Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D13
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: 64892201
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1760000 characters in sequence are not A, C, G, or T
File 124 of 221
Found at i:38219660 original size:7 final size:7
Alignment explanation
Indices: 38219648--38219692 Score: 90
Period size: 7 Copynumber: 6.4 Consensus size: 7
38219638 TTCGAACTTA
38219648 ATCAAAT
1 ATCAAAT
38219655 ATCAAAT
1 ATCAAAT
38219662 ATCAAAT
1 ATCAAAT
38219669 ATCAAAT
1 ATCAAAT
38219676 ATCAAAT
1 ATCAAAT
38219683 ATCAAAT
1 ATCAAAT
38219690 ATC
1 ATC
38219693 TACTAGTAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 38 1.00
ACGTcount: A:0.56, C:0.16, G:0.00, T:0.29
Consensus pattern (7 bp):
ATCAAAT
Found at i:38222409 original size:21 final size:22
Alignment explanation
Indices: 38222356--38222418 Score: 56
Period size: 21 Copynumber: 2.8 Consensus size: 22
38222346 AATAAAAATT
* *
38222356 TTAAATATTTCTAAATAATTAATG
1 TTAAATATTTATAAA-ATTTAA-G
*
38222380 TTAATTATTTATAAAATTTAA-
1 TTAAATATTTATAAAATTTAAG
* *
38222401 TTAAATATTAATACAATT
1 TTAAATATTTATAAAATT
38222419 GTATTATTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
21 15 0.45
23 5 0.15
24 13 0.39
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.48
Consensus pattern (22 bp):
TTAAATATTTATAAAATTTAAG
Found at i:38228950 original size:57 final size:57
Alignment explanation
Indices: 38228868--38229005 Score: 145
Period size: 57 Copynumber: 2.4 Consensus size: 57
38228858 TTTTTATAGT
** * * *
38228868 ATTATATATTATGATTTTCGTAAATTCATA-TAAAAATAGTTATATTAAAAATTTTATTAA
1 ATTATATATTAT--TTTTATTAAATT-ATATTAAAAATAATTATATT-AAAATATAATTAA
* *
38228928 ATTATATATTA-TTTTATTAAATTATATTTAATAATAATTATGTTAAAATATAATTAA
1 ATTATATATTATTTTTATTAAATTATA-TTAAAAATAATTATATTAAAATATAATTAA
*
38228985 ATTATTTATTATTTTTATTAA
1 ATTATATATTATTTTTATTAA
38229006 TGATCTTATT
Statistics
Matches: 67, Mismatches: 8, Indels: 8
0.81 0.10 0.10
Matches are distributed among these distances:
56 3 0.04
57 31 0.46
58 22 0.33
60 11 0.16
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.51
Consensus pattern (57 bp):
ATTATATATTATTTTTATTAAATTATATTAAAAATAATTATATTAAAATATAATTAA
Found at i:38229735 original size:15 final size:15
Alignment explanation
Indices: 38229715--38229769 Score: 55
Period size: 15 Copynumber: 3.8 Consensus size: 15
38229705 AAAATTAAAA
38229715 ATTTATATTTATATT
1 ATTTATATTTATATT
38229730 ATTTATAATTTA-A-T
1 ATTTAT-ATTTATATT
*
38229744 ATTTAATAATTATATT
1 ATTT-ATATTTATATT
38229760 -TTT-TATTTAT
1 ATTTATATTTAT
38229770 TAAAATTTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
13 6 0.18
14 9 0.26
15 13 0.38
16 6 0.18
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
ATTTATATTTATATT
Found at i:38230788 original size:7 final size:7
Alignment explanation
Indices: 38230776--38230824 Score: 64
Period size: 7 Copynumber: 6.7 Consensus size: 7
38230766 ATAAATATTT
38230776 TTTTTTA
1 TTTTTTA
38230783 TTTTTTA
1 TTTTTTA
38230790 TTTTTTAAA
1 TTTTTT--A
38230799 TATTTTTA
1 T-TTTTTA
38230807 -TTTTTA
1 TTTTTTA
38230813 TTTTTTA
1 TTTTTTA
38230820 TTTTT
1 TTTTT
38230825 AAAATAATTT
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
6 6 0.16
7 24 0.63
8 1 0.03
9 2 0.05
10 5 0.13
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (7 bp):
TTTTTTA
Found at i:38230813 original size:30 final size:29
Alignment explanation
Indices: 38230767--38230837 Score: 108
Period size: 30 Copynumber: 2.4 Consensus size: 29
38230757 CCAAATATAA
38230767 TAAATA-TTTTTTTTTATTTTTTATTTTT
1 TAAATATTTTTTTTTTATTTTTTATTTTT
38230795 TAAATATTTTTATTTTTATTTTTTATTTTT
1 TAAATATTTTT-TTTTTATTTTTTATTTTT
* *
38230825 AAAATAATTTTTT
1 TAAATATTTTTTT
38230838 AATGTTTATT
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
28 6 0.15
29 6 0.15
30 27 0.69
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (29 bp):
TAAATATTTTTTTTTTATTTTTTATTTTT
Found at i:38231708 original size:25 final size:23
Alignment explanation
Indices: 38231680--38231727 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 23
38231670 ACACACACAT
38231680 AAATTTTAAAAATGAAAAATAGAGG
1 AAATTTTAAAAAT-AAAAA-AGAGG
* *
38231705 AAATTTTCAAACTAAAAAAGAGG
1 AAATTTTAAAAATAAAAAAGAGG
38231728 GCTCAGATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 5 0.24
24 5 0.24
25 11 0.52
ACGTcount: A:0.58, C:0.04, G:0.15, T:0.23
Consensus pattern (23 bp):
AAATTTTAAAAATAAAAAAGAGG
Found at i:38232155 original size:132 final size:132
Alignment explanation
Indices: 38231918--38232167 Score: 378
Period size: 132 Copynumber: 1.9 Consensus size: 132
38231908 AGAAAAATAG
* * * *
38231918 ATAGAAGAGATGAACAAGAGAAGGCGGCGTCTATCGGTTGAGAGAGCCAGATATTTAAAGGGGAA
1 ATAGAAGAGATGAACAAGAGAAGGCGGCGACTAACGGTTAAGAGAGCCAGATATTTAAAGGGAAA
*
38231983 GAAATGAGAAGGTATAGGGTTTAAGTTTAGGTATTATGACAAATTTAACCTTTTACCTCTTCTAT
66 GAAATGAGAAGGTATAGGGTTTAAGTTTAGGTATAATGACAAATTTAACCTTTTACCTCTTCTAT
38232048 CA
131 CA
* * *
38232050 ATAGAATAGATGAACAGGAGAAGGCGGCGGAC-AACGGTTAAGATAGCCAGATATTTAAAGGGAA
1 ATAGAAGAGATGAACAAGAGAAGGCGGC-GACTAACGGTTAAGAGAGCCAGATATTTAAAGGGAA
* *
38232114 AGAAATGAGAAGGTATAGGGTTTAA-TATTAGGTGTAATGACAATTTTAACCTTT
65 AGAAATGAGAAGGTATAGGGTTTAAGT-TTAGGTATAATGACAAATTTAACCTTT
38232168 AATTTTTACA
Statistics
Matches: 106, Mismatches: 10, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
131 1 0.01
132 103 0.97
133 2 0.02
ACGTcount: A:0.38, C:0.10, G:0.26, T:0.26
Consensus pattern (132 bp):
ATAGAAGAGATGAACAAGAGAAGGCGGCGACTAACGGTTAAGAGAGCCAGATATTTAAAGGGAAA
GAAATGAGAAGGTATAGGGTTTAAGTTTAGGTATAATGACAAATTTAACCTTTTACCTCTTCTAT
CA
Found at i:38232494 original size:12 final size:13
Alignment explanation
Indices: 38232465--38232497 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
38232455 CACTAACATC
38232465 GTTAAAAATTTTA
1 GTTAAAAATTTTA
*
38232478 GTTAAAATTTTTA
1 GTTAAAAATTTTA
38232491 -TTAAAAA
1 GTTAAAAA
38232498 CTAGTTTAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
12 6 0.33
13 12 0.67
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (13 bp):
GTTAAAAATTTTA
Found at i:38236536 original size:19 final size:19
Alignment explanation
Indices: 38236495--38236544 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
38236485 TTGATGTTTT
* * *
38236495 TTTTATTGCTTTCTTGTTT
1 TTTTATTGTTTTCTTGCTA
*
38236514 TTTTATTGTTTTGTTGCTA
1 TTTTATTGTTTTCTTGCTA
*
38236533 TTTTCTTGTTTT
1 TTTTATTGTTTT
38236545 TTTCACTATT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.06, C:0.08, G:0.12, T:0.74
Consensus pattern (19 bp):
TTTTATTGTTTTCTTGCTA
Found at i:38236546 original size:31 final size:31
Alignment explanation
Indices: 38236504--38236573 Score: 97
Period size: 31 Copynumber: 2.3 Consensus size: 31
38236494 TTTTTATTGC
* * *
38236504 TTTCTTGTTTTTTT-ATTGTTTTGTTGCTAT
1 TTTCTTGTTTTTTTCACTATTTTGTTACTAT
38236534 TTTCTTGTTTTTTTCACTATTTTGTTACTAT
1 TTTCTTGTTTTTTTCACTATTTTGTTACTAT
*
38236565 TTTGTTGTT
1 TTTCTTGTT
38236574 ATTGTTTGGA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
30 14 0.40
31 21 0.60
ACGTcount: A:0.09, C:0.09, G:0.11, T:0.71
Consensus pattern (31 bp):
TTTCTTGTTTTTTTCACTATTTTGTTACTAT
Found at i:38237571 original size:19 final size:17
Alignment explanation
Indices: 38237547--38237590 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
38237537 AAAAAATTTA
38237547 AAATATATTTGTCTTTTT
1 AAATATATTT-TCTTTTT
*
38237565 AATATATACTTTCTTTTT
1 AA-ATATATTTTCTTTTT
38237583 AAATATAT
1 AAATATAT
38237591 AATAAAAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 5 0.22
18 11 0.48
19 7 0.30
ACGTcount: A:0.34, C:0.07, G:0.02, T:0.57
Consensus pattern (17 bp):
AAATATATTTTCTTTTT
Found at i:38237591 original size:19 final size:20
Alignment explanation
Indices: 38237543--38237591 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
38237533 TTCCAAAAAA
*
38237543 TTTAAA-ATATATTTGTCTT
1 TTTAAATATATACTTGTCTT
38237562 TTT-AATATATACTT-TCTT
1 TTTAAATATATACTTGTCTT
38237580 TTTAAATATATA
1 TTTAAATATATA
38237592 ATAAAAAAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
18 9 0.33
19 18 0.67
ACGTcount: A:0.35, C:0.06, G:0.02, T:0.57
Consensus pattern (20 bp):
TTTAAATATATACTTGTCTT
Found at i:38237873 original size:29 final size:29
Alignment explanation
Indices: 38237840--38237903 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
38237830 GGCTAAATTG
* *
38237840 AAAGATTGAAGATTTGGAGTTGGCTAGAT
1 AAAGATTGAAGATTTGAAATTGGCTAGAT
* *
38237869 AAAGATTGAAGATTTGAAATTGGTTGGAT
1 AAAGATTGAAGATTTGAAATTGGCTAGAT
38237898 AAAGAT
1 AAAGAT
38237904 CAAATTATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.39, C:0.02, G:0.28, T:0.31
Consensus pattern (29 bp):
AAAGATTGAAGATTTGAAATTGGCTAGAT
Found at i:38237964 original size:18 final size:18
Alignment explanation
Indices: 38237941--38237975 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
38237931 ATGTAATTAC
38237941 TTTAAAGTTGATCTTTAG
1 TTTAAAGTTGATCTTTAG
* *
38237959 TTTAAATTTGATTTTTA
1 TTTAAAGTTGATCTTTA
38237976 AAATTTTGAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.03, G:0.11, T:0.57
Consensus pattern (18 bp):
TTTAAAGTTGATCTTTAG
Found at i:38242682 original size:19 final size:19
Alignment explanation
Indices: 38242657--38242702 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
38242647 CTTGAATTCG
38242657 TAAAAAACAACAAAAAAGTA
1 TAAAAAACAACAAAAAA-TA
* *
38242677 -AAAAAATAATAAAAAATA
1 TAAAAAACAACAAAAAATA
38242695 TAAAAAAC
1 TAAAAAAC
38242703 GTCAAGTTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
18 2 0.09
19 20 0.91
ACGTcount: A:0.78, C:0.07, G:0.02, T:0.13
Consensus pattern (19 bp):
TAAAAAACAACAAAAAATA
Found at i:38243282 original size:29 final size:29
Alignment explanation
Indices: 38243210--38243270 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 29
38243200 AAAAAAGAGT
* *
38243210 GCTAGATTGAAAGATTGAAGATTTGAAGTTG
1 GCTAGA-T-AAAGATTGAAGATTTGAAATTA
38243241 GCTAGATAAAGATTGAAGATTTGAAATTA
1 GCTAGATAAAGATTGAAGATTTGAAATTA
38243270 G
1 G
38243271 TTGGGTAAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 21 0.75
30 1 0.04
31 6 0.21
ACGTcount: A:0.39, C:0.03, G:0.26, T:0.31
Consensus pattern (29 bp):
GCTAGATAAAGATTGAAGATTTGAAATTA
