Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168026.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_28, 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: 15507587
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 97000 characters in sequence are not A, C, G, or T
File 29 of 91
Found at i:5058541 original size:94 final size:94
Alignment explanation
Indices: 5058367--5058551 Score: 257
Period size: 95 Copynumber: 2.0 Consensus size: 94
5058357 AGCCTCTGTT
*
5058367 TAGAAGAGCCTTTATTTTTAAAAGTTGTTGAACCTCTATATAAAAGAGCTTTTTATTTTCTAAAA
1 TAGAAGAGCCTTTACTTTTAAAAGTTGTTGAACCTCTATATAAAAGAGCTTTTTATTTTCTAAAA
*
5058432 GTCATTGAGCCTCTATTTAGAGGAGCAAA
66 GTCATTGAGCCTCTATTTAGAAGAGCAAA
* * * * * * *
5058461 TAGATGAGCCTTTTACTTTTCAAAGTTGTTGAGCCTCTATTTAGAGGAGAC-TTTTATTTT-TCA
1 TAGAAGAGCC-TTTACTTTTAAAAGTTGTTGAACCTCTATATAAAAGAG-CTTTTTATTTTCTAA
5058524 AAGTCATTGAGCCTCTATTTAGAAGAGC
64 AAGTCATTGAGCCTCTATTTAGAAGAGC
5058552 CTTTTATTTC
Statistics
Matches: 80, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
94 38 0.47
95 41 0.51
96 1 0.01
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.38
Consensus pattern (94 bp):
TAGAAGAGCCTTTACTTTTAAAAGTTGTTGAACCTCTATATAAAAGAGCTTTTTATTTTCTAAAA
GTCATTGAGCCTCTATTTAGAAGAGCAAA
Found at i:5058589 original size:135 final size:135
Alignment explanation
Indices: 5058347--5058592 Score: 350
Period size: 135 Copynumber: 1.8 Consensus size: 135
5058337 TTATTTCTCT
* **
5058347 AAAGTTGTTGAGCCTCTGTTTAGAAGAGCCTTTATTTTTAAAAGTTGTTGAACCTCTATATAAAA
1 AAAGTTGTTGAGCCTCTATTTAGAAGAGCCTTTATTTTTAAAAGTCATTGAACCTCTATATAAAA
* *
5058412 GAGCTTTTTATTTTCTAAAAGTCATTGAGCCTCTATTTAGAGGAGCAAATAGATGAGCCTTTTAC
66 GAGCCTTTTATTTTCTAAAAGTCATTGAGCCTCTATTCAGAGGAGCAAATAGATGAGCCTTTTAC
5058477 TTTTC
131 TTTTC
* * * * * *
5058482 AAAGTTGTTGAGCCTCTATTTAGAGGAGACTTTTATTTTTCAAAGTCATTGAGCCTCTATTTAGA
1 AAAGTTGTTGAGCCTCTATTTAGAAGAG-CCTTTATTTTTAAAAGTCATTGAACCTCTATATAAA
* * *
5058547 AGAGCCTTTTA-TTTCTCAAAGTCATTGAGCCTTTGTTCAGAGGAGC
65 AGAGCCTTTTATTTTCTAAAAGTCATTGAGCCTCTATTCAGAGGAGC
5058593 CTTTTGTTTT
Statistics
Matches: 96, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
135 57 0.59
136 39 0.41
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.39
Consensus pattern (135 bp):
AAAGTTGTTGAGCCTCTATTTAGAAGAGCCTTTATTTTTAAAAGTCATTGAACCTCTATATAAAA
GAGCCTTTTATTTTCTAAAAGTCATTGAGCCTCTATTCAGAGGAGCAAATAGATGAGCCTTTTAC
TTTTC
Found at i:5059399 original size:21 final size:21
Alignment explanation
Indices: 5059373--5059421 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 21
5059363 ATTTGGATTA
* *
5059373 GAGAGAGAGAGAGAAAAGAAAGG
1 GAGA-AGAAAGAG-AAAGAAAAG
5059396 GAGAAGAAAGAGAAAGAAAAG
1 GAGAAGAAAGAGAAAGAAAAG
5059417 GAGAA
1 GAGAA
5059422 ATCTCAAGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 13 0.54
22 7 0.29
23 4 0.17
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (21 bp):
GAGAAGAAAGAGAAAGAAAAG
Found at i:5059409 original size:17 final size:17
Alignment explanation
Indices: 5059379--5059411 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
5059369 ATTAGAGAGA
5059379 GAGAGAGAAAAGAAAGG
1 GAGAGAGAAAAGAAAGG
5059396 GAGA-AGAAAGAGAAAG
1 GAGAGAGAAA-AGAAAG
5059412 AAAAGGAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (17 bp):
GAGAGAGAAAAGAAAGG
Found at i:5059676 original size:11 final size:11
Alignment explanation
Indices: 5059660--5059729 Score: 51
Period size: 11 Copynumber: 6.6 Consensus size: 11
5059650 CAAGTCGTTT
5059660 TATTTTTTTAG
1 TATTTTTTTAG
5059671 TA-TTTTTT--
1 TATTTTTTTAG
* *
5059679 TATTTATTCAG
1 TATTTTTTTAG
5059690 TATTTTATTTATG
1 TATTTT-TTTA-G
* *
5059703 TGTTTGTTT--
1 TATTTTTTTAG
5059712 TATTTTTTTAG
1 TATTTTTTTAG
5059723 TATTTTT
1 TATTTTT
5059730 GCATGATTAA
Statistics
Matches: 44, Mismatches: 8, Indels: 14
0.67 0.12 0.21
Matches are distributed among these distances:
8 2 0.05
9 11 0.25
10 6 0.14
11 14 0.32
12 6 0.14
13 5 0.11
ACGTcount: A:0.17, C:0.01, G:0.09, T:0.73
Consensus pattern (11 bp):
TATTTTTTTAG
Found at i:5067493 original size:7 final size:7
Alignment explanation
Indices: 5067481--5067511 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
5067471 ATAAAGAAAT
5067481 AAATTAA
1 AAATTAA
5067488 AAATTAA
1 AAATTAA
5067495 AAATTAA
1 AAATTAA
5067502 AAA-TAA
1 AAATTAA
5067508 AAAT
1 AAAT
5067512 AAACATGTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (7 bp):
AAATTAA
Found at i:5069374 original size:22 final size:21
Alignment explanation
Indices: 5069349--5069425 Score: 66
Period size: 22 Copynumber: 3.6 Consensus size: 21
5069339 ATAGAATACA
* *
5069349 TACATAATGCTTATAGGATTT
1 TACATAGTGCTTATAAGATTT
5069370 GTACAT-GTGCTTATAAGATATT
1 -TACATAGTGCTTATAAGAT-TT
* * * *
5069392 TATATATTGCTTATATGATATA
1 TACATAGTGCTTATAAGAT-TT
5069414 TACATAGTGCTT
1 TACATAGTGCTT
5069426 CTGAAATATG
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
21 15 0.33
22 30 0.67
ACGTcount: A:0.32, C:0.09, G:0.14, T:0.44
Consensus pattern (21 bp):
TACATAGTGCTTATAAGATTT
Found at i:5071141 original size:14 final size:14
Alignment explanation
Indices: 5071122--5071148 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5071112 CAGTTGATCA
5071122 AGTACCCTAAATGT
1 AGTACCCTAAATGT
5071136 AGTACCCTAAATG
1 AGTACCCTAAATG
5071149 AGTTTCTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.22, G:0.15, T:0.26
Consensus pattern (14 bp):
AGTACCCTAAATGT
Found at i:5071864 original size:44 final size:44
Alignment explanation
Indices: 5071816--5071900 Score: 109
Period size: 44 Copynumber: 1.9 Consensus size: 44
5071806 TAATGAAATG
* * *
5071816 TACATATAAGTATATCT-ATATGTGTATGTCCTATAAGTATAATA
1 TACATAT-ACTATAACTAATATGTGTATATCCTATAAGTATAATA
* *
5071860 TACATATCCTATAACTAATATGTTTATATCCTATAAGTATA
1 TACATATACTATAACTAATATGTGTATATCCTATAAGTATA
5071901 CAATCAAATT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
43 6 0.17
44 29 0.83
ACGTcount: A:0.39, C:0.12, G:0.08, T:0.41
Consensus pattern (44 bp):
TACATATACTATAACTAATATGTGTATATCCTATAAGTATAATA
Found at i:5071871 original size:22 final size:23
Alignment explanation
Indices: 5071844--5071900 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 23
5071834 TATGTGTATG
5071844 TCCTATAAGTATA-ATATACATA
1 TCCTATAAGTATATATATACATA
* * **
5071866 TCCTATAACTA-ATATGTTTATA
1 TCCTATAAGTATATATATACATA
5071888 TCCTATAAGTATA
1 TCCTATAAGTATA
5071901 CAATCAAATT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
21 1 0.04
22 26 0.93
23 1 0.04
ACGTcount: A:0.40, C:0.14, G:0.05, T:0.40
Consensus pattern (23 bp):
TCCTATAAGTATATATATACATA
Found at i:5072264 original size:21 final size:21
Alignment explanation
Indices: 5072233--5072290 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
5072223 TACATCAAAG
* *
5072233 CAAAGCAAATCAAAATACGATA
1 CAAA-CAAATCCAAATAAGATA
*
5072255 TAAACAAATCCAAATAAGATA
1 CAAACAAATCCAAATAAGATA
*
5072276 CAAGCAAATCCAAAT
1 CAAACAAATCCAAAT
5072291 TTGAAATCGA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
21 28 0.90
22 3 0.10
ACGTcount: A:0.59, C:0.19, G:0.07, T:0.16
Consensus pattern (21 bp):
CAAACAAATCCAAATAAGATA
Found at i:5074432 original size:12 final size:13
Alignment explanation
Indices: 5074410--5074442 Score: 50
Period size: 12 Copynumber: 2.5 Consensus size: 13
5074400 AGGTTTAAAG
5074410 TTTAGGGTTTAGGA
1 TTTA-GGTTTAGGA
5074424 -TTAGGTTTAGGA
1 TTTAGGTTTAGGA
5074436 TTTAGGT
1 TTTAGGT
5074443 CAGTGTTTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 9 0.50
13 9 0.50
ACGTcount: A:0.21, C:0.00, G:0.33, T:0.45
Consensus pattern (13 bp):
TTTAGGTTTAGGA
Found at i:5074450 original size:19 final size:19
Alignment explanation
Indices: 5074409--5074450 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
5074399 TAGGTTTAAA
* *
5074409 GTTTAGGGTTTAGGATTAG
1 GTTTAGGATTTAGGATCAG
5074428 GTTTAGGATTTAGG-TCAG
1 GTTTAGGATTTAGGATCAG
5074446 TGTTT
1 -GTTT
5074451 GGAGAAAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 3 0.15
19 17 0.85
ACGTcount: A:0.19, C:0.02, G:0.33, T:0.45
Consensus pattern (19 bp):
GTTTAGGATTTAGGATCAG
Found at i:5077541 original size:29 final size:31
Alignment explanation
Indices: 5077474--5077552 Score: 85
Period size: 29 Copynumber: 2.6 Consensus size: 31
5077464 AATATCATAA
*
5077474 ATGATTTTTAAATTATAATAAAATATTTAAT
1 ATGATATTTAAATTATAATAAAATATTTAAT
*
5077505 AT-ATTATTTAAATT-TAA-AAAATTTTTAAT
1 ATGA-TATTTAAATTATAATAAAATATTTAAT
*
5077534 TTGATATTTGAAA-TATAAT
1 ATGATATTT-AAATTATAAT
5077553 TTTAGTAATT
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
29 18 0.45
30 11 0.28
31 11 0.28
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (31 bp):
ATGATATTTAAATTATAATAAAATATTTAAT
Found at i:5079140 original size:87 final size:87
Alignment explanation
Indices: 5078984--5079142 Score: 196
Period size: 87 Copynumber: 1.8 Consensus size: 87
5078974 AAATTCAATA
* * * * * **
5078984 TCAAATAACTCAAAATCAAAAACATAAATTAAACTTAAATATAATAAAAAAATAAACCATAAATT
1 TCAAATAACCCAAAATCAAAAACATAAATCAAACTCAAATATAATAAAAAAATAAACAAAAAAAA
5079049 AAAAAAATTCTAAAACTCAGCC
66 AAAAAAATTCTAAAACTCAGCC
* * *
5079071 TCAACTAACCCAAAATCAAACACATATAA-CAAACTCAAATATAATAAAAAAA-AAGCTAAAAAA
1 TCAAATAACCCAAAATCAAAAACATA-AATCAAACTCAAATATAATAAAAAAATAAAC-AAAAAA
5079134 AAAAAAAAA
64 AAAAAAAAA
5079143 ATTTATTCAT
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
86 3 0.05
87 55 0.92
88 2 0.03
ACGTcount: A:0.64, C:0.16, G:0.01, T:0.19
Consensus pattern (87 bp):
TCAAATAACCCAAAATCAAAAACATAAATCAAACTCAAATATAATAAAAAAATAAACAAAAAAAA
AAAAAAATTCTAAAACTCAGCC
Found at i:5084516 original size:2 final size:2
Alignment explanation
Indices: 5084509--5084545 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
5084499 GTTCTAGCAA
5084509 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
5084546 TTTCATGGGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5086411 original size:2 final size:2
Alignment explanation
Indices: 5086406--5086439 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
5086396 ACACACACAC
5086406 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5086440 TGTCTTTGCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5087027 original size:3 final size:3
Alignment explanation
Indices: 5087019--5087063 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
5087009 ACATCGTTTA
*
5087019 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TGT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
5087064 GAGGTCTAGA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:5090328 original size:11 final size:11
Alignment explanation
Indices: 5090312--5090344 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
5090302 TTATCGTAAA
5090312 ATTGATATTTG
1 ATTGATATTTG
5090323 ATTGATATTT-
1 ATTGATATTTG
5090333 ATTGTATATTTG
1 ATTG-ATATTTG
5090345 TATATGATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 4 0.20
11 16 0.80
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (11 bp):
ATTGATATTTG
