Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr10
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: 57797951
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 1092422 characters in sequence are not A, C, G, or T
File 160 of 187
Found at i:48514980 original size:3 final size:3
Alignment explanation
Indices: 48514972--48515016 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
48514962 ACATCTTACT
48514972 CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA
1 CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA
48515017 TTCTTTTGCT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.67, G:0.00, T:0.00
Consensus pattern (3 bp):
CCA
Found at i:48517391 original size:11 final size:11
Alignment explanation
Indices: 48517375--48517404 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
48517365 TCAAAGACCG
48517375 ACCATCCATCC
1 ACCATCCATCC
48517386 ACCATCCATCC
1 ACCATCCATCC
48517397 ACCATCCA
1 ACCATCCA
48517405 ATAGCTACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.30, C:0.53, G:0.00, T:0.17
Consensus pattern (11 bp):
ACCATCCATCC
Found at i:48521061 original size:29 final size:29
Alignment explanation
Indices: 48521015--48521070 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
48521005 TAACGTCATT
* * *
48521015 TTATATTTATATATTATATATATAAATAA
1 TTATATTTATATAATATAAAAATAAATAA
*
48521044 TTATATTTATTTAATATAAAAATAAAT
1 TTATATTTATATAATATAAAAATAAAT
48521071 TGATGCATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (29 bp):
TTATATTTATATAATATAAAAATAAATAA
Found at i:48521997 original size:17 final size:17
Alignment explanation
Indices: 48521946--48522006 Score: 56
Period size: 17 Copynumber: 3.8 Consensus size: 17
48521936 TTCCTAAAAT
*
48521946 ATTATTTTTTCAATT-A
1 ATTAATTTTTCAATTAA
* * *
48521962 ATTTA-TATT-AATTAG
1 ATTAATTTTTCAATTAA
48521977 ATTAATTTTTCAATTAA
1 ATTAATTTTTCAATTAA
*
48521994 ATTATTTTTTCAA
1 ATTAATTTTTCAA
48522007 CCCAATTCTA
Statistics
Matches: 34, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
14 4 0.12
15 7 0.21
16 6 0.18
17 17 0.50
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.57
Consensus pattern (17 bp):
ATTAATTTTTCAATTAA
Found at i:48529818 original size:22 final size:22
Alignment explanation
Indices: 48529792--48529849 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
48529782 GTAAATATAT
*
48529792 ATATAATAATAT-AATAAGGTAA
1 ATATAATAAAATAAATAA-GTAA
48529814 ATATAATAAAATAAATAAGTAA
1 ATATAATAAAATAAATAAGTAA
48529836 ATGA-AAT-AAATAAA
1 AT-ATAATAAAATAAA
48529850 GAACAAAAGT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
21 7 0.21
22 20 0.61
23 6 0.18
ACGTcount: A:0.66, C:0.00, G:0.07, T:0.28
Consensus pattern (22 bp):
ATATAATAAAATAAATAAGTAA
Found at i:48529828 original size:14 final size:14
Alignment explanation
Indices: 48529783--48529830 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
48529773 AATATTTAAG
*
48529783 TAAATATATATATAA
1 TAAATATA-ATAAAA
**
48529798 T-AATATAATAAGG
1 TAAATATAATAAAA
48529811 TAAATATAATAAAA
1 TAAATATAATAAAA
48529825 TAAATA
1 TAAATA
48529831 AGTAAATGAA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
13 4 0.15
14 22 0.81
15 1 0.04
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.33
Consensus pattern (14 bp):
TAAATATAATAAAA
Found at i:48529893 original size:9 final size:8
Alignment explanation
Indices: 48529879--48529916 Score: 58
Period size: 9 Copynumber: 4.5 Consensus size: 8
48529869 ACAGGGAGAA
48529879 AAAGAAAGG
1 AAAGAAA-G
48529888 AAAGAAAG
1 AAAGAAAG
48529896 AAAAGAAAG
1 -AAAGAAAG
48529905 AAAGAAAG
1 AAAGAAAG
48529913 AAAG
1 AAAG
48529917 GAGAAACTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
8 13 0.46
9 15 0.54
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (8 bp):
AAAGAAAG
Found at i:48529894 original size:4 final size:4
Alignment explanation
Indices: 48529879--48529916 Score: 58
Period size: 4 Copynumber: 9.0 Consensus size: 4
48529869 ACAGGGAGAA
48529879 AAAG AAAGG AAAG AAAG AAAAG AAAG AAAG AAAG AAAG
1 AAAG AAA-G AAAG AAAG -AAAG AAAG AAAG AAAG AAAG
48529917 GAGAAACTAG
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
4 24 0.75
5 8 0.25
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:48529897 original size:13 final size:12
Alignment explanation
Indices: 48529879--48529916 Score: 58
Period size: 13 Copynumber: 3.0 Consensus size: 12
48529869 ACAGGGAGAA
48529879 AAAGAAAGGAAAG
1 AAAGAAA-GAAAG
48529892 AAAGAAAAGAAAG
1 AAAG-AAAGAAAG
48529905 AAAGAAAGAAAG
1 AAAGAAAGAAAG
48529917 GAGAAACTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 8 0.33
13 13 0.54
14 3 0.12
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (12 bp):
AAAGAAAGAAAG
Found at i:48534431 original size:40 final size:39
Alignment explanation
Indices: 48534382--48534493 Score: 134
Period size: 39 Copynumber: 2.8 Consensus size: 39
48534372 AGTGGCTTTG
* *
48534382 TGCCGGTGTATTTATCGGGCTTTGTGCCTAGTAGGCTTTA
1 TGCCAGTGTATTTATCGGGCTTTGTGCCTAGCAGG-TTTA
* * *
48534422 TGCTAGTGTATTTATCGGGGTTTGTGCCTAGCAGGTTTG
1 TGCCAGTGTATTTATCGGGCTTTGTGCCTAGCAGGTTTA
* * * *
48534461 TGCCAGTGTGTTTATCAGGTTTTGTACCTAGCA
1 TGCCAGTGTATTTATCGGGCTTTGTGCCTAGCA
48534494 TGCATTGTGC
Statistics
Matches: 62, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
39 31 0.50
40 31 0.50
ACGTcount: A:0.14, C:0.16, G:0.29, T:0.40
Consensus pattern (39 bp):
TGCCAGTGTATTTATCGGGCTTTGTGCCTAGCAGGTTTA
Found at i:48534485 original size:39 final size:40
Alignment explanation
Indices: 48534375--48534503 Score: 152
Period size: 40 Copynumber: 3.2 Consensus size: 40
48534365 ACGAGTTAGT
* *
48534375 GGCTTTGTGCCGGTGTATTTATCGGGCTTTGTGCCTAGTA
1 GGCTTTGTGCCAGTGTATTTATCGGGCTTTGTGCCTAGCA
* * *
48534415 GGCTTTATGCTAGTGTATTTATCGGGGTTTGTGCCTAGCA
1 GGCTTTGTGCCAGTGTATTTATCGGGCTTTGTGCCTAGCA
* * * *
48534455 GG-TTTGTGCCAGTGTGTTTATCAGGTTTTGTACCTAGCA
1 GGCTTTGTGCCAGTGTATTTATCGGGCTTTGTGCCTAGCA
* *
48534494 TGCATTGTGC
1 GGCTTTGTGC
48534504 TGGTGTTGTA
Statistics
Matches: 75, Mismatches: 13, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
39 32 0.43
40 43 0.57
ACGTcount: A:0.13, C:0.16, G:0.30, T:0.40
Consensus pattern (40 bp):
GGCTTTGTGCCAGTGTATTTATCGGGCTTTGTGCCTAGCA
Found at i:48542052 original size:69 final size:69
Alignment explanation
Indices: 48541930--48542061 Score: 169
Period size: 69 Copynumber: 1.9 Consensus size: 69
48541920 GGAAAGTTAC
* * *
48541930 CTATGAAGCCTTTGTGGCTCATTCTATAGAGCCTTTGTGGCAGAATTAATGAAGGCTTTGTGGTA
1 CTATGAAGCCTTTGTAGCGCATTCTATAGAGCCTTTGTGGCAGAATTAATGAAGCCTTTGTGGTA
48541995 TAAT
66 TAAT
* * * *
48541999 CTATGAAGCCTTTGTAGCGCACTT-TTTGGAGCCTTTGTGGCATAATCT-TTGAAGCCTTTGTGG
1 CTATGAAGCCTTTGTAGCGCA-TTCTATAGAGCCTTTGTGGCAGAAT-TAATGAAGCCTTTGTGG
48542062 CATATTCTGT
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
69 51 0.94
70 3 0.06
ACGTcount: A:0.21, C:0.17, G:0.25, T:0.37
Consensus pattern (69 bp):
CTATGAAGCCTTTGTAGCGCATTCTATAGAGCCTTTGTGGCAGAATTAATGAAGCCTTTGTGGTA
TAAT
Found at i:48542078 original size:23 final size:23
Alignment explanation
Indices: 48541933--48542072 Score: 88
Period size: 23 Copynumber: 6.1 Consensus size: 23
48541923 AAGTTACCTA
* *
48541933 TGAAGCCTTTGTGGC-TCATTCTA
1 TGAAGCCTTTGTGGCAT-AATCTG
* *
48541956 T-AGAGCCTTTGTGGCAGAAT-TAA
1 TGA-AGCCTTTGTGGCATAATCT-G
* * *
48541979 TGAAGGCTTTGTGGTATAATCTA
1 TGAAGCCTTTGTGGCATAATCTG
* ** * * *
48542002 TGAAGCCTTTGTAGCGCACTTTT
1 TGAAGCCTTTGTGGCATAATCTG
* *
48542025 TGGAGCCTTTGTGGCATAATCTT
1 TGAAGCCTTTGTGGCATAATCTG
*
48542048 TGAAGCCTTTGTGGCATATTCTG
1 TGAAGCCTTTGTGGCATAATCTG
48542071 TG
1 TG
48542073 GCGCCTAAAT
Statistics
Matches: 90, Mismatches: 22, Indels: 10
0.74 0.18 0.08
Matches are distributed among these distances:
22 2 0.02
23 86 0.96
24 2 0.02
ACGTcount: A:0.21, C:0.16, G:0.25, T:0.38
Consensus pattern (23 bp):
TGAAGCCTTTGTGGCATAATCTG
Found at i:48543787 original size:27 final size:27
Alignment explanation
Indices: 48543751--48543806 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
48543741 AACAATGTTT
48543751 CTGACAATAAAG-TCTTTAATAGAGTTC
1 CTGACAATAAAGTTC-TTAATAGAGTTC
* *
48543778 CTGACGATAAGGTTCTTAATAGAGTTC
1 CTGACAATAAAGTTCTTAATAGAGTTC
48543805 CT
1 CT
48543807 ATCAATCACA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 24 0.92
28 2 0.08
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (27 bp):
CTGACAATAAAGTTCTTAATAGAGTTC
Found at i:48543983 original size:34 final size:34
Alignment explanation
Indices: 48543939--48544058 Score: 168
Period size: 34 Copynumber: 3.5 Consensus size: 34
48543929 ACACGGTTAA
* * *
48543939 CCATCTAGCACATCAGATGCTCGTAAGAGCTAAT
1 CCATCCAGCACATCAAATGCTCGTATGAGCTAAT
*
48543973 CCATCCAGCACATCAAATGCTCATATGAGCTAAT
1 CCATCCAGCACATCAAATGCTCGTATGAGCTAAT
* * *
48544007 CCATCTAGCACACCAAATGCTCGTATGAGTTAAT
1 CCATCCAGCACATCAAATGCTCGTATGAGCTAAT
*
48544041 CCATCCAGCACACCAAAT
1 CCATCCAGCACATCAAAT
48544059 CCATCCACCT
Statistics
Matches: 77, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 77 1.00
ACGTcount: A:0.34, C:0.30, G:0.13, T:0.23
Consensus pattern (34 bp):
CCATCCAGCACATCAAATGCTCGTATGAGCTAAT
Found at i:48545346 original size:22 final size:22
Alignment explanation
Indices: 48545282--48545346 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 22
48545272 TGCCAGTAGT
*
48545282 CAGAATGGCTA-AGAGCCTTAAA
1 CAGAATGGCTATA-AGCCATAAA
* * * **
48545304 CAGTATAGTTATAAGTTATAAA
1 CAGAATGGCTATAAGCCATAAA
48545326 CAGAATGGCTATAAGCCATAA
1 CAGAATGGCTATAAGCCATAA
48545347 GTATAGTAAT
Statistics
Matches: 31, Mismatches: 11, Indels: 2
0.70 0.25 0.05
Matches are distributed among these distances:
22 30 0.97
23 1 0.03
ACGTcount: A:0.43, C:0.14, G:0.18, T:0.25
Consensus pattern (22 bp):
CAGAATGGCTATAAGCCATAAA
Found at i:48545434 original size:32 final size:32
Alignment explanation
Indices: 48545358--48545572 Score: 193
Period size: 32 Copynumber: 6.7 Consensus size: 32
48545348 TATAGTAATG
* * * * *
48545358 TGATTGGCACAAAGCCATCAGTAGCAGTGATA
1 TGATCGGCACAAAGCCATCAGTAACGGTAACA
* * *
48545390 TGA-CTGGGACACAGCCATTAGTAACGGTAACA
1 TGATC-GGCACAAAGCCATCAGTAACGGTAACA
* * * **
48545422 TGATCGGCACACAGACATCAGTGATAGTGAA-A
1 TGATCGGCACAAAGCCATCAGTAACGGT-AACA
* * * * * *
48545454 TGATCGACACACAGCCATCGGTAGCAGTAATA
1 TGATCGGCACAAAGCCATCAGTAACGGTAACA
48545486 TGATCGGCACAAAGCCATCAGTAACGGT-ACTA
1 TGATCGGCACAAAGCCATCAGTAACGGTAAC-A
* *
48545518 TGATCAGCACAAAGCCATCAGTAACGGTAATA
1 TGATCGGCACAAAGCCATCAGTAACGGTAACA
48545550 TGATCGGCACAAAGCCATCAGTA
1 TGATCGGCACAAAGCCATCAGTA
48545573 GTATCGCAGC
Statistics
Matches: 148, Mismatches: 29, Indels: 12
0.78 0.15 0.06
Matches are distributed among these distances:
