Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 ID=Chr08-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 57128820
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 677448 characters in sequence are not A, C, G, or T
File 62 of 190
Found at i:17912946 original size:101 final size:101
Alignment explanation
Indices: 17912788--17912969 Score: 249
Period size: 101 Copynumber: 1.8 Consensus size: 101
17912778 AAAGTGATAG
* * * * * * *
17912788 TCACGTGTGTAGTACTATGTGTAGGCTACTACGTGTACCGGAATGAAAGGTCTCATGTGTAGTAC
1 TCACGTGTCTAGTACTATGTGCAGGCTACTACGTGAACCGGAAAGAAAGATCACATGTATAGTAC
17912853 TATGT-ACAGGCTACTATGCGTACCGGATAGCTTCGA
66 TATGTGA-AGGCTACTATGCGTACCGGATAGCTTCGA
* ***
17912889 TCACGTGTCTAGTACTATGTGCAGGCTACTACGTGAACTGGAAAGTTTGATCACATGTATAGTAC
1 TCACGTGTCTAGTACTATGTGCAGGCTACTACGTGAACCGGAAAGAAAGATCACATGTATAGTAC
17912954 TATGTGAAGGCTACTA
66 TATGTGAAGGCTACTA
17912970 CGTGTATCGA
Statistics
Matches: 69, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
101 68 0.99
102 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.30
Consensus pattern (101 bp):
TCACGTGTCTAGTACTATGTGCAGGCTACTACGTGAACCGGAAAGAAAGATCACATGTATAGTAC
TATGTGAAGGCTACTATGCGTACCGGATAGCTTCGA
Found at i:17920500 original size:9 final size:9
Alignment explanation
Indices: 17920483--17920513 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
17920473 TCGAGTTGAT
17920483 TCGAATAAC
1 TCGAATAAC
*
17920492 TCGATTAAC
1 TCGAATAAC
17920501 TCGAATAAC
1 TCGAATAAC
17920510 TCGA
1 TCGA
17920514 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:17935959 original size:31 final size:31
Alignment explanation
Indices: 17935921--17935982 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
17935911 AGCACAAAGT
17935921 AATGTGGGCAATTAAG-CAAGTGAACATGGAC
1 AATGTGGGCAATTAAGCCAA-TGAACATGGAC
17935952 AATGTGGGCAATTAAGCCAATGAACATGGAC
1 AATGTGGGCAATTAAGCCAATGAACATGGAC
17935983 TATGAAGCTG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
31 27 0.90
32 3 0.10
ACGTcount: A:0.39, C:0.15, G:0.27, T:0.19
Consensus pattern (31 bp):
AATGTGGGCAATTAAGCCAATGAACATGGAC
Found at i:17938679 original size:17 final size:17
Alignment explanation
Indices: 17938657--17938690 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
17938647 TGTTAGTGCA
*
17938657 TATTGTCATTGCATTTT
1 TATTGTCATTACATTTT
17938674 TATTGTCATTACATTTT
1 TATTGTCATTACATTTT
17938691 AATGTTAGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.21, C:0.12, G:0.09, T:0.59
Consensus pattern (17 bp):
TATTGTCATTACATTTT
Found at i:17941795 original size:61 final size:61
Alignment explanation
Indices: 17941707--17941822 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 61
17941697 AATTAATCAC
*
17941707 ATTAATATAACATGAATAAAATATTATCAAGATAAATATTAAATTAAATTTAATACCTCAT
1 ATTAATATAACATGAATAAAATATTATCAAGATAAATATTAAATTAAAATTAATACCTCAT
* * * * *
17941768 ATTAATATTAA-ATTAATACAATGTTATCTAGGTAAATATTAAATTAAAATTAATA
1 ATTAATA-TAACATGAATAAAATATTATCAAGATAAATATTAAATTAAAATTAATA
17941823 TAATACTATA
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
61 45 0.94
62 3 0.06
ACGTcount: A:0.52, C:0.06, G:0.04, T:0.38
Consensus pattern (61 bp):
ATTAATATAACATGAATAAAATATTATCAAGATAAATATTAAATTAAAATTAATACCTCAT
Found at i:17941807 original size:37 final size:36
Alignment explanation
Indices: 17941766--17941859 Score: 107
Period size: 37 Copynumber: 2.5 Consensus size: 36
17941756 TTAATACCTC
** * *
17941766 ATATTAATATTAAATTAATACAATGTTATCTAGGTAA
1 ATATTAA-ATTAAATTAATACAATACTATATAGATAA
*
17941803 ATATTAAATTAAAATTAATATAATACTATATAGATAA
1 ATATTAAATT-AAATTAATACAATACTATATAGATAA
*
17941840 ATATGAAATTAAATTTAATA
1 ATATTAAATTAAA-TTAATA
17941860 TTAAATTTAT
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
36 6 0.12
37 43 0.88
ACGTcount: A:0.52, C:0.03, G:0.05, T:0.39
Consensus pattern (36 bp):
ATATTAAATTAAATTAATACAATACTATATAGATAA
Found at i:17941841 original size:61 final size:60
Alignment explanation
Indices: 17941721--17941841 Score: 136
Period size: 61 Copynumber: 2.0 Consensus size: 60
17941711 ATATAACATG
* * * *
17941721 AATAAAATATTATCAAGATAAATATTAAATTAAATTTAATACCTCATATTAATATTAAATT
1 AATAAAATATTATCAAGATAAATATTAAATTAAAATTAATA-CTAATACTAATAATAAATT
* * * *
17941782 AATACAATGTTATCTAGGTAAATATTAAATTAAAATTAATA-TAATACTATATAGATAAAT
1 AATAAAATATTATCAAGATAAATATTAAATTAAAATTAATACTAATACTA-ATA-ATAAAT
17941842 ATGAAATTAA
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
59 6 0.12
60 3 0.06
61 41 0.82
ACGTcount: A:0.52, C:0.06, G:0.04, T:0.38
Consensus pattern (60 bp):
AATAAAATATTATCAAGATAAATATTAAATTAAAATTAATACTAATACTAATAATAAATT
Found at i:17947753 original size:26 final size:26
Alignment explanation
Indices: 17947699--17947753 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
17947689 ATAAAGGGGG
* *
17947699 TTGCTAAGTGCTGATTCCCCAAGGGA
1 TTGCTAAGTGCTGATTCCCCAACGCA
* *
17947725 TTGCTAAGTGCTGATTCCCCGACTCA
1 TTGCTAAGTGCTGATTCCCCAACGCA
17947751 TTG
1 TTG
17947754 GCCGTTGCTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.20, C:0.25, G:0.24, T:0.31
Consensus pattern (26 bp):
TTGCTAAGTGCTGATTCCCCAACGCA
Found at i:17947934 original size:27 final size:27
Alignment explanation
Indices: 17947896--17947948 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
17947886 TTTAAATGTG
*
17947896 AAGGGGTTGCTAAGTACTGATTCCCCC
1 AAGGGGCTGCTAAGTACTGATTCCCCC
**
17947923 AAGGGGCTGCTAAGTGTTGATTCCCC
1 AAGGGGCTGCTAAGTACTGATTCCCC
17947949 GAATCATTGG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.21, C:0.25, G:0.28, T:0.26
Consensus pattern (27 bp):
AAGGGGCTGCTAAGTACTGATTCCCCC
Found at i:17947944 original size:101 final size:102
Alignment explanation
Indices: 17947695--17948024 Score: 457
Period size: 103 Copynumber: 3.2 Consensus size: 102
17947685 GAATATAAAG
* * **
17947695 GGGGTTGCTAAGTGCTGATT-CCCCAAGGGATTGCTAAGTGCTGATTCCCCGACTCATTGGCCGT
1 GGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGT
* * *
17947759 TGCTAAGTGCTGATTCCACAGTATCTTTGAATATAAA
66 TGCTAAGTGCTGATTCCACCGTATCTTTGAATGTGAA
* * * *
17947796 GGGGGTTGCTAAGTGCTGATTCCCCCAAGGAGTTGCTAAGTGCTGATTCCCTGATTCATTAGTGG
1 -GGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGG
* *
17947861 TTGCTAAGTGCTGATCCCACCGTAT-TTTAAATGTGAA
65 TTGCTAAGTGCTGATTCCACCGTATCTTTGAATGTGAA
* * *
17947898 GGGGTTGCTAAGTACTGATTCCCCCAAGGGGCTGCTAAGTGTTGATTCCCCGAATCATTGGTGGT
1 GGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGT
* *
17947963 TGCTAAGTGCTGATTCCATCATATCTTTGAATGTGAAA
66 TGCTAAGTGCTGATTCCACCGTATCTTTGAATGTG-AA
*
17948001 GGGGTTGCTAAGTGCTGGTTCCCC
1 GGGGTTGCTAAGTGCTGATTCCCC
17948025 AAATCACTGG
Statistics
Matches: 200, Mismatches: 25, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
101 79 0.40
102 38 0.19
103 83 0.41
ACGTcount: A:0.21, C:0.21, G:0.27, T:0.32
Consensus pattern (102 bp):
GGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGT
TGCTAAGTGCTGATTCCACCGTATCTTTGAATGTGAA
Found at i:17955291 original size:33 final size:33
Alignment explanation
Indices: 17955249--17955401 Score: 120
Period size: 33 Copynumber: 4.5 Consensus size: 33
17955239 ATATAAAGGG
17955249 GGTTGCTAAGTGCTGATTCCTCGACTAATTGGT
1 GGTTGCTAAGTGCTGATTCCTCGACTAATTGGT
* * *
17955282 GGTTGCTAAGTGTTGATTCCACCGTATCTTTGAATATAAAGGG
1 GGTTGCTAAGTGCTGATTCC-TCG-A-C--T-AAT-T---GGT
*
17955325 GGTTGCTAAGTGCTGATTCC-C--CCAA--GG-
1 GGTTGCTAAGTGCTGATTCCTCGACTAATTGGT
* *
17955352 GGTTGCTAAGTGCTGATTCCTCGATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCTCGACTAATTGGT
17955385 GGTTGCTAAGTGCTGAT
1 GGTTGCTAAGTGCTGAT
17955402 CCCACCGTAT
Statistics
Matches: 96, Mismatches: 8, Indels: 32
0.71 0.06 0.24
Matches are distributed among these distances:
27 20 0.21
28 3 0.03
30 1 0.01
32 2 0.02
33 36 0.38
34 4 0.04
35 1 0.01
36 1 0.01
37 1 0.01
38 1 0.01
39 3 0.03
40 1 0.01
41 1 0.01
43 21 0.22
ACGTcount: A:0.20, C:0.18, G:0.28, T:0.35
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCTCGACTAATTGGT
Found at i:17955371 original size:103 final size:103
Alignment explanation
Indices: 17955247--17955551 Score: 454
Period size: 102 Copynumber: 3.0 Consensus size: 103
17955237 GAATATAAAG
* * *
17955247 GGGGTTGCTAAGTGCTGATTCCTCGACTAATTGGTGGTTGCTAAGTGTTGATTCCACCGTATCTT
1 GGGGTTGCTAAGTGCTGATTCCTCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATCTT
*
17955312 TGAATATAAAGGGGGTTGCTAAGTGCTGATTCCCCCAA
66 TGAATGTAAAGGGGGTTGCTAAGTGCTGATTCCCCCAA
* *
17955350 GGGGTTGCTAAGTGCTGATTCCTCGATTCATTGGTGGTTGCTAAGTGCTGATCCCACCGTAT-TT
1 GGGGTTGCTAAGTGCTGATTCCTCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATCTT
* * *
17955414 TAAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCCAG
66 TGAATGTAAAGGGGGTTGCTAAGTGCTGATTCCCCCAA
* * *
17955452 GGGGCTGCTAAGTGCTGATTCC-CTGAATCATTGGTGGTTTCTAAGTGCTGATTCCACCATATCT
1 GGGGTTGCTAAGTGCTGATTCCTC-GAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATCT
*
17955516 TTGAATGTGAAA-GGGTTTGCTAAGTGCTGATTCCCC
65 TTGAATGT-AAAGGGGGTTGCTAAGTGCTGATTCCCC
17955552 GAATCACTGG
Statistics
Matches: 183, Mismatches: 16, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
101 1 0.01
102 91 0.50
103 89 0.49
104 2 0.01
ACGTcount: A:0.20, C:0.19, G:0.28, T:0.33
Consensus pattern (103 bp):
GGGGTTGCTAAGTGCTGATTCCTCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATCTT
TGAATGTAAAGGGGGTTGCTAAGTGCTGATTCCCCCAA
Found at i:17955461 original size:27 final size:27
Alignment explanation
Indices: 17955423--17955474 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
17955413 TTAAATGTGA
*
17955423 AGGGGGTTGCTAAGTGCTGATTCCCCC
1 AGGGGGCTGCTAAGTGCTGATTCCCCC
17955450 AGGGGGCTGCTAAGTGCTGATTCCC
1 AGGGGGCTGCTAAGTGCTGATTCCC
17955475 TGAATCATTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.15, C:0.25, G:0.35, T:0.25
Consensus pattern (27 bp):
AGGGGGCTGCTAAGTGCTGATTCCCCC
Found at i:17955483 original size:102 final size:103
Alignment explanation
Indices: 17955245--17955551 Score: 465
Period size: 103 Copynumber: 3.0 Consensus size: 103
17955235 TTGAATATAA
* * *
17955245 AGGGGGTTGCTAAGTGCTGATTCCTCGACTAATTGGTGGTTGCTAAGTGTTGATTCCACCGTATC
1 AGGGGGTTGCTAAGTGCTGATTCCTCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
* *
17955310 TTTGAATATAAAGGGGGTTGCTAAGTGCTGATTCCCCC
66 TTTGAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCC
* * *
17955348 AAGGGGTTGCTAAGTGCTGATTCCTCGATTCATTGGTGGTTGCTAAGTGCTGATCCCACCGTAT-
1 AGGGGGTTGCTAAGTGCTGATTCCTCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
*
17955412 TTTAAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCC
66 TTTGAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCC
* * *
17955450 AGGGGGCTGCTAAGTGCTGATTCC-CTGAATCATTGGTGGTTTCTAAGTGCTGATTCCACCATAT
1 AGGGGGTTGCTAAGTGCTGATTCCTC-GAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTAT
* *
17955514 CTTTGAATGTGAAAGGGTTTGCTAAGTGCTGATTCCCC
65 CTTTGAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCC
17955552 GAATCACTGG
Statistics
Matches: 185, Mismatches: 17, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
101 1 0.01
102 91 0.49
103 93 0.50
ACGTcount: A:0.20, C:0.19, G:0.28, T:0.33
Consensus pattern (103 bp):
AGGGGGTTGCTAAGTGCTGATTCCTCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
TTTGAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCC
Found at i:17969425 original size:39 final size:39
Alignment explanation
Indices: 17969348--17969603 Score: 194
Period size: 37 Copynumber: 6.8 Consensus size: 39
17969338 GATTCTATTT
* * * * * * * *
17969348 AAAGTATGCTCAATCGAGCCATACCCATTGATTCTATTG
1 AAAGTATGCTCAAACGAGCAATATCTACTGAATATACTG
*
17969387 AAAGTATGCTCAAACGAGCAATATCTACTGAATATATTG
1 AAAGTATGCTCAAACGAGCAATATCTACTGAATATACTG
* *
17969426 AATGT-T-CTCAAAC-AACTAATATCTACTGAATATACTG
1 AAAGTATGCTCAAACGAGC-AATATCTACTGAATATACTG
*
17969463 -AAG--TGCTCAAATGAGCAATATCTACTGAATATACTG
1 AAAGTATGCTCAAACGAGCAATATCTACTGAATATACTG
* **
17969499 -AA-TGTGCTCAAACGAGCAATGCCTACTGAATATACT-
1 AAAGTATGCTCAAACGAGCAATATCTACTGAATATACTG
* * *
17969535 AAA-TGA-GCTCAAAAGAGCAATGTCTACTGATTATACT-
1 AAAGT-ATGCTCAAACGAGCAATATCTACTGAATATACTG
* * * * *
17969572 AAATGTTTTCTCAAATGAGCATTATCAACTGA
1 AAA-GTATGCTCAAACGAGCAATATCTACTGA
17969604 TCATATTGAA
Statistics
Matches: 181, Mismatches: 26, Indels: 20
0.80 0.11 0.09
Matches are distributed among these distances:
35 1 0.01
36 32 0.18
37 91 0.50
38 1 0.01
39 56 0.31
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.29
Consensus pattern (39 bp):
AAAGTATGCTCAAACGAGCAATATCTACTGAATATACTG
Found at i:17969480 original size:73 final size:74
Alignment explanation
Indices: 17969393--17969578 Score: 241
Period size: 73 Copynumber: 2.5 Consensus size: 74
17969383 ATTGAAAGTA
* * *
17969393 TGCTCAAACGAGCAATATCTACTGAATATATTGAATGTTCTCAAAC-AACTAATATCTACTGAAT
1 TGCTCAAAAGAGCAATATCTACTGAATATACTGAATGTTCTCAAACGAAC-AATACCTACTGAAT
*
17969457 ATACTGAA-G
65 ATACTAAATG
* * * *
17969466 TGCTCAAATGAGCAATATCTACTGAATATACTGAATGTGCTCAAACGAGCAATGCCTACTGAATA
1 TGCTCAAAAGAGCAATATCTACTGAATATACTGAATGTTCTCAAACGAACAATACCTACTGAATA
17969531 TACTAAATG
66 TACTAAATG
* * * *
17969540 AGCTCAAAAGAGCAATGTCTACTGATTATACTAAATGTT
1 TGCTCAAAAGAGCAATATCTACTGAATATACTGAATGTT
17969579 TTCTCAAATG
Statistics
Matches: 98, Mismatches: 13, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
73 62 0.63
74 36 0.37
ACGTcount: A:0.39, C:0.18, G:0.15, T:0.29
Consensus pattern (74 bp):
TGCTCAAAAGAGCAATATCTACTGAATATACTGAATGTTCTCAAACGAACAATACCTACTGAATA
TACTAAATG
Found at i:17972031 original size:16 final size:17
Alignment explanation
Indices: 17971999--17972031 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
17971989 AGTATCATGG
*
17971999 ATTAAATTATGATGTTA
1 ATTAAATTATAATGTTA
17972016 ATTAAATT-TAATGTTA
1 ATTAAATTATAATGTTA
17972032 TATTTGAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.48
Consensus pattern (17 bp):
ATTAAATTATAATGTTA
Found at i:17987930 original size:18 final size:17
Alignment explanation
Indices: 17987897--17987935 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
17987887 TTGTATAAAT
17987897 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
17987915 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
17987932 TGTG
1 TGTG
17987936 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:17988053 original size:8 final size:8
Alignment explanation
Indices: 17988040--17988068 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
17988030 CACTAGAGAC
17988040 CAGTGTTA
1 CAGTGTTA
17988048 CAGTGTTA
1 CAGTGTTA
17988056 CAGTGTTA
1 CAGTGTTA
17988064 CAGTG
1 CAGTG
17988069 AGTCCCGGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.24, C:0.14, G:0.28, T:0.34
Consensus pattern (8 bp):
CAGTGTTA
Found at i:17988182 original size:23 final size:23
Alignment explanation
Indices: 17988155--17988230 Score: 143
Period size: 23 Copynumber: 3.3 Consensus size: 23
17988145 AGTGTTATTG
17988155 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
17988178 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
17988201 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
17988224 ATCAGTG
1 ATCAGTG
17988231 TGGCACTTAT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:17995273 original size:18 final size:17
Alignment explanation
Indices: 17995240--17995278 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
17995230 TTGTATAAAT
17995240 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
17995258 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
17995275 TGTG
1 TGTG
17995279 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:17995396 original size:8 final size:8
Alignment explanation
Indices: 17995383--17995411 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
17995373 CACTAGAGAC
17995383 CAGTGTTA
1 CAGTGTTA
17995391 CAGTGTTA
1 CAGTGTTA
17995399 CAGTGTTA
1 CAGTGTTA
17995407 CAGTG
1 CAGTG
17995412 AGTCCCGGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.24, C:0.14, G:0.28, T:0.34
Consensus pattern (8 bp):
CAGTGTTA
Found at i:17995525 original size:23 final size:23
Alignment explanation
Indices: 17995498--17995573 Score: 143
Period size: 23 Copynumber: 3.3 Consensus size: 23
17995488 AGTGTTATTG
17995498 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
17995521 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
17995544 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
17995567 ATCAGTG
1 ATCAGTG
17995574 TGGCACTTAT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:17997424 original size:61 final size:61
Alignment explanation
Indices: 17997345--17997465 Score: 179
Period size: 61 Copynumber: 2.0 Consensus size: 61
17997335 AATTGAGATG
* *
17997345 GTTTAGATTATAGAAACACAAGCCGTAAACTCTGAGATATTCATCGATGACTTTGTCTTTA
1 GTTTAGATTATAGAAACACAAACCGTAAACTCCGAGATATTCATCGATGACTTTGTCTTTA
* * * **
17997406 GTTTGGATTATAGAAACACAAACCGTAATCTCCGAGCTATTTGTCGATGACTTTGTCTTT
1 GTTTAGATTATAGAAACACAAACCGTAAACTCCGAGATATTCATCGATGACTTTGTCTTT
17997466 TCCTTTCTTT
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
61 53 1.00
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Consensus pattern (61 bp):
GTTTAGATTATAGAAACACAAACCGTAAACTCCGAGATATTCATCGATGACTTTGTCTTTA
Found at i:18008075 original size:45 final size:45
Alignment explanation
Indices: 18008009--18008100 Score: 148
Period size: 45 Copynumber: 2.0 Consensus size: 45
18007999 CAGATACTCA
* *
18008009 GTGGATTCAGCACATAACAACCACCTTATTAATCAATGATGTCCG
1 GTGGAATCAGCACATAACAACCACCTTACTAATCAATGATGTCCG
* *
18008054 GTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTTCG
1 GTGGAATCAGCACATAACAACCACCTTACTAATCAATGATGTCCG
18008099 GT
1 GT
18008101 TCACATAGTA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (45 bp):
GTGGAATCAGCACATAACAACCACCTTACTAATCAATGATGTCCG
Found at i:18008169 original size:51 final size:50
Alignment explanation
Indices: 18008102--18008291 Score: 231
Period size: 51 Copynumber: 3.8 Consensus size: 50
18008092 ATGTTCGGTT
*
18008102 CACATAGTAGCTTGCACATAGTACTACACATGTGACCATTACCATCTGATA
1 CACATAGTAGCCTGCACATAGTACTACACATGTGACCA-TACCATCTGATA
* * * * * **
18008153 CACGTAGTAGCCTGCACATAGTACTACACACGTGATCGAAACTATCCAATA
1 CACATAGTAGCCTGCACATAGTACTACACATGTGA-CCATACCATCTGATA
* * * *
18008204 CGCATAGTAGCCTGCACATAGTACTACACATGCGA-C-TATCATTCTGGTA
1 CACATAGTAGCCTGCACATAGTACTACACATGTGACCATACCA-TCTGATA
18008253 CACATAGTAGCCTGCACATAGTACTACACATGTGACCAT
1 CACATAGTAGCCTGCACATAGTACTACACATGTGACCAT
18008292 CACTTTCACT
Statistics
Matches: 114, Mismatches: 21, Indels: 8
0.80 0.15 0.06
Matches are distributed among these distances:
48 2 0.02
49 37 0.32
50 1 0.01
51 72 0.63
52 2 0.02
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.25
Consensus pattern (50 bp):
CACATAGTAGCCTGCACATAGTACTACACATGTGACCATACCATCTGATA
Found at i:18008280 original size:100 final size:101
Alignment explanation
Indices: 18008104--18008287 Score: 282
Period size: 100 Copynumber: 1.8 Consensus size: 101
18008094 GTTCGGTTCA
* * *
18008104 CATAGTAGCTTGCACATAGTACTACACATGTGACCATTACCATCTGATACACGTAGTAGCCTGCA
1 CATAGTAGCCTGCACATAGTACTACACATGCGACCA-TACCATCTGATACACATAGTAGCCTGCA
18008169 CATAGTACTACACACGTGATCGAAACTATCCAATACG
65 CATAGTACTACACACGTGATCGAAACTATCCAATACG
* *
18008206 CATAGTAGCCTGCACATAGTACTACACATGCGA-C-TATCATTCTGGTACACATAGTAGCCTGCA
1 CATAGTAGCCTGCACATAGTACTACACATGCGACCATACCA-TCTGATACACATAGTAGCCTGCA
*
18008269 CATAGTACTACACATGTGA
65 CATAGTACTACACACGTGA
18008288 CCATCACTTT
Statistics
Matches: 75, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
99 4 0.05
100 39 0.52
101 1 0.01
102 31 0.41
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.25
Consensus pattern (101 bp):
CATAGTAGCCTGCACATAGTACTACACATGCGACCATACCATCTGATACACATAGTAGCCTGCAC
ATAGTACTACACACGTGATCGAAACTATCCAATACG
Found at i:18018467 original size:6 final size:6
Alignment explanation
Indices: 18018456--18018485 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
18018446 TCATACATAT
18018456 TTATGA TTATGA TTATGA TTATGA TTATGA
1 TTATGA TTATGA TTATGA TTATGA TTATGA
18018486 AAAAAAATGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (6 bp):
TTATGA
Found at i:18024641 original size:24 final size:23
Alignment explanation
Indices: 18024609--18024662 Score: 81
Period size: 24 Copynumber: 2.3 Consensus size: 23
18024599 TAGGAGTGTG
*
18024609 TGGGCCTACATGGGCTCGCATTA
1 TGGGCCTACACGGGCTCGCATTA
*
18024632 TGGGTCCTACACGGGCTCGTATTA
1 TGGG-CCTACACGGGCTCGCATTA
18024656 TGGGCCT
1 TGGGCCT
18024663 TGGGCCCAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 7 0.25
24 21 0.75
ACGTcount: A:0.15, C:0.26, G:0.31, T:0.28
Consensus pattern (23 bp):
TGGGCCTACACGGGCTCGCATTA
Found at i:18024823 original size:27 final size:27
Alignment explanation
Indices: 18024793--18024964 Score: 265
Period size: 27 Copynumber: 6.4 Consensus size: 27
18024783 CCTCACGTGG
18024793 TAAAATGACTATTATGCCCCTATGTTA
1 TAAAATGACTATTATGCCCCTATGTTA
**
18024820 TAAAATGACGGTTATGCCCCTATGTTA
1 TAAAATGACTATTATGCCCCTATGTTA
*
18024847 TAAAATGA-TGGTTATGCCCCTATGTTA
1 TAAAATGACT-ATTATGCCCCTATGTTA
** *
18024874 TAAAATGAAGATTATGCTCCTATGTTA
1 TAAAATGACTATTATGCCCCTATGTTA
*
18024901 TAAAATGACTATTATGCCCCTATATTA
1 TAAAATGACTATTATGCCCCTATGTTA
18024928 TAAAATGACTATTATGCCCCTATGTTA
1 TAAAATGACTATTATGCCCCTATGTTA
18024955 TAAAATGACT
1 TAAAATGACT
18024965 GTATGCTTAA
Statistics
Matches: 132, Mismatches: 11, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
27 132 1.00
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.36
Consensus pattern (27 bp):
TAAAATGACTATTATGCCCCTATGTTA
