Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 ID=Chr10-JGI_221_v2.0
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: 62175169
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 981721 characters in sequence are not A, C, G, or T
File 126 of 202
Found at i:39026068 original size:42 final size:43
Alignment explanation
Indices: 39025979--39026076 Score: 126
Period size: 42 Copynumber: 2.3 Consensus size: 43
39025969 CTTACACGTG
* ** * *
39025979 GTCTTACATGTAATCAAATAACGATGCCAGTGTCCCAAACAAG
1 GTCTTACACGTAATCAAATAACGACACCAATGTCCCAAACAAC
* *
39026022 GTCTTACACGTAATCATAT-ACGACACCAATGTCCCAAACATC
1 GTCTTACACGTAATCAAATAACGACACCAATGTCCCAAACAAC
39026064 GTCTTACACGTAA
1 GTCTTACACGTAA
39026077 ATTTCAAATT
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
42 31 0.65
43 17 0.35
ACGTcount: A:0.36, C:0.27, G:0.13, T:0.24
Consensus pattern (43 bp):
GTCTTACACGTAATCAAATAACGACACCAATGTCCCAAACAAC
Found at i:39044276 original size:9 final size:9
Alignment explanation
Indices: 39044262--39044298 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
39044252 AAATGCTCGT
39044262 GAAAAAAAA
1 GAAAAAAAA
39044271 GAAAAAAAA
1 GAAAAAAAA
39044280 G--AAAAAA
1 GAAAAAAAA
39044287 GAAAAGAAAA
1 GAAAA-AAAA
39044297 GA
1 GA
39044299 GAGTATATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
7 7 0.28
9 12 0.48
10 6 0.24
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (9 bp):
GAAAAAAAA
Found at i:39044284 original size:16 final size:17
Alignment explanation
Indices: 39044265--39044298 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
39044255 TGCTCGTGAA
39044265 AAAAAAGAAAA-AAAAG
1 AAAAAAGAAAAGAAAAG
39044281 AAAAAAGAAAAGAAAAG
1 AAAAAAGAAAAGAAAAG
39044298 A
1 A
39044299 GAGTATATGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (17 bp):
AAAAAAGAAAAGAAAAG
Found at i:39059593 original size:29 final size:29
Alignment explanation
Indices: 39059560--39059619 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
39059550 GATAACTACT
39059560 CGTAGTAAAGTGGATAGAACTCGGTTGAC
1 CGTAGTAAAGTGGATAGAACTCGGTTGAC
39059589 CGTAGTAAAGTGGATAGAACTCGGTTGAC
1 CGTAGTAAAGTGGATAGAACTCGGTTGAC
39059618 CG
1 CG
39059620 CCTCCATTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.30, C:0.15, G:0.32, T:0.23
Consensus pattern (29 bp):
CGTAGTAAAGTGGATAGAACTCGGTTGAC
Found at i:39061913 original size:22 final size:23
Alignment explanation
Indices: 39061888--39061934 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
39061878 TTCACTTTTC
*
39061888 TTTTCTTTTTC-AT-TTTCTCTTT
1 TTTTCTTATTCAATCTTT-TCTTT
39061910 TTTTCTTATTCAATCTTTTCTTT
1 TTTTCTTATTCAATCTTTTCTTT
39061933 TT
1 TT
39061935 CTTTCATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 10 0.45
23 9 0.41
24 3 0.14
ACGTcount: A:0.09, C:0.17, G:0.00, T:0.74
Consensus pattern (23 bp):
TTTTCTTATTCAATCTTTTCTTT
Found at i:39077535 original size:30 final size:27
Alignment explanation
Indices: 39077492--39077574 Score: 103
Period size: 28 Copynumber: 2.9 Consensus size: 27
39077482 CAGTAGCAGT
*
39077492 ACAGTGTGGGCCTTAGCCCATTACATCA
1 ACAGTGTGGGCCTTAGCCCAATACAT-A
*
39077520 ACAGTGTGAGGGCCTTAGCCCAATACCGTA
1 ACAGTGT--GGGCCTTAGCCCAATA-CATA
*
39077550 ACAATGTGGGCCTTAGCCCAATACA
1 ACAGTGTGGGCCTTAGCCCAATACA
39077575 GTTATCATCC
Statistics
Matches: 48, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
27 1 0.02
28 23 0.48
30 22 0.46
31 2 0.04
ACGTcount: A:0.28, C:0.28, G:0.23, T:0.22
Consensus pattern (27 bp):
ACAGTGTGGGCCTTAGCCCAATACATA
Found at i:39077569 original size:28 final size:29
Alignment explanation
Indices: 39077496--39077573 Score: 97
Period size: 30 Copynumber: 2.7 Consensus size: 29
39077486 AGCAGTACAG
* *
39077496 TGTGGGCCTTAGCCCATTA-CATCAACAG
1 TGTGGGCCTTAGCCCAATACCATCAACAA
*
39077524 TGTGAGGGCCTTAGCCCAATACCGT-AACAA
1 TGT--GGGCCTTAGCCCAATACCATCAACAA
39077554 TGTGGGCCTTAGCCCAATAC
1 TGTGGGCCTTAGCCCAATAC
39077574 AGTTATCATC
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
28 20 0.45
30 22 0.50
31 2 0.05
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (29 bp):
TGTGGGCCTTAGCCCAATACCATCAACAA
Found at i:39077740 original size:26 final size:26
Alignment explanation
Indices: 39077667--39077742 Score: 89
Period size: 26 Copynumber: 2.9 Consensus size: 26
39077657 CACGAATATC
* * * *
39077667 GCAGCAAAGCTGCGAGTAATAATGAT
1 GCAGCAAAGCTGCCAGTAACAGTAAT
* *
39077693 GCAGCATAGTTGCCAGTAACAGTAAT
1 GCAGCAAAGCTGCCAGTAACAGTAAT
*
39077719 GCAGCAAAGCTGCCACTAACAGTA
1 GCAGCAAAGCTGCCAGTAACAGTA
39077743 TATGTGGCAA
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 41 1.00
ACGTcount: A:0.37, C:0.21, G:0.24, T:0.18
Consensus pattern (26 bp):
GCAGCAAAGCTGCCAGTAACAGTAAT
Found at i:39078021 original size:27 final size:27
Alignment explanation
Indices: 39077915--39078141 Score: 226
Period size: 27 Copynumber: 8.4 Consensus size: 27
39077905 AGGGGTATAA
*
39077915 CAGTCATTTTACCCTAT-GGGGGTATTT
1 CAGTCATTTTACCC-ATCGAGGGTATTT
** * *
39077942 TTGTCATTTTACCCTTCGGGGGTATTT
1 CAGTCATTTTACCCATCGAGGGTATTT
** *
39077969 TGGTCATTTTA-CCATTCAAGGGTATTT
1 CAGTCATTTTACCCA-TCGAGGGTATTT
*
39077996 CAGTCATTTTACCCTTCGAGGGTATTT
1 CAGTCATTTTACCCATCGAGGGTATTT
** * *
39078023 TGGTCATTTTACCCATCAAGGGTACTT
1 CAGTCATTTTACCCATCGAGGGTATTT
*
39078050 CAGTCATTTTACCCATCAAGGGTATTT
1 CAGTCATTTTACCCATCGAGGGTATTT
*** *
39078077 TTTTTATTTTACCCATCGAGGGTATTT
1 CAGTCATTTTACCCATCGAGGGTATTT
*
39078104 C-GTTCATTTTTACACATCGAGGGTATTT
1 CAG-TCA-TTTTACCCATCGAGGGTATTT
39078132 CAGTCATTTT
1 CAGTCATTTT
39078142 CTCATGAATC
Statistics
Matches: 166, Mismatches: 28, Indels: 12
0.81 0.14 0.06
Matches are distributed among these distances:
26 3 0.02
27 136 0.82
28 26 0.16
29 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.18, T:0.43
Consensus pattern (27 bp):
CAGTCATTTTACCCATCGAGGGTATTT
Found at i:39078029 original size:81 final size:81
Alignment explanation
Indices: 39077915--39078141 Score: 269
Period size: 81 Copynumber: 2.8 Consensus size: 81
39077905 AGGGGTATAA
* * * * **
39077915 CAGTCATTTTACCCTAT-GGGGGTATTTTTGTCATTTTACCCTTCGGGGGTATTTTGGTCATTTT
1 CAGTCATTTTACCCT-TCGAGGGTATTTTGGTCATTTTACCCATCGAGGGTATTTCAGTCATTTT
39077979 A-CCATTCAAGGGTATTT
65 ACCCA-TCAAGGGTATTT
* *
39077996 CAGTCATTTTACCCTTCGAGGGTATTTTGGTCATTTTACCCATCAAGGGTACTTCAGTCATTTTA
1 CAGTCATTTTACCCTTCGAGGGTATTTTGGTCATTTTACCCATCGAGGGTATTTCAGTCATTTTA
39078061 CCCATCAAGGGTATTT
66 CCCATCAAGGGTATTT
*** * * * * *
39078077 TTTTTATTTTACCCATCGAGGGTATTTCGTTCATTTTTACACATCGAGGGTATTTCAGTCATTTT
1 CAGTCATTTTACCCTTCGAGGGTATTTTGGTCA-TTTTACCCATCGAGGGTATTTCAGTCATTTT
39078142 CTCATGAATC
Statistics
Matches: 125, Mismatches: 18, Indels: 5
0.84 0.12 0.03
Matches are distributed among these distances:
80 1 0.01
81 93 0.74
82 31 0.25
ACGTcount: A:0.20, C:0.19, G:0.18, T:0.43
Consensus pattern (81 bp):
CAGTCATTTTACCCTTCGAGGGTATTTTGGTCATTTTACCCATCGAGGGTATTTCAGTCATTTTA
CCCATCAAGGGTATTT
Found at i:39081794 original size:22 final size:23
Alignment explanation
Indices: 39081778--39081821 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
39081768 AAAAATTCTC
*
39081778 CTGTAATATCCCGAAAATTACGA
1 CTGTAATACCCCGAAAATTACGA
39081801 CTGTAATACCCCGAAAATTAC
1 CTGTAATACCCCGAAAATTAC
39081822 TACAGTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.39, C:0.25, G:0.11, T:0.25
Consensus pattern (23 bp):
CTGTAATACCCCGAAAATTACGA
Found at i:39081829 original size:23 final size:23
Alignment explanation
Indices: 39081780--39081829 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
39081770 AAATTCTCCT
* *
39081780 GTAATATCCCGAAAATTACGACT
1 GTAATACCCCGAAAATTACGACA
*
39081803 GTAATACCCCGAAAATTACTACA
1 GTAATACCCCGAAAATTACGACA
39081826 GTAA
1 GTAA
39081830 AAAGTAGGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.42, C:0.22, G:0.12, T:0.24
Consensus pattern (23 bp):
GTAATACCCCGAAAATTACGACA
Found at i:39084483 original size:22 final size:20
Alignment explanation
Indices: 39084455--39084514 Score: 61
Period size: 20 Copynumber: 2.9 Consensus size: 20
39084445 ACACCACACC
39084455 AAAGGCATCAAAGATGCATAAT
1 AAAGGCATCAAAG-TGCA-AAT
*
39084477 AAAGGCATCGAAGTGCAAAT
1 AAAGGCATCAAAGTGCAAAT
39084497 AGAA-GCA-CAAATGTGCAA
1 A-AAGGCATCAAA-GTGCAA
39084515 TTAGAGGCAC
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
19 3 0.09
20 13 0.38
21 6 0.18
22 12 0.35
ACGTcount: A:0.48, C:0.15, G:0.22, T:0.15
Consensus pattern (20 bp):
AAAGGCATCAAAGTGCAAAT
Found at i:39084512 original size:20 final size:20
Alignment explanation
Indices: 39084487--39084554 Score: 75
Period size: 20 Copynumber: 3.4 Consensus size: 20
39084477 AAAGGCATCG
39084487 AAGTGCAAATAGAAGCAC-A
1 AAGTGCAAATAGAAGCACTA
* * *
39084506 AATGTGCAATTAGAGGCACTG
1 AA-GTGCAAATAGAAGCACTA
* *
39084527 AAGTGCAAACAGATGCACTA
1 AAGTGCAAATAGAAGCACTA
39084547 AAGTGCAA
1 AAGTGCAA
39084555 TCCCATACAA
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
19 2 0.05
20 36 0.90
21 2 0.05
ACGTcount: A:0.44, C:0.16, G:0.24, T:0.16
Consensus pattern (20 bp):
AAGTGCAAATAGAAGCACTA
Found at i:39091907 original size:12 final size:12
Alignment explanation
Indices: 39091890--39091914 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39091880 GCAAGTAGGT
39091890 TAAGGATAGGCC
1 TAAGGATAGGCC
39091902 TAAGGATAGGCC
1 TAAGGATAGGCC
39091914 T
1 T
39091915 GTAACCAACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.16, G:0.32, T:0.20
Consensus pattern (12 bp):
TAAGGATAGGCC
Found at i:39096886 original size:22 final size:22
Alignment explanation
Indices: 39096858--39096900 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
39096848 CAGTTAAACC
39096858 TAAGTTTGTGTCTAAATGGTCT
1 TAAGTTTGTGTCTAAATGGTCT
39096880 TAAGTTTGTGTCTAAATGGTC
1 TAAGTTTGTGTCTAAATGGTC
39096901 ATATTTCATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.23, C:0.09, G:0.23, T:0.44
Consensus pattern (22 bp):
TAAGTTTGTGTCTAAATGGTCT
Found at i:39103562 original size:25 final size:25
Alignment explanation
Indices: 39103504--39103565 Score: 88
Period size: 25 Copynumber: 2.5 Consensus size: 25
39103494 ACGAGCTGTA
39103504 AACGGTAAGCTCCTCCGAGCTAAAT
1 AACGGTAAGCTCCTCCGAGCTAAAT
** *
39103529 AACAATAAGCTCCTCCGAGCTGAAT
1 AACGGTAAGCTCCTCCGAGCTAAAT
*
39103554 AATGGTAAGCTC
1 AACGGTAAGCTC
39103566 ATAGAAGCTG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.21
Consensus pattern (25 bp):
AACGGTAAGCTCCTCCGAGCTAAAT
Found at i:39107718 original size:40 final size:40
Alignment explanation
Indices: 39107674--39107796 Score: 165
Period size: 40 Copynumber: 3.1 Consensus size: 40
39107664 TGATTGGGAC
* * * *
39107674 CACCAAAGGGCAAACAGCGGTACATATGTGCATTCAGGGG
1 CACCAAAGTGCAAACAGAGGCACAGATGTGCATTCAGGGG
* *
39107714 CACCAAAGTACAAACAGGGGCACAGATGTGCATTCAGGGG
1 CACCAAAGTGCAAACAGAGGCACAGATGTGCATTCAGGGG
* * *
39107754 CACCAAAGTGCAAACAAAGGCACAGATATGCATTTAGGGG
1 CACCAAAGTGCAAACAGAGGCACAGATGTGCATTCAGGGG
39107794 CAC
1 CAC
39107797 TTTTTCATTT
Statistics
Matches: 73, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 73 1.00
ACGTcount: A:0.36, C:0.23, G:0.28, T:0.14
Consensus pattern (40 bp):
CACCAAAGTGCAAACAGAGGCACAGATGTGCATTCAGGGG
Found at i:39107733 original size:20 final size:20
Alignment explanation
Indices: 39107708--39107769 Score: 72
Period size: 20 Copynumber: 3.1 Consensus size: 20
39107698 TATGTGCATT
*
39107708 CAGGGGCACCAAAGTACAAA
1 CAGGGGCACCAAAGTGCAAA
* **
39107728 CAGGGGCA-CAGATGTGCATT
1 CAGGGGCACCA-AAGTGCAAA
39107748 CAGGGGCACCAAAGTGCAAA
1 CAGGGGCACCAAAGTGCAAA
39107768 CA
1 CA
39107770 AAGGCACAGA
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
19 2 0.06
20 29 0.88
21 2 0.06
ACGTcount: A:0.37, C:0.24, G:0.29, T:0.10
Consensus pattern (20 bp):
CAGGGGCACCAAAGTGCAAA
Found at i:39119554 original size:152 final size:152
Alignment explanation
Indices: 39119278--39119578 Score: 496
Period size: 152 Copynumber: 2.0 Consensus size: 152
39119268 GATAGAGAGA
* *
39119278 TAGAATTTTCAATAGAATTGGAACCCAGAACAGCTTCTATATCGTGGACACCCTATAGGATGGCA