31 3 0.02
32 141 0.95
33 4 0.03
ACGTcount: A:0.36, C:0.22, G:0.23, T:0.19
Consensus pattern (32 bp):
TGATCGGCACAAAGCCATCAGTAACGGTAACA
Found at i:48545451 original size:64 final size:64
Alignment explanation
Indices: 48545352--48545572 Score: 248
Period size: 64 Copynumber: 3.5 Consensus size: 64
48545342 CATAAGTATA
* * * * *
48545352 GTAATGTGATTGGCACAAAGCCATCAGTAGCAGTGATATGA-CTGGGACACAGCCATTAGTAACG
1 GTAATATGATCGGCACAAAGCCATCAGTAACAGTGATATGATC-GGCACACAGCCATCAGTAACG
* * * * * * * * * *
48545416 GTAACATGATCGGCACACAGACATCAGTGATAGTGAAATGATCGACACACAGCCATCGGTAGCA
1 GTAATATGATCGGCACAAAGCCATCAGTAACAGTGATATGATCGGCACACAGCCATCAGTAACG
* * *
48545480 GTAATATGATCGGCACAAAGCCATCAGTAACGGT-ACTATGATCAGCACAAAGCCATCAGTAACG
1 GTAATATGATCGGCACAAAGCCATCAGTAACAGTGA-TATGATCGGCACACAGCCATCAGTAACG
48545544 GTAATATGATCGGCACAAAGCCATCAGTA
1 GTAATATGATCGGCACAAAGCCATCAGTA
48545573 GTATCGCAGC
Statistics
Matches: 127, Mismatches: 28, Indels: 4
0.80 0.18 0.03
Matches are distributed among these distances:
63 1 0.01
64 125 0.98
65 1 0.01
ACGTcount: A:0.36, C:0.22, G:0.23, T:0.19
Consensus pattern (64 bp):
GTAATATGATCGGCACAAAGCCATCAGTAACAGTGATATGATCGGCACACAGCCATCAGTAACG
Found at i:48545513 original size:96 final size:96
Alignment explanation
Indices: 48545365--48545573 Score: 253
Period size: 96 Copynumber: 2.2 Consensus size: 96
48545355 ATGTGATTGG
* * * * *
48545365 CACAAAGCCATCAGTAGCAGTGATATGACTGGGACACAGCCATTAGTAACGGTAAC-ATGATCGG
1 CACAAAGCCATCAGTAGCAGTAATATGACTGGCACAAAGCCATCAGTAACGGT-ACTATGATCAG
*
48545429 CACACAGACATCAGTGATAGTGAAATGATCGA
65 CACAAAGACATCAGTGATAGTGAAATGATCGA
* *
48545461 CACACAGCCATCGGTAGCAGTAATATGA-TCGGCACAAAGCCATCAGTAACGGTACTATGATCAG
1 CACAAAGCCATCAGTAGCAGTAATATGACT-GGCACAAAGCCATCAGTAACGGTACTATGATCAG
* * ** *
48545525 CACAAAGCCATCAGTAACGGT-AATATGATCGG
65 CACAAAGACATCAGTGATAGTGAA-ATGATCGA
48545557 CACAAAGCCATCAGTAG
1 CACAAAGCCATCAGTAG
48545574 TATCGCAGCA
Statistics
Matches: 95, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
95 5 0.05
96 90 0.95
ACGTcount: A:0.36, C:0.23, G:0.22, T:0.18
Consensus pattern (96 bp):
CACAAAGCCATCAGTAGCAGTAATATGACTGGCACAAAGCCATCAGTAACGGTACTATGATCAGC
ACAAAGACATCAGTGATAGTGAAATGATCGA
Found at i:48545744 original size:24 final size:23
Alignment explanation
Indices: 48545717--48545775 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 23
48545707 CCATGCTCAG
*
48545717 AATCAGTCATTCAAATCACAGACA
1 AATCAGTCATTCAAA-CACAAACA
* *
48545741 AATCAGTTATACCAAACACAAACA
1 AATCAGTCAT-TCAAACACAAACA
48545765 AATCAGTCATT
1 AATCAGTCATT
48545776 TAACCATAGA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
24 25 0.86
25 4 0.14
ACGTcount: A:0.47, C:0.24, G:0.07, T:0.22
Consensus pattern (23 bp):
AATCAGTCATTCAAACACAAACA
Found at i:48546058 original size:27 final size:27
Alignment explanation
Indices: 48545836--48546137 Score: 259
Period size: 27 Copynumber: 11.2 Consensus size: 27
48545826 TACCCACTAA
* * *
48545836 GGCATTACTGTCATTTTACCTTACAAG
1 GGCATTACGGTCATTTTACCCTACAGG
* *
48545863 GACATTACGATCATTTTACCCTACAGG
1 GGCATTACGGTCATTTTACCCTACAGG
**
48545890 GGCATTACATTCATTTTACCCTACAGG
1 GGCATTACGGTCATTTTACCCTACAGG
* *
48545917 GGCATTACGGTCAATTTACCCTATAGG
1 GGCATTACGGTCATTTTACCCTACAGG
* *
48545944 GGTATTACGATCATTTTACCCTACAGG
1 GGCATTACGGTCATTTTACCCTACAGG
* *
48545971 GGCATTACGGTCATTTTATCCTACAAG
1 GGCATTACGGTCATTTTACCCTACAGG
* * * *
48545998 GGTATTACGATTATTTTACCCTATAGG
1 GGCATTACGGTCATTTTACCCTACAGG
* * * *
48546025 GGCATTACGGTTATTTTACCCCATAAG
1 GGCATTACGGTCATTTTACCCTACAGG
* * * * *
48546052 GGTATTACTGTTATTTTATCCTA-TGG
1 GGCATTACGGTCATTTTACCCTACAGG
* * * *
48546078 AGGTATTTCGAT-ATTCTACCCTAC-GAG
1 -GGCATTACGGTCATTTTACCCTACAG-G
* ** *
48546105 GGTATTTTGGTCATTTTACCCTACGGG
1 GGCATTACGGTCATTTTACCCTACAGG
48546132 GGCATT
1 GGCATT
48546138 TTAGCCATTT
Statistics
Matches: 225, Mismatches: 45, Indels: 10
0.80 0.16 0.04
Matches are distributed among these distances:
26 20 0.09
27 204 0.91
28 1 0.00
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.36
Consensus pattern (27 bp):
GGCATTACGGTCATTTTACCCTACAGG
Found at i:48546108 original size:26 final size:27
Alignment explanation
Indices: 48546079--48546180 Score: 68
Period size: 27 Copynumber: 3.8 Consensus size: 27
48546069 ATCCTATGGA
48546079 GGTATTTCGAT-ATTCTACCCTACGAG
1 GGTATTTCGATCATTCTACCCTACGAG
* * * *
48546105 GGTATTTTGGTCATTTTACCCTACGGG
1 GGTATTTCGATCATTCTACCCTACGAG
* * * *
48546132 GGCATTT-TAGCCATTTTACCC-ATCGAG
1 GGTATTTCGA-TCATTCTACCCTA-CGAG
*
48546159 GGTATTTC-AGTCATTTTACCCT
1 GGTATTTCGA-TCATTCTACCCT
48546181 TTGCACATAT
Statistics
Matches: 60, Mismatches: 11, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
26 10 0.17
27 50 0.83
ACGTcount: A:0.20, C:0.23, G:0.20, T:0.38
Consensus pattern (27 bp):
GGTATTTCGATCATTCTACCCTACGAG
Found at i:48546146 original size:27 final size:27
Alignment explanation
Indices: 48546094--48546180 Score: 113
Period size: 27 Copynumber: 3.2 Consensus size: 27
48546084 TTCGATATTC
*
48546094 TACCCTACGAGGGTATTTTGGTCATTT
1 TACCCTACGAGGGTATTTTAGTCATTT
* * *
48546121 TACCCTACGGGGGCATTTTAGCCATTT
1 TACCCTACGAGGGTATTTTAGTCATTT
*
48546148 TACCC-ATCGAGGGTATTTCAGTCATTT
1 TACCCTA-CGAGGGTATTTTAGTCATTT
48546175 TACCCT
1 TACCCT
48546181 TTGCACATAT
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
26 1 0.02
27 49 0.98
ACGTcount: A:0.20, C:0.24, G:0.20, T:0.37
Consensus pattern (27 bp):
TACCCTACGAGGGTATTTTAGTCATTT
Found at i:48550665 original size:37 final size:37
Alignment explanation
Indices: 48550612--48550706 Score: 115
Period size: 37 Copynumber: 2.6 Consensus size: 37
48550602 AGTACACACG
*
48550612 TAATCCAACCGA-AACACGCCAAATGAT-CATAAGCGA
1 TAATCCAACCGATAACACGCCAAATGATCCA-AAGAGA
* * *
48550648 TAATCCAACCGATAACACACCAAATGCTCCAAAGAGC
1 TAATCCAACCGATAACACGCCAAATGATCCAAAGAGA
48550685 TAA-CACAACCGATAACACGCCA
1 TAATC-CAACCGATAACACGCCA
48550707 CGACACTAAG
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
36 13 0.25
37 36 0.71
38 2 0.04
ACGTcount: A:0.44, C:0.32, G:0.12, T:0.13
Consensus pattern (37 bp):
TAATCCAACCGATAACACGCCAAATGATCCAAAGAGA
Found at i:48558013 original size:14 final size:13
Alignment explanation
Indices: 48557996--48558050 Score: 53
Period size: 14 Copynumber: 4.3 Consensus size: 13
48557986 CGTGAATATC
48557996 TTCAGTCTAATAGT
1 TTCAGTCT-ATAGT
* *
48558010 TTCA-ACTACAGT
1 TTCAGTCTATAGT
48558022 TTACAGTCTATAGT
1 TT-CAGTCTATAGT
48558036 TT--GTCTATAGT
1 TTCAGTCTATAGT
48558047 TTCA
1 TTCA
48558051 TTAGTAAGAG
Statistics
Matches: 33, Mismatches: 4, Indels: 9
0.72 0.09 0.20
Matches are distributed among these distances:
11 11 0.33
12 6 0.18
13 4 0.12
14 12 0.36
ACGTcount: A:0.27, C:0.16, G:0.13, T:0.44
Consensus pattern (13 bp):
TTCAGTCTATAGT
Found at i:48565090 original size:58 final size:59
Alignment explanation
Indices: 48564979--48565090 Score: 149
Period size: 58 Copynumber: 1.9 Consensus size: 59
48564969 TTCACTTTAA
* * * *
48564979 TATTAAATTAATATAATATTTATCAAGATAAATATTAGATTATTTTTAATATTATATCT
1 TATTAAATTAATAGAATATATATCAAGATAAATATTAAATTATATTTAATATTATATCT
48565038 TATTAAATTAATAGAATATATA-CAAGAT-AATCATTAAATT-TAATTTAATATTA
1 TATTAAATTAATAGAATATATATCAAGATAAAT-ATTAAATTAT-ATTTAATATTA
48565091 AGATAATCAC
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
57 4 0.09
58 23 0.49
59 20 0.43
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.46
Consensus pattern (59 bp):
TATTAAATTAATAGAATATATATCAAGATAAATATTAAATTATATTTAATATTATATCT
Found at i:48565175 original size:68 final size:68
Alignment explanation
Indices: 48565038--48565178 Score: 162
Period size: 68 Copynumber: 2.1 Consensus size: 68
48565028 TATTATATCT
* * ***
48565038 TATTAAATTAATAGAATATATACAAGATAATCATTAAATTTAATTTAATATTAAGATAATCACTT
1 TATTAAATTAATAAAATATATACAAGATAATCATTAAATTTAATTTAATATCAAGATAATCAAAA
48565103 TAA
66 TAA
** *
48565106 TATTAAATTAATAAAATACTAT-TGAGATAAGT-ATTAAATTTAATTTAATATCAA-ATATATTA
1 TATTAAATTAATAAAATA-TATACAAGATAA-TCATTAAATTTAATTTAATATCAAGATA-ATCA
48565168 AAATAA
63 AAATAA
48565174 TATTA
1 TATTA
48565179 TATTTGGAAT
Statistics
Matches: 62, Mismatches: 8, Indels: 6
0.82 0.11 0.08
Matches are distributed among these distances:
67 3 0.05
68 55 0.89
69 4 0.06
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.40
Consensus pattern (68 bp):
TATTAAATTAATAAAATATATACAAGATAATCATTAAATTTAATTTAATATCAAGATAATCAAAA
TAA
Found at i:48575351 original size:17 final size:17
Alignment explanation
Indices: 48575331--48575371 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
48575321 GATAAGTATA
* *
48575331 CATTGTTATTGCATATT
1 CATTGTCATTACATATT
48575348 CATTGTCATTACATATT
1 CATTGTCATTACATATT
48575365 CA-TGTCA
1 CATTGTCA
48575372 GTGTATTGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.27, C:0.17, G:0.10, T:0.46
Consensus pattern (17 bp):
CATTGTCATTACATATT
Found at i:48584983 original size:25 final size:24
Alignment explanation
Indices: 48584955--48585002 Score: 78
Period size: 25 Copynumber: 2.0 Consensus size: 24
48584945 TTGGCTCTCA
*
48584955 CGAGCTTCCCGTTATATGGTTCTTG
1 CGAGCTTCCCGTTA-ATAGTTCTTG
48584980 CGAGCTTCCCGTTAATAGTTCTT
1 CGAGCTTCCCGTTAATAGTTCTT
48585003 CAAAGCATCC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 8 0.36
25 14 0.64
ACGTcount: A:0.15, C:0.25, G:0.21, T:0.40
Consensus pattern (24 bp):
CGAGCTTCCCGTTAATAGTTCTTG
Found at i:48598287 original size:2 final size:2
Alignment explanation
Indices: 48598280--48598309 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
48598270 GGTAGTTAGA
48598280 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
48598310 ACTTTGTAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:48600695 original size:16 final size:17
Alignment explanation
Indices: 48600663--48600712 Score: 59
Period size: 16 Copynumber: 3.0 Consensus size: 17
48600653 ATTTAGAGTT
*
48600663 AAATATATATAAATAATA
1 AAATATAT-TTAATAATA
48600681 AAATA-ATTTAATAATA
1 AAATATATTTAATAATA
*
48600697 TAATATATTT-ATAATA
1 AAATATATTTAATAATA
48600713 TATTAAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
16 18 0.62
17 6 0.21
18 5 0.17
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
AAATATATTTAATAATA
Found at i:48602571 original size:6 final size:6
Alignment explanation
Indices: 48602560--48602635 Score: 53
Period size: 6 Copynumber: 12.0 Consensus size: 6
48602550 ATTTAGCCAT
* * * **
48602560 TTTTTA TTTTTA TTTTTA GTTTTA GTTTTA GTTTTA GTTTTCG TTTTAATA
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA -TTTTTA TTTT--TA
* *
48602611 TTTTTTA TTTTTA ATTTAA TTTTTA
1 -TTTTTA TTTTTA TTTTTA TTTTTA
48602636 CATTCTAATT
Statistics
Matches: 56, Mismatches: 10, Indels: 8
