Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A04
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: 82679320
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4050000 characters in sequence are not A, C, G, or T
File 132 of 255
Found at i:42421074 original size:2 final size:2
Alignment explanation
Indices: 42421063--42421097 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
42421053 AGGCATTTAT
*
42421063 CA CA CA -A CA CA CA CA CA CA CA CA CA TA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
42421098 TATAATACAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.51, C:0.46, G:0.00, T:0.03
Consensus pattern (2 bp):
CA
Found at i:42430439 original size:42 final size:41
Alignment explanation
Indices: 42430356--42430500 Score: 125
Period size: 43 Copynumber: 3.4 Consensus size: 41
42430346 GTCCTGGACG
* * *
42430356 TGGTCTTACATGTAAT-TCAATGTCGATGCCTCTGTCTCAGACA
1 TGGTCTTACACG-AATATCAA--TCGATGCCTATGTCCCAGACA
* *
42430399 AGGTCTTACACGAA-ATCAGATACGATGCCAATGTCCCAGACA
1 TGGTCTTACACGAATATCA-AT-CGATGCCTATGTCCCAGACA
* * * *
42430441 TGGTCTTATACGTGAATCTCAATCGAGGCCTGTGTCCCAGACA
1 TGGTCTTACAC--GAATATCAATCGATGCCTATGTCCCAGACA
42430484 TGGTCTTACACG-ATATC
1 TGGTCTTACACGAATATC
42430501 TCAGATAGAT
Statistics
Matches: 83, Mismatches: 13, Indels: 15
0.75 0.12 0.14
Matches are distributed among these distances:
40 4 0.05
41 2 0.02
42 31 0.37
43 38 0.46
44 5 0.06
45 3 0.04
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.28
Consensus pattern (41 bp):
TGGTCTTACACGAATATCAATCGATGCCTATGTCCCAGACA
Found at i:42432618 original size:13 final size:13
Alignment explanation
Indices: 42432600--42432646 Score: 85
Period size: 13 Copynumber: 3.6 Consensus size: 13
42432590 TCGAATAAAG
42432600 GGCACACGGCCAA
1 GGCACACGGCCAA
*
42432613 GGCACACAGCCAA
1 GGCACACGGCCAA
42432626 GGCACACGGCCAA
1 GGCACACGGCCAA
42432639 GGCACACG
1 GGCACACG
42432647 CCCATGGCCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 32 1.00
ACGTcount: A:0.32, C:0.38, G:0.30, T:0.00
Consensus pattern (13 bp):
GGCACACGGCCAA
Found at i:42433831 original size:46 final size:45
Alignment explanation
Indices: 42433570--42433937 Score: 215
Period size: 46 Copynumber: 7.8 Consensus size: 45
42433560 ATAGGTTAAG
* * *
42433570 ATGCCGACGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATATAGC
1 ATGCCGATG-CATGTCCCAGACAT-GTCTTACACTAGCTCTCATCT--C
* * *
42433619 GAGGCCGATGCCATGTCCCAGACAGGTCTTACACTGGCTCTCATCTATC
1 -ATGCCGATG-CATGTCCCAGACATGTCTTACACTAGCTCTCATC--TC
* ** * * * * * * *
42433668 GGTGTTGATGCCATATCCTAGACAGGTCTTACACT-G-ACACACCAC
1 -ATGCCGATG-CATGTCCCAGACATGTCTTACACTAGCTCTCATCTC
* * * * *
42433713 ATGCTGACGCCATGTCCCAGACAGGTCTTACACTAGCT-TGTATATTAC
1 ATGCCGATG-CATGTCCCAGACATGTCTTACACTAGCTCT-CAT-CT-C
*
42433761 GAGGCCGATGCATGTCCCAGACATGTCTTACACTAGCTCTCATCTC
1 -ATGCCGATGCATGTCCCAGACATGTCTTACACTAGCTCTCATCTC
* *
42433807 AATACCGATGCATGTCCCAGACATGTCTTACACTAGCT-TAAATATCTC
1 -ATGCCGATGCATGTCCCAGACATGTCTTACACTAGCTCT---CATCTC
* * * * * *
42433855 GAGGCCAATGCATGTCCCAAACATGCCATACACTGGCTCTCATGCT-
1 -ATGCCGATGCATGTCCCAGACATGTCTTACACTAGCTCTCAT-CTC
* *
42433901 GTGGCTGATGCATGTCCCAGACATGTCTTACACTAGC
1 AT-GCCGATGCATGTCCCAGACATGTCTTACACTAGC
42433938 ACACATATCA
Statistics
Matches: 251, Mismatches: 52, Indels: 34
0.74 0.15 0.10
Matches are distributed among these distances:
44 29 0.12
45 3 0.01
46 67 0.27
47 7 0.03
48 66 0.26
49 57 0.23
50 21 0.08
51 1 0.00
ACGTcount: A:0.24, C:0.30, G:0.20, T:0.26
Consensus pattern (45 bp):
ATGCCGATGCATGTCCCAGACATGTCTTACACTAGCTCTCATCTC
Found at i:42433946 original size:94 final size:94
Alignment explanation
Indices: 42433723--42433937 Score: 283
Period size: 94 Copynumber: 2.3 Consensus size: 94
42433713 ATGCTGACGC
* ** * * *
42433723 CATGTCCCAGACAGGTCTTACACTAGCTTGTATAT-TACGAGGCCGATGCATGTCCCAGACATGT
1 CATGTCCCAGACATGTCTTACACTAGCTTAAATATCTACGAGGCCAATGCATGTCCCAAACATGC
*
42433787 CTTACACTAGCTCTCATCTCAATACCGATG
66 CATACACTAGCTCTCATCT-AATACCGATG
42433817 CATGTCCCAGACATGTCTTACACTAGCTTAAATATCT-CGAGGCCAATGCATGTCCCAAACATGC
1 CATGTCCCAGACATGTCTTACACTAGCTTAAATATCTACGAGGCCAATGCATGTCCCAAACATGC
* * * *
42433881 CATACACTGGCTCTCATGCT-GTGGCTGATG
66 CATACACTAGCTCTCAT-CTAAT-ACCGATG
42433911 CATGTCCCAGACATGTCTTACACTAGC
1 CATGTCCCAGACATGTCTTACACTAGC
42433938 ACACATATCA
Statistics
Matches: 107, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
93 1 0.01
94 103 0.96
95 3 0.03
ACGTcount: A:0.26, C:0.29, G:0.18, T:0.27
Consensus pattern (94 bp):
CATGTCCCAGACATGTCTTACACTAGCTTAAATATCTACGAGGCCAATGCATGTCCCAAACATGC
CATACACTAGCTCTCATCTAATACCGATG
Found at i:42442371 original size:6 final size:6
Alignment explanation
Indices: 42442360--42442391 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
42442350 CACTGAAACT
*
42442360 TACACA TACACA TACACA TACGCA TACACA TA
1 TACACA TACACA TACACA TACACA TACACA TA
42442392 TAACATTCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.47, C:0.31, G:0.03, T:0.19
Consensus pattern (6 bp):
TACACA
Found at i:42444350 original size:42 final size:43
Alignment explanation
Indices: 42444250--42444363 Score: 133
Period size: 43 Copynumber: 2.7 Consensus size: 43
42444240 CAATGCCAAC
* * *
42444250 GTCCCAGACGTGGTCTTACATGTAATCAAATATCGATGCAATT
1 GTCCCAGACATGGTCTTACACGAAATCAAATATCGATGCAATT
* * *
42444293 GTCCCAGACAGGGTCTTACACGAAATCCAATAT-GATATCAA-T
1 GTCCCAGACATGGTCTTACACGAAATCAAATATCGAT-GCAATT
*
42444335 GTCCTAGACATGGTCTTACACGTAAATCA
1 GTCCCAGACATGGTCTTACACG-AAATCA
42444364 TAAGTCGATG
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
42 24 0.40
43 36 0.60
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (43 bp):
GTCCCAGACATGGTCTTACACGAAATCAAATATCGATGCAATT
Found at i:42449947 original size:27 final size:27
Alignment explanation
Indices: 42449904--42449962 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
42449894 AAAGACGTTC
*
42449904 CTTTCATATTATGCTACAAAGG-TTCTT
1 CTTTCATATTATACTACAAAGGCTT-TT
42449931 CTTTCATATT-TCACTACAAAGGCTTTT
1 CTTTCATATTAT-ACTACAAAGGCTTTT
42449958 CTTTC
1 CTTTC
42449963 TTGATATGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 1 0.03
27 26 0.90
28 2 0.07
ACGTcount: A:0.24, C:0.22, G:0.08, T:0.46
Consensus pattern (27 bp):
CTTTCATATTATACTACAAAGGCTTTT
Found at i:42452751 original size:119 final size:118
Alignment explanation
Indices: 42452541--42452777 Score: 318
Period size: 119 Copynumber: 2.0 Consensus size: 118
42452531 GGTTAGTAAC
* * *
42452541 ATTGGCGAACTCAATCAAAAGACTAAGGATGGCTAGAGGAGGAATGAAGAGAGTGATGGATGGTC
1 ATTGGCGAACTCAATCAAAAGACTAAGCATGGCTAGAGAAGGAATGAAGAGAGCGATGGATGGTC
* *
42452606 AAGCGTGGGGAGTGTGGTATTGGGCACAAAAT-AAGGAATAGAAATTTCATCCT
66 AAGCGCGGGGAGTGTGGTATTGGGCACAAAATGAA-GAACAGAAATTTCATCCT
* *
42452659 ATTGGCGAACTCAA-CTAGAAGACTGAGCATGGCTAGAGAAGGAAATGAAGAGAGCGATGGA-GA
1 ATTGGCGAACTCAATC-AAAAGACTAAGCATGGCTAGAGAAGG-AATGAAGAGAGCGATGGATG-
* * * *
42452722 GTCAAGTGCGGGGATTGTGGTATTGGGCACAAACTGAAGAACATAAATTTCATCCT
63 GTCAAGCGCGGGGAGTGTGGTATTGGGCACAAAATGAAGAACAGAAATTTCATCCT
42452778 CTAGATGGAT
Statistics
Matches: 104, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
117 1 0.01
118 37 0.36
119 64 0.62
120 2 0.02
ACGTcount: A:0.35, C:0.13, G:0.31, T:0.21
Consensus pattern (118 bp):
ATTGGCGAACTCAATCAAAAGACTAAGCATGGCTAGAGAAGGAATGAAGAGAGCGATGGATGGTC
AAGCGCGGGGAGTGTGGTATTGGGCACAAAATGAAGAACAGAAATTTCATCCT
Found at i:42459625 original size:40 final size:40
Alignment explanation
Indices: 42459536--42459715 Score: 197
Period size: 40 Copynumber: 4.5 Consensus size: 40
42459526 ACCCAAGTAT
** * *
42459536 CTTCGGGAT-TTAG-CCGGATATAACCACTAGCA-CAAGGC
1 CTTCGGG-TCTTAGCCCGGATATAGTCACTAGCATAAATGC
* *
42459574 CTTCGGGTCTTAGCCTGGATATGGTCACTAGCATAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCATAAATGC
* * *
42459614 CTTCGGGTCTTAGCCCGGATATAG-CAACTCGTACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGTC-ACTAGCATAAATGC
* * *
42459654 CTTCGGATCTTAGTCCGGATATAGTCACTAGCATAAAAGC
1 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCATAAATGC
*
42459694 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGTCTTAGCCCGGATAT
42459716 CATTCGAATA
Statistics
Matches: 117, Mismatches: 20, Indels: 8
0.81 0.14 0.06
Matches are distributed among these distances:
37 1 0.01
38 11 0.09
39 16 0.14
40 88 0.75
41 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.23, T:0.26
Consensus pattern (40 bp):
CTTCGGGTCTTAGCCCGGATATAGTCACTAGCATAAATGC
Found at i:42466693 original size:38 final size:39
Alignment explanation
Indices: 42466638--42466779 Score: 182
Period size: 38 Copynumber: 3.6 Consensus size: 39
42466628 AGTGACAATA
*
42466638 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGATACTAAT
* *
42466678 TCCGGGCTAAG-CCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGATACTAAT
*
42466716 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATACT-AT
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGATACTAAT
* *
42466754 AACCGGGCTATGTCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCGAAGGCATTTG
42466780 AACGAGGAGC
Statistics
Matches: 90, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
38 49 0.54
39 13 0.14
40 28 0.31
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:42466797 original size:78 final size:77
Alignment explanation
Indices: 42466651--42466812 Score: 195
Period size: 78 Copynumber: 2.1 Consensus size: 77
42466641 GGACTAAGAT
* ** *
42466651 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCGAAGGCATTTGTGCGAGTTACTAAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCGAAGGCATTTGAACGAGTGACTAAA
*
42466716 TCCGGGTTAAGTC
66 TCC-GGTTAAATC
*
42466729 CCGAAGGCATTTGTGCGA-ATACT-ATAACCGGGCTATGTCCGAAGGCATTTGAACGAG-GAGCT
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCGAAGGCATTTGAACGAGTGA-CT
* *
42466791 ATATCCGGTTAAATT
63 AAATCCGGTTAAATC
42466806 CCGAAGG
1 CCGAAGG
42466813 TACGTGATTT
Statistics
Matches: 73, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
76 2 0.03
77 29 0.40
78 42 0.58
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.25
Consensus pattern (77 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCGAAGGCATTTGAACGAGTGACTAAA
TCCGGTTAAATC
Found at i:42473858 original size:40 final size:40
Alignment explanation
Indices: 42473713--42473896 Score: 209
Period size: 40 Copynumber: 4.7 Consensus size: 40
42473703 TTGAATGATG
* *
42473713 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGAC-AATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAA-A
* * * *
42473752 TCTGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
42473792 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
42473831 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
42473872 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
42473897 AACGAGGAGC
Statistics
Matches: 124, Mismatches: 14, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
39 52 0.42
40 62 0.50
41 10 0.08
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:42473918 original size:79 final size:79
Alignment explanation
Indices: 42473765--42473929 Score: 194
Period size: 79 Copynumber: 2.1 Consensus size: 79
42473755 GGACTAAGAT
* ** *
42473765 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAA
*
42473830 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
*
42473844 CCGAAGGCATTTGTGCGA-ATTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAG
1 CCGAAGGCATTTGTGCGAGA-TACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTGA-
* *
42473906 CTATATCC-GGTTAAATT
62 CTAAATCCGGGTTAAATC
42473923 CCGAAGG
1 CCGAAGG
42473930 TACGTGATTT
Statistics
Matches: 74, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
78 3 0.04
79 46 0.62
80 25 0.34
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAA
ATCCGGGTTAAATC
Found at i:42485453 original size:13 final size:13
Alignment explanation
Indices: 42485435--42485461 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
