Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr2
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: 61750188
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1877335 characters in sequence are not A, C, G, or T
File 127 of 186
Found at i:42192063 original size:31 final size:31
Alignment explanation
Indices: 42192027--42192096 Score: 103
Period size: 27 Copynumber: 2.4 Consensus size: 31
42192017 TGTGTTGTTG
42192027 GATTAAATTGAATGAAATTGTGTTTGAATGA
1 GATTAAATTGAATGAAATTGTGTTTGAATGA
42192058 GATT-AATT---TGAAATTGTGTTTGAATGA
1 GATTAAATTGAATGAAATTGTGTTTGAATGA
*
42192085 GATTAATTTGAA
1 GATTAAATTGAA
42192097 ATTTTATAGA
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
27 23 0.68
28 3 0.09
30 4 0.12
31 4 0.12
ACGTcount: A:0.37, C:0.00, G:0.21, T:0.41
Consensus pattern (31 bp):
GATTAAATTGAATGAAATTGTGTTTGAATGA
Found at i:42192071 original size:27 final size:27
Alignment explanation
Indices: 42192039--42192099 Score: 122
Period size: 27 Copynumber: 2.3 Consensus size: 27
42192029 TTAAATTGAA
42192039 TGAAATTGTGTTTGAATGAGATTAATT
1 TGAAATTGTGTTTGAATGAGATTAATT
42192066 TGAAATTGTGTTTGAATGAGATTAATT
1 TGAAATTGTGTTTGAATGAGATTAATT
42192093 TGAAATT
1 TGAAATT
42192100 TTATAGATCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.34, C:0.00, G:0.21, T:0.44
Consensus pattern (27 bp):
TGAAATTGTGTTTGAATGAGATTAATT
Found at i:42205515 original size:12 final size:12
Alignment explanation
Indices: 42205498--42205522 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
42205488 CTGTGTGTTC
42205498 TTTATTTTATTT
1 TTTATTTTATTT
42205510 TTTATTTTATTT
1 TTTATTTTATTT
42205522 T
1 T
42205523 CACATATTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTATTTTATTT
Found at i:42205766 original size:45 final size:45
Alignment explanation
Indices: 42205628--42205885 Score: 188
Period size: 45 Copynumber: 5.8 Consensus size: 45
42205618 ATGATTGAAG
* *
42205628 GATGCCATAGTGTCTTTCAACCATCGTCTTATTCATTCTCGTCTT
1 GATGCCATAATGTCTTTCAACCATGGTCTTATTCATTCTCGTCTT
* * * *
42205673 AATGCCATAGTGTCTTTCAACCATGGTCTTATACATTCTCGCCTT
1 GATGCCATAATGTCTTTCAACCATGGTCTTATTCATTCTCGTCTT
* * * * *
42205718 GATGCCATAATGTCTTTCAACGATGGTCTTGTTC-GTCTGAGTCAT
1 GATGCCATAATGTCTTTCAACCATGGTCTTATTCATTCT-CGTCTT
* * ** * ** * *
42205763 GATGCCACAACGTCTTTCTGCTATGGTCTTACACGTT-TCCAT-TAT
1 GATGCCATAATGTCTTTCAACCATGGTCTTATTCATTCT-CGTCT-T
* * * *
42205808 AATGCCATAGTGTCTTTCAACTATGGTCTTATTCAGTTC-CGGT-AT
1 GATGCCATAATGTCTTTCAACCATGGTCTTATTCA-TTCTC-GTCTT
*
42205853 -ACTGCCATAATATCTTTCAACCAT-GTCTTATTC
1 GA-TGCCATAATGTCTTTCAACCATGGTCTTATTC
42205886 GTTTCCTTCA
Statistics
Matches: 166, Mismatches: 40, Indels: 15
0.75 0.18 0.07
Matches are distributed among these distances:
44 13 0.08
45 149 0.90
46 4 0.02
ACGTcount: A:0.21, C:0.24, G:0.15, T:0.39
Consensus pattern (45 bp):
GATGCCATAATGTCTTTCAACCATGGTCTTATTCATTCTCGTCTT
Found at i:42212200 original size:46 final size:46
Alignment explanation
Indices: 42212102--42212222 Score: 163
Period size: 46 Copynumber: 2.6 Consensus size: 46
42212092 ATTATGAGAG
* * *
42212102 CCAGTGTAAGACCATGTCTGGGACATGGCATCGACATTGAGACGAATG
1 CCAGTATAAGA-CATGTCTGGGACAT-GCATCGACATCGAGACGAATA
* *
42212150 CCAGTATAAGACATGTCTGGGACATGCATCGACCTCGGGACGTAA-A
1 CCAGTATAAGACATGTCTGGGACATGCATCGACATCGAGACG-AATA
42212196 CCAGTATAAGACATGTCTGGGACATGC
1 CCAGTATAAGACATGTCTGGGACATGC
42212223 GACGGCTACG
Statistics
Matches: 67, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
46 41 0.61
47 16 0.24
48 10 0.15
ACGTcount: A:0.30, C:0.22, G:0.27, T:0.21
Consensus pattern (46 bp):
CCAGTATAAGACATGTCTGGGACATGCATCGACATCGAGACGAATA
Found at i:42217772 original size:86 final size:87
Alignment explanation
Indices: 42217638--42217798 Score: 252
Period size: 86 Copynumber: 1.9 Consensus size: 87
42217628 GGAATATTTG
* *
42217638 AGATGTAAAGAGACGTATTGGTAAGTGATGTGAAATGGATATTTTGAACAGGTATGTATTTAACC
1 AGATGTAAAGAGACGTATTGGTAAGTGATGTGAAATGGATACTTTGAACAGGTATGTACTTAACC
42217703 CTCGGGTTGAGAGGAATACTCA
66 CTCGGGTTGAGAGGAATACTCA
* * ** *
42217725 AGATG-AAAGGGATGTATTGGTAAGTTTTGTGAAATGGGTACTTTGAACAGGTATGTACTTAACC
1 AGATGTAAAGAGACGTATTGGTAAGTGATGTGAAATGGATACTTTGAACAGGTATGTACTTAACC
42217789 CTCGGGTTGA
66 CTCGGGTTGA
42217799 AAAATCGATA
Statistics
Matches: 67, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
86 62 0.93
87 5 0.07
ACGTcount: A:0.31, C:0.09, G:0.29, T:0.31
Consensus pattern (87 bp):
AGATGTAAAGAGACGTATTGGTAAGTGATGTGAAATGGATACTTTGAACAGGTATGTACTTAACC
CTCGGGTTGAGAGGAATACTCA
Found at i:42222859 original size:50 final size:48
Alignment explanation
Indices: 42222751--42222930 Score: 161
Period size: 50 Copynumber: 3.7 Consensus size: 48
42222741 CTTGTGTGAA
*
42222751 CTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCACATTATGAGAG
1 CTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCACAATATGAGAG
* * *
42222797 CCATTGTAAGACCATGTCTGGGACATGGCATCGG-CATGAATATGCGAGAG
1 CTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCA-CAATAT--GAGAG
** * * * *
42222847 CTAGTGTAAGACCATGTCTAAGACATGGCATCAGCCTCGATGATGATAG
1 CTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCACAAT-ATGAGAG
* * * *
42222896 -TAAGTTTGATACCATGTTTGGGACATGGCATCGGC
1 CT-AGTGTAAGACCATGTCTGGGACATGGCATCGGC
42222931 ACCTTACCCG
Statistics
Matches: 106, Mismatches: 20, Indels: 13
0.76 0.14 0.09
Matches are distributed among these distances:
46 9 0.08
47 16 0.15
48 12 0.11
49 30 0.28
50 36 0.34
51 3 0.03
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.25
Consensus pattern (48 bp):
CTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCACAATATGAGAG
Found at i:42237062 original size:28 final size:27
Alignment explanation
Indices: 42237025--42237119 Score: 77
Period size: 28 Copynumber: 3.4 Consensus size: 27
42237015 GATTTTAGGC
42237025 TTTAGAGTTTAGGGTTTAATGTTTAGTAA
1 TTTAG-GTTTAGGGTTTAA-GTTTAGTAA
* *
42237054 TTTAGGTTTAGGGGTTAAGATTT-GTTAT
1 TTTAGGTTTAGGGTTTAAG-TTTAG-TAA
* * *
42237082 TTTGGGTTTAGGGTTTTAGGTTTAG-GA
1 TTTAGGTTTAGGG-TTTAAGTTTAGTAA
42237109 TTTAGGGTTTA
1 TTTA-GGTTTA
42237120 TGATTTAGTG
Statistics
Matches: 53, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
27 5 0.09
28 38 0.72
29 10 0.19
ACGTcount: A:0.21, C:0.00, G:0.29, T:0.49
Consensus pattern (27 bp):
TTTAGGTTTAGGGTTTAAGTTTAGTAA
Found at i:42237117 original size:14 final size:14
Alignment explanation
Indices: 42237080--42237132 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 14
42237070 AAGATTTGTT
*
42237080 ATTTTGGGTTTAGGG
1 ATTTAGGGTTTA-GG
*
42237095 TTTTA-GGTTTAGG
1 ATTTAGGGTTTAGG
*
42237108 ATTTAGGGTTTATG
1 ATTTAGGGTTTAGG
*
42237122 ATTTAGTGTTT
1 ATTTAGGGTTT
42237133 TATAGTTAGG
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
13 6 0.19
14 23 0.72
15 3 0.09
ACGTcount: A:0.17, C:0.00, G:0.30, T:0.53
Consensus pattern (14 bp):
ATTTAGGGTTTAGG
Found at i:42237126 original size:21 final size:21
Alignment explanation
Indices: 42237088--42237127 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
42237078 TTATTTTGGG
*
42237088 TTTAGGGTTTTAGGTTTAGGA
1 TTTAGGGTTTTAGATTTAGGA
42237109 TTTAGGG-TTTATGATTTAG
1 TTTAGGGTTTTA-GATTTAG
42237128 TGTTTTATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.20, C:0.00, G:0.30, T:0.50
Consensus pattern (21 bp):
TTTAGGGTTTTAGATTTAGGA
Found at i:42238029 original size:22 final size:22
Alignment explanation
Indices: 42237985--42238029 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
42237975 TCCCCCAATT
* **
42237985 CAAAATCCCCAAATCTATTTCC
1 CAAAATCCCCAAATCAAAATCC
42238007 CAAAATCCCCAAATCAAAATCC
1 CAAAATCCCCAAATCAAAATCC
42238029 C
1 C
42238030 TTTTATTTTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.42, C:0.38, G:0.00, T:0.20
Consensus pattern (22 bp):
CAAAATCCCCAAATCAAAATCC
Found at i:42239751 original size:22 final size:23
Alignment explanation
Indices: 42239705--42239751 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
42239695 GGAAAGATAG
* **
42239705 TTTTCTATACTTATGTAATTTCT
1 TTTTCTATACTTAGGTAATGGCT
42239728 TTTTCTATACTTAGGTAA-GGCT
1 TTTTCTATACTTAGGTAATGGCT
42239750 TT
1 TT
42239752 GATCCTCCAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 4 0.19
23 17 0.81
ACGTcount: A:0.21, C:0.13, G:0.11, T:0.55
Consensus pattern (23 bp):
TTTTCTATACTTAGGTAATGGCT
Found at i:42240390 original size:9 final size:10
Alignment explanation
Indices: 42240373--42240410 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
42240363 TTTAATATTT
42240373 AATATTTTTA
1 AATATTTTTA
42240383 AATATTTTTA
1 AATATTTTTA
* *
42240393 AA-ACTTATA
1 AATATTTTTA
42240402 AATATTTTT
1 AATATTTTT
42240411 TTATCAATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
9 7 0.30
10 16 0.70
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (10 bp):
AATATTTTTA
Found at i:42240653 original size:18 final size:18
Alignment explanation
Indices: 42240630--42240665 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
42240620 AATATTTAAA
42240630 GAATAAAAGATAACTTTG
1 GAATAAAAGATAACTTTG
42240648 GAATAAAAGATAACTTTG
1 GAATAAAAGATAACTTTG
42240666 CTATAAATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.06, G:0.17, T:0.28
Consensus pattern (18 bp):
GAATAAAAGATAACTTTG
Found at i:42240671 original size:18 final size:18
Alignment explanation
Indices: 42240631--42240672 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
42240621 ATATTTAAAG
*
42240631 AATAAAAGATAACTTTGG
1 AATAAAAGATAACTTTGC
42240649 AATAAAAGATAACTTTGC
1 AATAAAAGATAACTTTGC
*
42240667 TATAAA
1 AATAAA
42240673 TGACTTCTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.52, C:0.07, G:0.12, T:0.29
Consensus pattern (18 bp):
AATAAAAGATAACTTTGC
Found at i:42240856 original size:9 final size:9
Alignment explanation
Indices: 42240817--42240922 Score: 67
Period size: 9 Copynumber: 11.8 Consensus size: 9
42240807 CTTTGGATCT
42240817 TAACTTA-A
1 TAACTTACA
*
42240825 TAACTTATA
1 TAACTTACA
*
42240834 TATATCATATCA
1 TA-A-CTTA-CA
42240846 TAACTTACA
1 TAACTTACA
*
42240855 TAACTCACA
1 TAACTTACA
*
42240864 TTACTTACA
1 TAACTTACA
42240873 TAACTTACA
1 TAACTTACA
*
42240882 TAA--TATA
1 TAACTTACA
* *
42240889 TAA-ATATA
1 TAACTTACA
* *
42240897 TATCATATCA
1 TAACTTA-CA
42240907 TAACTTACA
1 TAACTTACA
42240916 TAACTTA
1 TAACTTA
42240923 ATTATACTTA
Statistics
Matches: 79, Mismatches: 12, Indels: 13
0.76 0.12 0.12
Matches are distributed among these distances:
7 6 0.08
8 13 0.16
9 43 0.54
10 10 0.13
11 4 0.05
12 3 0.04
ACGTcount: A:0.45, C:0.17, G:0.00, T:0.38
Consensus pattern (9 bp):
TAACTTACA
Found at i:42246364 original size:21 final size:21
Alignment explanation
Indices: 42246335--42246384 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
42246325 CTATAGCTTA
*
42246335 AAGCGGAGGCAGCAGCGAGGG
1 AAGCAGAGGCAGCAGCGAGGG
* *
42246356 AAGCAGAGGTAGCAGTGAGGG
1 AAGCAGAGGCAGCAGCGAGGG
42246377 AAGCAGAG
1 AAGCAGAG
42246385 CAGAGCAGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.34, C:0.14, G:0.48, T:0.04
Consensus pattern (21 bp):
AAGCAGAGGCAGCAGCGAGGG
Found at i:42246783 original size:43 final size:44
Alignment explanation
Indices: 42246736--42246979 Score: 182
Period size: 43 Copynumber: 5.7 Consensus size: 44
42246726 ATAAAAGCGG
* * **
42246736 CGCTAAAGGTAC-TGTTCTTTAGTGGTGTTTGTAAAAAAAACGC
1 CGCTAAAGGTACATGTTCTTTAGCGGCGTTTGTAAAAAAAGTGC
* * * *
42246779 CGCTAAAGGT-CATGCTT-TTTAGCGACATTTGTCATAAAAGTGC
1 CGCTAAAGGTACATG-TTCTTTAGCGGCGTTTGTAAAAAAAGTGC
*
42246822 CGCTAAAGG-ACATGTTCTATAGCGGCGTTTGTAAAAAAAGTGC
1 CGCTAAAGGTACATGTTCTTTAGCGGCGTTTGTAAAAAAAGTGC
* * * * * *
42246865 CGCTAAAGGT-TATGTTCTTTAGCAGCATTTATGATAAAA--GC
1 CGCTAAAGGTACATGTTCTTTAGCGGCGTTTGTAAAAAAAGTGC
* * * * ** ** *
42246906 ATGCTAAAGGT-CATGTTCTATAGTGCCAATTGTGGAAAAAGCGC
1 -CGCTAAAGGTACATGTTCTTTAGCGGCGTTTGTAAAAAAAGTGC
*
42246950 CGCTAAAGGT-CTTGTTCTTTAGCGGCGTTT
1 CGCTAAAGGTACATGTTCTTTAGCGGCGTTT
42246980 TTTCACATAA
Statistics
Matches: 156, Mismatches: 37, Indels: 16
0.75 0.18 0.08
Matches are distributed among these distances:
41 2 0.01
42 32 0.21
43 118 0.76
44 4 0.03
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.32
Consensus pattern (44 bp):
CGCTAAAGGTACATGTTCTTTAGCGGCGTTTGTAAAAAAAGTGC
Found at i:42246854 original size:86 final size:85
Alignment explanation
Indices: 42246710--42246973 Score: 277
Period size: 86 Copynumber: 3.1 Consensus size: 85
42246700 GAACGATACT
* * *
42246710 TTTAGCAGA-ATTTGTGATAAAAGCGGCGCTAAAGGTAC-TGTTCTTTAGTGGTGTTTGTAAAAA
1 TTTAGC-GACATTTGTGATAAAAG-GCCGCTAAAGG-ACATGTTCTATAGTGGCGTTTGTAAAAA
*
42246773 AAACGCCGCTAAAGGTCATGCTT-
63 AAGCGCCGCTAAAGGTCATG-TTC
* *
42246796 TTTAGCGACATTTGTCATAAAAGTGCCGCTAAAGGACATGTTCTATAGCGGCGTTTGTAAAAAAA