0.76 0.14 0.11
Matches are distributed among these distances:
6 47 0.84
7 5 0.09
9 4 0.07
ACGTcount: A:0.20, C:0.01, G:0.07, T:0.72
Consensus pattern (6 bp):
TTTTTA
Found at i:48602588 original size:18 final size:18
Alignment explanation
Indices: 48602561--48602607 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
48602551 TTTAGCCATT
* *
48602561 TTTTATTTTTATTTTTAG
1 TTTTAGTTTTAGTTTTAG
48602579 TTTTAGTTTTAGTTTTAG
1 TTTTAGTTTTAGTTTTAG
*
48602597 TTTTCGTTTTA
1 TTTTAGTTTTA
48602608 ATATTTTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.15, C:0.02, G:0.11, T:0.72
Consensus pattern (18 bp):
TTTTAGTTTTAGTTTTAG
Found at i:48602623 original size:34 final size:35
Alignment explanation
Indices: 48602579--48602655 Score: 84
Period size: 34 Copynumber: 2.2 Consensus size: 35
48602569 TTATTTTTAG
* * * * *
48602579 TTTTAGTTTTAGTTTTAGTTTT-CGTTTTAATATT
1 TTTTATTTTTAATTTAAGTTTTACATTCTAATATT
* *
48602613 TTTTATTTTTAATTTAATTTTTACATTCTAATTTT
1 TTTTATTTTTAATTTAAGTTTTACATTCTAATATT
48602648 TTTTATTT
1 TTTTATTT
48602656 GATTCTTACA
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
34 18 0.51
35 17 0.49
ACGTcount: A:0.21, C:0.04, G:0.05, T:0.70
Consensus pattern (35 bp):
TTTTATTTTTAATTTAAGTTTTACATTCTAATATT
Found at i:48604251 original size:20 final size:20
Alignment explanation
Indices: 48604223--48604263 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
48604213 ATATATCCTG
*
48604223 ATTTTATTTGATTCTAATCA
1 ATTTAATTTGATTCTAATCA
*
48604243 ATTTAATTTGATTTTAATCA
1 ATTTAATTTGATTCTAATCA
48604263 A
1 A
48604264 ATTGATTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.34, C:0.07, G:0.05, T:0.54
Consensus pattern (20 bp):
ATTTAATTTGATTCTAATCA
Found at i:48604271 original size:20 final size:20
Alignment explanation
Indices: 48604228--48604271 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
48604218 TCCTGATTTT
*
48604228 ATTTGATTCTAATCAATTTA
1 ATTTGATTCTAATCAAATTA
* *
48604248 ATTTGATTTTAATCAAATTG
1 ATTTGATTCTAATCAAATTA
48604268 ATTT
1 ATTT
48604272 AATAGCCCCT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.07, G:0.07, T:0.52
Consensus pattern (20 bp):
ATTTGATTCTAATCAAATTA
Found at i:48604739 original size:20 final size:22
Alignment explanation
Indices: 48604714--48604753 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
48604704 TATTCAATTT
48604714 ATATTT-TAT-TTTATATATAA
1 ATATTTGTATATTTATATATAA
*
48604734 ATATTTGTTTATTTATATAT
1 ATATTTGTATATTTATATAT
48604754 TTATATATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 2 0.12
22 9 0.53
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (22 bp):
ATATTTGTATATTTATATATAA
Found at i:48604759 original size:22 final size:20
Alignment explanation
Indices: 48604710--48604759 Score: 55
Period size: 22 Copynumber: 2.4 Consensus size: 20
48604700 AAATTATTCA
48604710 ATTTATATTTTATTTTATAT
1 ATTTATATTTTATTTTATAT
** *
48604730 ATAAATATTTGTTTATTTATAT
1 ATTTATATTT-TAT-TTTATAT
48604752 ATTTATAT
1 ATTTATAT
48604760 ATTTTGTTCA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
20 8 0.35
21 2 0.09
22 13 0.57
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (20 bp):
ATTTATATTTTATTTTATAT
Found at i:48604761 original size:24 final size:23
Alignment explanation
Indices: 48604718--48604763 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
48604708 CAATTTATAT
48604718 TTTATTTTATATATAAATATTTG
1 TTTATTTTATATATAAATATTTG
* *
48604741 TTTATTTATATATTTATATATTT
1 TTTATTT-TATATATAAATATTT
48604764 TGTTCACTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (23 bp):
TTTATTTTATATATAAATATTTG
Found at i:48608411 original size:20 final size:20
Alignment explanation
Indices: 48608386--48608438 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
48608376 ATATATCCTT
48608386 ATTTTATTTGATTCTAATCA
1 ATTTTATTTGATTCTAATCA
48608406 ATTTTATTTGATTCTAATCA
1 ATTTTATTTGATTCTAATCA
*
48608426 ATTTGATTTGATT
1 ATTTTATTTGATT
48608439 TTTATCAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.28, C:0.08, G:0.08, T:0.57
Consensus pattern (20 bp):
ATTTTATTTGATTCTAATCA
Found at i:48608445 original size:20 final size:20
Alignment explanation
Indices: 48608386--48608454 Score: 93
Period size: 20 Copynumber: 3.5 Consensus size: 20
48608376 ATATATCCTT
*
48608386 ATTTTATTTGATTCTAATCA
1 ATTTGATTTGATTCTAATCA
*
48608406 ATTTTATTTGATTCTAATCA
1 ATTTGATTTGATTCTAATCA
* *
48608426 ATTTGATTTGATTTTTATCA
1 ATTTGATTTGATTCTAATCA
*
48608446 AATTGATTT
1 ATTTGATTT
48608455 AATAGCCACT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.29, C:0.07, G:0.07, T:0.57
Consensus pattern (20 bp):
ATTTGATTTGATTCTAATCA
Found at i:48608943 original size:22 final size:23
Alignment explanation
Indices: 48608897--48608948 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
48608887 CTATTCAATT
48608897 TATA-TTTTATTTTATATATAAA
1 TATATTTTTATTTTATATATAAA
* **
48608919 TATTTTTTTA-TTTATATATTTA
1 TATATTTTTATTTTATATATAAA
48608941 TATATTTT
1 TATATTTT
48608949 GTTCGCTAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
22 20 0.80
23 5 0.20
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (23 bp):
TATATTTTTATTTTATATATAAA
Found at i:48618300 original size:16 final size:16
Alignment explanation
Indices: 48618279--48618309 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
48618269 AAGAGCAAAT
48618279 ACGCTAGTAAATAAAC
1 ACGCTAGTAAATAAAC
48618295 ACGCTAGTAAATAAA
1 ACGCTAGTAAATAAA
48618310 ATACTAGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.52, C:0.16, G:0.13, T:0.19
Consensus pattern (16 bp):
ACGCTAGTAAATAAAC
Found at i:48629854 original size:15 final size:14
Alignment explanation
Indices: 48629834--48629868 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
48629824 GCAAAAGGTT
48629834 AAGAAAAGAAAAACA
1 AAGAAAAG-AAAACA
*
48629849 AAGAAATGAAAACA
1 AAGAAAAGAAAACA
48629863 AAGAAA
1 AAGAAA
48629869 TTATCGCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.77, C:0.06, G:0.14, T:0.03
Consensus pattern (14 bp):
AAGAAAAGAAAACA
Found at i:48629862 original size:14 final size:14
Alignment explanation
Indices: 48629843--48629869 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
48629833 TAAGAAAAGA
48629843 AAAACAAAGAAATG
1 AAAACAAAGAAATG
48629857 AAAACAAAGAAAT
1 AAAACAAAGAAAT
48629870 TATCGCAAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.74, C:0.07, G:0.11, T:0.07
Consensus pattern (14 bp):
AAAACAAAGAAATG
Found at i:48632160 original size:97 final size:97
Alignment explanation
Indices: 48631875--48632171 Score: 397
Period size: 97 Copynumber: 3.0 Consensus size: 97
48631865 GACATTCTAG
* *
48631875 TGAGTGAAAAGAATAAAGGGCCTGTTGTCTCAAAAGTGAAACAGTCAGT-CGTACTGCTTTTGTT
1 TGAGTGAAAAGAATAAAGGGTCTGTTGTCTCAAAAGTGAAACAGTC-GTAC-TA-T--TCTTGTT
48631939 TCAGGATTTTATTAGAACACTACATATCCTTTTAGCC
61 TCAGGATTTTATTAGAACACTACATATCCTTTTAGCC
*
48631976 TGAGTGAAAAGAATAAAGGGTCTGTTGTCTCAAAAGTGAAACAGTCGTACTATTCTTGTCTTTTA
1 TGAGTGAAAAGAATAAAGGGTCTGTTGTCTCAAAAGTGAAACAGTCGTACTATTCTTG--TTTCA
** ** * *
48632041 -GCCTGAATT---ACAGTGGAGATATCCTTTTAGCC
64 GGATTTTATTAGAACACT--ACATATCCTTTTAGCC
48632073 TGAGTGAAAAGAATAAAGGGTCTGTTGTCTCAAAAGTGAAACAGTCGTACTATTCTTGTTTCAGG
1 TGAGTGAAAAGAATAAAGGGTCTGTTGTCTCAAAAGTGAAACAGTCGTACTATTCTTGTTTCAGG
48632138 ATTTTATTAGAACACTACATATCCTTTTAGCC
66 ATTTTATTAGAACACTACATATCCTTTTAGCC
48632170 TG
1 TG
48632172 TCTTTGCATT
Statistics
Matches: 171, Mismatches: 16, Indels: 22
0.82 0.08 0.11
Matches are distributed among these distances:
95 8 0.05
96 5 0.03
97 94 0.55
98 5 0.03
99 9 0.05
100 4 0.02
101 46 0.27
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (97 bp):
TGAGTGAAAAGAATAAAGGGTCTGTTGTCTCAAAAGTGAAACAGTCGTACTATTCTTGTTTCAGG
ATTTTATTAGAACACTACATATCCTTTTAGCC
Found at i:48632937 original size:29 final size:29
Alignment explanation
Indices: 48632904--48632961 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
48632894 GGATTAATGT
48632904 CATTTCGTTTTCTTCTAAACTAATTTGTG
1 CATTTCGTTTTCTTCTAAACTAATTTGTG
48632933 CATTTCGTTTTCTTCTAAACTAATTTGTG
1 CATTTCGTTTTCTTCTAAACTAATTTGTG
48632962 ATTCTTTCTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.21, C:0.17, G:0.10, T:0.52
Consensus pattern (29 bp):
CATTTCGTTTTCTTCTAAACTAATTTGTG
Found at i:48632969 original size:25 final size:28
Alignment explanation
Indices: 48632904--48632976 Score: 98
Period size: 29 Copynumber: 2.6 Consensus size: 28
48632894 GGATTAATGT
48632904 CATTTCGTTTTCTTCTAAACTAATTTGTG
1 CATTTCG-TTTCTTCTAAACTAATTTGTG
48632933 CATTTCGTTTTCTTCTAAACTAATTTGTG
1 CATTTCG-TTTCTTCTAAACTAATTTGTG
*
48632962 -A-TTC-TTTCTGCTAAA
1 CATTTCGTTTCTTCTAAA
48632977 ACCTTTGAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
25 10 0.23
27 3 0.07
28 1 0.02
29 29 0.67
ACGTcount: A:0.22, C:0.18, G:0.10, T:0.51
Consensus pattern (28 bp):
CATTTCGTTTCTTCTAAACTAATTTGTG
Found at i:48640893 original size:20 final size:20
Alignment explanation
Indices: 48640833--48640893 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
48640823 CAGTAGTAAT
*
48640833 ACAATAGAGAAATGATAGCAAA
1 ACAATAAAGAAA--ATAGCAAA
* *
48640855 ACAATAAA-AATAGTGGCAAA
1 ACAATAAAGAA-AATAGCAAA
48640875 ACAATAAAGAAAATAGCAA
1 ACAATAAAGAAAATAGCAA
48640894 CAATTTTTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
20 20 0.62
21 4 0.12
22 8 0.25
ACGTcount: A:0.62, C:0.10, G:0.15, T:0.13
Consensus pattern (20 bp):
ACAATAAAGAAAATAGCAAA
Found at i:48651358 original size:44 final size:44
Alignment explanation
Indices: 48651298--48651826 Score: 291
Period size: 44 Copynumber: 11.3 Consensus size: 44
48651288 TCCCTAAGCA
*
48651298 ACAGTGGAGCAGATTGAAGCCAGAAATCTTATCTCCCTGAGATT
1 ACAGTGGAGCAGATTGAAGCTAGAAATCTTATCTCCCTGAGATT
* * ** *
48651342 ACAGCGGAGCAGATTGAAGCTAGTAATCCGATCTCCCTGAGGTT
1 ACAGTGGAGCAGATTGAAGCTAGAAATCTTATCTCCCTGAGATT
* ** *
48651386 ACAGTGGAGCTGATT-AAAATA-AATGATCTTATCTCTCTGAAGTTACTGT
1 ACAGTGGAGCAGATTGAAGCTAGAA--ATCTTATCTCCCTG-AG--A-T-T
* * * *
48651435 AGAGTAGATTGCATCAGATTGAAGCCAGAAATCTTATCTCACTGAGATT
1 ACAGT-G---G-AGCAGATTGAAGCTAGAAATCTTATCTCCCTGAGATT
*** * *
48651484 ACA-ACAAGGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATT
1 ACAGTGGA-GCAGATTGAAGCTAGAAATCTTATCTCCCTGAGATT
* ** * *
48651528 ACAGTGGAGTAGATT-AAAATA-AAGGATTTTATCTCTCTGA-AGTT
1 ACAGTGGAGCAGATTGAAGCTAGAA--ATCTTATCTCCCTGAGA-TT
48651572 ACAGTAGAGTAGATTGCATCAGATTGAAGCTAGAAATCTTATCTCCCTGAGATT
1 ACAGT---G--GA--G---CAGATTGAAGCTAGAAATCTTATCTCCCTGAGATT
* * *
48651626 ACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATT
1 ACAGTGGAGCAGATTGAAGCTAGAAATCTTATCTCCCTGAGATT
* ** *
48651670 ACAGTGGAGCGGATT-AAAATA-AAGGATCTTATCTCTCTGAAGTTATAGT