42485425 CGTTTTTGAT
42485435 AAAACGCCACTAA
1 AAAACGCCACTAA
42485448 AAAACGCCACTAA
1 AAAACGCCACTAA
42485461 A
1 A
42485462 GCCCTATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.30, G:0.07, T:0.07
Consensus pattern (13 bp):
AAAACGCCACTAA
Found at i:42485979 original size:16 final size:14
Alignment explanation
Indices: 42485957--42485999 Score: 50
Period size: 16 Copynumber: 2.9 Consensus size: 14
42485947 TCCCTTGCAT
42485957 GTTAGATTAACATG
1 GTTAGATTAACATG
*
42485971 GATTTAGATTAAAATG
1 G--TTAGATTAACATG
42485987 GTTAGATGTAACA
1 GTTAGAT-TAACA
42486000 CCCCTCACCC
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
14 7 0.29
15 4 0.17
16 13 0.54
ACGTcount: A:0.40, C:0.05, G:0.21, T:0.35
Consensus pattern (14 bp):
GTTAGATTAACATG
Found at i:42493685 original size:38 final size:39
Alignment explanation
Indices: 42493574--42493701 Score: 156
Period size: 38 Copynumber: 3.3 Consensus size: 39
42493564 CAATCACGTA
* * *
42493574 CCTTCGGAATTTAACCGGATATAGCT-ACTCG-TCAAATG
1 CCTTCGGGACTTAACCGGATATAG-TAACTCGCACAAATG
* * *
42493612 CCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTA-ACCGGATATAGTAACTCGCACAAATG
42493652 CCTTCGGGACTTAACCGGAT-TAGTAACTCGCACAAATG
1 CCTTCGGGACTTAACCGGATATAGTAACTCGCACAAATG
42493690 CCTTCGGG-CTTA
1 CCTTCGGGACTTA
42493702 GCCCGGAAAA
Statistics
Matches: 78, Mismatches: 9, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
37 4 0.05
38 37 0.47
39 19 0.24
40 18 0.23
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.26
Consensus pattern (39 bp):
CCTTCGGGACTTAACCGGATATAGTAACTCGCACAAATG
Found at i:42493708 original size:38 final size:40
Alignment explanation
Indices: 42493588--42493775 Score: 169
Period size: 38 Copynumber: 5.1 Consensus size: 40
42493578 CGGAATTTAA
* *
42493588 CCGGATATAGCT-ACTCG-TCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
42493627 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTA-A
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
42493666 CCGGAT-TAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
42493704 CCGGA-A-AAT-ACT-GCA-AAATG-CTTC--GACTTAGT
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
42493736 CCGGATAT--TCACTAGCA-AAA-GCCTTC-GGACTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
42493771 CCGGA
1 CCGGA
42493776 ATCATTCAAT
Statistics
Matches: 129, Mismatches: 9, Indels: 26
0.79 0.05 0.16
Matches are distributed among these distances:
31 1 0.01
32 11 0.09
33 9 0.07
34 15 0.12
35 15 0.12
36 3 0.02
37 6 0.05
38 32 0.25
39 19 0.15
40 18 0.14
ACGTcount: A:0.28, C:0.27, G:0.22, T:0.23
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:42493775 original size:35 final size:33
Alignment explanation
Indices: 42493684--42493776 Score: 100
Period size: 32 Copynumber: 2.8 Consensus size: 33
42493674 GTAACTCGCA
* *
42493684 CAAATGCCTTCGGGCTTAGCCCGGAAAATACTG
1 CAAAAGCCTTCGGACTTAGCCCGGAAAATACTG
* * *
42493717 CAAAATG-CTTC-GACTTAGTCCGGATATTCACTAG
1 CAAAA-GCCTTCGGACTTAGCCCGGAAAAT-ACT-G
42493751 CAAAAGCCTTCGGACTTAGCCCGGAA
1 CAAAAGCCTTCGGACTTAGCCCGGAA
42493777 TCATTCAATA
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
32 13 0.27
33 12 0.25
34 11 0.23
35 12 0.25
ACGTcount: A:0.29, C:0.27, G:0.22, T:0.23
Consensus pattern (33 bp):
CAAAAGCCTTCGGACTTAGCCCGGAAAATACTG
Found at i:42501767 original size:40 final size:40
Alignment explanation
Indices: 42501712--42501903 Score: 278
Period size: 40 Copynumber: 4.8 Consensus size: 40
42501702 ATAACCACAA
* * * *
42501712 GCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
42501752 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
42501792 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
* * * *
42501832 GCACAAATGCCTTCAGGTCTTAGCCTGGATAAAATC-ACTA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGAT-ATATCAACTC
* *
42501872 GCATAAATGCCTTCGGGACTTAGCCCGGATAT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATAT
42501904 CATTCAAATG
Statistics
Matches: 138, Mismatches: 13, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
39 1 0.01
40 133 0.96
41 4 0.03
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
Found at i:42504198 original size:40 final size:40
Alignment explanation
Indices: 42504148--42504291 Score: 191
Period size: 40 Copynumber: 3.6 Consensus size: 40
42504138 CTCGCACAAG
* *
42504148 GCCTTTGGGTCTTAGCCCGGATATGGTCACTAGCATAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCATAAAT
* *
42504188 GCCTTCGGGTCTTAGCCCGGATATAG-CAACTCGCACAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTC-ACTAGCATAAAT
* * *
42504228 GCCTTCGGATCTTAGTCCGGATATAGTCACTAGCATAAAA
1 GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCATAAAT
* *
42504268 GCCTTCGGGACTTAGCCTGGATAT
1 GCCTTCGGGTCTTAGCCCGGATAT
42504292 CATTCGAATA
Statistics
Matches: 89, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
39 1 0.01
40 87 0.98
41 1 0.01
ACGTcount: A:0.24, C:0.25, G:0.24, T:0.27
Consensus pattern (40 bp):
GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCATAAAT
Found at i:42504248 original size:80 final size:79
Alignment explanation
Indices: 42504112--42504291 Score: 229
Period size: 80 Copynumber: 2.3 Consensus size: 79
42504102 ACCCAAGTAT
* * * * *
42504112 CTTCGGGAT-TTAG-CCAGATATAACCACTCGCACAAGGCCTTTGGGTCTTAGCCCGGATATGGT
1 CTTCGGG-TCTTAGCCCGGATATAACAACTCGCACAAGGCCTTCGGATCTTAGCCCGGATATAGT
*
42504175 CACTAGCATAAATGC
65 CACTAGCATAAAAGC
* * *
42504190 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGCCTTCGGATCTTAGTCCGGATATAGT
1 CTTCGGGTCTTAGCCCGGATATAACAACTCGCAC-AAGGCCTTCGGATCTTAGCCCGGATATAGT
42504255 CACTAGCATAAAAGC
65 CACTAGCATAAAAGC
* *
42504270 CTTCGGGACTTAGCCTGGATAT
1 CTTCGGGTCTTAGCCCGGATAT
42504292 CATTCGAATA
Statistics
Matches: 88, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
77 1 0.01
78 11 0.12
79 17 0.19
80 59 0.67
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.26
Consensus pattern (79 bp):
CTTCGGGTCTTAGCCCGGATATAACAACTCGCACAAGGCCTTCGGATCTTAGCCCGGATATAGTC
ACTAGCATAAAAGC
Found at i:42512936 original size:14 final size:15
Alignment explanation
Indices: 42512907--42512936 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
42512897 AATCATTTTC
42512907 ATGTTATTTATTAAT
1 ATGTTATTTATTAAT
42512922 ATGTTATTT-TTAAT
1 ATGTTATTTATTAAT
42512936 A
1 A
42512937 ATATAGTGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (15 bp):
ATGTTATTTATTAAT
Found at i:42514034 original size:41 final size:41
Alignment explanation
Indices: 42513917--42514312 Score: 391
Period size: 41 Copynumber: 9.7 Consensus size: 41
42513907 CTTAATTATT
* * * * *
42513917 CCCTAAATTACACATACATGGCCTTGTTTGTACTTCAGTAC
1 CCCTAAATTGCACATACGTGCCCCTGTTTGTACTTCGGTAC
* *
42513958 CTCCAAAATTGCACATACGTGCCCCTATTTGTACTTCGGTAC
1 C-CCTAAATTGCACATACGTGCCCCTGTTTGTACTTCGGTAC
* * * * **
42514000 CCCTGAATTACACATACGTGCCCTTGTTTATACTTCAATA-
1 CCCTAAATTGCACATACGTGCCCCTGTTTGTACTTCGGTAC
* * * * * **
42514040 CCTTGAATTTCACATATGTTCCCCTGTTTACACTTCGGTAC
1 CCCTAAATTGCACATACGTGCCCCTGTTTGTACTTCGGTAC
* * * *
42514081 CCCTGAATTACACATACATGCCCCTGTTTGTACTTCGATAC
1 CCCTAAATTGCACATACGTGCCCCTGTTTGTACTTCGGTAC
* * * * * *
42514122 CCCTAGATGGCACATACGTACCCCTATTTATAATTCGGTAC
1 CCCTAAATTGCACATACGTGCCCCTGTTTGTACTTCGGTAC
* *
42514163 CCCTAAATTGCATATACGTGCCCCTGTTTGTACTTTGGTAC
1 CCCTAAATTGCACATACGTGCCCCTGTTTGTACTTCGGTAC
* * *
42514204 CCCTAAATTGCACATACATACCCCTGTTTGTACTTCGATAC
1 CCCTAAATTGCACATACGTGCCCCTGTTTGTACTTCGGTAC
* * * *
42514245 CCTTAAATTGTACATATGTGCCCCTGTTTGTACTTTGGTAC
1 CCCTAAATTGCACATACGTGCCCCTGTTTGTACTTCGGTAC
* * *
42514286 CCCTGAATAGCACCTACGTG-CCCTGTT
1 CCCTAAATTGCACATACGTGCCCCTGTT
42514313 AACACTCCGA
Statistics
Matches: 286, Mismatches: 67, Indels: 5
0.80 0.19 0.01
Matches are distributed among these distances:
40 39 0.14
41 213 0.74
42 34 0.12
ACGTcount: A:0.23, C:0.29, G:0.14, T:0.34
Consensus pattern (41 bp):
CCCTAAATTGCACATACGTGCCCCTGTTTGTACTTCGGTAC
Found at i:42514288 original size:20 final size:20
Alignment explanation
Indices: 42514183--42514290 Score: 56
Period size: 20 Copynumber: 5.3 Consensus size: 20
42514173 CATATACGTG
42514183 CCCCTGTTTGTACTTTGGTA
1 CCCCTGTTTGTACTTTGGTA
** * * ***
42514203 CCCCTAAATTGCACATACATA
1 CCCCT-GTTTGTACTTTGGTA
* *
42514224 CCCCTGTTTGTACTTCGATA
1 CCCCTGTTTGTACTTTGGTA
* ** * *
42514244 CCCTTAAATTGTACATAT-GTG
1 CCCCT-GTTTGTAC-TTTGGTA
42514265 CCCCTGTTTGTACTTTGGTA
1 CCCCTGTTTGTACTTTGGTA
42514285 CCCCTG
1 CCCCTG
42514291 AATAGCACCT
Statistics
Matches: 59, Mismatches: 25, Indels: 8
0.64 0.27 0.09
Matches are distributed among these distances:
19 2 0.03
20 32 0.54
21 24 0.41
22 1 0.02
ACGTcount: A:0.19, C:0.29, G:0.15, T:0.37
Consensus pattern (20 bp):
CCCCTGTTTGTACTTTGGTA
Found at i:42518803 original size:42 final size:42
Alignment explanation
Indices: 42518716--42518868 Score: 146
Period size: 42 Copynumber: 3.6 Consensus size: 42
42518706 AGATGCCAAT
* * * *
42518716 CCATGTCCCAGACATGGTCTTACATGCGATT-TCACATCGATG
1 CCATATCCCAGACATGGTCTTACATG-AATTCTCATATCGACG
* * *
42518758 CCATATCCCAGATATGGTCTTATATGAATTCTCATTTCGACG
1 CCATATCCCAGACATGGTCTTACATGAATTCTCATATCGACG
* * * * * *
42518800 CCATGTCCTAGACATGGTCTTACACGAAATCTCGTATCAACG
1 CCATATCCCAGACATGGTCTTACATGAATTCTCATATCGACG
* * *
42518842 CTATATCCCGGATATGGTCTTACATGA
1 CCATATCCCAGACATGGTCTTACATGA
42518869 TAACTCATAT
Statistics
Matches: 88, Mismatches: 22, Indels: 2
0.79 0.20 0.02
Matches are distributed among these distances:
41 3 0.03
42 85 0.97
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.31
Consensus pattern (42 bp):
CCATATCCCAGACATGGTCTTACATGAATTCTCATATCGACG
Found at i:42530434 original size:55 final size:55
Alignment explanation
Indices: 42530343--42530483 Score: 147
Period size: 55 Copynumber: 2.6 Consensus size: 55
42530333 TGTGACATGG
* * * * * * * * ** *
42530343 CCGTGGGCGAACCGGCCAAAATAGCACGGACGTGCGACACGTACGTGCCTTGAAC
1 CCGTGGCCGAACCTGTCAAATTAACACGGGCATGCGACACGCACGTGCCAAGAAA
* *
42530398 CCGTGGCTGAACCTGTCAAATTAACACGGGCATGCGACACGCCCGTGCCAAGAAA
1 CCGTGGCCGAACCTGTCAAATTAACACGGGCATGCGACACGCACGTGCCAAGAAA
* *
42530453 CCGTGGCCGAACCTGTTAAATTAACATGGGC
1 CCGTGGCCGAACCTGTCAAATTAACACGGGC
42530484 GTGGGCCTAC
Statistics
Matches: 70, Mismatches: 16, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
55 70 1.00
ACGTcount: A:0.27, C:0.30, G:0.28, T:0.16
Consensus pattern (55 bp):
CCGTGGCCGAACCTGTCAAATTAACACGGGCATGCGACACGCACGTGCCAAGAAA
Found at i:42535934 original size:13 final size:13
Alignment explanation
Indices: 42535916--42535940 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42535906 TAATAAGGCC
42535916 TCTTTGGATTTTA
1 TCTTTGGATTTTA
42535929 TCTTTGGATTTT
1 TCTTTGGATTTT
42535941 TAATTGCTTT
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:0.08, G:0.16, T:0.64
Consensus pattern (13 bp):
TCTTTGGATTTTA
Found at i:42535956 original size:16 final size:17
Alignment explanation
Indices: 42535930--42535964 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
42535920 TGGATTTTAT
*
42535930 CTTTGGATTTTTAATTG
1 CTTTGGATTTTTAACTG
42535947 CTTT-GATTTTTAACTG
1 CTTTGGATTTTTAACTG
42535963 CT
1 CT
42535965 AGCAGTAGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.17, C:0.11, G:0.14, T:0.57
Consensus pattern (17 bp):
CTTTGGATTTTTAACTG
Found at i:42542815 original size:46 final size:47
Alignment explanation
Indices: 42542707--42542827 Score: 160
Period size: 46 Copynumber: 2.6 Consensus size: 47
42542697 AAGCCAACGC
* *
42542707 CATGTCCCAGACAGGTCTTACACTAGCTTGTATATCGTGAAGACGATG
1 CATGTCCCAGACATGTCTTACACTAGCTTCTATATCGTG-AGACGATG
42542755 CATGTCCCAGACATGTCTTACACTAGCTCTCT-TA-CGGTG-G-CTGATG
1 CATGTCCCAGACATGTCTTACACTAGCT-TCTATATC-GTGAGAC-GATG
42542801 CATGTCCCAGACATGTCTTACACTAGC
1 CATGTCCCAGACATGTCTTACACTAGC
42542828 ACACACATCA
Statistics
Matches: 68, Mismatches: 2, Indels: 8
0.87 0.03 0.10
Matches are distributed among these distances:
45 1 0.01
46 32 0.47
47 1 0.01
48 32 0.47
49 2 0.03
ACGTcount: A:0.24, C:0.27, G:0.21, T:0.28
Consensus pattern (47 bp):
CATGTCCCAGACATGTCTTACACTAGCTTCTATATCGTGAGACGATG
Found at i:42544029 original size:22 final size:22
Alignment explanation
Indices: 42543999--42544055 Score: 80
Period size: 22 Copynumber: 2.6 Consensus size: 22
42543989 GTCCCAAGGT
*
42543999 CACACGGGCGTGTCCCTTGGAC
1 CACATGGGCGTGTCCCTTGGAC
*
42544021 CACATGGGCGCGTCCCTTGGAC
1 CACATGGGCGTGTCCCTTGGAC
42544043 CAC-TCGGGCGTGT
1 CACAT-GGGCGTGT
42544056 GACCCCTGTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
21 1 0.03
22 30 0.97
ACGTcount: A:0.12, C:0.35, G:0.33, T:0.19
Consensus pattern (22 bp):
CACATGGGCGTGTCCCTTGGAC
Found at i:42546472 original size:93 final size:93
Alignment explanation
Indices: 42546358--42546529 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
42546348 CGCCCATAAG
* *
42546358 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
42546423 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
* *
42546451 CGAACTTGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
42546516 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
42546530 TCAACCATCC
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.22
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:42546526 original size:46 final size:46
Alignment explanation
Indices: 42546351--42546526 Score: 207
Period size: 46 Copynumber: 3.8 Consensus size: 46
42546341 TGTAACCCGC
* * *
42546351 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
42546397 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
* *
42546447 -C-TCA-CGAACTTGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
42546490 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
42546527 TGCTCAACCA
Statistics
Matches: 109, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 62 0.57
47 28 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:42550478 original size:48 final size:48
Alignment explanation
Indices: 42550281--42550599 Score: 216
Period size: 48 Copynumber: 6.6 Consensus size: 48
42550271 GGTGAATTTT
* * * * * ** * *
42550281 CGATGCCATGTTCCAAACATGGTCTTATACTGGCTCACATGTCGAGGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCAAATCAATGC
* * * * ***
42550329 CAATGCCATGTCCCTGGCATGGTCTTACACTAGCTTTCGTCTCAATGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCAAATCAATGC
* * * *
42550377 TGATGCCATGTCCTAGACATGGTCTTACACTAGCTCTTATAAT--ATGGT
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCA-AATCAAT-GC
* * * *
42550425 TGATGCCATGTCCCAGACATGGTCTTACACTAGCGCACAAATCAATAC
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCAAATCAATGC
** * * * *
42550473 CGATGCCATGTAACAGACATGGTCTTACACTGGCTCTC-ATTACATTAC
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCAAAT-CAATGC
* * * * * * *
42550521 CGATGTCATGTTCCAAACATGGTCTTACACTGGCCCTCATATC-GTGGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCAAATCAAT-GC
*
42550569 CGATGCCATATCCCA-ATCATGGTCTTACACT
1 CGATGCCATGTCCCAGA-CATGGTCTTACACT
42550600 GGTATACATA
Statistics
Matches: 213, Mismatches: 50, Indels: 16
0.76 0.18 0.06
Matches are distributed among these distances:
47 9 0.04
48 200 0.94
49 4 0.02
ACGTcount: A:0.24, C:0.28, G:0.18, T:0.29
Consensus pattern (48 bp):
CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCAAATCAATGC
Found at i:42554947 original size:42 final size:42
Alignment explanation
Indices: 42554895--42554992 Score: 153
Period size: 42 Copynumber: 2.3 Consensus size: 42
42554885 ATAGCCCATC
*
42554895 TATGGTCTTACACAAAATCTCAT-ATCGATGCCATATCCCGGA
1 TATGGTCTTACACAAAATCTCATAAT-GATGCCATATCCCAGA
* *
42554937 TATGGTCTTACACGAAATCTCATAATGATGTCATATCCCAGA
1 TATGGTCTTACACAAAATCTCATAATGATGCCATATCCCAGA
42554979 TATGGTCTTACACA
1 TATGGTCTTACACA
42554993 TAGCCTCGGT
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
42 49 0.96
43 2 0.04
ACGTcount: A:0.32, C:0.23, G:0.14, T:0.31
Consensus pattern (42 bp):
TATGGTCTTACACAAAATCTCATAATGATGCCATATCCCAGA
Found at i:42556817 original size:42 final size:41
Alignment explanation
Indices: 42556699--42556830 Score: 140
Period size: 42 Copynumber: 3.1 Consensus size: 41
42556689 ACAACAATGT
* * * *
42556699 CATATCCTAGATATGGCCTTACATGGAATCTCGTATCGATGC
1 CATATCCAAGATATGGTCTTACAT-GAAACTCATATCGATGC
* * * *
42556741 CAATAGCCCAGCTATGGTCTTACACGAAATCTCATATCGATGC
1 C-ATATCCAAGATATGGTCTTACATGAAA-CTCATATCGATGC
42556784 CATATCCAAGATATGGTCTTACATGAAGACTCATAAT-GATGC
1 CATATCCAAGATATGGTCTTACATGAA-ACTCAT-ATCGATGC
42556826 CATAT
1 CATAT
42556831 ACCCTAATGT
Statistics
Matches: 75, Mismatches: 11, Indels: 8
0.80 0.12 0.09
Matches are distributed among these distances:
42 41 0.55
43 34 0.45
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.29
Consensus pattern (41 bp):
CATATCCAAGATATGGTCTTACATGAAACTCATATCGATGC
Found at i:42563457 original size:43 final size:42
Alignment explanation
Indices: 42563395--42563508 Score: 138
Period size: 43 Copynumber: 2.7 Consensus size: 42
42563385 TGCTACACCA
* ****
42563395 ATGCCATATCCCAGTTATGGTCTTACATGGGATCTCATATCG
1 ATGCCATATCCCAGCTATGGTCTTACACAAAATCTCATATCG
*
42563437 ATGCCAATAGCCCAGCTATGGTCTTACACAAAATCTCATATCG
1 ATGCC-ATATCCCAGCTATGGTCTTACACAAAATCTCATATCG
* * *
42563480 ATTCCATATCCCAGCTATCGTCTTTCACA
1 ATGCCATATCCCAGCTATGGTCTTACACA
42563509 TAGCCTCGGT
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
42 26 0.43
43 35 0.57
ACGTcount: A:0.27, C:0.28, G:0.14, T:0.31
Consensus pattern (42 bp):
ATGCCATATCCCAGCTATGGTCTTACACAAAATCTCATATCG
Found at i:42573582 original size:14 final size:14
Alignment explanation
Indices: 42573565--42573595 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
42573555 ATGTTTTATA
42573565 TTATAATATAACAT
1 TTATAATATAACAT
*
42573579 TTATAATATAATAT
1 TTATAATATAACAT
42573593 TTA
1 TTA
42573596 ATTTACTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (14 bp):
TTATAATATAACAT
Found at i:42574952 original size:12 final size:12
Alignment explanation
Indices: 42574935--42574961 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
42574925 TCTTGATAAA
42574935 AAGGGTCAAATT
1 AAGGGTCAAATT
42574947 AAGGGTCAAATT
1 AAGGGTCAAATT
42574959 AAG
1 AAG
42574962 TAAGAGGATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.44, C:0.07, G:0.26, T:0.22
Consensus pattern (12 bp):
AAGGGTCAAATT
Found at i:42575970 original size:6 final size:6
Alignment explanation
Indices: 42575959--42576040 Score: 60
Period size: 6 Copynumber: 13.7 Consensus size: 6
42575949 AAGAAAATTG
* * * * *
42575959 AAAAAT AAAAAT CAAAAG GAAAAT AAGAAT AAAATAA ATAAAAT AAAAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAA-AT A-AAAAT AAAAAT
* * *
42576009 AAAAAT AAGAAT --AAAT AACATT AAAAAT AAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAA
42576041 TAGGAGGATT
Statistics
Matches: 57, Mismatches: 15, Indels: 8
0.71 0.19 0.10
Matches are distributed among these distances:
4 3 0.05
6 47 0.82
7 4 0.07
8 3 0.05
ACGTcount: A:0.76, C:0.02, G:0.05, T:0.17
Consensus pattern (6 bp):
AAAAAT
Found at i:42576014 original size:32 final size:34
Alignment explanation
Indices: 42575964--42576040 Score: 97
Period size: 32 Copynumber: 2.3 Consensus size: 34
42575954 AATTGAAAAA
* **
42575964 TAAAAATCAAAAGGAAAATAAGAATAAAATAA-A-
1 TAAAAATAAAAATAAAAATAAGAAT-AAATAACAT
42575997 T-AAAATAAAAATAAAAATAAGAATAAATAACAT
1 TAAAAATAAAAATAAAAATAAGAATAAATAACAT
42576030 TAAAAATAAAA
1 TAAAAATAAAA
42576041 TAGGAGGATT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
31 6 0.16
32 21 0.55
33 2 0.05
34 9 0.24
ACGTcount: A:0.74, C:0.03, G:0.05, T:0.18
Consensus pattern (34 bp):
TAAAAATAAAAATAAAAATAAGAATAAATAACAT
Found at i:42576021 original size:27 final size:27
Alignment explanation
Indices: 42575978--42576040 Score: 92
Period size: 26 Copynumber: 2.3 Consensus size: 27
42575968 AATCAAAAGG
*
42575978 AAAATAAGAATAAAATAAATAA-AATA
1 AAAATAAAAATAAAATAAATAACAATA
*
42576004 AAAATAAAAATAAGAATAAATAACATTA
1 AAAATAAAAATAA-AATAAATAACAATA
42576032 AAAATAAAA
1 AAAATAAAA
42576041 TAGGAGGATT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
26 12 0.36
27 9 0.27
28 12 0.36
ACGTcount: A:0.76, C:0.02, G:0.03, T:0.19
Consensus pattern (27 bp):
AAAATAAAAATAAAATAAATAACAATA
Found at i:42576033 original size:22 final size:21
Alignment explanation
Indices: 42575959--42576042 Score: 73
Period size: 22 Copynumber: 3.9 Consensus size: 21
42575949 AAGAAAATTG
*
42575959 AAAAATAAAAATCAAAAGGAAAAT
1 AAAAATAAAAAT-AAAA--TAAAT
*
42575983 AAGAAT-AAAAT-AAATAAAAT
1 AAAAATAAAAATAAAAT-AAAT
42576003 AAAAATAAAAATAAGAATAAAT
1 AAAAATAAAAATAA-AATAAAT
* *
42576025 AACATTAAAAATAAAATA
1 AAAAATAAAAATAAAATA
42576043 GGAGGATTCA
Statistics
Matches: 51, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
20 9 0.18
21 12 0.24
22 17 0.33
23 8 0.16
24 5 0.10
ACGTcount: A:0.75, C:0.02, G:0.05, T:0.18
Consensus pattern (21 bp):
AAAAATAAAAATAAAATAAAT
Found at i:42576041 original size:27 final size:25
Alignment explanation
Indices: 42575978--42576042 Score: 85
Period size: 27 Copynumber: 2.4 Consensus size: 25
42575968 AATCAAAAGG
42575978 AAAATAAGAATAAAATAAATAAAATA
1 AAAATAA-AATAAAATAAATAAAATA
*
42576004 AAAATAAAAATAAGAATAAATAACATTA
1 AAAAT-AAAATAA-AATAAATAA-AATA
42576032 AAAATAAAATA
1 AAAATAAAATA
42576043 GGAGGATTCA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
26 10 0.29
27 17 0.49
28 8 0.23
ACGTcount: A:0.75, C:0.02, G:0.03, T:0.20
Consensus pattern (25 bp):
AAAATAAAATAAAATAAATAAAATA
Found at i:42583307 original size:25 final size:25
Alignment explanation
Indices: 42583278--42583325 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
42583268 TTATAATATG
* * *
42583278 AAAATGACCATTTTGCCCCTAGGTA
1 AAAATAACCATTATACCCCTAGGTA
42583303 AAAATAACCATTATACCCCTAGG
1 AAAATAACCATTATACCCCTAGG
42583326 GTTTAGATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.38, C:0.25, G:0.12, T:0.25
Consensus pattern (25 bp):
AAAATAACCATTATACCCCTAGGTA
Found at i:42583409 original size:11 final size:11
Alignment explanation
Indices: 42583373--42583428 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
42583363 CATGGTATGT
42583373 ATGATATGCAC
1 ATGATATGCAC
* *
42583384 ATGACATG--T
1 ATGATATGCAC
42583393 ATGATATGCAC
1 ATGATATGCAC
*
42583404 ATGATATG--T
1 ATGATATGCAC
42583413 ATGATATGCAC
1 ATGATATGCAC
42583424 ATGAT
1 ATGAT
42583429 GTATTCATAA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:42583428 original size:20 final size:20
Alignment explanation
Indices: 42583362--42583428 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
42583352 ATTTTGATAA
*
42583362 ACATGGTATGTATGATATGC
1 ACATGATATGTATGATATGC
*
42583382 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
42583402 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
42583422 ACATGAT
1 ACATGAT
42583429 GTATTCATAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.33
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:42583505 original size:24 final size:24
Alignment explanation
Indices: 42583477--42583645 Score: 250
Period size: 24 Copynumber: 7.0 Consensus size: 24
42583467 GGAGGAAGTG
42583477 CAAAAGGGCTTATGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
* *
42583501 TAAAAGGGCTTATGCCCCAGTTGT
1 CAAAAGGGCTTATGCCCCAGTTAT
42583525 CAAAAGGGCTTATGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
42583549 CAAAAGGGCTTATGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
42583573 CAAAAGGGCTTATGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
* * *
42583597 TAAAAGAGCTTTTGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
* *
42583621 TAAAAGAGGC-TAGGCCTCCAGTTAT
1 CAAAAG-GGCTTATGCC-CCAGTTAT
42583646 ATGATAAAGC
Statistics
Matches: 133, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
24 123 0.92
25 10 0.08
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (24 bp):
CAAAAGGGCTTATGCCCCAGTTAT