1 TTTAGCGACATTTGTGATAAAAG-GCCGCTAAAGGACATGTTCTATAGTGGCGTTTGTAAAAAAA
* *
42246861 GTGCCGCTAAAGGTTATGTTC
65 GCGCCGCTAAAGGTCATGTTC
* * * * ** **
42246882 TTTAGC-AGCATTTATGATAAAA-GCATGCTAAAGGTCATGTTCTATAGTGCCAATTGTGGAAAA
1 TTTAGCGA-CATTTGTGATAAAAGGC-CGCTAAAGGACATGTTCTATAGTGGCGTTTGTAAAAAA
*
42246945 AGCGCCGCTAAAGGTCTTGTTC
64 AGCGCCGCTAAAGGTCATGTTC
42246967 TTTAGCG
1 TTTAGCG
42246974 GCGTTTTTTC
Statistics
Matches: 150, Mismatches: 22, Indels: 12
0.82 0.12 0.07
Matches are distributed among these distances:
84 2 0.01
85 62 0.41
86 86 0.57
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (85 bp):
TTTAGCGACATTTGTGATAAAAGGCCGCTAAAGGACATGTTCTATAGTGGCGTTTGTAAAAAAAG
CGCCGCTAAAGGTCATGTTC
Found at i:42246956 original size:85 final size:85
Alignment explanation
Indices: 42246764--42246973 Score: 230
Period size: 85 Copynumber: 2.5 Consensus size: 85
42246754 TTAGTGGTGT
* * *
42246764 TTGTAAAAAAAACGCCGCTAAAGGTCATGCTT-TTTAGCGACATTTGTCATAAAAGTGCCGCTAA
1 TTGTAAAAAAAGCGCCGCTAAAGGTTATG-TTCTTTAGCGACATTTATCATAAAAG-GCCGCTAA
* **
42246828 AGGACATGTTCTATAGCGGCGT
64 AGGACATGTTCTATAGCGCCAA
* * *
42246850 TTGTAAAAAAAGTGCCGCTAAAGGTTATGTTCTTTAGC-AGCATTTATGATAAAA-GCATGCTAA
1 TTGTAAAAAAAGCGCCGCTAAAGGTTATGTTCTTTAGCGA-CATTTATCATAAAAGGC-CGCTAA
* *
42246913 AGGTCATGTTCTATAGTGCCAA
64 AGGACATGTTCTATAGCGCCAA
**
42246935 TTGTGGAAAAAGCGCCGCTAAAGGTCT-TGTTCTTTAGCG
1 TTGTAAAAAAAGCGCCGCTAAAGGT-TATGTTCTTTAGCG
42246974 GCGTTTTTTC
Statistics
Matches: 105, Mismatches: 14, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
84 2 0.02
85 58 0.55
86 45 0.43
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30
Consensus pattern (85 bp):
TTGTAAAAAAAGCGCCGCTAAAGGTTATGTTCTTTAGCGACATTTATCATAAAAGGCCGCTAAAG
GACATGTTCTATAGCGCCAA
Found at i:42249168 original size:8 final size:8
Alignment explanation
Indices: 42249126--42249150 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
42249116 ATATAGACTA
42249126 AATAAAAT
1 AATAAAAT
42249134 AATAAAAT
1 AATAAAAT
42249142 AATAAAAT
1 AATAAAAT
42249150 A
1 A
42249151 TCTTATTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AATAAAAT
Found at i:42249200 original size:29 final size:30
Alignment explanation
Indices: 42249130--42249201 Score: 71
Period size: 31 Copynumber: 2.4 Consensus size: 30
42249120 AGACTAAATA
*
42249130 AAATAA-TA-AAATAATAAAATATCTTATT
1 AAATAATTATAAATAATAAAATATCTAATT
*
42249158 AAA-ATATTAAATAAATAAT-AATTATCTAATT
1 AAATA-ATT--ATAAATAATAAAATATCTAATT
42249189 AAATAATTATAAA
1 AAATAATTATAAA
42249202 ATATTACCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 11
0.73 0.04 0.22
Matches are distributed among these distances:
27 1 0.03
28 4 0.11
29 6 0.17
31 17 0.47
32 8 0.22
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (30 bp):
AAATAATTATAAATAATAAAATATCTAATT
Found at i:42249429 original size:24 final size:22
Alignment explanation
Indices: 42249396--42249439 Score: 61
Period size: 24 Copynumber: 1.9 Consensus size: 22
42249386 GATCATTCCA
42249396 CCCTTAAAATATTTTCACTATTAT
1 CCCTTAAAAT-TTTTCA-TATTAT
*
42249420 CCCTTCAAATTTTTCATATT
1 CCCTTAAAATTTTTCATATT
42249440 TACACTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 4 0.21
23 6 0.32
24 9 0.47
ACGTcount: A:0.30, C:0.23, G:0.00, T:0.48
Consensus pattern (22 bp):
CCCTTAAAATTTTTCATATTAT
Found at i:42252725 original size:13 final size:12
Alignment explanation
Indices: 42252703--42252737 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
42252693 TAATACATTC
42252703 ATATTATTATAT
1 ATATTATTATAT
42252715 ATATATATTATAT
1 ATAT-TATTATAT
42252728 AGTATTATTA
1 A-TATTATTA
42252738 ATAATTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 4 0.19
13 14 0.67
14 3 0.14
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (12 bp):
ATATTATTATAT
Found at i:42252944 original size:11 final size:11
Alignment explanation
Indices: 42252928--42252953 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
42252918 TATATGTACA
42252928 TATTTATGTAG
1 TATTTATGTAG
42252939 TATTTATGTAG
1 TATTTATGTAG
42252950 TATT
1 TATT
42252954 ATTAATAGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (11 bp):
TATTTATGTAG
Found at i:42253018 original size:5 final size:6
Alignment explanation
Indices: 42252992--42253023 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
42252982 ATCATTTCTA
42252992 ATATGT ATATGT -TATGT ATATGT -TATGT ATAT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATAT
42253024 ATTTTAATAC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
5 10 0.42
6 14 0.58
ACGTcount: A:0.31, C:0.00, G:0.16, T:0.53
Consensus pattern (6 bp):
ATATGT
Found at i:42253050 original size:11 final size:11
Alignment explanation
Indices: 42252993--42253073 Score: 81
Period size: 11 Copynumber: 7.0 Consensus size: 11
42252983 TCATTTCTAA
*
42252993 TATGTATATGT
1 TATGTATATAT
*
42253004 TATGTATATGT
1 TATGTATATAT
42253015 TATGTATATAT
1 TATGTATATAT
* *
42253026 TTTAATACTATAT
1 TAT-GTA-TATAT
42253039 TATGTATATATT
1 TATGTATATA-T
*
42253051 CTATATATATAT
1 -TATGTATATAT
42253063 TATGTATATAT
1 TATGTATATAT
42253074 ATTTTTAATA
Statistics
Matches: 59, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
11 37 0.63
12 6 0.10
13 16 0.27
ACGTcount: A:0.35, C:0.02, G:0.09, T:0.54
Consensus pattern (11 bp):
TATGTATATAT
Found at i:42253061 original size:13 final size:13
Alignment explanation
Indices: 42253043--42253076 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
42253033 CTATATTATG
*
42253043 TATATATTCTATA
1 TATATATTATATA
*
42253056 TATATATTATGTA
1 TATATATTATATA
42253069 TATATATT
1 TATATATT
42253077 TTTAATATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (13 bp):
TATATATTATATA
Found at i:42253066 original size:48 final size:47
Alignment explanation
Indices: 42253008--42253220 Score: 153
Period size: 48 Copynumber: 4.6 Consensus size: 47
42252998 ATATGTTATG
* *
42253008 TATATGTTATGTATATA-TTTTAATACTATATTATGTATATATTCTATA
1 TATATATTATGTATATACTTTTAATACTATATTAT-TATATATT-TTTA
42253056 TATATATTATGTATATA-TATTT--T--TA-A-TATTAT-T-TTTTTA
1 TATATATTATGTATATACT-TTTAATACTATATTATTATATATTTTTA
* * *
42253095 TATATGTTATGTATATATTTTTAATA-TCACATTATTCATATAGTTTTTA
1 TATATATTATGTATATACTTTTAATACT-ATATTATT-ATATA-TTTTTA
* * * * *
42253144 TAT-TATCCCATGTAAATACTTTCAATACTATATTATGCATATATTTTTG
1 TATATAT--TATGTATATACTTTTAATACTATATTAT-TATATATTTTTA
* *
42253193 TCTATATTATATATATACTTTTAATACT
1 TATATATTATGTATATACTTTTAATACT
42253221 CAATACTATT
Statistics
Matches: 132, Mismatches: 16, Indels: 34
0.73 0.09 0.19
Matches are distributed among these distances:
39 22 0.17
40 3 0.02
41 2 0.02
42 4 0.03
43 4 0.03
44 2 0.02
45 6 0.05
46 2 0.02
47 2 0.02
48 36 0.27
49 19 0.14
50 29 0.22
51 1 0.01
ACGTcount: A:0.34, C:0.07, G:0.05, T:0.54
Consensus pattern (47 bp):
TATATATTATGTATATACTTTTAATACTATATTATTATATATTTTTA
Found at i:42253084 original size:24 final size:23
Alignment explanation
Indices: 42253009--42253084 Score: 89
Period size: 24 Copynumber: 3.2 Consensus size: 23
42252999 TATGTTATGT
*
42253009 ATATGTTATGTATATATTTTAATA
1 ATATATTATGTATATATTTT-ATA
* *
42253033 CTATATTATGTATATATTCTATA
1 ATATATTATGTATATATTTTATA
*
42253056 TATATATTATGTATATATATTTTTA
1 -ATATATTATGTATATAT-TTTATA
42253081 ATAT
1 ATAT
42253085 TATTTTTTTA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
23 3 0.07
24 37 0.84
25 4 0.09
ACGTcount: A:0.37, C:0.03, G:0.05, T:0.55
Consensus pattern (23 bp):
ATATATTATGTATATATTTTATA
Found at i:42253090 original size:12 final size:13
Alignment explanation
Indices: 42253055--42253121 Score: 52
Period size: 13 Copynumber: 5.3 Consensus size: 13
42253045 TATATTCTAT
*
42253055 ATATATATTATGT-
1 ATATATATT-TTTA
42253068 ATATATATTTTTA
1 ATATATATTTTTA
42253081 ATAT-TATTTTT-
1 ATATATATTTTTA
* *
42253092 TTATATA-TGTTA
1 ATATATATTTTTA
*
42253104 TGTATATATTTTTA
1 -ATATATATTTTTA
42253118 ATAT
1 ATAT
42253122 CACATTATTC
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
11 6 0.14
12 11 0.26
13 22 0.51
14 4 0.09
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.61
Consensus pattern (13 bp):
ATATATATTTTTA
Found at i:42253116 original size:24 final size:24
Alignment explanation
Indices: 42252997--42253073 Score: 95
Period size: 24 Copynumber: 3.2 Consensus size: 24
42252987 TTCTAATATG
* *
42252997 TATATGTTATGTATATGTTATGTA
1 TATATGTTATATATATATTATGTA
*
42253021 TATATTTTA-ATACTATATTATGTA
1 TATATGTTATATA-TATATTATGTA
42253045 TATAT-TCTATATATATATTATGTA
1 TATATGT-TATATATATATTATGTA
42253069 TATAT
1 TATAT
42253074 ATTTTTAATA
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
23 3 0.06
24 41 0.87
25 3 0.06
ACGTcount: A:0.35, C:0.03, G:0.08, T:0.55
Consensus pattern (24 bp):
TATATGTTATATATATATTATGTA
Found at i:42253208 original size:23 final size:23
Alignment explanation
Indices: 42253171--42253214 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
42253161 ACTTTCAATA
* *
42253171 CTATATTATGCATATATTTTTGT
1 CTATATTATACATATACTTTTGT
*
42253194 CTATATTATATATATACTTTT
1 CTATATTATACATATACTTTT
42253215 AATACTCAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.30, C:0.09, G:0.05, T:0.57
Consensus pattern (23 bp):
CTATATTATACATATACTTTTGT
Found at i:42256725 original size:22 final size:22
Alignment explanation
Indices: 42256699--42256743 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
42256689 ATTCATGACT
*
42256699 AACATTCATTCGTTATTTATTC
1 AACATTCATTCGTCATTTATTC
*
42256721 AACATTCATTTGTCATTTATTC
1 AACATTCATTCGTCATTTATTC
42256743 A
1 A
42256744 TTCATCCATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.29, C:0.18, G:0.04, T:0.49
Consensus pattern (22 bp):
AACATTCATTCGTCATTTATTC
Found at i:42264150 original size:27 final size:27
Alignment explanation
Indices: 42264112--42264166 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
42264102 GTGGAGCTTT
*
42264112 GATTCTCACTGAGATGGATGGGAAAGA
1 GATTCTCACTGAGATGGATAGGAAAGA
42264139 GATTCTCACTGAGATGGATAGGAAAGA
1 GATTCTCACTGAGATGGATAGGAAAGA
42264166 G
1 G
42264167 TTACCTAACC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.35, C:0.11, G:0.33, T:0.22
Consensus pattern (27 bp):
GATTCTCACTGAGATGGATAGGAAAGA
Found at i:42265323 original size:75 final size:75
Alignment explanation
Indices: 42265205--42266195 Score: 1540
Period size: 75 Copynumber: 12.8 Consensus size: 75
42265195 GCCTTTCAAA
42265205 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTTCAATT
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTTCAATT
42265270 TTTGTCTTTC
66 TTTGTCTTTC
*
42265280 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGT-ATTTTTAATT
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTTCAA--
*
42265344 TCTGTTTTTCAATTTAC
64 T-T-TTTGTC--TTT-C
*
42265361 GTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTTC
1 ----AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTTC
42265426 AATTTTTGTCTTTC
62 AATTTTTGTCTTTC
42265440 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTTCAATT
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTTCAATT
42265505 TTTGTCTTTC
66 TTTGTCTTTC
42265515 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTTCAATT
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTTCAATT
42265580 TTTGTCTTTC
66 TTTGTCTTTC
42265590 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTTCAATT
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTTCAATT
42265655 TTTGTCTTTC
66 TTTGTCTTTC
42265665 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTTCAATT
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTTCAATT
42265730 TTTGTCTTTC
66 TTTGTCTTTC
42265740 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTTCAATT
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTTCAATT
42265805 TTTGTCTTTC
66 TTTGTCTTTC
42265815 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTTCAATT
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTTCAATT
42265880 TTTGTCTTTC
66 TTTGTCTTTC
42265890 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTTCAATT
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTTCAATT
42265955 TTTGTCTTTC
66 TTTGTCTTTC
*
42265965 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGT-ATTTTTAATT
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTTCAA--
*
42266029 TCTGTTTTTCAATTTAC
64 T-T-TTTGTC--TTT-C
* ** *
42266046 GTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGT-ATTTTC
1 ----AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTTC
* *
42266110 AATTTCTGTTTTTC
62 AATTTTTGTCTTTC
* *
42266124 AATTTATGTTTCAAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGT
1 -----A------AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGT
42266189 -ATTTTCA
55 AATTTTCA
42266196 GTTTCTATTT
Statistics
