size: 62 Copynumber: 2.4 Consensus size: 62
510011 AATTTCGCGT
* * *
510021 TGCGATTTTCCCAATTCGCAATGCGAA-TAAGTAAATCGCAATGCGAAT-TTGGAAAATCGCAA
1 TGCGATTTTCCAAATTCGCAATGCGAATTAAGAAAATCGCAATG-GAATACT-GAAAATCGCAA
* ** * ** * **
510083 TGCGAATTTGGAAAATCGCAATGCGAATTTGGAAAATCGCAATGGGATACTGACTATCGCAA
1 TGCGATTTTCCAAATTCGCAATGCGAATTAAGAAAATCGCAATGGAATACTGAAAATCGCAA
* *
510145 TGCGATTTTCCTAATTCGCATTGCGA
1 TGCGATTTTCCAAATTCGCAATGCGA
510171 TTTACGTATT
Statistics
Matches: 68, Mismatches: 18, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
62 54 0.79
63 14 0.21
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (62 bp):
TGCGATTTTCCAAATTCGCAATGCGAATTAAGAAAATCGCAATGGAATACTGAAAATCGCAA
Found at i:510164 original size:41 final size:41
Alignment explanation
Indices: 510139--510279 Score: 103
Period size: 41 Copynumber: 3.5 Consensus size: 41
510129 ATACTGACTA
* * *
510139 TCGCAATGCGATTTTCCTAATTCGCATTGCGATTTACGTAT
1 TCGCAATGCGATTTTCATAATTCGCAATGCGATTGACGTAT
** * *
510180 TCGCGTTGCGATTTTCATAATTCGCAATGCGAAT-ACGTAAA
1 TCGCAATGCGATTTTCATAATTCGCAATGCGATTGACGT-AT
* * * *
510221 TCGCAACGCGA-ATT-AGTAAATCGCAATGCGAATCTTAC-TA-
1 TCGCAATGCGATTTTCA-TAATTCGCAATGCG-AT-TGACGTAT
*
510261 TCGCAATGCGATTTGCATA
1 TCGCAATGCGATTTTCATA
510280 GCGCCATTCG
Statistics
Matches: 78, Mismatches: 15, Indels: 14
0.73 0.14 0.13
Matches are distributed among these distances:
39 1 0.01
40 29 0.37
41 43 0.55
42 3 0.04
43 2 0.03
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.32
Consensus pattern (41 bp):
TCGCAATGCGATTTTCATAATTCGCAATGCGATTGACGTAT
Found at i:510169 original size:21 final size:21
Alignment explanation
Indices: 510139--510211 Score: 85
Period size: 21 Copynumber: 3.5 Consensus size: 21
510129 ATACTGACTA
*
510139 TCGCAATGCGATTTTCCTAAT
1 TCGCAATGCGATTTTCATAAT
* * *
510160 TCGCATTGCGATTTACGT-AT
1 TCGCAATGCGATTTTCATAAT
**
510180 TCGCGTTGCGATTTTCATAAT
1 TCGCAATGCGATTTTCATAAT
510201 TCGCAATGCGA
1 TCGCAATGCGA
510212 ATACGTAAAT
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 17 0.40
21 26 0.60
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.37
Consensus pattern (21 bp):
TCGCAATGCGATTTTCATAAT
Found at i:510226 original size:20 final size:20
Alignment explanation
Indices: 510201--510271 Score: 83
Period size: 20 Copynumber: 3.5 Consensus size: 20
510191 TTTTCATAAT
510201 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
510221 TCGCAACGCGAATTA-GTAAA
1 TCGCAATGCGAA-TACGTAAA
* *
510241 TCGCAATGCGAAT-CTTACTA
1 TCGCAATGCGAATACGTA-AA
510261 TCGCAATGCGA
1 TCGCAATGCGA
510272 TTTGCATAGC
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
19 3 0.07
20 39 0.89
21 2 0.05
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.23
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:510658 original size:24 final size:24
Alignment explanation
Indices: 510624--510677 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
510614 CTGAAACATC
*
510624 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
510648 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
510672 ATCAAA
1 ATCAAA
510678 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:511510 original size:21 final size:20
Alignment explanation
Indices: 511463--511514 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
511453 TTTTCCTAAT
*
511463 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGAAAA
* **
511483 TCACAATGCGAATTTGGAAAA
1 TCGCAATGCGAA-TAAGAAAA
511504 TCGCAATGCGA
1 TCGCAATGCGA
511515 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATAAGAAAA
Found at i:511536 original size:20 final size:20
Alignment explanation
Indices: 511503--511576 Score: 60
Period size: 20 Copynumber: 3.6 Consensus size: 20
511493 AATTTGGAAA
* *
511503 ATCGCAATGCGATACTGACT
1 ATCGCAACGAGATACTGACT
* *
511523 ATCGCAACGAGATAAT-ACAAA
1 ATCGCAACGAGATACTGAC--T
* *
511544 ATCACAACGAGATTCTGACT
1 ATCGCAACGAGATACTGACT
*
511564 TTCGCAACGAGAT
1 ATCGCAACGAGAT
511577 TCTAAAAATC
Statistics
Matches: 41, Mismatches: 10, Indels: 6
0.72 0.18 0.11
Matches are distributed among these distances:
19 2 0.05
20 24 0.59
21 13 0.32
22 2 0.05
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.22
Consensus pattern (20 bp):
ATCGCAACGAGATACTGACT
Found at i:511545 original size:41 final size:40
Alignment explanation
Indices: 511500--511591 Score: 112
Period size: 41 Copynumber: 2.3 Consensus size: 40
511490 GCGAATTTGG
*
511500 AAAATCGCAATGCGATACTGACTATCGCAACGAGATAATA
1 AAAATCGCAATGAGATACTGACTATCGCAACGAGATAATA
* * * * **
511540 CAAAATCACAACGAGATTCTGACTTTCGCAACGAGATTCTA
1 -AAAATCGCAATGAGATACTGACTATCGCAACGAGATAATA
511581 AAAATCGCAAT
1 AAAATCGCAAT
511592 CATCTTCAAA
Statistics
Matches: 42, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
40 9 0.21
41 33 0.79
ACGTcount: A:0.41, C:0.22, G:0.15, T:0.22
Consensus pattern (40 bp):
AAAATCGCAATGAGATACTGACTATCGCAACGAGATAATA
Found at i:511588 original size:20 final size:20
Alignment explanation
Indices: 511523--511590 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 20
511513 GATACTGACT
**
511523 ATCGCAACGAGATAATACAAA
1 ATCGCAACGAGATTCTA-AAA
* * **
511544 ATCACAACGAGATTCTGACT
1 ATCGCAACGAGATTCTAAAA
*
511564 TTCGCAACGAGATTCTAAAA
1 ATCGCAACGAGATTCTAAAA
511584 ATCGCAA
1 ATCGCAA
511591 TCATCTTCAA
Statistics
Matches: 35, Mismatches: 12, Indels: 1
0.73 0.25 0.02
Matches are distributed among these distances:
20 22 0.63
21 13 0.37
ACGTcount: A:0.43, C:0.22, G:0.15, T:0.21
Consensus pattern (20 bp):
ATCGCAACGAGATTCTAAAA
Found at i:511922 original size:14 final size:14
Alignment explanation
Indices: 511903--511956 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
511893 GAAAATCGCA
511903 TTGCGATTTTCTCG
1 TTGCGATTTTCTCG
511917 TTGCGATTTTCATTTCG
1 TTGCGATTTTC---TCG
511934 CATTGCGATTTTCTCG
1 --TTGCGATTTTCTCG
511950 TTGCGAT
1 TTGCGAT
511957 AGTCAGTTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 18 0.51
16 3 0.09
17 3 0.09
19 11 0.31
ACGTcount: A:0.11, C:0.20, G:0.20, T:0.48
Consensus pattern (14 bp):
TTGCGATTTTCTCG
Found at i:511922 original size:33 final size:33
Alignment explanation
Indices: 511885--511955 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 33
511875 AAAATCGCAA
511885 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
** ** **
511918 TGCGATTTTCATTTCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
511951 TGCGA
1 TGCGA
511956 TAGTCAGTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.39
Consensus pattern (33 bp):
TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
Found at i:513600 original size:21 final size:20
Alignment explanation
Indices: 513512--513609 Score: 72
Period size: 21 Copynumber: 4.8 Consensus size: 20
513502 TGGAATGGTG
* *
513512 GGAGGGACCTCTTCAACGAT
1 GGAGGGGCCTCTTGAACGAT
* *
513532 GACAGTGGCCTCTTGAACGAT
1 G-GAGGGGCCTCTTGAACGAT
* * **
513553 GGGGGGGACTCTTGAGGGA-
1 GGAGGGGCCTCTTGAACGAT
513572 GGATAGGGGCCTCTTGAACGATT
1 GG--AGGGGCCTCTTGAACGA-T
*
513595 GGAGGGGACTCTTGA
1 GGAGGGGCCTCTTGA
513610 GGGATGACAG
Statistics
