Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A12
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: 103038859
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4950000 characters in sequence are not A, C, G, or T
File 125 of 320
Found at i:40651301 original size:55 final size:55
Alignment explanation
Indices: 40651242--40651351 Score: 202
Period size: 55 Copynumber: 2.0 Consensus size: 55
40651232 TAGTTAATAT
*
40651242 GTTTGATTTTGAGGTTGTGTATATATTAAGCCATGCAAAAATGGCTAAGTATAAA
1 GTTTGATTTTGAGGTTGTGTATATATTAAACCATGCAAAAATGGCTAAGTATAAA
*
40651297 GTTTGATTTTGAGGTTGTGTATATATTAAACCATGCTAAAATGGCTAAGTATAAA
1 GTTTGATTTTGAGGTTGTGTATATATTAAACCATGCAAAAATGGCTAAGTATAAA
40651352 TTTTAAGTTT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.35, C:0.07, G:0.21, T:0.37
Consensus pattern (55 bp):
GTTTGATTTTGAGGTTGTGTATATATTAAACCATGCAAAAATGGCTAAGTATAAA
Found at i:40655633 original size:31 final size:31
Alignment explanation
Indices: 40655586--40655669 Score: 134
Period size: 31 Copynumber: 2.7 Consensus size: 31
40655576 TCAGTCTCAA
*
40655586 CATAT-ACTGGGTCGAAGCCTTTTCATTATT
1 CATATCACTGGGCCGAAGCCTTTTCATTATT
*
40655616 CATATCACTGGGCCGAAGCCTTTTCATTTTT
1 CATATCACTGGGCCGAAGCCTTTTCATTATT
*
40655647 CATATCACTGGGCTGAAGCCTTT
1 CATATCACTGGGCCGAAGCCTTT
40655670 ACTGTAAACG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
30 5 0.10
31 45 0.90
ACGTcount: A:0.21, C:0.24, G:0.18, T:0.37
Consensus pattern (31 bp):
CATATCACTGGGCCGAAGCCTTTTCATTATT
Found at i:40656018 original size:10 final size:10
Alignment explanation
Indices: 40656005--40656042 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
40655995 CATATATGAA
40656005 CATATCATGG
1 CATATCATGG
*
40656015 CATATCAAGTG
1 CATATCATG-G
40656026 CATATCATGG
1 CATATCATGG
40656036 CATATCA
1 CATATCA
40656043 CGTACAATAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 16 0.64
11 9 0.36
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.29
Consensus pattern (10 bp):
CATATCATGG
Found at i:40656123 original size:25 final size:25
Alignment explanation
Indices: 40656084--40656134 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
40656074 ATAACATATC
* *
40656084 CCTAGGGGTATAATGGTCATTTTCA
1 CCTAGGGGCAAAATGGTCATTTTCA
40656109 CCTAGGGGCAAAATGGTCATTTTCA
1 CCTAGGGGCAAAATGGTCATTTTCA
40656134 C
1 C
40656135 ATTATAAGGG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (25 bp):
CCTAGGGGCAAAATGGTCATTTTCA
Found at i:40662823 original size:30 final size:30
Alignment explanation
Indices: 40662789--40662848 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
40662779 ATTTAATACG
40662789 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
40662819 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
40662849 GGTTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:40665239 original size:39 final size:40
Alignment explanation
Indices: 40665138--40665361 Score: 271
Period size: 40 Copynumber: 5.7 Consensus size: 40
40665128 TCGAATGATG
* *
40665138 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAT
* *
40665177 ATCCAGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
40665218 TCCGGGCTAAG-CCCAAAGGCATTGGTGCGAGTTACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
40665257 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
*
40665296 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
40665335 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
40665362 AACGAGTAGC
Statistics
Matches: 162, Mismatches: 16, Indels: 12
0.85 0.08 0.06
Matches are distributed among these distances:
39 73 0.45
40 79 0.49
41 10 0.06
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
Found at i:40665384 original size:79 final size:79
Alignment explanation
Indices: 40665138--40665361 Score: 269
Period size: 79 Copynumber: 2.8 Consensus size: 79
40665128 TCGAATGATG
* * * * *
40665138 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATATCCAGACTAAGAT-CCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATATCCGGGCTAAG-TCCCGAAGGCAT
40665201 TTGTGCGAGTTACTAA
64 TTGTGCGAGTTACTAA
* * *
40665217 TTCCGGGCTAAG-CCCAAAGGCATTGGTGCGAGTTACTA-ATTCCGGGCTAAG-CCCGAAGGCAT
1 -TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-TCCGGGCTAAGTCCCGAAGGCAT
*
40665279 TGGTGCGAGTTACTAAA
64 TTGTGCGAGTTACT-AA
* *
40665296 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTT
40665361 G
66 G
40665362 AACGAGTAGC
Statistics
Matches: 124, Mismatches: 13, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
78 34 0.27
79 59 0.48
80 31 0.25
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (79 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTT
GTGCGAGTTACTAA
Found at i:40665392 original size:79 final size:79
Alignment explanation
Indices: 40665191--40665394 Score: 209
Period size: 79 Copynumber: 2.6 Consensus size: 79
40665181 AGACTAAGAT
* ** * * * *
40665191 CCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCT-AAGCCCAAAGGCATTGGTGCGAGTTACTA
1 CCGAAGGCATTGGAACGAGTTACTAAATCCGGGTTAAATCCCGAAGGCATTGGTGCGAGTTACTA
*
40665255 ATTCCGGGCTAAGC
66 ATACCGGGCTAAGC
** * *
40665269 CCGAAGGCATTGGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-
1 CCGAAGGCATTGGAACGAGTTACTAAATCCGGGTTAAATCCCGAAGGCATTGGTGCGAGTTACTA
*
40665333 ATAACCGGGCTATGTC
66 AT-ACCGGGCTAAG-C
* * *
40665349 CCGAAGGCATTTGAACGAG-TAGCTATATCC-GGTTAAATTCCGAAGG
1 CCGAAGGCATTGGAACGAGTTA-CTAAATCCGGGTTAAATCCCGAAGG
40665395 TACGTGATTC
Statistics
Matches: 107, Mismatches: 15, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
78 34 0.32
79 49 0.46
80 24 0.22
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTGGAACGAGTTACTAAATCCGGGTTAAATCCCGAAGGCATTGGTGCGAGTTACTA
ATACCGGGCTAAGC
Found at i:40667737 original size:27 final size:27
Alignment explanation
Indices: 40667707--40667834 Score: 150
Period size: 27 Copynumber: 4.8 Consensus size: 27
40667697 TACTGAAATG
*
40667707 CCCTCGATTTGTAGAATTACCATTTTA
1 CCCTCGATTTATAGAATTACCATTTTA
** *
40667734 CCCTCGATTTATAGAATTACTGTTTCA
1 CCCTCGATTTATAGAATTACCATTTTA
* * **
40667761 ACCTCGATTTACA-AATTACTGTTTTA
1 CCCTCGATTTATAGAATTACCATTTTA
* *
40667787 CCCTCAATTTATAGAATTAGCATTTTA
1 CCCTCGATTTATAGAATTACCATTTTA
*
40667814 CCCTCGATTTACAGAATTACC
1 CCCTCGATTTATAGAATTACC
40667835 GAAATACCCT
Statistics
Matches: 84, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
26 22 0.26
27 62 0.74
ACGTcount: A:0.29, C:0.23, G:0.09, T:0.39
Consensus pattern (27 bp):
CCCTCGATTTATAGAATTACCATTTTA
Found at i:40667797 original size:53 final size:54
Alignment explanation
Indices: 40667708--40667833 Score: 159
Period size: 53 Copynumber: 2.4 Consensus size: 54
40667698 ACTGAAATGC
** ** *
40667708 CCTCGATTTGTAGAATTACCATTTTACCCTCGATTTATAGAATTA-C-TGTTTCAA
1 CCTCGATTTACAGAATTACTGTTTTACCCTCAATTTATAGAATTAGCAT-TTT-AA
*
40667762 CCTCGATTTACA-AATTACTGTTTTACCCTCAATTTATAGAATTAGCATTTTAC
1 CCTCGATTTACAGAATTACTGTTTTACCCTCAATTTATAGAATTAGCATTTTAA
40667815 CCTCGATTTACAGAATTAC
1 CCTCGATTTACAGAATTAC
40667834 CGAAATACCC
Statistics
Matches: 63, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
53 42 0.67
54 20 0.32
55 1 0.02
ACGTcount: A:0.29, C:0.21, G:0.10, T:0.40
Consensus pattern (54 bp):
CCTCGATTTACAGAATTACTGTTTTACCCTCAATTTATAGAATTAGCATTTTAA
Found at i:40667860 original size:27 final size:27
Alignment explanation
Indices: 40667826--40668163 Score: 495
Period size: 27 Copynumber: 12.6 Consensus size: 27
40667816 CTCGATTTAC
*
40667826 AGAATTACCGAAATACCCTTGTAGGGT
1 AGAATTACCGAAATACCCCTGTAGGGT
* *
40667853 AGATTTACCGAAATACCACTGTAGGGT
1 AGAATTACCGAAATACCCCTGTAGGGT
*
40667880 AGAATTACCGAAATACCCCTGTAGGAT
1 AGAATTACCGAAATACCCCTGTAGGGT
*
40667907 AGAATTATCGAAATACCCCTGTAGGGT
1 AGAATTACCGAAATACCCCTGTAGGGT
40667934 AGAATTACCGAAATA-CCCTGTAGGGT
1 AGAATTACCGAAATACCCCTGTAGGGT
* *
40667960 AGAATTATC-ACAATACCCCTATAGGGT
1 AGAATTACCGA-AATACCCCTGTAGGGT
* *
40667987 AGAATTACCGAAATACCCTTGTTGGGT
1 AGAATTACCGAAATACCCCTGTAGGGT
40668014 AGAATTACCGAAATACCCCTGTAGGGT
1 AGAATTACCGAAATACCCCTGTAGGGT
40668041 AGAATTACCGAAATA-CCCTGTAGGGT
1 AGAATTACCGAAATACCCCTGTAGGGT
40668067 AGAATTACCGAAATA-CCCTGTAGGGT
1 AGAATTACCGAAATACCCCTGTAGGGT
*
40668093 AGAATTACCAAAATACCCCTGTAGGGT
1 AGAATTACCGAAATACCCCTGTAGGGT
** **
40668120 AGAATTACTAAAATACCCCTACAGGGT
1 AGAATTACCGAAATACCCCTGTAGGGT
* *
40668147 AGAATTATCGAGATACC
1 AGAATTACCGAAATACC
40668164 TTGTGGGATA
Statistics
Matches: 282, Mismatches: 25, Indels: 8
0.90 0.08 0.03
Matches are distributed among these distances:
25 1 0.00
26 74 0.26
27 206 0.73
28 1 0.00
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.24
Consensus pattern (27 bp):
AGAATTACCGAAATACCCCTGTAGGGT
Found at i:40667999 original size:80 final size:81
Alignment explanation
Indices: 40667826--40668163 Score: 495
Period size: 80 Copynumber: 4.2 Consensus size: 81
40667816 CTCGATTTAC
* * *
40667826 AGAATTACCGAAATACCCTTGTAGGGTAGATTTACCGAAATACCACTGTAGGGTAGAATTACCGA
1 AGAATTACCGAAATACCCCTGTAGGGTAGAATTACCGAAATACCCCTGTAGGGTAGAATTACCGA
* *
40667891 AATACCCCTGTAGGAT
66 AATACCCCTATAGGGT
* *
40667907 AGAATTATCGAAATACCCCTGTAGGGTAGAATTACCGAAATA-CCCTGTAGGGTAGAATTATC-A
1 AGAATTACCGAAATACCCCTGTAGGGTAGAATTACCGAAATACCCCTGTAGGGTAGAATTACCGA
40667970 CAATACCCCTATAGGGT
66 -AATACCCCTATAGGGT
* *
40667987 AGAATTACCGAAATACCCTTGTTGGGTAGAATTACCGAAATACCCCTGTAGGGTAGAATTACCGA
1 AGAATTACCGAAATACCCCTGTAGGGTAGAATTACCGAAATACCCCTGTAGGGTAGAATTACCGA
*
40668052 AATA-CCCTGTAGGGT
66 AATACCCCTATAGGGT
* **
40668067 AGAATTACCGAAATA-CCCTGTAGGGTAGAATTACCAAAATACCCCTGTAGGGTAGAATTACTAA
1 AGAATTACCGAAATACCCCTGTAGGGTAGAATTACCGAAATACCCCTGTAGGGTAGAATTACCGA
*
40668131 AATACCCCTACAGGGT
66 AATACCCCTATAGGGT
* *
40668147 AGAATTATCGAGATACC
1 AGAATTACCGAAATACC
40668164 TTGTGGGATA
Statistics
Matches: 231, Mismatches: 21, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
79 49 0.21
80 118 0.51
81 63 0.27
82 1 0.00
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.24
Consensus pattern (81 bp):
AGAATTACCGAAATACCCCTGTAGGGTAGAATTACCGAAATACCCCTGTAGGGTAGAATTACCGA
AATACCCCTATAGGGT
Found at i:40668652 original size:22 final size:22
Alignment explanation
Indices: 40668600--40668664 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 22
40668590 TTAAAGCCTT
* *
40668600 CTGATTATGGCTTTGTGTCAAC
1 CTGATTATGGCTCTGTGCCAAC
*
40668622 CT-ACATATGGCTCTGTGCCAAC
1 CTGA-TTATGGCTCTGTGCCAAC
*
40668644 CTGATTATGGCTGTGTGCCAA
1 CTGATTATGGCTCTGTGCCAA
40668665 ACGTATTTGC
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
21 1 0.03
22 34 0.94
23 1 0.03
ACGTcount: A:0.20, C:0.23, G:0.23, T:0.34
Consensus pattern (22 bp):
CTGATTATGGCTCTGTGCCAAC
Found at i:40668853 original size:27 final size:27
Alignment explanation
Indices: 40668823--40668924 Score: 116
Period size: 27 Copynumber: 3.8 Consensus size: 27
40668813 ATTCTGTTAA
* * *
40668823 GTGGCTTTGCTACATTATCTGTTTCTG
1 GTGGCTATGCCACAATATCTGTTTCTG
40668850 GTGGCTATGCCACAAATATCTG-TTCTG
1 GTGGCTATGCCAC-AATATCTGTTTCTG
* *
40668877 GTGGCTCTGCCACAATATCTGTATCTG
1 GTGGCTATGCCACAATATCTGTTTCTG
* * *
40668904 GTGACTCTGTCACAATATCTG
1 GTGGCTATGCCACAATATCTG
40668925 ATAACTGAGC
Statistics
Matches: 66, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
26 8 0.12
27 51 0.77
28 7 0.11
ACGTcount: A:0.19, C:0.23, G:0.22, T:0.37
Consensus pattern (27 bp):
GTGGCTATGCCACAATATCTGTTTCTG
Found at i:40668881 original size:54 final size:53
Alignment explanation
Indices: 40668823--40668924 Score: 132
Period size: 54 Copynumber: 1.9 Consensus size: 53
40668813 ATTCTGTTAA
* * * * *
40668823 GTGGCTTTGCTACATTATCTGTTTCTGGTGGCTATGCCACAAATATCTGTTCTG
1 GTGGCTCTGCCACAATATCTGTATCTGGTGACTATGCCAC-AATATCTGTTCTG
* *
40668877 GTGGCTCTGCCACAATATCTGTATCTGGTGACTCTGTCACAATATCTG