Matches: 865, Mismatches: 21, Indels: 50
0.92 0.02 0.05
Matches are distributed among these distances:
74 14 0.02
75 632 0.73
76 2 0.00
77 2 0.00
78 11 0.01
79 7 0.01
80 9 0.01
81 5 0.01
82 6 0.01
83 2 0.00
84 1 0.00
85 167 0.19
86 7 0.01
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (75 bp):
AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTTCAATT
TTTGTCTTTC
Found at i:42266124 original size:14 final size:14
Alignment explanation
Indices: 42266105--42266134 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
42266095 CGTTGAGGTA
*
42266105 TTTTCAATTTCTGT
1 TTTTCAATTTATGT
42266119 TTTTCAATTTATGT
1 TTTTCAATTTATGT
42266133 TT
1 TT
42266135 CAAAAATCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.17, C:0.10, G:0.07, T:0.67
Consensus pattern (14 bp):
TTTTCAATTTATGT
Found at i:42266163 original size:170 final size:174
Alignment explanation
Indices: 42265946--42266262 Score: 457
Period size: 170 Copynumber: 1.8 Consensus size: 174
42265936 GCTGAGGTAA
* *
42265946 TTTTCAATTTTTGTCTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACAC
1 TTTTCAATTTATG-CTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACAC
* * *
42266011 GCTGAGGTATTTTTAATTTCTGTTTTTCAATTTAC-G-TT-TCAAAAATCA-ACTCATATTGCGA
65 GCTGAGGTATTTTCAATTTCTATTTTTCAAATT-CTGTTTATCAAAAATCAGA-TCATATTGCGA
*
42266072 GAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCTGT
128 GAGGTGAGTGGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCTGT
*
42266119 TTTTCAATTTATG-TTTC-AAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCAGGACACG
1 TTTTCAATTTATGCTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACG
* * *
42266182 CTGAGGTATTTTCAGTTTCTATTTTTCAAATTCTGTTTTTATCAAAAGTCAGATCATATTGTGAG
66 CTGAGGTATTTTCAATTTCTATTTTTCAAATTCTG--TTTATCAAAAATCAGATCATATTGCGAG
42266247 AGGTGAGTGGAGCCTC
129 AGGTGAGTGGAGCCTC
42266263 GGGTCACATG
Statistics
Matches: 128, Mismatches: 10, Indels: 11
0.86 0.07 0.07
Matches are distributed among these distances:
169 1 0.01
170 73 0.57
171 4 0.03
173 14 0.11
174 35 0.27
175 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.20, T:0.38
Consensus pattern (174 bp):
TTTTCAATTTATGCTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACG
CTGAGGTATTTTCAATTTCTATTTTTCAAATTCTGTTTATCAAAAATCAGATCATATTGCGAGAG
GTGAGTGGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCTGT
Found at i:42266429 original size:21 final size:21
Alignment explanation
Indices: 42266383--42266431 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
42266373 AGCAGAGCCC
**
42266383 TAAAGTTACAGTGGAGCTGAT
1 TAAAGTTACAGTGGAGCACAT
*
42266404 CAAAGTTACAGTGGAGCACAT
1 TAAAGTTACAGTGGAGCACAT
42266425 TAAAGTT
1 TAAAGTT
42266432 GCAGATTTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.37, C:0.12, G:0.24, T:0.27
Consensus pattern (21 bp):
TAAAGTTACAGTGGAGCACAT
Found at i:42271819 original size:30 final size:30
Alignment explanation
Indices: 42271785--42271846 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
42271775 CTTAACAAGT
42271785 AAATGACTCTAAAATAATAACAAAATTAAC
1 AAATGACTCTAAAATAATAACAAAATTAAC
* *
42271815 AAATGTCTTTAAAATAATAACAAAATTAAC
1 AAATGACTCTAAAATAATAACAAAATTAAC
42271845 AA
1 AA
42271847 TAAAATAAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.60, C:0.11, G:0.03, T:0.26
Consensus pattern (30 bp):
AAATGACTCTAAAATAATAACAAAATTAAC
Found at i:42272505 original size:48 final size:47
Alignment explanation
Indices: 42272420--42272511 Score: 107
Period size: 48 Copynumber: 1.9 Consensus size: 47
42272410 ATTTTTATTA
* *
42272420 TATTTAAAAATTATAAATTTAATTTAATAAATATTATTAATATATAT
1 TATTTAAAAATTATAAATTTAACTTAAAAAATATTATTAATATATAT
* *
42272467 TATTTAAAAAATTAT-ATTTTAAACTTAAAACAAT-TTATTATTATA
1 TATTT-AAAAATTATAAATTT-AACTTAAAA-AATATTATTAATATA
42272512 ACATTAGAGG
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
47 9 0.24
48 26 0.68
49 3 0.08
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (47 bp):
TATTTAAAAATTATAAATTTAACTTAAAAAATATTATTAATATATAT
Found at i:42274702 original size:20 final size:20
Alignment explanation
Indices: 42274674--42274714 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
42274664 TATTATTATA
42274674 TTTTTTTTGT-ATCAATAAT
1 TTTTTTTTGTAATCAATAAT
*
42274693 TTTTTATTTGTAATTAATAAT
1 TTTTT-TTTGTAATCAATAAT
42274714 T
1 T
42274715 ATAAGAAGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 5 0.26
20 5 0.26
21 9 0.47
ACGTcount: A:0.29, C:0.02, G:0.05, T:0.63
Consensus pattern (20 bp):
TTTTTTTTGTAATCAATAAT
Found at i:42275300 original size:29 final size:29
Alignment explanation
Indices: 42275262--42275322 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
42275252 TTAATTTAAT
*
42275262 AAATAATAAAATTGT-ACTTTAATCTTTTA
1 AAATAATAAAATTGTGA-TCTAATCTTTTA
*
42275291 AAATAATAAAATTTTGATCTAATCTTTTA
1 AAATAATAAAATTGTGATCTAATCTTTTA
42275320 AAA
1 AAA
42275323 ATTATAAAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 28 0.97
30 1 0.03
ACGTcount: A:0.48, C:0.07, G:0.03, T:0.43
Consensus pattern (29 bp):
AAATAATAAAATTGTGATCTAATCTTTTA
Found at i:42275409 original size:5 final size:5
Alignment explanation
Indices: 42275399--42275428 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
42275389 AATTCTACCT
*
42275399 TCACC TCACC TTACC TCACC TCACC TCACC
1 TCACC TCACC TCACC TCACC TCACC TCACC
42275429 AAATTTAACA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.20, C:0.57, G:0.00, T:0.23
Consensus pattern (5 bp):
TCACC
Found at i:42275416 original size:10 final size:10
Alignment explanation
Indices: 42275395--42275428 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
42275385 ACTTAATTCT
42275395 ACCTTCACCTC
1 ACCTT-ACCTC
42275406 ACCTTACCTC
1 ACCTTACCTC
*
42275416 ACCTCACCTC
1 ACCTTACCTC
42275426 ACC
1 ACC
42275429 AAATTTAACA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 17 0.77
11 5 0.23
ACGTcount: A:0.21, C:0.56, G:0.00, T:0.24
Consensus pattern (10 bp):
ACCTTACCTC
Found at i:42275419 original size:15 final size:16
Alignment explanation
Indices: 42275394--42275424 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
42275384 CACTTAATTC
42275394 TACCTTCACCTCACCT
1 TACCTTCACCTCACCT
42275410 TACC-TCACCTCACCT
1 TACCTTCACCTCACCT
42275425 CACCAAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.19, C:0.52, G:0.00, T:0.29
Consensus pattern (16 bp):
TACCTTCACCTCACCT
Found at i:42289851 original size:22 final size:21
Alignment explanation
Indices: 42289807--42289848 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
42289797 TTTAATCAAC
*
42289807 ACAAAAAGTATCGATACTTTT
1 ACAAAAAGTACCGATACTTTT
42289828 ACAAAAAGTACCGATACTTTT
1 ACAAAAAGTACCGATACTTTT
42289849 TACCAGGTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.43, C:0.17, G:0.10, T:0.31
Consensus pattern (21 bp):
ACAAAAAGTACCGATACTTTT
Found at i:42291647 original size:25 final size:25
Alignment explanation
Indices: 42291619--42291727 Score: 87
Period size: 25 Copynumber: 4.4 Consensus size: 25
42291609 CATGTAAACA
*
42291619 GGAAGCTCTTTCGAGCCATATAACG
1 GGAAGCTCATTCGAGCCATATAACG
* * *
42291644 GGAAACTCATGT-GAGCTATATAACA
1 GGAAGCTCAT-TCGAGCCATATAACG
* * ** *
42291669 GGAGGCTCAATCGAGCTGTATATCG
1 GGAAGCTCATTCGAGCCATATAACG
* *
42291694 AGAAGCTCATGCGAGCCATA-AATCG
1 GGAAGCTCATTCGAGCCATATAA-CG
42291719 GGAAGCTCA
1 GGAAGCTCA
42291728 AGAGAGCCAT
Statistics
Matches: 63, Mismatches: 18, Indels: 6
0.72 0.21 0.07
Matches are distributed among these distances:
24 2 0.03
25 60 0.95
26 1 0.02
ACGTcount: A:0.32, C:0.21, G:0.26, T:0.21
Consensus pattern (25 bp):
GGAAGCTCATTCGAGCCATATAACG
Found at i:42291757 original size:25 final size:25
Alignment explanation
Indices: 42291690--42291761 Score: 90
Period size: 25 Copynumber: 2.9 Consensus size: 25
42291680 CGAGCTGTAT
*
42291690 ATCGAGAAGCTCATGCGAGCCATAA
1 ATCGAGAAGCTCATGAGAGCCATAA
* * *
42291715 ATCGGGAAGCTCAAGAGAGCCATTA
1 ATCGAGAAGCTCATGAGAGCCATAA
**
42291740 ATCGAGAAGCTTGTGAGAGCCA
1 ATCGAGAAGCTCATGAGAGCCA
42291762 AATATCGGGA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.35, C:0.21, G:0.28, T:0.17
Consensus pattern (25 bp):
ATCGAGAAGCTCATGAGAGCCATAA
Found at i:42291768 original size:25 final size:25
Alignment explanation
Indices: 42291688--42291768 Score: 76
Period size: 25 Copynumber: 3.2 Consensus size: 25
42291678 ATCGAGCTGT
*
42291688 ATATCGAGAAGCTCATGCGAGCCATA
1 ATATCGAGAAGCTCATGAGAGCCA-A
* *
42291714 A-ATCGGGAAGCTCAAGAGAGCC-A
1 ATATCGAGAAGCTCATGAGAGCCAA
* **
42291737 TTAATCGAGAAGCTTGTGAGAGCCAA
1 AT-ATCGAGAAGCTCATGAGAGCCAA
42291763 ATATCG
1 ATATCG
42291769 GGATACTTAT
Statistics
Matches: 43, Mismatches: 9, Indels: 7
0.73 0.15 0.12
Matches are distributed among these distances:
23 1 0.02
25 39 0.91
26 3 0.07
ACGTcount: A:0.36, C:0.20, G:0.26, T:0.19
Consensus pattern (25 bp):
ATATCGAGAAGCTCATGAGAGCCAA
Found at i:42291975 original size:21 final size:21
Alignment explanation
Indices: 42291946--42291993 Score: 87
Period size: 21 Copynumber: 2.2 Consensus size: 21
42291936 CACACACAAC
42291946 AATATTCAATTCAAATCATACA
1 AATA-TCAATTCAAATCATACA
42291968 AATATCAATTCAAATCATACA
1 AATATCAATTCAAATCATACA
42291989 AATAT
1 AATAT
42291994 AGAATTTAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 22 0.85
22 4 0.15
ACGTcount: A:0.52, C:0.17, G:0.00, T:0.31
Consensus pattern (21 bp):
AATATCAATTCAAATCATACA
Found at i:42295017 original size:10 final size:10
Alignment explanation
Indices: 42295002--42295181 Score: 85
Period size: 9 Copynumber: 18.6 Consensus size: 10
42294992 AGTTGTAAAT
42295002 AAATTATTAA
1 AAATTATTAA
42295012 AAATTA-TAA
1 AAATTATTAA
*
42295021 AAAATATTTAA
1 AAATTA-TTAA
42295032 AAATTA-TAA
1 AAATTATTAA
42295041 AAATTA-TAA
1 AAATTATTAA
* *
42295050 AAAGTATT-T
1 AAATTATTAA
*
42295059 AAATTATAAA
1 AAATTATTAA
*
42295069 AAAATATTTAA
1 AAATTA-TTAA
*
42295080 AAATT-GTAA
1 AAATTATTAA
*
42295089 ATGATTATTAA
1 A-AATTATTAA
* *
42295100 ATATTGTTAA
1 AAATTATTAA
42295110 AATATT-TT-A
1 AA-ATTATTAA
* *
42295119 AAATTGTAAA
1 AAATTATTAA
*
42295129 AAAATA-TAA
1 AAATTATTAA
*
42295138 AAA-TAATAA
1 AAATTATTAA
42295147 AATATTATT--
1 AA-ATTATTAA
* *
42295156 TAATTTTTAA
1 AAATTATTAA
*
42295166 AAAATATTAA
1 AAATTATTAA
*
42295176 TAATTA
1 AAATTA
42295182 ACAAATCAAA
Statistics
Matches: 127, Mismatches: 28, Indels: 30
0.69 0.15 0.16
Matches are distributed among these distances:
8 10 0.08
9 50 0.39
10 42 0.33
11 25 0.20
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (10 bp):
AAATTATTAA
Found at i:42295031 original size:20 final size:20
Alignment explanation
Indices: 42295002--42295158 Score: 76
Period size: 19 Copynumber: 8.0 Consensus size: 20
42294992 AGTTGTAAAT
* *
42295002 AAATTATTAAAAAT-TATAA
1 AAATTATAAAAAATATTTAA
* * *
42295021 AAAATATTTAAAAAT-TATAA
1 AAATTA-TAAAAAATATTTAA
*
42295041 AAATTATAAAAAGTATTT--
1 AAATTATAAAAAATATTTAA
42295059 AAATTATAAAAAAATATTTAA
1 AAATTAT-AAAAAATATTTAA
* **
42295080 AAATTGTAAATGAT-TATTAA
1 AAATTATAAAAAATAT-TTAA
* * * *
42295100 ATATTGT-TAAAATATTTTA
1 AAATTATAAAAAATATTTAA
* *
42295119 AAATTGTAAAAAA-ATATAA
1 AAATTATAAAAAATATTTAA
* *
42295138 AAATAATAAAATATTATTTAA
1 AAATTATAAAA-AATATTTAA
42295159 TTTTTAAAAA
Statistics
Matches: 106, Mismatches: 22, Indels: 18
0.73 0.15 0.12
Matches are distributed among these distances:
18 7 0.07
19 47 0.44
20 41 0.39
21 11 0.10
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (20 bp):
AAATTATAAAAAATATTTAA
Found at i:42295073 original size:29 final size:27
Alignment explanation
Indices: 42295001--42295070 Score: 104
Period size: 29 Copynumber: 2.5 Consensus size: 27
42294991 AAGTTGTAAA
42295001 TAAATTATTAAAAATTATAAAAAATATT
1 TAAATTA-TAAAAATTATAAAAAATATT
*
42295029 TAAAAATTATAAAAATTATAAAAAGTATT
1 T--AAATTATAAAAATTATAAAAAATATT
42295058 TAAATTATAAAAA
1 TAAATTATAAAAA
42295071 AATATTTAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
27 12 0.31
28 1 0.03
29 20 0.51
30 6 0.15
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (27 bp):
TAAATTATAAAAATTATAAAAAATATT
Found at i:42295423 original size:10 final size:10
Alignment explanation
Indices: 42295408--42295513 Score: 63
Period size: 10 Copynumber: 10.4 Consensus size: 10
42295398 GTTCATAGTT
42295408 TTTTTTATAA
1 TTTTTTATAA
*
42295418 TTTTTTACAA
1 TTTTTTATAA
*
42295428 TTATTTAATAA
1 TT-TTTTATAA
* *
42295439 TTTTTCAAAA
1 TTTTTTATAA
42295449 TTTTTTGAT--
1 TTTTTT-ATAA
*
42295458 TTTTTTACAA
1 TTTTTTATAA
* *
42295468 ATTTTAATTAA
1 TTTTTTA-TAA
*
42295479 TGTTTTATAA
1 TTTTTTATAA
*
42295489 TTTTTAATAA
1 TTTTTTATAA
* *
42295499 CTTTGTTACAA
1 -TTTTTTATAA
42295510 TTTT
1 TTTT
42295514 AAAATATTTT
Statistics
Matches: 70, Mismatches: 20, Indels: 12
0.69 0.20 0.12