1 TAGAATTTTCAATAGAATTAGAACCCAGAACAGCTCCTATATCGTGGACACCCTATAGGATGGCA
* * * *
39119343 CTGGTAGAACTTAAGGAATTAAAAGAAAATTTGCAGGACATGTTAAGTAAATGTTTCATAAGGCC
66 CCGATAGAACTTAAGGAATTAAAAGAAAATTTGCAGGACACGTTAAGTAAAGGTTTCATAAGGCC
39119408 TAGTATATCTCATTGGGGGTGC
131 TAGTATATCTCATTGGGGGTGC
*
39119430 TAGAATTTTCAATAGAATTAGAACCCGGAACAGCTCCTATATCGTGGACACCCTATAGGATGGCA
1 TAGAATTTTCAATAGAATTAGAACCCAGAACAGCTCCTATATCGTGGACACCCTATAGGATGGCA
* * *
39119495 CCGATAGAACTTAAGGAATTAAAATAACAA-TTGTAGGACACGTTAAGTAAAGGTTTCATAGGGC
66 CCGATAGAACTTAAGGAATTAAAAGAA-AATTTGCAGGACACGTTAAGTAAAGGTTTCATAAGGC
39119559 CTAGTATATCTCATTGGGGG
130 CTAGTATATCTCATTGGGGG
39119579 CGCCAATCTT
Statistics
Matches: 138, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
152 136 0.99
153 2 0.01
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.27
Consensus pattern (152 bp):
TAGAATTTTCAATAGAATTAGAACCCAGAACAGCTCCTATATCGTGGACACCCTATAGGATGGCA
CCGATAGAACTTAAGGAATTAAAAGAAAATTTGCAGGACACGTTAAGTAAAGGTTTCATAAGGCC
TAGTATATCTCATTGGGGGTGC
Found at i:39125913 original size:28 final size:27
Alignment explanation
Indices: 39125807--39125927 Score: 113
Period size: 27 Copynumber: 4.4 Consensus size: 27
39125797 AAATGAATAT
* * *
39125807 ATAATTTACATAACTTACATAAATATAT
1 ATAATTTACATAACTCACATAACT-TAC
* * * * *
39125835 ATCATAT-CAAAAATCACATAACTTAT
1 ATAATTTACATAACTCACATAACTTAC
39125861 ATAATTTACATAACTCACATAACTTAC
1 ATAATTTACATAACTCACATAACTTAC
39125888 ATAATTTA-ATAAC-CATATCATAACTTAC
1 ATAATTTACATAACTC--A-CATAACTTAC
39125916 ATAATTTACATA
1 ATAATTTACATA
39125928 CCTTTAAAGA
Statistics
Matches: 77, Mismatches: 11, Indels: 9
0.79 0.11 0.09
Matches are distributed among these distances:
25 1 0.01
26 13 0.17
27 37 0.48
28 23 0.30
29 3 0.04
ACGTcount: A:0.48, C:0.17, G:0.00, T:0.36
Consensus pattern (27 bp):
ATAATTTACATAACTCACATAACTTAC
Found at i:39126062 original size:47 final size:47
Alignment explanation
Indices: 39125996--39126126 Score: 174
Period size: 47 Copynumber: 2.7 Consensus size: 47
39125986 TCATAACTTA
* *
39125996 CATAACTGACAT-ACATACATAACTTAATAACTTAAATATATCATAT
1 CATAACTCACATAACATACATAACTTAATAACTTAAATATATCATAC
* *
39126042 CATAACTCACATAACTTACATAACTTAATAACTTATATATATCATAC
1 CATAACTCACATAACATACATAACTTAATAACTTAAATATATCATAC
* *
39126089 CATAACTTACAAAACAAATACATAACTTACATAACTTA
1 CATAACTCACATAAC--ATACATAACTTA-ATAACTTA
39126127 CATAATACAT
Statistics
Matches: 74, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
46 11 0.15
47 44 0.59
49 11 0.15
50 8 0.11
ACGTcount: A:0.48, C:0.20, G:0.01, T:0.31
Consensus pattern (47 bp):
CATAACTCACATAACATACATAACTTAATAACTTAAATATATCATAC
Found at i:39126121 original size:29 final size:29
Alignment explanation
Indices: 39126050--39126128 Score: 88
Period size: 29 Copynumber: 2.7 Consensus size: 29
39126040 ATCATAACTC
* **
39126050 ACATAACTTACATAACTTA-ATAACTTAT
1 ACATAACTTACATAACTTACAAAACAAAT
* * *
39126078 ATATATCATACCATAACTTACAAAACAAAT
1 ACATAACTTA-CATAACTTACAAAACAAAT
39126108 ACATAACTTACATAACTTACA
1 ACATAACTTACATAACTTACA
39126129 TAATACATAA
Statistics
Matches: 40, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
28 7 0.17
29 20 0.50
30 13 0.32
ACGTcount: A:0.49, C:0.20, G:0.00, T:0.30
Consensus pattern (29 bp):
ACATAACTTACATAACTTACAAAACAAAT
Found at i:39126175 original size:165 final size:163
Alignment explanation
Indices: 39125974--39126405 Score: 626
Period size: 165 Copynumber: 2.6 Consensus size: 163
39125964 TTAATAACTT
* *
39125974 ATATATATCAGATCATAACTTACATAACTGACATACATACATAACTTAATAACTTAAATATATCA
1 ATATATATCATATCATAACTTACATAACTCACATACATACATAACTTAATAACTTAAATATATCA
39126039 TATCATAACTCACATAACTTACATAACTTAATAACTTATATATATCATACCATAACTTACAAAAC
66 TATCATAACTCACATAACTTACATAACTTAATAACTTATATATATCATACCATAACTTACAAAAC
39126104 AAAT-ACATAACTTACATAACTTACATAATACATAA
131 ---TCACATAACTTACATAACTTACATAATACATAA
* * *
39126139 ATATATATCATATCATAACTTACATAACTCACATACATACATAACTTAATGACTTATATGTATCA
1 ATATATATCATATCATAACTTACATAACTCACATACATACATAACTTAATAACTTAAATATATCA
* **
39126204 TATCATAACTCACATAACTTACGTAACTTAATAACTTATATATATCATACCATAACTTACGTAAC
66 TATCATAACTCACATAACTTACATAACTTAATAACTTATATATATCATACCATAACTTACAAAAC
39126269 TCACATAACTTACATAACTTACATAATACATAA
131 TCACATAACTTACATAACTTACATAATACATAA
* *
39126302 ATATATATCATATCATAACTTACATAACTTA-AT-TATACTTATAACTTACA-AA---AATATAT
1 ATATATATCATATCATAACTTACATAACTCACATACATAC--ATAACTTA-ATAACTTAA-ATAT
* *
39126361 ATCATATCATAACTTACATAATTTACATAACTTAATTATACTTAT
62 ATCATATCATAACTCACATAACTTACATAACTTAA-TA-ACTTAT
39126406 CCTTAAACCC
Statistics
Matches: 244, Mismatches: 16, Indels: 16
0.88 0.06 0.06
Matches are distributed among these distances:
160 1 0.00
161 39 0.16
162 5 0.02
163 76 0.31
164 1 0.00
165 122 0.50
ACGTcount: A:0.46, C:0.18, G:0.01, T:0.34
Consensus pattern (163 bp):
ATATATATCATATCATAACTTACATAACTCACATACATACATAACTTAATAACTTAAATATATCA
TATCATAACTCACATAACTTACATAACTTAATAACTTATATATATCATACCATAACTTACAAAAC
TCACATAACTTACATAACTTACATAATACATAA
Found at i:39126240 original size:8 final size:9
Alignment explanation
Indices: 39125850--39126394 Score: 219
Period size: 9 Copynumber: 59.1 Consensus size: 9
39125840 ATCAAAAATC
39125850 ACATAACTT
1 ACATAACTT
* *
39125859 ATATAATTT
1 ACATAACTT
*
39125868 ACATAACTC
1 ACATAACTT
39125877 ACATAACTT
1 ACATAACTT
*
39125886 ACATAATTT
1 ACATAACTT
*
39125895 A-ATAACCAT
1 ACATAA-CTT
39125904 ATCATAACTT
1 A-CATAACTT
*
39125914 ACATAATTT
1 ACATAACTT
*
39125923 ACATACCTTT
1 ACATAAC-TT
* *
39125933 AAAGAA-TT
1 ACATAACTT
* *
39125941 AAAAAAAAACTTT
1 ---ACATAAC-TT
*
39125954 GGATCTTAACTT
1 --A-CATAACTT
39125966 A-ATAACTT
1 ACATAACTT
* **
39125974 ATATATATCAG
1 ACATA-A-CTT
39125985 ATCATAACTT
1 A-CATAACTT
*
39125995 ACATAACTG
1 ACATAACTT
*
39126004 ACAT-ACAT
1 ACATAACTT
39126012 ACATAACTT
1 ACATAACTT
39126021 A-ATAACTT
1 ACATAACTT
* *
39126029 AAATATATCAT
1 ACATA-A-CTT
*
39126040 ATCATAACTC
1 A-CATAACTT
39126050 ACATAACTT
1 ACATAACTT
39126059 ACATAACTT
1 ACATAACTT
39126068 A-ATAACTT
1 ACATAACTT
* *
39126076 ATATATATCAT
1 ACATA-A-CTT
39126087 ACCATAACTT
1 A-CATAACTT
* *
39126097 ACAAAACAAAT
1 ACATAAC--TT
39126108 ACATAACTT
1 ACATAACTT
39126117 ACATAACTT
1 ACATAACTT
39126126 ACATAA--T
1 ACATAACTT
*
39126133 ACATAA-AT
1 ACATAACTT
* * *
39126141 ATATATCAT
1 ACATAACTT
39126150 ATCATAACTT
1 A-CATAACTT
*
39126160 ACATAACTC
1 ACATAACTT
*
39126169 ACAT-ACAT
1 ACATAACTT
39126177 ACATAACTT
1 ACATAACTT
*
39126186 A-ATGACTT
1 ACATAACTT
* * *
39126194 ATATGTATCAT
1 ACA--TAACTT
*
39126205 ATCATAACTC
1 A-CATAACTT
39126215 ACATAACTT
1 ACATAACTT
*
39126224 ACGTAACTT
1 ACATAACTT
39126233 A-ATAACTT
1 ACATAACTT
* *
39126241 ATATATATCAT
1 ACATA-A-CTT
39126252 ACCATAACTT
1 A-CATAACTT
* *
39126262 ACGTAACTC
1 ACATAACTT
39126271 ACATAACTT
1 ACATAACTT
39126280 ACATAACTT
1 ACATAACTT
39126289 ACATAA--T
1 ACATAACTT
*
39126296 ACATAA-AT
1 ACATAACTT
* * *
39126304 ATATATCAT
1 ACATAACTT
39126313 ATCATAACTT
1 A-CATAACTT
39126323 ACATAACTT
1 ACATAACTT
39126332 A-ATTATACTT
1 ACA-TA-ACTT
39126342 --ATAACTT
1 ACATAACTT
**
39126349 ACA-AAAAT
1 ACATAACTT
* * *
39126357 ATATATCAT
1 ACATAACTT
39126366 ATCATAACTT
1 A-CATAACTT
*
39126376 ACATAATTT
1 ACATAACTT
39126385 ACATAACTT
1 ACATAACTT
39126394 A
1 A
39126395 ATTATACTTA
Statistics
Matches: 404, Mismatches: 86, Indels: 92
0.69 0.15 0.16
Matches are distributed among these distances:
7 18 0.04
8 73 0.18
9 208 0.51
10 49 0.12
11 35 0.09
12 16 0.04
13 5 0.01
ACGTcount: A:0.46, C:0.18, G:0.02, T:0.34
Consensus pattern (9 bp):
ACATAACTT
Found at i:39126241 original size:47 final size:47
Alignment explanation
Indices: 39126109--39126289 Score: 179
Period size: 47 Copynumber: 3.7 Consensus size: 47
39126099 AAAACAAATA
* *
39126109 CATAACTTACATAACTTACATAA--TACATAAATATATATCATATCATAAC
1 CATAACTCACATAACTTACATAACTTA-ATAACT-TATAT-ATATCAT-AC
* * * *
39126158 TTACATAACTCACAT-ACATACATAACTTAATGACTTATATGTATCATAT
1 ---CATAACTCACATAACTTACATAACTTAATAACTTATATATATCATAC
*
39126207 CATAACTCACATAACTTACGTAACTTAATAACTTATATATATCATAC
1 CATAACTCACATAACTTACATAACTTAATAACTTATATATATCATAC
* * *
39126254 CATAACTTACGTAACTCACATAACTTACATAACTTA
1 CATAACTCACATAACTTACATAACTTA-ATAACTTA
39126290 CATAATACAT
Statistics
Matches: 110, Mismatches: 15, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
46 12 0.11
47 52 0.47
48 8 0.07
49 1 0.01
50 6 0.05
51 14 0.13
52 15 0.14
53 2 0.02
ACGTcount: A:0.44, C:0.20, G:0.02, T:0.34
Consensus pattern (47 bp):
CATAACTCACATAACTTACATAACTTAATAACTTATATATATCATAC
Found at i:39129065 original size:21 final size:21
Alignment explanation
Indices: 39129038--39129147 Score: 139
Period size: 21 Copynumber: 5.2 Consensus size: 21
39129028 CTACAACTTA
* *
39129038 AAGCAGAGGCAGCAATGAAGG
1 AAGCAGAGGCAGCAGTGAGGG
* * *
39129059 AAACAGAGGCAGTAGCGAGGG
1 AAGCAGAGGCAGCAGTGAGGG
39129080 AAGCAGAGGCAGCAGTGAGGG
1 AAGCAGAGGCAGCAGTGAGGG
* * *
39129101 AAGCAGAGGCAGTAGCGAGAG
1 AAGCAGAGGCAGCAGTGAGGG
*
39129122 AAGCAGAGGCAGCAGCGAGGG
1 AAGCAGAGGCAGCAGTGAGGG
39129143 AAGCA
1 AAGCA
39129148 AAGCAGAGCA
Statistics
Matches: 76, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 76 1.00
ACGTcount: A:0.38, C:0.15, G:0.43, T:0.04
Consensus pattern (21 bp):
AAGCAGAGGCAGCAGTGAGGG
Found at i:39129136 original size:42 final size:42
Alignment explanation
Indices: 39129038--39129147 Score: 175
Period size: 42 Copynumber: 2.6 Consensus size: 42
39129028 CTACAACTTA
* * * *
39129038 AAGCAGAGGCAGCAATGAAGGAAACAGAGGCAGTAGCGAGGG
1 AAGCAGAGGCAGCAGTGAGGGAAGCAGAGGCAGTAGCGAGAG
39129080 AAGCAGAGGCAGCAGTGAGGGAAGCAGAGGCAGTAGCGAGAG
1 AAGCAGAGGCAGCAGTGAGGGAAGCAGAGGCAGTAGCGAGAG
*
39129122 AAGCAGAGGCAGCAGCGAGGGAAGCA
1 AAGCAGAGGCAGCAGTGAGGGAAGCA
39129148 AAGCAGAGCA
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 63 1.00
ACGTcount: A:0.38, C:0.15, G:0.43, T:0.04
Consensus pattern (42 bp):
AAGCAGAGGCAGCAGTGAGGGAAGCAGAGGCAGTAGCGAGAG
Found at i:39129533 original size:43 final size:43
Alignment explanation
Indices: 39129449--39129731 Score: 349
Period size: 42 Copynumber: 6.7 Consensus size: 43
39129439 GTAAAATGCT
* *
39129449 GCTAAAGGTCATG-TTTTTAGCGGCATTTGCTATAAAAGCGCC
1 GCTAAAGGTCATGATCTTTAGCGGCGTTTGCTATAAAAGCGCC
* * * * * * *
39129491 GCTAAATGTTATGTTTTTTAGCGGCGTTTTCTACAAAGGCGCC
1 GCTAAAGGTCATGATCTTTAGCGGCGTTTGCTATAAAAGCGCC
* **
39129534 GCTAAAGGTCATGTTCTTTAGTAGCGTTT-CTATAAAAGCGCC
1 GCTAAAGGTCATGATCTTTAGCGGCGTTTGCTATAAAAGCGCC
* * *
39129576 GCTAAAGGTCATGTTC-TTAGTGGCGTTTTCTATAAAAGCGCC
1 GCTAAAGGTCATGATCTTTAGCGGCGTTTGCTATAAAAGCGCC
* *
39129618 GCTAAAGGTCATGATCTTTAGTGGCG-TTGCTATAAAAGCGTC
1 GCTAAAGGTCATGATCTTTAGCGGCGTTTGCTATAAAAGCGCC
* * *
39129660 GCTAAATGTCATGATCTATAGCGGCGTTTGCTATAAAAGTGCC
1 GCTAAAGGTCATGATCTTTAGCGGCGTTTGCTATAAAAGCGCC
*
39129703 GCTAAAGGTCATGACCTTTAGCGGCGTTT
1 GCTAAAGGTCATGATCTTTAGCGGCGTTT
39129732 ATGTGAAAAA
Statistics
Matches: 212, Mismatches: 25, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
41 11 0.05
42 103 0.49
43 98 0.46
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.33
Consensus pattern (43 bp):
GCTAAAGGTCATGATCTTTAGCGGCGTTTGCTATAAAAGCGCC
Found at i:39129571 original size:85 final size:84
Alignment explanation
Indices: 39129424--39129731 Score: 361
Period size: 85 Copynumber: 3.7 Consensus size: 84
39129414 GATGCCAAAG
* * * * *
39129424 TTAGTGGCGTTTT-TAGTAAAA-TGCTGCTAAAGGTCATGTT-TTTAGCGGCATTTGCTATAAAA
1 TTAGCGGCGTTTTCTA-TAAAAGCGCCGCTAAAGGTCATGTTCTTTAGTGGCGTTT-CTATAAAA
*
39129486 GCGCCGCTAAATGTTATGTTTT
64 GCGCCGCTAAATGTCATG-TTT
* * *
39129508 TTAGCGGCGTTTTCTACAAAGGCGCCGCTAAAGGTCATGTTCTTTAGTAGCGTTTCTATAAAAGC
1 TTAGCGGCGTTTTCTATAAAAGCGCCGCTAAAGGTCATGTTCTTTAGTGGCGTTTCTATAAAAGC
* *
39129573 GCCGCTAAAGGTCATGTTC
66 GCCGCTAAATGTCATGTTT
* * *
39129592 TTAGTGGCGTTTTCTATAAAAGCGCCGCTAAAGGTCATGATCTTTAGTGGCGTTGCTATAAAAGC
1 TTAGCGGCGTTTTCTATAAAAGCGCCGCTAAAGGTCATGTTCTTTAGTGGCGTTTCTATAAAAGC
* *
39129657 GTCGCTAAATGTCATGATCT
66 GCCGCTAAATGTCATG-TTT
* * * ** *
