Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012099.1 Kokia drynarioides strain JFW-HI SEQ_127098, whole genome shotgun sequence
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: 338792
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 49 characters in sequence are not A, C, G, or T
Found at i:663 original size:23 final size:23
Alignment explanation
Indices: 537--662 Score: 164
Period size: 23 Copynumber: 5.4 Consensus size: 23
527 AGGTGTTGGG
*
537 AAACAGAGAGCACACACAGTGCT
1 AAACAGAGAACACACACAGTGCT
*
560 AAACAGAGAACACACAAAGTGCT
1 AAACAGAGAACACACACAGTGCT
*
583 AATCAGAGAACACACACAGTGCT
1 AAACAGAGAACACACACAGTGCT
*
606 AATCAGAGAACACACACAGTGCT
1 AAACAGAGAACACACACAGTGCT
* *
629 AATAACAGAGAGCACTAGAC-GTGCT
1 -A-AACAGAGAACAC-ACACAGTGCT
654 AAACAGAGA
1 AAACAGAGA
663 GAGCGCTAGT
Statistics
Matches: 93, Mismatches: 7, Indels: 6
0.88 0.07 0.06
Matches are distributed among these distances:
23 73 0.78
24 2 0.02
25 15 0.16
26 3 0.03
ACGTcount: A:0.46, C:0.23, G:0.20, T:0.11
Consensus pattern (23 bp):
AAACAGAGAACACACACAGTGCT
Found at i:5713 original size:21 final size:21
Alignment explanation
Indices: 5689--5765 Score: 50
Period size: 21 Copynumber: 3.5 Consensus size: 21
5679 CCTGCAACTT
5689 CTACCGATACATGCATACAAA
1 CTACCGATACATGCATACAAA
* *
5710 CTACTGAAACAT-CAATACACATAA
1 CTACCGATACATGC-AT--ACA-AA
* * *
5734 CTACCGATACTTGTA-ATCCAA
1 CTACCGATACATGCATA-CAAA
5755 CTACCGATACA
1 CTACCGATACA
5766 ACTCAAGTCA
Statistics
Matches: 42, Mismatches: 8, Indels: 12
0.68 0.13 0.19
Matches are distributed among these distances:
20 1 0.02
21 25 0.60
22 1 0.02
23 3 0.07
24 12 0.29
ACGTcount: A:0.42, C:0.29, G:0.08, T:0.22
Consensus pattern (21 bp):
CTACCGATACATGCATACAAA
Found at i:11170 original size:23 final size:23
Alignment explanation
Indices: 11140--11188 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
11130 TAAAACTAAG
11140 TAAGAAATGTCTATCATGCATGC
1 TAAGAAATGTCTATCATGCATGC
11163 TAAGAAATGTCTATCATGCATGC
1 TAAGAAATGTCTATCATGCATGC
11186 TAA
1 TAA
11189 ATATACCATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (23 bp):
TAAGAAATGTCTATCATGCATGC
Found at i:15260 original size:24 final size:24
Alignment explanation
Indices: 15233--15287 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
15223 AATGCTTCTA
*
15233 TCTTTTTCCCCAATTCTGAATTTT
1 TCTTTTCCCCCAATTCTGAATTTT
15257 TCTTTTCCCCCAATTCTGAATTTT
1 TCTTTTCCCCCAATTCTGAATTTT
15281 TCTTTTC
1 TCTTTTC
15288 AAAGTCTTGC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.15, C:0.27, G:0.04, T:0.55
Consensus pattern (24 bp):
TCTTTTCCCCCAATTCTGAATTTT
Found at i:16688 original size:63 final size:65
Alignment explanation
Indices: 16555--16739 Score: 268
Period size: 63 Copynumber: 2.9 Consensus size: 65
16545 CCAATTCTAT
* *
16555 TTTTCTTATTTATTTATAATTTTATGAATATAAATAAATAAATAAATATAAAAAATATTAATTTT
1 TTTTATTATTTATTTATTATTTTATGAATATAAATAAATAAAT-AATATAAAAAATATTAATTTT
*
16620 G
65 A
* * *
16621 TTTTATTATTTATTTATTATTGTATGAATATAAATAAATAAAT-GTA-AAATAATATTAATTTTA
1 TTTTATTATTTATTTATTATTTTATGAATATAAATAAATAAATAATATAAAAAATATTAATTTTA
*
16684 TTTTATTATTTATTTATTATTTTATGAATATAGATAAATAAATAA-ATAAATAAATA
1 TTTTATTATTTATTTATTATTTTATGAATATAAATAAATAAATAATATAAA-AAATA
16740 ATAAACCCAA
Statistics
Matches: 106, Mismatches: 10, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
63 57 0.54
64 5 0.05
65 4 0.04
66 40 0.38
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.49
Consensus pattern (65 bp):
TTTTATTATTTATTTATTATTTTATGAATATAAATAAATAAATAATATAAAAAATATTAATTTTA
Found at i:19169 original size:21 final size:21
Alignment explanation
Indices: 19143--19185 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
19133 AAATGCGTAG
19143 GTTCTCTGTGGTACATTTGTT
1 GTTCTCTGTGGTACATTTGTT
*
19164 GTTCTCTGTGGTATATTTGTT
1 GTTCTCTGTGGTACATTTGTT
19185 G
1 G
19186 ATACATTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.09, C:0.12, G:0.26, T:0.53
Consensus pattern (21 bp):
GTTCTCTGTGGTACATTTGTT
Found at i:28829 original size:40 final size:40
Alignment explanation
Indices: 28774--29265 Score: 378
Period size: 40 Copynumber: 12.4 Consensus size: 40
28764 GAAGTCACCT
* * *
28774 CATCCAATCTCTTACCCCAACCATGGGGCAGATTGAAGAC
1 CATCCAATCTTTTACCCTAATCATGGGGCAGATTGAAGAC
* * *
28814 CATCCAATCTTTTACCCCAATCATGGGGAAAATTGAAG-C
1 CATCCAATCTTTTACCCTAATCATGGGGCAGATTGAAGAC
* * * **
28853 AATTCAATCTGTTACCCCGATCATGGGGGCAGATTGAAG-C
1 CATCCAATCTTTTACCCTAATCAT-GGGGCAGATTGAAGAC
* *
28893 AATCCAATATTTTACCCTAATCA-GAGGGCAGATTGAAGAC
1 CATCCAATCTTTTACCCTAATCATG-GGGCAGATTGAAGAC
* ** ** * *
28933 CGTTTAATCTTTTACCCTAATCAAAGGGTAGATTGAAGGC
1 CATCCAATCTTTTACCCTAATCATGGGGCAGATTGAAGAC
* * * *
28973 CATCCAATCTTTTACTCTAATTA-GAGAGTAGATTGAAGAC
1 CATCCAATCTTTTACCCTAATCATG-GGGCAGATTGAAGAC
* * *
29013 CAACCAATCTTTTACCCTAACCATGGGGTAGATTGAAG--
1 CATCCAATCTTTTACCCTAATCATGGGGCAGATTGAAGAC
* * *
29051 C-TCCAATCTTTTACCCCT-ACCATGAGGCAAATTGAAG-C
1 CATCCAATCTTTTA-CCCTAATCATGGGGCAGATTGAAGAC
* * * * * *
29089 AATCTAATCTTTTATCCTAATTA-GAGGGCAAATTGAAGAT
1 CATCCAATCTTTTACCCTAATCATG-GGGCAGATTGAAGAC
* *
29129 CATCCAATCTTTTACCATAATCA-GAGGGCAGATTGAAGAT
1 CATCCAATCTTTTACCCTAATCATG-GGGCAGATTGAAGAC
* * * * * *
29169 TATTCAATCTTTTACCCTGATTATGGGGCAAACTGAAG-C
1 CATCCAATCTTTTACCCTAATCATGGGGCAGATTGAAGAC
* * ** * *
29208 AATCCAATCTTTTACCCTAACCAAAGGGCAGATTAAAGAT
1 CATCCAATCTTTTACCCTAATCATGGGGCAGATTGAAGAC
* *
29248 CATCCAAACTTTTTCCCT
1 CATCCAATCTTTTACCCT
29266 TAAAGTTATG
Statistics
Matches: 363, Mismatches: 75, Indels: 28
0.78 0.16 0.06
Matches are distributed among these distances:
37 27 0.07
38 10 0.03
39 87 0.24
40 237 0.65
41 2 0.01
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.28
Consensus pattern (40 bp):
CATCCAATCTTTTACCCTAATCATGGGGCAGATTGAAGAC
Found at i:29138 original size:156 final size:157
Alignment explanation
Indices: 28799--29224 Score: 371
Period size: 156 Copynumber: 2.7 Consensus size: 157
28789 CCCAACCATG
* ** * * * *
28799 GGGCAGATTGAAGACCATCCAATCTTTTACCCCAATCATG-GGGAAAATTGAAG--CAATTCAAT
1 GGGCAAATTGAAGACCATCCAATCTTTTACCATAATCA-GAGAGCAGATTGAAGACCAA-CCAAT
* ** * * * * * *
28861 CTGTTACCCCGATCATGGGGGCAGATTGAAGCAATCCAATATTTTA-CCCTAATCA-GAGGGCAG
64 CTTTTACCCTAACCAT-GGGGCAAACTGAAGC-ATCCAATCTTTTACCCCT-ACCATGA-GGCAA
** *
28924 ATTGAAGACCGTTTAATCTTTTACCCTAATCAAA
125 ATTGAAG-CAATCTAATCTTTTACCCTAATCAAA
* * * * *
28958 GGGTAGATTGAAGGCCATCCAATCTTTTACTC-TAATTAGAGAGTAGATTGAAGACCAACCAATC
1 GGGCAAATTGAAGACCATCCAATCTTTTAC-CATAATCAGAGAGCAGATTGAAGACCAACCAATC
* * *
29022 TTTTACCCTAACCATGGGGTAGATTGAAGC-TCCAATCTTTTACCCCTACCATGAGGCAAATTGA
65 TTTTACCCTAACCATGGGGCAAACTGAAGCATCCAATCTTTTACCCCTACCATGAGGCAAATTGA
* * *
29086 AGCAATCTAATCTTTTATCCTAATTAGA
130 AGCAATCTAATCTTTTACCCTAATCAAA
* * ** **
29114 GGGCAAATTGAAGATCATCCAATCTTTTACCATAATCAGAGGGCAGATTGAAGATTATTCAATCT
1 GGGCAAATTGAAGACCATCCAATCTTTTACCATAATCAGAGAGCAGATTGAAGACCAACCAATCT
* **
29179 TTTACCCTGATTATGGGGCAAACTGAAGCAATCCAATCTTTTACCC
66 TTTACCCTAACCATGGGGCAAACTGAAGC-ATCCAATCTTTTACCC
29225 TAACCAAAGG
Statistics
Matches: 219, Mismatches: 39, Indels: 19
0.79 0.14 0.07
Matches are distributed among these distances:
155 1 0.00
156 95 0.43
157 25 0.11
158 22 0.10
159 56 0.26
160 17 0.08
161 3 0.01
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (157 bp):
GGGCAAATTGAAGACCATCCAATCTTTTACCATAATCAGAGAGCAGATTGAAGACCAACCAATCT
TTTACCCTAACCATGGGGCAAACTGAAGCATCCAATCTTTTACCCCTACCATGAGGCAAATTGAA
GCAATCTAATCTTTTACCCTAATCAAA
Found at i:29227 original size:119 final size:119
Alignment explanation
Indices: 28773--29265 Score: 471
Period size: 119 Copynumber: 4.2 Consensus size: 119
28763 CGAAGTCACC
* * *
28773 TCATCCAATCTCTTACCCCAACCATGGGGCAGATTGAAGACCATCCAATCTTTTACCCCAATCAT
1 TCATCCAATCTTTTACCCTAACCATGGGGCAGATTGAAGACCATCCAATCTTTTACCCTAATCAT
* * * ** *
28838 GGGGAAAATTGAAGCAATTCAATCTGTTACCCCGATCATGGGGGCAGATTGAAG-
66 GGGGCAAATTGAAGCAATCCAATCTTTTACCCTAATCA-GAGGGCAGATTGAAGA
* * * **
28892 -CAATCCAATATTTTACCCTAATCA-GAGGGCAGATTGAAGACCGTTTAATCTTTTACCCTAATC
1 TC-ATCCAATCTTTTACCCTAACCATG-GGGCAGATTGAAGACCATCCAATCTTTTACCCTAATC
** * * * * * * *
28955 AAAGGGTAGATTGAAGGCCATCCAATCTTTTACTCTAATTAGAGAGTAGATTGAAGA
64 ATGGGGCAAATTGAA-GCAATCCAATCTTTTACCCTAATCAGAGGGCAGATTGAAGA
* * * *
29012 CCAACCAATCTTTTACCCTAACCATGGGGTAGATTGAAG--C-TCCAATCTTTTACCCCT-ACCA
1 TCATCCAATCTTTTACCCTAACCATGGGGCAGATTGAAGACCATCCAATCTTTTA-CCCTAATCA
* * * * *
29073 TGAGGCAAATTGAAGCAATCTAATCTTTTATCCTAATTAGAGGGCAAATTGAAGA
65 TGGGGCAAATTGAAGCAATCCAATCTTTTACCCTAATCAGAGGGCAGATTGAAGA
* * ** * * *
29128 TCATCCAATCTTTTACCATAATCA-GAGGGCAGATTGAAGATTATTCAATCTTTTACCCTGATTA
1 TCATCCAATCTTTTACCCTAACCATG-GGGCAGATTGAAGACCATCCAATCTTTTACCCTAATCA
* * * *
29192 TGGGGCAAACTGAAGCAATCCAATCTTTTACCCTAACCAAAGGGCAGATTAAAGA
65 TGGGGCAAATTGAAGCAATCCAATCTTTTACCCTAATCAGAGGGCAGATTGAAGA
* *
29247 TCATCCAAACTTTTTCCCT
1 TCATCCAATCTTTTACCCT
29266 TAAAGTTATG
Statistics
Matches: 300, Mismatches: 62, Indels: 24
0.78 0.16 0.06
Matches are distributed among these distances:
115 1 0.00
116 66 0.22
117 22 0.07
118 11 0.04
119 149 0.50
120 49 0.16
121 2 0.01
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.28
Consensus pattern (119 bp):
TCATCCAATCTTTTACCCTAACCATGGGGCAGATTGAAGACCATCCAATCTTTTACCCTAATCAT
GGGGCAAATTGAAGCAATCCAATCTTTTACCCTAATCAGAGGGCAGATTGAAGA
Found at i:33750 original size:21 final size:22
Alignment explanation
Indices: 33726--33778 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
33716 TTGTGCTAGC
33726 TCTACCGATACAAGT-ATG-AA
1 TCTACCGATACAAGTCATGCAA
*
33746 TTCTACTGATACAAGTCATGCAA
1 -TCTACCGATACAAGTCATGCAA
33769 -CTACCGATAC
1 TCTACCGATAC
33779 CAAAAACTCC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 23 0.82
