Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009639.1 Hibiscus syriacus cultivar Beakdansim tig00117048_pilon, 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: 15077257
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 29 of 62
Found at i:6209121 original size:91 final size:91
Alignment explanation
Indices: 6209008--6209189 Score: 364
Period size: 91 Copynumber: 2.0 Consensus size: 91
6208998 CGTTGTGGAG
6209008 TTTAGATTTGAATTGGATGTCTTTCGTTGTGAAGTTGAAATCTACTCTTATGAATTGCATCGCTT
1 TTTAGATTTGAATTGGATGTCTTTCGTTGTGAAGTTGAAATCTACTCTTATGAATTGCATCGCTT
6209073 TCGAGTTTAATATCTTTCGCTGTGAA
66 TCGAGTTTAATATCTTTCGCTGTGAA
6209099 TTTAGATTTGAATTGGATGTCTTTCGTTGTGAAGTTGAAATCTACTCTTATGAATTGCATCGCTT
1 TTTAGATTTGAATTGGATGTCTTTCGTTGTGAAGTTGAAATCTACTCTTATGAATTGCATCGCTT
6209164 TCGAGTTTAATATCTTTCGCTGTGAA
66 TCGAGTTTAATATCTTTCGCTGTGAA
6209190 GTTAAAATTT
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
91 91 1.00
ACGTcount: A:0.23, C:0.13, G:0.20, T:0.44
Consensus pattern (91 bp):
TTTAGATTTGAATTGGATGTCTTTCGTTGTGAAGTTGAAATCTACTCTTATGAATTGCATCGCTT
TCGAGTTTAATATCTTTCGCTGTGAA
Found at i:6209964 original size:61 final size:62
Alignment explanation
Indices: 6209892--6210013 Score: 149
Period size: 63 Copynumber: 2.0 Consensus size: 62
6209882 AACATATCTT
* * *
6209892 ATTTTTCTCTTTTTT-ATTGTTTT-TTCAATTTAGGGCGCCCTTTCGGGTTTTCACCCTAAAC
1 ATTTTTCTCTTTTTTCATT-TTTTCTTCAACTTAGGACGCCCTCTCGGGTTTTCACCCTAAAC
* * * *
6209953 ATTTTTTTCTTTTTTCCCTTTTTTCTTCAACTTAGGATGCCCTCTCGGGTTTTCATCCTAA
1 ATTTTTCTCTTTTTT-CATTTTTTCTTCAACTTAGGACGCCCTCTCGGGTTTTCACCCTAA
6210014 GCGAAATATT
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
61 14 0.27
62 4 0.08
63 33 0.65
ACGTcount: A:0.14, C:0.23, G:0.11, T:0.52
Consensus pattern (62 bp):
ATTTTTCTCTTTTTTCATTTTTTCTTCAACTTAGGACGCCCTCTCGGGTTTTCACCCTAAAC
Found at i:6219189 original size:17 final size:18
Alignment explanation
Indices: 6219158--6219194 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
6219148 ATTAGTTAGT
*
6219158 AAAATAGAAATAATGATA
1 AAAATAGAAAAAATGATA
6219176 AAAATA-AAAAAATGATA
1 AAAATAGAAAAAATGATA
6219193 AA
1 AA
6219195 TTGCATGATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.73, C:0.00, G:0.08, T:0.19
Consensus pattern (18 bp):
AAAATAGAAAAAATGATA
Found at i:6220438 original size:20 final size:19
Alignment explanation
Indices: 6220396--6220439 Score: 63
Period size: 18 Copynumber: 2.3 Consensus size: 19
6220386 GGCTAATGTT
*
6220396 TAAAAAAGAATATAAATGA
1 TAAAAAAGAATATAAAAGA
6220415 -AAAAAAGAATATAAAAAGA
1 TAAAAAAGAATAT-AAAAGA
6220434 TAAAAA
1 TAAAAA
6220440 CAAAGTTAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 12 0.55
19 5 0.23
20 5 0.23
ACGTcount: A:0.75, C:0.00, G:0.09, T:0.16
Consensus pattern (19 bp):
TAAAAAAGAATATAAAAGA
Found at i:6221143 original size:74 final size:74
Alignment explanation