Found at i:42584837 original size:46 final size:48
Alignment explanation
Indices: 42584718--42584837 Score: 147
Period size: 48 Copynumber: 2.5 Consensus size: 48
42584708 TGTCTTCGAC
** * * *
42584718 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATATATAAT
1 ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCATATAAATATAAT
* *
42584766 ATGGGCTTACATGGCTCATTCCTGTCTCCAAAGCCATA-AAAT-TGAT
1 ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCATATAAATATAAT
42584812 ATGGACTTACATGGCTCACTT-CTGTC
1 ATGGACTTACATGGCTCA-TTCCTGTC
42584838 CTGTCCTGTC
Statistics
Matches: 63, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
46 25 0.40
47 5 0.08
48 33 0.52
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.34
Consensus pattern (48 bp):
ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCATATAAATATAAT
Found at i:42588561 original size:79 final size:81
Alignment explanation
Indices: 42588425--42588607 Score: 232
Period size: 79 Copynumber: 2.3 Consensus size: 81
42588415 TCGAATGATG
* *
42588425 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
42588489 TGTGCGAGTTACTA-A
66 TGTGCGAGTTACTATA
* * * **
42588504 TTCCGGGCTAAG-CCCGAAGGCATTGGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
42588566 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGTTACTATA
* *
42588584 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
42588608 TGAACGAGTA
Statistics
Matches: 90, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 1 0.01
79 59 0.66
80 30 0.33
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGTTACTATA
Found at i:42588623 original size:40 final size:40
Alignment explanation
Indices: 42588426--42588609 Score: 216
Period size: 40 Copynumber: 4.6 Consensus size: 40
42588416 CGAATGATGT
* * * *
42588426 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* *
42588466 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
*
42588506 CCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
42588544 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
42588585 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
42588610 AACGAGTAGC
Statistics
Matches: 126, Mismatches: 11, Indels: 14
0.83 0.07 0.09
Matches are distributed among these distances:
39 35 0.28
40 81 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:42588631 original size:79 final size:79
Alignment explanation
Indices: 42588478--42588632 Score: 208
Period size: 79 Copynumber: 2.0 Consensus size: 79
42588468 GGACTAAGAT
* **
42588478 CCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
42588543 ATCCGGGTTAAGTC
66 ATCCGGGTTAAGTC
* *
42588557 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGTTACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTTA-C
*
42588620 TATATCC-GGTTAA
63 TAAATCCGGGTTAA
42588633 ATTCTGAAGG
Statistics
Matches: 67, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
78 2 0.03
79 41 0.61
80 24 0.36
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
ATCCGGGTTAAGTC
Found at i:42590629 original size:13 final size:13
Alignment explanation
Indices: 42590607--42590639 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
42590597 AAGGGTTTGT
42590607 TTAT-TAAACTAA
1 TTATCTAAACTAA
42590619 TTATCTAAACTAA
1 TTATCTAAACTAA
*
42590632 TTAACTAA
1 TTATCTAA
42590640 TTTAATCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.39
Consensus pattern (13 bp):
TTATCTAAACTAA
Found at i:42595523 original size:30 final size:30
Alignment explanation
Indices: 42595487--42595545 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
42595477 GCACCTACGT
*
42595487 AAGTCACAAAAATTTCTTAAAATTTTTGAA
1 AAGTCACAAAAATTTCTTAAAACTTTTGAA
42595517 AAGTCACAAAAATTTCTTAAAACTTTTGA
1 AAGTCACAAAAATTTCTTAAAACTTTTGA
42595546 TTAAGTCCCG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.46, C:0.12, G:0.07, T:0.36
Consensus pattern (30 bp):
AAGTCACAAAAATTTCTTAAAACTTTTGAA
Found at i:42602360 original size:54 final size:53
Alignment explanation
Indices: 42602244--42602666 Score: 329
Period size: 54 Copynumber: 8.0 Consensus size: 53
42602234 TTACTCGGGA
* * * * * *
42602244 ACCTTTTCCTTTTTGAACTTACCATTGCCATGTCTTGACATGGTCTTACGTGG
1 ACCTTTGCCTTATAGAACTCACCAATGCCATGTCTTGACATGGTCTTACATGG
* *
42602297 TATCC-TTGCCTTAT-GAACTCACCAATGCCATGCCTTTGGCATGGTCTTACATAGG
1 -A-CCTTTGCCTTATAGAACTCACCAATGCCATGTC-TTGACATGGTCTTACAT-GG
*
42602352 ACCTTTGCCTTATAGTAACTCATCAATGCCATGTCTTGACATGGTCTTACAT-G
1 ACCTTTGCCTTATAG-AACTCACCAATGCCATGTCTTGACATGGTCTTACATGG
* * * * *
42602405 ATTTCC-TTGCCTTATAGAACTTATCAATTCCATGCCTTGGCATGGTCTTACAT-G
1 A---CCTTTGCCTTATAGAACTCACCAATGCCATGTCTTGACATGGTCTTACATGG
* * * ***
42602459 A--TAT--CTT-T--ATCTTACCAAATGCCATGTTCCAAACATGGTCTTACATGG
1 ACCTTTGCCTTATAGAACTCACC-AATGCCATG-TCTTGACATGGTCTTACATGG
* *
42602507 TATCC-TTGTCTTAT-GAACTCACCAATGCCTTGTCTTGACATGGTCTTACATAGG
1 -A-CCTTTGCCTTATAGAACTCACCAATGCCATGTCTTGACATGGTCTTACAT-GG
*
42602561 ACCTTTGCCTTATAGTAACTCATCAATGCCATGTCTTGACATGGTCTT-CAT-G
1 ACCTTTGCCTTATAG-AACTCACCAATGCCATGTCTTGACATGGTCTTACATGG
** * * * *
42602613 ATTTTCTTGCCTTATAGAACTTATCAATGCCATGCCTTGGCATGGTCTTACATG
1 A-CCT-TTGCCTTATAGAACTCACCAATGCCATGTCTTGACATGGTCTTACATG
42602667 ATATCCTTAT
Statistics
Matches: 302, Mismatches: 38, Indels: 57
0.76 0.10 0.14
Matches are distributed among these distances:
45 6 0.02
46 8 0.03
47 15 0.05
48 4 0.01
49 1 0.00
50 1 0.00
51 1 0.00
52 4 0.01
53 79 0.26
54 96 0.32
55 68 0.23
56 19 0.06
ACGTcount: A:0.23, C:0.24, G:0.16, T:0.37
Consensus pattern (53 bp):
ACCTTTGCCTTATAGAACTCACCAATGCCATGTCTTGACATGGTCTTACATGG
Found at i:42602664 original size:208 final size:210
Alignment explanation
Indices: 42602281--42602727 Score: 799
Period size: 208 Copynumber: 2.1 Consensus size: 210
42602271 CCATGTCTTG
* * *
42602281 ACATGGTCTTACGTGGTATCCTTGCCTTATGAACTCACCAATGCCATGCCTTTGGCATGGTCTTA
1 ACATGGTCTTACATGGTATCCTTGTCTTATGAACTCACCAATGCCATGCCTTTGACATGGTCTTA
42602346 CATAGGACCTTTGCCTTATAGTAACTCATCAATGCCATGTCTTGACATGGTCTTACATGATTTCC
66 CATAGGACCTTTGCCTTATAGTAACTCATCAATGCCATGTCTTGACATGGTCTTACATGATTTCC
* *
42602411 TTGCCTTATAGAACTTATCAATTCCATGCCTTGGCATGGTCTTACATGATATCTTTATCTTACCA
131 TTGCCTTATAGAACTTATCAATGCCATGCCTTGGCATGGTCTTACATGATATCCTTATCTTACCA
42602476 AATGCCATGTTCCAA
196 AATGCCATGTTCCAA
* *
42602491 ACATGGTCTTACATGGTATCCTTGTCTTATGAACTCACCAATGCCTTGTC-TTGACATGGTCTTA
1 ACATGGTCTTACATGGTATCCTTGTCTTATGAACTCACCAATGCCATGCCTTTGACATGGTCTTA
*
42602555 CATAGGACCTTTGCCTTATAGTAACTCATCAATGCCATGTCTTGACATGGTCTT-CATGATTTTC
66 CATAGGACCTTTGCCTTATAGTAACTCATCAATGCCATGTCTTGACATGGTCTTACATGATTTCC
42602619 TTGCCTTATAGAACTTATCAATGCCATGCCTTGGCATGGTCTTACATGATATCCTTATCTTACCA
131 TTGCCTTATAGAACTTATCAATGCCATGCCTTGGCATGGTCTTACATGATATCCTTATCTTACCA
42602684 AATGCCATGTTCCAA
196 AATGCCATGTTCCAA
*
42602699 ACATGGTATTACATGGTATCCTTGTCTTA
1 ACATGGTCTTACATGGTATCCTTGTCTTA
42602728 CCAAATGTCA
Statistics
Matches: 228, Mismatches: 9, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
208 115 0.50
209 67 0.29
210 46 0.20
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.36
Consensus pattern (210 bp):
ACATGGTCTTACATGGTATCCTTGTCTTATGAACTCACCAATGCCATGCCTTTGACATGGTCTTA
CATAGGACCTTTGCCTTATAGTAACTCATCAATGCCATGTCTTGACATGGTCTTACATGATTTCC
TTGCCTTATAGAACTTATCAATGCCATGCCTTGGCATGGTCTTACATGATATCCTTATCTTACCA
AATGCCATGTTCCAA
Found at i:42602711 original size:47 final size:47
Alignment explanation
Indices: 42602653--42602821 Score: 293
Period size: 47 Copynumber: 3.6 Consensus size: 47
42602643 CATGCCTTGG
* *
42602653 CATGGTCTTACATGATATCCTTATCTTACCAAATGCCATGTTCCAAA
1 CATGGTCTTACATGGTATCCTTGTCTTACCAAATGCCATGTTCCAAA
* *
42602700 CATGGTATTACATGGTATCCTTGTCTTACCAAATGTCATGTTCCAAA
1 CATGGTCTTACATGGTATCCTTGTCTTACCAAATGCCATGTTCCAAA
42602747 CATGGTCTTACATGGTATCCTTGTCTTACCAAATGCCATGTTCCAAA
1 CATGGTCTTACATGGTATCCTTGTCTTACCAAATGCCATGTTCCAAA
*
42602794 CATAGTCTTACATGGTATCCTTGTCTTA
1 CATGGTCTTACATGGTATCCTTGTCTTA
42602822 GTGCCAATGC
Statistics
Matches: 115, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 115 1.00
ACGTcount: A:0.27, C:0.24, G:0.14, T:0.36
Consensus pattern (47 bp):
CATGGTCTTACATGGTATCCTTGTCTTACCAAATGCCATGTTCCAAA
Found at i:42603025 original size:44 final size:44
Alignment explanation
Indices: 42602960--42603044 Score: 109
Period size: 44 Copynumber: 1.9 Consensus size: 44
42602950 ATCCTTAACC
* *
42602960 ATCAATTCCTCCTTAAATGCCATGTTATGAA-CATGGACTTTTCT
1 ATCAATTCCTCCTTAAATGCCATGGTA-CAACCATGGACTTTTCT
* * *
42603004 ATCATTTCTTCCTTAATTGCCATGGTACAACCATGGACTTT
1 ATCAATTCCTCCTTAAATGCCATGGTACAACCATGGACTTT
42603045 GAGATATCAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
43 2 0.06
44 33 0.94
ACGTcount: A:0.26, C:0.24, G:0.12, T:0.39
Consensus pattern (44 bp):
ATCAATTCCTCCTTAAATGCCATGGTACAACCATGGACTTTTCT
Found at i:42604816 original size:15 final size:15
Alignment explanation
Indices: 42604796--42604827 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
42604786 GGTAGAAAAT
*
42604796 GAAAGTTTGTTCATA
1 GAAAGTCTGTTCATA
42604811 GAAAGTCTGTTCATA
1 GAAAGTCTGTTCATA
42604826 GA
1 GA
42604828 TAAACAACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.34, C:0.09, G:0.22, T:0.34
Consensus pattern (15 bp):
GAAAGTCTGTTCATA
Found at i:42613729 original size:78 final size:78
Alignment explanation
Indices: 42613600--42613745 Score: 283
Period size: 78 Copynumber: 1.9 Consensus size: 78
42613590 CATCCCGGTG
*
42613600 AATGTAGGATGAATAACTAGGCTTGCTTCAAATGTGGCTCCCAAGATCACTTTATCTGAGACTGC
1 AATGTAGGATGAATAACTAGGCTTGCTTCAAATGTGGCTCCCAAGATCACTTTATCTGAGACTAC
42613665 CCTAAAATGGCTA
66 CCTAAAATGGCTA
42613678 AATGTAGGATGAATAACTAGGCTTGCTTCAAATGTGGCTCCCAAGATCACTTTATCTGAGACTAC
1 AATGTAGGATGAATAACTAGGCTTGCTTCAAATGTGGCTCCCAAGATCACTTTATCTGAGACTAC
42613743 CCT
66 CCT
42613746 GAAACGACTA
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
78 67 1.00
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.29
Consensus pattern (78 bp):
AATGTAGGATGAATAACTAGGCTTGCTTCAAATGTGGCTCCCAAGATCACTTTATCTGAGACTAC
CCTAAAATGGCTA
Found at i:42622108 original size:40 final size:40
Alignment explanation
Indices: 42621870--42622094 Score: 344
Period size: 40 Copynumber: 5.6 Consensus size: 40
42621860 GGATTGATAC
* *
42621870 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
* * *
42621909 TCTGGGCTAAGTCCCGAAGGCATTTGTACGAGTTACTATAT
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
42621950 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATCA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
* *
42621990 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTTACTATCA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
* *
42622030 CCAGGCTAAGTCCCAAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
42622070 CCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
42622095 AGCTAGTAGC
Statistics
Matches: 168, Mismatches: 16, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
40 167 0.99
41 1 0.01
ACGTcount: A:0.24, C:0.24, G:0.26, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:42629339 original size:85 final size:85
Alignment explanation
Indices: 42629196--42629374 Score: 358
Period size: 85 Copynumber: 2.1 Consensus size: 85
42629186 GGCCGGCCAT
42629196 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
42629261 GTAAGGATTAATAAAATAAA
66 GTAAGGATTAATAAAATAAA
42629281 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
42629346 GTAAGGATTAATAAAATAAA
66 GTAAGGATTAATAAAATAAA
42629366 GAGCATGGG
1 GAGCATGGG
42629375 CAATAAAATA
Statistics
Matches: 94, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
85 94 1.00
ACGTcount: A:0.38, C:0.08, G:0.27, T:0.26
Consensus pattern (85 bp):
GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
GTAAGGATTAATAAAATAAA
Found at i:42630641 original size:39 final size:40
Alignment explanation
Indices: 42630540--42630724 Score: 191
Period size: 40 Copynumber: 4.7 Consensus size: 40