22 3 0.11
23 2 0.07
ACGTcount: A:0.36, C:0.25, G:0.13, T:0.26
Consensus pattern (22 bp):
TCTACCGATACAAGTCATGCAA
Found at i:46727 original size:21 final size:20
Alignment explanation
Indices: 46681--46733 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 20
46671 TTGTGCTAGC
46681 TCTACCGATACAAGTATGAA
1 TCTACCGATACAAGTATGAA
*
46701 TTCTACTGATACAAGTCATGCAA
1 -TCTACCGATACAAGT-ATG-AA
46724 -CTACCGATAC
1 TCTACCGATAC
46734 CAAAAACTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 23 0.82
22 3 0.11
23 2 0.07
ACGTcount: A:0.36, C:0.25, G:0.13, T:0.26
Consensus pattern (20 bp):
TCTACCGATACAAGTATGAA
Found at i:48887 original size:30 final size:30
Alignment explanation
Indices: 48851--48966 Score: 146
Period size: 30 Copynumber: 3.9 Consensus size: 30
48841 CATTAAAATT
48851 GGGTCAAATTTGAATTTTTGGAAAGTTCAA
1 GGGTCAAATTTGAATTTTTGGAAAGTTCAA
*
48881 GGGTCAAATTTGAATTTTTAGG-AAGTTCGA
1 GGGTCAAATTTGAATTTTT-GGAAAGTTCAA
* * * *
48911 -GGTTAAATTAGAATTTTTGGAAAGTTTAG
1 GGGTCAAATTTGAATTTTTGGAAAGTTCAA
* *
48940 GGGTTAAATTTAAATTTTTGGAAAGTT
1 GGGTCAAATTTGAATTTTTGGAAAGTT
48967 TAGGGGTAAA
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
28 2 0.03
29 21 0.28
30 50 0.67
31 2 0.03
ACGTcount: A:0.33, C:0.03, G:0.24, T:0.40
Consensus pattern (30 bp):
GGGTCAAATTTGAATTTTTGGAAAGTTCAA
Found at i:48986 original size:30 final size:30
Alignment explanation
Indices: 48922--48987 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 30
48912 GTTAAATTAG
* **
48922 AATTTTTGGAAAGTTTAGGGGTTAAATTTA
1 AATTTTTGGAAAGTTTAGGGGTAAAACATA
48952 AATTTTTGGAAAGTTTAGGGGTAAAAACAT-
1 AATTTTTGGAAAGTTTAGGGGT-AAAACATA
48982 AATTTT
1 AATTTT
48988 AAAATAAAGC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
30 28 0.88
31 4 0.12
ACGTcount: A:0.36, C:0.02, G:0.21, T:0.41
Consensus pattern (30 bp):
AATTTTTGGAAAGTTTAGGGGTAAAACATA
Found at i:50623 original size:4 final size:4
Alignment explanation
Indices: 50600--50637 Score: 58
Period size: 4 Copynumber: 9.0 Consensus size: 4
50590 GTGTATATAA
50600 ATTT ATATT ATTT ATATT ATTT ATTT ATTT ATTT ATTT
1 ATTT AT-TT ATTT AT-TT ATTT ATTT ATTT ATTT ATTT
50638 TTGGGTTATA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
4 24 0.75
5 8 0.25
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (4 bp):
ATTT
Found at i:50629 original size:8 final size:9
Alignment explanation
Indices: 50600--50637 Score: 62
Period size: 9 Copynumber: 4.4 Consensus size: 9
50590 GTGTATATAA
50600 ATTTATATT
1 ATTTATATT
50609 ATTTATATT
1 ATTTATATT
50618 ATTTAT-TT
1 ATTTATATT
50626 ATTTAT-TT
1 ATTTATATT
50634 ATTT
1 ATTT
50638 TTGGGTTATA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
8 14 0.48
9 15 0.52
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (9 bp):
ATTTATATT
Found at i:51519 original size:60 final size:60
Alignment explanation
Indices: 51409--51735 Score: 288
Period size: 60 Copynumber: 5.5 Consensus size: 60
51399 GGTGGTGTTT
* * *
51409 GTAGCCCCAAGTGATCAGCAACAACATTTGAGGAGCTACCCTCCCCAAATGAAGGCCTTG
1 GTAGCCCCAAGTGATCAACAACAACATTTGAGGAGCTACCCTCACTAAATGAAGGCCTTG
* * * *
51469 GCAGCCCCAAATGATCAACAACAACAGTTGAGGAG-TGACCTTCACTAAATGGAA-GCCTTG
1 GTAGCCCCAAGTGATCAACAACAACATTTGAGGAGCT-ACCCTCACTAAAT-GAAGGCCTTG
* * * * * *
51529 GTTGTCCTAAGTGATCAA-AACCAACATTTAAAGAGCTACCCTCACTAAATGAAGGCATTG
1 GTAGCCCCAAGTGATCAACAA-CAACATTTGAGGAGCTACCCTCACTAAATGAAGGCCTTG
* * * **
51589 GTAGCCCTAAGTGATCAACAACAACATTTGAGGTGCTACCCTCACCAGCT-AGAGGCCTTG
1 GTAGCCCCAAGTGATCAACAACAACATTTGAGGAGCTACCCTCACTAAATGA-AGGCCTTG
* ** * * * * *
51649 GTAGTCCCAAGCCAT-AAGCAACAACATTTGAGGAGTTGTCCAT-ACCAAATGGAGGCCTTG
1 GTAGCCCCAAGTGATCAA-CAACAACATTTGAGGAGCT-ACCCTCACTAAATGAAGGCCTTG
* * * *
51709 GCAGCCCCAAGCGATCAATAGCAACAT
1 GTAGCCCCAAGTGATCAACAACAACAT
51736 CAGAAGAGCT
Statistics
Matches: 214, Mismatches: 42, Indels: 22
0.77 0.15 0.08
Matches are distributed among these distances:
59 9 0.04
60 194 0.91
61 11 0.05
ACGTcount: A:0.33, C:0.26, G:0.21, T:0.20
Consensus pattern (60 bp):
GTAGCCCCAAGTGATCAACAACAACATTTGAGGAGCTACCCTCACTAAATGAAGGCCTTG
Found at i:51745 original size:180 final size:180
Alignment explanation
Indices: 51409--51746 Score: 396
Period size: 180 Copynumber: 1.9 Consensus size: 180
51399 GGTGGTGTTT
* *
51409 GTAGCCCCAAGTGATCAGCAACAACATTTGAGGAGCTACCCTCCCCAAATGAAGGCCTTGGCAGC
1 GTAGCCCCAAGTGATCAACAACAACATTTGAGGAGCTACCCTCACCAAATGAAGGCCTTGGCAGC
** * * ** * *
51474 CCCAAATGATCAACAACAACAGTTGAGGAGTGACCTTCACTAAATGGAAGCCTTGGTTGTCCTAA
66 CCCAAACCATCAACAACAACAGTTGAGGAGTGACCATCACCAAATGGAAGCCTTGGCAGCCCCAA
* *
51539 GTGATCAAAACCAACATTTAAAGAGCTACCCTCACTAAATGAAGGCATTG
131 GCGATCAAAACCAACATTCAAAGAGCTACCCTCACTAAATGAAGGCATTG
* * ** *
51589 GTAGCCCTAAGTGATCAACAACAACATTTGAGGTGCTACCCTCACCAGCT-AGAGGCCTTGGTAG
1 GTAGCCCCAAGTGATCAACAACAACATTTGAGGAGCTACCCTCACCAAATGA-AGGCCTTGGCAG
* * * * *
51653 TCCCAAGCCAT-AAGCAACAACATTTGAGGAGTTGTCCAT-ACCAAATGGAGGCCTTGGCAGCCC
65 CCCCAAACCATCAA-CAACAACAGTTGAGGAG-TGACCATCACCAAATGGAAGCCTTGGCAGCCC
* *
51716 CAAGCGATCAATAGCAACA-TCAGAAGAGCTA
128 CAAGCGATCAAAACCAACATTCA-AAGAGCTA
51747 ACATCACCAA
Statistics
Matches: 130, Mismatches: 24, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
179 5 0.04
180 120 0.92
181 5 0.04
ACGTcount: A:0.33, C:0.26, G:0.21, T:0.20
Consensus pattern (180 bp):
GTAGCCCCAAGTGATCAACAACAACATTTGAGGAGCTACCCTCACCAAATGAAGGCCTTGGCAGC
CCCAAACCATCAACAACAACAGTTGAGGAGTGACCATCACCAAATGGAAGCCTTGGCAGCCCCAA
GCGATCAAAACCAACATTCAAAGAGCTACCCTCACTAAATGAAGGCATTG
Found at i:61177 original size:93 final size:93
Alignment explanation
Indices: 61018--61204 Score: 365
Period size: 93 Copynumber: 2.0 Consensus size: 93
61008 CATAAGATAA
*
61018 AATAGGATCATATTGGGAGAACATATATTATCCCAAAGAGATCAATGATATTCTATGAGGGTAAT
1 AATAGGATCATATTGGGAGAACATATATTATCCCAAAGAGATCAATGATATTCTATGAGAGTAAT
61083 ACACTTATGACAAGGTCATTGGACGAGC
66 ACACTTATGACAAGGTCATTGGACGAGC
61111 AATAGGATCATATTGGGAGAACATATATTATCCCAAAGAGATCAATGATATTCTATGAGAGTAAT
1 AATAGGATCATATTGGGAGAACATATATTATCCCAAAGAGATCAATGATATTCTATGAGAGTAAT
61176 ACACTTATGACAAGGTCATTGGACGAGC
66 ACACTTATGACAAGGTCATTGGACGAGC
61204 A
1 A
61205 TTGAGTAGTT
Statistics
Matches: 93, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 93 1.00
ACGTcount: A:0.39, C:0.14, G:0.21, T:0.27
Consensus pattern (93 bp):
AATAGGATCATATTGGGAGAACATATATTATCCCAAAGAGATCAATGATATTCTATGAGAGTAAT
ACACTTATGACAAGGTCATTGGACGAGC
Found at i:61719 original size:27 final size:26
Alignment explanation
Indices: 61664--61718 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
61654 AGTTTTATCG
* *
61664 AAATTTTATCAGGGATAAAACCGTCA
1 AAATTTTACCAGGGATAAAACCATCA
*
61690 AAATTTTACCGAGGG-TAAAATCATCA
1 AAATTTTACC-AGGGATAAAACCATCA
61716 AAA
1 AAA
61719 AAAATTGGAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 21 0.84
27 4 0.16
ACGTcount: A:0.45, C:0.15, G:0.15, T:0.25
Consensus pattern (26 bp):
AAATTTTACCAGGGATAAAACCATCA
Found at i:64106 original size:79 final size:79
Alignment explanation
Indices: 63964--64163 Score: 219
Period size: 79 Copynumber: 2.5 Consensus size: 79
63954 TCATGACACT
* ** * *
63964 TAGTGCCTAGCGGATAAACTGCAAGTGTGAGCCTAGCTTTAGTTGGATTAGCCAACAACGTCCGT
1 TAGTGCCTAGCGGATAAACCGCAAAAGTGAGCCTAGCTCTAGTTGGATTAACCAACAACGTCCGT
*
64029 AAAATCTTGGCATCC
66 AAAATCTTGG-AACC
* * *
64044 -AGTGCCTAGCGGATAAACCGCAAAAGCT-AG-CTCAGCTCTAGTTGGATTAACTATCAATGTCC
1 TAGTGCCTAGCGGATAAACCGCAAAAG-TGAGCCT-AGCTCTAGTTGGATTAACCAACAACGTCC
*
64106 GTTAAATCTTGGAACC
64 GTAAAATCTTGGAACC
* * * *
64122 TAATGCCTAGCGGTTAAACCG-TAATGTGAGCCTAGCTCTAGT
1 TAGTGCCTAGCGGATAAACCGCAAAAGTGAGCCTAGCTCTAGT
64164 CAGTTAAACT
Statistics
Matches: 101, Mismatches: 14, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
77 1 0.01
78 19 0.19
79 80 0.79
80 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.27
Consensus pattern (79 bp):
TAGTGCCTAGCGGATAAACCGCAAAAGTGAGCCTAGCTCTAGTTGGATTAACCAACAACGTCCGT
AAAATCTTGGAACC
Found at i:74469 original size:13 final size:13
Alignment explanation
Indices: 74451--74485 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
74441 GCAAATATTT
74451 TTTTCTTCTTTTA
1 TTTTCTTCTTTTA
74464 TTTTC-TCTTTTA
1 TTTTCTTCTTTTA
74476 TTTT-TTCTTT
1 TTTTCTTCTTT
74486 CTTTTTCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 16 0.76
13 5 0.24
ACGTcount: A:0.06, C:0.14, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTCTTCTTTTA
Found at i:74474 original size:12 final size:12
Alignment explanation
Indices: 74451--74499 Score: 55
Period size: 12 Copynumber: 3.9 Consensus size: 12
74441 GCAAATATTT
74451 TTTTCTTCTTTTA
1 TTTTC-TCTTTTA
74464 TTTTCTCTTTTA
1 TTTTCTCTTTTA
*
74476 TTTTTTCTTTCT-
1 TTTTCTCTTT-TA
74488 TTTTCTCATTTT
1 TTTTCTC-TTTT
74500 CCTTTTCTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
12 23 0.72
13 9 0.28
ACGTcount: A:0.06, C:0.16, G:0.00, T:0.78
Consensus pattern (12 bp):
TTTTCTCTTTTA
Found at i:74491 original size:24 final size:26
Alignment explanation
Indices: 74451--74499 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 26
74441 GCAAATATTT
74451 TTTTCTTCTTTTATTTTCTC-TTTTA
1 TTTTCTTCTTTTATTTTCTCATTTTA
74476 TTTT-TTCTTTCT-TTTTCTCATTTT
1 TTTTCTTCTTT-TATTTTCTCATTTT
74500 CCTTTTCTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 13 0.59
25 9 0.41
ACGTcount: A:0.06, C:0.16, G:0.00, T:0.78
Consensus pattern (26 bp):
TTTTCTTCTTTTATTTTCTCATTTTA
Found at i:74500 original size:14 final size:13
Alignment explanation
Indices: 74450--74507 Score: 50
Period size: 12 Copynumber: 4.5 Consensus size: 13
74440 AGCAAATATT
74450 TTTTTCTTCTTTT-
1 TTTTTC-TCTTTTC
* *
74463 ATTTTCTCTTTTA
1 TTTTTCTCTTTTC
74476 TTTTT-TC-TTTC