Found at i:38243337 original size:18 final size:18
Alignment explanation
Indices: 38243316--38243354 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
38243306 AATTCTATAA
38243316 TTAGTTTAAATTTGATCT
1 TTAGTTTAAATTTGATCT
38243334 TTAGTTTAAATTTGATCT
1 TTAGTTTAAATTTGATCT
38243352 TTA
1 TTA
38243355 AAATTTTGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.28, C:0.05, G:0.10, T:0.56
Consensus pattern (18 bp):
TTAGTTTAAATTTGATCT
Found at i:38249360 original size:18 final size:17
Alignment explanation
Indices: 38249327--38249365 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
38249317 TTTTATAAAT
38249327 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
38249345 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
38249362 TGTG
1 TGTG
38249366 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:38249618 original size:23 final size:23
Alignment explanation
Indices: 38249591--38249712 Score: 174
Period size: 23 Copynumber: 5.3 Consensus size: 23
38249581 AGTGTTATTG
38249591 ATCAGTGGTAGCTTCGGCTACA-
1 ATCAGTGGTAGCTTCGGCTACAT
* *
38249613 ATTCAGTGGTAGCTACGGCTCCAT
1 A-TCAGTGGTAGCTTCGGCTACAT
38249637 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* * * *
38249660 TTCAGTGGTAGCTACGACTACGT
1 ATCAGTGGTAGCTTCGGCTACAT
38249683 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
38249706 ATCAGTG
1 ATCAGTG
38249713 TGGCACTCAT
Statistics
Matches: 86, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
22 1 0.01
23 84 0.98
24 1 0.01
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.30
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:38249644 original size:46 final size:46
Alignment explanation
Indices: 38249591--38249712 Score: 192
Period size: 46 Copynumber: 2.7 Consensus size: 46
38249581 AGTGTTATTG
* *
38249591 ATCAGTGGTAGCTTCGGCTACAATTCAGTGGTAGCTACGGCTCCAT
1 ATCAGTGGTAGCTTCGGCTACAATTCAGTGGTAGCTACGACTACAT
* *
38249637 ATCAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTACGACTACGT
1 ATCAGTGGTAGCTTCGGCTACAATTCAGTGGTAGCTACGACTACAT
38249683 ATCAGTGGTAGCTTCGGCTAC-ATATCAGTG
1 ATCAGTGGTAGCTTCGGCTACAAT-TCAGTG
38249713 TGGCACTCAT
Statistics
Matches: 70, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
45 1 0.01
46 69 0.99
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.30
Consensus pattern (46 bp):
ATCAGTGGTAGCTTCGGCTACAATTCAGTGGTAGCTACGACTACAT
Found at i:38254177 original size:3 final size:3
Alignment explanation
Indices: 38254169--38254197 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
38254159 TCTCCATTCT
38254169 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
38254198 AGCCAAACTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:38259712 original size:23 final size:23
Alignment explanation
Indices: 38259595--38259716 Score: 113
Period size: 23 Copynumber: 5.3 Consensus size: 23
38259585 AGTGTTATTG
*
38259595 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCAGCTACAT
* * * *
38259618 TTTAATGGTAGCTATGA-CTACAT
1 ATCAGTGGTAGCT-TCAGCTACAT
* * *
38259641 ATCAATGATAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCAGCTACAT
* * *
38259664 TTCAGTGGTAGCTATGA-CTACGT
1 ATCAGTGGTAGCT-TCAGCTACAT
38259687 ATCAGTGGTAGCTTCAGCTACAT
1 ATCAGTGGTAGCTTCAGCTACAT
38259710 ATCAGTG
1 ATCAGTG
38259717 TGGCATTTAT
Statistics
Matches: 76, Mismatches: 19, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
22 3 0.04
23 71 0.93
24 2 0.03
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.33
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCAGCTACAT
Found at i:38259715 original size:46 final size:46
Alignment explanation
Indices: 38259595--38259716 Score: 181
Period size: 46 Copynumber: 2.7 Consensus size: 46
38259585 AGTGTTATTG
* *
38259595 ATCAGTGGTAGCTTCGGCTACATTTTAATGGTAGCTATGACTACAT
1 ATCAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTATGACTACAT
* * *
38259641 ATCAATGATAGCTTCGGCTACATTTCAGTGGTAGCTATGACTACGT
1 ATCAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTATGACTACAT
* *
38259687 ATCAGTGGTAGCTTCAGCTACATATCAGTG
1 ATCAGTGGTAGCTTCGGCTACATTTCAGTG
38259717 TGGCATTTAT
Statistics
Matches: 67, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 67 1.00
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.33
Consensus pattern (46 bp):
ATCAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTATGACTACAT
Found at i:38276562 original size:23 final size:22
Alignment explanation
Indices: 38276517--38276564 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
38276507 CAAGTATTAC
*
38276517 TAAAATGTTAGAATGATAAATA
1 TAAAATGTTAAAATGATAAATA
* *
38276539 TAAAATTTTAAAATTGATACATA
1 TAAAATGTTAAAA-TGATAAATA
38276562 TAA
1 TAA
38276565 TGTAACCCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 11 0.50
23 11 0.50
ACGTcount: A:0.54, C:0.02, G:0.08, T:0.35
Consensus pattern (22 bp):
TAAAATGTTAAAATGATAAATA
Found at i:38281145 original size:69 final size:69
Alignment explanation
Indices: 38281034--38281173 Score: 210
Period size: 69 Copynumber: 2.0 Consensus size: 69
38281024 GGAGAAGGGC
* * *
38281034 TAATAGGGTGTGATTCCCCTCATATGTATTATGATGAGGATTCGGGTCTCTCATTGTATTGGGCA
1 TAATAGAGTGTGATTCCCCTCATATGTATTATGATGAGGATTCGGGCCTCTCATTGTATTGAGCA
38281099 CAAT
66 CAAT
* * *
38281103 TAATAGAGTGTGTTTCCCCTTATATGTATTATGATCG-GGATTCGGGCCTTTCATTGTATTGAGC
1 TAATAGAGTGTGATTCCCCTCATATGTATTATGAT-GAGGATTCGGGCCTCTCATTGTATTGAGC
38281167 ACAAT
65 ACAAT
38281172 TA
1 TA
38281174 TATGTGTTTT
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
69 63 0.98
70 1 0.02
ACGTcount: A:0.24, C:0.16, G:0.23, T:0.38
Consensus pattern (69 bp):
TAATAGAGTGTGATTCCCCTCATATGTATTATGATGAGGATTCGGGCCTCTCATTGTATTGAGCA
CAAT
Found at i:38285941 original size:93 final size:94
Alignment explanation
Indices: 38285782--38285967 Score: 347
Period size: 93 Copynumber: 2.0 Consensus size: 94
38285772 TTTTGGTTTC
*
38285782 AGGTGATGGTTGAGTGATTAAAATTAAATTAAATTAAAAATTTGGGAACTAAAATGATAC-TTTT
1 AGGTGATGGTTGAGTGATTAAAATTAAATTAAATTAAAAATTTGGGAACAAAAATGATACTTTTT
38285846 TTTATGAATAATAAAGATATGGATTTTAT
66 TTTATGAATAATAAAGATATGGATTTTAT
38285875 AGGTGATGGTTGAGTGATTAAAATTAAATTAAATTAAAAATTTGGGAACAAAAATGATACTTTTT
1 AGGTGATGGTTGAGTGATTAAAATTAAATTAAATTAAAAATTTGGGAACAAAAATGATACTTTTT
*
38285940 TTTATGAATAATAATGATATGGATTTTA
66 TTTATGAATAATAAAGATATGGATTTTA
38285968 CTTTAACTAC
Statistics
Matches: 90, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
93 59 0.66
94 31 0.34
ACGTcount: A:0.42, C:0.02, G:0.17, T:0.39
Consensus pattern (94 bp):
AGGTGATGGTTGAGTGATTAAAATTAAATTAAATTAAAAATTTGGGAACAAAAATGATACTTTTT
TTTATGAATAATAAAGATATGGATTTTAT
Found at i:38286493 original size:30 final size:30
Alignment explanation
Indices: 38286459--38286518 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
38286449 GGCGGTGCAG
38286459 TGTGGATAGCGACATGGAAACCTTGGCCTT
1 TGTGGATAGCGACATGGAAACCTTGGCCTT
38286489 TGTGGATAGCGACATGGAAACCTTGGCCTT
1 TGTGGATAGCGACATGGAAACCTTGGCCTT
38286519 ACTTTGCACT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.23, C:0.20, G:0.30, T:0.27
Consensus pattern (30 bp):
TGTGGATAGCGACATGGAAACCTTGGCCTT
Found at i:38288041 original size:15 final size:15
Alignment explanation
Indices: 38288021--38288051 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
38288011 ATGATGTACT
*
38288021 ATCTATGTAAAAATC
1 ATCTATGCAAAAATC
38288036 ATCTATGCAAAAATC
1 ATCTATGCAAAAATC
38288051 A
1 A
38288052 AATGAAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.06, T:0.29
Consensus pattern (15 bp):
ATCTATGCAAAAATC
Found at i:38294394 original size:21 final size:22
Alignment explanation
Indices: 38294369--38294412 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
38294359 CAAATATAAG
*
38294369 TATTGTAT-TAACCAAATCATT
1 TATTGAATATAACCAAATCATT
38294390 TATTGAATATAACCAAATCATT
1 TATTGAATATAACCAAATCATT
38294412 T
1 T
38294413 TCATATGCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.41, C:0.14, G:0.05, T:0.41
Consensus pattern (22 bp):
TATTGAATATAACCAAATCATT
Found at i:38295017 original size:13 final size:13
Alignment explanation
Indices: 38294999--38295025 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
38294989 AAATACTCAA
38294999 ATTTCTCAAAAGC
1 ATTTCTCAAAAGC
38295012 ATTTCTCAAAAGC
1 ATTTCTCAAAAGC
38295025 A
1 A
38295026 ATAAAGAACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.22, G:0.07, T:0.30
Consensus pattern (13 bp):
ATTTCTCAAAAGC
Found at i:38296825 original size:3 final size:3
Alignment explanation
Indices: 38296817--38296846 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
38296807 CTGAAGTTGG
38296817 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
38296847 ATTATTAGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:38306385 original size:26 final size:26
Alignment explanation
Indices: 38306349--38306400 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
38306339 AAGCCCATGT
38306349 ATGCAAATCAGACAGAGTGTGAAGAA
1 ATGCAAATCAGACAGAGTGTGAAGAA
*
38306375 ATGCAAATCAGATAGAGTGTGAAGAA
1 ATGCAAATCAGACAGAGTGTGAAGAA
38306401 CTTGATGAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.46, C:0.10, G:0.27, T:0.17
Consensus pattern (26 bp):
ATGCAAATCAGACAGAGTGTGAAGAA
Found at i:38308373 original size:30 final size:30
Alignment explanation
Indices: 38308339--38308404 Score: 71
Period size: 31 Copynumber: 2.2 Consensus size: 30
38308329 TTGAATTGTG
*
38308339 TAATTCATATTCGAGTTAAATCGAAA-AACT
1 TAATTCATATTCGAGTT-AATCCAAATAACT
** *
38308369 TAATTTTTTATTCGAGTTGATCCAAATAACT
1 TAA-TTCATATTCGAGTTAATCCAAATAACT
38308400 TAATT
1 TAATT
38308405 AACTCAAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
30 11 0.37
31 19 0.63
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.41
Consensus pattern (30 bp):
TAATTCATATTCGAGTTAATCCAAATAACT
Found at i:38308381 original size:31 final size:31
Alignment explanation
Indices: 38308346--38308404 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
38308336 GTGTAATTCA
*
38308346 TATTCGAGTTAAATCGAAA-AACTTAATTTTT
1 TATTCGAGTT-AATCCAAATAACTTAATTTTT
*
38308377 TATTCGAGTTGATCCAAATAACTTAATT
1 TATTCGAGTTAATCCAAATAACTTAATT
38308405 AACTCAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 6 0.24