1 GTGGCTCTGCCACAATATCTGTATCTGGTGACTATGCCACAATATCTG
40668925 ATAACTGAGC
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
53 8 0.20
54 33 0.80
ACGTcount: A:0.19, C:0.23, G:0.22, T:0.37
Consensus pattern (53 bp):
GTGGCTCTGCCACAATATCTGTATCTGGTGACTATGCCACAATATCTGTTCTG
Found at i:40669121 original size:12 final size:12
Alignment explanation
Indices: 40669104--40669138 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
40669094 ATTTTGTCAC
40669104 CTAATTCTGATT
1 CTAATTCTGATT
*
40669116 CTAATTCTAATT
1 CTAATTCTGATT
*
40669128 CTAGTTCTGAT
1 CTAATTCTGAT
40669139 AATGTTTCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.26, C:0.17, G:0.09, T:0.49
Consensus pattern (12 bp):
CTAATTCTGATT
Found at i:40670563 original size:46 final size:49
Alignment explanation
Indices: 40670457--40670579 Score: 144
Period size: 50 Copynumber: 2.6 Consensus size: 49
40670447 TGTCTTCGAC
** * *
40670457 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCGTATATATATATAAT
1 ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCG-ATATATATATAAT
* * *
40670507 ATGGGCTTACATGGCTCATTCCTGTCTCCAAAGCC-ATATA-A-CTGAT
1 ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCGATATATATATAAT
*
40670553 ATGGACTTACATGGCTCATTTCTGTCT
1 ATGGACTTACATGGCTCATTCCTGTCT
40670580 TGTCCTGTCC
Statistics
Matches: 64, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
46 28 0.44
47 1 0.02
48 5 0.08
50 30 0.47
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.36
Consensus pattern (49 bp):
ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCGATATATATATAAT
Found at i:40674336 original size:31 final size:31
Alignment explanation
Indices: 40674297--40674367 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
40674287 TCAGAACTAG
*
40674297 AATCAGAATCAGA-ATAAGGTGACAGAATCAA
1 AATCAGAATCA-ATATAAGGTAACAGAATCAA
* *
40674328 AATTAGAATCAATATCAGGTAACAGAATCAA
1 AATCAGAATCAATATAAGGTAACAGAATCAA
*
40674359 TATCAGAAT
1 AATCAGAAT
40674368 GTGAATGTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
30 1 0.03
31 33 0.97
ACGTcount: A:0.51, C:0.13, G:0.15, T:0.21
Consensus pattern (31 bp):
AATCAGAATCAATATAAGGTAACAGAATCAA
Found at i:40674631 original size:27 final size:26
Alignment explanation
Indices: 40674583--40674634 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
40674573 GCGAGGCTGC
*
40674583 CAGATATTGTGACGAAGTCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
* *
40674609 CAGATATATGTGGCGAGGCCACCAGA
1 CAGATAT-TGTGACGAAGCCACCAGA
40674635 TTGTAGCGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.35, C:0.21, G:0.27, T:0.17
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:40674900 original size:27 final size:27
Alignment explanation
Indices: 40674870--40675038 Score: 221
Period size: 27 Copynumber: 6.2 Consensus size: 27
40674860 TAACACCCTA
** *
40674870 AGGGTAAAATGGTAATTTTATAAATCG
1 AGGGTAAAACAGTAATTTTGTAAATCG
** * *
40674897 AGGGTAAAATGGTAATTCTGTAAATTG
1 AGGGTAAAACAGTAATTTTGTAAATCG
40674924 AGGGTAAAACAGTAATTTTGTAAATCG
1 AGGGTAAAACAGTAATTTTGTAAATCG
* *
40674951 AGGGTAAAACAGTAATTCTGTCAATCG
1 AGGGTAAAACAGTAATTTTGTAAATCG
*
40674978 AGGGTAAAACAATAATTTTGTAAATCG
1 AGGGTAAAACAGTAATTTTGTAAATCG
* *
40675005 AGGGTAAAATAGTAATTTTTGTAATTCG
1 AGGGTAAAACAGTAA-TTTTGTAAATCG
40675033 AGGGTA
1 AGGGTA
40675039 CTTTGATAAT
Statistics
Matches: 126, Mismatches: 15, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
27 109 0.87
28 17 0.13
ACGTcount: A:0.39, C:0.07, G:0.23, T:0.31
Consensus pattern (27 bp):
AGGGTAAAACAGTAATTTTGTAAATCG
Found at i:40675090 original size:27 final size:27
Alignment explanation
Indices: 40675060--40675184 Score: 105
Period size: 27 Copynumber: 4.7 Consensus size: 27
40675050 TTACATGTCG
*
40675060 AGGGTATTTCAGTAATTTTGCAAACTA
1 AGGGTATTTCAGTAATTTTACAAACTA
*
40675087 AGGGTATTTC-GATAATTTTACAAA-TCG
1 AGGGTATTTCAG-TAATTTTACAAACT-A
* ** *
40675114 AGGATATTTGGGTAATTTTATAAACTA
1 AGGGTATTTCAGTAATTTTACAAACTA
* *
40675141 AGGGTACTTT-GGTAATTTTAC-AACTG
1 AGGGTA-TTTCAGTAATTTTACAAACTA
* *
40675167 GGGGTATTTTAGTAATTT
1 AGGGTATTTCAGTAATTT
40675185 AGTAAACTAA
Statistics
Matches: 81, Mismatches: 11, Indels: 13
0.77 0.10 0.12
Matches are distributed among these distances:
25 3 0.04
26 18 0.22
27 55 0.68
28 5 0.06
ACGTcount: A:0.31, C:0.08, G:0.21, T:0.40
Consensus pattern (27 bp):
AGGGTATTTCAGTAATTTTACAAACTA
Found at i:40675103 original size:54 final size:54
Alignment explanation
Indices: 40675033--40675194 Score: 193
Period size: 54 Copynumber: 3.0 Consensus size: 54
40675023 TTGTAATTCG
** *
40675033 AGGGTACTTTGATAATTTTACATGTCGAGGGTATTTCAGTAATTTTGCAAACTA
1 AGGGTACTTTGATAATTTTACAAATCGAGGGTATTTCAGTAATTTTGTAAACTA
* ** *
40675087 AGGGTA-TTTCGATAATTTTACAAATCGAGGATATTTGGGTAATTTTATAAACTA
1 AGGGTACTTT-GATAATTTTACAAATCGAGGGTATTTCAGTAATTTTGTAAACTA
* * * * *
40675141 AGGGTACTTTGGTAATTTTACAACT-GGGGGTATTTTAGTAATTTAGTAAACTA
1 AGGGTACTTTGATAATTTTACAAATCGAGGGTATTTCAGTAATTTTGTAAACTA
40675194 A
1 A
40675195 AGTATTCTAA
Statistics
Matches: 91, Mismatches: 15, Indels: 5
0.82 0.14 0.05
Matches are distributed among these distances:
53 26 0.29
54 62 0.68
55 3 0.03
ACGTcount: A:0.32, C:0.09, G:0.20, T:0.39
Consensus pattern (54 bp):
AGGGTACTTTGATAATTTTACAAATCGAGGGTATTTCAGTAATTTTGTAAACTA
Found at i:40677419 original size:31 final size:30
Alignment explanation
Indices: 40677372--40677455 Score: 114
Period size: 31 Copynumber: 2.7 Consensus size: 30
40677362 TCAGTCTCAA
*
40677372 CATATACTGGGTCGAAGCCTTTTCGTTAAT
1 CATATACTGGGTCGAAGCCTTTTCATTAAT
* *
40677402 CATATGACTGGGCCGAAGCCTTTTCATTATT
1 CATAT-ACTGGGTCGAAGCCTTTTCATTAAT
*
40677433 CATATCACTAGGTCGAAGCCTTT
1 CATAT-ACTGGGTCGAAGCCTTT
40677456 ACTATAAATG
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
30 5 0.11
31 42 0.89
ACGTcount: A:0.24, C:0.23, G:0.19, T:0.35
Consensus pattern (30 bp):
CATATACTGGGTCGAAGCCTTTTCATTAAT
Found at i:40677734 original size:25 final size:24
Alignment explanation
Indices: 40677668--40677745 Score: 104
Period size: 25 Copynumber: 3.2 Consensus size: 24
40677658 GGCCTTGCCT
* *
40677668 CTTTTAAT-AACTAGGGCAAAGCC
1 CTTTTGATAAACTGGGGCAAAGCC
*
40677691 CTTTTGATGAACTGGGGCAAAGCC
1 CTTTTGATAAACTGGGGCAAAGCC
*
40677715 CTTTTCGGTAAACTGGGGCAAAGCC
1 CTTTT-GATAAACTGGGGCAAAGCC
40677740 CTTTTG
1 CTTTTG
40677746 CACTTCCTCC
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
23 7 0.14
24 20 0.41
25 22 0.45
ACGTcount: A:0.26, C:0.22, G:0.24, T:0.28
Consensus pattern (24 bp):
CTTTTGATAAACTGGGGCAAAGCC
Found at i:40677803 original size:10 final size:10
Alignment explanation
Indices: 40677790--40677829 Score: 62
Period size: 10 Copynumber: 3.9 Consensus size: 10
40677780 CATATATAAA
40677790 CATATCATGG
1 CATATCATGG
*
40677800 CATATCAGGTG
1 CATATCATG-G
40677811 CATATCATGG
1 CATATCATGG
40677821 CATATCATG
1 CATATCATG
40677830 TACAATACAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
10 18 0.67
11 9 0.33
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (10 bp):
CATATCATGG
Found at i:40684229 original size:27 final size:27
Alignment explanation
Indices: 40684199--40684375 Score: 160
Period size: 27 Copynumber: 6.5 Consensus size: 27
40684189 ATATTGAGCC
* *
40684199 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* * *
40684226 CGCACACTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
* *
40684253 CCCACACTTAGTGCTACATAGTCAGACT
1 CGCACACTTAGTGCTACATAATCA-ACT
** ** *
40684281 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
40684308 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* *
40684335 CGCACACTTAGTGCAACATAGTCGAA-T
1 CGCACACTTAGTGCTACATAATC-AACT
40684362 CGCACACTTAGTGC
1 CGCACACTTAGTGC
40684376 CGCACAATTT
Statistics
Matches: 125, Mismatches: 21, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
27 101 0.81
28 24 0.19
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:40684341 original size:82 final size:81
Alignment explanation
Indices: 40684220--40684379 Score: 223
Period size: 82 Copynumber: 2.0 Consensus size: 81
40684210 TGCTATATAA
* * *
40684220 TCAACTCGCACACTTAGTGCCACGTAATCAAATCCCACACTTAGTGCTACATAGTCAGACTCGCA
1 TCAACTCGCACACTTAGTGCCACATAATCAAATCCCACACTTAGTGCAACATAGTC-GAATCGCA
40684285 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * ** *
40684302 TCAATTCGCACACTTAGTG-CATCATATTCATTTCGCACACTTAGTGCAACATAGTCGAATCGCA
1 TCAACTCGCACACTTAGTGCCA-CATAATCAAATCCCACACTTAGTGCAACATAGTCGAATCGCA
40684366 CACTTAGTGCCGCA
65 CACTTAGTGCCGCA
40684380 CAATTTAATC
Statistics
Matches: 69, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
81 23 0.33
82 46 0.67
ACGTcount: A:0.28, C:0.30, G:0.16, T:0.26
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCCACATAATCAAATCCCACACTTAGTGCAACATAGTCGAATCGCAC
ACTTAGTGCCGCATGG
Found at i:40698251 original size:40 final size:40
Alignment explanation
Indices: 40698221--40698406 Score: 225
Period size: 40 Copynumber: 4.7 Consensus size: 40
40698211 GCTACTCGTT
* *
40698221 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
40698261 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
40698301 CAAATGCCTTTGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
** * * * * *
40698341 CAAATGCCTTC-GGATCTTAGTCCAGATATGGTCAGCTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGT-AACTCGCA
*
40698382 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
40698407 CATCATTCAA
Statistics
Matches: 129, Mismatches: 13, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
39 3 0.02
40 111 0.86
41 15 0.12
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:40703073 original size:13 final size:13
Alignment explanation
Indices: 40703055--40703079 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40703045 CCAAGCACAC
40703055 GCTCGTGTCCCTA
1 GCTCGTGTCCCTA
40703068 GCTCGTGTCCCT
1 GCTCGTGTCCCT
40703080 CACACGGCCC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.04, C:0.40, G:0.24, T:0.32
Consensus pattern (13 bp):
GCTCGTGTCCCTA
Found at i:40715610 original size:17 final size:17
Alignment explanation
Indices: 40715588--40715628 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
40715578 TTTGAGTCCC
40715588 TTTATTTTACTATTATT
1 TTTATTTTACTATTATT
* *
40715605 TTTATTTTTCTTTTATT
1 TTTATTTTACTATTATT
40715622 TTTATTT
1 TTTATTT
40715629 AAACTTTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.17, C:0.05, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTATTTTACTATTATT
Found at i:40723527 original size:43 final size:43
Alignment explanation
Indices: 40723461--40723589 Score: 156
Period size: 43 Copynumber: 3.0 Consensus size: 43
40723451 AGCTCGTACA
* *
40723461 ATGCCAATGTCCCAGACGTGGTCTTACATGTAATCACATATCG
1 ATGCCACTGTCCCAGACGTGGTCTTACATGAAATCACATATCG
* * * *
40723504 ATGCCACTGTCCCAGACAG-GGTCTTTCACGCAAATCACAAATTG
1 ATGCCACTGTCCCAGAC-GTGGTCTTACATG-AAATCACATATCG
40723548 ATGCCAAC-GTCCCAG-CGTGGTCTTACATGAAATCACATATCG
1 ATGCC-ACTGTCCCAGACGTGGTCTTACATGAAATCACATATCG
40723590 GAATCCTATG
Statistics
Matches: 72, Mismatches: 10, Indels: 9
0.79 0.11 0.10
Matches are distributed among these distances:
42 12 0.17
43 35 0.49
44 23 0.32
45 2 0.03
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.25
Consensus pattern (43 bp):
ATGCCACTGTCCCAGACGTGGTCTTACATGAAATCACATATCG
Found at i:40742944 original size:43 final size:42
Alignment explanation
Indices: 40742879--40743029 Score: 162
Period size: 43 Copynumber: 3.5 Consensus size: 42
40742869 TTTCAGACAT
* *
40742879 CGTGTAAGACCGTGTCTGGGACACAGGCCTCGATTTAGATTTA
1 CGTGTAAGACCATGTCTGGGACACAGGCATCGATTT-GATTTA
* *
40742922 CGTATAAGACCATGTCTGGGACATC-GGCATCGTATCTGATTT-
1 CGTGTAAGACCATGTCTGGGACA-CAGGCATCG-ATTTGATTTA
* * *
