Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008013.1 Hibiscus syriacus cultivar Beakdansim tig00110478_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: 1461402
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 6
Found at i:192689 original size:15 final size:14
Alignment explanation
Indices: 192650--192715 Score: 59
Period size: 14 Copynumber: 4.7 Consensus size: 14
192640 AGATTCAATC
192650 AGAACAAAAAGGGAAA
1 AGAACAAAAA--GAAA
192666 A-AACAAAAAAGAAA
1 AGAAC-AAAAAGAAA
*
192680 AGAAGCAAAAA-AGA
1 AGAA-CAAAAAGAAA
192694 AGAA-AAAAAG-AA
1 AGAACAAAAAGAAA
192706 AGAACAAAAA
1 AGAACAAAAA
192716 TCAAAAAGAA
Statistics
Matches: 43, Mismatches: 2, Indels: 13
0.74 0.03 0.22
Matches are distributed among these distances:
12 10 0.23
13 5 0.12
14 11 0.26
15 10 0.23
16 7 0.16
ACGTcount: A:0.77, C:0.06, G:0.17, T:0.00
Consensus pattern (14 bp):
AGAACAAAAAGAAA
Found at i:192693 original size:11 final size:11
Alignment explanation
Indices: 192663--192715 Score: 52
Period size: 11 Copynumber: 4.5 Consensus size: 11
192653 ACAAAAAGGG
* *
192663 AAAAAACAAAA
1 AAAAAAGAAGA
*
192674 AAGAAAAGAAGC
1 AA-AAAAGAAGA
192686 AAAAAAGAAGA
1 AAAAAAGAAGA
192697 AAAAAAGAAAGA
1 AAAAAAG-AAGA
192709 ACAAAAA
1 A-AAAAA
192716 TCAAAAAGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
11 17 0.49
12 13 0.37
13 5 0.14
ACGTcount: A:0.81, C:0.06, G:0.13, T:0.00
Consensus pattern (11 bp):
AAAAAAGAAGA
Found at i:192702 original size:22 final size:23
Alignment explanation
Indices: 192663--192727 Score: 62
Period size: 23 Copynumber: 2.8 Consensus size: 23
192653 ACAAAAAGGG
192663 AAAAAACAAAAAAGAAAAGAAGC
1 AAAAAACAAAAAAGAAAAGAAGC
* *
192686 AAAAAAGAAGAAA-AAAAGAAAGAAC
1 AAAAAACAAAAAAGAAAAG-AAG--C
*
192711 AAAAATC-AAAAAGAAAA
1 AAAAAACAAAAAAGAAAA
192728 AGGGACAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
22 5 0.15
23 14 0.42
24 4 0.12
25 10 0.30
ACGTcount: A:0.80, C:0.06, G:0.12, T:0.02
Consensus pattern (23 bp):
AAAAAACAAAAAAGAAAAGAAGC
Found at i:192727 original size:26 final size:27
Alignment explanation
Indices: 192665--192729 Score: 71
Period size: 26 Copynumber: 2.4 Consensus size: 27
192655 AAAAAGGGAA
*
192665 AAAACAAAAAAGAAAAGAAGCAAAAAAG
1 AAAA-AAAAAAGAAAAGAAGCAAAAAAC
* *
192693 AAGAAAAAAAG-AAAGAA-CAAAAATC
1 AAAAAAAAAAGAAAAGAAGCAAAAAAC
192718 AAAAAGAAAAAG
1 AAAAA-AAAAAG
192730 GGACAAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
25 10 0.31
26 12 0.38
27 7 0.22
28 3 0.09
ACGTcount: A:0.78, C:0.06, G:0.14, T:0.02
Consensus pattern (27 bp):
AAAAAAAAAAGAAAAGAAGCAAAAAAC
Found at i:193362 original size:22 final size:22
Alignment explanation
Indices: 193331--193385 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
193321 GCTATCCCAT
*
193331 CAAACATTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
193353 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
193375 CAAACCTTTGA
1 CAAACCTTTGA
193386 CCAAACACAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.38, C:0.25, G:0.13, T:0.24
Consensus pattern (22 bp):
CAAACCTTTGAGCATCAAATGC
Found at i:194468 original size:106 final size:106
Alignment explanation
Indices: 194308--195159 Score: 1276
Period size: 106 Copynumber: 8.0 Consensus size: 106
194298 ATATCGTGCC
* * *
194308 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGA-CGACTGGTTGTCAACAAACAACTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG-CTGGTTGTCAACAAACAACTTCC
*
194372 CAAATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * * *
194414 ACTCTAGACAACACAAGCTCAGCTTCACAACGAAGGGACCGCTGGTTGTTAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
194479 AATTTCAGAGCCAATTTCAACTTCACAACAAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
194520 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTAGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
194585 AATTTCAGAGCCAATTTCAACTTCACAGCGAAAGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
194626 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
**
194691 AATTTTGGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
194732 ACTCCAGACAACGCAAGTTCAACTTCACGATGAAGGGACCGTTGGTTGTCGACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
194797 AATTTCAGAGCCAATTTCAACTTCACAACGAAAGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
194838 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
194903 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
194944 ACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAATAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* ***
195009 AATTTCGGAGCCAATTTCAACTTCACAATAAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * *
195050 ACTCGAGACAACACAAGTTCGACTTCACAACGAAGGGACAGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * *
195115 GATTCCAGAGCCAATTTCAACTTCAC-GACGGAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGG
195156 ACTC
1 ACTC
195160 AGAACAATGC
Statistics
Matches: 682, Mismatches: 62, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
106 680 1.00
107 2 0.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.22
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:195997 original size:37 final size:37
Alignment explanation
Indices: 195911--196003 Score: 123
Period size: 37 Copynumber: 2.5 Consensus size: 37
195901 TTTGTCCTAC
* **
195911 TAGGATTCAAACTCCTAAAAATAGGATAGAATTTTGC
1 TAGGATTCAAACTCCTAAAAATAGGATAGAATTATAA
*
195948 TAGGATTCAAACTCCTAAAAATAGGATAGAGTTATAA
1 TAGGATTCAAACTCCTAAAAATAGGATAGAATTATAA
** *
195985 TATTATTTAAACTCCTAAA
1 TAGGATTCAAACTCCTAAA
196004 GATAAGATCC
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 49 1.00
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.31
Consensus pattern (37 bp):
TAGGATTCAAACTCCTAAAAATAGGATAGAATTATAA
Found at i:196649 original size:21 final size:20
Alignment explanation
Indices: 196625--196732 Score: 69
Period size: 21 Copynumber: 5.3 Consensus size: 20
196615 TTTTAGTTAA
196625 TATTATATATATATATATATT
1 TATTATATATATAT-TATATT
* *
196646 TATTATTTATTTATTAT-TAT
1 TATTATATATATATTATAT-T
*
196666 TATTACTATTTAGTATTATATT
1 TATTA-TATATA-TATTATATT
* * * *
196688 ATATTATACATACATTTTTTT
1 -TATTATATATATATTATATT
*
196709 TATT-TTTATATA-TATATT
1 TATTATATATATATTATATT
*
196727 TTTTAT
1 TATTAT
196733 TATTTTATTT
Statistics
Matches: 65, Mismatches: 16, Indels: 14
0.68 0.17 0.15
Matches are distributed among these distances:
18 7 0.11
19 7 0.11
20 13 0.20
21 21 0.32
22 11 0.17
23 6 0.09
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.63
Consensus pattern (20 bp):
TATTATATATATATTATATT
Found at i:196692 original size:23 final size:21
Alignment explanation
Indices: 196605--196693 Score: 62
Period size: 23 Copynumber: 4.2 Consensus size: 21
196595 TATTTCTATG
196605 ATTACTATTT-TTT-TAGTTAAT
1 ATTACTATTTATTTATA-TT-AT
* *
196626 ATTA-TATATATATATA-TAT
1 ATTACTATTTATTTATATTAT
*
196645 -TTATTATTTATTTATTATTATT
1 ATTACTATTTATTTA-TATTA-T
196667 ATTACTATTTAGTATTATATTAT
1 ATTACTATTTA-T-TTATATTAT
196690 ATTA
1 ATTA
196694 TACATACATT
Statistics
Matches: 54, Mismatches: 5, Indels: 16
0.72 0.07 0.21
Matches are distributed among these distances:
18 3 0.06
19 10 0.19
20 7 0.13
21 8 0.15
22 3 0.06
23 14 0.26
24 6 0.11
25 3 0.06
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (21 bp):
ATTACTATTTATTTATATTAT
Found at i:196694 original size:10 final size:10
Alignment explanation
Indices: 196624--196695 Score: 60
Period size: 10 Copynumber: 6.8 Consensus size: 10
196614 TTTTTAGTTA
196624 ATATTATATAT
1 ATATTATAT-T
196635 ATATATATATT
1 ATAT-TATATT
196646 -TATTAT-TT
1 ATATTATATT
196654 AT-TTATTATT
1 ATATTA-TATT
196664 ATTATTACTATTT
1 A-TATTA-TA-TT
196677 AGTATTATATT
1 A-TATTATATT
196688 ATATTATA
1 ATATTATA
196696 CATACATTTT
Statistics
Matches: 52, Mismatches: 2, Indels: 15
0.75 0.03 0.22
Matches are distributed among these distances:
8 5 0.10
9 5 0.10
10 13 0.25
11 9 0.17
12 12 0.23
13 8 0.15
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.60
Consensus pattern (10 bp):
ATATTATATT
Found at i:196727 original size:23 final size:23
Alignment explanation
Indices: 196691--196772 Score: 73
Period size: 23 Copynumber: 3.7 Consensus size: 23
196681 TTATATTATA
* *
196691 TTATACATACATTTTTTTTATTT
1 TTATATATATATTTTTTTTATTT
196714 TTATATATATATTTTTTATTA-TT
1 TTATATATATATTTTTT-TTATTT
* *
196737 TTATTTATACTA-TTTATTTATTT
1 TTATATATA-TATTTTTTTTATTT
*
196760 TCAT-TATAT-TTTT
1 TTATATATATATTTT
196773 AATTTCTTTA
Statistics
Matches: 50, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
21 4 0.08
22 7 0.14
23 34 0.68
24 5 0.10
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (23 bp):
TTATATATATATTTTTTTTATTT
Found at i:196728 original size:22 final size:21
Alignment explanation
Indices: 196703--196772 Score: 63
Period size: 25 Copynumber: 3.2 Consensus size: 21
196693 ATACATACAT
196703 TTTTTTTATTTTTA-TATATA
1 TTTTTTTATTTTTATTATATA
196723 TATTTTTTATTATTTTATTTATACTA
1 T-TTTTTTA-T-TTTTA-TTATA-TA
* *
196749 TTTATTTATTTTCATTATAT-
1 TTTTTTTATTTTTATTATATA
196769 TTTT
1 TTTT
196773 AATTTCTTTA
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
20 4 0.10
21 8 0.20
22 6 0.15
23 9 0.22
24 1 0.02
25 10 0.24
26 3 0.07
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (21 bp):
TTTTTTTATTTTTATTATATA
Found at i:196757 original size:46 final size:45
Alignment explanation
Indices: 196654--196772 Score: 105
Period size: 51 Copynumber: 2.5 Consensus size: 45
196644 TTTATTATTT
* *
196654 ATTTATTATTATTATTACTATTTAGTATTATATTATATTATACATACATTTT
1 ATTTATTTTTATTA-TA-TATTTTGTATTATATTAT-TTATAC-T--A-TTT
* * *
196706 TTTTATTTTTATATATATATTTTTTATTATTTTATTTATACTATTT
1 ATTTATTTTTAT-TATATATTTTGTATTATATTATTTATACTATTT
*