Matches: 58, Mismatches: 15, Indels: 9
0.71 0.18 0.11
Matches are distributed among these distances:
19 2 0.03
20 13 0.22
21 41 0.71
23 2 0.03
ACGTcount: A:0.21, C:0.18, G:0.39, T:0.21
Consensus pattern (20 bp):
GGAGGGGCCTCTTGAACGAT
Found at i:514037 original size:19 final size:20
Alignment explanation
Indices: 513982--514037 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
513972 GAAATTTAAA
**
513982 ATCGCAACGCAAAAATGACT
1 ATCGCAACGCGGAAATGACT
*
514002 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGCGGAAATGACT
*
514022 ATCGCAATGC-GAAATG
1 ATCGCAACGCGGAAATG
514038 CAAATCGCAA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 6 0.19
20 26 0.81
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGGAAATGACT
Found at i:514044 original size:19 final size:18
Alignment explanation
Indices: 514022--514145 Score: 110
Period size: 14 Copynumber: 7.4 Consensus size: 18
514012 GGAAATGGCT
514022 ATCGCAATGCGAAATGCAA
1 ATCGCAATGCGAAATG-AA
*
514041 ATCGCAA--CGACA--AA
1 ATCGCAATGCGAAATGAA
514055 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATG-AA
*
514074 ATCGCAA--CGACA--AA
1 ATCGCAATGCGAAATGAA
514088 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATG-AA
*
514107 ATCGCAA--CGACA--AA
1 ATCGCAATGCGAAATGAA
514121 ATCGCAATGCGAAATGAA
1 ATCGCAATGCGAAATGAA
514139 ATCGCAA
1 ATCGCAA
514146 CGACAAAATC
Statistics
Matches: 85, Mismatches: 6, Indels: 29
0.71 0.05 0.24
Matches are distributed among these distances:
14 27 0.32
16 12 0.14
17 12 0.14
18 9 0.11
19 25 0.29
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.13
Consensus pattern (18 bp):
ATCGCAATGCGAAATGAA
Found at i:514058 original size:14 final size:14
Alignment explanation
Indices: 514039--514161 Score: 84
Period size: 14 Copynumber: 7.8 Consensus size: 14
514029 TGCGAAATGC
514039 AAATCGCAACGACA
1 AAATCGCAACGACA
*
514053 AAATCGCAATGCGAAATGA
1 AAATCGCAA--CG--A-CA
514072 AAATCGCAACGACA
1 AAATCGCAACGACA
*
514086 AAATCGCAATGCGAAATGA
1 AAATCGCAA--CG--A-CA
514105 AAATCGCAACGACA
1 AAATCGCAACGACA
*
514119 AAATCGCAATGCGAAA
1 AAATCGCAA--CGACA
514135 TGAAATCGCAACGACA
1 --AAATCGCAACGACA
*
514151 AAATCCCAACG
1 AAATCGCAACG
514162 CGAAACACAA
Statistics
Matches: 88, Mismatches: 7, Indels: 28
0.72 0.06 0.23
Matches are distributed among these distances:
14 39 0.44
15 2 0.02
16 12 0.14
17 4 0.05
18 11 0.12
19 20 0.23
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.11
Consensus pattern (14 bp):
AAATCGCAACGACA
Found at i:514059 original size:33 final size:33
Alignment explanation
Indices: 514022--514166 Score: 256
Period size: 33 Copynumber: 4.4 Consensus size: 33
514012 GGAAATGGCT
*
514022 ATCGCAATGCGAAATGCAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
514055 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
514088 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
514121 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
* *
514153 ATCCCAACGCGAAA
1 ATCGCAATGCGAAA
514167 CACAAATCGC
Statistics
Matches: 109, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
32 28 0.26
33 81 0.74
ACGTcount: A:0.47, C:0.23, G:0.18, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:514195 original size:19 final size:19
Alignment explanation
Indices: 514173--514269 Score: 97
Period size: 19 Copynumber: 5.6 Consensus size: 19
514163 GAAACACAAA
514173 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
514192 TCGCGTTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
514208 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
