Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008209.1 Hibiscus syriacus cultivar Beakdansim tig00110831_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: 6561538
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 30
Found at i:476985 original size:22 final size:22
Alignment explanation
Indices: 476960--477035 Score: 127
Period size: 22 Copynumber: 3.5 Consensus size: 22
476950 AATAAAGCTT
476960 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
476982 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
477004 TCATATTTG-AAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
477025 TCATCTTTGAA
1 TCATCTTTGAA
477036 GAGTGTAGAT
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
21 20 0.41
22 29 0.59
ACGTcount: A:0.41, C:0.13, G:0.12, T:0.34
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:481921 original size:18 final size:20
Alignment explanation
Indices: 481894--481933 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
481884 CTTGATTCAA
481894 TTTTC-CTTTTT-CTTTTTT
1 TTTTCTCTTTTTCCTTTTTT
*
481912 TTTTCTTTTTTTCCTTTTTT
1 TTTTCTCTTTTTCCTTTTTT
481932 TT
1 TT
481934 ACCTAATGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 5 0.26
19 5 0.26
20 9 0.47
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (20 bp):
TTTTCTCTTTTTCCTTTTTT
Found at i:484435 original size:13 final size:13
Alignment explanation
Indices: 484417--484463 Score: 71
Period size: 13 Copynumber: 3.8 Consensus size: 13
484407 ATTTGTTTTT
484417 CAAAAAAAAAATG
1 CAAAAAAAAAATG
*
484430 CAAAAAAAAATTG
1 CAAAAAAAAAATG
484443 C--AAAAAAAATG
1 CAAAAAAAAAATG
484454 CAAAAAAAAA
1 CAAAAAAAAA
484464 GCCAAAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
11 10 0.33
13 20 0.67
ACGTcount: A:0.77, C:0.09, G:0.06, T:0.09
Consensus pattern (13 bp):
CAAAAAAAAAATG
Found at i:484470 original size:12 final size:12
Alignment explanation
Indices: 484419--484463 Score: 74
Period size: 12 Copynumber: 3.8 Consensus size: 12
484409 TTGTTTTTCA
484419 AAAAAAAAATGC
1 AAAAAAAAATGC
484431 AAAAAAAAATTGC
1 AAAAAAAAA-TGC
484444 -AAAAAAAATGC
1 AAAAAAAAATGC
484455 AAAAAAAAA
1 AAAAAAAAA
484464 GCCAAAATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
11 3 0.10
12 25 0.81
13 3 0.10
ACGTcount: A:0.78, C:0.07, G:0.07, T:0.09
Consensus pattern (12 bp):
AAAAAAAAATGC
Found at i:494540 original size:3 final size:3
Alignment explanation
Indices: 494532--494594 Score: 83
Period size: 3 Copynumber: 20.7 Consensus size: 3
494522 GGCTTGTTTG
* *
494532 TAA TAA TAA TAA TAT TAA TAA TAA AAA TATA TAA TAAA TAA TAA T-A
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA T-AA TAA TAA TAA
494578 TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TA
494595 TAAATAAAAC
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
2 2 0.04
3 45 0.85
4 6 0.11
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:496130 original size:20 final size:19
Alignment explanation
Indices: 496088--496130 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
496078 AAATTGACCC
* *
496088 AATTTCACATTCTAACATC
1 AATTTCACAATCTAACATA
*
496107 AATTTCAACAATCTAATATA
1 AATTTC-ACAATCTAACATA
496127 AATT
1 AATT
496131 ACCAGCATAG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.44, C:0.19, G:0.00, T:0.37
Consensus pattern (19 bp):
AATTTCACAATCTAACATA
Found at i:498194 original size:12 final size:12
Alignment explanation
Indices: 498163--498192 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
498153 CACTTGTGCA
498163 ATACTTTCCAAG
1 ATACTTTCCAAG
498175 ATACTTTCCAAG
1 ATACTTTCCAAG
498187 A-ACTTT
1 ATACTTT
498193 TCATATTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 5 0.28
12 13 0.72
ACGTcount: A:0.33, C:0.23, G:0.07, T:0.37
Consensus pattern (12 bp):
ATACTTTCCAAG
Found at i:502275 original size:43 final size:46
Alignment explanation
Indices: 502152--502277 Score: 143
Period size: 47 Copynumber: 2.8 Consensus size: 46
502142 TATAAAATCT
*
502152 CTTACCATTT-ATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTAATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * * *
502197 CTTACCATTTAAATTCCATAAGCTCATAAACTTATTTTATCAATATA
1 CTTACCATTT-AATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * *
502244 CTTGCCA-TT-ATT-CATAAACTTGTAAGCTTATTTT
1 CTTACCATTTAATTCCATAAGCTCGTAAGCTTATTTT
502278 CATTCTTACC
Statistics
Matches: 69, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
43 18 0.26
44 3 0.04
45 10 0.14
46 2 0.03
47 36 0.52
ACGTcount: A:0.33, C:0.21, G:0.06, T:0.40
Consensus pattern (46 bp):
CTTACCATTTAATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:507312 original size:29 final size:30
Alignment explanation
Indices: 507239--507312 Score: 75
Period size: 29 Copynumber: 2.5 Consensus size: 30
507229 GAAAATTACC
* *
507239 ATTTTGGTCCCTAAACGTTTCCAAATTTAT
1 ATTTTTGTCACTAAACGTTTCCAAATTTAT
*
507269 A-TTTTGCCA-TGAAAC-TTT-CAAATTTTAT
1 ATTTTTGTCACT-AAACGTTTCCAAA-TTTAT
507297 ATTTTTGTCACTAAAC
1 ATTTTTGTCACTAAAC
507313 AAAATTTAGG
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
27 4 0.11
28 10 0.28
29 20 0.56
30 2 0.06
ACGTcount: A:0.30, C:0.18, G:0.08, T:0.45
Consensus pattern (30 bp):
ATTTTTGTCACTAAACGTTTCCAAATTTAT
Found at i:508416 original size:26 final size:28
Alignment explanation
Indices: 508387--508449 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 28
508377 GCTATGAAAA
508387 TGAATATG-AAAG-TATTGAAATGTGAT
1 TGAATATGAAAAGATATTGAAATGTGAT
508413 TGAATA-GAAAAGAATCTATTGAAATGTGAT
1 TGAATATGAAAAG-A--TATTGAAATGTGAT
508443 TGAATAT
1 TGAATAT
508450 AAATGAATCT
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
25 1 0.03
26 10 0.32
30 20 0.65
ACGTcount: A:0.44, C:0.02, G:0.21, T:0.33
Consensus pattern (28 bp):
TGAATATGAAAAGATATTGAAATGTGAT
Found at i:508435 original size:30 final size:30
Alignment explanation
Indices: 508399--508460 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
508389 AATATGAAAG
508399 TATTGAAATGTGATTGAATAGAAAAGAATC
1 TATTGAAATGTGATTGAATAGAAAAGAATC
* *
508429 TATTGAAATGTGATTGAATATAAATGAATC
1 TATTGAAATGTGATTGAATAGAAAAGAATC
508459 TA
1 TA
508461 CAATGATTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.45, C:0.03, G:0.18, T:0.34
Consensus pattern (30 bp):
TATTGAAATGTGATTGAATAGAAAAGAATC
Found at i:515839 original size:45 final size:48
Alignment explanation
Indices: 515768--515865 Score: 114
Period size: 50 Copynumber: 2.1 Consensus size: 48
515758 CAATGAATAA
*
515768 AATAATAATAAAAACACATGTCTTAA-CT-C-TAATTCCTAATAAAAT
1 AATAATAATAAAAACACATATCTTAACCTACGTAATTCCTAATAAAAT
* *
515813 AATAATAACTAAAAATA-ATATTTTAACCTAACCGTAATTCCTAATAAAAT
1 AATAATAA-TAAAAACACATATCTTAACCT-A-CGTAATTCCTAATAAAAT
515863 AAT
1 AAT
515866 TAGTCTAATC
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
45 15 0.34
46 9 0.20
49 1 0.02
50 19 0.43
ACGTcount: A:0.52, C:0.14, G:0.02, T:0.32
Consensus pattern (48 bp):
AATAATAATAAAAACACATATCTTAACCTACGTAATTCCTAATAAAAT
Found at i:517725 original size:19 final size:20
Alignment explanation
Indices: 517678--517728 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
517668 TAAACCCCTT
**
517678 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
517698 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
517717 TGAAGATACATG
1 TGAAAATACATG
517729 CTCGTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:519686 original size:24 final size:21
Alignment explanation
Indices: 519651--519693 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
519641 GGCACATTCT
*
519651 TTTGAATTTCAAGAGGTACATCC
1 TTTGAATGTCAA-AGG-ACATCC
519674 TTTGAAATGTCAAAGGACAT
1 TTTG-AATGTCAAAGGACAT
519694 GTCTTGTGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 7 0.39
24 7 0.39
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (21 bp):
TTTGAATGTCAAAGGACATCC
Found at i:530554 original size:62 final size:61
Alignment explanation
Indices: 530457--530585 Score: 177
Period size: 62 Copynumber: 2.1 Consensus size: 61
530447 GCGGGTTTAT
* * * * *
530457 ATTAGCACTAAAGTGTAAACCTAGTGTAGGTGGTGGGCACGACCCCTACGTATCATATTCGG
1 ATTAGCACGAAAGTGTAAACCTAGTGTAGGCGGTGGGCAC-AACCCTACGTATCATATCCAG
* * *
530519 ATTAGCACGAGAGTGTAAACCTAGTGTAGGCGGTGGGCACAACCTTATGTATCATATCCAG
1 ATTAGCACGAAAGTGTAAACCTAGTGTAGGCGGTGGGCACAACCCTACGTATCATATCCAG
530580 ATTAGC
1 ATTAGC
530586 CCTAGAGCAT
Statistics
Matches: 59, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
61 22 0.37
62 37 0.63
ACGTcount: A:0.29, C:0.20, G:0.26, T:0.26
Consensus pattern (61 bp):
ATTAGCACGAAAGTGTAAACCTAGTGTAGGCGGTGGGCACAACCCTACGTATCATATCCAG
Found at i:530605 original size:61 final size:62
Alignment explanation
Indices: 530472--530609 Score: 161
Period size: 61 Copynumber: 2.2 Consensus size: 62
530462 CACTAAAGTG
* * * * **
530472 TAAACCTAGTGTAGGTGGTGGGCACGACCCCTACGTATCATATTCGGATTAGCACGAGAGTG
1 TAAACCTAGTGTAGGCGGTGGGCACGAACCCTACGTATCATATCCAGATTAGCACGAGAGCA
* * * *
530534 TAAACCTAGTGTAGGCGGTGGGCAC-AACCTTATGTATCATATCCAGATTAGCCCTAGAGCA
1 TAAACCTAGTGTAGGCGGTGGGCACGAACCCTACGTATCATATCCAGATTAGCACGAGAGCA
* *
530595 TACACTTAGTGTAGG
1 TAAACCTAGTGTAGG
530610 TTTAGCACTA
Statistics
Matches: 64, Mismatches: 12, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
61 40 0.62
62 24 0.38
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.25
Consensus pattern (62 bp):
TAAACCTAGTGTAGGCGGTGGGCACGAACCCTACGTATCATATCCAGATTAGCACGAGAGCA
Found at i:532682 original size:61 final size:61
Alignment explanation
Indices: 532595--532709 Score: 176
Period size: 61 Copynumber: 1.9 Consensus size: 61
532585 TAAGGTGGAT
* * *
532595 ACGACCTAATGTATCATGTCCGGATTAGCACTATAGCGTAAGCTTAGTGTAGGTGGTGGGC
1 ACGACCTAATGTATCATATCCCGATTAGCACTATAGCGTAAGCTTAGTGCAGGTGGTGGGC
* * *
532656 ACGACCTTATGTGTCATATCCCGATTAGCACTATGGCGTAAGCTTAGTGCAGGT
1 ACGACCTAATGTATCATATCCCGATTAGCACTATAGCGTAAGCTTAGTGCAGGT
532710 TTAGCACTAC
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (61 bp):
ACGACCTAATGTATCATATCCCGATTAGCACTATAGCGTAAGCTTAGTGCAGGTGGTGGGC
Found at i:532909 original size:47 final size:47
Alignment explanation
Indices: 532819--533023 Score: 292
Period size: 47 Copynumber: 4.4 Consensus size: 47
532809 GTAAGTATGC
* *
532819 AAATAAGCTTACGAGCTTAT-GAA--T-ACTGGCAAGTATATTGATA
1 AAATAAGCTTACGAGCTTATGGAATTTAAATGGCAAGTATTTTGATA
* * *
532862 AATTAAGCTTTCGAGCTTATGGAATTTAAATGGCAAGTATGTTGATA
1 AAATAAGCTTACGAGCTTATGGAATTTAAATGGCAAGTATTTTGATA
* * *
532909 AAATAAGCTTACGAGCTTATGAAATTTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGAATTTAAATGGCAAGTATTTTGATA
* *
532956 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGAATTTAAATGGCAAGTATTTTGATA
533003 AAATAAGCTTACGAGCTTATG
1 AAATAAGCTTACGAGCTTATG
533024 AGATAAATGG
Statistics
Matches: 147, Mismatches: 11, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
43 18 0.12
44 3 0.02
46 1 0.01
47 125 0.85
ACGTcount: A:0.37, C:0.09, G:0.20, T:0.34
Consensus pattern (47 bp):
AAATAAGCTTACGAGCTTATGGAATTTAAATGGCAAGTATTTTGATA
Found at i:535907 original size:20 final size:17
Alignment explanation
Indices: 535884--535964 Score: 65
Period size: 20 Copynumber: 4.4 Consensus size: 17
535874 AAATTATATA
535884 AGAAAAAAAAATGAAGAAAT
1 AGAAAAAAAAA-G-A-AAAT
535904 AGAAAAAGAAAAGAAAAT
1 AGAAAAA-AAAAGAAAAT
*
535922 AGAAAAAAATGAAAAAAAAT
1 AG-AAAAAA--AAAGAAAAT
*
535942 AGAAAATGAAAAGAAAAT