Indices: 6221022--6221172 Score: 302
Period size: 74 Copynumber: 2.0 Consensus size: 74
6221012 TAATCGTTAA
6221022 TTTCTAAAATTTTAAAAGGGATAAATTTATAAAATTAAATTAAATATAAAATAAATGTTTAGGCT
1 TTTCTAAAATTTTAAAAGGGATAAATTTATAAAATTAAATTAAATATAAAATAAATGTTTAGGCT
6221087 ATAGTGGTT
66 ATAGTGGTT
6221096 TTTCTAAAATTTTAAAAGGGATAAATTTATAAAATTAAATTAAATATAAAATAAATGTTTAGGCT
1 TTTCTAAAATTTTAAAAGGGATAAATTTATAAAATTAAATTAAATATAAAATAAATGTTTAGGCT
6221161 ATAGTGGTT
66 ATAGTGGTT
6221170 TTT
1 TTT
6221173 ATGAACAGGT
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 77 1.00
ACGTcount: A:0.45, C:0.03, G:0.12, T:0.40
Consensus pattern (74 bp):
TTTCTAAAATTTTAAAAGGGATAAATTTATAAAATTAAATTAAATATAAAATAAATGTTTAGGCT
ATAGTGGTT
Found at i:6222348 original size:68 final size:67
Alignment explanation
Indices: 6222262--6222490 Score: 212
Period size: 68 Copynumber: 3.3 Consensus size: 67
6222252 TATTTATCTT
* *
6222262 TTTAATTTGAATATTATTAGAATAATAATAT-TCTTTTGAATATTTCAAATTAAAAGGTATTTAT
1 TTTAATTTTAA-A-TATTA-AA-AATAATATATCTTTTGAATATTTCAAATTAAAAGATATTTAT
*
6222326 TATAAA
62 TATATA
* *
6222332 TTTAATTTTAAATATTAAAAAAATAATTATATATTTTTGATTATTTCAAATTAAAAGAT-TTATA
1 TTTAATTTTAAATATT--AAAAATAA-TATAT-CTTTTGAATATTTCAAATTAAAAGATATT-TA
* *
6222396 TTATCTC
61 TTATATA
* * * * *
6222403 TTTAA-TTTGAGTATTAAAAGGTATCTATATCTTTTGAATATTTCAAATTAAAATATATTTATTA
1 TTTAATTTTAAATATTAAAA-ATA-ATATATCTTTTGAATATTTCAAATTAAAAGATATTTATTA
6222467 TATA
64 TATA
* *
6222471 TTTAAATTTGAATATTAAAA
1 TTTAATTTTAAATATTAAAA
6222491 GATATCTATT
Statistics
Matches: 132, Mismatches: 17, Indels: 21
0.78 0.10 0.12
Matches are distributed among these distances:
68 48 0.36
69 28 0.21
70 22 0.17
71 34 0.26
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.48
Consensus pattern (67 bp):
TTTAATTTTAAATATTAAAAATAATATATCTTTTGAATATTTCAAATTAAAAGATATTTATTATA
TA
Found at i:6222377 original size:71 final size:69
Alignment explanation
Indices: 6222262--6222490 Score: 248
Period size: 71 Copynumber: 3.3 Consensus size: 69
6222252 TATTTATCTT
** * * *
6222262 TTTAATTTGAATATTATTAGAATAATAATATTCTTTTGAATATTTCAAATTAAAAGGTATTTATT
1 TTTAATTTGAATATTAAAAAAATAATTATATT-TTTTGAATATTTCAAATTAAAAGATATTTATT
*
6222327 ATAAA
65 ATATA
* *
6222332 TTTAATTTTAAATATTAAAAAAATAATTATATATTTTTGATTATTTCAAATTAAAAGAT-TTATA
1 TTTAA-TTTGAATATTAAAAAAATAATTATAT-TTTTTGAATATTTCAAATTAAAAGATATT-TA
* *
6222396 TTATCTC
63 TTATATA
* ** * *
6222403 TTTAATTTGAGTATT-AAAAGGT-ATCTATATCTTTTGAATATTTCAAATTAAAATATATTTATT
1 TTTAATTTGAATATTAAAAAAATAAT-TATATTTTTTGAATATTTCAAATTAAAAGATATTTATT
6222466 ATATA
65 ATATA
6222471 TTTAAATTTGAATATTAAAA
1 TTT-AATTTGAATATTAAAA
6222491 GATATCTATT
Statistics
Matches: 132, Mismatches: 20, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
68 35 0.27
69 23 0.17
70 18 0.14
71 55 0.42
72 1 0.01
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.48
Consensus pattern (69 bp):