Found at i:5091240 original size:34 final size:33
Alignment explanation
Indices: 5091165--5091240 Score: 80
Period size: 34 Copynumber: 2.2 Consensus size: 33
5091155 AAAATTATTG
* * *
5091165 AAGATTTTCAAAAATAGATGTTCGGAATCGTTA
1 AAGACTTTCAAAAATACATGTTCGGAATCCTTA
* * *
5091198 AAGAACTTTCAAAAATTCATTTTCGGAGTCCTTAA
1 AAG-ACTTTCAAAAATACATGTTCGGAATCCTT-A
5091233 AAGACTTT
1 AAGACTTT
5091241 TTGATATCTA
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
33 3 0.09
34 28 0.80
35 4 0.11
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.34
Consensus pattern (33 bp):
AAGACTTTCAAAAATACATGTTCGGAATCCTTA
Found at i:5092724 original size:21 final size:20
Alignment explanation
Indices: 5092691--5092779 Score: 58
Period size: 20 Copynumber: 4.5 Consensus size: 20
5092681 AAAATTTTTT
*
5092691 TTTTATAAA-TCTA-AAAAGA
1 TTTTAAAAATTCTATAAAA-A
5092710 TTTTGAAAAATTCTATAAAAA
1 TTTT-AAAAATTCTATAAAAA
* * * **
5092731 TTTTAAAATTTTTTTTTAAA
1 TTTTAAAAATTCTATAAAAA
* *
5092751 TTATTTAAAATTC-AAAAAAA
1 TT-TTAAAAATTCTATAAAAA
5092771 TTTTAAAAA
1 TTTTAAAAA
5092780 ATTTCGTAGT
Statistics
Matches: 52, Mismatches: 14, Indels: 8
0.70 0.19 0.11
Matches are distributed among these distances:
19 10 0.19
20 22 0.42
21 16 0.31
22 4 0.08
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.44
Consensus pattern (20 bp):
TTTTAAAAATTCTATAAAAA
Found at i:5093928 original size:9 final size:9
Alignment explanation
Indices: 5093916--5093979 Score: 56
Period size: 9 Copynumber: 6.8 Consensus size: 9
5093906 TAAATTTTTT
5093916 AAAATTTAA
1 AAAATTTAA
5093925 AAAATTTAA
1 AAAATTTAA
*
5093934 AGAATTTAA
1 AAAATTTAA
**
5093943 AATTTTTTCAA
1 AA-AATTT-AA
*
5093954 AAATTTTCAA
1 AAAATTT-AA
*
5093964 AAATTTTAA
1 AAAATTTAA
5093973 AAAATTT
1 AAAATTT
5093980 TTTAGATTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
9 26 0.55
10 17 0.36
11 4 0.09
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.41
Consensus pattern (9 bp):
AAAATTTAA
Found at i:5093981 original size:11 final size:10
Alignment explanation
Indices: 5093947--5093980 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
5093937 ATTTAAAATT
5093947 TTTTCAAAAA
1 TTTTCAAAAA
5093957 TTTTCAAAAA
1 TTTTCAAAAA
*
5093967 TTTTAAAAAA
1 TTTTCAAAAA
5093977 TTTT
1 TTTT
5093981 TTAGATTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (10 bp):
TTTTCAAAAA
Found at i:5097348 original size:5 final size:5
Alignment explanation
Indices: 5097340--5097367 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
5097330 AGTATACATT
5097340 TTTTA TTTTA TTTTA TTTTA TTTTA TTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTT
5097368 CAAGTCATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTA
Found at i:5098052 original size:21 final size:21
Alignment explanation
Indices: 5098004--5098053 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
5097994 TTCGAACGGG
* *
5098004 TGTTTTGAGTGAGGAATTGTT
1 TGTTTTGAGTGAGGAATTATC
* *
5098025 TGCTTTGAGTGAGTAATTATC
1 TGTTTTGAGTGAGGAATTATC
5098046 TGTTTTGA
1 TGTTTTGA
5098054 TTAAAAATTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.20, C:0.04, G:0.28, T:0.48
Consensus pattern (21 bp):
TGTTTTGAGTGAGGAATTATC
Found at i:5099863 original size:62 final size:64
Alignment explanation
Indices: 5099690--5099865 Score: 164
Period size: 62 Copynumber: 2.8 Consensus size: 64
5099680 TCTTCTTATC
* * * * *
5099690 ATTTAT-AAAAAGATTAATTAAGGCGTTTGATTATACAAACAACTTAATTGATCATTCATATAAA
1 ATTTATAAAAAAGATCAATTAAGACATTTGGTTACACAAACAACTTAATTGAT-ATTCATATAAA
** *** *
5099754 ATTTATAAAAAAGATCAATTAAGACATTTGTGCAAC-CAAATGCCTTAATTGAT-TTC-TTTACA
1 ATTTATAAAAAAGATCAATTAAGACATTTG-GTTACACAAACAACTTAATTGATATTCATATA-A
5099816 A
64 A
** *
5099817 ATTT-TGCAAAAGATCATTTAAGACATTTGGTTACACAAACAACTTAATT
1 ATTTATAAAAAAGATCAATTAAGACATTTGGTTACACAAACAACTTAATT
5099866 AATCAAGTAT
Statistics
Matches: 89, Mismatches: 19, Indels: 10
0.75 0.16 0.08
Matches are distributed among these distances:
61 3 0.03
62 36 0.40
63 9 0.10
64 6 0.07
65 34 0.38
66 1 0.01
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.35
Consensus pattern (64 bp):
ATTTATAAAAAAGATCAATTAAGACATTTGGTTACACAAACAACTTAATTGATATTCATATAAA
Found at i:5099977 original size:73 final size:73
Alignment explanation
Indices: 5099858--5099994 Score: 168
Period size: 73 Copynumber: 1.9 Consensus size: 73
5099848 TACACAAACA
* *
5099858 ACTTAATTAATCAAGTATTTAAGGCATTTTTATATACAAACACCTTAAATGATAATTTTATTTTT
1 ACTTAATTAATCAAGTATTTAAGGCATTTCTATACACAAACACCTTAAATGATAATTTTATTTTT
5099923 TTATAACG
66 TTATAACG
* * * * * * **
5099931 ACTTAATTTATCAA-TCCTTTAAGGTATTTCTGTACACAAATACCTTAATTGATCCTTTTATTTT
1 ACTTAATTAATCAAGT-ATTTAAGGCATTTCTATACACAAACACCTTAAATGATAATTTTATTTT
5099995 AATAATTGAT
Statistics
Matches: 53, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
72 1 0.02
73 52 0.98
ACGTcount: A:0.34, C:0.14, G:0.07, T:0.45
Consensus pattern (73 bp):
ACTTAATTAATCAAGTATTTAAGGCATTTCTATACACAAACACCTTAAATGATAATTTTATTTTT
TTATAACG
Found at i:5100250 original size:131 final size:128
Alignment explanation
Indices: 5099876--5100417 Score: 539
Period size: 127 Copynumber: 4.2 Consensus size: 128
5099866 AATCAAGTAT
* * * * * *
5099876 TTAAGGCATTTTTATATACAAACACCTTAAATGATAATTTTATTTTTTTATAACGACTTAATTTA
1 TTAAGGCATTTATGTACAAAAACACCTTAAATG---ATTTT-TTTTTTT-TAACGCCTTAATTGA
* * * *
5099941 TCAATCCTTTAAGGTATTTCTGTACACAAATACCTTAATTGATCCTTTT-ATTTTAATAATTGAT
61 TCAATCATTTAAGGCATTTCTGTACACAAACACCTTAATTGATCCTTTTAATTTTTATAATTGAT
5100005 CAA
126 CAA
** * * * * ** * * ***
5100008 TTAAGGTGTTTATATATAGAAACATCTTAAATGATCTTTTTTTTAATAACACCATAAAAAAATCA
1 TTAAGGCATTTATGTACAAAAACACCTTAAATGAT-TTTTTTTTTTTAACGCC-TTAATTGATCA
* * ** * * * * *
5100073 ATCATTTAAGGCATTTTTATACACAAATGCCCTAATTGATCATTTTATTTTTTATAAGTAATCAA
64 ATCATTTAAGGCATTTCTGTACACAAACACCTTAATTGATCCTTTTAATTTTTATAATTGATCAA
* *
5100138 TTAAGGCATTTATGTACAAAAACATCTTAAATGATTTTTTAATTTTTTTAATGCCTTAATTGATC
1 TTAAGGCATTTATGTACAAAAACACCTTAAATGA-TTTTT--TTTTTTTAACGCCTTAATTGATC
* * * *
5100203 AATCATTTAAGGCGTTTCTGTACGCAAACGCTTTAATTGATCCTTTTAATTTTTATAATTGATCA
63 AATCATTTAAGGCATTTCTGTACACAAACACCTTAATTGATCCTTTTAATTTTTATAATTGATCA
5100268 A
128 A
** * ** *
5100269 TTAAGGTGTTTATGTACAAAAGCACCTTAAATGA-TCCTTTTTTTTAATGCCTTAATTGATCAAT
1 TTAAGGCATTTATGTACAAAAACACCTTAAATGATTTTTTTTTTTTAACGCCTTAATTGATCAAT
* * * *
5100333 CATTTAAGGAATTTCTGTACATAAACACCTTAATTGATCCTTTTAATTTTTATAACTGATTAA
66 CATTTAAGGCATTTCTGTACACAAACACCTTAATTGATCCTTTTAATTTTTATAATTGATCAA
*
5100396 TTAAGGCATTTGTGTACAAAAA
1 TTAAGGCATTTATGTACAAAAA
5100418 TGCTTTAAAT
Statistics
Matches: 338, Mismatches: 66, Indels: 17
0.80 0.16 0.04
Matches are distributed among these distances:
127 99 0.29
128 5 0.01
129 55 0.16
130 50 0.15
131 92 0.27
132 37 0.11
ACGTcount: A:0.35, C:0.13, G:0.09, T:0.43
Consensus pattern (128 bp):
TTAAGGCATTTATGTACAAAAACACCTTAAATGATTTTTTTTTTTTAACGCCTTAATTGATCAAT
CATTTAAGGCATTTCTGTACACAAACACCTTAATTGATCCTTTTAATTTTTATAATTGATCAA
Found at i:5100304 original size:60 final size:59
Alignment explanation
Indices: 5100235--5100416 Score: 170
Period size: 67 Copynumber: 2.9 Consensus size: 59
5100225 CGCAAACGCT
**
5100235 TTAATTGATCCTTTTAATTTTTATAATTGATCAATTAAGGTGTTTATGTACAAAAGCACC
1 TTAATTGATCCTTTTAATTTTTATAATTGATCAATTAAGGAATTTATGTACAAAA-CACC
* * *
5100295 TTAAATGATCCTTTT--TTTTAATGCCTTAATTGATCAATCATTTAAGGAATTTCTGTACATAAA
1 TTAATTGATCCTTTTAATTTT--T---ATAATTGATC-A--A-TTAAGGAATTTATGTACA-AAA
5100358 CACC
56 CACC
* * * *
5100362 TTAATTGATCCTTTTAATTTTTATAACTGATTAATTAAGGCATTTGTGTACAAAA
1 TTAATTGATCCTTTTAATTTTTATAATTGATCAATTAAGGAATTTATGTACAAAA
5100417 ATGCTTTAAA
Statistics
Matches: 99, Mismatches: 11, Indels: 25
0.73 0.08 0.19
Matches are distributed among these distances:
58 4 0.04
59 3 0.03
60 31 0.31
61 1 0.01
63 10 0.10
64 8 0.08
66 1 0.01
67 34 0.34
68 3 0.03
69 4 0.04
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.43
Consensus pattern (59 bp):
TTAATTGATCCTTTTAATTTTTATAATTGATCAATTAAGGAATTTATGTACAAAACACC
Found at i:5100353 original size:67 final size:66
Alignment explanation
Indices: 5100180--5100376 Score: 205
Period size: 67 Copynumber: 3.0 Consensus size: 66
5100170 GATTTTTTAA
* * * *
5100180 TTTTTTTAATGCCTTAATTGATCAATCATTTAAGGCGTTTCTGTACGCAAACGCTTTAATTGATC
1 TTTTTTTAATGCCTTAATTGATCAATCATTTAAGGAGTTTCTGTAC-AAAACACCTTAATTGATC
5100245 CT
65 CT
* * * *
5100247 TTTAATTTT--T---ATAATTGATC-A--A-TTAAGGTGTTTATGTACAAAAGCACCTTAAATGA
1 TTT--TTTTAATGCCTTAATTGATCAATCATTTAAGGAGTTTCTGTACAAAA-CACCTTAATTGA
5100303 TCCT
63 TCCT
*
5100307 TTTTTTTAATGCCTTAATTGATCAATCATTTAAGGAATTTCTGTACATAAACACCTTAATTGATC
1 TTTTTTTAATGCCTTAATTGATCAATCATTTAAGGAGTTTCTGTACA-AAACACCTTAATTGATC
5100372 CT
65 CT
5100374 TTT
1 TTT
5100377 AATTTTTATA
Statistics
Matches: 105, Mismatches: 12, Indels: 26
0.73 0.08 0.18
Matches are distributed among these distances:
58 4 0.04
59 3 0.03
60 32 0.30
61 1 0.01
63 10 0.10
64 10 0.10
66 1 0.01
67 37 0.35
68 3 0.03
69 4 0.04
ACGTcount: A:0.30, C:0.15, G:0.11, T:0.44
Consensus pattern (66 bp):
TTTTTTTAATGCCTTAATTGATCAATCATTTAAGGAGTTTCTGTACAAAACACCTTAATTGATCC
T
Found at i:5100374 original size:127 final size:125
Alignment explanation
Indices: 5099918--5100493 Score: 532
Period size: 127 Copynumber: 4.5 Consensus size: 125
5099908 GATAATTTTA
* * * * * *
5099918 TTTTTTTATAACGACTTAATTTATCAATCCTTTAAGGTATTTCTGTACACAAATACCTTAATTGA
1 TTTTTTT-TAATGCCTTAATTGATCAATCATTTAAGGCATTTCTGTACACAAACACCTTAATTGA
* ** * *
5099983 TCCTTTT-ATTTTAATAATTGATCAATTAAGGTGTTTATATATAGAAACATCTTAAATGATC
65 TCCTTTTAATTTTTATAATTGATCAATTAAGGCATTTATGTACA-AAACATCTTAAATGATC
* * *** * * ** *
5100044 TTTTTTTTAATAACACCATAAAAAAATCAATCATTTAAGGCATTTTTATACACAAATGCCCTAAT
1 TTTTTTTTAAT---GCC-TTAATTGATCAATCATTTAAGGCATTTCTGTACACAAACACCTTAAT
* * * *
5100109 TGATCATTTTATTTTTTATAAGTAATCAATTAAGGCATTTATGTACAAAAACATCTTAAATGATT
62 TGATCCTTTTAATTTTTATAATTGATCAATTAAGGCATTTATGTAC-AAAACATCTTAAATGA--
*
5100174 TTT
124 -TC
* * * *
5100177 TAATTTTTTTAATGCCTTAATTGATCAATCATTTAAGGCGTTTCTGTACGCAAACGCTTTAATTG
1 T--TTTTTTTAATGCCTTAATTGATCAATCATTTAAGGCATTTCTGTACACAAACACCTTAATTG
** *
5100242 ATCCTTTTAATTTTTATAATTGATCAATTAAGGTGTTTATGTACAAAAGCACCTTAAATGATCC
64 ATCCTTTTAATTTTTATAATTGATCAATTAAGGCATTTATGTACAAAA-CATCTTAAATGAT-C
* *
5100306 TTTTTTTTAATGCCTTAATTGATCAATCATTTAAGGAATTTCTGTACATAAACACCTTAATTGAT
1 TTTTTTTTAATGCCTTAATTGATCAATCATTTAAGGCATTTCTGTACACAAACACCTTAATTGAT
* * *
5100371 CCTTTTAATTTTTATAACTGATTAATTAAGGCATTTGTGTACAAAA-ATGCTTTAAATGATC
66 CCTTTTAATTTTTATAATTGATCAATTAAGGCATTTATGTACAAAACAT-C-TTAAATGATC
* * *** * * * * *
5100432 ATATTTTATAATATATAAATTG---AATCAATTAAGGCATTTCTATTCACAAACACCTTCATTGA
1 -TTTTTTTTAATGCCTTAATTGATCAATCATTTAAGGCATTTCTGTACACAAACACCTTAATTGA
5100494 CCTAAAAATT
Statistics
Matches: 367, Mismatches: 67, Indels: 34
0.78 0.14 0.07
Matches are distributed among these distances:
124 34 0.09
125 4 0.01
126 9 0.02
127 123 0.34
128 2 0.01
129 47 0.13
130 46 0.13
131 88 0.24
132 2 0.01
133 2 0.01
135 10 0.03
