Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015266.1 Kokia drynarioides strain JFW-HI SEQ_130311, 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: 514914
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 275 characters in sequence are not A, C, G, or T
File 2 of 3
Found at i:269225 original size:22 final size:22
Alignment explanation
Indices: 269199--269240 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
269189 TTAATATACT
269199 ATTTGGTA-TATGAGTTTTTTCA
1 ATTTGGTACT-TGAGTTTTTTCA
269221 ATTTGGTACTTGAGTTTTTT
1 ATTTGGTACTTGAGTTTTTT
269241 TTTTCCATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 18 0.95
23 1 0.05
ACGTcount: A:0.19, C:0.05, G:0.19, T:0.57
Consensus pattern (22 bp):
ATTTGGTACTTGAGTTTTTTCA
Found at i:274894 original size:110 final size:110
Alignment explanation
Indices: 274700--274919 Score: 395
Period size: 110 Copynumber: 2.0 Consensus size: 110
274690 ATAACAGAAT
* * * *
274700 ACACTACCTTTGCATGACACTCAGTCAATAGATGGGAGAGACATGCACCTCGGTGGTTCGATGTT
1 ACACTACCTCTACATGACACTCAGTCAATAGATGGGAGAGACATGCACCTCAGTGGCTCGATGTT
*
274765 CAATGTTGGGAATACTTATTGGGGAATGGCATCAACTTCCAGTGG
66 CAATGTTGGGAATAATTATTGGGGAATGGCATCAACTTCCAGTGG
274810 ACACTACCTCTACATGACACTCAGTCAATAGATGGGAGAGACATGCACCTCAGTGGCTCGATGTT
1 ACACTACCTCTACATGACACTCAGTCAATAGATGGGAGAGACATGCACCTCAGTGGCTCGATGTT
274875 CAATGTTGGGAATAATTATTGGGGAATGGCATCAACTTCCAGTGG
66 CAATGTTGGGAATAATTATTGGGGAATGGCATCAACTTCCAGTGG
274920 TTGACAGTCG
Statistics
Matches: 105, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
110 105 1.00
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.26
Consensus pattern (110 bp):
ACACTACCTCTACATGACACTCAGTCAATAGATGGGAGAGACATGCACCTCAGTGGCTCGATGTT
CAATGTTGGGAATAATTATTGGGGAATGGCATCAACTTCCAGTGG
Found at i:277578 original size:58 final size:59
Alignment explanation
Indices: 277456--277598 Score: 243
Period size: 58 Copynumber: 2.4 Consensus size: 59
277446 TATGAAGATC
* * *
277456 ATGTGTACAAAAATATTCAAAAGAACTTTTATTTTATTAAATGATATAATATAAAAATA
1 ATGTGTACAAAAATATTCAAAAGAACTTCTATTTTATTAAAAGATACAATATAAAAATA
277515 ATGTGTACAAAAATATTCAAAAGAACTTCTA-TTTATTAAAAGATACAATATAAAAATA
1 ATGTGTACAAAAATATTCAAAAGAACTTCTATTTTATTAAAAGATACAATATAAAAATA
*
277573 ATGTGTACAAAAATAGTCAAAAGAAC
1 ATGTGTACAAAAATATTCAAAAGAAC
277599 ATCAATGCAT
Statistics
Matches: 80, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
58 50 0.62
59 30 0.38
ACGTcount: A:0.52, C:0.08, G:0.08, T:0.31
Consensus pattern (59 bp):
ATGTGTACAAAAATATTCAAAAGAACTTCTATTTTATTAAAAGATACAATATAAAAATA
Found at i:277722 original size:33 final size:33
Alignment explanation
Indices: 277670--277732 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
277660 ATTCCTTCCT
* *
277670 GGTTCAGCTTCTGACCAAGGTTGTTGTTGTTCG
1 GGTTCAGCTTCCGACCAAGGTTGTGGTTGTTCG
* *
277703 GGTTTAGCTTCCGAGCAAGGTTGTGGTTGT
1 GGTTCAGCTTCCGACCAAGGTTGTGGTTGT
277733 GGTTATGGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.13, C:0.16, G:0.33, T:0.38
Consensus pattern (33 bp):
GGTTCAGCTTCCGACCAAGGTTGTGGTTGTTCG
Found at i:279869 original size:15 final size:17
Alignment explanation
Indices: 279849--279880 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
279839 GACTATATAG
279849 CCGTT-GGAAAA-ATGA
1 CCGTTGGGAAAACATGA
279864 CCGTTGGGAAAACATGA
1 CCGTTGGGAAAACATGA
279881 GGTAAAGTGC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.33
16 6 0.40
17 4 0.27
ACGTcount: A:0.38, C:0.16, G:0.28, T:0.19
Consensus pattern (17 bp):
CCGTTGGGAAAACATGA
Found at i:281812 original size:15 final size:16
Alignment explanation
Indices: 281770--281804 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
281760 GTATTTTTTA
281770 ATTTAATATTAAAGTG
1 ATTTAATATTAAAGTG
281786 ATTTAATATTAAAGTG
1 ATTTAATATTAAAGTG
281802 ATT
1 ATT
281805 AAGTTTAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.46
Consensus pattern (16 bp):
ATTTAATATTAAAGTG
Found at i:282697 original size:38 final size:38
Alignment explanation
Indices: 282655--282761 Score: 126
Period size: 38 Copynumber: 2.8 Consensus size: 38
282645 CCACCCTATT
* *
282655 GAATACATGTTGGA-CATGTTTACTGTTAGTGATGGATG
1 GAATACATGTT-GACCATGTTTACTGCTAGTGATGAATG
* * *
282693 GAATACATGATGACCATGTTTGCTGCTAGTGATGAATT
1 GAATACATGTTGACCATGTTTACTGCTAGTGATGAATG
* * *
282731 GAATACATGTTAAGCATGTTTACTACTAGTG
1 GAATACATGTTGACCATGTTTACTGCTAGTG
282762 TTGTTTTGTT
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
37 2 0.03
38 56 0.97
ACGTcount: A:0.29, C:0.11, G:0.24, T:0.36
Consensus pattern (38 bp):
GAATACATGTTGACCATGTTTACTGCTAGTGATGAATG
Found at i:284898 original size:19 final size:19
Alignment explanation
Indices: 284874--284924 Score: 70
Period size: 18 Copynumber: 2.8 Consensus size: 19
284864 AAAAATATTC
*
284874 ATTTTTTATATTTTTAACA
1 ATTTTTTATATTTTTAAAA
284893 A-TTTTTA-ATTTTTAAAA
1 ATTTTTTATATTTTTAAAA
*
284910 ATATTTTATATTTTT
1 ATTTTTTATATTTTT
284925 TGAATTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 10 0.36
18 11 0.39
19 7 0.25
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (19 bp):
ATTTTTTATATTTTTAAAA
Found at i:284903 original size:17 final size:18
Alignment explanation
Indices: 284876--284924 Score: 73
Period size: 17 Copynumber: 2.7 Consensus size: 18
284866 AAATATTCAT
*
284876 TTTTTATATTTTTAACAA
1 TTTTTATATTTTTAAAAA
284894 TTTTTA-ATTTTTAAAAA
1 TTTTTATATTTTTAAAAA
284911 TATTTTATATTTTT
1 T-TTTTATATTTTT
284925 TGAATTTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 11 0.39
18 11 0.39
19 6 0.21
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTTTATATTTTTAAAAA
Found at i:284934 original size:18 final size:18
Alignment explanation
Indices: 284874--284934 Score: 54
Period size: 18 Copynumber: 3.4 Consensus size: 18
284864 AAAAATATTC
284874 ATTTTTTATA-TTTTTAA
1 ATTTTTTATATTTTTTAA
* *
284891 CAATTTTTA-ATTTTTAAAA
1 -ATTTTTTATATTTTT-TAA
* *
284910 ATATTTTATATTTTTTGA
1 ATTTTTTATATTTTTTAA
284928 ATTTTTT
1 ATTTTTT
284935 TTAAATTTTA
Statistics
Matches: 33, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
17 1 0.03
18 24 0.73
19 8 0.24
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (18 bp):
ATTTTTTATATTTTTTAA
Found at i:299741 original size:17 final size:17
Alignment explanation
Indices: 299709--299803 Score: 91
Period size: 17 Copynumber: 5.5 Consensus size: 17
299699 AAAAATTTAG
* * *
299709 ATTTTAATTTTTAATTC
1 ATTTTAAATTTAAATTT
*
299726 ATTTTAAGTTTAAATTT
1 ATTTTAAATTTAAATTT
* **
299743 ATTGTAAATTTAAGCTT
1 ATTTTAAATTTAAATTT
** *
299760 ATTTGGAGTTTAAATTT
1 ATTTTAAATTTAAATTT
299777 ATTTTAAATTTAAATTT
1 ATTTTAAATTTAAATTT
299794 ATTTTGAAAT
1 ATTTT-AAAT
299804 AAAATTTTAA
Statistics
Matches: 61, Mismatches: 16, Indels: 1
0.78 0.21 0.01
Matches are distributed among these distances:
17 57 0.93
18 4 0.07
ACGTcount: A:0.35, C:0.02, G:0.07, T:0.56
Consensus pattern (17 bp):
ATTTTAAATTTAAATTT
Found at i:299796 original size:34 final size:34
Alignment explanation
Indices: 299709--299797 Score: 106
Period size: 34 Copynumber: 2.6 Consensus size: 34
299699 AAAAATTTAG
* * * *
299709 ATTTTAATTTTTAATTCATTTTAAGTTTAAATTT
1 ATTTTAAATTTAAATTTATTTGAAGTTTAAATTT
* ** *
299743 ATTGTAAATTTAAGCTTATTTGGAGTTTAAATTT
1 ATTTTAAATTTAAATTTATTTGAAGTTTAAATTT
299777 ATTTTAAATTTAAATTTATTT
1 ATTTTAAATTTAAATTTATTT
299798 TGAAATAAAA
Statistics
Matches: 44, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
34 44 1.00
ACGTcount: A:0.34, C:0.02, G:0.07, T:0.57
Consensus pattern (34 bp):
ATTTTAAATTTAAATTTATTTGAAGTTTAAATTT
Found at i:301689 original size:29 final size:29
Alignment explanation
Indices: 301649--301957 Score: 145
Period size: 29 Copynumber: 10.5 Consensus size: 29
301639 AATTTTCCAA
* *
301649 AAAATTACATTTTT-ACCACCGAACTTTCT
1 AAAATTACATTTTTAACC-CCAAACTTTCC
* *
301678 AAAATT-CTATTTTTAACCCTAAAATTTCC
1 AAAATTAC-ATTTTTAACCCCAAACTTTCC
* * * * *
301707 AAAATTCCTTTTTTAACCCTAAATTTTCTA
1 AAAATTACATTTTTAACCCCAAACTTTC-C
*
301737 AAAATTACATTTTT-ACCCTCGAACTTTCC
1 AAAATTACATTTTTAACCC-CAAACTTTCC
* * * *
301766 AAAATTCCATTTTTTTTACCCAAAATTTTCC
1 AAAATTACA--TTTTTAACCCCAAACTTTCC
301797 AAAAATTACA--TTT-ACCCCTAAACTTTCC
1 -AAAATTACATTTTTAACCCC-AAACTTTCC
* * *
301825 AAAATTACCA-TTTTACCCCCAAA-TGTCTA
1 AAAATTA-CATTTTTAACCCCAAACTTTC-C
* * * *
301854 AAAATTCCATTTTTTACCCCAAACCTTCAA
1 AAAATTACATTTTTAACCCCAAACTTTC-C
* * *
301884 AAAATTACCA-TTTT-ACCCCTGAA-TGTCTA
1 AAAATTA-CATTTTTAACCCC-AAACTTTC-C
* * * *
301913 AAAATTCCATTTTTAACCTCGAACCTTTCG
1 AAAATTACATTTTTAACC-CCAAACTTTCC
*
301943 AAAATTACAATTTTA
1 AAAATTACATTTTTA
301958 TTCCCGAGGC
Statistics
Matches: 216, Mismatches: 42, Indels: 43
0.72 0.14 0.14
Matches are distributed among these distances:
27 11 0.05
28 21 0.10
29 96 0.44
30 58 0.27
31 18 0.08
32 12 0.06
ACGTcount: A:0.36, C:0.24, G:0.02, T:0.38
Consensus pattern (29 bp):
AAAATTACATTTTTAACCCCAAACTTTCC
Found at i:301770 original size:59 final size:58
Alignment explanation
Indices: 301673--301957 Score: 219
Period size: 59 Copynumber: 4.9 Consensus size: 58
301663 ACCACCGAAC
* *
301673 TTTCT-AAAATT-CTATTTTTAACCCT-AAAATTTCCAAAATT-CCTTTTTTAACCCTAAA
1 TTTCTAAAAATTAC-ATTTTT-ACCCTCAAACTTTCCAAAATTACC-ATTTTAACCCTAAA
* * *
301730 TTTTCTAAAAATTACATTTTTACCCTCGAACTTTCCAAAATT-CCATTTTTTTTACCCAAAA
1 -TTTCTAAAAATTACATTTTTACCCTCAAACTTTCCAAAATTACCA---TTTTAACCCTAAA
* * *
301791 TTTTCCAAAAATTACA--TTTACCC-CTAAACTTTCCAAAATTACCATTTTACCCCCAAA
1 -TTTCTAAAAATTACATTTTTACCCTC-AAACTTTCCAAAATTACCATTTTAACCCTAAA
* * * * * *
301848 TGTCTAAAAATTCCATTTTTTACCC-CAAACCTTCAAAAAATTACCATTTTACCCCTGAA
1 TTTCTAAAAATTACA-TTTTTACCCTCAAACTTTC-CAAAATTACCATTTTAACCCTAAA
* * * * * *
301907 TGTCTAAAAATTCCATTTTTAACCTCGAACCTTTCGAAAATTACAATTTTA
1 TTTCTAAAAATTACATTTTTACCCTC-AAACTTTCCAAAATTACCATTTTA
301958 TTCCCGAGGC
Statistics
Matches: 191, Mismatches: 22, Indels: 27
0.80 0.09 0.11
Matches are distributed among these distances:
56 12 0.06
57 10 0.05
58 26 0.14
59 107 0.56
60 10 0.05
61 26 0.14
ACGTcount: A:0.35, C:0.24, G:0.02, T:0.39
Consensus pattern (58 bp):
TTTCTAAAAATTACATTTTTACCCTCAAACTTTCCAAAATTACCATTTTAACCCTAAA
Found at i:301770 original size:88 final size:89
Alignment explanation
Indices: 301605--301779 Score: 246
Period size: 88 Copynumber: 2.0 Consensus size: 89
301595 CCTTGAAGGT
* * * *
301605 CCCTAAACTTCCCAAAATTCCATTTTTGACCTTGAATTTTCCAAAAAATTACATTTTTACCACCG
1 CCCTAAAATTCCCAAAATTCCATTTTTAACCCTAAATTTTCCAAAAAATTACATTTTTACCACCG
* *
301670 AACTTTCTAAAATTCTATTTTTAA
66 AACTTTCCAAAATTCCATTTTTAA
* * *
301694 CCCTAAAATTTCCAAAATTCCTTTTTTAACCCTAAATTTT-CTAAAAATTACATTTTTACC-CTC
1 CCCTAAAATTCCCAAAATTCCATTTTTAACCCTAAATTTTCCAAAAAATTACATTTTTACCAC-C
301757 GAACTTTCCAAAATTCCATTTTT
65 GAACTTTCCAAAATTCCATTTTT
301780 TTTACCCAAA
Statistics
Matches: 76, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
87 1 0.01
88 41 0.54
89 34 0.45
ACGTcount: A:0.33, C:0.24, G:0.02, T:0.41
Consensus pattern (89 bp):
CCCTAAAATTCCCAAAATTCCATTTTTAACCCTAAATTTTCCAAAAAATTACATTTTTACCACCG
AACTTTCCAAAATTCCATTTTTAA
Found at i:301829 original size:88 final size:85
Alignment explanation
Indices: 301648--301948 Score: 252
Period size: 88 Copynumber: 3.4 Consensus size: 85
301638 GAATTTTCCA
* * *
301648 AAAAATTACATTTTTACCACCGAACTTTCTAAAATTCTA-TTTTTAACCCTAAAATTTCC-AAAA
1 AAAAATTACATTTTTACC-CCGAACTTTCAAAAATTCCATTTTTTTACCC-AAAATTTCCAAAAA
* * *
301711 TTCCTTTTTTAACCCTAAATTTTCT
64 TTAC--ATTTACCCCTAAA-TTTCT
*
301736 AAAAATTACATTTTTACCCTCGAACTTTCCAAAATTCCATTTTTTTTACCCAAAATTTTCCAAAA
1 AAAAATTACATTTTTACCC-CGAACTTTCAAAAATTCCA-TTTTTTTACCCAAAA-TTTCCAAAA
301801 ATTACATTTACCCCTAAACTTTC-
63 ATTACATTTACCCCTAAA-TTTCT
* * * * ** *
301824 CAAAATTACCA-TTTTACCCCCAAATGTCTAAAAATTCCA-TTTTTTACCCCAAACCTTCAAAAA
1 AAAAATTA-CATTTTTACCCCGAACTTTC-AAAAATTCCATTTTTTTA-CCCAAAATTTCCAAAA
* *
301887 ATTACCATTTTACCCCTGAATGTCT
63 ATTA-CA-TTTACCCCTAAATTTCT
* * *
301912 AAAAATTCCATTTTTAACCTCGAACCTTTCGAAAATT
1 AAAAATTACATTTTT-ACCCCGAA-CTTTCAAAAATT
301949 ACAATTTTAT
Statistics
Matches: 175, Mismatches: 24, Indels: 27
0.77 0.11 0.12
Matches are distributed among these distances:
86 18 0.10
87 20 0.11
88 80 0.46
89 33 0.19
90 17 0.10
91 7 0.04
ACGTcount: A:0.36, C:0.25, G:0.02, T:0.38
Consensus pattern (85 bp):