514225 TCGCATTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
514241 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
514258 TCGCATTGCGAT
1 TCGCATTGCGAT
514270 AGCCATTTCC
Statistics
Matches: 63, Mismatches: 5, Indels: 20
0.72 0.06 0.23
Matches are distributed among these distances:
14 12 0.19
15 6 0.10
16 8 0.13
17 8 0.13
18 6 0.10
19 23 0.37
ACGTcount: A:0.12, C:0.20, G:0.22, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:514214 original size:14 final size:14
Alignment explanation
Indices: 514195--514253 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
514185 TTTCATTTCG
514195 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
514209 CGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TGT
514226 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
514242 CGTTGCGATTTT
1 CGTTGCGATTTT
514254 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 18 0.47
15 3 0.08
16 4 0.11
17 4 0.11
18 3 0.08
19 6 0.16
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.49
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:514220 original size:33 final size:33
Alignment explanation
Indices: 514178--514269 Score: 175
Period size: 33 Copynumber: 2.8 Consensus size: 33
514168 ACAAATCGCA
*
514178 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
514211 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
514244 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
514270 AGCCATTTCC
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.12, C:0.18, G:0.22, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:514306 original size:20 final size:20
Alignment explanation
Indices: 514254--514297 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
514244 TTGCGATTTT
*
514254 CATTT-CGCATTGCGATAGC
1 CATTTCCGCGTTGCGATAGC
*
514273 CATTTCCGCGTTGCGATAGT
1 CATTTCCGCGTTGCGATAGC
514293 CATTT
1 CATTT
514298 TCGTGTTGCA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.18, C:0.25, G:0.20, T:0.36
Consensus pattern (20 bp):
CATTTCCGCGTTGCGATAGC
Found at i:514816 original size:18 final size:18
Alignment explanation
Indices: 514790--514834 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
514780 GTCGATCAGA
*
514790 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
514808 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
514826 TGATGGCTC
1 TGATGGCTC
514835 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:516202 original size:20 final size:20
Alignment explanation
Indices: 516154--516212 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
516144 AATAGTTTCT
* *
516154 GAAAATGAAAATCGCAACAC
1 GAAAATGACAATCGCAACGC
516174 GAAAATGACAATCGCAACGC
1 GAAAATGACAATCGCAACGC
** *
516194 GAATTTGACTATCGCAACG
1 GAAAATGACAATCGCAACG
516213 AGAGAATAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.44, C:0.22, G:0.19, T:0.15
Consensus pattern (20 bp):
GAAAATGACAATCGCAACGC
Found at i:516732 original size:20 final size:20
Alignment explanation
Indices: 516707--516758 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
516697 CTTATGTATT
516707 ATCGCGTTGCGAAAGTCAAA
1 ATCGCGTTGCGAAAGTCAAA
**
516727 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGAAAGTCAAA
*
516747 ATCTCGTTGCGA
1 ATCGCGTTGCGA
516759 TTTTGTATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (20 bp):
ATCGCGTTGCGAAAGTCAAA
Found at i:516819 original size:41 final size:41
Alignment explanation
Indices: 516727--516821 Score: 102
Period size: 41 Copynumber: 2.3 Consensus size: 41