39129677 ATAGCGGCGTTTGCTATAAAAGTGCCGCTAAAGGTCATGACCTTTAGCGGCGTTT
1 TTAGCGGCGTTTTCTATAAAAGCGCCGCTAAAGGTCATGTTCTTTAGTGGCGTTT
39129732 ATGTGAAAAA
Statistics
Matches: 192, Mismatches: 28, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
84 90 0.47
85 92 0.48
86 10 0.05
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (84 bp):
TTAGCGGCGTTTTCTATAAAAGCGCCGCTAAAGGTCATGTTCTTTAGTGGCGTTTCTATAAAAGC
GCCGCTAAATGTCATGTTT
Found at i:39129694 original size:127 final size:127
Alignment explanation
Indices: 39129449--39129715 Score: 347
Period size: 127 Copynumber: 2.1 Consensus size: 127
39129439 GTAAAATGCT
* * * * *
39129449 GCTAAAGGTCATGTTTTTAGCGGCATTTGCTATAAAAGCGCCGCTAAATGTTATGTTTTTTAGCG
1 GCTAAAGGTCATGTTCTTAGCGGCATTTGCTATAAAAGCGCCGCTAAAGGTCATGATCTTTAGCG
* * * * *
39129514 GCGTTTTCTACAAAGGCGCCGCTAAAGGTCATGTTCTTTAGTAGCGTTTCTATAAAAGCGCC
66 GCGTTTGCTACAAAAGCGCCGCTAAAGGTCATGATCTATAGCAGCGTTTCTATAAAAGCGCC
* * * *
39129576 GCTAAAGGTCATGTTCTTAGTGGCGTTTTCTATAAAAGCGCCGCTAAAGGTCATGATCTTTAGTG
1 GCTAAAGGTCATGTTCTTAGCGGCATTTGCTATAAAAGCGCCGCTAAAGGTCATGATCTTTAGCG
* * * * *
39129641 GCG-TTGCTATAAAAGCGTCGCTAAATGTCATGATCTATAGCGGCGTTTGCTATAAAAGTGCC
66 GCGTTTGCTACAAAAGCGCCGCTAAAGGTCATGATCTATAGCAGCGTTT-CTATAAAAGCGCC
39129703 GCTAAAGGTCATG
1 GCTAAAGGTCATG
39129716 ACCTTTAGCG
Statistics
Matches: 120, Mismatches: 19, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
126 36 0.30
127 84 0.70
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.32
Consensus pattern (127 bp):
GCTAAAGGTCATGTTCTTAGCGGCATTTGCTATAAAAGCGCCGCTAAAGGTCATGATCTTTAGCG
GCGTTTGCTACAAAAGCGCCGCTAAAGGTCATGATCTATAGCAGCGTTTCTATAAAAGCGCC
Found at i:39130085 original size:18 final size:18
Alignment explanation
Indices: 39130051--39130103 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
39130041 ATTCACCTAA
*
39130051 ACCCAATCCAGACCCAAGT
1 ACCCAACCCA-ACCCAAGT
** *
39130070 ATTCAACCCAACCCAATT
1 ACCCAACCCAACCCAAGT
39130088 ACCCAACCCAACCCAA
1 ACCCAACCCAACCCAA
39130104 TCATAAAAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
18 21 0.75
19 7 0.25
ACGTcount: A:0.40, C:0.45, G:0.04, T:0.11
Consensus pattern (18 bp):
ACCCAACCCAACCCAAGT
Found at i:39130221 original size:9 final size:9
Alignment explanation
Indices: 39130207--39130325 Score: 134
Period size: 9 Copynumber: 13.2 Consensus size: 9
39130197 GTAGTGATTC
39130207 AATTCGGTT
1 AATTCGGTT
39130216 AATTCGGTT
1 AATTCGGTT
*
39130225 AATTCGGGT
1 AATTCGGTT
39130234 AATTCGGTT
1 AATTCGGTT
*
39130243 AATTCGGGT
1 AATTCGGTT
39130252 AATTCGGTT
1 AATTCGGTT
*
39130261 AATTCGATT
1 AATTCGGTT
**
39130270 AATTCAATT
1 AATTCGGTT
39130279 AATTCAGG-T
1 AATTC-GGTT
**
39130288 AATTCAATT
1 AATTCGGTT
39130297 AATTCAGG-T
1 AATTC-GGTT
39130306 AATTCGGTT
1 AATTCGGTT
*
39130315 AATTCAGTT
1 AATTCGGTT
39130324 AA
1 AA
39130326 CCGACCGAAT
Statistics
Matches: 93, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
8 2 0.02
9 91 0.98
ACGTcount: A:0.30, C:0.11, G:0.18, T:0.40
Consensus pattern (9 bp):
AATTCGGTT
Found at i:39136273 original size:7 final size:7
Alignment explanation
Indices: 39136263--39136287 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
39136253 TATATTAATG
39136263 ATAAATT
1 ATAAATT
39136270 ATAAATT
1 ATAAATT
39136277 ATAAATT
1 ATAAATT
39136284 ATAA
1 ATAA
39136288 TATATAGAGA
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (7 bp):
ATAAATT
Found at i:39137783 original size:3 final size:3
Alignment explanation
Indices: 39137775--39137812 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
39137765 ACAAATTTTA
39137775 TAT TAT TAT TAT TAT TAT TAT T-T TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
39137813 ATATATCATT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:39138089 original size:2 final size:2
Alignment explanation
Indices: 39138071--39138107 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
39138061 TGGCTTCTTT
* *
39138071 TA TA TC TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
39138108 TTATCTTATT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:39138160 original size:13 final size:14
Alignment explanation
Indices: 39138141--39138179 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
39138131 CATGCACATT
*
39138141 TTTATATGTATATA
1 TTTATATATATATA
39138155 -TTATATATATATA
1 TTTATATATATATA
39138168 TTTATATA-ATAT
1 TTTATATATATAT
39138180 TTATACGCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 16 0.70
14 7 0.30
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (14 bp):
TTTATATATATATA
Found at i:39138167 original size:21 final size:21
Alignment explanation
Indices: 39138143--39138184 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
39138133 TGCACATTTT
*
39138143 TATATGTATATATTATATATA
1 TATATGTATATAATATATATA
* *
39138164 TATATTTATATAATATTTATA
1 TATATGTATATAATATATATA
39138185 CGCATTTGCG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (21 bp):
TATATGTATATAATATATATA
Found at i:39138179 original size:11 final size:12
Alignment explanation
Indices: 39138149--39138184 Score: 56
Period size: 11 Copynumber: 3.0 Consensus size: 12
39138139 TTTTTATATG
39138149 TATATATTATATA
1 TATATATT-TATA
39138162 TATATATTTATA
1 TATATATTTATA
39138174 TA-ATATTTATA
1 TATATATTTATA
39138185 CGCATTTGCG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 9 0.39
12 6 0.26
13 8 0.35
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
TATATATTTATA
Found at i:39142380 original size:6 final size:6
Alignment explanation
Indices: 39142349--39142408 Score: 63
Period size: 6 Copynumber: 10.3 Consensus size: 6
39142339 GTTCATACTC
* *
39142349 AAAA-A AAAACA ACAAA-A AAAATA AAAACA AAAACA AAAACA AAAATA
1 AAAACA AAAACA A-AAACA AAAACA AAAACA AAAACA AAAACA AAAACA
*
39142396 AAAA-A AAATCA AA
1 AAAACA AAAACA AA
39142409 GTCAAAAAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
5 11 0.23
6 34 0.71
7 3 0.06
ACGTcount: A:0.85, C:0.10, G:0.00, T:0.05
Consensus pattern (6 bp):
AAAACA
Found at i:39142392 original size:24 final size:22
Alignment explanation
Indices: 39142349--39142408 Score: 84
Period size: 24 Copynumber: 2.6 Consensus size: 22
39142339 GTTCATACTC
39142349 AAAAAAAAACAACAAAAAAAATA
1 AAAAAAAAACAA-AAAAAAAATA
39142372 AAAACAAAAACAAAAACAAAAATA
1 AAAA-AAAAACAAAAA-AAAAATA
*
39142396 AAAAAAAATCAAA
1 AAAAAAAAACAAA
39142409 GTCAAAAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
23 15 0.44
24 19 0.56
ACGTcount: A:0.85, C:0.10, G:0.00, T:0.05
Consensus pattern (22 bp):
AAAAAAAAACAAAAAAAAAATA
Found at i:39144822 original size:170 final size:169
Alignment explanation
Indices: 39144375--39145015 Score: 980
Period size: 170 Copynumber: 3.7 Consensus size: 169
39144365 GTTCATTATA
*
39144375 CAGGTCTTATTTCCCTGAGATTACAATGGAACAGACAGAAGAATTTCAGATCTTATCTCCCTGAG
1 CAGGTCTTATTTCCCTGAGATTACAGTGGAACAGAC-GAAGAATTTCAGATCTTATCTCCCTGAG
* *
39144440 ATTACAGCAGAGCAGATCGATA-CTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAA
65 ATTACAGCGGAGCAGATTGA-AGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGA-T--
* *
39144504 AATAAAGGATCTTATCTCTCTGAGGTTACAGTAGAGTAGATCGCGT
126 --TAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCGC
* * *
39144550 CAGGTCTTATCTCCCTGATATTACAGTGGAGCAGACGAAGAATTTCAGATCTTATCTCCCTGAGA
1 CAGGTCTTATTTCCCTGAGATTACAGTGGAACAGACGAAGAATTTCAGATCTTATCTCCCTGAGA
* *
39144615 TTACAGCGGAGCAGATTGAAGATAGTAATCCTATCTCCCTGAGATTACAGTAGAGCGGATTAAAG
66 TTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAG
*
39144680 GATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCAC
131 GATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCGC
* * *
39144719 CAGGTCTCATTTCCCTAAGATTACAGTGGAACAGATCGAAGAATTTCAGATCTTATCTCCCTGAT
1 CAGGTCTTATTTCCCTGAGATTACAGTGGAACAGA-CGAAGAATTTCAGATCTTATCTCCCTGAG
* * *
39144784 ATTACAGCGGAGCAAATTGAAGCTAGTAATCTTATCTCCCTGAGATTACAGCGGAGCGGATTAAA
65 ATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAA
*
39144849 GGATCTTGTCTCTCTGAAGTTACAGTAGAGTAGATCGCGC
130 GGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCGC
39144889 CAGGTCTTATTTCCCTGAGATTACAGTGGAACAGATCGAAGAATTTCAGATCTTATCTCCCTGAG
1 CAGGTCTTATTTCCCTGAGATTACAGTGGAACAGA-CGAAGAATTTCAGATCTTATCTCCCTGAG
* * * *
39144954 ATTACAGCGGAGCAGATTGAAGCCAG-AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATT
65 ATTACAGCGGAGCAGATTGAAGCTAGTA-ATCCTATCTCCCTGAGATTACAGTGGAGCGGATT
39145016 GAAGATAGTA
Statistics
Matches: 433, Mismatches: 30, Indels: 11
0.91 0.06 0.02
Matches are distributed among these distances:
169 72 0.17
170 245 0.57
173 2 0.00
174 82 0.19
175 32 0.07
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (169 bp):
CAGGTCTTATTTCCCTGAGATTACAGTGGAACAGACGAAGAATTTCAGATCTTATCTCCCTGAGA
TTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAG
GATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCGC
Found at i:39145000 original size:90 final size:88
Alignment explanation
Indices: 39144554--39145059 Score: 277
Period size: 90 Copynumber: 5.9 Consensus size: 88
39144544 TCGCGTCAGG
* * * * *
39144554 TCTTATCTCCCTGATATTACAGTGGAGCAGA-CGAAGA-ATTTCAGATCTTATCTCCCTGAGATT
1 TCTTATCTCCCTGAGATTACAGCGGAACAGATCGAAGATA-GT-A-ATCCTATCTCCCTGAGATT
**
39144617 ACAGCGGAGCAGATTGAAGATAGTA-A
63 ACAGCGGAGCAGATTGAAGCCAG-AGA
* ** * * * * * *
39144643 TCCTATCTCCCTGAGATTACAGTAGAGCGGAT--TA-A-AG-GATCTTATCTCTCTGA-AGTTAC
1 TCTTATCTCCCTGAGATTACAGCGGAACAGATCGAAGATAGTAATCCTATCTCCCTGAGA-TTAC
** * * *
39144702 AGTAGAGTAGATCGCA-CCAG-G-
65 AGCGGAGCAGATTGAAGCCAGAGA
* * * * * * *
39144723 TCTCATTTCCCTAAGATTACAGTGGAACAGATCGAAGA-ATTTCAGATCTTATCTCCCTGATATT
1 TCTTATCTCCCTGAGATTACAGCGGAACAGATCGAAGATA-GT-A-ATCCTATCTCCCTGAGATT
* *
39144787 ACAGCGGAGCAAATTGAAGCTAGTA-A
63 ACAGCGGAGCAGATTGAAGCCAG-AGA
* * * * * * *
39144813 TCTTATCTCCCTGAGATTACAGCGGAGCGGAT--TA-A-AG-GATCTTGTCTCTCTGA-AGTTAC
1 TCTTATCTCCCTGAGATTACAGCGGAACAGATCGAAGATAGTAATCCTATCTCCCTGAGA-TTAC
** * * *
39144872 AGTAGAGTAGATCG-CGCCAG-G-
65 AGCGGAGCAGATTGAAGCCAGAGA
* * * *
39144893 TCTTATTTCCCTGAGATTACAGTGGAACAGATCGAAGA-ATTTCAGATCTTATCTCCCTGAGATT
1 TCTTATCTCCCTGAGATTACAGCGGAACAGATCGAAGATA-GT-A-ATCCTATCTCCCTGAGATT
39144957 ACAGCGGAGCAGATTGAAGCCAGAGA
63 ACAGCGGAGCAGATTGAAGCCAGAGA
* *
39144983 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGATAGTAATCCTATCTCCCTGAGATTACA
1 TCTTATCTCCCTGAGATTACAGCGGAACAGATCGAAGATAGTAATCCTATCTCCCTGAGATTACA
* *
39145048 GTGGAGCGGATT
66 GCGGAGCAGATT
39145060 AAAATAAAGG
Statistics
Matches: 315, Mismatches: 73, Indels: 59
0.70 0.16 0.13
Matches are distributed among these distances:
80 53 0.17
82 10 0.03
83 59 0.19
87 59 0.19
88 43 0.14
89 29 0.09
90 61 0.19
91 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (88 bp):
TCTTATCTCCCTGAGATTACAGCGGAACAGATCGAAGATAGTAATCCTATCTCCCTGAGATTACA
GCGGAGCAGATTGAAGCCAGAGA
Found at i:39145078 original size:44 final size:44
Alignment explanation
Indices: 39144372--39145321 Score: 372
Period size: 44 Copynumber: 21.9 Consensus size: 44
39144362 TAGGTTCATT
* * * **
39144372 ATACAGG-TCTTATTTCCCTGAGATTACAATGGAACAGACAGAAGA
1 ATACAGGATCTTATCTCCCTGAGATTACAGTGGAGCAGA-TTAA-A
* ** **
39144417 ATTTCA-GATCTTATCTCCCTGAGATTACAGCAGAGCAGA-T-CG
1 A-TACAGGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAA
* * *
39144459 ATACTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAA
1 ATAC-AG-GATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAA
* * * * * ***
39144505 ATAAAGGATCTTATCTCTCTGAGGTTACAGTAGAGTAGA-TCGC
1 ATACAGGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAA
* * **
39144548 GT-CAGG-TCTTATCTCCCTGATATTACAGTGGAGCAGACGAAGA
1 ATACAGGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAA-A
* * *
39144591 ATTTCA-GATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAG
1 A-TACAGGATCTTATCTCCCTGAGATTACAGTGGAGCAGATT-AAA
* * * *
39144636 AT--AGTAATCCTATCTCCCTGAGATTACAGTAGAGCGGATT---
1 ATACAG-GATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAA
* * * ***
39144676 A-A-AGGATCTTATCTCTCTGA-AGTTACAGTAGAGTAGA-TCGC