1 ACAGTGGAGCAGATTGAAGCTAGAA--ATCTTATCTCCCTG-AG--AT--T
* * *
48651719 AGAGTAGATTGCATCAGATTGAAGCCAGAAATCTTATCTCCCTGAGATT
1 ACAGT-G---G-AGCAGATTGAAGCTAGAAATCTTATCTCCCTGAGATT
* ** * * *
48651768 ATAGCAGAGCAGATTGAAGCTAGTAGTCCTATCTCCCTGAGATT
1 ACAGTGGAGCAGATTGAAGCTAGAAATCTTATCTCCCTGAGATT
*
48651812 ACAGTGGAGCGGATT
1 ACAGTGGAGCAGATT
48651827 AAAATAAAGG
Statistics
Matches: 364, Mismatches: 75, Indels: 92
0.69 0.14 0.17
Matches are distributed among these distances:
42 3 0.01
43 14 0.04
44 222 0.61
45 6 0.02
47 4 0.01
48 1 0.00
49 21 0.06
50 3 0.01
51 5 0.01
53 6 0.02
54 62 0.17
55 11 0.03
56 6 0.02
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (44 bp):
ACAGTGGAGCAGATTGAAGCTAGAAATCTTATCTCCCTGAGATT
Found at i:48651563 original size:142 final size:142
Alignment explanation
Indices: 48651307--48651876 Score: 962
Period size: 142 Copynumber: 4.0 Consensus size: 142
48651297 AACAGTGGAG
* *
48651307 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCG
1 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCAGAGCAGATTGAAGCTAGTAATCCT
* * * *
48651372 ATCTCCCTGAGGTTACAGTGGAGCTGATTAAAATAAATGATCTTATCTCTCTGAAGTTACTGTAG
66 ATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAG
48651437 AGTAGATTGCAT
131 AGTAGATTGCAT
* *
48651449 CAGATTGAAGCCAGAAATCTTATCTCACTGAGATTACAACA-AGGCAGATTGAAGCTAGTAATCC
1 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCAGA-GCAGATTGAAGCTAGTAATCC
** *
48651513 TATCTCCCTGAGATTACAGTGGAGTAGATTAAAATAAAGGATTTTATCTCTCTGAAGTTACAGTA
65 TATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTA
48651578 GAGTAGATTGCAT
130 GAGTAGATTGCAT
* *
48651591 CAGATTGAAGCTAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCT
1 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCAGAGCAGATTGAAGCTAGTAATCCT
*
48651656 ATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTATAGTAG
66 ATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAG
48651721 AGTAGATTGCAT
131 AGTAGATTGCAT
* *
48651733 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTATAGCAGAGCAGATTGAAGCTAGTAGTCCT
1 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCAGAGCAGATTGAAGCTAGTAATCCT
*
48651798 ATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTTTGAAGTTACAGTAG
66 ATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAG
*
48651863 AGTAGATCGCAT
131 AGTAGATTGCAT
48651875 CA
1 CA
48651877 AGTCTTATCT
Statistics
Matches: 401, Mismatches: 25, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
141 1 0.00
142 399 1.00
143 1 0.00
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (142 bp):
CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCAGAGCAGATTGAAGCTAGTAATCCT
ATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAG
AGTAGATTGCAT
Found at i:48651672 original size:98 final size:97
Alignment explanation
Indices: 48651493--48651674 Score: 224
Period size: 98 Copynumber: 1.9 Consensus size: 97
48651483 TACAACAAGG
* * * * **
48651493 CAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGTAGATTAAAATAAAGGATTTT
1 CAGATTGAAGCTAGAAATCCTATCTCCCTGAGATTACAGCGGAGCAGATTAAAAT-AAGAATCCT
*
48651558 ATCTCTCTGAAGTTACAGTAGAGTAGATTGCAT
65 ATCTCCCTGAAGTTACAGTAGAGTAGATTGCAT
* **
48651591 CAGATTGAAGCTAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCT-AGTAATCC
1 CAGATTGAAGCTAGAAATCCTATCTCCCTGAGATTACAGCGGAGCAGATT-AAAATAAG-AATCC
48651655 TATCTCCCTG-AGATTACAGT
64 TATCTCCCTGAAG-TTACAGT
48651675 GGAGCGGATT
Statistics
Matches: 71, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
97 4 0.06
98 64 0.90
99 3 0.04
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (97 bp):
CAGATTGAAGCTAGAAATCCTATCTCCCTGAGATTACAGCGGAGCAGATTAAAATAAGAATCCTA
TCTCCCTGAAGTTACAGTAGAGTAGATTGCAT
Found at i:48658795 original size:45 final size:45
Alignment explanation
Indices: 48658737--48658830 Score: 102
Period size: 45 Copynumber: 2.1 Consensus size: 45
48658727 ATATGTTGAT
* *
48658737 TTCATCGGATACCAATG-GTTATATAAGTTATTGCTATGTCCTGAA
1 TTCATCGGATACCAATGAG-TATAAAAGTGATTGCTATGTCCTGAA
* * * *
48658782 TTCATCTGG-TACCATTGAGTATAAAAGTGGTTGCTATGTGCTGAT
1 TTCATC-GGATACCAATGAGTATAAAAGTGATTGCTATGTCCTGAA
48658827 TTCA
1 TTCA
48658831 CCGAGTACTA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
45 38 0.93
46 3 0.07
ACGTcount: A:0.27, C:0.15, G:0.20, T:0.38
Consensus pattern (45 bp):
TTCATCGGATACCAATGAGTATAAAAGTGATTGCTATGTCCTGAA
Found at i:48662168 original size:15 final size:15
Alignment explanation
Indices: 48662148--48662176 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
48662138 ATTCATAATA
48662148 TTATAATATACAGTT
1 TTATAATATACAGTT
48662163 TTATAATATACAGT
1 TTATAATATACAGT
48662177 AATATTATGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.45
Consensus pattern (15 bp):
TTATAATATACAGTT
Found at i:48662293 original size:83 final size:83
Alignment explanation
Indices: 48662154--48662396 Score: 468
Period size: 83 Copynumber: 2.9 Consensus size: 83
48662144 AATATTATAA
*
48662154 TATACAGTTTTATAATATACAGTAATATTATGATTTACTAATACTATTGGTTTTTAGTGGTTCAT
1 TATACAATTTTATAATATACAGTAATATTATGATTTACTAATACTATTGGTTTTTAGTGGTTCAT
48662219 GCGTTAAACATACAATTG
66 GCGTTAAACATACAATTG
48662237 TATACAATTTTATAATATACAGTAATATTATGATTTACTAATACTATTGGTTTTTAGTGGTTCAT
1 TATACAATTTTATAATATACAGTAATATTATGATTTACTAATACTATTGGTTTTTAGTGGTTCAT
48662302 GCGTTAAACATACAATTG
66 GCGTTAAACATACAATTG
*
48662320 TATACAATTTTATAATATACAGTAATATTATGATTTACTAATACTATTGTTTTTTAGTGGTTCAT
1 TATACAATTTTATAATATACAGTAATATTATGATTTACTAATACTATTGGTTTTTAGTGGTTCAT
48662385 GCGTTAAACATA
66 GCGTTAAACATA
48662397 TATCCGTTAA
Statistics
Matches: 158, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
83 158 1.00
ACGTcount: A:0.35, C:0.09, G:0.12, T:0.44
Consensus pattern (83 bp):
TATACAATTTTATAATATACAGTAATATTATGATTTACTAATACTATTGGTTTTTAGTGGTTCAT
GCGTTAAACATACAATTG
Found at i:48663709 original size:95 final size:95
Alignment explanation
Indices: 48663546--48663721 Score: 334
Period size: 95 Copynumber: 1.9 Consensus size: 95
48663536 AGTTTCATGG
*
48663546 AACTTAAATTTTAGGCCTTCATTAACCAGCTTATTTCGCTTATACCAAAGGGCCCACAAAGAGAT
1 AACTTAAATTTTAGGCCTTCATTAACAAGCTTATTTCGCTTATACCAAAGGGCCCACAAAGAGAT
48663611 AGCAATGAGTTTCTTATTTCGTCTTGCGGC
66 AGCAATGAGTTTCTTATTTCGTCTTGCGGC
*
48663641 AACTTAAATTTTAGGCCTTCATTAACAAGCTTATTTTGCTTATACCAAAGGGCCCACAAAGAGAT
1 AACTTAAATTTTAGGCCTTCATTAACAAGCTTATTTCGCTTATACCAAAGGGCCCACAAAGAGAT
48663706 AGCAATGAGTTTCTTA
66 AGCAATGAGTTTCTTA
48663722 GAATTCATAT
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
95 79 1.00
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.32
Consensus pattern (95 bp):
AACTTAAATTTTAGGCCTTCATTAACAAGCTTATTTCGCTTATACCAAAGGGCCCACAAAGAGAT
AGCAATGAGTTTCTTATTTCGTCTTGCGGC
Found at i:48669161 original size:12 final size:12
Alignment explanation
Indices: 48669144--48669170 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
48669134 CCTCCTTACC
48669144 TTAATTTATTTT
1 TTAATTTATTTT
48669156 TTAATTTATTTT
1 TTAATTTATTTT
48669168 TTA
1 TTA
48669171 TCGATTATTT
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:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (12 bp):
TTAATTTATTTT
Found at i:48671012 original size:17 final size:17
Alignment explanation
Indices: 48670990--48671024 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
48670980 GTAAATATTT
48670990 ATTAAAAATATTTACGA
1 ATTAAAAATATTTACGA
48671007 ATTAAAAATATTTACGA
1 ATTAAAAATATTTACGA
48671024 A
1 A
48671025 GTTAGTTGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.54, C:0.06, G:0.06, T:0.34
Consensus pattern (17 bp):
ATTAAAAATATTTACGA
Found at i:48671372 original size:11 final size:11
Alignment explanation
Indices: 48671317--48671412 Score: 55
Period size: 11 Copynumber: 8.7 Consensus size: 11
48671307 AAATAAATGA
48671317 AAGAAAAAGA-
1 AAGAAAAAGAG
48671327 ATAG-AAAA-AG
1 A-AGAAAAAGAG
48671337 AAGAACAAAGTAG
1 AAGAA-AAAG-AG
*
48671350 AACGAAACAGAG
1 AA-GAAAAAGAG
48671362 AAGAAAAAGAG
1 AAGAAAAAGAG
48671373 -AGAAAGAA-A-
1 AAGAAA-AAGAG
48671382 AAG-AAAAGAAG
1 AAGAAAAAG-AG
48671393 AAAGAAAAAGGAG
1 -AAGAAAAA-GAG
48671406 AA-AAAAA
1 AAGAAAAA
48671413 TTAGGATTTT
Statistics
Matches: 69, Mismatches: 2, Indels: 29
0.69 0.02 0.29
Matches are distributed among these distances:
8 2 0.03
9 5 0.07
10 16 0.23
11 20 0.29
12 9 0.13
13 13 0.19
14 4 0.06
ACGTcount: A:0.72, C:0.03, G:0.23, T:0.02
Consensus pattern (11 bp):
AAGAAAAAGAG
Found at i:48671376 original size:25 final size:26
Alignment explanation
Indices: 48671331--48671397 Score: 68
Period size: 25 Copynumber: 2.7 Consensus size: 26
48671321 AAAAGAATAG
* *
48671331 AAAA-AGAAGAACAAAG-TAGAACGA
1 AAAAGAGAAGAACAAAGAGAGAAAGA
*
48671355 AACAGAGAAGAA-AAAGAGAGAAAGA
1 AAAAGAGAAGAACAAAGAGAGAAAGA
* *
48671380 AAAAGAAAAGAAGAAAGA
1 AAAAGAGAAGAACAAAGA
48671398 AAAAGGAGAA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
24 7 0.20
25 23 0.66
26 5 0.14
ACGTcount: A:0.70, C:0.04, G:0.24, T:0.01
Consensus pattern (26 bp):
AAAAGAGAAGAACAAAGAGAGAAAGA
Found at i:48671381 original size:14 final size:14
Alignment explanation
Indices: 48671358--48671412 Score: 53
Period size: 18 Copynumber: 3.9 Consensus size: 14
48671348 AGAACGAAAC
48671358 AGAG-AAGAAAAAG
1 AGAGAAAGAAAAAG
48671371 AGAGAAAGAAAAAG
1 AGAGAAAGAAAAAG
48671385 AAAAGAAGAAAGAAAAAG
1 ---AG-AGAAAGAAAAAG
48671403 -GAGAAA-AAAA
1 AGAGAAAGAAAA
48671413 TTAGGATTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
12 4 0.11
13 9 0.24
14 10 0.27
17 2 0.05
18 12 0.32
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (14 bp):
AGAGAAAGAAAAAG
Found at i:48671398 original size:12 final size:11
Alignment explanation
Indices: 48671316--48671400 Score: 57
Period size: 11 Copynumber: 7.3 Consensus size: 11
48671306 AAAATAAATG
48671316 AAAGAAAAAGA
1 AAAGAAAAAGA
*
48671327 ATAGAAAAAG-
1 AAAGAAAAAGA
48671337 -AAGAACAAAGTA
1 AAAGAA-AAAG-A
* *
48671349 GAACGAAACAGA
1 -AAAGAAAAAGA
*
48671361 GAAGAAAAAGAGA
1 AAAG-AAAA-AGA
48671374 GAAAGAAAAAGA
1 -AAAGAAAAAGA
48671386 AAAGAAGAAAGA
1 AAAGAA-AAAGA
48671398 AAA
1 AAA
48671401 AGGAGAAAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 17
0.70 0.10 0.21
Matches are distributed among these distances:
9 4 0.07
10 4 0.07
11 17 0.30
12 15 0.26
13 10 0.18
14 7 0.12
ACGTcount: A:0.72, C:0.04, G:0.22, T:0.02
Consensus pattern (11 bp):
AAAGAAAAAGA
Found at i:48684008 original size:23 final size:21
Alignment explanation
Indices: 48683982--48684031 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
48683972 GTAATTATAA
48683982 ATACATGTGTAATAAATATATGT
1 ATACATGTGTAAT-AA-ATATGT
* *
48684005 ATACATTTGTAATTAATATGT
1 ATACATGTGTAATAAATATGT
48684026 ATACAT
1 ATACAT