196752 ATTTATTTTCATTATAT-TTTT
1 ATTTATTTTTATTATATATTTT
196773 AATTTCTTTA
Statistics
Matches: 59, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
44 4 0.07
45 5 0.08
46 13 0.22
47 1 0.02
49 1 0.02
50 6 0.10
51 15 0.25
52 12 0.20
53 2 0.03
ACGTcount: A:0.29, C:0.04, G:0.01, T:0.66
Consensus pattern (45 bp):
ATTTATTTTTATTATATATTTTGTATTATATTATTTATACTATTT
Found at i:196769 original size:28 final size:27
Alignment explanation
Indices: 196708--196770 Score: 65
Period size: 28 Copynumber: 2.3 Consensus size: 27
196698 TACATTTTTT
* *
196708 TTATTTTTATATATATATTTTTTATTA
1 TTATATTTATATATATATTTTTTATCA
* *
196735 TTTTATTTATACTATTTATTTATTT-TCA
1 TTATATTTATA-TATATATTT-TTTATCA
196763 TTATATTT
1 TTATATTT
196771 TTAATTTCTT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
27 9 0.31
28 17 0.59
29 3 0.10
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (27 bp):
TTATATTTATATATATATTTTTTATCA
Found at i:196777 original size:22 final size:21
Alignment explanation
Indices: 196705--196773 Score: 63
Period size: 22 Copynumber: 3.3 Consensus size: 21
196695 ACATACATTT
* *
196705 TTTTTATTT-TTATATATATA
1 TTTTTATTTATTTTATTTATA
196725 TTTTT-TATTATTTTATTTATA
1 TTTTTAT-TTATTTTATTTATA
*
196746 CTATTTATTTATTTTCA-TTATA
1 -TTTTTATTTATTTT-ATTTATA
196768 TTTTTA
1 TTTTTA
196774 ATTTCTTTAC
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
19 1 0.03
20 7 0.17
21 14 0.35
22 16 0.40
23 2 0.05
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (21 bp):
TTTTTATTTATTTTATTTATA
Found at i:196777 original size:26 final size:27
Alignment explanation
Indices: 196748--196799 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 27
196738 TATTTATACT
*
196748 ATTTATTTA-TTTTCATTA-TATTTTTA
1 ATTTATTTACTCTT-ATTATTATTTTTA
*
196774 ATTTCTTTACTCTTATTATTATTTTT
1 ATTTATTTACTCTTATTATTATTTTT
196800 CTTTTTAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
26 12 0.55
27 10 0.45
ACGTcount: A:0.23, C:0.08, G:0.00, T:0.69
Consensus pattern (27 bp):
ATTTATTTACTCTTATTATTATTTTTA
Found at i:196883 original size:20 final size:19
Alignment explanation
Indices: 196856--196911 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
196846 TTTTATCTTC
196856 ATTTATTTTATTTTATTCA
1 ATTTATTTTATTTTATTCA
*
196875 ATTTCATTTT-TTTTCATCCA
1 ATTT-ATTTTATTTT-ATTCA
196895 A-TTATTTTATGTTTATT
1 ATTTATTTTAT-TTTATT
196912 ATTATTGGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
18 5 0.16
19 13 0.42
20 13 0.42
ACGTcount: A:0.23, C:0.09, G:0.02, T:0.66
Consensus pattern (19 bp):
ATTTATTTTATTTTATTCA
Found at i:202500 original size:35 final size:35
Alignment explanation
Indices: 202460--202546 Score: 104
Period size: 36 Copynumber: 2.5 Consensus size: 35
202450 ATGTTAAAAG
*
202460 TTTCAAAGTTTGGTAA-CCAACTTTGGAAAATGTTT
1 TTTCAAAGTTTGGTAATCCAACTTTGAAAAATG-TT
****
202495 TTTCAAAGTTTGGTAAATGTTTCTTTGAAAAATGTT
1 TTTCAAAGTTTGGT-AATCCAACTTTGAAAAATGTT
202531 TTTCAAAGTTTGGTAA
1 TTTCAAAGTTTGGTAA
202547 AATTTTGGTA
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
35 16 0.36
36 18 0.40
37 11 0.24
ACGTcount: A:0.31, C:0.08, G:0.17, T:0.44
Consensus pattern (35 bp):
TTTCAAAGTTTGGTAATCCAACTTTGAAAAATGTT
Found at i:203003 original size:16 final size:16
Alignment explanation
Indices: 202982--203015 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
202972 TTACTATTCA
*
202982 CGTGAATAGTGAATTT
1 CGTGAATAGTGAAATT
202998 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
203014 CG
1 CG
203016 GTCGGCGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.32
Consensus pattern (16 bp):
CGTGAATAGTGAAATT
Found at i:207084 original size:35 final size:35
Alignment explanation
Indices: 207038--207124 Score: 104
Period size: 36 Copynumber: 2.5 Consensus size: 35
207028 TTGTTAAAAG
*
207038 TTTCAAAGTTTGGTAA-CCAACTTTGGAAAATGTTT
1 TTTCAAAGTTTGGTAATCCAACTTTGAAAAATG-TT
****
207073 TTTCAAAGTTTGGTAAATGTTTCTTTGAAAAATGTT
1 TTTCAAAGTTTGGT-AATCCAACTTTGAAAAATGTT
207109 TTTCAAAGTTTGGTAA
1 TTTCAAAGTTTGGTAA
207125 AATTTTGGTA
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
35 16 0.36
36 18 0.40
37 11 0.24
ACGTcount: A:0.31, C:0.08, G:0.17, T:0.44
Consensus pattern (35 bp):
TTTCAAAGTTTGGTAATCCAACTTTGAAAAATGTT
Found at i:207985 original size:22 final size:22
Alignment explanation
Indices: 207959--208002 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
207949 ACATCCAAAA
207959 CAACTCAAAATTCAATATCCGT
1 CAACTCAAAATTCAATATCCGT
* *
207981 CAACTCGAAATTCGATATCCGT
1 CAACTCAAAATTCAATATCCGT
208003 TGCATCGGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.36, C:0.27, G:0.09, T:0.27
Consensus pattern (22 bp):
CAACTCAAAATTCAATATCCGT
Found at i:219338 original size:16 final size:16
Alignment explanation
Indices: 219317--219349 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
219307 TAATAAATAA
219317 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
219333 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
219349 A
1 A
219350 AAATGTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:219430 original size:10 final size:10
Alignment explanation
Indices: 219415--219488 Score: 50
Period size: 10 Copynumber: 7.6 Consensus size: 10
219405 CATTTAATAA
219415 ATAAACGAAC
1 ATAAACGAAC
219425 ATAAACGAAC
1 ATAAACGAAC
*
219435 ----ACAAAC
1 ATAAACGAAC
219441 ATAAACGAAC
1 ATAAACGAAC
** *
219451 ACGAAC-ATAA
1 ATAAACGA-AC
219461 ATGAACACGAAC
1 AT-AA-ACGAAC
219473 ATAAACGAAC
1 ATAAACGAAC
219483 ATAAAC
1 ATAAAC
219489 ATTGGAGACC
Statistics
Matches: 48, Mismatches: 8, Indels: 16
0.67 0.11 0.22
Matches are distributed among these distances:
6 5 0.10
9 1 0.02
10 33 0.69
11 3 0.06
12 5 0.10
13 1 0.02
ACGTcount: A:0.59, C:0.22, G:0.09, T:0.09
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:219443 original size:16 final size:16
Alignment explanation
Indices: 219422--219490 Score: 102
Period size: 16 Copynumber: 4.3 Consensus size: 16
219412 TAAATAAACG
219422 AACATAAACGAACACA
1 AACATAAACGAACACA
*
219438 AACATAAACGAACACG
1 AACATAAACGAACACA
* *
219454 AACATAAATGAACACG
1 AACATAAACGAACACA
*
219470 AACATAAACGAACATA
1 AACATAAACGAACACA
219486 AACAT
1 AACAT
219491 TGGAGACCCT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 48 1.00
ACGTcount: A:0.59, C:0.22, G:0.09, T:0.10
Consensus pattern (16 bp):
AACATAAACGAACACA
Found at i:220178 original size:24 final size:24
Alignment explanation
Indices: 220143--220243 Score: 150
Period size: 24 Copynumber: 4.2 Consensus size: 24
220133 GATTGACTTA
* **
220143 AACATAAATGAATGAACATAAACG
1 AACATAACTGAACAAACATAAACG
220167 AACATAACTGAACAAACATAAACG
1 AACATAACTGAACAAACATAAACG
220191 AACATAACTGAACAAACATAAACG
1 AACATAACTGAACAAACATAAACG
*
220215 AACATAACTGAACGAACAT-AACTG
1 AACATAACTGAACAAACATAAAC-G
220239 AACAT
1 AACAT
220244 TCACGAACGT
Statistics
Matches: 72, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
23 3 0.04
24 69 0.96
ACGTcount: A:0.56, C:0.19, G:0.10, T:0.15
Consensus pattern (24 bp):
AACATAACTGAACAAACATAAACG
Found at i:220186 original size:14 final size:14
Alignment explanation
Indices: 220167--220242 Score: 69
Period size: 14 Copynumber: 6.0 Consensus size: 14
220157 AACATAAACG
220167 AACATAACTGAACA
1 AACATAACTGAACA
*
220181 AACAT-A---AACG
1 AACATAACTGAACA
220191 AACATAACTGAACA
1 AACATAACTGAACA
*
220205 AACAT-A---AACG
1 AACATAACTGAACA
*
220215 AACATAACTGAACG
1 AACATAACTGAACA
220229 AACATAACTGAACA
1 AACATAACTGAACA
220243 TTCACGAACG
Statistics
Matches: 50, Mismatches: 4, Indels: 16
0.71 0.06 0.23
Matches are distributed among these distances:
10 16 0.32
11 2 0.04
13 2 0.04
14 30 0.60
ACGTcount: A:0.57, C:0.21, G:0.09, T:0.13
Consensus pattern (14 bp):
AACATAACTGAACA
Found at i:220209 original size:38 final size:38
Alignment explanation
Indices: 220167--220242 Score: 111
Period size: 38 Copynumber: 2.0 Consensus size: 38
220157 AACATAAACG
220167 AACAT-AACTGAACA-AACATAAACGAACATAACTGAACA
1 AACATAAAC-GAACATAAC-TAAACGAACATAACTGAACA
*
220205 AACATAAACGAACATAACTGAACGAACATAACTGAACA
1 AACATAAACGAACATAACTAAACGAACATAACTGAACA
220243 TTCACGAACG
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
38 29 0.83
39 6 0.17
ACGTcount: A:0.57, C:0.21, G:0.09, T:0.13
Consensus pattern (38 bp):
AACATAAACGAACATAACTAAACGAACATAACTGAACA
Found at i:224575 original size:86 final size:86
Alignment explanation
Indices: 224425--224634 Score: 379
Period size: 86 Copynumber: 2.5 Consensus size: 86
224415 TTTGAAGAGG
* *
224425 CGTTCAGTGGGCTAAGACTCAGATACTGATCGTTATCTCCAACCGATCACCGAGTCCAGCAGCTA
1 CGTTAAGTGGGCTAAGACTCAGATACTGATCGTTATCTCCAACCGATCACCGAGTCCAGAAGCTA
*
224490 CAAACCGCAGATAGGGTCGGC
66 CAAACCGCAGATAGGGTCAGC
224511 CGTTAAGTGGGCTAAGACTCAGATACTGATCGTTATCTCCAACCGATCACCGAGTCCAGAAGCTA
1 CGTTAAGTGGGCTAAGACTCAGATACTGATCGTTATCTCCAACCGATCACCGAGTCCAGAAGCTA
224576 CAAACCGCAGATAGGGTCAGC
66 CAAACCGCAGATAGGGTCAGC
224597 CGTTAAGTGGGCT--GACTCAGATACTGATCGTTATCTCC
1 CGTTAAGTGGGCTAAGACTCAGATACTGATCGTTATCTCC
224635 TTTAAGTGCC
Statistics
Matches: 121, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
84 25 0.21
86 96 0.79
ACGTcount: A:0.27, C:0.27, G:0.24, T:0.22
Consensus pattern (86 bp):
CGTTAAGTGGGCTAAGACTCAGATACTGATCGTTATCTCCAACCGATCACCGAGTCCAGAAGCTA
CAAACCGCAGATAGGGTCAGC
Found at i:225095 original size:24 final size:23
Alignment explanation
Indices: 225060--225107 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 23
225050 CAATGGCTTT
225060 TAGTTGGATCAATTGTATTAGCA
1 TAGTTGGATCAATTGTATTAGCA
225083 TAGTTGGGATCAATTGTATTAGCA
1 TAGTT-GGATCAATTGTATTAGCA
225107 T
1 T
225108 TTATATTGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 5 0.21
24 19 0.79
ACGTcount: A:0.29, C:0.08, G:0.23, T:0.40
Consensus pattern (23 bp):
TAGTTGGATCAATTGTATTAGCA