1 ATACAGGATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTAAA
* * * * * *
39144717 A-CCAGG-TCTCATTTCCCTAAGATTACAGTGGAACAGATCGAAGA
1 ATACAGGATCTTATCTCCCTGAGATTACAGTGGAGCAGAT-TAA-A
* * * * *
39144761 ATTTCA-GATCTTATCTCCCTGATATTACAGCGGAGCAAATT-GA
1 A-TACAGGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAA
* * * *
39144804 A-GCTAGTAATCTTATCTCCCTGAGATTACAGCGGAGCGGATT---
1 ATAC-AG-GATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAA
* * * * **
39144846 A-A-AGGATCTTGTCTCTCTGA-AGTTACAGTAGAGTAGA-T-CG
1 ATACAGGATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTAAA
*** * * *
39144886 CGCCAGG-TCTTATTTCCCTGAGATTACAGTGGAACAGATCGAAGA
1 ATACAGGATCTTATCTCCCTGAGATTACAGTGGAGCAGAT-TAA-A
* * *
39144931 ATTTCA-GATCTTATCTCCCTGAGATTACAGCGGAGCAGATT-GA
1 A-TACAGGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAA
** * *
39144974 AGCCAGAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAG
1 ATACAG-GATCTTATCTCCCTGAGATTACAGTGGAGCAGATT-AAA
* * *
39145020 AT--AGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAA
1 ATACAG-GATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAA
* * ** * ***
39145063 ATAAAGGATCTTATCTCTCTGA-AGTTACAGCAGAGTAGA-TCGC
1 ATACAGGATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTAAA
* * **
39145106 AT-CAGG-TCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAATA
1 ATACAGGATCTTATCTCCCTGAGATTACAGTGGAGCAGA-TTAA-A
* * * * *
39145150 ATTTCA-GATCTTGTCTCCCTAACATTATAGTGGAGCAGATT-AA
1 A-TACAGGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAA
** * * *
39145193 AGCCAAAGATCTTATCTCCCTGAGATTACAGTGGAGCAGGTTGAAG
1 ATAC-AGGATCTTATCTCCCTGAGATTACAGTGGAGCAGATT-AAA
* *
39145239 ATACA-AATCTTATCTCCCTGA-AGTTGCAGTGGAGC-GAATTAAA
1 ATACAGGATCTTATCTCCCTGAGA-TTACAGTGGAGCAG-ATTAAA
* * *
39145282 ACCACA-GATCTTATCTCTCTGA-AGTTACAGTAGAGCAGAT
1 A-TACAGGATCTTATCTCCCTGAGA-TTACAGTGGAGCAGAT
39145322 CGCATCAAGT
Statistics
Matches: 674, Mismatches: 166, Indels: 131
0.69 0.17 0.13
Matches are distributed among these distances:
38 4 0.01
39 50 0.07
40 5 0.01
41 101 0.15
42 22 0.03
43 22 0.03
44 302 0.45
45 45 0.07
46 123 0.18
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.28
Consensus pattern (44 bp):
ATACAGGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAA
Found at i:39145158 original size:219 final size:219
Alignment explanation
Indices: 39144766--39145337 Score: 789
Period size: 219 Copynumber: 2.6 Consensus size: 219
39144756 GAAGAATTTC
* * *
39144766 AGATCTTATCTCCCTGATATTACAGCGGAGCAAATTGAAGCTAGTAATCTTATCTCCCTGAGATT
1 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGATAGTAATCTTATCTCCCTGAGATT
* * **
39144831 ACAGCGGAGCGGA-T----TAAAGGATCTTGTCTCTCTGAAGTTACAGTAGAGTAGATCGCGCCA
66 ACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCA
* * * *
39144891 GGTCTTATTTCCCTGAGATTACAGTGGAACAGATCGAAGAATTTCAGATCTTATCTCCCTGAGAT
131 GGTCTTATCTCCCTGAGATTACAGTGGAACAGACCGAAGAATTTCAGATCTTATCTCCCTAACAT
* *
39144956 TACAGCGGAGCAGATTGAAGCCAG
196 TACAGCGGAGCAGATTAAAGCCAA
*
39144980 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGATAGTAATCCTATCTCCCTGAGATT
1 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGATAGTAATCTTATCTCCCTGAGATT
*
39145045 ACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCATCA
66 ACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCA
* ** * *
39145110 GGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAATAATTTCAGATCTTGTCTCCCTAACAT
131 GGTCTTATCTCCCTGAGATTACAGTGGAACAGACCGAAGAATTTCAGATCTTATCTCCCTAACAT
* *
39145175 TATAGTGGAGCAGATTAAAGCCAA
196 TACAGCGGAGCAGATTAAAGCCAA
* * **
39145199 AGATCTTATCTCCCTGAGATTACAGTGGAGCAGGTTGAAGATACAAATCTTATCTCCCTGA-AGT
1 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGATAGTAATCTTATCTCCCTGAGA-T
* * * * *
39145263 TGCAGTGGAGCGAATTAAAACCACA-GATCTTATCTCTCTGAAGTTACAGTAGAGCAGATCGCAT
65 TACAGTGGAGCGGATTAAAA-TAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCAT
*
39145327 CAAGTCTTATC
129 CAGGTCTTATC
39145338 CCTAAGCAGT
Statistics
Matches: 317, Mismatches: 34, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
214 73 0.23
215 1 0.00
218 1 0.00
219 240 0.76
220 2 0.01
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (219 bp):
AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGATAGTAATCTTATCTCCCTGAGATT
ACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCA
GGTCTTATCTCCCTGAGATTACAGTGGAACAGACCGAAGAATTTCAGATCTTATCTCCCTAACAT
TACAGCGGAGCAGATTAAAGCCAA
Found at i:39147326 original size:3 final size:3
Alignment explanation
Indices: 39147318--39147376 Score: 91
Period size: 3 Copynumber: 19.3 Consensus size: 3
39147308 ACAAATTTTA
39147318 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT ATAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT
* *
39147367 CAT TGT TAT T
1 TAT TAT TAT T
39147377 CTCATTATAT
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
3 48 0.94
4 3 0.06
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:39147636 original size:6 final size:6
Alignment explanation
Indices: 39147621--39147675 Score: 83
Period size: 6 Copynumber: 9.2 Consensus size: 6
39147611 TGGCTTCTTT
* *
39147621 TATATC TATACA TATATA TATATA TATATA TATATA TATATA TATATA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
*
39147669 GATATA T
1 TATATA T
39147676 TTATCTTATT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 44 1.00
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (6 bp):
TATATA
Found at i:39147643 original size:8 final size:8
Alignment explanation
Indices: 39147621--39147675 Score: 83
Period size: 8 Copynumber: 6.9 Consensus size: 8
39147611 TGGCTTCTTT
*
39147621 TATATCTA
1 TATATATA
*
39147629 TACATATA
1 TATATATA
39147637 TATATATA
1 TATATATA
39147645 TATATATA
1 TATATATA
39147653 TATATATA
1 TATATATA
39147661 TATATATA
1 TATATATA
*
39147669 GATATAT
1 TATATAT
39147676 TTATCTTATT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 43 1.00
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (8 bp):
TATATATA
Found at i:39147731 original size:2 final size:2
Alignment explanation
Indices: 39147711--39147754 Score: 54
Period size: 2 Copynumber: 22.5 Consensus size: 2
39147701 TGCACATTTT
* * *
39147711 TA TA TG TA TA TA T- TT TA TA TA TA TA TA TA TA TA TA TA TG TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
39147752 TA T
1 TA T
39147755 TTTACGGNNN
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.55
Consensus pattern (2 bp):
TA
Found at i:39149273 original size:4 final size:4
Alignment explanation
Indices: 39149264--39149292 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
39149254 TTATTACTAT
39149264 TTTA TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA T
39149293 ATGTCTATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:39149306 original size:3 final size:3
Alignment explanation
Indices: 39149298--39149381 Score: 168
Period size: 3 Copynumber: 28.0 Consensus size: 3
39149288 TTTATATGTC
39149298 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
39149346 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
39149382 GCTTTAGTTT
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 81 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:39150586 original size:27 final size:27
Alignment explanation
Indices: 39150555--39150609 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
39150545 TTAAGAAGGA
39150555 TAAGCACGAAGTTTGAAAAATTAATTT
1 TAAGCACGAAGTTTGAAAAATTAATTT
**
39150582 TAAGCACGAAGTTTGAAATTTTAATTT
1 TAAGCACGAAGTTTGAAAAATTAATTT
39150609 T
1 T
39150610 CATAAATAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.40, C:0.07, G:0.15, T:0.38
Consensus pattern (27 bp):
TAAGCACGAAGTTTGAAAAATTAATTT
Found at i:39152171 original size:33 final size:33
Alignment explanation
Indices: 39152108--39152173 Score: 82
Period size: 33 Copynumber: 2.0 Consensus size: 33
39152098 GTAGTTTCTT
* *
39152108 AAATAATTTTAAAACATTATAGAAATTTTTAAA
1 AAATAATTATAAAACATTATAGAAAATTTTAAA
39152141 AAATAATTATAAGAA-ATTATA-AATAATTTTAAA
1 AAATAATTATAA-AACATTATAGAA-AATTTTAAA
39152174 TTTTATTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
32 2 0.07
33 25 0.86
34 2 0.07
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.38
Consensus pattern (33 bp):
AAATAATTATAAAACATTATAGAAAATTTTAAA
Found at i:39152800 original size:27 final size:27
Alignment explanation
Indices: 39152770--39152841 Score: 78
Period size: 27 Copynumber: 2.6 Consensus size: 27
39152760 AAAGTTAGAA
39152770 AAATTTTATCAAAAATTAGAAATT-AT-T
1 AAATTTTAT-AAAAATTA-AAATTGATAT
*
39152797 AAATATTTAAAAAATATTAAAATTGATAT
1 AAAT-TTTATAAAA-ATTAAAATTGATAT
39152826 AAA-TTTATAAAAATTA
1 AAATTTTATAAAAATTA
39152842 TAAAAAAAAG
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
26 4 0.10
27 21 0.54
28 10 0.26
29 4 0.10
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.39
Consensus pattern (27 bp):
AAATTTTATAAAAATTAAAATTGATAT
Found at i:39152846 original size:28 final size:26
Alignment explanation
Indices: 39152774--39152846 Score: 69
Period size: 29 Copynumber: 2.7 Consensus size: 26
39152764 TTAGAAAAAT
*
39152774 TTTATCAAAAATTA-GAAATTATTAAA
1 TTTAT-AAAAATTATAAAATTATTAAA
*
39152800 TATT-TAAAAAATATTAAAATTGATATAAA
1 T-TTATAAAAATTA-TAAAATT-AT-TAAA
39152829 TTTATAAAAATTATAAAA
1 TTTATAAAAATTATAAAA
39152847 AAAAGTATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
25 7 0.18
26 2 0.05
27 7 0.18
28 9 0.24
29 13 0.34
ACGTcount: A:0.58, C:0.01, G:0.03, T:0.38
Consensus pattern (26 bp):
TTTATAAAAATTATAAAATTATTAAA
Found at i:39153002 original size:21 final size:19
Alignment explanation
Indices: 39152956--39153016 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 19
39152946 AAAATGTATT
* *
39152956 AAAATTCTATAAAAAATTA
1 AAAATTATAAAAAAAATTA
39152975 AAAATTATAAAAAAAATATA
1 AAAATTATAAAAAAAAT-TA
* *
39152995 AGATATTAT-AAGAAAATTA
1 A-AAATTATAAAAAAAATTA
39153014 AAA
1 AAA
39153017 TTGATATTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
18 1 0.03
19 18 0.51
20 10 0.29
21 6 0.17
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.28
Consensus pattern (19 bp):
AAAATTATAAAAAAAATTA
Found at i:39153348 original size:19 final size:19
Alignment explanation
Indices: 39153320--39153359 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
39153310 TATATACTAA
* *
39153320 TAGTTGGATAATAAAATTT
1 TAGTTGGATAAAAAAAATT
*
39153339 TAGTTTGATAAAAAAAATT
1 TAGTTGGATAAAAAAAATT
39153358 TA
1 TA
39153360 AAAATAAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.40
Consensus pattern (19 bp):
TAGTTGGATAAAAAAAATT
Found at i:39155511 original size:24 final size:25
Alignment explanation
Indices: 39155468--39155530 Score: 65
Period size: 24 Copynumber: 2.5 Consensus size: 25
39155458 AATTTATGTA
*
39155468 TTTTTTTTAATTCGGCACTT-AAGT
1 TTTTTTTTAATTCAGCACTTGAAGT
* * *
39155492 TTTTTTTTAATTTAGTACTTGAATT
1 TTTTTTTTAATTCAGCACTTGAAGT
39155517 TAATTTTTTTAATT
1 T--TTTTTTTAATT
39155531 GAATTTGACA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
24 17 0.53
25 4 0.12
27 11 0.34
ACGTcount: A:0.24, C:0.06, G:0.08, T:0.62
Consensus pattern (25 bp):
TTTTTTTTAATTCAGCACTTGAAGT
Found at i:39156399 original size:10 final size:10
Alignment explanation
Indices: 39156384--39156409 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
39156374 ATTTATAACA
39156384 ATCCATTTTC
1 ATCCATTTTC
39156394 ATCCATTTTC
1 ATCCATTTTC
39156404 ATCCAT
1 ATCCAT
39156410 ATACAACTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.23, C:0.31, G:0.00, T:0.46
Consensus pattern (10 bp):
ATCCATTTTC
Found at i:39156996 original size:3 final size:3
Alignment explanation
Indices: 39156988--39157018 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
39156978 CTATGGAGAA
*
39156988 ATG ATG ATG ATG ATG ATG ATG ACG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
39157019 GAGAGAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.35, C:0.03, G:0.32, T:0.29
Consensus pattern (3 bp):