48684032 ATTTATTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 12 0.48
22 1 0.04
23 12 0.48
ACGTcount: A:0.42, C:0.06, G:0.10, T:0.42
Consensus pattern (21 bp):
ATACATGTGTAATAAATATGT
Found at i:48684117 original size:18 final size:18
Alignment explanation
Indices: 48684084--48684122 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
48684074 TTAATTAAAC
48684084 AAAAGAAAGAAATGAAAAT
1 AAAAGAAAGAAATG-AAAT
*
48684103 AAAAGAAA-CAATGAAAT
1 AAAAGAAAGAAATGAAAT
48684120 AAA
1 AAA
48684123 GATAGAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 7 0.37
18 4 0.21
19 8 0.42
ACGTcount: A:0.74, C:0.03, G:0.13, T:0.10
Consensus pattern (18 bp):
AAAAGAAAGAAATGAAAT
Found at i:48684177 original size:12 final size:12
Alignment explanation
Indices: 48684147--48684191 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
48684137 AAAAAAGATC
48684147 AAGAAAAGGAAAGA
1 AAGAAAAGG-AA-A
48684161 AAGAAAAGGAAA
1 AAGAAAAGGAAA
48684173 AAGAAAA-GAAA
1 AAGAAAAGGAAA
48684184 AAGGAAAA
1 AA-GAAAA
48684192 ATAGGGTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
11 6 0.20
12 13 0.43
13 2 0.07
14 9 0.30
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (12 bp):
AAGAAAAGGAAA
Found at i:48689220 original size:18 final size:18
Alignment explanation
Indices: 48689187--48689225 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
48689177 TTAATTAAAC
48689187 AAAAGAAAGAAATGAAAAT
1 AAAAGAAAGAAATG-AAAT
*
48689206 AAAAGAAA-CAATGAAAT
1 AAAAGAAAGAAATGAAAT
48689223 AAA
1 AAA
48689226 GATAGAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 7 0.37
18 4 0.21
19 8 0.42
ACGTcount: A:0.74, C:0.03, G:0.13, T:0.10
Consensus pattern (18 bp):
AAAAGAAAGAAATGAAAT
Found at i:48696049 original size:13 final size:13
Alignment explanation
Indices: 48696033--48696060 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
48696023 GAGAGCCATC
48696033 AGCAAAGGAACAA
1 AGCAAAGGAACAA
48696046 AGCAAAGGAACAA
1 AGCAAAGGAACAA
48696059 AG
1 AG
48696061 GAGCCTTGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.61, C:0.14, G:0.25, T:0.00
Consensus pattern (13 bp):
AGCAAAGGAACAA
Found at i:48720287 original size:6 final size:6
Alignment explanation
Indices: 48720276--48720303 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
48720266 AGGTTTCAAA
48720276 AAATGG AAATGG AAATGG AAATGG AAAT
1 AAATGG AAATGG AAATGG AAATGG AAAT
48720304 AATCCATTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.54, C:0.00, G:0.29, T:0.18
Consensus pattern (6 bp):
AAATGG
Found at i:48722394 original size:22 final size:22
Alignment explanation
Indices: 48722366--48722410 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
48722356 ATACTTAAGG
48722366 ATTTGACTAACTCAGATGTACT
1 ATTTGACTAACTCAGATGTACT
48722388 ATTTGACTAACTCAGATGTACT
1 ATTTGACTAACTCAGATGTACT
48722410 A
1 A
48722411 ACGTCCATAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (22 bp):
ATTTGACTAACTCAGATGTACT
Found at i:48730670 original size:18 final size:18
Alignment explanation
Indices: 48730629--48730671 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
48730619 ACACATAAAT
48730629 AAATAAATATCAGATAAGA
1 AAAT-AATATCAGATAAGA
*
48730648 CAATAATATCA-ATAATGA
1 AAATAATATCAGATAA-GA
48730666 AAATAA
1 AAATAA
48730672 ATTATAAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 4 0.19
18 14 0.67
19 3 0.14
ACGTcount: A:0.63, C:0.07, G:0.07, T:0.23
Consensus pattern (18 bp):
AAATAATATCAGATAAGA
Found at i:48731106 original size:21 final size:21
Alignment explanation
Indices: 48731065--48731106 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
48731055 TTGTAAAAGA
* *
48731065 TTTAAATATATATAAATATAT
1 TTTAAATATATAAAAACATAT
48731086 TTTAAA-ATATAAAGAACATAT
1 TTTAAATATATAAA-AACATAT
48731107 ACAAGTATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (21 bp):
TTTAAATATATAAAAACATAT
Found at i:48745357 original size:27 final size:27
Alignment explanation
Indices: 48745327--48745711 Score: 324
Period size: 27 Copynumber: 14.4 Consensus size: 27
48745317 ACCCAAAAAT
* *
48745327 AGGTAGAATGAATGAAATACCCTCATA
1 AGGTAAAATGAATGAAATACCCCCATA
*
48745354 AGGTAAAAT-AACCGAAATACCCCCATA
1 AGGTAAAATGAA-TGAAATACCCCCATA
* * * *
48745381 GGGTAAAATGACTAAAATACCCTCATA
1 AGGTAAAATGAATGAAATACCCCCATA
* *
48745408 AGGTAAAATGACTGAAATACCCCTATA
1 AGGTAAAATGAATGAAATACCCCCATA
* **
48745435 AGGTAGAATGACCGAAATA-CCCCATA
1 AGGTAAAATGAATGAAATACCCCCATA
*
48745461 GGGTAAAATG-ATCGAAATACCCCCATA
1 AGGTAAAATGAAT-GAAATACCCCCATA
48745488 AGGTAAAATG-ATCGAAATACCCCCATA
1 AGGTAAAATGAAT-GAAATACCCCCATA
* **
48745515 GGGTAAAATGACCGAAATACCCCCATA
1 AGGTAAAATGAATGAAATACCCCCATA
* *
48745542 GGGTAAAAT-AATAGAAATACCCCCAGA
1 AGGTAAAATGAAT-GAAATACCCCCATA
* * * *
48745569 GGGTAAAATG-ATAAAAATACTCCTATA
1 AGGTAAAATGAAT-GAAATACCCCCATA
* *** *
48745596 GGGTAAAATGACCAAAATACCCTCATA
1 AGGTAAAATGAATGAAATACCCCCATA
* *
48745623 GGGTAAAATG-ATCGAAATA-CCCCACA
1 AGGTAAAATGAAT-GAAATACCCCCATA
* *
48745649 AGGTAGAATG-ACGAAATACCCCCAT-
1 AGGTAAAATGAATGAAATACCCCCATA
*
48745674 AGAGTAAAATG-ATCGAAATACCCCAATA
1 AG-GTAAAATGAAT-GAAATACCCCCATA
*
48745702 AAGTAAAATG
1 AGGTAAAATG
48745712 GTTGTTATAC
Statistics
Matches: 297, Mismatches: 48, Indels: 26
0.80 0.13 0.07
Matches are distributed among these distances:
25 8 0.03
26 50 0.17
27 237 0.80
28 2 0.01
ACGTcount: A:0.45, C:0.20, G:0.17, T:0.18
Consensus pattern (27 bp):
AGGTAAAATGAATGAAATACCCCCATA
Found at i:48745399 original size:54 final size:54
Alignment explanation
Indices: 48745327--48745711 Score: 413
Period size: 54 Copynumber: 7.2 Consensus size: 54
48745317 ACCCAAAAAT
* * * * * * *
48745327 AGGTAGAATGAATGAAATACCCTCATAAGGTAAAATAACCGAAATACCCCCATA
1 AGGTAAAATGACTAAAATACCCCCATAGGGTAAAATGATCGAAATACCCCCATA
* * * *
48745381 GGGTAAAATGACTAAAATACCCTCATAAGGTAAAATGA-CTGAAATACCCCTATA
1 AGGTAAAATGACTAAAATACCCCCATAGGGTAAAATGATC-GAAATACCCCCATA
* **
48745435 AGGTAGAATGACCGAAATA-CCCCATAGGGTAAAATGATCGAAATACCCCCATA
1 AGGTAAAATGACTAAAATACCCCCATAGGGTAAAATGATCGAAATACCCCCATA
* *
48745488 AGGTAAAATGA-TCGAAATACCCCCATAGGGTAAAATGACCGAAATACCCCCATA
1 AGGTAAAATGACT-AAAATACCCCCATAGGGTAAAATGATCGAAATACCCCCATA
* * * ** * *
48745542 GGGTAAAAT-AATAGAAATACCCCCAGAGGGTAAAATGATAAAAATACTCCTATA
1 AGGTAAAATGACTA-AAATACCCCCATAGGGTAAAATGATCGAAATACCCCCATA
* * * *
48745596 GGGTAAAATGACCAAAATACCCTCATAGGGTAAAATGATCGAAATA-CCCCACA
1 AGGTAAAATGACTAAAATACCCCCATAGGGTAAAATGATCGAAATACCCCCATA
* * * *
48745649 AGGTAGAATGAC-GAAATACCCCCATAGAGTAAAATGATCGAAATACCCCAATA
1 AGGTAAAATGACTAAAATACCCCCATAGGGTAAAATGATCGAAATACCCCCATA
*
48745702 AAGTAAAATG
1 AGGTAAAATG
48745712 GTTGTTATAC
Statistics
Matches: 281, Mismatches: 42, Indels: 17
0.83 0.12 0.05
Matches are distributed among these distances:
52 30 0.11
53 74 0.26
54 175 0.62
55 2 0.01
ACGTcount: A:0.45, C:0.20, G:0.17, T:0.18
Consensus pattern (54 bp):
AGGTAAAATGACTAAAATACCCCCATAGGGTAAAATGATCGAAATACCCCCATA
Found at i:48745578 original size:81 final size:80
Alignment explanation
Indices: 48745340--48745697 Score: 443
Period size: 81 Copynumber: 4.5 Consensus size: 80
48745330 TAGAATGAAT
* * * * *
48745340 GAAATACCCTCATAAGGTAAAATAACCGAAATACCCCCATAGGGTAAAATGACTA-AAATACCCT
1 GAAATACCCCCATAGGGTAAAATGACCGAAATACCCCCATAGGGTAAAAT-AATAGAAATACCCC
48745404 CATAAGGTAAAATGAC
65 CATAAGGTAAAATGAC
* * * * *
48745420 TGAAATACCCCTATAAGGTAGAATGACCGAAATA-CCCCATAGGGTAAAATGATCGAAATACCCC
1 -GAAATACCCCCATAGGGTAAAATGACCGAAATACCCCCATAGGGTAAAATAATAGAAATACCCC
48745484 CATAAGGTAAAATGATC
65 CATAAGGTAAAATGA-C
48745501 GAAATACCCCCATAGGGTAAAATGACCGAAATACCCCCATAGGGTAAAATAATAGAAATACCCCC
1 GAAATACCCCCATAGGGTAAAATGACCGAAATACCCCCATAGGGTAAAATAATAGAAATACCCCC
* * *
48745566 AGAGGGTAAAATGATA
66 ATAAGGTAAAATGA-C
* * * * * * *
48745582 AAAATACTCCTATAGGGTAAAATGACCAAAATACCCTCATAGGGTAAAATGATCGAAATA-CCCC
1 GAAATACCCCCATAGGGTAAAATGACCGAAATACCCCCATAGGGTAAAATAATAGAAATACCCCC
* *
48745646 ACAAGGTAGAATGAC
66 ATAAGGTAAAATGAC
* *
48745661 GAAATACCCCCATAGAGTAAAATGATCGAAATACCCC
1 GAAATACCCCCATAGGGTAAAATGACCGAAATACCCC
48745698 AATAAAGTAA
Statistics
Matches: 240, Mismatches: 34, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
79 31 0.13
80 84 0.35
81 125 0.52
ACGTcount: A:0.44, C:0.22, G:0.16, T:0.18
Consensus pattern (80 bp):
GAAATACCCCCATAGGGTAAAATGACCGAAATACCCCCATAGGGTAAAATAATAGAAATACCCCC
ATAAGGTAAAATGAC
Found at i:48747271 original size:71 final size:71
Alignment explanation
Indices: 48747155--48747435 Score: 562
Period size: 71 Copynumber: 4.0 Consensus size: 71
48747145 TTTCGGAGAG
48747155 AATGGTCCATCATTACCTCTCACTGTCACTATTTTCCACATAACACTATGTGGTCTTCGAGTTTC
1 AATGGTCCATCATTACCTCTCACTGTCACTATTTTCCACATAACACTATGTGGTCTTCGAGTTTC
48747220 CTCGTC
66 CTCGTC
48747226 AATGGTCCATCATTACCTCTCACTGTCACTATTTTCCACATAACACTATGTGGTCTTCGAGTTTC
1 AATGGTCCATCATTACCTCTCACTGTCACTATTTTCCACATAACACTATGTGGTCTTCGAGTTTC
48747291 CTCGTC
66 CTCGTC
48747297 AATGGTCCATCATTACCTCTCACTGTCACTATTTTCCACATAACACTATGTGGTCTTCGAGTTTC
1 AATGGTCCATCATTACCTCTCACTGTCACTATTTTCCACATAACACTATGTGGTCTTCGAGTTTC
48747362 CTCGTC
66 CTCGTC
48747368 AATGGTCCATCATTACCTCTCACTGTCACTATTTTCCACATAACACTATGTGGTCTTCGAGTTTC
1 AATGGTCCATCATTACCTCTCACTGTCACTATTTTCCACATAACACTATGTGGTCTTCGAGTTTC
48747433 CTC
66 CTC
48747436 ATCTCTAAGA
Statistics
Matches: 210, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 210 1.00
ACGTcount: A:0.21, C:0.30, G:0.12, T:0.37
Consensus pattern (71 bp):
AATGGTCCATCATTACCTCTCACTGTCACTATTTTCCACATAACACTATGTGGTCTTCGAGTTTC
CTCGTC
Found at i:48749750 original size:17 final size:17
Alignment explanation
Indices: 48749728--48749760 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
48749718 AACATAAAAA
48749728 TTAAAATTAAAATAAAC
1 TTAAAATTAAAATAAAC
*
48749745 TTAAAATTGAAATAAA
1 TTAAAATTAAAATAAA
48749761 AAATTAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.30
Consensus pattern (17 bp):
TTAAAATTAAAATAAAC
Found at i:48753485 original size:30 final size:30
Alignment explanation
Indices: 48753435--48753537 Score: 102
Period size: 30 Copynumber: 3.5 Consensus size: 30
48753425 AGAATTAGTC
* *
48753435 TGGGCCATAGCCCTATACAGTAGCAGTGTG
1 TGGGCCATAGCCCAATACAGTAACAGTGTG
* * * ***
48753465 TGGGTCATAACCCAATACAGTATCAACATG
1 TGGGCCATAGCCCAATACAGTAACAGTGTG
*
48753495 TGGGCCTTAGCCCAATACAGTAACA--GTG
1 TGGGCCATAGCCCAATACAGTAACAGTGTG
*
48753523 TGGGCCTTAGCCCAA
1 TGGGCCATAGCCCAA
48753538 AATAGTAATC
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
28 17 0.28
30 44 0.72
ACGTcount: A:0.28, C:0.25, G:0.24, T:0.22
Consensus pattern (30 bp):
TGGGCCATAGCCCAATACAGTAACAGTGTG
Found at i:48753544 original size:28 final size:27
Alignment explanation
Indices: 48753489--48753545 Score: 87