Found at i:18029054 original size:21 final size:21
Alignment explanation
Indices: 18029015--18029055 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
18029005 AAGTTAATCA
* * *
18029015 AAAGAATAATAACACATAATG
1 AAAGAAGAATAAAAAATAATG
18029036 AAAGAAGAATAAAAAATAAT
1 AAAGAAGAATAAAAAATAAT
18029056 AGTCAGATAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.68, C:0.05, G:0.10, T:0.17
Consensus pattern (21 bp):
AAAGAAGAATAAAAAATAATG
Found at i:18030216 original size:9 final size:10
Alignment explanation
Indices: 18030192--18030228 Score: 74
Period size: 10 Copynumber: 3.7 Consensus size: 10
18030182 CAAGAAATAA
18030192 GTTTTTCTAG
1 GTTTTTCTAG
18030202 GTTTTTCTAG
1 GTTTTTCTAG
18030212 GTTTTTCTAG
1 GTTTTTCTAG
18030222 GTTTTTC
1 GTTTTTC
18030229 ATTTCATGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.08, C:0.11, G:0.19, T:0.62
Consensus pattern (10 bp):
GTTTTTCTAG
Found at i:18030637 original size:61 final size:63
Alignment explanation
Indices: 18030534--18030660 Score: 179
Period size: 62 Copynumber: 2.0 Consensus size: 63
18030524 TTTTTGAAAA
* * *
18030534 TTTTAGAATTAGAACCAAATTGATAAATTTTTGTAAATATTGAGGG-TAAATTTATTGAATTT
1 TTTTAGAATTAGAACCAAAATGACAAATTTTTGTAAACATTGAGGGCTAAATTTATTGAATTT
* *
18030596 TTTTAGAATTTAG-ACTAAAATGACAAA-TTTTGTAAACATTGAGGGCTAAATTTGTTGAATTT
1 TTTTAGAA-TTAGAACCAAAATGACAAATTTTTGTAAACATTGAGGGCTAAATTTATTGAATTT
18030658 TTT
1 TTT
18030661 AGATTTTGAA
Statistics
Matches: 58, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
61 17 0.29
62 37 0.64
63 4 0.07
ACGTcount: A:0.37, C:0.05, G:0.15, T:0.43
Consensus pattern (63 bp):
TTTTAGAATTAGAACCAAAATGACAAATTTTTGTAAACATTGAGGGCTAAATTTATTGAATTT
Found at i:18030691 original size:61 final size:62
Alignment explanation
Indices: 18030534--18030713 Score: 154
Period size: 62 Copynumber: 2.9 Consensus size: 62
18030524 TTTTTGAAAA
* * * * *
18030534 TTTTAGAA-TTAGAACCAAATTGATAAATTTTTGTAAATATTGAGGG-TAAATTTATTGAATTT
1 TTTTAGAATTTAGAA-TAAAATGACAAA-TTGTGTAAATATTGAGGGCTAAATTTGTTGAATTT
* * *
18030596 TTTTAGAATTTAGACTAAAATGACAAATTTTGTAAACATTGAGGGCTAAATTTGTTGAA-TT
1 TTTTAGAATTTAGAATAAAATGACAAATTGTGTAAATATTGAGGGCTAAATTTGTTGAATTT
* * ** **
18030657 TTTTAG-ATTTTGAATCAAATTGATTTAA-TGTGTAAATATTGGATAGCTAAATTTGTT
1 TTTTAGAATTTAGAAT-AAAATGA-CAAATTGTGTAAATATT-GAGGGCTAAATTTGTT
18030714 ATTAGACCAA
Statistics
Matches: 98, Mismatches: 15, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
60 7 0.07
61 41 0.42
62 45 0.46
63 5 0.05
ACGTcount: A:0.37, C:0.04, G:0.16, T:0.43
Consensus pattern (62 bp):
TTTTAGAATTTAGAATAAAATGACAAATTGTGTAAATATTGAGGGCTAAATTTGTTGAATTT
Found at i:18036675 original size:27 final size:27
Alignment explanation
Indices: 18036638--18036723 Score: 145
Period size: 27 Copynumber: 3.2 Consensus size: 27
18036628 AGGTCAAAAT
* *
18036638 ATGACCGAAATACCCCCATAGGGTAAA
1 ATGACCAAAATACCCTCATAGGGTAAA
18036665 ATGACCAAAATACCCTCATAGGGTAAA
1 ATGACCAAAATACCCTCATAGGGTAAA
*
18036692 ATGACCAAAATACCCTTATAGGGTAAA
1 ATGACCAAAATACCCTCATAGGGTAAA
18036719 ATGAC
1 ATGAC
18036724 TATTATACCC
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 56 1.00
ACGTcount: A:0.43, C:0.22, G:0.16, T:0.19
Consensus pattern (27 bp):
ATGACCAAAATACCCTCATAGGGTAAA
Found at i:18045432 original size:26 final size:26
Alignment explanation
Indices: 18045364--18045466 Score: 86
Period size: 26 Copynumber: 4.0 Consensus size: 26
18045354 TTAATCATTC
* *
18045364 CTATTTTATCCC-AACAAAATTTTGA
1 CTATTTTGTCCCTAATAAAATTTTGA
* * * *
18045389 CAATTTT-ACCTTTGATAAAATTTTGA
1 CTATTTTGTCC-CTAATAAAATTTTGA
18045415 CTATTTTGTCCCTAATAAAATTTTGA
1 CTATTTTGTCCCTAATAAAATTTTGA
* **
18045441 -TGACTTTGTCCCTGGTAAAATTTTGA
1 CT-ATTTTGTCCCTAATAAAATTTTGA
18045467 GAAAATATGT
Statistics
Matches: 62, Mismatches: 12, Indels: 7
0.77 0.15 0.09
Matches are distributed among these distances:
24 2 0.03
25 7 0.11
26 51 0.82
27 2 0.03
ACGTcount: A:0.31, C:0.16, G:0.10, T:0.44
Consensus pattern (26 bp):
CTATTTTGTCCCTAATAAAATTTTGA
Found at i:18045627 original size:12 final size:12
Alignment explanation
Indices: 18045610--18045639 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
18045600 TGCACATGGA
18045610 TCATTTCCATTT
1 TCATTTCCATTT
18045622 TCATTTCCATTT
1 TCATTTCCATTT
*
18045634 CCATTT
1 TCATTT
18045640 TCTGGAAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.17, C:0.27, G:0.00, T:0.57
Consensus pattern (12 bp):
TCATTTCCATTT
Found at i:18045751 original size:18 final size:16
Alignment explanation
Indices: 18045713--18045755 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 16
18045703 TTCCTGAATG
*
18045713 TTTCTCATTTCTTTTTT
1 TTTCT-ATTTATTTTTT
18045730 TTTCTATTTATTTTTT
1 TTTCTATTTATTTTTT
18045746 CATTTCTATT
1 --TTTCTATT
18045756 GAAAACACGC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 10 0.43
17 5 0.22
18 8 0.35
ACGTcount: A:0.12, C:0.14, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTCTATTTATTTTTT
Found at i:18047732 original size:26 final size:24
Alignment explanation
Indices: 18047693--18047745 Score: 88
Period size: 26 Copynumber: 2.1 Consensus size: 24
18047683 GGGATAATAA
18047693 TTTTTAATTAATATTCAACTGATT
1 TTTTTAATTAATATTCAACTGATT
18047717 TTTTTAAAGTTAATATTCAACTGATT
1 TTTTT-AA-TTAATATTCAACTGATT
18047743 TTT
1 TTT
18047746 AAAACAAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
24 5 0.19
25 2 0.07
26 20 0.74
ACGTcount: A:0.32, C:0.08, G:0.06, T:0.55
Consensus pattern (24 bp):
TTTTTAATTAATATTCAACTGATT
Found at i:18047755 original size:24 final size:25
Alignment explanation
Indices: 18047702--18047755 Score: 65
Period size: 26 Copynumber: 2.2 Consensus size: 25
18047692 ATTTTTAATT
***
18047702 AATATTCAACTGATTTTTTTAAAGTT
1 AATATTCAACTGA-TTTTTTAAAACA
18047728 AATATTCAACTGA-TTTTTAAAACA
1 AATATTCAACTGATTTTTTAAAACA
18047752 AATA
1 AATA
18047756 AGTATCCACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 12 0.48
26 13 0.52
ACGTcount: A:0.43, C:0.09, G:0.06, T:0.43
Consensus pattern (25 bp):
AATATTCAACTGATTTTTTAAAACA
Found at i:18049924 original size:15 final size:15
Alignment explanation
Indices: 18049904--18049934 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
18049894 AAAACAACAT
18049904 AACTCTTGACCTTTC
1 AACTCTTGACCTTTC
18049919 AACTCTTGACCTTTC
1 AACTCTTGACCTTTC
18049934 A
1 A
18049935 CTTACATAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.23, C:0.32, G:0.06, T:0.39
Consensus pattern (15 bp):
AACTCTTGACCTTTC
Found at i:18054264 original size:15 final size:15
Alignment explanation
Indices: 18054244--18054274 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
18054234 AAAACAACAT
18054244 AACTCTTAACCTTTC
1 AACTCTTAACCTTTC
*
18054259 AACTCTTGACCTTTC
1 AACTCTTAACCTTTC
18054274 A
1 A
18054275 CTTGCATATC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.26, C:0.32, G:0.03, T:0.39
Consensus pattern (15 bp):
AACTCTTAACCTTTC
Found at i:18061937 original size:9 final size:8
Alignment explanation
Indices: 18061901--18061937 Score: 65
Period size: 8 Copynumber: 4.5 Consensus size: 8
18061891 TTTAAGACTT
18061901 TTAAAATA
1 TTAAAATA
18061909 TTAAAATA
1 TTAAAATA
18061917 TTAAAATA
1 TTAAAATA
18061925 TTAAAATTA
1 TTAAAA-TA
18061934 TTAA
1 TTAA
18061938 TTTATGTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
8 22 0.79
9 6 0.21
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (8 bp):
TTAAAATA
Found at i:18062602 original size:22 final size:24
Alignment explanation
Indices: 18062550--18062603 Score: 60
Period size: 22 Copynumber: 2.3 Consensus size: 24
18062540 TTTTTTATGA
18062550 TTAAATTATTGTTATTAAATATGCT
1 TTAAATTATTGTTATT-AATATGCT
*
18062575 TGAAATTATTG-TATT-ATAT-CTT
1 TTAAATTATTGTTATTAATATGC-T
18062597 TTAAATT
1 TTAAATT
18062604 GAATTTATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
21 1 0.04
22 11 0.42
24 4 0.15
25 10 0.38
ACGTcount: A:0.35, C:0.04, G:0.07, T:0.54
Consensus pattern (24 bp):
TTAAATTATTGTTATTAATATGCT
Found at i:18063870 original size:10 final size:10
Alignment explanation
Indices: 18063855--18063883 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
18063845 CCGGAAGAGA
18063855 ATGTAATAAT
1 ATGTAATAAT
18063865 ATGTAATAAT
1 ATGTAATAAT
18063875 ATGTAATAA
1 ATGTAATAA
18063884 ATTCGAAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.10, T:0.38
Consensus pattern (10 bp):
ATGTAATAAT
Found at i:18068168 original size:41 final size:42
Alignment explanation
Indices: 18068083--18068168 Score: 104
Period size: 42 Copynumber: 2.1 Consensus size: 42
18068073 CCTTATGTAA
* * *
18068083 TAAGTCTAAAATTTTTATGAACCTAAAAATATATGTATGCAG
1 TAAGTCTAAAATTTTTAAGAACCTAAAAATATAAGTATACAG
* *
18068125 TAAGTCTAAAATTTTTAAGCACCT-AAAATGTAAGTA-ACTAG
1 TAAGTCTAAAATTTTTAAGAACCTAAAAATATAAGTATAC-AG
18068166 TAA
1 TAA
18068169 CCGGATAATT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
40 1 0.03
41 15 0.39
42 22 0.58
ACGTcount: A:0.44, C:0.10, G:0.12, T:0.34
Consensus pattern (42 bp):
TAAGTCTAAAATTTTTAAGAACCTAAAAATATAAGTATACAG
Found at i:18071465 original size:51 final size:49
Alignment explanation
Indices: 18071400--18071575 Score: 196
Period size: 49 Copynumber: 3.5 Consensus size: 49
18071390 AAAGGTCGCA
*
18071400 TGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGCTTCGATCACG
1 TGTGTAGTACTATGTGCAGGCTACTA-GCGTACCGGATAG-TTTGATCACG
*
18071451 TGTGTAGTACTATGTGCAGGCTACTA-CGTATCGGATA-TTAATGATCACG
1 TGTGTAGTACTATGTGCAGGCTACTAGCGTACCGGATAGTT--TGATCACG
* * * *
18071500 TGTGTAGTACTATGTGCAGGCTAATA-CGTGAACCGGAAAGTTTGATTAAG
1 TGTGTAGTACTATGTGCAGGCTACTAGCGT--ACCGGATAGTTTGATCACG
* * *
18071550 TGTGTAGTATTATATGAAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
18071576 CGTGTATCGA
Statistics
Matches: 109, Mismatches: 11, Indels: 11
0.83 0.08 0.08
Matches are distributed among these distances:
47 2 0.02
49 45 0.41
50 28 0.26
51 32 0.29
52 2 0.02
ACGTcount: A:0.27, C:0.15, G:0.26, T:0.32
Consensus pattern (49 bp):
TGTGTAGTACTATGTGCAGGCTACTAGCGTACCGGATAGTTTGATCACG
Found at i:18072876 original size:2 final size:2
Alignment explanation
Indices: 18072869--18072897 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
18072859 ATGGATAATG
18072869 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
18072898 GTGACAATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:18073806 original size:433 final size:433
Alignment explanation
Indices: 18072994--18073868 Score: 1633
Period size: 433 Copynumber: 2.0 Consensus size: 433
18072984 TACGGATAAA
*
18072994 TTCAGGTACTCAGGACGAATTCAACAAGCAAGTGAAAATTTATAAATTCATACGACGAGGAAGTG
1 TTCAGATACTCAGGACGAATTCAACAAGCAAGTGAAAATTTATAAATTCATACGACGAGGAAGTG
18073059 AAAGATTGTGAGTATATTTAGCCAAGAAAACCCTAATTAACGACTCGAGAATAACAACTTGAAAA