42630530 TCGAATGATG
* * * *
42630540 TCCGGACTAAGTCCCGAAGGC-TTTGTGCTAAGTGAC-CAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAT
**
42630579 ATCCGAACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAT
* * *
42630620 TCCGAGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
*
42630659 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
42630698 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
42630725 AACGAGTAGC
Statistics
Matches: 125, Mismatches: 14, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
39 35 0.28
40 80 0.64
41 10 0.08
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
Found at i:42630746 original size:79 final size:79
Alignment explanation
Indices: 42630593--42630757 Score: 192
Period size: 79 Copynumber: 2.1 Consensus size: 79
42630583 GAACTAAGAT
* **
42630593 CCGAAGGCATTTGTGCGAGTTACTAATTCCGAGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGTTACTAATACCGAGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
*
42630658 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* * *
42630672 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGTTACTAAT-ACCGAGCTAAG-CCCGAAGGCATTGGAACGAGTTA-C
* * *
42630735 TATAT-CTGGTTAAATT
63 TAAATCCGGGTTAAATC
42630751 CCGAAGG
1 CCGAAGG
42630758 TACGTGATTC
Statistics
Matches: 73, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
78 2 0.03
79 49 0.67
80 22 0.30
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGTTACTAATACCGAGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:42633332 original size:40 final size:40
Alignment explanation
Indices: 42633094--42633318 Score: 353
Period size: 40 Copynumber: 5.6 Consensus size: 40
42633084 AGATTGATAC
* *
42633094 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
* *
42633133 TCCGGGCTAAGTCCCGAAGGCATTTGTACGAGTTACTATAT
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
42633174 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATCA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
* *
42633214 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTTACTATCA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
* *
42633254 CCAGGCTAAGTCCCAAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
42633294 CCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
42633319 AGCTAGTAGC
Statistics
Matches: 170, Mismatches: 14, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
40 169 0.99
41 1 0.01
ACGTcount: A:0.24, C:0.24, G:0.26, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:42637506 original size:20 final size:20
Alignment explanation
Indices: 42637478--42637527 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
42637468 TGGAGCAGGA
*
42637478 ATATCGATACCTTAGGAAAT
1 ATATCGATACCTTAAGAAAT
*
42637498 ATATTGATACCTTAAGAAA-
1 ATATCGATACCTTAAGAAAT
42637517 AGTATCGATAC
1 A-TATCGATAC
42637528 GAGATCGATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 1 0.04
20 25 0.96
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (20 bp):
ATATCGATACCTTAAGAAAT
Found at i:42640803 original size:16 final size:16
Alignment explanation
Indices: 42640784--42640831 Score: 62
Period size: 16 Copynumber: 3.0 Consensus size: 16
42640774 AATAAAATTT
42640784 TTTTAAAAGTAT-TAAA
1 TTTTAAAA-TATATAAA
42640800 TTTTAAAATATATAAA
1 TTTTAAAATATATAAA
* *
42640816 TTATAAAAAATATAAA
1 TTTTAAAATATATAAA
42640832 AATCATAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 3 0.10
16 26 0.90
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (16 bp):
TTTTAAAATATATAAA
Found at i:42640827 original size:18 final size:18
Alignment explanation
Indices: 42640804--42640843 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
42640794 ATTAAATTTT
* *
42640804 AAAATATATAAATTATAA
1 AAAATATAAAAATCATAA
42640822 AAAATATAAAAATCATAA
1 AAAATATAAAAATCATAA
42640840 AAAA
1 AAAA
42640844 AATTATAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (18 bp):
AAAATATAAAAATCATAA
Found at i:42640854 original size:9 final size:9
Alignment explanation
Indices: 42640804--42640895 Score: 51
Period size: 9 Copynumber: 9.3 Consensus size: 9
42640794 ATTAAATTTT
42640804 AAAA-TATA
1 AAAATTATA
*
42640812 TAAATTATA
1 AAAATTATA
*
42640821 AAAAATATA
1 AAAATTATA
*
42640830 AAAATCATAAAA
1 AAAAT--T-ATA
42640842 AAAATTATAAAA
1 AAAATTAT---A
*
42640854 AAAATTGTA
1 AAAATTATA
42640863 AAAATTTATA
1 AAAA-TTATA
*
42640873 AAAAGTTTAAA
1 AAAA--TTATA
42640884 AAAATTATA
1 AAAATTATA
42640893 AAA
1 AAA
42640896 GGCATTTTAA
Statistics
Matches: 65, Mismatches: 10, Indels: 17
0.71 0.11 0.18
Matches are distributed among these distances:
8 3 0.05
9 28 0.43
10 9 0.14
11 10 0.15
12 15 0.23
ACGTcount: A:0.68, C:0.01, G:0.02, T:0.28
Consensus pattern (9 bp):
AAAATTATA
Found at i:42640859 original size:12 final size:12
Alignment explanation
Indices: 42640829--42640866 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
42640819 TAAAAAATAT
*
42640829 AAAAATCATAAA
1 AAAAATTATAAA
42640841 AAAAATTATAAA
1 AAAAATTATAAA
*
42640853 AAAAATTGTAAA
1 AAAAATTATAAA
42640865 AA
1 AA
42640867 TTTATAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.21
Consensus pattern (12 bp):
AAAAATTATAAA
Found at i:42640865 original size:42 final size:42
Alignment explanation
Indices: 42640813--42640895 Score: 107
Period size: 42 Copynumber: 2.0 Consensus size: 42
42640803 TAAAATATAT
42640813 AAATTATAAAAA-ATATAAAAA-TCATAAAAAAAATTATAAAAA
1 AAATTATAAAAATATATAAAAAGT--TAAAAAAAATTATAAAAA
* * *
42640855 AAATTGTAAAAATTTATAAAAAGTTTAAAAAAATTATAAAA
1 AAATTATAAAAATATATAAAAAGTTAAAAAAAATTATAAAA
42640896 GGCATTTTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
42 27 0.75
43 8 0.22
44 1 0.03
ACGTcount: A:0.69, C:0.01, G:0.02, T:0.28
Consensus pattern (42 bp):
AAATTATAAAAATATATAAAAAGTTAAAAAAAATTATAAAAA
Found at i:42641094 original size:9 final size:9
Alignment explanation
Indices: 42641080--42641206 Score: 57
Period size: 9 Copynumber: 13.2 Consensus size: 9
42641070 TTTTGGTAGA
42641080 ATAATTTTT
1 ATAATTTTT
42641089 ATAATTTTT
1 ATAATTTTT
*
42641098 TTACATTTTTTT
1 ATA-A--TTTTT
42641110 ATAATTTTCT
1 ATAATTTT-T
*
42641120 -TACGA-CTTT
1 ATA--ATTTTT
*
42641129 ATAAAATTTT
1 AT-AATTTTT
42641139 ATAATTCTTT
1 ATAATT-TTT
42641149 -TAGGATTTTT
1 ATA--ATTTTT
42641159 ATAATTTTT
1 ATAATTTTT
*
42641168 TTAAATTTTT
1 AT-AATTTTT
*
42641178 AATAAATTTT
1 -ATAATTTTT
42641188 A-AATTTTT
1 ATAATTTTT
42641196 -TAAATTTTT
1 AT-AATTTTT
42641205 AT
1 AT
42641207 TAAAATTTAA
Statistics
Matches: 91, Mismatches: 9, Indels: 35
0.67 0.07 0.26
Matches are distributed among these distances:
8 6 0.07
9 39 0.43
10 30 0.33
11 9 0.10
12 7 0.08
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.61
Consensus pattern (9 bp):
ATAATTTTT
Found at i:42641100 original size:11 final size:11
Alignment explanation
Indices: 42641084--42641117 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
42641074 GGTAGAATAA
42641084 TTTTTATAATT
1 TTTTTATAATT
*
42641095 TTTTTA-CATT
1 TTTTTATAATT
42641105 TTTTTATAATT
1 TTTTTATAATT
42641116 TT
1 TT
42641118 CTTACGACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (11 bp):
TTTTTATAATT
Found at i:42641183 original size:11 final size:10
Alignment explanation
Indices: 42641126--42641206 Score: 59
Period size: 9 Copynumber: 8.5 Consensus size: 10
42641116 TTCTTACGAC
*
42641126 TTTATAAAAT
1 TTTATAAATT
42641136 TTTAT-AATT
1 TTTATAAATT
*
42641145 CTTT-TAGGATT
1 -TTTATA-AATT
42641156 TTTAT-AATT
1 TTTATAAATT
*
42641165 TTTTTAAATT
1 TTTATAAATT
42641175 TTTAATAAA--
1 TTT-ATAAATT
42641184 TTT-TAAATT
1 TTTATAAATT
42641193 TTT-TAAATT
1 TTTATAAATT
42641202 TTTAT
1 TTTAT
42641207 TAAAATTTAA
Statistics
Matches: 57, Mismatches: 5, Indels: 18
0.71 0.06 0.22
Matches are distributed among these distances:
7 4 0.07
9 26 0.46
10 19 0.33
11 8 0.14
ACGTcount: A:0.35, C:0.01, G:0.02, T:0.62
Consensus pattern (10 bp):
TTTATAAATT
Found at i:42641194 original size:27 final size:28
Alignment explanation
Indices: 42641155--42641216 Score: 90
Period size: 27 Copynumber: 2.2 Consensus size: 28
42641145 CTTTTAGGAT
42641155 TTTTATAATTTTTTTAAATTTTTAATAAA
1 TTTTA-AATTTTTTTAAATTTTTAATAAA
*
42641184 TTTTAAA-TTTTTTAAATTTTTATTAAA
1 TTTTAAATTTTTTTAAATTTTTAATAAA
*
42641211 ATTTAA
1 TTTTAA
42641217 TCATTTTTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
27 24 0.77
28 2 0.06
29 5 0.16
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (28 bp):
TTTTAAATTTTTTTAAATTTTTAATAAA
Found at i:42644046 original size:22 final size:22
Alignment explanation
Indices: 42644021--42644070 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
42644011 CATTTATGTG
*
42644021 TTTAAATTTCTATT-TTAATTAT
1 TTTAAATTT-TATTATTAATTAA
*
42644043 TTTATATTTTATTATTAATTAA
1 TTTAAATTTTATTATTAATTAA
42644065 TTTAAA
1 TTTAAA
42644071 ATAATAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 4 0.17
22 20 0.83
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (22 bp):
TTTAAATTTTATTATTAATTAA
Found at i:42645701 original size:3 final size:3
Alignment explanation
Indices: 42645693--42645739 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
42645683 CATAAATCAA
42645693 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
42645740 AAGACAAGTG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:42647678 original size:27 final size:27
Alignment explanation
Indices: 42647647--42647700 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
42647637 ATGTTTATAT
* *
42647647 TAAATAAA-AAACTATTTAATTATAAAA
1 TAAATAAATAAA-AATTTAATAATAAAA
42647674 TAAATAAATAAAAATTTAATAATAAAA
1 TAAATAAATAAAAATTTAATAATAAAA
42647701 AGGTTATATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 21 0.88
28 3 0.12
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (27 bp):
TAAATAAATAAAAATTTAATAATAAAA
Found at i:42649546 original size:12 final size:12
Alignment explanation
Indices: 42649527--42649562 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
42649517 GGTCCAGCTG
42649527 TATTATTTTTTA
1 TATTATTTTTTA
*
42649539 TTTTATTTTTTA
1 TATTATTTTTTA
*
42649551 TATAATTTTTTA
1 TATTATTTTTTA
42649563 AAAAATATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (12 bp):
TATTATTTTTTA
Found at i:42649796 original size:23 final size:23
Alignment explanation
Indices: 42649770--42649820 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
42649760 CAAAATAGTG
*
42649770 AAAAAAACAACAATAAAACAATA
1 AAAAAAACAACAAGAAAACAATA
* * *
42649793 AAAAGAACAACAAGAAAGCAGTA
1 AAAAAAACAACAAGAAAACAATA
42649816 AAAAA
1 AAAAA
42649821 TTATTTTTTT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.75, C:0.12, G:0.08, T:0.06
Consensus pattern (23 bp):
AAAAAAACAACAAGAAAACAATA
Found at i:42654390 original size:45 final size:44
Alignment explanation
Indices: 42654321--42654457 Score: 150
Period size: 44 Copynumber: 3.1 Consensus size: 44
42654311 ATTAACTTAA
* * * * * *
42654321 GAAAAGAGAAAGACCCTGGTTGAAAGATA-TCATGGCATTTTACCC
1 GAAATGAGAAAGACCCTAGTTGAAAGATACT-ATGACA-ATAAACC
* *
42654366 GAAATGAGAAAGACCATAGTTGAAAGATACTATGACAATAAACT
1 GAAATGAGAAAGACCCTAGTTGAAAGATACTATGACAATAAACC
* * *
42654410 GAAATGAGGAAGACCCTAGTTGAAAGATACTATGACACTAAATC
1 GAAATGAGAAAGACCCTAGTTGAAAGATACTATGACAATAAACC
42654454 GAAA
1 GAAA
42654458 AATAAACAAG
Statistics
Matches: 78, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
44 46 0.59
45 31 0.40
46 1 0.01
ACGTcount: A:0.45, C:0.15, G:0.20, T:0.20
Consensus pattern (44 bp):
GAAATGAGAAAGACCCTAGTTGAAAGATACTATGACAATAAACC
Found at i:42654430 original size:44 final size:44
Alignment explanation
Indices: 42654366--42654534 Score: 157
Period size: 44 Copynumber: 3.8 Consensus size: 44
42654356 CATTTTACCC
42654366 GAAATGAGAAAGACCATAGTTGAAAGATACTATGACAATAAACT
1 GAAATGAGAAAGACCATAGTTGAAAGATACTATGACAATAAACT
* * *
42654410 GAAATGAGGAAGACCCTAGTTGAAAGATACTATGACACTAAA-T
1 GAAATGAGAAAGACCATAGTTGAAAGATACTATGACAATAAACT
* * * * * *