Matches are distributed among these distances:
8 1 0.01
9 6 0.09
10 41 0.59
11 22 0.31
ACGTcount: A:0.32, C:0.05, G:0.03, T:0.60
Consensus pattern (10 bp):
TTTTTTATAA
Found at i:42295438 original size:21 final size:20
Alignment explanation
Indices: 42295408--42295536 Score: 95
Period size: 21 Copynumber: 6.3 Consensus size: 20
42295398 GTTCATAGTT
*
42295408 TTTTTTATAATTTTTTACAA
1 TTTTTAATAATTTTTTACAA
* *
42295428 TTATTTAATAATTTTTCAAAA
1 TT-TTTAATAATTTTTTACAA
*
42295449 TTTTT--TGATTTTTTTACAA
1 TTTTTAAT-AATTTTTTACAA
* * *
42295468 ATTTTAATTAATGTTTTATAA
1 TTTTTAA-TAATTTTTTACAA
*
42295489 TTTTTAATAACTTTGTTACAA
1 TTTTTAATAA-TTTTTTACAA
42295510 -TTTTAA-AATATTTTTAACAA
1 TTTTTAATAAT-TTTTT-ACAA
42295530 TATTTTA
1 T-TTTTA
42295537 TTTTTAAAAA
Statistics
Matches: 84, Mismatches: 15, Indels: 18
0.72 0.13 0.15
Matches are distributed among these distances:
18 2 0.02
19 19 0.23
20 18 0.21
21 39 0.46
22 6 0.07
ACGTcount: A:0.35, C:0.05, G:0.02, T:0.58
Consensus pattern (20 bp):
TTTTTAATAATTTTTTACAA
Found at i:42295464 original size:40 final size:40
Alignment explanation
Indices: 42295418--42295493 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 40
42295408 TTTTTTATAA
*
42295418 TTTTTTACAATTATTTAA-TAAT-TTTTCAAAATTTTTTGAT
1 TTTTTTACAAAT-TTTAATTAATGTTTT-AAAATTTTTTGAT
*
42295458 TTTTTTACAAATTTTAATTAATGTTTTATAATTTTT
1 TTTTTTACAAATTTTAATTAATGTTTTAAAATTTTT
42295494 AATAACTTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
39 5 0.16
40 23 0.72
41 4 0.12
ACGTcount: A:0.32, C:0.04, G:0.03, T:0.62
Consensus pattern (40 bp):
TTTTTTACAAATTTTAATTAATGTTTTAAAATTTTTTGAT
Found at i:42295551 original size:15 final size:17
Alignment explanation
Indices: 42295518--42295551 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
42295508 AATTTTAAAA
42295518 TATTTTTAACAATATTT
1 TATTTTTAACAATATTT
42295535 TATTTTTAA-AA-ATTT
1 TATTTTTAACAATATTT
42295550 TA
1 TA
42295552 AAATTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
16 2 0.12
17 9 0.53
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (17 bp):
TATTTTTAACAATATTT
Found at i:42297421 original size:21 final size:21
Alignment explanation
Indices: 42297397--42297437 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
42297387 TGGGTGAATT
*
42297397 AGCTCTTACTAGCTTCTGTTA
1 AGCTCTTACAAGCTTCTGTTA
*
42297418 AGCTTTTACAAGCTTCTGTT
1 AGCTCTTACAAGCTTCTGTT
42297438 TAGATTTTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.22, G:0.15, T:0.44
Consensus pattern (21 bp):
AGCTCTTACAAGCTTCTGTTA
Found at i:42297445 original size:21 final size:21
Alignment explanation
Indices: 42297402--42297458 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
42297392 GAATTAGCTC
* *
42297402 TTACTAGCTTCTGTTAAGCTT
1 TTACAAGCTTCTGTTAAGATT
*
42297423 TTACAAGCTTCTGTTTAGATT
1 TTACAAGCTTCTGTTAAGATT
*
42297444 TT--GAGCTTCTGTTAA
1 TTACAAGCTTCTGTTAA
42297459 CTTATTCGGG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
19 11 0.35
21 20 0.65
ACGTcount: A:0.21, C:0.16, G:0.16, T:0.47
Consensus pattern (21 bp):
TTACAAGCTTCTGTTAAGATT
Found at i:42299061 original size:23 final size:25
Alignment explanation
Indices: 42299035--42299081 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
42299025 TATCATTCAT
*
42299035 TTCATTATAT-CA-ATATTTTATGC
1 TTCATCATATCCATATATTTTATGC
*
42299058 TTCATCATTTCCATATATTTTATG
1 TTCATCATATCCATATATTTTATG
42299082 TATATTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 8 0.40
24 2 0.10
25 10 0.50
ACGTcount: A:0.28, C:0.15, G:0.04, T:0.53
Consensus pattern (25 bp):
TTCATCATATCCATATATTTTATGC
Found at i:42299510 original size:46 final size:46
Alignment explanation
Indices: 42299352--42299607 Score: 305
Period size: 46 Copynumber: 5.7 Consensus size: 46
42299342 TGCCATAATG
* * * * * *
42299352 TCTTTCAACTATGGTTTTACTCATTTTC-TGTCATGTTGTCATGGTA
1 TCTTTCAACCATGGTCTTACACA-TTTCATATCAGGTTGCCATGGTA
** * * *
42299398 TCTTTCAACCATGGTCTTATTCTTTTCATGTCACGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTA
*
42299444 TCTTTCAACCATGGTCTTACACATCTCATATCAGGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTA
* *
42299490 TCTTTCAACCATAGTCTT--ACA---C--A-CAGGTTGCCATGATA
1 TCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTA
*
42299528 TCTTTCAACCATGGTCTTACACATTTCATATTAGGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTA
42299574 TCTTTCAACCATGGTCTTACACATTTCATATCAG
1 TCTTTCAACCATGGTCTTACACATTTCATATCAG
42299608 AGAGCACACT
Statistics
Matches: 183, Mismatches: 18, Indels: 18
0.84 0.08 0.08
Matches are distributed among these distances:
38 31 0.17
39 1 0.01
40 3 0.02
41 1 0.01
43 1 0.01
44 3 0.02
45 5 0.03
46 138 0.75
ACGTcount: A:0.23, C:0.23, G:0.14, T:0.40
Consensus pattern (46 bp):
TCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTA
Found at i:42299530 original size:38 final size:39
Alignment explanation
Indices: 42299473--42299597 Score: 162
Period size: 38 Copynumber: 3.1 Consensus size: 39
42299463 CACATCTCAT
*
42299473 ATCAGGTTGCCATGGTATCTTTCAACCATAGTCTTACAC
1 ATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
*
42299512 A-CAGGTTGCCATGATATCTTTCAACCATGGTCTTACAC
1 ATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
42299550 ATTTCATATTAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
1 A--TC-----AGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
42299596 AT
1 AT
42299598 TTCATATCAG
Statistics
Matches: 75, Mismatches: 3, Indels: 11
0.84 0.03 0.12
Matches are distributed among these distances:
38 36 0.48
39 1 0.01
41 1 0.01
44 1 0.01
46 36 0.48
ACGTcount: A:0.26, C:0.24, G:0.15, T:0.35
Consensus pattern (39 bp):
ATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
Found at i:42299573 original size:84 final size:84
Alignment explanation
Indices: 42299432--42299596 Score: 294
Period size: 84 Copynumber: 2.0 Consensus size: 84
42299422 TTCATGTCAC
*
42299432 GTTGCCATGGTATCTTTCAACCATGGTCTTACACATCTCATATCAGGTTGCCATGGTATCTTTCA
1 GTTGCCATGATATCTTTCAACCATGGTCTTACACATCTCATATCAGGTTGCCATGGTATCTTTCA
42299497 ACCATAGTCTTACACACAG
66 ACCATAGTCTTACACACAG
* *
42299516 GTTGCCATGATATCTTTCAACCATGGTCTTACACATTTCATATTAGGTTGCCATGGTATCTTTCA
1 GTTGCCATGATATCTTTCAACCATGGTCTTACACATCTCATATCAGGTTGCCATGGTATCTTTCA
*
42299581 ACCATGGTCTTACACA
66 ACCATAGTCTTACACA
42299597 TTTCATATCA
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
84 77 1.00
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.35
Consensus pattern (84 bp):
GTTGCCATGATATCTTTCAACCATGGTCTTACACATCTCATATCAGGTTGCCATGGTATCTTTCA
ACCATAGTCTTACACACAG
Found at i:42303866 original size:49 final size:47
Alignment explanation
Indices: 42303752--42303887 Score: 173
Period size: 49 Copynumber: 2.8 Consensus size: 47
42303742 CCTGGGATAA
*
42303752 AATGTCGATGCCATGTCCCAGACATGGTCTTACACTGGCTAGCACATT
1 AATGTCGATGCCATGTCCCAGACA-GGTCTTACACTGGCTAGCACATC
* * * * **
42303800 AAAGTCGATGCCGTGTCCCAGACAGGTCATACATTGGCTCTCATCTATC
1 AATGTCGATGCCATGTCCCAGACAGGTCTTACACTGGCTAGCA-C-ATC
*
42303849 AGTGTCGATGCCATGTCCCAGACAGGTCTTACACTGGCT
1 AATGTCGATGCCATGTCCCAGACAGGTCTTACACTGGCT
42303888 TGTATATCTT
Statistics
Matches: 74, Mismatches: 12, Indels: 3
0.83 0.13 0.03
Matches are distributed among these distances:
47 15 0.20
48 23 0.31
49 36 0.49
ACGTcount: A:0.24, C:0.28, G:0.22, T:0.26
Consensus pattern (47 bp):
AATGTCGATGCCATGTCCCAGACAGGTCTTACACTGGCTAGCACATC
Found at i:42303907 original size:49 final size:49
Alignment explanation
Indices: 42303755--42303931 Score: 166
Period size: 48 Copynumber: 3.7 Consensus size: 49
42303745 GGGATAAAAT
* * *
42303755 GTCGATGCCATGTCCCAGACATGGTCTTACACTGGCTAGCACA--TTAAA
1 GTCGATGCCATGTCCCAGACA-GGTCTTACACTGGCTTGTACATCTTAAG
* * * * *
42303803 GTCGATGCCGTGTCCCAGACAGGTCATACATTGGC-TCT-CATCTATCAG
1 GTCGATGCCATGTCCCAGACAGGTCTTACACTGGCTTGTACATCT-TAAG
* *
42303851 TGTCGATGCCATGTCCCAGACAGGTCTTACACTGGCTTGTATATCTTGAG
1 -GTCGATGCCATGTCCCAGACAGGTCTTACACTGGCTTGTACATCTTAAG
* * * *
42303901 GCCGATG-TATGTCCCAGACATGTCTTGCACT
1 GTCGATGCCATGTCCCAGACAGGTCTTACACT
42303932 AGCTCACATG
Statistics
Matches: 105, Mismatches: 18, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
45 2 0.02
47 13 0.12
48 43 0.41
49 38 0.36
50 5 0.05
51 4 0.04
ACGTcount: A:0.22, C:0.27, G:0.23, T:0.28
Consensus pattern (49 bp):
GTCGATGCCATGTCCCAGACAGGTCTTACACTGGCTTGTACATCTTAAG
Found at i:42308176 original size:22 final size:22
Alignment explanation
Indices: 42308151--42308194 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
42308141 CCCGAAGAAC
42308151 ATCCCCGCTTTCACACTTCAAT
1 ATCCCCGCTTTCACACTTCAAT
42308173 ATCCCCGCTTTCACACTTCAAT
1 ATCCCCGCTTTCACACTTCAAT
42308195 TTAATAAGTT
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:0.23, C:0.41, G:0.05, T:0.32
Consensus pattern (22 bp):
ATCCCCGCTTTCACACTTCAAT
Found at i:42310403 original size:28 final size:28
Alignment explanation
Indices: 42310371--42310488 Score: 191
Period size: 28 Copynumber: 4.2 Consensus size: 28
42310361 GTCCATGGCT
*
42310371 CGTGTCCCTCACACGGCTATGACACGCC
1 CGTGTCCCTCACACGGCCATGACACGCC
42310399 CGTGTCCCTCACACGGCCATGACACGCC
1 CGTGTCCCTCACACGGCCATGACACGCC
*
42310427 CGTGTCTCTCACACGGCCATGACACGCC
1 CGTGTCCCTCACACGGCCATGACACGCC
* * *
42310455 CGTGTTCCTCACACGGCCATGAAACACC
1 CGTGTCCCTCACACGGCCATGACACGCC
42310483 CGTGTC
1 CGTGTC
42310489 ATATCCCATG
Statistics
Matches: 83, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 83 1.00
ACGTcount: A:0.19, C:0.42, G:0.21, T:0.18
Consensus pattern (28 bp):
CGTGTCCCTCACACGGCCATGACACGCC
Found at i:42311606 original size:49 final size:48
Alignment explanation
Indices: 42311545--42311762 Score: 200
Period size: 49 Copynumber: 4.6 Consensus size: 48
42311535 ACATTAAAGT
*
42311545 CGATGCCGTGTCCCAGACAGGTCTTACACTGACTTTCATATATCGAGGC
1 CGATGCCATGTCCCAGACAGGTCTTACACTGACTTTCATATATC-AGGC
* * * *
42311594 CGATGCCATGTCCCAGACAGGTCTTAAACTGGCTCTCA-ACTATCAGTGT
1 CGATGCCATGTCCCAGACAGGTCTTACACTGACTTTCATA-TATCAG-GC
* * * *
42311643 CGATGCCATGTCCCAGACAGGTCTTACATTGAC--ACACA-A-CAAGC
1 CGATGCCATGTCCCAGACAGGTCTTACACTGACTTTCATATATCAGGC
* * * *
42311687 TGATGCCATGTCCCATACAGGTCTTACACT-AGCTTGT-ATATCTTGAGGC
1 CGATGCCATGTCCCAGACAGGTCTTACACTGA-CTT-TCATAT-ATCAGGC
*
42311736 CGATG-CATGTCCCAGACATGTCTTACA
1 CGATGCCATGTCCCAGACAGGTCTTACA
42311763 TGGGCTCTTG
Statistics
Matches: 137, Mismatches: 22, Indels: 21
0.76 0.12 0.12
Matches are distributed among these distances:
43 1 0.01
44 29 0.21
45 2 0.01
46 3 0.02
47 2 0.01
48 24 0.18
49 76 0.55
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.26
Consensus pattern (48 bp):
CGATGCCATGTCCCAGACAGGTCTTACACTGACTTTCATATATCAGGC
Found at i:42314718 original size:25 final size:25
Alignment explanation
Indices: 42314690--42314749 Score: 102
Period size: 25 Copynumber: 2.4 Consensus size: 25
42314680 TTCCCTGCTG
42314690 ATTTGATGTTGTTACCCTTTCTAGA
1 ATTTGATGTTGTTACCCTTTCTAGA
* *
42314715 ATTTGATGTTGTTACCCTTTTTGGA
1 ATTTGATGTTGTTACCCTTTCTAGA
42314740 ATTTGATGTT
1 ATTTGATGTT
42314750 ATACTGAGTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.18, C:0.12, G:0.18, T:0.52
Consensus pattern (25 bp):
ATTTGATGTTGTTACCCTTTCTAGA
Found at i:42317012 original size:19 final size:19
Alignment explanation
Indices: 42316988--42317068 Score: 92
Period size: 19 Copynumber: 4.3 Consensus size: 19
42316978 AAAAGCAATG
42316988 TGTTATACGGATGAATTAC
1 TGTTATACGGATGAATTAC
* * *
42317007 TGTTATATGGATGAAGTGC
1 TGTTATACGGATGAATTAC
*
42317026 TGTTTATACGGATGAGTTAC
1 TG-TTATACGGATGAATTAC
* *
42317046 TATTAT-CGAATGAATTAC
1 TGTTATACGGATGAATTAC
42317064 TGTTA
1 TGTTA
42317069 ATATGATTGA
Statistics
Matches: 50, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
18 14 0.28
19 22 0.44
20 14 0.28
ACGTcount: A:0.30, C:0.09, G:0.22, T:0.40
Consensus pattern (19 bp):
TGTTATACGGATGAATTAC
Found at i:42323495 original size:24 final size:22
Alignment explanation
Indices: 42323458--42323524 Score: 80
Period size: 24 Copynumber: 2.9 Consensus size: 22
42323448 TACTGGTATA
*
42323458 TCAGCTCGTAAGAGCTTACTGCTC
1 TCAGCTCAT-AGAGCTTACTG-TC
*
42323482 TCAGCTCATCAGAGCTTACTGTT
1 TCAGCTCAT-AGAGCTTACTGTC
42323505 TCAGCTCAATAGAGCTTACT
1 TCAGCTC-ATAGAGCTTACT
42323525 ATCCATCAGC
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
23 18 0.46
24 21 0.54
ACGTcount: A:0.24, C:0.27, G:0.18, T:0.31
Consensus pattern (22 bp):
TCAGCTCATAGAGCTTACTGTC
Found at i:42323634 original size:19 final size:19
Alignment explanation
Indices: 42323610--42323648 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
42323600 TTAAACTATG
*
42323610 TGTTATACGGATGAATTAC
1 TGTTATACGGATGAAGTAC
*
42323629 TGTTATATGGATGAAGTAC
1 TGTTATACGGATGAAGTAC
42323648 T
1 T