ACGTcount: A:0.35, C:0.13, G:0.09, T:0.42
Consensus pattern (125 bp):
TTTTTTTTAATGCCTTAATTGATCAATCATTTAAGGCATTTCTGTACACAAACACCTTAATTGAT
CCTTTTAATTTTTATAATTGATCAATTAAGGCATTTATGTACAAAACATCTTAAATGATC
Found at i:5112441 original size:6 final size:7
Alignment explanation
Indices: 5112410--5112434 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
5112400 CAAAAATAAT
5112410 TAAAATA
1 TAAAATA
5112417 TAAAATA
1 TAAAATA
5112424 TAAAATA
1 TAAAATA
5112431 TAAA
1 TAAA
5112435 TAAAAATGGA
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:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (7 bp):
TAAAATA
Found at i:5112750 original size:44 final size:44
Alignment explanation
Indices: 5112678--5112993 Score: 327
Period size: 44 Copynumber: 7.2 Consensus size: 44
5112668 AACTTTTGAA
* * * *
5112678 AAAAATAAATAAAGCTCCTATAAACAGAGGCTTC-ATGACTTTGG
1 AAAAATAAATAAAGTTCCTCTAATCAGAGGC-TCAACGACTTTGG
* * *
5112722 AAAAGTAAATAAAGTTCCTCTAATCAGAGGCTCAACAACTTTGA
1 AAAAATAAATAAAGTTCCTCTAATCAGAGGCTCAACGACTTTGG
*
5112766 AAAAATAAATAAAGCTCCTCTAATCAGAGGCTCAACGACTTTGG
1 AAAAATAAATAAAGTTCCTCTAATCAGAGGCTCAACGACTTTGG
* * * **
5112810 AAAAGTAAATAAGGCTT-CTCTAAGCAGAGGCTCAA-GAACTTTTC
1 AAAAATAAATAAAG-TTCCTCTAATCAGAGGCTCAACG-ACTTTGG
* * * *
5112854 AAAAATAAATAAGGTTCCTCTAATTAGAGGCTCAACAACTTTTG
1 AAAAATAAATAAAGTTCCTCTAATCAGAGGCTCAACGACTTTGG
* * * *
5112898 AAAAATAAATAAGGTTTCTCTAATCAGAGGCTCAACAACTTTGA
1 AAAAATAAATAAAGTTCCTCTAATCAGAGGCTCAACGACTTTGG
* * * **
5112942 AAAAATAAAT-AAGACTCCTATAATCAAAGGCTCAATAACTTT-G
1 AAAAATAAATAAAG-TTCCTCTAATCAGAGGCTCAACGACTTTGG
5112985 AAAAATAAA
1 AAAAATAAA
5112994 GCTCATTGAC
Statistics
Matches: 233, Mismatches: 33, Indels: 13
0.84 0.12 0.05
Matches are distributed among these distances:
43 16 0.07
44 216 0.93
45 1 0.00
ACGTcount: A:0.44, C:0.17, G:0.14, T:0.25
Consensus pattern (44 bp):
AAAAATAAATAAAGTTCCTCTAATCAGAGGCTCAACGACTTTGG
Found at i:5112794 original size:88 final size:87
Alignment explanation
Indices: 5112648--5112993 Score: 412
Period size: 88 Copynumber: 3.9 Consensus size: 87
5112638 GACATAAAAC
* *
5112648 TCTCATAAGCAGAGGCTC-ACAACTTTTGAAAAAAATAAATAAAGCTCCTATAAACAGAGGCTTC
1 TCTC-TAATCAGAGGCTCAACAAC-TTTG-AAAAAATAAATAAAGCTCCTATAATCAGAGGC-TC
* *
5112712 -ATGACTTTGGAAAAGTAAATAAAGT
62 AACGACTTTGGAAAAGTAAATAAGGT
*
5112737 TCCTCTAATCAGAGGCTCAACAACTTTGAAAAAATAAATAAAGCTCCTCTAATCAGAGGCTCAAC
1 T-CTCTAATCAGAGGCTCAACAACTTTGAAAAAATAAATAAAGCTCCTATAATCAGAGGCTCAAC
5112802 GACTTTGGAAAAGTAAATAAGGCT
65 GACTTTGGAAAAGTAAATAAGG-T
* * ** * * * * *
5112826 TCTCTAAGCAGAGGCTCAAGAACTTTTCAAAAATAAATAAGGTTCCTCTAATTAGAGGCTCAACA
1 TCTCTAATCAGAGGCTCAACAACTTTGAAAAAATAAATAAAGCTCCTATAATCAGAGGCTCAACG
* *
5112891 ACTTTTGAAAAATAAATAAGGTT
66 ACTTTGGAAAAGTAAATAAGG-T
* *
5112914 TCTCTAATCAGAGGCTCAACAACTTTGAAAAAATAAAT-AAGACTCCTATAATCAAAGGCTCAAT
1 TCTCTAATCAGAGGCTCAACAACTTTGAAAAAATAAATAAAG-CTCCTATAATCAGAGGCTCAAC
* *
5112978 AACTTT-GAAAAATAAA
65 GACTTTGGAAAAGTAAA
5112994 GCTCATTGAC
Statistics
Matches: 226, Mismatches: 26, Indels: 12
0.86 0.10 0.05
Matches are distributed among these distances:
87 14 0.06
88 185 0.82
89 19 0.08
90 8 0.04
ACGTcount: A:0.43, C:0.17, G:0.14, T:0.25
Consensus pattern (87 bp):
TCTCTAATCAGAGGCTCAACAACTTTGAAAAAATAAATAAAGCTCCTATAATCAGAGGCTCAACG
ACTTTGGAAAAGTAAATAAGGT
Found at i:5112851 original size:132 final size:131
Alignment explanation
Indices: 5112657--5112993 Score: 428
Period size: 132 Copynumber: 2.5 Consensus size: 131
5112647 CTCTCATAAG
* *
5112657 CAGAGGCTC-ACAACTTTTGAAAAAAATAAATAAAGCTCCTATAAACAGAGGCTTCATG-ACTTT
1 CAGAGGCTCAACAAC-TTTG-AAAAAATAAATAAGGCTCCTATAAACAGAGGC-TCAAGAACTTT
*
5112720 GGAAAAGTAAATAAAGTTCCTCTAATCAGAGGCTCAACAAC-TTTGAAAAAATAAATAAAGCTCC
63 -GAAAAATAAATAAAGTTCCTCTAATCAGAGGCTCAACAACTTTTG-AAAAATAAATAAAGCTCC
5112784 TCTAAT
126 TCTAAT
* * * * * * *
5112790 CAGAGGCTCAACGACTTTGGAAAAGTAAATAAGGCTTCTCTAAGCAGAGGCTCAAGAACTTTTCA
1 CAGAGGCTCAACAACTTTGAAAAAATAAATAAGGCTCCTATAAACAGAGGCTCAAGAAC-TTTGA
* * * * *
5112855 AAAATAAATAAGGTTCCTCTAATTAGAGGCTCAACAACTTTTGAAAAATAAATAAGGTTTCTCTA
65 AAAATAAATAAAGTTCCTCTAATCAGAGGCTCAACAACTTTTGAAAAATAAATAAAGCTCCTCTA
5112920 AT
130 AT
* * * *
5112922 CAGAGGCTCAACAACTTTGAAAAAATAAATAAGACTCCTATAATCAAAGGCTCAATAACTTTGAA
1 CAGAGGCTCAACAACTTTGAAAAAATAAATAAGGCTCCTATAAACAGAGGCTCAAGAACTTTGAA
5112987 AAATAAA
66 AAATAAA
5112994 GCTCATTGAC
Statistics
Matches: 175, Mismatches: 25, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
131 16 0.09
132 135 0.77
133 20 0.11
134 4 0.02
ACGTcount: A:0.43, C:0.17, G:0.14, T:0.25
Consensus pattern (131 bp):
CAGAGGCTCAACAACTTTGAAAAAATAAATAAGGCTCCTATAAACAGAGGCTCAAGAACTTTGAA
AAATAAATAAAGTTCCTCTAATCAGAGGCTCAACAACTTTTGAAAAATAAATAAAGCTCCTCTAA
T
Found at i:5113180 original size:21 final size:21
Alignment explanation
Indices: 5113156--5113196 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
5113146 AAAGATTTAT
* *
5113156 ATTCAGATTCTAGAGATTCAC
1 ATTCAAATTATAGAGATTCAC
*
5113177 ATTCAAATTATAGTGATTCA
1 ATTCAAATTATAGAGATTCA
5113197 TACCCAATTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.37
Consensus pattern (21 bp):
ATTCAAATTATAGAGATTCAC
Found at i:5113401 original size:43 final size:44
Alignment explanation
Indices: 5113318--5113403 Score: 104
Period size: 44 Copynumber: 2.0 Consensus size: 44
5113308 CTCCTCGTTC
* * *
5113318 AAGTTCAAAGATTCACATTTAATAAATCTTAGAGTTTCACATCT
1 AAGTTCAAAGATTCACATTTAAAAAATCTTAAAGATTCACATCT
**
5113362 AAGTTCAAAGATTTTC-TTTAAAAAAAT-TTAAAGATTCACATC
1 AAGTTCAAAGATTCACATTT-AAAAAATCTTAAAGATTCACATC
5113404 CAAAATTTCA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
43 16 0.44
44 20 0.56
ACGTcount: A:0.42, C:0.14, G:0.08, T:0.36
Consensus pattern (44 bp):
AAGTTCAAAGATTCACATTTAAAAAATCTTAAAGATTCACATCT
Found at i:5113527 original size:22 final size:21
Alignment explanation
Indices: 5113484--5113567 Score: 123
Period size: 21 Copynumber: 4.0 Consensus size: 21
5113474 TTCATATCTG
5113484 AAAGATTCTCATTTGAAACTA
1 AAAGATTCTCATTTGAAACTA
5113505 AAAGATTCTCATTTGAAAACTA
1 AAAGATTCTCATTTG-AAACTA
* * *
5113527 AAAAATTCTCATTTGAAATTG
1 AAAGATTCTCATTTGAAACTA
*
5113548 AATGATTCTCATTTGAAACT
1 AAAGATTCTCATTTGAAACT
5113568 CATAATTTTA
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
21 36 0.64
22 20 0.36
ACGTcount: A:0.42, C:0.13, G:0.10, T:0.36
Consensus pattern (21 bp):
AAAGATTCTCATTTGAAACTA
Found at i:5114040 original size:79 final size:79
Alignment explanation
Indices: 5113936--5114128 Score: 251
Period size: 79 Copynumber: 2.4 Consensus size: 79
5113926 TTCTATCAAT
* * * * *
5113936 TGATCCACATCATTTGCATCATTTGATCCCAACTTACAAGCTTCTCATCATTAGCAATTTCAGCA
1 TGATCCACATCATTTTCATCATTTGATCCCAACTCACAAGCTTCTCAACACTAGCAATTTCAACA
*
5114001 TAAATTTCATCTAC
66 TAAATTTCATCCAC
* ** * * * *
5114015 TGATCCATATCATTTTCATTGTTTGATCTCAACTCATAGGCTTCTTAACACTAGCAATTTCAACA
1 TGATCCACATCATTTTCATCATTTGATCCCAACTCACAAGCTTCTCAACACTAGCAATTTCAACA
5114080 TAAATTTCATCCAC
66 TAAATTTCATCCAC
* *
5114094 TGATCCACATCATTTTCATCACTTGATCACAACTC
1 TGATCCACATCATTTTCATCATTTGATCCCAACTC
5114129 CTAAGTTACG
Statistics
Matches: 96, Mismatches: 18, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
79 96 1.00
ACGTcount: A:0.30, C:0.26, G:0.07, T:0.36
Consensus pattern (79 bp):
TGATCCACATCATTTTCATCATTTGATCCCAACTCACAAGCTTCTCAACACTAGCAATTTCAACA
TAAATTTCATCCAC
Found at i:5114690 original size:24 final size:24
Alignment explanation
Indices: 5114663--5114724 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 24
5114653 TCAATTTGAG
*
5114663 TTTTCCTTTTTT-TTTCTTTTACATT
1 TTTTCCTTTTTTCATTC-TTT-CATT
*
5114688 TTTTCATTTTTTCATTCTTTCA-T
1 TTTTCCTTTTTTCATTCTTTCATT
5114711 TTTTCTCTTTTTTC
1 TTTTC-CTTTTTTC
5114725 CTTTATTTCT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
23 6 0.19
24 9 0.28
25 14 0.44
26 3 0.09
ACGTcount: A:0.08, C:0.18, G:0.00, T:0.74
Consensus pattern (24 bp):
TTTTCCTTTTTTCATTCTTTCATT
Found at i:5114724 original size:16 final size:15
Alignment explanation
Indices: 5114672--5114829 Score: 93
Period size: 16 Copynumber: 10.3 Consensus size: 15
5114662 GTTTTCCTTT
*
5114672 TTTTTTC-TTTTACA
1 TTTTTTCTTTTTTCA
5114686 TTTTTTCATTTTTTCA
1 TTTTTTC-TTTTTTCA
*
5114702 TTCTTTCATTTTTCTC-
1 TTTTTTC-TTTTT-TCA
5114718 TTTTTTCCTTTATTTC-
1 TTTTTT-CTTT-TTTCA
5114734 TTTCTTT-TGTTTTTC-
1 TTT-TTTCT-TTTTTCA
5114749 TTGTTTTCTCTTTTTC-
1 TT-TTTTCT-TTTTTCA
5114765 -TTTTTC-TTTTTCA
1 TTTTTTCTTTTTTCA
5114778 TTTTTT-TTATTTTCA
1 TTTTTTCTT-TTTTCA
* *
5114793 TTTATTTTTATTTTTTA
1 TTT-TTTCT-TTTTTCA
5114810 TTTTTT-TATTTTTCA
1 TTTTTTCT-TTTTTCA
5114825 TTTTT
1 TTTTT
5114830 GATATCTCTC
Statistics
Matches: 122, Mismatches: 6, Indels: 31
0.77 0.04 0.19
Matches are distributed among these distances:
12 6 0.05
14 18 0.15
15 33 0.27
16 47 0.39
17 17 0.14
18 1 0.01
ACGTcount: A:0.09, C:0.13, G:0.01, T:0.77
Consensus pattern (15 bp):
TTTTTTCTTTTTTCA
Found at i:5114829 original size:8 final size:8
Alignment explanation
Indices: 5114679--5114829 Score: 78
Period size: 8 Copynumber: 19.5 Consensus size: 8
5114669 TTTTTTTTTC
*
5114679 TTTTACAT
1 TTTTTCAT
5114687 TTTTTCAT
1 TTTTTCAT
5114695 TTTTTCAT
1 TTTTTCAT
*
5114703 TCTTTCAT
1 TTTTTCAT
5114711 TTTTCTC-T
1 TTTT-TCAT
*
5114719 TTTTTCCT
1 TTTTTCAT
5114727 TTATTTC-T
1 TT-TTTCAT
5114735 TTCTTT--T
1 TT-TTTCAT
5114742 GTTTTTC-T
1 -TTTTTCAT
5114750 TGTTTTC-T
1 T-TTTTCAT
5114758 CTTTTTC--
1 -TTTTTCAT
5114765 TTTTTC--
1 TTTTTCAT
5114771 TTTTTCAT
1 TTTTTCAT
5114779 TTTTT--T
1 TTTTTCAT
5114785 TATTTTCATT
1 T-TTTTCA-T
*
5114795 TATTTTTAT
1 T-TTTTCAT
5114804 TTTTT-AT
1 TTTTTCAT
*
5114811 TTTTTTA-
1 TTTTTCAT
5114818 TTTTTCAT
1 TTTTTCAT
5114826 TTTT
1 TTTT
5114830 GATATCTCTC
Statistics
Matches: 122, Mismatches: 6, Indels: 30
0.77 0.04 0.19
Matches are distributed among these distances:
6 14 0.11
7 24 0.20
8 67 0.55
9 9 0.07
10 8 0.07
ACGTcount: A:0.09, C:0.13, G:0.01, T:0.77
Consensus pattern (8 bp):
TTTTTCAT
Found at i:5115205 original size:15 final size:14
Alignment explanation
Indices: 5115173--5115225 Score: 54
Period size: 14 Copynumber: 3.7 Consensus size: 14
5115163 GTGGCATTTA
*
5115173 ATTTTTCTTTTCTCT
1 ATTTTT-TTTTCTTT
*
5115188 -TTTTTTTTGCTTT
1 ATTTTTTTTTCTTT
*
5115201 GTTTTGTTTTTCTTT
1 ATTTT-TTTTTCTTT
5115216 ATTTTTTTTT
1 ATTTTTTTTT
5115226 TACTTTCTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
13 6 0.19
14 14 0.44
15 12 0.38
ACGTcount: A:0.04, C:0.09, G:0.06, T:0.81
Consensus pattern (14 bp):
ATTTTTTTTTCTTT
Found at i:5121687 original size:18 final size:18
Alignment explanation
Indices: 5121656--5121694 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
5121646 AATAATAAAT
*
5121656 AGGGTAAAGTCAGAAACTA
1 AGGGTAAAGCCAGAAAC-A
5121675 AGGG-AAAGCCAGAAACA
1 AGGGTAAAGCCAGAAACA
5121692 AGG
1 AGG
5121695 AAACCTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 4 0.21
18 11 0.58
19 4 0.21
ACGTcount: A:0.49, C:0.13, G:0.31, T:0.08
Consensus pattern (18 bp):
AGGGTAAAGCCAGAAACA