1 TTTTTCTCTTTTC
74487 TTTTTCTCATTTTC
1 TTTTTCTC-TTTTC
*
74501 CTTTTCT
1 TTTTTCT
74508 AAGTGACTGA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
11 8 0.22
12 10 0.27
13 9 0.24
14 10 0.27
ACGTcount: A:0.05, C:0.19, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTTCTCTTTTC
Found at i:74505 original size:31 final size:30
Alignment explanation
Indices: 74448--74505 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 30
74438 ACAGCAAATA
74448 TTTTTTTCTTCTTTTATTTTCTCTTTTATT
1 TTTTTTTCTTCTTTTATTTTCTCTTTTATT
74478 TTTTCTTTCTT-TTTCTCATTTTC-CTTTT
1 TTTT-TTTCTTCTTT-T-ATTTTCTCTTTT
74506 CTAAGTGACT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
30 7 0.28
31 12 0.48
32 6 0.24
ACGTcount: A:0.05, C:0.17, G:0.00, T:0.78
Consensus pattern (30 bp):
TTTTTTTCTTCTTTTATTTTCTCTTTTATT
Found at i:90355 original size:24 final size:24
Alignment explanation
Indices: 90309--90355 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
90299 GCAAAATGCA
*
90309 TGTAACTCCTACTCATGATTTTTT
1 TGTAACTCCTACTCATGAATTTTT
*
90333 TGTAACTCCTCACT-TTGAATTTT
1 TGTAACTCCT-ACTCATGAATTTT
90356 GAAAATATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 17 0.85
25 3 0.15
ACGTcount: A:0.21, C:0.21, G:0.09, T:0.49
Consensus pattern (24 bp):
TGTAACTCCTACTCATGAATTTTT
Found at i:90639 original size:14 final size:14
Alignment explanation
Indices: 90620--90652 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
90610 TCACCACCCT
90620 ACCACCAT-CAAATC
1 ACCACCATAC-AATC
90634 ACCACCATACAATC
1 ACCACCATACAATC
90648 ACCAC
1 ACCAC
90653 ACCACCACCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 17 0.94
15 1 0.06
ACGTcount: A:0.42, C:0.45, G:0.00, T:0.12
Consensus pattern (14 bp):
ACCACCATACAATC
Found at i:90658 original size:22 final size:22
Alignment explanation
Indices: 90633--90694 Score: 106
Period size: 22 Copynumber: 2.8 Consensus size: 22
90623 ACCATCAAAT
* *
90633 CACCACCATACAATCACCACAC
1 CACCACCATTCAACCACCACAC
90655 CACCACCATTCAACCACCACAC
1 CACCACCATTCAACCACCACAC
90677 CACCACCATTCAACCACC
1 CACCACCATTCAACCACC
90695 GTAGCATCAC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.37, C:0.53, G:0.00, T:0.10
Consensus pattern (22 bp):
CACCACCATTCAACCACCACAC
Found at i:90661 original size:11 final size:11
Alignment explanation
Indices: 90601--90684 Score: 53
Period size: 11 Copynumber: 7.6 Consensus size: 11
90591 ACACCTAACA
* *
90601 ACCACCAAATC
1 ACCACCACACC
90612 ACCACC-CTACC
1 ACCACCAC-ACC
* * *
90623 ACCATCAAATC
1 ACCACCACACC
* *
90634 ACCACCATACA
1 ACCACCACACC
*
90645 ATCACCACACC
1 ACCACCACACC
** *
90656 ACCACCATTCA
1 ACCACCACACC
90667 ACCACCACACC
1 ACCACCACACC
90678 ACCACCA
1 ACCACCA
90685 TTCAACCACC
Statistics
Matches: 52, Mismatches: 19, Indels: 4
0.69 0.25 0.05
Matches are distributed among these distances:
11 52 1.00
ACGTcount: A:0.39, C:0.51, G:0.00, T:0.10
Consensus pattern (11 bp):
ACCACCACACC
Found at i:90692 original size:11 final size:11
Alignment explanation
Indices: 90656--90694 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
90646 TCACCACACC
90656 ACCACCATTCA
1 ACCACCATTCA
** *
90667 ACCACCACACC
1 ACCACCATTCA
90678 ACCACCATTCA
1 ACCACCATTCA
90689 ACCACC
1 ACCACC
90695 GTAGCATCAC
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.36, C:0.54, G:0.00, T:0.10
Consensus pattern (11 bp):
ACCACCATTCA
Found at i:92308 original size:30 final size:30
Alignment explanation
Indices: 92266--92420 Score: 142
Period size: 29 Copynumber: 5.2 Consensus size: 30
92256 CATTAAAATC
**
92266 GGGTCAAAATTTGAATTTTTAAAAAGTTTGG
1 GGGTC-AAATTTGAATTTTTGGAAAGTTTGG
* *
92297 GGGTCAAATTTGAATTTTTTGAAAATTT-G
1 GGGTCAAATTTGAATTTTTGGAAAGTTTGG
*
92326 GGGT-AAGATTTTG-ATTTTTGGAAA-TTTCG
1 GGGTCAA-A-TTTGAATTTTTGGAAAGTTTGG
* * **
92355 GGGTAAAATTGGAATTTTTGGAAAGTTTAA
1 GGGTCAAATTTGAATTTTTGGAAAGTTTGG
*
92385 GGGT-AAAATTGAAATTTTT-GAAAGTTTGG
1 GGGTCAAATTTG-AATTTTTGGAAAGTTTGG
92414 GGGTCAA
1 GGGTCAA
92421 CTTAATTTTA
Statistics
Matches: 105, Mismatches: 11, Indels: 17
0.79 0.08 0.13
Matches are distributed among these distances:
28 8 0.08
29 50 0.48
30 42 0.40
31 5 0.05
ACGTcount: A:0.32, C:0.03, G:0.26, T:0.39
Consensus pattern (30 bp):
GGGTCAAATTTGAATTTTTGGAAAGTTTGG
Found at i:92329 original size:29 final size:29
Alignment explanation
Indices: 92266--92420 Score: 129
Period size: 30 Copynumber: 5.2 Consensus size: 29
92256 CATTAAAATC
*
92266 GGGTCAAAATTTGAATTTTTAAAAAGTTTGG
1 GGGTC-AAATTTGAATTTTTGAAAA-TTTGG
92297 GGGTCAAATTTGAATTTTTTGAAAATTT-G
1 GGGTCAAATTTGAA-TTTTTGAAAATTTGG
* *
92326 GGGT-AAGATTTTG-ATTTTTGGAAATTTCG
1 GGGTCAA-A-TTTGAATTTTTGAAAATTTGG
* * * **
92355 GGGTAAAATTGGAATTTTTGGAAAGTTTAA
1 GGGTCAAATTTGAATTTTT-GAAAATTTGG
* *
92385 GGGT-AAAATTGAAATTTTTGAAAGTTTGG
1 GGGTCAAATTTG-AATTTTTGAAAATTTGG
92414 GGGTCAA
1 GGGTCAA
92421 CTTAATTTTA
Statistics
Matches: 104, Mismatches: 11, Indels: 19
0.78 0.08 0.14
Matches are distributed among these distances:
28 17 0.16
29 36 0.35
30 37 0.36
31 14 0.13
ACGTcount: A:0.32, C:0.03, G:0.26, T:0.39
Consensus pattern (29 bp):
GGGTCAAATTTGAATTTTTGAAAATTTGG
Found at i:93663 original size:19 final size:19
Alignment explanation
Indices: 93612--93656 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
93602 GTATTTATTT
*
93612 AAATAATAAAT-AGATAAAC
1 AAATAA-AAATAAAATAAAC
93631 AAATAAAAATAAAATAAAC
1 AAATAAAAATAAAATAAAC
93650 AAATAAA
1 AAATAAA
93657 GTTAAAAACA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 4 0.17
19 20 0.83
ACGTcount: A:0.76, C:0.04, G:0.02, T:0.18
Consensus pattern (19 bp):
AAATAAAAATAAAATAAAC
Found at i:106701 original size:13 final size:14
Alignment explanation
Indices: 106675--106703 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
106665 ATTTTCTTTT
106675 TTTTTTATATTATG
1 TTTTTTATATTATG
106689 TTTTTTATA-TATG
1 TTTTTTATATTATG
106702 TT
1 TT
106704 GAATGAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.21, C:0.00, G:0.07, T:0.72
Consensus pattern (14 bp):
TTTTTTATATTATG
Found at i:107120 original size:17 final size:16
Alignment explanation
Indices: 107086--107144 Score: 50
Period size: 17 Copynumber: 3.6 Consensus size: 16
107076 TTTAGGGGTT
*
107086 TATTAATCTTAGATTAA
1 TATTAATATTAGATT-A
107103 TATTAATATTA-A-TA
1 TATTAATATTAGATTA
*
107117 TAATTAATATTATATTTA
1 T-ATTAATATTAGA-TTA
107135 TATTATATAT
1 TATTA-ATAT
107145 CTTAGGTGCA
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
14 2 0.06
15 11 0.31
16 2 0.06
17 14 0.39
18 7 0.19
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (16 bp):
TATTAATATTAGATTA
Found at i:107124 original size:21 final size:20
Alignment explanation
Indices: 107098--107137 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
107088 TTAATCTTAG
107098 ATTAATATTAATATTAATATA
1 ATTAATATT-ATATTAATATA
*
107119 ATTAATATTATATTTATAT
1 ATTAATATTATATTAATAT
107138 TATATATCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
ATTAATATTATATTAATATA
Found at i:107279 original size:29 final size:28
Alignment explanation
Indices: 107216--107280 Score: 87
Period size: 29 Copynumber: 2.3 Consensus size: 28
107206 CCAATAGCGA
*
107216 AATTATATATAAATTATGGTTTAATGTAC
1 AATTATATATAAATTATGATTT-ATGTAC
*
107245 AATTATATATAAATTATGATTT-TGTAT
1 AATTATATATAAATTATGATTTATGTAC
*
107272 AATTTTATA
1 AATTATATA
107281 CATAAAATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
27 12 0.36
29 21 0.64
ACGTcount: A:0.42, C:0.02, G:0.08, T:0.49
Consensus pattern (28 bp):
AATTATATATAAATTATGATTTATGTAC
Found at i:107714 original size:16 final size:16
Alignment explanation
Indices: 107693--107725 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
107683 TAATTTTAAG
107693 TAAATTTTTTATTTGA
1 TAAATTTTTTATTTGA
107709 TAAATTTTTTATTTGA
1 TAAATTTTTTATTTGA
107725 T
1 T
107726 CTTTGAAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (16 bp):
TAAATTTTTTATTTGA
Found at i:109056 original size:22 final size:24
Alignment explanation
Indices: 109016--109063 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 24
109006 TTGATAATTT
*
109016 AAAAAAAATAACAATAATT-CAAA
1 AAAAAAAAAAACAATAATTACAAA
*
109039 AAAAAAAAAAAGAA-AATTACAAA
1 AAAAAAAAAAACAATAATTACAAA
109062 AA
1 AA
109064 TTATAAAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 4 0.18
23 18 0.82
ACGTcount: A:0.79, C:0.06, G:0.02, T:0.12
Consensus pattern (24 bp):
AAAAAAAAAAACAATAATTACAAA
Found at i:110976 original size:20 final size:19
Alignment explanation
Indices: 110916--110987 Score: 99
Period size: 19 Copynumber: 3.7 Consensus size: 19
110906 ATGGCCCGTG
110916 GTATCGATATTTTTTAAGA
1 GTATCGATATTTTTTAAGA
*
110935 GTATCGATATTTTTTACGA
1 GTATCGATATTTTTTAAGA
* *
110954 GTATCGAGATTTTTGTAAAA
1 GTATCGATATTTTT-TAAGA
110974 GTATCGATAATTTT
1 GTATCGAT-ATTTT
110988 ATATTAGCAT
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
19 31 0.67
20 10 0.22
21 5 0.11
ACGTcount: A:0.31, C:0.07, G:0.17, T:0.46
Consensus pattern (19 bp):
GTATCGATATTTTTTAAGA
Found at i:113822 original size:26 final size:26
Alignment explanation
Indices: 113786--113838 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
113776 TTCTGGGCGT
*
113786 AATTCTGGACACGTTTATGCAGCGAC
1 AATTCTGGACACGTTCATGCAGCGAC
* *
113812 AATTCTGGACATGTTCATGTAGCGAC
1 AATTCTGGACACGTTCATGCAGCGAC
113838 A
1 A
113839 TTCCTAGGTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (26 bp):
AATTCTGGACACGTTCATGCAGCGAC
Found at i:113873 original size:37 final size:37
Alignment explanation
Indices: 113832--113912 Score: 90
Period size: 37 Copynumber: 2.2 Consensus size: 37
113822 ATGTTCATGT
* * *
113832 AGCGACATTCCTAGGTGCAATTGAAGAATGCTTATGC
1 AGCGACACTCCTAGATGCAATTGAAGAATACTTATGC
* * * *