1 AGAAAA-AAAAAGAAAAT
535960 A-AAAA
1 AGAAAA
535965 TGAGAGATGA
Statistics
Matches: 53, Mismatches: 3, Indels: 13
0.77 0.04 0.19
Matches are distributed among these distances:
17 4 0.08
18 16 0.30
19 10 0.19
20 19 0.36
21 4 0.08
ACGTcount: A:0.78, C:0.00, G:0.14, T:0.09
Consensus pattern (17 bp):
AGAAAAAAAAAGAAAAT
Found at i:535909 original size:18 final size:19
Alignment explanation
Indices: 535888--535947 Score: 72
Period size: 18 Copynumber: 3.2 Consensus size: 19
535878 TATATAAGAA
535888 AAAAAAATGAAG-AAATAG
1 AAAAAAATGAAGAAAATAG
535906 AAAAAGAA--AAGAAAATAG
1 AAAAA-AATGAAGAAAATAG
*
535924 AAAAAAATGAAAAAAAATAG
1 AAAAAAATG-AAGAAAATAG
535944 AAAA
1 AAAA
535948 TGAAAAGAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
17 5 0.14
18 16 0.44
19 2 0.06
20 13 0.36
ACGTcount: A:0.78, C:0.00, G:0.13, T:0.08
Consensus pattern (19 bp):
AAAAAAATGAAGAAAATAG
Found at i:535920 original size:11 final size:11
Alignment explanation
Indices: 535897--535964 Score: 54
Period size: 11 Copynumber: 6.2 Consensus size: 11
535887 AAAAAAAATG
535897 AAGAAATAGAAA
1 AAGAAA-AGAAA
535909 AAGAAAAGAAA
1 AAGAAAAGAAA
535920 ATAG-AAA-AAA
1 A-AGAAAAGAAA
*
535930 ATGAAAA-AAA
1 AAGAAAAGAAA
535940 ATAGAAAATG-AA
1 A-AGAAAA-GAAA
*
535952 AAGAAAATAAA
1 AAGAAAAGAAA
535963 AA
1 AA
535965 TGAGAGATGA
Statistics
Matches: 47, Mismatches: 3, Indels: 13
0.75 0.05 0.21
Matches are distributed among these distances:
9 1 0.02
10 11 0.23
11 24 0.51
12 11 0.23
ACGTcount: A:0.78, C:0.00, G:0.13, T:0.09
Consensus pattern (11 bp):
AAGAAAAGAAA
Found at i:535926 original size:38 final size:39
Alignment explanation
Indices: 535884--535964 Score: 107
Period size: 38 Copynumber: 2.2 Consensus size: 39
535874 AAATTATATA
*
535884 AGAAAAAAAAATG-AAGAAATAGAAAAAGAAAAGAAAAT
1 AGAAAAAAAAATGAAAAAAATAGAAAAAGAAAAGAAAAT
*
535922 AG--AAAAAAATGAAAAAAAATAGAAAATGAAAAGAAAAT
1 AGAAAAAAAAATG-AAAAAAATAGAAAAAGAAAAGAAAAT
535960 A-AAAA
1 AGAAAA
535965 TGAGAGATGA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
36 9 0.24
38 26 0.70
39 2 0.05
ACGTcount: A:0.78, C:0.00, G:0.14, T:0.09
Consensus pattern (39 bp):
AGAAAAAAAAATGAAAAAAATAGAAAAAGAAAAGAAAAT
Found at i:535935 original size:27 final size:27
Alignment explanation
Indices: 535883--535953 Score: 85
Period size: 26 Copynumber: 2.7 Consensus size: 27
535873 AAAATTATAT
* *
535883 AAGAAAAAAAAATG-AAGAAATAGAAA
1 AAGAAAAGAAAATGAAAAAAATAGAAA
535909 AAGAAAAGAAAATAGAAAAAAAT-GAAA
1 AAGAAAAGAAAAT-GAAAAAAATAGAAA
535936 AA-AAATAGAAAATGAAAA
1 AAGAAA-AGAAAATGAAAA
535954 GAAAATAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
26 20 0.50
27 14 0.35
28 6 0.15
ACGTcount: A:0.77, C:0.00, G:0.14, T:0.08
Consensus pattern (27 bp):
AAGAAAAGAAAATGAAAAAAATAGAAA
Found at i:535948 original size:17 final size:18
Alignment explanation
Indices: 535900--535967 Score: 86
Period size: 17 Copynumber: 3.7 Consensus size: 18
535890 AAAAATGAAG
*
535900 AAATAGAAAAAGAAAAGA
1 AAATAGAAAATGAAAAGA
535918 AAATAGAAAAAAATGAAAA-A
1 AAATAG---AAAATGAAAAGA
535938 AAATAGAAAATGAAAAGA
1 AAATAGAAAATGAAAAGA
535956 AAATA-AAAATGA
1 AAATAGAAAATGA
535968 GAGATGAAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
17 17 0.38
18 12 0.27
20 7 0.16
21 9 0.20
ACGTcount: A:0.76, C:0.00, G:0.13, T:0.10
Consensus pattern (18 bp):
AAATAGAAAATGAAAAGA
Found at i:539806 original size:47 final size:47
Alignment explanation
Indices: 539718--539876 Score: 227
Period size: 47 Copynumber: 3.5 Consensus size: 47
539708 GTAAGTATGC
539718 AAATAAGCTTACGAGCTTAT-GAA--T-AATGGCAAGTATATTGATA
1 AAATAAGCTTACGAGCTTATGGAATTTAAATGGCAAGTATATTGATA
* * *
539761 AATTAAGCTTTCGAGCTTATGGAATTTAAATGGCAAGTATGTTGATA
1 AAATAAGCTTACGAGCTTATGGAATTTAAATGGCAAGTATATTGATA
* * * *
539808 AAATCAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGAATTTAAATGGCAAGTATATTGATA
539855 AAATAAGCTTACGAGCTTATGG
1 AAATAAGCTTACGAGCTTATGG
539877 GATAAATGGT
Statistics
Matches: 102, Mismatches: 10, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
43 18 0.18
44 3 0.03
46 1 0.01
47 80 0.78
ACGTcount: A:0.36, C:0.09, G:0.21, T:0.33
Consensus pattern (47 bp):
AAATAAGCTTACGAGCTTATGGAATTTAAATGGCAAGTATATTGATA
Found at i:542882 original size:21 final size:21
Alignment explanation
Indices: 542858--542898 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
542848 CAATTATGAG
*
542858 TATTCAATGTTGAAATTTAAT
1 TATTCAATGATGAAATTTAAT
* *
542879 TATTTAATGATGAATTTTAA
1 TATTCAATGATGAAATTTAA
542899 GTTAGAATGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.39, C:0.02, G:0.10, T:0.49
Consensus pattern (21 bp):
TATTCAATGATGAAATTTAAT
Found at i:543881 original size:21 final size:22
Alignment explanation
Indices: 543857--543901 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
543847 TGCATTAAAT
*
543857 TTAGCTCATATGTCTTATA-CA
1 TTAGCTCACATGTCTTATATCA
*
543878 TTAGCTCACATGTGTTATATCA
1 TTAGCTCACATGTCTTATATCA
543900 TT
1 TT
543902 TTATACTTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.27, C:0.18, G:0.11, T:0.44
Consensus pattern (22 bp):
TTAGCTCACATGTCTTATATCA
Found at i:546087 original size:81 final size:81
Alignment explanation
Indices: 545949--546440 Score: 743
Period size: 81 Copynumber: 6.1 Consensus size: 81
545939 CTGTTCTAAA
* * * * * * *
545949 TAAAATATTAATGACCTAGTTGTGCA-TTGATAGAAATGTGTCAATTATGCCAATTAGATAAAAT
1 TAAAAGATTAATGGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
546013 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * * **
546029 TAAAAGATTTATGGCCTAGGTGTGCATTTGACAGAAAGCTGTCAATTATGTAAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
546094 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * *
546110 TAAAAGATTAATGGCCTAGTTGTGCATTTGATAGAAAGATGTCAATTGTGCCAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
546175 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * *
546191 TAAAAGATTAATGGCCTAGCTGTGTATTTGACATAAAGGTGTCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
*
546256 GTTAAATAACTTTGAG
66 GTTAAATACCTTTGAG
* * *
546272 TAAAAGATTAATGGCCTAGTTGTGCATTTGAAAGAAAGGTGTCAATTATGTCAGTTACATGAAAG
1 TAAAAGATTAATGGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
546337 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * * *
546353 TAAAAGATTAATGGCCTAGATGTGCATTTGACATAAAGGTGTCAATTATGCCAGTTAGATAAAAT
1 TAAAAGATTAATGGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
546418 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
546434 TAAAAGA
1 TAAAAGA
546441 CTAAATGCTT
Statistics
Matches: 371, Mismatches: 40, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
80 22 0.06
81 349 0.94
ACGTcount: A:0.37, C:0.10, G:0.21, T:0.32
Consensus pattern (81 bp):
TAAAAGATTAATGGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
GTTAAATACCTTTGAG
Found at i:551302 original size:350 final size:347
Alignment explanation
Indices: 550654--551351 Score: 1328
Period size: 350 Copynumber: 2.0 Consensus size: 347
550644 ATTGGCCTAG
550654 ATTTGATGAAAAAAATGGAGGAGAAAGTAAAAATTATCAGGATAATTTGTAGATAGCCTCCGATC
1 ATTTGATGAAAAAAATGGAGGAGAAAGTAAAAATTATCAGGATAATTTGTAGATAGCCTCCGATC
*
550719 AACCGAAGTCTTATGATGATTTGAACGAAAAGAAATCAAATTTCGAGTGGGAGACAAAGTATTTC
66 AACCGAAGTCTTATGATGATTTGAACGAAAAGAAATCAAATTTCGAGTGAGAGACAAAGTATTTC
550784 TAAAGGTACCGCCTTGGAAAAAGGTATTGCGATTTGTACAAAAGAAAGCTGAGTCTGAGATTCAT
131 TAAAGGTACCGCCTTGGAAAAAGGTATTGCGATTTGTACAAAAGAAAGCTGAGTCTGAGATTCAT
550849 TGGACCTTATGACATCTTGAAATGGGTTGGACCTGTAGCTTATCAAATAGATTTACCTTTGGATA
196 TGGACCTTATGACATCTTGAAATGGGTTGGACCTGTAGCTTATCAAATAGATTTACCTTTGGATA
550914 TGGTAAAAATTCACAATGTTTTCCACGTATCGATGCTTAGAAGGTACAGATTGGATCCATCCCAT
261 TGGTAAAAATTCACAATGTTTTCCACGTATCGATGCTTAGAAGGTACAGATTGGATCCATCCCAT
550979 GTAA-CCACGCCAGAAGAGATACA
326 GTAACCCA-GCCAG-AGAGATACA
551002 ATTTGATGAAAAAAAATGGAGGAGAAAGTAAAAATTATCCAGGATAATTTGTAGATAGCCTCCGA
1 ATTTGATG-AAAAAAATGGAGGAGAAAGTAAAAATTAT-CAGGATAATTTGTAGATAGCCTCCGA
551067 TCAACCGAAGTCTTATGATGATTTGAACGAAAAGAAATCAAATTTCGAGTGAG-GACAAAGTATT
64 TCAACCGAAGTCTTATGATGATTTGAACGAAAAGAAATCAAATTTCGAGTGAGAGACAAAGTATT
551131 TCTAAAGGTACCGCCTTGGAAAAAGGTATTGCGATTTGTACAAAAGAAAAGCTGAGTCTGAGATT
129 TCTAAAGGTACCGCCTTGGAAAAAGGTATTGCGATTTGTACAAAAG-AAAGCTGAGTCTGAGATT
551196 CATTGGACCTTATGACATCTTGAAATGGGTTGGACCTGTAGCTTATCAAATAGATTTACCTTTGG
193 CATTGGACCTTATGACATCTTGAAATGGGTTGGACCTGTAGCTTATCAAATAGATTTACCTTTGG
551261 ATATGGTAAAAATTCACAATGTTTTCCACGTATCGATGCTTAGAAGGTACAGATTGGATCCATCC
258 ATATGGTAAAAATTCACAATGTTTTCCACGTATCGATGCTTAGAAGGTACAGATTGGATCCATCC
551326 CATGTAACCCAGCCAGAGAGATACA
323 CATGTAACCCAGCCAGAGAGATACA
551351 A
1 A
551352 ATCCAACCAG
Statistics
Matches: 345, Mismatches: 1, Indels: 7
0.98 0.00 0.02
Matches are distributed among these distances:
348 8 0.02
349 96 0.28
350 238 0.69
351 3 0.01
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28
Consensus pattern (347 bp):
ATTTGATGAAAAAAATGGAGGAGAAAGTAAAAATTATCAGGATAATTTGTAGATAGCCTCCGATC
AACCGAAGTCTTATGATGATTTGAACGAAAAGAAATCAAATTTCGAGTGAGAGACAAAGTATTTC
TAAAGGTACCGCCTTGGAAAAAGGTATTGCGATTTGTACAAAAGAAAGCTGAGTCTGAGATTCAT
TGGACCTTATGACATCTTGAAATGGGTTGGACCTGTAGCTTATCAAATAGATTTACCTTTGGATA
TGGTAAAAATTCACAATGTTTTCCACGTATCGATGCTTAGAAGGTACAGATTGGATCCATCCCAT
GTAACCCAGCCAGAGAGATACA
Found at i:552208 original size:19 final size:19
Alignment explanation
Indices: 552184--552254 Score: 79
Period size: 19 Copynumber: 3.5 Consensus size: 19
552174 TGCAAAAATG
552184 GTATCGATACCATAGTATA
1 GTATCGATACCATAGTATA
*
552203 GTATCGTTACCATAGTATATTA
1 GTATCGATACCATAG--TA-TA
* *
552225 GTATCGATACCATGGTATGG
1 GTATCGATACCATAGTAT-A
552245 GTATCGATAC
1 GTATCGATAC
552255 TGAGGAGCCA
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
19 15 0.34
20 12 0.27
21 2 0.05
22 15 0.34
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.34
Consensus pattern (19 bp):
GTATCGATACCATAGTATA
Found at i:552229 original size:22 final size:21
Alignment explanation
Indices: 552184--552242 Score: 77
Period size: 22 Copynumber: 2.9 Consensus size: 21
552174 TGCAAAAATG
552184 GTATCGATACCATAG--TATA
1 GTATCGATACCATAGTATATA
*
552203 GTATCGTTACCATAGTATATTA
1 GTATCGATACCATAGTATA-TA
*
552225 GTATCGATACCATGGTAT
1 GTATCGATACCATAGTAT
552243 GGGTATCGAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
19 14 0.41
21 2 0.06
22 18 0.53
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (21 bp):
GTATCGATACCATAGTATATA
Found at i:552668 original size:55 final size:54
Alignment explanation
Indices: 552579--552927 Score: 491
Period size: 55 Copynumber: 6.4 Consensus size: 54
552569 CTATGTGTAC
* *
552579 TACAGGCACTAAGTGTACAAAACCACGGAATTCATCATGAGTTGATGAATAATCG
1 TACAGGCACTAAGTGTGCAAAACCACAGAATTCATCATGAGTTGATGAATAA-CG
* * * *
552634 TACATGCACTAAATGTGCAAAACCATAGAATTCATCATGAGTTGATGAATTAGCG
1 TACAGGCACTAAGTGTGCAAAACCACAGAATTCATCATGAGTTGATGAA-TAACG
* *
552689 TACATGCACTAAGTGTGCAAAACCACATAATTCATCATGAGTTGATGAATAATCG
1 TACAGGCACTAAGTGTGCAAAACCACAGAATTCATCATGAGTTGATGAATAA-CG
* * *
552744 TACAGGCACTAAGTGTGCAAAACAACAAAATTCATAATGAGTTGATGAATAACTG
1 TACAGGCACTAAGTGTGCAAAACCACAGAATTCATCATGAGTTGATGAATAAC-G
* * *
552799 TATAGACACTAAGTGTACAAAACCACAGAATTCATCATGAGTTGATGAATAACAG
1 TACAGGCACTAAGTGTGCAAAACCACAGAATTCATCATGAGTTGATGAATAAC-G
*
552854 TACAGGCACTAAGTGTGCAAAACCACAGAATTCATCATGAATTGATGAATAACCG
1 TACAGGCACTAAGTGTGCAAAACCACAGAATTCATCATGAGTTGATGAATAA-CG