Found at i:5122519 original size:60 final size:59
Alignment explanation
Indices: 5122449--5122721 Score: 221
Period size: 60 Copynumber: 4.5 Consensus size: 59
5122439 CAAAAAATAA
* *
5122449 TTTAAGGAAAAGTTGAAAATATCAATTTTTCTTGAAGATAAAATTTTTAAAAGATATTTT
1 TTTAAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAAATTTTTAAAA-ATATTTT
* * * *
5122509 TTTAAAGAAAAATTGAGAGTATCAATTTTTCTTGAAAATAAATTTTTTTAAAAAAATATATTT
1 TTTAAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAA-ATTTTT--AAAAATAT-TTT
* * ** * *
5122572 CTCAA-GAAACTTTTTTAAGGAAAGTATCAATTTTTCTTGAAAATAAAA-ATTTCAAAATATATT
1 TTTAAGGAAA---AGTT---GAAAGTATCAATTTTTCTTGAAAATAAAATTTTTAAAAATAT-TT
5122635 T
59 T
* * * * * * *
5122636 TTTGAGGAAAAGTTAAAAGTATAAATTTTTCTTAAAAATAAAA-ATTTCAAAA-ATCTT
1 TTTAAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAAATTTTTAAAAATATTTT
* *
5122693 TTTGAGGAAAAGTTGAAAGTAGCAATTTT
1 TTTAAGGAAAAGTTGAAAGTATCAATTTT
5122722 CCTTAAATAA
Statistics
Matches: 176, Mismatches: 26, Indels: 25
0.78 0.11 0.11
Matches are distributed among these distances:
57 28 0.16
58 2 0.01
59 35 0.20
60 37 0.21
61 5 0.03
62 10 0.06
63 10 0.06
64 13 0.07
65 6 0.03
66 3 0.02
68 27 0.15
ACGTcount: A:0.45, C:0.05, G:0.11, T:0.40
Consensus pattern (59 bp):
TTTAAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAAATTTTTAAAAATATTTT
Found at i:5122721 original size:57 final size:59
Alignment explanation
Indices: 5122591--5122728 Score: 208
Period size: 59 Copynumber: 2.4 Consensus size: 59
5122581 CTTTTTTAAG
* *
5122591 GAAAGTATCAATTTTTCTTGAAAATAAAAATTTCAAAATATATTTTTTGAGGAAAAGTT
1 GAAAGTATCAATTTTTCTTAAAAATAAAAATTTCAAAATATACTTTTTGAGGAAAAGTT
* *
5122650 AAAAGTATAAATTTTTCTTAAAAATAAAAATTTCAAAA-AT-CTTTTTGAGGAAAAGTT
1 GAAAGTATCAATTTTTCTTAAAAATAAAAATTTCAAAATATACTTTTTGAGGAAAAGTT
* *
5122707 GAAAGTAGCAATTTTCCTTAAA
1 GAAAGTATCAATTTTTCTTAAA
5122729 TAAAGGCATT
Statistics
Matches: 71, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
57 34 0.48
58 2 0.03
59 35 0.49
ACGTcount: A:0.46, C:0.07, G:0.11, T:0.37
Consensus pattern (59 bp):
GAAAGTATCAATTTTTCTTAAAAATAAAAATTTCAAAATATACTTTTTGAGGAAAAGTT
Found at i:5124537 original size:42 final size:42
Alignment explanation
Indices: 5124473--5124559 Score: 147
Period size: 42 Copynumber: 2.1 Consensus size: 42
5124463 CTATCAAAGA
*
5124473 AATGGATTATTTTGGCTCTATAGATGTAGCTGAACTATGCTT
1 AATGGATTATTTTGGCTCTATAGATGCAGCTGAACTATGCTT
* *
5124515 AATGGATTATTTTGGCTTTATAGATGCAGTTGAACTATGCTT
1 AATGGATTATTTTGGCTCTATAGATGCAGCTGAACTATGCTT
5124557 AAT
1 AAT
5124560 TCTAGATATG
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.28, C:0.10, G:0.21, T:0.41
Consensus pattern (42 bp):
AATGGATTATTTTGGCTCTATAGATGCAGCTGAACTATGCTT
Found at i:5126188 original size:18 final size:17
Alignment explanation
Indices: 5126162--5126195 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
5126152 CAAATAGGGT
*
5126162 AAAGTCAGAAACTAAGGC
1 AAAGCCAGAAAC-AAGGC
5126180 AAAGCCAGAAACAAGG
1 AAAGCCAGAAACAAGG
5126196 AAACCTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.53, C:0.18, G:0.24, T:0.06
Consensus pattern (17 bp):
AAAGCCAGAAACAAGGC
Found at i:5126603 original size:19 final size:19
Alignment explanation
Indices: 5126579--5126621 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
5126569 AAAGATCGAT
*
5126579 AAAAAA-TTGTAAAAAGAGA
1 AAAAAACTTATAAAAAG-GA
*
5126598 AAAAAACTTATAAAATGGA
1 AAAAAACTTATAAAAAGGA
5126617 AAAAA
1 AAAAA
5126622 CGTTTAAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.70, C:0.02, G:0.12, T:0.16
Consensus pattern (19 bp):
AAAAAACTTATAAAAAGGA
Found at i:5127390 original size:10 final size:10
Alignment explanation
Indices: 5127362--5127405 Score: 63
Period size: 10 Copynumber: 4.5 Consensus size: 10
5127352 CTTTTCCCTT
5127362 TCTCTC-TTC
1 TCTCTCTTTC
* *
5127371 TTTCTTTTTC
1 TCTCTCTTTC
5127381 TCTCTCTTTC
1 TCTCTCTTTC
5127391 TCTCTCTTTC
1 TCTCTCTTTC
5127401 TCTCT
1 TCTCT
5127406 AGAAACCCAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
9 4 0.13
10 26 0.87
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (10 bp):
TCTCTCTTTC
Found at i:5132240 original size:47 final size:51
Alignment explanation
Indices: 5132128--5132242 Score: 129
Period size: 47 Copynumber: 2.4 Consensus size: 51
5132118 ACAAGAAGAT
*
5132128 TACAAAAGAAGAATTCT--AAGAAATAGGAAATCTTAATAGGTAAGTTTGAC
1 TACAAAAGAAGAATTCTAAAAGAAATAGG-AATCTTAATAGGCAAGTTTGAC
*
5132178 T-CAAAAGAA-AGATTCTAAAAGAAA-AGG-ATTTTAATA-GCAAGTTT-AC
1 TACAAAAGAAGA-ATTCTAAAAGAAATAGGAATCTTAATAGGCAAGTTTGAC
*
5132224 TACAAGAGAAGAATTCTAA
1 TACAAAAGAAGAATTCTAA
5132243 GAAAGGGATT
Statistics
Matches: 57, Mismatches: 3, Indels: 13
0.78 0.04 0.18
Matches are distributed among these distances:
46 3 0.05
47 21 0.37
48 10 0.18
49 13 0.23
50 4 0.07
51 6 0.11
ACGTcount: A:0.50, C:0.09, G:0.17, T:0.25
Consensus pattern (51 bp):
TACAAAAGAAGAATTCTAAAAGAAATAGGAATCTTAATAGGCAAGTTTGAC
Found at i:5132750 original size:31 final size:31
Alignment explanation
Indices: 5132711--5132795 Score: 136
Period size: 31 Copynumber: 2.7 Consensus size: 31
5132701 AGGCTTTTAG
*
5132711 CCCAACAAATGGTATCAGAGCTGTGGTA-TT
1 CCCAACAAATAGTATCAGAGCTGTGGTATTT
5132741 CTCCAACAAATAGTATCAGAGCTGTGGTATTT
1 C-CCAACAAATAGTATCAGAGCTGTGGTATTT
*
5132773 CCCAACAAGTAGTATCAGAGCTG
1 CCCAACAAATAGTATCAGAGCTG
5132796 AAGGTTCGAA
Statistics
Matches: 51, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
30 1 0.02
31 47 0.92
32 3 0.06
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (31 bp):
CCCAACAAATAGTATCAGAGCTGTGGTATTT
Found at i:5132841 original size:25 final size:25
Alignment explanation
Indices: 5132808--5132865 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 25
5132798 GGTTCGAAAC
*
5132808 ATGAAAAGAGTT-AAAGATTCAAGAT
1 ATGAGAAGAGTTGAAAG-TTCAAGAT
* *
5132833 ATGGGAAGAGTTGATAGTTCAAGAT
1 ATGAGAAGAGTTGAAAGTTCAAGAT
5132858 ATGAGAAG
1 ATGAGAAG
5132866 CGCATGGTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 25 0.89
26 3 0.11
ACGTcount: A:0.45, C:0.03, G:0.28, T:0.24
Consensus pattern (25 bp):
ATGAGAAGAGTTGAAAGTTCAAGAT
Found at i:5133122 original size:11 final size:11
Alignment explanation
Indices: 5133106--5133136 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
5133096 AATCCCATAA
5133106 GAGATTTGTTT
1 GAGATTTGTTT
5133117 GAGATTTGTTT
1 GAGATTTGTTT
5133128 GAGATTTGT
1 GAGATTTGT
5133137 CAGATATTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.19, C:0.00, G:0.29, T:0.52
Consensus pattern (11 bp):
GAGATTTGTTT
Found at i:5133249 original size:52 final size:52
Alignment explanation
Indices: 5133161--5133317 Score: 217
Period size: 52 Copynumber: 3.0 Consensus size: 52
5133151 TGGATAAAAA
* * *
5133161 GACTTGCAAAAGAAGAATTCCAAGA-GAAAAGGGATTCTTAATAGGTAAGTTT
1 GACTTGCAAGAGAAGAATTCTAAAAGGAAAA-GGATTCTTAATAGGTAAGTTT
*
5133213 GACTTGCAAGAGAAGAATTCTAAAAGGAAAAAGATTCTTAATAGGTAAGTTT
1 GACTTGCAAGAGAAGAATTCTAAAAGGAAAAGGATTCTTAATAGGTAAGTTT
* * * * *
5133265 GACTTACAGGAGAAGAATTCTAAAAGGAAATGGATTCTTAATGGGCAAGTTT
1 GACTTGCAAGAGAAGAATTCTAAAAGGAAAAGGATTCTTAATAGGTAAGTTT
5133317 G
1 G
5133318 TATGGTTATA
Statistics
Matches: 94, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
52 89 0.95
53 5 0.05
ACGTcount: A:0.41, C:0.09, G:0.24, T:0.26
Consensus pattern (52 bp):
GACTTGCAAGAGAAGAATTCTAAAAGGAAAAGGATTCTTAATAGGTAAGTTT
Found at i:5136329 original size:41 final size:40
Alignment explanation
Indices: 5136283--5136359 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 40
5136273 ATAGTAATAA
5136283 TTAAAAAAATTAAAAATTTTGC-AATATTCTTTATTAATTTT
1 TTAAAAAAATTAAAAATTTT-CTAATATTCTTT-TTAATTTT
* * *
5136324 TTAAAATATTTAAAAATTTTCTTATATTCTTTTTAA
1 TTAAAAAAATTAAAAATTTTCTAATATTCTTTTTAA
5136360 AATATTTTCT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
40 5 0.16
41 27 0.84
ACGTcount: A:0.42, C:0.05, G:0.01, T:0.52
Consensus pattern (40 bp):
TTAAAAAAATTAAAAATTTTCTAATATTCTTTTTAATTTT
Found at i:5136747 original size:76 final size:76
Alignment explanation
Indices: 5136607--5136781 Score: 235
Period size: 76 Copynumber: 2.3 Consensus size: 76
5136597 GAAGCAAGGG
* * * *
5136607 AAATTAAAGAAT-GCTAATGATGATTAGTAAGAGTTTTAAGTTATAACCAAGGTTAAAAGTTGAT
1 AAATCAAAGAATAG-TAATGATGATTAATAAGAGTTTTAAGCTATAACCAAGGCTAAAAGTTGAT
5136671 TTGCAACCGATT
65 TTGCAACCGATT
* * * * *
5136683 AAATCAGAGAGTATTAATGATGATTAATAAGAGTTTTAAGCTATAATCAAGGCTAGAAGTTGATT
1 AAATCAAAGAATAGTAATGATGATTAATAAGAGTTTTAAGCTATAACCAAGGCTAAAAGTTGATT
**
5136748 TGCAAGTGATT
66 TGCAACCGATT
5136759 AAATCAAAGAATAGTAATGATGA
1 AAATCAAAGAATAGTAATGATGA
5136782 AACATTAGCT
Statistics
Matches: 84, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
76 84 1.00
ACGTcount: A:0.42, C:0.07, G:0.19, T:0.31
Consensus pattern (76 bp):
AAATCAAAGAATAGTAATGATGATTAATAAGAGTTTTAAGCTATAACCAAGGCTAAAAGTTGATT
TGCAACCGATT
Found at i:5156626 original size:105 final size:105
Alignment explanation
Indices: 5156336--5156628 Score: 317
Period size: 105 Copynumber: 2.8 Consensus size: 105
5156326 CTACTTTTAG
* * *
5156336 CTTT-AAAGAAATGTAGTAATTGCCAT-ACCGATAATAAATGCTCATTAAATCAAAAGTAATT-T
1 CTTTAAAAGAAATGCAGTAATTGCCATAACC-ATAATAAATGCTCATTAAATCAAAAGTCATTAA
*
5156398 G-GAAATAAGATGAAAAAAATTAAATGCTAAATATTGTGTTT
65 GTCAAATAA-ATGAAAAAAATTAAATGCTAAATATTGTGTTT
* * * * * * *
5156439 CTTTAAACAAAAATGCAATAATTGCCATATCCATAATAAATACTTATTAAATCAAAAGCCATCAA
1 CTTTAAA-AGAAATGCAGTAATTGCCATAACCATAATAAATGCTCATTAAATCAAAAGTCATTAA
** * *
5156504 GTCAAGCAGATGAAAAAAATTAAATGC-CAATATTGTGTTT
65 GTCAAATAAATGAAAAAAATTAAATGCTAAATATTGTGTTT
* * * ** *
5156544 CTATTCAAAGAAATGCAGTAATTACCATAACCATAATAAACGCTCATTAAAGAAAAAATCATTAA
1 CT-TTAAAAGAAATGCAGTAATTGCCATAACCATAATAAATGCTCATTAAATCAAAAGTCATTAA
*
5156609 GTCAAATAAATGGAAAAAAT
65 GTCAAATAAATGAAAAAAAT
5156629 ACGAGTTACA
Statistics
Matches: 152, Mismatches: 32, Indels: 10
0.78 0.16 0.05
Matches are distributed among these distances:
103 4 0.03
104 2 0.01
105 118 0.78
106 25 0.16
107 3 0.02
ACGTcount: A:0.48, C:0.13, G:0.11, T:0.28
Consensus pattern (105 bp):
CTTTAAAAGAAATGCAGTAATTGCCATAACCATAATAAATGCTCATTAAATCAAAAGTCATTAAG
TCAAATAAATGAAAAAAATTAAATGCTAAATATTGTGTTT
Found at i:5163492 original size:143 final size:145
Alignment explanation
Indices: 5163301--5163625 Score: 355
Period size: 143 Copynumber: 2.3 Consensus size: 145
5163291 TCCAAATCCC
* * * *
5163301 TTAGGGTTATTTTCATAATTTGACCTTTTCGAA-GTT-GAATTTTTAT-AAAAACTTTTAAATCA
1 TTAGGGATATTTTTATAATTTGACCTTCTC-AAGGTTAGAATTTTCATAAAAAAC-TTTAAATCA
* **
5163363 TAATTAAATATTATTTTG-TGACTTTTGATGCATTAGAAA-CCTTGATCGTACATTG-AAAGT-T
64 TAATTAAATA-TAATTTGATGACTTTTGAAACATT-GAAAGCCTTGATCGTACATTGAAAAGTAT
*
5163424 ACAATATTACTAAAATACGC-
127 -CAA-ATCACTAAAATACGCT
* *
5163444 TTAGAGG-TATTTTTGTAATTTGACCTTCTCAAGGTTAGAA-TTTCATAAAAAACTTTAGATCAT
1 TTAG-GGATATTTTTATAATTTGACCTTCTCAAGGTTAGAATTTTCATAAAAAACTTTAAATCAT
* * * ** *
5163507 GATTTAATATAATTTGATGATTTTTGAAACATTGAAAGCCTTGATCGTATTTTGAAAAGTATGAA
65 AATTAAATATAATTTGATGACTTTTGAAACATTGAAAGCCTTGATCGTACATTGAAAAGTATCAA