ATG
Found at i:39158938 original size:2 final size:2
Alignment explanation
Indices: 39158933--39158968 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
39158923 TTATATTTTG
39158933 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39158969 GTAAATTCTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39164623 original size:37 final size:37
Alignment explanation
Indices: 39164573--39164646 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
39164563 TGCTGAGACC
39164573 GGGTATCAGACTTTGATAGCTGAGGATGATGCACTAT
1 GGGTATCAGACTTTGATAGCTGAGGATGATGCACTAT
*
39164610 GGGTATCAGACTTTGATAGCTGAGGATGGTGCACTAT
1 GGGTATCAGACTTTGATAGCTGAGGATGATGCACTAT
39164647 CTCAAGCTAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.26, C:0.14, G:0.31, T:0.30
Consensus pattern (37 bp):
GGGTATCAGACTTTGATAGCTGAGGATGATGCACTAT
Found at i:39171434 original size:14 final size:15
Alignment explanation
Indices: 39171409--39171437 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
39171399 ATTGAATTAC
39171409 TTTTAGTTTTATTTA
1 TTTTAGTTTTATTTA
39171424 TTTTA-TTTTATTTA
1 TTTTAGTTTTATTTA
39171438 ACATAATGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (15 bp):
TTTTAGTTTTATTTA
Found at i:39180418 original size:20 final size:20
Alignment explanation
Indices: 39180393--39180434 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
39180383 TTGTTGCTAA
39180393 ATGGTTGGCAAATATCTATC
1 ATGGTTGGCAAATATCTATC
39180413 ATGGTTGGCAAATATCTATC
1 ATGGTTGGCAAATATCTATC
39180433 AT
1 AT
39180435 TACATTATCG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.31, C:0.14, G:0.19, T:0.36
Consensus pattern (20 bp):
ATGGTTGGCAAATATCTATC
Found at i:39182668 original size:18 final size:17
Alignment explanation
Indices: 39182635--39182673 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
39182625 TTTTATAAAT
39182635 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
39182653 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
39182670 TGTG
1 TGTG
39182674 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:39182925 original size:23 final size:23
Alignment explanation
Indices: 39182899--39183043 Score: 182
Period size: 23 Copynumber: 6.3 Consensus size: 23
39182889 AGTGTTATTG
*
39182899 ATCAGTGGTAGCTACGGCTATAT
1 ATCAGTGGTAGCTACGGCTACAT
* *
39182922 ATCAGTGGTAGCTTCAGCTACAT
1 ATCAGTGGTAGCTACGGCTACAT
* *
39182945 TTCAGTGGTAGCTACGGCTATAT
1 ATCAGTGGTAGCTACGGCTACAT
** *
39182968 ATCAGTGGTAGCTTTGACTACAT
1 ATCAGTGGTAGCTACGGCTACAT
* * *
39182991 TTCAGTGGTAGCTACTGCTACGT
1 ATCAGTGGTAGCTACGGCTACAT
*
39183014 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTACGGCTACAT
39183037 ATCAGTG
1 ATCAGTG
39183044 TGGCACTTAT
Statistics
Matches: 100, Mismatches: 22, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 100 1.00
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTACGGCTACAT
Found at i:39182953 original size:46 final size:46
Alignment explanation
Indices: 39182900--39183043 Score: 218
Period size: 46 Copynumber: 3.1 Consensus size: 46
39182890 GTGTTATTGA
39182900 TCAGTGGTAGCTACGGCTATATATCAGTGGTAGCTTCAGCTACATT
1 TCAGTGGTAGCTACGGCTATATATCAGTGGTAGCTTCAGCTACATT
*
39182946 TCAGTGGTAGCTACGGCTATATATCAGTGGTAGCTT-TGACTACATT
1 TCAGTGGTAGCTACGGCTATATATCAGTGGTAGCTTCAG-CTACATT
* ** * *
39182992 TCAGTGGTAGCTACTGCTACGTATCAGTGGTAGCTTCGGCTACATA
1 TCAGTGGTAGCTACGGCTATATATCAGTGGTAGCTTCAGCTACATT
39183038 TCAGTG
1 TCAGTG
39183044 TGGCACTTAT
Statistics
Matches: 90, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
45 1 0.01
46 88 0.98
47 1 0.01
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (46 bp):
TCAGTGGTAGCTACGGCTATATATCAGTGGTAGCTTCAGCTACATT
Found at i:39184848 original size:42 final size:43
Alignment explanation
Indices: 39184801--39185007 Score: 233
Period size: 42 Copynumber: 4.9 Consensus size: 43
39184791 TGACCTTTAG
* * * *
39184801 CATGACTTTTAGCGGCGCTTTT-ACAAAAACGCTGCTAAAGGT
1 CATGACTTTTAGCGGCGCTTTTCACACAAACGCCGCTATAGAT
* * * * *
39184843 CATGACTTTTAACGACACTTAT-ACAACAAATGCCGCTATAGAT
1 CATGACTTTTAGCGGCGCTTTTCAC-ACAAACGCCGCTATAGAT
* * **
39184886 TATGAC-TTTAGCGGCGCTTTTCCCACAAACGATGCTATAGAT
1 CATGACTTTTAGCGGCGCTTTTCACACAAACGCCGCTATAGAT
* *
39184928 CATGACTTTTAGCGGCGATTTTCCCACAAACGCCGCTATAG-T
1 CATGACTTTTAGCGGCGCTTTTCACACAAACGCCGCTATAGAT
*
39184970 CATGACTTTTAGCGGCACTTTTCACACAAACGCCGCTA
1 CATGACTTTTAGCGGCGCTTTTCACACAAACGCCGCTA
39185008 AAAACATATC
Statistics
Matches: 137, Mismatches: 25, Indels: 6
0.82 0.15 0.04
Matches are distributed among these distances:
42 87 0.64
43 50 0.36
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.29
Consensus pattern (43 bp):
CATGACTTTTAGCGGCGCTTTTCACACAAACGCCGCTATAGAT
Found at i:39184957 original size:85 final size:85
Alignment explanation
Indices: 39184801--39185001 Score: 246
Period size: 85 Copynumber: 2.4 Consensus size: 85
39184791 TGACCTTTAG
* * *
39184801 CATGACTTTTAGCGGCGCTTTT-ACAAAAACGCTGCTAAAGGTCATGACTTTTAACGACACTTAT
1 CATGACTTTTAGCGGCGCTTTTCACACAAACGATGCTAAAGATCATGACTTTTAACGACACTTAT
*
39184865 ACAACAAATGCCGCTATAGAT
66 ACAACAAACGCCGCTATAG-T
* * * * * *
39184886 TATGAC-TTTAGCGGCGCTTTTCCCACAAACGATGCTATAGATCATGACTTTTAGCGGCGA-TTT
1 CATGACTTTTAGCGGCGCTTTTCACACAAACGATGCTAAAGATCATGACTTTTAACGAC-ACTTA
* *
39184949 TCCCACAAACGCCGCTATAGT
65 TACAACAAACGCCGCTATAGT
*
39184970 CATGACTTTTAGCGGCACTTTTCACACAAACG
1 CATGACTTTTAGCGGCGCTTTTCACACAAACG
39185002 CCGCTAAAAA
Statistics
Matches: 98, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
84 21 0.21
85 76 0.78
86 1 0.01
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (85 bp):
CATGACTTTTAGCGGCGCTTTTCACACAAACGATGCTAAAGATCATGACTTTTAACGACACTTAT
ACAACAAACGCCGCTATAGT
Found at i:39188742 original size:3 final size:3
Alignment explanation
Indices: 39188736--39188787 Score: 72
Period size: 3 Copynumber: 17.3 Consensus size: 3
39188726 TTTTTAACTG
39188736 TTA TTA TTA -TA TATA TTA TTA TTA TTA TTA TTA TTA TATA TTA TTA
1 TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA
39188782 TT- TTA T
1 TTA TTA T
39188788 AACATTCATG
Statistics
Matches: 45, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
2 4 0.09
3 35 0.78
4 6 0.13
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:39191814 original size:4 final size:4
Alignment explanation
Indices: 39191805--39191833 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
39191795 AAAAAAATAA
39191805 AAAG AAAG AAAG AAAG AAAG AAAG AAAG A
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG A
39191834 GGGGAATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:39192064 original size:23 final size:24
Alignment explanation
Indices: 39192023--39192067 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
39192013 AATAAAGACG
*
39192023 TTATTTTGTTTTGCTAAAAATTTT
1 TTATTTTGTTCTGCTAAAAATTTT
39192047 TTATTTTG-TCTGCTAAAAATT
1 TTATTTTGTTCTGCTAAAAATT
39192068 ATTAGTTAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.27, C:0.07, G:0.09, T:0.58
Consensus pattern (24 bp):
TTATTTTGTTCTGCTAAAAATTTT
Found at i:39192822 original size:14 final size:14
Alignment explanation
Indices: 39192804--39192999 Score: 128
Period size: 14 Copynumber: 13.8 Consensus size: 14
39192794 CCCCTAACTT
* *
39192804 CTAAACCCTAAATC
1 CTAAACCATAAACC
* *
39192818 ATAAAACATAAACC
1 CTAAACCATAAACC
* *
39192832 CTAAACCCTTAACCC
1 CTAAA-CCATAAACC
39192847 CTAAACCATAAA-C
1 CTAAACCATAAACC
* *
39192860 CTCAACCCTTAAACC
1 CT-AAACCATAAACC
*
39192875 ATAAACCATAAACC
1 CTAAACCATAAACC
* *
39192889 ATAAACCATAATCC
1 CTAAACCATAAACC
*
39192903 CTAAACCCATAATCC
1 CTAAA-CCATAAACC
* *
39192918 ATAATCCATAAA-C
1 CTAAACCATAAACC
* *
39192931 CTTAA-GATAGTAACTC
1 CTAAACCATA--AAC-C
**
39192947 CTAAACTTTAAACC
1 CTAAACCATAAACC
* *
39192961 CTAAACTATATACC
1 CTAAACCATAAACC
39192975 CTAAACCATAAACC
1 CTAAACCATAAACC
*
39192989 CTAAACTATAA
1 CTAAACCATAA
39193000 TAATAATTAA
Statistics
Matches: 141, Mismatches: 32, Indels: 18
0.74 0.17 0.09
Matches are distributed among these distances:
12 3 0.02
13 6 0.04
14 97 0.69
15 28 0.20
16 5 0.04
17 2 0.01
ACGTcount: A:0.46, C:0.31, G:0.01, T:0.21
Consensus pattern (14 bp):
CTAAACCATAAACC
Found at i:39192853 original size:8 final size:7
Alignment explanation
Indices: 39192775--39192994 Score: 95
Period size: 7 Copynumber: 30.9 Consensus size: 7
39192765 ACTAATTAAT
39192775 CTAAACC
1 CTAAACC
39192782 CTAAACC
1 CTAAACC
* *
39192789 TTTAACCC
1 -CTAAACC
*
39192797 CT-AACTT
1 CTAAAC-C
39192804 CTAAACC
1 CTAAACC
*
39192811 CTAAATC
1 CTAAACC
* *
39192818 ATAAAAC
1 CTAAACC
*
39192825 ATAAACC
1 CTAAACC
39192832 CTAAACC
1 CTAAACC
*
39192839 CTTAACCC
1 C-TAAACC
39192847 CTAAACC
1 CTAAACC
*
39192854 ATAAA-C
1 CTAAACC
*
39192860 CTCAACC
1 CTAAACC
39192867 CTTAAACC
1 C-TAAACC
*
39192875 ATAAACC
1 CTAAACC
*
39192882 ATAAACC
1 CTAAACC
*
39192889 ATAAACC
1 CTAAACC
* *
39192896 ATAATCC
1 CTAAACC
39192903 CTAAACC
1 CTAAACC
*
39192910 CATAATCC
1 C-TAAACC
* *
39192918 ATAATCC
1 CTAAACC
*
39192925 ATAAACC
1 CTAAACC
* **
39192932 TTAAGATA
1 CTAA-ACC
*
39192940 GT-AACTC
1 CTAAAC-C
*
39192947 CTAAACT
1 CTAAACC
*
39192954 TTAAACC
1 CTAAACC
*
39192961 CTAAACT
1 CTAAACC
* *
39192968 ATATACC
1 CTAAACC
39192975 CTAAACC
1 CTAAACC
*
39192982 ATAAACC
1 CTAAACC
39192989 CTAAAC
1 CTAAAC
39192995 TATAATAATA
Statistics
Matches: 160, Mismatches: 43, Indels: 20
0.72 0.19 0.09
Matches are distributed among these distances:
6 7 0.04
7 124 0.77
8 29 0.18
ACGTcount: A:0.45, C:0.33, G:0.01, T:0.22
Consensus pattern (7 bp):
CTAAACC
Found at i:39193173 original size:7 final size:7
Alignment explanation
Indices: 39193130--39193173 Score: 70
Period size: 7 Copynumber: 6.1 Consensus size: 7
39193120 ACCTAGCCTT
39193130 TAAACCA
1 TAAACCA
39193137 TAAACCA
1 TAAACCA
39193144 TAAACCA
1 TAAACCA
39193151 TAAACCA
1 TAAACCA
39193158 TAAACCCA
1 TAAA-CCA
*
39193166 TAATCCA
1 TAAACCA
39193173 T
1 T
39193174 GCATAAACCT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
7 29 0.83
8 6 0.17
ACGTcount: A:0.52, C:0.30, G:0.00, T:0.18
Consensus pattern (7 bp):
TAAACCA
Found at i:39193217 original size:14 final size:14
Alignment explanation
Indices: 39193197--39193245 Score: 62
Period size: 14 Copynumber: 3.5 Consensus size: 14
39193187 AATGGTAACA
*
39193197 CCTAAACCTTAAAC
1 CCTAAACCATAAAC
* *
39193211 TCTAAACCATATAC
1 CCTAAACCATAAAC
*
39193225 CCTAAACCAAAAAC
1 CCTAAACCATAAAC
39193239 CCTAAAC
1 CCTAAAC
39193246 TATAGTGATA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.47, C:0.35, G:0.00, T:0.18
Consensus pattern (14 bp):
CCTAAACCATAAAC
Found at i:39193775 original size:41 final size:41
Alignment explanation
Indices: 39193544--39193778 Score: 242
Period size: 41 Copynumber: 5.7 Consensus size: 41
39193534 TTTTTGCGGT
* * * *
39193544 GCTTTTTCAAAAATGCCGCTAAAGCCCCCGAGCATTAGCTGC
1 GCTTTTTTAAAAACGCCGCTAAAG-CCTCGAGCATTAGCAGC
* *** ** * *
39193586 GCTTATTGGCAAACGCCGCTAAA-AATAGAGCATTAGCGGC
1 GCTTTTTTAAAAACGCCGCTAAAGCCTCGAGCATTAGCAGC
**
39193626 GCTTTCCTAAAAACGCCGCTAAAGTCC-CGAGCATTAGCAGC
1 GCTTTTTTAAAAACGCCGCTAAAG-CCTCGAGCATTAGCAGC
* * * *
39193667 GCTTTCTGAAAAACGCCGCTAAAGCCCCGAGCATTAGC-GAT
1 GCTTTTTTAAAAACGCCGCTAAAGCCTCGAGCATTAGCAG-C
* *
39193708 GCTTTTTTAAAAACGCCGTTAAAGCCTTGAGCATTAGCAGC
1 GCTTTTTTAAAAACGCCGCTAAAGCCTCGAGCATTAGCAGC
39193749 GCTTTTTTAAAAACGCCGCTAAAGCCTCGA
1 GCTTTTTTAAAAACGCCGCTAAAGCCTCGA
39193779 AAGCTCGGAG
Statistics
Matches: 157, Mismatches: 31, Indels: 11
0.79 0.16 0.06
Matches are distributed among these distances:
40 32 0.20
41 106 0.68
42 19 0.12
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.23
Consensus pattern (41 bp):
GCTTTTTTAAAAACGCCGCTAAAGCCTCGAGCATTAGCAGC
Found at i:39193839 original size:39 final size:40
Alignment explanation
Indices: 39193795--39193878 Score: 98
Period size: 40 Copynumber: 2.1 Consensus size: 40
39193785 GGAGCTTAGG
* **
39193795 TTTTTTGCGGCACTTCTTGGAAAA-CGCCGCTAATGCTCTA
1 TTTTTAGCGG-ACTTCTTCAAAAAGCGCCGCTAATGCTCTA