31 19 0.76
ACGTcount: A:0.37, C:0.12, G:0.10, T:0.41
Consensus pattern (31 bp):
TATTCGAGTTAATCCAAATAACTTAATTTTT
Found at i:38311613 original size:18 final size:18
Alignment explanation
Indices: 38311578--38311611 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
38311568 TAAAATACTA
38311578 TAAATATAAGTATTAAAT
1 TAAATATAAGTATTAAAT
*
38311596 TAAATTTAA-TATTAAA
1 TAAATATAAGTATTAAA
38311612 ATATTAAAAT
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:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (18 bp):
TAAATATAAGTATTAAAT
Found at i:38313692 original size:38 final size:38
Alignment explanation
Indices: 38313591--38313707 Score: 119
Period size: 38 Copynumber: 3.1 Consensus size: 38
38313581 GTAATAGAAA
* * * *
38313591 AATTCAACACTACCAGTAAACATGCTTAACATGTATTC
1 AATTCAACATTAGCAATCAACATGCTTAACATGTATTC
*
38313629 AATTCAACATTGGCAATCAACATGCTTAACATGTATTC
1 AATTCAACATTAGCAATCAACATGCTTAACATGTATTC
* * * * *
38313667 ACTTTAACATTAGTAAT-AGATATGCTTAACGTGTACTTC
1 AATTCAACATTAGCAATCA-ACATGCTTAACATGTA-TTC
38313706 AA
1 AA
38313708 AAGGTGGTGA
Statistics
Matches: 65, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
37 1 0.02
38 60 0.92
39 4 0.06
ACGTcount: A:0.38, C:0.20, G:0.10, T:0.32
Consensus pattern (38 bp):
AATTCAACATTAGCAATCAACATGCTTAACATGTATTC
Found at i:38314138 original size:20 final size:21
Alignment explanation
Indices: 38314105--38314152 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
38314095 CATGGTGCAC
*
38314105 AAAAATAAATAAAAAAAGAAA
1 AAAAAGAAATAAAAAAAGAAA
*
38314126 AAAAAGAAA-AAAAAAAGAGA
1 AAAAAGAAATAAAAAAAGAAA
*
38314146 AAGAAGA
1 AAAAAGA
38314153 GAGACTTTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.83, C:0.00, G:0.12, T:0.04
Consensus pattern (21 bp):
AAAAAGAAATAAAAAAAGAAA
Found at i:38314140 original size:10 final size:9
Alignment explanation
Indices: 38314115--38314139 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
38314105 AAAAATAAAT
38314115 AAAAAAAGA
1 AAAAAAAGA
38314124 AAAAAAAGA
1 AAAAAAAGA
38314133 AAAAAAA
1 AAAAAAA
38314140 AAGAGAAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:38314589 original size:21 final size:21
Alignment explanation
Indices: 38314567--38314616 Score: 70
Period size: 19 Copynumber: 2.5 Consensus size: 21
38314557 AAATAGCTTA
*
38314567 TATATTAATTAAA-A-TTTAC
1 TATATTTATTAAATATTTTAC
38314586 TATATTTATTAAATATTTTAC
1 TATATTTATTAAATATTTTAC
38314607 TAT-TTTATTA
1 TATATTTATTA
38314617 GAGTAATAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 12 0.43
20 8 0.29
21 8 0.29
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (21 bp):
TATATTTATTAAATATTTTAC
Found at i:38316995 original size:9 final size:9
Alignment explanation
Indices: 38316978--38317014 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
38316968 TTCGAGTTCG
38316978 AATTCGAAT
1 AATTCGAAT
*
38316987 AACTCGAAT
1 AATTCGAAT
38316996 AATTCGAAT
1 AATTCGAAT
38317005 AATTCGAAT
1 AATTCGAAT
38317014 A
1 A
38317015 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:38317097 original size:30 final size:31
Alignment explanation
Indices: 38317063--38317123 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 31
38317053 AAACCTTTTT
* * *
38317063 ACTTTTCCCTCAAAACTTTTACT-CCTTCCC
1 ACTTTCCCCCCAAAACCTTTACTCCCTTCCC
38317093 ACTTTCCCCCCAAAACCTTTACTCCCTTCCC
1 ACTTTCCCCCCAAAACCTTTACTCCCTTCCC
38317124 CTCCCAACCC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 20 0.74
31 7 0.26
ACGTcount: A:0.20, C:0.46, G:0.00, T:0.34
Consensus pattern (31 bp):
ACTTTCCCCCCAAAACCTTTACTCCCTTCCC
Found at i:38318050 original size:5 final size:5
Alignment explanation
Indices: 38318040--38318065 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
38318030 CTCGAAAATT
38318040 TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA T
38318066 CGAATGCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:38319770 original size:7 final size:7
Alignment explanation
Indices: 38319758--38319782 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
38319748 CTTCTTTTTC
38319758 TTTTCTT
1 TTTTCTT
38319765 TTTTCTT
1 TTTTCTT
38319772 TTTTCTT
1 TTTTCTT
38319779 TTTT
1 TTTT
38319783 AATCTAAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTCTT
Found at i:38325482 original size:50 final size:51
Alignment explanation
Indices: 38325355--38325601 Score: 225
Period size: 50 Copynumber: 4.8 Consensus size: 51
38325345 GATAATAACA
* * * ** * * *
38325355 TGCCAAAGCCATGTCCTAGACATGGTCTTACATGAGATGTTTCATGTAC--
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCCGG
* * * * **
38325404 TGCCAATTCCATATCCCATATATGGTCTTACATGGGAGTTCTCATAT-CGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCCGG
** *
38325454 TGTCC-ATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCT-CGG
1 TG-CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCCGG
* *
38325504 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATCCCAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-AT-CC---GG
*
38325560 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
38325602 TTACCCAAAT
Statistics
Matches: 161, Mismatches: 27, Indels: 13
0.80 0.13 0.06
Matches are distributed among these distances:
48 1 0.01
49 38 0.24
50 77 0.48
51 3 0.02
53 1 0.01
56 41 0.25
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (51 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCCGG
Found at i:38331243 original size:53 final size:53
Alignment explanation
Indices: 38331166--38331270 Score: 192
Period size: 53 Copynumber: 2.0 Consensus size: 53
38331156 CAATTTGTTA
*
38331166 TTTCCAAATTCAACTTGTTATAAGTTAAAATAAACCTGAAATCACTTATATAT
1 TTTCCAAATTCAACTTATTATAAGTTAAAATAAACCTGAAATCACTTATATAT
*
38331219 TTTCCAAATTCAACTTATTATAAGTTAAAATAGACCTGAAATCACTTATATA
1 TTTCCAAATTCAACTTATTATAAGTTAAAATAAACCTGAAATCACTTATATA
38331271 CATTCTTATG
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 50 1.00
ACGTcount: A:0.42, C:0.15, G:0.06, T:0.37
Consensus pattern (53 bp):
TTTCCAAATTCAACTTATTATAAGTTAAAATAAACCTGAAATCACTTATATAT
Found at i:38331295 original size:53 final size:53
Alignment explanation
Indices: 38331183--38331295 Score: 138
Period size: 53 Copynumber: 2.1 Consensus size: 53
38331173 ATTCAACTTG
** * **
38331183 TTATAAGTTAAAATAAACCTGAAATCACTTATATATTTTCCAAATTCAACTTA
1 TTATAAGTTAAAATAAACCTGAAATCACTTATATACATTCCAAATGCAACCAA
* **
38331236 TTATAAGTTAAAATAGACCTGAAATCACTTATATACATT-CTTATGCAACCAA
1 TTATAAGTTAAAATAAACCTGAAATCACTTATATACATTCCAAATGCAACCAA
38331288 TTCATAAG
1 TT-ATAAG
38331296 CTTACCAAAT
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
52 10 0.20
53 41 0.80
ACGTcount: A:0.42, C:0.16, G:0.06, T:0.35
Consensus pattern (53 bp):
TTATAAGTTAAAATAAACCTGAAATCACTTATATACATTCCAAATGCAACCAA
Found at i:38333248 original size:30 final size:30
Alignment explanation
Indices: 38333192--38333248 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
38333182 TACGAGCCTA
* *
38333192 GGGGCAAAATCGTAATTTTGTGAAACTTTT
1 GGGGCAAAAACGTAATTTTGTCAAACTTTT
38333222 GGGGCAAAAACGTAATTTT-TCCAAACT
1 GGGGCAAAAACGTAATTTTGT-CAAACT
38333249 ATGATTTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 1 0.04
30 23 0.96
ACGTcount: A:0.33, C:0.14, G:0.21, T:0.32
Consensus pattern (30 bp):
GGGGCAAAAACGTAATTTTGTCAAACTTTT
Found at i:38333609 original size:51 final size:51
Alignment explanation
Indices: 38333475--38333659 Score: 207
Period size: 51 Copynumber: 3.6 Consensus size: 51
38333465 AGTGAAAGTG
* * *
38333475 ATGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGA-A-TG
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACTGGATAGTA
* * * *
38333524 ATAGGTCGCATGTATAGTACTATGTGCAGGCTACTATGCGTACTGGATAGT-
1 AT-GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACTGGATAGTA
* * * * *
38333575 TTCGATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTA-TCGAATGGTA
1 AT-GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACT-GGATAGTA
38333627 ATGGTCACATGTGTAGTACTATGTGCAGGCTAC
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTAC
38333660 CACCGGACAT
Statistics
Matches: 112, Mismatches: 19, Indels: 8
0.81 0.14 0.06
Matches are distributed among these distances:
49 2 0.02
50 39 0.35
51 69 0.62
52 2 0.02
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.31
Consensus pattern (51 bp):
ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACTGGATAGTA
Found at i:38339994 original size:51 final size:51
Alignment explanation
Indices: 38339906--38340024 Score: 163
Period size: 51 Copynumber: 2.4 Consensus size: 51
38339896 ATAGAAATGG
* *
38339906 TGAAAATAGAG-AATGAGAAATCATTTGAAAATTATTATGGTTTTCTCCAAAA
1 TGAAAATAGAGAAATG-G-AATCATTTGAAAATGATTATGGTTTTCTACAAAA
*
38339958 TGAAAATAGAGAAATGGAATCATTTGGAAATGATTATGGTTTTCTACAAAA
1 TGAAAATAGAGAAATGGAATCATTTGAAAATGATTATGGTTTTCTACAAAA
*
38340009 TCAAAAT-GA-AAATGGA
1 TGAAAATAGAGAAATGGA
38340025 TAAATGGAGT
Statistics
Matches: 62, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
49 7 0.11
50 2 0.03
51 37 0.60
52 12 0.19
53 4 0.06
ACGTcount: A:0.45, C:0.07, G:0.18, T:0.30
Consensus pattern (51 bp):
TGAAAATAGAGAAATGGAATCATTTGAAAATGATTATGGTTTTCTACAAAA
Found at i:38340065 original size:51 final size:51
Alignment explanation
Indices: 38339906--38340075 Score: 153
Period size: 57 Copynumber: 3.2 Consensus size: 51
38339896 ATAGAAATGG
* * *
38339906 TGAAAATAGAG-AATGAGAAATCATTTGAAAATTATTATGGTTTTCTCCAAAA
1 TGAAAATGGAGAAATG-G-AATCATTTGAAAATAATTATGGTTTTCACCAAAA
* * *
38339958 TGAAAATAGAGAAATGGAATCATTTGGAAATGATTATGGTTTTCTACAAAATCAAAA
1 TGAAAATGGAGAAATGGAATCATTTGAAAATAATTATGGTTTTC-AC-----CAAAA
* * * *
38340015 TGAAAATGGATAAATGGAGTCATTTGAAAATAAATGTGGTTTTCACCAAAAAA
1 TGAAAATGGAGAAATGGAATCATTTGAAAATAATTATGGTTTTCACC--AAAA
38340068 TGAAAATG
1 TGAAAATG
38340076 AAAATAGTGA
Statistics
Matches: 99, Mismatches: 10, Indels: 17
0.79 0.08 0.13
Matches are distributed among these distances:
51 26 0.26
52 13 0.13
53 16 0.16
56 2 0.02
57 42 0.42
ACGTcount: A:0.45, C:0.07, G:0.18, T:0.30
Consensus pattern (51 bp):
TGAAAATGGAGAAATGGAATCATTTGAAAATAATTATGGTTTTCACCAAAA
Found at i:38340089 original size:59 final size:59
Alignment explanation
Indices: 38339953--38340123 Score: 206