* *
552909 TAAAGGCACTATGTGTGCA
1 TACAGGCACTAAGTGTGCA
552928 TCTTAATAAA
Statistics
Matches: 263, Mismatches: 27, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
54 3 0.01
55 257 0.98
56 3 0.01
ACGTcount: A:0.40, C:0.17, G:0.18, T:0.25
Consensus pattern (54 bp):
TACAGGCACTAAGTGTGCAAAACCACAGAATTCATCATGAGTTGATGAATAACG
Found at i:554706 original size:27 final size:27
Alignment explanation
Indices: 554572--554757 Score: 155
Period size: 28 Copynumber: 6.7 Consensus size: 27
554562 TCCACATTCG
*
554572 AAAATTACCAAAATGTCACCTTTTTCAA
1 AAAATT-CCAGAATGTCACCTTTTTCAA
* * *
554600 ATAATACCCAGAATGTCACCTTTCTCAA
1 AAAAT-TCCAGAATGTCACCTTTTTCAA
* *
554628 AATAATTCCCAGAATGTCACCCTTTTCAC
1 AA-AATT-CCAGAATGTCACCTTTTTCAA
* * *
554657 AAAATTCCCGAAATGTCA-TTTTTTTAA
1 AAAATTCCAG-AATGTCACCTTTTTCAA
*
554684 AAAATTCCAGAATGTCACATTTTTTCACA
1 AAAATTCCAGAATGTCAC-CTTTTTCA-A
* *
554713 AAAA-T-CAAAATGTCA-CATTTTCAA
1 AAAATTCCAGAATGTCACCTTTTTCAA
554737 AATAATTCCTAGAATGTCACC
1 AA-AATTCC-AGAATGTCACC
554758 GGGTCGGGTC
Statistics
Matches: 126, Mismatches: 20, Indels: 23
0.75 0.12 0.14
Matches are distributed among these distances:
24 3 0.02
25 8 0.06
26 8 0.06
27 27 0.21
28 51 0.40
29 29 0.23
ACGTcount: A:0.39, C:0.23, G:0.06, T:0.32
Consensus pattern (27 bp):
AAAATTCCAGAATGTCACCTTTTTCAA
Found at i:554711 original size:55 final size:53
Alignment explanation
Indices: 554611--554757 Score: 161
Period size: 55 Copynumber: 2.7 Consensus size: 53
554601 TAATACCCAG
* * *
554611 AATGTCACCTTTCTCAAAATAATTCCCAGAATGTCACCCTTTTCACAAAATTCCCGA
1 AATGTCACATTT-TCAAAATAATT-CCAGAATGTCACCCTTTTCACAAAAAT--CAA
** * **
554668 AATGTCATTTTTTTAAAA-AATTCCAGAATGTCACATTTTTTCACAAAAATCAA
1 AATGTCACATTTTCAAAATAATTCCAGAATGTCAC-CCTTTTCACAAAAATCAA
554721 AATGTCACATTTTCAAAATAATTCCTAGAATGTCACC
1 AATGTCACATTTTCAAAATAATTCC-AGAATGTCACC
554758 GGGTCGGGTC
Statistics
Matches: 76, Mismatches: 11, Indels: 9
0.79 0.11 0.09
Matches are distributed among these distances:
53 17 0.22
54 18 0.24
55 26 0.34
56 5 0.07
57 10 0.13
ACGTcount: A:0.37, C:0.22, G:0.07, T:0.33
Consensus pattern (53 bp):
AATGTCACATTTTCAAAATAATTCCAGAATGTCACCCTTTTCACAAAAATCAA
Found at i:554780 original size:17 final size:17
Alignment explanation
Indices: 554757--554801 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 17
554747 AGAATGTCAC
*
554757 CGGGTCGGGTCGGGTTAA
1 CGGGTCGGGTC-GATTAA
554775 -GGGTCGGGTCGATTAA
1 CGGGTCGGGTCGATTAA
554791 CGGGTCGGGTC
1 CGGGTCGGGTC
554802 AGACCGGTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
16 5 0.20
17 20 0.80
ACGTcount: A:0.11, C:0.18, G:0.49, T:0.22
Consensus pattern (17 bp):
CGGGTCGGGTCGATTAA
Found at i:560914 original size:26 final size:26
Alignment explanation
Indices: 560885--560950 Score: 123
Period size: 26 Copynumber: 2.5 Consensus size: 26
560875 CATAGTCCAG
560885 TAAATCTCATAAAAATTGTACTGCAA
1 TAAATCTCATAAAAATTGTACTGCAA
*
560911 TAAATCTCATAAAAATTGTACTGCAG
1 TAAATCTCATAAAAATTGTACTGCAA
560937 TAAATCTCATAAAA
1 TAAATCTCATAAAA
560951 TAGTTACCCT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.47, C:0.15, G:0.08, T:0.30
Consensus pattern (26 bp):
TAAATCTCATAAAAATTGTACTGCAA
Found at i:562017 original size:29 final size:28
Alignment explanation
Indices: 561985--562134 Score: 146
Period size: 29 Copynumber: 5.3 Consensus size: 28
561975 AAATTATCAA
561985 AATGTCACCTTTTTCAAAATAATTCCCAG
1 AATGTCACCTTTTTCAAAA-AATTCCCAG
*
562014 AATGTCACATTTTTCACAAAAATTCCC-G
1 AATGTCACCTTTTTCA-AAAAATTCCCAG
* * * *
562042 AAATGTCA--TATTTAAAAAAAAT-CTAG
1 -AATGTCACCTTTTTCAAAAAATTCCCAG
* *
562068 AATGTCACATTTTTCACAAAAATTCCCAA
1 AATGTCACCTTTTTCA-AAAAATTCCCAG
* *
562097 AATATCACCTTTTTCATAATAATTCCCAG
1 AATGTCACCTTTTTCA-AAAAATTCCCAG
562126 AATGTCACC
1 AATGTCACC
562135 GGGTCGGGTC
Statistics
Matches: 98, Mismatches: 16, Indels: 14
0.77 0.12 0.11
Matches are distributed among these distances:
25 8 0.08
26 7 0.07
27 10 0.10
28 7 0.07
29 63 0.64
30 3 0.03
ACGTcount: A:0.39, C:0.22, G:0.06, T:0.33
Consensus pattern (28 bp):
AATGTCACCTTTTTCAAAAAATTCCCAG
Found at i:562168 original size:17 final size:18
Alignment explanation
Indices: 562129--562179 Score: 68
Period size: 17 Copynumber: 2.9 Consensus size: 18
562119 TTCCCAGAAT
*
562129 GTCACCGGGTCGGGTCGG
1 GTCAACGGGTCGGGTCGG
*
562147 GTCAACGGGTCTGGTC-G
1 GTCAACGGGTCGGGTCGG
*
562164 GTCAACGGGTTGGGTC
1 GTCAACGGGTCGGGTC
562180 AGACCGGTCA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
17 15 0.52
18 14 0.48
ACGTcount: A:0.10, C:0.24, G:0.45, T:0.22
Consensus pattern (18 bp):
GTCAACGGGTCGGGTCGG
Found at i:562205 original size:19 final size:19
Alignment explanation
Indices: 562178--562223 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
562168 ACGGGTTGGG
*
562178 TCAGACCGGTCATCCCGGT
1 TCAGACCGGTCAACCCGGT
*
562197 TCGGACCGGTCAACCCGGT
1 TCAGACCGGTCAACCCGGT
562216 TCAGACCG
1 TCAGACCG
562224 TTTTGGACCG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.17, C:0.37, G:0.28, T:0.17
Consensus pattern (19 bp):
TCAGACCGGTCAACCCGGT
Found at i:565476 original size:21 final size:22
Alignment explanation
Indices: 565444--565493 Score: 77
Period size: 21 Copynumber: 2.4 Consensus size: 22
565434 GCCCTTTGAT
565444 GATGT-TCTTAGGTGAAAATAA
1 GATGTATCTTAGGTGAAAATAA
*
565465 GATGTATC-TAGGTGGAAATAA
1 GATGTATCTTAGGTGAAAATAA
565486 GATGTATC
1 GATGTATC
565494 AGGATTTGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 25 0.93
22 2 0.07
ACGTcount: A:0.36, C:0.06, G:0.26, T:0.32
Consensus pattern (22 bp):
GATGTATCTTAGGTGAAAATAA
Found at i:568948 original size:95 final size:90
Alignment explanation
Indices: 568779--569023 Score: 344
Period size: 95 Copynumber: 2.7 Consensus size: 90
568769 TTATAATATT
*
568779 ATATATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTATGG
1 ATATATATACAATAAAGCTTGAGCTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTATGG
* *
568844 ATAATATTCAGCTAGCCTGATAAATGTG
66 ATAAGATTCAGCTAACCTGATAAA---G
568872 ATTATACTATACAATAAAGCTTGAGCTGTCCCTCTA-AGGCAATTGGTTAAACGCCCCGGCTTTA
1 A-TATA-TATACAATAAAGCTTGAGCTGTCCCTCTAGA-GCAATTGGTTAAACGCCCCGGCTTTA
568936 TGGATAAGATTCAGCTAACCTGATAAAG
63 TGGATAAGATTCAGCTAACCTGATAAAG
*
568964 ATAT-T-TAC-AT--A--TTGAGCTGTCCCTCTAGAGCAATTGGTAAAACGCCCCGGCTTTATGG
1 ATATATATACAATAAAGCTTGAGCTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTATGG
569022 AT
66 AT
569024 CCAGCTAGCC
Statistics
Matches: 144, Mismatches: 4, Indels: 18
0.87 0.02 0.11
Matches are distributed among these distances:
83 46 0.32
84 1 0.01
85 1 0.01
87 2 0.01
88 3 0.02
89 1 0.01
91 3 0.02
92 2 0.01
93 1 0.01
94 5 0.03
95 79 0.55
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (90 bp):
ATATATATACAATAAAGCTTGAGCTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTATGG
ATAAGATTCAGCTAACCTGATAAAG
Found at i:570105 original size:77 final size:75
Alignment explanation
Indices: 570014--570155 Score: 218
Period size: 77 Copynumber: 1.9 Consensus size: 75
570004 CAACCGTTGA
570014 TCAGGGGGAATCGGTA-CCCCTTGGGGGGGGAAATTGGTTCCCT-TCGAGC-ATACTGGAATTTC
1 TCAGGGGGAATCGGTACCCCCTT-GGGGGGG-AATTGGTTCCCTCT-GAGCAAT-CTGGAATTT-
570076 TTGGAGTCAAACCAT
61 TTGGAGTCAAACCAT
570091 TCAGGGGGAATCGGTACCCCCTTGGGGGGGAATTGGTTCCCTCTGAGCAATCTGGAATTTTTGGA
1 TCAGGGGGAATCGGTACCCCCTTGGGGGGGAATTGGTTCCCTCTGAGCAATCTGGAATTTTTGGA
570156 TTTGAAATGG
Statistics
Matches: 62, Mismatches: 0, Indels: 8
0.89 0.00 0.11
Matches are distributed among these distances:
75 5 0.08
76 25 0.40
77 26 0.42
78 6 0.10
ACGTcount: A:0.20, C:0.20, G:0.32, T:0.27
Consensus pattern (75 bp):
TCAGGGGGAATCGGTACCCCCTTGGGGGGGAATTGGTTCCCTCTGAGCAATCTGGAATTTTTGGA
GTCAAACCAT
Found at i:570147 original size:76 final size:76
Alignment explanation
Indices: 570014--570155 Score: 220
Period size: 76 Copynumber: 1.9 Consensus size: 76
570004 CAACCGTTGA
570014 TCAGGGGGAATCGGTACCCCTTGGGGGGGGAAATTGGTTCCCTTCGAGCATACTGGAATTTCTTG
1 TCAGGGGGAATCGGTACCCCTTGGGGGGGGAAATTGGTTCCCTTCGAGCATACTGGAATTT-TTG
570079 GAGTCAAACCAT
65 GAGTCAAACCAT
570091 TCAGGGGGAATCGGTACCCCCTT-GGGGGGG-AATTGGTTCCC-TCTGAGCA-ATCTGGAATTTT
1 TCAGGGGGAATCGGTA-CCCCTTGGGGGGGGAAATTGGTTCCCTTC-GAGCATA-CTGGAATTTT
570152 TGGA
63 TGGA
570156 TTTGAAATGG
Statistics
Matches: 62, Mismatches: 0, Indels: 8
0.89 0.00 0.11
Matches are distributed among these distances:
75 8 0.13
76 25 0.40
77 23 0.37
78 6 0.10
ACGTcount: A:0.20, C:0.20, G:0.32, T:0.27
Consensus pattern (76 bp):
TCAGGGGGAATCGGTACCCCTTGGGGGGGGAAATTGGTTCCCTTCGAGCATACTGGAATTTTTGG
AGTCAAACCAT
Found at i:572810 original size:22 final size:23
Alignment explanation
Indices: 572764--572824 Score: 97
Period size: 23 Copynumber: 2.7 Consensus size: 23
572754 CCCCTGTGGG
572764 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTTCCCCTTCAAA
572787 GGGGGAATCGGTTCCCCTTC-AA
1 GGGGGAATCGGTTCCCCTTCAAA
* *
572809 GGGGGTATCGATTCCC
1 GGGGGAATCGGTTCCC
572825 TCTACACTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
22 16 0.44
23 20 0.56
ACGTcount: A:0.18, C:0.26, G:0.33, T:0.23
Consensus pattern (23 bp):
GGGGGAATCGGTTCCCCTTCAAA
Found at i:576962 original size:47 final size:44
Alignment explanation
Indices: 576864--576981 Score: 146
Period size: 47 Copynumber: 2.6 Consensus size: 44
576854 GTAACCATGC
* * *
576864 AAATAAGCTTATGAGCTTACGGAATAATGGCAAGTATATTGGAA
1 AAATAAGCTTACGAGCTTATGGAATAATGACAAGTATATTGGAA
* * *
576908 AAATAAGCTTACGAGCTTATGGAATTTAAATGATAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGAA--T-AATGACAAGTATATTGGAA
*
576955 AAATAAGCTTACGAGCTTATGGGATAA
1 AAATAAGCTTACGAGCTTATGGAATAA
576982 ATGGTAAGAG
Statistics
Matches: 64, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
44 24 0.38
45 1 0.02
46 1 0.02
47 38 0.59
ACGTcount: A:0.40, C:0.08, G:0.21, T:0.31
Consensus pattern (44 bp):
AAATAAGCTTACGAGCTTATGGAATAATGACAAGTATATTGGAA
Found at i:584066 original size:47 final size:44
Alignment explanation
Indices: 583972--584089 Score: 146
Period size: 47 Copynumber: 2.6 Consensus size: 44
583962 GTAACCATGC
* * *
583972 AAATAAGCTTATGAGCTTACGGAATAATGACAAGTATATTGGAA
1 AAATAAGCTTACGAGCTTATGGAATAATGACAAGTATATTAGAA
* * *
584016 AAATAAGCTTACGAGCTTATGGAATTTAAATGATAAGTATTTTAGTA
1 AAATAAGCTTACGAGCTTATGGAA--T-AATGACAAGTATATTAGAA
*
584063 AAATAAGCTTACGAGCTTATGGGATAA
1 AAATAAGCTTACGAGCTTATGGAATAA
584090 ATGGTAAGAG
Statistics
Matches: 64, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
44 24 0.38
45 1 0.02
46 1 0.02
47 38 0.59
ACGTcount: A:0.42, C:0.08, G:0.19, T:0.31
Consensus pattern (44 bp):
AAATAAGCTTACGAGCTTATGGAATAATGACAAGTATATTAGAA
Found at i:584448 original size:23 final size:23
Alignment explanation
Indices: 584422--584495 Score: 68
Period size: 23 Copynumber: 3.4 Consensus size: 23
584412 AATTTTTGGG
584422 AATTTTTATAGTGATGAAAGGTT
1 AATTTTTATAGTGATGAAAGGTT
* * *
584445 AATTTTTATGAGT-TTTATA---T
1 AATTTTTAT-AGTGATGAAAGGTT
*
584465 -GTTTTTATAGTGATGAAAGGTT
1 AATTTTTATAGTGATGAAAGGTT
584487 AATTTTTAT
1 AATTTTTAT
584496 GAGTTTTATA
Statistics
Matches: 37, Mismatches: 8, Indels: 12
0.65 0.14 0.21
Matches are distributed among these distances:
18 3 0.08
19 10 0.27
20 1 0.03
22 1 0.03
23 19 0.51
24 3 0.08
ACGTcount: A:0.31, C:0.00, G:0.18, T:0.51
Consensus pattern (23 bp):
AATTTTTATAGTGATGAAAGGTT
Found at i:584471 original size:42 final size:42
Alignment explanation