66 AAAGATTGTGAGTATATTTAGCCAAGAAAACCCTAATTAACGACTCGAGAATAACAACTTGAAAA
* * *
18073124 TTTTAATTTAGATGAAATTTTACAACTTGGTTTACTACGGTTAAAAGTGTATATGTTTTGGTAAT
131 TTTTAATTTAGATGAAATTTTACAACTTGGTTTACTACAGTTAAAAGTGTATATGTTCTGCTAAT
18073189 ACCTCGTACCCTATTCCGGCATCGAATACGGGTAAGAGGTGTTACATTAATTGTATAAAATTGTT
196 ACCTCGTACCCTATTCCGGCATCGAATACGGGTAAGAGGTGTTACATTAATTGTATAAAATTGTT
* *
18073254 TATTTAAGTCCTGAAATGGTATTATTTGAATGAAATTATTATTTAGATTAAGAAACGCTGCAATC
261 TAGTTAAGTCCTGAAATGGTATTATTTGAATGAAATTATTATTTAGATCAAGAAACGCTGCAATC
*
18073319 AAATTTAAACCGAGGGAAAACCAAAGTTTCAGAGTAGTTATCAACTCCATTTTAGTAACCGTTTT
326 AAATTTAAACCGAGGGAAAACCAAAGTTTCAGACTAGTTATCAACTCCATTTTAGTAACCGTTTT
*
18073384 AGCTGAGGTAAGTTCTTATTTCCATTAAAATAATTCATTTAAG
391 AGCCGAGGTAAGTTCTTATTTCCATTAAAATAATTCATTTAAG
18073427 TTCAGATACTCAGGACGAATTCAACAAGCAAGTGAAAATTTATAAATTCATACGACGAGGAAGTG
1 TTCAGATACTCAGGACGAATTCAACAAGCAAGTGAAAATTTATAAATTCATACGACGAGGAAGTG
*
18073492 AAAGATTGTGAGTATATTTAGCCAAGAAAACCCTAATTAACGACTCGAGAATAACAACTTGAAAT
66 AAAGATTGTGAGTATATTTAGCCAAGAAAACCCTAATTAACGACTCGAGAATAACAACTTGAAAA
18073557 TTTTAATTTAGATGAAATTTTACAACTTGGTTTACTACAGTTAAAAGTGTATATGTTCTGCTAAT
131 TTTTAATTTAGATGAAATTTTACAACTTGGTTTACTACAGTTAAAAGTGTATATGTTCTGCTAAT
*
18073622 ACCTCGTACCCTTTTCCGGCATCGAATACGGGTAAGAGGTGTTACATTAATTGTATAAAATTGTT
196 ACCTCGTACCCTATTCCGGCATCGAATACGGGTAAGAGGTGTTACATTAATTGTATAAAATTGTT
*
18073687 TAGTTAAGTCCTGAAATGGTATTATTTGAATTAAATTATTATTTAGATCAAGAAACGCTGCAATC
261 TAGTTAAGTCCTGAAATGGTATTATTTGAATGAAATTATTATTTAGATCAAGAAACGCTGCAATC
18073752 AAATTTAAACCGAGGGAAAACCAAAGTTTCAGACTAGTTATCAACTCCATTTTAGTAACCGTTTT
326 AAATTTAAACCGAGGGAAAACCAAAGTTTCAGACTAGTTATCAACTCCATTTTAGTAACCGTTTT
*
18073817 AGCCGAGGTAAGTTCTTATTTCCATTAGAATAATTCATTTAAG
391 AGCCGAGGTAAGTTCTTATTTCCATTAAAATAATTCATTTAAG
18073860 TTCAAGATA
1 TTC-AGATA
18073869 TAAATTGATA
Statistics
Matches: 429, Mismatches: 12, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
433 424 0.99
434 5 0.01
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (433 bp):
TTCAGATACTCAGGACGAATTCAACAAGCAAGTGAAAATTTATAAATTCATACGACGAGGAAGTG
AAAGATTGTGAGTATATTTAGCCAAGAAAACCCTAATTAACGACTCGAGAATAACAACTTGAAAA
TTTTAATTTAGATGAAATTTTACAACTTGGTTTACTACAGTTAAAAGTGTATATGTTCTGCTAAT
ACCTCGTACCCTATTCCGGCATCGAATACGGGTAAGAGGTGTTACATTAATTGTATAAAATTGTT
TAGTTAAGTCCTGAAATGGTATTATTTGAATGAAATTATTATTTAGATCAAGAAACGCTGCAATC
AAATTTAAACCGAGGGAAAACCAAAGTTTCAGACTAGTTATCAACTCCATTTTAGTAACCGTTTT
AGCCGAGGTAAGTTCTTATTTCCATTAAAATAATTCATTTAAG
Found at i:18077101 original size:94 final size:94
Alignment explanation
Indices: 18076993--18077177 Score: 334
Period size: 94 Copynumber: 2.0 Consensus size: 94
18076983 TTTTAAAAAA
*
18076993 AAAATATAATTGTGAGATGAATTAATAGACATATAGTAAAATAACTTTTATTGATAAAATAGTAC
1 AAAATATAATTGTGAGATGAATTAATAGACATATAGTAAAATAACTTTTATTGATAAAATAGCAC
18077058 AAAATTAAATAATTGTGTTAATTAATAGT
66 AAAATTAAATAATTGTGTTAATTAATAGT
*
18077087 AAAATATAATTGTGAGATGAATTAATAGACATATGGTAAAATAACTTTTATTGATAAAATAGCAC
1 AAAATATAATTGTGAGATGAATTAATAGACATATAGTAAAATAACTTTTATTGATAAAATAGCAC
* *
18077152 AAAATTAAGTAATTGTGTTGATTAAT
66 AAAATTAAATAATTGTGTTAATTAAT
18077178 TTTGACTATA
Statistics
Matches: 87, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
94 87 1.00
ACGTcount: A:0.48, C:0.04, G:0.13, T:0.36
Consensus pattern (94 bp):
AAAATATAATTGTGAGATGAATTAATAGACATATAGTAAAATAACTTTTATTGATAAAATAGCAC
AAAATTAAATAATTGTGTTAATTAATAGT
Found at i:18077899 original size:24 final size:26
Alignment explanation
Indices: 18077844--18077900 Score: 68
Period size: 24 Copynumber: 2.3 Consensus size: 26
18077834 ATAAATAAAC
*
18077844 AAAC-ATAAATAATAATAAACATATT
1 AAACAATAAATAATAATAAACACATT
*
18077869 ATA-AATAAATAA-AATAAACACA-T
1 AAACAATAAATAATAATAAACACATT
18077892 AAACAATAA
1 AAACAATAA
18077901 TAGTATTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
23 3 0.11
24 14 0.52
25 10 0.37
ACGTcount: A:0.68, C:0.09, G:0.00, T:0.23
Consensus pattern (26 bp):
AAACAATAAATAATAATAAACACATT
Found at i:18081296 original size:25 final size:25
Alignment explanation
Indices: 18081265--18081457 Score: 123
Period size: 25 Copynumber: 7.9 Consensus size: 25
18081255 GTCCTATCTC
18081265 GAGCCATATAACGGGAAGCTCATGT
1 GAGCCATATAACGGGAAGCTCATGT
* * * **
18081290 GAGCCATGTAATGGGAAGCTTATCC
1 GAGCCATATAACGGGAAGCTCATGT
* * **
18081315 GAGCTATATAACGGGAAGCCCATAA
1 GAGCCATATAACGGGAAGCTCATGT
18081340 GAGCCATA-ATA-GGGAAGCTCATGT
1 GAGCCATATA-ACGGGAAGCTCATGT
* * *
18081364 GAGCC-TATAACGGGTAGCTC-CGAA
1 GAGCCATATAACGGGAAGCTCATG-T
**
18081388 GAGCCA-ATAACCAGAAGCTC-TGAAT
1 GAGCCATATAACGGGAAGCTCATG--T
* * * *
18081413 -AGCCATATATCGGGAAGTTCAAGC
1 GAGCCATATAACGGGAAGCTCATGT
*
18081437 GAGCCA-ATATCGGGAAGCTCA
1 GAGCCATATAACGGGAAGCTCA
18081458 CAAAGAGCCT
Statistics
Matches: 128, Mismatches: 31, Indels: 19
0.72 0.17 0.11
Matches are distributed among these distances:
23 4 0.03
24 61 0.48
25 62 0.48
26 1 0.01
ACGTcount: A:0.34, C:0.21, G:0.26, T:0.19
Consensus pattern (25 bp):
GAGCCATATAACGGGAAGCTCATGT
Found at i:18081324 original size:50 final size:50
Alignment explanation
Indices: 18081259--18081377 Score: 138
Period size: 50 Copynumber: 2.4 Consensus size: 50
18081249 TAGGAAGTCC
* **
18081259 TATCTCGAGCCATATAACGGGAAGCTCATGTGAGCCATGTAAT-GGGAAGCT
1 TATCTCGAGCCATATAACGGGAAGCCCATAAGAGCCA--TAATAGGGAAGCT
*
18081310 TATC-CGAGCTATATAACGGGAAGCCCATAAGAGCCATAATAGGGAAGCT
1 TATCTCGAGCCATATAACGGGAAGCCCATAAGAGCCATAATAGGGAAGCT
* *
18081359 CATGT-GAGCC-TATAACGGG
1 TATCTCGAGCCATATAACGGG
18081378 TAGCTCCGAA
Statistics
Matches: 59, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
48 13 0.22
49 14 0.24
50 28 0.47
51 4 0.07
ACGTcount: A:0.32, C:0.20, G:0.27, T:0.21
Consensus pattern (50 bp):
TATCTCGAGCCATATAACGGGAAGCCCATAAGAGCCATAATAGGGAAGCT
Found at i:18081465 original size:25 final size:25
Alignment explanation
Indices: 18081265--18081466 Score: 81
Period size: 24 Copynumber: 8.2 Consensus size: 25
18081255 GTCCTATCTC
* ***
18081265 GAGCCATATAACGGGAAGCTCATGT
1 GAGCCATATATCGGGAAGCTCAAAA
* * ***
18081290 GAGCCATGTAAT-GGGAAGCTTATCC
1 GAGCCATAT-ATCGGGAAGCTCAAAA
* * * *
18081315 GAGCTATATAACGGGAAGCCCATAA
1 GAGCCATATATCGGGAAGCTCAAAA
* ***
18081340 GAGCCATA-ATAGGGAAGCTCATGT
1 GAGCCATATATCGGGAAGCTCAAAA
* * **
18081364 GAGCC-TATAACGGGTAGCTCCGAA
1 GAGCCATATATCGGGAAGCTCAAAA
* ** **
18081388 GAGCCA-ATAACCAGAAGCTCTGAA
1 GAGCCATATATCGGGAAGCTCAAAA
* * **
18081412 TAGCCATATATCGGGAAGTTCAAGC
1 GAGCCATATATCGGGAAGCTCAAAA
18081437 GAGCCA-ATATCGGGAAGCTCACAAA
1 GAGCCATATATCGGGAAGCTCA-AAA
18081462 GAGCC
1 GAGCC
18081467 TTTAATCAAA
Statistics
Matches: 129, Mismatches: 42, Indels: 12
0.70 0.23 0.07
Matches are distributed among these distances:
23 2 0.02
24 64 0.50
25 62 0.48
26 1 0.01
ACGTcount: A:0.34, C:0.22, G:0.26, T:0.18
Consensus pattern (25 bp):
GAGCCATATATCGGGAAGCTCAAAA
Found at i:18083487 original size:57 final size:57
Alignment explanation
Indices: 18083419--18083533 Score: 221
Period size: 57 Copynumber: 2.0 Consensus size: 57
18083409 GGATAGTGTG
*
18083419 TCTGCTCCGACTTGAACTTTCGATCTACTAGGCTTCACGAAATTTACAAGAAAAACA
1 TCTGCTCCGACTTGAACTTTCAATCTACTAGGCTTCACGAAATTTACAAGAAAAACA
18083476 TCTGCTCCGACTTGAACTTTCAATCTACTAGGCTTCACGAAATTTACAAGAAAAACA
1 TCTGCTCCGACTTGAACTTTCAATCTACTAGGCTTCACGAAATTTACAAGAAAAACA
18083533 T
1 T
18083534 GATATGTAAG
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.34, C:0.24, G:0.13, T:0.29
Consensus pattern (57 bp):
TCTGCTCCGACTTGAACTTTCAATCTACTAGGCTTCACGAAATTTACAAGAAAAACA
Found at i:18083912 original size:43 final size:43
Alignment explanation
Indices: 18083859--18083947 Score: 117
Period size: 43 Copynumber: 2.1 Consensus size: 43
18083849 GTTTTATAGG
* * *
18083859 TAGTGGCATTTTTA-GTAGAAGTGTCACTAAATGTCATGTTCTT
1 TAGTGGCATTTTTATG-AGAAGCGCCACTAAAGGTCATGTTCTT
* *
18083902 TAGTGGCATTTTTATGAGAAGCGCCGCTAAAGGTCATGTTTTT
1 TAGTGGCATTTTTATGAGAAGCGCCACTAAAGGTCATGTTCTT
18083945 TAG
1 TAG
18083948 CGGCGTTTGT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
43 39 0.98
44 1 0.03
ACGTcount: A:0.25, C:0.12, G:0.24, T:0.39
Consensus pattern (43 bp):
TAGTGGCATTTTTATGAGAAGCGCCACTAAAGGTCATGTTCTT
Found at i:18084370 original size:66 final size:66
Alignment explanation
Indices: 18084243--18084370 Score: 186
Period size: 66 Copynumber: 1.9 Consensus size: 66
18084233 TCTAAAGCTA
* * * *
18084243 TAGCTGGAGTTCGTCATATTTTCTTGTTGCCTCTGCTTCTCTCGCTGCTGCCTCCGCTTTAATTT
1 TAGCTGGAGTTCATCATATTTTCTTGTAGCCTCTGCTTCTCTCGATGCTGCCTCCACTTTAATTT
18084308 G
66 G
* *
18084309 TAGCTGGAGTTCATCATATTTTCTT-TGAGCCTCTGCTTCTCTCGATGCTGCCTTCATTTTAA
1 TAGCTGGAGTTCATCATATTTTCTTGT-AGCCTCTGCTTCTCTCGATGCTGCCTCCACTTTAA
18084371 GCTGAGCAAT
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
65 1 0.02
66 54 0.98
ACGTcount: A:0.12, C:0.26, G:0.18, T:0.44
Consensus pattern (66 bp):
TAGCTGGAGTTCATCATATTTTCTTGTAGCCTCTGCTTCTCTCGATGCTGCCTCCACTTTAATTT
G
Found at i:18105588 original size:30 final size:30
Alignment explanation
Indices: 18105553--18105621 Score: 129
Period size: 30 Copynumber: 2.3 Consensus size: 30
18105543 GCTACAAAGG
18105553 ACACACGGCCGTGTAACCTAGCCATGTGTC
1 ACACACGGCCGTGTAACCTAGCCATGTGTC
*
18105583 ACACACGGCCGTGTCACCTAGCCATGTGTC
1 ACACACGGCCGTGTAACCTAGCCATGTGTC
18105613 ACACACGGC
1 ACACACGGC
18105622 TAAGACACAC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.23, C:0.36, G:0.23, T:0.17
Consensus pattern (30 bp):
ACACACGGCCGTGTAACCTAGCCATGTGTC
Found at i:18106789 original size:25 final size:25
Alignment explanation
Indices: 18106748--18106811 Score: 83
Period size: 25 Copynumber: 2.6 Consensus size: 25
18106738 TCATGTACAT
*
18106748 GTATGCTCACACAAGCTGTGAATCG
1 GTATGCTCACACAAGCTGTAAATCG
* *
18106773 GTATGCTCTCACGAGCTGTAAATCG
1 GTATGCTCACACAAGCTGTAAATCG
* *
18106798 GTAAGCTCATACAA
1 GTATGCTCACACAA
18106812 AATGAGAATC
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.30, C:0.23, G:0.22, T:0.25
Consensus pattern (25 bp):
GTATGCTCACACAAGCTGTAAATCG
Found at i:18107059 original size:25 final size:25
Alignment explanation
Indices: 18107003--18107062 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
18106993 TTAGTATACC
* **
18107003 CATACGAGCTATGAATCAGTATTCT
1 CATACGAGCTATAAATCAGTAAGCT
*
18107028 C-TCACGAGCTTTAAATCAGTAAGCT
1 CAT-ACGAGCTATAAATCAGTAAGCT
18107053 CATACGAGCT
1 CATACGAGCT
18107063 GAGAATTGGT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
24 1 0.03
25 27 0.93
26 1 0.03
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.28
Consensus pattern (25 bp):
CATACGAGCTATAAATCAGTAAGCT
Found at i:18107062 original size:50 final size:50
Alignment explanation
Indices: 18107003--18107113 Score: 136
Period size: 50 Copynumber: 2.2 Consensus size: 50
18106993 TTAGTATACC
** *
18107003 CATACGAGCT-ATGAATCAGTATTCTCTCACGAGCT-TTAAATCAGTAAGCT