Period size: 59 Copynumber: 2.9 Consensus size: 59
38339943 TGGTTTTCTC
* * *
38339953 CAAAATGAAAATAGAGAAATGGAATCATTTGGAAATGATTATGGTTTTCTA-C--AAAAT
1 CAAAATGAAAATAGTGAAATGGAATCATTTGGAAATGAATGTGGTTTTC-ACCAAAAAAT
* * * *
38340010 CAAAATGAAAATGGAT-AAATGGAGTCATTTGAAAATAAATGTGGTTTTCACCAAAAAAT
1 CAAAATGAAAATAG-TGAAATGGAATCATTTGGAAATGAATGTGGTTTTCACCAAAAAAT
* * *
38340069 GAAAATGAAAATAGTGAAATGGAATCATTTGGAAATGAATGTGATTTTCTCCAAA
1 CAAAATGAAAATAGTGAAATGGAATCATTTGGAAATGAATGTGGTTTTCACCAAA
38340124 TTGATAATGA
Statistics
Matches: 95, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
56 1 0.01
57 42 0.44
58 1 0.01
59 51 0.54
ACGTcount: A:0.46, C:0.08, G:0.18, T:0.29
Consensus pattern (59 bp):
CAAAATGAAAATAGTGAAATGGAATCATTTGGAAATGAATGTGGTTTTCACCAAAAAAT
Found at i:38341851 original size:183 final size:183
Alignment explanation
Indices: 38341543--38341913 Score: 715
Period size: 183 Copynumber: 2.0 Consensus size: 183
38341533 AAAATGGTCA
*
38341543 AAAAAATGACAACGAAAACGTGAAGTGGTATCGCAGTAGAAGTCCGTGGTGACAAAATTGAAGAT
1 AAAAAATGACAACGAAAACGTGAAGTGGTATCACAGTAGAAGTCCGTGGTGACAAAATTGAAGAT
*
38341608 CCAAAGTATGCTTTGGGGTGAATTTTTTAATTTTGTATTTTTTAGTTTTTCTAGGATGGAATTAT
66 CCAAAGTATGCTTTGGGGTGAATTTTTTAATTTTGCATTTTTTAGTTTTTCTAGGATGGAATTAT
38341673 GGAAACTTTTGTTGGTTAGAGTCATTTAAATTTTATGCTTTTATAGATGAGAT
131 GGAAACTTTTGTTGGTTAGAGTCATTTAAATTTTATGCTTTTATAGATGAGAT
*
38341726 AAAAAATGACAACGAAAACGTGAAGTGGTATCACAGTAGAAGTCGGTGGTGACAAAATTGAAGAT
1 AAAAAATGACAACGAAAACGTGAAGTGGTATCACAGTAGAAGTCCGTGGTGACAAAATTGAAGAT
38341791 CCAAAGTATGCTTTGGGGTGAATTTTTTAATTTTGCATTTTTTAGTTTTTCTAGGATGGAATTAT
66 CCAAAGTATGCTTTGGGGTGAATTTTTTAATTTTGCATTTTTTAGTTTTTCTAGGATGGAATTAT
38341856 GGAAACTTTTGTTGGTTAGAGTCATTTAAATTTTATGCTTTTATAGATGAGAT
131 GGAAACTTTTGTTGGTTAGAGTCATTTAAATTTTATGCTTTTATAGATGAGAT
38341909 AAAAA
1 AAAAA
38341914 TGGTGATATT
Statistics
Matches: 185, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
183 185 1.00
ACGTcount: A:0.33, C:0.08, G:0.22, T:0.37
Consensus pattern (183 bp):
AAAAAATGACAACGAAAACGTGAAGTGGTATCACAGTAGAAGTCCGTGGTGACAAAATTGAAGAT
CCAAAGTATGCTTTGGGGTGAATTTTTTAATTTTGCATTTTTTAGTTTTTCTAGGATGGAATTAT
GGAAACTTTTGTTGGTTAGAGTCATTTAAATTTTATGCTTTTATAGATGAGAT
Found at i:38350868 original size:105 final size:105
Alignment explanation
Indices: 38350734--38350940 Score: 396
Period size: 105 Copynumber: 2.0 Consensus size: 105
38350724 GATGTCATCT
38350734 GTTTAGGCTCCTCAGCAATAGTTTCCCCTTTATTAGCAATGGTTCCCAAATTCACTGATTCGACT
1 GTTTAGGCTCCTCAGCAATAGTTTCCCCTTTATTAGCAATGGTTCCCAAATTCACTGATTCGACT
*
38350799 CTGGCAGTAGGAGTTTGAGCTGGCTCCTCTGTAGCTTTAG
66 CTGGCAGTAGGAGTTTGAGCTGGCTCCTCTGCAGCTTTAG
38350839 GTTTAGGCTCCTCAGCAATAGTTTCCCCTTTATTAGCAATGGTTCCCAAATTCACTGATTCGACT
1 GTTTAGGCTCCTCAGCAATAGTTTCCCCTTTATTAGCAATGGTTCCCAAATTCACTGATTCGACT
*
38350904 CTGGCAGTATGAGTTTGAGCTGGCTCCTCTGCAGCTT
66 CTGGCAGTAGGAGTTTGAGCTGGCTCCTCTGCAGCTT
38350941 CAGGAATTGG
Statistics
Matches: 100, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
105 100 1.00
ACGTcount: A:0.20, C:0.25, G:0.21, T:0.34
Consensus pattern (105 bp):
GTTTAGGCTCCTCAGCAATAGTTTCCCCTTTATTAGCAATGGTTCCCAAATTCACTGATTCGACT
CTGGCAGTAGGAGTTTGAGCTGGCTCCTCTGCAGCTTTAG
Found at i:38354113 original size:12 final size:12
Alignment explanation
Indices: 38354096--38354121 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
38354086 ACAATTAAAA
38354096 AAATAAAGGAAG
1 AAATAAAGGAAG
38354108 AAATAAAGGAAG
1 AAATAAAGGAAG
38354120 AA
1 AA
38354122 CTTTGGGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.69, C:0.00, G:0.23, T:0.08
Consensus pattern (12 bp):
AAATAAAGGAAG
Found at i:38362520 original size:24 final size:24
Alignment explanation
Indices: 38362475--38362520 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
38362465 ATAAATAACT
**
38362475 GAAAAAAAAATCTAAAGCCTAAAA
1 GAAAAAAAAATCTAAAAACTAAAA
38362499 GAAAAGAAAAA-CTAAAAACTAA
1 GAAAA-AAAAATCTAAAAACTAA
38362521 TTACAGAGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 14 0.74
25 5 0.26
ACGTcount: A:0.70, C:0.11, G:0.09, T:0.11
Consensus pattern (24 bp):
GAAAAAAAAATCTAAAAACTAAAA
Found at i:38374120 original size:49 final size:50
Alignment explanation
Indices: 38374067--38374190 Score: 146
Period size: 48 Copynumber: 2.5 Consensus size: 50
38374057 GACGGACCAT
** * * * * **
38374067 TGGTAGGATATGTTAGTTGGTAATCAGA-TTGGCGTATATGTTGGGCCAC
1 TGGTAGGGCATGTTAGTTGCTAATCAGAGTTAGCGGAGATGAGGGGCCAC
38374116 TGGTAGGGCATGTTAG-TGCTAATCA-AGTTAGCGGAGATGAGGGGCCAC
1 TGGTAGGGCATGTTAGTTGCTAATCAGAGTTAGCGGAGATGAGGGGCCAC
*
38374164 TGGTAGGGCATGTTAGTTTCTAATCAG
1 TGGTAGGGCATGTTAGTTGCTAATCAG
38374191 CTTAGCGTTA
Statistics
Matches: 63, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
47 1 0.02
48 40 0.63
49 22 0.35
ACGTcount: A:0.23, C:0.12, G:0.34, T:0.31
Consensus pattern (50 bp):
TGGTAGGGCATGTTAGTTGCTAATCAGAGTTAGCGGAGATGAGGGGCCAC
Found at i:38374204 original size:48 final size:47
Alignment explanation
Indices: 38374067--38374232 Score: 145
Period size: 48 Copynumber: 3.4 Consensus size: 47
38374057 GACGGACCAT
** * * **
38374067 TGGTAGGATATGTTAGTTGGTAATCAGATTGGCGTATATGTTGGGCCAC
1 TGGTAGGGCATGTTAGTTGCTAATCAG-TTAGCGT-TATGAGGGGCCAC
**
38374116 TGGTAGGGCATGTTAG-TGCTAATCAAGTTAGCGGAGATGAGGGGCCAC
1 TGGTAGGGCATGTTAGTTGCTAATC-AGTTAGC-GTTATGAGGGGCCAC
* * * *
38374164 TGGTAGGGCATGTTAGTTTCTAATCAGCTTAGCGTTATGAGTGATGTCAT
1 TGGTAGGGCATGTTAGTTGCTAATCAG-TTAGCGTTATGAG-G-GGCCAC
*
38374214 TAGTAGGGCATGTTAGTTG
1 TGGTAGGGCATGTTAGTTG
38374233 TTAACCATGG
Statistics
Matches: 95, Mismatches: 16, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
48 45 0.47
49 30 0.32
50 20 0.21
ACGTcount: A:0.23, C:0.11, G:0.33, T:0.33
Consensus pattern (47 bp):
TGGTAGGGCATGTTAGTTGCTAATCAGTTAGCGTTATGAGGGGCCAC
Found at i:38396154 original size:40 final size:40
Alignment explanation
Indices: 38396071--38396373 Score: 396
Period size: 40 Copynumber: 7.6 Consensus size: 40
38396061 TTGAATGCTG
* * * * * *
38396071 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* * * * *
38396111 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
38396151 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
38396191 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
38396231 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
38396271 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
38396311 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
38396350 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
38396374 TGAACGAGGA
Statistics
Matches: 241, Mismatches: 19, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
39 35 0.15
40 198 0.82
41 8 0.03
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:38398811 original size:26 final size:27
Alignment explanation
Indices: 38398729--38398821 Score: 111
Period size: 27 Copynumber: 3.5 Consensus size: 27
38398719 GATTCGTGGG
*
38398729 AAAATGACTGAAATACCCTCAGAGGGT
1 AAAATGACTGAAATACCCTCGGAGGGT
* * *
38398756 AAAATGA-TCGAAATACCTTCGAAGGAT
1 AAAATGACT-GAAATACCCTCGGAGGGT
38398783 AAAATGACTG-AATACCC-CTGGAGGGT
1 AAAATGACTGAAATACCCTC-GGAGGGT
38398809 AAAATGACTGAAA
1 AAAATGACTGAAA
38398822 AGGGTAAAAT
Statistics
Matches: 55, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
25 1 0.02
26 22 0.40
27 31 0.56
28 1 0.02
ACGTcount: A:0.43, C:0.16, G:0.22, T:0.19
Consensus pattern (27 bp):
AAAATGACTGAAATACCCTCGGAGGGT
Found at i:38398882 original size:27 final size:28
Alignment explanation
Indices: 38398821--38398888 Score: 93
Period size: 28 Copynumber: 2.5 Consensus size: 28
38398811 AATGACTGAA
* *
38398821 AAGGGTAAAATGATCGAAATACCCCCCG
1 AAGGGTAAAATGAACGAAATACCCCCAG
* *
38398849 AAGGGTAAACTGAACGAAATACCCCCAT
1 AAGGGTAAAATGAACGAAATACCCCCAG
38398877 AA-GGTAAAATGA
1 AAGGGTAAAATGA
38398889 CTGTTATACT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
27 9 0.26
28 26 0.74
ACGTcount: A:0.44, C:0.21, G:0.21, T:0.15
Consensus pattern (28 bp):
AAGGGTAAAATGAACGAAATACCCCCAG
Found at i:38399284 original size:27 final size:28
Alignment explanation
Indices: 38399243--38399324 Score: 112
Period size: 27 Copynumber: 3.0 Consensus size: 28
38399233 ACTGTACTGG
38399243 TTACTGTATTGGGCTAAGGCCCACACTA
1 TTACTGTATTGGGCTAAGGCCCACACTA
* *
38399271 TT-CTGTATTGGGCTAAGGCCCACATTT
1 TTACTGTATTGGGCTAAGGCCCACACTA
* * *
38399298 TTATTGTTTTGGGTTAAGGCCCACACT
1 TTACTGTATTGGGCTAAGGCCCACACT
38399325 GTACTGTTAC
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
27 25 0.53
28 22 0.47
ACGTcount: A:0.21, C:0.22, G:0.22, T:0.35
Consensus pattern (28 bp):
TTACTGTATTGGGCTAAGGCCCACACTA
Found at i:38404114 original size:35 final size:35
Alignment explanation
Indices: 38404055--38404136 Score: 128
Period size: 35 Copynumber: 2.3 Consensus size: 35
38404045 TAGGCAATCC
*
38404055 AACACACCAGAAGCTCATAAGAGCTAATCCATCCGA
1 AACACACCA-AAGCTCATAAGAGCTAATCCATCCAA
* *
38404091 AACACACCAATGCTCATACGAGCTAATCCATCCAA
1 AACACACCAAAGCTCATAAGAGCTAATCCATCCAA
38404126 AACACACCAAA
1 AACACACCAAA
38404137 ACAGAGAGTA
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
35 33 0.79
36 9 0.21
ACGTcount: A:0.44, C:0.33, G:0.10, T:0.13
Consensus pattern (35 bp):
AACACACCAAAGCTCATAAGAGCTAATCCATCCAA
Found at i:38405737 original size:24 final size:22
Alignment explanation
Indices: 38405696--38405739 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 22
38405686 CATTATTCAA
*
38405696 ATTTCATATACATGTATCATAC
1 ATTTCATATACATATATCATAC
38405718 ATTTCATATATCAATATATCAT
1 ATTTCATATA-C-ATATATCAT
38405740 GTAACATCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 10 0.53
23 1 0.05
24 8 0.42
ACGTcount: A:0.39, C:0.16, G:0.02, T:0.43
Consensus pattern (22 bp):
ATTTCATATACATATATCATAC
Found at i:38413430 original size:24 final size:22
Alignment explanation
Indices: 38413389--38413432 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 22
38413379 CATTATTCAA
*
38413389 ATTTCATATATATGTATCATAC
1 ATTTCATATATATATATCATAC
38413411 ATTTCATATATCAATATATCAT
1 ATTTCATATAT--ATATATCAT
38413433 GTAACATCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 11 0.58
24 8 0.42
ACGTcount: A:0.39, C:0.14, G:0.02, T:0.45
Consensus pattern (22 bp):
ATTTCATATATATATATCATAC
Found at i:38413935 original size:14 final size:15