AAAAATTACATTTTTACCCCGAACTTTCAAAAATTCCATTTTTTTACCCAAAATTTCCAAAAATT
ACATTTACCCCTAAATTTCT
Found at i:301978 original size:29 final size:28
Alignment explanation
Indices: 301943--302013 Score: 72
Period size: 28 Copynumber: 2.5 Consensus size: 28
301933 GAACCTTTCG
*
301943 AAAATTACAATTTTATTCC-CGAGGCATCC
1 AAAATTACAATTTTA-CCCTCG-GGCATCC
**
301972 AAAATTACCGTTTTACCCTCGGGCATCC
1 AAAATTACAATTTTACCCTCGGGCATCC
* *
302000 AAAATCACATTTTT
1 AAAATTACAATTTT
302014 GACTCCGTTT
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
28 20 0.57
29 15 0.43
ACGTcount: A:0.32, C:0.25, G:0.10, T:0.32
Consensus pattern (28 bp):
AAAATTACAATTTTACCCTCGGGCATCC
Found at i:308878 original size:21 final size:21
Alignment explanation
Indices: 308830--308874 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
308820 TACATGAAAC
*
308830 ATCATGTCAATACTGTTAACG
1 ATCACGTCAATACTGTTAACG
308851 ATCACGTCAATACTG-TAACG
1 ATCACGTCAATACTGTTAACG
308871 ATCA
1 ATCA
308875 ACGTTAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 9 0.39
21 14 0.61
ACGTcount: A:0.36, C:0.22, G:0.13, T:0.29
Consensus pattern (21 bp):
ATCACGTCAATACTGTTAACG
Found at i:309868 original size:12 final size:13
Alignment explanation
Indices: 309851--309883 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
309841 TCACGATGTG
309851 TGTAAAAAATT-A
1 TGTAAAAAATTGA
309863 TGTAAAAAATTGA
1 TGTAAAAAATTGA
*
309876 TTTAAAAA
1 TGTAAAAA
309884 TTAAATGTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.58, C:0.00, G:0.09, T:0.33
Consensus pattern (13 bp):
TGTAAAAAATTGA
Found at i:311019 original size:18 final size:18
Alignment explanation
Indices: 310996--311032 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
310986 AATATACATC
310996 TTTTGAGAACTTGAAATT
1 TTTTGAGAACTTGAAATT
311014 TTTTGAGAACTTGAAATT
1 TTTTGAGAACTTGAAATT
311032 T
1 T
311033 CATATTGAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.05, G:0.16, T:0.46
Consensus pattern (18 bp):
TTTTGAGAACTTGAAATT
Found at i:311548 original size:29 final size:30
Alignment explanation
Indices: 311515--311582 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 30
311505 GATAAAATGC
*
311515 AATTTTTGGATAC-CCGGGGGTAAAACGGT
1 AATTTTTGGACACTCCGGGGGTAAAACGGT
*** *
311544 AA-TTTTGGACACTTTTGGGGTAAAATGGT
1 AATTTTTGGACACTCCGGGGGTAAAACGGT
311573 AATTTTTGGA
1 AATTTTTGGA
311583 GGTTCGGGGT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
28 9 0.28
29 16 0.50
30 7 0.22
ACGTcount: A:0.28, C:0.09, G:0.28, T:0.35
Consensus pattern (30 bp):
AATTTTTGGACACTCCGGGGGTAAAACGGT
Found at i:311596 original size:29 final size:28
Alignment explanation
Indices: 311531--312102 Score: 269
Period size: 29 Copynumber: 19.4 Consensus size: 28
311521 TGGATACCCG
* *
311531 GGGGTAAAACGGTAA-TTTTGGACACTTTT
1 GGGGTAAAATGGTAATTTTTGGA-A-GTTT
* *
311560 GGGGTAAAATGGTAATTTTTGGAGGTTC
1 GGGGTAAAATGGTAATTTTTGGAAGTTT
311588 GGGGTTAAAAAT-G-AATTTTTTGGAAGTTTT
1 GGGG-T-AAAATGGTAA-TTTTTGGAAG-TTT
* *
311618 AGGGT-AAATGGTAATTTTTGAAAAGTTT
1 GGGGTAAAATGGTAATTTTTG-GAAGTTT
* * * *
311646 GGGATCAAAAAT-GAAATTTTTGGAAATTC
1 GGGGT--AAAATGGTAATTTTTGGAAGTTT
* *
311675 GAGGGTAAAATGGCAATTTTTGGAAAATTT
1 G-GGGTAAAATGGTAATTTTTGG-AAGTTT
* * *
311705 GGGGTTAAAAATTG-AATTTATGGAAATTT
1 GGGG-T-AAAATGGTAATTTTTGGAAGTTT
* *
311734 AGGGTAAAATGATAATTTTT-GAAGTTT
1 GGGGTAAAATGGTAATTTTTGGAAGTTT
311761 GGGGTTAAAAAT-G-AAGTTTTTGGAAGTTT
1 GGGG-T-AAAATGGTAA-TTTTTGGAAGTTT
311790 GGGGGTAAAATGGTAATTTTTGGAAAGTTT
1 -GGGGTAAAATGGTAATTTTTGG-AAGTTT
* *
311820 GGGGTCAAATGG-AATTTTTGGAAGTTC
1 GGGGTAAAATGGTAATTTTTGGAAGTTT
*
311847 GAGGGTAAAATGGTAATTTTTGGGAAATTTT
1 G-GGGTAAAATGGTAATTTTT-GG-AAGTTT
* *** * *
311878 AGAAATTTAGGGGTAAAATGGTATTTTTTAGAAGTTT
1 -G------GGGTAAAA--TGGTAATTTTTGGAAGTTT
* * *
311915 GGGGTCAAAAATGG-AGTTTTTAGAAATTT
1 GGGGT--AAAATGGTAATTTTTGGAAGTTT
**
311944 AGGGGT--AATGGTTTTTTTTGGAAAGTTT
1 -GGGGTAAAATGGTAATTTTTGG-AAGTTT
* *
311972 AGGGTCAAAAAAGG-AATTTTTGGAAGTTT
1 GGGGT--AAAATGGTAATTTTTGGAAGTTT
** *
312001 GAGGGTAAAATTTTAATTTTTGGAAGTTCGA
1 G-GGGTAAAATGGTAATTTTTGGAAGTT--T
312032 GGGAGTAAAAAT-GTAATGTTTAT-GAAGTTT
1 GGG-GT-AAAATGGTAAT-TTT-TGGAAGTTT
312062 GGGGGTCAAAAT-GTAATTTTTGGAAAGTTT
1 -GGGGT-AAAATGGTAATTTTTGG-AAGTTT
*
312092 GAGGTTAAAAT
1 G-GGGTAAAAT
312103 ATGATTTATG
Statistics
Matches: 423, Mismatches: 62, Indels: 116
0.70 0.10 0.19
Matches are distributed among these distances:
26 5 0.01
27 36 0.09
28 73 0.17
29 140 0.33
30 102 0.24
31 28 0.07
32 17 0.04
33 1 0.00
36 1 0.00
37 9 0.02
38 1 0.00
39 10 0.02
ACGTcount: A:0.33, C:0.02, G:0.28, T:0.37
Consensus pattern (28 bp):
GGGGTAAAATGGTAATTTTTGGAAGTTT
Found at i:311606 original size:57 final size:56
Alignment explanation
Indices: 311546--311869 Score: 332
Period size: 57 Copynumber: 5.6 Consensus size: 56
311536 AAAACGGTAA
* *
311546 TTTTGGACACTTTTGGGGTAAAATGGTAATTTTTGGAGGTTCGGGGTTAAAAATGAATT
1 TTTTGGA-A-TTTTGGGGTAAAATGGTAATTTTTGGAAGTTTGGGGTTAAAAATGAA-T
* * * *
311605 TTTTGGAAGTTTTAGGGT-AAATGGTAATTTTTGAAAAGTTTGGGATCAAAAATGAAAT
1 TTTTGGAA-TTTTGGGGTAAAATGGTAATTTTTG-GAAGTTTGGGGTTAAAAATG-AAT
* * * *
311663 TTTTGGAAATTCGAGGGTAAAATGGCAATTTTTGGAAAATTTGGGGTTAAAAATTGAAT
1 TTTTGGAATTTTG-GGGTAAAATGGTAATTTTTGG-AAGTTTGGGGTTAAAAA-TGAAT
* * * *
311722 TTATGGAAATTTAGGGTAAAATGATAATTTTT-GAAGTTTGGGGTTAAAAATGAAGT
1 TTTTGGAATTTTGGGGTAAAATGGTAATTTTTGGAAGTTTGGGGTTAAAAATGAA-T
* *
311778 TTTTGGAAGTTTGGGGGTAAAATGGTAATTTTTGGAAAGTTTGGGG-T-CAAATGGAAT
1 TTTTGGAA-TTTTGGGGTAAAATGGTAATTTTTGG-AAGTTTGGGGTTAAAAAT-GAAT
* *
311835 TTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGG
1 TTTTGGAATTTTG-GGGTAAAATGGTAATTTTTGG
311870 GAAATTTTAG
Statistics
Matches: 224, Mismatches: 29, Indels: 26
0.80 0.10 0.09
Matches are distributed among these distances:
55 4 0.02
56 27 0.12
57 72 0.32
58 59 0.26
59 60 0.27
60 2 0.01
ACGTcount: A:0.32, C:0.02, G:0.28, T:0.38
Consensus pattern (56 bp):
TTTTGGAATTTTGGGGTAAAATGGTAATTTTTGGAAGTTTGGGGTTAAAAATGAAT
Found at i:311949 original size:154 final size:151
Alignment explanation
Indices: 311727--312023 Score: 416
Period size: 154 Copynumber: 1.9 Consensus size: 151
311717 TGAATTTATG
* * * *
311727 GAAATTTAGGGTAAAATGATAATTTTTGAAGTTTGGGGTTAAAAATGAAGTTTTTGGAAGTTTGG
1 GAAATTTAGGGTAAAATGATAATTTTTGAAGTTTGGGGTCAAAAATGAAGTTTTTAGAAATTTAG
* *
311792 GGGTAAAATGGTAATTTTTGGAAAGTTTGGGGTC-AAATGGAATTTTTGGAAGTTCGAGGGTAAA
66 GGGT--AATGGTAATTTTTGGAAAGTTTAGGGTCAAAAAGGAATTTTTGGAAGTTCGAGGGTAAA
311856 ATGGTAATTTTTGGGAAATTTTA
129 ATGGTAATTTTTGGGAAATTTTA
* * *
311879 GAAATTTAGGGGTAAAATGGTATTTTTTAGAAGTTTGGGGTCAAAAATGGAGTTTTTAGAAATTT
1 GAAATTTA-GGGTAAAATGATAATTTTT-GAAGTTTGGGGTCAAAAATGAAGTTTTTAGAAATTT
** *
311944 AGGGGTAATGGTTTTTTTTGGAAAGTTTAGGGTCAAAAAAGGAATTTTTGGAAGTTTGAGGGTAA
64 AGGGGTAATGGTAATTTTTGGAAAGTTTAGGGTC-AAAAAGGAATTTTTGGAAGTTCGAGGGTAA
**
312009 AATTTTAATTTTTGG
128 AATGGTAATTTTTGG
312024 AAGTTCGAGG
Statistics
Matches: 127, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
152 33 0.26
153 17 0.13
154 77 0.61
ACGTcount: A:0.32, C:0.01, G:0.28, T:0.38
Consensus pattern (151 bp):
GAAATTTAGGGTAAAATGATAATTTTTGAAGTTTGGGGTCAAAAATGAAGTTTTTAGAAATTTAG
GGGTAATGGTAATTTTTGGAAAGTTTAGGGTCAAAAAGGAATTTTTGGAAGTTCGAGGGTAAAAT
GGTAATTTTTGGGAAATTTTA
Found at i:311981 original size:57 final size:57
Alignment explanation
Indices: 311869--312009 Score: 169
Period size: 57 Copynumber: 2.5 Consensus size: 57
311859 GTAATTTTTG
* * *
311869 GGAAATTTTAGAAATTTAGGGGTAAAATGGTATTTTTTAGAAGTTTGGGGTCAAAAAT
1 GGAATTTTTAGAAATTTAGGGGT-AAATGGTATTTTTTAGAAGTTTAGGGTCAAAAAA
* * *
311927 GGAGTTTTTAGAAATTTAGGGGT-AATGGTTTTTTTTGGAAAGTTTAGGGTCAAAAAA
1 GGAATTTTTAGAAATTTAGGGGTAAATGGTATTTTTTAG-AAGTTTAGGGTCAAAAAA
* *
311984 GGAATTTTTGGAAGTTT-GAGGGTAAA
1 GGAATTTTTAGAAATTTAG-GGGTAAA
312010 ATTTTAATTT
Statistics
Matches: 71, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
56 14 0.20
57 34 0.48
58 23 0.32
ACGTcount: A:0.33, C:0.01, G:0.28, T:0.37
Consensus pattern (57 bp):
GGAATTTTTAGAAATTTAGGGGTAAATGGTATTTTTTAGAAGTTTAGGGTCAAAAAA
Found at i:312090 original size:30 final size:29
Alignment explanation
Indices: 311958--312095 Score: 129
Period size: 30 Copynumber: 4.6 Consensus size: 29
311948 GTAATGGTTT
* *
311958 TTTTTGGAAAGTTT-AGGGTCAAAAAAGGAA
1 TTTTTGG-AAGTTTGAGGGTC-AAAATGTAA
*
311988 TTTTTGGAAGTTTGAGGGT-AAAATTTTAA
1 TTTTTGGAAGTTTGAGGGTCAAAA-TGTAA
* *
312017 TTTTTGGAAGTTCGAGGGAGTAAAAATGTAA
1 TTTTTGGAAGTTTGA-GG-GTCAAAATGTAA
*
312048 TGTTTAT-GAAGTTTGGGGGTCAAAATGTAA
1 T-TTT-TGGAAGTTTGAGGGTCAAAATGTAA
312078 TTTTTGGAAAGTTTGAGG
1 TTTTTGG-AAGTTTGAGG
312096 TTAAAATATG
Statistics
Matches: 90, Mismatches: 9, Indels: 18
0.77 0.08 0.15
Matches are distributed among these distances:
28 5 0.06
29 26 0.29
30 35 0.39
31 9 0.10
32 14 0.16
33 1 0.01
ACGTcount: A:0.33, C:0.02, G:0.28, T:0.37
Consensus pattern (29 bp):
TTTTTGGAAGTTTGAGGGTCAAAATGTAA
Found at i:313225 original size:3 final size:3
Alignment explanation
Indices: 313217--313272 Score: 71
Period size: 3 Copynumber: 18.7 Consensus size: 3
313207 TCGTTTTCTT
*
313217 TTA TTA TTA TTA TTA TTA TTA TTA TTGA -TG TTA -TA TTTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA -TTA TTA TTA
313262 TTA TTA TTA TT
1 TTA TTA TTA TT
313273 TATTGATACT
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
2 2 0.04
3 42 0.89
4 3 0.06
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:314059 original size:26 final size:26
Alignment explanation
Indices: 314020--314070 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
314010 ATTTAAAAAT
* *
314020 AAATTTAAACTTAAATTAAATTTAAC
1 AAATTTAAACTTAAAATAAACTTAAC
*
314046 AAATTTAAATTTAAAATAAACTTAA
1 AAATTTAAACTTAAAATAAACTTAA
314071 TCTCAAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (26 bp):
AAATTTAAACTTAAAATAAACTTAAC
Found at i:314083 original size:43 final size:44
Alignment explanation
Indices: 314006--314093 Score: 124
Period size: 43 Copynumber: 2.0 Consensus size: 44
313996 TAGAGGAAGA
* * * *
314006 TTAAATTTAAAAATAAATTTAAACTTAAATTAAATTTAACAAAT
1 TTAAATTTAAAAATAAACTTAAACTCAAAATAAATTTAAAAAAT
*
314050 TTAAATTT-AAAATAAACTTAATCTCAAAATAAATTTAAAAAAT
1 TTAAATTTAAAAATAAACTTAAACTCAAAATAAATTTAAAAAAT
314093 T
1 T
314094 GGGTTTAGTT
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
43 31 0.79
44 8 0.21
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.38
Consensus pattern (44 bp):
TTAAATTTAAAAATAAACTTAAACTCAAAATAAATTTAAAAAAT
Found at i:315269 original size:183 final size:184
Alignment explanation
Indices: 314961--315502 Score: 900
Period size: 183 Copynumber: 3.0 Consensus size: 184
314951 ATAAGTCCTT
* * *
314961 GTACTATTCATATATTTGGAATTTAGTAAATTTATTTATATTTTTAAGGAATTTAG-TCTTTTAT
1 GTACTATTCATAAATTTGGAATTTAGTCAATTTACTTATATTTTTAAGGAATTTAGTTCTTTTA-
*
315025 CTTTTCATATTTCAAAATTTAGATCTAACTTTTATCACTGTTAAATTTATTTTATTAAATCGGAT
65 CTTTTCATATTTCAAAATTTAGATCCAACTTTTATCACTGTTAAATTTATTTTATTAAATCGGAT
315090 CCAATACAATACCAATTTTAATTACATATCTATTACGTGAGTATTTTTTTC-CCA
130 CCAATACAATACCAATTTTAATTACATATCTATTACGTGAGTATTTTTTTCTCCA
315144 GTACTATTCATAAATTTGGAATTTAGTCAATTTACTTATATTTTTAAGGAATTTAGTTCTTTTAC
1 GTACTATTCATAAATTTGGAATTTAGTCAATTTACTTATATTTTTAAGGAATTTAGTTCTTTTAC
* *
315209 TTTTTATATTTCAAAATTTAGATCCAATTTTTATCACTGTTAAATTTATTTTATTAAATCGGATC
66 TTTTCATATTTCAAAATTTAGATCCAACTTTTATCACTGTTAAATTTATTTTATTAAATCGGATC
* * * * *
315274 CAATACAATACCAATTTTAATTACATATATATTATGTGACTA-TATTTTCTCCT
131 CAATACAATACCAATTTTAATTACATATCTATTACGTGAGTATTTTTTTCTCCA
*
315327 GTACTATTCATAAATTTGGAATTTAGTCAATTTACTTATATTTTTAAGGAACTTAGTTCTTTTAC
1 GTACTATTCATAAATTTGGAATTTAGTCAATTTACTTATATTTTTAAGGAATTTAGTTCTTTTAC
*
315392 TTTTCATATTTCAAAATTTAGATCCAACTTGTATCACTGTTAAATTTATTTTATTAAATCGGATT
66 TTTTCATATTTCAAAATTTAGATCCAACTTTTATCACTGTTAAATTTATTTTATTAAATCGGA-T
315457 CC-ATAC-A-A-CAATTTTAATTACATATCTATTACGTGAGTATTTTTTT
130 CCAATACAATACCAATTTTAATTACATATCTATTACGTGAGTATTTTTTT
315503 ATTTCAAAAT
Statistics
Matches: 336, Mismatches: 19, Indels: 10
0.92 0.05 0.03
Matches are distributed among these distances:
180 28 0.08
181 6 0.02
182 7 0.02
183 285 0.85
184 10 0.03
ACGTcount: A:0.32, C:0.12, G:0.08, T:0.48
Consensus pattern (184 bp):
GTACTATTCATAAATTTGGAATTTAGTCAATTTACTTATATTTTTAAGGAATTTAGTTCTTTTAC