42323649 ATGTGACAGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.31, C:0.08, G:0.23, T:0.38
Consensus pattern (19 bp):
TGTTATACGGATGAAGTAC
Found at i:42327009 original size:49 final size:47
Alignment explanation
Indices: 42326807--42327070 Score: 397
Period size: 47 Copynumber: 5.6 Consensus size: 47
42326797 CCCTTCGGGA
* * * *
42326807 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* * * *
42326854 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCA--AGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
42326899 CTTATCACATATATACACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATAT--ACACTTTCACATTCATCACATTGGCCATTCGGC
*
42326948 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
42326995 CTTATCACATATATACACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATAT--ACACTTTCACATTCATCACATTGGCCATTCGGC
42327044 CTTATCACATATATACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
42327071 TATTCAAATA
Statistics
Matches: 198, Mismatches: 13, Indels: 12
0.89 0.06 0.05
Matches are distributed among these distances:
45 15 0.08
47 120 0.61
49 63 0.32
ACGTcount: A:0.28, C:0.31, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
Found at i:42327026 original size:96 final size:94
Alignment explanation
Indices: 42326807--42327070 Score: 433
Period size: 96 Copynumber: 2.8 Consensus size: 94
42326797 CCCTTCGGGA
* * * * * *
42326807 CTTATCACAT-T-TATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATAC
1 CTTATCACATATATACACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
42326870 ACTTTCACATTCATCACATCGGCCAAGGC
66 ACTTTCACATTCATCACATCGGCCAAGGC
42326899 CTTATCACATATATACACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
1 CTTATCACATATATACACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
*
42326964 ACTTTCACATTCATCACATTGGCCATTAGGC
66 ACTTTCACATTCATCACATCGGCCA--AGGC
42326995 CTTATCACATATATACACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
1 CTTATCACATATATACACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
42327060 ACTTTCACATT
66 ACTTTCACATT
42327071 TATTCAAATA
Statistics
Matches: 161, Mismatches: 7, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
92 10 0.06
93 1 0.01
94 70 0.43
96 80 0.50
ACGTcount: A:0.28, C:0.31, G:0.08, T:0.33
Consensus pattern (94 bp):
CTTATCACATATATACACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
ACTTTCACATTCATCACATCGGCCAAGGC
Found at i:42329880 original size:38 final size:38
Alignment explanation
Indices: 42329836--42329935 Score: 141
Period size: 38 Copynumber: 2.6 Consensus size: 38
42329826 TTAAAGACAT
* *
42329836 GCAGGCTATATGCTGGAATTATATCCGGGTTAAATCCC
1 GCAGGCTATGTGCTGGTATTATATCCGGGTTAAATCCC
*
42329874 GCAGGCT-TCGTGCTGGTATTATATCCGGGTTAAATCCT
1 GCAGGCTAT-GTGCTGGTATTATATCCGGGTTAAATCCC
42329912 GCAGGCCTA-GTGCTGGTATTATAT
1 GCAGG-CTATGTGCTGGTATTATAT
42329936 ATGAGTTTAA
Statistics
Matches: 56, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
37 1 0.02
38 53 0.95
39 2 0.04
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.32
Consensus pattern (38 bp):
GCAGGCTATGTGCTGGTATTATATCCGGGTTAAATCCC
Found at i:42329965 original size:40 final size:38
Alignment explanation
Indices: 42329846--42329973 Score: 130
Period size: 38 Copynumber: 3.3 Consensus size: 38
42329836 GCAGGCTATA
* * *
42329846 TGCTGGAATTATATCCGGGTTAAATCCCGCAGGCTTCG
1 TGCTGGTATTATATACGGGTTAAATCCCACAGGCTTCG
* ** * *
42329884 TGCTGGTATTATATCCGGGTTAAATCCTGCAGGCCTAG
1 TGCTGGTATTATATACGGGTTAAATCCCACAGGCTTCG
* * *
42329922 TGCTGGTATTATATATGAGTTTAAAGTCCCATAGGCTTCG
1 TGCTGGTATTATATACG-GGTTAAA-TCCCACAGGCTTCG
*
42329962 TGCTGGTGTTAT
1 TGCTGGTATTAT
42329974 GTTTGGGTTT
Statistics
Matches: 75, Mismatches: 13, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
38 49 0.65
39 6 0.08
40 20 0.27
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.34
Consensus pattern (38 bp):
TGCTGGTATTATATACGGGTTAAATCCCACAGGCTTCG
Found at i:42330905 original size:20 final size:20
Alignment explanation
Indices: 42330880--42330928 Score: 57
Period size: 18 Copynumber: 2.5 Consensus size: 20
42330870 GGGTGTTACA
** *
42330880 TACTGTTTATACGGATGAGT
1 TACTGTTTATACAAATGAAT
42330900 TACTG-TTAT-CAAATGAAT
1 TACTGTTTATACAAATGAAT
42330918 TACTGTTTATA
1 TACTGTTTATA
42330929 TGATTGAGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
18 11 0.46
19 8 0.33
20 5 0.21
ACGTcount: A:0.31, C:0.10, G:0.16, T:0.43
Consensus pattern (20 bp):
TACTGTTTATACAAATGAAT
Found at i:42333904 original size:48 final size:48
Alignment explanation
Indices: 42333714--42334191 Score: 451
Period size: 48 Copynumber: 9.9 Consensus size: 48
42333704 AAAGGGTAAG
* * * * * **
42333714 ATGCCGATGCCATGTCCCAGACATGGTCTTACACTGGTTCTCAGATATCG
1 ATGCCAATGCCATGTTCCAAACATGGTCTTACACTAG--CTCACATATAA
* * * **
42333764 GTG-CAGATGTCATGTTCCAAACATGGTCTTACTCTAGCTCACATATCG
1 ATGCCA-ATGCCATGTTCCAAACATGGTCTTACACTAGCTCACATATAA
* *
42333812 AGGCCAATGCCATG-TCCAAACATGGTCTTACACTAGCTCTCATATAA
1 ATGCCAATGCCATGTTCCAAACATGGTCTTACACTAGCTCACATATAA
* * * * *
42333859 ATACCTATGCCATGTTCCAAACATGGTCTTACATTGGCTCACATATCA
1 ATGCCAATGCCATGTTCCAAACATGGTCTTACACTAGCTCACATATAA
* ** * * **
42333907 AGGCTGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTTATATAA
1 ATGCCAATGCCATGTTCCAAACATGGTCTTACACTAGCTCACATATAA
* * * **
42333955 TTGTCAATGCCATGTTTCAAACATGGTCTTACACTAGCTCACATATCG
1 ATGCCAATGCCATGTTCCAAACATGGTCTTACACTAGCTCACATATAA
* * * ** *
42334003 AGGTCGATGCCATG-TCTCGGACATGGTCTTACACTAGCTCTCATATAA
1 ATGCCAATGCCATGTTC-CAAACATGGTCTTACACTAGCTCACATATAA
* * **
42334051 ATGCCGATGCCATGTTCCAAACATGGTCTTACACTGGCTCACATATCG
1 ATGCCAATGCCATGTTCCAAACATGGTCTTACACTAGCTCACATATAA
* * * **
42334099 AGGCCGATGCCATGTCCCAGAA-ATGGTCTTACACTAGCTCTTATATAA
1 ATGCCAATGCCATGTTCCA-AACATGGTCTTACACTAGCTCACATATAA
* *
42334147 ATGCCAATGTCATGTTCCAAACATGGTCTTACACTGGCTCACATA
1 ATGCCAATGCCATGTTCCAAACATGGTCTTACACTAGCTCACATA
42334192 ACCCTAGTAT
Statistics
Matches: 345, Mismatches: 76, Indels: 16
0.79 0.17 0.04
Matches are distributed among these distances:
47 43 0.12
48 267 0.77
49 7 0.02
50 28 0.08
ACGTcount: A:0.27, C:0.26, G:0.18, T:0.29
Consensus pattern (48 bp):
ATGCCAATGCCATGTTCCAAACATGGTCTTACACTAGCTCACATATAA
Found at i:42333978 original size:96 final size:96
Alignment explanation
Indices: 42333716--42334191 Score: 668
Period size: 96 Copynumber: 4.9 Consensus size: 96
42333706 AGGGTAAGAT
* * *** *
42333716 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGTTCTCAGATATCGGTG-CAGATGTCATGTT
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTC--ATATAAATGCCA-ATGCCATGTT
* *
42333780 CCAAACATGGTCTTACTCTAGCTCACATATCGAG
63 CCAAACATGGTCTTACACTGGCTCACATATCGAG
* * * *
42333814 GCCAATGCCATGT-CCAAACATGGTCTTACACTAGCTCTCATATAAATACCTATGCCATGTTCCA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATAAATGCCAATGCCATGTTCCA
* *
42333878 AACATGGTCTTACATTGGCTCACATATCAAG
66 AACATGGTCTTACACTGGCTCACATATCGAG
* * * * *
42333909 GCTGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTTATATAATTGTCAATGCCATGTTTCA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATAAATGCCAATGCCATGTTCCA
*
42333974 AACATGGTCTTACACTAGCTCACATATCGAG
66 AACATGGTCTTACACTGGCTCACATATCGAG
* * * *
42334005 GTCGATGCCATGTCTCGGACATGGTCTTACACTAGCTCTCATATAAATGCCGATGCCATGTTCCA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATAAATGCCAATGCCATGTTCCA
42334070 AACATGGTCTTACACTGGCTCACATATCGAG
66 AACATGGTCTTACACTGGCTCACATATCGAG
* * *
42334101 GCCGATGCCATGTCCCAGAAATGGTCTTACACTAGCTCTTATATAAATGCCAATGTCATGTTCCA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATAAATGCCAATGCCATGTTCCA
42334166 AACATGGTCTTACACTGGCTCACATA
66 AACATGGTCTTACACTGGCTCACATA
42334192 ACCCTAGTAT
Statistics
Matches: 333, Mismatches: 43, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
95 55 0.17
96 243 0.73
97 23 0.07
98 12 0.04
ACGTcount: A:0.27, C:0.26, G:0.18, T:0.29
Consensus pattern (96 bp):
GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATAAATGCCAATGCCATGTTCCA
AACATGGTCTTACACTGGCTCACATATCGAG
Found at i:42337983 original size:40 final size:40
Alignment explanation
Indices: 42337928--42338008 Score: 144
Period size: 40 Copynumber: 2.0 Consensus size: 40
42337918 AATTGGTCAA
*
42337928 ACAGATCATCGATCCTTGGCAAAGGATACTTGCTCTTCAC
1 ACAGATCATCGATCCTCGGCAAAGGATACTTGCTCTTCAC
*
42337968 ACAGATCATCGATCCTCGGCAAAGGATACTTGTTCTTCAC
1 ACAGATCATCGATCCTCGGCAAAGGATACTTGCTCTTCAC
42338008 A
1 A
42338009 GTCACCTTGT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.28, C:0.27, G:0.17, T:0.27
Consensus pattern (40 bp):
ACAGATCATCGATCCTCGGCAAAGGATACTTGCTCTTCAC
Found at i:42340789 original size:34 final size:33
Alignment explanation
Indices: 42340742--42340820 Score: 97
Period size: 34 Copynumber: 2.3 Consensus size: 33
42340732 AAGACTTTTT
*
42340742 CAGTAGCAATATCAGTGTGGGCCTCAG-CCAATTA
1 CAGTA-CAGTATCAGTGTGGGCCTCAGCCCAA-TA
* *
42340776 CGGTAACAGTATCAGTGTGGGCCTTAGCCCAATA
1 CAGT-ACAGTATCAGTGTGGGCCTCAGCCCAATA
42340810 CAGTACAGTAT
1 CAGTACAGTAT
42340821 TAGAGATGTA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
33 7 0.18
34 27 0.69
35 5 0.13
ACGTcount: A:0.29, C:0.23, G:0.24, T:0.24
Consensus pattern (33 bp):
CAGTACAGTATCAGTGTGGGCCTCAGCCCAATA
Found at i:42344662 original size:48 final size:48
Alignment explanation
Indices: 42344543--42344826 Score: 284
Period size: 48 Copynumber: 5.9 Consensus size: 48
42344533 GGGTAAGATG
* * *
42344543 CCGATGCCATGTCCCAGACATGGTCTTACACTTGCTCTCATATATC-AGTG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAG--CTCACATATCGAG-A
* * *
42344593 CCGATGCCATGTTCCAAACATGGTCTTACTCTAGCTCACATATCGAGA
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCGAGA
* * * ** *
42344641 CCGACGCCATGTCCTAGACATGGTCTTACACTAGCTCTCATATAAATA
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCGAGA
** * * * * *
42344689 TTGATGCCATGTTCAAAACATGGTCTTACACTGGCTCACATATCGAGG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCGAGA
* **
42344737 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATAAATG-
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCGA-GA
* * * *
42344785 TCGATGCCATGTTCCAAACATGGTCTTACACTGGCTCACATA
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATA
42344827 ACCCTAGTAT
Statistics
Matches: 191, Mismatches: 41, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
48 158 0.83
49 3 0.02
50 30 0.16
ACGTcount: A:0.26, C:0.28, G:0.17, T:0.28
Consensus pattern (48 bp):
CCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCGAGA
Found at i:42344732 original size:96 final size:96
Alignment explanation
Indices: 42344543--42344826 Score: 451
Period size: 96 Copynumber: 2.9 Consensus size: 96
42344533 GGGTAAGATG
* * *
42344543 CCGATGCCATGTCCCAGACATGGTCTTACACTTGCTCTCATATATCAGTGCCGATGCCATGTTCC
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATA--AATGTCGATGCCATGTTCC
* *
42344608 AAACATGGTCTTACTCTAGCTCACATATCGAGA
64 AAACATGGTCTTACACTGGCTCACATATCGAGA
* * * * *
42344641 CCGACGCCATGTCCTAGACATGGTCTTACACTAGCTCTCATATAAATATTGATGCCATGTTCAAA
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATAAATGTCGATGCCATGTTCCAA
*
42344706 ACATGGTCTTACACTGGCTCACATATCGAGG
66 ACATGGTCTTACACTGGCTCACATATCGAGA
42344737 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATAAATGTCGATGCCATGTTCCAA
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATAAATGTCGATGCCATGTTCCAA
42344802 ACATGGTCTTACACTGGCTCACATA
66 ACATGGTCTTACACTGGCTCACATA
42344827 ACCCTAGTAT
Statistics
Matches: 170, Mismatches: 16, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
96 129 0.76
98 41 0.24
ACGTcount: A:0.26, C:0.28, G:0.17, T:0.28
Consensus pattern (96 bp):
CCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATAAATGTCGATGCCATGTTCCAA
ACATGGTCTTACACTGGCTCACATATCGAGA
Found at i:42344807 original size:144 final size:146
Alignment explanation
Indices: 42344545--42344826 Score: 358
Period size: 144 Copynumber: 1.9 Consensus size: 146
42344535 GTAAGATGCC
* * * * *
42344545 GATGCCATGTCCCAGACATGGTCTTACACTTGCTCTCATATATCAGTGCCGATGCCATGTTCCAA
1 GATGCCATGTCCAAAACATGGTCTTACACTTGCGCTCACATATCAGTGCCGATGCCATGTCCCAA
* ** *
42344610 ACATGGTCTTACTCTAGCTCACATATCGAGACCGACGCCATGTCCTAGACATGGTCTTACACTAG
66 ACATGGTCTTACACTAGCTCACATATAAAGACCGACGCCATGTCCTAAACATGGTCTTACACTAG
*
42344675 CTCTCATATAAATATT
131 CTCACATATAAATATT
*
42344691 GATGCCATGTTCAAAACATGGTCTTACAC-TG-GCTCACATATCGAG-GCCGATGCCATGTCCCA
1 GATGCCATGTCCAAAACATGGTCTTACACTTGCGCTCACATATC-AGTGCCGATGCCATGTCCCA
* * * *
42344753 GACATGGTCTTACACTAGCTCTCATATAAATG-TCGATGCCATGTTCC-AAACATGGTCTTACAC
65 AACATGGTCTTACACTAGCTCACATATAAA-GACCGACGCCATG-TCCTAAACATGGTCTTACAC
*
42344816 TGGCTCACATA
128 TAGCTCACATA
42344827 ACCCTAGTAT
Statistics
Matches: 117, Mismatches: 16, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