1 CATACGAGCTGA-GAATCAGTAACCTCTCACGAGCTGCT-AATCAGTAAGCT
** *
18107053 CATACGAGCTGAGAATTGGTAACCTCTCACGAGCTGCTAATCTGTAAGCT
1 CATACGAGCTGAGAATCAGTAACCTCTCACGAGCTGCTAATCAGTAAGCT
18107103 CATACGAGCTG
1 CATACGAGCTG
18107114 TGGTGTGTCC
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
50 51 0.96
51 2 0.04
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.27
Consensus pattern (50 bp):
CATACGAGCTGAGAATCAGTAACCTCTCACGAGCTGCTAATCAGTAAGCT
Found at i:18107074 original size:25 final size:25
Alignment explanation
Indices: 18107041--18107113 Score: 78
Period size: 25 Copynumber: 2.9 Consensus size: 25
18107031 ACGAGCTTTA
*
18107041 AATCAGTAAGCTCATACGAGCTGAG
1 AATCTGTAAGCTCATACGAGCTGAG
* **
18107066 AAT-TGGTAACCTC-TCACGAGCTGCT
1 AATCT-GTAAGCTCAT-ACGAGCTGAG
18107091 AATCTGTAAGCTCATACGAGCTG
1 AATCTGTAAGCTCATACGAGCTG
18107114 TGGTGTGTCC
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
24 1 0.03
25 36 0.92
26 2 0.05
ACGTcount: A:0.30, C:0.23, G:0.22, T:0.25
Consensus pattern (25 bp):
AATCTGTAAGCTCATACGAGCTGAG
Found at i:18107216 original size:248 final size:248
Alignment explanation
Indices: 18106761--18107238 Score: 726
Period size: 248 Copynumber: 1.9 Consensus size: 248
18106751 TGCTCACACA
* * *
18106761 AGCTGTGAATCGGTATGCTCTCACGAGCTGTAAATCGGTAAGCTCATACAAAATGAGAATCAGTA
1 AGCTATGAATCAGTATGCTCTCACGAGCTGTAAATCAGTAAGCTCATACAAAATGAGAATCAGTA
*
18106826 AGCTCTCACGAGCTACAAATTGGTAAGCTCATACGAGCTGCGATGTGTCCGTAACACATGCAGGA
66 ACCTCTCACGAGCTACAAATTGGTAAGCTCATACGAGCTGCGATGTGTCCGTAACACATGCAGGA
* * * *
18106891 CCTCAACCAAATCAGTAACCCTAATGACATGTCATTTCTATCCTATGAATTCTTAAGGTTCAAAC
131 CCTCAACCAAATCAGTAACCCTAATGACATGTCAATTCTATCCTATAAATTCCTAAGGTTCAAAA
18106956 AGGGCTCGATAATCATCGTACGTCATC-AGATATGCAATTAGTATACCCATACG
196 AGGGCTCGATAATCATCGTACGTCATCGA-ATATGCAATTAGTATACCCATACG
* * * ** **
18107009 AGCTATGAATCAGTATTCTCTCACGAGCTTTAAATCAGTAAGCTCATACGAGCTGAGAATTGGTA
1 AGCTATGAATCAGTATGCTCTCACGAGCTGTAAATCAGTAAGCTCATACAAAATGAGAATCAGTA
* * * *
18107074 ACCTCTCACGAGCTGCTAATCT-GTAAGCTCATACGAGCTGTGGTGTGTCCGTAACACATGCAGG
66 ACCTCTCACGAGCTACAAAT-TGGTAAGCTCATACGAGCTGCGATGTGTCCGTAACACATGCAGG
* *
18107138 ACCTCAACCAAATCGGTAACCCTAATGACATGTCAATTGTATCCTATAAATTCCTAAGGTTCAAA
130 ACCTCAACCAAATCAGTAACCCTAATGACATGTCAATTCTATCCTATAAATTCCTAAGGTTCAAA
*
18107203 AAGGGCTCGATAATCGTCGTACGTCATCGAATATGC
195 AAGGGCTCGATAATCATCGTACGTCATCGAATATGC
18107239 CTATAGTAGC
Statistics
Matches: 206, Mismatches: 22, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
248 204 0.99
249 2 0.01
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.26
Consensus pattern (248 bp):
AGCTATGAATCAGTATGCTCTCACGAGCTGTAAATCAGTAAGCTCATACAAAATGAGAATCAGTA
ACCTCTCACGAGCTACAAATTGGTAAGCTCATACGAGCTGCGATGTGTCCGTAACACATGCAGGA
CCTCAACCAAATCAGTAACCCTAATGACATGTCAATTCTATCCTATAAATTCCTAAGGTTCAAAA
AGGGCTCGATAATCATCGTACGTCATCGAATATGCAATTAGTATACCCATACG
Found at i:18113150 original size:25 final size:25
Alignment explanation
Indices: 18113109--18113161 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
18113099 TCATGTACAT
**
18113109 GTATGCTCACACAAGCTGTGAATCG
1 GTATGCTCACACAAGCTACGAATCG
* *
18113134 GTATGCTCTCACGAGCTACGAATCG
1 GTATGCTCACACAAGCTACGAATCG
18113159 GTA
1 GTA
18113162 AGCTTGTACG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.26, C:0.25, G:0.25, T:0.25
Consensus pattern (25 bp):
GTATGCTCACACAAGCTACGAATCG
Found at i:18120723 original size:56 final size:50
Alignment explanation
Indices: 18120513--18120759 Score: 253
Period size: 50 Copynumber: 4.8 Consensus size: 50
18120503 AATAATAACA
* * ** * * * *
18120513 TGCCAAAGACATGTCCCAGACATGGTCTTACATGGGATGTTTCGTGT-AC
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAG
* * ** * *
18120562 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAG
* * **
18120612 TGCCTATGCCATGTCCCAAACATGGTCTTACGGGGGACCTCTCATCTCAG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAG
*
18120662 TGCCAATGCCACGTCCCAGACATGGTCTTACATGGGACCTCTCATAATCTCAATG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATCTC-A-G
*
18120717 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
18120760 TTACCCAAAT
Statistics
Matches: 163, Mismatches: 28, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
49 38 0.23
50 78 0.48
53 5 0.03
54 1 0.01
55 1 0.01
56 40 0.25
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAG
Found at i:18125343 original size:12 final size:12
Alignment explanation
Indices: 18125326--18125351 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
18125316 TAGACGGATG
18125326 GTCAATCTGAAT
1 GTCAATCTGAAT
18125338 GTCAATCTGAAT
1 GTCAATCTGAAT
18125350 GT
1 GT
18125352 ATGATTCAGA
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:0.31, C:0.15, G:0.19, T:0.35
Consensus pattern (12 bp):
GTCAATCTGAAT
Found at i:18139322 original size:14 final size:14
Alignment explanation
Indices: 18139303--18139330 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
18139293 ACAATTTATT
18139303 AATATATATTAATA
1 AATATATATTAATA
18139317 AATATATATTAATA
1 AATATATATTAATA
18139331 TATGTAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
AATATATATTAATA
Found at i:18139387 original size:32 final size:32
Alignment explanation
Indices: 18139351--18139435 Score: 93
Period size: 32 Copynumber: 2.6 Consensus size: 32
18139341 CTACTTTTCG
* *
18139351 GAAAATATTTTCAAGAAATCTGCCAAACAGCA
1 GAAAATATTTTCAAGAAATCTACCAAACACCA
*
18139383 GAAAATATTTTACACAG--ATTTACCAAACACCA
1 GAAAATATTTT-CA-AGAAATCTACCAAACACCA
*
18139415 GAAAATATTTTCCAGTAAATC
1 GAAAATATTTTCAAG-AAATC
18139436 ATTTTACAGA
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
30 2 0.05
31 1 0.02
32 34 0.79
33 4 0.09
34 2 0.05
ACGTcount: A:0.46, C:0.19, G:0.09, T:0.26
Consensus pattern (32 bp):
GAAAATATTTTCAAGAAATCTACCAAACACCA
Found at i:18141788 original size:22 final size:21
Alignment explanation
Indices: 18141749--18141789 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
18141739 TTTATTTTAA
* *
18141749 AGTTTAAATTAAATAAAGGCT
1 AGTTTAAAATAAAAAAAGGCT
18141770 AGTTTAATAATAAAAAAAGG
1 AGTTTAA-AATAAAAAAAGG
18141790 TAGGGTCATC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.54, C:0.02, G:0.15, T:0.29
Consensus pattern (21 bp):
AGTTTAAAATAAAAAAAGGCT
Found at i:18142675 original size:41 final size:41
Alignment explanation
Indices: 18142614--18142844 Score: 248
Period size: 41 Copynumber: 5.6 Consensus size: 41
18142604 ACTAAGTCCT
* * *
18142614 GCAGGCTTCATGCCATTGTATTATATCAAGCTTTGTGCCTA
1 GCAGGCTTCGTGCTAGTGTATTATATCAAGCTTTGTGCCTA
* * * * *
18142655 ACAAGCTTCGTGTTGGTGTATTATATCAAGCTTTATGCCTA
1 GCAGGCTTCGTGCTAGTGTATTATATCAAGCTTTGTGCCTA
* * * *
18142696 GTAGGCTTCGTGCCAATGTATTATATCAGGCTTTGTGCCTA
1 GCAGGCTTCGTGCTAGTGTATTATATCAAGCTTTGTGCCTA
* * *
18142737 GCAGGATTCGTGCTAGTGTATTATATCAGGCTTTATGCCTA
1 GCAGGCTTCGTGCTAGTGTATTATATCAAGCTTTGTGCCTA
* * * *
18142778 CCAGGATTCATGCTGGTGTATTATATCAAGCTTTGTGCCTA
1 GCAGGCTTCGTGCTAGTGTATTATATCAAGCTTTGTGCCTA
* * *
18142819 GCAAGCTTCATGC-CGATGTATTATAT
1 GCAGGCTTCGTGCTAG-TGTATTATAT
18142845 TAGGATTTGT
Statistics
Matches: 158, Mismatches: 31, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
40 1 0.01
41 157 0.99
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.37
Consensus pattern (41 bp):
GCAGGCTTCGTGCTAGTGTATTATATCAAGCTTTGTGCCTA
Found at i:18142756 original size:82 final size:82
Alignment explanation
Indices: 18142615--18142823 Score: 283
Period size: 82 Copynumber: 2.5 Consensus size: 82
18142605 CTAAGTCCTG
* * * * *
18142615 CAGGCTTCATGCCATTGTATTATATCAAGCTTTGTGCCTAACAAGCTTCGTGTTGGTGTATTATA
1 CAGGCTTCATGCCAATGTATTATATCAAGCTTTGTGCCTAGCAAGATTCGTGCTAGTGTATTATA
*
18142680 TCAAGCTTTATGCCTAG
66 TCAAGCTTTATGCCTAC
* * * *
18142697 TAGGCTTCGTGCCAATGTATTATATCAGGCTTTGTGCCTAGCAGGATTCGTGCTAGTGTATTATA
1 CAGGCTTCATGCCAATGTATTATATCAAGCTTTGTGCCTAGCAAGATTCGTGCTAGTGTATTATA
*
18142762 TCAGGCTTTATGCCTAC
66 TCAAGCTTTATGCCTAC
* ***
18142779 CAGGATTCATGCTGGTGTATTATATCAAGCTTTGTGCCTAGCAAG
1 CAGGCTTCATGCCAATGTATTATATCAAGCTTTGTGCCTAGCAAG
18142824 CTTCATGCCG
Statistics
Matches: 108, Mismatches: 19, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
82 108 1.00
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.36
Consensus pattern (82 bp):
CAGGCTTCATGCCAATGTATTATATCAAGCTTTGTGCCTAGCAAGATTCGTGCTAGTGTATTATA
TCAAGCTTTATGCCTAC
Found at i:18142838 original size:123 final size:122
Alignment explanation
Indices: 18142630--18143149 Score: 441
Period size: 123 Copynumber: 4.4 Consensus size: 122
18142620 TTCATGCCAT
* * * * *
18142630 TGTATTATATCAAGCTTTGTGCCTAACAAGCTTCGTGTTGGTGTATTATATCAAGCTTTATGCCT
1 TGTATTATATCAGGCTTTGTGCCTAGCAGGCTTCATGCTGGTGTATTATATCAAGCTTTATGCCT
* * *
18142695 AGTAGGCTTCGTGCCAATGTATTATATCAGGCTTTGTGCCTAGCAGGATTCGTG-CTAG
66 AGTAAGCTTCATGCCGATGTATTATATCAGGCTTTGTGCCTAGCAGGA-TCGTGTC-AG
* * * *
18142753 TGTATTATATCAGGCTTTATGCCTACCAGGATTCATGCTGGTGTATTATATCAAGCTTTGTGCCT
1 TGTATTATATCAGGCTTTGTGCCTAGCAGGCTTCATGCTGGTGTATTATATCAAGCTTTATGCCT
* * *
18142818 AGCAAGCTTCATGCCGATGTATTATATTAGG-ATT-TG--T-GC-----C--G---G
66 AGTAAGCTTCATGCCGATGTATTATATCAGGCTTTGTGCCTAGCAGGATCGTGTCAG
* * ** * *
18142860 TGTATTATATCAGGCTTTGTGCCTAGCAGACTTTATGCTTATGTATTATATCAGGATTTATGCCT
1 TGTATTATATCAGGCTTTGTGCCTAGCAGGCTTCATGCTGGTGTATTATATCAAGCTTTATGCCT
* * * * * *
18142925 AGTAGGCTTCGA-GTCGGTGTA-T-TATCAGGCTTTGTACCTAGCAGGCTTCATGTCAG
66 AGTAAGCTTC-ATGCCGATGTATTATATCAGGCTTTGTGCCTAGCAGG-ATCGTGTCAG
* ** * *
18142981 TGTATTATATCAGGCTTTGTGCCTAGCAGGCTTCGTGCCAGTGTATTATATTAAGCTTTGTGCCT
1 TGTATTATATCAGGCTTTGTGCCTAGCAGGCTTCATGCTGGTGTATTATATCAAGCTTTATGCCT
** * * * *
18143046 AG-AAGGCTTCATATCGGTGTGTTATATCAGGCTTTGAGCCTAACAGGCATCGTGTCAG
66 AGTAA-GCTTCATGCCGATGTATTATATCAGGCTTTGTGCCTAGCAGG-ATCGTGTCAG
* * * ** * *
18143104 TGTGTTATATCAGGCTTTGAGCTTAATAGGCTTCGTGCTAGTGTAT
1 TGTATTATATCAGGCTTTGTGCCTAGCAGGCTTCATGCTGGTGTAT
18143150 CAGGTAAGTT
Statistics
Matches: 321, Mismatches: 55, Indels: 42
0.77 0.13 0.10
Matches are distributed among these distances:
105 6 0.02
106 3 0.01
107 72 0.22
108 1 0.00
109 1 0.00
110 3 0.01
112 1 0.00
116 1 0.00
118 3 0.01
119 1 0.00
120 2 0.01
121 72 0.22
122 3 0.01
123 152 0.47
ACGTcount: A:0.22, C:0.17, G:0.24, T:0.37
Consensus pattern (122 bp):
TGTATTATATCAGGCTTTGTGCCTAGCAGGCTTCATGCTGGTGTATTATATCAAGCTTTATGCCT
AGTAAGCTTCATGCCGATGTATTATATCAGGCTTTGTGCCTAGCAGGATCGTGTCAG
Found at i:18142863 original size:25 final size:25
Alignment explanation
Indices: 18142829--18142882 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
18142819 GCAAGCTTCA
*
18142829 TGCCGATGTATTATATTAGGATTTG
1 TGCCGATGTATTATATCAGGATTTG
* *
18142854 TGCCGGTGTATTATATCAGGCTTTG
1 TGCCGATGTATTATATCAGGATTTG
18142879 TGCC
1 TGCC