*
5163572 ATCACTAAAATACTCT
130 ATCACTAAAATACGCT
*
5163588 TTAGGGATATTTTTATAATTTGACATTCTCAAGGTTAG
1 TTAGGGATATTTTTATAATTTGACCTTCTCAAGGTTAG
5163626 TTTTTTGTGA
Statistics
Matches: 154, Mismatches: 18, Indels: 19
0.81 0.09 0.10
Matches are distributed among these distances:
142 12 0.08
143 90 0.58
144 51 0.33
145 1 0.01
ACGTcount: A:0.35, C:0.10, G:0.14, T:0.41
Consensus pattern (145 bp):
TTAGGGATATTTTTATAATTTGACCTTCTCAAGGTTAGAATTTTCATAAAAAACTTTAAATCATA
ATTAAATATAATTTGATGACTTTTGAAACATTGAAAGCCTTGATCGTACATTGAAAAGTATCAAA
TCACTAAAATACGCT
Found at i:5165174 original size:13 final size:15
Alignment explanation
Indices: 5165142--5165179 Score: 53
Period size: 13 Copynumber: 2.7 Consensus size: 15
5165132 GCATATTTAC
5165142 ATTTTTGTCAATGGT
1 ATTTTTGTCAATGGT
*
5165157 ATTTTTGT-AAT-TT
1 ATTTTTGTCAATGGT
5165170 ATTTTTGTCA
1 ATTTTTGTCA
5165180 CATGCATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 9 0.43
14 4 0.19
15 8 0.38
ACGTcount: A:0.21, C:0.05, G:0.13, T:0.61
Consensus pattern (15 bp):
ATTTTTGTCAATGGT
Found at i:5165247 original size:7 final size:7
Alignment explanation
Indices: 5165234--5165281 Score: 53
Period size: 7 Copynumber: 6.9 Consensus size: 7
5165224 TTTAAATCCA
5165234 AAACCTT
1 AAACCTT
*
5165241 AAGCCTT
1 AAACCTT
5165248 AAACCTT
1 AAACCTT
* *
5165255 AAATCGT
1 AAACCTT
5165262 AAATCC-T
1 AAA-CCTT
5165269 AAACCTT
1 AAACCTT
5165276 AAACCT
1 AAACCT
5165282 AAAATCTAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
6 2 0.06
7 31 0.91
8 1 0.03
ACGTcount: A:0.42, C:0.27, G:0.04, T:0.27
Consensus pattern (7 bp):
AAACCTT
Found at i:5165259 original size:28 final size:26
Alignment explanation
Indices: 5165225--5165302 Score: 84
Period size: 28 Copynumber: 2.8 Consensus size: 26
5165215 ATTCTAAAAT
*
5165225 TTAAATCCAAAACCTTAAGCCTTAAACC
1 TTAAATCTAAAACC-TAA-CCTTAAACC
*
5165253 TTAAATCGTAAATCCTAAACCTTAAACC
1 TTAAATC-TAAAACCT-AACCTTAAACC
*
5165281 TAAAATCTAAAACCCTAACCTT
1 TTAAATCTAAAA-CCTAACCTT
5165303 GGCTCTATCC
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
27 10 0.23
28 26 0.60
29 7 0.16
ACGTcount: A:0.44, C:0.27, G:0.03, T:0.27
Consensus pattern (26 bp):
TTAAATCTAAAACCTAACCTTAAACC
Found at i:5165286 original size:21 final size:20
Alignment explanation
Indices: 5165247--5165291 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
5165237 CCTTAAGCCT
*
5165247 TAAACCTTAAATCGTAAATCC
1 TAAACCTTAAATCCTAAAT-C
5165268 TAAACCTTAAA-CCTAAAATC
1 TAAACCTTAAATCCT-AAATC
5165288 TAAA
1 TAAA
5165292 ACCCTAACCT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.49, C:0.22, G:0.02, T:0.27
Consensus pattern (20 bp):
TAAACCTTAAATCCTAAATC
Found at i:5166526 original size:2 final size:2
Alignment explanation
Indices: 5166519--5166557 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
5166509 GTTTAATCTA
5166519 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5166558 TTTGTTTTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:5168968 original size:23 final size:23
Alignment explanation
Indices: 5168942--5169013 Score: 81
Period size: 23 Copynumber: 3.0 Consensus size: 23
5168932 TAGTGTTTGC
*
5168942 GAACATATTTGTTTATTATTCAT
1 GAACATATTTATTTATTATTCAT
* *
5168965 GAACATGTTTATTTATATATGTTCGT
1 GAACATATTTATTTAT-TA--TTCAT
*
5168991 GAACATATTTATTTAATATTCAT
1 GAACATATTTATTTATTATTCAT
5169014 AAATAAGTTC
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
23 18 0.45
24 2 0.05
25 2 0.05
26 18 0.45
ACGTcount: A:0.32, C:0.08, G:0.10, T:0.50
Consensus pattern (23 bp):
GAACATATTTATTTATTATTCAT
Found at i:5172417 original size:121 final size:121
Alignment explanation
Indices: 5172131--5172418 Score: 325
Period size: 122 Copynumber: 2.4 Consensus size: 121
5172121 TTTATTGAAA
* **
5172131 GAGATTATTCAAGGCGTTTTTTACCAAAAACGTCTTGAATAATCCCTTGTCATTTTTTTAGGATT
1 GAGATTATTCAAGGCGTTTTTGA-CAAAAACACCTTGAATAATCCCTTGTCATTTTTTTAGGATT
* * * * *
5172196 ATTCAAAGTGTTTTTGGCTAGAAACACTTTGAATAATCTTTTTATAAAAAATTAAAC
65 ATTCAAAGCGTTTTTGGCTAAAAACACCTTGAATAATCTCTTTACAAAAAATTAAAC
* * *
5172253 GAGGTTATTCAAAGCGTTTTCTGTCAAAAACACCTTGAATAATCCCTTG-C-TATTTTTTAGAGA
1 GAGATTATTCAAGGCGTTTT-TGACAAAAACACCTTGAATAATCCCTTGTCAT-TTTTTTAG-GA
* * * *
5172316 TTATTTAAGGCGTTTTTGG-TCAAAAACGCCTTGAATAATC-CTTTACAAAAAATTGAATC
63 TTATTCAAAGCGTTTTTGGCT-AAAAACACCTTGAATAATCTCTTTACAAAAAATT-AAAC
* *
5172375 GA-ATTATTCAAGGCGTTTTTGGCTAAAAATACCTTGAATAATCC
1 GAGATTATTCAAGGCGTTTTTGAC-AAAAACACCTTGAATAATCC
5172419 ATTAACAAAA
Statistics
Matches: 141, Mismatches: 19, Indels: 13
0.82 0.11 0.08
Matches are distributed among these distances:
120 4 0.03
121 56 0.40
122 80 0.57
123 1 0.01
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.38
Consensus pattern (121 bp):
GAGATTATTCAAGGCGTTTTTGACAAAAACACCTTGAATAATCCCTTGTCATTTTTTTAGGATTA
TTCAAAGCGTTTTTGGCTAAAAACACCTTGAATAATCTCTTTACAAAAAATTAAAC
Found at i:5177114 original size:6 final size:6
Alignment explanation
Indices: 5177103--5177134 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
5177093 TTGTTTATTA
5177103 TTGCTT TTGCTT TTGCTT TT-CTT TTGCTT TTG
1 TTGCTT TTGCTT TTGCTT TTGCTT TTGCTT TTG
5177135 GATGCTTCCC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.00, C:0.16, G:0.16, T:0.69
Consensus pattern (6 bp):
TTGCTT
Found at i:5177128 original size:11 final size:12
Alignment explanation
Indices: 5177103--5177134 Score: 57
Period size: 11 Copynumber: 2.8 Consensus size: 12
5177093 TTGTTTATTA
5177103 TTGCTTTTGCTT
1 TTGCTTTTGCTT
5177115 TTGCTTTT-CTT
1 TTGCTTTTGCTT
5177126 TTGCTTTTG
1 TTGCTTTTG
5177135 GATGCTTCCC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 11 0.58
12 8 0.42
ACGTcount: A:0.00, C:0.16, G:0.16, T:0.69
Consensus pattern (12 bp):
TTGCTTTTGCTT
Found at i:5179803 original size:17 final size:16
Alignment explanation
Indices: 5179757--5179804 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 16
5179747 ATATAAAATT
*
5179757 TTTTATTATTTATTTAA
1 TTTTA-TATTTATATAA
**
5179774 TTTTATACATATATATA
1 TTTTATATTTATATA-A
5179791 TTTTATATTTATAT
1 TTTTATATTTATAT
5179805 TTTAAAAAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
16 7 0.28
17 18 0.72
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTTATATTTATATAA
Found at i:5179847 original size:18 final size:20
Alignment explanation
Indices: 5179795--5179844 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
5179785 TATATATTTT
*
5179795 ATATTTATATTTTAAAAAATA
1 ATATTT-TATATTAAAAAATA
*
5179816 ATATTTTATATTAAAAATTA
1 ATATTTTATATTAAAAAATA
5179836 ATATTTTAT
1 ATATTTTAT
5179845 TAATTTCAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 21 0.78
21 6 0.22
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
ATATTTTATATTAAAAAATA
Found at i:5182547 original size:23 final size:22
Alignment explanation
Indices: 5182507--5182551 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
5182497 AATACATGCA
5182507 TAATAAATATCAAATTTATCTTT
1 TAATAAATATCAAATTTA-CTTT
*
5182530 TAATAAATTAT-AATTTTACTTT
1 TAATAAA-TATCAAATTTACTTT
5182552 CTTTTTTCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 4 0.20
23 13 0.65
24 3 0.15
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.51
Consensus pattern (22 bp):
TAATAAATATCAAATTTACTTT
Found at i:5182575 original size:16 final size:16
Alignment explanation
Indices: 5182549--5182600 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 16
5182539 ATAATTTTAC
5182549 TTTCTTTTTTCTCTTTT
1 TTTC-TTTTTCTCTTTT
5182566 TTTC-TTTT-TCTTTT
1 TTTCTTTTTCTCTTTT
*
5182580 TTTCTCTTTCATCTTTT
1 TTTCTTTTTC-TCTTTT
5182597 TTTC
1 TTTC
5182601 CTCTTATACT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
14 10 0.32
15 7 0.23
17 14 0.45
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTCTTTTTCTCTTTT
Found at i:5182579 original size:14 final size:15
Alignment explanation
Indices: 5182555--5182600 Score: 67
Period size: 14 Copynumber: 3.0 Consensus size: 15
5182545 TTACTTTCTT
5182555 TTTTCTCTTTTTTTC
1 TTTTCTCTTTTTTTC
5182570 TTTT-TCTTTTTTTC
1 TTTTCTCTTTTTTTC
5182584 TCTTTCATCTTTTTTTC
1 T-TTTC-TCTTTTTTTC
5182601 CTCTTATACT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
14 11 0.39
15 7 0.25
17 10 0.36
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTTCTCTTTTTTTC
Found at i:5182594 original size:23 final size:23
Alignment explanation
Indices: 5182549--5182597 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
5182539 ATAATTTTAC
**
5182549 TTTCTTTTTTCTCTTTTTTTCTT
1 TTTCTTTTTTCTCTTTTCATCTT
5182572 TTTCTTTTTT-TCTCTTTCATCTT
1 TTTCTTTTTTCTCT-TTTCATCTT
5182595 TTT
1 TTT
5182598 TTCCTCTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 3 0.13
23 20 0.87
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (23 bp):
TTTCTTTTTTCTCTTTTCATCTT
Found at i:5182767 original size:22 final size:22
Alignment explanation
Indices: 5182722--5182770 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 22
5182712 GAGATTTTTC
*
5182722 AAAAATAAAATTTTAAGAATCTT
1 AAAAATAAAATTTTAAG-ACCTT
5182745 AAAAATAAAATTTTGAAG-CCTT
1 AAAAATAAAATTTT-AAGACCTT
5182767 AAAA
1 AAAA
5182771 GTTTCTCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 7 0.29
23 14 0.58
24 3 0.12
ACGTcount: A:0.57, C:0.06, G:0.06, T:0.31
Consensus pattern (22 bp):
AAAAATAAAATTTTAAGACCTT
Found at i:5187625 original size:22 final size:22
Alignment explanation
Indices: 5187595--5187678 Score: 80
Period size: 22 Copynumber: 3.8 Consensus size: 22
5187585 TACTAACAAT
* *
5187595 TAAGTTATCATTGATTTACTAC
1 TAAGATATCAATGATTTACTAC
* * *
5187617 TATGATATCAATAATTTACTAT
1 TAAGATATCAATGATTTACTAC
* *
5187639 TAAGCTATTAATGATTTACTAC
1 TAAGATATCAATGATTTACTAC
*
5187661 TAA-ATTATAAATGATTTA
1 TAAGA-TATCAATGATTTA
5187679 TTATAAATTG
Statistics
Matches: 49, Mismatches: 12, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
22 49 1.00
ACGTcount: A:0.39, C:0.10, G:0.07, T:0.44
Consensus pattern (22 bp):
TAAGATATCAATGATTTACTAC
Found at i:5187678 original size:44 final size:44
Alignment explanation
Indices: 5187593--5188046 Score: 173
Period size: 44 Copynumber: 10.2 Consensus size: 44
5187583 ATTACTAACA
* * * *
5187593 ATTAAGTTATCATTGATTTACTACTATGA-TATCAATAATTTACT
1 ATTAAGTTATTAATGATTTACTACTA-AATTATCAATGATTTACT
* * *
5187637 ATTAAGCTATTAATGATTTACTACTAAATTATAAATGATTTATT
1 ATTAAGTTATTAATGATTTACTACTAAATTATCAATGATTTACT
* *
5187681 ATAAATTGTTGATGATTTGAATGATTTACTACTAAATCGT-TGAA-GATTTACT
1 ATTAA--G-T--T-A-TT-AATGATTTACTACTAAAT--TATCAATGATTTACT
* * * *
5187733 ACTAAGTTACTAAT-TTTTTC-A-TAAAGTTAT-AATTGATTTACT
1 ATTAAGTTATTAATGATTTACTACTAAA-TTATCAA-TGATTTACT
* * * * *
5187775 ATTAATTTATCAATGATTTATTA-TAAAGTTATCAATAATTAACT
1 ATTAAGTTATTAATGATTTACTACTAAA-TTATCAATGATTTACT
* * * * * * * *
5187819 ATTAAATTATCACTAATTAACTATTAAGTTATCAATGATTTATT
1 ATTAAGTTATTAATGATTTACTACTAAATTATCAATGATTTACT
* * * *
5187863 ATTAAGTTA-TATTGATTTACTATTAAGTTAT-ATTGATTTACT
1 ATTAAGTTATTAATGATTTACTACTAAATTATCAATGATTTACT
* * ** * * * *