113869 AGCGATACTGCTAGATGCAGTTGAAGAATATTTATGC
1 AGCGACACTCCTAGATGCAATTGAAGAATACTTATGC
*
113906 ATCGACA
1 AGCGACA
113913 ATCTTTGGTG
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.27
Consensus pattern (37 bp):
AGCGACACTCCTAGATGCAATTGAAGAATACTTATGC
Found at i:113949 original size:37 final size:36
Alignment explanation
Indices: 113895--114001 Score: 90
Period size: 37 Copynumber: 2.9 Consensus size: 36
113885 GCAGTTGAAG
* * **
113895 AATATTTATGC-ATCGACAATCTTTGGTGCATTTTGGA
1 AATATTCATGCGA-CGACAAT-TTTGGTGCAATCCGGA
*
113932 AATATTCATGCGACGACAGTTTTGGGTGCAATCCGGA
1 AATATTCATGCGACGACAATTTT-GGTGCAATCCGGA
* ** *
113969 AGTGCTCATGCGACTACAATTTTTGGTGCAATC
1 AATATTCATGCGACGACAA-TTTTGGTGCAATC
114002 TAGAAGTGCT
Statistics
Matches: 57, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
36 3 0.05
37 49 0.86
38 5 0.09
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (36 bp):
AATATTCATGCGACGACAATTTTGGTGCAATCCGGA
Found at i:114008 original size:37 final size:37
Alignment explanation
Indices: 113937--114015 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
113927 TTGGAAATAT
* *
113937 TCATGCGACGACAGTTTTGGGTGCAATCCGGAAGTGC
1 TCATGCGACGACAATTTTGGGTGCAATCCAGAAGTGC
* * *
113974 TCATGCGACTACAATTTTTGGTGCAATCTAGAAGTGC
1 TCATGCGACGACAATTTTGGGTGCAATCCAGAAGTGC
114011 TCATG
1 TCATG
114016 TAGCGACATT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (37 bp):
TCATGCGACGACAATTTTGGGTGCAATCCAGAAGTGC
Found at i:117594 original size:16 final size:16
Alignment explanation
Indices: 117573--117603 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
117563 ATAATATGAA
117573 AATAAAGATAAAATGT
1 AATAAAGATAAAATGT
*
117589 AATAAAGGTAAAATG
1 AATAAAGATAAAATG
117604 GGATCTACAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.00, G:0.16, T:0.23
Consensus pattern (16 bp):
AATAAAGATAAAATGT
Found at i:121375 original size:16 final size:16
Alignment explanation
Indices: 121354--121384 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
121344 ATAATGTGAA
121354 AATAAAGATAAAATGT
1 AATAAAGATAAAATGT
*
121370 AATAAAGGTAAAATG
1 AATAAAGATAAAATG
121385 GAATCCACAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.00, G:0.16, T:0.23
Consensus pattern (16 bp):
AATAAAGATAAAATGT
Found at i:121613 original size:127 final size:127
Alignment explanation
Indices: 121387--121635 Score: 392
Period size: 127 Copynumber: 2.0 Consensus size: 127
121377 GTAAAATGGA
*
121387 ATCCACAACGTGAATAGTCAGTAAAAAACTAAGTGTGACTTACAAGGTTAAGAATAACAGGTAAT
1 ATCCACAACGTGAATAGTCAGCAAAAAACTAAGTGTGACTTACAAGGTTAAGAATAACAGGTAAT
* * * *
121452 TTGTTGGCGTAATGAATTACGATGAACATCTTACCAAACTTGGCTTTTCTATTAGATTTAGG
66 TTGTTGGCGCAATGAAGTACAATGAACATCTTACCAAACTTGGCTTTCCTATTAGATTTAGG
* * * *
121514 ATCCATAACGTGAATAGTCAGCATAAAACTGAGTGTGACTTACAAGGTTAAGAATAAGAGGTAAT
1 ATCCACAACGTGAATAGTCAGCAAAAAACTAAGTGTGACTTACAAGGTTAAGAATAACAGGTAAT
*
121579 TT-TTCGGCGCAATGAAGTGCAATGAACATCTTACCAAACTTGGCTTTCCTATTAGAT
66 TTGTT-GGCGCAATGAAGTACAATGAACATCTTACCAAACTTGGCTTTCCTATTAGAT
121636 CTATGACTTT
Statistics
Matches: 111, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
126 2 0.02
127 109 0.98
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.30
Consensus pattern (127 bp):
ATCCACAACGTGAATAGTCAGCAAAAAACTAAGTGTGACTTACAAGGTTAAGAATAACAGGTAAT
TTGTTGGCGCAATGAAGTACAATGAACATCTTACCAAACTTGGCTTTCCTATTAGATTTAGG
Found at i:122397 original size:37 final size:38
Alignment explanation
Indices: 122355--122431 Score: 95
Period size: 37 Copynumber: 2.1 Consensus size: 38
122345 GAACTTGTTC
*
122355 ATGTAGCGACA-TTCTTGGGTACAA-TTGAAGAATACTT
1 ATGTAGCGACAGTTC-TGGATACAATTTGAAGAATACTT
* * *
122392 ATGTAGCGATAGTTCTGGATGCAATTTGAAGAATATTT
1 ATGTAGCGACAGTTCTGGATACAATTTGAAGAATACTT
122430 AT
1 AT
122432 ACGGTGACAG
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
37 17 0.50
38 17 0.50
ACGTcount: A:0.32, C:0.10, G:0.22, T:0.35
Consensus pattern (38 bp):
ATGTAGCGACAGTTCTGGATACAATTTGAAGAATACTT
Found at i:124137 original size:22 final size:24
Alignment explanation
Indices: 124112--124155 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
124102 ATTTTTGTCA
124112 ATTTTAACTT-ATAT-TCAAAAAC
1 ATTTTAACTTGATATATCAAAAAC
*
124134 ATTTTAATTTGATATATCAAAA
1 ATTTTAACTTGATATATCAAAA
124156 TACTTTATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 4 0.21
24 6 0.32
ACGTcount: A:0.45, C:0.09, G:0.02, T:0.43
Consensus pattern (24 bp):
ATTTTAACTTGATATATCAAAAAC
Found at i:124835 original size:30 final size:30
Alignment explanation
Indices: 124799--124860 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
124789 ACTCATCGAC
124799 ATAAAACATGACATCCTTTGGCTTTGATGA
1 ATAAAACATGACATCCTTTGGCTTTGATGA
124829 ATAAAACATGACATCCTTTGGCTTTGATGA
1 ATAAAACATGACATCCTTTGGCTTTGATGA
124859 AT
1 AT
124861 TTTATTTGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (30 bp):
ATAAAACATGACATCCTTTGGCTTTGATGA
Found at i:125969 original size:21 final size:21
Alignment explanation
Indices: 125945--125998 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
125935 CTTGGGAAAG
*
125945 TTCTACCGATACAAGTGTA-AC
1 TTCTACCGATACAAGT-CACAC
*
125966 TTCTACCGAAACAAGTCACAC
1 TTCTACCGATACAAGTCACAC
125987 TTCTACCGATAC
1 TTCTACCGATAC
125999 TAAAAACTCC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 1 0.03
21 28 0.97
ACGTcount: A:0.33, C:0.30, G:0.11, T:0.26
Consensus pattern (21 bp):
TTCTACCGATACAAGTCACAC
Found at i:158262 original size:36 final size:36
Alignment explanation
Indices: 158125--158255 Score: 165
Period size: 36 Copynumber: 3.6 Consensus size: 36
158115 CTCATTATTT
*
158125 ATTTTACTCCCTGTTGGCCCGAAGGTCATGTTGCTC
1 ATTTTACTCCCTGTTGACCCGAAGGTCATGTTGCTC
* * *
158161 GTTTTACTCCCAT-TTAACCCGAAGGTCATGTTGCTT
1 ATTTTACTCCC-TGTTGACCCGAAGGTCATGTTGCTC
** *
158197 ATTTCGCTCCCTGTTGACCCGAAGTTCATGTTGCTC
1 ATTTTACTCCCTGTTGACCCGAAGGTCATGTTGCTC
* *
158233 ATTTTATTCCTTGTTGACCCGAA
1 ATTTTACTCCCTGTTGACCCGAA
158256 AATCATGCCT
Statistics
Matches: 79, Mismatches: 14, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
35 1 0.01
36 77 0.97
37 1 0.01
ACGTcount: A:0.17, C:0.27, G:0.18, T:0.38
Consensus pattern (36 bp):
ATTTTACTCCCTGTTGACCCGAAGGTCATGTTGCTC
Found at i:162271 original size:29 final size:29
Alignment explanation
Indices: 162238--162330 Score: 123
Period size: 29 Copynumber: 3.2 Consensus size: 29
162228 AAATGCAATT
* *
162238 TAACACAGATACAATTACAGATGTAGACG
1 TAACACAGATACAATTACAGATGCAGACA
* *
162267 TAACACATATACAATTACATATGCAGACA
1 TAACACAGATACAATTACAGATGCAGACA
* * *
162296 TAACACGGATACAGTTACAGATGCAGATA
1 TAACACAGATACAATTACAGATGCAGACA
162325 TAACAC
1 TAACAC
162331 CTTCATCAGT
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 55 1.00
ACGTcount: A:0.45, C:0.19, G:0.14, T:0.22
Consensus pattern (29 bp):
TAACACAGATACAATTACAGATGCAGACA
Found at i:173953 original size:23 final size:21
Alignment explanation
Indices: 173926--173998 Score: 62
Period size: 20 Copynumber: 3.5 Consensus size: 21
173916 GTTTTAAAAC
173926 ATAT-TATTACATTATGTAAT
1 ATATATATTACATTATGTAAT
*
173946 A-ATATATTACATAATGTAAT
1 ATATATATTACATTATGTAAT
* **
173966 A-ATAATATGTATATTAAATAAT
1 ATAT-ATAT-TACATTATGTAAT
173988 ATATATTATTA
1 ATATA-TATTA
173999 TTTTTTATTA
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
19 2 0.05
20 19 0.44
21 4 0.09
22 13 0.30
23 5 0.12
ACGTcount: A:0.48, C:0.03, G:0.04, T:0.45
Consensus pattern (21 bp):
ATATATATTACATTATGTAAT
Found at i:173955 original size:20 final size:20
Alignment explanation
Indices: 173930--173969 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
173920 TAAAACATAT
*
173930 TATTACATTATGTAATAATA
1 TATTACATAATGTAATAATA
173950 TATTACATAATGTAATAATA
1 TATTACATAATGTAATAATA
173970 ATATGTATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.42
Consensus pattern (20 bp):
TATTACATAATGTAATAATA
Found at i:177678 original size:18 final size:18
Alignment explanation
Indices: 177633--177681 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
177623 AAGGAGTAGC
177633 ATACTAGCTCGTTAGAGT
1 ATACTAGCTCGTTAGAGT
* * *
177651 TTATTGGCTCGTTAGAGT
1 ATACTAGCTCGTTAGAGT
177669 ATACTAGCTCGTT
1 ATACTAGCTCGTT
177682 TAAGCATACT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.22, C:0.16, G:0.22, T:0.39
Consensus pattern (18 bp):
ATACTAGCTCGTTAGAGT
Found at i:177690 original size:18 final size:18
Alignment explanation
Indices: 177630--177698 Score: 68
Period size: 18 Copynumber: 3.8 Consensus size: 18
177620 CGGAAGGAGT
177630 AGCATACTAGCTCGTTAG
1 AGCATACTAGCTCGTTAG
** * *
177648 AGTTTATTGGCTCGTTAG
1 AGCATACTAGCTCGTTAG
*
177666 AGTATACTAGCTCGTTTA-
1 AGCATACTAGCTCG-TTAG
*
177684 AGCATACTGGCTCGT
1 AGCATACTAGCTCGT
177699 AAAAGCAATA
Statistics
Matches: 41, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
17 1 0.02
18 37 0.90
19 3 0.07
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (18 bp):
AGCATACTAGCTCGTTAG
Found at i:179213 original size:50 final size:50
Alignment explanation
Indices: 179138--179433 Score: 310
Period size: 50 Copynumber: 5.9 Consensus size: 50
179128 TGTTGTTGTG
* * * * *
179138 GCTTCACTCTACCCTTCTATAGCTTTAGGGGTACAAGATTCGCTTTCGTA
1 GCTTCAATCTGCCCCTCTACAGCTTTAGGGGTATAAGATTCGCTTTCGTA
* * * **
179188 GCTTCAATATGCCTCTCTATAGCTTTAGGGGTATAAGATTCGCTTTCACA
1 GCTTCAATCTGCCCCTCTACAGCTTTAGGGGTATAAGATTCGCTTTCGTA
** * *
179238 GCTTCAATCTGCCTTTCTACAACTTTAGGGGTATAAGATTTGCCTTTGCG-A
1 GCTTCAATCTGCCCCTCTACAGCTTTAGGGGTATAAGATTCG-CTTT-CGTA
* ** ** *
179289 -CTTCAATTTGTACCTCTACAGCTTTAGCAGTATAAGATTCGCTTTTGTA
1 GCTTCAATCTGCCCCTCTACAGCTTTAGGGGTATAAGATTCGCTTTCGTA
* * * *
179338 GCTTCAATCTGCCCCTTTACAACTTTAGGGGTACAAGATTCGCCTTT-ATA
1 GCTTCAATCTGCCCCTCTACAGCTTTAGGGGTATAAGATTCG-CTTTCGTA