516717 GAAAGTCAAA
* * * * ** *
516727 ATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCAAT
*
516768 ATCGCATTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTT-CCAAT
516810 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
516822 TTACTTATTC
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
41 42 0.95
42 2 0.05
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.36
Consensus pattern (41 bp):
ATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCAAT
Found at i:516911 original size:21 final size:21
Alignment explanation
Indices: 516871--516911 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
516861 ACTGTAGACC
* *
516871 ATCGCAACGCGAATTTCAACT
1 ATCGCAACGCGAAATGCAACT
516892 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATGCAAC
516912 GCGAATTTGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.37, C:0.29, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATGCAACT
Found at i:517768 original size:20 final size:20
Alignment explanation
Indices: 517743--517787 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
517733 GTCATCTAAT
517743 TTTTTAAACCCCAGACCGGA
1 TTTTTAAACCCCAGACCGGA
517763 TTTTTAAACCCCAGACCGGA
1 TTTTTAAACCCCAGACCGGA
517783 TTTTT
1 TTTTT
517788 TTTCCGGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.27, C:0.27, G:0.13, T:0.33
Consensus pattern (20 bp):
TTTTTAAACCCCAGACCGGA
Found at i:518507 original size:12 final size:12
Alignment explanation
Indices: 518481--518514 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
518471 TTTTAGTGAG
518481 TAAATTAAAAAAA
1 TAAA-TAAAAAAA
*
518494 TAAATAAAATAA
1 TAAATAAAAAAA
518506 TAAATAAAA
1 TAAATAAAA
518515 CAAAACAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 16 0.80
13 4 0.20
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
TAAATAAAAAAA
Found at i:521704 original size:23 final size:23
Alignment explanation
Indices: 521678--521722 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
521668 CACCACAGCT
*
521678 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
* *
521701 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
521723 ATATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCG
Found at i:521889 original size:150 final size:149
Alignment explanation
Indices: 521690--522005 Score: 562
Period size: 150 Copynumber: 2.1 Consensus size: 149
521680 TATAAATGCA
*
521690 CCGAAGTG-CCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATATAA
1 CCGAAG-GACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAA
*
521754 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCCAAGACTTCACACATGT
65 TTCCTTAAGAATCATATACATATACTAAGGATCAAGTATGTGTCTTT-CAAGACTTCACACATGT
* *
521819 TCCACAGAATATATATATATC
129 TCCAAAGAATATACATATATC
521840 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
521905 TCCTTAAGAATCATATACATATACTAAGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
66 TCCTTAAGAATCATATACATATACTAAGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
*
521970 CAAAGAATATACATATGTC
131 CAAAGAATATACATATATC
521989 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
522006 CCCTCTACCC
Statistics
Matches: 160, Mismatches: 5, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
149 53 0.33
150 107 0.67
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (149 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
TCCTTAAGAATCATATACATATACTAAGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
CAAAGAATATACATATATC
Found at i:522518 original size:19 final size:20