40742964 CGTGTAAGACCCTGTCTGGGACAGAGGCATCGATATTGAATTA
1 CGTGTAAGACCATGTCTGGGACACAGGCATCGAT-TTGATTTA
* * *
40743007 CATGTAAGACCATATCCGGGACA
1 CGTGTAAGACCATGTCTGGGACA
40743030 TTGGCATTAT
Statistics
Matches: 90, Mismatches: 13, Indels: 10
0.80 0.12 0.09
Matches are distributed among these distances:
41 2 0.02
42 33 0.37
43 51 0.57
44 4 0.04
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.26
Consensus pattern (42 bp):
CGTGTAAGACCATGTCTGGGACACAGGCATCGATTTGATTTA
Found at i:40743028 original size:85 final size:85
Alignment explanation
Indices: 40742878--40743036 Score: 221
Period size: 85 Copynumber: 1.9 Consensus size: 85
40742868 GTTTCAGACA
* * * * * *
40742878 TCGTGTAAGACCGTGTCTGGGACACAGGCCTCGATTTAGATTTACGTATAAGACCATGTCTGGGA
1 TCGTGTAAGACCCTGTCTGGGACACAGGCATCGATTTAGAATTACATATAAGACCATATCCGGGA
40742943 CATCGGCATCGTATCTGATT
66 CATCGGCATCGTATCTGATT
* *
40742963 TCGTGTAAGACCCTGTCTGGGACAGAGGCATCGATATT-GAATTACATGTAAGACCATATCCGGG
1 TCGTGTAAGACCCTGTCTGGGACACAGGCATCGAT-TTAGAATTACATATAAGACCATATCCGGG
*
40743027 ACATTGGCAT
65 ACATCGGCAT
40743037 TATACTTGTT
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
85 62 0.97
86 2 0.03
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.28
Consensus pattern (85 bp):
TCGTGTAAGACCCTGTCTGGGACACAGGCATCGATTTAGAATTACATATAAGACCATATCCGGGA
CATCGGCATCGTATCTGATT
Found at i:40744427 original size:24 final size:24
Alignment explanation
Indices: 40744400--40744486 Score: 156
Period size: 24 Copynumber: 3.6 Consensus size: 24
40744390 GTCAGGAAAA
40744400 GATTTAGGAGCTGATAAGGGAGAG
1 GATTTAGGAGCTGATAAGGGAGAG
40744424 GATTTAGGAGCTGATAAGGGAGAG
1 GATTTAGGAGCTGATAAGGGAGAG
* *
40744448 GATTTAGGAGCTGATAAAGGAGAA
1 GATTTAGGAGCTGATAAGGGAGAG
40744472 GATTTAGGAGCTGAT
1 GATTTAGGAGCTGAT
40744487 CAAAGAACAA
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 61 1.00
ACGTcount: A:0.34, C:0.05, G:0.38, T:0.23
Consensus pattern (24 bp):
GATTTAGGAGCTGATAAGGGAGAG
Found at i:40746189 original size:33 final size:34
Alignment explanation
Indices: 40746112--40746192 Score: 94
Period size: 33 Copynumber: 2.4 Consensus size: 34
40746102 TATAGGCCAT
*
40746112 ACTGTTATCTGAATAAGGGGCTAAGGCCCAGTTT
1 ACTGTTATCTGAATAAGGGGCTAAGGCCCAGTTC
* * **
40746146 AATGTAATCTGAA-AA-GGGCTCTGGCCCAGTATC
1 ACTGTTATCTGAATAAGGGGCTAAGGCCCAGT-TC
40746179 ACTGTTATCTGAAT
1 ACTGTTATCTGAAT
40746193 GAGCTTAGGC
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
32 13 0.34
33 14 0.37
34 11 0.29
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (34 bp):
ACTGTTATCTGAATAAGGGGCTAAGGCCCAGTTC
Found at i:40752302 original size:24 final size:24
Alignment explanation
Indices: 40752275--40752349 Score: 123
Period size: 24 Copynumber: 3.1 Consensus size: 24
40752265 AAGGCTGTCA
40752275 GGAGAAGATTTAGGAGCTGATAAG
1 GGAGAAGATTTAGGAGCTGATAAG
* *
40752299 GGAGAGGATTTAGGAGCTGATAAA
1 GGAGAAGATTTAGGAGCTGATAAG
40752323 GGAGAAGATTTAGGAGCTGATCAAG
1 GGAGAAGATTTAGGAGCTGAT-AAG
40752348 GG
1 GG
40752350 CAGGAGTTGG
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
24 42 0.91
25 4 0.09
ACGTcount: A:0.36, C:0.05, G:0.39, T:0.20
Consensus pattern (24 bp):
GGAGAAGATTTAGGAGCTGATAAG
Found at i:40766610 original size:24 final size:24
Alignment explanation
Indices: 40766566--40766611 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
40766556 TAAAGAAATG
**
40766566 GAAAAAAAAGAGAAAGTAAATGAT
1 GAAAAAAAAGAGAAAAAAAATGAT
40766590 GAAAACAAAAGA-AAAAAAAATG
1 GAAAA-AAAAGAGAAAAAAAATG
40766612 TGTCCATCCT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 13 0.68
25 6 0.32
ACGTcount: A:0.72, C:0.02, G:0.17, T:0.09
Consensus pattern (24 bp):
GAAAAAAAAGAGAAAAAAAATGAT
Found at i:40768042 original size:40 final size:39
Alignment explanation
Indices: 40767852--40768035 Score: 203
Period size: 40 Copynumber: 4.6 Consensus size: 39
40767842 CGAATGATGT
* * * *
40767852 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTATGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGA-GTTACTA-AA
* *
40767892 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAA-A
*
40767932 CCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
40767970 TCTGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
40768011 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
40768036 AACGAGTAGC
Statistics
Matches: 124, Mismatches: 13, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
39 34 0.27
40 79 0.64
41 11 0.09
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.26
Consensus pattern (39 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:40768057 original size:79 final size:79
Alignment explanation
Indices: 40767904--40768068 Score: 201
Period size: 79 Copynumber: 2.1 Consensus size: 79
40767894 GGACTAAGAT
* **
40767904 CCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
* *
40767969 ATCTGGGTTAAGTC
66 ATCTCGGTTAAATC
* *
40767983 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGTTACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTTA-C
* *
40768046 TATATC-CGGTTAAATT
63 TAAATCTCGGTTAAATC
40768062 CCGAAGG
1 CCGAAGG
40768069 TACGTGATTC
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
78 2 0.03
79 49 0.66
80 23 0.31
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
ATCTCGGTTAAATC
Found at i:40774835 original size:16 final size:16
Alignment explanation
Indices: 40774793--40774835 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
40774783 GTAAATCGAC
40774793 AAATCTCGAAATGCCGA
1 AAAT-TCGAAATGCCGA
*
40774810 AAA-GCTGAAATGCCGA
1 AAATTC-GAAATGCCGA
40774826 AAATTCGAAA
1 AAATTCGAAA
40774836 GTTTGGCTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
15 1 0.05
16 17 0.77
17 4 0.18
ACGTcount: A:0.47, C:0.19, G:0.19, T:0.16
Consensus pattern (16 bp):
AAATTCGAAATGCCGA
Found at i:40775088 original size:28 final size:28
Alignment explanation
Indices: 40775048--40775138 Score: 139
Period size: 28 Copynumber: 3.2 Consensus size: 28
40775038 ATTGAATGAT
**
40775048 TATGAATGTGATTGGGCCTGACAGGCCA
1 TATGAATGTGATTGGGCCTGATGGGCCA
*
40775076 TATGAAAGTGATTGGGCCTGATGGGCCA
1 TATGAATGTGATTGGGCCTGATGGGCCA
40775104 TATGAATGTGATTGGG-CTCGATGGGCCA
1 TATGAATGTGATTGGGCCT-GATGGGCCA
40775132 TATGAAT
1 TATGAAT
40775139 AAGATTGGAC
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
27 2 0.03
28 56 0.97
ACGTcount: A:0.25, C:0.14, G:0.33, T:0.27
Consensus pattern (28 bp):
TATGAATGTGATTGGGCCTGATGGGCCA
Found at i:40779998 original size:46 final size:46
Alignment explanation
Indices: 40779897--40779984 Score: 122
Period size: 46 Copynumber: 1.9 Consensus size: 46
40779887 TGTAACCCGC
* * * *
40779897 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGCTCCCAT
* *
40779943 CCATAAGTGAACTCGGACTCAACTCAACGAGCTTGGATGCTC
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGCTC
40779985 AACCATCCTA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 37 1.00
ACGTcount: A:0.27, C:0.31, G:0.23, T:0.19
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGCTCCCAT
Found at i:40784741 original size:47 final size:47
Alignment explanation
Indices: 40784629--40785331 Score: 1179
Period size: 47 Copynumber: 15.1 Consensus size: 47
40784619 GAAATGATAG
*
40784629 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTACATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT--ATATATGTGA
40784678 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* *
40784725 TAAGGCCTAATAGCCGATGTGATGTATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
40784772 TAAGGCCTAACGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* *
40784819 TAAGGCCTAACGGCCGATGTGATGAATGTG--A---TATATGTGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
40784861 TAAGGCCTAAT-GCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
40784907 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
40784954 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
40785001 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
40785048 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
40785095 TAAGGCCTAA-GGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
40785141 TAAGGCCTAA-GGCCGATGTGATGAATGTGAAAGTGTATATATGTCA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
40785187 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
40785234 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*** * * * * * * *
40785281 CGGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGCATAAATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
40785328 TAAG
1 TAAG
40785332 TCCCGAAGGG
Statistics
Matches: 623, Mismatches: 24, Indels: 16
0.94 0.04 0.02
Matches are distributed among these distances:
41 18 0.03
42 20 0.03
43 1 0.00
45 1 0.00
46 112 0.18
47 435 0.70
49 36 0.06
ACGTcount: A:0.32, C:0.10, G:0.30, T:0.29
Consensus pattern (47 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
Found at i:40785044 original size:229 final size:231
Alignment explanation
Indices: 40784629--40785280 Score: 1166
Period size: 229 Copynumber: 2.8 Consensus size: 231
40784619 GAAATGATAG
40784629 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTACATATATGTGATAAGGCCTAATGGCCG
1 TAAGGCCTAAT-GCCGATGTGATGAATGTGAAAGTGT--ATATATGTGATAAGGCCTAATGGCCG
* *
40784694 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGTATGTGAAAG
63 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
*
40784759 TGTATATATGTGATAAGGCCTAACGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGG
128 TGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGG
*
40784824 CCTAACGGCCGATGTGATGAATGTG-A-TATATGTGTGA
193 CCTAACGGCCGATGTGATGAATGTGAAGTATATATGTGA
40784861 TAAGGCCTAATGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATG
1 TAAGGCCTAATGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATG
40784926 TGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT
66 TGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT
40784991 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCT
131 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCT
*
40785056 AATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
196 AACGGCCGATGTGATGAATGTG-AA--GTATATATGTGA
*
40785095 TAAGGCCTAAGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAA-GGCCGATG
1 TAAGGCCTAATGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATG
*
40785159 TGATGAATGTGAAAGTGTATATATGTCATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT
66 TGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT
40785224 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
131 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
40785281 CGGGGCCGAG
Statistics
Matches: 408, Mismatches: 7, Indels: 9
0.96 0.02 0.02
Matches are distributed among these distances:
229 177 0.43
231 26 0.06
232 11 0.03
233 129 0.32
234 65 0.16
ACGTcount: A:0.32, C:0.09, G:0.29, T:0.29
Consensus pattern (231 bp):
TAAGGCCTAATGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATG
TGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT
ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCT
AACGGCCGATGTGATGAATGTGAAGTATATATGTGA
Found at i:40785312 original size:280 final size:276
Alignment explanation
Indices: 40784629--40785331 Score: 1183
Period size: 280 Copynumber: 2.5 Consensus size: 276
40784619 GAAATGATAG
*
40784629 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTACATATATGTGATAAGGCCTAATGGCCG
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT--ATATATGTGATAAGGCCTAATGGCCG
* *
40784694 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGTATGTGAAAG
64 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
40784759 TGTATATATGTGATAAGGCCTAACGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGG
129 TGTATATATGTGATAAGGCCTAACGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGG
* *
40784824 CCTAACGGCCGATGTGATGAATGTGATATATGTGTGATAAGGCCTAATGCCGATGTGATGAATGT
194 CCTAACGGCCGATGTGATGAATGTGATATATATGTGATAAGGCCTAAGGCCGATGTGATGAATGT
*
40784889 GAAAGTGTATATATGTGA
259 GAAAGTGTATATATGTCA
40784907 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
40784972 GTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
66 GTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
*
40785037 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCC
131 TATATATGTGATAAGGCCTAACGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCC
40785102 TAA-GGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAAGGCCGATGTGATGAA
196 TAACGGCCGATGTGATGAATGTG--A---TATATATGTGATAAGGCCTAAGGCCGATGTGATGAA
40785166 TGTGAAAGTGTATATATGTCA
256 TGTGAAAGTGTATATATGTCA
40785187 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
*** * * * * *
40785252 GTGATGAATGTGAAAGTGTATATATGTGACGGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTG
66 GTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
* *
40785317 CATAAATGTGATAAG
131 TATATATGTGATAAG
40785332 TCCCGAAGGG
Statistics
Matches: 403, Mismatches: 17, Indels: 8
0.94 0.04 0.02
Matches are distributed among these distances:
275 19 0.05
276 158 0.39
277 1 0.00
278 36 0.09
280 189 0.47
ACGTcount: A:0.32, C:0.10, G:0.30, T:0.29
Consensus pattern (276 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
GTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
TATATATGTGATAAGGCCTAACGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCC
TAACGGCCGATGTGATGAATGTGATATATATGTGATAAGGCCTAAGGCCGATGTGATGAATGTGA
AAGTGTATATATGTCA
Found at i:40785506 original size:37 final size:37
Alignment explanation
Indices: 40785450--40785528 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
40785440 CCGAGCTCTA
* *
40785450 AAGACCCGATGACTACGTGTGG-GAATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAG-ATTATGTCCGGGT
*
40785487 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
40785524 AAGAC
1 AAGAC
40785529 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 37 0.97
38 1 0.03
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:40787432 original size:43 final size:43
Alignment explanation
Indices: 40787384--40787486 Score: 206
Period size: 43 Copynumber: 2.4 Consensus size: 43
40787374 TTGGTTTTCA
40787384 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
40787427 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
40787470 GCACTAAGTGTGCGGGC
1 GCACTAAGTGTGCGGGC
40787487 TTGAAATGCG
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 60 1.00
ACGTcount: A:0.22, C:0.16, G:0.36, T:0.26
Consensus pattern (43 bp):
GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
Found at i:40787986 original size:40 final size:40
Alignment explanation
Indices: 40787933--40788208 Score: 473
Period size: 40 Copynumber: 6.9 Consensus size: 40
40787923 GAGTTACTAA
40787933 ATCCGGGCT-AGTCCCGAAGAGCATTCATGCTAGTGATGT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
40787972 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
40788012 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
*
40788052 ATCCTGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
40788092 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
* * *
40788132 ATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATAT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
* * * *
40788172 ATCCGTGCTAAATCCCGAAGAGCAATCATGCTGGTGA
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGA
40788209 CGTGTATTCG
Statistics
Matches: 225, Mismatches: 11, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
39 9 0.04
40 216 0.96
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
Found at i:40791718 original size:47 final size:47
Alignment explanation
Indices: 40791611--40792184 Score: 889
Period size: 47 Copynumber: 12.1 Consensus size: 47
40791601 GAAATGATAG
*
40791611 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGA
*
40791660 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
40791707 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* * *
40791754 TAAGGCCTAACGGCCGATGTGATGAATGTGAATGTGTATATGTGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* * *
40791801 TAAGGCCTAATAGCCGGTGCGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
40791848 TAAGGCCTAATGGCCGATGCGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
40791895 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
40791942 TAAGGCCTAATGGCCGATGTGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCC-----GATGTGATGAATGTGAAAGTGTATATATGTGA
*
40791994 TAAGGCCTAAT-GCCGATGTGATGAATGTGAAAGTGTATATATGTAA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
40792040 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
40792087 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*** * * * * * * *
40792134 CGGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGCATAAATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
40792181 TAAG
1 TAAG
40792185 TCCCGAAGGG
Statistics
Matches: 491, Mismatches: 28, Indels: 14
0.92 0.05 0.03
Matches are distributed among these distances:
46 42 0.09
47 367 0.75
49 36 0.07
51 3 0.01
52 43 0.09
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (47 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
Found at i:40791994 original size:25 final size:25
Alignment explanation
Indices: 40791911--40791994 Score: 66
Period size: 25 Copynumber: 3.3 Consensus size: 25
40791901 CTAATGGCCG
40791911 ATGTGATGAATGTGAAAGTGTATAT
1 ATGTGATGAATGTGAAAGTGTATAT
* * * *
40791936 ATGTGAT-AAGGCCT-AATG-GCCGATGT
1 ATGTGATGAATG--TGAAAGTG--TATAT
40791962 GATGTGATGAATGTGAAAGTGTATAT
1 -ATGTGATGAATGTGAAAGTGTATAT
40791988 ATGTGAT
1 ATGTGAT
40791995 AAGGCCTAAT
Statistics
Matches: 43, Mismatches: 8, Indels: 16
0.64 0.12 0.24
Matches are distributed among these distances:
24 4 0.09
25 17 0.40
26 8 0.19
27 10 0.23
28 4 0.09
ACGTcount: A:0.32, C:0.05, G:0.30, T:0.33
Consensus pattern (25 bp):
ATGTGATGAATGTGAAAGTGTATAT
Found at i:40792359 original size:37 final size:37
Alignment explanation
Indices: 40792303--40792381 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
40792293 CCGAGCTCTA
* *
40792303 AAGACCCGATGACTACGTGTGG-GAATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAG-ATTATGTCCGGGT
*
40792340 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
40792377 AAGAC
1 AAGAC
40792382 TTTGTAATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 37 0.97
38 1 0.03
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:40804686 original size:24 final size:25
Alignment explanation
Indices: 40804659--40804710 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
40804649 GCCTAGCCTC
40804659 TTTTAAT-AACTGGGGAAAAGCCCT
1 TTTTAATAAACTGGGGAAAAGCCCT
* *
40804683 TTTTGATAAACTGGGGCAAAGCCCT
1 TTTTAATAAACTGGGGAAAAGCCCT
40804708 TTT
1 TTT
40804711 CGGTAAATTG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 6 0.24
25 19 0.76
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (25 bp):
TTTTAATAAACTGGGGAAAAGCCCT
Found at i:40804694 original size:25 final size:25
Alignment explanation
Indices: 40804666--40804736 Score: 88
Period size: 25 Copynumber: 2.8 Consensus size: 25
40804656 CTCTTTTAAT
*
40804666 AACTGGGGAAAAGCCCTTTTTGATA
1 AACTGGGGAAAAGCCCTTTTCGATA
* *
40804691 AACTGGGGCAAAGCCCTTTTCGGTA
1 AACTGGGGAAAAGCCCTTTTCGATA
* *
40804716 AATTGGGACAAAAGCCCTTTT
1 AACTGGG-GAAAAGCCCTTTT
40804737 GCACTTCCTC
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
25 28 0.72
26 11 0.28
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.27
Consensus pattern (25 bp):
AACTGGGGAAAAGCCCTTTTCGATA
Found at i:40812322 original size:30 final size:31
Alignment explanation
Indices: 40812252--40812334 Score: 134
Period size: 30 Copynumber: 2.7 Consensus size: 31
40812242 TCAATCTCAA
40812252 CATAT-ACTGGGCCGAAGCCTTTGCATTATT
1 CATATCACTGGGCCGAAGCCTTTGCATTATT
* *
40812282 CATGTCACTGGGCCGAAGCCTTTTCATTA-T
1 CATATCACTGGGCCGAAGCCTTTGCATTATT
40812312 CATATCACTGGGCCGAAGCCTTT
1 CATATCACTGGGCCGAAGCCTTT
40812335 ACTGTAAATG
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
30 27 0.55
31 22 0.45
ACGTcount: A:0.22, C:0.27, G:0.20, T:0.31
Consensus pattern (31 bp):
CATATCACTGGGCCGAAGCCTTTGCATTATT
Found at i:40812580 original size:24 final size:24
Alignment explanation
Indices: 40812530--40812625 Score: 88
Period size: 25 Copynumber: 3.8 Consensus size: 24
40812520 TTTATCATAT
40812530 AACTGGAGGCATAA-CCTCTTTTAAT-
1 AACTGG-GGCA-AAGCC-CTTTTAATA
*
40812555 AACTGGGGCAAAGCCCTTTCTGATA
1 AACTGGGGCAAAGCCCTTT-TAATA
* *
40812580 AACTAGGGCAAAGCCCTTTTCAGTA
1 AACTGGGGCAAAGCCCTTTT-AATA
*
40812605 AACTGGGGCAAAAGCTCTTTT
1 AACTGGGGC-AAAGCCCTTTT
40812626 GCACCTCCTC
Statistics
Matches: 60, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
23 6 0.10
24 10 0.17
25 34 0.57
26 10 0.17
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.27
Consensus pattern (24 bp):
AACTGGGGCAAAGCCCTTTTAATA
Found at i:40812618 original size:26 final size:26
Alignment explanation
Indices: 40812555--40812625 Score: 92
Period size: 25 Copynumber: 2.8 Consensus size: 26
40812545 CTCTTTTAAT
*
40812555 AACTGGGGCAAAGCCC-TTTCTGATA
1 AACTGGGGCAAAGCCCTTTTCAGATA
*
40812580 AACTAGGGCAAAGCCCTTTTCAG-TA
1 AACTGGGGCAAAGCCCTTTTCAGATA
*
40812605 AACTGGGGCAAAAGCTCTTTT
1 AACTGGGGC-AAAGCCCTTTT
40812626 GCACCTCCTC
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
25 25 0.62
26 15 0.38
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.25
Consensus pattern (26 bp):
AACTGGGGCAAAGCCCTTTTCAGATA
Found at i:40814835 original size:17 final size:16
Alignment explanation
Indices: 40814809--40814842 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
40814799 CGAGCTCATA
40814809 TAAAATTTTTAAAACT
1 TAAAATTTTTAAAACT
*
40814825 TAAACATTTTTCAAACT
1 TAAA-ATTTTTAAAACT
40814842 T
1 T
40814843 GTACAGGTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (16 bp):
TAAAATTTTTAAAACT
Found at i:40820173 original size:43 final size:43
Alignment explanation
Indices: 40820105--40820271 Score: 144
Period size: 43 Copynumber: 3.9 Consensus size: 43
40820095 ATCGAGATGT
40820105 GATTACATGTAAGACCATATCTGGGACAATGGCATTGTATTGA
1 GATTACATGTAAGACCATATCTGGGACAATGGCATTGTATTGA
* * * * *
40820148 GATTACATGTAAGACCATGTTTGGGACATTGGCATCAT-TAAT-C
1 GATTACATGTAAGACCATATCTGGGACAATGGCAT--TGTATTGA
* * * * * * * *
40820191 GATTTCGTGTAAGACCCTGTGTGGAACAATGGCATCG-ATATGT
1 GATTACATGTAAGACCATATCTGGGACAATGGCATTGTAT-TGA
* *
40820234 GATAACATGTAAGACCATATCTGGGA-TATGGCATTGTA
1 GATTACATGTAAGACCATATCTGGGACAATGGCATTGTA
40820272 CAAGATTATG
Statistics
Matches: 95, Mismatches: 23, Indels: 12
0.73 0.18 0.09
Matches are distributed among these distances:
41 1 0.01
42 9 0.09
43 81 0.85
44 3 0.03
45 1 0.01
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.31
Consensus pattern (43 bp):
GATTACATGTAAGACCATATCTGGGACAATGGCATTGTATTGA
Found at i:40823573 original size:28 final size:27
Alignment explanation
Indices: 40823531--40823620 Score: 101
Period size: 28 Copynumber: 3.2 Consensus size: 27
40823521 GTGACAGAGT
*
40823531 CACCAGATACAGATATTTTGTAGCAGTGC
1 CACCAGA-ACAGATA-TTTGTGGCAGTGC
** *
40823560 CACCAGAACAGATATACGTGGCAGGGC
1 CACCAGAACAGATATTTGTGGCAGTGC
40823587 CACCAGAACAGATAATTTGTGGCA-TAGC
1 CACCAGAACAGAT-ATTTGTGGCAGT-GC
40823615 CACCAG
1 CACCAG
40823621 GACGCTTCCT
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
27 22 0.42
28 23 0.44
29 7 0.13
ACGTcount: A:0.33, C:0.24, G:0.23, T:0.19
Consensus pattern (27 bp):
CACCAGAACAGATATTTGTGGCAGTGC