TTTAATTTGAATATTAAAAAAATAATTATATTTTTTGAATATTTCAAATTAAAAGATATTTATTA
TATA
Found at i:6222377 original size:139 final size:138
Alignment explanation
Indices: 6222226--6222490 Score: 322
Period size: 139 Copynumber: 1.9 Consensus size: 138
6222216 ATTTATATTC
* * **
6222226 TTTTTGAATATTTTAAA-AACTAA-ATATAT-TTATCTTTTTAATTTGAATATTATTAGA-ATAA
1 TTTTTGAATATTTCAAATAA--AAGATATATATTATCTCTTTAATTTGAATATTAAAAGATAT-A
* *
6222287 TAATATTCTTTTGAATATTTCAAATTAAAAGGTATTTATTATAAATTTAATTTTAAATATTAAAA
63 T-ATA-TCTTTTGAATATTTCAAATTAAAAGATATTTATTATAAATTTAAATTTAAATATTAAAA
6222352 AAATAATTATATA
126 AAATAATTATATA
* * * * *
6222365 TTTTTGATTATTTCAAATTAAAAGATTTATATTATCTCTTTAATTTGAGTATTAAAAGGTATCTA
1 TTTTTGAATATTTCAAA-TAAAAGATATATATTATCTCTTTAATTTGAATATTAAAAGATATATA
* * *
6222430 TATCTTTTGAATATTTCAAATTAAAATATATTTATTATATATTTAAATTTGAATATTAAAA
65 TATCTTTTGAATATTTCAAATTAAAAGATATTTATTATAAATTTAAATTTAAATATTAAAA
6222491 GATATCTATT
Statistics
Matches: 107, Mismatches: 14, Indels: 10
0.82 0.11 0.08
Matches are distributed among these distances:
139 71 0.66
140 8 0.07
141 26 0.24
142 2 0.02
ACGTcount: A:0.42, C:0.04, G:0.05, T:0.49
Consensus pattern (138 bp):
TTTTTGAATATTTCAAATAAAAGATATATATTATCTCTTTAATTTGAATATTAAAAGATATATAT
ATCTTTTGAATATTTCAAATTAAAAGATATTTATTATAAATTTAAATTTAAATATTAAAAAAATA
ATTATATA
Found at i:6222487 original size:69 final size:69
Alignment explanation
Indices: 6222293--6222499 Score: 249
Period size: 68 Copynumber: 3.0 Consensus size: 69
6222283 ATAATAATAT
* * * * *
6222293 TCTTTTGAATATTTCAAATTAAAAGGTATTTATTATAAATTTAATTTTAAATATTAAAAAAATAA
1 TCTTTTGAATATTTCAAATTAAAAGATATTTATTATATATTTAAATTTGAATATT-AAAAGAT-A
6222358 T-TATA
64 TCTATA
* * * * * *
6222363 TATTTTTGATTATTTCAAATTAAAAGAT-TTATATTATCTCTTT-AATTTGAGTATTAAAAGGTA
1 T-CTTTTGAATATTTCAAATTAAAAGATATT-TATTATATATTTAAATTTGAATATTAAAAGATA
6222426 TCTATA
64 TCTATA
*
6222432 TCTTTTGAATATTTCAAATTAAAATATATTTATTATATATTTAAATTTGAATATTAAAAGATATC
1 TCTTTTGAATATTTCAAATTAAAAGATATTTATTATATATTTAAATTTGAATATTAAAAGATATC
6222497 TAT
66 TAT
6222500 TTTGAGTAAA
Statistics
Matches: 114, Mismatches: 18, Indels: 11
0.80 0.13 0.08
Matches are distributed among these distances:
68 35 0.31
69 35 0.31
70 12 0.11
71 32 0.28
ACGTcount: A:0.42, C:0.04, G:0.06, T:0.48
Consensus pattern (69 bp):
TCTTTTGAATATTTCAAATTAAAAGATATTTATTATATATTTAAATTTGAATATTAAAAGATATC
TATA
Found at i:6228818 original size:45 final size:47
Alignment explanation
Indices: 6228734--6228822 Score: 119
Period size: 45 Copynumber: 1.9 Consensus size: 47
6228724 ATTTATTTTC
* *
6228734 ATTTTTTGAATAAATGCATGCGAACTAGATATCATGCGGTTAGGTTG
1 ATTTTTCGAATAAATGCATGCGAACTAGATATCACGCGGTTAGGTTG
* * *
6228781 ATTTTTCGAAT-AA-GCATGTGAATTATATATCACGCGGTTAGG
1 ATTTTTCGAATAAATGCATGCGAACTAGATATCACGCGGTTAGG
6228823 GTTTTTATGT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
45 25 0.68
46 2 0.05
47 10 0.27