Alignment explanation
Indices: 38413916--38413944 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
38413906 GAAGAAGAAA
38413916 ACTTATTTTT-TTTT
1 ACTTATTTTTGTTTT
38413930 ACTTATTTTTGTTTT
1 ACTTATTTTTGTTTT
38413945 GATTTTATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.14, C:0.07, G:0.03, T:0.76
Consensus pattern (15 bp):
ACTTATTTTTGTTTT
Found at i:38420051 original size:25 final size:24
Alignment explanation
Indices: 38420020--38420066 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 24
38420010 TTTTCTTTAA
38420020 TTTTA-TTAACCTTTATTTAATAATT
1 TTTTATTTAACC-TTA-TTAATAATT
38420045 TTTTATTTAACCTTATTAATAA
1 TTTTATTTAACCTTATTAATAA
38420067 CCTTTAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 7 0.33
25 8 0.38
26 6 0.29
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.57
Consensus pattern (24 bp):
TTTTATTTAACCTTATTAATAATT
Found at i:38426506 original size:27 final size:27
Alignment explanation
Indices: 38426468--38426698 Score: 254
Period size: 27 Copynumber: 8.4 Consensus size: 27
38426458 TCAGATTCGT
*
38426468 GGGTAAAATGATCGAAATACCCCCGAA
1 GGGTAAAATGATCGAAATACCCTCGAA
*
38426495 GGGTAAAATGATCGACCGAAATACCCTCAAA
1 GGGTAAAATGAT----CGAAATACCCTCGAA
* *
38426526 GGGTAAAATGACCGAAATACCCCCGAA
1 GGGTAAAATGATCGAAATACCCTCGAA
**
38426553 GGGTAAAATGA-CTGAAATACCCTTAAA
1 GGGTAAAATGATC-GAAATACCCTCGAA
* * *
38426580 GGGTAAAAT-AACAAAAATACCCTTGAA
1 GGGTAAAATGATC-GAAATACCCTCGAA
*
38426607 GGGTAAAATGATCGAAATACCCTTGAA
1 GGGTAAAATGATCGAAATACCCTCGAA
*
38426634 GGGTAAAATGATCGAAATACCC-CCACA
1 GGGTAAAATGATCGAAATACCCTCGA-A
*
38426661 GGGTAAAATGACCGAAATACCCTC-ATA
1 GGGTAAAATGATCGAAATACCCTCGA-A
38426688 GGGTAAAATGA
1 GGGTAAAATGA
38426699 CCATTATACC
Statistics
Matches: 178, Mismatches: 17, Indels: 18
0.84 0.08 0.08
Matches are distributed among these distances:
26 3 0.02
27 148 0.83
28 3 0.02
31 24 0.13
ACGTcount: A:0.43, C:0.19, G:0.20, T:0.17
Consensus pattern (27 bp):
GGGTAAAATGATCGAAATACCCTCGAA
Found at i:38426697 original size:54 final size:54
Alignment explanation
Indices: 38426468--38426698 Score: 295
Period size: 54 Copynumber: 4.2 Consensus size: 54
38426458 TCAGATTCGT
38426468 GGGTAAAATGATCGAAATACCCCCGAAGGGTAAAATGATCGACCGAAATACCCTCAAA
1 GGGTAAAATGATCGAAATACCCCCGAAGGGT-AAA--AT-GACCGAAATACCCTCAAA
* * *
38426526 GGGTAAAATGACCGAAATACCCCCGAAGGGTAAAATGACTGAAATACCCTTAAA
1 GGGTAAAATGATCGAAATACCCCCGAAGGGTAAAATGACCGAAATACCCTCAAA
* * ** * **
38426580 GGGTAAAAT-AACAAAAATACCCTTGAAGGGTAAAATGATCGAAATACCCTTGAA
1 GGGTAAAATGATC-GAAATACCCCCGAAGGGTAAAATGACCGAAATACCCTCAAA
*
38426634 GGGTAAAATGATCGAAATACCCCC-ACAGGGTAAAATGACCGAAATACCCTCATA
1 GGGTAAAATGATCGAAATACCCCCGA-AGGGTAAAATGACCGAAATACCCTCAAA
38426688 GGGTAAAATGA
1 GGGTAAAATGA
38426699 CCATTATACC
Statistics
Matches: 152, Mismatches: 18, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
53 3 0.02
54 112 0.74
55 4 0.03
57 3 0.02
58 30 0.20
ACGTcount: A:0.43, C:0.19, G:0.20, T:0.17
Consensus pattern (54 bp):
GGGTAAAATGATCGAAATACCCCCGAAGGGTAAAATGACCGAAATACCCTCAAA
Found at i:38427049 original size:28 final size:28
Alignment explanation
Indices: 38427017--38427105 Score: 110
Period size: 28 Copynumber: 3.2 Consensus size: 28
38427007 GGTTGCATTA
38427017 CCACATTGTTACTATAATGGGCTAAGGC
1 CCACATTGTTACTATAATGGGCTAAGGC
* *
38427045 CCACATTGTTTCTATATTGGGCTAAGGC
1 CCACATTGTTACTATAATGGGCTAAGGC
* *
38427073 CCTCATTATTAC-AGT-ATCGGGCTAAGGC
1 CCACATTGTTACTA-TAAT-GGGCTAAGGC
38427101 CCACA
1 CCACA
38427106 CTGTGCTATT
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
27 2 0.04
28 50 0.96
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.29
Consensus pattern (28 bp):
CCACATTGTTACTATAATGGGCTAAGGC
Found at i:38439472 original size:21 final size:20
Alignment explanation
Indices: 38439448--38439502 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 20
38439438 AAATAAAATA
38439448 TTTTATATTTAAATATTATTC
1 TTTTATA-TTAAATATTATTC
**
38439469 TTTTGATAGAAAATATTATTC
1 TTTT-ATATTAAATATTATTC
*
38439490 TTTAATATTAAAT
1 TTTTATATTAAAT
38439503 TGATGTGGAA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
20 7 0.25
21 18 0.64
22 3 0.11
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.55
Consensus pattern (20 bp):
TTTTATATTAAATATTATTC
Found at i:38443017 original size:12 final size:13
Alignment explanation
Indices: 38443000--38443028 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
38442990 AATTTAATTT
38443000 CTTTAA-TTTTAA
1 CTTTAATTTTTAA
38443012 CTTTAATTTTTAA
1 CTTTAATTTTTAA
38443025 CTTT
1 CTTT
38443029 TTACTAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.38
13 10 0.62
ACGTcount: A:0.28, C:0.10, G:0.00, T:0.62
Consensus pattern (13 bp):
CTTTAATTTTTAA
Found at i:38444471 original size:9 final size:9
Alignment explanation
Indices: 38444454--38444490 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
38444444 TGAGTTTTCG
38444454 AATTCGAAT
1 AATTCGAAT
*
38444463 AACTCGAAT
1 AATTCGAAT
38444472 AATTCGAAT
1 AATTCGAAT
38444481 AATTCGAAT
1 AATTCGAAT
38444490 A
1 A
38444491 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:38444738 original size:30 final size:31
Alignment explanation
Indices: 38444704--38444763 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
38444694 AAACCTTTTA
*
38444704 TTTTCCCCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
* * *
38444734 TTTTCGCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCA
38444764 TCCCACCTCT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.20, C:0.38, G:0.02, T:0.40
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:38444884 original size:19 final size:19
Alignment explanation
Indices: 38444838--38444898 Score: 58
Period size: 19 Copynumber: 3.4 Consensus size: 19
38444828 ACTCCTCCTA
38444838 TTTACTTTCCCTC--AAACT
1 TTTACTTTCCC-CAAAAACT
*
38444856 TTT-C-TTCCCCAAAAATT
1 TTTACTTTCCCCAAAAACT
**
38444873 TTTACTTTCCCCCTAAACT
1 TTTACTTTCCCCAAAAACT
38444892 TTTACTT
1 TTTACTT
38444899 CTTACCCTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
15 1 0.03
16 5 0.14
17 8 0.23
18 4 0.11
19 17 0.49
ACGTcount: A:0.23, C:0.31, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTACTTTCCCCAAAAACT
Found at i:38445849 original size:22 final size:22
Alignment explanation
Indices: 38445801--38445868 Score: 57
Period size: 22 Copynumber: 3.0 Consensus size: 22
38445791 ATCTACTTCT
* **
38445801 AAAAATTATAAAAAATCTATGTGA
1 AAAAATTATAAAAAAAC-AT-AAA
38445825 AAAAATTATAAAAAAACATAAA
1 AAAAATTATAAAAAAACATAAA
* * *
38445847 AAAATTTAGAAAACAACA-AAA
1 AAAAATTATAAAAAAACATAAA
38445868 A
1 A
38445869 TATGATTTCC
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
21 4 0.11
22 16 0.42
23 2 0.05
24 16 0.42
ACGTcount: A:0.69, C:0.06, G:0.04, T:0.21
Consensus pattern (22 bp):
AAAAATTATAAAAAAACATAAA
Found at i:38450729 original size:23 final size:24
Alignment explanation
Indices: 38450703--38450755 Score: 99
Period size: 23 Copynumber: 2.2 Consensus size: 24
38450693 CAAAGTAAAC
38450703 ATCAATTCATTCAAGCAATACCT-
1 ATCAATTCATTCAAGCAATACCTA
38450726 ATCAATTCATTCAAGCAATACCTA
1 ATCAATTCATTCAAGCAATACCTA
38450750 ATCAAT
1 ATCAAT
38450756 ACCTAACAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 23 0.79
24 6 0.21
ACGTcount: A:0.42, C:0.25, G:0.04, T:0.30
Consensus pattern (24 bp):
ATCAATTCATTCAAGCAATACCTA
Found at i:38459830 original size:22 final size:24
Alignment explanation
Indices: 38459783--38459835 Score: 67
Period size: 22 Copynumber: 2.3 Consensus size: 24
38459773 TTTAAATATT
*
38459783 TTTAAA-AGTATAACCATTATAAA
1 TTTAAATAGTATAACCATTACAAA
*
38459806 TTTAAATA-TATAA-CATTACATA
1 TTTAAATAGTATAACCATTACAAA
38459828 TTTAAATA
1 TTTAAATA
38459836 AATCCTAACC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
22 15 0.56
23 11 0.41
24 1 0.04
ACGTcount: A:0.51, C:0.08, G:0.02, T:0.40
Consensus pattern (24 bp):
TTTAAATAGTATAACCATTACAAA
Found at i:38461161 original size:150 final size:150
Alignment explanation
Indices: 38460989--38461295 Score: 551
Period size: 150 Copynumber: 2.0 Consensus size: 150
38460979 GAGGAGGAAG
* *
38460989 AGGAAGAGGTGGGAGAGGTTGTTAGGTTGAAAAGAGAACGGATATCTTCGGTAAGGGAGAGGAAG
1 AGGAAGAGGTGAGAGAGGTTGTTAGGTTGAAAAGAGAACGGATATCTTCGGAAAGGGAGAGGAAG
*
38461054 ATTGTGGATAAAAAATCTGTAAAGCAGGAAACCGTGTCTGTTGAAGAAGATGAAGACAAGGATTA
66 ATTGCGGATAAAAAATCTGTAAAGCAGGAAACCGTGTCTGTTGAAGAAGATGAAGACAAGGATTA
38461119 TGAGGAGGAAGAAGAAGAAA
131 TGAGGAGGAAGAAGAAGAAA
38461139 AGGAAGAGGTGAGAGAGGTTGTTAGGTTGAAAAGAGAACGGATATCTTCGGAAAGGGAGAGGAAG
1 AGGAAGAGGTGAGAGAGGTTGTTAGGTTGAAAAGAGAACGGATATCTTCGGAAAGGGAGAGGAAG
* * * *
38461204 ATTGCGGATAAAAAATCTGTCAAGCGGGAAAGCTTGTCTGTTGAAGAAGATGAAGACAAGGATTA
66 ATTGCGGATAAAAAATCTGTAAAGCAGGAAACCGTGTCTGTTGAAGAAGATGAAGACAAGGATTA
38461269 TGAGGAGGAAGAAGAAGAAA
131 TGAGGAGGAAGAAGAAGAAA
38461289 AGGAAGA
1 AGGAAGA
38461296 TGATGATGAG
Statistics
Matches: 150, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
150 150 1.00
ACGTcount: A:0.40, C:0.06, G:0.36, T:0.18
Consensus pattern (150 bp):
AGGAAGAGGTGAGAGAGGTTGTTAGGTTGAAAAGAGAACGGATATCTTCGGAAAGGGAGAGGAAG
ATTGCGGATAAAAAATCTGTAAAGCAGGAAACCGTGTCTGTTGAAGAAGATGAAGACAAGGATTA
TGAGGAGGAAGAAGAAGAAA
Found at i:38461341 original size:36 final size:36
Alignment explanation
Indices: 38461300--38461416 Score: 153
Period size: 36 Copynumber: 3.2 Consensus size: 36
38461290 GGAAGATGAT
* * ** *
38461300 GATGAGGAGTTCACTCCAGATTTAGAAGATTGTTTG
1 GATGAGGAATTCACTCCGGATGAAGAGGATTGTTTG
* *
38461336 GATGAGGAATTTACTCTGGATGAAGAGGATTGTTTG
1 GATGAGGAATTCACTCCGGATGAAGAGGATTGTTTG
* *
38461372 GATGAAGAATTCACTCCGGATGAAGAGGATTGTTTA
1 GATGAGGAATTCACTCCGGATGAAGAGGATTGTTTG
38461408 GATGAGGAA
1 GATGAGGAA
38461417 GAGGAATTGA
Statistics
Matches: 69, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 69 1.00
ACGTcount: A:0.31, C:0.09, G:0.31, T:0.30
Consensus pattern (36 bp):
GATGAGGAATTCACTCCGGATGAAGAGGATTGTTTG
Found at i:38463914 original size:33 final size:33
Alignment explanation
Indices: 38463872--38463936 Score: 130
Period size: 33 Copynumber: 2.0 Consensus size: 33
38463862 AGTCAATTTT
38463872 CTGCTTCTCAGTGCTGATTGCTTTTACTGCTTC
1 CTGCTTCTCAGTGCTGATTGCTTTTACTGCTTC
38463905 CTGCTTCTCAGTGCTGATTGCTTTTACTGCTT