42654453 CGAAAAAT-AAACAAGACCATAGTTGAAACATGCTATGGCATTAAATTT
1 -G--AAATGAGA-AAGACCATAGTTGAAAGATACTATGACAATAAA-CT
*
42654501 G-AATGAATGAAA-ACCATAGTTGAAAGATATTATG
1 GAAATG-A-GAAAGACCATAGTTGAAAGATACTATG
42654535 GCACCACTTC
Statistics
Matches: 102, Mismatches: 14, Indels: 17
0.77 0.11 0.13
Matches are distributed among these distances:
43 1 0.01
44 43 0.42
45 20 0.20
46 35 0.34
47 2 0.02
48 1 0.01
ACGTcount: A:0.47, C:0.12, G:0.18, T:0.23
Consensus pattern (44 bp):
GAAATGAGAAAGACCATAGTTGAAAGATACTATGACAATAAACT
Found at i:42656212 original size:12 final size:12
Alignment explanation
Indices: 42656195--42656220 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
42656185 TAATAAACCT
42656195 TAATCGAATTCA
1 TAATCGAATTCA
42656207 TAATCGAATTCA
1 TAATCGAATTCA
42656219 TA
1 TA
42656221 CTTGTGTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.35
Consensus pattern (12 bp):
TAATCGAATTCA
Found at i:42657887 original size:48 final size:48
Alignment explanation
Indices: 42657835--42658108 Score: 271
Period size: 48 Copynumber: 5.7 Consensus size: 48
42657825 TAATGTGTGC
* * *
42657835 GCTAGTGTAAGACTATGTTTGGGACATGGCATCGACATTGAAATGAGA
1 GCTAGTGTAAGACCATGTCTAGGACATGGCATCGACATTGAAATGAGA
* * * * * * *
42657883 GCTAGTTTAAGACCATGTCTAGGACATGGCATTGGCCTCGACATGTGA
1 GCTAGTGTAAGACCATGTCTAGGACATGGCATCGACATTGAAATGAGA
* * * * * * * *
42657931 GCCAGTGTAAAACCATATTTAGAATATGGCATCGACAATGTAATGAGA
1 GCTAGTGTAAGACCATGTCTAGGACATGGCATCGACATTGAAATGAGA
* * * * *
42657979 GCCAGTGTAAGACCATGTCT-GAGACATGGCATTGGCATTGAGACGAGA
1 GCTAGTGTAAGACCATGTCTAG-GACATGGCATCGACATTGAAATGAGA
* * * * *
42658027 GCTAGTGTAAGACCATGTTTGGGACACGGCATCGACATTGAGACGAGA
1 GCTAGTGTAAGACCATGTCTAGGACATGGCATCGACATTGAAATGAGA
*
42658075 GCTAGTGTAAGACCATGTCTAGGACATGACATCG
1 GCTAGTGTAAGACCATGTCTAGGACATGGCATCG
42658109 GCCTCAACAT
Statistics
Matches: 179, Mismatches: 45, Indels: 4
0.79 0.20 0.02
Matches are distributed among these distances:
47 1 0.01
48 177 0.99
49 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.28, T:0.24
Consensus pattern (48 bp):
GCTAGTGTAAGACCATGTCTAGGACATGGCATCGACATTGAAATGAGA
Found at i:42657976 original size:96 final size:95
Alignment explanation
Indices: 42657838--42658161 Score: 380
Period size: 96 Copynumber: 3.4 Consensus size: 95
42657828 TGTGTGCGCT
* * * *
42657838 AGTGTAAGACTATGTTTGGGACATGGCATCGACATTGAAATGAGAGCTAGTTTAAGACCATGTCT
1 AGTGTAAGACCATGTTTGGAACATGGCATCGACAATG-AATGAGAGCTAGTGTAAGACCATGTCT
42657903 AGGACATGGCATTGGCCTCGACATGTGAGCC
65 AGGACATGGCATTGGCCTCGACATGTGAGCC
* * * * *
42657934 AGTGTAAAACCATATTTAGAATATGGCATCGACAATGTAATGAGAGCCAGTGTAAGACCATGTCT
1 AGTGTAAGACCATGTTTGGAACATGGCATCGACAATG-AATGAGAGCTAGTGTAAGACCATGTCT
* * * * * *
42657999 -GAGACATGGCATTGGCATTGAGACGAGAGCT
65 AG-GACATGGCATTGGCCTCGACATGTGAGCC
* * * *
42658030 AGTGTAAGACCATGTTTGGGACACGGCATCGACATTGAGACGAGAGCTAGTGTAAGACCATGTCT
1 AGTGTAAGACCATGTTTGGAACATGGCATCGACAATGA-ATGAGAGCTAGTGTAAGACCATGTCT
* * * *
42658095 AGGACATGACATCGGCCTCAACATGTGAACC
65 AGGACATGGCATTGGCCTCGACATGTGAGCC
* *
42658126 AATGTAAGACCATGTTTGGAACATGGCATCGGCAAT
1 AGTGTAAGACCATGTTTGGAACATGGCATCGACAAT
42658162 TCACCCTCTT
Statistics
Matches: 185, Mismatches: 40, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
95 2 0.01
96 182 0.98
97 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.27, T:0.24
Consensus pattern (95 bp):
AGTGTAAGACCATGTTTGGAACATGGCATCGACAATGAATGAGAGCTAGTGTAAGACCATGTCTA
GGACATGGCATTGGCCTCGACATGTGAGCC
Found at i:42658108 original size:144 final size:144
Alignment explanation
Indices: 42657838--42658108 Score: 317
Period size: 144 Copynumber: 1.9 Consensus size: 144
42657828 TGTGTGCGCT
* * * * *
42657838 AGTGTAAGACTATGTTTGGGACATGGCATCGACATTGAAATGAGAGCTAGTTTAAGACCATGTCT
1 AGTGTAAGACCATGTCTGAGACATGGCATCGACATTGAAACGAGAGCTAGTGTAAGACCATGTCT
* * * * * * * * *
42657903 AGGACATGGCATTGGCCTCGACATGTGAGCCAGTGTAAAACCATATTTAGAATATGGCATCGACA
66 AGGACACGGCATCGACATCGACACGAGAGCCAGTGTAAAACCATATCTAGAACATGACATCGACA
42657968 ATGTAATGAGAGCC
131 ATGTAATGAGAGCC
* * * *
42657982 AGTGTAAGACCATGTCTGAGACATGGCATTGGCATTGAGACGAGAGCTAGTGTAAGACCATGTTT
1 AGTGTAAGACCATGTCTGAGACATGGCATCGACATTGAAACGAGAGCTAGTGTAAGACCATGTCT
* * * * * * *
42658047 GGGACACGGCATCGACATTGAGACGAGAGCTAGTGTAAGACCATGTCTAGGACATGACATCG
66 AGGACACGGCATCGACATCGACACGAGAGCCAGTGTAAAACCATATCTAGAACATGACATCG
42658109 GCCTCAACAT
Statistics
Matches: 102, Mismatches: 25, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
144 102 1.00
ACGTcount: A:0.31, C:0.17, G:0.28, T:0.24
Consensus pattern (144 bp):
AGTGTAAGACCATGTCTGAGACATGGCATCGACATTGAAACGAGAGCTAGTGTAAGACCATGTCT
AGGACACGGCATCGACATCGACACGAGAGCCAGTGTAAAACCATATCTAGAACATGACATCGACA
ATGTAATGAGAGCC
Found at i:42665650 original size:48 final size:48
Alignment explanation
Indices: 42665580--42665927 Score: 305
Period size: 48 Copynumber: 7.3 Consensus size: 48
42665570 ATATTCATGC
* *
42665580 CATGACATCGACATTGATATGTGCGCTAGTGTAAGACCATGTCTGGGA
1 CATGGCATCGACATTGATATGTGAGCTAGTGTAAGACCATGTCTGGGA
* * * * * *
42665628 CATGGCATCGACCTCGACATGTGAGTTAGTGTAAGACCATGTTTGGAA
1 CATGGCATCGACATTGATATGTGAGCTAGTGTAAGACCATGTCTGGGA
* * * * * *
42665676 CATGGCATTGGCAATG-TAATGAGAGCCAATGTAAGACCATGTCTGGGA
1 CATGGCATCGACATTGAT-ATGTGAGCTAGTGTAAGACCATGTCTGGGA
* *
42665724 TATGGCATCGACATTGATATGTGCGCTAGTGTAAGACCATGTCTGGGA
1 CATGGCATCGACATTGATATGTGAGCTAGTGTAAGACCATGTCTGGGA
* *
42665772 CATGGCATCAGCCACA-T--TATGAGAGCCAGTGTAAGACCATGTCTGGGA
1 CATGGCATC-G--ACATTGATATGTGAGCTAGTGTAAGACCATGTCTGGGA
* * * * * * * *
42665820 TATGGCATAG-CATTGAGACGAGAACTAGTATAAGACCATGTTTGGGA
1 CATGGCATCGACATTGATATGTGAGCTAGTGTAAGACCATGTCTGGGA
* * * * *
42665867 CATGGCATC-AGCCTAT-ACATATGAGCTAGTGTAAGACCATGTTTGGAA
1 CATGGCATCGA-CAT-TGATATGTGAGCTAGTGTAAGACCATGTCTGGGA
*
42665915 CATGACATCGACA
1 CATGGCATCGACA
42665928 ATTCACCCTC
Statistics
Matches: 236, Mismatches: 52, Indels: 24
0.76 0.17 0.08
Matches are distributed among these distances:
44 2 0.01
45 1 0.00
47 33 0.14
48 192 0.81
49 4 0.02
50 1 0.00
51 3 0.01
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.25
Consensus pattern (48 bp):
CATGGCATCGACATTGATATGTGAGCTAGTGTAAGACCATGTCTGGGA
Found at i:42665754 original size:96 final size:96
Alignment explanation
Indices: 42665609--42665879 Score: 350
Period size: 96 Copynumber: 2.8 Consensus size: 96
42665599 TGTGCGCTAG
* * * *
42665609 TGTAAGACCATGTCTGGGACATGGCATCGACCTCGACATGTGAGTTAGTGTAAGACCATGTTTGG
1 TGTAAGACCATGTCTGGGATATGGCATCGACATTGACATGTGAGCTAGTGTAAGACCATGTTTGG
* * *
42665674 AACATGGCAT-TGGCA-ATGTAATGAGAGCCAA
66 GACATGGCATCAGCCACAT-T-ATGAGAGCCAA
* * *
42665705 TGTAAGACCATGTCTGGGATATGGCATCGACATTGATATGTGCGCTAGTGTAAGACCATGTCTGG
1 TGTAAGACCATGTCTGGGATATGGCATCGACATTGACATGTGAGCTAGTGTAAGACCATGTTTGG
*
42665770 GACATGGCATCAGCCACATTATGAGAGCCAG
66 GACATGGCATCAGCCACATTATGAGAGCCAA
* * * * * *
42665801 TGTAAGACCATGTCTGGGATATGGCATAG-CATTGAGACGAGAACTAGTATAAGACCATGTTTGG
1 TGTAAGACCATGTCTGGGATATGGCATCGACATTGACATGTGAGCTAGTGTAAGACCATGTTTGG
42665865 GACATGGCATCAGCC
66 GACATGGCATCAGCC
42665880 TATACATATG
Statistics
Matches: 154, Mismatches: 19, Indels: 5
0.87 0.11 0.03
Matches are distributed among these distances:
95 43 0.28
96 105 0.68
97 4 0.03
98 2 0.01
ACGTcount: A:0.29, C:0.18, G:0.28, T:0.25
Consensus pattern (96 bp):
TGTAAGACCATGTCTGGGATATGGCATCGACATTGACATGTGAGCTAGTGTAAGACCATGTTTGG
GACATGGCATCAGCCACATTATGAGAGCCAA
Found at i:42674448 original size:16 final size:17
Alignment explanation
Indices: 42674429--42674465 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
42674419 TTACATTTTG
42674429 TTTTAATAGTTA-AAAT
1 TTTTAATAGTTATAAAT
*
42674445 TTTT-GTAGTTATAAAT
1 TTTTAATAGTTATAAAT
42674461 TTTTA
1 TTTTA
42674466 TGTTTTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.57
Consensus pattern (17 bp):
TTTTAATAGTTATAAAT
Found at i:42674453 original size:15 final size:16
Alignment explanation
Indices: 42674435--42674464 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
42674425 TTTGTTTTAA
42674435 TAGTTA-AAATTTTTG
1 TAGTTATAAATTTTTG
42674450 TAGTTATAAATTTTT
1 TAGTTATAAATTTTT
42674465 ATGTTTTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (16 bp):
TAGTTATAAATTTTTG
Found at i:42686745 original size:93 final size:93
Alignment explanation
Indices: 42686635--42686806 Score: 299
Period size: 93 Copynumber: 1.8 Consensus size: 93
42686625 CGCCCATAAG
* *
42686635 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGGGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGGGAACTCGGACTCAACTCA
*
42686700 ATGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
* *
42686728 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGGGAACTCGGACTCAACTCA
42686793 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
42686807 TCAACCATCC
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGGGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:42686803 original size:46 final size:46
Alignment explanation
Indices: 42686628--42686803 Score: 207
Period size: 46 Copynumber: 3.8 Consensus size: 46
42686618 TGTAACCCGC
* * *
42686628 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* * *
42686674 CCATAAGGGAACTCGGACTCAACTCAATGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
42686724 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
42686767 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
42686804 TGCTCAACCA
Statistics
Matches: 109, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 62 0.57
47 28 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.29, G:0.22, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:42694380 original size:19 final size:19
Alignment explanation
Indices: 42694356--42694403 Score: 80
Period size: 19 Copynumber: 2.5 Consensus size: 19
42694346 AGTTAATAAC
42694356 AAATTTGATTACTA-TGAGT
1 AAATTTGATTAC-AGTGAGT
42694375 AAATTTGATTACAGTGAGT
1 AAATTTGATTACAGTGAGT
42694394 AAATTTGATT
1 AAATTTGATT
42694404 CTGATGGATG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
18 1 0.04
19 27 0.96
ACGTcount: A:0.38, C:0.04, G:0.17, T:0.42
Consensus pattern (19 bp):
AAATTTGATTACAGTGAGT
Found at i:42695699 original size:18 final size:17
Alignment explanation
Indices: 42695676--42695719 Score: 54
Period size: 19 Copynumber: 2.5 Consensus size: 17
42695666 TTTATATATT
42695676 TAAAAATATTAATTACT-A
1 TAAAAATATTAA-TA-TGA
42695694 TAAAAAATATTAATATGA
1 T-AAAAATATTAATATGA
42695712 TAAAAATA
1 TAAAAATA
42695720 ATTTCTAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 8 0.33
18 5 0.21
19 11 0.46
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.34
Consensus pattern (17 bp):
TAAAAATATTAATATGA
Found at i:42696262 original size:58 final size:58
Alignment explanation
Indices: 42696197--42696400 Score: 178
Period size: 54 Copynumber: 3.7 Consensus size: 58
42696187 AAAAAAATTC
* *
42696197 AAAATTTTTTGGTGCTGGCCTTGTAATGGCCGACACCAGACTACCAGTATTTAAAAAA
1 AAAATTTTTTGGTGCTGGCCTTCTAATGGCCGGCACCAGACTACCAGTATTTAAAAAA
* * * * *
42696255 AAAATTTTTTGGTCCTGGTCTACTAATGGTCGGCACCA-ACTA--TG-A---AAAAAA
1 AAAATTTTTTGGTGCTGGCCTTCTAATGGCCGGCACCAGACTACCAGTATTTAAAAAA
* * * * * *
42696306 ATCAAATTTTTTTGGTACTGGCCTTGTAATGGTCGGCACTAGAGTACCAATATTTAAAAAA
1 A--AAA-TTTTTTGGTGCTGGCCTTCTAATGGCCGGCACCAGACTACCAGTATTTAAAAAA
*
42696367 AAAA----TTGGTGCTGGTCTTCTAATGGCCGGCACCA
1 AAAATTTTTTGGTGCTGGCCTTCTAATGGCCGGCACCA
42696401 AGTATGAAAA
Statistics
Matches: 116, Mismatches: 20, Indels: 24
0.73 0.12 0.15
Matches are distributed among these distances:
51 7 0.06
53 3 0.03
54 55 0.47
55 4 0.03
57 4 0.03
58 33 0.28
59 3 0.03
61 7 0.06
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (58 bp):
AAAATTTTTTGGTGCTGGCCTTCTAATGGCCGGCACCAGACTACCAGTATTTAAAAAA
Found at i:42696420 original size:108 final size:109
Alignment explanation
Indices: 42696155--42696516 Score: 413
Period size: 108 Copynumber: 3.2 Consensus size: 109
42696145 TTTTTTTGTT
* * * *