5187905 TTTAAATGT-CCAATGATTAACTACT-AGTTAT-TATTATTTACT
1 ATTAAGT-TATTAATGATTTACTACTAAATTATCAATGATTTACT
** * * * * *
5187947 GCTAAGTTTATCAATTAATTACTATTAAA--CTCAAATAGATTTACT
1 ATTAAG-TTATTAATGATTTACTACTAAATTATC-AAT-GATTTACT
* * * * * * *
5187992 ATTAAGTTATCACTAATTTATTATTAAATTATCATTGATTTATT
1 ATTAAGTTATTAATGATTTACTACTAAATTATCAATGATTTACT
5188036 ATTAAGTTATT
1 ATTAAGTTATT
5188047 GCTTATTTTT
Statistics
Matches: 309, Mismatches: 72, Indels: 58
0.70 0.16 0.13
Matches are distributed among these distances:
40 3 0.01
41 5 0.02
42 53 0.17
43 50 0.16
44 136 0.44
45 19 0.06
46 4 0.01
47 1 0.00
49 2 0.01
50 2 0.01
51 2 0.01
52 28 0.09
53 3 0.01
54 1 0.00
ACGTcount: A:0.37, C:0.09, G:0.07, T:0.46
Consensus pattern (44 bp):
ATTAAGTTATTAATGATTTACTACTAAATTATCAATGATTTACT
Found at i:5187704 original size:30 final size:31
Alignment explanation
Indices: 5187670--5187729 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
5187660 CTAAATTATA
* * *
5187670 AATGATTTATTA-TAAATTGTTGATGATTTG
1 AATGATTTACTACTAAATCGTTGAAGATTTG
5187700 AATGATTTACTACTAAATCGTTGAAGATTT
1 AATGATTTACTACTAAATCGTTGAAGATTT
5187730 ACTACTAAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 11 0.42
31 15 0.58
ACGTcount: A:0.35, C:0.05, G:0.15, T:0.45
Consensus pattern (31 bp):
AATGATTTACTACTAAATCGTTGAAGATTTG
Found at i:5187791 original size:22 final size:22
Alignment explanation
Indices: 5187756--5188045 Score: 202
Period size: 22 Copynumber: 13.3 Consensus size: 22
5187746 TTTTTTCATA
5187756 AAGTTAT-AATTGATTTACTATT
1 AAGTTATCAA-TGATTTACTATT
* * *
5187778 AATTTATCAATGATTTATTATA
1 AAGTTATCAATGATTTACTATT
* *
5187800 AAGTTATCAATAATTAACTATT
1 AAGTTATCAATGATTTACTATT
* * * *
5187822 AAATTATCACTAATTAACTATT
1 AAGTTATCAATGATTTACTATT
*
5187844 AAGTTATCAATGATTTATTATT
1 AAGTTATCAATGATTTACTATT
*
5187866 AAGTTAT-ATTGATTTACTATT
1 AAGTTATCAATGATTTACTATT
* *
5187887 AAGTTAT-ATTGATTTACTTTT
1 AAGTTATCAATGATTTACTATT
* * * *
5187908 AAATGT-CCAATGATTAACTACT
1 AAGT-TATCAATGATTTACTATT
* * **
5187930 -AGTTAT-TATTATTTACTGCT
1 AAGTTATCAATGATTTACTATT
* *
5187950 AAGTTTATCAATTAATTACTATT
1 AAG-TTATCAATGATTTACTATT
5187973 AA---ACTCAAATAGATTTACTATT
1 AAGTTA-TC-AAT-GATTTACTATT
* * *
5187995 AAGTTATCACTAATTTATTATT
1 AAGTTATCAATGATTTACTATT
* * *
5188017 AAATTATCATTGATTTATTATT
1 AAGTTATCAATGATTTACTATT
5188039 AAGTTAT
1 AAGTTAT
5188046 TGCTTATTTT
Statistics
Matches: 212, Mismatches: 43, Indels: 26
0.75 0.15 0.09
Matches are distributed among these distances:
19 1 0.00
20 13 0.06
21 42 0.20
22 137 0.65
23 16 0.08
24 2 0.01
25 1 0.00
ACGTcount: A:0.38, C:0.08, G:0.07, T:0.47
Consensus pattern (22 bp):
AAGTTATCAATGATTTACTATT
Found at i:5188054 original size:22 final size:21
Alignment explanation
Indices: 5187985--5188064 Score: 63
Period size: 22 Copynumber: 3.6 Consensus size: 21
5187975 ACTCAAATAG
* * *
5187985 ATTTACTATTAAGTTATCACTA
1 ATTTATTATTAAGTTAT-TCTT
*
5188007 ATTTATTATTAAATTA-TCATT
1 ATTTATTATTAAGTTATTC-TT
5188028 GATTTATTATTAAGTTATTGCTT
1 -ATTTATTATTAAGTTATT-CTT
*
5188051 ATTTTTTTATTAAG
1 A-TTTATTATTAAG
5188065 CTATCATTGA
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
20 1 0.02
21 1 0.02
22 30 0.64
23 14 0.30
24 1 0.02
ACGTcount: A:0.33, C:0.06, G:0.06, T:0.55
Consensus pattern (21 bp):
ATTTATTATTAAGTTATTCTT
Found at i:5188063 original size:45 final size:44
Alignment explanation
Indices: 5187984--5188078 Score: 118
Period size: 45 Copynumber: 2.1 Consensus size: 44
5187974 AACTCAAATA
*
5187984 GATTTACTATTAAGTTATCACTAATTTATTATTAAATTATCATT
1 GATTTACTATTAAGTTATCACTAATTTATTATTAAACTATCATT
* ** * * *
5188028 GATTTATTATTAAGTTATTGCTTATTTTTTTATTAAGCTATCATT
1 GATTTACTATTAAGTTATCAC-TAATTTATTATTAAACTATCATT
5188073 GATTTA
1 GATTTA
5188079 ATAATATGTT
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
44 18 0.42
45 25 0.58
ACGTcount: A:0.32, C:0.07, G:0.07, T:0.54
Consensus pattern (44 bp):
GATTTACTATTAAGTTATCACTAATTTATTATTAAACTATCATT
Found at i:5188400 original size:22 final size:22
Alignment explanation
Indices: 5188306--5188602 Score: 161
Period size: 22 Copynumber: 13.5 Consensus size: 22
5188296 AACTATAAAA
* *
5188306 AAATTATCAATGATTGACAATT
1 AAATTATCAATGATTTACTATT
* * *
5188328 AAATTATCATTAATTTACTACT
1 AAATTATCAATGATTTACTATT
** * * * * *
5188350 ATGTTATTAGTGATTTATTGTC
1 AAATTATCAATGATTTACTATT
*
5188372 AAGTTATCAATGATTTACTATT
1 AAATTATCAATGATTTACTATT
* * *
5188394 AAATTATTAATGAATTAGTA-T
1 AAATTATCAATGATTTACTATT
* * *
5188415 AAATTTATGAATTATTTACCATT
1 AAA-TTATCAATGATTTACTATT
** * *
5188438 AGGTTATGAATTATTTACTATT
1 AAATTATCAATGATTTACTATT
* *
5188460 AAGTTA-CGAATGATTTAGTATT
1 AAATTATC-AATGATTTACTATT
* *
5188482 AAGTTATGAATGATTTACTATT
1 AAATTATCAATGATTTACTATT
** *
5188504 AAATTATTGATGATTTACTACT
1 AAATTATCAATGATTTACTATT
* ** *
5188526 AAGTTATTGATGATTTATTA-T
1 AAATTATCAATGATTTACTATT
* * * *
5188547 AAAGTTAT-GATCAATTTATTACT
1 AAA-TTATCAAT-GATTTACTATT
* **
5188570 AATTTATCAATGATTTACTAAA
1 AAATTATCAATGATTTACTATT
5188592 AAATTATCAAT
1 AAATTATCAAT
5188603 AATTAATAAA
Statistics
Matches: 214, Mismatches: 53, Indels: 16
0.76 0.19 0.06
Matches are distributed among these distances:
21 10 0.05
22 197 0.92
23 7 0.03
ACGTcount: A:0.38, C:0.07, G:0.10, T:0.45
Consensus pattern (22 bp):
AAATTATCAATGATTTACTATT
Found at i:5188432 original size:44 final size:44
Alignment explanation
Indices: 5188340--5188598 Score: 193
Period size: 44 Copynumber: 5.9 Consensus size: 44
5188330 ATTATCATTA
* * * * * * * *
5188340 ATTTACTACTATGTTATTAGTGATTTATTGTCAAGTTATCAATG
1 ATTTACTATTAAGTTATGAATGATTTACTATAAAGTTATGAATG
* * * * * *
5188384 ATTTACTATTAAATTATTAATGAATTAGTATAAATTTATGAATT
1 ATTTACTATTAAGTTATGAATGATTTACTATAAAGTTATGAATG
* * * * *
5188428 ATTTACCATTAGGTTATGAATTATTTACTATTAAGTTACGAATG
1 ATTTACTATTAAGTTATGAATGATTTACTATAAAGTTATGAATG
*
5188472 ATTTAGTATTAAGTTATGAATGATTTACTATTAAA-TTATTG-ATG
1 ATTTACTATTAAGTTATGAATGATTTACTA-TAAAGTTA-TGAATG
* * *
5188516 ATTTACTACTAAGTTATTG-ATGATTTATTATAAAGTTATG-ATCA
1 ATTTACTATTAAGTTA-TGAATGATTTACTATAAAGTTATGAAT-G
* * * * * *
5188560 ATTTATTACTAATTTATCAATGATTTACTAAAAAATTAT
1 ATTTACTATTAAGTTATGAATGATTTACTATAAAGTTAT
5188599 CAATAATTAA
Statistics
Matches: 171, Mismatches: 38, Indels: 12
0.77 0.17 0.05
Matches are distributed among these distances:
43 9 0.05
44 156 0.91
45 6 0.04
ACGTcount: A:0.37, C:0.06, G:0.10, T:0.46
Consensus pattern (44 bp):
ATTTACTATTAAGTTATGAATGATTTACTATAAAGTTATGAATG
Found at i:5188432 original size:66 final size:66
Alignment explanation
Indices: 5188370--5188607 Score: 194
Period size: 66 Copynumber: 3.6 Consensus size: 66
5188360 TGATTTATTG
* * *
5188370 TCAAGTTATCAATGATTTACTATTAAATTATTAATGAATTAGTATAAATTTATGAATTATTTACC
1 TCAAGTTATCAATGATTTACTATTAAATTATTAATGAATTAGTATAAAGTTATGAATAATTTACT
5188435 A
66 A
* * * * * ** * * *
5188436 TTAGGTTATGAATTATTTACTATTAAGTTACGAATGATTTAGTATTAAGTTATGAATGATTTACT
1 TCAAGTTATCAATGATTTACTATTAAATTATTAATGAATTAGTATAAAGTTATGAATAATTTACT
5188501 A
66 A
* * ** * * * * * *
5188502 TTAAATTATTGATGATTTACTACTAAGTTATTGATGATTTATTATAAAGTTATG-ATCAATTTAT
1 TCAAGTTATCAATGATTTACTATTAAATTATTAATGAATTAGTATAAAGTTATGAAT-AATTTAC
5188566 TA
65 TA
* ** *
5188568 -CTAATTTATCAATGATTTACTAAAAAATTATCAAT-AATTA
1 TC-AAGTTATCAATGATTTACTATTAAATTATTAATGAATTA
5188608 ATAAATTTAT
Statistics
Matches: 135, Mismatches: 35, Indels: 5
0.77 0.20 0.03
Matches are distributed among these distances:
65 6 0.04
66 129 0.96
ACGTcount: A:0.39, C:0.06, G:0.10, T:0.45
Consensus pattern (66 bp):
TCAAGTTATCAATGATTTACTATTAAATTATTAATGAATTAGTATAAAGTTATGAATAATTTACT
A
Found at i:5188636 original size:22 final size:22
Alignment explanation
Indices: 5188611--5188826 Score: 111
Period size: 22 Copynumber: 9.8 Consensus size: 22
5188601 ATAATTAATA
* * *
5188611 AATTTATTACTAAATTATCATT
1 AATTTACTACTAAATTATTAGT
* *
5188633 AATTT-GTAGCCAAATTATTAGT
1 AATTTACTA-CTAAATTATTAGT
**
5188655 AATTTACTA-TATGTTATTAGT
1 AATTTACTACTAAATTATTAGT
*
5188676 AATTTACTACTAAATTA-TAAT
1 AATTTACTACTAAATTATTAGT
* * *
5188697 AATTTACTATTGAATTATTAAT
1 AATTTACTACTAAATTATTAGT
* * * *
5188719 GATTTACTATTATATTATTATAT
1 AATTTACTACTAAATTATTA-GT
* ** *
5188742 ATATTTATTACTATGTTATTATT
1 A-ATTTACTACTAAATTATTAGT
* *
5188765 GATTTACTACTTAAGTT-TT-GAT
1 AATTTACTAC-TAAATTATTAG-T
* *
5188787 TATTTACTACAAAATTATTA-T
1 AATTTACTACTAAATTATTAGT
* *
5188808 CGATTTACTATTAAATTAT
1 -AATTTACTACTAAATTAT
5188827 CCATTATTCA
Statistics
Matches: 152, Mismatches: 31, Indels: 22
0.74 0.15 0.11
Matches are distributed among these distances:
21 43 0.28
22 83 0.55
23 10 0.07
24 16 0.11
ACGTcount: A:0.37, C:0.07, G:0.06, T:0.50
Consensus pattern (22 bp):
AATTTACTACTAAATTATTAGT
Found at i:5188673 original size:21 final size:22
Alignment explanation
Indices: 5188647--5188775 Score: 104
Period size: 21 Copynumber: 5.9 Consensus size: 22
5188637 TGTAGCCAAA
*
5188647 TTATTAGTAATTTACTA-TATG
1 TTATTAATAATTTACTACTATG
* **
5188668 TTATTAGTAATTTACTACTAAA
1 TTATTAATAATTTACTACTATG
5188690 TTA-TAATAATTTACTA-T-TG
1 TTATTAATAATTTACTACTATG
* * *
5188709 AATTATTAATGATTTACTATTATA
1 --TTATTAATAATTTACTACTATG
*
5188733 TTATTATATATATTTATTACTATG
1 TTATTA-ATA-ATTTACTACTATG
* *
5188757 TTATTATTGATTTACTACT
1 TTATTAATAATTTACTACT
5188776 TAAGTTTTGA
Statistics
Matches: 86, Mismatches: 14, Indels: 15
0.75 0.12 0.13
Matches are distributed among these distances:
20 1 0.01
21 32 0.37
22 32 0.37
23 4 0.05
24 17 0.20
ACGTcount: A:0.36, C:0.06, G:0.05, T:0.53
Consensus pattern (22 bp):
TTATTAATAATTTACTACTATG
Found at i:5188715 original size:43 final size:42
Alignment explanation
Indices: 5188644--5188775 Score: 122
Period size: 43 Copynumber: 3.0 Consensus size: 42
5188634 ATTTGTAGCC
* *
5188644 AAATTATTAGTAATTTACTATATGTTATTAGTAATTTACTACT
1 AAATTA-TAATAATTTACTATATGTTATTAATAATTTACTACT
* *
5188687 AAATTATAATAATTTACTAT-TGAATTATTAATGATTTACTATT
1 AAATTATAATAATTTACTATATG--TTATTAATAATTTACTACT
* * * *
5188730 ATATTATTATATATATTTATTACTATGTTATTATTGATTTACTACT
1 AAATTA-TA-ATA-ATTTACTA-TATGTTATTAATAATTTACTACT
5188776 TAAGTTTTGA
Statistics
Matches: 74, Mismatches: 8, Indels: 11
0.80 0.09 0.12
Matches are distributed among these distances:
41 2 0.03
42 13 0.18
43 27 0.36
44 2 0.03
45 3 0.04
46 24 0.32
47 1 0.01
48 2 0.03
ACGTcount: A:0.37, C:0.06, G:0.05, T:0.52
Consensus pattern (42 bp):
AAATTATAATAATTTACTATATGTTATTAATAATTTACTACT
Found at i:5188817 original size:90 final size:88
Alignment explanation
Indices: 5188644--5188826 Score: 210
Period size: 90 Copynumber: 2.1 Consensus size: 88
5188634 ATTTGTAGCC
* *
5188644 AAATTATTA-GTA-ATTTACTATATGTTATTAGTAATTTACTACTAAATTATAATAATTTACTAT
1 AAATTATTATATATATTTACTATATGTTATTAGTAATTTACTACTAAATTATAATAATTTACTAC
**
5188707 TGAATTATTAATGATTTACTATT
66 AAAATTATTAATGATTTACTATT
* * * * * * * *
5188730 ATATTATTATATATATTTATTACTATGTTATTATTGATTTACTACTTAAGTTTTGATTATTTACT
1 AAATTATTATATATATTTACTA-TATGTTATTAGTAATTTACTAC-TAAATTATAATAATTTACT
5188795 ACAAAATTATT-ATCGATTTACTATT
64 ACAAAATTATTAAT-GATTTACTATT