144 83 0.71
145 8 0.07
146 26 0.22
ACGTcount: A:0.27, C:0.28, G:0.17, T:0.28
Consensus pattern (146 bp):
GATGCCATGTCCAAAACATGGTCTTACACTTGCGCTCACATATCAGTGCCGATGCCATGTCCCAA
ACATGGTCTTACACTAGCTCACATATAAAGACCGACGCCATGTCCTAAACATGGTCTTACACTAG
CTCACATATAAATATT
Found at i:42345742 original size:39 final size:39
Alignment explanation
Indices: 42345683--42345822 Score: 208
Period size: 39 Copynumber: 3.6 Consensus size: 39
42345673 ATCGTGATCT
* * *
42345683 GAAGCCCGAAGTCTAGCTGAAGCACATAAGTGCTAAACG
1 GAAGCCCGAAGGCTAACTGAAGCACAAAAGTGCTAAACG
42345722 GAAGCCCGAAGGCTAACTGAAGCACAAAAGTGCTAAACG
1 GAAGCCCGAAGGCTAACTGAAGCACAAAAGTGCTAAACG
* **
42345761 GAAGCCCGAATGCTAACTGAAGCACAAAAGTGCTAAATA
1 GAAGCCCGAAGGCTAACTGAAGCACAAAAGTGCTAAACG
* *
42345800 GAAGCCCAAAGGCTAATTGAAGC
1 GAAGCCCGAAGGCTAACTGAAGC
42345823 TCATCAGAGT
Statistics
Matches: 92, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 92 1.00
ACGTcount: A:0.40, C:0.22, G:0.24, T:0.14
Consensus pattern (39 bp):
GAAGCCCGAAGGCTAACTGAAGCACAAAAGTGCTAAACG
Found at i:42345809 original size:21 final size:20
Alignment explanation
Indices: 42345700--42345822 Score: 78
Period size: 19 Copynumber: 6.3 Consensus size: 20
42345690 GAAGTCTAGC
*
42345700 TGAAGCACATAAGTGCTAAA
1 TGAAGCACAAAAGTGCTAAA
* ** *
42345720 CGGAAGC-CCGAAG-GCTAAC
1 -TGAAGCACAAAAGTGCTAAA
42345739 TGAAGCACAAAAGTGCTAAA
1 TGAAGCACAAAAGTGCTAAA
* ** *
42345759 CGGAAGC-CCGAA-TGCTAAC
1 -TGAAGCACAAAAGTGCTAAA
42345778 TGAAGCACAAAAGTGCTAAA
1 TGAAGCACAAAAGTGCTAAA
* *
42345798 TAGAAGC-CCAAAG-GCTAAT
1 T-GAAGCACAAAAGTGCTAAA
42345817 TGAAGC
1 TGAAGC
42345823 TCATCAGAGT
Statistics
Matches: 78, Mismatches: 18, Indels: 15
0.70 0.16 0.14
Matches are distributed among these distances:
18 15 0.19
19 24 0.31
20 24 0.31
21 15 0.19
ACGTcount: A:0.41, C:0.21, G:0.24, T:0.14
Consensus pattern (20 bp):
TGAAGCACAAAAGTGCTAAA
Found at i:42354909 original size:13 final size:13
Alignment explanation
Indices: 42354893--42354927 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
42354883 TGTTGTATAA
42354893 TGATTTTATAAAG
1 TGATTTTATAAAG
42354906 TGATTTTATAAAG
1 TGATTTTATAAAG
42354919 TGATTTTAT
1 TGATTTTAT
42354928 TAAATATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.51
Consensus pattern (13 bp):
TGATTTTATAAAG
Found at i:42357896 original size:93 final size:93
Alignment explanation
Indices: 42357788--42358053 Score: 469
Period size: 93 Copynumber: 2.9 Consensus size: 93
42357778 CGCCCATAAG
* *
42357788 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
*
42357853 ACGAGTTCGGATGCCTAGTTACATTTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
* *
42357881 CGAACTCGGACTCAACTCAATGAGTTCGGACGTTCGCATCCATAAGTGAACTCGGACTCAACTGA
1 CGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
*
42357946 ATGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
42357974 CGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATCCATAAGTGAACTCAGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
42358039 ACGAGTTCGGATGCC
66 ACGAGTTCGGATGCC
42358054 CAAATATCCG
Statistics
Matches: 163, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 163 1.00
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:42357906 original size:47 final size:46
Alignment explanation
Indices: 42357835--42358003 Score: 198
Period size: 47 Copynumber: 3.6 Consensus size: 46
42357825 ATCCATAAGT
42357835 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATTTCAC
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACA-TTCAC
* * * * * * * *
42357882 GAACTCGGACTCAACTCAATGAGTTCGGACG-TTCGCATCCA-TAAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAG-TTACATTCA-C
* *
42357928 GAACTCGGACTCAACTGAATGAGTTCGGATGCCTAGTTACATCTCAC
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT-TCAC
42357975 GAACTCGGACTCAACTCAACGAGTTCGGA
1 GAACTCGGACTCAACTCAACGAGTTCGGA
42358004 CGTTCGCATC
Statistics
Matches: 99, Mismatches: 18, Indels: 10
0.78 0.14 0.08
Matches are distributed among these distances:
45 2 0.02
46 34 0.34
47 61 0.62
48 2 0.02
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (46 bp):
GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATTCAC
Found at i:42358049 original size:46 final size:46
Alignment explanation
Indices: 42357781--42358049 Score: 271
Period size: 46 Copynumber: 5.8 Consensus size: 46
42357771 TGTAACCCGC
* *
42357781 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCAT
* * * * *
42357827 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAG-TT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACG-TTCGCAT
* * *
42357873 ACATTTCA-CGAACTCGGACTCAACTCAATGAGTTCGGACGTTCGCAT
1 CCA--TAAGCGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCAT
* * * *
42357920 CCATAAGTGAACTCGGACTCAACTGAATGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C--GTTCGCAT
*
42357970 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCAT
* *
42358013 CCATAAGTGAACTCAGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
42358050 TGCCCAAATA
Statistics
Matches: 181, Mismatches: 28, Indels: 28
0.76 0.12 0.12
Matches are distributed among these distances:
42 3 0.02
43 3 0.02
44 2 0.01
45 4 0.02
46 96 0.53
47 61 0.34
48 4 0.02
49 2 0.01
50 3 0.02
51 3 0.02
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCAT
Found at i:42364902 original size:28 final size:27
Alignment explanation
Indices: 42364870--42364954 Score: 75
Period size: 28 Copynumber: 3.0 Consensus size: 27
42364860 ACCCAAATAA
42364870 GTCCATAT-ACATGCTTATGGCCCACTAG
1 GTCCA-ATCACAT-CTTATGGCCCACTAG
* * *
42364898 GTCCAATCTCATTCATATGGCCCATTAG
1 GTCCAATCACA-TCTTATGGCCCACTAG
*
42364926 GCCCAAATCACATCTATAT-GCCCACTAG
1 GTCC-AATCACATCT-TATGGCCCACTAG
42364954 G
1 G
42364955 CTTAATCACT
Statistics
Matches: 46, Mismatches: 7, Indels: 8
0.75 0.11 0.13
Matches are distributed among these distances:
27 2 0.04
28 34 0.74
29 10 0.22
ACGTcount: A:0.27, C:0.31, G:0.15, T:0.27
Consensus pattern (27 bp):
GTCCAATCACATCTTATGGCCCACTAG
Found at i:42364955 original size:28 final size:28
Alignment explanation
Indices: 42364885--42364955 Score: 83
Period size: 28 Copynumber: 2.5 Consensus size: 28
42364875 TATACATGCT
* *
42364885 TATGGCCCACTAGGTCCAATCTCATTCA
1 TATGGCCCACTAGGCCCAATCACATTCA
*
42364913 TATGGCCCATTAGGCCCAAATCACA-TCTA
1 TATGGCCCACTAGGCCC-AATCACATTC-A
42364942 TAT-GCCCACTAGGC
1 TATGGCCCACTAGGC
42364956 TTAATCACTT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
28 27 0.73
29 10 0.27
ACGTcount: A:0.27, C:0.32, G:0.15, T:0.25
Consensus pattern (28 bp):
TATGGCCCACTAGGCCCAATCACATTCA
Found at i:42365052 original size:17 final size:18
Alignment explanation
Indices: 42365030--42365063 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
42365020 TGTCTATTAT
42365030 GGGCCCA-ATAGCCCATC
1 GGGCCCATATAGCCCATC
*
42365047 GGGCCCATTTAGCCCAT
1 GGGCCCATATAGCCCAT
42365064 GCTGGCCCAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.21, C:0.38, G:0.24, T:0.18
Consensus pattern (18 bp):
GGGCCCATATAGCCCATC
Found at i:42365225 original size:16 final size:16
Alignment explanation
Indices: 42365183--42365227 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
42365173 ATAGCTAAAC
*
42365183 TTTTGGCTTTTCGGCA
1 TTTTGGCTTTTCAGCA
**
42365199 TTTCAGCTTTTCAGCA
1 TTTTGGCTTTTCAGCA
*
42365215 TTTTGGTTTTTCA
1 TTTTGGCTTTTCA
42365228 AGATTTGCTG
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.11, C:0.18, G:0.18, T:0.53
Consensus pattern (16 bp):
TTTTGGCTTTTCAGCA
Found at i:42375522 original size:6 final size:6
Alignment explanation
Indices: 42375492--42375566 Score: 73
Period size: 6 Copynumber: 12.3 Consensus size: 6
42375482 AAGAAACATT
* * * *
42375492 ATCAGA A-CTAGA ATCAAA ATGAGA ATCAGA ATCAAA ATCAGC ATCA-A
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA
42375539 ATAACAGA ATCAGA ATCAGA ATCAGA AT
1 AT--CAGA ATCAGA ATCAGA ATCAGA AT
42375567 GTGAATGCAA
Statistics
Matches: 56, Mismatches: 8, Indels: 10
0.76 0.11 0.14
Matches are distributed among these distances:
5 3 0.05
6 47 0.84
7 3 0.05
8 3 0.05
ACGTcount: A:0.53, C:0.16, G:0.13, T:0.17
Consensus pattern (6 bp):
ATCAGA
Found at i:42375720 original size:27 final size:26
Alignment explanation
Indices: 42375684--42375763 Score: 106
Period size: 26 Copynumber: 3.0 Consensus size: 26
42375674 AGCTTGGCTG
*
42375684 CCAGAACAGATATTGTGACAGAGTCA
1 CCAGAACAGATATTGTGACAGAGCCA
*
42375710 CCAGATACAGATATTGTGGCAGAGCCA
1 CCAGA-ACAGATATTGTGACAGAGCCA
* * *
42375737 CCAGAACAGATAATGTGGCAAAGCCA
1 CCAGAACAGATATTGTGACAGAGCCA
42375763 C
1 C
42375764 TTAACAGAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
26 25 0.51
27 24 0.49
ACGTcount: A:0.38, C:0.23, G:0.24, T:0.16
Consensus pattern (26 bp):
CCAGAACAGATATTGTGACAGAGCCA
Found at i:42376556 original size:27 final size:27
Alignment explanation
Indices: 42376498--42377401 Score: 474
Period size: 27 Copynumber: 33.0 Consensus size: 27
42376488 GGGGCAAAAT
* * * * *
42376498 GGTAATTTTACCCCACAAGGATATCTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
42376525 GGTAATTCTACCCTACAGGGGTATTTT
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
42376552 AGTAATTCTACCCTATAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
42376579 GGTAATTCTACCCTACA-GGGTATTGT-
1 GGTAATTCTACCCTACAGGGGTATT-TC
* *
42376605 GATAATTCTACCCTATAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
42376632 AGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
42376659 GGTATTTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
42376686 GATAATTCTACCCTAAAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
42376713 GATAATTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* * * *
42376740 GGTATTTCTATCCTACAAGGGTAGTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
42376767 GGTATTTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
42376794 GATAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
42376821 GGTAATTCTACCCTATAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
** * ** * ***
42376848 AATAATTTTGTA-AAT-CAAGGGTAAAAC
1 GGTAA--TTCTACCCTACAGGGGTATTTC
** *
42376875 GGTAATTCTGTA-AAT-CGGGGGTACTTT-
1 GGTAATTC--TACCCTACAGGGGTA-TTTC
* ** *
42376902 GGTAATTTTACAAGT-CAAGGGTATTTC
1 GGTAATTCTAC-CCTACAGGGGTATTTC
* * ** *
42376929 AGTAATTTTA-CAAATC-GAGGGTATTTT
1 GGTAATTCTACCCTA-CAG-GGGTATTTC
* ** ** *
42376956 AGTAATT-TTTCAAACTATGGGTATTTC
1 GGTAATTCTACCCTAC-AGGGGTATTTC
* * *** *
42376983 AGTAATTTCAAAAAT-CAGGGGTATTTT
1 GGTAA-TTCTACCCTACAGGGGTATTTC
* ** * *
42377010 GGTAATTTTA-CAAACCAAGGGTATTTT
1 GGTAATTCTACCCTA-CAGGGGTATTTC
* ** * *
42377037 GGTAATTTTA-CAAACCAGGAGTATTTT
1 GGTAATTCTACCCTA-CAGGGGTATTTC
* * ** * *** ***
42377064 GGTGATTTGGTAAACTAAAGTATTCTAAATAAG
1 GGT-AATT-CTACCCTACAG--GGGT--ATTTC
* ** ** ***
42377097 GGTATTTCGGTATTTCTAC---CCTATAGG
1 GGTAATTC--TA-CCCTACAGGGGTATTTC
* ** *
42377124 GGTATTTCGATAATTCTACCCTACAAGGGTATTTC
1 GGTAATTC--T-ACCCTAC-----AGGGGTATTTC
* *
42377159 GGTATTTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
42377186 GATAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
42377213 AGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
42377240 GGTATTTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
42377267 GATAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
42377294 AGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* * * *
42377321 GATATTTCTACCCTATAAGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
42377348 GATAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
42377375 GGTAATTCTACCCTATAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
42377402 AATAATTTTG
Statistics
Matches: 706, Mismatches: 131, Indels: 80
0.77 0.14 0.09
Matches are distributed among these distances:
25 5 0.01
26 31 0.04
27 618 0.88
28 8 0.01
29 11 0.02
30 1 0.00
31 1 0.00
32 9 0.01
33 8 0.01
34 3 0.00
35 11 0.02
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36
Consensus pattern (27 bp):
GGTAATTCTACCCTACAGGGGTATTTC
Found at i:42376722 original size:81 final size:82
Alignment explanation
Indices: 42376502--42377401 Score: 576
Period size: 81 Copynumber: 11.0 Consensus size: 82
42376492 CAAAATGGTA
* * * * * *
42376502 ATTT-TACCCCACAAGGATATCTCGGTAATTCTACCCTACAGGGGTATTT-TAGTAATTCTACCC
1 ATTTCTACCCTACAAGGGTATTTCGATAATTCTACCCTAAAGGGGTATTTCGAGTAATTCTACCC
*
42376565 TATAGGGGTATTTCGGT
66 TACAGGGGTATTTCGGT
* *
42376582 AATTCTACCCTAC-AGGGTATTGT-GATAATTCTACCCTATAGGGGTATTTC-AGTAATTCTACC
1 ATTTCTACCCTACAAGGGTATT-TCGATAATTCTACCCTAAAGGGGTATTTCGAGTAATTCTACC
42376644 CTACAGGGGTATTTCGGT
65 CTACAGGGGTATTTCGGT
42376662 ATTTCTACCCTACAAGGGTATTTCGATAATTCTACCCTAAAGGGGTATTTCGA-TAATTCTACCC