42696155 CTGGCCTTCTAATTGCCGGC-CCCAGTATGAAAAAAAAAATTCAAAATTTTTTGGTGCTGGCCTT
1 CTGGTCTTCTAATGGCCGGCACCAAGTATG---AAAAAAATTCAAATTTTTTTGGTGCTGGCCTT
* * *
42696219 GTAATGGCCGACACCAGACTACCAGTATTTAAAAAAAAAATTTTTTGGTC
63 GTAATGGCCGGCACCAGAGTACCAATATTTAAAAAAAAAA---TTTGGTC
* * * * *
42696269 CTGGTCTACTAATGGTCGGCACCAACTATGAAAAAAAATCAAATTTTTTTGGTACTGGCCTTGTA
1 CTGGTCTTCTAATGGCCGGCACCAAGTATGAAAAAAATTCAAATTTTTTTGGTGCTGGCCTTGTA
* * *
42696334 ATGGTCGGCACTAGAGTACCAATATTTAAAAAAAAAA-TTGGTG
66 ATGGCCGGCACCAGAGTACCAATATTTAAAAAAAAAATTTGGTC
*
42696377 CTGGTCTTCTAATGGCCGGCACCAAGTATGAAAAAAATTCAAATTTTTTTGGTGTTGGCCTTGTA
1 CTGGTCTTCTAATGGCCGGCACCAAGTATGAAAAAAATTCAAATTTTTTTGGTGCTGGCCTTGTA
* *
42696442 ATGGCCAGCACCAGAGTGCCAATATGTAAAAAATAAAAAAAAAATTTGGTC
66 ATGGCCGGCACCAGAGTACCAATAT-T------TAAAAAAAAAATTTGGTC
* *
42696493 CTAGTCTTCGAATGGCCGGCACCA
1 CTGGTCTTCTAATGGCCGGCACCA
42696517 GGAACTTTTT
Statistics
Matches: 211, Mismatches: 28, Indels: 16
0.83 0.11 0.06
Matches are distributed among these distances:
108 85 0.40
109 1 0.00
112 64 0.30
114 16 0.08
115 18 0.09
116 27 0.13
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (109 bp):
CTGGTCTTCTAATGGCCGGCACCAAGTATGAAAAAAATTCAAATTTTTTTGGTGCTGGCCTTGTA
ATGGCCGGCACCAGAGTACCAATATTTAAAAAAAAAATTTGGTC
Found at i:42696429 original size:54 final size:54
Alignment explanation
Indices: 42696259--42696454 Score: 144
Period size: 54 Copynumber: 3.6 Consensus size: 54
42696249 AAAAAAAAAA
* * * * * *
42696259 TTTTTTGGTCCTGGTCTACTAATGGTCGGCACCAACTATGAAAAAAAATCAAAT
1 TTTTTTGGTGCTGGCCTTCTAATGGCCGGCACCAAGTATGAAAAAAATTCAAAT
* * * * ** * * * *
42696313 TTTTTTGGTACTGGCCTTGTAATGGTCGGCACTAGAGTA--CCAATATTTAAAAAA
1 TTTTTTGGTGCTGGCCTTCTAATGGCCGGCACCA-AGTATGAAAAAAATT-CAAAT
**** *
42696367 AAAATTGGTGCTGGTCTTCTAATGGCCGGCACCAAGTATGAAAAAAATTCAAAT
1 TTTTTTGGTGCTGGCCTTCTAATGGCCGGCACCAAGTATGAAAAAAATTCAAAT
* * *
42696421 TTTTTTGGTGTTGGCCTTGTAATGGCCAGCACCA
1 TTTTTTGGTGCTGGCCTTCTAATGGCCGGCACCA
42696455 GAGTGCCAAT
Statistics
Matches: 102, Mismatches: 36, Indels: 8
0.70 0.25 0.05
Matches are distributed among these distances:
53 8 0.08
54 86 0.84
55 8 0.08
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.32
Consensus pattern (54 bp):
TTTTTTGGTGCTGGCCTTCTAATGGCCGGCACCAAGTATGAAAAAAATTCAAAT
Found at i:42702844 original size:49 final size:47
Alignment explanation
Indices: 42702759--42703040 Score: 197
Period size: 49 Copynumber: 5.9 Consensus size: 47
42702749 AAAGATTGAT
* * * *
42702759 AATTTAAATGAAATGAGAA-AAAAATAAATTGAAATGAAATGATACAA
1 AATTTAAATGAAATGA-AAGAAAGATAAATTTAAATGAAATGAGAAAA
42702806 AATTTAAATGAAAATTGAAAGAAAGATAAATTTAAATGAAATGAGGAAAA
1 AATTTAAATG-AAA-TGAAAGAAAGATAAATTTAAATGAAATGA-GAAAA
* * *
42702856 AATTTAATTCAAATGAAATGAGAA-A-AAAATTAAAT-AAATTTGAAAGAAAGATA
1 AATTTAAATGAAATGAAA-GA-AAGATAAATTTAAATGAAA--TG--AG-AA-A-A
* * * *
42702909 AATTTAAATGAAATGAGAGAAAAGTTTAATTGAAATGAAATGAGAGAAA
1 AATTTAAATGAAATGAAAG-AAAGATAAATTTAAATGAAATGAGA-AAA
* **
42702958 AA-TTACATG----GAAAGATTGAT-AATTTAAATGAAATGAGAAAA
1 AATTTAAATGAAATGAAAGAAAGATAAATTTAAATGAAATGAGAAAA
* *
42702999 AAATTAAATTAAATTTGAAAGAAAGATAAATTTAAATGAAAT
1 AATTTAAATGAAA--TGAAAGAAAGATAAATTTAAATGAAAT
42703041 TAGGGAAACT
Statistics
Matches: 185, Mismatches: 24, Indels: 50
0.71 0.09 0.19
Matches are distributed among these distances:
41 5 0.03
42 22 0.12
43 3 0.02
44 4 0.02
47 13 0.07
48 34 0.18
49 49 0.26
50 16 0.09
51 6 0.03
52 4 0.02
53 19 0.10
54 7 0.04
55 3 0.02
ACGTcount: A:0.59, C:0.01, G:0.15, T:0.26
Consensus pattern (47 bp):
AATTTAAATGAAATGAAAGAAAGATAAATTTAAATGAAATGAGAAAA
Found at i:42702850 original size:75 final size:74
Alignment explanation
Indices: 42702759--42703088 Score: 311
Period size: 75 Copynumber: 4.5 Consensus size: 74
42702749 AAAGATTGAT
* * *
42702759 AATTTAAATGAAATGAGAAAAAAATAAATTGAAATGAAATGATACAAAATTTAAATGAAAATTGA
1 AATTTAAATGAAATGAGAAAAAAATAAATTGAAATGAAATGAGAGAAAAATTAAATG-AAATTGA
42702824 AAGAAAGATA
65 AAGAAAGATA
* * * *
42702834 AATTTAAATGAAATGAGGAAAAAATTTAATTCAAATGAAATGAGAAAAAAATTAAAT-AAATTTG
1 AATTTAAATGAAATGA-GAAAAAAATAAATTGAAATGAAATGAGAGAAAAATTAAATGAAA-TTG
42702898 AAAGAAAGATA
64 AAAGAAAGATA
** * *
42702909 AATTTAAATGAAATGAGAGAAAAGTTTAATTGAAATGAAATGAGAGAAAAATTACATG-----GA
1 AATTTAAATGAAATGAGA-AAAAAATAAATTGAAATGAAATGAGAGAAAAATTAAATGAAATTGA
**
42702969 AAGATTGAT-
65 AAGAAAGATA
* *
42702978 AATTTAAATGAAATGAGAAAAAAATTAAATT-AAATTTGAAA-GAAAGATAAATTTAAATGAAAT
1 AATTTAAATGAAATGAGAAAAAAA-TAAATTGAAA--TGAAATGAGAGA-AAAATTAAATGAAAT
** ** *
42703041 T-AGGGAAACTTTT
62 TGAAAGAAA-GATA
* *
42703054 AATTTAAATGAAATTAGAAAAAAATAAATTTAAAT
1 AATTTAAATGAAATGAGAAAAAAATAAATTGAAAT
42703089 TAAAAAATAA
Statistics
Matches: 214, Mismatches: 25, Indels: 33
0.79 0.09 0.12
Matches are distributed among these distances:
68 7 0.03
69 28 0.13
70 23 0.11
74 9 0.04
75 87 0.41
76 60 0.28
ACGTcount: A:0.58, C:0.01, G:0.14, T:0.27
Consensus pattern (74 bp):
AATTTAAATGAAATGAGAAAAAAATAAATTGAAATGAAATGAGAGAAAAATTAAATGAAATTGAA
AGAAAGATA
Found at i:42702858 original size:22 final size:22
Alignment explanation
Indices: 42702759--42703121 Score: 125
Period size: 27 Copynumber: 15.1 Consensus size: 22
42702749 AAAGATTGAT
42702759 AATTTAAATGAAATGAGAAAAA
1 AATTTAAATGAAATGAGAAAAA
* *
42702781 AATAAATTGAAATGAAATGA-TACAA
1 AAT---TT-AAATGAAATGAGAAAAA
42702806 AATTTAAATGAAAATTGAAAGAAAGATA
1 AATTTAAATG-AAA-TG--AGAAA-A-A
42702834 AATTTAAATGAAATGAGGAAAAAA
1 AATTTAAATGAAATGA-G-AAAAA
*
42702858 TTTAATTCAAATGAAATGAGAAAAA
1 ---AATTTAAATGAAATGAGAAAAA
42702883 AA-TTAAAT-AAATTTGAAAGAAAGATA
1 AATTTAAATGAAA--TG--AGAAA-A-A
42702909 AATTTAAATGAAATGAGAGAAAA
1 AATTTAAATGAAATGAGA-AAAA
* *
42702932 GTTTAATTGAAATGAAATGAGAGAAA
1 ----AATTTAAATGAAATGAGAAAAA
* *** *
42702958 AA-TTACATGGAAA-GA-TTGAT
1 AATTTAAAT-GAAATGAGAAAAA
42702978 AATTTAAATGAAATGAGAAAAA
1 AATTTAAATGAAATGAGAAAAA
*
42703000 AA-TTAAATTAAATTTGAAAGAAAGATA
1 AATTTAAATGAAA--TG--AGAAA-A-A
* **
42703027 AATTTAAATGAAATTAGGGAAACTTTT
1 AATTTAAATGAAA-T-GAGAAA---AA
*
42703054 AATTTAAATGAAATTAGAAAAA
1 AATTTAAATGAAATGAGAAAAA
* *
42703076 AA--TAAATTTAAATTA-AAAAA
1 AATTTAAA-TGAAATGAGAAAAA
* *
42703096 TAATATAAATGAATTGAGAAAAA
1 -AATTTAAATGAAATGAGAAAAA
42703119 AAT
1 AAT
42703122 AATATAATTT
Statistics
Matches: 260, Mismatches: 33, Indels: 96
0.67 0.08 0.25
Matches are distributed among these distances:
20 19 0.07
21 41 0.16
22 31 0.12
23 14 0.05
24 11 0.04
25 28 0.11
26 32 0.12
27 60 0.23
28 24 0.09
ACGTcount: A:0.59, C:0.01, G:0.13, T:0.27
Consensus pattern (22 bp):
AATTTAAATGAAATGAGAAAAA
Found at i:42703008 original size:27 final size:26
Alignment explanation
Indices: 42702978--42703088 Score: 79
Period size: 26 Copynumber: 4.3 Consensus size: 26
42702968 AAAGATTGAT
42702978 AATTTAAATGAAATGAGAAAAAAATTA
1 AATTTAAATGAAATGAGAAAAAAA-TA
* *
42703005 AA-TTAAAT---TTGA-AAGAAAGATA
1 AATTTAAATGAAATGAGAA-AAAAATA
* * *** *
42703027 AATTTAAATGAAATTAGGGAAACTTTT
1 AATTTAAATGAAATGA-GAAAAAAATA
*
42703054 AATTTAAATGAAATTAGAAAAAAATA
1 AATTTAAATGAAATGAGAAAAAAATA
42703080 AATTTAAAT
1 AATTTAAAT
42703089 TAAAAAATAA
Statistics
Matches: 63, Mismatches: 14, Indels: 15
0.68 0.15 0.16
Matches are distributed among these distances:
22 6 0.10
23 13 0.21
26 22 0.35
27 21 0.33
28 1 0.02
ACGTcount: A:0.58, C:0.01, G:0.11, T:0.31
Consensus pattern (26 bp):
AATTTAAATGAAATGAGAAAAAAATA
Found at i:42703023 original size:118 final size:117
Alignment explanation
Indices: 42702860--42703078 Score: 357
Period size: 118 Copynumber: 1.9 Consensus size: 117
42702850 GGAAAAAATT
42702860 TAATTCAAATGAAATGAGAAAAAAATTAAATAAATTTGAAAGAAAGATAAATTTAAATGAAATGA
1 TAATTCAAATGAAATGAGAAAAAAATTAAATAAATTTGAAAGAAAGATAAATTTAAATGAAATGA
*
42702925 GAGAAAAGTTTAATTGAAATGAAATGAGAGAAAAATTACATGGAAAGATTGA
66 GAGAAAAGTTTAATTGAAATGAAATGAGAAAAAAATTACATGGAAAGATTGA
* *
42702977 TAATTTAAATGAAATGAGAAAAAAATTAAATTAAATTTGAAAGAAAGATAAATTTAAATGAAATT
1 TAATTCAAATGAAATGAGAAAAAAATTAAA-TAAATTTGAAAGAAAGATAAATTTAAATGAAATG
* ** * *
42703042 AGGGAAACTTTTAATTTAAATGAAATTAGAAAAAAAT
65 AGAGAAAAGTTTAATTGAAATGAAATGAGAAAAAAAT
42703079 AAATTTAAAT
Statistics
Matches: 93, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
117 29 0.31
118 64 0.69
ACGTcount: A:0.57, C:0.01, G:0.15, T:0.27
Consensus pattern (117 bp):
TAATTCAAATGAAATGAGAAAAAAATTAAATAAATTTGAAAGAAAGATAAATTTAAATGAAATGA
GAGAAAAGTTTAATTGAAATGAAATGAGAAAAAAATTACATGGAAAGATTGA
Found at i:42703089 original size:21 final size:20
Alignment explanation
Indices: 42703059--42703128 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 20
42703049 CTTTTAATTT
42703059 AAATGAAATTAGAAAAAAATA
1 AAAT-AAATTAGAAAAAAATA
*
42703080 AATTTAAATTA-AAAAATAATA
1 AA-ATAAATTAGAAAAA-AATA
*
42703101 TAAATGAATTGAGAAAAAAATA
1 -AAATAAATT-AGAAAAAAATA
*
42703123 ATATAA
1 AAATAA
42703129 TTTAAATGAA
Statistics
Matches: 39, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
20 5 0.13
21 21 0.54
22 8 0.21
23 5 0.13
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (20 bp):
AAATAAATTAGAAAAAAATA
Found at i:42703104 original size:17 final size:18
Alignment explanation
Indices: 42703072--42703105 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
42703062 TGAAATTAGA
*
42703072 AAAAAATAAATTTAAATT
1 AAAAAATAAATATAAATT
42703090 AAAAAAT-AATATAAAT
1 AAAAAATAAATATAAAT
42703106 GAATTGAGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
AAAAAATAAATATAAATT
Found at i:42703118 original size:118 final size:117
Alignment explanation
Indices: 42702866--42703121 Score: 334
Period size: 118 Copynumber: 2.2 Consensus size: 117
42702856 AATTTAATTC
42702866 AAATGAAATGAGAAAAAAATTAAATAAATTTGAAAGAAAGATAAATTTAAATGAAATGAGAGAAA
1 AAATGAAATGAGAAAAAAATTAAATAAATTTGAAAGAAAGATAAATTTAAATGAAATGAGAGAAA
* * * *** *
42702931 AGTTTAATTGAAATGAAATGAGAGAAAAATTACATGGAAAGATTGATAATTT
66 AGTTTAATTGAAATGAAATGAGAGAAAAAATAAATGGAAAAAAAAATAATAT
* *
42702983 AAATGAAATGAGAAAAAAATTAAATTAAATTTGAAAGAAAGATAAATTTAAATGAAATTAGGGAA
1 AAATGAAATGAGAAAAAAATTAAA-TAAATTTGAAAGAAAGATAAATTTAAATGAAATGAGAGAA
** * * **
42703048 ACTTTTAATTTAAATGAAATTAGA-AAAAAATAAATTTAAATTAAAAAATAATAT
65 AAGTTTAATTGAAATGAAATGAGAGAAAAAATAAATGGAAA--AAAAAATAATAT
*
42703102 AAATGAATTGAGAAAAAAAT
1 AAATGAAATGAGAAAAAAAT
42703122 AATATAATTT
Statistics
Matches: 120, Mismatches: 16, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
117 36 0.30
118 58 0.48
119 26 0.22
ACGTcount: A:0.59, C:0.01, G:0.14, T:0.27
Consensus pattern (117 bp):
AAATGAAATGAGAAAAAAATTAAATAAATTTGAAAGAAAGATAAATTTAAATGAAATGAGAGAAA
AGTTTAATTGAAATGAAATGAGAGAAAAAATAAATGGAAAAAAAAATAATAT
Found at i:42703134 original size:42 final size:43
Alignment explanation
Indices: 42703053--42703134 Score: 114
Period size: 43 Copynumber: 1.9 Consensus size: 43
42703043 GGGAAACTTT
* *
42703053 TAATTTAAATGAAATTAGAAAAAAATAAATTTAAATTAAAAAA
1 TAATATAAATGAAATTAGAAAAAAATAAATATAAATTAAAAAA
*
42703096 TAATATAAATG-AATTGAGAAAAAAAT-AATATAATTTAAA
1 TAATATAAATGAAATT-AGAAAAAAATAAATATAAATTAAA
42703135 TGAAATGAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
42 15 0.43
43 20 0.57
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.30
Consensus pattern (43 bp):
TAATATAAATGAAATTAGAAAAAAATAAATATAAATTAAAAAA
Found at i:42703164 original size:6 final size:5
Alignment explanation
Indices: 42703132--42703215 Score: 60
Period size: 5 Copynumber: 15.6 Consensus size: 5
42703122 AATATAATTT
* * *
42703132 AAATG AAATG AAATGG AAATAG GAATGG AAATG AAATT AGAACG AAATG
1 AAATG AAATG AAAT-G AAAT-G AAAT-G AAATG AAATG A-AATG AAATG
* * *
42703181 AAATTG GAATG AAATA AAATT AGAATG AAATG AAA
1 AAA-TG AAATG AAATG AAATG A-AATG AAATG AAA
42703216 ATGGAAAGAA
Statistics
Matches: 62, Mismatches: 13, Indels: 8
0.75 0.16 0.10
Matches are distributed among these distances:
5 38 0.61
6 24 0.39
ACGTcount: A:0.57, C:0.01, G:0.21, T:0.20
Consensus pattern (5 bp):
AAATG
Found at i:42703180 original size:16 final size:16