* *
179388 GTTTCAATCTGCCCCTCTATAGCTTTAGGGGTATAAGATTCGCTTT
1 GCTTCAATCTGCCCCTCTACAGCTTTAGGGGTATAAGATTCGCTTT
179434 TGCAACTTCA
Statistics
Matches: 203, Mismatches: 38, Indels: 11
0.81 0.15 0.04
Matches are distributed among these distances:
48 1 0.00
49 9 0.04
50 183 0.90
51 9 0.04
52 1 0.00
ACGTcount: A:0.22, C:0.23, G:0.18, T:0.37
Consensus pattern (50 bp):
GCTTCAATCTGCCCCTCTACAGCTTTAGGGGTATAAGATTCGCTTTCGTA
Found at i:179414 original size:150 final size:150
Alignment explanation
Indices: 179153--179443 Score: 386
Period size: 150 Copynumber: 1.9 Consensus size: 150
179143 ACTCTACCCT
* ** * * *
179153 TCTATAGCTTTAGGGGTACAAGATTCGCTTTCGTAGCTTCAATATGCCTCTCTATAGCTTTAGGG
1 TCTACAGCTTTAGCAGTACAAGATTCGCTTTCGTAGCTTCAATATGCCCCTCTACAACTTTAGGG
* ** *
179218 GTATAAGATTCGCTTTCACAGCTTCAATCTGCCTTTCTACAACTTTAGGGGTATAAGATTTGCCT
66 GTACAAGATTCGCTTTCACAGCTTCAATCTGCCCCTCTACAACTTTAGGGGTATAAGATTCGCCT
*
179283 TTGCGACTTCAATTTGTACC
131 TTGCAACTTCAATTTGTACC
* * * *
179303 TCTACAGCTTTAGCAGTATAAGATTCGCTTTTGTAGCTTCAATCTGCCCCTTTACAACTTTAGGG
1 TCTACAGCTTTAGCAGTACAAGATTCGCTTTCGTAGCTTCAATATGCCCCTCTACAACTTTAGGG
* * * * *
179368 GTACAAGATTCGCCTTT-ATAGTTTCAATCTGCCCCTCTATAGCTTTAGGGGTATAAGATTCGCT
66 GTACAAGATTCG-CTTTCACAGCTTCAATCTGCCCCTCTACAACTTTAGGGGTATAAGATTCGCC
179432 TTTGCAACTTCA
130 TTTGCAACTTCA
179444 CTCTATGTAA
Statistics
Matches: 120, Mismatches: 20, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
150 116 0.97
151 4 0.03
ACGTcount: A:0.23, C:0.22, G:0.18, T:0.37
Consensus pattern (150 bp):
TCTACAGCTTTAGCAGTACAAGATTCGCTTTCGTAGCTTCAATATGCCCCTCTACAACTTTAGGG
GTACAAGATTCGCTTTCACAGCTTCAATCTGCCCCTCTACAACTTTAGGGGTATAAGATTCGCCT
TTGCAACTTCAATTTGTACC
Found at i:179434 original size:100 final size:99
Alignment explanation
Indices: 179138--179443 Score: 355
Period size: 100 Copynumber: 3.1 Consensus size: 99
179128 TGTTGTTGTG
* * * * *
179138 GCTTCACTCTACCCTTCTATAGCTTTAGGGGTACAAGATTCG-CTTTCGTAGCTTCAATATGCCT
1 GCTTCAATCTGCCCTTCTACAACTTTAGGGGTACAAGATTCGCCTTT--TAGCTTCAATATGCCC
**
179202 CTCTATAGCTTTAGGGGTATAAGATTCGCTTTCACA
64 CTCTATAGCTTTAGGGGTATAAGATTCGCTTTTGCA
* * * ** * **
179238 GCTTCAATCTGCCTTTCTACAACTTTAGGGGTATAAGATTTGCCTTTGCGACTTCAATTTGTACC
1 GCTTCAATCTGCCCTTCTACAACTTTAGGGGTACAAGATTCGCCTTTTAG-CTTCAATATGCCCC
* ** *
179303 TCTACAGCTTTAGCAGTATAAGATTCGCTTTTGTA
65 TCTATAGCTTTAGGGGTATAAGATTCGCTTTTGCA
* *
179338 GCTTCAATCTGCCCCTT-TACAACTTTAGGGGTACAAGATTCGCCTTTATAGTTTCAATCTGCCC
1 GCTTCAATCTG-CCCTTCTACAACTTTAGGGGTACAAGATTCGCCTTT-TAGCTTCAATATGCCC
179402 CTCTATAGCTTTAGGGGTATAAGATTCGCTTTTGCA
64 CTCTATAGCTTTAGGGGTATAAGATTCGCTTTTGCA
*
179438 ACTTCA
1 GCTTCA
179444 CTCTATGTAA
Statistics
Matches: 169, Mismatches: 33, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
99 1 0.01
100 159 0.94
101 9 0.05
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.37
Consensus pattern (99 bp):
GCTTCAATCTGCCCTTCTACAACTTTAGGGGTACAAGATTCGCCTTTTAGCTTCAATATGCCCCT
CTATAGCTTTAGGGGTATAAGATTCGCTTTTGCA
Found at i:179761 original size:21 final size:21
Alignment explanation
Indices: 179737--179777 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
179727 CTTGAGATAG
*
179737 TTCTATCGATACAAGTCATGC
1 TTCTATCGATACAAGCCATGC
179758 TTCTATCGATACAAGCCATG
1 TTCTATCGATACAAGCCATG
179778 ATACTACCGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.32
Consensus pattern (21 bp):
TTCTATCGATACAAGCCATGC
Found at i:179788 original size:21 final size:21
Alignment explanation
Indices: 179743--179790 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
179733 ATAGTTCTAT
* * * *
179743 CGATACAAGTCATGCTTCTAT
1 CGATACAAGCCATGATACTAC
179764 CGATACAAGCCATGATACTAC
1 CGATACAAGCCATGATACTAC
179785 CGATAC
1 CGATAC
179791 TAAAAACTCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.33, C:0.27, G:0.15, T:0.25
Consensus pattern (21 bp):
CGATACAAGCCATGATACTAC
Found at i:180469 original size:42 final size:41
Alignment explanation
Indices: 180413--180528 Score: 119
Period size: 42 Copynumber: 2.8 Consensus size: 41
180403 AACATCCGAG
* * * **
180413 TCACAAGTTTTCCTTTAAACGTAATCTCATGTTCATTATGAA-
1 TCACGAGTCTTCCTTTAAACATAATCTCATGTTC-TT-CCAAC
*
180455 TCACGAGTCTTCCTTTAAATCATAA-CTTCACGTTCTTCCAAC
1 TCACGAGTCTTCCTTTAAA-CATAATC-TCATGTTCTTCCAAC
180497 TCACGAGTCTTCCTTTAATACATAATCTCATG
1 TCACGAGTCTTCCTTTAA-ACATAATCTCATG
180529 CTCAACCCGA
Statistics
Matches: 62, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
41 2 0.03
42 47 0.76
43 13 0.21
ACGTcount: A:0.28, C:0.25, G:0.09, T:0.38
Consensus pattern (41 bp):
TCACGAGTCTTCCTTTAAACATAATCTCATGTTCTTCCAAC
Found at i:180608 original size:40 final size:41
Alignment explanation
Indices: 180501--180679 Score: 227
Period size: 41 Copynumber: 4.3 Consensus size: 41
180491 TCCAACTCAC
** * *
180501 GAGTCTTCCTTTAATACATAATCTCATGCTCAACCCGAGACAT
1 GAGTCTTCCTTTAAT--ATCCTCTCATGCTCATCCCAAGACAT
*
180544 GAGTCTTCCTTTAATATTCC-CTCATGCTTATCCCAAGACAT
1 GAGTCTTCCTTTAATA-TCCTCTCATGCTCATCCCAAGACAT
*
180585 GAGT-TTCCTTTAATATCCTCTCATGCTCATCCAAAGACAT
1 GAGTCTTCCTTTAATATCCTCTCATGCTCATCCCAAGACAT
* * *
180625 GAGTCTTCTTTTAATATCCCCTCATGCTCATCCCGAGACAT
1 GAGTCTTCCTTTAATATCCTCTCATGCTCATCCCAAGACAT
180666 GAGTCTTCCATTTA
1 GAGTCTTCC-TTTA
180680 CACATCAAGT
Statistics
Matches: 120, Mismatches: 12, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
39 3 0.03
40 34 0.28
41 63 0.52
42 5 0.04
43 15 0.12
ACGTcount: A:0.26, C:0.28, G:0.11, T:0.35
Consensus pattern (41 bp):
GAGTCTTCCTTTAATATCCTCTCATGCTCATCCCAAGACAT
Found at i:180623 original size:81 final size:83
Alignment explanation
Indices: 180522--180679 Score: 239
Period size: 81 Copynumber: 1.9 Consensus size: 83
180512 TAATACATAA
** * *
180522 TCTCATGCTCAACCCGAGACATGAGTCTTCCTTTAATATTCCCTCATGCTTATCCCAAGACATGA
1 TCTCATGCTCAACCAAAGACATGAGTCTTCCTTTAATATCCCCTCATGCTCATCCCAAGACATGA
180587 GT-TTCC-TTTAATATCC
66 GTCTTCCATTTAATATCC
* * *
180603 TCTCATGCTCATCCAAAGACATGAGTCTTCTTTTAATATCCCCTCATGCTCATCCCGAGACATGA
1 TCTCATGCTCAACCAAAGACATGAGTCTTCCTTTAATATCCCCTCATGCTCATCCCAAGACATGA
180668 GTCTTCCATTTA
66 GTCTTCCATTTA
180680 CACATCAAGT
Statistics
Matches: 68, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
81 60 0.88
82 4 0.06
83 4 0.06
ACGTcount: A:0.25, C:0.30, G:0.11, T:0.34
Consensus pattern (83 bp):
TCTCATGCTCAACCAAAGACATGAGTCTTCCTTTAATATCCCCTCATGCTCATCCCAAGACATGA
GTCTTCCATTTAATATCC
Found at i:181886 original size:50 final size:50
Alignment explanation
Indices: 181803--181934 Score: 167
Period size: 50 Copynumber: 2.6 Consensus size: 50
181793 GCTATTACAC
* * * ** *
181803 TCTATCCTTCTATAACTTTAGTGGTATAAGATTCACTTTTGTAGCTTTAA
1 TCTATCCCTCTATAGCTTTAGGGGTATAAGATTCACTTTTACAGCTTCAA
* *
181853 TTTA-CTCGTCTATAGCTTTAGGGGTATAAGATTCACTTTTACAGCTTCAA
1 TCTATC-CCTCTATAGCTTTAGGGGTATAAGATTCACTTTTACAGCTTCAA
*
181903 TCTATCCCTTTATAGCTTTAGGGGTATAAGAT
1 TCTATCCCTCTATAGCTTTAGGGGTATAAGAT
181935 ACAACTTTGC
Statistics
Matches: 70, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
49 1 0.01
50 68 0.97
51 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.42
Consensus pattern (50 bp):
TCTATCCCTCTATAGCTTTAGGGGTATAAGATTCACTTTTACAGCTTCAA
Found at i:182003 original size:46 final size:45
Alignment explanation
Indices: 181948--182130 Score: 222
Period size: 46 Copynumber: 4.0 Consensus size: 45
181938 ACTTTGCGGC
*
181948 TTCAATCTGCCCCTCTAGATTTATGGGTATAATATTGGATGATGGT
1 TTCAATCTGCCCCTCTAGATTTATGGGTATAAGATTGGATG-TGGT
*
181994 TTCAATCTGCCCCTCTAGATTTAGGGGTATAAGATTGGATTGTGGT
1 TTCAATCTGCCCCTCTAGATTTATGGGTATAAGATTGGA-TGTGGT
* * * * * * * *
182040 TTTAATCCGCCCTTTTGGGTTTTTGGGTATAAGATTGGATGGTGGC
1 TTCAATCTGCCCCTCTAGATTTATGGGTATAAGATTGGAT-GTGGT
* * *
182086 TTCAATTTTCCCCTCTAGATTTAAGGGTATAAGATTGGATGTGGT
1 TTCAATCTGCCCCTCTAGATTTATGGGTATAAGATTGGATGTGGT
182131 GATGTAATTT
Statistics
Matches: 113, Mismatches: 22, Indels: 5
0.81 0.16 0.04
Matches are distributed among these distances:
45 5 0.04
46 106 0.94
47 2 0.02
ACGTcount: A:0.21, C:0.14, G:0.25, T:0.39
Consensus pattern (45 bp):
TTCAATCTGCCCCTCTAGATTTATGGGTATAAGATTGGATGTGGT
Found at i:182417 original size:99 final size:100
Alignment explanation
Indices: 182307--182853 Score: 493
Period size: 99 Copynumber: 5.6 Consensus size: 100
182297 CTTCAAGGGC
* * * * * *
182307 ATAGGATTTGGTGATGTAA-CTTTACTCCATTCCACTATAACTTCAGGGAGATTGAGATCCATTA
1 ATAGGATTTGGTGTTGTAAGCTTCACTCCATTCCACTGTAACCTCAAGGAGATTGAGATCCGTTA
*
182371 CTTATTTTAATCTGATCCACTGCAACTTTAGGGAT
66 CTTATTTTAATCTGATCCACTACAACTTTAGGGAT
* ** **
182406 ATAGGATTTGGTGTTG-AAGCTTCACTCCATTCCACTCTAACCTCAAAAAGATTGAGATATGCTT
1 ATAGGATTTGGTGTTGTAAGCTTCACTCCATTCCACTGTAACCTCAAGGAGATTGAGATCCG-TT
* * * * * * *
182470 -TTGTAACTTTAATCTGACCCTCTATAATTTTAGGGGT
65 ACT-T-ATTTTAATCTGATCCACTACAACTTTAGGGAT
* * * * * *
182507 ATAGGATTTGGTGTCGTAA-CTTCACTTCATTCCATTGTAACTTC-AGAGAGATTAAGATCTGTT
1 ATAGGATTTGGTGTTGTAAGCTTCACTCCATTCCACTGTAACCTCAAG-GAGATTGAGATCCGTT
* * *
182570 ACTTATTTTAATCCGATCCACTACAACTTCAAGGAT
65 ACTTATTTTAATCTGATCCACTACAACTTTAGGGAT
* * * *
182606 ATAGGATTTGGTGTTG-AAGCTTCACTCCATTGCACTATAACCTCAGGGAGATTGAGATCTACCT
1 ATAGGATTTGGTGTTGTAAGCTTCACTCCATTCCACTGTAACCTCAAGGAGATTGAGATC--CGT
* * *
182670 T--TTTTTTTACT-TCGATCC-TTACAAC-TT----AT
64 TACTTATTTTAATCT-GATCCACTACAACTTTAGGGAT
* ** * *
182699 A-AGG-TTTGGGGTTGTAA-CAGCACTCCATTCCACTGTAACCTCAAGGAGATTGAGATTCGTTG
1 ATAGGATTTGGTGTTGTAAGCTTCACTCCATTCCACTGTAACCTCAAGGAGATTGAGATCCGTTA
** * *
182761 CTTATTTTAATCCAATCCACTACAACTTCAGGGAA
66 CTTATTTTAATCTGATCCACTACAACTTTAGGGAT
*
182796 ATAGGATTTGGTGTT-AAAGCTTCACTCCATTCCACTGTAACCTCAAGGAGATTGAGAT
1 ATAGGATTTGGTGTTGTAAGCTTCACTCCATTCCACTGTAACCTCAAGGAGATTGAGAT
182854 TTGCTTTTAT
Statistics