18142883 TAGCAGACTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.19, C:0.15, G:0.26, T:0.41
Consensus pattern (25 bp):
TGCCGATGTATTATATCAGGATTTG
Found at i:18142886 original size:66 final size:66
Alignment explanation
Indices: 18142779--18142923 Score: 202
Period size: 66 Copynumber: 2.2 Consensus size: 66
18142769 TTATGCCTAC
* *
18142779 CAGGATTCATGCTGGTGTATTATATCAAGCTTTGTGCCTAGCA-AGCTTCATGCCGATGTATTAT
1 CAGGATTTATGCCGGTGTATTATATCAAGCTTTGTGCCTAGCAGA-CTTCATGCCGATGTATTAT
18142843 AT
65 AT
* * * * **
18142845 TAGGATTTGTGCCGGTGTATTATATCAGGCTTTGTGCCTAGCAGACTTTATGCTTATGTATTATA
1 CAGGATTTATGCCGGTGTATTATATCAAGCTTTGTGCCTAGCAGACTTCATGCCGATGTATTATA
18142910 T
66 T
18142911 CAGGATTTATGCC
1 CAGGATTTATGCC
18142924 TAGTAGGCTT
Statistics
Matches: 68, Mismatches: 10, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
66 67 0.99
67 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.22, T:0.39
Consensus pattern (66 bp):
CAGGATTTATGCCGGTGTATTATATCAAGCTTTGTGCCTAGCAGACTTCATGCCGATGTATTATA
T
Found at i:18142910 original size:148 final size:146
Alignment explanation
Indices: 18142712--18143003 Score: 378
Period size: 148 Copynumber: 2.0 Consensus size: 146
18142702 TTCGTGCCAA
* *
18142712 TGTATTATATCAGGCTTTGTGCCTAGCAGGATTCGTGCTAGTGTATTATATCAGGCTTTATGCCT
1 TGTATTATATCAGGCTTTGTGCCTAGCAGGATTCATGCTAGTGTATTATATCAGGATTTATGCCT
*
18142777 ACCAGGATTC-A-TGCTGGTGTATTATATCAAGCTTTGTGCCTAGCAAGCTTCATGCC-GATGTA
66 ACCAGGATTCGAGT-C-GGTGTA-T-TATCAAGCTTTGTACCTAGCAAGCTTCATGCCAG-TGTA
*
18142839 TTATATTAGGATTTGTGCCGG
126 TTATATCAGGATTTGTGCCGG
*
18142860 TGTATTATATCAGGCTTTGTGCCTAGCA-GACTTTATGCTTA-TGTATTATATCAGGATTTATGC
1 TGTATTATATCAGGCTTTGTGCCTAGCAGGA-TTCATGC-TAGTGTATTATATCAGGATTTATGC
** * * * *
18142923 CTAGTAGGCTTCGAGTCGGTGTATTATCAGGCTTTGTACCTAGCAGGCTTCATGTCAGTGTATTA
64 CTACCAGGATTCGAGTCGGTGTATTATCAAGCTTTGTACCTAGCAAGCTTCATGCCAGTGTATTA
*
18142988 TATCAGGCTTTGTGCC
129 TATCAGGATTTGTGCC
18143004 TAGCAGGCTT
Statistics
Matches: 127, Mismatches: 12, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
146 49 0.39
147 4 0.03
148 69 0.54
149 4 0.03
150 1 0.01
ACGTcount: A:0.21, C:0.17, G:0.23, T:0.38
Consensus pattern (146 bp):
TGTATTATATCAGGCTTTGTGCCTAGCAGGATTCATGCTAGTGTATTATATCAGGATTTATGCCT
ACCAGGATTCGAGTCGGTGTATTATCAAGCTTTGTACCTAGCAAGCTTCATGCCAGTGTATTATA
TCAGGATTTGTGCCGG
Found at i:18142946 original size:41 final size:41
Alignment explanation
Indices: 18142859--18143122 Score: 261
Period size: 41 Copynumber: 6.5 Consensus size: 41
18142849 ATTTGTGCCG
* * *
18142859 GTGTATTATATCAGGCTTTGTGCCTAGCAGACTT-TATGCTTA
1 GTGTATTATATCAGGCTTTGTGCCTAGCAGGCTTCGA-G-TCA
* * * *
18142901 -TGTATTATATCAGGATTTATGCCTAGTAGGCTTCGAGTCG
1 GTGTATTATATCAGGCTTTGTGCCTAGCAGGCTTCGAGTCA
*
18142941 GTGTA-T-TATCAGGCTTTGTACCTAGCAGGCTTC-ATGTCA
1 GTGTATTATATCAGGCTTTGTGCCTAGCAGGCTTCGA-GTCA
* *
18142980 GTGTATTATATCAGGCTTTGTGCCTAGCAGGCTTCGTGCCA
1 GTGTATTATATCAGGCTTTGTGCCTAGCAGGCTTCGAGTCA
* * * * *
18143021 GTGTATTATATTAAGCTTTGTGCCTAGAAGGCTTC-ATATCG
1 GTGTATTATATCAGGCTTTGTGCCTAGCAGGCTTCGA-GTCA
* * * * *
18143062 GTGTGTTATATCAGGCTTTGAGCCTAACAGGCATCGTGTCA
1 GTGTATTATATCAGGCTTTGTGCCTAGCAGGCTTCGAGTCA
*
18143103 GTGTGTTATATCAGGCTTTG
1 GTGTATTATATCAGGCTTTG
18143123 AGCTTAATAG
Statistics
Matches: 182, Mismatches: 32, Indels: 17
0.79 0.14 0.07
Matches are distributed among these distances:
38 1 0.01
39 31 0.17
40 3 0.02
41 146 0.80
42 1 0.01
ACGTcount: A:0.21, C:0.17, G:0.25, T:0.37
Consensus pattern (41 bp):
GTGTATTATATCAGGCTTTGTGCCTAGCAGGCTTCGAGTCA
Found at i:18143074 original size:82 final size:82
Alignment explanation
Indices: 18142853--18143122 Score: 303
Period size: 82 Copynumber: 3.3 Consensus size: 82
18142843 ATTAGGATTT
* * * * * *
18142853 GTGCCGGTGTATTATATCAGGCTTTGTGCCTAGCAGACTTTATGCTTA-TGTATTATATCAGGAT
1 GTGCCAGTGTATTATATCAGGCTTTGTGCCTAGCAGGCTTCAT-ATCAGTGTATTATATCAGGCT
* *
18142917 TTATGCCTAGTAGGCTTC
65 TTGTGCCTAGCAGGCTTC
* * * * *
18142935 GAGTCGGTGTA-T-TATCAGGCTTTGTACCTAGCAGGCTTCATGTCAGTGTATTATATCAGGCTT
1 GTGCCAGTGTATTATATCAGGCTTTGTGCCTAGCAGGCTTCATATCAGTGTATTATATCAGGCTT
18142998 TGTGCCTAGCAGGCTTC
66 TGTGCCTAGCAGGCTTC
* * * * *
18143015 GTGCCAGTGTATTATATTAAGCTTTGTGCCTAGAAGGCTTCATATCGGTGTGTTATATCAGGCTT
1 GTGCCAGTGTATTATATCAGGCTTTGTGCCTAGCAGGCTTCATATCAGTGTATTATATCAGGCTT
* * *
18143080 TGAGCCTAACAGGCATC
66 TGTGCCTAGCAGGCTTC
* *
18143097 GTGTCAGTGTGTTATATCAGGCTTTG
1 GTGCCAGTGTATTATATCAGGCTTTG
18143123 AGCTTAATAG
Statistics
Matches: 158, Mismatches: 27, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
79 2 0.01
80 65 0.41
81 2 0.01
82 89 0.56
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (82 bp):
GTGCCAGTGTATTATATCAGGCTTTGTGCCTAGCAGGCTTCATATCAGTGTATTATATCAGGCTT
TGTGCCTAGCAGGCTTC
Found at i:18147506 original size:40 final size:41
Alignment explanation
Indices: 18147422--18147510 Score: 153
Period size: 41 Copynumber: 2.2 Consensus size: 41
18147412 TTTCTGAATT
* *
18147422 AATGAAAAGGTTGAAAAGGATGTTATTCGAAAAGGATATCA
1 AATGAAAAGGTTGAAAAGGATGTTATTCCAAAAGGATAACA
18147463 AATGAAAAGGTTGAAAAGGATGTTA-TCCAAAAGGATAACA
1 AATGAAAAGGTTGAAAAGGATGTTATTCCAAAAGGATAACA
18147503 AATGAAAA
1 AATGAAAA
18147511 TGATGTATTT
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
40 21 0.46
41 25 0.54
ACGTcount: A:0.51, C:0.06, G:0.22, T:0.21
Consensus pattern (41 bp):
AATGAAAAGGTTGAAAAGGATGTTATTCCAAAAGGATAACA
Found at i:18147999 original size:2 final size:2
Alignment explanation
Indices: 18147992--18148020 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
18147982 CATATCTTTT
18147992 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
18148021 TCTTATAGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:18158809 original size:17 final size:17
Alignment explanation
Indices: 18158767--18158810 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
18158757 AATTCATAAA
18158767 AATGATGATACATGAAAT
1 AATGAT-ATACATGAAAT
*
18158785 ATTGATATA-ATGAAAT
1 AATGATATACATGAAAT
18158801 GAATGATATA
1 -AATGATATA
18158811 TGTTTATGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 7 0.30
17 11 0.48
18 5 0.22
ACGTcount: A:0.50, C:0.02, G:0.16, T:0.32
Consensus pattern (17 bp):
AATGATATACATGAAAT
Found at i:18167581 original size:26 final size:26
Alignment explanation
Indices: 18167547--18167682 Score: 125
Period size: 26 Copynumber: 5.2 Consensus size: 26
18167537 AAAGAGAACG
*
18167547 AAATAAAATAATATATAAAACAATTTA
1 AAAT-AAATAATATACAAAACAATTTA
** * *
18167574 AAGCAAATAGTAT--AAAACAATTCA
1 AAATAAATAATATACAAAACAATTTA
* * *
18167598 AAAGTAAATAATATGCAACACAAATTA
1 AAA-TAAATAATATACAAAACAATTTA
* * *
18167625 AAATAAATAACATACAAAGCAAATTA
1 AAATAAATAATATACAAAACAATTTA
18167651 AAATAAATAATATA-AAAGACAATTTA
1 AAATAAATAATATACAAA-ACAATTTA
18167677 AAATAA
1 AAATAA
18167683 TGTATAAAAT
Statistics
Matches: 88, Mismatches: 17, Indels: 9
0.77 0.15 0.08
Matches are distributed among these distances:
24 12 0.14
25 11 0.12
26 52 0.59
27 13 0.15
ACGTcount: A:0.64, C:0.08, G:0.04, T:0.24
Consensus pattern (26 bp):
AAATAAATAATATACAAAACAATTTA
Found at i:18167607 original size:25 final size:23
Alignment explanation
Indices: 18167556--18167607 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 23
18167546 GAAATAAAAT
*
18167556 AATATATAAAACAATTTAAAGCA
1 AATATATAAAACAATTAAAAGCA
*
18167579 AATAGTATAAAACAATTCAAAAGTA
1 AATA-TATAAAACAATT-AAAAGCA
18167604 AATA
1 AATA
18167608 ATATGCAACA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 4 0.16
24 12 0.48
25 9 0.36
ACGTcount: A:0.62, C:0.08, G:0.06, T:0.25
Consensus pattern (23 bp):
AATATATAAAACAATTAAAAGCA
Found at i:18167704 original size:24 final size:26
Alignment explanation
Indices: 18167677--18167735 Score: 68
Period size: 28 Copynumber: 2.3 Consensus size: 26
18167667 AGACAATTTA
*
18167677 AAATAATGTATAAA-A-TTTTAAAAT
1 AAATAATGTAAAAATAGTTTTAAAAT
*
18167701 AAATAATATGTAAAAATAGTTTTCAAAT
1 AAAT-A-ATGTAAAAATAGTTTTAAAAT
18167729 AAATAAT
1 AAATAAT
18167736 ATGCATAACA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
24 4 0.14
25 1 0.03
26 10 0.34
27 2 0.07
28 12 0.41
ACGTcount: A:0.58, C:0.02, G:0.05, T:0.36
Consensus pattern (26 bp):
AAATAATGTAAAAATAGTTTTAAAAT
Found at i:18169562 original size:44 final size:44
Alignment explanation
Indices: 18169446--18169609 Score: 181
Period size: 44 Copynumber: 3.7 Consensus size: 44
18169436 TCATCGTTTT
* * *
18169446 AATCCGCTCCACTGCAACTTC-AGTGAGATAGGATTATTTATCTTC
1 AATCTGCTCCACTGCAACTTCAAG-GAGATAAGATTA-GTATCTTC
* * *
18169491 AGTCTGCTCCACTGCAACTTTAGGGAGATAAGACTT-GTAAT-TTC
1 AATCTGCTCCACTGCAACTTCAAGGAGATAAGA-TTAGT-ATCTTC
* *
18169535 AATATGCTCCACTGCAACTTCAAGGAGATAAGATTGGTATCTTC
1 AATCTGCTCCACTGCAACTTCAAGGAGATAAGATTAGTATCTTC
* *
18169579 AACCTGCTCCACTGCAACTTCAGGGAGATAA
1 AATCTGCTCCACTGCAACTTCAAGGAGATAA
18169610 TGTTTGATAT
Statistics
Matches: 101, Mismatches: 13, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
43 4 0.04
44 66 0.65
45 28 0.28
46 3 0.03
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.29
Consensus pattern (44 bp):
AATCTGCTCCACTGCAACTTCAAGGAGATAAGATTAGTATCTTC
Found at i:18169797 original size:48 final size:46
Alignment explanation
Indices: 18169699--18169861 Score: 188
Period size: 46 Copynumber: 3.5 Consensus size: 46
18169689 CCTACTCTAT
* * * *
18169699 TGCAACTTCAGAGAGATAAGGTTTGCGGC--TTTAATCTGCTCCAC
1 TGCAACTTCAGGGAGATAAGATTTGAGCCATTTTAATCTGCTCCAC
18169743 TGCAACTTCAGGGAGATAAGATTTGTAGCCATTTTCAATCTGCTCCAC
1 TGCAACTTCAGGGAGATAAGATTTG-AGCCATTTT-AATCTGCTCCAC
* *** *
18169791 TGCAACTTTAGGGAGATAAGA-TTGATTTATTTTTAACCTGCTCCAC
1 TGCAACTTCAGGGAGATAAGATTTGAGCCA-TTTTAATCTGCTCCAC
*
18169837 TGCAACTTCAAGGAGATAAGATTTG
1 TGCAACTTCAGGGAGATAAGATTTG
18169862 CCATGATAAC
Statistics
Matches: 102, Mismatches: 11, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
44 23 0.23
45 2 0.02
46 32 0.31
47 13 0.13
48 32 0.31
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (46 bp):
TGCAACTTCAGGGAGATAAGATTTGAGCCATTTTAATCTGCTCCAC
Found at i:18170509 original size:45 final size:45
Alignment explanation
Indices: 18170424--18170510 Score: 102
Period size: 45 Copynumber: 1.9 Consensus size: 45
18170414 AGCTCGAAAC
* * * *
18170424 GAATAAATTTATCAAGATAGAAAATTTTGCTAGAATACAAAATGA
1 GAATAAATTAATCAAGATAGAAAATTTTGCCAAAACACAAAATGA
* ***
18170469 GAATAAATTAATCAAGATGGCGTATTTTGCCAAAACACAAAA
1 GAATAAATTAATCAAGATAGAAAATTTTGCCAAAACACAAAA
18170511 ATGAATAAAA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
45 34 1.00
ACGTcount: A:0.49, C:0.10, G:0.14, T:0.26
Consensus pattern (45 bp):
GAATAAATTAATCAAGATAGAAAATTTTGCCAAAACACAAAATGA
Found at i:18179336 original size:22 final size:22
Alignment explanation
Indices: 18179310--18179353 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