Period size: 28 Copynumber: 2.1 Consensus size: 27
48753479 ATACAGTATC
*
48753489 AACATGTGGGCCTTAGCCCAATACAGT
1 AACATGTGGGCCTTAGCCCAAAACAGT
*
48753516 AACAGTGTGGGCCTTAGCCCAAAATAGT
1 AACA-TGTGGGCCTTAGCCCAAAACAGT
48753544 AA
1 AA
48753546 TCAATACAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
27 4 0.15
28 23 0.85
ACGTcount: A:0.33, C:0.23, G:0.23, T:0.21
Consensus pattern (27 bp):
AACATGTGGGCCTTAGCCCAAAACAGT
Found at i:48753696 original size:26 final size:26
Alignment explanation
Indices: 48753657--48753752 Score: 113
Period size: 26 Copynumber: 3.7 Consensus size: 26
48753647 ACACCAATAT
48753657 CGCAGCAAAGCTGCCAGTATCAGTAA
1 CGCAGCAAAGCTGCCAGTATCAGTAA
* * *
48753683 CGTAGCAAAGCTGCCAGTAACAGTAT
1 CGCAGCAAAGCTGCCAGTATCAGTAA
* * **
48753709 CGCAGTAGAGCTGCTTGTATCAGTATA
1 CGCAGCAAAGCTGCCAGTATCAGTA-A
48753736 -GCAGCAAAGCTGCCAGT
1 CGCAGCAAAGCTGCCAGT
48753753 GACAGTATTT
Statistics
Matches: 55, Mismatches: 14, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
26 55 1.00
ACGTcount: A:0.31, C:0.24, G:0.25, T:0.20
Consensus pattern (26 bp):
CGCAGCAAAGCTGCCAGTATCAGTAA
Found at i:48753732 original size:52 final size:52
Alignment explanation
Indices: 48753654--48753760 Score: 144
Period size: 52 Copynumber: 2.1 Consensus size: 52
48753644 AACACACCAA
*
48753654 TATCGCAGCAAAGCTGCCAGTATCAGTA-ACGTAGCAAAGCTGCCAGTAACAG
1 TATCGCAGCAAAGCTGCCAGTATCAGTATA-GCAGCAAAGCTGCCAGTAACAG
* * ** *
48753706 TATCGCAGTAGAGCTGCTTGTATCAGTATAGCAGCAAAGCTGCCAGTGACAG
1 TATCGCAGCAAAGCTGCCAGTATCAGTATAGCAGCAAAGCTGCCAGTAACAG
48753758 TAT
1 TAT
48753761 TTGTGGCAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
52 47 0.98
53 1 0.02
ACGTcount: A:0.32, C:0.22, G:0.24, T:0.21
Consensus pattern (52 bp):
TATCGCAGCAAAGCTGCCAGTATCAGTATAGCAGCAAAGCTGCCAGTAACAG
Found at i:48753984 original size:27 final size:27
Alignment explanation
Indices: 48753954--48754472 Score: 523
Period size: 27 Copynumber: 19.2 Consensus size: 27
48753944 GTAAACGGTC
* * *
48753954 ATTTTACCCCTCGGGGGTATTTTGATA
1 ATTTTACCCTTCGAGGGTATTTCGATA
* *
48753981 ATTTTACCCTTCGAGGGCATTTCAATA
1 ATTTTACCCTTCGAGGGTATTTCGATA
* *
48754008 ATTTTACCCTTCGAGGGTATTTTGGTA
1 ATTTTACCCTTCGAGGGTATTTCGATA
* * *
48754035 ATTTTTCCCTTCAAGGGTATTTCAATA
1 ATTTTACCCTTCGAGGGTATTTCGATA
* *
48754062 ATTTTTACCCTTTGAGGGTGTTTCGATA
1 A-TTTTACCCTTCGAGGGTATTTCGATA
* *
48754090 ATTTTACCCTTCGAGGGAATTT-TAGTA
1 ATTTTACCCTTCGAGGGTATTTCGA-TA
* *
48754117 ATTTTACCCTT-TAGGGGTGTTTC-AGTA
1 ATTTTACCCTTCGA-GGGTATTTCGA-TA
**
48754144 ATTTTACCCTTTAAGGGTATTTCGATA
1 ATTTTACCCTTCGAGGGTATTTCGATA
*
48754171 ATTTTACCCTTCGGGGGTATTTC-AGTA
1 ATTTTACCCTTCGAGGGTATTTCGA-TA
* ** *
48754198 ATTTTACCATTCGAGATTATTTCGGTA
1 ATTTTACCCTTCGAGGGTATTTCGATA
* * *
48754225 ATTTTACCTTTTGAGGGTATTT-TAGTA
1 ATTTTACCCTTCGAGGGTATTTCGA-TA
* *
48754252 ATTTTACCCATT-GAGGGTATTTTGGTA
1 ATTTTACCC-TTCGAGGGTATTTCGATA
* * *
48754279 ATTTTACCCTTCAAAGGTGTTTCGATA
1 ATTTTACCCTTCGAGGGTATTTCGATA
**
48754306 ATTTTACCCTTTAAGGGTATTTC-AGTA
1 ATTTTACCCTTCGAGGGTATTTCGA-TA
* *
48754333 ATTTTACCCTTCTAGGGTGTTTC-AGTA
1 ATTTTACCCTTCGAGGGTATTTCGA-TA
*
48754360 ATTTTACCCTTCGAGGGTATTTCGGTA
1 ATTTTACCCTTCGAGGGTATTTCGATA
* *
48754387 ATTTTACCCATCGAAGGTATTTCGATA
1 ATTTTACCCTTCGAGGGTATTTCGATA
**
48754414 ATTTTACCCTTTAAGGGTATTTCGATA
1 ATTTTACCCTTCGAGGGTATTTCGATA
* *
48754441 ATTTTACCCTTCGAGAGTATTTCGGTA
1 ATTTTACCCTTCGAGGGTATTTCGATA
48754468 ATTTT
1 ATTTT
48754473 TCCTAAGAAT
Statistics
Matches: 408, Mismatches: 70, Indels: 28
0.81 0.14 0.06
Matches are distributed among these distances:
26 6 0.01
27 376 0.92
28 26 0.06
ACGTcount: A:0.23, C:0.16, G:0.18, T:0.43
Consensus pattern (27 bp):
ATTTTACCCTTCGAGGGTATTTCGATA
Found at i:48755573 original size:48 final size:48
Alignment explanation
Indices: 48755502--48755601 Score: 182
Period size: 48 Copynumber: 2.1 Consensus size: 48
48755492 CACACTCTCC
*
48755502 TCCTCTCCCACAAACTCCTTGATTTTCTCCATCAAATCCTCCCTAACT
1 TCCTCTCCCACAAACTCCTTGATTTTCTCCATCAAATCCTCCCCAACT
*
48755550 TCCTCTTCCACAAACTCCTTGATTTTCTCCATCAAATCCTCCCCAACT
1 TCCTCTCCCACAAACTCCTTGATTTTCTCCATCAAATCCTCCCCAACT
48755598 TCCT
1 TCCT
48755602 TCATGACCAG
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.22, C:0.42, G:0.02, T:0.34
Consensus pattern (48 bp):
TCCTCTCCCACAAACTCCTTGATTTTCTCCATCAAATCCTCCCCAACT
Found at i:48760366 original size:8 final size:8
Alignment explanation
Indices: 48760353--48760381 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
48760343 TCATTATACT
48760353 ATTTTATA
1 ATTTTATA
48760361 ATTTTATA
1 ATTTTATA
48760369 ATTTTATA
1 ATTTTATA
48760377 ATTTT
1 ATTTT
48760382 CCAATAAACT
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:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (8 bp):
ATTTTATA
Found at i:48761636 original size:7 final size:7
Alignment explanation
Indices: 48761624--48761682 Score: 100
Period size: 7 Copynumber: 8.4 Consensus size: 7
48761614 ATTAAAATTA
48761624 AAATTTC
1 AAATTTC
48761631 AAATTTC
1 AAATTTC
48761638 AAATTTC
1 AAATTTC
48761645 AAATTTC
1 AAATTTC
48761652 AAATTTC
1 AAATTTC
48761659 AAATTTC
1 AAATTTC
*
48761666 AAAATTC
1 AAATTTC
*
48761673 AAAATTC
1 AAATTTC
48761680 AAA
1 AAA
48761683 ATATAAAACA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
7 51 1.00
ACGTcount: A:0.49, C:0.14, G:0.00, T:0.37
Consensus pattern (7 bp):
AAATTTC
Found at i:48761683 original size:7 final size:7
Alignment explanation
Indices: 48761611--48761684 Score: 80
Period size: 7 Copynumber: 10.7 Consensus size: 7
48761601 TAATTAATAT
48761611 AAAATT-
1 AAAATTC
48761617 AAAATT-
1 AAAATTC
48761623 AAAATTTC
1 AAAA-TTC
*
48761631 AAATTTC
1 AAAATTC
*
48761638 AAATTTC
1 AAAATTC
*
48761645 AAATTTC
1 AAAATTC
*
48761652 AAATTTC
1 AAAATTC
*
48761659 AAATTTC
1 AAAATTC
48761666 AAAATTC
1 AAAATTC
48761673 AAAATTC
1 AAAATTC
48761680 AAAAT
1 AAAAT
48761685 ATAAAACATA
Statistics
Matches: 64, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
6 10 0.16
7 51 0.80
8 3 0.05
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.36
Consensus pattern (7 bp):
AAAATTC
Found at i:48761683 original size:14 final size:14
Alignment explanation
Indices: 48761611--48761684 Score: 89
Period size: 14 Copynumber: 5.4 Consensus size: 14
48761601 TAATTAATAT
*
48761611 AAAATT-AAAATT-
1 AAAATTCAAATTTC
48761623 AAAATTTCAAATTTC
1 AAAA-TTCAAATTTC
*
48761638 AAATTTCAAATTTC
1 AAAATTCAAATTTC
*
48761652 AAATTTCAAATTTC
1 AAAATTCAAATTTC
*
48761666 AAAATTCAAAATTC
1 AAAATTCAAATTTC
48761680 AAAAT
1 AAAAT
48761685 ATAAAACATA
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
12 4 0.07
13 2 0.04
14 46 0.84
15 3 0.05
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.36
Consensus pattern (14 bp):
AAAATTCAAATTTC
Found at i:48761690 original size:21 final size:20
Alignment explanation
Indices: 48761611--48761713 Score: 73
Period size: 21 Copynumber: 4.9 Consensus size: 20
48761601 TAATTAATAT
48761611 AAAATT-AAAATTAAAATTTC
1 AAAATTCAAAATTAAAA-TTC
* * *
48761631 AAATTTCAAATTTCAAATTTC
1 AAAATTCAAAATT-AAAATTC
* *
48761652 AAATTTCAAATTTCAAAATTC
1 AAAATTCAAAATT-AAAATTC
* *
48761673 AAAATTCAAAATATAAAACATA
1 AAAATTCAAAAT-TAAAA-TTC
*
48761695 AAAATATAAAAATTAAAAT
1 AAAAT-TCAAAATTAAAAT
48761714 AAACAAATTA
Statistics
Matches: 68, Mismatches: 10, Indels: 9
0.78 0.11 0.10
Matches are distributed among these distances:
20 5 0.07
21 42 0.62
22 15 0.22
23 6 0.09
ACGTcount: A:0.58, C:0.09, G:0.00, T:0.33
Consensus pattern (20 bp):
AAAATTCAAAATTAAAATTC
Found at i:48761700 original size:15 final size:14
Alignment explanation
Indices: 48761673--48761739 Score: 91
Period size: 14 Copynumber: 4.6 Consensus size: 14
48761663 TTCAAAATTC
48761673 AAAATTCAAAATATA
1 AAAATT-AAAATATA
*
48761688 AAACATAAAAATATA
1 AAA-ATTAAAATATA
48761703 AAAATTAAAATA-A
1 AAAATTAAAATATA
48761716 ACAAATTAAAATATA
1 A-AAATTAAAATATA
48761731 AAAATTAAA
1 AAAATTAAA
48761740 TTCACAGCTT
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
13 2 0.04
14 27 0.57
15 16 0.34
16 2 0.04
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.24
Consensus pattern (14 bp):
AAAATTAAAATATA
Found at i:48761703 original size:8 final size:8
Alignment explanation
Indices: 48761680--48761739 Score: 53
Period size: 8 Copynumber: 8.2 Consensus size: 8
48761670 TTCAAAATTC
48761680 AAAATAT-
1 AAAATATA
*
48761687 AAAACATA
1 AAAATATA
48761695 AAAATATA
1 AAAATATA
48761703 AAAAT-T-
1 AAAATATA
48761709 AAAATA-A
1 AAAATATA
48761716 ACAAAT-T-
1 A-AAATATA
48761723 AAAATATA
1 AAAATATA
48761731 AAAAT-TA
1 AAAATATA
48761738 AA
1 AA
48761740 TTCACAGCTT
Statistics
Matches: 44, Mismatches: 2, Indels: 14
0.73 0.03 0.23
Matches are distributed among these distances:
6 9 0.20
7 14 0.32
8 21 0.48
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.23
Consensus pattern (8 bp):
AAAATATA
Found at i:48761739 original size:7 final size:7
Alignment explanation
Indices: 48761666--48761739 Score: 55
Period size: 7 Copynumber: 10.3 Consensus size: 7
48761656 TTCAAATTTC
*
48761666 AAAATTC
1 AAAATTA
*
48761673 AAAATTC
1 AAAATTA
48761680 AAAATATA
1 AAAAT-TA
48761688 AAACA-TA
1 AAA-ATTA
48761695 AAAATATA
1 AAAAT-TA
48761703 AAAATT-
1 AAAATTA
*
48761709 AAAATAA
1 AAAATTA
48761716 ACAAATT-
1 A-AAATTA
48761723 AAAATATA
1 AAAAT-TA
48761731 AAAATTA
1 AAAATTA
48761738 AA
1 AA
48761740 TTCACAGCTT
Statistics
Matches: 56, Mismatches: 3, Indels: 16
0.75 0.04 0.21
Matches are distributed among these distances:
6 10 0.18
7 25 0.45
8 20 0.36
9 1 0.02
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.24
Consensus pattern (7 bp):
AAAATTA
Found at i:48766835 original size:39 final size:40
Alignment explanation
Indices: 48766734--48766918 Score: 200
Period size: 40 Copynumber: 4.7 Consensus size: 40
48766724 TTGAATGATG
* * * *
48766734 TCCGGGCTAAGTCCCGAAGGC-TTTATGCTAAGTGAC-CAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAT
* *
48766773 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
48766814 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
*
48766853 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
48766892 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
48766919 AACGAGTAGC
Statistics
Matches: 123, Mismatches: 16, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
39 35 0.28
40 79 0.64
41 9 0.07
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
Found at i:48766940 original size:79 final size:79
Alignment explanation
Indices: 48766787--48766951 Score: 201
Period size: 79 Copynumber: 2.1 Consensus size: 79
48766777 GGACTAAGAT
* **
48766787 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