Indices: 584424--584508 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
584414 TTTTTGGGAA
584424 TTTTTATAGTGATGAAAGGTTAATTTTTATGAGTTTTATATG
1 TTTTTATAGTGATGAAAGGTTAATTTTTATGAGTTTTATATG
584466 TTTTTATAGTGATGAAAGGTTAATTTTTATGAGTTTTATATG
1 TTTTTATAGTGATGAAAGGTTAATTTTTATGAGTTTTATATG
584508 T
1 T
584509 AAATTTTCGA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.28, C:0.00, G:0.19, T:0.53
Consensus pattern (42 bp):
TTTTTATAGTGATGAAAGGTTAATTTTTATGAGTTTTATATG
Found at i:584635 original size:25 final size:25
Alignment explanation
Indices: 584607--584654 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
584597 CAGGGAATCG
584607 ATTCCCCCACTATTCACTATTCACT
1 ATTCCCCCACTATTCACTATTCACT
****
584632 ATTCGGGTACTATTCACTATTCA
1 ATTCCCCCACTATTCACTATTCA
584655 TAAATAAAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.25, C:0.31, G:0.06, T:0.38
Consensus pattern (25 bp):
ATTCCCCCACTATTCACTATTCACT
Found at i:590460 original size:36 final size:36
Alignment explanation
Indices: 590369--590864 Score: 415
Period size: 36 Copynumber: 14.1 Consensus size: 36
590359 AATTTACTCA
* **
590369 AAACAAAGTTTTGTCTCTCTTGAGACAGATTCTCTCA
1 AAACAAA-TTTTGTCTCTCTTGAGACAGTTTCTCTTG
* *
590406 AAACAAAATTTTGTCTCTCTTGAGACAGTTTATCTTA
1 AAAC-AAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
* * * * *
590443 AAACAAATTTTGCCTCTCATGAGATATTTTCTCTTA
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
*
590479 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
* * * *
590515 AAACAAAATCTG--ACTC-T-----ATTTTC-CTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
* * * *
590542 GAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTC-TCTTG
* * *
590579 GAACTAAGTTTTGTCTCTCTAT-AGACAGTTTTTCTTG
1 AAAC-AAATTTTGTCTCTCT-TGAGACAGTTTCTCTTG
*
590616 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
* *
590652 AATCAAA--TTGTCTCTCTTGAGACAGTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
* * * *
590686 AAACAAA------ATCT-GTGA-ATATGTTT-TCCTTT
1 AAACAAATTTTGTCTCTCTTGAGACA-GTTTCT-CTTG
* * * *
590715 AAACAAATTTCGTCTCCCTTGAAACAGTTTCTTTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
* * *
590751 GAACTAAGTTTTGGCTCTCTTGAGACAGTTTCTCTTG
1 AAAC-AAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
590788 AAA-AAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTG
1 AAACAAA-TTTTGTCTCTCTTGAGACAGTTTCTCTTG
* *
590824 AAACAAGTTTTGTCTCTCTTGAGACAGTTTCTCCTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
590860 AAACA
1 AAACA
590865 CCAACCTTTG
Statistics
Matches: 371, Mismatches: 60, Indels: 57
0.76 0.12 0.12
Matches are distributed among these distances:
27 12 0.03
28 7 0.02
29 19 0.05
30 4 0.01
33 1 0.00
34 36 0.10
35 10 0.03
36 176 0.47
37 81 0.22
38 24 0.06
39 1 0.00
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.40
Consensus pattern (36 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
Found at i:590712 original size:173 final size:170
Alignment explanation
Indices: 590414--590864 Score: 629
Period size: 173 Copynumber: 2.6 Consensus size: 170
590404 CAAAACAAAA
* * * * * *
590414 TTTTGTCTCTCTTGAGACAGTTTATCTTAAAACAAATTTTGCCTCTCATGAGATATTTTCTCTTA
1 TTTTGTCTCTCTTGAGACAGTTTATCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
* * *
590479 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTGACTCTATTTTCCTTGGA
66 AAACAAA--TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTGAATATATTTTCCTTGAA
*
590544 ACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTTGGAACTAAG
129 ACAAATTTCGTCTCCCTTGAAACAGTTTC-TTTTGGAACTAAG
* *
590587 TTTTGTCTCTCTAT-AGACAGTTTTTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTT
1 TTTTGTCTCTCT-TGAGACAGTTTATCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTT
* * *
590651 GAATCAAATTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTGTGAATATGTTTTCCTTTA
65 GAAACAAATTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATC--TGAATATATTTTCCTTGA
590716 AACAAATTTCGTCTCCCTTGAAACAGTTTCTTTTGGAACTAAG
128 AACAAATTTCGTCTCCCTTGAAACAGTTTCTTTTGGAACTAAG
* *
590759 TTTTGGCTCTCTTGAGACAGTTTCTCTTGAAA-AAAGTTTTGTCTCTCTTGAGACAGTTTCTCTT
1 TTTTGTCTCTCTTGAGACAGTTTATCTTGAAACAAA-TTTTGTCTCTCTTGAGACAGTTTCTCTT
*
590823 GAAACAAGTTTTGTCTCTCTTGAGACAGTTTCTCC-TGAAACA
65 GAAACAA--ATTGTCTCTCTTGAGACAGTTTC-CCTTGAAACA
590865 CCAACCTTTG
Statistics
Matches: 250, Mismatches: 20, Indels: 15
0.88 0.07 0.05
Matches are distributed among these distances:
171 41 0.16
172 74 0.30
173 103 0.41
174 30 0.12
175 2 0.01
ACGTcount: A:0.25, C:0.20, G:0.14, T:0.41
Consensus pattern (170 bp):
TTTTGTCTCTCTTGAGACAGTTTATCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
AAACAAATTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTGAATATATTTTCCTTGAAAC
AAATTTCGTCTCCCTTGAAACAGTTTCTTTTGGAACTAAG
Found at i:590806 original size:21 final size:21
Alignment explanation
Indices: 590781--590845 Score: 61
Period size: 21 Copynumber: 3.4 Consensus size: 21
590771 TGAGACAGTT
590781 TCTCTTGAAAAAAGTTTTGTC
1 TCTCTTGAAAAAAGTTTTGTC
* *
590802 TCTCTTG-AGACAG---T-T-
1 TCTCTTGAAAAAAGTTTTGTC
*
590817 TCTCTTGAAACAAGTTTTGTC
1 TCTCTTGAAAAAAGTTTTGTC
590838 TCTCTTGA
1 TCTCTTGA
590846 GACAGTTTCT
Statistics
Matches: 33, Mismatches: 5, Indels: 12
0.66 0.10 0.24
Matches are distributed among these distances:
15 7 0.21
16 4 0.12
17 1 0.03
19 1 0.03
20 5 0.15
21 15 0.45
ACGTcount: A:0.23, C:0.18, G:0.15, T:0.43
Consensus pattern (21 bp):
TCTCTTGAAAAAAGTTTTGTC
Found at i:591049 original size:84 final size:83
Alignment explanation
Indices: 590897--591101 Score: 250
Period size: 84 Copynumber: 2.5 Consensus size: 83
590887 TTGAAACACA
* * * * * * *
590897 AAAGACCTTCGGGTTCGACTACGCTCAGCTCGAAGGCACACCATTTGCAGCATAGCTTAAGTTGA
1 AAAGACCTTCGAGTTCGATTACACTCAGCTCCAAGGCACACCATTTGCAGCATAACTCAAGCTGA
590962 GAAGGGCTATCTGCCAACC
66 GAAGGGCTATCTGCCAA-C
* * * *
590981 AAATACCTTCGAGTTCGATTACACTCGGCTCCAAGTCACATCATTTGCAGCATAACTCAAGGCT-
1 AAAGACCTTCGAGTTCGATTACACTCAGCTCCAAGGCACACCATTTGCAGCATAACTCAA-GCTG
* *
591045 AGAAGGGTTATCTGTCAAC
65 AGAAGGGCTATCTGCCAAC
* *
591064 AAAGACCTTCGAGTTCGATTACACTAAGCTCAAAGGCA
1 AAAGACCTTCGAGTTCGATTACACTCAGCTCCAAGGCA
591102 AATCAAATTT
Statistics
Matches: 102, Mismatches: 18, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
83 34 0.33
84 66 0.65
85 2 0.02
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.23
Consensus pattern (83 bp):
AAAGACCTTCGAGTTCGATTACACTCAGCTCCAAGGCACACCATTTGCAGCATAACTCAAGCTGA
GAAGGGCTATCTGCCAAC
Found at i:591144 original size:85 final size:82
Alignment explanation
Indices: 590901--591178 Score: 234
Period size: 84 Copynumber: 3.3 Consensus size: 82
590891 AACACAAAAG
* * * * * * * * * * ***
590901 ACCTTCGGGTTCGACTACGCTCAGCTCGAAGGCACACCATTTGCAGCATAGCTTAAGTTGAGAAG
1 ACCTTCGAGTTCGATTACACTAAGCTCAAAGGCAAATCATTTACAGCATAACTCAAGGCAAGAAG
* *
590966 GGCTATCTGCCAACCAAA
66 GGTTATCTGTCAA-CAAA
** * * * * *
590984 TACCTTCGAGTTCGATTACACTCGGCTCCAAGTCACATCATTTGCAGCATAACTCAAGGCTAGAA
1 -ACCTTCGAGTTCGATTACACTAAGCTCAAAGGCAAATCATTTACAGCATAACTCAAGGCAAGAA
591049 GGGTTATCTGTCAACAAA
65 GGGTTATCTGTCAACAAA
* * * *
591067 GACCTTCGAGTTCGATTACACTAAGCTCAAAGGCAAATCAAATTTATAGGATAGCTCAAGGCAAT
1 -ACCTTCGAGTTCGATTACACTAAGCTCAAAGGCAAATC--ATTTACAGCATAACTCAAGGCAAG
591132 AAGGGTTATCTGTCAACAAA
63 AAGGGTTATCTGTCAACAAA
* * *
591152 A-TTGTCGAGTTCGATTCCATTAAGCTC
1 ACCT-TCGAGTTCGATTACACTAAGCTC
591179 GATGACACCT
Statistics
Matches: 162, Mismatches: 29, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
83 38 0.23
84 86 0.53
85 38 0.23
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.26
Consensus pattern (82 bp):
ACCTTCGAGTTCGATTACACTAAGCTCAAAGGCAAATCATTTACAGCATAACTCAAGGCAAGAAG
GGTTATCTGTCAACAAA
Found at i:593112 original size:12 final size:13
Alignment explanation
Indices: 593090--593118 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
593080 CAAATTAAAT
593090 TTTTAAATTTTAA
1 TTTTAAATTTTAA
593103 TTTT-AATTTTAA
1 TTTTAAATTTTAA
593115 TTTT
1 TTTT
593119 CACAATTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTTAAATTTTAA
Found at i:593493 original size:32 final size:33
Alignment explanation
Indices: 593431--593511 Score: 137
Period size: 32 Copynumber: 2.5 Consensus size: 33
593421 GTTTTTATTA
* *
593431 GTTCGCCCAATGGATTTTTGTTTTTGAACAGGG
1 GTTCGCCCATTGAATTTTTGTTTTTGAACAGGG
593464 GTTCGCCCATTGAATTTTTG-TTTTGAACAGGG
1 GTTCGCCCATTGAATTTTTGTTTTTGAACAGGG
593496 GTTCGCCCATTGAATT
1 GTTCGCCCATTGAATT
593512 GCTTACACGC
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 28 0.61
33 18 0.39
ACGTcount: A:0.19, C:0.17, G:0.25, T:0.40
Consensus pattern (33 bp):
GTTCGCCCATTGAATTTTTGTTTTTGAACAGGG
Found at i:594846 original size:21 final size:20
Alignment explanation
Indices: 594808--594847 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
594798 AACCAAATTG
594808 ATTCAAACAAAAATAAAAAA
1 ATTCAAACAAAAATAAAAAA
* *
594828 ATTCAAACGAAAAGAAAAAA
1 ATTCAAACAAAAATAAAAAA
594848 CAGAGAGAAC
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:0.72, C:0.10, G:0.05, T:0.12
Consensus pattern (20 bp):
ATTCAAACAAAAATAAAAAA
Found at i:594874 original size:28 final size:29
Alignment explanation
Indices: 594838--594912 Score: 125
Period size: 28 Copynumber: 2.6 Consensus size: 29
594828 ATTCAAACGA
*
594838 AAAGAAAAAACAGAGAGAACCTTTCGGTG
1 AAAGAAAAAACAAAGAGAACCTTTCGGTG
594867 AAAGAAAAAA-AAAGAGAACCTTTCGGTG
1 AAAGAAAAAACAAAGAGAACCTTTCGGTG
*
594895 AAAGAAAAAACATAGAGA
1 AAAGAAAAAACAAAGAGA
594913 GAAAACAAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
28 27 0.63
29 16 0.37
ACGTcount: A:0.56, C:0.11, G:0.21, T:0.12
Consensus pattern (29 bp):
AAAGAAAAAACAAAGAGAACCTTTCGGTG
Found at i:596423 original size:190 final size:190
Alignment explanation
Indices: 596100--596476 Score: 673
Period size: 190 Copynumber: 2.0 Consensus size: 190
596090 TCTCTATTTT
596100 TTAATTTAGTTAGTTCTCCAAATATTATCTTATATCCTATTTATATTTATATGTGAACATATCAT
1 TTAATTTAGTTAGTTCTCCAAATATTATCTTATATCCTATTTATATTTATATGTGAACATATCAT
* *
596165 GAAATTACATTTACGTCATATTATACGTTTTTATCAATTCATATTTTAATAGACGTGTATTGTAT
66 GAAATTACATTTACGTAATATTATACGTTTTTATCAATTCATATTTTAATAGACGTGTACTGTAT
* *
596230 GTAAAGTATGTATTGTAAGTATTTTAATGTATGTATTTGTTTTAGGTATTAATATTCGTA
131 GTAAAGTATGTATGGTAAGTATTTTAATGTATGTATTTGGTTTAGGTATTAATATTCGTA
* * *
596290 TTAATTTAGTTAGTTCTTCATATATTATCTTATATCTTATTTATATTTATATGTGAACATATCAT
1 TTAATTTAGTTAGTTCTCCAAATATTATCTTATATCCTATTTATATTTATATGTGAACATATCAT
* *
596355 GAAATTACATTTACGTAATATTATATGTTTTTATCAATTGATATTTTAATAGACGTGTACTGTAT
66 GAAATTACATTTACGTAATATTATACGTTTTTATCAATTCATATTTTAATAGACGTGTACTGTAT
596420 GTAAAGTATGTATGGTAAGTATTTTAATGTATGTATTTGGTTTAGGTATTAATATTC
131 GTAAAGTATGTATGGTAAGTATTTTAATGTATGTATTTGGTTTAGGTATTAATATTC
596477 ATATAGCGTA
Statistics
Matches: 178, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
190 178 1.00
ACGTcount: A:0.32, C:0.07, G:0.12, T:0.49
Consensus pattern (190 bp):
TTAATTTAGTTAGTTCTCCAAATATTATCTTATATCCTATTTATATTTATATGTGAACATATCAT
GAAATTACATTTACGTAATATTATACGTTTTTATCAATTCATATTTTAATAGACGTGTACTGTAT
GTAAAGTATGTATGGTAAGTATTTTAATGTATGTATTTGGTTTAGGTATTAATATTCGTA
Found at i:597261 original size:10 final size:10
Alignment explanation
Indices: 597242--597272 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
597232 AAAAAAACAA
597242 AATAATCCAT
1 AATAATCCAT
*