Found at i:40823773 original size:28 final size:28
Alignment explanation
Indices: 40823726--40823790 Score: 112
Period size: 28 Copynumber: 2.3 Consensus size: 28
40823716 AAATTAACCC
*
40823726 TAGGGGTATAAAGGTCATTTTGCATACA
1 TAGGGGTATAAAGGTAATTTTGCATACA
*
40823754 TAGGGGTATAACGGTAATTTTGCATACA
1 TAGGGGTATAAAGGTAATTTTGCATACA
40823782 TAGGGGTAT
1 TAGGGGTAT
40823791 TCTAGTAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.31, C:0.09, G:0.28, T:0.32
Consensus pattern (28 bp):
TAGGGGTATAAAGGTAATTTTGCATACA
Found at i:40849566 original size:39 final size:39
Alignment explanation
Indices: 40849449--40849658 Score: 316
Period size: 39 Copynumber: 5.3 Consensus size: 39
40849439 GCTCCTCGTT
* *
40849449 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
40849489 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
40849529 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
*
40849568 CAAATGCCTTCGGGCTTTGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
40849607 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
40849646 CAAATGCCTTCGG
1 CAAATGCCTTCGG
40849659 ATCTTAGTCT
Statistics
Matches: 160, Mismatches: 8, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
39 112 0.70
40 46 0.29
41 2 0.01
ACGTcount: A:0.24, C:0.28, G:0.22, T:0.26
Consensus pattern (39 bp):
CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
Found at i:40849694 original size:78 final size:78
Alignment explanation
Indices: 40849449--40849710 Score: 302
Period size: 78 Copynumber: 3.3 Consensus size: 78
40849439 GCTCCTCGTT
* * *
40849449 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCACAAATGCCTTCGGGACTTAACCC
1 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGT-ATCTCGCACAAATGCCTTCGGG-CTTAGCCC
* * *
40849512 GGATTTAGTAACTCGCA
62 GGAATTAGTATCTAGCA
*
40849529 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGGCTTTGCCCGGAA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGGCTTAGCCCGGAA
*
40849594 TTAGTATCTCGCA
66 TTAGTATCTAGCA
* * *
40849607 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCTGGA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGG-GCTTAGCCCGGA
40849672 TATT-GTCA-CTTAGCA
65 -ATTAGT-ATC-TAGCA
40849687 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGG-CTTAGCCCGGA
40849711 CATCATTCAA
Statistics
Matches: 164, Mismatches: 11, Indels: 15
0.86 0.06 0.08
Matches are distributed among these distances:
78 84 0.51
79 56 0.34
80 24 0.15
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (78 bp):
CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGGCTTAGCCCGGAA
TTAGTATCTAGCA
Found at i:40849694 original size:117 final size:119
Alignment explanation
Indices: 40849449--40849710 Score: 324
Period size: 118 Copynumber: 2.2 Consensus size: 119
40849439 GCTCCTCGTT
* *
40849449 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCACAAATGCCTTCGGGACTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCACAAATGCCTTCGGGACTTAACCC
* *
40849512 GGATTTAGTAACTCGCACAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
64 GGAATTAGTAACTCGCACAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTAGCA
* *
40849568 CAAATGCCTTCGGG-CTTTGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGG-CTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGGACTTAACCCGG
* * * *
40849631 AATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCTGGATATT-GTCA-CTTAGCA
66 AATTAGTAACTCGCACAAATGCCTTCGG-GCTTAGCCCGGA-ATTAGT-ATC-TAGCA
40849687 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
40849711 CATCATTCAA
Statistics
Matches: 125, Mismatches: 11, Indels: 15
0.83 0.07 0.10
Matches are distributed among these distances:
117 46 0.37
118 55 0.44
119 24 0.19
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (119 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGGACTTAACCCGG
AATTAGTAACTCGCACAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTAGCA
Found at i:40851354 original size:28 final size:28
Alignment explanation
Indices: 40851303--40851388 Score: 120
Period size: 28 Copynumber: 3.1 Consensus size: 28
40851293 GGCTGTCACA
40851303 GCTATATAATC-AACTCGCACACTTAGT
1 GCTATATAATCAAACTCGCACACTTAGT
40851330 GCTATATAATCAAACTCGCACACTTAGT
1 GCTATATAATCAAACTCGCACACTTAGT
* * * *
40851358 GCTGTACAATTTAAACCCGCACACTTAGT
1 GCTATATAA-TCAAACTCGCACACTTAGT
40851387 GC
1 GC
40851389 CAACCTCATG
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 11 0.21
28 23 0.43
29 19 0.36
ACGTcount: A:0.33, C:0.27, G:0.13, T:0.28
Consensus pattern (28 bp):
GCTATATAATCAAACTCGCACACTTAGT
Found at i:40854864 original size:27 final size:26
Alignment explanation
Indices: 40854820--40854871 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
40854810 CTCACTGCAA
*
40854820 TCTGGTGGCCTCGCCACATATATCTGT
1 TCTGGTGACCTCGCCACA-ATATCTGT
* *
40854847 TCTGGTGACTTCGTCACAATATCTG
1 TCTGGTGACCTCGCCACAATATCTG
40854872 GCAGCCTCGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.17, C:0.27, G:0.21, T:0.35
Consensus pattern (26 bp):
TCTGGTGACCTCGCCACAATATCTGT
Found at i:40854939 original size:26 final size:27
Alignment explanation
Indices: 40854910--40854969 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
40854900 CCACATATAT
*
40854910 ATATCTGT-TCTGGTGGCCTAGCCACA
1 ATATCTGTATCTGGTGACCTAGCCACA
* * *
40854936 ATATCTGTATCTGGTGACTTCGTCACA
1 ATATCTGTATCTGGTGACCTAGCCACA
40854963 ATATCTG
1 ATATCTG
40854970 GCAGCCTCGC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35
Consensus pattern (27 bp):
ATATCTGTATCTGGTGACCTAGCCACA
Found at i:40863365 original size:40 final size:40
Alignment explanation
Indices: 40863321--40863591 Score: 366
Period size: 40 Copynumber: 6.8 Consensus size: 40
40863311 GGATATAGCT
* * * *
40863321 ACTCGCTCAAATGCCTTCAGGACATAGCCCGG-TTAGAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATT-TAGTA
*
40863361 ACTCGCACAATTGCCTTCGGGACTTAGCCCGGATTTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
*
40863401 ACTTGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
* * *
40863441 ACTCGCACAATTGCCTTCAGGATTTAGCCCGGATTTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
* *
40863481 ACTCGCACAAATCCCTTCGGGACTTAGCCCAGATTTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
** *
40863521 ACTCGCACAAATGCCTTCGGGACTT-GCCCGGAACTAGTC
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
* * *
40863560 ACTAGCGCAGATGCCTTCGGGACTTAGCCCGG
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGG
40863592 TTTTCATCCA
Statistics
Matches: 205, Mismatches: 24, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
39 32 0.16
40 171 0.83
41 2 0.01
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
Found at i:40868425 original size:25 final size:25
Alignment explanation
Indices: 40868397--40868454 Score: 116
Period size: 25 Copynumber: 2.3 Consensus size: 25
40868387 CCGAGGATAC
40868397 CATCAAATTCGTCAAACGGTAAAAG
1 CATCAAATTCGTCAAACGGTAAAAG
40868422 CATCAAATTCGTCAAACGGTAAAAG
1 CATCAAATTCGTCAAACGGTAAAAG
40868447 CATCAAAT
1 CATCAAAT
40868455 CGGCCGAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.45, C:0.21, G:0.14, T:0.21
Consensus pattern (25 bp):
CATCAAATTCGTCAAACGGTAAAAG
Found at i:40871534 original size:40 final size:40
Alignment explanation
Indices: 40871479--40871748 Score: 375
Period size: 40 Copynumber: 6.8 Consensus size: 40
40871469 GGATATAGCT
* * *
40871479 ACTCGCTCAAATGCCTTCGGGACATAGCCCGG-TTAGAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATT-TAGTA
* *
40871519 ACTCGCACAATTGCCTTCGGGACTTAGCCCGAATTTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
*
40871559 ACTCGCACAAATGCCTTCGGCACTTAGCCCGGATTTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
* * *
40871599 ACTCACACAATTGCCTTCGAGACTTAGCCCGGATTTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
40871639 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
** *
40871679 ACTCGCACAAATGCCTTCGGGACTT-GCCCGGAACTAGTC
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
* * *
40871718 ACTAGCGCAGATGCCTTC-GGACTTAGCCCGG
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGG
40871749 TTTTCATCCA
Statistics
Matches: 207, Mismatches: 21, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
38 6 0.03
39 32 0.15
40 167 0.81
41 2 0.01
ACGTcount: A:0.24, C:0.29, G:0.22, T:0.24
Consensus pattern (40 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
Found at i:40874279 original size:14 final size:14
Alignment explanation
Indices: 40874260--40874290 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
40874250 CATCTAAAAG
40874260 GTAAAATTCAAGGT
1 GTAAAATTCAAGGT
40874274 GTAAAATTCAAGGT
1 GTAAAATTCAAGGT
40874288 GTA
1 GTA
40874291 CTGGTAAGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.42, C:0.06, G:0.23, T:0.29
Consensus pattern (14 bp):
GTAAAATTCAAGGT
Found at i:40881926 original size:22 final size:22
Alignment explanation
Indices: 40881883--40881991 Score: 119
Period size: 22 Copynumber: 5.0 Consensus size: 22
40881873 CTGTGATATT
* * * *
40881883 TACGGCCTTTAGCCTTCTTGTC
1 TACGGCATTGAGCCATCCTGTC
*
40881905 TATGGCATTGAGCCATCCTGTC
1 TACGGCATTGAGCCATCCTGTC
*
40881927 TACGGCATTGAGCCGTCCTGTC
1 TACGGCATTGAGCCATCCTGTC
* * * *
40881949 TATGTCGTTGAGCCATCCTATC
1 TACGGCATTGAGCCATCCTGTC
*
40881971 TACGGCGTTGAGCCATCCTGT
1 TACGGCATTGAGCCATCCTGT
40881992 TGACTTAGTG
Statistics
Matches: 72, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 72 1.00
ACGTcount: A:0.15, C:0.29, G:0.23, T:0.33
Consensus pattern (22 bp):
TACGGCATTGAGCCATCCTGTC
Found at i:40881949 original size:44 final size:44
Alignment explanation
Indices: 40881883--40881991 Score: 137
Period size: 44 Copynumber: 2.5 Consensus size: 44
40881873 CTGTGATATT
* * * * *
40881883 TACGGCCTTTAGCCTTCTTGTCTATGGCATTGAGCCATCCTGTC
1 TACGGCATTGAGCCATCCTGTCTATGGCATTGAGCCATCCTATC
* * *
40881927 TACGGCATTGAGCCGTCCTGTCTATGTCGTTGAGCCATCCTATC
1 TACGGCATTGAGCCATCCTGTCTATGGCATTGAGCCATCCTATC
*
40881971 TACGGCGTTGAGCCATCCTGT
1 TACGGCATTGAGCCATCCTGT
40881992 TGACTTAGTG
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
44 56 1.00
ACGTcount: A:0.15, C:0.29, G:0.23, T:0.33
Consensus pattern (44 bp):
TACGGCATTGAGCCATCCTGTCTATGGCATTGAGCCATCCTATC
Found at i:40887180 original size:27 final size:27
Alignment explanation
Indices: 40887150--40887327 Score: 137
Period size: 27 Copynumber: 6.6 Consensus size: 27
40887140 ATATTGAGCC
* *
40887150 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* * * *
40887177 CGCACATTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
* *
40887204 CGCACACTTAGTGCTACATAGTCAAACC
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
40887232 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
40887259 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* *
40887286 CGCACACTTAGTGCAACA-AAGT-AGAAT
1 CGCACACTTAGTGCTACATAA-TCA-ACT
40887313 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
40887328 GTACAATTTA
Statistics
Matches: 121, Mismatches: 25, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
26 2 0.02
27 96 0.79
28 23 0.19
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:40887262 original size:55 final size:54
Alignment explanation
Indices: 40887150--40887327 Score: 164
Period size: 54 Copynumber: 3.3 Consensus size: 54
40887140 ATATTGAGCC
* * * * *
40887150 CGCACACTCAGTGCTATATAATCAACTCGCACATTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACCCGCACACTTAGTGCCACATAATCAAAT
* * ** *
40887204 CGCACACTTAGTGCTACATAGTCAAACCCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATC-AACCCGCACACTTAGTGCCACATAATCAAAT
* *** *
40887259 CGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACA-AAGT-AGAAT