TTTTCATATTTCAAAATTTAGATCCAACTTTTATCACTGTTAAATTTATTTTATTAAATCGGATC
CAATACAATACCAATTTTAATTACATATCTATTACGTGAGTATTTTTTTCTCCA
Found at i:315540 original size:14 final size:15
Alignment explanation
Indices: 315521--315549 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
315511 ATGTCAAATC
315521 AATAAA-TTTAACAA
1 AATAAATTTTAACAA
315535 AATAAATTTTAACAA
1 AATAAATTTTAACAA
315550 TTAGACCTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.31
Consensus pattern (15 bp):
AATAAATTTTAACAA
Found at i:316713 original size:29 final size:29
Alignment explanation
Indices: 316693--316749 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
316683 AAAAAATTTA
*
316693 AAAAAATTGACAGCATAAAAATAAAAAAT
1 AAAAAATTGAAAGCATAAAAATAAAAAAT
316722 AAAAAATTGAAAGCA-AAGAAATAAAAAA
1 AAAAAATTGAAAGCATAA-AAATAAAAAA
316750 CGATTAAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 2 0.08
29 24 0.92
ACGTcount: A:0.72, C:0.05, G:0.09, T:0.14
Consensus pattern (29 bp):
AAAAAATTGAAAGCATAAAAATAAAAAAT
Found at i:318601 original size:33 final size:33
Alignment explanation
Indices: 318562--318632 Score: 81
Period size: 33 Copynumber: 2.2 Consensus size: 33
318552 AAATAGCAAC
* *
318562 AAAAATAACAATAAAAACAAC-ACCAAAATAGTA
1 AAAAATAAC-ATAAAAACAACAACCAAAACAATA
* * *
318595 AAAAATAGCTTCAAAACAACAACCAAAACAATA
1 AAAAATAACATAAAAACAACAACCAAAACAATA
318628 AAAAA
1 AAAAA
318633 AGCACCCAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
32 9 0.28
33 23 0.72
ACGTcount: A:0.69, C:0.17, G:0.03, T:0.11
Consensus pattern (33 bp):
AAAAATAACATAAAAACAACAACCAAAACAATA
Found at i:318632 original size:22 final size:20
Alignment explanation
Indices: 318616--318714 Score: 99
Period size: 22 Copynumber: 4.7 Consensus size: 20
318606 CAAAACAACA
*
318616 ACCAAAACAATAAAAAAAGC
1 ACCAAAACAATAAAAAAAAC
*
318636 ACCCAAACAATAAAAACATAAC
1 ACCAAAACAATAAAAA-A-AAC
* *
318658 ACCAAAACAACAAAAAATAGC
1 ACCAAAACAATAAAAAA-AAC
*
318679 AACCAAAACAGTAAAAAAATAGC
1 -ACCAAAACAATAAAAAAA-A-C
318702 ACCAAAACAATAA
1 ACCAAAACAATAA
318715 TATAATTTTT
Statistics
Matches: 65, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
20 15 0.23
21 6 0.09
22 43 0.66
23 1 0.02
ACGTcount: A:0.67, C:0.22, G:0.04, T:0.07
Consensus pattern (20 bp):
ACCAAAACAATAAAAAAAAC
Found at i:318644 original size:32 final size:32
Alignment explanation
Indices: 318575--318645 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 32
318565 AATAACAATA
* * **
318575 AAAACAACACCAAAATAGTAAAAAATAGCTTC
1 AAAACAACACCAAAACAATAAAAAATAGCACC
318607 AAAACAACAACCAAAACAATAAAAAA-AGCACC
1 AAAACAAC-ACCAAAACAATAAAAAATAGCACC
*
318639 CAAACAA
1 AAAACAA
318646 TAAAAACATA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
32 18 0.55
33 15 0.45
ACGTcount: A:0.65, C:0.23, G:0.04, T:0.08
Consensus pattern (32 bp):
AAAACAACACCAAAACAATAAAAAATAGCACC
Found at i:318650 original size:53 final size:54
Alignment explanation
Indices: 318568--318670 Score: 129
Period size: 53 Copynumber: 1.9 Consensus size: 54
318558 CAACAAAAAT
* * * **
318568 AACAATAAAAACAACACCAAAATAGTAAAAA-ATAGCTTCAAAACAACAACCAA
1 AACAATAAAAACAACACCAAAACAATAAAAACATAACACCAAAACAACAACCAA
*
318621 AACAATAAAAA-AAGCACCCAAACAATAAAAACATAACACCAAAACAACAA
1 AACAATAAAAACAA-CACCAAAACAATAAAAACATAACACCAAAACAACAA
318671 AAAATAGCAA
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
52 2 0.05
53 25 0.60
54 15 0.36
ACGTcount: A:0.66, C:0.22, G:0.03, T:0.09
Consensus pattern (54 bp):
AACAATAAAAACAACACCAAAACAATAAAAACATAACACCAAAACAACAACCAA
Found at i:318705 original size:44 final size:42
Alignment explanation
Indices: 318607--318711 Score: 129
Period size: 44 Copynumber: 2.4 Consensus size: 42
318597 AAATAGCTTC
* * *
318607 AAAACAACAACCAAAACAATAAAAAAAGCACCCAAACAATAAA
1 AAAATAAC-ACCAAAACAACAAAAAAAGCACCAAAACAATAAA
* *
318650 AACATAACACCAAAACAACAAAAAATAGCAACCAAAACAGTAAA
1 AAAATAACACCAAAACAACAAAAAA-AGC-ACCAAAACAATAAA
*
318694 AAAATAGCACCAAAACAA
1 AAAATAACACCAAAACAA
318712 TAATATAATT
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
42 16 0.30
43 9 0.17
44 28 0.53
ACGTcount: A:0.68, C:0.23, G:0.04, T:0.06
Consensus pattern (42 bp):
AAAATAACACCAAAACAACAAAAAAAGCACCAAAACAATAAA
Found at i:323249 original size:103 final size:103
Alignment explanation
Indices: 323127--323351 Score: 281
Period size: 103 Copynumber: 2.2 Consensus size: 103
323117 ACAAAATGAT
* * *
323127 ATTGCCTCGATTTTAAAATAGGATATTCGATTA-TTTAGATCCAAAGAAAAATCATACCCAGTAC
1 ATTGCCTCGATTTTAAAATAGAATATTCAATTACTTT-GATCCAAAAAAAAATCATACCCAGTAC
* * * * * *
323191 GTTTGAGCATAATTTTTCGAGTTTCCTAAATAAAGAAAC
65 ATTTGAACACAATTTATCGAATTCCCTAAATAAAGAAAC
* * * * * *
323230 ATTGCTTCGTTTTTCAAATAGAATATTCAATTACTTTGGTTCAAAAAAAAATTATACCCAGTACA
1 ATTGCCTCGATTTTAAAATAGAATATTCAATTACTTTGATCCAAAAAAAAATCATACCCAGTACA
323295 TTTGAACACAATTTATCGAATTCCCTAAATAAAGAAAC
66 TTTGAACACAATTTATCGAATTCCCTAAATAAAGAAAC
* *
323333 ATTACCTCGATTTTGAAAT
1 ATTGCCTCGATTTTAAAAT
323352 TTTTAATTCT
Statistics
Matches: 102, Mismatches: 19, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
103 99 0.97
104 3 0.03
ACGTcount: A:0.39, C:0.16, G:0.11, T:0.34
Consensus pattern (103 bp):
ATTGCCTCGATTTTAAAATAGAATATTCAATTACTTTGATCCAAAAAAAAATCATACCCAGTACA
TTTGAACACAATTTATCGAATTCCCTAAATAAAGAAAC
Found at i:324793 original size:34 final size:34
Alignment explanation
Indices: 324751--324822 Score: 126
Period size: 34 Copynumber: 2.1 Consensus size: 34
324741 TTATTTTTAC
324751 ATATATATAAAATAAAATCAAGATCTATATATAT
1 ATATATATAAAATAAAATCAAGATCTATATATAT
* *
324785 ATATATATATAATAAAATCAAGATCTATGTATAT
1 ATATATATAAAATAAAATCAAGATCTATATATAT
324819 ATAT
1 ATAT
324823 GTATGTGTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.53, C:0.06, G:0.04, T:0.38
Consensus pattern (34 bp):
ATATATATAAAATAAAATCAAGATCTATATATAT
Found at i:324947 original size:14 final size:14
Alignment explanation
Indices: 324928--324968 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
324918 AAGATGTATC
324928 TATGTATGTATATG
1 TATGTATGTATATG
*
324942 TATGTATGTACATG
1 TATGTATGTATATG
* *
324956 TATATTTGTATAT
1 TATGTATGTATAT
324969 ATTCGTATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.29, C:0.02, G:0.17, T:0.51
Consensus pattern (14 bp):
TATGTATGTATATG
Found at i:325646 original size:17 final size:16
Alignment explanation
Indices: 325624--325669 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
325614 TTCATATGTA
325624 TAATAAATATATAAAAT
1 TAATAAATAT-TAAAAT
*
325641 TAATAATTATTAAAAT
1 TAATAAATATTAAAAT
325657 CT-ATAAA-ATTAAA
1 -TAATAAATATTAAA
325670 CCTTAATGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
15 6 0.23
16 10 0.38
17 10 0.38
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (16 bp):
TAATAAATATTAAAAT
Found at i:325656 original size:16 final size:17
Alignment explanation
Indices: 325624--325656 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
325614 TTCATATGTA
325624 TAATAAATATATAAAAT
1 TAATAAATATATAAAAT
*
325641 TAATAATTAT-TAAAAT
1 TAATAAATATATAAAAT
325657 CTATAAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
TAATAAATATATAAAAT
Found at i:326800 original size:27 final size:27
Alignment explanation
Indices: 326757--326820 Score: 83
Period size: 27 Copynumber: 2.4 Consensus size: 27
326747 ATCCAAAGAT
* *
326757 TACCAAAAAGGCGTCCTTTACAAGGAA
1 TACCACAAAGACGTCCTTTACAAGGAA
* *
326784 TGCCACAAAGACGTCCTTTATAAGGAA
1 TACCACAAAGACGTCCTTTACAAGGAA
*
326811 TACCATAAAG
1 TACCACAAAG
326821 GTTTTCCTTA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.41, C:0.22, G:0.17, T:0.20
Consensus pattern (27 bp):
TACCACAAAGACGTCCTTTACAAGGAA
Found at i:328803 original size:7 final size:6
Alignment explanation
Indices: 328776--328840 Score: 71
Period size: 6 Copynumber: 11.0 Consensus size: 6
328766 TTGAATTTAT
** *
328776 TTTAAA TTTAAA TTT-GT TTTACAA TTTAAA TTT-AA TTTAAG TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTA-AA TTTAAA TTTAAA TTTAAA TTTAAA
*
328823 TTTATA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA
328841 ATTATTCTAA
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
5 8 0.17
6 36 0.75
7 4 0.08
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:328803 original size:18 final size:17
Alignment explanation
Indices: 328748--328856 Score: 130
Period size: 17 Copynumber: 6.3 Consensus size: 17
328738 CTAAACCCAT
328748 TTTAAATTTATTTTAAGA
1 TTTAAATTTATTTTAA-A
*
328766 -TTGAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
328782 TTTAAATTTGTTTTACAA
1 TTTAAATTTATTTTA-AA
* *
328800 TTTAAATTTAATTTAAG
1 TTTAAATTTATTTTAAA
328817 TTTAAATTTATATTTAAA
1 TTTAAATTTAT-TTTAAA
* *
328835 TTTAAAATTATTCTAAA
1 TTTAAATTTATTTTAAA
328852 TTTAA
1 TTTAA
328857 GTAAATAATA
Statistics
Matches: 78, Mismatches: 10, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
16 1 0.01
17 47 0.60
18 30 0.38
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:328815 original size:35 final size:34
Alignment explanation
Indices: 328748--328856 Score: 123
Period size: 35 Copynumber: 3.1 Consensus size: 34
328738 CTAAACCCAT
* *
328748 TTTAAATTTATTTTAAGA-TTGAATTTATTTTAAA
1 TTTAAATTTATTTTAA-ATTTAAATTTAATTTAAA
* *
328782 TTTAAATTTGTTTTACAATTTAAATTTAATTTAAG
1 TTTAAATTTATTTTA-AATTTAAATTTAATTTAAA
*
328817 TTTAAATTTATATTTAAATTTAAAATT-ATTCTAAA
1 TTTAAATTTAT-TTTAAATTTAAATTTAATT-TAAA
328852 TTTAA
1 TTTAA
328857 GTAAATAATA
Statistics
Matches: 64, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
34 18 0.28
35 42 0.66
36 4 0.06
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (34 bp):
TTTAAATTTATTTTAAATTTAAATTTAATTTAAA
Found at i:328838 original size:24 final size:26
Alignment explanation
Indices: 328776--328839 Score: 84
Period size: 24 Copynumber: 2.7 Consensus size: 26
328766 TTGAATTTAT
328776 TTTAAATTTAAATTT--GTTTTACAA
1 TTTAAATTTAAATTTAAGTTTTACAA
328800 TTTAAATTT-AATTTAAG-TTTA-AA
1 TTTAAATTTAAATTTAAGTTTTACAA
*
328823 TTTATATTTAAATTTAA
1 TTTAAATTTAAATTTAA
328840 AATTATTCTA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
23 15 0.42
24 20 0.56
25 1 0.03
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.55
Consensus pattern (26 bp):
TTTAAATTTAAATTTAAGTTTTACAA
Found at i:329629 original size:30 final size:30
Alignment explanation
Indices: 329584--329656 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 30
329574 TGTAATAAAT
* * *
329584 ATATGTATTAAATGATTTTAATAACATTAATA
1 ATATATATT-AATGATATTAATAAC-CTAATA
329616 ATA-ATATTAATGATATTAATAACCTAATA
1 ATATATATTAATGATATTAATAACCTAATA
*
329645 ATATTTATTAAT
1 ATATATATTAAT
329657 AAAAAGAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
29 8 0.22
30 21 0.58
31 4 0.11
32 3 0.08
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (30 bp):
ATATATATTAATGATATTAATAACCTAATA
Found at i:330924 original size:30 final size:28
Alignment explanation
Indices: 330814--331113 Score: 167
Period size: 30 Copynumber: 10.1 Consensus size: 28
330804 CCTAAGAGGT
* *
330814 CCCTAAACTGTCCAAAAATTATATTTTGAG
1 CCCTAAACT-TCCAAAAATTACATTTT-AA
** * *
330844 CCCCGAACATTCTAAAAATTACATTTTTA
1 CCCTAAAC-TTCCAAAAATTACATTTTAA
** * * *
330873 CCACTAATTTTTTCTAGAAATTGCATTTTAA
1 CC-CTAA--ACTTCCAAAAATTACATTTTAA
**
330904 CCCTCAAACTTCACAAAAATTACATTTTTGC
1 CCCT-AAACTTC-CAAAAATTACA-TTTTAA
*
330935 CCCTAAACTTCCAAAAATTACATTTTTGA
1 CCCTAAACTTCCAAAAATTACA-TTTTAA
* * *
330964 CCATAAACTTTCTAAAAA-TACCATTTTAC
1 CCCTAAAC-TTCCAAAAATTA-CATTTTAA
*
330993 CCCTAAACTTTCAAAAATTACATATTTAA
1 CCCTAAACTTCCAAAAATTACAT-TTTAA
* * *
331022 CCCTAAATTTTCAAAAAATTATATTTTTAA
1 CCCTAAA-CTTCCAAAAATTACA-TTTTAA
* * *
331052 -CCTCAAATTTTTCAAAAATTATATTTTAA
1 CCCT-AAA-CTTCCAAAAATTACATTTTAA
*
331081 CCCTTGAA-TATCCAAAAATTACCATTTT-A
1 CCC-TAAACT-TCCAAAAATTA-CATTTTAA
331110 CCCT
1 CCCT
331114 CGTGCATAAA
Statistics
Matches: 214, Mismatches: 38, Indels: 38
0.74 0.13 0.13
Matches are distributed among these distances:
28 12 0.06
29 78 0.36
30 92 0.43
31 32 0.15
ACGTcount: A:0.38, C:0.22, G:0.03, T:0.37
Consensus pattern (28 bp):
CCCTAAACTTCCAAAAATTACATTTTAA
Found at i:331109 original size:59 final size:60
Alignment explanation
Indices: 330890--331114 Score: 164
Period size: 59 Copynumber: 3.8 Consensus size: 60
330880 TTTTTTCTAG
* * ** * *