597252 AATCATCCAT
1 AATAATCCAT
597262 AATAATCCAT
1 AATAATCCAT
597272 A
1 A
597273 GGTTCTAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.48, C:0.23, G:0.00, T:0.29
Consensus pattern (10 bp):
AATAATCCAT
Found at i:598891 original size:35 final size:35
Alignment explanation
Indices: 598850--598920 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
598840 ATCAATGCCT
598850 GATACTTAGTTCAACCTAGAACTAATCAAAAACTA
1 GATACTTAGTTCAACCTAGAACTAATCAAAAACTA
*
598885 GATACTTAGTTCAACCTATAACTAATCAAAAACTA
1 GATACTTAGTTCAACCTAGAACTAATCAAAAACTA
598920 G
1 G
598921 TCCTAAGTTC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.45, C:0.20, G:0.08, T:0.27
Consensus pattern (35 bp):
GATACTTAGTTCAACCTAGAACTAATCAAAAACTA
Found at i:605104 original size:65 final size:66
Alignment explanation
Indices: 605033--605187 Score: 174
Period size: 65 Copynumber: 2.4 Consensus size: 66
605023 TACACTAGGG
* * * *
605033 GTGCATCGGTACACT-AATTACATTCAATGTTTCAAAAGAGCCAGGAGTGCATCGATGCATG-GT
1 GTGCATCGGTACACTAAAATACATTCAATATTTCAAAAGAGCCAAGAGTGCATCGATGCATGACT
605096 CT
66 -T
* * * ***
605098 GTGCATCGGTACA-TAAAATGCATTCGATATTTCAAAATATTTAAGAGTGCATCGATGCATGACT
1 GTGCATCGGTACACTAAAATACATTCAATATTTCAAAAGAGCCAAGAGTGCATCGATGCATGACT
605162 T
66 T
*
605163 GTGCATCGGTACAC-AAAATGCATTC
1 GTGCATCGGTACACTAAAATACATTC
605188 GAAATGGGTG
Statistics
Matches: 77, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
64 1 0.01
65 75 0.97
66 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.29
Consensus pattern (66 bp):
GTGCATCGGTACACTAAAATACATTCAATATTTCAAAAGAGCCAAGAGTGCATCGATGCATGACT
T
Found at i:610441 original size:17 final size:17
Alignment explanation
Indices: 610419--610469 Score: 93
Period size: 17 Copynumber: 3.0 Consensus size: 17
610409 ATTAAAATTT
610419 AAAGGTTTAAATATATA
1 AAAGGTTTAAATATATA
610436 AAAGGTTTAAATATATA
1 AAAGGTTTAAATATATA
*
610453 AAAAGTTTAAATATATA
1 AAAGGTTTAAATATATA
610470 TTTGTTTTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 33 1.00
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.35
Consensus pattern (17 bp):
AAAGGTTTAAATATATA
Found at i:611409 original size:2 final size:2
Alignment explanation
Indices: 611402--611427 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
611392 CGTGGAGCTA
611402 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
611428 TCTTTAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:621609 original size:23 final size:22
Alignment explanation
Indices: 621583--621646 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 22
621573 CAGCTCATAT
621583 AATTGCACCTAAGTGCCACGTAG
1 AATTGCACCT-AGTGCCACGTAG
* *
621606 AATTGCACCGGAGTGCCGCGTAG
1 AATTGCACC-TAGTGCCACGTAG
621629 AATTGCACCGTAGTGCCA
1 AATTGCACC-TAGTGCCA
621647 TATAATAATG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (22 bp):
AATTGCACCTAGTGCCACGTAG
Found at i:621780 original size:101 final size:102
Alignment explanation
Indices: 621648--621877 Score: 410
Period size: 101 Copynumber: 2.3 Consensus size: 102
621638 GTAGTGCCAT
**
621648 ATAATA-ATGTCCATAAGGACCACATATCATTCCTTAAGAACCATATACATATGCCAAGGATCAA
1 ATAATATATGTCCCGAAGGACCACATATCATTCCTTAAGAACCATATACATATGCCAAGGATCAA
621712 GTATGTGTCTCACCAGACTTCACACATGTTCCAAAGA
66 GTATGTGTCTCACCAGACTTCACACATGTTCCAAAGA
*
621749 AT-ATATATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAA
1 ATAATATATGTCCCGAAGGACCACATATCATTCCTTAAGAACCATATACATATGCCAAGGATCAA
621813 GTATGTGTCTCACCAGACTTCACACATGTTCCAAAGA
66 GTATGTGTCTCACCAGACTTCACACATGTTCCAAAGA
621850 ATACATATATGTCCCGAAGGACCACATA
1 ATA-ATATATGTCCCGAAGGACCACATA
621878 GACCCTCTAC
Statistics
Matches: 123, Mismatches: 3, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
100 3 0.02
101 96 0.78
103 24 0.20
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (102 bp):
ATAATATATGTCCCGAAGGACCACATATCATTCCTTAAGAACCATATACATATGCCAAGGATCAA
GTATGTGTCTCACCAGACTTCACACATGTTCCAAAGA
Found at i:628334 original size:184 final size:188
Alignment explanation
Indices: 628019--628378 Score: 583
Period size: 184 Copynumber: 1.9 Consensus size: 188
628009 AAAATACAAT
** *
628019 AATATACATATGGTGATATAAGTTTACCAAATATTCAGCATCACAACCTTAACTCTTTAATTACA
1 AATATACATATAATGATATAAGTTTACCAAATATTCAGCATAACAACCTTAACTCTTTAATTACA
628084 TGCCAACATCCATTTTCATAACAAAATGACCTACTGATTAATTGCTTCTGATCTGATAGTTTGCA
66 TGCCAACATCCATTTTCATAACAAAATGACCTACTGATTAATTGCTTCTGATCTGATAGTTTGCA
628149 GGAGTAATG-T-TCCAGCTGCTTCACCTCGATCG-CTACTTTATCGATCAAAAACTAA
131 GGAGTAATGTTGTCCAGCTGCTTCACCTCGATCGTCTACTTTATCGATCAAAAACTAA
* *
628204 AATATACATATAAT-ATATAAGTTTGCCAAAATATTCAGAGTATAACAA-C-TAAC-CTTTAATT
1 AATATACATATAATGATATAAGTTTACC-AAATATTC--AGCATAACAACCTTAACTCTTTAATT
628265 ACATGCCAACATCCATTTTCATAACAAAATGACCTACTGATTAAGTTGCTTCTGATCTGATAG-T
63 ACATGCCAACATCCATTTTCATAACAAAATGACCTACTGATTAA-TTGCTTCTGATCTGATAGTT
628329 TGCAGGAGTAATGTTGTCCAGCTGCTTCACCTCGATCGTCTACTTTATCG
127 TGCAGGAGTAATGTTGTCCAGCTGCTTCACCTCGATCGTCTACTTTATCG
628379 GATCCTACGT
Statistics
Matches: 163, Mismatches: 5, Indels: 12
0.91 0.03 0.07
Matches are distributed among these distances:
184 78 0.48
185 43 0.26
186 23 0.14
187 19 0.12
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.33
Consensus pattern (188 bp):
AATATACATATAATGATATAAGTTTACCAAATATTCAGCATAACAACCTTAACTCTTTAATTACA
TGCCAACATCCATTTTCATAACAAAATGACCTACTGATTAATTGCTTCTGATCTGATAGTTTGCA
GGAGTAATGTTGTCCAGCTGCTTCACCTCGATCGTCTACTTTATCGATCAAAAACTAA
Found at i:632553 original size:51 final size:50
Alignment explanation
Indices: 632454--632651 Score: 314
Period size: 51 Copynumber: 4.0 Consensus size: 50
632444 CTGAATCAGA
*
632454 AGTAGAATCTAATTTATCATCATCTAAATGTTCTTTTTC--CTTTGCTTC
1 AGTAGAATCTGATTTATCATCATCTAAATGTTCTTTTTCTTCTTTGCTTC
*
632502 AGTAGAATGTGATTTATCATCATCTAAATGTTCTTTTTCTTCATTTGCTTC
1 AGTAGAATCTGATTTATCATCATCTAAATGTTCTTTTTCTTC-TTTGCTTC
*
632553 AGTAGAATCTGATTTATCATCATCTAAATGTTCTTTTTCTTCCTTTGCTAC
1 AGTAGAATCTGATTTATCATCATCTAAATGTTCTTTTTCTT-CTTTGCTTC
*
632604 AATAGAATCTGATTTATCATCATCTAAATGTTCTTTTTC--CTTTGCTTC
1 AGTAGAATCTGATTTATCATCATCTAAATGTTCTTTTTCTTCTTTGCTTC
632652 GGCTTCCTTA
Statistics
Matches: 140, Mismatches: 6, Indels: 8
0.91 0.04 0.05
Matches are distributed among these distances:
48 45 0.32
50 1 0.01
51 93 0.66
52 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.10, T:0.48
Consensus pattern (50 bp):
AGTAGAATCTGATTTATCATCATCTAAATGTTCTTTTTCTTCTTTGCTTC
Found at i:634648 original size:26 final size:23
Alignment explanation
Indices: 634592--634646 Score: 110
Period size: 23 Copynumber: 2.4 Consensus size: 23
634582 TAAGTAATTA
634592 TTTTTATTAAATAAAAATAATAT
1 TTTTTATTAAATAAAAATAATAT
634615 TTTTTATTAAATAAAAATAATAT
1 TTTTTATTAAATAAAAATAATAT
634638 TTTTTATTA
1 TTTTTATTA
634647 TTTTGGATCG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
TTTTTATTAAATAAAAATAATAT
Found at i:635824 original size:13 final size:12
Alignment explanation
Indices: 635780--635825 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
635770 ATTTTAAAAC
*
635780 GCATTTTATCAT
1 GCATTTTTTCAT
635792 GCA--TTTTCAT
1 GCATTTTTTCAT
*
635802 GTATTTTTTCAT
1 GCATTTTTTCAT
635814 GCATATTTTTCA
1 GCAT-TTTTTCA
635826 GATAATGCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
10 8 0.29
12 13 0.46
13 7 0.25
ACGTcount: A:0.22, C:0.15, G:0.09, T:0.54
Consensus pattern (12 bp):
GCATTTTTTCAT
Found at i:636783 original size:12 final size:12
Alignment explanation
Indices: 636768--636822 Score: 74
Period size: 12 Copynumber: 4.6 Consensus size: 12
636758 GTTATTTAAA
636768 CGGGTATTGGGC
1 CGGGTATTGGGC
*
636780 CGGGTATTGGGT
1 CGGGTATTGGGC
636792 CGGGTATTGGGC
1 CGGGTATTGGGC
* * *
636804 CGAGAATCGGGC
1 CGGGTATTGGGC
636816 CGGGTAT
1 CGGGTAT
636823 ATATATATAT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 36 1.00
ACGTcount: A:0.13, C:0.16, G:0.47, T:0.24
Consensus pattern (12 bp):
CGGGTATTGGGC
Found at i:642323 original size:3 final size:3
Alignment explanation
Indices: 642310--642372 Score: 85
Period size: 3 Copynumber: 21.7 Consensus size: 3
642300 TTCATCCTGA
* *
642310 TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT CAT CAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
642356 TAT TAA TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TA
642373 ATAAATACAT
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
2 4 0.07
3 50 0.93
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:642354 original size:29 final size:29
Alignment explanation
Indices: 642310--642372 Score: 99
Period size: 29 Copynumber: 2.2 Consensus size: 29
642300 TTCATCCTGA
* * *
642310 TATTATATTATTATTATTATTATTATTAT
1 TATTATATCATCATTATTATTAATATTAT
642339 TATTATATCATCATTATTATTAATATTAT
1 TATTATATCATCATTATTATTAATATTAT
642368 TATTA
1 TATTA
642373 ATAAATACAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (29 bp):
TATTATATCATCATTATTATTAATATTAT
Found at i:644654 original size:131 final size:130
Alignment explanation
Indices: 644413--644779 Score: 328
Period size: 131 Copynumber: 2.8 Consensus size: 130
644403 TGATATCAAG
* * *** * * *
644413 AATAGTAATATCTTTTCATTTCGGCCGGAGTAATAAATGACTTCTTTAAGGTATGATAGGTAATT
1 AATAATAATATCTCTTCATTTCGATTGGAGTAATAAATGACTTCTTTAATGTATGAAAGGTCATT
** * ** *
644478 TATTCTTGATTGGATGTAATTTGATAAT-TCTGTTTTTTCTCGAATT-AATATCAATTTTTAAGG
66 TATTCTTGATTGGAAAT-ATTAGATAATATC-GTTTTCACTCGAATTGAATATCAA-TTTTAAGA
* *
644541 TGG
128 CGA
* * * *
644544 AATAATGATATCTCTTCATTTCGATTGGAGCAATAAATGACTTCTTTAATGTATTAGAGGTCATT
1 AATAATAATATCTCTTCATTTCGATTGGAGTAATAAATGACTTCTTTAATGTATGAAAGGTCATT
* * * * * * *
644609 TATTCTAGATTGAAAATCATTAGATACTATCGTTTTCACTTGAATTGATTTTGAATTTTAAGACG
66 TATTCTTGATTGGAAAT-ATTAGATAATATCGTTTTCACTCGAATTGAATATCAATTTTAAGACG
644674 A
130 A
* * * * * * *
644675 AATAGTAATATATCTTTATTTCAATTGGTA-TAATAAATGACTGT-TTTATTGCACGAAAGGTCA
1 AATAATAATATCTCTTCATTTCGATTGG-AGTAATAAATGACT-TCTTTAATGTATGAAAGGTCA
* *
644738 TTTATTCTTGATTGGAAATATTAGATATTATCTTTTTCACTC
64 TTTATTCTTGATTGGAAATATTAGATAATATCGTTTTCACTC
644780 TTAAAATTAT
Statistics
Matches: 189, Mismatches: 43, Indels: 9
0.78 0.18 0.04
Matches are distributed among these distances:
130 20 0.11
131 160 0.85
132 9 0.05
ACGTcount: A:0.31, C:0.10, G:0.15, T:0.43
Consensus pattern (130 bp):
AATAATAATATCTCTTCATTTCGATTGGAGTAATAAATGACTTCTTTAATGTATGAAAGGTCATT
TATTCTTGATTGGAAATATTAGATAATATCGTTTTCACTCGAATTGAATATCAATTTTAAGACGA
Found at i:648523 original size:13 final size:13
Alignment explanation
Indices: 648505--648529 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
648495 TACATACATT
648505 GCATTTAATTTTC
1 GCATTTAATTTTC
648518 GCATTTAATTTT
1 GCATTTAATTTT
648530 ATTCATTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.12, G:0.08, T:0.56
Consensus pattern (13 bp):
GCATTTAATTTTC
Found at i:653101 original size:134 final size:134
Alignment explanation
Indices: 652851--653473 Score: 700
Period size: 134 Copynumber: 4.7 Consensus size: 134
652841 TCAAATCGAA
* * * *
652851 CTCGATTCAATCTTCCCTGAGTGATAGTGGAATGAATCAACAT-CCTCAGATCTGATTTCCCCTC
1 CTCGATTCAATCTTCCCTGAGTGACAGTGGAATGAATCAACATCCCT-AGATCTAATTTTCCCTT
* * * *
652915 AAGAAGAAGCAGAACATATCCTTCTCTTTCAAGATTTGATATTCC-CACAGTAACAGTGGAATAA
65 AAGAAGAAGCAGAACAAATCCCTCTCTTTCAAGATTTGATATTCCTTA-AGTAACAGTGGAACAA
* *
652979 GTTTGC
129 GTCTAC
* * * * *
652985 CTCGATTCAATCTTCCCTGAGTGATAGTGAAATGAATCGACATCCCTAGATATGATTTTCCCTTA