** *
39193835 TTTTTAGCGGTGTTTTTCAAAAAGCGCCGCTAATGCTCTA
1 TTTTTAGCGGACTTCTTCAAAAAGCGCCGCTAATGCTCTA
39193875 TTTT
1 TTTT
39193879 AGCAGCGTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
39 8 0.22
40 29 0.78
ACGTcount: A:0.20, C:0.21, G:0.19, T:0.39
Consensus pattern (40 bp):
TTTTTAGCGGACTTCTTCAAAAAGCGCCGCTAATGCTCTA
Found at i:39193890 original size:39 final size:39
Alignment explanation
Indices: 39193815--39193930 Score: 155
Period size: 39 Copynumber: 2.9 Consensus size: 39
39193805 CACTTCTTGG
*
39193815 AAAACGCCGCTAATGCTCTATTTTTAGCGGTGTTTTTCA-
1 AAAACGCCGCTAATGCTCTATTTTTAGCGGCGTTTTT-AT
*
39193854 AAAAGCGCCGCTAATGCTCTA-TTTTAGCAGCGTTTTTAT
1 AAAA-CGCCGCTAATGCTCTATTTTTAGCGGCGTTTTTAT
* *
39193893 AAATATGCCGCTAATGCTCGATTTTTAGCGGCGTTTTT
1 AAA-ACGCCGCTAATGCTCTATTTTTAGCGGCGTTTTT
39193931 GTTCAAACGC
Statistics
Matches: 68, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
38 1 0.01
39 35 0.51
40 32 0.47
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.38
Consensus pattern (39 bp):
AAAACGCCGCTAATGCTCTATTTTTAGCGGCGTTTTTAT
Found at i:39219606 original size:39 final size:39
Alignment explanation
Indices: 39219546--39219665 Score: 195
Period size: 39 Copynumber: 3.1 Consensus size: 39
39219536 ATTTTCAATA
* * *
39219546 CACCGGCACATAGCTTGCTAGGCACATAGCCTGAATAAT
1 CACCGGCACAAAGCCTGCTAGGCACATAGCCCGAATAAT
*
39219585 CACCGGCACAAAGCCTACTAGGCACATAGCCCGAATAAT
1 CACCGGCACAAAGCCTGCTAGGCACATAGCCCGAATAAT
*
39219624 CACCGGCACACAGCCTGCTAGGCACATAGCCCGAATAAT
1 CACCGGCACAAAGCCTGCTAGGCACATAGCCCGAATAAT
39219663 CAC
1 CAC
39219666 TAGATTTCTA
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 75 1.00
ACGTcount: A:0.33, C:0.33, G:0.19, T:0.15
Consensus pattern (39 bp):
CACCGGCACAAAGCCTGCTAGGCACATAGCCCGAATAAT
Found at i:39224279 original size:27 final size:26
Alignment explanation
Indices: 39224212--39224280 Score: 68
Period size: 27 Copynumber: 2.6 Consensus size: 26
39224202 AGATTTTTAA
*
39224212 TGAAATTGTCAAATATGGGCTAAATTG
1 TGAAATTGTGAAAT-TGGGCTAAATTG
* * *
39224239 AGAAA-TGTGAAAATTGTGTTAAATGTG
1 TGAAATTGTG-AAATTGGGCTAAAT-TG
39224266 TGAAATTGTGAAATT
1 TGAAATTGTGAAATT
39224281 CATGGTTGAT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
26 11 0.32
27 19 0.56
28 4 0.12
ACGTcount: A:0.39, C:0.03, G:0.23, T:0.35
Consensus pattern (26 bp):
TGAAATTGTGAAATTGGGCTAAATTG
Found at i:39229035 original size:27 final size:27
Alignment explanation
Indices: 39228996--39229055 Score: 111
Period size: 27 Copynumber: 2.2 Consensus size: 27
39228986 ATTCTTAGTG
*
39228996 GTTGTGCTTGTAGATATGTTTTGGCGA
1 GTTGTGCTCGTAGATATGTTTTGGCGA
39229023 GTTGTGCTCGTAGATATGTTTTGGCGA
1 GTTGTGCTCGTAGATATGTTTTGGCGA
39229050 GTTGTG
1 GTTGTG
39229056 TTCATAGGTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.13, C:0.08, G:0.35, T:0.43
Consensus pattern (27 bp):
GTTGTGCTCGTAGATATGTTTTGGCGA
Found at i:39234717 original size:43 final size:43
Alignment explanation
Indices: 39234668--39234947 Score: 434
Period size: 43 Copynumber: 6.5 Consensus size: 43
39234658 AGATAAGCGT
* * *
39234668 CGCTAAAGGTCATGTTCTTTAGCGGTGCTTCTATAGAAAAGGC
1 CGCTAAAGGTCATGTTCTTTAGCGGCGCTTCTATAGCAAACGC
*
39234711 CGCTAAAGGTCATGTTCTTTAGCGGAGCTTCTATAGCAAACGC
1 CGCTAAAGGTCATGTTCTTTAGCGGCGCTTCTATAGCAAACGC
*
39234754 CGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTATAGCAAACGC
1 CGCTAAAGGTCATGTTCTTTAGCGGCGCTTCTATAGCAAACGC
* * *
39234797 CGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTATATCAAACAC
1 CGCTAAAGGTCATGTTCTTTAGCGGCGCTTCTATAGCAAACGC
* * *
39234840 CGCTAAAGGTCATGTTCTTTAGCGGTGCTTCTATAGAAAATGC
1 CGCTAAAGGTCATGTTCTTTAGCGGCGCTTCTATAGCAAACGC
*
39234883 CGCTAAATGTCATGTTCTTTAGCGGCGCTTCTATAGCAAACGC
1 CGCTAAAGGTCATGTTCTTTAGCGGCGCTTCTATAGCAAACGC
* *
39234926 CGTTAAAGGTCACGTTCTTTAG
1 CGCTAAAGGTCATGTTCTTTAG
39234948 TGACACTTTT
Statistics
Matches: 217, Mismatches: 20, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 217 1.00
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.31
Consensus pattern (43 bp):
CGCTAAAGGTCATGTTCTTTAGCGGCGCTTCTATAGCAAACGC
Found at i:39235008 original size:129 final size:129
Alignment explanation
Indices: 39234668--39234994 Score: 379
Period size: 129 Copynumber: 2.5 Consensus size: 129
39234658 AGATAAGCGT
* *** * ** ** * *
39234668 CGCTAAAGGTCATGTTCTTTAGCGGTGCTTCTATAGAAAAGGCCGCTAAAGGTCATGTTCTTTAG
1 CGCTAAAGGTCACGTTCTTTAGCGACACTTTTATATCAAACACCGCTAAAAGTCACGTTCTTTAG
* * * * *
39234733 CGGAGCTTCTATAGCAAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTATAGCAAACGC
66 CGGTGCTTCTACAGAAAATGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTCTATAGCAAACGC
* * * * *
39234797 CGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTATATCAAACACCGCTAAAGGTCATGTTCTTTAG
1 CGCTAAAGGTCACGTTCTTTAGCGACACTTTTATATCAAACACCGCTAAAAGTCACGTTCTTTAG
* *
39234862 CGGTGCTTCTATAGAAAATGCCGCTAAATGTCATGTTCTTTAGCGGCGCTTCTATAGCAAACGC
66 CGGTGCTTCTACAGAAAATGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTCTATAGCAAACGC
* * *
39234926 CGTTAAAGGTCACGTTCTTTAGTGACACTTTT-TATCAAAAACGCCGCTAAAAG-CACCGTTCTT
1 CGCTAAAGGTCACGTTCTTTAGCGACACTTTTATATC--AAACACCGCTAAAAGTCA-CGTTCTT
39234989 TAGCGG
63 TAGCGG
39234995 CATTTTACGG
Statistics
Matches: 176, Mismatches: 19, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
128 4 0.02
129 147 0.84
130 25 0.14
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.31
Consensus pattern (129 bp):
CGCTAAAGGTCACGTTCTTTAGCGACACTTTTATATCAAACACCGCTAAAAGTCACGTTCTTTAG
CGGTGCTTCTACAGAAAATGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTCTATAGCAAACGC
Found at i:39248137 original size:83 final size:83
Alignment explanation
Indices: 39247978--39248498 Score: 524
Period size: 84 Copynumber: 6.2 Consensus size: 83
39247968 CTATTGCTTT
* * * *
39247978 CATAGTTGCGGCGTTTTCCGCAAAAAACGCTAATACAAAATTAAATTCCTGTACTGAAACGACGC
1 CATAGTTGCGGCGTTTTCCG-AAAAAACGCCACTA-AAAATTAAATTCCTGTAGTGAAACGGCGC
*
39248043 CGTTTTAAGAAACTTTAATA
64 CGTTTTGAGAAACTTTAATA
* * * * * * *
39248063 TATAGTTGCGGCGTTTTCCGTAAAAATGCCACTAAAAATTAAATTCCTGAAGAGAAATGGCGACG
1 CATAGTTGCGGCGTTTTCCGAAAAAACGCCACTAAAAATTAAATTCCTGTAGTGAAACGGCGCCG
*
39248128 TTTTGAGAAACATTAATA
66 TTTTGAGAAACTTTAATA
** ** * * *
39248146 CATTTTTGTAGCGTTTTCAAC-AAAAAACACCACTAAAAGATTACATTCCTGTAGTGAAACGGAG
1 CATAGTTGCGGCGTTTTC--CGAAAAAACGCCACTAAAA-ATTAAATTCCTGTAGTGAAACGGCG
* *
39248210 CCGTTTTGATAAATTTTAATA
63 CCGTTTTGAGAAACTTTAATA
* * ** **
39248231 CATATTTACGGCGTTTTCCGAAAAAACGCCACTAAAAATTTAAATTCCTAAACAGAAACGGCGCC
1 CATAGTTGCGGCGTTTTCCGAAAAAACGCCACTAAAAA-TTAAATTCCTGTAGTGAAACGGCGCC
* * *
39248296 GTTTAGAAAAACTTGAATA
65 GTTTTGAGAAACTTTAATA
* * * * * * *
39248315 CATAGTTCCGGCATTTTCAGTAAAAACGCCACTAAAAAATTTAATTCTTGTGGTGAAACGGCGCC
1 CATAGTTGCGGCGTTTTCCGAAAAAACGCCACT-AAAAATTAAATTCCTGTAGTGAAACGGCGCC
*
39248380 GTTTTGAGAAATTTTAATA
65 GTTTTGAGAAACTTTAATA
* ** * * *
39248399 CATAGTTGCGGCATTTT-TAAAAAAACGCCACTAAGAAATTAAATTCTTGTAGCGAAACGGCGCT
1 CATAGTTGCGGCGTTTTCCGAAAAAACGCCACTAA-AAATTAAATTCCTGTAGTGAAACGGCGCC
* * *
39248463 GTTTTGGGGAATTTTAATA
65 GTTTTGAGAAACTTTAATA
39248482 CATAGTTGCGGCGTTTT
1 CATAGTTGCGGCGTTTT
39248499 TTTCTAAAAA
Statistics
Matches: 357, Mismatches: 72, Indels: 16
0.80 0.16 0.04
Matches are distributed among these distances:
82 2 0.01
83 126 0.35
84 153 0.43
85 76 0.21
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Consensus pattern (83 bp):
CATAGTTGCGGCGTTTTCCGAAAAAACGCCACTAAAAATTAAATTCCTGTAGTGAAACGGCGCCG
TTTTGAGAAACTTTAATA
Found at i:39249080 original size:7 final size:7
Alignment explanation
Indices: 39249051--39249125 Score: 53
Period size: 7 Copynumber: 10.6 Consensus size: 7
39249041 CCCTGAATCC
39249051 TAAACCCT
1 TAAA-CCT
* *
39249059 TAACCCC
1 TAAACCT
*
39249066 TAACCCT
1 TAAACCT
39249073 TAAACCT
1 TAAACCT
39249080 TAAATCC-
1 TAAA-CCT
* *
39249087 CAACCCT
1 TAAACCT
*
39249094 TAAACCA
1 TAAACCT
39249101 TAAACCT
1 TAAACCT
* *
39249108 TAATCCA
1 TAAACCT
39249115 TAAACCT
1 TAAACCT
39249122 TAAA
1 TAAA
39249126 ATAGTAACTC
Statistics
Matches: 51, Mismatches: 14, Indels: 5
0.73 0.20 0.07
Matches are distributed among these distances:
6 2 0.04
7 44 0.86
8 5 0.10
ACGTcount: A:0.41, C:0.35, G:0.00, T:0.24
Consensus pattern (7 bp):
TAAACCT
Found at i:39249080 original size:21 final size:21
Alignment explanation
Indices: 39249034--39249125 Score: 89
Period size: 21 Copynumber: 4.3 Consensus size: 21
39249024 AACACCTATC
*
39249034 CCTTAAACCCTGAATCC-TAAA
1 CCTTAAACCCT-AACCCTTAAA
*
39249055 CCCTTAACCCCTAACCCTTAAA
1 -CCTTAAACCCTAACCCTTAAA
39249077 CCTTAAATCCC-AACCCTTAAA
1 CCTTAAA-CCCTAACCCTTAAA
* * * *
39249098 CCATAAACCTTAATCCATAAA
1 CCTTAAACCCTAACCCTTAAA
39249119 CCTTAAA
1 CCTTAAA
39249126 ATAGTAACTC
Statistics
Matches: 59, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
20 2 0.03
21 40 0.68
22 17 0.29
ACGTcount: A:0.39, C:0.36, G:0.01, T:0.24
Consensus pattern (21 bp):
CCTTAAACCCTAACCCTTAAA
Found at i:39249108 original size:14 final size:14
Alignment explanation
Indices: 39249073--39249125 Score: 63
Period size: 14 Copynumber: 3.8 Consensus size: 14
39249063 CCCTAACCCT
39249073 TAAACCTTAAATCC-
1 TAAACCTTAAA-CCA
* *
39249087 CAACCCTTAAACCA
1 TAAACCTTAAACCA
*
39249101 TAAACCTTAATCCA
1 TAAACCTTAAACCA
39249115 TAAACCTTAAA
1 TAAACCTTAAA
39249126 ATAGTAACTC
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
13 2 0.06
14 30 0.94
ACGTcount: A:0.45, C:0.30, G:0.00, T:0.25
Consensus pattern (14 bp):
TAAACCTTAAACCA
Found at i:39249548 original size:19 final size:19
Alignment explanation
Indices: 39249524--39249584 Score: 54
Period size: 19 Copynumber: 3.1 Consensus size: 19
39249514 CCGCTAATGC
39249524 TTGATATATAGCGGCATTT
1 TTGATATATAGCGGCATTT
*
39249543 TTGATA-A-AGCGCCGCTAATAT
1 TTGATATATAGCG--GC--ATTT
*
39249564 TCGATATATAGCGGCATTT
1 TTGATATATAGCGGCATTT
39249583 TT
1 TT
39249585 TATGAAGCGC
Statistics
Matches: 32, Mismatches: 4, Indels: 12
0.67 0.08 0.25
Matches are distributed among these distances:
17 4 0.12
18 1 0.03
19 12 0.38
21 10 0.31
22 1 0.03
23 4 0.12
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.38
Consensus pattern (19 bp):
TTGATATATAGCGGCATTT
Found at i:39249555 original size:40 final size:41
Alignment explanation
Indices: 39249495--39249604 Score: 143
Period size: 40 Copynumber: 2.7 Consensus size: 41
39249485 ATGTTTTTTA
* *
39249495 CGGCGTTTTTGACAAAGCGCCGCTAATGCTT-GATATATAG
1 CGGCATTTTTGATAAAGCGCCGCTAATGCTTCGATATATAG
*
39249535 CGGCATTTTTGATAAAGCGCCGCTAAT-ATTCGATATATAG
1 CGGCATTTTTGATAAAGCGCCGCTAATGCTTCGATATATAG
* * *
39249575 CGGCATTTTTTATGAAGCGCCAACTAATGC
1 CGGCATTTTTGATAAAGCGCC-GCTAATGC
39249605 CACTAAAGCT
Statistics
Matches: 60, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
39 2 0.03
40 53 0.88
41 5 0.08
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (41 bp):
CGGCATTTTTGATAAAGCGCCGCTAATGCTTCGATATATAG
Found at i:39249716 original size:40 final size:39
Alignment explanation
Indices: 39249661--39249776 Score: 151
Period size: 40 Copynumber: 2.9 Consensus size: 39
39249651 GGCATTTTTT
* *
39249661 AAAAAGTGCCGCTAATACTCGATCTATAGCGGCGTTTGTC
1 AAAAAGTGCCGCTAAT-CTCAATCTATAGCGGCGTTTCTC
* * *
39249701 AAAAAGTGCCGCTAATGTCAATCTTTAGCGGCATTTCTC
1 AAAAAGTGCCGCTAATCTCAATCTATAGCGGCGTTTCTC
* *
39249740 AAAATGCGCCGCTAATGCTCAATCTATAGCGGCGTTT
1 AAAAAGTGCCGCTAAT-CTCAATCTATAGCGGCGTTT
39249777 TTTATCCAAA
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
39 32 0.49
40 33 0.51
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (39 bp):
AAAAAGTGCCGCTAATCTCAATCTATAGCGGCGTTTCTC
Found at i:39252152 original size:12 final size:11
Alignment explanation
Indices: 39252137--39252187 Score: 57
Period size: 12 Copynumber: 4.4 Consensus size: 11
39252127 TTAGTGATTA
39252137 AAAACTTGATGG
1 AAAACTTGAT-G
*
39252149 AAAACTTGATT
1 AAAACTTGATG
*
39252160 AATGACTTGATG
1 AA-AACTTGATG
39252172 AAAGACTTGATG
1 AAA-ACTTGATG
39252184 AAAA
1 AAAA