*
48766852 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* * *
48766866 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTTA-C
* *
48766929 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
48766945 CCGAAGG
1 CCGAAGG
48766952 TATGTGATTT
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
78 2 0.03
79 48 0.65
80 24 0.32
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:48774862 original size:6 final size:6
Alignment explanation
Indices: 48774851--48774922 Score: 51
Period size: 6 Copynumber: 12.5 Consensus size: 6
48774841 TAATTCTAAG
* * * *
48774851 AAAATA AAAATA AAAAT- -AACTA AAAATA ACAATA AACATA AACAT-
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA
* * * *
48774896 AAAAGA AAAAGA AAACTA AAAAGA AAA
1 AAAATA AAAATA AAAATA AAAATA AAA
48774923 CAGAGAAACT
Statistics
Matches: 52, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
4 3 0.06
5 3 0.06
6 46 0.88
ACGTcount: A:0.76, C:0.07, G:0.04, T:0.12
Consensus pattern (6 bp):
AAAATA
Found at i:48774867 original size:26 final size:25
Alignment explanation
Indices: 48774802--48774869 Score: 66
Period size: 26 Copynumber: 2.6 Consensus size: 25
48774792 AGAAACAACC
*
48774802 ATAAAAATAAAAATATAGTCCAAAAG
1 ATAAAAATAAAAATA-AGTCCAAAAA
* * *
48774828 ATAAGAAAT-GAAATAATTCTAAGAAA
1 ATAA-AAATAAAAATAAGTCCAA-AAA
48774854 ATAAAAATAAAAATAA
1 ATAAAAATAAAAATAA
48774870 CTAAAAATAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
25 9 0.26
26 21 0.62
27 4 0.12
ACGTcount: A:0.68, C:0.04, G:0.07, T:0.21
Consensus pattern (25 bp):
ATAAAAATAAAAATAAGTCCAAAAA
Found at i:48774876 original size:16 final size:18
Alignment explanation
Indices: 48774854--48774899 Score: 60
Period size: 16 Copynumber: 2.7 Consensus size: 18
48774844 TTCTAAGAAA
48774854 ATAAAAATAAAAAT-AAC
1 ATAAAAATAAAAATAAAC
*
48774871 -TAAAAATAACAATAAAC
1 ATAAAAATAAAAATAAAC
*
48774888 ATAAACATAAAA
1 ATAAAAATAAAA
48774900 GAAAAAGAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
16 12 0.50
17 3 0.12
18 9 0.38
ACGTcount: A:0.74, C:0.09, G:0.00, T:0.17
Consensus pattern (18 bp):
ATAAAAATAAAAATAAAC
Found at i:48789465 original size:16 final size:16
Alignment explanation
Indices: 48789444--48789474 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
48789434 ATATTAATAA
48789444 TTTTATTAAATTATAT
1 TTTTATTAAATTATAT
48789460 TTTTATTAAATTATA
1 TTTTATTAAATTATA
48789475 ATTAATAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTTATTAAATTATAT
Found at i:48789620 original size:120 final size:120
Alignment explanation
Indices: 48789379--48789854 Score: 760
Period size: 120 Copynumber: 4.0 Consensus size: 120
48789369 ATTATTAATC
* *
48789379 TATATTATATAGTATTATATATTATGATTTTATTAAATTCATATAAGAATATTTAATATTAATAA
1 TATATTATATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAA
* *
48789444 TTTTATTAAA-T-TATATTTTTATTAAATTATAATTAATAATAATTATTTTAAAT
66 TTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAAT
* *
48789497 TATATTATATAGTATTATATATTATGATTTTATTAAATTCATATAAGAGTATTTAATATTAAGAA
1 TATATTATATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAA
48789562 TTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAAT
66 TTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAAT
* * *
48789617 TATATTTTATAGTATTATATATTATGATTTTAGAAAATTCATATAATAATATTTAATATTAAGAA
1 TATATTATATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAA
*
48789682 TTTTATTAAATTATATA-TTTTATTAAATTATATTTAATAATAATTATGTTAAAA
66 TTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAAT
* * * * * * *
48789736 TATATTTTATAGTATCATATGTTATTATTTTAGTAAATTCAGATAAGAATATTGACTATTAAGAA
1 TATATTATATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAA
* *
48789801 TTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAA
66 TTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAA
48789855 ATATGGTTAA
Statistics
Matches: 335, Mismatches: 20, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
118 73 0.22
119 111 0.33
120 151 0.45
ACGTcount: A:0.43, C:0.01, G:0.05, T:0.51
Consensus pattern (120 bp):
TATATTATATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAA
TTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAAT
Found at i:48789701 original size:17 final size:17
Alignment explanation
Indices: 48789681--48789714 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
48789671 AATATTAAGA
48789681 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
48789698 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
48789715 TTAATAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
ATTTTATTAAATTATAT
Found at i:48789816 original size:239 final size:238
Alignment explanation
Indices: 48789379--48789854 Score: 772
Period size: 239 Copynumber: 2.0 Consensus size: 238
48789369 ATTATTAATC
** *
48789379 TATATTATATAGTATTATATATTATGATTTTATTAAATTCATATAAGAATATTTAATATTAATAA
1 TATATTATATAGTATTATATATTATGATTTTAGAAAATTCATATAAGAATATTTAATATTAAGAA
* *
48789444 TTTTATTAAATTATATTTTTATTAAATTATAATTAATAATAATTATTTTAAATTATATTATATAG
66 TTTTATTAAATTATATTTTTATTAAATTATAATTAATAATAATTATGTTAAAATATATTATATAG
* * * * *
48789509 TATTATATATTATGATTTTATTAAATTCATATAAGAGTATTTAATATTAAGAATTTTATTAAATT
131 TATCATATATTATGATTTTAGTAAATTCAGATAAGAATATTGAATATTAAGAATTTTATTAAATT
* *
48789574 ATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAAT
196 ATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAAT
* *
48789617 TATATTTTATAGTATTATATATTATGATTTTAGAAAATTCATATAATAATATTTAATATTAAGAA
1 TATATTATATAGTATTATATATTATGATTTTAGAAAATTCATATAAGAATATTTAATATTAAGAA
* *
48789682 TTTTATTAAATTATATATTTTATTAAATTATATTTAATAATAATTATGTTAAAATATATTTTATA
66 TTTTATTAAATTATAT-TTTTATTAAATTATAATTAATAATAATTATGTTAAAATATATTATATA
* * *
48789747 GTATCATATGTTATTATTTTAGTAAATTCAGATAAGAATATTGACTATTAAGAATTTTATTAAAT
130 GTATCATATATTATGATTTTAGTAAATTCAGATAAGAATATTGAATATTAAGAATTTTATTAAAT
48789812 TATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAA
195 TATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAA
48789855 ATATGGTTAA
Statistics
Matches: 218, Mismatches: 19, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
238 76 0.35
239 142 0.65
ACGTcount: A:0.43, C:0.01, G:0.05, T:0.51
Consensus pattern (238 bp):
TATATTATATAGTATTATATATTATGATTTTAGAAAATTCATATAAGAATATTTAATATTAAGAA
TTTTATTAAATTATATTTTTATTAAATTATAATTAATAATAATTATGTTAAAATATATTATATAG
TATCATATATTATGATTTTAGTAAATTCAGATAAGAATATTGAATATTAAGAATTTTATTAAATT
ATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAAT
Found at i:48789828 original size:18 final size:17
Alignment explanation
Indices: 48789800--48789834 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
48789790 ACTATTAAGA
*
48789800 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
48789817 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
48789835 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:48790083 original size:45 final size:44
Alignment explanation
Indices: 48789997--48790086 Score: 110
Period size: 45 Copynumber: 2.0 Consensus size: 44
48789987 ACCTCTATTC
* *
48789997 CATTCAACCAAACACAAGAATACTATTGCACCTCTATTCCATTA
1 CATTCAACCAAACACAAGAATACTATTACACCTCTAATCCATTA
* * *
48790041 CATTCAACCAAACA-ATTGAATTGCTATTACGCCTCTAATCCATTA
1 CATTCAACCAAACACA-AGAA-TACTATTACACCTCTAATCCATTA
48790086 C
1 C
48790087 GCTTCTAATC
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
43 1 0.03
44 17 0.44
45 21 0.54
ACGTcount: A:0.37, C:0.29, G:0.06, T:0.29
Consensus pattern (44 bp):
CATTCAACCAAACACAAGAATACTATTACACCTCTAATCCATTA
Found at i:48790087 original size:16 final size:16
Alignment explanation
Indices: 48790066--48790134 Score: 102
Period size: 16 Copynumber: 4.3 Consensus size: 16
48790056 TTGAATTGCT
48790066 ATTACGCCTCTAATCC
1 ATTACGCCTCTAATCC
*
48790082 ATTACGCTTCTAATCC
1 ATTACGCCTCTAATCC
* *
48790098 ATTACGCCTCTATTAC
1 ATTACGCCTCTAATCC
*
48790114 ATTACGCCTCTATTCC
1 ATTACGCCTCTAATCC
48790130 ATTAC
1 ATTAC
48790135 AGCGAACCAA
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 48 1.00
ACGTcount: A:0.25, C:0.33, G:0.06, T:0.36
Consensus pattern (16 bp):
ATTACGCCTCTAATCC
Found at i:48792437 original size:48 final size:49
Alignment explanation
Indices: 48792335--48792438 Score: 140
Period size: 47 Copynumber: 2.1 Consensus size: 49
48792325 GGATTACTTA
* * *
48792335 AAAATGATCGGAAGAATGAGTTTATGTTTTTGAGATATTTTGAAGCCTG
1 AAAATGATCGGAAGAATGAGTTTATATTTTTCAGATATGTTGAAGCCTG
* *
48792384 GAAATGA-CGGAAGAATGAG-TTATATTTTTCAGCTATGTTGAAGCCTCG
1 AAAATGATCGGAAGAATGAGTTTATATTTTTCAGATATGTTGAAGCCT-G
48792432 AAAATGA
1 AAAATGA
48792439 AAATAAACCA
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
47 23 0.48
48 19 0.40
49 6 0.12
ACGTcount: A:0.35, C:0.09, G:0.24, T:0.33
Consensus pattern (49 bp):
AAAATGATCGGAAGAATGAGTTTATATTTTTCAGATATGTTGAAGCCTG
Found at i:48794849 original size:85 final size:85
Alignment explanation
Indices: 48794704--48794888 Score: 289
Period size: 85 Copynumber: 2.2 Consensus size: 85
48794694 CCTTTCTTTA
* * *
48794704 CAACAACACAAGTATTTTACCATATGTAAGACAATATTAGAAATAAGGTTAGAATTCAATTTAGG
1 CAACAACACAAGTATTTCACCATACGTAAGACAATATTAGAAATAAGGTTAGAATCCAATTTAGG
*
48794769 ATGATCCTGTGGCATACCTG
66 ATGATCCTGTGACATACCTG
* * * *
48794789 CAACAACATAAGTATTTCATCATACGTAAGACAATATTAGAGATAAGGTTAGAATCCAATTTGGG
1 CAACAACACAAGTATTTCACCATACGTAAGACAATATTAGAAATAAGGTTAGAATCCAATTTAGG
48794854 ATGATCCTGTGACATACCTG
66 ATGATCCTGTGACATACCTG
*
48794874 CAATAACACAAGTAT
1 CAACAACACAAGTAT
48794889 GTGGAGTGTT
Statistics
Matches: 90, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
85 90 1.00
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.28
Consensus pattern (85 bp):
CAACAACACAAGTATTTCACCATACGTAAGACAATATTAGAAATAAGGTTAGAATCCAATTTAGG
ATGATCCTGTGACATACCTG
Found at i:48795413 original size:18 final size:18
Alignment explanation
Indices: 48795376--48795414 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
48795366 CATCGGTTTT
*
48795376 AACTTCCTTTTCATTCTC
1 AACTTCCTTTTCATTATC
**
48795394 AACTTCCTTTTTGTTATC
1 AACTTCCTTTTCATTATC
48795412 AAC
1 AAC
48795415 CTAGTTGCAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.21, C:0.28, G:0.03, T:0.49
Consensus pattern (18 bp):
AACTTCCTTTTCATTATC
Found at i:48798263 original size:31 final size:31
Alignment explanation
Indices: 48798225--48798286 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
48798215 GAAAAAAAGA
48798225 AAACTTAATTTTTGTTGCTAAGGGTGTTGTT
1 AAACTTAATTTTTGTTGCTAAGGGTGTTGTT
48798256 AAACTTAATTTTTGTTGCTAAGGGTGTTGTT
1 AAACTTAATTTTTGTTGCTAAGGGTGTTGTT
48798287 TGAAAGAACT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.23, C:0.06, G:0.23, T:0.48
Consensus pattern (31 bp):