Found at i:229285 original size:20 final size:20
Alignment explanation
Indices: 229257--229298 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
229247 AGTTAACGGG
*
229257 TCAGATCGGTTCGGGTTGAC
1 TCAGATCGGTTCGGATTGAC
*
229277 TCAGGTCGGTTCGGATTGAC
1 TCAGATCGGTTCGGATTGAC
229297 TC
1 TC
229299 GGTTCAGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.14, C:0.21, G:0.33, T:0.31
Consensus pattern (20 bp):
TCAGATCGGTTCGGATTGAC
Found at i:245497 original size:24 final size:23
Alignment explanation
Indices: 245470--245545 Score: 57
Period size: 24 Copynumber: 3.2 Consensus size: 23
245460 TGGCTCTCCC
245470 AAATTACGAAATGATAAACTTAAA
1 AAATTAC-AAATGATAAACTTAAA
* * *
245494 AAATAACTAAAAT-TTAAGAGTTAAA
1 AAATTAC--AAATGATAA-ACTTAAA
*
245519 ATAACTA-AAATGATAAACTTAAA
1 A-AATTACAAATGATAAACTTAAA
245542 AAAT
1 AAAT
245546 AAACAGTTTA
Statistics
Matches: 39, Mismatches: 9, Indels: 10
0.67 0.16 0.17
Matches are distributed among these distances:
22 2 0.05
23 11 0.28
24 12 0.31
25 11 0.28
26 3 0.08
ACGTcount: A:0.61, C:0.07, G:0.07, T:0.26
Consensus pattern (23 bp):
AAATTACAAATGATAAACTTAAA
Found at i:245506 original size:25 final size:25
Alignment explanation
Indices: 245478--245547 Score: 92
Period size: 23 Copynumber: 2.9 Consensus size: 25
245468 CCAAATTACG
245478 AAATGATAAACTTAAAAAATAACTA
1 AAATGATAAACTTAAAAAATAACTA
* *
245503 AAAT-TTAAGAGTT--AAAATAACTA
1 AAATGATAA-ACTTAAAAAATAACTA
245526 AAATGATAAACTTAAAAAATAA
1 AAATGATAAACTTAAAAAATAA
245548 ACAGTTTATT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
23 17 0.46
24 6 0.16
25 14 0.38
ACGTcount: A:0.63, C:0.06, G:0.06, T:0.26
Consensus pattern (25 bp):
AAATGATAAACTTAAAAAATAACTA
Found at i:248545 original size:3 final size:3
Alignment explanation
Indices: 248537--248563 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
248527 CCTTATTTAC
248537 CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT
248564 TTATTTCCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:248580 original size:69 final size:70
Alignment explanation
Indices: 248500--248634 Score: 254
Period size: 69 Copynumber: 1.9 Consensus size: 70
248490 TCGCTTTCTA
248500 TCCCTATAAAACTATTATTTCTTTTCTCCTTATTTACCTTCTTCTTCTT-CTTCTTCTTCTTCTT
1 TCCCTATAAAACTATTATTTCTTTTCTCCTTATTTACCTTCTTCTTCTTCCTTCTTCTTCTTCTT
248564 TTATT
66 TTATT
248569 TCCCTATAAAACTATTATTTCTTTTCTCCTTATTTACCTTCTTCTTCTTCCCTTCTTCTTCTTCT
1 TCCCTATAAAACTATTATTTCTTTTCTCCTTATTTACCTTCTTCTTCTT-CCTTCTTCTTCTTCT
248634 T
65 T
248635 CTTTTATTTC
Statistics
Matches: 64, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
69 49 0.77
71 15 0.23
ACGTcount: A:0.14, C:0.28, G:0.00, T:0.58
Consensus pattern (70 bp):
TCCCTATAAAACTATTATTTCTTTTCTCCTTATTTACCTTCTTCTTCTTCCTTCTTCTTCTTCTT
TTATT
Found at i:248614 original size:23 final size:22
Alignment explanation
Indices: 248587--248639 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
248577 AAACTATTAT
248587 TTCTTTTCTCCTTATT-TACCTTC
1 TTCTTTTC-CCTTATTCT-CCTTC
* *
248610 TTCTTCTTCCCTTCTTCTTCTTC
1 TTCTT-TTCCCTTATTCTCCTTC
248633 TTCTTTT
1 TTCTTTT
248640 ATTTCCCTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 2 0.08
23 20 0.77
24 4 0.15
ACGTcount: A:0.04, C:0.32, G:0.00, T:0.64
Consensus pattern (22 bp):
TTCTTTTCCCTTATTCTCCTTC
Found at i:248624 original size:14 final size:14
Alignment explanation
Indices: 248605--248632 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
248595 TCCTTATTTA
248605 CCTTCTTCTTCTTC
1 CCTTCTTCTTCTTC
248619 CCTTCTTCTTCTTC
1 CCTTCTTCTTCTTC
248633 TTCTTTTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.00, C:0.43, G:0.00, T:0.57
Consensus pattern (14 bp):
CCTTCTTCTTCTTC
Found at i:257090 original size:6 final size:6
Alignment explanation
Indices: 257079--257111 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
257069 ACAAAATAAG
257079 TTCTAA TTCTAA TTCTAA TTCTAA TTCTAA TTC
1 TTCTAA TTCTAA TTCTAA TTCTAA TTCTAA TTC
257112 AACTCCTTGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.30, C:0.18, G:0.00, T:0.52
Consensus pattern (6 bp):
TTCTAA
Found at i:260178 original size:2 final size:2
Alignment explanation
Indices: 260166--260195 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
260156 AGGCACAACC
*
260166 AT AT CT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
260196 TGTACAATGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:261648 original size:44 final size:45
Alignment explanation
Indices: 261576--261662 Score: 122
Period size: 44 Copynumber: 2.0 Consensus size: 45
261566 TCTAAAGAGG
* *
261576 AACTCAAAACAGAAAATAGGAGGAGGATCTTATCCTCCGAAAAAT
1 AACTCAAAACAGAAAATAAGAGGAGGATCTTATCCACCGAAAAAT
* * *
261621 AACTCAAATC-GAAAATAAGATGTGGATCTTATCCACCGAAAA
1 AACTCAAAACAGAAAATAAGAGGAGGATCTTATCCACCGAAAA
261663 GGAACAATGG
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
44 28 0.76
45 9 0.24
ACGTcount: A:0.46, C:0.18, G:0.16, T:0.20
Consensus pattern (45 bp):
AACTCAAAACAGAAAATAAGAGGAGGATCTTATCCACCGAAAAAT
Found at i:261955 original size:2 final size:2
Alignment explanation
Indices: 261944--261984 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
261934 AAATAAATTT
261944 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
261985 AATTACTTGA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:277253 original size:15 final size:15
Alignment explanation
Indices: 277204--277280 Score: 50
Period size: 15 Copynumber: 5.1 Consensus size: 15
277194 TTTATAATAT
* * *
277204 ATGTGTGTATGATGA
1 ATGTATGTATAATTA
*
277219 ATGTTATG-ATAATATG
1 ATG-TATGTATAAT-TA
*
277235 ATGTATGTATATTTA
1 ATGTATGTATAATTA
*
277250 ATGTATGTTATACTT-
1 ATGTATG-TATAATTA
*
277265 ATGCATGTATAATTA
1 ATGTATGTATAATTA
277280 A
1 A
277281 CTATAAATTA
Statistics
Matches: 48, Mismatches: 9, Indels: 10
0.72 0.13 0.15
Matches are distributed among these distances:
14 6 0.12
15 26 0.54
16 16 0.33
ACGTcount: A:0.34, C:0.03, G:0.18, T:0.45
Consensus pattern (15 bp):
ATGTATGTATAATTA
Found at i:277617 original size:2 final size:2
Alignment explanation
Indices: 277610--277643 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
277600 AACATAGGTA
277610 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
277644 GGAATATGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:278257 original size:16 final size:16
Alignment explanation
Indices: 278217--278249 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
278207 TATTACTAAT
*
278217 AAGTCGGGTAAATATC
1 AAGTCAGGTAAATATC
278233 AAGTCAGGTAAATATC
1 AAGTCAGGTAAATATC
278249 A
1 A
278250 TATCAGGTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.42, C:0.12, G:0.21, T:0.24
Consensus pattern (16 bp):
AAGTCAGGTAAATATC
Found at i:278292 original size:16 final size:16
Alignment explanation
Indices: 278271--278306 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
278261 TCAATAACAA
278271 GTCAGATCATTTACAG
1 GTCAGATCATTTACAG
278287 GTCAGATCATTTACAG
1 GTCAGATCATTTACAG
278303 GTCA
1 GTCA
278307 TGTTCATAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (16 bp):
GTCAGATCATTTACAG
Found at i:278613 original size:20 final size:21
Alignment explanation
Indices: 278574--278614 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
278564 TTTGATTCAA
*
278574 GTCGGTTCAGTTAGTTTTACAT
1 GTCGGGTCAGTTA-TTTTACAT
278596 GTCGGGTCAGTT-TTTTACA
1 GTCGGGTCAGTTATTTTACA
278615 ACCCTAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
22 11 0.61
ACGTcount: A:0.17, C:0.15, G:0.24, T:0.44
Consensus pattern (21 bp):
GTCGGGTCAGTTATTTTACAT
Found at i:279245 original size:16 final size:16
Alignment explanation
Indices: 279224--279258 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
279214 TGTAATCGCT
*
279224 ATTTAATTATTATATG
1 ATTTAATTACTATATG
279240 ATTTAATTACTATATG
1 ATTTAATTACTATATG
279256 ATT
1 ATT
279259 GCGATATTCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.37, C:0.03, G:0.06, T:0.54
Consensus pattern (16 bp):
ATTTAATTACTATATG
Found at i:288307 original size:114 final size:114
Alignment explanation
Indices: 288102--288320 Score: 384
Period size: 114 Copynumber: 1.9 Consensus size: 114
288092 GATTAAGATA
*
288102 TTTTGAGACCGGGTGGAGTAGGAATTTTTAGAGCCCGACATTTTATCGGTGGATTCTGTCCACTT
1 TTTTGAGACCGGGTGGAGTAGGAATTTTTAGAGCCAGACATTTTATCGGTGGATTCTGTCCACTT
*
288167 GATGTTAAATAGATGAAACTCATGCGAACGATGATAATTAACTGTTTAT
66 GATGTTAAATAGATGAAACTCATGCGAAAGATGATAATTAACTGTTTAT
* * *
288216 TTTTTAGACCGGGTGGAGTATGAATTTTTAGAGCCAGACATTTTGTCGGTGGATTCTGTCCACTT
1 TTTTGAGACCGGGTGGAGTAGGAATTTTTAGAGCCAGACATTTTATCGGTGGATTCTGTCCACTT
*
288281 GCTGTTAAATAGATGAAACTCATGCGAAAGATGATAATTA
66 GATGTTAAATAGATGAAACTCATGCGAAAGATGATAATTA
288321 TCGAGTGCTC
Statistics
Matches: 99, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
114 99 1.00
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.34
Consensus pattern (114 bp):
TTTTGAGACCGGGTGGAGTAGGAATTTTTAGAGCCAGACATTTTATCGGTGGATTCTGTCCACTT
GATGTTAAATAGATGAAACTCATGCGAAAGATGATAATTAACTGTTTAT
Found at i:297148 original size:2 final size:2
Alignment explanation
Indices: 297141--297210 Score: 133
Period size: 2 Copynumber: 35.5 Consensus size: 2
297131 AGGATAGGGG
297141 TA TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
297182 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
297211 GTTTTAAAAG
Statistics
Matches: 67, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 66 0.99
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:302163 original size:3 final size:3
Alignment explanation
Indices: 302155--302228 Score: 130
Period size: 3 Copynumber: 24.7 Consensus size: 3
302145 TAATATATTT
* *
302155 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAG TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