Matches: 352, Mismatches: 71, Indels: 50
0.74 0.15 0.11
Matches are distributed among these distances:
89 3 0.01
91 55 0.16
92 11 0.03
93 4 0.01
97 3 0.01
98 15 0.04
99 176 0.50
100 8 0.02
101 75 0.21
102 2 0.01
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35
Consensus pattern (100 bp):
ATAGGATTTGGTGTTGTAAGCTTCACTCCATTCCACTGTAACCTCAAGGAGATTGAGATCCGTTA
CTTATTTTAATCTGATCCACTACAACTTTAGGGAT
Found at i:182517 original size:101 final size:101
Alignment explanation
Indices: 182235--182904 Score: 415
Period size: 99 Copynumber: 6.8 Consensus size: 101
182225 ATTTGGTGTG
* * * * **
182235 TTCCATTATAACATCA-AGGAGATTGAGATATACTTTTGTAACTTTAAT-TCGACCCATTGTAAC
1 TTCCACTATAACCTCAGA-GAGATTGAGATATGCTTTTGTAACTTTAATCT-GACCCACTACAAC
** * *
182298 TTCAAGGGCATAGGATTTGGTGATGTAACTTTACTCCA
64 TTCAAGGATATAGGATTTGGTGTTGTAACTTCACTCCA
* * * * ** * * * *
182336 TTCCACTATAACTTCAGGGAGATTGAG--ATCCATTACTTATTTTAATCTGATCCACTGCAACTT
1 TTCCACTATAACCTCAGAGAGATTGAGATATGCTTTTGTAACTTTAATCTGACCCACTACAACTT
* *
182399 TAGGGATATAGGATTTGGTGTTG-AAGCTTCACTCCA
66 CAAGGATATAGGATTTGGTGTTGTAA-CTTCACTCCA
* * * * * *
182435 TTCCACTCTAACCTCAAAAAGATTGAGATATGCTTTTGTAACTTTAATCTGACCCTCTATAATTT
1 TTCCACTATAACCTCAGAGAGATTGAGATATGCTTTTGTAACTTTAATCTGACCCACTACAACTT
* * * * *
182500 TAGGGGTATAGGATTTGGTGTCGTAACTTCACTTCA
66 CAAGGATATAGGATTTGGTGTTGTAACTTCACTCCA
* * * * * * * * *
182536 TTCCATTGTAACTTCAGAGAGATTAAGATCTG-TTACT-T-ATTTTAATCCGATCCACTACAACT
1 TTCCACTATAACCTCAGAGAGATTGAGATATGCTT-TTGTAACTTTAATCTGACCCACTACAACT
182598 TCAAGGATATAGGATTTGGTGTTG-AAGCTTCACTCCA
65 TCAAGGATATAGGATTTGGTGTTGTAA-CTTCACTCCA
* * * * * * * *
182635 TTGCACTATAACCTCAGGGAGATTGAGATCTACCTTTT-T--TTTTACT-TCGATCC-TTACAAC
1 TTCCACTATAACCTCAGAGAGATTGAGATAT-GCTTTTGTAACTTTAATCT-GACCCACTACAAC
* **
182695 TT-----ATA-AGG-TTTGGGGTTGTAACAGCACTCCA
64 TTCAAGGATATAGGATTTGGTGTTGTAACTTCACTCCA
* * * * ** *
182726 TTCCACTGTAACCTCA-AGGAGATTGAGAT-T-C-GTTGCTTATTTTAATCCAATCCACTACAAC
1 TTCCACTATAACCTCAGA-GAGATTGAGATATGCTTTTG-TAACTTTAATCTGACCCACTACAAC
* * *
182787 TTCAGGGAAATAGGATTTGGTGTT-AAAGCTTCACTCCA
64 TTCAAGGATATAGGATTTGGTGTTGTAA-CTTCACTCCA
* * * *
182825 TTCCACTGTAACCTCA-AGGAGATTGAGATTTGCTTTTATAACTTTAAT-TCGACCCACTGCAAC
1 TTCCACTATAACCTCAGA-GAGATTGAGATATGCTTTTGTAACTTTAATCT-GACCCACTACAAC
* *
182888 TTCAGGGGTATAGGATT
64 TTCAAGGATATAGGATT
182905 CTCCATTCCA
Statistics
Matches: 445, Mismatches: 93, Indels: 62
0.74 0.16 0.10
Matches are distributed among these distances:
87 2 0.00
88 1 0.00
89 1 0.00
90 1 0.00
91 52 0.12
92 13 0.03
93 3 0.01
97 2 0.00
98 17 0.04
99 202 0.45
100 7 0.02
101 140 0.31
102 4 0.01
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.35
Consensus pattern (101 bp):
TTCCACTATAACCTCAGAGAGATTGAGATATGCTTTTGTAACTTTAATCTGACCCACTACAACTT
CAAGGATATAGGATTTGGTGTTGTAACTTCACTCCA
Found at i:182608 original size:200 final size:198
Alignment explanation
Indices: 182235--182904 Score: 754
Period size: 200 Copynumber: 3.4 Consensus size: 198
182225 ATTTGGTGTG
* * * **
182235 TTCCATTATAACATCAAGGAGATTGAGATATACTTTTGTAACTTTAATTCGACCCATTGTAACTT
1 TTCCACTATAACCTCAAGGAGATTGAGATATGCTTTTGTAACTTTAATTCGACCC-TTACAACTT
* * * * *
182300 CAAGGGCATAGGATTTGGTGATGTAACTTTACTCCATTCCACTATAACTTCAGGGAGATTGAGAT
65 CAGGGGTATAGGATTTGGTG-TGTAACTTCACTCCATTCCACTGTAACTTCAGAGAGATTGAGAT
** * * *
182365 CCATTACTTATTTTAATCTGATCCACTGCAACTTTAGGGATATAGGATTTGGTGTTGAAGCTTCA
129 CTGTTACTTATTTTAATCCGATCCACTACAACTTCAGGGATATAGGATTTGGTGTTGAAGCTTCA
182430 CTCCA
194 CTCCA
* ** * *
182435 TTCCACTCTAACCTCAAAAAGATTGAGATATGCTTTTGTAACTTTAA-TCTGACCCTCTATAATT
1 TTCCACTATAACCTCAAGGAGATTGAGATATGCTTTTGTAACTTTAATTC-GACCCT-TACAACT
* * * *
182499 TTAGGGGTATAGGATTTGGTGTCGTAACTTCACTTCATTCCATTGTAACTTCAGAGAGATTAAGA
64 TCAGGGGTATAGGATTTGGTGT-GTAACTTCACTCCATTCCACTGTAACTTCAGAGAGATTGAGA
*
182564 TCTGTTACTTATTTTAATCCGATCCACTACAACTTCAAGGATATAGGATTTGGTGTTGAAGCTTC
128 TCTGTTACTTATTTTAATCCGATCCACTACAACTTCAGGGATATAGGATTTGGTGTTGAAGCTTC
182629 ACTCCA
193 ACTCCA
* * * * * * *
182635 TTGCACTATAACCTCAGGGAGATTGAGATCTACCTTTT-T--TTTTACTTCGATCCTTACAACTT
1 TTCCACTATAACCTCAAGGAGATTGAGATAT-GCTTTTGTAACTTTAATTCGACCCTTACAACTT
* ** *
182697 -A----TA-AGG-TTTGGGGTTGTAACAGCACTCCATTCCACTGTAACCTCA-AGGAGATTGAGA
65 CAGGGGTATAGGATTTGGTG-TGTAACTTCACTCCATTCCACTGTAACTTCAGA-GAGATTGAGA
* * * *
182754 T-TCGTTGCTTATTTTAATCCAATCCACTACAACTTCAGGGAAATAGGATTTGGTGTTAAAGCTT
128 TCT-GTTACTTATTTTAATCCGATCCACTACAACTTCAGGGATATAGGATTTGGTGTTGAAGCTT
182818 CACTCCA
192 CACTCCA
* * * * *
182825 TTCCACTGTAACCTCAAGGAGATTGAGATTTGCTTTTATAACTTTAATTCGACCCACTGCAACTT
1 TTCCACTATAACCTCAAGGAGATTGAGATATGCTTTTGTAACTTTAATTCGACCC-TTACAACTT
182890 CAGGGGTATAGGATT
65 CAGGGGTATAGGATT
182905 CTCCATTCCA
Statistics
Matches: 394, Mismatches: 57, Indels: 38
0.81 0.12 0.08
Matches are distributed among these distances:
189 7 0.02
190 132 0.34
191 4 0.01
192 13 0.03
193 7 0.02
194 1 0.00
196 1 0.00
197 6 0.02
198 11 0.03
199 9 0.02
200 198 0.50
201 5 0.01
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.35
Consensus pattern (198 bp):
TTCCACTATAACCTCAAGGAGATTGAGATATGCTTTTGTAACTTTAATTCGACCCTTACAACTTC
AGGGGTATAGGATTTGGTGTGTAACTTCACTCCATTCCACTGTAACTTCAGAGAGATTGAGATCT
GTTACTTATTTTAATCCGATCCACTACAACTTCAGGGATATAGGATTTGGTGTTGAAGCTTCACT
CCA
Found at i:185595 original size:23 final size:22
Alignment explanation
Indices: 185560--185606 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 22
185550 TTTGAAATTT
*
185560 AATGCATGATAAAATGAAATGCA
1 AATGAATGATAAAATG-AATGCA
* *
185583 AATGAATGGTAAAATGCATGCA
1 AATGAATGATAAAATGAATGCA
185605 AA
1 AA
185607 GAGACGTTGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 7 0.33
23 14 0.67
ACGTcount: A:0.51, C:0.09, G:0.19, T:0.21
Consensus pattern (22 bp):
AATGAATGATAAAATGAATGCA
Found at i:189681 original size:16 final size:15
Alignment explanation
Indices: 189640--189677 Score: 58
Period size: 16 Copynumber: 2.5 Consensus size: 15
189630 CATAAAAATA
*
189640 TTATTAATTATTTTT
1 TTATTAATAATTTTT
189655 TCTATTAATAATTTTT
1 T-TATTAATAATTTTT
189671 TTATTAA
1 TTATTAA
189678 ATAAACATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 7 0.33
16 14 0.67
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (15 bp):
TTATTAATAATTTTT
Found at i:193097 original size:31 final size:32
Alignment explanation
Indices: 193062--193131 Score: 83
Period size: 29 Copynumber: 2.3 Consensus size: 32
193052 ACATCAACTA
*
193062 TAATTTAATGTGCAATTGTATACAT-AAATTT
1 TAATTTAATGTGCAATTGTATAAATGAAATTT
* *
193093 TAATTT--TGTGTAATTTTATAAATGAAATTT
1 TAATTTAATGTGCAATTGTATAAATGAAATTT
*
193123 TGATTTAAT
1 TAATTTAAT
193132 CCAATTCTTG
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
29 14 0.44
30 11 0.34
31 6 0.19
32 1 0.03
ACGTcount: A:0.37, C:0.03, G:0.10, T:0.50
Consensus pattern (32 bp):
TAATTTAATGTGCAATTGTATAAATGAAATTT
Found at i:193307 original size:31 final size:29
Alignment explanation
Indices: 193271--193352 Score: 87
Period size: 31 Copynumber: 2.8 Consensus size: 29
193261 AATTAAATCA
193271 AAATTAAAGTTTCAAGTATACATTTGAACC
1 AAATTAAAGTTTCAAGTATACA-TTGAACC
* *
193301 ACAATTAAAGTTTCACATGCATA-ATTGCACC
1 A-AATTAAAGTTTCA-A-GTATACATTGAACC
*
193332 AAATTAAAG-TTCATGTATACA
1 AAATTAAAGTTTCAAGTATACA
193353 ATTACATATT
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
27 4 0.09
28 1 0.02
29 4 0.09
30 9 0.20
31 20 0.45
32 2 0.05
33 4 0.09
ACGTcount: A:0.43, C:0.16, G:0.10, T:0.32
Consensus pattern (29 bp):
AAATTAAAGTTTCAAGTATACATTGAACC
Found at i:197192 original size:22 final size:21
Alignment explanation
Indices: 197167--197250 Score: 78
Period size: 22 Copynumber: 3.9 Consensus size: 21
197157 AATGAGGGTG
*
197167 AGATATGATATGATATGATATA
1 AGATATGCTATGATATG-TATA
* *
197189 AGATATGCTATGATATGTTTTG
1 AGATATGCTATGATATG-TATA
* *
197211 AGATTTGCTATCATATGTCATA
1 AGATATGCTATGATATGT-ATA
* *
197233 ATATATGTTATGATATGT
1 AGATATGCTATGATATGT
197251 TACACGATAT
Statistics
Matches: 49, Mismatches: 12, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
21 1 0.02
22 48 0.98
ACGTcount: A:0.35, C:0.05, G:0.18, T:0.43
Consensus pattern (21 bp):
AGATATGCTATGATATGTATA
Found at i:201476 original size:5 final size:5
Alignment explanation
Indices: 201466--201504 Score: 60
Period size: 5 Copynumber: 7.8 Consensus size: 5
201456 ATGTGTAGCG
* *
201466 GATAC GATAC GATAC GATAC GATAC GATAT GATAT GATA
1 GATAC GATAC GATAC GATAC GATAC GATAC GATAC GATA
201505 TGATGTGAGA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.41, C:0.13, G:0.21, T:0.26
Consensus pattern (5 bp):
GATAC
Found at i:201505 original size:5 final size:5
Alignment explanation
Indices: 201466--201549 Score: 51
Period size: 5 Copynumber: 16.0 Consensus size: 5
201456 ATGTGTAGCG
* * * * * *
201466 GATAC GATAC GATAC GATAC GATAC GATAT GATAT GATAT GATGT GAGATAT
1 GATAT GATAT GATAT GATAT GATAT GATAT GATAT GATAT GATAT --GATAT
* * *
201518 GTTAT GATAT CATAT GCGATAT GCTAT GATAT
1 GATAT GATAT GATAT --GATAT GATAT GATAT
201550 TTTATGAGAT
Statistics
Matches: 66, Mismatches: 9, Indels: 8
0.80 0.11 0.10
Matches are distributed among these distances:
5 58 0.88
7 8 0.12
ACGTcount: A:0.36, C:0.10, G:0.21, T:0.33
Consensus pattern (5 bp):
GATAT
Found at i:201523 original size:22 final size:22
Alignment explanation
Indices: 201491--201594 Score: 86
Period size: 22 Copynumber: 4.7 Consensus size: 22
201481 GATACGATAC
* *
201491 GATATGATATGATATGATGTGA
1 GATATGTTATGATATGATATGA
* *
201513 GATATGTTATGATATCATATGC
1 GATATGTTATGATATGATATGA
* **
201535 GATATGCTATGATATTTTATGA
1 GATATGTTATGATATGATATGA
* * *
201557 GAT-TCATTATGATTTG-TGATAA
1 GATAT-GTTATGATATGAT-ATGA
201579 GATATGTTATGATATG
1 GATATGTTATGATATG