1 CTCGATTCAATCTTCCCTGAGTGACAGTGGAATGAATCAACATCCCTAGATCTAATTTTCCCTTA
* * * * *
653050 AGAAGAAGCGGAATAAATCCCTCTCTTTCAAGATTGGACATTACC-TAAGTAACAGTGGTACAAG
66 AGAAGAAGCAGAACAAATCCCTCTCTTTCAAGATTTGATATT-CCTTAAGTAACAGTGGAACAAG
*
653114 TCTGC
130 TCTAC
** * * *
653119 CTCGATTCAATCTTCCCTGAGTGACAGTGGAATGAATCAATGTCCCCATATCTAATTTTCCCTCA
1 CTCGATTCAATCTTCCCTGAGTGACAGTGGAATGAATCAACATCCCTAGATCTAATTTTCCCTTA
* * *
653184 AGAAGAAGC-GCAACAGATCACTCTCTTTCAAGATTTGATATTCCTTGAGTAACAGTGGAACAAG
66 AGAAGAAGCAG-AACAAATCCCTCTCTTTCAAGATTTGATATTCCTTAAGTAACAGTGGAACAAG
653248 TCTAC
130 TCTAC
* * *** *** * *
653253 CTCGATTCAATGTTCCCTAAACAACAGTAGG-ATGAATCAATGCCCCTATATCTAATTTTTCCTT
1 CTCGATTCAATCTTCCCTGAGTGACAGT-GGAATGAATCAACATCCCTAGATCTAATTTTCCCTT
* * * * * *
653317 AAAAAGAATCAAAACAAATCCCTCT-TTTCAAGATTTGATATTCCTTGAGTAATAGTGGAATAAG
65 AAGAAGAAGCAGAACAAATCCCTCTCTTTCAAGATTTGATATTCCTTAAGTAACAGTGGAACAAG
653381 TCTAC
130 TCTAC
* * * * *
653386 CTCGATTCAATATTCCCCGAGTGACAGTGGAATGAATCAACAACCCCAGATCTAATTTTACCTTA
1 CTCGATTCAATCTTCCCTGAGTGACAGTGGAATGAATCAACATCCCTAGATCTAATTTTCCCTTA
*
653451 AGAAGAAGCAGAACATATCCCTC
66 AGAAGAAGCAGAACAAATCCCTC
653474 ATCATATTCC
Statistics
Matches: 417, Mismatches: 65, Indels: 15
0.84 0.13 0.03
Matches are distributed among these distances:
132 2 0.00
133 114 0.27
134 293 0.70
135 8 0.02
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.29
Consensus pattern (134 bp):
CTCGATTCAATCTTCCCTGAGTGACAGTGGAATGAATCAACATCCCTAGATCTAATTTTCCCTTA
AGAAGAAGCAGAACAAATCCCTCTCTTTCAAGATTTGATATTCCTTAAGTAACAGTGGAACAAGT
CTAC
Found at i:653605 original size:3 final size:3
Alignment explanation
Indices: 653597--653677 Score: 85
Period size: 3 Copynumber: 27.7 Consensus size: 3
653587 TTTGTCCCAC
* *
653597 TAT TAT TAT TA- TAT TAT TAT TAT T-T TAT TAT TTT TAT TAT TAT TAA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * *
653643 TAT CAT TAT TAA TAT TAA TAT TAA TAT TAA TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
653678 ATAAGTACAT
Statistics
Matches: 62, Mismatches: 14, Indels: 4
0.77 0.17 0.05
Matches are distributed among these distances:
2 4 0.06
3 58 0.94
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:655319 original size:12 final size:12
Alignment explanation
Indices: 655302--655369 Score: 54
Period size: 12 Copynumber: 6.0 Consensus size: 12
655292 ACTATACAAT
655302 ATGAACAGTACC
1 ATGAACAGTACC
655314 ATGAACAGTA--
1 ATGAACAGTACC
*
655324 ATGAACAGTATC
1 ATGAACAGTACC
* **
655336 GTGAACA--ATG
1 ATGAACAGTACC
655346 ATGAACAGTACC
1 ATGAACAGTACC
* *
655358 GTAAACAGTACC
1 ATGAACAGTACC
655370 GAATGCTAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
10 18 0.40
12 27 0.60
ACGTcount: A:0.43, C:0.19, G:0.19, T:0.19
Consensus pattern (12 bp):
ATGAACAGTACC
Found at i:655328 original size:22 final size:22
Alignment explanation
Indices: 655302--655367 Score: 87
Period size: 22 Copynumber: 3.0 Consensus size: 22
655292 ACTATACAAT
*
655302 ATGAACAGTACCATGAACAGTA
1 ATGAACAGTACCGTGAACAGTA
* * *
655324 ATGAACAGTATCGTGAACAATG
1 ATGAACAGTACCGTGAACAGTA
*
655346 ATGAACAGTACCGTAAACAGTA
1 ATGAACAGTACCGTGAACAGTA
655368 CCGAATGCTA
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.44, C:0.17, G:0.20, T:0.20
Consensus pattern (22 bp):
ATGAACAGTACCGTGAACAGTA
Found at i:655329 original size:10 final size:11
Alignment explanation
Indices: 655302--655356 Score: 51
Period size: 10 Copynumber: 5.0 Consensus size: 11
655292 ACTATACAAT
655302 ATGAACAGTACC
1 ATGAACAGTA-C
655314 ATGAACAGTA-
1 ATGAACAGTAC
655324 ATGAACAGTATC
1 ATGAACAGTA-C
* * *
655336 GTGAACAAT-G
1 ATGAACAGTAC
655346 ATGAACAGTAC
1 ATGAACAGTAC
655357 CGTAAACAGT
Statistics
Matches: 34, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
10 17 0.50
12 17 0.50
ACGTcount: A:0.44, C:0.16, G:0.20, T:0.20
Consensus pattern (11 bp):
ATGAACAGTAC
Found at i:656089 original size:32 final size:32
Alignment explanation
Indices: 656035--656270 Score: 386
Period size: 32 Copynumber: 7.4 Consensus size: 32
656025 GTTCCTAAGA
* *
656035 ACATAGGTAA-CC-ATCTATATGTCCCGAAAG
1 ACATAGGTAATCCTGTCCATATGTCCCGAAAG
*
656065 ACATAGGCAATCCTGTCCATATGTCCCGAAAG
1 ACATAGGTAATCCTGTCCATATGTCCCGAAAG
* *
656097 ACATAGGTAATCCTATCCATATATCCCGAAAG
1 ACATAGGTAATCCTGTCCATATGTCCCGAAAG
656129 ACATAGGTAATCCTGTCCATATGTCCCGAAAG
1 ACATAGGTAATCCTGTCCATATGTCCCGAAAG
*
656161 ACATAGGTAATCATGTCCATATGTCCCGAAAG
1 ACATAGGTAATCCTGTCCATATGTCCCGAAAG
* *
656193 ACATTGGTAATCCTGTCCATATGTCTCGAAAG
1 ACATAGGTAATCCTGTCCATATGTCCCGAAAG
656225 ACATAGGTAATCCTGTCCATATGTCCCGAAAG
1 ACATAGGTAATCCTGTCCATATGTCCCGAAAG
656257 ACATAGGTAATCCT
1 ACATAGGTAATCCT
656271 CGACTCTTGG
Statistics
Matches: 190, Mismatches: 14, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
30 9 0.05
31 2 0.01
32 179 0.94
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.25
Consensus pattern (32 bp):
ACATAGGTAATCCTGTCCATATGTCCCGAAAG
Found at i:656470 original size:24 final size:25
Alignment explanation
Indices: 656423--656470 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
656413 CAAATATTCA
*
656423 CATATATATCACATATACTTTTTCTT
1 CATATATAT-ACATATACTATTTCTT
*
656449 CATATATAT-CATATCCTATTTC
1 CATATATATACATATACTATTTC
656471 CTATCTTGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 11 0.55
26 9 0.45
ACGTcount: A:0.31, C:0.21, G:0.00, T:0.48
Consensus pattern (25 bp):
CATATATATACATATACTATTTCTT
Found at i:664727 original size:48 final size:48
Alignment explanation
Indices: 664647--664788 Score: 195
Period size: 50 Copynumber: 3.0 Consensus size: 48
664637 CTGAATCAGA
*
664647 AGTAGAATCT-AATT-T-ATCATCTAAATGTTCTTTTCCCTTTGCTTC
1 AGTAGAATCTGATTTATCATCATCTAAATGTTCTTTTCCCTTTGCTTC
* *
664692 AGTAGAATGTGATTTATCATCATCTAAATGTTCTTTTTCTTCATTTGC-TC
1 AGTAGAATCTGATTTATCATCATCTAAATGTTC-TTTTC--CCTTTGCTTC
664742 AGTAGAATCTGATTTATCATCATCTAAATGTTCTTTT-CCTTTGCTTC
1 AGTAGAATCTGATTTATCATCATCTAAATGTTCTTTTCCCTTTGCTTC
664789 GGCTTCCTTA
Statistics
Matches: 85, Mismatches: 5, Indels: 12
0.83 0.05 0.12
Matches are distributed among these distances:
45 9 0.11
46 9 0.11
47 3 0.04
48 15 0.18
49 9 0.11
50 34 0.40
51 6 0.07
ACGTcount: A:0.24, C:0.18, G:0.11, T:0.47
Consensus pattern (48 bp):
AGTAGAATCTGATTTATCATCATCTAAATGTTCTTTTCCCTTTGCTTC
Found at i:667175 original size:15 final size:15
Alignment explanation
Indices: 667155--667184 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
667145 AGAAAACATA
667155 TAATTTTTCTATTTT
1 TAATTTTTCTATTTT
667170 TAATTTTTCTATTTT
1 TAATTTTTCTATTTT
667185 CTTTAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.73
Consensus pattern (15 bp):
TAATTTTTCTATTTT
Found at i:672632 original size:180 final size:180
Alignment explanation
Indices: 672330--672678 Score: 689
Period size: 180 Copynumber: 1.9 Consensus size: 180
672320 CAAAATAATC
672330 AAGGCCTTCTATTTGTCGGTAATCTTTTATTACCAATCTAGCCTTATACTTATTAATTGTTTCAT
1 AAGGCCTTCTATTTGTCGGTAATCTTTTATTACCAATCTAGCCTTATACTTATTAATTGTTTCAT
*
672395 CTGCTTTTATTTTCCATTTGAAAATTCATTTCAAACTTAGTGGTTTCATTCCCGGAGGATGATCC
66 CTGATTTTATTTTCCATTTGAAAATTCATTTCAAACTTAGTGGTTTCATTCCCGGAGGATGATCC
672460 ACTAATTTTCATGTATGATTTTGCCTGATGGAATTGATCGATATCAAAAT
131 ACTAATTTTCATGTATGATTTTGCCTGATGGAATTGATCGATATCAAAAT
672510 AAGGCCTTCTATTTGTCGGTAATCTTTTATTACCAATCTAGCCTTATACTTATTAATTGTTTCAT
1 AAGGCCTTCTATTTGTCGGTAATCTTTTATTACCAATCTAGCCTTATACTTATTAATTGTTTCAT
672575 CTGATTTTATTTTCCATTTGAAAATTCATTTCAAACTTAGTGGTTTCATTCCCGGAGGATGATCC
66 CTGATTTTATTTTCCATTTGAAAATTCATTTCAAACTTAGTGGTTTCATTCCCGGAGGATGATCC
672640 ACTAATTTTCATGTATGATTTTGCCTGATGGAATTGATC
131 ACTAATTTTCATGTATGATTTTGCCTGATGGAATTGATC
672679 TCACTTTTAA
Statistics
Matches: 168, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
180 168 1.00
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.43
Consensus pattern (180 bp):
AAGGCCTTCTATTTGTCGGTAATCTTTTATTACCAATCTAGCCTTATACTTATTAATTGTTTCAT
CTGATTTTATTTTCCATTTGAAAATTCATTTCAAACTTAGTGGTTTCATTCCCGGAGGATGATCC
ACTAATTTTCATGTATGATTTTGCCTGATGGAATTGATCGATATCAAAAT
Found at i:674381 original size:16 final size:16
Alignment explanation
Indices: 674360--674399 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
674350 TAGGATTTTC
674360 TTTGGAACTCTTCCTT
1 TTTGGAACTCTTCCTT
* *
674376 TTTGGAAATTCTTCTTT
1 TTTGG-AACTCTTCCTT
674393 TTTGGAA
1 TTTGGAA
674400 ATTCCACCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 7 0.33
17 14 0.67
ACGTcount: A:0.17, C:0.15, G:0.15, T:0.53
Consensus pattern (16 bp):
TTTGGAACTCTTCCTT
Found at i:674394 original size:17 final size:17
Alignment explanation
Indices: 674368--674403 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
674358 TCTTTGGAAC
674368 TCTTCCTTTTTGGAAAT
1 TCTTCCTTTTTGGAAAT
*
674385 TCTTCTTTTTTGGAAAT
1 TCTTCCTTTTTGGAAAT
674402 TC
1 TC
674404 CACCTTTAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.56
Consensus pattern (17 bp):
TCTTCCTTTTTGGAAAT
Found at i:678742 original size:25 final size:28
Alignment explanation
Indices: 678716--678768 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 28
678706 CAAAAGAAAG
678716 AAAAGAAAA-AGAAGAAAATT-CAAAGA
1 AAAAGAAAAGAGAAGAAAATTGCAAAGA
* *
678742 AAAAGAAAAGTGAAGAAAGTTGCAAAG
1 AAAAGAAAAGAGAAGAAAATTGCAAAG
678769 TACAGTCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 9 0.39
27 9 0.39
28 5 0.22
ACGTcount: A:0.66, C:0.04, G:0.21, T:0.09
Consensus pattern (28 bp):
AAAAGAAAAGAGAAGAAAATTGCAAAGA
Found at i:683434 original size:30 final size:30
Alignment explanation
Indices: 683398--683632 Score: 149
Period size: 30 Copynumber: 7.9 Consensus size: 30
683388 TATGATTCAA
* * *
683398 TCCTTTAAATTTTTGTTTGTGCTATTTTGG
1 TCCTTTAAATTTATGTTTTTGCTATTTTAG
* * *** *
683428 TCCTTTAACTTTCTGTTTCCACT-TTTTTG
1 TCCTTTAAATTTATGTTTTTGCTATTTTAG
* * * *
683457 T-CTCTTAAGTTTTTATTTTTGTTATTTTAG
1 TCCT-TTAAATTTATGTTTTTGCTATTTTAG
* *
683487 TCCTTTAAATGTCT-TTATTTGCTA-TTTAG
1 TCCTTTAAATTTATGTT-TTTGCTATTTTAG
* * * * *
683516 ACCCTTAAGTTTCTG-TTTTACTATTTTAG
1 TCCTTTAAATTTATGTTTTTGCTATTTTAG
* *
683545 -CCTTTTAAATTTATATTTTTGCCATTTTAG
1 TCC-TTTAAATTTATGTTTTTGCTATTTTAG
* * * *
683575 TTCTTTAAATTCATGTTTGTACTATTTTAG
1 TCCTTTAAATTTATGTTTTTGCTATTTTAG
* *
683605 TCCTTTGAGTTTATGTTTTTGCTATTTT
1 TCCTTTAAATTTATGTTTTTGCTATTTT
683633 GGTTCTTGTA
Statistics
Matches: 155, Mismatches: 41, Indels: 18
0.72 0.19 0.08
Matches are distributed among these distances:
28 10 0.06
29 49 0.32
30 93 0.60
31 3 0.02
ACGTcount: A:0.17, C:0.13, G:0.11, T:0.59
Consensus pattern (30 bp):
TCCTTTAAATTTATGTTTTTGCTATTTTAG
Found at i:683561 original size:21 final size:23
Alignment explanation
Indices: 683532--683573 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
683522 AAGTTTCTGT
683532 TTTACTATTTTAGCC-TTTTAAA
1 TTTACTATTTTAGCCATTTTAAA
*
683554 TTTA-TATTTTTGCCATTTTA
1 TTTACTATTTTAGCCATTTTA
683574 GTTCTTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.24, C:0.12, G:0.05, T:0.60
Consensus pattern (23 bp):
TTTACTATTTTAGCCATTTTAAA
Found at i:685502 original size:32 final size:32
Alignment explanation
Indices: 685466--685527 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 32
685456 TCTTACCTGT
*
685466 ACTAAC-TAATTTATTTTCTTTTGTTTGTGTGC
1 ACTAACAT-ATTTATTTTCTGTTGTTTGTGTGC
*
685498 ACTAACATATTTCTTTTCTGTTGTTTGTGT
1 ACTAACATATTTATTTTCTGTTGTTTGTGT