39252188 AAACAATTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
11 3 0.09
12 30 0.91
ACGTcount: A:0.45, C:0.08, G:0.20, T:0.27
Consensus pattern (11 bp):
AAAACTTGATG
Found at i:39252158 original size:24 final size:24
Alignment explanation
Indices: 39252131--39252188 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 24
39252121 AAAAACTTAG
39252131 TGATTAAAAACTTGATGGAAA-ACT
1 TGATTAAAAACTTGAT-GAAAGACT
**
39252155 TGATTAATGACTTGATGAAAGACT
1 TGATTAAAAACTTGATGAAAGACT
*
39252179 TGATGAAAAA
1 TGATTAAAAA
39252189 AACAATTAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
23 4 0.14
24 24 0.86
ACGTcount: A:0.45, C:0.07, G:0.19, T:0.29
Consensus pattern (24 bp):
TGATTAAAAACTTGATGAAAGACT
Found at i:39252211 original size:12 final size:12
Alignment explanation
Indices: 39252194--39252219 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
39252184 AAAAAAACAA
39252194 TTAATGAATGAC
1 TTAATGAATGAC
39252206 TTAATGAATGAC
1 TTAATGAATGAC
39252218 TT
1 TT
39252220 GATCCAAGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.38
Consensus pattern (12 bp):
TTAATGAATGAC
Found at i:39252775 original size:26 final size:27
Alignment explanation
Indices: 39252721--39252777 Score: 71
Period size: 26 Copynumber: 2.1 Consensus size: 27
39252711 AATTTTAAAA
* * *
39252721 TATTTTTAAAATACATTTTTTTATTTT
1 TATTTTTAAAATACAATTTTTGATGTT
*
39252748 TATTTTTAAAATA-AATTTTTGGTGTT
1 TATTTTTAAAATACAATTTTTGATGTT
39252774 TATT
1 TATT
39252778 AAAAAAAGGC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 13 0.50
27 13 0.50
ACGTcount: A:0.30, C:0.02, G:0.05, T:0.63
Consensus pattern (27 bp):
TATTTTTAAAATACAATTTTTGATGTT
Found at i:39255188 original size:97 final size:97
Alignment explanation
Indices: 39255085--39255850 Score: 647
Period size: 97 Copynumber: 7.8 Consensus size: 97
39255075 TAATGTAAAA
* * *
39255085 TTATTTTGTTAGTAATTTAAGATTAGTTTATAAATTGTTAGTGTTTTGTGTTTTATGAAGTTTTA
1 TTATTTTGTTAGTAATTTATGATTAGTTTATAAATTGTTAGTGTTTTGTGTTTTGTGAATTTTTA
39255150 GTAATGTAAATTCTTTTTAAAAAATGTTATAG
66 GTAATGTAAATTCTTTTTAAAAAATGTTATAG
*
39255182 TTATTTTGTTAGTAATTTATGATTAGTTTATAATTTGTTAGTGTTTTGTGTTTTGTG-ATTTATT
1 TTATTTTGTTAGTAATTTATGATTAGTTTATAAATTGTTAGTGTTTTGTGTTTTGTGAATTT-TT
*
39255246 AGTAATGTAAATTCTTTTTTAAAAATGTTATAG
65 AGTAATGTAAATTCTTTTTAAAAAATGTTATAG
*** * *
39255279 TTATTTTGTTAGTAATTTATGATTAGTTTA-GGGTT-TT-GTG-ATT-T-TTTAGT-AA---TT-
1 TTATTTTGTTAGTAATTTATGATTAGTTTATAAATTGTTAGTGTTTTGTGTTTTGTGAATTTTTA
* ** * *
39255333 -TAAT-T---TTTTTTAAAAATAATTG-TATAA
66 GTAATGTAAATTCTTTTTAAA-AAATGTTATAG
* *
39255360 TTATGTTGTTAGTAATTTATGGTTAGGTTATATAAATTGTTAGTGTTTTGTGTTTTGTG-ATTTA
1 TTATTTTGTTAGTAATTTATGATTA-GTT-TATAAATTGTTAGTGTTTTGTGTTTTGTGAATTT-
*
39255424 TTAGTAATGTAAATTCTTTTTTTAAAAATGTTATAG
63 TTAGTAATGTAAATTC-TTTTTAAAAAATGTTATAG
* *
39255460 TTATTTTGTTAGTAATTTATAATTAGTTTATAAATTGTTAGTGTTTAGTTTAGGATTTTGTGAAT
1 TTATTTTGTTAGTAATTTATGATTAGTTTATAAATTGTTAGTGTTT--TGT--G-TTTTGTGAAT
* **
39255525 TTTTAGTAATGT-AA----TTTAAAAGAAAAATTATAG
61 TTTTAGTAATGTAAATTCTTTTTAAA-AAATGTTATAG
* * **
39255558 TTGTTTTGTTAGTAAGTTATGATTAGGTTATATAAATTGAAAAGTGTTTTGTGTTTTGTG-ATTT
1 TTATTTTGTTAGTAATTTATGATTA-GTT-TATAAATTG-TTAGTGTTTTGTGTTTTGTGAATTT
* *
39255622 ATTAGTAATGT-AATTCTTTTAAAAAAAATGTTATAA
63 -TTAGTAATGTAAATTCTTTT-TAAAAAATGTTATAG
* * * * *
39255658 TTATTTTTTTACTAATTTATGATTAGTTTATAAATTATTAGTGTTTAGTTTAGGGTTTTGTGATT
1 TTATTTTGTTAGTAATTTATGATTAGTTTATAAATTGTTAGTG--T--TTT-GTGTTTTGTGAAT
*** *
39255723 TTTTAGTAATGT-AATT-TTAAAAAAATATATAACTTTATAG
61 TTTTAGTAATGTAAATTCTTTTTAAAA-A-AT---GTTATAG
*
39255763 TTATTTTGTTAGTAATTTATGATTAAGTTATATAAACTGTTAGTGTTTAGTTTAGTGTTTTGT-A
1 TTATTTTGTTAGTAATTTATGATT-AGTT-TATAAATTGTTAGTG--T--TTT-GTGTTTTGTGA
*
39255827 ATTTTTTATTAATGTAAATT-TTTT
59 A-TTTTTAGTAATGTAAATTCTTTT
39255851 ATAATATAAT
Statistics
Matches: 546, Mismatches: 68, Indels: 99
0.77 0.10 0.14
Matches are distributed among these distances:
81 34 0.06
82 7 0.01
83 2 0.00
84 3 0.01
85 6 0.01
86 3 0.01
87 4 0.01
88 1 0.00
89 6 0.01
91 6 0.01
92 1 0.00
93 4 0.01
94 3 0.01
95 10 0.02
96 25 0.05
97 128 0.23
98 57 0.10
99 18 0.03
100 79 0.14
101 17 0.03
102 28 0.05
103 20 0.04
104 4 0.01
105 27 0.05
106 5 0.01
107 42 0.08
108 6 0.01
ACGTcount: A:0.30, C:0.01, G:0.15, T:0.54
Consensus pattern (97 bp):
TTATTTTGTTAGTAATTTATGATTAGTTTATAAATTGTTAGTGTTTTGTGTTTTGTGAATTTTTA
GTAATGTAAATTCTTTTTAAAAAATGTTATAG
Found at i:39255320 original size:80 final size:80
Alignment explanation
Indices: 39255231--39255385 Score: 215
Period size: 81 Copynumber: 1.9 Consensus size: 80
39255221 AGTGTTTTGT
* *
39255231 GTTTTGTGATTTATTAGTAATGTAAATTCTTTTTTAAAAAT-GT-TATAGTTATTTTGTTAGTAA
1 GTTTTGTGATTTATTAGTAAT-TAAATT-TTTTTTAAAAATAGTGTATAATTATGTTGTTAGTAA
39255294 TTTATGATTAGTTTAGG
64 TTTATGATTAGTTTAGG
* * *
39255311 GTTTTGTGATTTTTTAGTAATTTAATTTTTTTTAAAAATAATTGTATAATTATGTTGTTAGTAAT
1 GTTTTGTGATTTATTAGTAATTAAATTTTTTTTAAAAAT-AGTGTATAATTATGTTGTTAGTAAT
*
39255376 TTATGGTTAG
65 TTATGATTAG
39255386 GTTATATAAA
Statistics
Matches: 66, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
78 12 0.18
79 5 0.08
80 21 0.32
81 28 0.42
ACGTcount: A:0.29, C:0.01, G:0.15, T:0.55
Consensus pattern (80 bp):
GTTTTGTGATTTATTAGTAATTAAATTTTTTTTAAAAATAGTGTATAATTATGTTGTTAGTAATT
TATGATTAGTTTAGG
Found at i:39255491 original size:100 final size:96
Alignment explanation
Indices: 39255311--39255849 Score: 469
Period size: 100 Copynumber: 5.3 Consensus size: 96
39255301 TTAGTTTAGG
* * * *
39255311 GTTTTGTGATTTTTTAGTAATTTAATTTTTTTTAAAAATAAT-TGTATAATTATGTTGTTAGTAA
1 GTTTTGTGATTTTTTAGTAATGTAA---TTTTTAAAAAAAATGT-TATAGTTATTTTGTTAGTAA
*
39255375 TTTATGGTTAGGTTATATAAATTGTTAGTGTTTTGT
62 TTTATGATTA-GTTATATAAATTGTTAGTGTTTTGT
* ***
39255411 GTTTTGTGATTTATTAGTAATGTAAATTCTTTTTTTAAAAATGTTATAGTTATTTTGTTAGTAAT
1 GTTTTGTGATTTTTTAGTAATGT-AA-T-TTTTAAAAAAAATGTTATAGTTATTTTGTTAGTAAT
* *
39255476 TTATAATTAGTT-TATAAATTGTTAGTGTTTAGTTT
63 TTATGATTAGTTATATAAATTGTTAGTGTTT--TGT
* * *
39255511 AGGATTTTGTGAATTTTTAGTAATGTAA--TTTAAAAGAAAA-ATTATAGTTGTTTTGTTAGTAA
1 --G-TTTTGTGATTTTTTAGTAATGTAATTTTTAAAA-AAAATGTTATAGTTATTTTGTTAGTAA
* **
39255573 GTTATGATTAGGTTATATAAATTGAAAAGTGTTTTGT
62 TTTATGATTA-GTTATATAAATTG-TTAGTGTTTTGT
* * * *
39255610 GTTTTGTGATTTATTAGTAATGTAATTCTTTTAAAAAAAATGTTATAATTATTTTTTTACTAATT
1 GTTTTGTGATTTTTTAGTAATGTAA-T-TTTTAAAAAAAATGTTATAGTTATTTTGTTAGTAATT
* *
39255675 TATGATTAGTT-TATAAATTATTAGTGTTTAGTTTAGG
64 TATGATTAGTTATATAAATTGTTAGTG--T--TTT-GT
* *
39255712 GTTTTGTGATTTTTTAGTAATGTAATTTTAAAAAAATATATAACTTTATAGTTATTTTGTTAGTA
1 GTTTTGTGATTTTTTAGTAATGTAATTTTTAAAAAA-A-AT---GTTATAGTTATTTTGTTAGTA
*
39255777 ATTTATGATTAAGTTATATAAACTGTTAGTGTTTAGTTTAGT
61 ATTTATGATT-AGTTATATAAATTGTTAGTG--T--TTT-GT
* *
39255819 GTTTTGTAATTTTTTATTAATGTAAATTTTT
1 GTTTTGTGATTTTTTAGTAATGT-AATTTTT
39255850 TATAATATAA
Statistics
Matches: 362, Mismatches: 47, Indels: 52
0.79 0.10 0.11
Matches are distributed among these distances:
96 22 0.06
97 5 0.01
98 58 0.16
99 22 0.06
100 109 0.30
101 15 0.04
102 30 0.08
103 20 0.06
105 27 0.07
106 4 0.01
107 44 0.12
108 6 0.02
ACGTcount: A:0.31, C:0.01, G:0.15, T:0.53
Consensus pattern (96 bp):
GTTTTGTGATTTTTTAGTAATGTAATTTTTAAAAAAAATGTTATAGTTATTTTGTTAGTAATTTA
TGATTAGTTATATAAATTGTTAGTGTTTTGT
Found at i:39255651 original size:198 final size:204
Alignment explanation
Indices: 39255301--39255851 Score: 663
Period size: 198 Copynumber: 2.7 Consensus size: 204
39255291 TAATTTATGA
* * * **** * *
39255301 TTAGTTTAGGGTTTTGTGATTTTTTAGTAATTTAATTTTTTTTAAA-A-ATAATTGTATAATTAT
1 TTAGTTTAGGATTTTGTGAATTTTTAGTAATGTAATTTTAAAAAAATATATAACT-TATAGTTAT
* * **
39255364 GTTGTTAGTAATTTATGGTTAGGTTATATAAATTGTTAGTGTTTTGTGTTTTGTGATTTATTAGT
65 TTTGTTAGTAATTTATGATTAGGTTATATAAATTGAAAGTGTTTTGTGTTTTGTGATTTATTAGT
*** * *
39255429 AATGTAAATTCTTTTTTTAAAAATGTTATAGTTATTTTGTTAGTAATTTATAATTAGTTTATAAA
130 AATGTAAATTCTTTTAAAAAAAATGTTATAATTATTTTGTTACTAATTTATAATTAGTTTATAAA
*
39255494 TTGTTAGTGT
195 TTATTAGTGT
* *
39255504 TTAGTTTAGGATTTTGTGAATTTTTAGTAATGTAA-TTT-AAAAGA-A-A-AA-TTATAGTTGTT
1 TTAGTTTAGGATTTTGTGAATTTTTAGTAATGTAATTTTAAAAAAATATATAACTTATAGTTATT
*
39255563 TTGTTAGTAAGTTATGATTAGGTTATATAAATTGAAAAGTGTTTTGTGTTTTGTGATTTATTAGT
66 TTGTTAGTAATTTATGATTAGGTTATATAAATTG-AAAGTGTTTTGTGTTTTGTGATTTATTAGT
* *
39255628 AATGT-AATTCTTTTAAAAAAAATGTTATAATTATTTTTTTACTAATTTATGATTAGTTTATAAA
130 AATGTAAATTCTTTTAAAAAAAATGTTATAATTATTTTGTTACTAATTTATAATTAGTTTATAAA
39255692 TTATTAGTGT
195 TTATTAGTGT
* *
39255702 TTAGTTTAGGGTTTTGTGATTTTTTAGTAATGTAATTTTAAAAAAATATATAACTTTATAGTTAT
1 TTAGTTTAGGATTTTGTGAATTTTTAGTAATGTAATTTTAAAAAAATATATAAC-TTATAGTTAT
* * ** * *
39255767 TTTGTTAGTAATTTATGATTAAGTTATATAAACTGTTAGTGTTTAGTTTAGTGTTTTGTAATTTT
65 TTTGTTAGTAATTTATGATTAGGTTATATAAATTGAAAGTG--T--TTT-GTGTTTTGTGATTTA
*
39255832 TTATTAATGTAAATT-TTTTA
125 TTAGTAATGTAAATTCTTTTA
39255852 TAATATAATT
Statistics
Matches: 300, Mismatches: 34, Indels: 22
0.84 0.10 0.06
Matches are distributed among these distances:
198 133 0.44
199 37 0.12
200 7 0.02
201 5 0.02
202 4 0.01
203 34 0.11
204 4 0.01
205 41 0.14
206 1 0.00
208 3 0.01
209 27 0.09
210 4 0.01
ACGTcount: A:0.31, C:0.01, G:0.15, T:0.53
Consensus pattern (204 bp):
TTAGTTTAGGATTTTGTGAATTTTTAGTAATGTAATTTTAAAAAAATATATAACTTATAGTTATT
TTGTTAGTAATTTATGATTAGGTTATATAAATTGAAAGTGTTTTGTGTTTTGTGATTTATTAGTA
ATGTAAATTCTTTTAAAAAAAATGTTATAATTATTTTGTTACTAATTTATAATTAGTTTATAAAT
TATTAGTGT
Found at i:39261004 original size:41 final size:41
Alignment explanation
Indices: 39260938--39261069 Score: 219
Period size: 41 Copynumber: 3.2 Consensus size: 41
39260928 TTTTTCAAGA
39260938 GCGTTTTTCAAGAAGCGCCGCTAATGCGCAGACCTTTAGCG
1 GCGTTTTTCAAGAAGCGCCGCTAATGCGCAGACCTTTAGCG
* * *
39260979 GCGCTTTTAAAGAAGCGCCGTTAATGCGCAGACCTTTAGCG
1 GCGTTTTTCAAGAAGCGCCGCTAATGCGCAGACCTTTAGCG
*
39261020 GCGTTTTTTCAAGACGCGCCGCTAATGCGCAGACCTTTAGCG
1 GCG-TTTTTCAAGAAGCGCCGCTAATGCGCAGACCTTTAGCG
39261062 GCGTTTTT
1 GCGTTTTT
39261070 GGTGAAGCGC
Statistics
Matches: 83, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
41 46 0.55
42 37 0.45
ACGTcount: A:0.20, C:0.26, G:0.27, T:0.27
Consensus pattern (41 bp):
GCGTTTTTCAAGAAGCGCCGCTAATGCGCAGACCTTTAGCG
Found at i:39261052 original size:42 final size:42
Alignment explanation
Indices: 39260941--39261069 Score: 215
Period size: 42 Copynumber: 3.1 Consensus size: 42
39260931 TTCAAGAGCG
39260941 TTTTTCAAGAAGCGCCGCTAATGCGCAGACCTTTAGCGGCG-
1 TTTTTCAAGAAGCGCCGCTAATGCGCAGACCTTTAGCGGCGT
* * *
39260982 CTTTTAAAGAAGCGCCGTTAATGCGCAGACCTTTAGCGGCGT
1 TTTTTCAAGAAGCGCCGCTAATGCGCAGACCTTTAGCGGCGT
*
39261024 TTTTTCAAGACGCGCCGCTAATGCGCAGACCTTTAGCGGCGT
1 TTTTTCAAGAAGCGCCGCTAATGCGCAGACCTTTAGCGGCGT
39261066 TTTT
1 TTTT
39261070 GGTGAAGCGC
Statistics
Matches: 80, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
41 38 0.47
42 42 0.52
ACGTcount: A:0.21, C:0.26, G:0.26, T:0.28
Consensus pattern (42 bp):
TTTTTCAAGAAGCGCCGCTAATGCGCAGACCTTTAGCGGCGT
Found at i:39261717 original size:14 final size:15
Alignment explanation
Indices: 39261691--39261720 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
39261681 TGTTAAATAA
39261691 GGTTCAGGGGTTAGG
1 GGTTCAGGGGTTAGG
39261706 GGTTCA-GGGTTAGG
1 GGTTCAGGGGTTAGG
39261720 G
1 G
39261721 ACTGGGGGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.13, C:0.07, G:0.53, T:0.27
Consensus pattern (15 bp):
GGTTCAGGGGTTAGG
Found at i:39261919 original size:21 final size:21
Alignment explanation
Indices: 39261885--39261946 Score: 65
Period size: 21 Copynumber: 2.9 Consensus size: 21
39261875 ATTGGTGCAA
39261885 TTAGGG-TTATGAGTTTGGGA-
1 TTAGGGTTTA-GAGTTTGGGAT
* *
39261905 TTAGAGGTTTAGAGTTAGAGAT
1 TTAG-GGTTTAGAGTTTGGGAT
39261927 TTAGGGTTTAGAGATTTGGG
1 TTAGGGTTTAGAG-TTTGGG
39261947 GTCGAGTTAG
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
20 4 0.12
21 19 0.56
22 11 0.32
ACGTcount: A:0.24, C:0.00, G:0.37, T:0.39
Consensus pattern (21 bp):
TTAGGGTTTAGAGTTTGGGAT
Found at i:39262715 original size:12 final size:12