302203 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
302229 TGGATAAAAA
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 67 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:302795 original size:113 final size:113
Alignment explanation
Indices: 302550--302985 Score: 739
Period size: 113 Copynumber: 3.9 Consensus size: 113
302540 AGAATTATGC
* * * *
302550 AAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
302615 TATGAA-CTTCTCTGGAAAAGATAATCCATCAATTGATGAATTCAGGT
66 TATGAACCTTCTCTGGAAAAGATAATCCATCAATTGATGAATTCAGGT
*
302662 AAAAGGTTAAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
302727 TATGAACTTTCTCTGGAAAAGATAATCCATCAATTGATGAATTCAGGT
66 TATGAACCTTCTCTGGAAAAGATAATCCATCAATTGATGAATTCAGGT
* *
302775 AAAAGGTTGAATAGATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * *
302840 TATGAACCTTCTCTGGCAAAGATGATCCATCAAATGATGGATTCAGGT
66 TATGAACCTTCTCTGGAAAAGATAATCCATCAATTGATGAATTCAGGT
302888 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* *
302953 TATGAACCTTCTCTGGCAAAGATGATCCATCAA
66 TATGAACCTTCTCTGGAAAAGATAATCCATCAA
302986 GTGGATTCGA
Statistics
Matches: 307, Mismatches: 16, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
112 66 0.21
113 241 0.79
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (113 bp):
AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACCTTCTCTGGAAAAGATAATCCATCAATTGATGAATTCAGGT
Found at i:303863 original size:83 final size:83
Alignment explanation
Indices: 303724--304184 Score: 784
Period size: 83 Copynumber: 5.5 Consensus size: 83
303714 GTTCCTACCA
*
303724 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATT
303789 CAATGATTGGTTCTGTCC
66 CAATGATTGGTTCTGTCC
* *
303807 AACCAGATAAGATAACTCAAAGAACACTTCCAAAAGATGCTATTGGCAAATTCATCTTCTAAATT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATT
303872 CAATGATTGGTTCTGTCC
66 CAATGATTGGTTCTGTCC
303890 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATT
303955 CAATGATTGGTTCTGTCC
66 CAATGATTGGTTCTGTCC
* * *
303973 AACCAGATCAGATAACTCAAAGAATACTTCCAGAAGATGCTA-TGGACACATTC-TCTTCCAAAT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGG-CAAATTCATCTTCTAAAT
304036 TCAATGATTGGTTCTGTCC
65 TCAATGATTGGTTCTGTCC
* *
304055 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATT-ATTCTTCCAAA
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-GCAAATTCA-TCTTCTAAA
304119 TTCAATGATTGGTTCTGTCC
64 TTCAATGATTGGTTCTGTCC
*
304139 AACCAGATCAGATAACTCAAAGAACACTTCCCAAAAGATGCTATTG
1 AACCAGATCAGATAACTCAAAGAACACTT-CCAGAAGATGCTATTG
304185 AGCACATTAT
Statistics
Matches: 362, Mismatches: 10, Indels: 10
0.95 0.03 0.03
Matches are distributed among these distances:
82 72 0.20
83 216 0.60
84 59 0.16
85 15 0.04
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.28
Consensus pattern (83 bp):
AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATT
CAATGATTGGTTCTGTCC
Found at i:305371 original size:11 final size:11
Alignment explanation
Indices: 305355--305379 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
305345 TCCTTTTCAC
305355 TTTTTTCTTTT
1 TTTTTTCTTTT
305366 TTTTTTCTTTT
1 TTTTTTCTTTT
305377 TTT
1 TTT
305380 CTTCAAGCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTTTCTTTT
Found at i:312726 original size:15 final size:15
Alignment explanation
Indices: 312706--312737 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
312696 TGAATGATGA
*
312706 ATGTATGCAAAATGT
1 ATGTATGCAAAAGGT
312721 ATGTATGCAAAAGGT
1 ATGTATGCAAAAGGT
312736 AT
1 AT
312738 TGATCCCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.41, C:0.06, G:0.22, T:0.31
Consensus pattern (15 bp):
ATGTATGCAAAAGGT
Found at i:315978 original size:13 final size:15
Alignment explanation
Indices: 315956--315992 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
315946 TTTGACAGAA
315956 AAAT-AAATAC-TG-
1 AAATAAAATACTTGC
315968 AAATAAAATACTTGC
1 AAATAAAATACTTGC
315983 AAATAAAATA
1 AAATAAAATA
315993 AAATGAAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 4 0.18
13 6 0.27
14 2 0.09
15 10 0.45
ACGTcount: A:0.62, C:0.08, G:0.05, T:0.24
Consensus pattern (15 bp):
AAATAAAATACTTGC
Found at i:316721 original size:13 final size:13
Alignment explanation
Indices: 316684--316723 Score: 55
Period size: 14 Copynumber: 3.1 Consensus size: 13
316674 TCGATATTGA
316684 AAAATAAATA-TT
1 AAAATAAATATTT
*
316696 AAAATAATTTATTT
1 AAAATAA-ATATTT
316710 AAAATAAATATTT
1 AAAATAAATATTT
316723 A
1 A
316724 TTTATTATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 7 0.29
13 8 0.33
14 9 0.38
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AAAATAAATATTT
Found at i:318165 original size:3 final size:3
Alignment explanation
Indices: 318147--318259 Score: 183
Period size: 3 Copynumber: 37.7 Consensus size: 3
318137 TATATATATT
* *
318147 TAA TATA TAT TAA TAA TAA TAA TAA -AA TGA TAA TAA TAA TAA TAA
1 TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
318192 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAG TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
318240 TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TA
318260 TGGATAAAAA
Statistics
Matches: 102, Mismatches: 6, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
2 2 0.02
3 97 0.95
4 3 0.03
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:335142 original size:27 final size:27
Alignment explanation
Indices: 335104--335171 Score: 136
Period size: 27 Copynumber: 2.5 Consensus size: 27
335094 AAGGTAAAAT
335104 GAAAATTATATTAAATTCAACCAACAA
1 GAAAATTATATTAAATTCAACCAACAA
335131 GAAAATTATATTAAATTCAACCAACAA
1 GAAAATTATATTAAATTCAACCAACAA
335158 GAAAATTATATTAA
1 GAAAATTATATTAA
335172 CTGATAAATT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.56, C:0.12, G:0.04, T:0.28
Consensus pattern (27 bp):
GAAAATTATATTAAATTCAACCAACAA
Found at i:337507 original size:18 final size:18
Alignment explanation
Indices: 337481--337515 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
337471 ACACCAAATT
337481 TCAAGAATACTTTTAATC
1 TCAAGAATACTTTTAATC
*
337499 TCAATAATACTTTTAAT
1 TCAAGAATACTTTTAAT
337516 AGAAAATACT
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:0.40, C:0.14, G:0.03, T:0.43
Consensus pattern (18 bp):
TCAAGAATACTTTTAATC
Found at i:343607 original size:263 final size:252
Alignment explanation
Indices: 343319--343849 Score: 689
Period size: 263 Copynumber: 2.0 Consensus size: 252
343309 ATAAAAAAAA
343319 TTATTCAATAAAAGCAGTGACTTAATTGGAAAAAAAA-TAGAGAGAGAGGGGTATTATTGTAATT
1 TTATTCAATAAAAGCAGTGACTTAATT-GAAAAAAAATTAGAGAGAGAGGGGTATTATTGTAATT
* *
343383 ATTCCTAAATATATAAGGTAAAATTATATATTTTTGGGTCGGGTCGAGTATTTTTCACCCTAAA-
65 ATTCCTAAATATATAAGGTAAAATTATATATATTT---TCGAGTCGAGTATTTTTCACCCTAAAC
*
343447 C-CT-GA-ACCTGACCCGAATATCACACTTAAAAAAAACCTACCCGACCCGACCAAAATA-AAGT
127 CACTCGACACCCGACCCGAATATCACACTT-AAAAAAA--T---CGACCCGACCAAAATACAA-T
* * *
343508 TTCACCCGACCCGACCCGAATATATGAATTAGAAATCCTACCCGACCCGACCCAAAATAATAAAA
185 TTCACCCAACCCGACCCGAATATATGAATTAG-AA----ACCCAACCCAACCCAAAATAATAAAA
343573 AAATTATTT
245 AAA-TATTT
* * *
343582 TTATTCAATAGAAA-CAGTGACTTAATTGAAAAAAAATTATATATAGAGGGGTATTATTGTAATT
1 TTATTCAATA-AAAGCAGTGACTTAATTGAAAAAAAATTAGAGAGAGAGGGGTATTATTGTAATT
*
343646 ATTCCTAAATATATAAGGTAAAATTATATATATTTTCGAGTCGGGTATTTTTCACCCTAAACCCG
65 ATTCCTAAATATATAAGGTAAAATTATATATATTTTCGAGTCGAGTATTTTTCACCCTAAA-CC-
343711 AACTCGACCCGACCCGACCCGAATATCACACTTAAAAAAATCGACCCGACCAAAATACAATTTCA
128 -ACTCGA--C-ACCCGACCCGAATATCACACTTAAAAAAATCGACCCGACCAAAATACAATTTCA
*
343776 CCCAACCCGACCCGAATATATGAATTAGAAACCCAACCCAACCTAAAATAATAAAAAAATATTT
189 CCCAACCCGACCCGAATATATGAATTAGAAACCCAACCCAACCCAAAATAATAAAAAAATATTT
*
343840 TTATTTAATA
1 TTATTCAATA
343850 TATGAATAAG
Statistics
Matches: 243, Mismatches: 12, Indels: 31
0.85 0.04 0.11
Matches are distributed among these distances:
258 14 0.06
259 26 0.11
260 24 0.10
262 10 0.04
263 83 0.34
264 51 0.21
265 4 0.02
266 2 0.01
267 1 0.00
269 7 0.03
270 21 0.09
ACGTcount: A:0.41, C:0.20, G:0.12, T:0.27
Consensus pattern (252 bp):
TTATTCAATAAAAGCAGTGACTTAATTGAAAAAAAATTAGAGAGAGAGGGGTATTATTGTAATTA
TTCCTAAATATATAAGGTAAAATTATATATATTTTCGAGTCGAGTATTTTTCACCCTAAACCACT
CGACACCCGACCCGAATATCACACTTAAAAAAATCGACCCGACCAAAATACAATTTCACCCAACC
CGACCCGAATATATGAATTAGAAACCCAACCCAACCCAAAATAATAAAAAAATATTT
Found at i:367890 original size:2 final size:2
Alignment explanation
Indices: 367883--367908 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
367873 TGGGTTTTTC
367883 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
367909 GGGATAAGGT
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:372788 original size:2 final size:2
Alignment explanation
Indices: 372781--372845 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
372771 AATGTATCAT
372781 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
372823 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
372846 TAGAATATTG
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:392974 original size:24 final size:24
Alignment explanation
Indices: 392913--392963 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
392903 GATTGGGTTA
**
392913 AACATAAATGAACGAACATAAACG
1 AACATAACCGAACGAACATAAACG
*
392937 AACATAACCGAACGAACATAACCG
1 AACATAACCGAACGAACATAAACG
392961 AAC
1 AAC
392964 GTTCACGAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.55, C:0.24, G:0.12, T:0.10
Consensus pattern (24 bp):
AACATAACCGAACGAACATAAACG
Found at i:396870 original size:53 final size:53
Alignment explanation
Indices: 396812--397009 Score: 213
Period size: 53 Copynumber: 3.7 Consensus size: 53
396802 TGGCGGTGTT
*
396812 AATGCTTAAATACCAGCGTTAAACCTACGCAACGTTCTCCTCGTGATGTTGCA