685528 TTTTTTTTCG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
32 26 0.96
33 1 0.04
ACGTcount: A:0.18, C:0.13, G:0.13, T:0.56
Consensus pattern (32 bp):
ACTAACATATTTATTTTCTGTTGTTTGTGTGC
Found at i:689104 original size:48 final size:48
Alignment explanation
Indices: 688997--689105 Score: 121
Period size: 48 Copynumber: 2.3 Consensus size: 48
688987 TATATCAAAA
* * * *
688997 ATCAAAACATAATCCAAGTAAAGTATCATATCAGAATCTAGGTCAAGT
1 ATCAGAACAGAATCCAAGTAAAGTATCAAATCAGAATCCAGGTCAAGT
* * * * *
689045 ATCAGACCAGAATCCAGGTCAAGTATCAAATCAGAATCCATGTCAGGT
1 ATCAGAACAGAATCCAAGTAAAGTATCAAATCAGAATCCAGGTCAAGT
689093 ATC-GTAACAGAAT
1 ATCAG-AACAGAAT
689106 TCAAATCAGA
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
47 1 0.02
48 49 0.98
ACGTcount: A:0.42, C:0.19, G:0.16, T:0.23
Consensus pattern (48 bp):
ATCAGAACAGAATCCAAGTAAAGTATCAAATCAGAATCCAGGTCAAGT
Found at i:689105 original size:24 final size:24
Alignment explanation
Indices: 688997--689095 Score: 108
Period size: 24 Copynumber: 4.1 Consensus size: 24
688987 TATATCAAAA
* * * *
688997 ATCAAAACATAATCCAAGTAAAGT
1 ATCAAATCAGAATCCAGGTCAAGT
* *
689021 ATCATATCAGAATCTAGGTCAAGT
1 ATCAAATCAGAATCCAGGTCAAGT
* *
689045 ATCAGACCAGAATCCAGGTCAAGT
1 ATCAAATCAGAATCCAGGTCAAGT
* *
689069 ATCAAATCAGAATCCATGTCAGGT
1 ATCAAATCAGAATCCAGGTCAAGT
689093 ATC
1 ATC
689096 GTAACAGAAT
Statistics
Matches: 62, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 62 1.00
ACGTcount: A:0.41, C:0.20, G:0.15, T:0.23
Consensus pattern (24 bp):
ATCAAATCAGAATCCAGGTCAAGT
Found at i:693199 original size:14 final size:13
Alignment explanation
Indices: 693174--693202 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
693164 AACTTTTCAG
693174 ATATTTTTAAAAT
1 ATATTTTTAAAAT
693187 ATATTTTTAAAA-
1 ATATTTTTAAAAT
693199 ATAT
1 ATAT
693203 GAACACTACC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.25
13 12 0.75
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
ATATTTTTAAAAT
Found at i:693412 original size:24 final size:24
Alignment explanation
Indices: 693370--693468 Score: 99
Period size: 24 Copynumber: 4.1 Consensus size: 24
693360 TATATCAAAA
* * * *
693370 ATCAAAACATAATTCAGGTTAAGT
1 ATCAAATCAGAATCCAGGTCAAGT
** *
693394 ATCATTTCAGAATCTAGGTCAAGT
1 ATCAAATCAGAATCCAGGTCAAGT
* *
693418 ATCAGATCAGAATCCATGTCAAGT
1 ATCAAATCAGAATCCAGGTCAAGT
* *
693442 ATCAAATCAGAATCCATGTCAGGT
1 ATCAAATCAGAATCCAGGTCAAGT
693466 ATC
1 ATC
693469 GTAACAGAAT
Statistics
Matches: 62, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 62 1.00
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.28
Consensus pattern (24 bp):
ATCAAATCAGAATCCAGGTCAAGT
Found at i:693478 original size:24 final size:24
Alignment explanation
Indices: 693390--693468 Score: 104
Period size: 24 Copynumber: 3.3 Consensus size: 24
693380 AATTCAGGTT
** * *
693390 AAGTATCATTTCAGAATCTAGGTC
1 AAGTATCAAATCAGAATCCATGTC
*
693414 AAGTATCAGATCAGAATCCATGTC
1 AAGTATCAAATCAGAATCCATGTC
693438 AAGTATCAAATCAGAATCCATGTC
1 AAGTATCAAATCAGAATCCATGTC
*
693462 AGGTATC
1 AAGTATC
693469 GTAACAGAAT
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 49 1.00
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.28
Consensus pattern (24 bp):
AAGTATCAAATCAGAATCCATGTC
Found at i:698145 original size:42 final size:41
Alignment explanation
Indices: 698098--698280 Score: 120
Period size: 42 Copynumber: 4.3 Consensus size: 41
698088 GACTGACCTT
* *
698098 CTCATCACGTAGGAGCCATGTCACCCCTGATAACCAGCCGTC
1 CTCATCACGTAGGAACCGTGTCACCCCTGAT-ACCAGCCGTC
* *** ** *
698140 CTCATCACTTAGGAACCGTGTTATCATTACTAAAGATGGCATGCAGTC
1 CTCATCACGTAGGAACCGTG---TCACCCCT---GATACCA-GCCGTC
*
698188 CTCATCACGTAGGAACTGTGTCATCCCCTG--ACCAGACC-TC
1 CTCATCACGTAGGAACCGTGTCA-CCCCTGATACCAG-CCGTC
* * * *
698228 CTCATCACGTAGGAGCTGTGTCACCCCTGATAACCAACCATC
1 CTCATCACGTAGGAACCGTGTCACCCCTGAT-ACCAGCCGTC
698270 CTCATCACGTA
1 CTCATCACGTA
698281 AGAATCGTTT
Statistics
Matches: 109, Mismatches: 19, Indels: 26
0.71 0.12 0.17
Matches are distributed among these distances:
39 6 0.06
40 25 0.23
41 5 0.05
42 34 0.31
43 1 0.01
45 8 0.07
46 2 0.02
47 2 0.02
48 26 0.24
ACGTcount: A:0.26, C:0.33, G:0.17, T:0.23
Consensus pattern (41 bp):
CTCATCACGTAGGAACCGTGTCACCCCTGATACCAGCCGTC
Found at i:698241 original size:40 final size:40
Alignment explanation
Indices: 698186--698280 Score: 131
Period size: 40 Copynumber: 2.3 Consensus size: 40
698176 TGGCATGCAG
698186 TCCTCATCACGTAGGAACTGTGTCATCCCCTG-ACCAGACC-
1 TCCTCATCACGTAGGAACTGTGTCA-CCCCTGAACCA-ACCA
*
698226 TCCTCATCACGTAGGAGCTGTGTCACCCCTGATAACCAACCA
1 TCCTCATCACGTAGGAACTGTGTCACCCCTG--AACCAACCA
698268 TCCTCATCACGTA
1 TCCTCATCACGTA
698281 AGAATCGTTT
Statistics
Matches: 50, Mismatches: 1, Indels: 6
0.88 0.02 0.11
Matches are distributed among these distances:
39 6 0.12
40 24 0.48
41 3 0.06
42 17 0.34
ACGTcount: A:0.24, C:0.37, G:0.16, T:0.23
Consensus pattern (40 bp):
TCCTCATCACGTAGGAACTGTGTCACCCCTGAACCAACCA
Found at i:698272 original size:130 final size:130
Alignment explanation
Indices: 698039--698506 Score: 512
Period size: 130 Copynumber: 3.6 Consensus size: 130
698029 AACCATATTC
* * * * * * * * * *
698039 CCTAAAGATGGCCTACCGTCCTCATCGCGTAGGGACCGTGACATCCACCGA-CTGACCTTCTCAT
1 CCTAAAGATGGCATGCAGTCCTCATCACGTAGGAACTGTGTCATCCCCCGACCAGACCTCCTCAT
** * * *
698103 CACGTAGGAGCCATGTCACCCCTGATAACCAGCCGTCCTCATCACTTAGGAACCGTGTTATCATT
66 CACGTAGGAGCTGTGTCACCCCTGATAACCAGCCATCCTCATCACGTAAGAACCGTGTTATCATT
* *
698168 ACTAAAGATGGCATGCAGTCCTCATCACGTAGGAACTGTGTCATCCCCTGACCAGACCTCCTCAT
1 CCTAAAGATGGCATGCAGTCCTCATCACGTAGGAACTGTGTCATCCCCCGACCAGACCTCCTCAT
* * *
698233 CACGTAGGAGCTGTGTCACCCCTGATAACCAACCATCCTCATCACGTAAGAATCGTTTTATCATT
66 CACGTAGGAGCTGTGTCACCCCTGATAACCAGCCATCCTCATCACGTAAGAACCGTGTTATCATT
** *
698298 CCTAAAGATGGCATGTTGTCCTCATCACGTAGGAACAT-TTTCATCCCCCGACCAGACCTCCTCA
1 CCTAAAGATGGCATGCAGTCCTCATCACGTAGGAAC-TGTGTCATCCCCCGACCAGACCTCCTCA
* * * *
698362 TCACGTAGGAG-TCGTGTCACCCCAGATAACTAGTCATCCTCACCACGTAAGAACCGTGTTATCA
65 TCACGTAGGAGCT-GTGTCACCCCTGATAACCAGCCATCCTCATCACGTAAGAACCGTGTTATC-
698426 ACCTT
128 A--TT
* * * * * * * *
698431 CCTAAAGATTGCCAAGAACTCTTCATCACGTATGG-GCAGTGTCATCCCCCGACCAGATCTCCTC
1 CCTAAAGA-TGGCATGCAGTCCTCATCACGTA-GGAACTGTGTCATCCCCCGACCAGACCTCCTC
* *
698495 CTCATGTAGGAG
64 ATCACGTAGGAG
698507 ATGCATCACC
Statistics
Matches: 286, Mismatches: 44, Indels: 13
0.83 0.13 0.04
Matches are distributed among these distances:
129 42 0.15
130 179 0.63
131 2 0.01
133 10 0.03
134 51 0.18
135 2 0.01
ACGTcount: A:0.25, C:0.32, G:0.18, T:0.24
Consensus pattern (130 bp):
CCTAAAGATGGCATGCAGTCCTCATCACGTAGGAACTGTGTCATCCCCCGACCAGACCTCCTCAT
CACGTAGGAGCTGTGTCACCCCTGATAACCAGCCATCCTCATCACGTAAGAACCGTGTTATCATT
Found at i:698747 original size:18 final size:18
Alignment explanation
Indices: 698732--698766 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
698722 TATATTATAT
698732 TTATATTTATTATTATTA
1 TTATATTTATTATTATTA
*
698750 TTATATTTATTAATATT
1 TTATATTTATTATTATT
698767 TTTAATACAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
TTATATTTATTATTATTA
Found at i:698771 original size:9 final size:10
Alignment explanation
Indices: 698723--698773 Score: 54
Period size: 9 Copynumber: 5.3 Consensus size: 10
698713 AAATATTCTT
*
698723 ATATTATATTT
1 ATATT-TATTA
698734 ATATTTATTA
1 ATATTTATTA
*
698744 TTA-TTATT-
1 ATATTTATTA
698752 ATATTTATTA
1 ATATTTATTA
698762 ATATTT-TTA
1 ATATTTATTA
698771 ATA
1 ATA
698774 CAATTTTTTG
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
8 2 0.06
9 16 0.46
10 12 0.34
11 5 0.14
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (10 bp):
ATATTTATTA
Found at i:700353 original size:29 final size:29
Alignment explanation
Indices: 700321--700395 Score: 71
Period size: 29 Copynumber: 2.6 Consensus size: 29
700311 GTTTCCACTT
* *
700321 TTTTGTCCCTTAAGTTTCTATTTTTGTTA
1 TTTTGTCCCTTAAGTTTCTATATTTGCTA
* * *
700350 TTTTAGT-CCTTAAATGTCTCTATTTGCTA
1 TTTT-GTCCCTTAAGTTTCTATATTTGCTA
* *
700379 TTTAGACCCTTAAGTTT
1 TTTTGTCCCTTAAGTTT
700396 TTGTTTTTAC
Statistics
Matches: 35, Mismatches: 9, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
28 1 0.03
29 32 0.91
30 2 0.06
ACGTcount: A:0.19, C:0.16, G:0.11, T:0.55
Consensus pattern (29 bp):
TTTTGTCCCTTAAGTTTCTATATTTGCTA
Found at i:701627 original size:26 final size:27
Alignment explanation
Indices: 701597--701648 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 27
701587 TTAATTAATT
701597 ATAAAAATTCAAATAAATTA-TAAAAA
1 ATAAAAATTCAAATAAATTACTAAAAA
* *
701623 ATAAAAATTTAAATAATTTACTAAAA
1 ATAAAAATTCAAATAAATTACTAAAA
701649 TAAATGCATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 18 0.78
27 5 0.22
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (27 bp):
ATAAAAATTCAAATAAATTACTAAAAA
Found at i:703296 original size:88 final size:88
Alignment explanation
Indices: 703181--703465 Score: 272
Period size: 88 Copynumber: 3.1 Consensus size: 88
703171 CACATAAATC
*
703181 ATTTAAAATATAAAAATATTATATTTTTAATGGAAGATTTACCATAAAAATAAATTGAATAGAAA
1 ATTTAAAATATAAAAATATTATATTTTTAATGGAAGATTTACAAT-AAAATAAATTGAATAGAAA
*
703246 TGGTTAAAAATAAATTGAATGTTTT
65 T-GTTAAAAATAAATTGAATATTTT
* * *
703271 -TTTAAGATAT-AAAATATTATATTTTTAATGGAAGATTTACAATAAAATAAATTTAATGGAAAT
1 ATTTAAAATATAAAAATATTATATTTTTAATGGAAGATTTACAATAAAATAAATTGAATAGAAAT
*
703334 GTTTAAAATAAATTTAATATTTTATTTATATTTAT
66 G-TT--AA-AAA--TAA-A-TTGA---ATATTT-T
* * *
703369 TTTTAAAATATAAAAATATTATA-TTTTAATGGAA-ATTTTACAATAAAAATAAATTTAATGGAA
1 ATTTAAAATATAAAAATATTATATTTTTAATGGAAGA-TTTACAAT-AAAATAAATTGAATAG-A
* *
703432 AATTTTAAAAATAAATTTAATATTTAAT
63 AATGTTAAAAATAAATTGAATATTT--T
703460 ATTTAA
1 ATTTAA
703466 TTTATATTAA
Statistics
Matches: 168, Mismatches: 9, Indels: 35
0.79 0.04 0.17
Matches are distributed among these distances:
86 1 0.01
87 20 0.12
88 32 0.19
89 11 0.07
90 9 0.05
91 7 0.04
92 3 0.02
93 5 0.03
94 4 0.02
95 3 0.02
97 8 0.05
98 4 0.02
99 28 0.17
100 29 0.17
101 4 0.02
ACGTcount: A:0.49, C:0.01, G:0.07, T:0.42
Consensus pattern (88 bp):
ATTTAAAATATAAAAATATTATATTTTTAATGGAAGATTTACAATAAAATAAATTGAATAGAAAT
GTTAAAAATAAATTGAATATTTT
Found at i:703380 original size:99 final size:101
Alignment explanation
Indices: 703269--703470 Score: 308
Period size: 99 Copynumber: 2.0 Consensus size: 101
703259 ATTGAATGTT
*
703269 TTTTTAAGATAT-AAAATATTATATTTTTAATGGAAGA-TTTACAAT-AAAATAAATTTAATGG-
1 TTTTTAAAATATAAAAATATTATA-TTTTAATGGAA-ATTTTACAATAAAAATAAATTTAATGGA
703330 AAATGTTT-AAAATAAATTTAATATTT-TATTTATATTTA
64 AAAT-TTTAAAAATAAATTTAATATTTATATTTA-ATTTA
703368 TTTTTAAAATATAAAAATATTATATTTTAATGGAAATTTTACAATAAAAATAAATTTAATGGAAA
1 TTTTTAAAATATAAAAATATTATATTTTAATGGAAATTTTACAATAAAAATAAATTTAATGGAAA
703433 ATTTTAAAAATAAATTTAATATTTAATATTTAATTTA
66 ATTTTAAAAATAAATTTAATATTT-ATATTTAATTTA
703470 T
1 T
703471 ATTAAATTTT
Statistics
Matches: 95, Mismatches: 1, Indels: 11
0.89 0.01 0.10
Matches are distributed among these distances:
98 1 0.01
99 30 0.32
100 30 0.32
101 22 0.23
102 6 0.06
103 6 0.06
ACGTcount: A:0.48, C:0.01, G:0.05, T:0.46
Consensus pattern (101 bp):
TTTTTAAAATATAAAAATATTATATTTTAATGGAAATTTTACAATAAAAATAAATTTAATGGAAA
ATTTTAAAAATAAATTTAATATTTATATTTAATTTA
Found at i:703458 original size:7 final size:7
Alignment explanation
Indices: 703446--703490 Score: 51
Period size: 7 Copynumber: 6.9 Consensus size: 7