Alignment explanation
Indices: 39262698--39262730 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
39262688 CGTGATTTAA
39262698 AATTTTAAAATG
1 AATTTTAAAATG
39262710 AATTTTAAAA-G
1 AATTTTAAAATG
39262721 -ATTTTAAAAT
1 AATTTTAAAAT
39262731 TTTTAAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 9 0.45
11 1 0.05
12 10 0.50
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (12 bp):
AATTTTAAAATG
Found at i:39262724 original size:29 final size:29
Alignment explanation
Indices: 39262693--39262763 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 29
39262683 TTTTTCGTGA
*
39262693 TTTAAAATTTTAAAATGAATTT-TAAAAGAT
1 TTTAAAATTTTAAAA--AATTTAAAAAAGAT
*
39262723 TTTAAAATTTTTAAAAATTTAAAAAAGAT
1 TTTAAAATTTTAAAAAATTTAAAAAAGAT
*
39262752 TTTAAACTTTTA
1 TTTAAAATTTTA
39262764 TTTTTATAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
28 5 0.14
29 17 0.47
30 14 0.39
ACGTcount: A:0.49, C:0.01, G:0.04, T:0.45
Consensus pattern (29 bp):
TTTAAAATTTTAAAAAATTTAAAAAAGAT
Found at i:39262726 original size:10 final size:10
Alignment explanation
Indices: 39262699--39262757 Score: 59
Period size: 10 Copynumber: 5.8 Consensus size: 10
39262689 GTGATTTAAA
39262699 ATTTTAAAATG
1 ATTTTAAAA-G
39262710 AATTTTAAAAG
1 -ATTTTAAAAG
39262721 ATTTTAAAA-
1 ATTTTAAAAG
*
39262730 TTTTTAAAA-
1 ATTTTAAAAG
*
39262739 ATTTAAAAAAG
1 ATTT-TAAAAG
39262750 ATTTTAAA
1 ATTTTAAA
39262758 CTTTTATTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
9 11 0.27
10 16 0.39
11 5 0.12
12 9 0.22
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (10 bp):
ATTTTAAAAG
Found at i:39264369 original size:57 final size:58
Alignment explanation
Indices: 39264281--39264397 Score: 227
Period size: 57 Copynumber: 2.0 Consensus size: 58
39264271 TTTTGAATGT
39264281 CTCATAGCTTTTTCTCCTCATTAGTTGTGC-TTTTTTTTATAACTACTATAATTGGCA
1 CTCATAGCTTTTTCTCCTCATTAGTTGTGCTTTTTTTTTATAACTACTATAATTGGCA
39264338 CTCATAGCTTTTTCTCCTCATTAGTTGTGCTTTTTTTTTATAACTACTATAATTGGCA
1 CTCATAGCTTTTTCTCCTCATTAGTTGTGCTTTTTTTTTATAACTACTATAATTGGCA
39264396 CT
1 CT
39264398 TTTTAGATTA
Statistics
Matches: 59, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
57 30 0.51
58 29 0.49
ACGTcount: A:0.21, C:0.20, G:0.10, T:0.50
Consensus pattern (58 bp):
CTCATAGCTTTTTCTCCTCATTAGTTGTGCTTTTTTTTTATAACTACTATAATTGGCA
Found at i:39267605 original size:43 final size:43
Alignment explanation
Indices: 39267515--39267850 Score: 423
Period size: 43 Copynumber: 7.8 Consensus size: 43
39267505 TTTTTGCTAG
* * **
39267515 AAGCGCCGCTAAAGGT-TTGTTCTTTAGCGGCGTTT-T-CAAT
1 AAGCGCCGCTAAAGGTCTTGGTCTTTAGCAGCGTTTGTGGGAT
* * *
39267555 AAAAGCGCCGCTAAATGTCATGGTCTATAGCAGCGTTTGTGGGAT
1 --AAGCGCCGCTAAAGGTCTTGGTCTTTAGCAGCGTTTGTGGGAT
*
39267600 AAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGGA-
1 AAGCGCCGCTAAAGGTCTTGGTCTTTAGCAGCGTTTGT-GGGAT
* * *
39267643 AAGTGCCGCTAAAGGTTTTGGTATTTAGCAGCGTTTGTGGGAT
1 AAGCGCCGCTAAAGGTCTTGGTCTTTAGCAGCGTTTGTGGGAT
*
39267686 AAGCGCCGCTAAAGGTCTTGGTCTTTAG-AGGCTTTTGTGGGAT
1 AAGCGCCGCTAAAGGTCTTGGTCTTTAGCA-GCGTTTGTGGGAT
* *
39267729 AAACGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAT
1 AAGCGCCGCTAAAGGTCTTGGTCTTTAGCAGCGTTTGTGGGAT
* *
39267772 AAACACCGCTAAAGGTCTTGGTCTTTAGCAGCGTTTGTGGGGA-
1 AAGCGCCGCTAAAGGTCTTGGTCTTTAGCAGCGTTTGT-GGGAT
* *
39267815 AAGCGCCGCTAAAGGTTTTGGTCTTTAGCGGCGTTT
1 AAGCGCCGCTAAAGGTCTTGGTCTTTAGCAGCGTTT
39267851 TTTTCTAAAA
Statistics
Matches: 258, Mismatches: 28, Indels: 15
0.86 0.09 0.05
Matches are distributed among these distances:
42 20 0.08
43 227 0.88
44 9 0.03
45 2 0.01
ACGTcount: A:0.20, C:0.18, G:0.31, T:0.31
Consensus pattern (43 bp):
AAGCGCCGCTAAAGGTCTTGGTCTTTAGCAGCGTTTGTGGGAT
Found at i:39270816 original size:20 final size:20
Alignment explanation
Indices: 39270774--39270832 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
39270764 GACTTGTTTG
*
39270774 AAAATCATTTTGA-TGTG-TT
1 AAAATCATTTTAACT-TGATT
*
39270793 AAAATGATTTTAACTTGATT
1 AAAATCATTTTAACTTGATT
*
39270813 AAAATCATTTTCACTTGATT
1 AAAATCATTTTAACTTGATT
39270833 TTAAAATTGT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
19 13 0.38
20 21 0.62
ACGTcount: A:0.36, C:0.08, G:0.10, T:0.46
Consensus pattern (20 bp):
AAAATCATTTTAACTTGATT
Found at i:39273295 original size:21 final size:21
Alignment explanation
Indices: 39273248--39273323 Score: 89
Period size: 21 Copynumber: 3.5 Consensus size: 21
39273238 TACGGCACAT
* **
39273248 AAGTGCCTGAAACGACAAACG
1 AAGTGCCTGATACGACAAATA
*
39273269 AGGTGCCTGATACGACAAATA
1 AAGTGCCTGATACGACAAATA
*
39273290 AAGTGCCTGAGATACGACACATA
1 AAGTGCCT--GATACGACAAATA
39273313 AAGTGCCTGAT
1 AAGTGCCTGAT
39273324 CGGCAAAGCC
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
21 27 0.57
23 20 0.43
ACGTcount: A:0.38, C:0.21, G:0.24, T:0.17
Consensus pattern (21 bp):
AAGTGCCTGATACGACAAATA
Found at i:39276419 original size:40 final size:41
Alignment explanation
Indices: 39276374--39276454 Score: 112
Period size: 40 Copynumber: 2.0 Consensus size: 41
39276364 GTAACAGTTT
** *
39276374 GGGCCTTAGCCCATCTTAGTAT-AGTATCAAAT-ATGCAGTA
1 GGGCCTTAGCCCATCACAGTATCAGTAGC-AATCATGCAGTA
39276414 GGGCCTTAGCCCATCACAGTATCAGTAGCAATCATGCAGTA
1 GGGCCTTAGCCCATCACAGTATCAGTAGCAATCATGCAGTA
39276455 TTTAGTAACA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
40 23 0.64
41 13 0.36
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26
Consensus pattern (41 bp):
GGGCCTTAGCCCATCACAGTATCAGTAGCAATCATGCAGTA
Found at i:39277756 original size:40 final size:41
Alignment explanation
Indices: 39277686--39277766 Score: 112
Period size: 40 Copynumber: 2.0 Consensus size: 41
39277676 TGTTACTAAA
* **
39277686 TACTGCATGATTGCTACTGATACTGTGATGGGCTAAGGCCC
1 TACTGCATGATTGATACTGATACTAAGATGGGCTAAGGCCC
39277727 TACTGCAT-ATTTGATACT-ATACTAAGATGGGCTAAGGCCC
1 TACTGCATGA-TTGATACTGATACTAAGATGGGCTAAGGCCC
39277767 AAACTGTTAC
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
40 21 0.58
41 15 0.42
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (41 bp):
TACTGCATGATTGATACTGATACTAAGATGGGCTAAGGCCC
Found at i:39281830 original size:137 final size:137
Alignment explanation
Indices: 39281672--39281945 Score: 539
Period size: 137 Copynumber: 2.0 Consensus size: 137
39281662 TTCTTCTACT
39281672 ACTAAAGTTCTTTTGTTAAAAACTCGATAAGCTTTAGAATTTAAAAAATAACCAAGAAAATTTTC
1 ACTAAAGTTCTTTTGTTAAAAACTCGATAAGCTTTAGAATTTAAAAAATAACCAAGAAAATTTTC
39281737 TTTATAACTTTTTACATCAAATTTACCAAGATTATCTTTGTCATTGTTTAAAACAAAACATTTTC
66 TTTATAACTTTTTACATCAAATTTACCAAGATTATCTTTGTCATTGTTTAAAACAAAACATTTTC
39281802 ATCCAAA
131 ATCCAAA
39281809 ACTAAAGTTCTTTTGTTAAAAACTCGATAAGCTTTAGAATTTAAAAAATAACCAAGAAAATTTTC
1 ACTAAAGTTCTTTTGTTAAAAACTCGATAAGCTTTAGAATTTAAAAAATAACCAAGAAAATTTTC
*
39281874 TTTATCACTTTTTACATCAAATTTACCAAGATTATCTTTGTCATTGTTTAAAACAAAACATTTTC
66 TTTATAACTTTTTACATCAAATTTACCAAGATTATCTTTGTCATTGTTTAAAACAAAACATTTTC
39281939 ATCCAAA
131 ATCCAAA
39281946 GGGATGAAAA
Statistics
Matches: 136, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
137 136 1.00
ACGTcount: A:0.41, C:0.15, G:0.07, T:0.38
Consensus pattern (137 bp):
ACTAAAGTTCTTTTGTTAAAAACTCGATAAGCTTTAGAATTTAAAAAATAACCAAGAAAATTTTC
TTTATAACTTTTTACATCAAATTTACCAAGATTATCTTTGTCATTGTTTAAAACAAAACATTTTC
ATCCAAA
Found at i:39288760 original size:114 final size:115
Alignment explanation
Indices: 39288446--39288776 Score: 488
Period size: 114 Copynumber: 2.9 Consensus size: 115
39288436 GCGAACAATA
* *
39288446 GCTTTAGCGGTGTTTTTAAGAAAGCGCCGCAAAAAACCTAAGCAAAAACGACGTCGTTTTGTGAG
1 GCTTTAGCGGCGTTTTTAAGAAAGCGCCGCAAAAAACCTAAGCCAAAACGACGTCGTTTTGTGAG
* *
39288511 CTTTTGGGGATTTAGCGGCG-CTTTAAGGAAAGCGCCGCTAATGCTCAGG
66 CTTTCGGGGATTTAGCGGCGTTTTTAAGGAAAGCGCCGCTAATGCTCAGG
* * * *
39288560 GCTTTAGCGGCGTTTTTGAGAAAGCGCTGCAAAAAACCTAAGCCAAAACAACGCCGTTTTGTGAG
1 GCTTTAGCGGCGTTTTTAAGAAAGCGCCGCAAAAAACCTAAGCCAAAACGACGTCGTTTTGTGAG
39288625 CTTTCGGGGATTTAGCGGCGTTTTTAA-GAAAGCGCCGCTAATGCTCAGG
66 CTTTCGGGGATTTAGCGGCGTTTTTAAGGAAAGCGCCGCTAATGCTCAGG
* * * * *
39288674 GCTTTAGTGGCGTTTTCAAGAAAGCCCCGCAAAGAACCTAAGCCAAAACGACGTTGTTTTGTGAG
1 GCTTTAGCGGCGTTTTTAAGAAAGCGCCGCAAAAAACCTAAGCCAAAACGACGTCGTTTTGTGAG
* * * *
39288739 CTTTGGGGGATTTAGGGGCGTTTTTGAGG-AGGCGCCGC
66 CTTTCGGGGATTTAGCGGCGTTTTTAAGGAAAGCGCCGC
39288777 AAAAAACCTA
Statistics
Matches: 194, Mismatches: 21, Indels: 4
0.89 0.10 0.02
Matches are distributed among these distances:
114 188 0.97
115 6 0.03
ACGTcount: A:0.25, C:0.20, G:0.29, T:0.26
Consensus pattern (115 bp):
GCTTTAGCGGCGTTTTTAAGAAAGCGCCGCAAAAAACCTAAGCCAAAACGACGTCGTTTTGTGAG
CTTTCGGGGATTTAGCGGCGTTTTTAAGGAAAGCGCCGCTAATGCTCAGG
Found at i:39288795 original size:73 final size:72
Alignment explanation
Indices: 39288700--39288840 Score: 210
Period size: 73 Copynumber: 1.9 Consensus size: 72
39288690 CAAGAAAGCC
* ** ** *
39288700 CCGCAAAGAACCTAAGCCAAAACGACGTTGTTTTGTGAGCTTTGGGGGATTTAGGGGCGTTTTTG
1 CCGCAAAAAACCTAAGCCAAAACGACGCCGTTTTGTGAGCTTTCAGGGATTTAGCGGCGTTTTT-
39288765 AGGAGGCG
65 AGGAGGCG
*
39288773 CCGCAAAAAACCTAAGCCAAAACGGCGCCGTTTTGTGAGCTTTCAGGGATTTAGCGGCGTTTTTA
1 CCGCAAAAAACCTAAGCCAAAACGACGCCGTTTTGTGAGCTTTCAGGGATTTAGCGGCGTTTTTA
39288838 GGA
66 GGA
39288841 AAGCGCTGCT
Statistics
Matches: 61, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
72 4 0.07
73 57 0.93
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.26
Consensus pattern (72 bp):
CCGCAAAAAACCTAAGCCAAAACGACGCCGTTTTGTGAGCTTTCAGGGATTTAGCGGCGTTTTTA
GGAGGCG
Found at i:39289052 original size:14 final size:14
Alignment explanation
Indices: 39289033--39289072 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
39289023 TATCACTATA
*
39289033 GTTTAGGGTTTTTG
1 GTTTAGGGTTTATG
*
39289047 GTTTAGGGTATATG
1 GTTTAGGGTTTATG
*
39289061 GTTTAGAGTTTA
1 GTTTAGGGTTTA
39289073 AAGTTTAGGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.17, C:0.00, G:0.33, T:0.50
Consensus pattern (14 bp):
GTTTAGGGTTTATG
Found at i:39289116 original size:22 final size:21
Alignment explanation
Indices: 39289091--39289138 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
39289081 GTGTTACCAT
* *
39289091 TTTAAGGTTTATGGATTATGGG
1 TTTAAGGGTTATAGATTAT-GG
* *
39289113 TTTAGGGGTTATAGTTTATGG
1 TTTAAGGGTTATAGATTATGG
39289134 TTTAA
1 TTTAA
39289139 AGGCTGGGGT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.23, C:0.00, G:0.29, T:0.48
Consensus pattern (21 bp):
TTTAAGGGTTATAGATTATGG
Found at i:39289199 original size:7 final size:7
Alignment explanation
Indices: 39289177--39289220 Score: 54
Period size: 7 Copynumber: 6.3 Consensus size: 7
39289167 GTGCATGTTA
39289177 AGGGTTT
1 AGGGTTT
*
39289184 ATGGTTTT
1 A-GGGTTT
39289192 AGGGTTT
1 AGGGTTT
39289199 A-GGTTT
1 AGGGTTT
*
39289205 ATGGTTT
1 AGGGTTT
39289212 AGGGTTT
1 AGGGTTT
39289219 AG
1 AG
39289221 ATTAACTAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
6 6 0.19
7 20 0.62
8 6 0.19
ACGTcount: A:0.16, C:0.00, G:0.36, T:0.48
Consensus pattern (7 bp):
AGGGTTT
Found at i:39289204 original size:21 final size:20
Alignment explanation
Indices: 39289179--39289220 Score: 75
Period size: 20 Copynumber: 2.0 Consensus size: 20
39289169 GCATGTTAAG
39289179 GGTTTATGGTTTTAGGGTTTA
1 GGTTTATGG-TTTAGGGTTTA
39289200 GGTTTATGGTTTAGGGTTTA
1 GGTTTATGGTTTAGGGTTTA
39289220 G
1 G
39289221 ATTAACTAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.14, C:0.00, G:0.36, T:0.50
Consensus pattern (20 bp):
GGTTTATGGTTTAGGGTTTA
Found at i:39289217 original size:14 final size:13
Alignment explanation
Indices: 39289177--39289220 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
39289167 GTGCATGTTA
39289177 AGGGTTTATGGTTTT
1 AGGGTTTA-GG-TTT
39289192 AGGGTTTAGGTTT
1 AGGGTTTAGGTTT
*
39289205 ATGGTTTAGGGTTT
1 AGGGTTTA-GGTTT
39289219 AG
1 AG
39289221 ATTAACTAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
13 10 0.38
14 8 0.31
15 8 0.31
ACGTcount: A:0.16, C:0.00, G:0.36, T:0.48
Consensus pattern (13 bp):
AGGGTTTAGGTTT
Done.