18179300 CCTCTTCGCC
18179310 AAACTCGTTGTCGATTGTCGTT
1 AAACTCGTTGTCGATTGTCGTT
18179332 AAACTCGTTGTCGATTGTCGTT
1 AAACTCGTTGTCGATTGTCGTT
18179354 CTCTTTAGGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.18, C:0.18, G:0.23, T:0.41
Consensus pattern (22 bp):
AAACTCGTTGTCGATTGTCGTT
Found at i:18180399 original size:29 final size:29
Alignment explanation
Indices: 18180357--18180418 Score: 124
Period size: 29 Copynumber: 2.1 Consensus size: 29
18180347 GTAACATGTG
18180357 TGTTTGGAATATTGTATTCGTATTTTGTA
1 TGTTTGGAATATTGTATTCGTATTTTGTA
18180386 TGTTTGGAATATTGTATTCGTATTTTGTA
1 TGTTTGGAATATTGTATTCGTATTTTGTA
18180415 TGTT
1 TGTT
18180419 AATGGAAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.19, C:0.03, G:0.21, T:0.56
Consensus pattern (29 bp):
TGTTTGGAATATTGTATTCGTATTTTGTA
Found at i:18184435 original size:23 final size:22
Alignment explanation
Indices: 18184382--18184438 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
18184372 ATGTTTTGGA
*
18184382 AATGACTAAATGTGGTACATTT
1 AATGCCTAAATGTGGTACATTT
* *
18184404 AATGGCTAAATGTGGTACGTTTT
1 AATGCCTAAATGTGGTAC-ATTT
*
18184427 AGTGCCTAAATG
1 AATGCCTAAATG
18184439 GACTAGAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
22 17 0.57
23 13 0.43
ACGTcount: A:0.32, C:0.11, G:0.23, T:0.35
Consensus pattern (22 bp):
AATGCCTAAATGTGGTACATTT
Found at i:18190070 original size:24 final size:24
Alignment explanation
Indices: 18190042--18190090 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
18190032 CCAATAAGTA
18190042 AGATTCACATACTTCAAATTGTTC
1 AGATTCACATACTTCAAATTGTTC
18190066 AGATTCACATACTTCAAATTGTTC
1 AGATTCACATACTTCAAATTGTTC
18190090 A
1 A
18190091 AAAACAAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.35, C:0.20, G:0.08, T:0.37
Consensus pattern (24 bp):
AGATTCACATACTTCAAATTGTTC
Found at i:18209315 original size:44 final size:46
Alignment explanation
Indices: 18209261--18209353 Score: 136
Period size: 44 Copynumber: 2.1 Consensus size: 46
18209251 TTACACCTCT
* * *
18209261 ATTCTATTCAACCAAACACAAGAA-TACC-ATTATGCCTCTATTCC
1 ATTCCATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCC
*
18209305 ATTCCATTCAACCAAACAAAATAATTACCTATTACGCCTCTATTCC
1 ATTCCATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCC
18209351 ATT
1 ATT
18209354 ATACATCTAT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
44 21 0.49
45 4 0.09
46 18 0.42
ACGTcount: A:0.37, C:0.29, G:0.03, T:0.31
Consensus pattern (46 bp):
ATTCCATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCC
Found at i:18209362 original size:16 final size:16
Alignment explanation
Indices: 18209343--18209386 Score: 79
Period size: 16 Copynumber: 2.8 Consensus size: 16
18209333 CTATTACGCC
18209343 TCTATTCCATTATACA
1 TCTATTCCATTATACA
*
18209359 TCTATTCCATTATGCA
1 TCTATTCCATTATACA
18209375 TCTATTCCATTA
1 TCTATTCCATTA
18209387 CAGCGAACCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.27, C:0.25, G:0.02, T:0.45
Consensus pattern (16 bp):
TCTATTCCATTATACA
Found at i:18213146 original size:4 final size:4
Alignment explanation
Indices: 18213137--18213161 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
18213127 GTTTTTAGAA
18213137 TAAT TAAT TAAT TAAT TAAT TAAT T
1 TAAT TAAT TAAT TAAT TAAT TAAT T
18213162 GAAGTTCGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TAAT
Found at i:18215028 original size:53 final size:53
Alignment explanation
Indices: 18214970--18215078 Score: 218
Period size: 53 Copynumber: 2.1 Consensus size: 53
18214960 ATGTCATATA
18214970 ATTTAGGAAAAGAATGTCACACGTACTTGCCATGTATATATTGATCATTCATT
1 ATTTAGGAAAAGAATGTCACACGTACTTGCCATGTATATATTGATCATTCATT
18215023 ATTTAGGAAAAGAATGTCACACGTACTTGCCATGTATATATTGATCATTCATT
1 ATTTAGGAAAAGAATGTCACACGTACTTGCCATGTATATATTGATCATTCATT
18215076 ATT
1 ATT
18215079 GAAACTAGAC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 56 1.00
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.37
Consensus pattern (53 bp):
ATTTAGGAAAAGAATGTCACACGTACTTGCCATGTATATATTGATCATTCATT
Found at i:18217858 original size:21 final size:21
Alignment explanation
Indices: 18217834--18217876 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
18217824 GTTGAGTAAA
*
18217834 TTATTTAATTGGAAAATTAAT
1 TTATTTAACTGGAAAATTAAT
*
18217855 TTATTTAACTGGGAAATTAAT
1 TTATTTAACTGGAAAATTAAT
18217876 T
1 T
18217877 AATTAAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.40, C:0.02, G:0.12, T:0.47
Consensus pattern (21 bp):
TTATTTAACTGGAAAATTAAT
Found at i:18222785 original size:15 final size:15
Alignment explanation
Indices: 18222758--18222791 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
18222748 AATTGTATAG
18222758 AAATAATATAAATAA
1 AAATAATATAAATAA
18222773 TAAATAA-ATAAATAA
1 -AAATAATATAAATAA
18222788 AAAT
1 AAAT
18222792 CAATGACATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 4 0.22
15 8 0.44
16 6 0.33
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (15 bp):
AAATAATATAAATAA
Found at i:18223287 original size:23 final size:23
Alignment explanation
Indices: 18223246--18223293 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 23
18223236 ATATTAGTTG
18223246 AAAAAAATAAATATGTACATATAT
1 AAAAAAATAAATA-GTACATATAT
18223270 AAAAGAAATAAATA-TACATATAT
1 AAAA-AAATAAATAGTACATATAT
18223293 A
1 A
18223294 TAGATTTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 10 0.43
24 4 0.17
25 9 0.39
ACGTcount: A:0.65, C:0.04, G:0.04, T:0.27
Consensus pattern (23 bp):
AAAAAAATAAATAGTACATATAT
Found at i:18223294 original size:25 final size:24
Alignment explanation
Indices: 18223246--18223295 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
18223236 ATATTAGTTG
**
18223246 AAAAAAATAAATATGTACATATAT
1 AAAAAAATAAATATACACATATAT
*
18223270 AAAAGAAATAAATATACATATATAT
1 AAAA-AAATAAATATACACATATAT
18223295 A
1 A
18223296 GATTTAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 4 0.18
25 18 0.82
ACGTcount: A:0.64, C:0.04, G:0.04, T:0.28
Consensus pattern (24 bp):
AAAAAAATAAATATACACATATAT
Found at i:18224955 original size:44 final size:44
Alignment explanation
Indices: 18224907--18225022 Score: 121
Period size: 44 Copynumber: 2.6 Consensus size: 44
18224897 CTAATCCACT
* * *
18224907 CCACTACAACTTTAGGGAGATAGGA-TTTGTTCATTCAGTCTGCC
1 CCACTACAACTTTAGGGAGATAAGACTTTCTT-ACTCAGTCTGCC
* *
18224951 CCACTGCAA-TTTCAGGG-GAATAAGACTTTCTTACTCAGTCTGCT
1 CCACTACAACTTT-AGGGAG-ATAAGACTTTCTTACTCAGTCTGCC
* *
18224995 CCATTACAACTTCAGGGAGATAAGACTT
1 CCACTACAACTTTAGGGAGATAAGACTT
18225023 ACGCGATCTA
Statistics
Matches: 59, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
43 4 0.07
44 47 0.80
45 8 0.14
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (44 bp):
CCACTACAACTTTAGGGAGATAAGACTTTCTTACTCAGTCTGCC
Found at i:18225098 original size:44 final size:44
Alignment explanation
Indices: 18225035--18225148 Score: 131
Period size: 44 Copynumber: 2.6 Consensus size: 44
18225025 GCGATCTACT
** *
18225035 CTCTGCAACTTCAAAGAGATAAGATCT-GTAATTTTAATCCACTC
1 CTCTGCAACTTCAGGGAGATAAGAT-TAGTAACTTTAATCCACTC
* * ** *
18225079 CTCTGCAACTTCAGGGAGATAGGATTATTGGCTTTAATCTACTC
1 CTCTGCAACTTCAGGGAGATAAGATTAGTAACTTTAATCCACTC
*
18225123 CACTGCAACTTCAGGGAGATAAGATT
1 CTCTGCAACTTCAGGGAGATAAGATT
18225149 CACCATCTTC
Statistics
Matches: 59, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
43 1 0.02
44 58 0.98
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.31
Consensus pattern (44 bp):
CTCTGCAACTTCAGGGAGATAAGATTAGTAACTTTAATCCACTC
Found at i:18225649 original size:44 final size:44
Alignment explanation
Indices: 18225603--18225855 Score: 337
Period size: 44 Copynumber: 5.8 Consensus size: 44
18225593 CAAGGTCTAC
* * * * **
18225603 AATCTTTCACCTATTCCACTGCTGACGAGGGAGATAGGATTCAC
1 AATCTTTAACTTATTCCACTGCTGACCAGGGAGATAAGATTCGT
* ** *
18225647 AATCCTCCACTTATTCCACTGCTGAACAGGGAGATAAGATTCGT
1 AATCTTTAACTTATTCCACTGCTGACCAGGGAGATAAGATTCGT
* *
18225691 ATTCTTCAACTTATTCCACTGCTGACCAGGGAGATAAGATTCGT
1 AATCTTTAACTTATTCCACTGCTGACCAGGGAGATAAGATTCGT
*
18225735 AATCTTTAACTTATTCCACTGCTGACCAGGGAGATAAAATTCGT
1 AATCTTTAACTTATTCCACTGCTGACCAGGGAGATAAGATTCGT
*
18225779 AAT-TTTAACTTATTTCACTGCTGACCAGGGAGATAAGATTCGT
1 AATCTTTAACTTATTCCACTGCTGACCAGGGAGATAAGATTCGT
* * **
18225822 AATCTTTAACCTATTCCATTGCTGTTCAGGGAGA
1 AATCTTTAACTTATTCCACTGCTGACCAGGGAGA
18225856 AAGGGTTGGG
Statistics
Matches: 186, Mismatches: 22, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
43 41 0.22
44 145 0.78
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (44 bp):
AATCTTTAACTTATTCCACTGCTGACCAGGGAGATAAGATTCGT
Found at i:18225984 original size:88 final size:88
Alignment explanation
Indices: 18225870--18226084 Score: 322
Period size: 88 Copynumber: 2.4 Consensus size: 88
18225860 GTTGGGGTCA
* * *
18225870 TCGATCTGCTTCGCTATCAGTGCAGGAATACCAGATCTGCTATTTTTAACCTGCTCCACCGCAAC
1 TCGATCTGCTTCGCTATCGGTGCAGGAAGACAAGATCTGCTATTTTTAACCTGCTCCACCGCAAC
18225935 CCAGGGAGGCAAGGCTGGTGTCT
66 CCAGGGAGGCAAGGCTGGTGTCT
* * ** * *
18225958 TCGATCTGCTTCGCTGTCGGTACAGGAAGGGAAGATCTGCTATTTTTAACCTGCTCCGCTGCAAC
1 TCGATCTGCTTCGCTATCGGTGCAGGAAGACAAGATCTGCTATTTTTAACCTGCTCCACCGCAAC
18226023 CCAGGGAGGCAAGGCTGGTGTCT
66 CCAGGGAGGCAAGGCTGGTGTCT
* * *
18226046 TCGATCTGCTTCACTATCGGTGCAGGAAGGCAAAATCTG
1 TCGATCTGCTTCGCTATCGGTGCAGGAAGACAAGATCTG
18226085 TTATCTTCAC
Statistics
Matches: 113, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
88 113 1.00
ACGTcount: A:0.21, C:0.26, G:0.27, T:0.26
Consensus pattern (88 bp):
TCGATCTGCTTCGCTATCGGTGCAGGAAGACAAGATCTGCTATTTTTAACCTGCTCCACCGCAAC
CCAGGGAGGCAAGGCTGGTGTCT
Found at i:18228108 original size:25 final size:23
Alignment explanation
Indices: 18228079--18228124 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 23
18228069 AAGAAAATCC
*
18228079 AAAAGAATGAAAGAATAATTATTTA
1 AAAAGAAT-AAA-AAAAATTATTTA
18228104 AAAAGAATAAAAAAAATTATT
1 AAAAGAATAAAAAAAATTATT
18228125 GGCTCAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 9 0.45
24 3 0.15
25 8 0.40
ACGTcount: A:0.65, C:0.00, G:0.09, T:0.26
Consensus pattern (23 bp):
AAAAGAATAAAAAAAATTATTTA
Found at i:18232299 original size:49 final size:47
Alignment explanation
Indices: 18232246--18232337 Score: 130
Period size: 49 Copynumber: 1.9 Consensus size: 47
18232236 TTTAAAAAAA
* *
18232246 TGAAAAATAAATAAATGTATATATATATAAATATGAAAAAAATATTAGT
1 TGAAAAATAAATAAATATATACATATATAAA-A-GAAAAAAATATTAGT
* *
18232295 TGAAAAATAAATAAATATGTACATATATAAAAGAAATAAATAT
1 TGAAAAATAAATAAATATATACATATATAAAAGAAAAAAATAT
18232338 GCATATATAT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
47 10 0.26
48 1 0.03
49 28 0.72
ACGTcount: A:0.61, C:0.01, G:0.08, T:0.30
Consensus pattern (47 bp):
TGAAAAATAAATAAATATATACATATATAAAAGAAAAAAATATTAGT