1 AATGCTTAAATCCCAGCGTTAAACCTACGCAACGTTCTCCTCGTGATGTTGCA
* * *
396865 AATGCTTAAATCCCAGCGTTAAACCTATGCAATGTTCTCCTCGTGATGTTGCT
1 AATGCTTAAATCCCAGCGTTAAACCTACGCAACGTTCTCCTCGTGATGTTGCA
* * **** *
396918 AATGC--AATGTTCTCC-TCGTGATGTTGCTAATGCAACGTTCTCCTCGTGATGTTGCA
1 AATGCTTAA--ATC-CCAGCGT--TAAACCT-ACGCAACGTTCTCCTCGTGATGTTGCA
*
396974 AATGCTTAAATCCCAGCATTAAACCTACGCAACGTT
1 AATGCTTAAATCCCAGCGTTAAACCTACGCAACGTT
397010 ATGCTTAAAT
Statistics
Matches: 116, Mismatches: 20, Indels: 18
0.75 0.13 0.12
Matches are distributed among these distances:
51 2 0.02
53 68 0.59
54 5 0.04
55 5 0.04
56 34 0.29
58 2 0.02
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.31
Consensus pattern (53 bp):
AATGCTTAAATCCCAGCGTTAAACCTACGCAACGTTCTCCTCGTGATGTTGCA
Found at i:396923 original size:28 final size:28
Alignment explanation
Indices: 396891--396978 Score: 158
Period size: 28 Copynumber: 3.1 Consensus size: 28
396881 CGTTAAACCT
396891 ATGCAATGTTCTCCTCGTGATGTTGCTA
1 ATGCAATGTTCTCCTCGTGATGTTGCTA
396919 ATGCAATGTTCTCCTCGTGATGTTGCTA
1 ATGCAATGTTCTCCTCGTGATGTTGCTA
* *
396947 ATGCAACGTTCTCCTCGTGATGTTGCAA
1 ATGCAATGTTCTCCTCGTGATGTTGCTA
396975 ATGC
1 ATGC
396979 TTAAATCCCA
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 58 1.00
ACGTcount: A:0.19, C:0.23, G:0.22, T:0.36
Consensus pattern (28 bp):
ATGCAATGTTCTCCTCGTGATGTTGCTA
Found at i:397021 original size:35 final size:35
Alignment explanation
Indices: 396975--397044 Score: 104
Period size: 35 Copynumber: 2.0 Consensus size: 35
396965 GATGTTGCAA
396975 ATGCTTAAATCCCAGCATTAAACCTACGCAACGTT
1 ATGCTTAAATCCCAGCATTAAACCTACGCAACGTT
* ** *
397010 ATGCTTAAATCCTAGTTTTAAACCTATGCAACGTT
1 ATGCTTAAATCCCAGCATTAAACCTACGCAACGTT
397045 CTCGTGATGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.33, C:0.24, G:0.11, T:0.31
Consensus pattern (35 bp):
ATGCTTAAATCCCAGCATTAAACCTACGCAACGTT
Found at i:397649 original size:2 final size:2
Alignment explanation
Indices: 397642--397671 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
397632 TTGTGAAATG
397642 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
397672 AATATAGCAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:399274 original size:22 final size:23
Alignment explanation
Indices: 399243--399289 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
399233 TAATTGCGAG
399243 TTTAGAAGATACGA-TTATGGGC
1 TTTAGAAGATACGATTTATGGGC
* *
399265 TTTAGCAGATACGATTTTTGGGC
1 TTTAGAAGATACGATTTATGGGC
399288 TT
1 TT
399290 ATTTAGGGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 13 0.59
23 9 0.41
ACGTcount: A:0.26, C:0.11, G:0.26, T:0.38
Consensus pattern (23 bp):
TTTAGAAGATACGATTTATGGGC
Found at i:400980 original size:141 final size:141
Alignment explanation
Indices: 400726--400994 Score: 414
Period size: 141 Copynumber: 1.9 Consensus size: 141
400716 TGCAGGCCGG
* * **
400726 CATCTTTGTTTTGTATATTGCAATTGTCATCATTTGAATCATTGCGACTCAGATTTGGAATCTCT
1 CATCTTTGTTTTGTATATCGCAATTGTCAACATTCAAATCATTGCGACTCAGATTTGGAATCTCT
* *
400791 AAATCGTATGGCTTCAAGCATAGGCTTAGATCCAAACCTGCAGCATCTCTGTTATTGACCTCGCA
66 AAATCGTATGGCGTCAAGCACAGGCTTAGATCCAAACCTGCAGCATCTCTGTTATTGACCTCGCA
400856 GATGGAGTCGT
131 GATGGAGTCGT
* * *
400867 CATCTTTGTTTTGTATATCGCAAATT-TCAACGTTCAAATCGTTGCGACTCGGATTTGGAATCTC
1 CATCTTTGTTTTGTATATCGC-AATTGTCAACATTCAAATCATTGCGACTCAGATTTGGAATCTC
** *
400931 TAAATCGTATGGCGTCAAGTGCAGGCTTAGATCCAAACCTGCAGCATCTCTGTTTTTGACCTCG
65 TAAATCGTATGGCGTCAAGCACAGGCTTAGATCCAAACCTGCAGCATCTCTGTTATTGACCTCG
400995 AAGGTGGGCT
Statistics
Matches: 115, Mismatches: 12, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
141 111 0.97
142 4 0.03
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.35
Consensus pattern (141 bp):
CATCTTTGTTTTGTATATCGCAATTGTCAACATTCAAATCATTGCGACTCAGATTTGGAATCTCT
AAATCGTATGGCGTCAAGCACAGGCTTAGATCCAAACCTGCAGCATCTCTGTTATTGACCTCGCA
GATGGAGTCGT
Found at i:404228 original size:60 final size:59
Alignment explanation
Indices: 404104--404265 Score: 155
Period size: 60 Copynumber: 2.7 Consensus size: 59
404094 TGAATTTAAA
* * * * * *
404104 GATGAAATTAGAA-GATTTAGAAGTTTAAGGATTAATTTAGAATTAAGATCATTGTTGGAT
1 GATGAAATTAGAATG-TTTAAAAGTTTAAAGATTAATTTA-AAATAAGATAATAGTTGGAC
* * *
404164 GATGAAATTAGAATGTTCAAAAGTTTAAAGATTAATTTAAAATGAGTATAATAGTTTGAC
1 GATGAAATTAGAATGTTTAAAAGTTTAAAGATTAATTTAAAATAAG-ATAATAGTTGGAC
* * * * **
404224 GATGAAATTAAAATATTTAAAAGTCTAGAGACCAATTTAAAA
1 GATGAAATTAGAATGTTTAAAAGTTTAAAGATTAATTTAAAA
404266 CGGAGATCAT
Statistics
Matches: 84, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
59 5 0.06
60 78 0.93
61 1 0.01
ACGTcount: A:0.45, C:0.04, G:0.17, T:0.34
Consensus pattern (59 bp):
GATGAAATTAGAATGTTTAAAAGTTTAAAGATTAATTTAAAATAAGATAATAGTTGGAC
Found at i:405989 original size:60 final size:60
Alignment explanation
Indices: 405894--406011 Score: 159
Period size: 60 Copynumber: 2.0 Consensus size: 60
405884 TATTATTAAG
* * *
405894 ATCATAATTAGAGGATGAAATTAGAATGTTCAAAAGTTTAAAGACTATTTTAAAATGAGT
1 ATCATAATTAGAGGATGAAATAAGAATGTTCAAAAGTTTAAAGACCAATTTAAAATGAGT
* *
405954 ATCATAGTTTGAGGATGAAACTAAGATAT-TT-AAAAGTTTAAAGACCAATTTAAAATGA
1 ATCATAATTAGAGGATGAAA-TAAGA-ATGTTCAAAAGTTTAAAGACCAATTTAAAATGA
406012 AGATAATAGT
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
60 43 0.84
61 6 0.12
62 2 0.04
ACGTcount: A:0.46, C:0.06, G:0.16, T:0.32
Consensus pattern (60 bp):
ATCATAATTAGAGGATGAAATAAGAATGTTCAAAAGTTTAAAGACCAATTTAAAATGAGT
Found at i:410280 original size:7 final size:7
Alignment explanation
Indices: 410268--410296 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
410258 TATATACACT
410268 CCCTCCC
1 CCCTCCC
410275 CCCTCCC
1 CCCTCCC
410282 CCCTCCC
1 CCCTCCC
410289 CCCTCCC
1 CCCTCCC
410296 C
1 C
410297 GGGATCTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.00, C:0.86, G:0.00, T:0.14
Consensus pattern (7 bp):
CCCTCCC
Found at i:412931 original size:4 final size:4
Alignment explanation
Indices: 412922--412964 Score: 86
Period size: 4 Copynumber: 10.8 Consensus size: 4
412912 TAGATGACAT
412922 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
412965 ACATGTATAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 39 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:415442 original size:34 final size:32
Alignment explanation
Indices: 415389--415458 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
415379 ACCTTACAAC
*
415389 TCCCTAGTTTTTCCGGGCTAAACTAGAACATT
1 TCCCTAGTTTTACCGGGCTAAACTAGAACATT
* *
415421 TCCCTAGCTTTTACACGGGCTAAGCTATAACATT
1 TCCCTAG-TTTTAC-CGGGCTAAACTAGAACATT
415455 TCCC
1 TCCC
415459 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.24, C:0.29, G:0.14, T:0.33
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAACTAGAACATT
Found at i:415768 original size:21 final size:21
Alignment explanation
Indices: 415742--415783 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
415732 CCAGAATGGG
*
415742 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
415763 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
415784 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:415913 original size:19 final size:19
Alignment explanation
Indices: 415889--415955 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
415879 GAGCCTCGGG
*
415889 TTACTGTTCAAACAGTGAT
1 TTACTGTTCAAACAGTAAT
*
415908 TTACTGTTCAAATAGTAAT
1 TTACTGTTCAAACAGTAAT
* *
415927 TTACTGTTCAAATAGTAAA
1 TTACTGTTCAAACAGTAAT
*
415946 TTACTATTCA
1 TTACTGTTCA
415956 TAAAAACATT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 44 1.00
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.40
Consensus pattern (19 bp):
TTACTGTTCAAACAGTAAT
Found at i:416052 original size:29 final size:31
Alignment explanation
Indices: 416020--416079 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
416010 AAATTTTGAA
*
416020 TAAATTCAATT-AAGTCCAAATA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
416049 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
416080 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 10 0.36
31 7 0.25
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.35
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:420381 original size:2 final size:2
Alignment explanation
Indices: 420374--420402 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
420364 GGTAGAAAGT
420374 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
420403 TACTTTAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:420845 original size:37 final size:36
Alignment explanation
Indices: 420770--420845 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
420760 TTTTTATATT
*
420770 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* *
420806 TTTAATTTTTTAAATAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
420843 TTT
1 TTT
420846 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
36 26 0.74
37 9 0.26
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:421027 original size:20 final size:20
Alignment explanation
Indices: 420991--421028 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
420981 ATCCTATTCC
**
420991 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
421011 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
421029 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:421192 original size:2 final size:2
Alignment explanation
Indices: 421185--421218 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
421175 AACATTGATC
421185 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
421219 GCATGCGTGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:422356 original size:29 final size:29
Alignment explanation
Indices: 422323--422384 Score: 106
Period size: 29 Copynumber: 2.1 Consensus size: 29