Alignment explanation
Indices: 522481--522518 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
522471 TTTTTTCTCA
*
522481 TGGGGGAATCGGTTCCCCCC
1 TGGGGGAATCGATTCCCCCC
*
522501 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
522519 TCTAGCATTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.11, C:0.32, G:0.34, T:0.24
Consensus pattern (20 bp):
TGGGGGAATCGATTCCCCCC
Found at i:528661 original size:23 final size:23
Alignment explanation
Indices: 528635--528679 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
528625 CACCACAGCT
*
528635 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
* *
528658 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
528680 ATATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCG
Found at i:528846 original size:150 final size:148
Alignment explanation
Indices: 528647--528961 Score: 542
Period size: 150 Copynumber: 2.1 Consensus size: 148
528637 TATAAATGCA
* *
528647 CCGAAGTG-CCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCGCATATAA
1 CCGAAG-GACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAA
*
528711 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCCAAGACTTCACACATGT
65 TTCCTTAAGAATCATATACATATACTAAGGATCAAGTATGTGTCTTT-CAAGACTTCACACATGT
* *
528776 TCCACAGAATATATATATAT
129 TCCAAAGAATATACATATAT
528796 CCCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAA
1 -CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAA
528861 TTCCTTAAGAATCATATACATATACTAAGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTT
65 TTCCTTAAGAATCATATACATATACTAAGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTT
*
528926 CCAAAGAATATACATATGT
130 CCAAAGAATATACATATAT
528945 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
528962 CCCTCTACCC
Statistics
Matches: 158, Mismatches: 6, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
148 17 0.11
149 35 0.22
150 106 0.67
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (148 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
TCCTTAAGAATCATATACATATACTAAGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
CAAAGAATATACATATAT
Found at i:533809 original size:40 final size:41
Alignment explanation
Indices: 533758--533913 Score: 117
Period size: 40 Copynumber: 3.9 Consensus size: 41
533748 TAACGCGGAT
* **
533758 ATGT-AAA-TCGCAACGTGAATTTGTAATTCGCAACACAT-A
1 ATGTCAAATTCGCAACGCGAATTTCAAATTCGCAACAC-TGA
**
533797 A-GTCAAATTCGCAACGCGGTTTTCAAATTCGCAACACTGA
1 ATGTCAAATTCGCAACGCGAATTTCAAATTCGCAACACTGA
* * * *
533837 ATTTCAAATTCGCAACTCG-ATTTCTGAATTCGCAAC-TTGA
1 ATGTCAAATTCGCAACGCGAATTTC-AAATTCGCAACACTGA
* * * * * *
533877 TTTTCGAATTCGCAACACGAATTTTAATTTCGCAACA
1 ATGTCAAATTCGCAACGCGAATTTCAAATTCGCAACA
533914 GATTTTATTT
Statistics
Matches: 94, Mismatches: 16, Indels: 12
0.77 0.13 0.10
Matches are distributed among these distances:
38 2 0.02
39 5 0.05
40 58 0.62
41 29 0.31
ACGTcount: A:0.33, C:0.22, G:0.14, T:0.31
Consensus pattern (41 bp):
ATGTCAAATTCGCAACGCGAATTTCAAATTCGCAACACTGA
Found at i:533822 original size:20 final size:20
Alignment explanation
Indices: 533799--533912 Score: 104
Period size: 20 Copynumber: 5.7 Consensus size: 20
533789 AACACATAAG
* **
533799 TCAAATTCGCAACGCGGTTT
1 TCAAATTCGCAACTCGAATT
*
533819 TCAAATTCGCAACACTGAATT
1 TCAAATTCGCAACTC-GAATT
533840 TCAAATTCGCAACTCG-ATT
1 TCAAATTCGCAACTCGAATT
* * *
533859 TCTGAATTCGCAACTTGATTT
1 TC-AAATTCGCAACTCGAATT
* *
533880 TCGAATTCGCAACACGAATT
1 TCAAATTCGCAACTCGAATT
* *
533900 TTAATTTCGCAAC
1 TCAAATTCGCAAC