1 CTGCTTCTCAGTGCTGATTGCTTTTACTGCTT
38463937 GAGTTCTTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.09, C:0.26, G:0.18, T:0.46
Consensus pattern (33 bp):
CTGCTTCTCAGTGCTGATTGCTTTTACTGCTTC
Found at i:38463926 original size:17 final size:17
Alignment explanation
Indices: 38463873--38463927 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 17
38463863 GTCAATTTTC
38463873 TGCTTCTCAGTGCTGAT
1 TGCTTCTCAGTGCTGAT
* * ***
38463890 TGCTT-TTACTGCTTCC
1 TGCTTCTCAGTGCTGAT
38463906 TGCTTCTCAGTGCTGAT
1 TGCTTCTCAGTGCTGAT
38463923 TGCTT
1 TGCTT
38463928 TTACTGCTTG
Statistics
Matches: 27, Mismatches: 10, Indels: 2
0.69 0.26 0.05
Matches are distributed among these distances:
16 11 0.41
17 16 0.59
ACGTcount: A:0.09, C:0.25, G:0.20, T:0.45
Consensus pattern (17 bp):
TGCTTCTCAGTGCTGAT
Found at i:38469095 original size:18 final size:17
Alignment explanation
Indices: 38469062--38469103 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
38469052 AGCTTCTCAG
* *
38469062 AAATACTTTTGGGATAA
1 AAATATTTTTGAGATAA
38469079 AAAGTATTTTTGAGATAA
1 AAA-TATTTTTGAGATAA
38469097 AAATATT
1 AAATATT
38469104 GTTAAATAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.45, C:0.02, G:0.14, T:0.38
Consensus pattern (17 bp):
AAATATTTTTGAGATAA
Found at i:38471285 original size:19 final size:20
Alignment explanation
Indices: 38471263--38471302 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
38471253 AAAAAGTATG
*
38471263 TATAAAATCTAAAAA-AAAA
1 TATAAAATATAAAAATAAAA
*
38471282 TATAAATTATAAAAATAAAA
1 TATAAAATATAAAAATAAAA
38471302 T
1 T
38471303 TTACAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.28
Consensus pattern (20 bp):
TATAAAATATAAAAATAAAA
Found at i:38471405 original size:17 final size:18
Alignment explanation
Indices: 38471363--38471405 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
38471353 TTATTACAAA
*
38471363 AAAATTAT-AAAAATTGT
1 AAAATTATAAAAAAATGT
*
38471380 AAAAATATAAAAAAATGT
1 AAAATTATAAAAAAATGT
38471398 -AAATTATA
1 AAAATTATA
38471406 TTTTTAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 14 0.64
18 8 0.36
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (18 bp):
AAAATTATAAAAAAATGT
Found at i:38471406 original size:19 final size:18
Alignment explanation
Indices: 38471362--38471400 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
38471352 ATTATTACAA
*
38471362 AAAAAT-TATAAAAATTGT
1 AAAAATATA-AAAAAATGT
38471380 AAAAATATAAAAAAATGT
1 AAAAATATAAAAAAATGT
38471398 AAA
1 AAA
38471401 TTATATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 17 0.89
19 2 0.11
ACGTcount: A:0.69, C:0.00, G:0.05, T:0.26
Consensus pattern (18 bp):
AAAAATATAAAAAAATGT
Found at i:38471448 original size:24 final size:24
Alignment explanation
Indices: 38471388--38471434 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
38471378 GTAAAAATAT
*
38471388 AAAAAAATGTAAATTATATTTTTA
1 AAAAAAATTTAAATTATATTTTTA
*
38471412 AAAAAAATTTAAATTATTTTTTT
1 AAAAAAATTTAAATTATATTTTT
38471435 TATAAAATTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (24 bp):
AAAAAAATTTAAATTATATTTTTA
Found at i:38474851 original size:20 final size:20
Alignment explanation
Indices: 38474828--38474868 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
38474818 CTTAAACAAA
*
38474828 TTAAGATTTATTTAA-TTAAT
1 TTAAG-TTTAATTAACTTAAT
38474848 TTAAGTTTAATTAACTTAAT
1 TTAAGTTTAATTAACTTAAT
38474868 T
1 T
38474869 AACAAATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.54
Consensus pattern (20 bp):
TTAAGTTTAATTAACTTAAT
Found at i:38475464 original size:49 final size:50
Alignment explanation
Indices: 38475392--38475521 Score: 183
Period size: 49 Copynumber: 2.6 Consensus size: 50
38475382 TGCCTTTGGT
* * * *
38475392 TGAAAATCATCATTGTCGGGCTATCCGAGATGA-TAGGATAAGTAAATTG
1 TGAAAACCATCATTTTCAGGCTATCCGTGATGAGTAGGATAAGTAAATTG
** *
38475441 TGAAAACCATTGTTTTCAGGCTATCTGTGAT-AGTAGGATAAGTAAATTG
1 TGAAAACCATCATTTTCAGGCTATCCGTGATGAGTAGGATAAGTAAATTG
38475490 TGAAAACCATCATTTTCAGGCTATCCGTGATG
1 TGAAAACCATCATTTTCAGGCTATCCGTGATG
38475522 GTAAAATGTA
Statistics
Matches: 69, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
48 1 0.01
49 68 0.99
ACGTcount: A:0.32, C:0.14, G:0.22, T:0.32
Consensus pattern (50 bp):
TGAAAACCATCATTTTCAGGCTATCCGTGATGAGTAGGATAAGTAAATTG
Found at i:38475606 original size:23 final size:23
Alignment explanation
Indices: 38475579--38475625 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
38475569 TGATAATGTA
38475579 TTGTATAGTGCGAACCATCGTTG
1 TTGTATAGTGCGAACCATCGTTG
38475602 TTGTATAGTGCGAACCATCGTTG
1 TTGTATAGTGCGAACCATCGTTG
38475625 T
1 T
38475626 CGGGCCACTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.21, C:0.17, G:0.26, T:0.36
Consensus pattern (23 bp):
TTGTATAGTGCGAACCATCGTTG
Found at i:38482921 original size:32 final size:32
Alignment explanation
Indices: 38482865--38482932 Score: 100
Period size: 32 Copynumber: 2.1 Consensus size: 32
38482855 TTTTTGGAGG
* * *
38482865 TTGATTAATGCAAATCCTTAAAGAAATTAGAA
1 TTGATTAATACAAACCCCTAAAGAAATTAGAA
*
38482897 TTGATTAATACAAACCCCTGAAGAAATTAGAA
1 TTGATTAATACAAACCCCTAAAGAAATTAGAA
38482929 TTGA
1 TTGA
38482933 ATAGAAAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.46, C:0.12, G:0.13, T:0.29
Consensus pattern (32 bp):
TTGATTAATACAAACCCCTAAAGAAATTAGAA
Found at i:38484456 original size:4 final size:4
Alignment explanation
Indices: 38484449--38484554 Score: 185
Period size: 4 Copynumber: 26.5 Consensus size: 4
38484439 GTTAAAATAA
*
38484449 ATGT ATGT GTGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* *
38484497 ATGT ATGT GTGT ATGT GTGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
38484545 ATGT ATGT AT
1 ATGT ATGT AT
38484555 ATGTTGAATT
Statistics
Matches: 96, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 96 1.00
ACGTcount: A:0.23, C:0.00, G:0.27, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:38494124 original size:125 final size:125
Alignment explanation
Indices: 38493896--38494167 Score: 424
Period size: 125 Copynumber: 2.2 Consensus size: 125
38493886 TTATTTCGAG
* **
38493896 TTGACGTTTCTG-GTCAAATAGTATAAAATCGCTTCTACCAAGATGCTATCAGAGAAGAAATTGT
1 TTGACGTTTCTGAG-CAAATAGTATAAAATCACTGATACCAAGATGCTATCAGAGAAGAAATTGT
* *
38493960 GAAATCGTGCCCTTGTGGACGCGATTTCGGTACAGTTGGTCATGTAAGAAATAATT-TTTT
65 GAAATCGCGCCCTTGTGGACGCGATTTCGCTACAGTTGGTCATGTAAGAAATAATTATTTT
*
38494020 TTGACGTTTTCTGAGCAAATAGTATAAAATCACTGATACCAGGATGCTAT-ATGAGAAGAAATTG
1 TTGACG-TTTCTGAGCAAATAGTATAAAATCACTGATACCAAGATGCTATCA-GAGAAGAAATTG
* *
38494084 TGAAATTGCGCCCTTGTGGACGCGATTTCGCTACAGTTGGTCATGTAGGAAATAATTATTTT
64 TGAAATCGCGCCCTTGTGGACGCGATTTCGCTACAGTTGGTCATGTAAGAAATAATTATTTT
38494146 TTGACGTTTCTGAGCAAATAGT
1 TTGACGTTTCTGAGCAAATAGT
38494168 GTCAGATCGC
Statistics
Matches: 136, Mismatches: 8, Indels: 7
0.90 0.05 0.05
Matches are distributed among these distances:
124 7 0.05
125 118 0.87
126 11 0.08
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (125 bp):
TTGACGTTTCTGAGCAAATAGTATAAAATCACTGATACCAAGATGCTATCAGAGAAGAAATTGTG
AAATCGCGCCCTTGTGGACGCGATTTCGCTACAGTTGGTCATGTAAGAAATAATTATTTT
Found at i:38497352 original size:29 final size:29
Alignment explanation
Indices: 38497302--38498222 Score: 1139
Period size: 29 Copynumber: 31.5 Consensus size: 29
38497292 ATTAAAATGA
**
38497302 GTTTTTAATTAAATTAGTTTAGGGTTAGG
1 GTTTTTAATTAAATTAAATTAGGGTTAGG
* ***
38497331 GTTTTTAATTAAAATGGGTTAGGGTTAGG
1 GTTTTTAATTAAATTAAATTAGGGTTAGG
*
38497360 GTTTTTAATTAAATTAGATTAGGGTTTAGG
1 GTTTTTAATTAAATTAAATTAGGG-TTAGG
** *
38497390 GTTTTTAATTAAATTAGGTTAGGGTTTAGT
1 GTTTTTAATTAAATTAAATTAGGG-TTAGG
*
38497420 G-TTTTAATTAAATTAAACTAGGGTTAGG
1 GTTTTTAATTAAATTAAATTAGGGTTAGG
* **
38497448 GTTTTTAATTAACTTAGGTTAGGGTTTAGG
1 GTTTTTAATTAAATTAAATTAGGG-TTAGG
38497478 G-TTTTAATTAAATTAAATTAGGGTTAGG
1 GTTTTTAATTAAATTAAATTAGGGTTAGG
*
38497506 GTTTTTAATTAAATTAAACTAGGGTTAGG
1 GTTTTTAATTAAATTAAATTAGGGTTAGG
* * *
38497535 GTTTTTAATTAAAATGAGTTAGGGTTAGG
1 GTTTTTAATTAAATTAAATTAGGGTTAGG
*
38497564 GTTTTTAATTAAATTAAATTAGGGTTAAG
1 GTTTTTAATTAAATTAAATTAGGGTTAGG
38497593 GTTTTTAATTAAATTAAATTAAACTAGGGTTAGG
1 GTTTTTAATTAAATTAAA-T----TAGGGTTAGG
*
38497627 GTTTTTAATTAAATTAAACTAGGGTTAGG
1 GTTTTTAATTAAATTAAATTAGGGTTAGG
* *** *
38497656 GTTTTTAATTAAAATGGGTTAGGGTTAGA
1 GTTTTTAATTAAATTAAATTAGGGTTAGG
*
38497685 GTTTTTAATTAAATTAAACTAGGGTTAGG
1 GTTTTTAATTAAATTAAATTAGGGTTAGG
* **
38497714 GTTTTTATTTAAATTAGGTTAGGGTTTAGG
1 GTTTTTAATTAAATTAAATTAGGG-TTAGG
38497744 G-TTTTAATTAAATTAAATTAGGGTTAGG
1 GTTTTTAATTAAATTAAATTAGGGTTAGG
*
38497772 GTTTTTACTTAAATTAAATTAGGGTTAGG
1 GTTTTTAATTAAATTAAATTAGGGTTAGG
***
38497801 GTTTTTAATT-AATATGGGTTAGGGTTAGG
1 GTTTTTAATTAAAT-TAAATTAGGGTTAGG
38497830 GTTTTTAATTAAATTAAATTAAACTAGGGTTAGG
1 GTTTTTAATTAAATTAAA-T----TAGGGTTAGG
* *
38497864 GTTTTTAATTAAATTAAACTAGGGTTAGA
1 GTTTTTAATTAAATTAAATTAGGGTTAGG
* * **
38497893 ATTTTTATTTAAATTAGGTTAGGGTTTAGG
1 GTTTTTAATTAAATTAAATTAGGG-TTAGG
38497923 G-TTTTAATTAAATTAAATTAGGGTTAGG
1 GTTTTTAATTAAATTAAATTAGGGTTAGG
*
38497951 GTTTTTAATTAAATTAAACTAGGGTTAGG
1 GTTTTTAATTAAATTAAATTAGGGTTAGG
* *
38497980 GTTTTTAATTAAAATAGATTAGGGTTAGG
1 GTTTTTAATTAAATTAAATTAGGGTTAGG
38498009 GTTTTTAATTAAATTAAATTAAATTAGGGTTAGG
1 G--TTT--TT-AATTAAATTAAATTAGGGTTAGG
*
38498043 GTTTTTAATTAAATTAAAATAGGGTTAGG
1 GTTTTTAATTAAATTAAATTAGGGTTAGG
*
38498072 GTTTTTAATTAAATTAAATTAGGGTCAGG
1 GTTTTTAATTAAATTAAATTAGGGTTAGG
*
38498101 GTTTTTAATTAAATTAAACTAGGGTTAGG
1 GTTTTTAATTAAATTAAATTAGGGTTAGG
38498130 GTTTTTAATT--A--AAA-T-GGGTTAGG
1 GTTTTTAATTAAATTAAATTAGGGTTAGG
*
38498153 GTTTTTAATTAAATTAAATTA-GGTTTGG
1 GTTTTTAATTAAATTAAATTAGGGTTAGG
38498181 GTTTTTAATTAAATTAAATTA-GGTTAGG
1 GTTTTTAATTAAATTAAATTAGGGTTAGG
*
38498209 GTTTTTAATCAAAT
1 GTTTTTAATTAAAT
38498223 AATATCAAAA
Statistics
Matches: 778, Mismatches: 83, Indels: 63
0.84 0.09 0.07
Matches are distributed among these distances:
23 18 0.02
24 1 0.00
25 4 0.01
27 4 0.01
28 73 0.09
29 536 0.69
30 57 0.07
31 3 0.00
32 3 0.00
33 2 0.00
34 77 0.10
ACGTcount: A:0.33, C:0.01, G:0.22, T:0.44
Consensus pattern (29 bp):
GTTTTTAATTAAATTAAATTAGGGTTAGG
Found at i:38497465 original size:24 final size:23
Alignment explanation