330890 AAATTGCAT-TTTAACCCTCAAACT-TCACAAAAATTA-CATTTTTGCCCCTAAACTTCCAA
1 AAATTACATATTTAACCCT-AAATTATCA-AAAAATTACCATTTTAACCTCTAAACTTTCAA
* * * * *
330949 AAATTACATTTTTGACCATAAACTT-TCTAAAAA-TACCATTTT-ACCCCTAAACTTTCAA
1 AAATTACATATTTAACCCTAAA-TTATCAAAAAATTACCATTTTAACCTCTAAACTTTCAA
* * *
331007 AAATTACATATTTAACCCTAAATTTTCAAAAAATTA-TATTTTTAACCTC-AAATTTTTCAA
1 AAATTACATATTTAACCCTAAATTATCAAAAAATTACCA-TTTTAACCTCTAAA-CTTTCAA
* * * *
331067 AAATTATAT-TTTAACCCTTGAA-TATCCAAAAATTACCATTTTACCCTC
1 AAATTACATATTTAACCC-TAAATTATCAAAAAATTACCATTTTAACCTC
331115 GTGCATAAAA
Statistics
Matches: 136, Mismatches: 20, Indels: 20
0.77 0.11 0.11
Matches are distributed among these distances:
57 2 0.01
58 43 0.32
59 59 0.43
60 32 0.24
ACGTcount: A:0.40, C:0.22, G:0.02, T:0.37
Consensus pattern (60 bp):
AAATTACATATTTAACCCTAAATTATCAAAAAATTACCATTTTAACCTCTAAACTTTCAA
Found at i:343443 original size:209 final size:205
Alignment explanation
Indices: 343064--343629 Score: 713
Period size: 207 Copynumber: 2.7 Consensus size: 205
343054 AGTGACACGA
* * * * * * *
343064 TCATCTTCTTGATGAGATACTGAGAAG-GGAACCAACTCAATGGAATAAAACTCAATGCTAGCGA
1 TCATCTTCCTGATGAGATACTGAGAAGAAG-ACCAAATCAAT-GAATCAAGCTCAAAG-TAGCAA
* * * *
343128 AACTTCGAATCCCAGATTCCTGATGAGATACTGAGAAGCAGGTCAAAGCAATATAATGGTTAGCT
63 AACTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCT
* * *
343193 TCTTGATGAGATACTGAGAAGTTGACCATATTCATCTTCCTGATGAGATACAGAGAAGCGGATTG
128 TCCTGATGAGATACTGAGAAGTTGACCAAATTCACCTTCCTGATGAGAT--AGAGAAGCGGATTG
343258 AAACAAGTGATGCAG
191 AAACAAGTGATGCAG
*
343273 TCATCTTCCTGATGAGATATTGAGAAGAAGACCAAATCAATGAAGTCAAGCTCAAAGTGAGCAAA
1 TCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAATGAA-TCAAGCTCAAAGT-AGCAAA
* *
343338 ACTTCGAACCCCAGCTTCCTGATAAGATACTGAGAAGCAGGACGAAGCAATAAAATGGTTAGCTT
64 ACTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTT
** * *
343403 CCTGATGAGATACTGAGAAG-TGAACCAAATTTGCCTTCCTGATGAGATATAGAAGTGGATTGAA
129 CCTGATGAGATACTGAGAAGTTG-ACCAAATTCACCTTCCTGATGAGATAGAGAAGCGGATTGAA
*
343467 ACAAGTGATGCGG
193 ACAAGTGATGCAG
* * *
343480 TCATCTTCCTGATGAGACACTGAGAAGAAGGCCAAATCAATGAAACTAAGCTCAAAGTAAGCAAA
1 TCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAATGAATC-AAGCTCAAAGT-AGCAAA
* * * * * ** * *
343545 TCTTCAAACCCAAGCTTCTTGATGAGATACTGAGAAACAGGTCGAAGCAATAAAGCGATTACCTT
64 ACTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTT
*
343610 CCTGATGAGATACAGAGAAG
129 CCTGATGAGATACTGAGAAG
343630 CGGATTGAAA
Statistics
Matches: 313, Mismatches: 39, Indels: 12
0.86 0.11 0.03
Matches are distributed among these distances:
206 1 0.00
207 157 0.50
208 6 0.02
209 148 0.47
210 1 0.00
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.23
Consensus pattern (205 bp):
TCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAATGAATCAAGCTCAAAGTAGCAAAAC
TTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCC
TGATGAGATACTGAGAAGTTGACCAAATTCACCTTCCTGATGAGATAGAGAAGCGGATTGAAACA
AGTGATGCAG
Found at i:343619 original size:48 final size:49
Alignment explanation
Indices: 343559--343677 Score: 125
Period size: 49 Copynumber: 2.4 Consensus size: 49
343549 CAAACCCAAG
* *
343559 CTTCTTGATGAGATACTGAGAAACAGG-TCGAAGCAA-TAAAGCGATTAC
1 CTTCCTGATGAGATACTGAGAAAC-GGATCGAAACAAGTAAAGCGATTAC
* * * * * * * *
343607 CTTCCTGATGAGATACAGAGAAGCGGATTGAAATAAGTGATGCGGTTAT
1 CTTCCTGATGAGATACTGAGAAACGGATCGAAACAAGTAAAGCGATTAC
343656 CTTCCTGATGAGATACTGAGAA
1 CTTCCTGATGAGATACTGAGAA
343678 GTAGACCAAA
Statistics
Matches: 58, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
47 2 0.03
48 27 0.47
49 29 0.50
ACGTcount: A:0.34, C:0.15, G:0.25, T:0.25
Consensus pattern (49 bp):
CTTCCTGATGAGATACTGAGAAACGGATCGAAACAAGTAAAGCGATTAC
Found at i:344021 original size:17 final size:16
Alignment explanation
Indices: 343996--344118 Score: 102
Period size: 18 Copynumber: 7.1 Consensus size: 16
343986 TAAACCCATT
343996 TTAAATTTATTTTAAGA
1 TTAAATTTATTTTAA-A
* *
344013 TTGAATTTATTTTTAAT
1 TTAAATTTA-TTTTAAA
344030 TTAAATTTACTTTTAAA
1 TTAAATTTA-TTTTAAA
*
344047 TTTAAATTTGTTTTAAAA
1 -TTAAATTTATTTT-AAA
* *
344065 TTTAAATTTAATTTAAGT
1 -TTAAATTTATTTTAA-A
344083 TTAAATTTATATTTAAA
1 TTAAATTTAT-TTTAAA
* *
344100 TTTAAAATTATTCTAAA
1 -TTAAATTTATTTTAAA
344117 TT
1 TT
344119 TAAGTAAATA
Statistics
Matches: 87, Mismatches: 13, Indels: 13
0.77 0.12 0.12
Matches are distributed among these distances:
16 2 0.02
17 42 0.48
18 43 0.49
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.55
Consensus pattern (16 bp):
TTAAATTTATTTTAAA
Found at i:344036 original size:6 final size:6
Alignment explanation
Indices: 344027--344105 Score: 81
Period size: 6 Copynumber: 13.3 Consensus size: 6
344017 ATTTATTTTT
** **
344027 AATTTA AATTTA CTTTTA AATTTA AATTT- GTTTTAA AATTTA AATTT-
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTT-A AATTTA AATTTA
* *
344074 AATTTA AGTTTA AATTTA TATTTA AATTTA AA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AA
344106 ATTATTCTAA
Statistics
Matches: 58, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
5 8 0.14
6 47 0.81
7 3 0.05
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (6 bp):
AATTTA
Found at i:344043 original size:18 final size:17
Alignment explanation
Indices: 343995--344121 Score: 148
Period size: 17 Copynumber: 7.3 Consensus size: 17
343985 CTAAACCCAT
343995 TTTAAATTTATTTTAAGA
1 TTTAAATTTATTTTAA-A
* *
344013 -TTGAATTTATTTTTAA
1 TTTAAATTTATTTTAAA
344029 TTTAAATTTACTTTTAAA
1 TTTAAATTTA-TTTTAAA
*
344047 TTTAAATTTGTTTTAAAA
1 TTTAAATTTATTTT-AAA
* *
344065 TTTAAATTTAATTTAAG
1 TTTAAATTTATTTTAAA
344082 TTTAAATTTATATTTAAA
1 TTTAAATTTAT-TTTAAA
* *
344100 TTTAAAATTATTCTAAA
1 TTTAAATTTATTTTAAA
344117 TTTAA
1 TTTAA
344122 GTAAATAATA
Statistics
Matches: 93, Mismatches: 12, Indels: 9
0.82 0.11 0.08
Matches are distributed among these distances:
16 1 0.01
17 47 0.51
18 45 0.48
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.55
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:344877 original size:30 final size:30
Alignment explanation
Indices: 344832--344904 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 30
344822 TGTAATAAAT
* * *
344832 ATATGTATTAAATGATTTTAATAACATTAATA
1 ATATATATT-AATGATATTAATAAC-CTAATA
344864 ATA-ATATTAATGATATTAATAACCTAATA
1 ATATATATTAATGATATTAATAACCTAATA
*
344893 ATATTTATTAAT
1 ATATATATTAAT
344905 AAAAAGAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
29 8 0.22
30 21 0.58
31 4 0.11
32 3 0.08
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (30 bp):
ATATATATTAATGATATTAATAACCTAATA
Found at i:346133 original size:29 final size:29
Alignment explanation
Indices: 346063--346298 Score: 205
Period size: 29 Copynumber: 8.1 Consensus size: 29
346053 CCCAAGAGGT
* * **
346063 CCCTAAACTATCCAAAAAATTGTATTTTTA
1 CCCTAAAATTTCC-AAAAATTACATTTTTA
*
346093 CCCTAAACTTTCC-AAAATTACATTTTTA
1 CCCTAAAATTTCCAAAAATTACATTTTTA
* * *
346121 CCCTTTAATTTTCCAAAAATTACATTTTGA
1 CCC-TAAAATTTCCAAAAATTACATTTTTA
**
346151 CCCCT-AAATTTCCAAAAATTACATTTTGC
1 -CCCTAAAATTTCCAAAAATTACATTTTTA
*
346180 CCCT-AAACTTCCAAAAATTACATTTTTGA
1 CCCTAAAATTTCCAAAAATTACATTTTT-A
* * *
346209 -CCTCAAATTTTCTAAAAATCACATTTTTA
1 CCCT-AAAATTTCCAAAAATTACATTTTTA
* *
346238 TCCTAAAACTTCCAAAAATTACA-TTTTA
1 CCCTAAAATTTCCAAAAATTACATTTTTA
* **
346266 CCCTAAATTTTTTTAAAAA-TACATTTTTA
1 CCCTAAA-ATTTCCAAAAATTACATTTTTA
346295 CCCT
1 CCCT
346299 CGAACATCCA
Statistics
Matches: 173, Mismatches: 24, Indels: 19
0.80 0.11 0.09
Matches are distributed among these distances:
28 59 0.34
29 62 0.36
30 49 0.28
31 3 0.02
ACGTcount: A:0.37, C:0.22, G:0.02, T:0.39
Consensus pattern (29 bp):
CCCTAAAATTTCCAAAAATTACATTTTTA
Found at i:346184 original size:87 final size:86
Alignment explanation
Indices: 346088--346299 Score: 250
Period size: 87 Copynumber: 2.4 Consensus size: 86
346078 AAAATTGTAT
** *
346088 TTTTACCCTAAACTTTCCAAAATTACATTTTTACCCTTTAATTTTCCAAAAATTACATTTTGACC
1 TTTTACCCTAAACTTTCCAAAATTACATTTTTACCCTCAAATTTTCCAAAAATCACATTTTGA-C
*
346153 CCT-AAATTTCCAAAAATTACA
65 CCTAAAACTTCCAAAAATTACA
* * *
346174 TTTTGCCCCTAAAC-TTCCAAAAATTACATTTTTGA-CCTCAAATTTTCTAAAAATCACATTTTT
1 TTTT-ACCCTAAACTTTCC-AAAATTACATTTTT-ACCCTCAAATTTTCCAAAAATCACATTTTG
*
346237 ATCCTAAAACTTCCAAAAATTACA
63 ACCCTAAAACTTCCAAAAATTACA
* ** *
346261 TTTTACCCTAAATTTTTTTAAAAATACATTTTTACCCTC
1 TTTTACCCTAAA-CTTTCCAAAATTACATTTTTACCCTC
346300 GAACATCCAA
Statistics
Matches: 106, Mismatches: 13, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
86 19 0.18
87 84 0.79
88 3 0.03
ACGTcount: A:0.36, C:0.23, G:0.01, T:0.40
Consensus pattern (86 bp):
TTTTACCCTAAACTTTCCAAAATTACATTTTTACCCTCAAATTTTCCAAAAATCACATTTTGACC
CTAAAACTTCCAAAAATTACA
Found at i:350435 original size:16 final size:18
Alignment explanation
Indices: 350402--350438 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
350392 TAAACAATAA
*
350402 TATATAATATACTTTTAT
1 TATATAATATACTATTAT
350420 TATAT-ATA-ACTATTAT
1 TATATAATATACTATTAT
350436 TAT
1 TAT
350439 TTTTATATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 10 0.56
17 3 0.17
18 5 0.28
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (18 bp):
TATATAATATACTATTAT
Found at i:352026 original size:2 final size:2
Alignment explanation
Indices: 352014--352046 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
352004 ATTCTGACCA
352014 AT AT A- 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
352047 TAAAAGATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:352145 original size:17 final size:17
Alignment explanation
Indices: 352123--352156 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
352113 TAGCAAAGCA
352123 TAATATTATTAA-AAAAT
1 TAATA-TATTAATAAAAT
352140 TAATATATTAATAAAAT
1 TAATATATTAATAAAAT
352157 AATTTTTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TAATATATTAATAAAAT
Found at i:352159 original size:16 final size:16
Alignment explanation
Indices: 352122--352159 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 16
352112 CTAGCAAAGC
352122 ATAATATTATTAAAAA
1 ATAATATTATTAAAAA
352138 ATTAATA-TATTAATAAA
1 A-TAATATTATTAA-AAA
352155 ATAAT
1 ATAAT
352160 TTTTTTCTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
ATAATATTATTAAAAA
Found at i:364706 original size:16 final size:16
Alignment explanation
Indices: 364664--364703 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
364654 CAAATGATTG
*
364664 TAAAAT-TATTTTTTT
1 TAAAATATAATTTTTT
364679 TAAAATATAATTTTTT
1 TAAAATATAATTTTTT
364695 T-AAATATAA
1 TAAAATATAA
364704 ATTATTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TAAAATATAATTTTTT
Found at i:364713 original size:21 final size:23
Alignment explanation
Indices: 364679--364732 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 23
364669 TTATTTTTTT
*
364679 TAAAATATAATTTTTTT-AAAT-A
1 TAAAAT-TATTTTTTTTGAAATAA
364701 T-AAATTATTTTTTTTGAAATAA
1 TAAAATTATTTTTTTTGAAATAA
364723 TAAAATTATT
1 TAAAATTATT
364733 AAATAATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 9 0.32
21 8 0.29
22 3 0.11
23 8 0.29
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (23 bp):
TAAAATTATTTTTTTTGAAATAA
Found at i:364735 original size:37 final size:36
Alignment explanation
Indices: 364666--364737 Score: 99
Period size: 36 Copynumber: 2.0 Consensus size: 36
364656 AATGATTGTA
** *
364666 AAATTATTTTTTTTAAAATATAATTTTTTTAAATAT
1 AAATTATTTTTTTTAAAATATAAAATTATTAAATAT
*
364702 AAATTATTTTTTTTGAAATAATAAAATTATTAAATA
1 AAATTATTTTTTTTAAAAT-ATAAAATTATTAAATA
364738 ATTTTAATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
36 18 0.58
37 13 0.42
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (36 bp):
AAATTATTTTTTTTAAAATATAAAATTATTAAATAT
Found at i:365999 original size:14 final size:14
Alignment explanation
Indices: 365980--366008 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
365970 TATTTTTAAT
365980 ATTTTTTAATTTTA
1 ATTTTTTAATTTTA
365994 ATTTTTTAATTTTA
1 ATTTTTTAATTTTA
366008 A
1 A
366009 AAGCATTTGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (14 bp):
ATTTTTTAATTTTA
Found at i:367371 original size:20 final size:20
Alignment explanation
Indices: 367348--367386 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
367338 AAAAAACTTT
* *