533913 AGATTTTATT
Statistics
Matches: 78, Mismatches: 13, Indels: 6
0.80 0.13 0.06
Matches are distributed among these distances:
19 5 0.06
20 52 0.67
21 21 0.27
ACGTcount: A:0.31, C:0.24, G:0.13, T:0.32
Consensus pattern (20 bp):
TCAAATTCGCAACTCGAATT
Found at i:533913 original size:20 final size:18
Alignment explanation
Indices: 533802--533932 Score: 84
Period size: 20 Copynumber: 6.7 Consensus size: 18
533792 ACATAAGTCA
* *
533802 AATTCGCAACGCGGTTTT
1 AATTCGCAACACGATTTT
*
533820 CAAATTCGCAACACTGAATTTCA
1 --AATTCGCAACAC-G-ATTT-T
*
533843 AATTCGCAACTCGATTTCT
1 AATTCGCAACACGATTT-T
**
533862 GAATTCGCAACTTGATTTT
1 -AATTCGCAACACGATTTT
533881 CGAATTCGCAACACGAATTTT
1 --AATTCGCAACACG-ATTTT
533902 AATTTCGCAACA-GATTTT
1 AA-TTCGCAACACGATTTT
*
533920 ATTTTCGCAACAC
1 A-ATTCGCAACAC
533933 AAATATTTTG
Statistics
Matches: 93, Mismatches: 9, Indels: 19
0.77 0.07 0.16
Matches are distributed among these distances:
18 15 0.16
19 9 0.10
20 49 0.53
21 17 0.18
22 3 0.03
ACGTcount: A:0.31, C:0.23, G:0.13, T:0.34
Consensus pattern (18 bp):
AATTCGCAACACGATTTT
Found at i:534088 original size:14 final size:15
Alignment explanation
Indices: 534069--534106 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
534059 TCCCCATCTC
534069 TAATTTTTTT-TACA
1 TAATTTTTTTCTACA
*
534083 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
534099 TAATTTTT
1 TAATTTTT
534107 CAATGATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:534901 original size:24 final size:24
Alignment explanation
Indices: 534843--534889 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
534833 AGTCAGTATT
* *
534843 CGAAATTTGATCTTGGTTAATACC
1 CGAACTTTGATCTTGGTCAATACC
534867 CGAACTTTGATCTTGGTCAATAC
1 CGAACTTTGATCTTGGTCAATAC
534890 TCGGATTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Consensus pattern (24 bp):
CGAACTTTGATCTTGGTCAATACC
Found at i:537462 original size:20 final size:20
Alignment explanation
Indices: 537437--537484 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
537427 TGCGATTGTT
*
537437 GCGAAAGTCAAATTCGCAAC
1 GCGAAAGTCAAAATCGCAAC
*
537457 GCGAAAGTCAAAATCGCAAT
1 GCGAAAGTCAAAATCGCAAC
537477 GCGAAAGT
1 GCGAAAGT
537485 ATACCTTCAA
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:0.42, C:0.21, G:0.23, T:0.15
Consensus pattern (20 bp):
GCGAAAGTCAAAATCGCAAC
Found at i:538977 original size:21 final size:19
Alignment explanation
Indices: 538953--539025 Score: 74
Period size: 21 Copynumber: 3.5 Consensus size: 19
538943 GTGAATCGAG
538953 CTCTTGAACTGTGGGAGGGAC
1 CTCTTGAAC-GTGGGAGGG-C
**
538974 CTCTTGAACGATGACAGGGGC
1 CTCTTGAACG-TGGGA-GGGC
538995 CTCTTGAACGGTGGGAGAGGC
1 CTCTTGAAC-GTGGGAG-GGC
539016 CTCTTGAACG
1 CTCTTGAACG
539026 ATAACAGGTG
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
20 3 0.07
21 37 0.84
22 4 0.09
ACGTcount: A:0.21, C:0.22, G:0.36, T:0.22
Consensus pattern (19 bp):
CTCTTGAACGTGGGAGGGC
Found at i:539019 original size:42 final size:42
Alignment explanation
Indices: 538953--539033 Score: 128
Period size: 42 Copynumber: 1.9 Consensus size: 42
538943 GTGAATCGAG
* *
538953 CTCTTGAACTGTGGGAGGGACCTCTTGAACGATGACAGGGGC
1 CTCTTGAACGGTGGGAGGGACCTCTTGAACGATAACAGGGGC
538995 CTCTTGAACGGTGGGAGAGG-CCTCTTGAACGATAACAGG
1 CTCTTGAACGGTGGGAG-GGACCTCTTGAACGATAACAGG
539034 TGAATCAGGT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
42 34 0.94
43 2 0.06
ACGTcount: A:0.23, C:0.21, G:0.35, T:0.21
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGGGACCTCTTGAACGATAACAGGGGC