Indices: 38497430--38497474 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 23
38497420 GTTTTAATTA
38497430 AATTAAACTAGGGTTAGGGTTTTT
1 AATTAAACTA-GGTTAGGGTTTTT
38497454 AATT-AACTTAGGTTAGGGTTT
1 AATTAAAC-TAGGTTAGGGTTT
38497475 AGGGTTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.29, C:0.04, G:0.24, T:0.42
Consensus pattern (23 bp):
AATTAAACTAGGTTAGGGTTTTT
Found at i:38497667 original size:179 final size:175
Alignment explanation
Indices: 38497302--38498222 Score: 1160
Period size: 179 Copynumber: 5.2 Consensus size: 175
38497292 ATTAAAATGA
** * ****
38497302 GTTTTTAATTAAATTAGTTTAGGGTTAGGGTTTTTAATTAAAATGGGTTAGGGTTAGGGTTTTTA
1 GTTTTTAATTAAATTAAATTAGGGTTAGGGTTTTTAATTAAATTAAACTAGGGTTAGGGTTTTTA
** *
38497367 ATT-AAATTAGATTAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTA-GTGTTTTAATTA
66 ATTAAAATTAG-TTAGGGTTTAGGGTTTTTAATTAAATTAAATTAGGG-TTAGGTTTTTTAATTA
* *
38497430 AATTAAACTAGGGTTAGGGTTTTTAATTAACTTAGGTTAGGGTTTAGG
129 AATTAAACTAGGGTTAGGGTTTTTAATTAAATTAGATTAGGG-TTAGG
38497478 G-TTTTAATTAAATTAAATTAGGGTTAGGGTTTTTAATTAAATTAAACTAGGGTTAGGGTTTTTA
1 GTTTTTAATTAAATTAAATTAGGGTTAGGGTTTTTAATTAAATTAAACTAGGGTTAGGGTTTTTA
*
38497542 ATTAAAATGAGTTAGGG-TTAGGGTTTTTAATTAAATTAAATTAGGGTTAAGGTTTTTAATTAAA
66 ATTAAAATTAGTTAGGGTTTAGGGTTTTTAATTAAATTAAATTAGGGTT-AGG-TTTT--TT-AA
* *
38497606 TTAAATTAAACTAGGGTTAGGGTTTTTAATTAAATTAAACTAGGGTTAGG
126 TTAAATTAAACTAGGGTTAGGGTTTTTAATTAAATTAGATTAGGGTTAGG
* *** *
38497656 GTTTTTAATTAAAATGGGTTAGGGTTAGAGTTTTTAATTAAATTAAACTAGGGTTAGGGTTTTT-
1 GTTTTTAATTAAATTAAATTAGGGTTAGGGTTTTTAATTAAATTAAACTAGGGTTAGGGTTTTTA
* * *
38497720 ATTTAAATTAGGTTAGGGTTTAGGG-TTTTAATTAAATTAAATTAGGGTTAGGGTTTTTACTTAA
66 ATTAAAATTA-GTTAGGGTTTAGGGTTTTTAATTAAATTAAATTAGGGTTAGGTTTTTTAATTAA
* * *
38497784 ATTAAATTAGGGTTAGGGTTTTTAATT-AATATGGGTTAGGGTTAGG
130 ATTAAACTAGGGTTAGGGTTTTTAATTAAAT-TAGATTAGGGTTAGG
**
38497830 GTTTTTAATTAAATTAAATTAAACTAGGGTTAGGGTTTTTAATTAAATTAAACTAGGGTTAGAAT
1 GTTTTTAATTAAATTAAA-T----TAGGGTTAGGGTTTTTAATTAAATTAAACTAGGGTTAGGGT
* *
38497895 TTTT-ATTTAAATTAGGTTAGGGTTTAGGG-TTTTAATTAAATTAAATTAGGGTTAGGGTTTTTA
61 TTTTAATTAAAATTA-GTTAGGGTTTAGGGTTTTTAATTAAATTAAATTAGGGTTAGGTTTTTTA
*
38497958 ATTAAATTAAACTAGGGTTAGGGTTTTTAATTAAAATAGATTAGGGTTAGG
125 ATTAAATTAAACTAGGGTTAGGGTTTTTAATTAAATTAGATTAGGGTTAGG
*
38498009 GTTTTTAATTAAATTAAATTAAATTAGGGTTAGGGTTTTTAATTAAATTAAAATAGGGTTAGGGT
1 G--TTT--TT-AATTAAATTAAATTAGGGTTAGGGTTTTTAATTAAATTAAACTAGGGTTAGGGT
* * * *
38498074 TTTTAATT-AAATTAAATTAGGG-TCAGGGTTTTTAATTAAATTAAACTAGGGTTAGGGTTTTTA
61 TTTTAATTAAAATT-AGTTAGGGTTTAGGGTTTTTAATTAAATTAAATTAGGGTTAGGTTTTTTA
* *
38498137 ATT--A--AAA-T-GGGTTAGGGTTTTTAATTAAATTAAATTA-GGTTTGG
125 ATTAAATTAAACTAGGGTTAGGGTTTTTAATTAAATTAGATTAGGGTTAGG
*
38498181 GTTTTTAATTAAATTAAATTA-GGTTAGGGTTTTTAATCAAAT
1 GTTTTTAATTAAATTAAATTAGGGTTAGGGTTTTTAATTAAAT
38498223 AATATCAAAA
Statistics
Matches: 669, Mismatches: 51, Indels: 60
0.86 0.07 0.08
Matches are distributed among these distances:
166 20 0.03
167 15 0.02
168 2 0.00
170 3 0.00
172 7 0.01
173 32 0.05
174 85 0.13
175 72 0.11
176 10 0.01
177 4 0.01
178 24 0.04
179 365 0.55
180 12 0.02
181 3 0.00
183 3 0.00
184 12 0.02
ACGTcount: A:0.33, C:0.01, G:0.22, T:0.44
Consensus pattern (175 bp):
GTTTTTAATTAAATTAAATTAGGGTTAGGGTTTTTAATTAAATTAAACTAGGGTTAGGGTTTTTA
ATTAAAATTAGTTAGGGTTTAGGGTTTTTAATTAAATTAAATTAGGGTTAGGTTTTTTAATTAAA
TTAAACTAGGGTTAGGGTTTTTAATTAAATTAGATTAGGGTTAGG
Found at i:38499396 original size:7 final size:7
Alignment explanation
Indices: 38499386--38499417 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
38499376 TTATATACAT
38499386 AATACTA
1 AATACTA
38499393 AATACTA
1 AATACTA
38499400 AATACTA
1 AATACTA
38499407 AATACTA
1 AATACTA
38499414 AATA
1 AATA
38499418 TCAATCCACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:38500392 original size:14 final size:15
Alignment explanation
Indices: 38500375--38500408 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
38500365 AATAATTATC
38500375 TAAAAATA-CATAAA
1 TAAAAATATCATAAA
*
38500389 TAAAAATATCTTAAA
1 TAAAAATATCATAAA
38500404 TAAAA
1 TAAAA
38500409 TTTAAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (15 bp):
TAAAAATATCATAAA
Found at i:38500557 original size:28 final size:28
Alignment explanation
Indices: 38500506--38500561 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
38500496 TTGAAACTAT
*
38500506 TAAAAATTTTAAAATTATTTTTAAAAAA
1 TAAAAATTTTAAAATTATTCTTAAAAAA
38500534 TAAAAATATTTAAAATT-TTCTTAAAAAA
1 TAAAAAT-TTTAAAATTATTCTTAAAAAA
38500562 ATGAAATTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 17 0.65
29 9 0.35
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (28 bp):
TAAAAATTTTAAAATTATTCTTAAAAAA
Found at i:38500568 original size:28 final size:28
Alignment explanation
Indices: 38500506--38500563 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 28
38500496 TTGAAACTAT
*
38500506 TAAAAATTTTAAAATTATTTTTAAAAAA
1 TAAAAATTTTAAAATTATTTTAAAAAAA
38500534 TAAAAATATTTAAAATT-TTCTTAAAAAAA
1 TAAAAAT-TTTAAAATTATT-TTAAAAAAA
38500563 T
1 T
38500564 GAAATTGAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 9 0.33
29 18 0.67
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (28 bp):
TAAAAATTTTAAAATTATTTTAAAAAAA
Found at i:38500625 original size:22 final size:21
Alignment explanation
Indices: 38500597--38500647 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 21
38500587 AAATATGGAT
*
38500597 TTGAGAGATTTTTTGAAGGAAA
1 TTGAGAGA-TTTTGGAAGGAAA
*
38500619 TTGAGAGGATTTTGGAAGGAAT
1 TTGAGA-GATTTTGGAAGGAAA
38500641 TTGAGAG
1 TTGAGAG
38500648 TTTAAGAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 1 0.04
22 23 0.88
23 2 0.08
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (21 bp):
TTGAGAGATTTTGGAAGGAAA
Found at i:38500670 original size:52 final size:52
Alignment explanation
Indices: 38500600--38500699 Score: 164
Period size: 52 Copynumber: 1.9 Consensus size: 52
38500590 TATGGATTTG
* * * *
38500600 AGAGATTTTTTGAAGGAAATTGAGAGGATTTTGGAAGGAATTTGAGAGTTTA
1 AGAGAATTTTGGAAGGAAATTGAGAGAATTTTGGAAGGAAATTGAGAGTTTA
38500652 AGAGAATTTTGGAAGGAAATTGAGAGAATTTTGGAAGGAAATTGAGAG
1 AGAGAATTTTGGAAGGAAATTGAGAGAATTTTGGAAGGAAATTGAGAG
38500700 AATATTTGTT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 44 1.00
ACGTcount: A:0.38, C:0.00, G:0.32, T:0.30
Consensus pattern (52 bp):
AGAGAATTTTGGAAGGAAATTGAGAGAATTTTGGAAGGAAATTGAGAGTTTA
Found at i:38500716 original size:24 final size:22
Alignment explanation
Indices: 38500652--38500707 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
38500642 TGAGAGTTTA
38500652 AGAGAATTTTGGAAGGAAATTG
1 AGAGAATTTTGGAAGGAAATTG
38500674 AGAGAATTTTGGAAGGAAATTG
1 AGAGAATTTTGGAAGGAAATTG
38500696 AGAGAATATTTG
1 AGAGAAT-TTTG
38500708 TTTGTGAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 29 0.88
23 4 0.12
ACGTcount: A:0.41, C:0.00, G:0.30, T:0.29
Consensus pattern (22 bp):
AGAGAATTTTGGAAGGAAATTG
Found at i:38512313 original size:21 final size:21
Alignment explanation
Indices: 38512289--38512358 Score: 68
Period size: 21 Copynumber: 3.3 Consensus size: 21
38512279 TCTTTTGAGC
*
38512289 TTCTGTTTAACCCTTATGGGT
1 TTCTGTTCAACCCTTATGGGT
* * * * *
38512310 TTCTGTTCAGCTCTTACGAGC
1 TTCTGTTCAACCCTTATGGGT
*
38512331 TTCCGTTCAACCCTTATGGGT
1 TTCTGTTCAACCCTTATGGGT
*
38512352 TTTTGTT
1 TTCTGTT
38512359 TAGCTTTCAT
Statistics
Matches: 35, Mismatches: 14, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.13, C:0.23, G:0.19, T:0.46
Consensus pattern (21 bp):
TTCTGTTCAACCCTTATGGGT
Found at i:38512324 original size:42 final size:42
Alignment explanation
Indices: 38512234--38512381 Score: 138
Period size: 42 Copynumber: 3.5 Consensus size: 42
38512224 CTTTCCATTT
* * * * * * *
38512234 AGCTCTCACGAGCTTTTGTTCAACTCATATGAGTTT-TCGTTT
1 AGCTCTTATGAGCTTCTGTTCAACCCTTATGGGTTTCT-GTTC
* * *
38512276 AACTCTTTTGAGCTTCTGTTTAACCCTTATGGGTTTCTGTTC
1 AGCTCTTATGAGCTTCTGTTCAACCCTTATGGGTTTCTGTTC
* * * *
38512318 AGCTCTTACGAGCTTCCGTTCAACCCTTATGGGTTTTTGTTT
1 AGCTCTTATGAGCTTCTGTTCAACCCTTATGGGTTTCTGTTC
38512360 AGCT-TTCATGAGCTTCTGTTCA
1 AGCTCTT-ATGAGCTTCTGTTCA
38512382 GCCTTCAGGC
Statistics
Matches: 85, Mismatches: 19, Indels: 4
0.79 0.18 0.04
Matches are distributed among these distances:
41 2 0.02
42 82 0.96
43 1 0.01
ACGTcount: A:0.16, C:0.22, G:0.18, T:0.44
Consensus pattern (42 bp):
AGCTCTTATGAGCTTCTGTTCAACCCTTATGGGTTTCTGTTC
Found at i:38512388 original size:21 final size:20
Alignment explanation
Indices: 38512284--38512386 Score: 62
Period size: 21 Copynumber: 5.0 Consensus size: 20
38512274 TTAACTCTTT
* *
38512284 TGAGCTTCTGTTTAACCCTTA
1 TGAGCTTCTG-TTCAGCCTTA
* *
38512305 TGGGTTTCTGTTCAGCTCTTA
1 TGAGCTTCTGTTCAGC-CTTA
* * *
38512326 CGAGCTTCCGTTCAACCCTTA
1 TGAGCTTCTGTTC-AGCCTTA
* * * * *
38512347 TGGGTTTTTGTTTAGCTTTCA
1 TGAGCTTCTGTTCAGCCTT-A
38512368 TGAGCTTCTGTTCAGCCTT
1 TGAGCTTCTGTTCAGCCTT
38512387 CAGGCTTCTA
Statistics
Matches: 57, Mismatches: 22, Indels: 6
0.67 0.26 0.07
Matches are distributed among these distances:
20 8 0.14
21 47 0.82
22 2 0.04
ACGTcount: A:0.14, C:0.23, G:0.19, T:0.44
Consensus pattern (20 bp):
TGAGCTTCTGTTCAGCCTTA
Found at i:38514814 original size:50 final size:50
Alignment explanation
Indices: 38514671--38514917 Score: 185
Period size: 50 Copynumber: 4.8 Consensus size: 50
38514661 GATAATAACA
* * ** * * *
38514671 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTTCTTGTAC--
1 TGCCAACGCCATGTCCCAGATATGGTCTTACATGGGACCTCTCATAT-CGG
* * * ** *
38514720 TGCCAATGCCATATCCCAAATATGGTCTTACATGGGAGTTCTCATATTGG
1 TGCCAACGCCATGTCCCAGATATGGTCTTACATGGGACCTCTCATATCGG
* * * ** *
38514770 TG-CACATGTCATGTCTCAGATATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCA-ACGCCATGTCCCAGATATGGTCTTACATGGGACCTCTCATATCGG
* *
38514820 TGCCAACGCCATGTCCCAGAAATGGTCTTACATGGGACCTCTCATAACCTCAATGA
1 TGCCAACGCCATGTCCCAGATATGGTCTTACATGGGACCTCTCAT-A--TC---GG
* * *
38514876 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 TGCCAACGCCATGTCCCAGATATGGTCTTACATGGGACCTCT
38514918 TTACCCAAAT
Statistics
Matches: 157, Mismatches: 31, Indels: 13
0.78 0.15 0.06
Matches are distributed among these distances:
49 40 0.25
50 73 0.46
51 2 0.01
53 2 0.01
56 40 0.25