422313 TTCTACAGTA
*
422323 ACCTTGGAGGTCGCCATGGCATCCGGGCG
1 ACCTTGGAGGTCGCCATGGCATCCGAGCG
*
422352 ACCTTGGAGGTCGCCATGGCATCTGAGCG
1 ACCTTGGAGGTCGCCATGGCATCCGAGCG
422381 ACCT
1 ACCT
422385 GTGTGTATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.16, C:0.31, G:0.34, T:0.19
Consensus pattern (29 bp):
ACCTTGGAGGTCGCCATGGCATCCGAGCG
Found at i:423030 original size:28 final size:30
Alignment explanation
Indices: 422989--423059 Score: 103
Period size: 28 Copynumber: 2.4 Consensus size: 30
422979 TAAAACTAAA
*
422989 ATATAGTTA-ATTAGTTTGTTAGTTTAAG-T
1 ATATA-TTATATTAGTTTATTAGTTTAAGTT
423018 -TATATTATATTAGTTTATTAGTTTAAGTT
1 ATATATTATATTAGTTTATTAGTTTAAGTT
423047 ATATATTATATTA
1 ATATATTATATTA
423060 TATAAAAAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
27 3 0.08
28 22 0.58
29 1 0.03
30 12 0.32
ACGTcount: A:0.34, C:0.00, G:0.11, T:0.55
Consensus pattern (30 bp):
ATATATTATATTAGTTTATTAGTTTAAGTT
Found at i:423890 original size:26 final size:25
Alignment explanation
Indices: 423861--423919 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
423851 AAATCATATT
*
423861 ATTATTAAATCATTAAATATCAAATC
1 ATTATTAAAT-AGTAAATATCAAATC
*
423887 ATTAGATT-AATAGTAATTATCAAATC
1 ATT--ATTAAATAGTAAATATCAAATC
423913 ATTATTA
1 ATTATTA
423920 GGTTTATTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
24 3 0.11
26 19 0.68
27 3 0.11
28 3 0.11
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.41
Consensus pattern (25 bp):
ATTATTAAATAGTAAATATCAAATC
Found at i:426832 original size:26 final size:26
Alignment explanation
Indices: 426806--426940 Score: 147
Period size: 26 Copynumber: 5.3 Consensus size: 26
426796 GATGATTTAG
*
426806 TAATGATTTGATAATAATCATTATAG
1 TAATGATTTGATAATAATCATTATAA
426832 TAATGATTTGATAATAATCATTATAA
1 TAATGATTTGATAATAATCATTATAA
426858 TAATGATTT-AGTAATAATCATTATAA
1 TAATGATTTGA-TAATAATCATTATAA
* * *
426884 AAATGATTTAATAATGAT--TTAGTAA
1 TAATGATTTGATAATAATCATTA-TAA
* * *
426909 TAATCA-TT-ATAAAAATGATT-TAA
1 TAATGATTTGATAATAATCATTATAA
426932 TAATGATTT
1 TAATGATTT
426941 AAATATTTAA
Statistics
Matches: 95, Mismatches: 8, Indels: 14
0.81 0.07 0.12
Matches are distributed among these distances:
23 14 0.15
24 7 0.07
25 10 0.11
26 63 0.66
27 1 0.01
ACGTcount: A:0.46, C:0.03, G:0.09, T:0.42
Consensus pattern (26 bp):
TAATGATTTGATAATAATCATTATAA
Found at i:426976 original size:161 final size:161
Alignment explanation
Indices: 426748--427065 Score: 627
Period size: 161 Copynumber: 2.0 Consensus size: 161
426738 ATGTATTTAT
*
426748 TAATCATTATAAAATTGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
426813 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAATAATCA
66 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAATAATCA
426878 TTATAAAAATGATTTAATAATGATTTAGTAA
131 TTATAAAAATGATTTAATAATGATTTAGTAA
426909 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
426974 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAATAATCA
66 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAATAATCA
427039 TTATAAAAATGATTTAATAATGATTTA
131 TTATAAAAATGATTTAATAATGATTTA
427066 AATATTTAAT
Statistics
Matches: 156, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
161 156 1.00
ACGTcount: A:0.44, C:0.03, G:0.10, T:0.43
Consensus pattern (161 bp):
TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAATAATCA
TTATAAAAATGATTTAATAATGATTTAGTAA
Found at i:426993 original size:26 final size:25
Alignment explanation
Indices: 426852--427175 Score: 164
Period size: 26 Copynumber: 13.1 Consensus size: 25
426842 ATAATAATCA
* *
426852 TTATAATAATGATT-TAGTAATAAT
1 TTATAATAATCATTATAGTAATGAT
* * *
426876 CATTATAAAAATGATT-TAATAATGAT
1 --TTATAATAATCATTATAGTAATGAT
**
426902 TTAGTAATAATCATTATAAAAATGA-
1 TTA-TAATAATCATTATAGTAATGAT
*
426927 TT-TAATAATGATT-TA--AAT-AT
1 TTATAATAATCATTATAGTAATGAT
* * *
426947 TTAATGATTTGATGATT-TAGTAATGAT
1 TT-AT-A-ATAATCATTATAGTAATGAT
426974 TTGATAATAATCATTATAGTAATGAT
1 TT-ATAATAATCATTATAGTAATGAT
*
427000 TTGATAATAATCATTATAATAATGAT
1 TT-ATAATAATCATTATAGTAATGAT
**
427026 TTAGTAATAATCATTATAAAAATGA-
1 TTA-TAATAATCATTATAGTAATGAT
*
427051 TT-TAATAATGATT-TA--AAT-AT
1 TTATAATAATCATTATAGTAATGAT
* * *
427071 TTAATGATTTGATGATT-TAGTAATGATT
1 TT-AT-A-ATAATCATTATAGTAATGA-T
*
427099 TTATAATAATCATTATAATAATGATT
1 TTATAATAATCATTATAGTAATGA-T
* * *
427125 TTATAATAATTATT-TAGTTATTAT
1 TTATAATAATCATTATAGTAATGAT
* *
427149 TTAGTAATTAT--TTATAATAATGAT
1 TTA-TAATAATCATTATAGTAATGAT
427173 TTA
1 TTA
427176 ATACTAATGA
Statistics
Matches: 244, Mismatches: 30, Indels: 50
0.75 0.09 0.15
Matches are distributed among these distances:
19 2 0.01
20 10 0.04
22 6 0.02
23 24 0.10
24 35 0.14
25 38 0.16
26 117 0.48
27 9 0.04
28 3 0.01
ACGTcount: A:0.44, C:0.02, G:0.09, T:0.46
Consensus pattern (25 bp):
TTATAATAATCATTATAGTAATGAT
Found at i:426994 original size:124 final size:122
Alignment explanation
Indices: 426854--427178 Score: 476
Period size: 124 Copynumber: 2.6 Consensus size: 122
426844 AATAATCATT
* * * *
426854 ATAATAATGATT-TAGTAATAATCATTATAAAAATGATTTAATAATGATTTAGTAATAATCATTA
1 ATAATAATCATTATAGTAATGAT--TTATAATAATCATTTAATAATGATTTAGTAATAATCATTA
426918 TAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATTTG
64 TAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATTTG
426977 ATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAATAATCATTA
1 ATAATAATCATTATAGTAATGATTT-ATAATAATCATT-TAATAATGATTTAGTAATAATCATTA
*
427042 TAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATTTT
64 TAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATTTG
* * * * * *
427101 ATAATAATCATTATAATAATGATTTTATAATAATTATTTAGTTATTATTTAGTAATTAT--TTAT
1 ATAATAATCATTATAGTAATGA-TTTATAATAATCATTTAATAATGATTTAGTAATAATCATTAT
*
427164 AATAATGATTTAATA
65 AAAAATGATTTAATA
427179 CTAATGATTT
Statistics
Matches: 186, Mismatches: 12, Indels: 10
0.89 0.06 0.05
Matches are distributed among these distances:
121 18 0.10
122 2 0.01
123 38 0.20
124 125 0.67
125 3 0.02
ACGTcount: A:0.44, C:0.02, G:0.09, T:0.45
Consensus pattern (122 bp):
ATAATAATCATTATAGTAATGATTTATAATAATCATTTAATAATGATTTAGTAATAATCATTATA
AAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATTTG
Found at i:427114 original size:12 final size:13
Alignment explanation
Indices: 427098--427140 Score: 52
Period size: 12 Copynumber: 3.3 Consensus size: 13
427088 TAGTAATGAT
427098 TTTATAATAATCA
1 TTTATAATAATCA
*
427111 -TTATAATAATGA
1 TTTATAATAATCA
*
427123 TTTTATAATAATTA
1 -TTTATAATAATCA
427137 TTTA
1 TTTA
427141 GTTATTATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
12 11 0.42
13 4 0.15
14 11 0.42
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (13 bp):
TTTATAATAATCA
Found at i:427163 original size:35 final size:37
Alignment explanation
Indices: 426806--427210 Score: 128
Period size: 37 Copynumber: 10.8 Consensus size: 37
426796 GATGATTTAG
* * * * *
426806 TAATGATTTGATAATAATCATTATAGTAATGATTTGATAA
1 TAATGATTTAATAATTAT--TTATAATAATTATTTAAT-A
* * *
426846 TAATCATTATAATAATGATTTAGTAATAATCATTATAA-A
1 TAATGATT-TAATAATTATTTA-TAATAATTATT-TAATA
* *
426885 -AATGATTTAATAATGATTTAGTAATAATCATTATAA-A
1 TAATGATTTAATAATTATTTA-TAATAATTATT-TAATA
* * * * *
426922 -AATGATTTAATAATGATTTA-AATATTTA-ATGATT
1 TAATGATTTAATAATTATTTATAATAATTATTTAATA
* * * *
426956 TGATGATTTAGTAATGATTTGATAATAATCA-TT-ATA
1 TAATGATTTAATAATTATTT-ATAATAATTATTTAATA
* * * *
426992 GTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
1 -TAATGATTTAATAATTAT--TTATAATAATTATTTAAT-A
* * * *
427033 TAATCATTATAAAAATGA-TT-TAATAATGATTTAAATA
1 TAATGATT-TAATAATTATTTATAATAATTATTT-AATA
* * *
427070 TTTAATGA-TT--TGATGATTTAGTAATGATT-TTATAATAA
1 --TAATGATTTAATAATTATTTA-TAATAATTATT-TAAT-A
* * * * *
427108 TCATTATAATAATGA-T-TTTATAATAATTATTTAGT-
1 TAATGAT-TTAATAATTATTTATAATAATTATTTAATA
* * *
427143 T-ATTATTTAGTAATTATTTATAATAATGATTTAATA
1 TAATGATTTAATAATTATTTATAATAATTATTTAATA
427179 CTAATGATTTAATAATTA-TTACTAATAATTAT
1 -TAATGATTTAATAATTATTTA-TAATAATTAT
427211 AGAATACTAA
Statistics
Matches: 284, Mismatches: 48, Indels: 68
0.71 0.12 0.17
Matches are distributed among these distances:
33 6 0.02
34 6 0.02
35 45 0.16
36 9 0.03
37 104 0.37
38 57 0.20
39 13 0.05
40 27 0.10
41 17 0.06
ACGTcount: A:0.44, C:0.02, G:0.09, T:0.45
Consensus pattern (37 bp):
TAATGATTTAATAATTATTTATAATAATTATTTAATA
Found at i:427185 original size:14 final size:14
Alignment explanation
Indices: 426806--427194 Score: 149
Period size: 14 Copynumber: 29.1 Consensus size: 14
426796 GATGATTTAG
*
426806 TAATGATTTGATAA
1 TAATGATTTAATAA
* *
426820 TAATCA-TT-ATAG
1 TAATGATTTAATAA
*
426832 TAATGATTTGATAA
1 TAATGATTTAATAA
*
426846 TAATCA-TT-ATAA
1 TAATGATTTAATAA
*
426858 TAATGATTTAGTAA
1 TAATGATTTAATAA
*
426872 TAATCA-TT-ATAA
1 TAATGATTTAATAA
*
426884 AAATGA-TT--TAA
1 TAATGATTTAATAA
*
426895 TAATGATTTAGTAA
1 TAATGATTTAATAA
*
426909 TAATCA-TT-ATAA
1 TAATGATTTAATAA
*
426921 AAATGA-TT--TAA
1 TAATGATTTAATAA
*
426932 TAATGATTTAAATATT
1 TAATGATTT-AATA-A
*
426948 TAATGATTTGATGATTTAG
1 TAATGATTT-A--A--TAA
*
426967 TAATGATTTGATAA
1 TAATGATTTAATAA
* *
426981 TAATCA-TT-ATAG
1 TAATGATTTAATAA
*
426993 TAATGATTTGATAA
1 TAATGATTTAATAA
*
427007 TAATCA-TT-ATAA
1 TAATGATTTAATAA
*
427019 TAATGATTTAGTAA
1 TAATGATTTAATAA
*
427033 TAATCA-TT-ATAA
1 TAATGATTTAATAA
*
427045 AAATGA-TT--TAA
1 TAATGATTTAATAA
*
427056 TAATGATTTAAATATT
1 TAATGATTT-AATA-A
*
427072 TAATGATTTGATGATTTAG
1 TAATGATTT-A--A--TAA
*
427091 TAATGATTTTATAA
1 TAATGATTTAATAA
*
427105 TAATCA-TT-ATAA
1 TAATGATTTAATAA
*
427117 TAATGATTTTATAA
1 TAATGATTTAATAA
* *
427131 TAATTATTTAGT--
1 TAATGATTTAATAA
* *
427143 T-ATTATTTAGTAA
1 TAATGATTTAATAA
427156 T--T-ATTT-ATAA
1 TAATGATTTAATAA
*
427166 TAATGATTTAATAC