AAACTTAATTTTTGTTGCTAAGGGTGTTGTT
Found at i:48800283 original size:77 final size:77
Alignment explanation
Indices: 48800156--48800317 Score: 315
Period size: 77 Copynumber: 2.1 Consensus size: 77
48800146 TGAGACAATC
48800156 TTAAAGTGTTATGTCAATAAAATTTTATATATTTCAAGTTCAAAGATTAAAATATATCTAATTGT
1 TTAAAGTGTTATGTCAATAAAATTTTATATATTTCAAGTTCAAAGATTAAAATATATCTAATTGT
48800221 CAAGTTCAATTA
66 CAAGTTCAATTA
*
48800233 TTAAAGTGTTATGTCAATATAATTTTATATATTTCAAGTTCAAAGATTAAAATATATCTAATTGT
1 TTAAAGTGTTATGTCAATAAAATTTTATATATTTCAAGTTCAAAGATTAAAATATATCTAATTGT
48800298 CAAGTTCAATTA
66 CAAGTTCAATTA
48800310 TTAAAGTG
1 TTAAAGTG
48800318 GACAAAAAAT
Statistics
Matches: 84, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
77 84 1.00
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.42
Consensus pattern (77 bp):
TTAAAGTGTTATGTCAATAAAATTTTATATATTTCAAGTTCAAAGATTAAAATATATCTAATTGT
CAAGTTCAATTA
Found at i:48800715 original size:56 final size:57
Alignment explanation
Indices: 48800606--48800738 Score: 146
Period size: 56 Copynumber: 2.3 Consensus size: 57
48800596 TATATTATTA
* *
48800606 TATATTATGATTTTAGTAAATTAATATAAGAATAATTATATTAAGAATTTTATTAAAT
1 TATA-TATTATTTTATTAAATTAATATAAGAATAATTATATTAAGAATTTTATTAAAT
* * *
48800664 TATATATT-TTTTATTAAATTATATTTAATAATAATTAT-TTTA-AATTATTATTAAAT
1 TATATATTATTTTATTAAATTA-ATATAAGAATAATTATATTAAGAATT-TTATTAAAT
* *
48800720 TGTTTATTATTTATATTAA
1 TATATATTATTT-TATTAA
48800739 TAATCTTATT
Statistics
Matches: 64, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
55 4 0.06
56 30 0.47
57 20 0.31
58 10 0.16
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (57 bp):
TATATATTATTTTATTAAATTAATATAAGAATAATTATATTAAGAATTTTATTAAAT
Found at i:48800888 original size:39 final size:39
Alignment explanation
Indices: 48800834--48800932 Score: 171
Period size: 39 Copynumber: 2.5 Consensus size: 39
48800824 TTTTCTTATG
*
48800834 CTATTATGCCTCTATTCCATTCAACCAAATACAAGAATA
1 CTATTATGCCTCTATTCCATTCAACCAAACACAAGAATA
* *
48800873 CTATTACGCCTCTATTTCATTCAACCAAACACAAGAATA
1 CTATTATGCCTCTATTCCATTCAACCAAACACAAGAATA
48800912 CTATTATGCCTCTATTCCATT
1 CTATTATGCCTCTATTCCATT
48800933 ATATTCAATC
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 55 1.00
ACGTcount: A:0.34, C:0.27, G:0.05, T:0.33
Consensus pattern (39 bp):
CTATTATGCCTCTATTCCATTCAACCAAACACAAGAATA
Found at i:48800980 original size:16 final size:16
Alignment explanation
Indices: 48800959--48801011 Score: 61
Period size: 16 Copynumber: 3.3 Consensus size: 16
48800949 TTGAATTGCT
48800959 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
* * *
48800975 ATTACGTCTTTATTTC
1 ATTACGCCTCTATTCC
**
48800991 ATTACGCCTGAATTCC
1 ATTACGCCTCTATTCC
48801007 ATTAC
1 ATTAC
48801012 AGCGAACCAA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.23, C:0.28, G:0.08, T:0.42
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:48807159 original size:14 final size:15
Alignment explanation
Indices: 48807129--48807167 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
48807119 AATCGAAAAA
48807129 AATCGAATTTCGAGTT
1 AATCGAA-TTCGAGTT
48807145 AATCGAATT-GAGTT
1 AATCGAATTCGAGTT
*
48807159 ATTCGAATT
1 AATCGAATT
48807168 ATTCAAGTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 13 0.59
15 2 0.09
16 7 0.32
ACGTcount: A:0.33, C:0.10, G:0.18, T:0.38
Consensus pattern (15 bp):
AATCGAATTCGAGTT
Found at i:48807360 original size:19 final size:19
Alignment explanation
Indices: 48807316--48807367 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 19
48807306 AAAAATTACA
48807316 AAAAATTCAAAATAAATTTT
1 AAAAATTCAAAAT-AATTTT
*
48807336 -ATAATTCAAAAT-ATTTAT
1 AAAAATTCAAAATAATTT-T
48807354 AAAAATTTCAAAAT
1 AAAAA-TTCAAAAT
48807368 TCATATTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
17 4 0.15
18 1 0.04
19 14 0.52
20 8 0.30
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.37
Consensus pattern (19 bp):
AAAAATTCAAAATAATTTT
Found at i:48807688 original size:20 final size:20
Alignment explanation
Indices: 48807663--48807702 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
48807653 AATAAAATGA
*
48807663 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
48807683 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
48807703 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:48807864 original size:22 final size:24
Alignment explanation
Indices: 48807839--48807889 Score: 56
Period size: 26 Copynumber: 2.2 Consensus size: 24
48807829 TTATTTATAA
48807839 ATAAATAA-A-TCAA-ATT-AAAT
1 ATAAATAATACTCAATATTAAAAT
48807859 ATATAATAATACTCAATTATTAAAAT
1 ATA-AATAATACTCAA-TATTAAAAT
48807885 ATAAA
1 ATAAA
48807890 AGCATTGCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
20 3 0.12
21 5 0.20
22 1 0.04
23 4 0.16
25 5 0.20
26 7 0.28
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (24 bp):
ATAAATAATACTCAATATTAAAAT
Found at i:48811439 original size:23 final size:23
Alignment explanation
Indices: 48811413--48811511 Score: 162
Period size: 23 Copynumber: 4.3 Consensus size: 23
48811403 ATAAGTGCAA
48811413 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
48811436 CACTGTTATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
48811459 CACTAAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
48811482 CACTGTTATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
48811505 CACTGAT
1 CACTGAT
48811512 CAATAACACT
Statistics
Matches: 68, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 68 1.00
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.23
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:48814186 original size:220 final size:220
Alignment explanation
Indices: 48813803--48814805 Score: 1877
Period size: 220 Copynumber: 4.6 Consensus size: 220
48813793 TACTAAATAA
* *
48813803 TGTGTTTTATAGTTTATTAAAAGTCAAAATAATTCATATA-ATATATATTTTGTGTTACACATTT
1 TGTGTTTTATGGTTTATTAAAAGTCAAAAT-ATTAATATATA-ATATATTTTGTGTTACACATTT
48813867 CTTCAAGCACTTATATTTTATTAAATCAGGAATAAACCAAATTTGATGGATTATTGAACTGTGTT
64 CTTCAAGCACTTATATTTTATTAAATCAGGAATAAACCAAATTTGATGGATTATTGAACTGTGTT
48813932 TTATGATTTATCAAAAGTAAAAAAAAAAATCATATATAATATATTTTATGGTATACACATCTCTT
129 TTATGATTTATCAAAAGTAAAAAAAAAAATCATATATAATATATTTTATGGTATACACATCTCTT
48813997 TATGTACTTATATATTTTTTAAATCAG
194 TATGTACTTATATATTTTTTAAATCAG
48814024 TGTGTTTTATGGTTTATTAAAAGTCAAAATATTAATATATAATATATTTTGTGTTACACATTTCT
1 TGTGTTTTATGGTTTATTAAAAGTCAAAATATTAATATATAATATATTTTGTGTTACACATTTCT
48814089 TCAAGCACTTATATTTTATTAAATCAGGAATAAACCAAATTTGATGGATTATTGAACTGTGTTTT
66 TCAAGCACTTATATTTTATTAAATCAGGAATAAACCAAATTTGATGGATTATTGAACTGTGTTTT
48814154 ATGATTTATCAAAAGTAAAAAAAAAAATCATATATAATATATTTTATGGTATACACATCTCTTTA
131 ATGATTTATCAAAAGTAAAAAAAAAAATCATATATAATATATTTTATGGTATACACATCTCTTTA
48814219 TGTACTTATATATTTTTTAAATCAG
196 TGTACTTATATATTTTTTAAATCAG
48814244 TGTGTTTTATGGTTTATTAAAAGTCAAAATATTAATATATAATATATTTTGTGTTACACATTTCT
1 TGTGTTTTATGGTTTATTAAAAGTCAAAATATTAATATATAATATATTTTGTGTTACACATTTCT
48814309 TCAAGCACTTATATTTTATTAAATCAGGAATAAACCAAATTTGATGGATTATTGAACTGTGTTTT
66 TCAAGCACTTATATTTTATTAAATCAGGAATAAACCAAATTTGATGGATTATTGAACTGTGTTTT
48814374 ATGATTTATCAAAAGTAAAAAAAAAAATCATATATAATATATTTTATGGTATACACATCTCTTTA
131 ATGATTTATCAAAAGTAAAAAAAAAAATCATATATAATATATTTTATGGTATACACATCTCTTTA
48814439 TGTACTTATATATTTTTTAAATCAG
196 TGTACTTATATATTTTTTAAATCAG
48814464 TGTGTTTTATGGTTTATTAAAAGTCAAAATATTAATATATAATATATTTTGTGTTACACATTTCT
1 TGTGTTTTATGGTTTATTAAAAGTCAAAATATTAATATATAATATATTTTGTGTTACACATTTCT
48814529 TCAAGCACTTATATTTTATTAAATCAGGAATAAACCAAATTTGATGGATTATTGAACTGTGTTTT
66 TCAAGCACTTATATTTTATTAAATCAGGAATAAACCAAATTTGATGGATTATTGAACTGTGTTTT
48814594 ATGATTTATCAAAAGTAAAAAAAAAAATCATATATAATATATTTTATGGTATACACATCTCTTTA
131 ATGATTTATCAAAAGTAAAAAAAAAAATCATATATAATATATTTTATGGTATACACATCTCTTTA
48814659 TGTACTTATATATTTTTTAAATCAG
196 TGTACTTATATATTTTTTAAATCAG
48814684 TGTGTTTTATGGTTTATTAAAAGTCAAAATATTAATATATAATATATTTTGTGTTACACATTTCT
1 TGTGTTTTATGGTTTATTAAAAGTCAAAATATTAATATATAATATATTTTGTGTTACACATTTCT
* * * ** * *
48814749 TCAAGTATTTATA-TTTATTTAAA-CGGGAATAAAAGAATTTTGATGGATTACTGAACT
66 TCAAGCACTTATATTTTA-TTAAATCAGGAATAAACCAAATTTGATGGATTATTGAACT
48814806 TATTAAAAGT
Statistics
Matches: 771, Mismatches: 9, Indels: 6
0.98 0.01 0.01
Matches are distributed among these distances:
219 33 0.04
220 708 0.92
221 30 0.04
ACGTcount: A:0.38, C:0.08, G:0.10, T:0.43
Consensus pattern (220 bp):
TGTGTTTTATGGTTTATTAAAAGTCAAAATATTAATATATAATATATTTTGTGTTACACATTTCT
TCAAGCACTTATATTTTATTAAATCAGGAATAAACCAAATTTGATGGATTATTGAACTGTGTTTT
ATGATTTATCAAAAGTAAAAAAAAAAATCATATATAATATATTTTATGGTATACACATCTCTTTA
TGTACTTATATATTTTTTAAATCAG
Found at i:48817698 original size:22 final size:23
Alignment explanation
Indices: 48817645--48817700 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
48817635 TTTAATTAAA
* * *
48817645 ATTAAAATTAAAATTATTTTTTT
1 ATTAAAATTAAAACTATATTGTT
*
48817668 AATAAAATTAAAACTA-ATTGTT
1 ATTAAAATTAAAACTATATTGTT
48817690 ATTAAAATTAA
1 ATTAAAATTAA
48817701 TTGTTAGTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 14 0.50
23 14 0.50
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
ATTAAAATTAAAACTATATTGTT
Found at i:48817713 original size:16 final size:16
Alignment explanation
Indices: 48817676--48817715 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
48817666 TTAATAAAAT
* *
48817676 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
48817692 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
48817708 TAAAATTA
1 TAAAATTA
48817716 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:48817794 original size:59 final size:59
Alignment explanation
Indices: 48817726--48817865 Score: 271
Period size: 59 Copynumber: 2.4 Consensus size: 59
48817716 TCAAATTATT
*
48817726 AATTGTTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
1 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
48817785 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
1 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
48817844 AATTATTAATTGTATTAATTGT
1 AATTATTAATTGTATTAATTGT
48817866 ATTAATTGTT
Statistics
Matches: 80, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
59 80 1.00
ACGTcount: A:0.39, C:0.04, G:0.09, T:0.47
Consensus pattern (59 bp):
AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
Found at i:48817859 original size:9 final size:9
Alignment explanation
Indices: 48817847--48817874 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
48817837 TTTATCAAAT
48817847 TATTAATTG
1 TATTAATTG
48817856 TATTAATTG
1 TATTAATTG
48817865 TATTAATTG
1 TATTAATTG
48817874 T
1 T
48817875 TGTAACAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Done.