5188820 AAATTAT
1 AAATTAT
5188827 CCATTATTCA
Statistics
Matches: 79, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
86 8 0.10
87 2 0.03
88 7 0.09
89 22 0.28
90 40 0.51
ACGTcount: A:0.37, C:0.07, G:0.05, T:0.51
Consensus pattern (88 bp):
AAATTATTATATATATTTACTATATGTTATTAGTAATTTACTACTAAATTATAATAATTTACTAC
AAAATTATTAATGATTTACTATT
Found at i:5188833 original size:44 final size:43
Alignment explanation
Indices: 5188668--5188987 Score: 193
Period size: 44 Copynumber: 7.3 Consensus size: 43
5188658 TTACTATATG
* * * * * *
5188668 TTATTAGTAATTTACTACTAAATTATAATAATTTACTATTGAA
1 TTATTATTGATTTACTATTAAATTATAATTATTTACTACTAAA
* * * **
5188711 TTATTAATGATTTACTATTATATTATTATATATATTTATTACTATG
1 TTATTATTGATTTACTATTAAATTA-TA-AT-TATTTACTACTAAA
* * * *
5188757 TTATTATTGATTTACTACTTAAGTTTTGATTATTTACTACAAAA
1 TTATTATTGATTTACTA-TTAAATTATAATTATTTACTACTAAA
* * * *
5188801 TTATTATCGATTTACTATTAAATTATCCATTATTCACTATTAAA
1 TTATTATTGATTTACTATTAAATTAT-AATTATTTACTACTAAA
** * *
5188845 TTATCGTTGATTTA-TATTAAATTATTTATGT-TTTACTATTAAA
1 TTATTATTGATTTACTATTAAATTA-TAAT-TATTTACTACTAAA
* * * * **
5188888 TTATTGATT-ATTTATTATTAAGTTA-CACTATTTACTTTTAAA
1 TTATT-ATTGATTTACTATTAAATTATAATTATTTACTACTAAA
* * * * *
5188930 TT-TTCAATGATTAACTATTAAAATATCAATTATTTACTATTAAG
1 TTATT-ATTGATTTACTATTAAATTAT-AATTATTTACTACTAAA
*
5188974 TTA-TGTTGATTTAC
1 TTATTATTGATTTAC
5188988 CACAAAGTTA
Statistics
Matches: 213, Mismatches: 50, Indels: 28
0.73 0.17 0.10
Matches are distributed among these distances:
41 5 0.02
42 26 0.12
43 67 0.31
44 81 0.38
45 4 0.02
46 25 0.12
47 5 0.02
ACGTcount: A:0.36, C:0.08, G:0.05, T:0.51
Consensus pattern (43 bp):
TTATTATTGATTTACTATTAAATTATAATTATTTACTACTAAA
Found at i:5188839 original size:22 final size:22
Alignment explanation
Indices: 5188810--5188977 Score: 130
Period size: 22 Copynumber: 7.8 Consensus size: 22
5188800 ATTATTATCG
5188810 ATTTACTATTAAATTATCCATT
1 ATTTACTATTAAATTATCCATT
* *
5188832 ATTCACTATTAAATTAT-CGTT
1 ATTTACTATTAAATTATCCATT
**
5188853 GATTTA-TATTAAATTATTTATGT
1 -ATTTACTATTAAATTATCCAT-T
**
5188876 -TTTACTATTAAATTATTGATT
1 ATTTACTATTAAATTATCCATT
* * *
5188897 ATTTATTATTAAGTTA--CACT
1 ATTTACTATTAAATTATCCATT
* * * *
5188917 ATTTACTTTTAAATTTTCAATG
1 ATTTACTATTAAATTATCCATT
* * *
5188939 ATTAACTATTAAAATATCAATT
1 ATTTACTATTAAATTATCCATT
*
5188961 ATTTACTATTAAGTTAT
1 ATTTACTATTAAATTAT
5188978 GTTGATTTAC
Statistics
Matches: 114, Mismatches: 25, Indels: 14
0.75 0.16 0.09
Matches are distributed among these distances:
20 14 0.12
21 19 0.17
22 80 0.70
23 1 0.01
ACGTcount: A:0.36, C:0.08, G:0.04, T:0.51
Consensus pattern (22 bp):
ATTTACTATTAAATTATCCATT
Found at i:5188880 original size:65 final size:66
Alignment explanation
Indices: 5188677--5189007 Score: 227
Period size: 65 Copynumber: 5.1 Consensus size: 66
5188667 GTTATTAGTA
* * *** *
5188677 ATTTACTACTAAATTAT-AATAATTTACTATTGAA-TTATTAATGATTTACTATTATATTATTAT
1 ATTTACTATTAAATTATCAATTATTTACTATT-AAGTTATCGTTGATTTACTATTAAATTATT-T
*
5188740 ATAT
64 AT-G
* * ** * * **
5188744 ATTTATTACTATGTTAT-TATTGATTTACTACTTAAGTT-TTGATT-ATTTACTACAAAATTA-T
1 ATTTACTATTAAATTATCAATT-ATTTACTA-TTAAGTTATCG-TTGATTTACTATTAAATTATT
5188805 TATCG
63 TAT-G
* * *
5188810 ATTTACTATTAAATTATCCATTATTCACTATTAAATTATCGTTGATTTA-TATTAAATTATTTAT
1 ATTTACTATTAAATTATCAATTATTTACTATTAAGTTATCGTTGATTTACTATTAAATTATTTAT
5188874 G
66 G
* ** * ** * *
5188875 TTTTACTATTAAATTATTGATTATTTATTATTAAGTTA-CACT-ATTTACTTTTAAATT-TTCAA
1 ATTTACTATTAAATTATCAATTATTTACTATTAAGTTATCGTTGATTTACTATTAAATTATT-TA
5188937 TG
65 TG
* * * *
5188939 ATTAACTATTAAAATATCAATTATTTACTATTAAGTTAT-GTTGATTTACCA-CAAAGTTATTTA
1 ATTTACTATTAAATTATCAATTATTTACTATTAAGTTATCGTTGATTTACTATTAAA-TTATTTA
5189002 TG
65 TG
5189004 ATTT
1 ATTT
5189008 CTTAGCATCA
Statistics
Matches: 205, Mismatches: 45, Indels: 30
0.73 0.16 0.11
Matches are distributed among these distances:
63 7 0.03
64 49 0.24
65 63 0.31
66 36 0.18
67 20 0.10
68 25 0.12
69 5 0.02
ACGTcount: A:0.36, C:0.08, G:0.05, T:0.51
Consensus pattern (66 bp):
ATTTACTATTAAATTATCAATTATTTACTATTAAGTTATCGTTGATTTACTATTAAATTATTTAT
G
Found at i:5188883 original size:43 final size:45
Alignment explanation
Indices: 5188809--5188987 Score: 142
Period size: 43 Copynumber: 4.2 Consensus size: 45
5188799 AATTATTATC
5188809 GATTTACTATTAAATTATCCATTATTCACTATTAAATTATCG-TT
1 GATTTACTATTAAATTATCCATTATTCACTATTAAATTATCGATT
** * *
5188853 GATTTA-TATTAAATTATTTATGT-TTTACTATTAAATTATTGATT
1 GATTTACTATTAAATTATCCAT-TATTCACTATTAAATTATCGATT
* * * * * * *
5188897 -ATTTATTATTAAGTTA--CACTATTTACTTTTAAATTTTC-AAT
1 GATTTACTATTAAATTATCCATTATTCACTATTAAATTATCGATT
* * * * *
5188938 GATTAACTATTAAAATATCAATTATTTACTATTAAGTTAT-G-TT
1 GATTTACTATTAAATTATCCATTATTCACTATTAAATTATCGATT
5188981 GATTTAC
1 GATTTAC
5188988 CACAAAGTTA
Statistics
Matches: 105, Mismatches: 22, Indels: 17
0.73 0.15 0.12
Matches are distributed among these distances:
41 3 0.03
42 27 0.26
43 41 0.39
44 34 0.32
ACGTcount: A:0.35, C:0.08, G:0.06, T:0.51
Consensus pattern (45 bp):
GATTTACTATTAAATTATCCATTATTCACTATTAAATTATCGATT
Found at i:5189127 original size:47 final size:44
Alignment explanation
Indices: 5189041--5189128 Score: 104
Period size: 44 Copynumber: 1.9 Consensus size: 44
5189031 AAATTGAAAC
* * *
5189041 TAATTTACTATTAAATTACCATTGATTTATTACTAAGTTATAAA
1 TAATTAACTACTAAATTACCATTGATTTATTAATAAGTTATAAA
* *
5189085 TAATTAACTACTAAATTATCATTTGTTATTTTTTAATAAGTTAT
1 TAATTAACTACTAAATTACCA-TTG--ATTTATTAATAAGTTAT
5189129 CTTTAATTTA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
44 18 0.50
45 3 0.08
47 15 0.42
ACGTcount: A:0.39, C:0.08, G:0.05, T:0.49
Consensus pattern (44 bp):
TAATTAACTACTAAATTACCATTGATTTATTAATAAGTTATAAA
Found at i:5189205 original size:43 final size:41
Alignment explanation
Indices: 5189147--5189236 Score: 112
Period size: 43 Copynumber: 2.1 Consensus size: 41
5189137 TACTACTATG
*
5189147 AGTTATGTATTTACTATTATGTTA-TAATTGATCATTTATTACTA
1 AGTTATGTATATACTATTATGTTACT-ATTG---ATTTATTACTA
5189191 AGTTAT-TATATACTATTATGTTACTATTGATTTATTACTA
1 AGTTATGTATATACTATTATGTTACTATTGATTTATTACTA
*
5189231 AATTAT
1 AGTTAT
5189237 CAATTATCGA
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
40 16 0.37
43 20 0.47
44 7 0.16
ACGTcount: A:0.33, C:0.07, G:0.08, T:0.52
Consensus pattern (41 bp):
AGTTATGTATATACTATTATGTTACTATTGATTTATTACTA
Found at i:5189337 original size:22 final size:22
Alignment explanation
Indices: 5189246--5189346 Score: 89
Period size: 22 Copynumber: 4.6 Consensus size: 22
5189236 TCAATTATCG
*
5189246 ACTATTGAAA-TATCATTAATTT
1 ACTATT-AAATTATCACTAATTT
* * *
5189268 ATTATTAAGTAATCACTAATTT
1 ACTATTAAATTATCACTAATTT
** * *
5189290 GGTATTAACTTATCTA-TGATTT
1 ACTATTAAATTATC-ACTAATTT
*
5189312 ACTATTAAATTATCACTAATTA
1 ACTATTAAATTATCACTAATTT
5189334 ACTATTAAATTAT
1 ACTATTAAATTAT
5189347 TGATGATTAC
Statistics
Matches: 62, Mismatches: 14, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
21 3 0.05
22 58 0.94
23 1 0.02
ACGTcount: A:0.40, C:0.10, G:0.05, T:0.46
Consensus pattern (22 bp):
ACTATTAAATTATCACTAATTT
Found at i:5189340 original size:44 final size:44
Alignment explanation
Indices: 5189264--5189367 Score: 113
Period size: 44 Copynumber: 2.4 Consensus size: 44
5189254 AATATCATTA
* * *** *
5189264 ATTTATTATTAAGTAATCACTAATTTGGTATTAACTTATCT-ATG
1 ATTTACTATTAAGTTATCACTAATTAACTATTAAATTAT-TGATG
*
5189308 ATTTACTATTAAATTATCACTAATTAACTATTAAATTATTGATG
1 ATTTACTATTAAGTTATCACTAATTAACTATTAAATTATTGATG
*
5189352 A-TTACTACTAAGTTAT
1 ATTTACTATTAAGTTAT
5189368 GTTGATTACT
Statistics
Matches: 50, Mismatches: 9, Indels: 3
0.81 0.15 0.05
Matches are distributed among these distances:
43 14 0.28
44 36 0.72
ACGTcount: A:0.38, C:0.10, G:0.07, T:0.46
Consensus pattern (44 bp):
ATTTACTATTAAGTTATCACTAATTAACTATTAAATTATTGATG
Found at i:5189355 original size:22 final size:21
Alignment explanation
Indices: 5189292--5189355 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 21
5189282 ACTAATTTGG
* *
5189292 TATTAACTTATCTATGATTTAC
1 TATTAAATTAT-TATGATTAAC
* *
5189314 TATTAAATTATCACTAATTAAC
1 TATTAAATTATTA-TGATTAAC
5189336 TATTAAATTATTGATGATTA
1 TATTAAATTATT-ATGATTA
5189356 CTACTAAGTT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
21 1 0.03
22 32 0.94
23 1 0.03
ACGTcount: A:0.39, C:0.09, G:0.05, T:0.47
Consensus pattern (21 bp):
TATTAAATTATTATGATTAAC
Found at i:5189367 original size:21 final size:20
Alignment explanation
Indices: 5189305--5189377 Score: 56
Period size: 22 Copynumber: 3.5 Consensus size: 20
5189295 TAACTTATCT
* *
5189305 ATGATTTACTATTAAATTATC
1 ATGA-TTACTACTAAATTATG
* *
5189326 ACTAATTAACTATTAAATTATTG
1 A-TGATT-ACTACTAAATTA-TG
*
5189349 ATGATTACTACTAAGTTATG
1 ATGATTACTACTAAATTATG
*
5189369 TTGATTACT
1 ATGATTACT
5189378 TTTAAGTTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
20 10 0.23
21 13 0.30
22 18 0.42
23 2 0.05
ACGTcount: A:0.37, C:0.10, G:0.08, T:0.45
Consensus pattern (20 bp):
ATGATTACTACTAAATTATG
Found at i:5189429 original size:15 final size:14
Alignment explanation
Indices: 5189389--5189462 Score: 55
Period size: 14 Copynumber: 5.4 Consensus size: 14
5189379 TTAAGTTTTC
*
5189389 AATTATTAATTATA
1 AATTATCAATTATA
*
5189403 AATTATCTATTATTA
1 AATTATCAATTA-TA
*
5189418 AGTTATCAA-T-T-
1 AATTATCAATTATA
* *
5189429 AATTACTAAATTATC
1 AATTA-TCAATTATA
*
5189444 AATTATCAATTATT
1 AATTATCAATTATA
5189458 AATTA
1 AATTA
5189463 CTAGATTGAA
Statistics
Matches: 47, Mismatches: 8, Indels: 10
0.72 0.12 0.15
Matches are distributed among these distances:
11 4 0.09
12 4 0.09
13 1 0.02
14 24 0.51
15 14 0.30
ACGTcount: A:0.45, C:0.07, G:0.01, T:0.47
Consensus pattern (14 bp):
AATTATCAATTATA
Found at i:5189442 original size:19 final size:18
Alignment explanation
Indices: 5189393--5189448 Score: 64
Period size: 19 Copynumber: 3.2 Consensus size: 18
5189383 GTTTTCAATT
*
5189393 ATTAATTATAAATTATCT
1 ATTAATTATAAATTATCA
*
5189411 ATT-A-T-TAAGTTATCA
1 ATTAATTATAAATTATCA
5189426 ATTAATTACTAAATTATCA
1 ATTAATTA-TAAATTATCA
5189445 ATTA
1 ATTA
5189449 TCAATTATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
15 11 0.35
16 2 0.06
17 2 0.06
18 3 0.10
19 13 0.42
ACGTcount: A:0.45, C:0.07, G:0.02, T:0.46
Consensus pattern (18 bp):
ATTAATTATAAATTATCA
Found at i:5201318 original size:13 final size:13
Alignment explanation
Indices: 5201302--5201350 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
5201292 TTAGGCTTAA
*
5201302 GGTTTAGGTTTGG
1 GGTTTAAGTTTGG
5201315 GGTTTAAGTTT-G
1 GGTTTAAGTTTGG
* *
5201327 GGTCTAAGTTTAG
1 GGTTTAAGTTTGG
*
5201340 GGTCTAAGTTT
1 GGTTTAAGTTT
5201351 ATGGTTTAGT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
12 11 0.33
13 22 0.67
ACGTcount: A:0.16, C:0.04, G:0.35, T:0.45
Consensus pattern (13 bp):
GGTTTAAGTTTGG
Found at i:5201351 original size:13 final size:13
Alignment explanation
Indices: 5201309--5201351 Score: 61
Period size: 13 Copynumber: 3.4 Consensus size: 13