201595 TTACACGATA
Statistics
Matches: 64, Mismatches: 15, Indels: 6
0.75 0.18 0.07
Matches are distributed among these distances:
21 2 0.03
22 61 0.95
23 1 0.02
ACGTcount: A:0.33, C:0.04, G:0.21, T:0.42
Consensus pattern (22 bp):
GATATGTTATGATATGATATGA
Found at i:202440 original size:24 final size:24
Alignment explanation
Indices: 202412--202474 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
202402 AGAAATAATC
*
202412 TTTCAGTTAAACTCTGTTTCTTTG
1 TTTCAGTTAAACTCTGTTTATTTG
* *
202436 TTTCAATTAAACTCAGTTTATTTG
1 TTTCAGTTAAACTCTGTTTATTTG
* *
202460 TTTTAGTCAAACTCT
1 TTTCAGTTAAACTCT
202475 TATTCGTCTA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.24, C:0.16, G:0.10, T:0.51
Consensus pattern (24 bp):
TTTCAGTTAAACTCTGTTTATTTG
Found at i:204585 original size:40 final size:40
Alignment explanation
Indices: 204541--204667 Score: 148
Period size: 40 Copynumber: 3.2 Consensus size: 40
204531 AGCTACTGCA
*
204541 TAGCAGGCTATGAGCCAATGTTAAAAATCAAGCTTAGGCT
1 TAGCAGGCTATGAGCCAGTGTTAAAAATCAAGCTTAGGCT
* * * *
204581 TAGCAGGTTATGAGCCGGTGTTAAAAATCAAGCTTCGACT
1 TAGCAGGCTATGAGCCAGTGTTAAAAATCAAGCTTAGGCT
* * * * *
204621 TAGCAGGGTGTAAGCCAGTGTTAAGATTCAAG-TTATGGCT
1 TAGCAGGCTATGAGCCAGTGTTAAAAATCAAGCTTA-GGCT
204661 TAGCAGG
1 TAGCAGG
204668 TGGTAAGCCG
Statistics
Matches: 73, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
39 2 0.03
40 71 0.97
ACGTcount: A:0.31, C:0.16, G:0.27, T:0.27
Consensus pattern (40 bp):
TAGCAGGCTATGAGCCAGTGTTAAAAATCAAGCTTAGGCT
Found at i:210364 original size:31 final size:33
Alignment explanation
Indices: 210329--210399 Score: 110
Period size: 33 Copynumber: 2.2 Consensus size: 33
210319 AATATAATAA
*
210329 TTGGTATTTGAATTT-A-ACATTTTTTCTTAAT
1 TTGGTATTTAAATTTGACACATTTTTTCTTAAT
*
210360 TTGGTATTTAAATTTGACACTTTTTTTCTTAAT
1 TTGGTATTTAAATTTGACACATTTTTTCTTAAT
210393 TTGGTAT
1 TTGGTAT
210400 CTAATTTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
31 14 0.39
32 1 0.03
33 21 0.58
ACGTcount: A:0.24, C:0.07, G:0.11, T:0.58
Consensus pattern (33 bp):
TTGGTATTTAAATTTGACACATTTTTTCTTAAT
Found at i:210433 original size:59 final size:56
Alignment explanation
Indices: 210348--210468 Score: 136
Period size: 59 Copynumber: 2.1 Consensus size: 56
210338 GAATTTAACA
* * * * *
210348 TTTTTTCTTAATTTGGTATTTAAATTTGACACTTTTTTTCTTAATTTGGTATCT-AATT
1 TTTTTTCTTAATTTGATACTTAAATTTGACA--TATTTAC-TAATTTGGTACCTAAATT
* *
210406 TTTTTTGTTCAATTTGATACTTGAATTTGACATATTTACTAATTTGGTACCTAAATT
1 TTTTTTCTT-AATTTGATACTTAAATTTGACATATTTACTAATTTGGTACCTAAATT
210463 TTTTTT
1 TTTTTT
210469 TAGGTTTAAA
Statistics
Matches: 54, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
56 12 0.22
57 15 0.28
58 8 0.15
59 19 0.35
ACGTcount: A:0.24, C:0.09, G:0.09, T:0.58
Consensus pattern (56 bp):
TTTTTTCTTAATTTGATACTTAAATTTGACATATTTACTAATTTGGTACCTAAATT
Found at i:211852 original size:56 final size:57
Alignment explanation
Indices: 211792--211902 Score: 145
Period size: 61 Copynumber: 1.9 Consensus size: 57
211782 AACAAATCCA
*
211792 AAATAAATAATAA-A-AATTTAAATTTAAAATATATTTTAAAATTAATTTTTTGGTAC
1 AAATAAATAATAACATAATTTAAATTTAAAACATATTTT-AAATTAATTTTTTGGTAC
* *
211848 AAATAAATAATAACATTTGAATTTGAATTTAAAACATATTTTAAATTATTTTTTT
1 AAATAAATAATAACA--T-AATTTAAATTTAAAACATATTTTAAATTAATTTTTT
211903 TGTATATGTC
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
56 13 0.28
57 1 0.02
60 12 0.26
61 21 0.45
ACGTcount: A:0.49, C:0.03, G:0.04, T:0.45
Consensus pattern (57 bp):
AAATAAATAATAACATAATTTAAATTTAAAACATATTTTAAATTAATTTTTTGGTAC
Found at i:212193 original size:28 final size:25
Alignment explanation
Indices: 212153--212216 Score: 92
Period size: 28 Copynumber: 2.4 Consensus size: 25
212143 ACTACTATCT
212153 TAAAATATATGTATTGTTAAATTTTA
1 TAAAATATATGTATTGTTAAA-TTTA
*
212179 TATTAAATATATGTATTGTTATATTTA
1 TA--AAATATATGTATTGTTAAATTTA
212206 TAAAATATATG
1 TAAAATATATG
212217 GAAGATAAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
25 9 0.26
26 2 0.06
27 6 0.17
28 18 0.51
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (25 bp):
TAAAATATATGTATTGTTAAATTTA
Found at i:223104 original size:15 final size:14
Alignment explanation
Indices: 223086--223128 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
223076 AATATATTTT
223086 TATTGTTTTATTTAA
1 TATT-TTTTATTTAA
**
223101 TATTTAATATTTTAA
1 TATTTTTTA-TTTAA
223116 TATTTTTTATTTA
1 TATTTTTTATTTA
223129 TTGAAATTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
14 7 0.30
15 16 0.70
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (14 bp):
TATTTTTTATTTAA
Found at i:229437 original size:15 final size:16
Alignment explanation
Indices: 229417--229446 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
229407 TTGACTTGAA
229417 AATTTTTTA-AATTAT
1 AATTTTTTAGAATTAT
229432 AATTTTTTAGAATTA
1 AATTTTTTAGAATTA
229447 AAATAAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (16 bp):
AATTTTTTAGAATTAT
Found at i:234840 original size:31 final size:31
Alignment explanation
Indices: 234805--234922 Score: 86
Period size: 31 Copynumber: 3.9 Consensus size: 31
234795 CCTACTTAAA
234805 AAAAAGTGTCAAATTTAGGTACCAAATTAGG
1 AAAAAGTGTCAAATTTAGGTACCAAATTAGG
* *
234836 AAAAAGTGTCAAGTTT-GACTACCAAATT-GG
1 AAAAAGTGTCAAATTTAG-GTACCAAATTAGG
* *
234866 ATAAAA----AAAATGTTCAGGTACCAAGTTAGG
1 A-AAAAGTGTCAAAT-TT-AGGTACCAAATTAGG
* * * *
234896 AAAAATTGTCAAGTTTAAGTATCAAAT
1 AAAAAGTGTCAAATTTAGGTACCAAAT
234923 GTTATATTAA
Statistics
Matches: 66, Mismatches: 11, Indels: 20
0.68 0.11 0.21
Matches are distributed among these distances:
27 3 0.05
28 2 0.03
29 12 0.18
30 8 0.12
31 36 0.55
32 2 0.03
33 3 0.05
ACGTcount: A:0.45, C:0.10, G:0.18, T:0.27
Consensus pattern (31 bp):
AAAAAGTGTCAAATTTAGGTACCAAATTAGG
Found at i:246846 original size:25 final size:25
Alignment explanation
Indices: 246818--247080 Score: 203
Period size: 25 Copynumber: 10.6 Consensus size: 25
246808 CCAGATAGAG
*
246818 TATCGCTCTTACGAGCTAAACAGAA
1 TATCGCTCTTACGAGCCAAACAGAA
* *
246843 TATCGCTCTTATGAGTCAAACAGAA
1 TATCGCTCTTACGAGCCAAACAGAA
****
246868 TATCGCTCTTACGAGATTGACAGAA
1 TATCGCTCTTACGAGCCAAACAGAA
**
246893 TA-CTGCTCTTACGAGCCAGGCA-AA
1 TATC-GCTCTTACGAGCCAAACAGAA
* * * *
246917 AATCACTCTTACAAGCCAAACATAA
1 TATCGCTCTTACGAGCCAAACAGAA
* **
246942 TACCGCTCCCACGAGCCAAAC-GAAA
1 TATCGCTCTTACGAGCCAAACAG-AA
*
246967 TATCGCTCTTACGAGCCAAGA-AGAG
1 TATCGCTCTTACGAGCCAA-ACAGAA
** *
246992 T-TTACTCTTACGAGTCAAACAGAA
1 TATCGCTCTTACGAGCCAAACAGAA
* * * *
247016 TACCGCTCTTACAAGCCAGATAGAA
1 TATCGCTCTTACGAGCCAAACAGAA
* * *
247041 TATCGCTTTTACAAGCCAGACAGAA
1 TATCGCTCTTACGAGCCAAACAGAA
* *
247066 TATCACTCTTTCGAG
1 TATCGCTCTTACGAG
247081 TTAGATACAA
Statistics
Matches: 184, Mismatches: 46, Indels: 16
0.75 0.19 0.07
Matches are distributed among these distances:
23 1 0.01
24 36 0.20
25 145 0.79
26 2 0.01
ACGTcount: A:0.35, C:0.26, G:0.16, T:0.23
Consensus pattern (25 bp):
TATCGCTCTTACGAGCCAAACAGAA
Found at i:247033 original size:74 final size:74
Alignment explanation
Indices: 246921--247058 Score: 172
Period size: 74 Copynumber: 1.9 Consensus size: 74
246911 GGCAAAAATC
* * *
246921 ACTCTTACAAGCCAAACATAATACCGCTCCCACGAGCCA-A-ACGAAATATCGCTCTTACGAGCC
1 ACTCTTACAAGCCAAACAGAATACCGCTCCCACAAGCCAGATA-G-AATATCGCTCTTACAAGCC
246984 AAGAAGAGTTT
64 AAGAAGAGTTT
* * ** *
246995 ACTCTTACGAGTCAAACAGAATACCGCTCTTACAAGCCAGATAGAATATCGCTTTTACAAGCCA
1 ACTCTTACAAGCCAAACAGAATACCGCTCCCACAAGCCAGATAGAATATCGCTCTTACAAGCCA
247059 GACAGAATAT
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
74 51 0.94
75 2 0.04
76 1 0.02
ACGTcount: A:0.36, C:0.28, G:0.14, T:0.21
Consensus pattern (74 bp):
ACTCTTACAAGCCAAACAGAATACCGCTCCCACAAGCCAGATAGAATATCGCTCTTACAAGCCAA
GAAGAGTTT
Found at i:257427 original size:48 final size:48
Alignment explanation
Indices: 257356--257449 Score: 163
Period size: 48 Copynumber: 2.0 Consensus size: 48
257346 GAAAGTATCT
*
257356 AGAAATGTTTAGTGACAAATGAACACATTCCAAAAAAGGAACAACTCC
1 AGAAAGGTTTAGTGACAAATGAACACATTCCAAAAAAGGAACAACTCC
257404 AGAAAGGTTTAGTGA-AAACTGAACACATTCCAAAAAAGGAACAACT
1 AGAAAGGTTTAGTGACAAA-TGAACACATTCCAAAAAAGGAACAACT
257450 TGTAGATATC
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
47 3 0.07
48 41 0.93
ACGTcount: A:0.49, C:0.17, G:0.16, T:0.18
Consensus pattern (48 bp):
AGAAAGGTTTAGTGACAAATGAACACATTCCAAAAAAGGAACAACTCC
Found at i:269840 original size:24 final size:24
Alignment explanation
Indices: 269812--269877 Score: 80
Period size: 24 Copynumber: 2.8 Consensus size: 24
269802 AAACTTTGCT
*
269812 TGGGCTCGAATGAGCTAACTTATC
1 TGGGCTCGAATGAGCTAACCTATC
*
269836 TGGGCTC-ATAAGAGCTAACCTATC
1 TGGGCTCGA-ATGAGCTAACCTATC
* *
269860 TGGGCTTGTATGAGCTAA
1 TGGGCTCGAATGAGCTAA
269878 TTTTGTTTGG
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
23 1 0.03
24 34 0.97
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.29
Consensus pattern (24 bp):
TGGGCTCGAATGAGCTAACCTATC
Found at i:275164 original size:31 final size:31
Alignment explanation
Indices: 275126--275187 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
275116 TCAATCATGC
*
275126 ATTGTTGACGCATTTCCAGGTGAGTAATTAT
1 ATTGTTGACGCATTTCCAGGTGAGCAATTAT
275157 ATTGTTGACGCATTTCCAGGTGAGCAATTAT
1 ATTGTTGACGCATTTCCAGGTGAGCAATTAT
275188 TTCTTATCGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.37
Consensus pattern (31 bp):
ATTGTTGACGCATTTCCAGGTGAGCAATTAT
Found at i:293838 original size:23 final size:23
Alignment explanation
Indices: 293811--294102 Score: 365
Period size: 23 Copynumber: 12.8 Consensus size: 23
293801 ATCTTAATTC
293811 TTTAAGCACAAATCATATTAATA
1 TTTAAGCACAAATCATATTAATA
* * * *
293834 TTTAATCATAATTTATATTAATA
1 TTTAAGCACAAATCATATTAATA