ACGTcount: A:0.23, C:0.26, G:0.21, T:0.29
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGATATGGTCTTACATGGGACCTCTCATATCGG
Found at i:38525238 original size:22 final size:22
Alignment explanation
Indices: 38525210--38525254 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
38525200 GATCCTTAAC
38525210 TTTGAAAGTAATTTAATGAAAT
1 TTTGAAAGTAATTTAATGAAAT
38525232 TTTGAAAGTAATTTAATGAAAT
1 TTTGAAAGTAATTTAATGAAAT
38525254 T
1 T
38525255 CAAGCTTAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.44, C:0.00, G:0.13, T:0.42
Consensus pattern (22 bp):
TTTGAAAGTAATTTAATGAAAT
Found at i:38525487 original size:26 final size:28
Alignment explanation
Indices: 38525422--38525493 Score: 85
Period size: 28 Copynumber: 2.6 Consensus size: 28
38525412 ATAAGAAAAT
* *
38525422 TTATTATTAAGAATTTTATGAAATTATATA
1 TTATTATT-A-AATTATATGAAATAATATA
*
38525452 TTATTATTAAATTATATGTAATAATA-A
1 TTATTATTAAATTATATGAAATAATATA
38525479 TTATT-TTAAATTATA
1 TTATTATTAAATTATA
38525494 CAAATTCATA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
26 10 0.26
27 6 0.15
28 14 0.36
29 1 0.03
30 8 0.21
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.51
Consensus pattern (28 bp):
TTATTATTAAATTATATGAAATAATATA
Found at i:38525611 original size:59 final size:56
Alignment explanation
Indices: 38525523--38525733 Score: 146
Period size: 54 Copynumber: 3.6 Consensus size: 56
38525513 TTATTAGTTA
*
38525523 TAATTATTTTAAATT-TTATTAA--ATCATATATTTTAATTAAAATATATTTAATAT
1 TAATTA-TTTAAATTATTTTTAAGTATCATATATTTTAATTAAAATATATTTAATAT
* * **
38525577 TAATTATTTCAAATTATCTTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATA
1 TAATTATTT-AAATTAT-TTTTA-AGTATCATATATT-TTAATT-A--AAA-T-ATAT-TTAATA
38525642 T
56 T
* * * * *
38525643 TAATTATTAAGAATT-TTATTAA--ATTATATATTTTAATTATAATATATTTAATAA
1 TAATTATTTA-AATTATTTTTAAGTATCATATATTTTAATTAAAATATATTTAATAT
*
38525697 TAATTATATTAATTTATATTTTACAGTATCATATATT
1 TAATTAT-TTAAATTAT-TTTTA-AGTATCATATATT
38525734 ATGATTTCAG
Statistics
Matches: 119, Mismatches: 18, Indels: 35
0.69 0.10 0.20
Matches are distributed among these distances:
53 3 0.03
54 25 0.21
55 8 0.07
56 9 0.08
57 4 0.03
59 20 0.17
60 8 0.07
61 10 0.08
63 4 0.03
64 5 0.04
65 6 0.05
66 17 0.14
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.51
Consensus pattern (56 bp):
TAATTATTTAAATTATTTTTAAGTATCATATATTTTAATTAAAATATATTTAATAT
Found at i:38525642 original size:66 final size:62
Alignment explanation
Indices: 38525572--38525770 Score: 164
Period size: 66 Copynumber: 3.2 Consensus size: 62
38525562 AAATATATTT
38525572 AATATTAATTATTTCAAATTATCTTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAA
1 AATATTAATTATTT-AAATTAT-TTTTA-AGTATCATATATTATGATTT-AGTAAATTCATATAA
38525637 G
62 G
* * * * * **
38525638 AATATTAATTATTAAGAATT-TTATTAA--ATTATATATT-TTAATTA-T-AA-T-ATAT-TT
1 AATATTAATTATTTA-AATTATTTTTAAGTATCATATATTATGATTTAGTAAATTCATATAAG
* * *
38525692 AATAATAATTATATTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAATTTCATATAA
1 AATATTAATTAT-TTAAATTAT-TTTTA-AGTATCATATATTATGATTT-AGTAAATTCATATAA
38525757 G
62 G
38525758 AATATTAATTATT
1 AATATTAATTATT
38525771 AAGAATTTTA
Statistics
Matches: 101, Mismatches: 18, Indels: 29
0.68 0.12 0.20
Matches are distributed among these distances:
54 14 0.14
55 7 0.07
56 5 0.05
57 3 0.03
58 1 0.01
59 10 0.10
60 8 0.08
61 10 0.10
62 1 0.01
63 2 0.02
64 5 0.05
65 7 0.07
66 28 0.28
ACGTcount: A:0.42, C:0.04, G:0.05, T:0.49
Consensus pattern (62 bp):
AATATTAATTATTTAAATTATTTTTAAGTATCATATATTATGATTTAGTAAATTCATATAAG
Found at i:38525658 original size:120 final size:120
Alignment explanation
Indices: 38525534--38525823 Score: 492
Period size: 120 Copynumber: 2.4 Consensus size: 120
38525524 AATTATTTTA
* * * *
38525534 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTATCTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATATT-AAATTATATTT
* *
38525598 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
65 TACAGTATCATATATTATGATTTCAGTAAATTCATATAAGAATATTAATTATTAAG
*
38525654 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATATTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATATTAAATTATATTTT
*
38525719 ACAGTATCATATATTATGATTTCAGTAATTTCATATAAGAATATTAATTATTAAG
66 ACAGTATCATATATTATGATTTCAGTAAATTCATATAAGAATATTAATTATTAAG
38525774 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTAT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTAT
38525824 GTTTAAATAT
Statistics
Matches: 161, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
120 159 0.99
121 2 0.01
ACGTcount: A:0.43, C:0.03, G:0.04, T:0.50
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATATTAAATTATATTTT
ACAGTATCATATATTATGATTTCAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:38525694 original size:15 final size:15
Alignment explanation
Indices: 38525659--38525820 Score: 58
Period size: 15 Copynumber: 10.9 Consensus size: 15
38525649 TTAAGAATTT
*
38525659 TATTAAATTAT-ATA
1 TATTTAATTATAATA
38525673 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
38525687 TATTTAATAATAAT-
1 TATTTAATTATAATA
38525701 TATATTAATT-T-ATA
1 TAT-TTAATTATAATA
* *
38525715 T-TTTACAGTATCATA
1 TATTTA-ATTATAATA
* *
38525730 TATTATGATT-TCAGTA
1 TATT-TAATTAT-AATA
* *
38525746 -ATTTCA-TATAAGA
1 TATTTAATTATAATA
*
38525759 -ATATTAATTATTAAGA
1 TAT-TTAATTA-TAATA
* *
38525775 -ATTTTATTAAATTATA
1 TATTTAATT--ATAATA
38525791 TATTTTAATTATAATA
1 TA-TTTAATTATAATA
*
38525807 TATTTAATAATAAT
1 TATTTAATTATAAT
38525821 TATGTTTAAA
Statistics
Matches: 112, Mismatches: 18, Indels: 35
0.68 0.11 0.21
Matches are distributed among these distances:
12 3 0.03
13 18 0.16
14 17 0.15
15 42 0.38
16 23 0.21
17 3 0.03
18 6 0.05
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.51
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:38525809 original size:16 final size:16
Alignment explanation
Indices: 38525788--38525829 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
38525778 TTATTAAATT
*
38525788 ATATATTTTAATTATA
1 ATATATTTTAATAATA
38525804 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
38525819 AT-TATGTTTAA
1 ATATAT-TTTAA
38525830 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:38526321 original size:50 final size:50
Alignment explanation
Indices: 38526206--38526440 Score: 215
Period size: 50 Copynumber: 4.6 Consensus size: 50
38526196 CCAAAGCTAG
* * * *
38526206 GTCCCAGACATGGTCTTACATGGGATG-TTTCTTGTAC--TGCCAATGTCAT
1 GTCCCAGACATGGTCTTACATGGGA-GCTCTCATAT-CGGTGCCAATGCCAT
* * * *
38526255 ATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGGTGCCCATGCCAT
1 GTCCCAGACATGGTCTTACATGGGAGCTCTCATATCGGTGCCAATGCCAT
* ** * *
38526305 GTCCCAGATATGGTCTTACGGGGGAACTCTCATCTCGGTGCCAATGCCAT
1 GTCCCAGACATGGTCTTACATGGGAGCTCTCATATCGGTGCCAATGCCAT
* * *
38526355 GTCCCAGACATGGTCTTACATGGGACCTCTCATAACCTCAATGATGCCACTGCCAT
1 GTCCCAGACATGGTCTTACATGGGAGCTCTCAT-A--TC---GGTGCCAATGCCAT
* *
38526411 GTCCCAGACATGGTTTTACATGGGATCTCT
1 GTCCCAGACATGGTCTTACATGGGAGCTCT
38526441 TTACCCAAAT
Statistics
Matches: 154, Mismatches: 23, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
48 2 0.01
49 28 0.18
50 82 0.53
53 2 0.01
56 40 0.26
ACGTcount: A:0.22, C:0.27, G:0.22, T:0.29
Consensus pattern (50 bp):
GTCCCAGACATGGTCTTACATGGGAGCTCTCATATCGGTGCCAATGCCAT
Found at i:38528917 original size:54 final size:54
Alignment explanation
Indices: 38528843--38528973 Score: 160
Period size: 54 Copynumber: 2.4 Consensus size: 54
38528833 AAATTGTTTT
* * * *
38528843 TTTTTTG-TGTTGCCGATGTGTTAAGTGGCACT-G-GTGTCAGTTTAAAAAAAAAA
1 TTTTTTGTTGTCGCCGGTGTGTCAAGTGGCACTAGTGTGT-A-TGTAAAAAAAAAA
* * *
38528896 TTTTTTGTTGTCGTCTGTGTGTCAAGTGGCACTAGTGTGTATGTAAAAAAATAA
1 TTTTTTGTTGTCGCCGGTGTGTCAAGTGGCACTAGTGTGTATGTAAAAAAAAAA
38528950 TTTTTTGTTGTCGCCGGTGTGTCA
1 TTTTTTGTTGTCGCCGGTGTGTCA
38528974 GGCGACACCT
Statistics
Matches: 66, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
53 7 0.11
54 53 0.80
55 2 0.03
56 4 0.06
ACGTcount: A:0.23, C:0.11, G:0.25, T:0.41
Consensus pattern (54 bp):
TTTTTTGTTGTCGCCGGTGTGTCAAGTGGCACTAGTGTGTATGTAAAAAAAAAA
Found at i:38532331 original size:21 final size:21
Alignment explanation
Indices: 38532307--38532373 Score: 50
Period size: 21 Copynumber: 3.2 Consensus size: 21
38532297 GAGTATTCTG
38532307 TCGAATACTCGTTTGTATCAT
1 TCGAATACTCGTTTGTATCAT
** **
38532328 TCG-ATCAC-AATGAGTATTCTAT
1 TCGAAT-ACTCGTTTGTA-TC-AT
38532350 -CGAATACTCGTTTGTATCAT
1 TCGAATACTCGTTTGTATCAT
38532370 TCGA
1 TCGA
38532374 TCACAATTTA
Statistics
Matches: 32, Mismatches: 8, Indels: 12
0.62 0.15 0.23
Matches are distributed among these distances:
20 8 0.25
21 16 0.50
22 8 0.25
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.39
Consensus pattern (21 bp):
TCGAATACTCGTTTGTATCAT
Found at i:38532356 original size:42 final size:42
Alignment explanation
Indices: 38532297--38532380 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
38532287 AGAGTGCTAC
*
38532297 GAGTATTCTGTCGAATACTCGTTTGTATCATTCGATCACAAT
1 GAGTATTCTATCGAATACTCGTTTGTATCATTCGATCACAAT
38532339 GAGTATTCTATCGAATACTCGTTTGTATCATTCGATCACAAT
1 GAGTATTCTATCGAATACTCGTTTGTATCATTCGATCACAAT
38532381 TTAAAATAGC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.38
Consensus pattern (42 bp):
GAGTATTCTATCGAATACTCGTTTGTATCATTCGATCACAAT
Found at i:38532719 original size:13 final size:13
Alignment explanation
Indices: 38532703--38532728 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
38532693 CCAATCCATC
38532703 CCTCAACTCCAGT
1 CCTCAACTCCAGT
38532716 CCTCAACTCCAGT
1 CCTCAACTCCAGT
38532729 GCTGCAACAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.46, G:0.08, T:0.23
Consensus pattern (13 bp):
CCTCAACTCCAGT
Found at i:38536690 original size:18 final size:18
Alignment explanation
Indices: 38536640--38536692 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
38536630 CATAAATTCA
*
38536640 TTTTTCA-TGTCATTTTTC
1 TTTTTCATTTTCA-TTTTC
*
38536658 TTTTTC-TTTCCCATTTTC
1 TTTTTCATTT-TCATTTTC
38536676 TTTTTCATTTTCATTTT
1 TTTTTCATTTTCATTTT
38536693 GGAGAAACCC
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
18 24 0.83
19 5 0.17
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (18 bp):
TTTTTCATTTTCATTTTC
Done.