1 TAATGATTTAATAA
427180 TAATGATTTAATAA
1 TAATGATTTAATAA
427194 T
1 T
427195 TATTACTAAT
Statistics
Matches: 291, Mismatches: 47, Indels: 74
0.71 0.11 0.18
Matches are distributed among these distances:
10 4 0.01
11 38 0.13
12 79 0.27
13 31 0.11
14 89 0.31
15 4 0.01
16 22 0.08
18 2 0.01
19 18 0.06
20 4 0.01
ACGTcount: A:0.44, C:0.02, G:0.09, T:0.45
Consensus pattern (14 bp):
TAATGATTTAATAA
Found at i:427189 original size:161 final size:159
Alignment explanation
Indices: 426748--427135 Score: 523
Period size: 161 Copynumber: 2.4 Consensus size: 159
426738 ATGTATTTAT
* * * *
426748 TAATCATTATAAAATTGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1 TAATCATTAT-AAA-TGATTTAATAATGATTTAAATATATAATGATATAATGATTTAGTAATAAT
426813 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAATAATCA
64 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAATAATCA
*
426878 TTATAAAAATGATTTAATAATGATTTAGTAA
129 TTATAAAAATGATTTAATAATGATTTAATAA
* * * *
426909 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1 TAATCATTAT--AAATGATTTAATAATGATTTAAATATATAATGATATAATGATTTAGTAATAAT
426974 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAATAATCA
64 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAATAATCA
*
427039 TTATAAAAATGATTTAATAATGATTTAAATATT
129 TTATAAAAATGATTTAATAATGATTT-AATA-A
* * * * *
427072 TAATGATT-T-GATGATTTAGTAATGATTTTATAATA-ATCATTATAATAATGATTTTA-TAATA
1 TAATCATTATAAATGATTTAATAATGA-TTTA-AATATATAATGAT-ATAATGA-TTTAGTAATA
427133 ATT
62 ATT
427136 ATTTAGTTAT
Statistics
Matches: 209, Mismatches: 11, Indels: 14
0.89 0.05 0.06
Matches are distributed among these distances:
159 14 0.07
160 9 0.04
161 167 0.80
162 12 0.06
163 7 0.03
ACGTcount: A:0.44, C:0.02, G:0.10, T:0.44
Consensus pattern (159 bp):
TAATCATTATAAATGATTTAATAATGATTTAAATATATAATGATATAATGATTTAGTAATAATTT
GATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAATAATCATT
ATAAAAATGATTTAATAATGATTTAATAA
Found at i:427217 original size:38 final size:38
Alignment explanation
Indices: 427147--427220 Score: 96
Period size: 38 Copynumber: 1.9 Consensus size: 38
427137 TTTAGTTATT
* **
427147 ATTTAGTAATTATTTATAATAATGATTTAATACTAATG
1 ATTTAATAATTATTTATAATAATGATAGAATACTAATG
*
427185 ATTTAATAATTA-TTACTAATAATTATAGAATACTAA
1 ATTTAATAATTATTTA-TAATAATGATAGAATACTAA
427221 CAAATGAGTG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
37 3 0.10
38 28 0.90
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (38 bp):
ATTTAATAATTATTTATAATAATGATAGAATACTAATG
Found at i:427427 original size:17 final size:17
Alignment explanation
Indices: 427402--427434 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
427392 ACTAAATATT
*
427402 TAATTATTTGATACTAG
1 TAATGATTTGATACTAG
427419 TAATGATTTGATACTA
1 TAATGATTTGATACTA
427435 AAAATCATTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.06, G:0.12, T:0.45
Consensus pattern (17 bp):
TAATGATTTGATACTAG
Found at i:428380 original size:15 final size:14
Alignment explanation
Indices: 428357--428387 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
428347 TACAACACTA
428357 AACTTTAATATAAT
1 AACTTTAATATAAT
428371 AACTTATAATATAAT
1 AACTT-TAATATAAT
428386 AA
1 AA
428388 ACTAACAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (14 bp):
AACTTTAATATAAT
Found at i:428521 original size:32 final size:34
Alignment explanation
Indices: 428441--428522 Score: 93
Period size: 34 Copynumber: 2.5 Consensus size: 34
428431 CTAAACCCTT
*
428441 AAAC-AACTAATAAAATATTCTTTTATATAACTA
1 AAACTAACTAATAAACTATTCTTTTATATAACTA
428474 AAACTAACTAATAAACTATT-TTTTCATTATAA-T-
1 AAACTAACTAATAAACTATTCTTTT-A-TATAACTA
*
428507 ATACT-ACTAATAAACT
1 AAACTAACTAATAAACT
428523 TACTAACTAA
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
32 11 0.25
33 12 0.27
34 16 0.36
35 5 0.11
ACGTcount: A:0.49, C:0.13, G:0.00, T:0.38
Consensus pattern (34 bp):
AAACTAACTAATAAACTATTCTTTTATATAACTA
Found at i:428639 original size:45 final size:45
Alignment explanation
Indices: 428562--428694 Score: 136
Period size: 45 Copynumber: 3.0 Consensus size: 45
428552 TCAACAAACA
*
428562 AATATAACTTAACTATTTAACTAACACAAACTAATTAAATAATTTTTT
1 AATATAAC-TAACTA-TTAAC-AAAACAAACTAATTAAATAATTTTTT
* *
428610 TATATAACTAACTATTAACAAAACAAACTAATT-AATTATTTTTT
1 AATATAACTAACTATTAACAAAACAAACTAATTAAATAATTTTTT
428654 AACTAT-A-TAACTA-T--C-AAACATATACTAATTAAATAATTTTT
1 AA-TATAACTAACTATTAACAAAACA-A-ACTAATTAAATAATTTTT
428695 AATTTATGTA
Statistics
Matches: 76, Mismatches: 5, Indels: 14
0.80 0.05 0.15
Matches are distributed among these distances:
39 5 0.07
40 2 0.03
41 7 0.09
42 10 0.13
43 6 0.08
44 12 0.16
45 16 0.21
46 5 0.07
47 6 0.08
48 7 0.09
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (45 bp):
AATATAACTAACTATTAACAAAACAAACTAATTAAATAATTTTTT
Found at i:428722 original size:41 final size:40
Alignment explanation
Indices: 428634--428722 Score: 90
Period size: 41 Copynumber: 2.2 Consensus size: 40
428624 TTAACAAAAC
* *
428634 AAACTAATTAATTATTTTTTAACTATATAACTATCAAACAT
1 AAACTAATTAAATAATTTTTAACTATATAACTAT-AAACAT
* * * *
428675 ATACTAATTAAATAATTTTTAATTTATGTATACTAT-AACTT
1 AAACTAATTAAATAATTTTTAA-CTATATA-ACTATAAACAT
428716 AAACTAA
1 AAACTAA
428723 CAATCATAAC
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
41 29 0.74
42 5 0.13
43 5 0.13
ACGTcount: A:0.46, C:0.10, G:0.01, T:0.43
Consensus pattern (40 bp):
AAACTAATTAAATAATTTTTAACTATATAACTATAAACAT
Found at i:428924 original size:23 final size:23
Alignment explanation
Indices: 428890--428935 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
428880 TCTTTCTCGG
428890 CTGCAATATCTTCTCCCTTTCTT
1 CTGCAATATCTTCTCCCTTTCTT
*
428913 CTGCAATCTCTTCTCCCTTTCTT
1 CTGCAATATCTTCTCCCTTTCTT
428936 TCTTTCTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.11, C:0.37, G:0.04, T:0.48
Consensus pattern (23 bp):
CTGCAATATCTTCTCCCTTTCTT
Found at i:429112 original size:27 final size:27
Alignment explanation
Indices: 429082--429137 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
429072 AATAATTCAC
429082 GGCTCAAATGGTTCACATGCATGCATT
1 GGCTCAAATGGTTCACATGCATGCATT
429109 GGCTCAAATGGTTCACATGCATGCATT
1 GGCTCAAATGGTTCACATGCATGCATT
429136 GG
1 GG
429138 GAGCTGTAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.29
Consensus pattern (27 bp):
GGCTCAAATGGTTCACATGCATGCATT
Found at i:429245 original size:29 final size:29
Alignment explanation
Indices: 429213--429292 Score: 108
Period size: 29 Copynumber: 2.8 Consensus size: 29
429203 ATGGGAATGG
429213 CGCCGGGACTACATGGTGACCTACAAGGT
1 CGCCGGGACTACATGGTGACCTACAAGGT
* *
429242 CGCCGGGACTACATGGCGACCTATAAGGT
1 CGCCGGGACTACATGGTGACCTACAAGGT
* *
429271 CGCCTAGG-CTGCATGGTGACCT
1 CGCC-GGGACTACATGGTGACCT
429293 CTCTATTGGC
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
29 43 0.96
30 2 0.04
ACGTcount: A:0.21, C:0.29, G:0.31, T:0.19
Consensus pattern (29 bp):
CGCCGGGACTACATGGTGACCTACAAGGT
Found at i:429343 original size:28 final size:28
Alignment explanation
Indices: 429311--429367 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
429301 GCTCGTACGA
* *
429311 CTCGTCTAAGCCTGCATGGCGACCTCTC
1 CTCGTATAAGACTGCATGGCGACCTCTC
429339 CTCGTATAAGACTGCATGGCGACCTCTC
1 CTCGTATAAGACTGCATGGCGACCTCTC
429367 C
1 C
429368 ATTGGCTCGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.18, C:0.37, G:0.21, T:0.25
Consensus pattern (28 bp):
CTCGTATAAGACTGCATGGCGACCTCTC
Found at i:429384 original size:9 final size:9
Alignment explanation
Indices: 429370--429409 Score: 53
Period size: 9 Copynumber: 4.2 Consensus size: 9
429360 ACCTCTCCAT
429370 TGGCTCGTA
1 TGGCTCGTA
429379 TGGCTCGTATA
1 TGGCTCG--TA
*
429390 TGGCTTGTA
1 TGGCTCGTA
429399 TGGCTCGTA
1 TGGCTCGTA
429408 TG
1 TG
429410 TCACCCCGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
9 19 0.70
11 8 0.30
ACGTcount: A:0.12, C:0.17, G:0.33, T:0.38
Consensus pattern (9 bp):
TGGCTCGTA
Found at i:429399 original size:20 final size:20
Alignment explanation
Indices: 429370--429408 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
429360 ACCTCTCCAT
429370 TGGCTCGTATGGCTCGTATA
1 TGGCTCGTATGGCTCGTATA
*
429390 TGGCTTGTATGGCTCGTAT
1 TGGCTCGTATGGCTCGTAT
429409 GTCACCCCGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.13, C:0.18, G:0.31, T:0.38
Consensus pattern (20 bp):
TGGCTCGTATGGCTCGTATA
Found at i:434809 original size:10 final size:10
Alignment explanation
Indices: 434794--434833 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
434784 GACCGTTGAC
434794 CGTTGACCGA
1 CGTTGACCGA
434804 CGTTGACC-A
1 CGTTGACCGA
434813 CAGTTGACCGA
1 C-GTTGACCGA
*
434824 CTTTGACCGA
1 CGTTGACCGA
434834 GAATTAAATG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
9 2 0.07
10 23 0.85
11 2 0.07
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.23
Consensus pattern (10 bp):
CGTTGACCGA
Found at i:434809 original size:17 final size:17
Alignment explanation
Indices: 434787--434832 Score: 56
Period size: 20 Copynumber: 2.5 Consensus size: 17
434777 AATGGTCGAC
434787 CGTTGACCGTTGACCGA
1 CGTTGACCGTTGACCGA
434804 CGTTGACCACAGTTGACCGA
1 CGTTGA-C-C-GTTGACCGA
*
434824 CTTTGACCG
1 CGTTGACCG
434833 AGAATTAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
17 7 0.28
18 2 0.08
19 2 0.08
20 14 0.56
ACGTcount: A:0.20, C:0.30, G:0.26, T:0.24
Consensus pattern (17 bp):
CGTTGACCGTTGACCGA
Found at i:437361 original size:24 final size:24
Alignment explanation
Indices: 437267--437358 Score: 132
Period size: 24 Copynumber: 3.8 Consensus size: 24
437257 TTCGATTTGA
437267 ATTCTGATCTGATACTTGACATGG
1 ATTCTGATCTGATACTTGACATGG
437291 ATTCTGATCTGATA-TCTGACATGG
1 ATTCTGATCTGATACT-TGACATGG
*
437315 ATTCTGATCTGATACTTGACCTGG
1 ATTCTGATCTGATACTTGACATGG
* * *