1 ATTTCTACCCTACAAGGGTATTTCGATAATTCTACCCTAAAGGGGTATTTCGAGTAATTCTACCC
*
42376726 TACAAGGGTATTTCGGT
66 TACAGGGGTATTTCGGT
* * * *
42376743 ATTTCTATCCTACAAGGGTAGTTCGGTATTTCTACCCTACAA-GGGTATTTCGA-TAATTCTACC
1 ATTTCTACCCTACAAGGGTATTTCGATAATTCTACCCTA-AAGGGGTATTTCGAGTAATTCTACC
42376806 CTACAGGGGTATTTCGGT
65 CTACAGGGGTATTTCGGT
* * * * * ** * ***
42376824 AATTCTACCCTATAGGGGTATTTCAATAATTTTGTA-AATCAA-GGGTAAAACG-GTAATTCTGT
1 ATTTCTACCCTACAAGGGTATTTCGATAA--TTCTACCCTAAAGGGGTATTTCGAGTAATTC--T
** *
42376886 A-AAT-CGGGGGTACTTT-GGT
62 ACCCTACAGGGGTA-TTTCGGT
** * *
42376905 AATTT-TACAAGT-CAAGGGTATTTC-AGTAATTTTA--C-AAATCGAGGGTATTT-TAGTAATT
1 -ATTTCTAC-CCTACAAGGGTATTTCGA-TAATTCTACCCTAAA--G-GGGTATTTCGAGTAATT
** ** * *
42376963 -TTTCAAACTATGGGTATTTCAGT
60 CTACCCTAC-AGGGGTATTTCGGT
* *** * * * * * *
42376986 AATTTCAAAAAT-CAGGGGTATTTTGGTAATTTTACAAACC--AA-GGGTATTTTG-GTAATTTT
1 -ATTTCTACCCTACAAGGGTATTTCGATAATTCTAC---CCTAAAGGGGTATTTCGAGTAATTCT
** * *
42377046 A-CAAACCAGGAGTATTTTGGT
62 ACCCTA-CAGGGGTATTTCGGT
* ** ** ** ** *
42377067 GATTTGGTAAACTA-AA--GTATTCTAAATAAGGGTATTTCGGTATTTCTACCCTATAGGG-GTA
1 -ATTT-CTACCCTACAAGGGTATT-TCGAT-A----A-TTC--TA---C--CCTAAAGGGGTAT-
** *
42377128 TT-TCGATAATTCTACCCTACAAGGGTATTTCGGT
49 TTCGAG-TAATTCTACCCTACAGGGGTATTTCGGT
*
42377162 ATTTCTACCCTACAAGGGTATTTCGATAATTCTACCCTACAGGGGTATTTC-AGTAATTCTACCC
1 ATTTCTACCCTACAAGGGTATTTCGATAATTCTACCCTAAAGGGGTATTTCGAGTAATTCTACCC
42377226 TACAGGGGTATTTCGGT
66 TACAGGGGTATTTCGGT
*
42377243 ATTTCTACCCTACAAGGGTATTTCGATAATTCTACCCTACAGGGGTATTTC-AGTAATTCTACCC
1 ATTTCTACCCTACAAGGGTATTTCGATAATTCTACCCTAAAGGGGTATTTCGAGTAATTCTACCC
*
42377307 TACAGGGGTATTTCGAT
66 TACAGGGGTATTTCGGT
* *
42377324 ATTTCTACCCTATAAGGGTATTTCGATAATTCTACCCTACAGGGGTATTTCG-GTAATTCTACCC
1 ATTTCTACCCTACAAGGGTATTTCGATAATTCTACCCTAAAGGGGTATTTCGAGTAATTCTACCC
*
42377388 TATAGGGGTATTTC
66 TACAGGGGTATTTC
42377402 AATAATTTTG
Statistics
Matches: 660, Mismatches: 98, Indels: 123
0.75 0.11 0.14
Matches are distributed among these distances:
77 2 0.00
78 1 0.00
79 5 0.01
80 85 0.13
81 463 0.70
82 29 0.04
83 7 0.01
84 1 0.00
85 2 0.00
86 2 0.00
87 4 0.01
89 5 0.01
90 1 0.00
91 3 0.00
92 1 0.00
93 7 0.01
94 13 0.02
95 22 0.03
96 7 0.01
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36
Consensus pattern (82 bp):
ATTTCTACCCTACAAGGGTATTTCGATAATTCTACCCTAAAGGGGTATTTCGAGTAATTCTACCC
TACAGGGGTATTTCGGT
Found at i:42376870 original size:54 final size:54
Alignment explanation
Indices: 42376498--42377401 Score: 576
Period size: 54 Copynumber: 17.0 Consensus size: 54
42376488 GGGGCAAAAT
* * * * * * *
42376498 GGTAATTTTACCCCACAAGGATATCTCGGTAATTCTACCCTACAGGGGTATTTT
1 GGTAATTCTACCCTACAAGGGTATTTCGATAATTCTACCCTACAAGGGTATTTC
* * * *
42376552 AGTAATTCTACCCTATAGGGGTATTTCGGTAATTCTACCCTAC-AGGGTATTGT-
1 GGTAATTCTACCCTACAAGGGTATTTCGATAATTCTACCCTACAAGGGTATT-TC
* * * *
42376605 GATAATTCTACCCTATAGGGGTATTTC-AGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTCGA-TAATTCTACCCTACAAGGGTATTTC
*
42376659 GGTATTTCTACCCTACAAGGGTATTTCGATAATTCTACCCTA-AAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTCGATAATTCTACCCTACAA-GGGTATTTC
* * * * *
42376713 GATAATTCTACCCTACAAGGGTATTTCGGTATTTCTATCCTACAAGGGTAGTTC
1 GGTAATTCTACCCTACAAGGGTATTTCGATAATTCTACCCTACAAGGGTATTTC
* *
42376767 GGTATTTCTACCCTACAAGGGTATTTCGATAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTCGATAATTCTACCCTACAAGGGTATTTC
* * * * ** ***
42376821 GGTAATTCTACCCTATAGGGGTATTTCAATAATTTTGTA-AAT-CAAGGGTAAAAC
1 GGTAATTCTACCCTACAAGGGTATTTCGATAA--TTCTACCCTACAAGGGTATTTC
** ** * * **
42376875 GGTAATTCTGTA-AAT-CGGGGGTACTTT-GGTAATTTTACAAGT-CAAGGGTATTTC
1 GGTAATTC--TACCCTACAAGGGTA-TTTCGATAATTCTAC-CCTACAAGGGTATTTC
* * ** * * ** ** *
42376929 AGTAATTTTA-CAAATCGAGGGTATTT-TAGTAATT-TTTCAAACTATGGGTATTTC
1 GGTAATTCTACCCTA-CAAGGGTATTTCGA-TAATTCTACCCTAC-AAGGGTATTTC
* * *** * * * * ** *
42376983 AGTAATTTCAAAAAT-CAGGGGTATTTTGGTAATTTTA-CAAACCAAGGGTATTTT
1 GGTAA-TTCTACCCTACAAGGGTATTTCGATAATTCTACCCTA-CAAGGGTATTTC
* ** * * * * * **
42377037 GGTAATTTTA-CAAACCAGGAGTATTTTGGTGATTTGGTAAACTA-AA--GTA-TTC
1 GGTAATTCTACCCTACAAGG-GTATTTCGAT-AATT-CTACCCTACAAGGGTATTTC
* * * *
42377089 --TAA----A---T--AAGGGTATTTCGGTATTTCTACCCTATAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTCGATAATTCTACCCTACAAGGGTATTTC
* * *
42377132 GATAATTCTACCCTACAAGGGTATTTCGGTATTTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTCGATAATTCTACCCTACAAGGGTATTTC
* * *
42377186 GATAATTCTACCCTACAGGGGTATTTC-AGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTCGA-TAATTCTACCCTACAAGGGTATTTC
* *
42377240 GGTATTTCTACCCTACAAGGGTATTTCGATAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTCGATAATTCTACCCTACAAGGGTATTTC
* * * *
42377294 AGTAATTCTACCCTACAGGGGTATTTCGATATTTCTACCCTATAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTCGATAATTCTACCCTACAAGGGTATTTC
* * * * *
42377348 GATAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCCTATAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTCGATAATTCTACCCTACAAGGGTATTTC
42377402 AATAATTTTG
Statistics
Matches: 688, Mismatches: 116, Indels: 92
0.77 0.13 0.10
Matches are distributed among these distances:
39 5 0.01
40 5 0.01
41 9 0.01
42 6 0.01
43 3 0.00
45 3 0.00
46 1 0.00
49 1 0.00
50 3 0.00
52 11 0.02
53 62 0.09
54 550 0.80
55 19 0.03
56 9 0.01
57 1 0.00
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36
Consensus pattern (54 bp):
GGTAATTCTACCCTACAAGGGTATTTCGATAATTCTACCCTACAAGGGTATTTC
Found at i:42377423 original size:27 final size:27
Alignment explanation
Indices: 42377393--42377658 Score: 185
Period size: 27 Copynumber: 9.9 Consensus size: 27
42377383 TACCCTATAG
* *
42377393 GGGTATTTCAATAATTTTGTAAATCAA
1 GGGTATTTCAGTAATTTTGCAAATCAA
*** * * * **
42377420 GGGTAAAACGGTAATTCTGTAAATCGG
1 GGGTATTTCAGTAATTTTGCAAATCAA
* * *
42377447 GGGTACTTT-GGTAATTTTACAAGTCAA
1 GGGTA-TTTCAGTAATTTTGCAAATCAA
*
42377474 GGGTATTTCAGTAATTTTACAAATCAA
1 GGGTATTTCAGTAATTTTGCAAATCAA
**
42377501 GGGTATTTCAGTAATTTTGCAAA-CTG
1 GGGTATTTCAGTAATTTTGCAAATCAA
* ** *
42377527 GGGATATTTTAGTAATTTCACAAATCAT
1 GGG-TATTTCAGTAATTTTGCAAATCAA
** * *
42377555 GGGTATTTTGGTAATTTTACAAACCAA
1 GGGTATTTCAGTAATTTTGCAAATCAA
** * *
42377582 GGGTATTTTGGTAATTTTACAAACCAA
1 GGGTATTTCAGTAATTTTGCAAATCAA
** * *
42377609 GGGTATTTTGGTAATTTTACAAACCAA
1 GGGTATTTCAGTAATTTTGCAAATCAA
** *
42377636 GGGTATTTTGGTAATTTTACAAA
1 GGGTATTTCAGTAATTTTGCAAA
42377659 CCAGGAGTAT
Statistics
Matches: 204, Mismatches: 31, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
26 7 0.03
27 193 0.95
28 4 0.02
ACGTcount: A:0.33, C:0.10, G:0.20, T:0.37
Consensus pattern (27 bp):
GGGTATTTCAGTAATTTTGCAAATCAA
Found at i:42377424 original size:54 final size:54
Alignment explanation
Indices: 42377094--42378026 Score: 521
Period size: 54 Copynumber: 17.5 Consensus size: 54
42377084 TATTCTAAAT
* *
42377094 AAGGGTATTTCGGTATTTCTACCCTATAGGGGTATTTCGATAATTCTACCCTAC
1 AAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCGATAATTCTACCCTAC
* *
42377148 AAGGGTATTTCGGTATTTCTACCCTACAAGGGTATTTCGATAATTCTACCCTAC
1 AAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCGATAATTCTACCCTAC
* * * *
42377202 AGGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTCGGTATTTCTACCCTAC
1 AAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCGATAATTCTACCCTAC
*
42377256 AAGGGTATTTCGATAATTCTACCCTACAGGGGTATTTC-AGTAATTCTACCCTAC
1 AAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCGA-TAATTCTACCCTAC
* * * * *
42377310 AGGGGTATTTCGATATTTCTACCCTATAAGGGTATTTCGATAATTCTACCCTAC
1 AAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCGATAATTCTACCCTAC
* * * * **
42377364 AGGGGTATTTCGGTAATTCTACCCTATAGGGGTATTTCAATAATTTTGTA-AAT-C
1 AAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCGATAA--TTCTACCCTAC
*** ** * * * **
42377418 AAGGGTAAAACGGTAATTCTGTA-AAT-CGGGGGTACTTT-GGTAATTTTACAAGT-C
1 AAGGGTATTTCGGTAATTC--TACCCTACAGGGGTA-TTTCGATAATTCTAC-CCTAC
* * ** * ** **
42377472 AAGGGTATTTCAGTAATTTTA-CAAATCAAGGGTATTTC-AGTAATT-TTGCAAAC
1 AAGGGTATTTCGGTAATTCTACCCTA-CAGGGGTATTTCGA-TAATTCTACCCTAC
** ** ** * * * * **
42377525 TGGGGATATTTTAGTAATT-T-CACAAATCATGGGTATTTTGGTAATTTTA-CAAACC
1 AAGGG-TATTTCGGTAATTCTAC-CCTA-CAGGGGTATTTCGATAATTCTACCCTA-C
* * ** * * * * **
42377580 AAGGGTATTTTGGTAATTTTA-CAAACCAAGGGTATTTTGGTAATTTTA-CAAACC
1 AAGGGTATTTCGGTAATTCTACCCTA-CAGGGGTATTTCGATAATTCTACCCTA-C
* * ** * * * * * **
42377634 AAGGGTATTTTGGTAATTTTA-CAAACCAGGAGTATTTTGGTGATTTGGTAAACTA-
1 AAGGGTATTTCGGTAATTCTACCCTA-CAGGGGTATTTCGAT-AATT-CTACCCTAC
* * *
42377689 AA--GTA-TTC--TAA----A---TA-A-GGGTATTTCGGTATTTCTACCCTAT
1 AAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCGATAATTCTACCCTAC
* * * *
42377729 AGGGGTATTTCGATAATTCTACCCTATAGGGGTATTTC-AGTATTTCTACCCTAC
1 AAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCGA-TAATTCTACCCTAC
* * *
42377783 AAGGGTATTTCGGTATTTCTACCCTACAAGGGTATTT-TAGTAATTCTACCCTAC
1 AAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCGA-TAATTCTACCCTAC
* * * * * * *
42377837 AGGGGTATTTCGATAATTCTACCCTACAGTGGTATTTAGGTATTTCTACCCTAG
1 AAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCGATAATTCTACCCTAC
* * ** * * *
42377891 AAGGGTATTTCAGTATTTCTACCCTACAATGGTATTTCGGTATTTTTACCCTAC
1 AAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCGATAATTCTACCCTAC
* * * *
42377945 AGGGGTATTGT-AGTAATTCTACCCTATAGGGGTATTTCGGTAATTCTACCCTAC
1 AAGGGTATT-TCGGTAATTCTACCCTACAGGGGTATTTCGATAATTCTACCCTAC
* *
42377999 AAAGGTATTTTGGTAATTCTACCCTACA
1 AAGGGTATTTCGGTAATTCTACCCTACA
42378027 AGTATATTTC
Statistics
Matches: 720, Mismatches: 114, Indels: 90
0.78 0.12 0.10
Matches are distributed among these distances:
39 5 0.01
40 5 0.01
41 10 0.01
42 4 0.01
43 3 0.00
44 1 0.00
45 3 0.00
46 1 0.00
49 1 0.00
50 3 0.00
52 11 0.02
53 14 0.02
54 632 0.88
55 18 0.03
56 8 0.01
57 1 0.00
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.37
Consensus pattern (54 bp):
AAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCGATAATTCTACCCTAC
Found at i:42377515 original size:81 final size:80
Alignment explanation
Indices: 42377393--42377658 Score: 280
Period size: 81 Copynumber: 3.3 Consensus size: 80
42377383 TACCCTATAG
* ** *** * * *
42377393 GGGTATTTCAATAATTTTGTAAATCAAGGGTAAAACGGTAATTCTGTAAATCGGGGGTACTTTGG
1 GGGTATTTCAGTAATTTTACAAATCAAGGGTATTTCGGTAATTTTGCAAA-CGGGGGTATTTTGG
*
42377458 TAATTTTACAAGTCAA
65 TAATTTTACAAATCAA
* * *
42377474 GGGTATTTCAGTAATTTTACAAATCAAGGGTATTTCAGTAATTTTGCAAACTGGGGATATTTTAG
1 GGGTATTTCAGTAATTTTACAAATCAAGGGTATTTCGGTAATTTTGCAAAC-GGGGGTATTTTGG
* *
42377539 TAATTTCACAAATCAT
65 TAATTTTACAAATCAA
** * * * **
42377555 GGGTATTTTGGTAATTTTACAAACCAAGGGTATTTTGGTAATTTTACAAACCAAGGGTATTTTGG
1 GGGTATTTCAGTAATTTTACAAATCAAGGGTATTTCGGTAATTTTGCAAA-CGGGGGTATTTTGG
*
42377620 TAATTTTACAAACCAA
65 TAATTTTACAAATCAA
**
42377636 GGGTATTTTGGTAATTTTACAAA
1 GGGTATTTCAGTAATTTTACAAA
42377659 CCAGGAGTAT
Statistics
Matches: 155, Mismatches: 28, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
80 1 0.01
81 153 0.99
82 1 0.01
ACGTcount: A:0.33, C:0.10, G:0.20, T:0.37
Consensus pattern (80 bp):
GGGTATTTCAGTAATTTTACAAATCAAGGGTATTTCGGTAATTTTGCAAACGGGGGTATTTTGGT
AATTTTACAAATCAA
Found at i:42377686 original size:27 final size:27
Alignment explanation
Indices: 42377447--42377679 Score: 290
Period size: 27 Copynumber: 8.6 Consensus size: 27
42377437 TGTAAATCGG
* **
42377447 GGGTACTTTGGTAATTTTACAAGTCAA
1 GGGTATTTTGGTAATTTTACAAACCAA
** *
42377474 GGGTATTTCAGTAATTTTACAAATCAA
1 GGGTATTTTGGTAATTTTACAAACCAA
** * **
42377501 GGGTATTTCAGTAATTTTGCAAA-CTG
1 GGGTATTTTGGTAATTTTACAAACCAA
* * * *
42377527 GGGATATTTTAGTAATTTCACAAATCAT
1 GGG-TATTTTGGTAATTTTACAAACCAA
42377555 GGGTATTTTGGTAATTTTACAAACCAA
1 GGGTATTTTGGTAATTTTACAAACCAA
42377582 GGGTATTTTGGTAATTTTACAAACCAA
1 GGGTATTTTGGTAATTTTACAAACCAA
42377609 GGGTATTTTGGTAATTTTACAAACCAA
1 GGGTATTTTGGTAATTTTACAAACCAA
42377636 GGGTATTTTGGTAATTTTACAAACC-A
1 GGGTATTTTGGTAATTTTACAAACCAA
*
42377662 GGAGTATTTTGGTGATTT
1 GG-GTATTTTGGTAATTT
42377680 GGTAAACTAA
Statistics
Matches: 186, Mismatches: 17, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
26 7 0.04
27 175 0.94
28 4 0.02
ACGTcount: A:0.31, C:0.10, G:0.20, T:0.39
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTACAAACCAA
Found at i:42378035 original size:27 final size:27
Alignment explanation
Indices: 42377702--42378028 Score: 379
Period size: 27 Copynumber: 12.1 Consensus size: 27
42377692 TATTCTAAAT
* *
42377702 AAGGGTATTTCGGTATTTCTACCCTAT
1 AAGGGTATTTCGGTAATTCTACCCTAC
* * *
42377729 AGGGGTATTTCGATAATTCTACCCTAT
1 AAGGGTATTTCGGTAATTCTACCCTAC
* * *
42377756 AGGGGTATTTCAGTATTTCTACCCTAC
1 AAGGGTATTTCGGTAATTCTACCCTAC
*