367348 AAAAAA-AATTAAAACTATA
1 AAAAAATAAATAAAAATATA
367367 AAAAAATAAATAAAAATATA
1 AAAAAATAAATAAAAATATA
367387 TTAAAATTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.21
Consensus pattern (20 bp):
AAAAAATAAATAAAAATATA
Found at i:367392 original size:20 final size:21
Alignment explanation
Indices: 367346--367418 Score: 58
Period size: 25 Copynumber: 3.3 Consensus size: 21
367336 AAAAAAAACT
* *
367346 TTAAAAAAAATTAAAACTATA
1 TTAAAATAAATTAAAAATATA
**
367367 AAAAAATAAA-TAAAAATATA
1 TTAAAATAAATTAAAAATATA
*
367387 TTAAAATTCAAAAATTAAAAATATT
1 TTAAAA-T---AAATTAAAAATATA
367412 TTAAAAT
1 TTAAAAT
367419 GTTTCATAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
20 13 0.32
21 8 0.20
24 4 0.10
25 15 0.38
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (21 bp):
TTAAAATAAATTAAAAATATA
Found at i:367410 original size:25 final size:26
Alignment explanation
Indices: 367374--367440 Score: 84
Period size: 25 Copynumber: 2.5 Consensus size: 26
367364 ATAAAAAAAT
367374 AAATAAAAATATATTAAAA-TTCA-A
1 AAATAAAAATATATTAAAATTTCATA
*
367398 AAATTAAAAATATTTTAAAATGTTTCATA
1 AAA-TAAAAATATATTAAAA--TTTCATA
367427 AAATAAAAATATAT
1 AAATAAAAATATAT
367441 ATTTAAATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
24 3 0.08
25 15 0.42
28 14 0.39
29 4 0.11
ACGTcount: A:0.61, C:0.03, G:0.01, T:0.34
Consensus pattern (26 bp):
AAATAAAAATATATTAAAATTTCATA
Found at i:367832 original size:22 final size:21
Alignment explanation
Indices: 367778--367832 Score: 53
Period size: 22 Copynumber: 2.6 Consensus size: 21
367768 AAATAATAAA
367778 ATAA-TAAATTT-TATATTTT
1 ATAATTAAATTTATATATTTT
*
367797 -TAATTCATATTTTATATAATTTT
1 ATAATT-A-AATTTATAT-ATTTT
367820 ATAATTAAATTTA
1 ATAATTAAATTTA
367833 AATTAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 9
0.72 0.05 0.23
Matches are distributed among these distances:
18 3 0.11
19 1 0.04
20 1 0.04
21 4 0.14
22 8 0.29
23 6 0.21
24 5 0.18
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (21 bp):
ATAATTAAATTTATATATTTT
Found at i:367870 original size:37 final size:38
Alignment explanation
Indices: 367803--367876 Score: 98
Period size: 37 Copynumber: 2.0 Consensus size: 38
367793 TTTTTAATTC
367803 ATATTTTATATAATTTTATAATTAAATTTAAATTAAAAA
1 ATATTTTATATAATTTTATAATTAAATTTAAA-TAAAAA
* * *
367842 ATATTTTTTATTA-TTTA-AATTGAATTTAAATAAAA
1 ATATTTTATATAATTTTATAATTAAATTTAAATAAAA
367877 TCAAATCGAC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
36 5 0.16
37 12 0.38
38 4 0.12
39 11 0.34
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (38 bp):
ATATTTTATATAATTTTATAATTAAATTTAAATAAAAA
Found at i:368330 original size:25 final size:25
Alignment explanation
Indices: 368282--368346 Score: 96
Period size: 25 Copynumber: 2.6 Consensus size: 25
368272 GATAGAATCA
* *
368282 AATCGAATGATAA-AATTTTGAGTT
1 AATCGAATGATAACTATTTCGAGTT
368306 AATCGAATGATAACTATTTCGAGTT
1 AATCGAATGATAACTATTTCGAGTT
368331 AATCGAATTGATAACT
1 AATCGAA-TGATAACT
368347 CCTATTTTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
24 13 0.35
25 16 0.43
26 8 0.22
ACGTcount: A:0.40, C:0.09, G:0.15, T:0.35
Consensus pattern (25 bp):
AATCGAATGATAACTATTTCGAGTT
Found at i:375037 original size:46 final size:46
Alignment explanation
Indices: 374970--375061 Score: 175
Period size: 46 Copynumber: 2.0 Consensus size: 46
374960 AATGATGAGA
*
374970 ATGATACTGACAATCAAGGTGATGATTCTTTGAATACTTTCTAGGT
1 ATGATAATGACAATCAAGGTGATGATTCTTTGAATACTTTCTAGGT
375016 ATGATAATGACAATCAAGGTGATGATTCTTTGAATACTTTCTAGGT
1 ATGATAATGACAATCAAGGTGATGATTCTTTGAATACTTTCTAGGT
375062 TATCTTCCTA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.32, C:0.12, G:0.20, T:0.37
Consensus pattern (46 bp):
ATGATAATGACAATCAAGGTGATGATTCTTTGAATACTTTCTAGGT
Found at i:375741 original size:6 final size:7
Alignment explanation
Indices: 375726--375750 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
375716 TCCCTACTGC
375726 TTTTGTT
1 TTTTGTT
375733 TTTTGTT
1 TTTTGTT
375740 TTTTGTT
1 TTTTGTT
375747 TTTT
1 TTTT
375751 CGACAATCGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (7 bp):
TTTTGTT
Found at i:375910 original size:97 final size:97
Alignment explanation
Indices: 375809--376003 Score: 336
Period size: 97 Copynumber: 2.0 Consensus size: 97
375799 TCAATATTAT
* *
375809 ACTATCTTTACAGGTGAAGCTTTTTTTTCTCTCGATAAAATGAAATTTATTGAAAGGATAAAGTT
1 ACTATCTTTACAGGTGAAGCTTTTTTTTCTCTCAACAAAATGAAATTTATTGAAAGGATAAAGTT
* *
375874 AATCACTAGTAGAGAAACCTATTAGGGATTTG
66 AATCACTAGAAAAGAAACCTATTAGGGATTTG
* *
375906 ACTATTTTTACAGGTGAAGCTTTTTTTTCTCTCAACAAAATGGAATTTATTGAAAGGATAAAGTT
1 ACTATCTTTACAGGTGAAGCTTTTTTTTCTCTCAACAAAATGAAATTTATTGAAAGGATAAAGTT
375971 AATCACTAGAAAAGAAACCTATTAGGGATTTG
66 AATCACTAGAAAAGAAACCTATTAGGGATTTG
376003 A
1 A
376004 TTTTGATTTT
Statistics
Matches: 92, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
97 92 1.00
ACGTcount: A:0.36, C:0.11, G:0.17, T:0.35
Consensus pattern (97 bp):
ACTATCTTTACAGGTGAAGCTTTTTTTTCTCTCAACAAAATGAAATTTATTGAAAGGATAAAGTT
AATCACTAGAAAAGAAACCTATTAGGGATTTG
Found at i:378465 original size:112 final size:112
Alignment explanation
Indices: 378310--378511 Score: 323
Period size: 112 Copynumber: 1.8 Consensus size: 112
378300 AATGTTTGTC
* * * *
378310 ATTTTTAATCTTTTCATTCATGCGAGCTTTGCCTCTAAGAAAATTCAATTTTATCCACCTTAAAA
1 ATTTTTAATCTTTACATTCACGCGAGCTTCGCCTCCAAGAAAATTCAATTTTATCCACCTTAAAA
*
378375 CCTTGTTCAAGCATGTTTGCATTGAGATAACAGTTAGTGGACTGATG
66 CATTGTTCAAGCATGTTTGCATTGAGATAACAGTTAGTGGACTGATG
* * *
378422 ATTTTTAATCTTTACATTCACGTGAGCTTCGCCTCCAATAAAATTCAATTTTATCCACCTTACAA
1 ATTTTTAATCTTTACATTCACGCGAGCTTCGCCTCCAAGAAAATTCAATTTTATCCACCTTAAAA
*
378487 CATTGTTCAAGCATTTTTGCATTGA
66 CATTGTTCAAGCATGTTTGCATTGA
378512 AATGATGGTT
Statistics
Matches: 81, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
112 81 1.00
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.39
Consensus pattern (112 bp):
ATTTTTAATCTTTACATTCACGCGAGCTTCGCCTCCAAGAAAATTCAATTTTATCCACCTTAAAA
CATTGTTCAAGCATGTTTGCATTGAGATAACAGTTAGTGGACTGATG
Found at i:379341 original size:99 final size:99
Alignment explanation
Indices: 378960--379638 Score: 542
Period size: 99 Copynumber: 6.9 Consensus size: 99
378950 GGAAACATAG
* * * * **
378960 AGATATGAAGGGAAAGGTT-AGGGCCGTAACTG-TGAACCCGGTACCTTAGAAGACATGATGGGA
1 AGATATAAAGGGAAAGGTTGA-GGCCGCAAC-GACGAACCCGATACCTTAGAAGATGTGATGGGA
* * * * * **
379023 AAGATCGAGGTCGTAACGAG-GGATCTAGTACCATG-
64 AGGATTGAGGCCGCAACG-GCGAATCCGGTACCATGA
* * * * * * *
379058 -GAAATAAAGGGAAAGGTTGAGGTCACAACGGCGAATCCGATACCTTAAAAGATGTGATGGAAAG
1 AGATATAAAGGGAAAGGTTGAGGCCGCAACGACGAACCCGATACCTTAGAAGATGTGATGGGAAG
* * * *
379122 GATTGAGGTCGTAACGGCAAATCCGATACCATGA
66 GATTGAGGCCGCAACGGCGAATCCGGTACCATGA
* ** ** ** * *
379156 TGATATGCAGGGAAAGGTTGACACCATAATGACGAACCCGATACCTTGGAAGATGTGATGGGAAG
1 AGATATAAAGGGAAAGGTTGAGGCCGCAACGACGAACCCGATACCTTAGAAGATGTGATGGGAAG
* * * **
379221 GATTGAGCCCGTAACGACGAATCCAATACCATGA
66 GATTGAGGCCGCAACGGCGAATCCGGTACCATGA
* * * **
379255 AGATATAAAGGGAAAGGTTGAGGTCGTAATGACGAACCCGATACCTTAGAAGATGTGATAAGAAG
1 AGATATAAAGGGAAAGGTTGAGGCCGCAACGACGAACCCGATACCTTAGAAGATGTGATGGGAAG
* * ** * * **
379320 AATTAAGGTTGGAATGGCGAATTTGGTACCATGA
66 GATTGAGGCCGCAACGGCGAATCCGGTACCATGA
* * * ** * * *
379354 AGATATGAATGGAAAAGTTGAGGCCGCAACGGTGAACCCGGTATCTTAGAAGATGTGATGCGAAG
1 AGATATAAAGGGAAAGGTTGAGGCCGCAACGACGAACCCGATACCTTAGAAGATGTGATGGGAAG
* * *
379419 GATTGAGACCGCAACAGTGAATCCGGTACCATGA
66 GATTGAGGCCGCAACGGCGAATCCGGTACCATGA
* * * * * *
379453 AGATATGAAGGGAAATGTTGAGGCTGCAACGGCGAACCCGATACCTTAAAAGATGTGATGGGAAT
1 AGATATAAAGGGAAAGGTTGAGGCCGCAACGACGAACCCGATACCTTAGAAGATGTGATGGGAAG
* * ** *
379518 GATTGAGGCTGCAACGACGAATCTTGTACCATGG
66 GATTGAGGCCGCAACGGCGAATCCGGTACCATGA
* * ** * * * *
379552 AGATATAGAGGGAAAGGTTGAAGCCGCAACGACGAACCTTATACCTTAG-AGATATTAAGGGAAA
1 AGATATAAAGGGAAAGGTTGAGGCCGCAACGACGAACCCGATACCTTAGAAGATGTGATGGGAAG
* *
379616 GAGTGAGGCCGCAACGGTGAATC
66 GATTGAGGCCGCAACGGCGAATC
379639 TCATACCCTG
Statistics
Matches: 460, Mismatches: 116, Indels: 10
0.78 0.20 0.02
Matches are distributed among these distances:
96 2 0.00
97 72 0.16
98 31 0.07
99 355 0.77
ACGTcount: A:0.35, C:0.16, G:0.30, T:0.20
Consensus pattern (99 bp):
AGATATAAAGGGAAAGGTTGAGGCCGCAACGACGAACCCGATACCTTAGAAGATGTGATGGGAAG
GATTGAGGCCGCAACGGCGAATCCGGTACCATGA
Found at i:379482 original size:49 final size:49
Alignment explanation
Indices: 378960--379632 Score: 229
Period size: 50 Copynumber: 13.7 Consensus size: 49
378950 GGAAACATAG
* * * *
378960 AGATATGAAGGGAAAGGTT-AGGGCCGTAACTGTGAACCCGGTACCTTAGA
1 AGATATGAAGGGAAAGGTTGA-GGCCGCAACGGCGAACCCGGTACCAT-GA
* * * * * * * * **
379010 AGACATGATGGGAAAGATCGAGGTCGTAACGAG-GGATCTAGTACCATGGA
1 AGATATGAAGGGAAAGGTTGAGGCCGCAACG-GCGAACCCGGTACCAT-GA
* * * * * *
379060 A-ATA--AAGGGAAAGGTTGAGGTCACAACGGCGAATCCGATACCTTAAA
1 AGATATGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCAT-GA
* * * * * * *
379107 AGATGTG-ATGGAAAGGATTGAGGTCGTAACGGCAAATCCGATACCATGA
1 AGATATGAAGGGAAAGG-TTGAGGCCGCAACGGCGAACCCGGTACCATGA
* * ** ** * * * *
379156 TGATATGCAGGGAAAGGTTGACACCATAATGACGAACCCGATACCTTGGA
1 AGATATGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCAT-GA
* * * * * * **
379206 AGATGTGATGGG-AAGGATTGAGCCCGTAACGACGAATCCAATACCATGA
1 AGATATGAAGGGAAAGG-TTGAGGCCGCAACGGCGAACCCGGTACCATGA
* * * * * * *
379255 AGATATAAAGGGAAAGGTTGAGGTCGTAATGACGAACCCGATACCTTAGA
1 AGATATGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCAT-GA
* * * * ** * * ***
379305 AGATGTGATA-AG-AAGAATTAAGGTTGGAATGGCGAATTTGGTACCATGA
1 AGATATGA-AGGGAAAG-GTTGAGGCCGCAACGGCGAACCCGGTACCATGA
* * * * *
379354 AGATATGAATGGAAAAGTTGAGGCCGCAACGGTGAACCCGGTATCTTAGA
1 AGATATGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCAT-GA
* * * * * * *
379404 AGATGTGATGCG-AAGGATTGAGACCGCAACAGTGAATCCGGTACCATGA
1 AGATATGAAGGGAAAGG-TTGAGGCCGCAACGGCGAACCCGGTACCATGA
* * * * *
379453 AGATATGAAGGGAAATGTTGAGGCTGCAACGGCGAACCCGATACCTTAAA
1 AGATATGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCAT-GA
* * * * * * * ** *
379503 AGATGTGATGGGAATGATTGAGGCTGCAACGACGAATCTTGTACCATGG
1 AGATATGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCATGA
* * *** *
379552 AGATAT-AGAGGGAAAGGTTGAAGCCGCAACGACGAACCTTATACC-TTA
1 AGATATGA-AGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCATGA
*
379600 GAGATATTAAGGGAAAGAG-TGAGGCCGCAACGG
1 -AGATATGAAGGGAAAG-GTTGAGGCCGCAACGG
379633 TGAATCTCAT
Statistics
Matches: 460, Mismatches: 139, Indels: 49
0.71 0.21 0.08
Matches are distributed among these distances:
46 1 0.00
47 30 0.07
48 5 0.01
49 206 0.45
50 215 0.47
51 3 0.01
ACGTcount: A:0.35, C:0.16, G:0.30, T:0.20
Consensus pattern (49 bp):
AGATATGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCATGA
Found at i:379499 original size:297 final size:297
Alignment explanation
Indices: 379067--379601 Score: 676
Period size: 297 Copynumber: 1.8 Consensus size: 297
379057 GGAAATAAAG
* * * **
379067 GGAAAGGTTGAGGTCACAACGGCGAATCCGATACCTTAAAAGATGTGATGGAAAGGATTGAGGTC
1 GGAAAAGTTGAGGCCACAACGGCGAACCCGATACCTTAAAAGATGTGATGGAAAGGATTGAGACC
* * * * * *
379132 GTAACGGCAAATCCGATACCATGATGATATGCAGGGAAAGGTTGACACCATAATGACGAACCCGA
66 GCAACAGCAAATCCGATACCATGAAGATATGAAGGGAAAGGTTGACACCACAACGACGAACCCGA
** *
379197 TACCTTGGAAGATGTGATGGGAAGGATTGAGCCCGTAACGACGAATCCAATACCATGAAGATATA
131 TACCTTAAAAGATGTGATGGGAAGGATTGAGCCCGCAACGACGAATCCAATACCATGAAGATATA
* * * *
379262 AAGGGAAAGGTTGAGGTCGTAATGACGAACCCGATACCTTAGAAGATGTGATAAGAAGAATTAAG
196 AAGGGAAAGGTTGAAGCCGCAACGACGAACCCGATACCTTAGAAGATGTGATAAGAAGAATTAAG
379327 GTTGGAATGGCGAATTTGGTACCATGAAGATATGAAT
261 GTTGGAATGGCGAATTTGGTACCATGAAGATATGAAT
* * * * *
379364 GGAAAAGTTGAGGCCGCAACGGTGAACCCGGTATCTTAGAAGATGTGATGCG-AAGGATTGAGAC
1 GGAAAAGTTGAGGCCACAACGGCGAACCCGATACCTTAAAAGATGTGATG-GAAAGGATTGAGAC
** * * ** ** *
379428 CGCAACAGTGAATCCGGTACCATGAAGATATGAAGGGAAATGTTGAGGCTGCAACGGCGAACCCG
65 CGCAACAGCAAATCCGATACCATGAAGATATGAAGGGAAAGGTTGACACCACAACGACGAACCCG
* * * *** *
379493 ATACCTTAAAAGATGTGATGGGAATGATTGAGGCTGCAACGACGAATCTTGTACCATGGAGATAT
130 ATACCTTAAAAGATGTGATGGGAAGGATTGAGCCCGCAACGACGAATCCAATACCATGAAGATAT
* **
379558 AGAGGGAAAGGTTGAAGCCGCAACGACGAACCTTATACCTTAGA
195 AAAGGGAAAGGTTGAAGCCGCAACGACGAACCCGATACCTTAGA