1 CGCACACTTAGTGCTA-CATAATCAACCCGCACACTTAGTGCCACATAA-TCA-AAT
40887313 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
40887328 GTACAATTTA
Statistics
Matches: 100, Mismatches: 19, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
53 1 0.01
54 55 0.55
55 44 0.44
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAATCAACCCGCACACTTAGTGCCACATAATCAAAT
Found at i:40900732 original size:31 final size:31
Alignment explanation
Indices: 40900697--40900758 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
40900687 ATGTTTGTGG
* *
40900697 CTAATTGCTTGATTAGTCAAATTGTTGGAAA
1 CTAATTACTTGATTAGTCAAATTGTTAGAAA
*
40900728 CTAATTACTTGATTAGTGAAATTGTTAGAAA
1 CTAATTACTTGATTAGTCAAATTGTTAGAAA
40900759 AGAGAGAGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.35, C:0.08, G:0.18, T:0.39
Consensus pattern (31 bp):
CTAATTACTTGATTAGTCAAATTGTTAGAAA
Found at i:40904543 original size:13 final size:13
Alignment explanation
Indices: 40904525--40904549 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40904515 AGTAATCTCG
40904525 CACGGGCGTGTCA
1 CACGGGCGTGTCA
40904538 CACGGGCGTGTC
1 CACGGGCGTGTC
40904550 CCTGTCAAGC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.32, G:0.40, T:0.16
Consensus pattern (13 bp):
CACGGGCGTGTCA
Found at i:40907732 original size:31 final size:31
Alignment explanation
Indices: 40907687--40907770 Score: 143
Period size: 31 Copynumber: 2.7 Consensus size: 31
40907677 TTAGTCTTGA
40907687 CATAT-ACTGGGCCGAAGCCTTTCCATAAAT
1 CATATCACTGGGCCGAAGCCTTTCCATAAAT
* *
40907717 CATATCATTGGGCCGAAGCCTTTTCATAAAT
1 CATATCACTGGGCCGAAGCCTTTCCATAAAT
40907748 CATATCACTGGGCCGAAGCCTTT
1 CATATCACTGGGCCGAAGCCTTT
40907771 ACTGTAAAAG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
30 5 0.10
31 45 0.90
ACGTcount: A:0.27, C:0.26, G:0.18, T:0.29
Consensus pattern (31 bp):
CATATCACTGGGCCGAAGCCTTTCCATAAAT
Found at i:40908046 original size:26 final size:26
Alignment explanation
Indices: 40907980--40908246 Score: 333
Period size: 26 Copynumber: 10.3 Consensus size: 26
40907970 CTGGAGGCCT
*
40907980 AGCCTCTTTT-AAT-AACTGGGGCAAA
1 AGCC-CTTTTCAATAAACTGGGGCATA
** *
40908005 AGCCC-TTTCGGTAAACTGGGGCGTA
1 AGCCCTTTTCAATAAACTGGGGCATA
**
40908030 AGCCCTTTTCAATAAACTAAGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
**
40908056 AGCCCTTTTCGGTAAACTGGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
*
40908082 AGCCCTTTCCAATAAACTGGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
* ** *
40908108 ATCCCTTTTCTGTAAACTGAGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
* *
40908134 AACCCTTTCCAATAAACTGGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
40908160 AGCCCTTTTCAATAAACTGGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
* * *
40908186 AACTCTTTTCAATAAACTAGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
*
40908212 AGCCCTTTTCAATAAACTAGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
40908238 AGCCCTTTT
1 AGCCCTTTT
40908247 GCACTTCCTC
Statistics
Matches: 206, Mismatches: 33, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
23 3 0.01
24 2 0.01
25 19 0.09
26 182 0.88
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.28
Consensus pattern (26 bp):
AGCCCTTTTCAATAAACTGGGGCATA
Found at i:40909288 original size:27 final size:26
Alignment explanation
Indices: 40909154--40909388 Score: 184
Period size: 27 Copynumber: 8.7 Consensus size: 26
40909144 TCATCCTACA
* * * *
40909154 AGGGTGTTTTGGTAAATCTACAAACCA
1 AGGGTATTTTGGTAATTTTACAAA-CT
* **
40909181 AGGGTATTTTAGTAATTTTGTAAACT
1 AGGGTATTTTGGTAATTTTACAAACT
* * * *
40909207 AATGGTATTTCT-ATAATTTTTAAAAAGTCA
1 -AGGGTATTT-TGGTAA-TTTTACAAA--CT
* ** *
40909237 AGGGTATTTTTGTAATTTTGTAAATCC
1 AGGGTATTTTGGTAATTTTACAAA-CT
*
40909264 AGGGTATTTTGGTAATTTTACAAATT
1 AGGGTATTTTGGTAATTTTACAAACT
* *
40909290 GAGGGTATTTCGGTAATTTCACAAACT
1 -AGGGTATTTTGGTAATTTTACAAACT
*
40909317 AGTGGTATTTCGGTAATTTTACAAACT
1 AG-GGTATTTTGGTAATTTTACAAACT
*
40909344 AGGGGTATTTTTGTAATTTTACAAACT
1 A-GGGTATTTTGGTAATTTTACAAACT
40909371 AGGGGTATTTTGGTAATT
1 A-GGGTATTTTGGTAATT
40909389 CTATCCTACA
Statistics
Matches: 170, Mismatches: 29, Indels: 18
0.78 0.13 0.08
Matches are distributed among these distances:
26 3 0.02
27 138 0.81
28 17 0.10
29 11 0.06
30 1 0.01
ACGTcount: A:0.31, C:0.08, G:0.20, T:0.42
Consensus pattern (26 bp):
AGGGTATTTTGGTAATTTTACAAACT
Found at i:40909324 original size:54 final size:54
Alignment explanation
Indices: 40909265--40909421 Score: 183
Period size: 54 Copynumber: 2.9 Consensus size: 54
40909255 TGTAAATCCA
*
40909265 GGGTATTTTGGTAATTTTACAAA-TTGAGGGTATTTCGGTAATTTCACAAACTAG
1 GGGTATTTTGGTAATTTTACAAACTAG-GGGTATTTCGGTAATTTCACAAACTAG
* * ** *
40909319 TGGTATTTCGGTAATTTTACAAACTAGGGGTATTTTTGTAATTTTACAAACTAG
1 GGGTATTTTGGTAATTTTACAAACTAGGGGTATTTCGGTAATTTCACAAACTAG
* ** **
40909373 GGGTATTTTGGTAATTCTATCCTAC-AGGGGTATTTTAGTAATTTCACAA
1 GGGTATTTTGGTAATTTTA-CAAACTAGGGGTATTTCGGTAATTTCACAA
40909422 TCGAAGGTAA
Statistics
Matches: 88, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
54 83 0.94
55 5 0.06
ACGTcount: A:0.29, C:0.10, G:0.20, T:0.41
Consensus pattern (54 bp):
GGGTATTTTGGTAATTTTACAAACTAGGGGTATTTCGGTAATTTCACAAACTAG
Found at i:40909401 original size:27 final size:27
Alignment explanation
Indices: 40909265--40909415 Score: 128
Period size: 27 Copynumber: 5.6 Consensus size: 27
40909255 TGTAAATCCA
* * *
40909265 GGGTATTTTGGTAATTTTACAAA-TTG
1 GGGTATTTTAGTAATTCTACAAACTAG
**
40909291 AGGGTATTTCGGTAATT-TCACAAACTAG
1 -GGGTATTTTAGTAATTCT-ACAAACTAG
* ** *
40909319 TGGTATTTCGGTAATTTTACAAACTAG
1 GGGTATTTTAGTAATTCTACAAACTAG
* *
40909346 GGGTATTTTTGTAATTTTACAAACTAG
1 GGGTATTTTAGTAATTCTACAAACTAG
* **
40909373 GGGTATTTTGGTAATTCTATCCTAC-AG
1 GGGTATTTTAGTAATTCTA-CAAACTAG
40909400 GGGTATTTTAGTAATT
1 GGGTATTTTAGTAATT
40909416 TCACAATCGA
Statistics
Matches: 109, Mismatches: 11, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
26 1 0.01
27 102 0.94
28 6 0.06
ACGTcount: A:0.28, C:0.09, G:0.21, T:0.42
Consensus pattern (27 bp):
GGGTATTTTAGTAATTCTACAAACTAG
Found at i:40909405 original size:81 final size:81
Alignment explanation
Indices: 40909265--40909421 Score: 185
Period size: 81 Copynumber: 1.9 Consensus size: 81
40909255 TGTAAATCCA
* * *
40909265 GGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAACTAGTGGTATTTCGG
1 GGGTATTTTGGTAATTTTACAAATAGAGGGTATTTCGGTAATTTCACAAACTAGGGGTATTTCAG
*
40909330 TAATTTTACAAACTAG
66 TAATTTCACAAACTAG
* * **
40909346 GGGTATTTTTGTAATTTTACAAACTAG-GGGTATTTTGGTAA-TTCTATCCTAC-AGGGGTATTT
1 GGGTATTTTGGTAATTTTACAAA-TAGAGGGTATTTCGGTAATTTC-A-CAAACTAGGGGTATTT
*
40909408 TAGTAATTTCACAA
63 CAGTAATTTCACAA
40909422 TCGAAGGTAA
Statistics
Matches: 64, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
80 3 0.05
81 56 0.88
82 5 0.08
ACGTcount: A:0.29, C:0.10, G:0.20, T:0.41
Consensus pattern (81 bp):
GGGTATTTTGGTAATTTTACAAATAGAGGGTATTTCGGTAATTTCACAAACTAGGGGTATTTCAG
TAATTTCACAAACTAG
Found at i:40909458 original size:27 final size:27
Alignment explanation
Indices: 40909420--40909617 Score: 236
Period size: 27 Copynumber: 7.3 Consensus size: 27
40909410 GTAATTTCAC
* * *
40909420 AATCGAAGGTAAAACGGTAATTTTGTA
1 AATCGAGGGTAAAACGGTAATTCTATA
* * * * *
40909447 AA-CTAAAGGTAAAATGGTAATTTTGTA
1 AATC-GAGGGTAAAACGGTAATTCTATA
40909474 AATCGAGGGTAAAACGGTAATTCTATA
1 AATCGAGGGTAAAACGGTAATTCTATA
* *
40909501 AATTGAGGGTAAAATGGTAATTCTATA
1 AATCGAGGGTAAAACGGTAATTCTATA
40909528 AATCGAGGGTAAAACGGTAATTCTATA
1 AATCGAGGGTAAAACGGTAATTCTATA
* *
40909555 AATCGAGGGTAAAATGGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTATA
* * *
40909582 AATCGAGGGTAAAATGGTAATTTTACA
1 AATCGAGGGTAAAACGGTAATTCTATA
*
40909609 AATTGAGGG
1 AATCGAGGG
40909618 CTTTTCAGTA
Statistics
Matches: 152, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
26 1 0.01
27 150 0.99
28 1 0.01
ACGTcount: A:0.40, C:0.07, G:0.23, T:0.29
Consensus pattern (27 bp):
AATCGAGGGTAAAACGGTAATTCTATA
Found at i:40909488 original size:54 final size:53
Alignment explanation
Indices: 40909420--40909617 Score: 270
Period size: 54 Copynumber: 3.7 Consensus size: 53
40909410 GTAATTTCAC
* * * * * *
40909420 AATCGAAGGTAAAACGGTAATTTTGTAAACTAAAGGTAAAATGGTAATTTTGTA
1 AATCGAGGGTAAAACGGTAATTCTATAAA-TGAGGGTAAAATGGTAATTCTGTA
*
40909474 AATCGAGGGTAAAACGGTAATTCTATAAATTGAGGGTAAAATGGTAATTCTATA
1 AATCGAGGGTAAAACGGTAATTCTATAAA-TGAGGGTAAAATGGTAATTCTGTA
40909528 AATCGAGGGTAAAACGGTAATTCTATAAATCGAGGGTAAAATGGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTATAAAT-GAGGGTAAAATGGTAATTCTGTA
* * *
40909582 AATCGAGGGTAAAATGGTAATTTTACAAATTGAGGG
1 AATCGAGGGTAAAACGGTAATTCTATAAA-TGAGGG
40909618 CTTTTCAGTA
Statistics
Matches: 130, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
53 1 0.01
54 128 0.98
55 1 0.01
ACGTcount: A:0.40, C:0.07, G:0.23, T:0.29
Consensus pattern (53 bp):
AATCGAGGGTAAAACGGTAATTCTATAAATGAGGGTAAAATGGTAATTCTGTA
Found at i:40915552 original size:12 final size:12
Alignment explanation
Indices: 40915527--40915565 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
40915517 TCAGAGAGTT
* *
40915527 ACACGGGGTAGG
1 ACACGGGCTGGG
40915539 ACACGGGCTGGG
1 ACACGGGCTGGG
*
40915551 ACACAGGCTGGG
1 ACACGGGCTGGG
40915563 ACA
1 ACA
40915566 TAGCCATGTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.26, C:0.23, G:0.44, T:0.08
Consensus pattern (12 bp):
ACACGGGCTGGG
Found at i:40916668 original size:48 final size:48
Alignment explanation
Indices: 40916616--40916714 Score: 198
Period size: 48 Copynumber: 2.1 Consensus size: 48
40916606 AAACAAGGTC
40916616 ATATAACTGTAACTGAGTATAAAAGAAAATTCATAAGGCTAAGTAAAT
1 ATATAACTGTAACTGAGTATAAAAGAAAATTCATAAGGCTAAGTAAAT
40916664 ATATAACTGTAACTGAGTATAAAAGAAAATTCATAAGGCTAAGTAAAT
1 ATATAACTGTAACTGAGTATAAAAGAAAATTCATAAGGCTAAGTAAAT
40916712 ATA
1 ATA
40916715 CTCGAGAATG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 51 1.00
ACGTcount: A:0.51, C:0.08, G:0.14, T:0.27
Consensus pattern (48 bp):
ATATAACTGTAACTGAGTATAAAAGAAAATTCATAAGGCTAAGTAAAT
Found at i:40923956 original size:38 final size:38
Alignment explanation
Indices: 40923905--40923979 Score: 150
Period size: 38 Copynumber: 2.0 Consensus size: 38
40923895 TCTAATAGCT
40923905 ATGGAACATTAAAGTGGAGGTCCTTATGTGGTAATTAA
1 ATGGAACATTAAAGTGGAGGTCCTTATGTGGTAATTAA
40923943 ATGGAACATTAAAGTGGAGGTCCTTATGTGGTAATTA
1 ATGGAACATTAAAGTGGAGGTCCTTATGTGGTAATTA
40923980 GACCATTTGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.33, C:0.08, G:0.27, T:0.32
Consensus pattern (38 bp):
ATGGAACATTAAAGTGGAGGTCCTTATGTGGTAATTAA
Found at i:40927240 original size:44 final size:42
Alignment explanation
Indices: 40927182--40927346 Score: 167
Period size: 43 Copynumber: 3.9 Consensus size: 42
40927172 CTCTGATATG
*
40927182 TGATTT-CATGTAAGACCATGTCTGGGACGTTGGCATCGATT
1 TGATTTACGTGTAAGACCATGTCTGGGACGTTGGCATCGATT
* * *
40927223 TGAGGTTTACGTGTAAGACCATGTCTAGGACATTGGCATCGTATA
1 TGA--TTTACGTGTAAGACCATGTCTGGGACGTTGGCATCG-ATT
* * *
40927268 TGATTT-TGTGTAAGACCTTATCTGGGACAG-TGGCATCGATAGT
1 TGATTTACGTGTAAGACCATGTCTGGGAC-GTTGGCATCGAT--T
* *
40927311 TGA-TTACATGTAAGACCACGTCTGGGACGTTGGCAT
1 TGATTTACGTGTAAGACCATGTCTGGGACGTTGGCAT
40927347 TGTATGAGCT
Statistics
Matches: 100, Mismatches: 15, Indels: 16
0.76 0.11 0.12
Matches are distributed among these distances:
41 5 0.05
42 29 0.29
43 32 0.32
44 29 0.29
45 5 0.05
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.32
Consensus pattern (42 bp):
TGATTTACGTGTAAGACCATGTCTGGGACGTTGGCATCGATT
Found at i:40927296 original size:42 final size:43
Alignment explanation
Indices: 40927190--40927354 Score: 160
Period size: 42 Copynumber: 3.9 Consensus size: 43
40927180 TGTGATTTCA
* *