Found at i:18232326 original size:25 final size:25
Alignment explanation
Indices: 18232298--18232348 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
18232288 TATTAGTTGA
* *
18232298 AAAATAAATAAATATGTACATATAT
1 AAAAGAAATAAATATGCACATATAT
*
18232323 AAAAGAAATAAATATGCATATATAT
1 AAAAGAAATAAATATGCACATATAT
18232348 A
1 A
18232349 TATATATTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.61, C:0.04, G:0.06, T:0.29
Consensus pattern (25 bp):
AAAAGAAATAAATATGCACATATAT
Found at i:18241330 original size:23 final size:23
Alignment explanation
Indices: 18241280--18241321 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
18241270 TTTTCTACTA
18241280 GTTTAGCATGTCTTCTGCTTGTT
1 GTTTAGCATGTCTTCTGCTTGTT
18241303 GTTTAGCATGT-TTCT-CTTG
1 GTTTAGCATGTCTTCTGCTTG
18241322 CTTCTTTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 4 0.21
22 4 0.21
23 11 0.58
ACGTcount: A:0.10, C:0.17, G:0.21, T:0.52
Consensus pattern (23 bp):
GTTTAGCATGTCTTCTGCTTGTT
Found at i:18243088 original size:25 final size:25
Alignment explanation
Indices: 18243060--18243153 Score: 125
Period size: 25 Copynumber: 3.8 Consensus size: 25
18243050 ACGAGTTATG
*
18243060 AATCGGGAAGCTCATACGAGCTGCA
1 AATCAGGAAGCTCATACGAGCTGCA
*
18243085 AATCAGGAAGCTCATACGAGCTGTA
1 AATCAGGAAGCTCATACGAGCTGCA
* * * * *
18243110 AATTAGAAAGTTCATACGAGTTACA
1 AATCAGGAAGCTCATACGAGCTGCA
18243135 AATCAGGAAGCTCATACGA
1 AATCAGGAAGCTCATACGA
18243154 ACTGTGGTGT
Statistics
Matches: 58, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 58 1.00
ACGTcount: A:0.38, C:0.19, G:0.22, T:0.20
Consensus pattern (25 bp):
AATCAGGAAGCTCATACGAGCTGCA
Found at i:18247070 original size:27 final size:27
Alignment explanation
Indices: 18247040--18247210 Score: 177
Period size: 27 Copynumber: 6.3 Consensus size: 27
18247030 TAAAGGACCA
* * *
18247040 AAATACCCTCGAAGGGTAAACTCACTG
1 AAATACCCCCGAAGGGTAAAATGACTG
* *
18247067 AAATACCCTCAAAGGGTAAAATGA-TCG
1 AAATACCCCCGAAGGGTAAAATGACT-G
*
18247094 AAATACCCCCGAAGGGTAAAATAACT-
1 AAATACCCCCGAAGGGTAAAATGACTG
*
18247120 ACAATACCCCCGAAGGGTAAAATGACCG
1 A-AATACCCCCGAAGGGTAAAATGACTG
*
18247148 AAATACCCCCGAAGGGTTAAATGA-TCG
1 AAATACCCCCGAAGGGTAAAATGACT-G
* * *
18247175 AAATACCCTCGAAGTGTAAAATAACTG
1 AAATACCCCCGAAGGGTAAAATGACTG
**
18247202 TTATACCCC
1 AAATACCCC
18247211 TAGGAGTTGA
Statistics
Matches: 121, Mismatches: 17, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
26 2 0.02
27 116 0.96
28 3 0.02
ACGTcount: A:0.40, C:0.24, G:0.18, T:0.18
Consensus pattern (27 bp):
AAATACCCCCGAAGGGTAAAATGACTG
Found at i:18247126 original size:54 final size:53
Alignment explanation
Indices: 18247035--18247196 Score: 198
Period size: 54 Copynumber: 3.0 Consensus size: 53
18247025 GGGCCTAAAG
* * * * *
18247035 GACCAAAATACCCTCGAAGGGTAAACTCACTGAAATACCCTCAAAGGGTAAAAT
1 GACCGAAATACCCCCGAAGGGTAAAATAACT-AAATACCCTCGAAGGGTAAAAT
* *
18247089 GATCGAAATACCCCCGAAGGGTAAAATAACTACAATACCCCCGAAGGGTAAAAT
1 GACCGAAATACCCCCGAAGGGTAAAATAACTA-AATACCCTCGAAGGGTAAAAT
* * * *
18247143 GACCGAAATACCCCCGAAGGGTTAAATGATCGAAATACCCTCGAAGTGTAAAAT
1 GACCGAAATACCCCCGAAGGGTAAAAT-AACTAAATACCCTCGAAGGGTAAAAT
18247197 AACTGTTATA
Statistics
Matches: 93, Mismatches: 13, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
53 1 0.01
54 89 0.96
55 3 0.03
ACGTcount: A:0.41, C:0.23, G:0.19, T:0.17
Consensus pattern (53 bp):
GACCGAAATACCCCCGAAGGGTAAAATAACTAAATACCCTCGAAGGGTAAAAT
Found at i:18247210 original size:81 final size:81
Alignment explanation
Indices: 18247041--18247200 Score: 239
Period size: 81 Copynumber: 2.0 Consensus size: 81
18247031 AAAGGACCAA
* * * *
18247041 AATACCCTCGAAGGGTAAACTCACTGAAATACCCTCAAAGGGTAAAATGATCGAAATACCCCCGA
1 AATACCCCCGAAGGGTAAAATCACCGAAATACCCCCAAAGGGTAAAATGATCGAAATACCCCCGA
18247106 AGGGTAAAATAACTAC
66 AGGGTAAAATAACTAC
* * * *
18247122 AATACCCCCGAAGGGTAAAATGACCGAAATACCCCCGAAGGGTTAAATGATCGAAATACCCTCGA
1 AATACCCCCGAAGGGTAAAATCACCGAAATACCCCCAAAGGGTAAAATGATCGAAATACCCCCGA
*
18247187 AGTGTAAAATAACT
66 AGGGTAAAATAACT
18247201 GTTATACCCC
Statistics
Matches: 70, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
81 70 1.00
ACGTcount: A:0.41, C:0.23, G:0.18, T:0.17
Consensus pattern (81 bp):
AATACCCCCGAAGGGTAAAATCACCGAAATACCCCCAAAGGGTAAAATGATCGAAATACCCCCGA
AGGGTAAAATAACTAC
Found at i:18248458 original size:17 final size:18
Alignment explanation
Indices: 18248433--18248468 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
18248423 TTGTTAAAGT
18248433 AAACAGAAA-CTGTAGGG
1 AAACAGAAATCTGTAGGG
*
18248450 AAACTGAAATCTGTAGGG
1 AAACAGAAATCTGTAGGG
18248468 A
1 A
18248469 GACTTTTGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.44, C:0.11, G:0.28, T:0.17
Consensus pattern (18 bp):
AAACAGAAATCTGTAGGG
Found at i:18253289 original size:32 final size:32
Alignment explanation
Indices: 18253248--18253312 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
18253238 TATATGGGAG
18253248 TGTTCGAGAAGTCTAGGTTCAAGTCTTGGCTT
1 TGTTCGAGAAGTCTAGGTTCAAGTCTTGGCTT
*
18253280 TGTTCGAGAAGTCTGGGTTCAAGTCTTGGCTT
1 TGTTCGAGAAGTCTAGGTTCAAGTCTTGGCTT
18253312 T
1 T
18253313 TGCAGAATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.17, C:0.15, G:0.29, T:0.38
Consensus pattern (32 bp):
TGTTCGAGAAGTCTAGGTTCAAGTCTTGGCTT
Found at i:18255022 original size:27 final size:27
Alignment explanation
Indices: 18254688--18255022 Score: 329
Period size: 27 Copynumber: 12.4 Consensus size: 27
18254678 TTAATGGGCC
** * *
18254688 TAAAATGACCAAAATACTCTCAAAGGG
1 TAAAATGACTGAAATACCCTCGAAGGG
*
18254715 TAAAATGA-TCGAAATACCCTCAAAGGG
1 TAAAATGACT-GAAATACCCTCGAAGGG
* * * * * *
18254742 TATAATAATTGAAACACCCTCAAAGGA
1 TAAAATGACTGAAATACCCTCGAAGGG
* *
18254769 TAAAATGACTGAAATACCCCCGAAGGA
1 TAAAATGACTGAAATACCCTCGAAGGG
* * *
18254796 TAAAATGACAGAATTACCCTCGAATGG
1 TAAAATGACTGAAATACCCTCGAAGGG
* **
18254823 TAAAATGACCGAAATACCCGAGAAGGG
1 TAAAATGACTGAAATACCCTCGAAGGG
*
18254850 TAAAATGA-TAGAAATACCCCCGAAGGG
1 TAAAATGACT-GAAATACCCTCGAAGGG
*
18254877 TAAAATGA-TCGAAATACCCTCGAAGCG
1 TAAAATGACT-GAAATACCCTCGAAGGG
* * *
18254904 TAAAATGA-TCGAAATACCTTTGAAGAG
1 TAAAATGACT-GAAATACCCTCGAAGGG
*
18254931 TAAAATGACCGAAATACACC-CGAAGGG
1 TAAAATGACTGAAATAC-CCTCGAAGGG
* * *
18254958 TAAAATAACTGAAATACCCCCGAAGGT
1 TAAAATGACTGAAATACCCTCGAAGGG
18254985 TAAAATGACTGAAATACCCTCGAAGGG
1 TAAAATGACTGAAATACCCTCGAAGGG
*
18255012 TAAAATAACTG
1 TAAAATGACTG
18255023 TTATACCCCT
Statistics
Matches: 259, Mismatches: 43, Indels: 12
0.82 0.14 0.04
Matches are distributed among these distances:
26 2 0.01
27 255 0.98
28 2 0.01
ACGTcount: A:0.44, C:0.19, G:0.19, T:0.18
Consensus pattern (27 bp):
TAAAATGACTGAAATACCCTCGAAGGG
Found at i:18255268 original size:26 final size:26
Alignment explanation
Indices: 18255195--18255288 Score: 109
Period size: 26 Copynumber: 3.6 Consensus size: 26
18255185 TTGCCACATA
* *
18255195 TACTGTTACAGGCAGCCTTGCTGTGT
1 TACTATTACTGGCAGCCTTGCTGTGT
*
18255221 TACTATTAATGGCAGCCTTGCTGTGT
1 TACTATTACTGGCAGCCTTGCTGTGT
*
18255247 TACTATTACTGGCAG-CTCTGCTGCGT
1 TACTATTACTGGCAGCCT-TGCTGTGT
* * *
18255273 CATTATTACTAGCAGC
1 TACTATTACTGGCAGC
18255289 TTCTCTGCGA
Statistics
Matches: 58, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
25 2 0.03
26 56 0.97
ACGTcount: A:0.19, C:0.23, G:0.22, T:0.35
Consensus pattern (26 bp):
TACTATTACTGGCAGCCTTGCTGTGT
Found at i:18258244 original size:25 final size:25
Alignment explanation
Indices: 18258206--18258253 Score: 80
Period size: 25 Copynumber: 1.9 Consensus size: 25
18258196 TCATATTCAT
18258206 GTATGCTCATACGAGCTATGAATCA
1 GTATGCTCATACGAGCTATGAATCA
18258231 GTATGCTC-TCACGAGCTATGAAT
1 GTATGCTCAT-ACGAGCTATGAAT
18258254 TGGGAAGCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 1 0.05
25 21 0.95
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (25 bp):
GTATGCTCATACGAGCTATGAATCA
Found at i:18258269 original size:25 final size:25
Alignment explanation
Indices: 18258210--18258270 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
18258200 ATTCATGTAT
* *
18258210 GCTCATACGAGCTATGAATCAGTAT
1 GCTCATACGAGCTATGAATCAGGAA
**
18258235 GCTC-TCACGAGCTATGAATTGGGAA
1 GCTCAT-ACGAGCTATGAATCAGGAA
18258260 GCTCATACGAG
1 GCTCATACGAG
18258271 TTGTGGTGTG
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
24 1 0.03
25 28 0.93
26 1 0.03
ACGTcount: A:0.30, C:0.21, G:0.25, T:0.25
Consensus pattern (25 bp):
GCTCATACGAGCTATGAATCAGGAA
Found at i:18276078 original size:27 final size:27
Alignment explanation
Indices: 18276048--18276112 Score: 103
Period size: 27 Copynumber: 2.4 Consensus size: 27
18276038 CTATTTCCCT
* * *
18276048 CAAAGACTTTATTTTATGATTTTGAAA
1 CAAAGACTTGATATTATAATTTTGAAA
18276075 CAAAGACTTGATATTATAATTTTGAAA
1 CAAAGACTTGATATTATAATTTTGAAA
18276102 CAAAGACTTGA
1 CAAAGACTTGA
18276113 GTGTGAAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.37
Consensus pattern (27 bp):
CAAAGACTTGATATTATAATTTTGAAA
Found at i:18280202 original size:27 final size:27
Alignment explanation
Indices: 18280172--18280230 Score: 100
Period size: 27 Copynumber: 2.2 Consensus size: 27
18280162 AAAAAAAAAA
18280172 CCTTTCTGGAAATCTATGAAAAGGAAG
1 CCTTTCTGGAAATCTATGAAAAGGAAG
**
18280199 CCTTTCTGGCTATCTATGAAAAGGAAG
1 CCTTTCTGGAAATCTATGAAAAGGAAG
18280226 CCTTT
1 CCTTT
18280231 GTGACGATCT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.31
Consensus pattern (27 bp):
CCTTTCTGGAAATCTATGAAAAGGAAG
Found at i:18280240 original size:27 final size:27
Alignment explanation
Indices: 18280183--18280260 Score: 95
Period size: 27 Copynumber: 2.9 Consensus size: 27
18280173 CTTTCTGGAA
* * *
18280183 ATCTATGAAAAGGAAGCCTTTCTGGCT
1 ATCTATGAAAAGGAAGCCTTTGTGACG
18280210 ATCTATGAAAAGGAAGCCTTTGTGACG
1 ATCTATGAAAAGGAAGCCTTTGTGACG
* *
18280237 ATCTAT-AAAGGGAATGCATTTGTG
1 ATCTATGAAAAGGAA-GCCTTTGTG
18280261 GTGCACTTTA
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
26 7 0.16
27 38 0.84
ACGTcount: A:0.32, C:0.14, G:0.24, T:0.29
Consensus pattern (27 bp):
ATCTATGAAAAGGAAGCCTTTGTGACG
Found at i:18284647 original size:13 final size:13
Alignment explanation
Indices: 18284629--18284705 Score: 100
Period size: 13 Copynumber: 5.9 Consensus size: 13
18284619 AGTTCTTTAT
18284629 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
*
18284642 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
* *
18284655 TGCTGTGGAAAAG
1 TGCTTTTGAAAAG
*
18284668 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
*
18284681 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
*
18284694 TACTTTTGAAAA
1 TGCTTTTGAAAA
18284706 TTTTGAATGT
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 55 1.00
ACGTcount: A:0.29, C:0.08, G:0.27, T:0.36
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Done.