437339 ATTTTGATATGATACGTGAC
1 ATTCTGATCTGATACTTGAC
437359 CTGATTTATG
Statistics
Matches: 62, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
23 1 0.02
24 60 0.97
25 1 0.02
ACGTcount: A:0.25, C:0.16, G:0.21, T:0.38
Consensus pattern (24 bp):
ATTCTGATCTGATACTTGACATGG
Found at i:438733 original size:21 final size:21
Alignment explanation
Indices: 438709--438749 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
438699 CTTATGGGTT
*
438709 AAATTAAAATTTTATCTAAAG
1 AAATTAAAATTTTATATAAAG
*
438730 AAATTAATATTTTATATAAA
1 AAATTAAAATTTTATATAAA
438750 ATTTATGGGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.41
Consensus pattern (21 bp):
AAATTAAAATTTTATATAAAG
Found at i:438866 original size:32 final size:30
Alignment explanation
Indices: 438825--438890 Score: 98
Period size: 32 Copynumber: 2.1 Consensus size: 30
438815 AAAGTCTCAA
438825 TGATCAAAATGTTAGTAA-ATTAATAACATAAG
1 TGATCAAAATGTTA-TAATA-T-ATAACATAAG
438857 TGATCAAAATGTTATAATATATAACATAAG
1 TGATCAAAATGTTATAATATATAACATAAG
438887 TGAT
1 TGAT
438891 TAAGACTTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
30 14 0.42
31 4 0.12
32 15 0.45
ACGTcount: A:0.48, C:0.06, G:0.12, T:0.33
Consensus pattern (30 bp):
TGATCAAAATGTTATAATATATAACATAAG
Found at i:438883 original size:30 final size:32
Alignment explanation
Indices: 438825--438890 Score: 102
Period size: 30 Copynumber: 2.1 Consensus size: 32
438815 AAAGTCTCAA
438825 TGATCAAAATGTTAGTAAATTAATAACATAAG
1 TGATCAAAATGTTAGTAAATTAATAACATAAG
438857 TGATCAAAATGTTA-T-AA-TATATAACATAAG
1 TGATCAAAATGTTAGTAAATTA-ATAACATAAG
438887 TGAT
1 TGAT
438891 TAAGACTTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
29 2 0.06
30 16 0.48
31 1 0.03
32 14 0.42
ACGTcount: A:0.48, C:0.06, G:0.12, T:0.33
Consensus pattern (32 bp):
TGATCAAAATGTTAGTAAATTAATAACATAAG
Found at i:441776 original size:16 final size:16
Alignment explanation
Indices: 441755--441793 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
441745 TTTCAACATT
441755 TGCATGCTACTTTCGG
1 TGCATGCTACTTTCGG
441771 TGCATGCTACTTTCGG
1 TGCATGCTACTTTCGG
441787 TGCATGC
1 TGCATGC
441794 ATATTAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.13, C:0.26, G:0.26, T:0.36
Consensus pattern (16 bp):
TGCATGCTACTTTCGG
Found at i:445640 original size:370 final size:370
Alignment explanation
Indices: 444956--445695 Score: 1381
Period size: 370 Copynumber: 2.0 Consensus size: 370
444946 CTTCTACGGT
*
444956 GGTTGACGCTTCACAGCATATAACATCTCCATCATCTGAAGTGTCTGCGGTATTGCCTTGTGGAT
1 GGTTGACGCTTCACAGCATATAACATCTCCATCATCTGAAATGTCTGCGGTATTGCCTTGTGGAT
*
445021 TGGAGTTTTTATTTAGACCCCAACAATCCTTTTTCAAGTGACCATTCTTTCCAAAGTTGTAGCAC
66 TGGAGTTTTTATTTAGACCCCAACAATCCTTCTTCAAGTGACCATTCTTTCCAAAGTTGTAGCAC
445086 TTTAAATTCTTCTTGCTCCTCGACTTCGATCTACCATGTTTGTGACTGTTGCTTTGACCACGTTC
131 TTTAAATTCTTCTTGCTCCTCGACTTCGATCTACCATGTTTGTGACTGTTGCTTTGACCACGTTC
* *
445151 TGTTGATCTCCCTCTCATCGTTGTCAACGCTTCTGCTTGTTGCAGATTTACTTGTCTATCTTCCT
196 TGTTGATATCCCTCTCATCGTTGTCAACGCTTCTGCTTGTTGCAGATTTACTTGTATATCTTCCT
*
445216 TGTTCTTGCGCCGATTTTCTTCTTGGAGAACAGCAGCTGCAACATCATCGAAGACTAGAGTGGTG
261 TGTTCTTGCGCCGATTTTCTTCTTGGAGAACAGCAGCTGCAACATCAACGAAGACTAGAGTGGTG
445281 ACATTACTATTTGTCAAGTTGATGATGAGTTGATCATACGAATCA
326 ACATTACTATTTGTCAAGTTGATGATGAGTTGATCATACGAATCA
*
445326 GGTTGACGCTTCACAGCATATAACATCTCCATCATCTGAAATGTTTGCGGTATTGCCTTGTGGAT
1 GGTTGACGCTTCACAGCATATAACATCTCCATCATCTGAAATGTCTGCGGTATTGCCTTGTGGAT
445391 TGGAGTTTTTATTTAGACCCCAACAATCCTTCTTCAAGTGACCATTCTTTCCAAAGTTGTAGCAC
66 TGGAGTTTTTATTTAGACCCCAACAATCCTTCTTCAAGTGACCATTCTTTCCAAAGTTGTAGCAC
* * *
445456 TTTAAATTTTTCTTGCTCCTCGACTTCGATCTACCATGTTTGTGACTGTTGCTTTGGCCACGTTT
131 TTTAAATTCTTCTTGCTCCTCGACTTCGATCTACCATGTTTGTGACTGTTGCTTTGACCACGTTC
*
445521 TGTTGATATCCCTCTCATCGTTGTCAACGCTTCTGCTTGTTGCAGATTTACTTGTATGTCTTCCT
196 TGTTGATATCCCTCTCATCGTTGTCAACGCTTCTGCTTGTTGCAGATTTACTTGTATATCTTCCT
*
445586 TGTTCTTGCGCCGATTTTCTTCTTGGAGAACAGCAGCTGCAACGTCAACGAAGACTAGAGTGGTG
261 TGTTCTTGCGCCGATTTTCTTCTTGGAGAACAGCAGCTGCAACATCAACGAAGACTAGAGTGGTG
445651 ACATTACTATTTGTCAAGTTGATGATGAGTTGATCATACGAATCA
326 ACATTACTATTTGTCAAGTTGATGATGAGTTGATCATACGAATCA
445696 TGTAGACTTT
Statistics
Matches: 359, Mismatches: 11, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
370 359 1.00
ACGTcount: A:0.21, C:0.22, G:0.19, T:0.37
Consensus pattern (370 bp):
GGTTGACGCTTCACAGCATATAACATCTCCATCATCTGAAATGTCTGCGGTATTGCCTTGTGGAT
TGGAGTTTTTATTTAGACCCCAACAATCCTTCTTCAAGTGACCATTCTTTCCAAAGTTGTAGCAC
TTTAAATTCTTCTTGCTCCTCGACTTCGATCTACCATGTTTGTGACTGTTGCTTTGACCACGTTC
TGTTGATATCCCTCTCATCGTTGTCAACGCTTCTGCTTGTTGCAGATTTACTTGTATATCTTCCT
TGTTCTTGCGCCGATTTTCTTCTTGGAGAACAGCAGCTGCAACATCAACGAAGACTAGAGTGGTG
ACATTACTATTTGTCAAGTTGATGATGAGTTGATCATACGAATCA
Found at i:452157 original size:17 final size:17
Alignment explanation
Indices: 452135--452174 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
452125 ACACCCTCTC
452135 ACATTTGTGAAGAAGAT
1 ACATTTGTGAAGAAGAT
452152 ACATTTGTGAAGAAGAT
1 ACATTTGTGAAGAAGAT
*
452169 AAATTT
1 ACATTT
452175 CTACCCAGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.42, C:0.05, G:0.20, T:0.33
Consensus pattern (17 bp):
ACATTTGTGAAGAAGAT
Found at i:453867 original size:2 final size:2
Alignment explanation
Indices: 453860--453900 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
453850 GCAACTTACA
453860 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
453901 GTTTCATTCA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:454268 original size:18 final size:19
Alignment explanation
Indices: 454245--454284 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
454235 AGTATTATAT
454245 AAATATATATAT-TTTTAA
1 AAATATATATATATTTTAA
* *
454263 AAATATTTATTTATTTTAA
1 AAATATATATATATTTTAA
454282 AAA
1 AAA
454285 ATTATGCATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
AAATATATATATATTTTAA
Found at i:455340 original size:12 final size:12
Alignment explanation
Indices: 455323--455347 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
455313 ACAAAGCACC
455323 ATTTGGTGCCTA
1 ATTTGGTGCCTA
455335 ATTTGGTGCCTA
1 ATTTGGTGCCTA
455347 A
1 A
455348 ATTATTTGAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.20, C:0.16, G:0.24, T:0.40
Consensus pattern (12 bp):
ATTTGGTGCCTA
Found at i:459961 original size:12 final size:12
Alignment explanation
Indices: 459944--459968 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
459934 ACAAAGCACC
459944 ATTTGGTGCCTA
1 ATTTGGTGCCTA
459956 ATTTGGTGCCTA
1 ATTTGGTGCCTA
459968 A
1 A
459969 ATTATTTGAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.20, C:0.16, G:0.24, T:0.40
Consensus pattern (12 bp):
ATTTGGTGCCTA
Found at i:465325 original size:2 final size:2
Alignment explanation
Indices: 465318--465347 Score: 51
Period size: 2 Copynumber: 14.5 Consensus size: 2
465308 ATGAAAAATG
465318 TA TA TA TA TA TA TA TA TA TA TA TCA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T-A TA TA T
465348 GGTTAGAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 25 0.93
3 2 0.07
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:474978 original size:188 final size:185
Alignment explanation
Indices: 474632--475024 Score: 637
Period size: 188 Copynumber: 2.1 Consensus size: 185
474622 TTTTCTAATT
* * *
474632 TATATAA-AAATTAAATATTTTTTAATTAAAAAAACAGTTTATAATTAATTTAAATAATATATAA
1 TATATAATATATTTAATATTTTTTAATTAAAAAAACAGTTTACAATTAATTTAAATAATATATAA
*
474696 TTATAAAATAAAAATTTTATATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTAT
66 TTATAAAATAAAAATTTTATATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAATTAT
* * *
474761 TGGATCTTAAATTATTAATTAGGTTTTAAATGGTTTTGGCTGAGCTCATATGTTA
131 TGGATCTTAAATTATTAATTAGGTTTTAAATGGTTTGGGCTGAACACATATGTTA
474816 TATATAATATATTTAATATTTTTTAATTCAAAAAAAAACAGTTTACAATTAATTTAAATAATATA
1 TATATAATATATTTAATATTTTTTAATT---AAAAAAACAGTTTACAATTAATTTAAATAATATA
* *
474881 TAATTATAAAATATAAATTTTATATAAATTTTTTAATTAATTAATATTTATTTAGGTTTAAAAAT
63 TAATTATAAAATAAAAATTTTATATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAAT
*
474946 TATTGGATCTTAAATTATTAATT-GGATTTTAAATGGTTTGGGTTGAACACATATGTTA
128 TATTGGATCTTAAATTATTAATTAGG-TTTTAAATGGTTTGGGCTGAACACATATGTTA
*
475004 TATATAATATATTTAAAATTT
1 TATATAATATATTTAATATTT
475025 AATTTCGGTT
Statistics
Matches: 193, Mismatches: 11, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
184 7 0.04
185 18 0.09
187 2 0.01
188 166 0.86
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.46
Consensus pattern (185 bp):
TATATAATATATTTAATATTTTTTAATTAAAAAAACAGTTTACAATTAATTTAAATAATATATAA
TTATAAAATAAAAATTTTATATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAATTAT
TGGATCTTAAATTATTAATTAGGTTTTAAATGGTTTGGGCTGAACACATATGTTA
Found at i:480793 original size:62 final size:62
Alignment explanation
Indices: 480717--480842 Score: 252
Period size: 62 Copynumber: 2.0 Consensus size: 62
480707 CAAAACAAAT
480717 CCTAATCTTTCAGTTGAATGCAGCTAACTTTTAGCCTTGAAAAAGTGGATGGTCTAGTTATC
1 CCTAATCTTTCAGTTGAATGCAGCTAACTTTTAGCCTTGAAAAAGTGGATGGTCTAGTTATC
480779 CCTAATCTTTCAGTTGAATGCAGCTAACTTTTAGCCTTGAAAAAGTGGATGGTCTAGTTATC
1 CCTAATCTTTCAGTTGAATGCAGCTAACTTTTAGCCTTGAAAAAGTGGATGGTCTAGTTATC
480841 CC
1 CC
480843 AAAGGAAATG
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 64 1.00
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (62 bp):
CCTAATCTTTCAGTTGAATGCAGCTAACTTTTAGCCTTGAAAAAGTGGATGGTCTAGTTATC
Found at i:482413 original size:2 final size:2
Alignment explanation
Indices: 482406--482435 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
482396 AAAATGTGCA
482406 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
482436 GATTGATTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.