379602 GATATTAAGG
Statistics
Matches: 195, Mismatches: 42, Indels: 2
0.82 0.18 0.01
Matches are distributed among these distances:
297 194 0.99
298 1 0.01
ACGTcount: A:0.35, C:0.16, G:0.29, T:0.20
Consensus pattern (297 bp):
GGAAAAGTTGAGGCCACAACGGCGAACCCGATACCTTAAAAGATGTGATGGAAAGGATTGAGACC
GCAACAGCAAATCCGATACCATGAAGATATGAAGGGAAAGGTTGACACCACAACGACGAACCCGA
TACCTTAAAAGATGTGATGGGAAGGATTGAGCCCGCAACGACGAATCCAATACCATGAAGATATA
AAGGGAAAGGTTGAAGCCGCAACGACGAACCCGATACCTTAGAAGATGTGATAAGAAGAATTAAG
GTTGGAATGGCGAATTTGGTACCATGAAGATATGAAT
Found at i:379645 original size:49 final size:49
Alignment explanation
Indices: 379453--379645 Score: 117
Period size: 49 Copynumber: 3.9 Consensus size: 49
379443 GGTACCATGA
* * * * *
379453 AGATAT-GAAGGGAAATGTTGAGGCTGCAACGGCGAACC-CGATACCTTAAA
1 AGATATAG-AGGGAAAGGTTGAAGCCGCAACGACGAACCTC-ATACCTT-AG
* * * * * * ** * *
379503 AGATGT-GATGGGAATGATTGAGGCTGCAACGACGAATCTTGTACCATGG
1 AGATATAGA-GGGAAAGGTTGAAGCCGCAACGACGAACCTCATACCTTAG
*
379552 AGATATAGAGGGAAAGGTTGAAGCCGCAACGACGAACCTTATACCTTAG
1 AGATATAGAGGGAAAGGTTGAAGCCGCAACGACGAACCTCATACCTTAG
* ** *
379601 AGATATTA-AGGGAAAGAG-TGAGGCCGCAACGGTGAATCTCATACC
1 AGATA-TAGAGGGAAAG-GTTGAAGCCGCAACGACGAACCTCATACC
379646 CTGAAGATGA
Statistics
Matches: 113, Mismatches: 25, Indels: 11
0.76 0.17 0.07
Matches are distributed among these distances:
49 73 0.65
50 40 0.35
ACGTcount: A:0.34, C:0.17, G:0.29, T:0.20
Consensus pattern (49 bp):
AGATATAGAGGGAAAGGTTGAAGCCGCAACGACGAACCTCATACCTTAG
Found at i:379926 original size:42 final size:42
Alignment explanation
Indices: 379872--380332 Score: 479
Period size: 42 Copynumber: 11.3 Consensus size: 42
379862 CAAAGACAAC
* ** *
379872 CCAATCTCTTACCTCGATCATAAGGCAAATTGAAGACATCAT
1 CCAATCTCTTACCCCGATCATGGGGCAGATTGAAGACATCAT
* * *
379914 CCAATCTTTTACCCCGATCATGGGGCAAATTGAAG-C--CAC
1 CCAATCTCTTACCCCGATCATGGGGCAGATTGAAGACATCAT
* * *
379953 CCAATATCTTATCTCGATCATGGGGCAGATTGAAGACATCAT
1 CCAATCTCTTACCCCGATCATGGGGCAGATTGAAGACATCAT
* *
379995 CCAATCTCTTACCCCGATCATAGGGTAGATTGAAGACA-CA-
1 CCAATCTCTTACCCCGATCATGGGGCAGATTGAAGACATCAT
*
380035 CCAATATCTTACCCCGATCATGGGGCAGATTGAAGACA-CA-
1 CCAATCTCTTACCCCGATCATGGGGCAGATTGAAGACATCAT
* * *
380075 CAAATCTC-TAACCCGATCATGGGGTAGATTGAAGACATCAT
1 CCAATCTCTTACCCCGATCATGGGGCAGATTGAAGACATCAT
* *
380116 CCAATCTCTTACCACGATCATGGGGTAGATTGAAG-CAT--T
1 CCAATCTCTTACCCCGATCATGGGGCAGATTGAAGACATCAT
** * *
380155 -CAATCGT-TTACCCTAATCA-GAAGGTAGATTGAAGACATCAT
1 CCAATC-TCTTACCCCGATCATG-GGGCAGATTGAAGACATCAT
* **
380196 CCGATCTCTTACCCCGATCATGGGTTAGATTGAAGACATCAT
1 CCAATCTCTTACCCCGATCATGGGGCAGATTGAAGACATCAT
* * * * *
380238 CTAGTCCCTTACCCCGATCATGGGGCAGATTAAAGACAACAT
1 CCAATCTCTTACCCCGATCATGGGGCAGATTGAAGACATCAT
* * *
380280 TCAATCTCTTACCCCGATAATGGGGCAAATTGAAG-C--CAT
1 CCAATCTCTTACCCCGATCATGGGGCAGATTGAAGACATCAT
*
380319 CCGATCTCTTACCC
1 CCAATCTCTTACCC
380333 TAATCAAGAG
Statistics
Matches: 353, Mismatches: 52, Indels: 31
0.81 0.12 0.07
Matches are distributed among these distances:
37 1 0.00
38 26 0.07
39 79 0.22
40 46 0.13
41 16 0.05
42 184 0.52
43 1 0.00
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (42 bp):
CCAATCTCTTACCCCGATCATGGGGCAGATTGAAGACATCAT
Found at i:379969 original size:81 final size:81
Alignment explanation
Indices: 379864--380319 Score: 406
Period size: 81 Copynumber: 5.6 Consensus size: 81
379854 GAGCAAAGCA
* ** *
379864 AAGACAACCCAATCTCTTACCTCGATCATAAGGCAAATTGAAGACATCATCCAATCTTTTACCCC
1 AAGAC-ACCCAATATCTTACCTCGATCATGGGGCAGATTGAAGACATCATCCAATCTTTTACCCC
* *
379929 GATCATGGGGCAAATTG
65 GATCATGGGGTAGATTG
* * *
379946 AAGCCACCCAATATCTTATCTCGATCATGGGGCAGATTGAAGACATCATCCAATCTCTTACCCCG
1 AAGACACCCAATATCTTACCTCGATCATGGGGCAGATTGAAGACATCATCCAATCTTTTACCCCG
*
380011 ATCATAGGGTAGATTG
66 ATCATGGGGTAGATTG
* * * *
380027 AAGACACACCAATATCTTACCCCGATCATGGGGCAGATTGAAGACA-CA-CAAATC-TCTAACCC
1 AAGACAC-CCAATATCTTACCTCGATCATGGGGCAGATTGAAGACATCATCCAATCTTTTACCCC
380089 GATCATGGGGTAGATTG
65 GATCATGGGGTAGATTG
* * * *
380106 AAGACATCATCCAATCTCTTACCACGATCATGGGGTAGATTGAAG-CAT--T-CAATCGTTTACC
1 AAGACA-C--CCAATATCTTACCTCGATCATGGGGCAGATTGAAGACATCATCCAATCTTTTACC
** *
380167 CTAATCA-GAAGGTAGATTG
63 CCGATCATG-GGGTAGATTG
* * * ** * * **
380186 AAGACATCATCCGATCTCTTACCCCGATCATGGGTTAGATTGAAGACATCATCTAGTCCCTTACC
1 AAGACA-C--CCAATATCTTACCTCGATCATGGGGCAGATTGAAGACATCATCCAATCTTTTACC
* *
380251 CCGATCATGGGGCAGATTA
63 CCGATCATGGGGTAGATTG
* * * * * *
380270 AAGACAACATTCAATCTCTTACCCCGATAATGGGGCAAATTGAAGCCATC
1 AAGAC-AC--CCAATATCTTACCTCGATCATGGGGCAGATTGAAGACATC
380320 CGATCTCTTA
Statistics
Matches: 314, Mismatches: 47, Indels: 24
0.82 0.12 0.06
Matches are distributed among these distances:
79 32 0.10
80 68 0.22
81 110 0.35
82 40 0.13
83 1 0.00
84 61 0.19
85 2 0.01
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (81 bp):
AAGACACCCAATATCTTACCTCGATCATGGGGCAGATTGAAGACATCATCCAATCTTTTACCCCG
ATCATGGGGTAGATTG
Found at i:380092 original size:121 final size:122
Alignment explanation
Indices: 379872--380314 Score: 477
Period size: 121 Copynumber: 3.6 Consensus size: 122
379862 CAAAGACAAC
* * * *
379872 CCAATCTCTTACCTCGATCATAAGGCAAATTGAAGACATCATCCAATCTTTTACCCCGATCATGG
1 CCAATCTCTTACCCCGATCATAGGGCAGATTGAAGACA-CATCCAATCTCTTACCCCGATCATGG
* * * * *
379937 GGCAAATTGAAGCCACCCAATATCT-TATCTCGATCATGGGGCAGATTGAAGACATCAT
65 GGCAAATTGAAGACACACAA-ATCTCTAACCCGATCATGGGGTAGATTGAAGACATCAT
* *
379995 CCAATCTCTTACCCCGATCATAGGGTAGATTGAAGACACA-CCAATATCTTACCCCGATCATGGG
1 CCAATCTCTTACCCCGATCATAGGGCAGATTGAAGACACATCCAATCTCTTACCCCGATCATGGG
*
380059 GCAGATTGAAGACACACAAATCTCTAACCCGATCATGGGGTAGATTGAAGACATCAT
66 GCAAATTGAAGACACACAAATCTCTAACCCGATCATGGGGTAGATTGAAGACATCAT
* * * * **
380116 CCAATCTCTTACCACGATCATGGGGTAGATTGAAG---CATTCAATCGT-TTACCCTAATCA-GA
1 CCAATCTCTTACCCCGATCATAGGGCAGATTGAAGACACATCCAATC-TCTTACCCCGATCATG-
* * * ** * *
380176 AGGTAGATTGAAGACATCATCCGATCTCTTACCCCGATCATGGGTTAGATTGAAGACATCAT
64 GGGCAAATTGAAGACA-CA-CAAATCTC-TAACCCGATCATGGGGTAGATTGAAGACATCAT
* * * * * * *
380238 CTAGTCCCTTACCCCGATCATGGGGCAGATTAAAGACAACATTCAATCTCTTACCCCGATAATGG
1 CCAATCTCTTACCCCGATCATAGGGCAGATTGAAGAC-ACATCCAATCTCTTACCCCGATCATGG
380303 GGCAAATTGAAG
65 GGCAAATTGAAG
380315 CCATCCGATC
Statistics
Matches: 271, Mismatches: 36, Indels: 23
0.82 0.11 0.07
Matches are distributed among these distances:
118 3 0.01
119 28 0.10
120 7 0.03
121 107 0.39
122 62 0.23
123 34 0.13
125 1 0.00
126 28 0.10
127 1 0.00
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (122 bp):
CCAATCTCTTACCCCGATCATAGGGCAGATTGAAGACACATCCAATCTCTTACCCCGATCATGGG
GCAAATTGAAGACACACAAATCTCTAACCCGATCATGGGGTAGATTGAAGACATCAT
Found at i:380230 original size:80 final size:81
Alignment explanation
Indices: 379953--380314 Score: 315
Period size: 80 Copynumber: 4.4 Consensus size: 81
379943 TTGAAGCCAC
* * * * * * *
379953 CCAATATCTTATCTCGATCATGGGGCAGATTGAAGACATCATCCAATCTCTTACCCCGATCAT-A
1 CCAATCTCTTACCCCGATCATGGGGTAGATTGAAGACA-CA-CAAATCTC-TAACCCAATCATGA
380017 GGGTAGATTGAAGACA-CA-
63 -GGTAGATTGAAGACATCAT
* * * *
380035 CCAATATCTTACCCCGATCATGGGGCAGATTGAAGACACACAAATCTCTAACCCGATCATGGGGT
1 CCAATCTCTTACCCCGATCATGGGGTAGATTGAAGACACACAAATCTCTAACCCAATCATGAGGT
380100 AGATTGAAGACATCAT
66 AGATTGAAGACATCAT
* ** *
380116 CCAATCTCTTACCACGATCATGGGGTAGATTGAAG-CATTC-AATCGT-TTACCCTAATCA-GAA
1 CCAATCTCTTACCCCGATCATGGGGTAGATTGAAGACACACAAATC-TCTAACCC-AATCATG-A
380177 GGTAGATTGAAGACATCAT
63 GGTAGATTGAAGACATCAT
* * * * * * * *
380196 CCGATCTCTTACCCCGATCATGGGTTAGATTGAAGACATCATCTAGTCCCTTACCCCGATCATGG
1 CCAATCTCTTACCCCGATCATGGGGTAGATTGAAGACA-CA-CAAATCTC-TAACCCAATCATGA
* * *
380261 GGCAGATTAAAGACAACAT
63 GGTAGATTGAAGACATCAT
* * * *
380280 TCAATCTCTTACCCCGATAATGGGGCAAATTGAAG
1 CCAATCTCTTACCCCGATCATGGGGTAGATTGAAG
380315 CCATCCGATC
Statistics
Matches: 234, Mismatches: 33, Indels: 24
0.80 0.11 0.08
Matches are distributed among these distances:
79 36 0.15
80 68 0.29
81 36 0.15
82 36 0.15
83 1 0.00
84 52 0.22
85 5 0.02
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.25
Consensus pattern (81 bp):
CCAATCTCTTACCCCGATCATGGGGTAGATTGAAGACACACAAATCTCTAACCCAATCATGAGGT
AGATTGAAGACATCAT
Found at i:380753 original size:16 final size:16
Alignment explanation
Indices: 380716--380762 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
380706 CTGGCCCAGT
*
380716 ACAAAATAAAACAAAAA
1 ACAAAACAAAA-AAAAA
* *
380733 CCAAAAGAAAAAAAAA
1 ACAAAACAAAAAAAAA
380749 ACAAAACAAAAAAA
1 ACAAAACAAAAAAA
380763 TAAATAATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
16 17 0.65
17 9 0.35
ACGTcount: A:0.83, C:0.13, G:0.02, T:0.02
Consensus pattern (16 bp):
ACAAAACAAAAAAAAA
Found at i:382105 original size:20 final size:20
Alignment explanation
Indices: 382063--382105 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
382053 AAAATTGCCC
**
382063 TTTAATTTTAGTTTTTTTTT
1 TTTAATTTTAGTTTTTTACT
382083 TTTAA-TTTAGTTATTTTACT
1 TTTAATTTTAGTT-TTTTACT
382103 TTT
1 TTT
382106 GGAGGCACAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.19, C:0.02, G:0.05, T:0.74
Consensus pattern (20 bp):
TTTAATTTTAGTTTTTTACT
Found at i:384356 original size:30 final size:28
Alignment explanation
Indices: 384320--384419 Score: 83
Period size: 30 Copynumber: 3.4 Consensus size: 28
384310 AGAGGTTCCC
384320 AAACTTTCCAACAATCACATTTTAACCCTT
1 AAACTTTCCAA-AAT-ACATTTTAACCCTT
* ** *
384350 AAACTTTCCAAAAATTCATATTTAGTCCTC
1 AAACTTTCC-AAAATACAT-TTTAACCCTT
* *
384380 AAACTTTCTAAATATTACATTTTAACCCCT
1 AAACTTTCCAAA-A-TACATTTTAACCCTT
*
384410 AACCTTTCCA
1 AAACTTTCCA
384420 TAATTCAAAT
Statistics
Matches: 54, Mismatches: 12, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
29 6 0.11
30 42 0.78
31 6 0.11
ACGTcount: A:0.36, C:0.27, G:0.01, T:0.36
Consensus pattern (28 bp):
AAACTTTCCAAAATACATTTTAACCCTT
Found at i:384491 original size:29 final size:29
Alignment explanation
Indices: 384470--384525 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
384460 TTGACCCTTG
384470 AACTTTCCAAAATTTAGATTTGACCCCCA
1 AACTTTCCAAAATTTAGATTTGACCCCCA
*
384499 AACTTTCCAAAACTTAGATTTGACCCC
1 AACTTTCCAAAATTTAGATTTGACCCC
384526 TAAAAGCCCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.34, C:0.29, G:0.07, T:0.30
Consensus pattern (29 bp):
AACTTTCCAAAATTTAGATTTGACCCCCA
Found at i:385063 original size:104 final size:103
Alignment explanation
Indices: 384905--385108 Score: 291
Period size: 104 Copynumber: 2.0 Consensus size: 103
384895 AAATATTTTC
* *
384905 AAAATCGAGGCAATATTTCTTTATTTAGGGAACTCGAGAAATTGTGCTCAAACGTATTGGGTACG
1 AAAATCGAGGCAATATTTCTTTATTTAGGGAACTCGAGAAATTGTGCCCAAACGTATTGAGTACG
* *
384970 ATTTTTCTTTAAACCTAAGTAATTGAATATCCTATTCA
66 ATTGTTCTTTAAACCTAAATAATTGAATATCCTATTCA
* * * * * * *
385008 AAAATCGAGGCAATGTTTTTTTATTTTAGGGAAGTCGAGGAATTGTGCCCTAACGTGTTGAGTAT
1 AAAATCGAGGCAATATTTCTTTA-TTTAGGGAACTCGAGAAATTGTGCCCAAACGTATTGAGTAC
*
385073 GATTGTTCTTTGAACCTAAATAATTGAATATCCTAT
65 GATTGTTCTTTAAACCTAAATAATTGAATATCCTAT
385109 GCGGAACCAA
Statistics
Matches: 88, Mismatches: 12, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
103 21 0.24
104 67 0.76
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.37
Consensus pattern (103 bp):
AAAATCGAGGCAATATTTCTTTATTTAGGGAACTCGAGAAATTGTGCCCAAACGTATTGAGTACG
ATTGTTCTTTAAACCTAAATAATTGAATATCCTATTCA
Found at i:391139 original size:3 final size:3
Alignment explanation
Indices: 391131--391160 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
391121 ATTGTCACAA
391131 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
391161 CAAGGGTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:392504 original size:159 final size:159
Alignment explanation
Indices: 392215--392533 Score: 595
Period size: 159 Copynumber: 2.0 Consensus size: 159
392205 AAAATTAGAC
392215 TATGTTTATGAACATGTCATGCATTCACCTATGTCTAGAGTCTGCATGCATGCAATTCCAAACCA
1 TATGTTTATGAACATGTCATGCATTCACCTATGTCTAGAGTCTGCATGCATGCAATTCCAAACCA
392280 AAAAAAAATTGAATGAAATAATAAAATAACTCAGATTAAAACTTGAACATTAAAAGAAAATAAAA
66 AAAAAAAATTGAATGAAATAATAAAATAACTCAGATTAAAACTTGAACATTAAAAGAAAATAAAA
392345 GTATCATCTAGTAACCCAACTCAATGAGT
131 GTATCATCTAGTAACCCAACTCAATGAGT
392374 TATGTTTATGAACATGTCATGCATTCACCTATGTCTAGAGTCTGCATGCATGCAATTCCAAA-CA