Alignment explanation
Indices: 42703138--42703215 Score: 95
Period size: 16 Copynumber: 4.8 Consensus size: 16
42703128 ATTTAAATGA
42703138 AATGAAATGGAAA-TAGG
1 AATGAAAT-GAAATTA-G
42703155 AATGGAAATGAAATTAG
1 AAT-GAAATGAAATTAG
* *
42703172 AACGAAATGAAATTGG
1 AATGAAATGAAATTAG
*
42703188 AATGAAATAAAATTAG
1 AATGAAATGAAATTAG
42703204 AATGAAATGAAA
1 AATGAAATGAAA
42703216 ATGGAAAGAA
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
16 36 0.68
17 10 0.19
18 7 0.13
ACGTcount: A:0.56, C:0.01, G:0.22, T:0.21
Consensus pattern (16 bp):
AATGAAATGAAATTAG
Found at i:42703182 original size:193 final size:192
Alignment explanation
Indices: 42702789--42703184 Score: 423
Period size: 193 Copynumber: 2.1 Consensus size: 192
42702779 AAAATAAATT
* * *
42702789 GAAATGAAATGATACAAAATTTAAATGAAAATTGAAAGAAAGATAAATTTAAATGAAATGAGGAA
1 GAAATGAAATGAGAAAAAAATTAAATGAAAATTGAAAGAAAGATAAATTTAAATGAAATGAGGAA
*
42702854 AAAATTTAATTCAAATGAAATGAGAAAAAAATTAAATAAATTTGAAAGAAAGATAAATTTAAATG
66 AAAATTTAATTCAAATGAAATGAGAAAAAAATTAAATAAATTT-AAAGAAAGATAAATATAAATG
* * * ** * *
42702919 AAATGAGAGAAAAGTTTAATTGAAATGAAATGAGAGAAAAATTACATGGAAAGATTGATAATT
130 AAATGAGAAAAAAATTTAATTGAAATGAAATGAAAGAAAAAGGACATGGAAAGATTGAGAATC
* * * * *
42702982 TAAATGAAATGAGAAAAAAATTAAATTAAATTTGAAAGAAAGATAAATTTAAATGAAATTAGGGA
1 GAAATGAAATGAGAAAAAAATTAAATGAAAATTGAAAGAAAGATAAATTTAAATGAAATGAGGAA
** * *
42703047 AACTTTTAATTTAAATGAAATTAGAAAAAAA-TAAATTTAAA-TT-AA-AAA-AT-AATATAAAT
66 AAAATTTAATTCAAATGAAATGAGAAAAAAATTAAA--TAAATTTAAAGAAAGATAAATATAAAT
* * *
42703106 GAATTGAGAAAAAAATAATATAATTTAAATGAAATGAAATGGAAATAGGA-ATGGAAATGAAATT
129 GAAATGAGAAAAAAAT--T-TAATTGAAATGAAATGAAA--GAAAAAGGACATGGAAA-G--ATT
42703170 -AGAA-C
186 GAGAATC
42703175 GAAATGAAAT
1 GAAATGAAAT
42703185 TGGAATGAAA
Statistics
Matches: 169, Mismatches: 24, Indels: 20
0.79 0.11 0.09
Matches are distributed among these distances:
188 21 0.12
189 2 0.01
190 4 0.02
191 19 0.11
192 11 0.07
193 102 0.60
194 7 0.04
195 3 0.02
ACGTcount: A:0.58, C:0.01, G:0.15, T:0.26
Consensus pattern (192 bp):
GAAATGAAATGAGAAAAAAATTAAATGAAAATTGAAAGAAAGATAAATTTAAATGAAATGAGGAA
AAAATTTAATTCAAATGAAATGAGAAAAAAATTAAATAAATTTAAAGAAAGATAAATATAAATGA
AATGAGAAAAAAATTTAATTGAAATGAAATGAAAGAAAAAGGACATGGAAAGATTGAGAATC
Found at i:42703201 original size:32 final size:32
Alignment explanation
Indices: 42703141--42703231 Score: 119
Period size: 32 Copynumber: 2.8 Consensus size: 32
42703131 TAAATGAAAT
* *
42703141 GAAATGGAAATAGGAATGGAAATGAAATTAGAAC
1 GAAAT-GAAATTGGAAT-GAAATAAAATTAGAAC
*
42703175 GAAATGAAATTGGAATGAAATAAAATTAGAAT
1 GAAATGAAATTGGAATGAAATAAAATTAGAAC
* *
42703207 GAAATGAAAATGGAAAGAAATAAAA
1 GAAATGAAATTGGAATGAAATAAAA
42703232 AAAAAAGAGT
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
32 37 0.71
33 10 0.19
34 5 0.10
ACGTcount: A:0.58, C:0.01, G:0.22, T:0.19
Consensus pattern (32 bp):
GAAATGAAATTGGAATGAAATAAAATTAGAAC
Found at i:42703211 original size:11 final size:10
Alignment explanation
Indices: 42703132--42703215 Score: 60
Period size: 11 Copynumber: 7.8 Consensus size: 10
42703122 AATATAATTT
42703132 AAATGAAATG
1 AAATGAAATG
42703142 AAATGGAAATAG
1 AAAT-GAAAT-G
*
42703154 GAATGGAAATG
1 AAAT-GAAATG
* *
42703165 AAATTAGAACG
1 AAATGA-AATG
42703176 AAATGAAATTG
1 AAATGAAA-TG
* *
42703187 GAATGAAATA
1 AAATGAAATG
*
42703197 AAATTAGAATG
1 AAATGA-AATG
42703208 AAATGAAA
1 AAATGAAA
42703216 ATGGAAAGAA
Statistics
Matches: 57, Mismatches: 12, Indels: 10
0.72 0.15 0.13
Matches are distributed among these distances:
10 14 0.25
11 33 0.58
12 10 0.18
ACGTcount: A:0.57, C:0.01, G:0.21, T:0.20
Consensus pattern (10 bp):
AAATGAAATG
Found at i:42703232 original size:16 final size:16
Alignment explanation
Indices: 42703132--42703232 Score: 67
Period size: 16 Copynumber: 6.2 Consensus size: 16
42703122 AATATAATTT
* **
42703132 AAATGAAATGAAATGG
1 AAATGGAATGAAATAA
*
42703148 AAATAGGAATGGAAATGA
1 AAAT-GGAAT-GAAATAA
* * * *
42703166 AATTAGAACGAAATGA
1 AAATGGAATGAAATAA
*
42703182 AATTGGAATGAAATAA
1 AAATGGAATGAAATAA
* * *
42703198 AATTAGAATGAAATGA
1 AAATGGAATGAAATAA
*
42703214 AAATGGAAAGAAATAA
1 AAATGGAATGAAATAA
42703230 AAA
1 AAA
42703233 AAAAAGAGTT
Statistics
Matches: 69, Mismatches: 14, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
16 53 0.77
17 7 0.10
18 9 0.13
ACGTcount: A:0.59, C:0.01, G:0.21, T:0.19
Consensus pattern (16 bp):
AAATGGAATGAAATAA
Found at i:42703558 original size:18 final size:18
Alignment explanation
Indices: 42703518--42703558 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
42703508 AAGAAGTACC
*
42703518 AAAATGAAAATAAAAATT
1 AAAATGAAAATAAAAATA
*
42703536 TAAATGAAAATAAAAATA
1 AAAATGAAAATAAAAATA
42703554 AAAAT
1 AAAAT
42703559 ATGAAAGAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.22
Consensus pattern (18 bp):
AAAATGAAAATAAAAATA
Found at i:42704099 original size:13 final size:13
Alignment explanation
Indices: 42704083--42704121 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
42704073 TTATTTTATT
42704083 TTATTTAGTTTTA
1 TTATTTAGTTTTA
42704096 TTATTTA-TTTTA
1 TTATTTAGTTTTA
*
42704108 TTAATTTAGCTTTA
1 TT-ATTTAGTTTTA
42704122 GCCTATTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
12 7 0.30
13 12 0.52
14 4 0.17
ACGTcount: A:0.26, C:0.03, G:0.05, T:0.67
Consensus pattern (13 bp):
TTATTTAGTTTTA
Found at i:42707885 original size:15 final size:16
Alignment explanation
Indices: 42707865--42707894 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
42707855 ATACACGAAA
42707865 ATAT-AAAAAATACAG
1 ATATAAAAAAATACAG
42707880 ATATAAAAAAATACA
1 ATATAAAAAAATACA
42707895 AACATTCTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.70, C:0.07, G:0.03, T:0.20
Consensus pattern (16 bp):
ATATAAAAAAATACAG
Found at i:42708610 original size:105 final size:105
Alignment explanation
Indices: 42708492--42708785 Score: 317
Period size: 107 Copynumber: 2.8 Consensus size: 105
42708482 ATATATAAGG
* *
42708492 TTTGGTGCCGGCCATTAGAAGGCCAAATCCAGAAAAAAATT-AATTTTTTTTCGTATTGGAGTCG
1 TTTGGTGCCGGCCATTACAAGGCC-AA-CCAGAAAAAAATTGAATTTTTTTTCGTATTGGTGTCG
* *
42708556 ACCATTAGAAGGCTAAAACAATTTTTTTT-AAATATTGGTAC
64 GCCATTAGAAGGCCAAAACAATTTTTTTTAAAATATTGGTAC
* * * *
42708597 TTTGGTGCCGGCCATTACAAGGTC-AGCAGCAAAAAAATTTGAATTTTTTTTCATACTTGGTGCC
1 TTTGGTGCCGGCCATTACAAGGCCAACCAG-AAAAAAA-TTGAATTTTTTTTCGTA-TTGGTGTC
** * * *
42708661 GGTTATTAGAAGACCAAGACAATTTTTTTTAAAATATTGGTAG
63 GGCCATTAGAAGGCCAAAACAATTTTTTTTAAAATATTGGTAC
* * * *
42708704 TCTGGTGTCGGCCATTACAAGGCCAGCACCA-AAAAAATTTGAATTTTTTTTTTCGTACTGGTGT
1 TTTGGTGCCGGCCATTACAAGGCCA--ACCAGAAAAAAATTGAA--TTTTTTTTCGTATTGGTGT
*
42708768 TGGCCATTAGAAGGCCAA
62 CGGCCATTAGAAGGCCAA
42708786 GAAAAAAAAT
Statistics
Matches: 154, Mismatches: 25, Indels: 17
0.79 0.13 0.09
Matches are distributed among these distances:
102 3 0.02
103 8 0.05
104 2 0.01
105 35 0.23
106 30 0.19
107 37 0.24
108 25 0.16
109 11 0.07
110 3 0.02
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.34
Consensus pattern (105 bp):
TTTGGTGCCGGCCATTACAAGGCCAACCAGAAAAAAATTGAATTTTTTTTCGTATTGGTGTCGGC
CATTAGAAGGCCAAAACAATTTTTTTTAAAATATTGGTAC
Found at i:42708752 original size:106 final size:106
Alignment explanation
Indices: 42708494--42708754 Score: 321
Period size: 107 Copynumber: 2.5 Consensus size: 106
42708484 ATATAAGGTT
* * * * * *
42708494 TGGTGCCGGCCATTAGAAGGCCA-AATCCAGAAAAAAATT-AATTTTTTTTCGTA-TTGGAGTCG
1 TGGTGCCGGCCATTACAAGGCCAGCA-CCA-AAAAAATTTGAATTTTTTTTCATACTTGGTGCCG
*** * * *
42708556 ACCATTAGAAGGCTAAAACAATTTTTTTTAAATATTGGTACTT
64 GTTATTAGAAGACCAAAACAATTTTTTTTAAATATTGGTACTC
* *
42708599 TGGTGCCGGCCATTACAAGGTCAGCAGCAAAAAAATTTGAATTTTTTTTCATACTTGGTGCCGGT
1 TGGTGCCGGCCATTACAAGGCCAGCACCAAAAAAATTTGAATTTTTTTTCATACTTGGTGCCGGT
* *
42708664 TATTAGAAGACCAAGACAATTTTTTTTAAAATATTGGTAGTC
66 TATTAGAAGACCAAAACAATTTTTTTT-AAATATTGGTACTC
*
42708706 TGGTGTCGGCCATTACAAGGCCAGCACCAAAAAAATTTGAATTTTTTTT
1 TGGTGCCGGCCATTACAAGGCCAGCACCAAAAAAATTTGAATTTTTTTT
42708755 TTCGTACTGG
Statistics
Matches: 133, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
104 8 0.06
105 36 0.27
106 31 0.23
107 58 0.44
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.34
Consensus pattern (106 bp):
TGGTGCCGGCCATTACAAGGCCAGCACCAAAAAAATTTGAATTTTTTTTCATACTTGGTGCCGGT
TATTAGAAGACCAAAACAATTTTTTTTAAATATTGGTACTC
Found at i:42708799 original size:107 final size:106
Alignment explanation
Indices: 42708494--42708843 Score: 287
Period size: 106 Copynumber: 3.3 Consensus size: 106
42708484 ATATAAGGTT
* * * * * *
42708494 TGGTGCCGGCCATTAGAAGGCCA-AATCCAGAAAAAAATT-AATTTTTTTTCGTA-TTGGAGTCG
1 TGGTGCCGGCCATTACAAGGCCAGCA-CCA-AAAAAATTTGAATTTTTTTTCATACTTGGTGCCG
* * * * ***** * *
42708556 ACCATTAGAAGGCTAAAACAATTTTTTTTAAATATTGGTACTT
64 GCCATTAGAAGACCAAGACAAAAAAATTTAAATATTGGTAGTC
* * *
42708599 TGGTGCCGGCCATTACAAGGTCAGCAGCAAAAAAATTTGAATTTTTTTTCATACTTGGTGCCGGT
1 TGGTGCCGGCCATTACAAGGCCAGCACCAAAAAAATTTGAATTTTTTTTCATACTTGGTGCCGGC
* *****
42708664 TATTAGAAGACCAAGACAATTTTTTTTAAAATATTGGTAGTC
66 CATTAGAAGACCAAGACAAAAAAATTT-AAATATTGGTAGTC
* * **
42708706 TGGTGTCGGCCATTACAAGGCCAGCACCAAAAAAATTTGAATTTTTTTTTTCGTAC-TGGTGTTG
1 TGGTGCCGGCCATTACAAGGCCAGCACCAAAAAAATTTGAA--TTTTTTTTCATACTTGGTGCCG
* * *
42708770 GCCATTAGAAGGCCAAGA-AAAAAAATTTAAATAGTGTTAGTC
64 GCCATTAGAAGACCAAGACAAAAAAATTTAAATATTGGTAGTC
* * * *
42708812 TGGTGCCAGCCATTATAAGGGCAACACCAAAA
1 TGGTGCCGGCCATTACAAGGCCAGCACCAAAA
42708844 TTTTTTTAAA
Statistics
Matches: 202, Mismatches: 37, Indels: 11
0.81 0.15 0.04
Matches are distributed among these distances:
104 8 0.04
105 36 0.18
106 70 0.35
107 55 0.27
108 21 0.10
109 12 0.06
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.32
Consensus pattern (106 bp):
TGGTGCCGGCCATTACAAGGCCAGCACCAAAAAAATTTGAATTTTTTTTCATACTTGGTGCCGGC
CATTAGAAGACCAAGACAAAAAAATTTAAATATTGGTAGTC
Found at i:42708840 original size:106 final size:107
Alignment explanation
Indices: 42708494--42708843 Score: 273
Period size: 107 Copynumber: 3.3 Consensus size: 107
42708484 ATATAAGGTT
* * * * * *
42708494 TGGTGCCGGCCATTAGAAGGCCA-AATCCAGAAAAAAATT-AATTTTTTTTCGTA-TTGGAGTCG
1 TGGTGCCGGCCATTACAAGGCCAGCA-CCA-AAAAAATTTGAATTTTTTTTCATACTTGGTGCCG
* * * * **** * * * *
42708556 ACCATTAGAAGGCTAAAAC-AATTTTTTTTAAATATTGGTACTT
64 GCCATTAGAAGACCAAGACAAAAAAATTTAAAATAGTGGTAGTC
* * *
42708599 TGGTGCCGGCCATTACAAGGTCAGCAGCAAAAAAATTTGAATTTTTTTTCATACTTGGTGCCGGT
1 TGGTGCCGGCCATTACAAGGCCAGCACCAAAAAAATTTGAATTTTTTTTCATACTTGGTGCCGGC
* ***** *
42708664 TATTAGAAGACCAAGACAATTTTTTTTAAAATATTGGTAGTC
66 CATTAGAAGACCAAGACAAAAAAATTTAAAATAGTGGTAGTC
* * **
42708706 TGGTGTCGGCCATTACAAGGCCAGCACCAAAAAAATTTGAATTTTTTTTTTCGTAC-TGGTGTTG
1 TGGTGCCGGCCATTACAAGGCCAGCACCAAAAAAATTTGAA--TTTTTTTTCATACTTGGTGCCG
* *
42708770 GCCATTAGAAGGCCAAGA-AAAAAAATTT-AAATAGTGTTAGTC
64 GCCATTAGAAGACCAAGACAAAAAAATTTAAAATAGTGGTAGTC
* * * *
42708812 TGGTGCCAGCCATTATAAGGGCAACACCAAAA
1 TGGTGCCGGCCATTACAAGGCCAGCACCAAAA
42708844 TTTTTTTAAA
Statistics
Matches: 200, Mismatches: 39, Indels: 11
0.80 0.16 0.04
Matches are distributed among these distances:
104 8 0.04
105 36 0.18
106 60 0.30
107 63 0.31
108 21 0.10
109 12 0.06
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.32
Consensus pattern (107 bp):
TGGTGCCGGCCATTACAAGGCCAGCACCAAAAAAATTTGAATTTTTTTTCATACTTGGTGCCGGC
CATTAGAAGACCAAGACAAAAAAATTTAAAATAGTGGTAGTC
Found at i:42710658 original size:24 final size:23
Alignment explanation
Indices: 42710605--42710667 Score: 65
Period size: 25 Copynumber: 2.6 Consensus size: 23
42710595 TATTTTTATT
42710605 AAAAATATAATTTTTTATAAAATC
1 AAAAATATAA-TTTTTATAAAATC
*
42710629 ACAAAATATAGATTTTTAT-ACATAC
1 A-AAAATATA-ATTTTTATAAAAT-C
42710654 AAAAATATATATTT
1 AAAAATATA-ATTT
42710668 AGTAAAAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
24 16 0.47
25 17 0.50
26 1 0.03
ACGTcount: A:0.52, C:0.06, G:0.02, T:0.40
Consensus pattern (23 bp):
AAAAATATAATTTTTATAAAATC
Done.