40927190 TGTAAGACCATGTCTGGGACGTTGGCATCGATTTGAGGTTTACG
1 TGTAAGACCATGTCTGGGACATTGGCATCGATATGA-GTTTACG
* *
40927234 TGTAAGACCATGTCTAGGACATTGGCATCGTATATGA-TTT-TG
1 TGTAAGACCATGTCTGGGACATTGGCATCG-ATATGAGTTTACG
* * * *
40927276 TGTAAGACCTTATCTGGGACAGTGGCATCGATAGTTGA--TTACA
1 TGTAAGACCATGTCTGGGACATTGGCATCGATA--TGAGTTTACG
* * *
40927319 TGTAAGACCACGTCTGGGACGTTGGCATTG-TATGAG
1 TGTAAGACCATGTCTGGGACATTGGCATCGATATGAG
40927355 CTTTTTGAGC
Statistics
Matches: 100, Mismatches: 16, Indels: 13
0.78 0.12 0.10
Matches are distributed among these distances:
40 3 0.03
41 3 0.03
42 31 0.31
43 30 0.30
44 28 0.28
45 5 0.05
ACGTcount: A:0.24, C:0.16, G:0.28, T:0.32
Consensus pattern (43 bp):
TGTAAGACCATGTCTGGGACATTGGCATCGATATGAGTTTACG
Found at i:40930817 original size:125 final size:124
Alignment explanation
Indices: 40930595--40930846 Score: 468
Period size: 125 Copynumber: 2.0 Consensus size: 124
40930585 ATACTGCTAA
*
40930595 ACCTAGTCAAAATAAAAGTGTATAGTTAGGATATGTTTACTTATGAATTAGCTATTTAGGTTTGG
1 ACCTAGTCAAAATAAAAGTGTATAGTTAGGATATGTTTACTTATGAATTAGCTATTTAGGTTCGG
40930660 TCATGAATCTCAATGAATGAATAAAATTTTTAAAAGTCACATTGAAGTTATTTTCCATTG
66 TCATGAATCTCAATGAATGAATAAAATTTTTAAAAGTCACATTGAAGTTA-TTTCCATTG
*
40930720 ACCTAGTCCAAATAAAAGTGTATAGTTAGGATATGTTTACTTATGAATTAGCTATTTAGGTTCGG
1 ACCTAGTCAAAATAAAAGTGTATAGTTAGGATATGTTTACTTATGAATTAGCTATTTAGGTTCGG
*
40930785 TCATGAATCTCAATGAATGAATAAAATTTTTAAAAGTCACATTGAAGTTATTTCTATTG
66 TCATGAATCTCAATGAATGAATAAAATTTTTAAAAGTCACATTGAAGTTATTTCCATTG
40930844 ACC
1 ACC
40930847 GAATGTTGGC
Statistics
Matches: 124, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
124 11 0.09
125 113 0.91
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.38
Consensus pattern (124 bp):
ACCTAGTCAAAATAAAAGTGTATAGTTAGGATATGTTTACTTATGAATTAGCTATTTAGGTTCGG
TCATGAATCTCAATGAATGAATAAAATTTTTAAAAGTCACATTGAAGTTATTTCCATTG
Found at i:40932593 original size:46 final size:46
Alignment explanation
Indices: 40932540--40932715 Score: 178
Period size: 46 Copynumber: 3.8 Consensus size: 46
40932530 TGTTTGGGCA
* *
40932540 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTAAACG
* * * *
40932586 TCTGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTAA--A--CG
* * *
40932633 TCCGAACTCTTTGAGTTGAGTCCGAGTTCACTCATGGATGTGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTAAACG
* * * *
40932679 CCCGAGCTCGTTGAGTTGAGTCTGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
40932716 GCAGGTTACA
Statistics
Matches: 105, Mismatches: 18, Indels: 14
0.77 0.13 0.10
Matches are distributed among these distances:
43 6 0.06
45 3 0.03
46 60 0.57
47 27 0.26
48 3 0.03
50 6 0.06
ACGTcount: A:0.21, C:0.20, G:0.28, T:0.31
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTAAACG
Found at i:40932695 original size:93 final size:93
Alignment explanation
Indices: 40932536--40932708 Score: 265
Period size: 93 Copynumber: 1.9 Consensus size: 93
40932526 AGGATGTTTG
* * * *
40932536 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCTGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACGCCCGAACTCGTTGAG
40932601 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
* ** *
40932629 GGCATCCGAACTCTTTGAGTTGAGTCCGAGTTCACTCATGGATGTGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACGCCCGAACTCGTTGAG
*
40932694 TTGAGTCTGAGTTCG
66 TTGAGTCCGAGTTCG
40932709 CTTATGGGCA
Statistics
Matches: 71, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.21, C:0.20, G:0.29, T:0.29
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:40935658 original size:15 final size:15
Alignment explanation
Indices: 40935638--40935693 Score: 87
Period size: 15 Copynumber: 3.7 Consensus size: 15
40935628 GTATCTTGGG
40935638 TTTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
40935653 TTTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
*
40935668 TTTCTCTA-TCTTGGA
1 TTTCTTTATTC-TGGA
40935683 TTTCTTTATTC
1 TTTCTTTATTC
40935694 GGTTTCCTTG
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
14 2 0.05
15 33 0.89
16 2 0.05
ACGTcount: A:0.12, C:0.16, G:0.11, T:0.61
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:40938140 original size:46 final size:46
Alignment explanation
Indices: 40938090--40938265 Score: 169
Period size: 46 Copynumber: 3.8 Consensus size: 46
40938080 TGTTTGGGCA
* *
40938090 TCCGAACTCGTTCAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * *
40938136 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-CTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
* ** * *
40938183 TTCGAACTCGTTGAGTTCTGTCCGAGTTCACTCATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * **
40938229 CCCGAGCTCGTTGAGTTGAGTCCGAGTTTGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
40938266 GCGGGTTACA
Statistics
Matches: 103, Mismatches: 20, Indels: 14
0.75 0.15 0.10
Matches are distributed among these distances:
43 6 0.06
45 4 0.04
46 58 0.56
47 26 0.25
48 4 0.04
50 5 0.05
ACGTcount: A:0.20, C:0.22, G:0.27, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:40938245 original size:93 final size:93
Alignment explanation
Indices: 40938086--40938256 Score: 261
Period size: 93 Copynumber: 1.8 Consensus size: 93
40938076 AGGATGTTTG
* * * *
40938086 GGCATCCGAACTCGTTCAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTCAGTTCAGTCCGAGTTCACTCATGGATGCAAACGCCCGAACTCGTTGAG
40938151 TTGAGTCCGAGTTCCTGAGATGTAACTA
66 TTGAGTCCGAGTTCCTGAGATGTAACTA
* * * * *
40938179 GGCATTCGAACTCGTTGAGTTCTGTCCGAGTTCACTCATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTCAGTTCAGTCCGAGTTCACTCATGGATGCAAACGCCCGAACTCGTTGAG
40938244 TTGAGTCCGAGTT
66 TTGAGTCCGAGTT
40938257 TGCTTATGGG
Statistics
Matches: 69, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
93 69 1.00
ACGTcount: A:0.21, C:0.23, G:0.27, T:0.29
Consensus pattern (93 bp):
GGCATCCGAACTCGTTCAGTTCAGTCCGAGTTCACTCATGGATGCAAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCCTGAGATGTAACTA
Found at i:40959058 original size:13 final size:13
Alignment explanation
Indices: 40959040--40959087 Score: 53
Period size: 13 Copynumber: 3.6 Consensus size: 13
40959030 GGGGGATAGG
40959040 ATTCTGTATATCT
1 ATTCTGTATATCT
* *
40959053 ATTCTGCATATTT
1 ATTCTGTATATCT
40959066 GATTCTGT-TATCT
1 -ATTCTGTATATCT
40959079 ATATCTGTA
1 AT-TCTGTA
40959088 CCTATAAAGG
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
12 2 0.07
13 20 0.71
14 6 0.21
ACGTcount: A:0.23, C:0.15, G:0.10, T:0.52
Consensus pattern (13 bp):
ATTCTGTATATCT
Found at i:40979726 original size:38 final size:39
Alignment explanation
Indices: 40979635--40979796 Score: 249
Period size: 39 Copynumber: 4.2 Consensus size: 39
40979625 TAATGGAGGA
*
40979635 TTATATCCGGGCCAAGTCCCGAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
*
40979674 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTACTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
40979713 -TATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
* *
40979751 TTATATCCGGGCTAAAGTCCC-ACAGGC-TTTGTGCTGGTA
1 TTATATCCGGGCT-AAGTCCCGA-AGGCATTCGTGCTGGTG
40979790 TTATATC
1 TTATATC
40979797 TGAGCTTAAA
Statistics
Matches: 115, Mismatches: 5, Indels: 6
0.91 0.04 0.05
Matches are distributed among these distances:
38 37 0.32
39 67 0.58
40 11 0.10
ACGTcount: A:0.20, C:0.23, G:0.28, T:0.29
Consensus pattern (39 bp):
TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
Found at i:40979807 original size:40 final size:39
Alignment explanation
Indices: 40979634--40979828 Score: 134
Period size: 39 Copynumber: 5.0 Consensus size: 39
40979624 ATAATGGAGG
* * *
40979634 ATTATATCCGGGC-CAAGTCCCGA-AGGCATTCGTGCTGGT
1 ATTATATCCGAGCTAAAGTCCC-ACAGGC-TTTGTGCTGGT
* * * *
40979673 GTTATATCCGGGCT-AAGTCCCGA-AGGCATTCGTACTGGT
1 ATTATATCCGAGCTAAAGTCCC-ACAGGC-TTTGTGCTGGT
* * *
40979712 -GTATATCCGGGCT-AAGTCCCGA-AGGCATTCGTGCTGGT
1 ATTATATCCGAGCTAAAGTCCC-ACAGGC-TTTGTGCTGGT
* *
40979750 GTTATATCCGGGCTAAAGTCCCACAGGCTTTGTGCTGGT
1 ATTATATCCGAGCTAAAGTCCCACAGGCTTTGTGCTGGT
* * * *
40979789 ATTATATCTGAGCTTAAAGTCCCGCATGCTTTGTGGTGGT
1 ATTATATCCGAGC-TAAAGTCCCACAGGCTTTGTGCTGGT
40979829 GATTGGATTT
Statistics
Matches: 139, Mismatches: 12, Indels: 9
0.87 0.08 0.06
Matches are distributed among these distances:
38 36 0.26
39 69 0.50
40 34 0.24
ACGTcount: A:0.19, C:0.23, G:0.28, T:0.30
Consensus pattern (39 bp):
ATTATATCCGAGCTAAAGTCCCACAGGCTTTGTGCTGGT
Found at i:40981562 original size:17 final size:17
Alignment explanation
Indices: 40981540--40981585 Score: 83
Period size: 17 Copynumber: 2.7 Consensus size: 17
40981530 TGGCTGGCAA
40981540 TGTGCGAGACACGGCCG
1 TGTGCGAGACACGGCCG
*
40981557 TGTGCGAGACATGGCCG
1 TGTGCGAGACACGGCCG
40981574 TGTGCGAGACAC
1 TGTGCGAGACAC
40981586 AGCCATGTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.20, C:0.26, G:0.39, T:0.15
Consensus pattern (17 bp):
TGTGCGAGACACGGCCG
Found at i:40981583 original size:34 final size:36
Alignment explanation
Indices: 40981540--40981635 Score: 106
Period size: 40 Copynumber: 2.6 Consensus size: 36
40981530 TGGCTGGCAA
*
40981540 TGTGCGAGACACGGCCGTGTG-CGAGA-CATGGCCG
1 TGTGCGAGACACGGCCGTGTGACAAGAGCATGGCCG
*
40981574 TGTGCGAGACACAGCCATGTGTTTGACAAGAGCATGGCCG
1 TGTGCGAGACACGGCC--GTG--TGACAAGAGCATGGCCG
* *
40981614 TGTGCAAGACACGACCGTGTGA
1 TGTGCGAGACACGGCCGTGTGA
40981636 TGGTGTGCGC
Statistics
Matches: 51, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
34 15 0.29
36 6 0.12
38 5 0.10
39 4 0.08
40 21 0.41
ACGTcount: A:0.23, C:0.24, G:0.35, T:0.18
Consensus pattern (36 bp):
TGTGCGAGACACGGCCGTGTGACAAGAGCATGGCCG
Found at i:40981594 original size:17 final size:17
Alignment explanation
Indices: 40981539--40981594 Score: 76
Period size: 17 Copynumber: 3.3 Consensus size: 17
40981529 GTGGCTGGCA
40981539 ATGTGCGAGACACGGCC
1 ATGTGCGAGACACGGCC
* *
40981556 GTGTGCGAGACATGGCC
1 ATGTGCGAGACACGGCC
* *
40981573 GTGTGCGAGACACAGCC
1 ATGTGCGAGACACGGCC
40981590 ATGTG
1 ATGTG
40981595 TTTGACAAGA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 34 1.00
ACGTcount: A:0.21, C:0.25, G:0.38, T:0.16
Consensus pattern (17 bp):
ATGTGCGAGACACGGCC
Found at i:40984455 original size:26 final size:25
Alignment explanation
Indices: 40984426--40984477 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
40984416 CTCTTTTGAG
* *
40984426 TTAATAAATTCTCTTTGAGTTTTTTT
1 TTAAGAAATTCTC-TTGAGTTTCTTT
*
40984452 TTAAGAATTTCTCTTGAGTTTCTTT
1 TTAAGAAATTCTCTTGAGTTTCTTT
40984477 T
1 T
40984478 GGAAGAGTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 12 0.52
26 11 0.48
ACGTcount: A:0.21, C:0.10, G:0.10, T:0.60
Consensus pattern (25 bp):
TTAAGAAATTCTCTTGAGTTTCTTT
Found at i:40984483 original size:26 final size:26
Alignment explanation
Indices: 40984434--40984483 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
40984424 AGTTAATAAA
**
40984434 TTCTCTTTGAGTTTTTTTTTAAGAAT
1 TTCTCTTTGAGTTTTTTTGGAAGAAT
40984460 TTCTC-TTGAGTTTCTTTTGGAAGA
1 TTCTCTTTGAGTTT-TTTTGGAAGA
40984484 GTTTTAACAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 8 0.38
26 13 0.62
ACGTcount: A:0.18, C:0.10, G:0.16, T:0.56
Consensus pattern (26 bp):
TTCTCTTTGAGTTTTTTTGGAAGAAT
Found at i:40989305 original size:46 final size:46
Alignment explanation
Indices: 40989255--40989475 Score: 225
Period size: 46 Copynumber: 4.8 Consensus size: 46
40989245 ACATCTCGTA
*
40989255 GCCGATGCATGTCCCAGACATGTCTTATACTAGCTTATGTCTCGAG
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGCTTATGTCTCGAG
* *
40989301 GCCGATGCATGTCCCAGACATGTCTTATACTAGCTTAAGTCTCGAG
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGCTTATGTCTCGAG
* * * * *
40989347 GCCGATGCATGTTCCAGACAAGTCTTACACTAGC--ACTCATCTCAAT
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGCTTA-T-GTCTCGAG