1 TATGTTTATGAACATGTCATGCATTCACCTATGTCTAGAGTCTGCATGCATGCAATTCCAAACCA
** *
392438 AAAAAATTTTTGAATGAAATAGTAAAATAACTCAGATTAAAACTTGAACATTAAAAGAAAATAAA
66 AAAAAA-AATTGAATGAAATAATAAAATAACTCAGATTAAAACTTGAACATTAAAAGAAAATAAA
392503 AGTATCATCTAGTAACCCAACTCAATGAGT
130 AGTATCATCTAGTAACCCAACTCAATGAGT
392533 T
1 T
392534 TTTAGCTCAT
Statistics
Matches: 156, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
158 8 0.05
159 148 0.95
ACGTcount: A:0.44, C:0.16, G:0.12, T:0.28
Consensus pattern (159 bp):
TATGTTTATGAACATGTCATGCATTCACCTATGTCTAGAGTCTGCATGCATGCAATTCCAAACCA
AAAAAAAATTGAATGAAATAATAAAATAACTCAGATTAAAACTTGAACATTAAAAGAAAATAAAA
GTATCATCTAGTAACCCAACTCAATGAGT
Found at i:392936 original size:55 final size:55
Alignment explanation
Indices: 392877--392986 Score: 175
Period size: 55 Copynumber: 2.0 Consensus size: 55
392867 AGCACACAAT
* * *
392877 CTATGCTCCCCCTTTTTCAAGTGGATCCTTCTAGTGCATTGTACAGTTGGTTGAG
1 CTATGCTCCCCCTTTTTCAAGTGGATCCTTCTAGTGCATTGCACAGCTGATTGAG
* *
392932 CTATGCTCCCCTTTTTTGAAGTGGATCCTTCTAGTGCATTGCACAGCTGATTGAG
1 CTATGCTCCCCCTTTTTCAAGTGGATCCTTCTAGTGCATTGCACAGCTGATTGAG
392987 ATGGCATGCT
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
55 50 1.00
ACGTcount: A:0.17, C:0.24, G:0.22, T:0.37
Consensus pattern (55 bp):
CTATGCTCCCCCTTTTTCAAGTGGATCCTTCTAGTGCATTGCACAGCTGATTGAG
Found at i:394147 original size:23 final size:22
Alignment explanation
Indices: 394121--394191 Score: 97
Period size: 23 Copynumber: 3.1 Consensus size: 22
394111 TGAACTCTTC
394121 TTCATATCACTTTCAATTTACAA
1 TTCATATCACTTTCAATTT-CAA
*
394144 TTCATATCACTTTCAATTCCAA
1 TTCATATCACTTTCAATTTCAA
*
394166 TTTCACTTTCACTTTCAATTTCAA
1 -TTCA-TATCACTTTCAATTTCAA
394190 TT
1 TT
394192 TTGATCACAA
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
22 3 0.07
23 24 0.56
24 16 0.37
ACGTcount: A:0.30, C:0.24, G:0.00, T:0.46
Consensus pattern (22 bp):
TTCATATCACTTTCAATTTCAA
Found at i:394175 original size:6 final size:6
Alignment explanation
Indices: 394131--394192 Score: 56
Period size: 6 Copynumber: 10.5 Consensus size: 6
394121 TTCATATCAC
* * * * *
394131 TTTCAA TTTACAA -TTC-A TATCAC TTTCAA TTCCAA TTTCAC TTTCAC
1 TTTCAA TTT-CAA TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA
394178 TTTCAA TTTCAA TTT
1 TTTCAA TTTCAA TTT
394193 TGATCACAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
4 1 0.02
5 3 0.07
6 38 0.84
7 3 0.07
ACGTcount: A:0.29, C:0.23, G:0.00, T:0.48
Consensus pattern (6 bp):
TTTCAA
Found at i:404303 original size:2 final size:2
Alignment explanation
Indices: 404296--404338 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
404286 TAATCATAAC
* *
404296 TA TA TA TA AA TA TA TA TA TA TC 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
404338 T
1 T
404339 TACATTTTGG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:406529 original size:27 final size:27
Alignment explanation
Indices: 406470--406522 Score: 76
Period size: 25 Copynumber: 2.0 Consensus size: 27
406460 TATATTATTC
406470 AAAATTAATTATAACATATTAAATAAA
1 AAAATTAATTATAACATATTAAATAAA
406497 AAAATTAAATTA-AA-ATA-TAAATAAA
1 AAAATT-AATTATAACATATTAAATAAA
406522 A
1 A
406523 CGAAATTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
25 9 0.36
26 3 0.12
27 8 0.32
28 5 0.20
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (27 bp):
AAAATTAATTATAACATATTAAATAAA
Found at i:409080 original size:27 final size:26
Alignment explanation
Indices: 409032--409082 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
409022 ATTTTTTTTT
* *
409032 TTCAATTTTTAAAGTGCTAAAAAAAA
1 TTCAACTTTTAAAGGGCTAAAAAAAA
* *
409058 TTCAACTTTTAAAGGGTTCAAAAAA
1 TTCAACTTTTAAAGGGCTAAAAAAA
409083 TTTCTTCAAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.47, C:0.10, G:0.10, T:0.33
Consensus pattern (26 bp):
TTCAACTTTTAAAGGGCTAAAAAAAA
Found at i:412364 original size:28 final size:28
Alignment explanation
Indices: 412326--412385 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 28
412316 CTAATCACTT
* *
412326 AAAAAATACATTGTTTAACGATACAATA
1 AAAAAACACATTGTTTAACAATACAATA
*
412354 AAAAAACACATTGTTTAACAATACGATA
1 AAAAAACACATTGTTTAACAATACAATA
412382 AAAA
1 AAAA
412386 CATCTCTTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.57, C:0.12, G:0.07, T:0.25
Consensus pattern (28 bp):
AAAAAACACATTGTTTAACAATACAATA
Found at i:417191 original size:21 final size:20
Alignment explanation
Indices: 417153--417191 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
417143 TTTCATAACT
* *
417153 TCAAAATCTAACACTTTCTA
1 TCAAAATCAAACAATTTCTA
417173 TCAAAACTCAAACAATTTC
1 TCAAAA-TCAAACAATTTC
417192 ACTCTAAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.44, C:0.26, G:0.00, T:0.31
Consensus pattern (20 bp):
TCAAAATCAAACAATTTCTA
Found at i:420655 original size:11 final size:11
Alignment explanation
Indices: 420639--420735 Score: 69
Period size: 11 Copynumber: 9.0 Consensus size: 11
420629 ACCGAGCCCC
420639 TTTTAAATTTA
1 TTTTAAATTTA
420650 TTTT-AA---A
1 TTTTAAATTTA
*
420657 -TTTAGATTTA
1 TTTTAAATTTA
420667 TTTTAAATTTGA
1 TTTTAAATTT-A
* *
420679 ATTTAAATTAA
1 TTTTAAATTTA
*
420690 TTTTCAATTTAA
1 TTTTAAATTT-A
* *
420702 ATTTAATTTTA
1 TTTTAAATTTA
*
420713 ATTTAAATTTA
1 TTTTAAATTTA
420724 TTTTCAAATTTA
1 TTTT-AAATTTA
420736 AAAAAATTAT
Statistics
Matches: 66, Mismatches: 12, Indels: 15
0.71 0.13 0.16
Matches are distributed among these distances:
6 3 0.05
7 2 0.03
10 3 0.05
11 34 0.52
12 24 0.36
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (11 bp):
TTTTAAATTTA
Found at i:420660 original size:6 final size:6
Alignment explanation
Indices: 420640--420737 Score: 80
Period size: 6 Copynumber: 17.0 Consensus size: 6
420630 CCGAGCCCCT
* * * *
420640 TTTAAA TTT-AT TTTAAA TTTAGA TTT-AT TTTAAA TTTGAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * * *
420686 -TTAAT TTTCAA TTTAAA TTT-AA TTTTAA TTTAAA TTT-AT TTTCAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA
420732 TTTAAA
1 TTTAAA
420738 AAAATTATTA
Statistics
Matches: 71, Mismatches: 15, Indels: 12
0.72 0.15 0.12
Matches are distributed among these distances:
5 20 0.28
6 47 0.66
7 4 0.06
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:420665 original size:17 final size:17
Alignment explanation
Indices: 420640--420737 Score: 90
Period size: 17 Copynumber: 5.4 Consensus size: 17
420630 CCGAGCCCCT
420640 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
420657 TTTAGATTTATTTTAAATTTGAA
1 TTTAAATTTATTTT--A----AA
* *
420680 TTTAAATTAATTTTCAA
1 TTTAAATTTATTTTAAA
420697 TTTAAATTTAATTTT-AA
1 TTTAAATTT-ATTTTAAA
420714 TTTAAATTTATTTTCAAA
1 TTTAAATTTATTTT-AAA
420732 TTTAAA
1 TTTAAA
420738 AAAATTATTA
Statistics
Matches: 67, Mismatches: 5, Indels: 17
0.75 0.06 0.19
Matches are distributed among these distances:
16 5 0.07
17 34 0.51
18 13 0.19
19 1 0.01
23 14 0.21
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:420735 original size:23 final size:23
Alignment explanation
Indices: 420651--420736 Score: 86
Period size: 23 Copynumber: 3.7 Consensus size: 23
420641 TTAAATTTAT
* *
420651 TTTAAATTTAGATTTATTTTAAA
1 TTTAAATTTAAATTTAATTTAAA
* *
420674 TTTGAATTTAAA-TTAATTTTCAA
1 TTTAAATTTAAATTTAA-TTTAAA
*
420697 TTTAAATTTAATTTTAATTTAAA
1 TTTAAATTTAAATTTAATTTAAA
*
420720 TTT-ATTTTCAAATTTAA
1 TTTAAATTT-AAATTTAA
420737 AAAAATTATT
Statistics
Matches: 51, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
22 7 0.14
23 40 0.78
24 4 0.08
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (23 bp):
TTTAAATTTAAATTTAATTTAAA
Found at i:422753 original size:59 final size:58
Alignment explanation
Indices: 422651--422932 Score: 182
Period size: 59 Copynumber: 4.8 Consensus size: 58
422641 AAAGGTCCCT
* * * ** *
422651 AAACTATCCAAAAATTATATTTTAACCCCAAACTTCTTTAAAATTCCATTTTTAACCTTG
1 AAACT-TCAAAAAATTATATTTTTACCCAAAACTTC-CAAAAATTACATTTTTAACCTTG
** * * *
422711 AAACTTTTAAAAATTATATTTTTACCCTAAAACTTCCAAAAATTATATTTTT-ACCCTC
1 AAACTTCAAAAAATTATATTTTTACCC-AAAACTTCCAAAAATTACATTTTTAACCTTG
* ** * * * *
422769 AAACTTCCAAAAATTCCATTTTTGATGCCAAAACTTTCAAAAATTACATTTTTACCCTCG
1 AAACTTCAAAAAATTATATTTTT-A-CCCAAAACTTCCAAAAATTACATTTTTAACCTTG
* * *
422829 -AACTTCAAAAAATCCTA-ATTTTGACCCCGAAACTTCCAAAAATTACCA-TTTTATCCCTT-
1 AAACTTCAAAAAAT--TATATTTTTA-CCCAAAACTTCCAAAAATTA-CATTTTTA-ACCTTG
* **
422888 -AACTTCCAAAAATTCCATTTTTGACCCCAAAAC-TCTCAAAAATTA
1 AAACTTCAAAAAATTATATTTTT-A-CCCAAAACTTC-CAAAAATTA
422933 TCCTTTTACC
Statistics
Matches: 178, Mismatches: 33, Indels: 23
0.76 0.14 0.10
Matches are distributed among these distances:
57 1 0.01
58 30 0.17
59 119 0.67
60 27 0.15
61 1 0.01
ACGTcount: A:0.39, C:0.23, G:0.02, T:0.35
Consensus pattern (58 bp):
AAACTTCAAAAAATTATATTTTTACCCAAAACTTCCAAAAATTACATTTTTAACCTTG
Found at i:422754 original size:88 final size:86
Alignment explanation
Indices: 422647--422933 Score: 262
Period size: 88 Copynumber: 3.2 Consensus size: 86
422637 CCCTAAAGGT
**
422647 CCCTAAACTATCCAAAAATTATATTTTAACCCCAAACTTCTTTAAAATTCCATTTTT-A-ACCTT
1 CCCTAAACT-TCCAAAAATTATATTTTAACCCCAAACTTC-CAAAAATTCCATTTTTGATACC--
* * *
422710 GAAACTTTTAAAAATTATATTTTTA
62 AAAACTTTCAAAAATTACATTTTTA
* *
422735 CCCTAAAACTTCCAAAAATTATATTTTTACCCTCAAACTTCCAAAAATTCCATTTTTGATGCCAA
1 CCCT-AAACTTCCAAAAATTATATTTTAACCC-CAAACTTCCAAAAATTCCATTTTTGATACCAA
422800 AACTTTCAAAAATTACATTTTTA
64 AACTTTCAAAAATTACATTTTTA
* * * *
422823 CCCTCGAACTTCAAAAAATCCTA-ATTTTGACCCCGAAACTTCCAAAAATTACCA-TTTT-ATCC
1 CCCT-AAACTTCCAAAAAT--TATATTTTAACCCC-AAACTTCCAAAAATT-CCATTTTTGATAC
** * *
422885 CTTAACTTCCAAAAATTCCATTTTTGA
61 CAAAACTTTCAAAAATTACATTTTT-A
*
422912 CCCCAAAAC-TCTCAAAAATTAT
1 -CCCTAAACTTC-CAAAAATTAT
422934 CCTTTTACCT
Statistics
Matches: 168, Mismatches: 19, Indels: 24
0.80 0.09 0.11
Matches are distributed among these distances:
87 2 0.01
88 104 0.62
89 52 0.31
90 10 0.06
ACGTcount: A:0.38, C:0.24, G:0.02, T:0.36
Consensus pattern (86 bp):
CCCTAAACTTCCAAAAATTATATTTTAACCCCAAACTTCCAAAAATTCCATTTTTGATACCAAAA
CTTTCAAAAATTACATTTTTA
Found at i:422789 original size:29 final size:29
Alignment explanation
Indices: 422647--422931 Score: 192
Period size: 29 Copynumber: 9.7 Consensus size: 29
422637 CCCTAAAGGT
** *
422647 CCCT-AAACTATCCAAAAATTATATTTTAA
1 CCCTCAAACT-TCCAAAAATTCCATTTTTA
**
422676 CCC-CAAACTTCTTTAAAATTCCATTTTTAA
1 CCCTCAAACTTC-CAAAAATTCCATTTTT-A
* * ** **
422706 CCTTGAAACTTTTAAAAATTATATTTTTA
1 CCCTCAAACTTCCAAAAATTCCATTTTTA
* **
422735 CCCTAAAACTTCCAAAAATTATATTTTTA
1 CCCTCAAACTTCCAAAAATTCCATTTTTA
422764 CCCTCAAACTTCCAAAAATTCCATTTTTGA
1 CCCTCAAACTTCCAAAAATTCCATTTTT-A
* * * *
422794 TGCC-AAAACTTTCAAAAATTACATTTTTA
1 -CCCTCAAACTTCCAAAAATTCCATTTTTA
* * *
422823 CCCTCGAACTT-CAAAAAATCCTAATTTTGA
1 CCCTCAAACTTCCAAAAATTCC--ATTTTTA
422853 CCC-CGAAACTTCCAAAAATTACCA-TTTTA
1 CCCTC-AAACTTCCAAAAATT-CCATTTTTA
*
422882 TCCCT-TAACTTCCAAAAATTCCATTTTTGA
1 -CCCTCAAACTTCCAAAAATTCCATTTTT-A
422912 CCC-CAAAAC-TCTCAAAAATT
1 CCCTC-AAACTTC-CAAAAATT
422932 ATCCTTTTAC
Statistics
Matches: 204, Mismatches: 33, Indels: 37
0.74 0.12 0.14
Matches are distributed among these distances:
28 15 0.07
29 104 0.51
30 68 0.33
31 15 0.07
32 2 0.01
ACGTcount: A:0.38, C:0.24, G:0.02, T:0.35
Consensus pattern (29 bp):
CCCTCAAACTTCCAAAAATTCCATTTTTA
Found at i:422940 original size:59 final size:59
Alignment explanation
Indices: 422719--422940 Score: 222
Period size: 59 Copynumber: 3.8 Consensus size: 59
422709 TGAAACTTTT
** * **
422719 AAAAATTATATTTTT-ACCCTAAAACTTCCAAAAATTATATTTT-TACCCTCAAACTTCC
1 AAAAATTCCATTTTTGACCCCAAAACTTCCAAAAATTACCTTTTAT-CCCTCAAACTTCC
** * * *
422777 AAAAATTCCATTTTTGATGCCAAAACTTTCAAAAATTACATTTT-TACCCTCGAACTT-C
1 AAAAATTCCATTTTTGACCCCAAAACTTCCAAAAATTACCTTTTAT-CCCTCAAACTTCC
* * * *
422835 AAAAAATCCTAATTTTGACCCCGAAACTTCCAAAAATTACCATTTTATCCCT-TAACTTCC
1 AAAAATTCC-ATTTTTGACCCCAAAACTTCCAAAAATTACC-TTTTATCCCTCAAACTTCC
422895 AAAAATTCCATTTTTGACCCCAAAAC-TCTCAAAAATTATCCTTTTA
1 AAAAATTCCATTTTTGACCCCAAAACTTC-CAAAAATTA-CCTTTTA
422941 CCTTCGGATG
Statistics
Matches: 138, Mismatches: 19, Indels: 13
0.81 0.11 0.08
Matches are distributed among these distances:
58 24 0.17
59 94 0.68
60 19 0.14
61 1 0.01
ACGTcount: A:0.38, C:0.24, G:0.03, T:0.35
Consensus pattern (59 bp):