*
293857 TTTAAGCACAAA-CACATTAATA
1 TTTAAGCACAAATCATATTAATA
*
293879 TTTGAGCACAAATCATATTAATA
1 TTTAAGCACAAATCATATTAATA
*
293902 TTTAAGCACAAATCACATTAATA
1 TTTAAGCACAAATCATATTAATA
* *
293925 TTTGAGCACAAATCACATTAATA
1 TTTAAGCACAAATCATATTAATA
*
293948 TTTGAGCACAAATCATATTAATA
1 TTTAAGCACAAATCATATTAATA
* * * *
293971 TTGAAACACATATCACATTAATA
1 TTTAAGCACAAATCATATTAATA
* *
293994 TTTAAGCATAAATCACATTAATA
1 TTTAAGCACAAATCATATTAATA
**
294017 TTGGAGCACAAATCATATTAATA
1 TTTAAGCACAAATCATATTAATA
294040 TTTAAGCACAAATCATATTAATA
1 TTTAAGCACAAATCATATTAATA
* *
294063 TTTGAA-AAAAAATCATATTAATA
1 TTT-AAGCACAAATCATATTAATA
*
294086 TTTAAACACAAAT-ATAT
1 TTTAAGCACAAATCATAT
294103 AAGCAAAAAT
Statistics
Matches: 232, Mismatches: 34, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
22 25 0.11
23 205 0.88
24 2 0.01
ACGTcount: A:0.47, C:0.13, G:0.05, T:0.34
Consensus pattern (23 bp):
TTTAAGCACAAATCATATTAATA
Found at i:296450 original size:531 final size:528
Alignment explanation
Indices: 295356--296387 Score: 1762
Period size: 531 Copynumber: 1.9 Consensus size: 528
295346 GTGGACTCAA
* * ** *
295356 CTCTACTACTCCGTACTACTATTTTTATATTATTTTATCGTAAGAATATATTATTTGGTGGTTTC
1 CTCTACTAATCCGAACTACTA-TTGCATATTATTTTATCATAAGAATATATTATTTGGTGGTTTC
* *
295421 GACGTGTATCATTGAAATATATAAAAATATAAAAAAATGTGTCATAGTTGGTTATGCCAGAATCT
65 GACATGTATCATTGAAATATATAAAAATATAAAAAAATGTGTCATAGTTGGTTATGCCAGAAACT
295486 TATGGTTGGTAGCACCGAACCTTATTGTTTCAAACTTCTTCAAGATGTAGATAGATTAATAATGA
130 TATGGTTGGTAGCACCGAACCTTATTGTTTCAAACTTCTTCAAGATGTAGATAGATTAATAATGA
295551 TCCAACATGGAGGAGTATAAAACATCTAACAAATAGAAGAGGGTGTGGGTGAAAGAAGATAAATC
195 TCCAACATGGAGGAGTATAAAACATCTAACAAATAGAAGAGGGTGTGGGTGAAAGAAGATAAATC
295616 ATTTATACAGTATGAAGATTAACAGAAGATTAAAGCTACTGTTAAAGATGATGTTGAAACAAAAG
260 ATTTATACAGTATGAAGATTAACAGAAGATTAAAGCTACTGTTAAAGATGATGTTGAAACAAAAG
295681 ATGAGACACTTGTAGATCAAATTAAAGATGTATTACCATGAATCTATCATTGAAGGCAGATTATA
325 ATGAGACACTTGTAGATCAAATTAAAGATGTATTACCATGAATCTATCATTGAAGGCAGATTATA
295746 GGGATATGGTCAGAGGTTGTGCAAGATGAATAATTGAGAGACACAAATAACAATAGAAACATGTC
390 GGGATATGGTCAGAGGTTGTGCAAGATGAATAATTGAGAGACACAAATAACAATAGAAACATGTC
* * ** * ** * *
295811 ATTTTTGTAAGTAATATATTTTTGAATGTTTTATTTTTCTTTTTAGAGGGATATCCATCACTTGG
455 ATTTTTGTAAGTAATATATTTTTGAATCTTTGATGATACTGCTTAGA-GGATAT-CATCACGTGA
*
295876 TTGTGTACTAAG
518 TTGTGGAC-AAG
* * **
295888 CTCTACTACTCCGTACTACTATTTTATATTATTTTATCATAAGAATATATTATTTGGTGGTTTCG
1 CTCTACTAATCCGAACTACTATTGCATATTATTTTATCATAAGAATATATTATTTGGTGGTTTCG
295953 ACATGTATCATTGAAATATATAAAAATATAAAAAAATGTGTCATAGTTGGTTAT-CCAAGAAACT
66 ACATGTATCATTGAAATATATAAAAATATAAAAAAATGTGTCATAGTTGGTTATGCC-AGAAACT
296017 TATGGTTGGTAGCACCGAACCTTATTGTTTCAAACTTCTTCAAGATGTAGATAGATTAATAATGA
130 TATGGTTGGTAGCACCGAACCTTATTGTTTCAAACTTCTTCAAGATGTAGATAGATTAATAATGA
296082 TCCAACATGGAGGAGTATAAAACATCTAACAAATAGAAGAGGGTGTGGGTGAAAGAAGATAAATC
195 TCCAACATGGAGGAGTATAAAACATCTAACAAATAGAAGAGGGTGTGGGTGAAAGAAGATAAATC
296147 ATTTATACAGTATGAAGATTAACAGAAGATTAAAGCTACTGTTAAAGATGATGTTGAAACAAAAG
260 ATTTATACAGTATGAAGATTAACAGAAGATTAAAGCTACTGTTAAAGATGATGTTGAAACAAAAG
* *
296212 ATGAGACACTTGTAGATCAAATTAAAGATGTATTACCATGAATCTGTCATTGAAGGTAGATTATA
325 ATGAGACACTTGTAGATCAAATTAAAGATGTATTACCATGAATCTATCATTGAAGGCAGATTATA
296277 GGGATATGGTCAGAGGTTGTGCAAGATGAATAATTGAGAGACACAAATAACAATAGAAACATGTC
390 GGGATATGGTCAGAGGTTGTGCAAGATGAATAATTGAGAGACACAAATAACAATAGAAACATGTC
*
296342 ATTTTTGTAAGTAATATA-TTTTGATATCTATATGATGATAGTGCTT
455 ATTTTTGTAAGTAATATATTTTTGA-ATCT-T-TGATGATACTGCTT
296388 CGAGTTATAG
Statistics
Matches: 483, Mismatches: 13, Indels: 7
0.96 0.03 0.01
Matches are distributed among these distances:
530 8 0.02
531 446 0.92
532 22 0.05
533 7 0.01
ACGTcount: A:0.38, C:0.11, G:0.19, T:0.33
Consensus pattern (528 bp):
CTCTACTAATCCGAACTACTATTGCATATTATTTTATCATAAGAATATATTATTTGGTGGTTTCG
ACATGTATCATTGAAATATATAAAAATATAAAAAAATGTGTCATAGTTGGTTATGCCAGAAACTT
ATGGTTGGTAGCACCGAACCTTATTGTTTCAAACTTCTTCAAGATGTAGATAGATTAATAATGAT
CCAACATGGAGGAGTATAAAACATCTAACAAATAGAAGAGGGTGTGGGTGAAAGAAGATAAATCA
TTTATACAGTATGAAGATTAACAGAAGATTAAAGCTACTGTTAAAGATGATGTTGAAACAAAAGA
TGAGACACTTGTAGATCAAATTAAAGATGTATTACCATGAATCTATCATTGAAGGCAGATTATAG
GGATATGGTCAGAGGTTGTGCAAGATGAATAATTGAGAGACACAAATAACAATAGAAACATGTCA
TTTTTGTAAGTAATATATTTTTGAATCTTTGATGATACTGCTTAGAGGATATCATCACGTGATTG
TGGACAAG
Found at i:303456 original size:26 final size:25
Alignment explanation
Indices: 303427--303486 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 25
303417 ATTACGTAAT
*
303427 TTTATTTTATTTTATTTTTACATTTG
1 TTTATTTTATTTTATTTCT-CATTTG
* *
303453 TTTAAGTTTGTTTTATTTCTCATTTG
1 TTT-ATTTTATTTTATTTCTCATTTG
*
303479 TTTTTTTT
1 TTTATTTT
303487 TTGCAAAATA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
25 3 0.11
26 12 0.43
27 13 0.46
ACGTcount: A:0.15, C:0.05, G:0.07, T:0.73
Consensus pattern (25 bp):
TTTATTTTATTTTATTTCTCATTTG
Found at i:310185 original size:14 final size:14
Alignment explanation
Indices: 310147--310186 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
310137 AAATTAAAAA
*
310147 TAAAACAAAATAAAT
1 TAAAAC-AAATAAAG
*
310162 TAAAATAAATAAAG
1 TAAAACAAATAAAG
310176 TAAAACAAATA
1 TAAAACAAATA
310187 TTGTTGCAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
14 17 0.77
15 5 0.23
ACGTcount: A:0.72, C:0.05, G:0.03, T:0.20
Consensus pattern (14 bp):
TAAAACAAATAAAG
Found at i:310280 original size:17 final size:17
Alignment explanation
Indices: 310258--310292 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
310248 AGCCTCAGCC
310258 TTAGTTCTCTCCTAACT
1 TTAGTTCTCTCCTAACT
310275 TTAGTTCTCTCCTAACT
1 TTAGTTCTCTCCTAACT
310292 T
1 T
310293 GAACCAATCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.17, C:0.29, G:0.06, T:0.49
Consensus pattern (17 bp):
TTAGTTCTCTCCTAACT
Found at i:312144 original size:103 final size:103
Alignment explanation
Indices: 311959--312187 Score: 323
Period size: 103 Copynumber: 2.2 Consensus size: 103
311949 TTGCGAGTCC
* *
311959 TCGATAGCTCGTGTGAGCAGCATCGTGATTCAAAAAAGATATATGAATCCTAAATGGACTGTAGA
1 TCGATAGCTCGTGTGAGCAGCATCGTGATTCAAAAAAGAGATATGAATCCTAAATGGACTATAGA
* * *
312024 CCCTTTTGCTGGCTGGGACTTATGCTTTATGCATACTA
66 CCCATTCGATGGCTGGGACTTATGCTTTATGCATACTA
* * * * *
312062 TCGACAGCTCGTGTGAGCAGCATCGTGATTCGAAAAGGAGATATGAATCCTAAATGGATTATAGG
1 TCGATAGCTCGTGTGAGCAGCATCGTGATTCAAAAAAGAGATATGAATCCTAAATGGACTATAGA
* *
312127 CCCATTCGATGGTTGGGACTTATGCTTTATGCATACTC
66 CCCATTCGATGGCTGGGACTTATGCTTTATGCATACTA
* * *
312165 CCAATAACTCGTGTGAGCAGCAT
1 TCGATAGCTCGTGTGAGCAGCAT
312188 TGTTAGGGAA
Statistics
Matches: 110, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
103 110 1.00
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.29
Consensus pattern (103 bp):
TCGATAGCTCGTGTGAGCAGCATCGTGATTCAAAAAAGAGATATGAATCCTAAATGGACTATAGA
CCCATTCGATGGCTGGGACTTATGCTTTATGCATACTA
Found at i:313012 original size:21 final size:22
Alignment explanation
Indices: 312986--313035 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
312976 TTAGTATAAC
*
312986 TAGAAGTA-AGACTTGTTTCGG
1 TAGAAGTAGAGACTTGTATCGG
* *
313007 TAGAAG-AGATATTTGTATCGG
1 TAGAAGTAGAGACTTGTATCGG
313028 TAGAAGTA
1 TAGAAGTA
313036 TGCACTATTC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 22 0.92
22 1 0.04
ACGTcount: A:0.34, C:0.06, G:0.28, T:0.32
Consensus pattern (22 bp):
TAGAAGTAGAGACTTGTATCGG
Found at i:315881 original size:15 final size:15
Alignment explanation
Indices: 315849--315899 Score: 61
Period size: 15 Copynumber: 3.4 Consensus size: 15
315839 GGAGCAATTC
*
315849 CTTCTTTTTCCTTC-T
1 CTTCTATTT-CTTCTT
315864 CTTCT-TTTCTCTCTT
1 CTTCTATTTCT-TCTT
315879 CTTCTATTTCTTCTT
1 CTTCTATTTCTTCTT
315894 CTTCTA
1 CTTCTA
315900 CTACAATACC
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
13 2 0.06
14 5 0.15
15 21 0.64
16 5 0.15
ACGTcount: A:0.04, C:0.31, G:0.00, T:0.65
Consensus pattern (15 bp):
CTTCTATTTCTTCTT
Found at i:323677 original size:24 final size:24
Alignment explanation
Indices: 323644--323690 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
323634 GTTAAGAGTA
*
323644 AAAACTGTCAGTGCAAATGTAATAT
1 AAAACTGTCAGAGCAAAT-TAATAT
323669 AAAA-TGTCAGAGCAAATTAATA
1 AAAACTGTCAGAGCAAATTAATA
323691 AAAGATGAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 5 0.24
24 12 0.57
25 4 0.19
ACGTcount: A:0.49, C:0.11, G:0.15, T:0.26
Consensus pattern (24 bp):
AAAACTGTCAGAGCAAATTAATAT
Found at i:325052 original size:12 final size:11
Alignment explanation
Indices: 325032--325063 Score: 55
Period size: 12 Copynumber: 2.8 Consensus size: 11
325022 TTGATAAGGG
325032 TTTGGTTTTTA
1 TTTGGTTTTTA
325043 TTTGGGTTTTTA
1 TTT-GGTTTTTA
325055 TTTGGTTTT
1 TTTGGTTTT
325064 AAAGGAAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 9 0.45
12 11 0.55
ACGTcount: A:0.06, C:0.00, G:0.22, T:0.72
Consensus pattern (11 bp):
TTTGGTTTTTA
Found at i:330618 original size:13 final size:14
Alignment explanation
Indices: 330589--330618 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
330579 TTCAGTACAT
330589 TGACATTTAACCTC
1 TGACATTTAACCTC
330603 TGACATTTAA-CTC
1 TGACATTTAACCTC
330616 TGA
1 TGA
330619 TTGCGTTGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.37
Consensus pattern (14 bp):
TGACATTTAACCTC
Found at i:336456 original size:20 final size:21
Alignment explanation
Indices: 336423--336461 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
336413 CATTTTTCTA
336423 TTTACTTTTATTTGTTTCAGT
1 TTTACTTTTATTTGTTTCAGT
336444 TTTACTTTT-TTTGTTTCA
1 TTTACTTTTATTTGTTTCA
336462 AATTCCTTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.13, C:0.10, G:0.08, T:0.69
Consensus pattern (21 bp):
TTTACTTTTATTTGTTTCAGT
Done.