* * ** *
40989393 ACCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCAT-AAT-GTG
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTAGCT-T-ATGTCTCGAG
* *
40989441 GCTGATGCATGTCCCAGGCATGTCTTACACTAGCT
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGCT
40989476 CACAATAACC
Statistics
Matches: 146, Mismatches: 21, Indels: 16
0.80 0.11 0.09
Matches are distributed among these distances:
44 1 0.01
46 100 0.68
47 25 0.17
48 17 0.12
49 1 0.01
51 1 0.01
52 1 0.01
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.28
Consensus pattern (46 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTAGCTTATGTCTCGAG
Found at i:40989351 original size:92 final size:95
Alignment explanation
Indices: 40989255--40989475 Score: 240
Period size: 94 Copynumber: 2.4 Consensus size: 95
40989245 ACATCTCGTA
* * * *
40989255 GCCGATGCATGTCCCAGACATGTCTTATACTAGCTTA-T-GTCTCGAGGCCGATG-CATGTCCCA
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGC-TACTCATCTCAAGACCGATGCCATGTCCCA
* *
40989317 GACAT-GTCTTATACTAGCT-TAAGT-CTCGAG
65 GACATGGTCTTACACTAGCTCTAA-TAAT-GAG
* * *
40989347 GCCGATGCATGTTCCAGACAAGTCTTACACTAGC-ACTCATCTCAATACCGATGCCATGTCCCAG
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGCTACTCATCTCAAGACCGATGCCATGTCCCAG
* * *
40989411 ACATGGTCTTACACTGGCTCTCATAATGTG
66 ACATGGTCTTACACTAGCTCTAATAATGAG
* *
40989441 GCTGATGCATGTCCCAGGCATGTCTTACACTAGCT
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGCT
40989476 CACAATAACC
Statistics
Matches: 106, Mismatches: 16, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
90 1 0.01
91 1 0.01
92 42 0.40
93 14 0.13
94 45 0.42
95 3 0.03
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.28
Consensus pattern (95 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTAGCTACTCATCTCAAGACCGATGCCATGTCCCAG
ACATGGTCTTACACTAGCTCTAATAATGAG
Found at i:41001256 original size:64 final size:64
Alignment explanation
Indices: 41001177--41001360 Score: 194
Period size: 67 Copynumber: 2.8 Consensus size: 64
41001167 AGACATTATG
* *
41001177 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * *
41001241 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
41001306 AA
63 AA
* * * *
41001308 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAGC
41001361 CGAACTATAT
Statistics
Matches: 98, Mismatches: 17, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 21 0.21
65 8 0.08
66 16 0.16
67 31 0.32
68 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:41013057 original size:39 final size:39
Alignment explanation
Indices: 41012998--41013075 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
41012988 GAAAAAAGAT
41012998 TTACCTAAACTTTCTTGTGCGCCAAAACTATCTCAAGGA
1 TTACCTAAACTTTCTTGTGCGCCAAAACTATCTCAAGGA
*
41013037 TTACTTAAACTTTCTTGTGCGCCAAAACTATCTCAAGGA
1 TTACCTAAACTTTCTTGTGCGCCAAAACTATCTCAAGGA
41013076 CCAAAGATAT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.31, C:0.24, G:0.13, T:0.32
Consensus pattern (39 bp):
TTACCTAAACTTTCTTGTGCGCCAAAACTATCTCAAGGA
Found at i:41015936 original size:11 final size:11
Alignment explanation
Indices: 41015920--41015946 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
41015910 CCTAAATGAC
41015920 AAATTCATCAA
1 AAATTCATCAA
41015931 AAATTCATCAA
1 AAATTCATCAA
41015942 AAATT
1 AAATT
41015947 TCTTTACAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.30
Consensus pattern (11 bp):
AAATTCATCAA
Found at i:41024669 original size:55 final size:54
Alignment explanation
Indices: 41024574--41024723 Score: 149
Period size: 55 Copynumber: 2.8 Consensus size: 54
41024564 CTACTTTGTT
* ** * *
41024574 GCACTAAGTGTGCGAAATGAATATGAT-GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAATGTGCGAGTTGACTAT-ATAGCACTAAGTGTGCGAATTGACCACGCG
* * * * ** *
41024628 GCACTAAGTGTGCGGGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTG
1 GCACTAAATGTGCGAG-TTGACTATATAGCACTAAGTGTGCGAATTGACCACGCG
* *
41024683 GCACTAAATGTGCGAGTTGATTATATAGCACTGAGTGTGCG
1 GCACTAAATGTGCGAGTTGACTATATAGCACTAAGTGTGCG
41024724 GGCTCAATAT
Statistics
Matches: 79, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
54 37 0.47
55 42 0.53
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29
Consensus pattern (54 bp):
GCACTAAATGTGCGAGTTGACTATATAGCACTAAGTGTGCGAATTGACCACGCG
Found at i:41024686 original size:27 final size:27
Alignment explanation
Indices: 41024546--41024723 Score: 146
Period size: 27 Copynumber: 6.6 Consensus size: 27
41024536 TAAATTGTAC
41024546 AGCACTAAGTGTGCGATTCT-ACTT-TGT
1 AGCACTAAGTGTGCGATT-TGA-TTATGT
* ** *
41024573 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGATTATGT
* ** *
41024599 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGATTATGT
* * *
41024627 GGCACTAAGTGTGCGGGTTTGACTATGT
1 AGCACTAAGTGTGC-GATTTGATTATGT
*
41024655 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGATTATGT
* * * *
41024682 GGCACTAAATGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGATTATGT
*
41024709 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
41024724 GGCTCAATAT
Statistics
Matches: 121, Mismatches: 25, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
26 2 0.02
27 97 0.80
28 22 0.18
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGATTATGT
Found at i:41024687 original size:82 final size:81
Alignment explanation
Indices: 41024547--41024702 Score: 190
Period size: 82 Copynumber: 1.9 Consensus size: 81
41024537 AAATTGTACA
* * * *
41024547 GCACTAAGTGTGCGATTCTACTTTGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAAGTGT
1 GCACTAAGTGTGCGATTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAATGT
41024612 GCGAATTGACCATGCG
66 GCGAATTGACCATGCG
* ** *
41024628 GCACTAAGTGTGCGGGTT-TGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TGGCACTAAA
1 GCACTAAGTGTGC-GATTCT-ACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACTAAA
*
41024691 TGTGCGAGTTGA
63 TGTGCGAATTGA
41024703 TTATATAGCA
Statistics
Matches: 63, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
81 15 0.24
82 48 0.76
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAATGT
GCGAATTGACCATGCG
Found at i:41039712 original size:34 final size:35
Alignment explanation
Indices: 41039674--41039748 Score: 111
Period size: 34 Copynumber: 2.2 Consensus size: 35
41039664 CCTTTTCTAG
41039674 TAACAGTAG-CAGTCTGGGCCTTAGCCCATTTCAA
1 TAACAGTAGACAGTCTGGGCCTTAGCCCATTTCAA
* *
41039708 TAACAAT-GACAGTCTGGGCCTTAGCCCATTTCAG
1 TAACAGTAGACAGTCTGGGCCTTAGCCCATTTCAA
41039742 T-ACAGTA
1 TAACAGTA
41039749 TGCAAGAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
33 5 0.14
34 31 0.86
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.27
Consensus pattern (35 bp):
TAACAGTAGACAGTCTGGGCCTTAGCCCATTTCAA
Found at i:41043356 original size:19 final size:19
Alignment explanation
Indices: 41043319--41043356 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
41043309 ACGTATCAGA
*
41043319 AGAAAATAAATGAAGAATT
1 AGAAAATAAATGAAAAATT
41043338 AGAAAATAAAAT-AAAAATT
1 AGAAAAT-AAATGAAAAATT
41043357 TAAATTGCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.68, C:0.00, G:0.11, T:0.21
Consensus pattern (19 bp):
AGAAAATAAATGAAAAATT
Found at i:41050957 original size:40 final size:39
Alignment explanation
Indices: 41050859--41050978 Score: 168
Period size: 39 Copynumber: 3.1 Consensus size: 39
41050849 TCCTCGTTCA
* * * *
41050859 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC
1 AATGCCTTTGGGACATAACCCGGATTTAGTAACTCGCAC
*
41050898 AATGCCTTTGGGACATAACCCGGATTTAATAACTCGCAC
1 AATGCCTTTGGGACATAACCCGGATTTAGTAACTCGCAC
* *
41050937 GAATGCCTTTGGGACTTAACCCGGATTTAGTATCTCGCAC
1 -AATGCCTTTGGGACATAACCCGGATTTAGTAACTCGCAC
41050977 AA
1 AA
41050979 AGGCCTTCGG
Statistics
Matches: 72, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
39 36 0.50
40 36 0.50
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.27
Consensus pattern (39 bp):
AATGCCTTTGGGACATAACCCGGATTTAGTAACTCGCAC
Found at i:41050985 original size:40 final size:40
Alignment explanation
Indices: 41050857--41050985 Score: 170
Period size: 40 Copynumber: 3.2 Consensus size: 40
41050847 GCTCCTCGTT
* * * *
41050857 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTTGGGACATAACCCGGATTTAGTAACTCGCA
*
41050897 C-AATGCCTTTGGGACATAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTTGGGACATAACCCGGATTTAGTAACTCGCA
* * *
41050936 CGAATGCCTTTGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTTGGGACATAACCCGGATTTAGTAACTCGCA
*
41050976 CAAAGGCCTT
1 CAAATGCCTT
41050986 CGGATCTTAG
Statistics
Matches: 78, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
39 34 0.44
40 44 0.56
ACGTcount: A:0.27, C:0.26, G:0.20, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTTGGGACATAACCCGGATTTAGTAACTCGCA
Found at i:41051050 original size:41 final size:41
Alignment explanation
Indices: 41050973--41051050 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
41050963 TTAGTATCTC
* * *
41050973 GCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
41051014 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAAGGCCTTC-GGATCTTAGCCCGGACA-CATTCA
41051051 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (41 bp):
GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:41057762 original size:39 final size:40
Alignment explanation
Indices: 41057717--41057848 Score: 176
Period size: 40 Copynumber: 3.3 Consensus size: 40
41057707 GCTCCTCGTT
* * *
41057717 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
*
41057757 C-AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * * *
41057796 CGAATGCCTTTGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
*
41057836 CAAAGGCCTTCGG
1 CAAATGCCTTCGG
41057849 ATCTTAGTCC
Statistics
Matches: 80, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
39 35 0.44
40 45 0.56
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
Found at i:41057910 original size:41 final size:41
Alignment explanation
Indices: 41057833--41057910 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
41057823 TTAGTATCTC
* * *
41057833 GCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
41057874 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAAGGCCTTC-GGATCTTAGCCCGGACA-CATTCA
41057911 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (41 bp):
GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:41064218 original size:27 final size:27
Alignment explanation
Indices: 41064166--41064219 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
41064156 GGTTTTATAT
*
41064166 TAATTAATAAAGGTTATATATGTAAAA
1 TAATTAATAAAGGTTATATATATAAAA
*
41064193 TAATTAAT-AATGTTATATAATATAAAA
1 TAATTAATAAAGGTTATAT-ATATAAAA
41064220 CATAAAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 9 0.38
27 15 0.62
ACGTcount: A:0.54, C:0.00, G:0.07, T:0.39
Consensus pattern (27 bp):
TAATTAATAAAGGTTATATATATAAAA
Found at i:41065193 original size:56 final size:56
Alignment explanation
Indices: 41065124--41065290 Score: 226
Period size: 56 Copynumber: 3.0 Consensus size: 56
41065114 ACCATGGGAT
* ** * *
41065124 CGATATATGTGTGCAAGTAAGACCACGTTTAATATGTTGCCATCGATATGTGATTT
1 CGATATATGTGTGCGAGTAAGACCACGTTTAATACATTGGCATCGATATGTGATTC
* * *
41065180 TGATATTTGTGTGCGAGTAAGACCATGTTTAATACATTGGCATCGATATGTGATTC
1 CGATATATGTGTGCGAGTAAGACCACGTTTAATACATTGGCATCGATATGTGATTC
* * * *
41065236 CGATATATGTGTGTGAGTAAGACCACATCTAGTACATTGGCATCGATATGTGATT
1 CGATATATGTGTGCGAGTAAGACCACGTTTAATACATTGGCATCGATATGTGATT
41065291 ATATGTAAGA
Statistics
Matches: 96, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
56 96 1.00
ACGTcount: A:0.28, C:0.14, G:0.23, T:0.35
Consensus pattern (56 bp):
CGATATATGTGTGCGAGTAAGACCACGTTTAATACATTGGCATCGATATGTGATTC
Done.