5201299 TAAGGTTTAG
* *
5201309 GTTTGGGGTTTAA
1 GTTTAGGGTCTAA
5201322 GTTT-GGGTCTAA
1 GTTTAGGGTCTAA
5201334 GTTTAGGGTCTAA
1 GTTTAGGGTCTAA
5201347 GTTTA
1 GTTTA
5201352 TGGTTTAGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
12 11 0.39
13 17 0.61
ACGTcount: A:0.19, C:0.05, G:0.33, T:0.44
Consensus pattern (13 bp):
GTTTAGGGTCTAA
Found at i:5201361 original size:25 final size:24
Alignment explanation
Indices: 5201302--5201362 Score: 59
Period size: 25 Copynumber: 2.4 Consensus size: 24
5201292 TTAGGCTTAA
* *
5201302 GGTTTAGGTTTGGGGTTTAAGTTTG
1 GGTTTA-GTTTAGGGTCTAAGTTTG
* *
5201327 GGTCTAAGTTTAGGGTCTAAGTTTAT
1 GGT-TTAGTTTAGGGTCTAAGTTT-G
5201353 GGTTTAGTTT
1 GGTTTAGTTT
5201363 TAAGGTTTGA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
25 24 0.83
26 5 0.17
ACGTcount: A:0.16, C:0.03, G:0.33, T:0.48
Consensus pattern (24 bp):
GGTTTAGTTTAGGGTCTAAGTTTG
Found at i:5201387 original size:17 final size:18
Alignment explanation
Indices: 5201365--5201402 Score: 69
Period size: 17 Copynumber: 2.2 Consensus size: 18
5201355 TTTAGTTTTA
5201365 AGGTTTGACCTA-GGTTT
1 AGGTTTGACCTAGGGTTT
5201382 AGGTTTGACCTAGGGTTT
1 AGGTTTGACCTAGGGTTT
5201400 AGG
1 AGG
5201403 GTTTTAATGT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.18, C:0.11, G:0.34, T:0.37
Consensus pattern (18 bp):
AGGTTTGACCTAGGGTTT
Found at i:5204263 original size:31 final size:31
Alignment explanation
Indices: 5204225--5204283 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
5204215 GGCATTGGGA
5204225 TAGTATTGATATCTTCAAATGGAGATTAGGG
1 TAGTATTGATATCTTCAAATGGAGATTAGGG
**
5204256 TAGTATTGATATCTTTTAATGGAGATTA
1 TAGTATTGATATCTTCAAATGGAGATTA
5204284 TTATCCTAGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.32, C:0.05, G:0.22, T:0.41
Consensus pattern (31 bp):
TAGTATTGATATCTTCAAATGGAGATTAGGG
Found at i:5205900 original size:18 final size:17
Alignment explanation
Indices: 5205877--5205914 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
5205867 TTAAAAATTC
5205877 AAAATAAA-AAGAAATGAA
1 AAAATAAACAA-AAAT-AA
5205895 AAAATAAACAAAAATAA
1 AAAATAAACAAAAATAA
5205912 AAA
1 AAA
5205915 GAAAGAATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 5 0.26
18 12 0.63
19 2 0.11
ACGTcount: A:0.82, C:0.03, G:0.05, T:0.11
Consensus pattern (17 bp):
AAAATAAACAAAAATAA
Found at i:5207292 original size:51 final size:51
Alignment explanation
Indices: 5207116--5207303 Score: 186
Period size: 51 Copynumber: 3.6 Consensus size: 51
5207106 CCTGTAAACA
5207116 TTTCATGGATGAA-ATCTTTTAAAGTTTCAAAACCTCTCTATATGTAAA-AAGCT
1 TTTCATGGAT-AAGATCTTTTAAAGTTTCAAAA-C-CTCTATAT-TAAATAAGCT
** * * * * *
5207169 TTTCACAGACAATG-TCTTTTAAAGTTGCAAAAGCTCTGTATTAAATGAGCT
1 TTTCATGGATAA-GATCTTTTAAAGTTTCAAAACCTCTATATTAAATAAGCT
* * * *
5207220 TTTCATCGAT-GGAGTTTTTTAAAGTTTCAAAACCTCTATATAAAATAAGCT
1 TTTCATGGATAAGA-TCTTTTAAAGTTTCAAAACCTCTATATTAAATAAGCT
*
5207271 TTTCATGGATAAGATCATTTAAAGTTTCAAAAC
1 TTTCATGGATAAGATCTTTTAAAGTTTCAAAAC
5207304 ATCTGCTTAT
Statistics
Matches: 108, Mismatches: 21, Indels: 14
0.76 0.15 0.10
Matches are distributed among these distances:
49 1 0.01
50 4 0.04
51 75 0.69
52 4 0.04
53 24 0.22
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.37
Consensus pattern (51 bp):
TTTCATGGATAAGATCTTTTAAAGTTTCAAAACCTCTATATTAAATAAGCT
Found at i:5209420 original size:21 final size:21
Alignment explanation
Indices: 5209395--5209438 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
5209385 AACCAAAAGT
5209395 AAAACTTTAAGTCTAACATGA
1 AAAACTTTAAGTCTAACATGA
5209416 AAAACTTTAAGTCTAACATGA
1 AAAACTTTAAGTCTAACATGA
5209437 AA
1 AA
5209439 TCGAGACCCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.50, C:0.14, G:0.09, T:0.27
Consensus pattern (21 bp):
AAAACTTTAAGTCTAACATGA
Found at i:5209502 original size:19 final size:19
Alignment explanation
Indices: 5209466--5209541 Score: 50
Period size: 19 Copynumber: 4.1 Consensus size: 19
5209456 AACCATAAAA
* *
5209466 CTAACCCTAATTCTAAACC
1 CTAACCCTAAATCCAAACC
* *
5209485 CTAACCTTAAATCCAAACT
1 CTAACCCTAAATCCAAACC
* *
5209504 ATAACCC-ATAGT-CAAACC
1 CTAACCCTA-AATCCAAACC
* *
5209522 CTAACCGTAAA-CCTAACC
1 CTAACCCTAAATCCAAACC
5209540 CT
1 CT
5209542 TAAACCGAGA
Statistics
Matches: 42, Mismatches: 12, Indels: 7
0.69 0.20 0.11
Matches are distributed among these distances:
18 19 0.45
19 23 0.55
ACGTcount: A:0.39, C:0.36, G:0.03, T:0.22
Consensus pattern (19 bp):
CTAACCCTAAATCCAAACC
Found at i:5209594 original size:24 final size:24
Alignment explanation
Indices: 5209560--5209619 Score: 66
Period size: 25 Copynumber: 2.5 Consensus size: 24
5209550 GACCTCAAAA
* * **
5209560 CCAAACTCTAAGCTTAACGTTAGC
1 CCAAACCCTAACCTTAACCCTAGC
5209584 CCAAACCCTAAACCTTAACCCTAGC
1 CCAAACCCT-AACCTTAACCCTAGC
*
5209609 CAAAACCCTAA
1 CCAAACCCTAA
5209620 ATTCCAAACC
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
24 10 0.33
25 20 0.67
ACGTcount: A:0.38, C:0.37, G:0.07, T:0.18
Consensus pattern (24 bp):
CCAAACCCTAACCTTAACCCTAGC
Found at i:5210780 original size:2 final size:2
Alignment explanation
Indices: 5210773--5210813 Score: 57
Period size: 2 Copynumber: 20.5 Consensus size: 2
5210763 CAACTTGAGT
*
5210773 TA TA TA TA TA GA TA TA TA TA TA TA TA TA TA TA -A GTA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA T
5210814 TTTATTATTC
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 1 0.03
2 33 0.94
3 1 0.03
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (2 bp):
TA
Found at i:5212821 original size:21 final size:22
Alignment explanation
Indices: 5212796--5212837 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
5212786 CCCCTTTAAA
5212796 ATACAC-CCCAAAATTTTCTTT
1 ATACACTCCCAAAATTTTCTTT
*
5212817 ATACACTTCCAAAATTTTCTT
1 ATACACTCCCAAAATTTTCTT
5212838 CTAAAAATAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.33, C:0.26, G:0.00, T:0.40
Consensus pattern (22 bp):
ATACACTCCCAAAATTTTCTTT
Found at i:5213800 original size:34 final size:34
Alignment explanation
Indices: 5213756--5213822 Score: 89
Period size: 34 Copynumber: 2.0 Consensus size: 34
5213746 AAAATTGACT
*
5213756 TTCTTGAAAATAGATATCCAAGAAGACTCAAAGA
1 TTCTTAAAAATAGATATCCAAGAAGACTCAAAGA
** * *
5213790 TTCTTAAAAATTTATTTCCGAGAAGACTCAAAG
1 TTCTTAAAAATAGATATCCAAGAAGACTCAAAG
5213823 CTTTTCAGGA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.43, C:0.15, G:0.13, T:0.28
Consensus pattern (34 bp):
TTCTTAAAAATAGATATCCAAGAAGACTCAAAGA
Found at i:5214993 original size:141 final size:139
Alignment explanation
Indices: 5214736--5215006 Score: 343
Period size: 141 Copynumber: 1.9 Consensus size: 139
5214726 ATATTTCAAT
** **
5214736 TTTTAAAATAAATTATTATATTTTTTAATCCAAATAAGTCTTTATCTTTTGATTTATATCAAAAT
1 TTTTAAAATAAATTATTATATTTTTTAATCCAAATAAGTCCCTATCGATTGATTTATATCAAAAT
* * * * *
5214801 AAATTTTTATTTAAAAAAAAATTAATTTATGTTAAAGATTTGTTTGATTATAAATTAAAAGTTAA
66 AAATTTTCACTCAAAAAAAAATTAATTTATGTTAAAGATGTGTTTGATTATAAATAAAAAGTTAA
5214866 CTAATTCAC
131 CTAATTCAC
5214875 TTTT-AAATAAACTT-TTATACTTTTTTTAATCCAAATAAG-CCCTATCGATTGATTTATATCAA
1 TTTTAAAATAAA-TTATTATA--TTTTTTAATCCAAATAAGTCCCTATCGATTGATTTATATCAA
* * * *
5214937 AATAAGTCTTTCCCTCAACGAAAAAATTAATTTATGTTAAGGATGTGTTT-AGTTATAAATAAAA
63 AATAAAT-TTTCACTCAA-AAAAAAATTAATTTATGTTAAAGATGTGTTTGA-TTATAAATAAAA
5215001 AGTTAA
125 AGTTAA
5215007 GAGTATATTT
Statistics
Matches: 113, Mismatches: 13, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
138 12 0.11
139 31 0.27
140 25 0.22
141 45 0.40
ACGTcount: A:0.41, C:0.08, G:0.07, T:0.44
Consensus pattern (139 bp):
TTTTAAAATAAATTATTATATTTTTTAATCCAAATAAGTCCCTATCGATTGATTTATATCAAAAT
AAATTTTCACTCAAAAAAAAATTAATTTATGTTAAAGATGTGTTTGATTATAAATAAAAAGTTAA
CTAATTCAC
Found at i:5217106 original size:25 final size:25
Alignment explanation
Indices: 5217078--5217131 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
5217068 CTTTAGTTAG
* *
5217078 ATTTAATTGTTTC-CAATTTTATTTT
1 ATTTAATTATTTCTCAATATT-TTTT
*
5217103 ATTTATTTATTTCTCAATATTTTTT
1 ATTTAATTATTTCTCAATATTTTTT
5217128 ATTT
1 ATTT
5217132 TATTTTGGCT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 19 0.76
26 6 0.24
ACGTcount: A:0.24, C:0.07, G:0.02, T:0.67
Consensus pattern (25 bp):
ATTTAATTATTTCTCAATATTTTTT
Found at i:5217819 original size:12 final size:11
Alignment explanation
Indices: 5217802--5217847 Score: 51
Period size: 12 Copynumber: 4.1 Consensus size: 11
5217792 ATATTAACAC
5217802 TTAAAATTATTT
1 TTAAAA-TATTT
5217814 TTAAAA-ATTT
1 TTAAAATATTT
5217824 TT-AAATATTTT
1 TTAAAATA-TTT
5217835 TTAAAATAATTT
1 TTAAAAT-ATTT
5217847 T
1 T
5217848 CATATTTCTA
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
9 3 0.10
10 7 0.23
11 5 0.17
12 14 0.47
13 1 0.03
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (11 bp):
TTAAAATATTT
Found at i:5223699 original size:20 final size:20
Alignment explanation
Indices: 5223674--5223735 Score: 88
Period size: 20 Copynumber: 3.1 Consensus size: 20
5223664 ACCTCCTACG
* *
5223674 ATCTTGGAACAATGTATTGC
1 ATCTTGGAATAATGTCTTGC
*
5223694 ATCTTGGAATAGTGTCTTGC
1 ATCTTGGAATAATGTCTTGC
*
5223714 ATTTTGGAATAATGTCTTGC
1 ATCTTGGAATAATGTCTTGC
5223734 AT
1 AT
5223736 TGCTTTCATT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.26, C:0.13, G:0.21, T:0.40
Consensus pattern (20 bp):
ATCTTGGAATAATGTCTTGC
Found at i:5224121 original size:40 final size:40
Alignment explanation
Indices: 5224065--5224144 Score: 124
Period size: 40 Copynumber: 2.0 Consensus size: 40
5224055 TCACGATCAT
* * *
5224065 GTATAACTAATTGACAATTTCTTTATCCCTAAATTACTCA
1 GTATAACTAATCGACAACTTCCTTATCCCTAAATTACTCA
*
5224105 GTATAACTAATCGACAACTTCCTTATCCTTAAATTACTCA
1 GTATAACTAATCGACAACTTCCTTATCCCTAAATTACTCA
5224145 ACAAACTCCT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.35, C:0.23, G:0.05, T:0.38
Consensus pattern (40 bp):
GTATAACTAATCGACAACTTCCTTATCCCTAAATTACTCA
Found at i:5229980 original size:23 final size:23
Alignment explanation
Indices: 5229953--5229999 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
5229943 CATGATTTGT
*
5229953 AAGATCTCGAA-GCATAATCTTAA
1 AAGATCTC-AATGCATAATCATAA
5229976 AAGATCTCAATGCATAATCATAA
1 AAGATCTCAATGCATAATCATAA
5229999 A
1 A
5230000 GACCTCTAGG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 2 0.09
23 20 0.91
ACGTcount: A:0.47, C:0.17, G:0.11, T:0.26
Consensus pattern (23 bp):
AAGATCTCAATGCATAATCATAA
Found at i:5230122 original size:33 final size:33
Alignment explanation
Indices: 5230085--5230167 Score: 105
Period size: 33 Copynumber: 2.5 Consensus size: 33
5230075 AGTCCAAGTC
*
5230085 ATTTCATTTTTAAACTTTAGCTCAATCTAGGCT
1 ATTTCATTTTCAAACTTTAGCTCAATCTAGGCT
* *
5230118 ATTTCGTTTTCAAACTTTAGTTCAATCTAGG-T
1 ATTTCATTTTCAAACTTTAGCTCAATCTAGGCT
* *
5230150 CATTGCATTTTCATACTT
1 -ATTTCATTTTCAAACTT
5230168 CAAGTCAGTC
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
32 1 0.02
33 42 0.98
ACGTcount: A:0.25, C:0.18, G:0.10, T:0.47
Consensus pattern (33 bp):
ATTTCATTTTCAAACTTTAGCTCAATCTAGGCT
Done.