703436 TTAAAAATAA
703446 ATTTAAT
1 ATTTAAT
703453 ATTTAAT
1 ATTTAAT
703460 ATTT-A-
1 ATTTAAT
703465 ATTT-AT
1 ATTTAAT
*
703471 ATTAAAT
1 ATTTAAT
*
703478 TTTTAAT
1 ATTTAAT
703485 ATTTAA
1 ATTTAA
703491 ACCAACGTCC
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
5 5 0.16
6 4 0.12
7 23 0.72
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (7 bp):
ATTTAAT
Found at i:703482 original size:18 final size:19
Alignment explanation
Indices: 703445--703484 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
703435 TTTAAAAATA
*
703445 AATTTAATATTTAATATTT
1 AATTTAATATTAAATATTT
*
703464 AATTT-ATATTAAATTTTT
1 AATTTAATATTAAATATTT
703482 AAT
1 AAT
703485 ATTTAAACCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
AATTTAATATTAAATATTT
Found at i:705707 original size:22 final size:22
Alignment explanation
Indices: 705682--705727 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
705672 GACTTGGAAC
705682 TGGTCCAAAAGAGTTTGGCAAG
1 TGGTCCAAAAGAGTTTGGCAAG
705704 TGGTCCAAAAGAGTTTGGCAAG
1 TGGTCCAAAAGAGTTTGGCAAG
705726 TG
1 TG
705728 ATGGAATTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.30, C:0.13, G:0.33, T:0.24
Consensus pattern (22 bp):
TGGTCCAAAAGAGTTTGGCAAG
Found at i:705996 original size:21 final size:20
Alignment explanation
Indices: 705972--706044 Score: 62
Period size: 21 Copynumber: 3.7 Consensus size: 20
705962 CATTGTATAC
705972 ATTATATTCATATTATATAAT
1 ATTATATT-ATATTATATAAT
* * *
705993 ATTATACATATATTGTATAGT
1 ATTATA-TTATATTATATAAT
*
706014 ATTATA-TATA-TATATTAT
1 ATTATATTATATTATATAAT
*
706032 ATGATATT-TATTA
1 ATTATATTATATTA
706045 ATGTTGTTTG
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
18 12 0.29
19 7 0.17
21 22 0.52
22 1 0.02
ACGTcount: A:0.41, C:0.03, G:0.04, T:0.52
Consensus pattern (20 bp):
ATTATATTATATTATATAAT
Found at i:706039 original size:23 final size:23
Alignment explanation
Indices: 705981--706039 Score: 70
Period size: 21 Copynumber: 2.7 Consensus size: 23
705971 CATTATATTC
*
705981 ATATTATATAATATTATACATAT
1 ATATTATATGATATTATACATAT
*
706004 AT-TGTATA-G-TATTATATATAT
1 ATAT-TATATGATATTATACATAT
706025 ATATTATATGATATT
1 ATATTATATGATATT
706040 TATTAATGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
21 17 0.57
22 3 0.10
23 10 0.33
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (23 bp):
ATATTATATGATATTATACATAT
Found at i:708035 original size:94 final size:96
Alignment explanation
Indices: 707874--708079 Score: 292
Period size: 94 Copynumber: 2.2 Consensus size: 96
707864 TAATGAAGTG
* *
707874 GTATCGAAT-CCATGGTGAGGGTATCGATACCCAGTAACATCGAACCTAATTTTGGTATAGATAC
1 GTATC-AATACCATGGTGAGGGTATCGATACCAAGGAACATCGAACCTAATTTTGGTATAGATAC
* *
707938 CGGAA-GGCG-TATCGATACCTTAGCATGGTA
65 CGGAATGGCGTTATCGATACCATAGCAGGGTA
* * *
707968 GTATCAATACCATGGTGAGGGTATCGATACCAAGGCACATCGAAGCTAATTTTGGTATCGATACC
1 GTATCAATACCATGGTGAGGGTATCGATACCAAGGAACATCGAACCTAATTTTGGTATAGATACC
* *
708033 GGAATGGGGTTATCGATACCATAGTAGGGTA
66 GGAATGGCGTTATCGATACCATAGCAGGGTA
*
708064 GTATCGATACCATGGT
1 GTATCAATACCATGGT
708080 AGATGTATTG
Statistics
Matches: 99, Mismatches: 10, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
93 3 0.03
94 60 0.61
95 3 0.03
96 33 0.33
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.27
Consensus pattern (96 bp):
GTATCAATACCATGGTGAGGGTATCGATACCAAGGAACATCGAACCTAATTTTGGTATAGATACC
GGAATGGCGTTATCGATACCATAGCAGGGTA
Found at i:708675 original size:107 final size:108
Alignment explanation
Indices: 708425--708717 Score: 401
Period size: 107 Copynumber: 2.7 Consensus size: 108
708415 AGGCACCAAT
* * * * * **
708425 TGTGCATTTCACGAAATTCATCCTAGGTGGATGAATAACTGTTTTGACACTAAATGTAAATTTCA
1 TGTGCATTCCACGGAATTCATCCTATGTGGATGAATAACTGTTTCGACACTAAGTGTGCATTTCA
* * **
708490 CGAAATTCATCCTATGTGGATGAATAACTGTTTCGGCACTAAG
66 CGGAATTCATCCTAGGTGGATGAATAACTGTTTCAACACTAAG
* * * *
708533 TGTGCATTCCACAGAATTCATCCTATGTGGATGAATAATTGTTTCGGCACTAAGTGTGCATTCCA
1 TGTGCATTCCACGGAATTCATCCTATGTGGATGAATAACTGTTTCGACACTAAGTGTGCATTTCA
**
708598 CGGAATTCATGTTAGGTGGATGAATAA-TCG-TTCAACACTAAG
66 CGGAATTCATCCTAGGTGGATGAATAACT-GTTTCAACACTAAG
*
708640 TGTGCATTCCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGACACTAAGTGTGCATTTCA
1 TGTGCATTCCACGGAATTCATCCTATGTGGATGAATAACTGTTTCGACACTAAGTGTGCATTTCA
708705 CGGAATTCATCCT
66 CGGAATTCATCCT
708718 CTTAGGATGA
Statistics
Matches: 160, Mismatches: 24, Indels: 3
0.86 0.13 0.02
Matches are distributed among these distances:
107 82 0.51
108 78 0.49
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32
Consensus pattern (108 bp):
TGTGCATTCCACGGAATTCATCCTATGTGGATGAATAACTGTTTCGACACTAAGTGTGCATTTCA
CGGAATTCATCCTAGGTGGATGAATAACTGTTTCAACACTAAG
Found at i:708753 original size:54 final size:54
Alignment explanation
Indices: 708416--708742 Score: 397
Period size: 54 Copynumber: 6.1 Consensus size: 54
708406 TTACCCAATA
* * * * * * *
708416 GGCACCAATTGTGCATTTCACGAAATTCATCCTAGGTGGATGAATAACTGTTTT
1 GGCACTAAGTGTGCATTCCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * ** * * *
708470 GACACTAAATGTAAATTTCACGAAATTCATCCTATGTGGATGAATAACTGTTTC
1 GGCACTAAGTGTGCATTCCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* **
708524 GGCACTAAGTGTGCATTCCACAGAATTCATCCTATGTGGATGAATAATTGTTTC
1 GGCACTAAGTGTGCATTCCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
** * *
708578 GGCACTAAGTGTGCATTCCACGGAATTCATGTTAGGTGGATGAATAATCG-TTC
1 GGCACTAAGTGTGCATTCCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
**
708631 AACACTAAGTGTGCATTCCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
1 GGCACTAAGTGTGCATTCCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * *
708685 GACACTAAGTGTGCATTTCACGGAATTCATCCTCT-TAGGATGAATAACCGTTTC
1 GGCACTAAGTGTGCATTCCACGGAATTCATCCTATGT-GGATGAATAACCGTTTC
708739 GGCA
1 GGCA
708743 GTCGGTGTGC
Statistics
Matches: 241, Mismatches: 30, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
53 48 0.20
54 193 0.80
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.31
Consensus pattern (54 bp):
GGCACTAAGTGTGCATTCCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
Found at i:708753 original size:161 final size:162
Alignment explanation
Indices: 708416--708742 Score: 435
Period size: 161 Copynumber: 2.0 Consensus size: 162
708406 TTACCCAATA
* * * **
708416 GGCACCAATTGTGCATTTCACGAAATTCATCCTAGGTGGATGAATAACTGTTTTGACACTAAATG
1 GGCACTAAGTGTGCATTCCACGAAATTCATCCTAGGTGGATGAATAACTGTTTCAACACTAAATG
* * *
708481 TAAATTTCACGAAATTCATCCTATGTGGATGAATAACTGTTTCGGCACTAAGTGTGCATTCCACA
66 TAAATTCCACGAAATTCATCCTATGTGGATGAATAACCGTTTCGACACTAAGTGTGCATTCCACA
**
708546 GAATTCATCCTATGTGGATGAATAATTGTTTC
131 GAATTCATCCTATGTGGATGAATAACCGTTTC
* ** *
708578 GGCACTAAGTGTGCATTCCACGGAATTCATGTTAGGTGGATGAATAA-TCG-TTCAACACTAAGT
1 GGCACTAAGTGTGCATTCCACGAAATTCATCCTAGGTGGATGAATAACT-GTTTCAACACTAAAT
** * *
708641 GTGCATTCCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGACACTAAGTGTGCATTTCAC
65 GTAAATTCCACGAAATTCATCCTATGTGGATGAATAACCGTTTCGACACTAAGTGTGCATTCCAC
* *
708706 GGAATTCATCCTCT-TAGGATGAATAACCGTTTC
130 AGAATTCATCCTATGT-GGATGAATAACCGTTTC
708739 GGCA
1 GGCA
708743 GTCGGTGTGC
Statistics
Matches: 143, Mismatches: 20, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
160 1 0.01
161 100 0.70
162 42 0.29
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.31
Consensus pattern (162 bp):
GGCACTAAGTGTGCATTCCACGAAATTCATCCTAGGTGGATGAATAACTGTTTCAACACTAAATG
TAAATTCCACGAAATTCATCCTATGTGGATGAATAACCGTTTCGACACTAAGTGTGCATTCCACA
GAATTCATCCTATGTGGATGAATAACCGTTTC
Found at i:712445 original size:83 final size:83
Alignment explanation
Indices: 712337--712498 Score: 252
Period size: 83 Copynumber: 2.0 Consensus size: 83
712327 ATACAATCAC
* * * * *
712337 GACACACGAATGTGTCATTTTCATTTATGACGGGGGCTTTAATGACATGCAATATAAGTCATAAA
1 GACACACAAATGTGTCATCTTCATTTATGACGAGGGCTTCAATGACACGCAATATAAGTCATAAA
*
712402 TGCGTGTCATAAATTTAT
66 TGCGCGTCATAAATTTAT
* *
712420 GACACACAAATGTGTCATCTTCATTTATGACGAGGGCTTCAATGACGCGCAATGTAAGTCATAAA
1 GACACACAAATGTGTCATCTTCATTTATGACGAGGGCTTCAATGACACGCAATATAAGTCATAAA
712485 TGCGCGTCATAAAT
66 TGCGCGTCATAAAT
712499 GCACGTCATA
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
83 71 1.00
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (83 bp):
GACACACAAATGTGTCATCTTCATTTATGACGAGGGCTTCAATGACACGCAATATAAGTCATAAA
TGCGCGTCATAAATTTAT
Found at i:712493 original size:13 final size:13
Alignment explanation
Indices: 712477--712511 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
712467 CGCAATGTAA
*
712477 GTCATAAATGCGC
1 GTCATAAATGCAC
712490 GTCATAAATGCAC
1 GTCATAAATGCAC
712503 GTCATAAAT
1 GTCATAAAT
712512 TTATGACGCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.26
Consensus pattern (13 bp):
GTCATAAATGCAC
Found at i:713179 original size:26 final size:26
Alignment explanation
Indices: 713142--713198 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
713132 AAACTATCAT
* * *
713142 CTTGGTTCTCTCATTTTACCCACCAA
1 CTTGGTTATCTCAGTTTAACCACCAA
*
713168 CTTGGTTATCTCAGTTTAACCATCAA
1 CTTGGTTATCTCAGTTTAACCACCAA
713194 CTTGG
1 CTTGG
713199 ATGCTAAATG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.21, C:0.28, G:0.12, T:0.39
Consensus pattern (26 bp):
CTTGGTTATCTCAGTTTAACCACCAA
Found at i:716925 original size:25 final size:26
Alignment explanation
Indices: 716885--716941 Score: 80
Period size: 25 Copynumber: 2.2 Consensus size: 26
716875 AGTCCTTTTG
* *
716885 TTAACAGATATATTACTCTTCAGC-T
1 TTAACAGACATATTACTATTCAGCAT
*
716910 TTAACAGACATGTTACTATTCAGCAT
1 TTAACAGACATATTACTATTCAGCAT
716936 TTAACA
1 TTAACA
716942 AATAACAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
25 21 0.75
26 7 0.25
ACGTcount: A:0.35, C:0.19, G:0.09, T:0.37
Consensus pattern (26 bp):
TTAACAGACATATTACTATTCAGCAT
Found at i:720951 original size:78 final size:78
Alignment explanation
Indices: 720802--720989 Score: 218
Period size: 78 Copynumber: 2.4 Consensus size: 78
720792 ATAGAACTAA
* * * * ** *
720802 GAACCAACAATATAAC-AATATGGGATGGATATAAATGGTCGGAGATGCGTCGTAACTCACTAGT
1 GAACCAACGATATAACAAAAATGGAATGGATAGAAATGGTAAGAGATGCGTCGTAACCCACTAGT
* *
720866 TATAAAGAAATAG
66 CACAAAGAAATAG
* * *
720879 GAACCAACGATATAACAAAAATGGAATGGATAGAACTGGTAAGAGTTG-GATCGTGACCCACTAG
1 GAACCAACGATATAACAAAAATGGAATGGATAGAAATGGTAAGAGATGCG-TCGTAACCCACTAG
*
720943 TCACAAAGAACTAG
65 TCACAAAGAAATAG
* *
720957 GAACCAACGATATAACAAAAATGAAATGAATAG
1 GAACCAACGATATAACAAAAATGGAATGGATAG
720990 CCATAAGAAC
Statistics
Matches: 94, Mismatches: 15, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
77 16 0.17
78 78 0.83
ACGTcount: A:0.45, C:0.14, G:0.21, T:0.20
Consensus pattern (78 bp):
GAACCAACGATATAACAAAAATGGAATGGATAGAAATGGTAAGAGATGCGTCGTAACCCACTAGT
CACAAAGAAATAG
Found at i:722441 original size:22 final size:20
Alignment explanation
Indices: 722385--722449 Score: 85
Period size: 21 Copynumber: 3.1 Consensus size: 20
722375 GGCATGTGAA
*
722385 ATCTATGTCCCGAAGGACACC
1 ATCTATGTCCCGAAGGAC-CT
*
722406 ATCTATATCCCGAAGGACCT
1 ATCTATGTCCCGAAGGACCT
722426 ATACATATGTCCCGAAGGACCT
1 AT-C-TATGTCCCGAAGGACCT
722448 AT
1 AT
722450 GTAACCCTCG
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
20 3 0.08
21 18 0.46
22 18 0.46
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.23
Consensus pattern (20 bp):
ATCTATGTCCCGAAGGACCT
Done.