Found at i:539204 original size:4 final size:4
Alignment explanation
Indices: 539172--539217 Score: 56
Period size: 4 Copynumber: 11.5 Consensus size: 4
539162 GGGCCACTAA
* * * *
539172 AAAT AAAT TAAT ACAT AAAT CAGT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
539218 TGCCGAAAAA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.26
Consensus pattern (4 bp):
AAAT
Found at i:539394 original size:63 final size:62
Alignment explanation
Indices: 539327--539448 Score: 147
Period size: 63 Copynumber: 1.9 Consensus size: 62
539317 CGTAGAGCGG
* *
539327 CTACCTAATCACGTAAAGTA-GATACCTCACCACGTAAAGCACCATTGTCATCACGTAAAACAT
1 CTACCTAACCACGTAAAG-ACG-TACCTCACCACGCAAAGCACCATTGTCATCACGTAAAACAT
* * * * *
539390 CTACCTCACCACGTAAAGACCGTACCTCATCACGCCATGCACCATTGTCCTCACGTAAA
1 CTACCTAACCACGTAAAGA-CGTACCTCACCACGCAAAGCACCATTGTCATCACGTAAA
539449 GTACCGACCT
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
62 1 0.02
63 48 0.96
64 1 0.02
ACGTcount: A:0.34, C:0.34, G:0.11, T:0.21
Consensus pattern (62 bp):
CTACCTAACCACGTAAAGACGTACCTCACCACGCAAAGCACCATTGTCATCACGTAAAACAT
Found at i:539415 original size:21 final size:20
Alignment explanation
Indices: 539349--539423 Score: 55
Period size: 21 Copynumber: 3.6 Consensus size: 20
539339 GTAAAGTAGA
539349 TACCTCACCACGTAAAGCACC
1 TACCTCACCACGTAAAG-ACC
** *
539370 -ATTGTCATCACGTAAA-ACATC
1 TA-CCTCACCACGTAAAGAC--C
539391 TACCTCACCACGTAAAGACC
1 TACCTCACCACGTAAAGACC
*
539411 GTACCTCATCACG
1 -TACCTCACCACG
539424 CCATGCACCA
Statistics
Matches: 41, Mismatches: 7, Indels: 12
0.68 0.12 0.20
Matches are distributed among these distances:
19 2 0.05
20 2 0.05
21 34 0.83
22 3 0.07
ACGTcount: A:0.33, C:0.36, G:0.11, T:0.20
Consensus pattern (20 bp):
TACCTCACCACGTAAAGACC
Found at i:539464 original size:21 final size:21
Alignment explanation
Indices: 539440--539489 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
539430 ACCATTGTCC
**
539440 TCACGTAAAGTACCGACCTCA
1 TCACGTAAAACACCGACCTCA
* **
539461 TCACGCAAAACATTGACCTCA
1 TCACGTAAAACACCGACCTCA
539482 TCACGTAA
1 TCACGTAA
539490 CTCCCCTAAC
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.36, C:0.32, G:0.12, T:0.20
Consensus pattern (21 bp):
TCACGTAAAACACCGACCTCA
Found at i:539486 original size:42 final size:42
Alignment explanation
Indices: 539374--539489 Score: 107
Period size: 42 Copynumber: 2.8 Consensus size: 42
539364 AGCACCATTG
* *
539374 TCATCACGTAAAACATCT-ACCTCACCACGTAAAGACCGTACC
1 TCATCACGCAAAACAT-TGACCTCATCACGTAAAGACCGTACC
* * *
539416 TCATCACGCCATGCACCATTG---TCCTCACGTAAAGTACCG-ACC
1 TCATCACG-CA--AAACATTGACCTCATCACGTAAAG-ACCGTACC
539458 TCATCACGCAAAACATTGACCTCATCACGTAA
1 TCATCACGCAAAACATTGACCTCATCACGTAA
539490 CTCCCCTAAC
Statistics
Matches: 58, Mismatches: 8, Indels: 16
0.71 0.10 0.20
Matches are distributed among these distances:
39 6 0.10
41 2 0.03
42 40 0.69
43 5 0.09
44 1 0.02
45 4 0.07
ACGTcount: A:0.33, C:0.35, G:0.11, T:0.21
Consensus pattern (42 bp):
TCATCACGCAAAACATTGACCTCATCACGTAAAGACCGTACC
Found at i:541015 original size:19 final size:19
Alignment explanation
Indices: 540964--541017 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 19
540954 GGTAGTTTCT
*
540964 GAAACTTAAATTCGCAACGC
1 GAAAC-TAAAATCGCAACGC
*
540984 GAAAATGAAAATCGCAACGC
1 GAAACT-AAAATCGCAACGC
541004 GAAACTAAAATCGC
1 GAAACTAAAATCGC
541018 GTTGCCATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
19 9 0.30
20 21 0.70
ACGTcount: A:0.46, C:0.22, G:0.17, T:0.15
Consensus pattern (19 bp):
GAAACTAAAATCGCAACGC
Done.