42377783 AAGGGTATTTCGGTATTTCTACCCTAC
1 AAGGGTATTTCGGTAATTCTACCCTAC
**
42377810 AAGGGTATTTTAGTAATTCTACCCTAC
1 AAGGGTATTTCGGTAATTCTACCCTAC
* *
42377837 AGGGGTATTTCGATAATTCTACCCTAC
1 AAGGGTATTTCGGTAATTCTACCCTAC
* * *
42377864 -AGTGGTATTTAGGTATTTCTACCCTAG
1 AAG-GGTATTTCGGTAATTCTACCCTAC
* *
42377891 AAGGGTATTTCAGTATTTCTACCCTAC
1 AAGGGTATTTCGGTAATTCTACCCTAC
* * *
42377918 AATGGTATTTCGGTATTTTTACCCTAC
1 AAGGGTATTTCGGTAATTCTACCCTAC
* * *
42377945 AGGGGTATTGT-AGTAATTCTACCCTAT
1 AAGGGTATT-TCGGTAATTCTACCCTAC
*
42377972 AGGGGTATTTCGGTAATTCTACCCTAC
1 AAGGGTATTTCGGTAATTCTACCCTAC
* *
42377999 AAAGGTATTTTGGTAATTCTACCCTAC
1 AAGGGTATTTCGGTAATTCTACCCTAC
42378026 AAG
1 AAG
42378029 TATATTTCAA
Statistics
Matches: 257, Mismatches: 39, Indels: 8
0.85 0.13 0.03
Matches are distributed among these distances:
26 2 0.01
27 252 0.98
28 3 0.01
ACGTcount: A:0.25, C:0.19, G:0.18, T:0.37
Consensus pattern (27 bp):
AAGGGTATTTCGGTAATTCTACCCTAC
Found at i:42378096 original size:27 final size:27
Alignment explanation
Indices: 42378031--42378261 Score: 164
Period size: 27 Copynumber: 8.6 Consensus size: 27
42378021 CCTACAAGTA
* **
42378031 TATTTCAATAATTTTGTAAATCGAGGG
1 TATTTCAGTAATTTTACAAATCGAGGG
*** * *
42378058 TAAAACAGTAATTCTATAAATCGAGGG
1 TATTTCAGTAATTTTACAAATCGAGGG
* * *
42378085 TGCTTTGA-TAATTTTACAAGTCGAGGG
1 T-ATTTCAGTAATTTTACAAATCGAGGG
42378112 TATTTCAGTAATTTTACAAATCGAGGG
1 TATTTCAGTAATTTTACAAATCGAGGG
* * *
42378139 TATTTTAGTAATTTTTCAAA-CTATGGG
1 TATTTCAGTAATTTTACAAATCGA-GGG
* *
42378166 TATTTCAGTAATTTCAAAAATC-AGGGG
1 TATTTCAGTAATTTTACAAATCGA-GGG
** * *
42378193 TATTTTGGTAATTTTACAAACCAAGGG
1 TATTTCAGTAATTTTACAAATCGAGGG
** * *
42378220 TATTTTGGTAATTTTATAAA-CCAGGGG
1 TATTTCAGTAATTTTACAAATCGA-GGG
**
42378247 TATTTTGGTAATTTT
1 TATTTCAGTAATTTT
42378262 GTAAACTAAG
Statistics
Matches: 166, Mismatches: 32, Indels: 12
0.79 0.15 0.06
Matches are distributed among these distances:
26 8 0.05
27 155 0.93
28 3 0.02
ACGTcount: A:0.32, C:0.09, G:0.19, T:0.39
Consensus pattern (27 bp):
TATTTCAGTAATTTTACAAATCGAGGG
Found at i:42378151 original size:54 final size:54
Alignment explanation
Indices: 42378063--42378314 Score: 219
Period size: 54 Copynumber: 4.7 Consensus size: 54
42378053 GAGGGTAAAA
* ** * * *
42378063 CAGTAATTCTATAAATCGA-GGGTGCTTTGATAATTTTACAAGTCGAGGGTATTT
1 CAGTAATTTTATAAATCGAGGGGTATTTTGGTAATTTTACAA-ACAAGGGTATTT
* * * *
42378117 CAGTAATTTTACAAATCGA-GGGTATTTTAGTAATTTTTCAAACTATGGGTATTT
1 CAGTAATTTTATAAATCGAGGGGTATTTTGGTAATTTTACAAAC-AAGGGTATTT
* *
42378171 CAGTAATTTCAAAAATC-AGGGGTATTTTGGTAATTTTACAAACCAAGGGTATTT
1 CAGTAATTTTATAAATCGAGGGGTATTTTGGTAATTTTACAAA-CAAGGGTATTT
** * ** *
42378225 TGGTAATTTTATAAA-CCAGGGGTATTTTGGTAATTTTGTAAACTAAGTGTAGTTT
1 CAGTAATTTTATAAATCGAGGGGTATTTTGGTAATTTTACAAAC-AAGGGTA-TTT
* * * *
42378280 -GGTAATTTTACAAA-CCAGGGGTATTTTGGTGATTT
1 CAGTAATTTTATAAATCGAGGGGTATTTTGGTAATTT
42378315 GGTAAACTAA
Statistics
Matches: 168, Mismatches: 24, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
53 4 0.02
54 160 0.95
55 4 0.02
ACGTcount: A:0.31, C:0.09, G:0.21, T:0.40
Consensus pattern (54 bp):
CAGTAATTTTATAAATCGAGGGGTATTTTGGTAATTTTACAAACAAGGGTATTT
Found at i:42378320 original size:54 final size:54
Alignment explanation
Indices: 42378119--42378324 Score: 220
Period size: 54 Copynumber: 3.8 Consensus size: 54
42378109 GGGTATTTCA
* * * * *
42378119 GTAATTTTACAAATC-GAGGGTATTTTAGTAATTTT-TCAAACTATGGGTA-TTTCA
1 GTAATTTTAAAAACCAG-GGGTATTTTGGTAATTTTGT-AAACTAAGGGTAGTTT-G
* * ** * *
42378173 GTAATTTCAAAAATCAGGGGTATTTTGGTAATTTTACAAACCAAGGGTATTTTG
1 GTAATTTTAAAAACCAGGGGTATTTTGGTAATTTTGTAAACTAAGGGTAGTTTG
* *
42378227 GTAATTTTATAAACCAGGGGTATTTTGGTAATTTTGTAAACTAAGTGTAGTTTG
1 GTAATTTTAAAAACCAGGGGTATTTTGGTAATTTTGTAAACTAAGGGTAGTTTG
* * *
42378281 GTAATTTTACAAACCAGGGGTATTTTGGTGATTTGGTAAACTAA
1 GTAATTTTAAAAACCAGGGGTATTTTGGTAATTTTGTAAACTAA
42378325 AGTATTCTAA
Statistics
Matches: 131, Mismatches: 18, Indels: 6
0.85 0.12 0.04
Matches are distributed among these distances:
54 127 0.97
55 4 0.03
ACGTcount: A:0.32, C:0.08, G:0.20, T:0.40
Consensus pattern (54 bp):
GTAATTTTAAAAACCAGGGGTATTTTGGTAATTTTGTAAACTAAGGGTAGTTTG
Found at i:42378321 original size:27 final size:27
Alignment explanation
Indices: 42378109--42378314 Score: 191
Period size: 27 Copynumber: 7.6 Consensus size: 27
42378099 TACAAGTCGA
** * *
42378109 GGGTATTTCAGTAATTTTACAAATC-G
1 GGGTATTTTGGTAATTTTATAAACCAG
* * *
42378135 AGGGTATTTTAGTAATTTT-TCAAACTAT
1 -GGGTATTTTGGTAATTTTAT-AAACCAG
** * * *
42378163 GGGTATTTCAGTAATTTCAAAAATCAG
1 GGGTATTTTGGTAATTTTATAAACCAG
* *
42378190 GGGTATTTTGGTAATTTTACAAACCAA
1 GGGTATTTTGGTAATTTTATAAACCAG
42378217 GGGTATTTTGGTAATTTTATAAACCAG
1 GGGTATTTTGGTAATTTTATAAACCAG
* * *
42378244 GGGTATTTTGGTAATTTTGTAAACTAA
1 GGGTATTTTGGTAATTTTATAAACCAG
* * *
42378271 GTGTAGTTTGGTAATTTTACAAACCAG
1 GGGTATTTTGGTAATTTTATAAACCAG
*
42378298 GGGTATTTTGGTGATTT
1 GGGTATTTTGGTAATTT
42378315 GGTAAACTAA
Statistics
Matches: 145, Mismatches: 31, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
27 145 1.00
ACGTcount: A:0.30, C:0.08, G:0.21, T:0.41
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTATAAACCAG
Found at i:42380232 original size:46 final size:46
Alignment explanation
Indices: 42380122--42380250 Score: 170
Period size: 46 Copynumber: 2.8 Consensus size: 46
42380112 TACGAGGAAT
* * * * *
42380122 CCGAACTCGTTGAGTTGCGTTCTGAGTTCACCTATAGATGAAAGCAT
1 CCGAACTCGTTGAGTTGTGTTCCGAGTTCA-TTATGGATGAAAGCAC
*
42380169 CCGAACTCGTTGAGTTGTGTTCCGAGTTCATTATGGATGCGAA-CAC
1 CCGAACTCGTTGAGTTGTGTTCCGAGTTCATTATGGATG-AAAGCAC
*
42380215 CCGAGCTCGTTGAGTTGTGTTCCGAGTTCATTATGG
1 CCGAACTCGTTGAGTTGTGTTCCGAGTTCATTATGG
42380251 GTGAGATTAT
Statistics
Matches: 74, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
46 44 0.59
47 30 0.41
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (46 bp):
CCGAACTCGTTGAGTTGTGTTCCGAGTTCATTATGGATGAAAGCAC
Found at i:42383969 original size:29 final size:29
Alignment explanation
Indices: 42383906--42383973 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
42383896 TAATCAACCG
42383906 CGCACACTTAGTGCCATGCACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
42383935 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
42383964 CGCACACTTA
1 CGCACACTTA
42383974 CCTTTTCCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 3 0.09
29 31 0.91
ACGTcount: A:0.28, C:0.31, G:0.13, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:42384143 original size:29 final size:29
Alignment explanation
Indices: 42384080--42384147 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
42384070 TAATCAACCG
42384080 CGCACACTTAGTGCCATGCACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
42384109 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
42384138 CGCACACTTA
1 CGCACACTTA
42384148 CCTTTTCCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 3 0.09
29 31 0.91
ACGTcount: A:0.28, C:0.31, G:0.13, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:42384288 original size:29 final size:29
Alignment explanation
Indices: 42384249--42384327 Score: 104
Period size: 29 Copynumber: 2.7 Consensus size: 29
42384239 CTTAATAATC
* *
42384249 AACCGCGCACACTTAGTGCCATGCACTTTA
1 AACC-CGCACACTTAGTGCCATACAATTTA
* **
42384279 AACTCGCACACTTAGTGCTGTACAATTTA
1 AACCCGCACACTTAGTGCCATACAATTTA
42384308 AACCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
42384328 ATCTCATGAC
Statistics
Matches: 41, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
29 38 0.93
30 3 0.07
ACGTcount: A:0.29, C:0.32, G:0.15, T:0.24
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATACAATTTA
Found at i:42384321 original size:174 final size:174
Alignment explanation
Indices: 42383795--42384296 Score: 977
Period size: 174 Copynumber: 2.9 Consensus size: 174
42383785 AACTCAAGGT
* *
42383795 ACTTACCTTTTCCGCTGTCCAAAATTGACTCGGTAAAGTCGCACCCTTCATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
42383860 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
42383925 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
131 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
42383969 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
42384034 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
42384099 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
131 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
42384143 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
42384208 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
*
42384273 ACTTTAAACTCGCACACTTAGTGC
131 ACTTTAAACTCACACACTTAGTGC
42384297 TGTACAATTT
Statistics
Matches: 325, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
174 325 1.00
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29
Consensus pattern (174 bp):
ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
Found at i:42387656 original size:49 final size:50
Alignment explanation
Indices: 42387576--42387696 Score: 147
Period size: 49 Copynumber: 2.5 Consensus size: 50
42387566 TCGGGTCTAG
* * *
42387576 GACCTATCTGGGACATGGCATC-GACTCCGATAGATGAGAGCCAGTATAA
1 GACCTGTCTGGGACATGGCATCGGACTCCGATAGATGAAAGCCAATATAA
* * * * *
42387625 GACTTGTCTGGGACATGGCATCGGCCT-CGATATATGAAAGTCAATGTAA
1 GACCTGTCTGGGACATGGCATCGGACTCCGATAGATGAAAGCCAATATAA
*
42387674 GACCTGTCTGGGACACGGCATCG
1 GACCTGTCTGGGACATGGCATCG
42387697 ACTTTAATGT
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
49 58 0.95
50 3 0.05
ACGTcount: A:0.27, C:0.22, G:0.28, T:0.22
Consensus pattern (50 bp):
GACCTGTCTGGGACATGGCATCGGACTCCGATAGATGAAAGCCAATATAA
Found at i:42390467 original size:33 final size:33
Alignment explanation
Indices: 42390425--42390497 Score: 103
Period size: 33 Copynumber: 2.2 Consensus size: 33
42390415 CCGTGTGACC
* *
42390425 CACACGGCCTAGCCACAC-AGGTGTGTGGGATCT
1 CACATGGCCTAGCCACACGA-GCGTGTGGGATCT
*
42390458 CACATGGCCTGGCCACACGAGCGTGTGGGATCT
1 CACATGGCCTAGCCACACGAGCGTGTGGGATCT
42390491 CACATGG
1 CACATGG
42390498 GCGTGAGAGA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
33 35 0.97
34 1 0.03
ACGTcount: A:0.21, C:0.30, G:0.32, T:0.18
Consensus pattern (33 bp):
CACATGGCCTAGCCACACGAGCGTGTGGGATCT
Found at i:42390832 original size:26 final size:26
Alignment explanation
Indices: 42390794--42390863 Score: 81
Period size: 26 Copynumber: 2.7 Consensus size: 26
42390784 TTAATCACCC
42390794 TATTT-TTATTTTATTTTATTTTATT-T
1 TATTTATTA-TTTATTTTATTTT-TTAT
*
42390820 TATTTATTATTTATTATATTTTTTAT
1 TATTTATTATTTATTTTATTTTTTAT
* *
42390846 TTTTTATTTTTTATTTTA
1 TATTTATTATTTATTTTA
42390864 CTAACTTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
25 2 0.05
26 33 0.87
27 3 0.08
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (26 bp):
TATTTATTATTTATTTTATTTTTTAT
Found at i:42390847 original size:23 final size:21
Alignment explanation
Indices: 42390796--42390862 Score: 68
Period size: 23 Copynumber: 3.1 Consensus size: 21
42390786 AATCACCCTA
42390796 TTTTTA-TT-TTATTTTATT-T
1 TTTTTATTTATTATTTT-TTAT
42390815 TATTTTATTTATTATTTATTATAT
1 T-TTTTATTTATTATTT-TT-TAT
*
42390839 TTTTTATTTTTTATTTTTTAT
1 TTTTTATTTATTATTTTTTAT
42390860 TTT
1 TTT
42390863 ACTAACTTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
19 1 0.02
20 5 0.12
21 8 0.20
22 9 0.22
23 16 0.39
24 2 0.05
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (21 bp):
TTTTTATTTATTATTTTTTAT
Found at i:42390876 original size:43 final size:43
Alignment explanation
Indices: 42390796--42390894 Score: 112
Period size: 43 Copynumber: 2.3 Consensus size: 43
42390786 AATCACCCTA
* *
42390796 TTTTTATTTTATTTTATTTTATTTTATTTATTATTTATTATAT
1 TTTTTATTTTATTTTATTTTATTTTACTAATTATTTATTATAT
* *
42390839 TTTTTATTTT-TTATT-TTTTATTTTACTAACTTTTTTATTTTAT
1 TTTTTATTTTATT-TTATTTTATTTTACTAA-TTATTTATTATAT
*
42390882 TTATTATTCTTAT
1 TTTTTATT-TTAT
42390895 ACTTATATTT
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
42 14 0.30
43 30 0.64
44 2 0.04
45 1 0.02
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (43 bp):
TTTTTATTTTATTTTATTTTATTTTACTAATTATTTATTATAT
Found at i:42390879 original size:7 final size:7
Alignment explanation
Indices: 42390802--42390862 Score: 70
Period size: 7 Copynumber: 8.3 Consensus size: 7
42390792 CCTATTTTTA
42390802 TTTTATT
1 TTTTATT
42390809 TTATT-TT
1 TT-TTATT
42390816 ATTTTATT
1 -TTTTATT
*
42390824 TATTATT
1 TTTTATT
42390831 TATTATATT
1 T-TT-TATT
42390840 TTTTATT
1 TTTTATT
42390847 TTTTATT
1 TTTTATT
42390854 TTTTATT
1 TTTTATT
42390861 TT
1 TT
42390863 ACTAACTTTT
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
7 33 0.70
8 9 0.19
9 5 0.11
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (7 bp):
TTTTATT
Done.