AAAAATTCCATTTTTGACCCCAAAACTTCCAAAAATTACCTTTTATCCCTCAAACTTCC
Found at i:422955 original size:59 final size:57
Alignment explanation
Indices: 422719--422967 Score: 211
Period size: 59 Copynumber: 4.2 Consensus size: 57
422709 TGAAACTTTT
** * ** * *
422719 AAAAATTATATTTTT-ACCCTAAAACTTCCAAAAATTATATTTTTACCCTCAAACTTCC
1 AAAAATTCCATTTTTGACCCCAAAACTT-CAAAAATTA-CCTTTTACCTTCGAACTTCC
** * *
422777 AAAAATTCCATTTTTGATGCCAAAACTTTCAAAAATTACATTTTTACCCTCGAACTT-C
1 AAAAATTCCATTTTTGACCCCAAAAC-TTCAAAAATTAC-CTTTTACCTTCGAACTTCC
* * *
422835 AAAAAATCCTAATTTTGACCCCGAAACTTCCAAAAATTACCATTTTATCCCTT--AACTTCC
1 AAAAATTCC-ATTTTTGACCCCAAAACTT-CAAAAATTACC-TTTTA--CCTTCGAACTTCC
*
422895 AAAAATTCCATTTTTGACCCCAAAACTCTCAAAAATTATCCTTTTACCTTCGGA-TGTCC
1 AAAAATTCCATTTTTGACCCCAAAACT-TCAAAAATTA-CCTTTTACCTTCGAACT-TCC
*
422954 AAAAATTCTATTTT
1 AAAAATTCCATTTT
422968 CGATCCTATT
Statistics
Matches: 158, Mismatches: 19, Indels: 27
0.77 0.09 0.13
Matches are distributed among these distances:
57 4 0.03
58 25 0.16
59 112 0.71
60 14 0.09
61 3 0.02
ACGTcount: A:0.37, C:0.24, G:0.04, T:0.36
Consensus pattern (57 bp):
AAAAATTCCATTTTTGACCCCAAAACTTCAAAAATTACCTTTTACCTTCGAACTTCC
Found at i:425390 original size:18 final size:18
Alignment explanation
Indices: 425367--425402 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
425357 AAAAATTTAC
425367 TTAGTTTACATCAGTAGT
1 TTAGTTTACATCAGTAGT
425385 TTAGTTTACATCAGTAGT
1 TTAGTTTACATCAGTAGT
425403 CATTGAAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.11, G:0.17, T:0.44
Consensus pattern (18 bp):
TTAGTTTACATCAGTAGT
Found at i:432367 original size:206 final size:206
Alignment explanation
Indices: 432006--432597 Score: 999
Period size: 206 Copynumber: 2.9 Consensus size: 206
431996 GCGCTTGATA
* *
432006 TGAGCAAATCTTCGAATCCCAGCTTCCTGATGAGATATTGAGAAGCGGGGTCGAAGCAATAAAAT
1 TGAGCAAATCTTCGAATCCCAGCTTTCTGATGAGATACTGAGAAGC-GGGTCGAAGCAATAAAAT
*
432071 GGTTAGCTTCCTGATGAGATATTGAGAAGTGGACTAAATTCGTCTTCCCT-ATGAGATACAGAGA
65 GGTTAGCTTCCTGATGAGATACTGAGAAGTGGACTAAATTCGTCTT-CCTGATGAGATACAGAGA
*
432135 AGCGGATTGAAACAAACGACGCGGTCATCTTCTTGATGAGATACTGAGAAGAAGACCAAATCAAA
129 AGCGGATTGAAACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAA
432200 CCCATGCTCGATG
194 CCCATGCTCGATG
* *
432213 TGAGCAAATCTTCGAATCCCAACTTTCTGATGAGATACTGAGAAGCGGGTCGAATCAATAAAATG
1 TGAGCAAATCTTCGAATCCCAGCTTTCTGATGAGATACTGAGAAGCGGGTCGAAGCAATAAAATG
* * * * *
432278 GTTAGCTTCTTGATGAGATACTAAGAAGTGGACTAAATTCATCTTCTTGATGAGATACAGATAAG
66 GTTAGCTTCCTGATGAGATACTGAGAAGTGGACTAAATTCGTCTTCCTGATGAGATACAGAGAAG
*
432343 CGGATTGAAACAAACGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACC
131 CGGATTGAAACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACC
432408 CATGCTCGATG
196 CATGCTCGATG
*
432419 TGAGCAAATCTTCGAATCCCAGC-TTCTTGATGAGATACTGAGAAGCGGGTCGAAGCAATAAAAC
1 TGAGCAAATCTTCGAATCCCAGCTTTC-TGATGAGATACTGAGAAGCGGGTCGAAGCAATAAAAT
*
432483 GGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAA
65 GGTTAGCTTCCTGATGAGATACTGAGAAGTGGACTAAATTCGTCTTCCTGATGAGATACAGAGAA
* *
432548 GCGGATTGAAACAAATGACGCGGTCATCTTCCTGATGAGATATTGAGAAG
130 GCGGATTGAAACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAG
432598 CAGGTCGAAG
Statistics
Matches: 359, Mismatches: 24, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
205 5 0.01
206 311 0.87
207 43 0.12
ACGTcount: A:0.34, C:0.18, G:0.24, T:0.24
Consensus pattern (206 bp):
TGAGCAAATCTTCGAATCCCAGCTTTCTGATGAGATACTGAGAAGCGGGTCGAAGCAATAAAATG
GTTAGCTTCCTGATGAGATACTGAGAAGTGGACTAAATTCGTCTTCCTGATGAGATACAGAGAAG
CGGATTGAAACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACC
CATGCTCGATG
Found at i:432498 original size:48 final size:48
Alignment explanation
Indices: 432439--432645 Score: 157
Period size: 48 Copynumber: 4.5 Consensus size: 48
432429 TTCGAATCCC
*
432439 AGCTTCTTGATGAGATACTGAGAAGCGGGTCGAAGCAATAAAACGGTT
1 AGCTTCCTGATGAGATACTGAGAAGCGGGTCGAAGCAATAAAACGGTT
* * **
432487 AGCTTCCTGATGAGATACTGAGAA----GT-GGA-CCA-AATTC-G-T
1 AGCTTCCTGATGAGATACTGAGAAGCGGGTCGAAGCAATAAAACGGTT
* * * * * ** *
432526 --CTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAATGACGCGGTC
1 AGCTTCCTGATGAGATACTGAGAAGCGGGTCGAAGC-AATAAAACGGTT
* * * *
432573 ATCTTCCTGATGAGATATTGAGAAGCAGGTCGAAGCAATAAAATGGTT
1 AGCTTCCTGATGAGATACTGAGAAGCGGGTCGAAGCAATAAAACGGTT
* *
432621 AGCTTCTTGATGAGATACGGAGAAG
1 AGCTTCCTGATGAGATACTGAGAAG
432646 TGAACCAAAT
Statistics
Matches: 119, Mismatches: 28, Indels: 24
0.70 0.16 0.14
Matches are distributed among these distances:
37 21 0.18
39 1 0.01
40 1 0.01
41 4 0.03
42 4 0.03
43 3 0.03
44 3 0.03
45 2 0.02
46 1 0.01
48 51 0.43
49 28 0.24
ACGTcount: A:0.33, C:0.15, G:0.28, T:0.24
Consensus pattern (48 bp):
AGCTTCCTGATGAGATACTGAGAAGCGGGTCGAAGCAATAAAACGGTT
Found at i:432709 original size:134 final size:134
Alignment explanation
Indices: 432441--432731 Score: 420
Period size: 134 Copynumber: 2.2 Consensus size: 134
432431 CGAATCCCAG
* *
432441 CTTCTTGATGAGATACTGAGAAGCGGGTCGAAGCAATAAAACGGTTAGCTTCCTGATGAGATACT
1 CTTCTTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAACGGTTAGCTTCCTGATGAGATACG
* * * ** * *
432506 GAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAATGACGCGG
66 GAGAAGTGAACCAAATTCGTCTTCCTGATGAAACACAGAGAAGCGGATCAAAACAAACGACGCGA
432571 TCAT
131 TCAT
* * * *
432575 CTTCCTGATGAGATATTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCTTGATGAGATACG
1 CTTCTTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAACGGTTAGCTTCCTGATGAGATACG
* * * * *
432640 GAGAAGTGAACCAAATTCGTCTTCCTGATGAAACACATAGAAGTGGATCAAAAGAAGCGATGCGA
66 GAGAAGTGAACCAAATTCGTCTTCCTGATGAAACACAGAGAAGCGGATCAAAACAAACGACGCGA
432705 TCAT
131 TCAT
432709 CTTCTTGATGAGATACTGAGAAG
1 CTTCTTGATGAGATACTGAGAAG
432732 AAGGCCAAAT
Statistics
Matches: 137, Mismatches: 20, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
134 137 1.00
ACGTcount: A:0.34, C:0.16, G:0.26, T:0.24
Consensus pattern (134 bp):
CTTCTTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAACGGTTAGCTTCCTGATGAGATACG
GAGAAGTGAACCAAATTCGTCTTCCTGATGAAACACAGAGAAGCGGATCAAAACAAACGACGCGA
TCAT
Found at i:434130 original size:23 final size:22
Alignment explanation
Indices: 434104--434149 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
434094 TTTTAGAACG
434104 AAATGAGAAAAGGATTTTAAAAA
1 AAAT-AGAAAAGGATTTTAAAAA
* *
434127 AAATCGAAAAGGCTTTTAAAAA
1 AAATAGAAAAGGATTTTAAAAA
434149 A
1 A
434150 GGGGAAATAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.59, C:0.04, G:0.15, T:0.22
Consensus pattern (22 bp):
AAATAGAAAAGGATTTTAAAAA
Found at i:434325 original size:25 final size:25
Alignment explanation
Indices: 434291--434341 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
434281 CGTATTGTGC
*
434291 ATGACGCGAAACCCAGGCGGCTAGG
1 ATGACGCGAAACCCAGGCGACTAGG
434316 ATGACGCGAAACCCAGGCGACTAGG
1 ATGACGCGAAACCCAGGCGACTAGG
434341 A
1 A
434342 CTTCAGGCGG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.31, C:0.27, G:0.33, T:0.08
Consensus pattern (25 bp):
ATGACGCGAAACCCAGGCGACTAGG
Found at i:435073 original size:29 final size:28
Alignment explanation
Indices: 434997--435298 Score: 223
Period size: 29 Copynumber: 10.2 Consensus size: 28
434987 CTTTAAACAG
**
434997 TCCAAAAATTATATTTTAACCCCTAAACT
1 TCCAAAAATTCCATTTTAACCCC-AAACT
435026 TCTTC-AAAATTCCATTTTTAACCCCAAAACT
1 TC--CAAAAATTCCA-TTTTAACCCC-AAACT
* *
435057 TCCAAAACTTCCATTTTTAACCTCAAAACT
1 TCCAAAAATTCCA-TTTTAACC-CCAAACT
* * * *
435087 TCTAAAAATTACATTTTTACCCTCGAACT
1 TCCAAAAATTCCATTTTAACCC-CAAACT
* * * *
435116 TCTAAAAATTACATTTTTACCCTCGAACTT
1 TCCAAAAATTCCATTTTAACCC-CAAAC-T
**
435146 TTAAAAAATTCCATTTTAACCCCAAAACT
1 TCCAAAAATTCCATTTTAACCCC-AAACT
* *
435175 TCCAAAAATTACATTTAAACCCTCAAACT
1 TCCAAAAATTCCATTTTAACCC-CAAACT
* *
435204 TCCAAAAATCCCAATTTAACCCCAAAACT
1 TCCAAAAATTCCATTTTAACCCC-AAACT
* *
435233 TGCAAAAATTACCATTTT-ACCCTCGAACT
1 TCCAAAAATT-CCATTTTAACCC-CAAACT
*
435262 T-CAAAAATTTCCATTTTTGACCCCGAAACT
1 TCCAAAAA-TTCCA-TTTTAACCCC-AAACT
*
435292 CCCAAAA
1 TCCAAAA
435299 TTATCCTTTC
Statistics
Matches: 226, Mismatches: 30, Indels: 32
0.78 0.10 0.11
Matches are distributed among these distances:
28 11 0.05
29 114 0.50
30 77 0.34
31 24 0.11
ACGTcount: A:0.39, C:0.27, G:0.02, T:0.32
Consensus pattern (28 bp):
TCCAAAAATTCCATTTTAACCCCAAACT
Found at i:435153 original size:59 final size:58
Alignment explanation
Indices: 434997--435298 Score: 286
Period size: 59 Copynumber: 5.1 Consensus size: 58
434987 CTTTAAACAG
* * **
434997 TCCAAAAATTATATTTTAACCC-CTAAACTTCTTCAAAATTCCATTTTTAACCCCAAAACT
1 TCCAAAAATTACATTTTTACCCTC-AAACTTC-AAAAAATTCCATTTTT-ACCCCAAAACT
* * * * * *
435057 TCCAAAACTTCCATTTTTAACCTCAAAACTTCTAAAAATTACATTTTTACCCTC-GAACT
1 TCCAAAAATTACATTTTTACCCTC-AAACTTCAAAAAATTCCATTTTTACCC-CAAAACT
* * * *
435116 TCTAAAAATTACATTTTTACCCTCGAACTTTTAAAAAATTCCATTTTAACCCCAAAACT
1 TCCAAAAATTACATTTTTACCCTCAAAC-TTCAAAAAATTCCATTTTTACCCCAAAACT
** * * * *
435175 TCCAAAAATTACATTTAAACCCTCAAACTTCCAAAAATCCCAATTTAACCCCAAAACT
1 TCCAAAAATTACATTTTTACCCTCAAACTTCAAAAAATTCCATTTTTACCCCAAAACT
* * * *
435233 TGCAAAAATTACCA-TTTTACCCTCGAACTTCAAAAATTTCCATTTTTGACCCCGAAACT
1 TCCAAAAATTA-CATTTTTACCCTCAAACTTCAAAAAATTCCATTTTT-ACCCCAAAACT
*
435292 CCCAAAA
1 TCCAAAA
435299 TTATCCTTTC
Statistics
Matches: 197, Mismatches: 39, Indels: 13
0.79 0.16 0.05
Matches are distributed among these distances:
58 65 0.33
59 92 0.47
60 32 0.16
61 8 0.04
ACGTcount: A:0.39, C:0.27, G:0.02, T:0.32
Consensus pattern (58 bp):
TCCAAAAATTACATTTTTACCCTCAAACTTCAAAAAATTCCATTTTTACCCCAAAACT
Found at i:435291 original size:88 final size:87
Alignment explanation
Indices: 434999--435298 Score: 247
Period size: 88 Copynumber: 3.4 Consensus size: 87
434989 TTAAACAGTC
* * * * *
434999 CAAAAATTATATTTTAACCC-CTAAACTTCTTCAAAATTC-CATTTTTAACCCCAAAACTTCCAA
1 CAAAAATTACATTTTTACCCTCGAAACTTC--CAAAAATCACA-ATTTAACCCCAAAACTTCCAA
* *
435062 AACTTCCATTTTTAACCTCAAAACTT
63 AAATTCCA-TTTTACCCTCAAAACTT
* * * * * **
435088 CTAAAAATTACATTTTTACCCTCG-AACTTCTAAAAATTACATTTTTACCCTC-GAACTTTTAAA
1 C-AAAAATTACATTTTTACCCTCGAAACTTCCAAAAATCACAATTTAACCC-CAAAAC-TTCCAA
435151 AAATTCCATTTTAACCC-CAAAACTT
63 AAATTCCATTTT-ACCCTCAAAACTT
** * *
435176 CCAAAAATTACATTTAAACCCTC-AAACTTCCAAAAATCCCAATTTAACCCCAAAACTTGCAAAA
1 -CAAAAATTACATTTTTACCCTCGAAACTTCCAAAAATCACAATTTAACCCCAAAACTTCCAAAA
*
435240 ATTACCATTTTACCCTC-GAACTT
65 ATT-CCATTTTACCCTCAAAACTT
* *
435263 CAAAAATTTCCATTTTTGACCC-CGAAACTCCCAAAA
1 CAAAAA-TTACATTTTT-ACCCTCGAAACTTCCAAAA
435299 TTATCCTTTC
Statistics
Matches: 170, Mismatches: 27, Indels: 29
0.75 0.12 0.13
Matches are distributed among these distances:
86 6 0.04
87 27 0.16
88 94 0.55
89 19 0.11
90 23 0.14
91 1 0.01
ACGTcount: A:0.39, C:0.27, G:0.02, T:0.32
Consensus pattern (87 bp):
CAAAAATTACATTTTTACCCTCGAAACTTCCAAAAATCACAATTTAACCCCAAAACTTCCAAAAA
TTCCATTTTACCCTCAAAACTT
Found at i:441743 original size:24 final size:24
Alignment explanation
Indices: 441711--441756 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
441701 AAGTTACTAG
*
441711 AAAAACTTCTTAAACTTATCATAA
1 AAAAACTTCTCAAACTTATCATAA
441735 AAAAACTTCTCAAACTTATCAT
1 AAAAACTTCTCAAACTTATCAT
441757 CACATTCTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.48, C:0.20, G:0.00, T:0.33
Consensus pattern (24 bp):
AAAAACTTCTCAAACTTATCATAA
Found at i:447882 original size:16 final size:17
Alignment explanation
Indices: 447854--447885 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
447844 TAATTTTTTA
447854 AAAATATTATTTAATAT
1 AAAATATTATTTAATAT
447871 AAAATATT-TTTAATA
1 AAAATATTATTTAATA
447886 CTGTAACTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
AAAATATTATTTAATAT
Found at i:447998 original size:24 final size:25
Alignment explanation
Indices: 447971--448033 Score: 85
Period size: 24 Copynumber: 2.6 Consensus size: 25
447961 AATGATAAAA
447971 TAATAATATAATATAT-ACTACTAC
1 TAATAATATAATATATAACTACTAC
* *
447995 TAATAATATAATATGTAACTATTAC
1 TAATAATATAATATATAACTACTAC
*
448020 TAAT-ACATAATATA
1 TAATAATATAATATA
448034 ATAATATATT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
24 23 0.68
25 11 0.32
ACGTcount: A:0.51, C:0.10, G:0.02, T:0.38
Consensus pattern (25 bp):
TAATAATATAATATATAACTACTAC
Done.