ACGTcount: A:0.30, C:0.11, G:0.22, T:0.36
Consensus pattern (47 bp):
ATTTTTCGAATAAATGCATGCGAACTAGATATCACGCGGTTAGGTTG
Found at i:6235299 original size:14 final size:13
Alignment explanation
Indices: 6235276--6235323 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
6235266 ATTTTGCTTG
6235276 AAGAATAAAAGAAA
1 AAGAA-AAAAGAAA
*
6235290 AAGATAAAAAAAAA
1 AAGA-AAAAAGAAA
6235304 AAGAAAAAAGGAAA
1 AAGAAAAAA-GAAA
*
6235318 ATGAAA
1 AAGAAA
6235324 GAATGAAAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
13 5 0.17
14 23 0.79
15 1 0.03
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.06
Consensus pattern (13 bp):
AAGAAAAAAGAAA
Found at i:6236774 original size:37 final size:37
Alignment explanation
Indices: 6236710--6236824 Score: 167
Period size: 37 Copynumber: 3.1 Consensus size: 37
6236700 GTTTGATCTT
* *
6236710 TGAAACAAGTCAATCTTAAGCCTTCACGAAAGAGTAG
1 TGAAGCAATTCAATCTTAAGCCTTCACGAAAGAGTAG
* **
6236747 TGAAGCAATTCAATCTTAAGCCGTCACGAAAGAACAG
1 TGAAGCAATTCAATCTTAAGCCTTCACGAAAGAGTAG
* *
6236784 TGAAGCAATTGAATCTTAAGCCTTCACGGAAGAGTAG
1 TGAAGCAATTCAATCTTAAGCCTTCACGAAAGAGTAG
6236821 TGAA
1 TGAA
6236825 ACAAACTCAT
Statistics
Matches: 68, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 68 1.00
ACGTcount: A:0.39, C:0.18, G:0.21, T:0.22
Consensus pattern (37 bp):
TGAAGCAATTCAATCTTAAGCCTTCACGAAAGAGTAG
Found at i:6236980 original size:55 final size:55
Alignment explanation
Indices: 6236844--6237311 Score: 412
Period size: 55 Copynumber: 8.6 Consensus size: 55
6236834 TTTATGAAGA
* *
6236844 TCGAGTCCTATACTCTCTGAAAGAATAGGGAGTGGACACGTTTGTTGAAGA----
1 TCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACACGTTTGTTGAAGATTGT
* *
6236895 CCGAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACACGTTTGTTGAAGATTGT
1 TCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACACGTTTGTTGAAGATTGT
* * * *
6236950 TCAAGTCCTATATTCTCTGAAGGAATAGGGAGCGGACTCGTTTGTTGAAGATTTT
1 TCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACACGTTTGTTGAAGATTGT
** ** * * * *
6237005 TTTAGTTATATACTCTCTGGAGGAATAGGGAGTGGACCCATTTGTTGAAGATTGT
1 TCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACACGTTTGTTGAAGATTGT
* * * *
6237060 TCGAGTTCTATACTATCTGAAGGAATAGAGAGCGAAC-CTGTTT-TATGAAGATTGT
1 TCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAC-GTTTGT-TGAAGATTGT
* * * * * * * * *
6237115 TTGAGTTCTATACTCCCTGAACGAATTGGGAGCGAACCCGTTTATTGAATATTGT
1 TCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACACGTTTGTTGAAGATTGT
* * ** ** * *
6237170 TCGAGTCTTATACTCCCTGAACAAATAGGGAGTAGACACGTTTGCTGAAAATTGT
1 TCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACACGTTTGTTGAAGATTGT
* * ** * * * *
6237225 TCGAGTCTTATATTC-CTTGAACAAATACGGAGCAGATACGTTTGTTAAAGATTGT
1 TCGAGTCCTATACTCTC-TGAAGGAATAGGGAGCGGACACGTTTGTTGAAGATTGT
** *
6237280 TCGAGTTTTATACTAC-CTGAAGGAATAAGGAG
1 TCGAGTCCTATACT-CTCTGAAGGAATAGGGAG
6237312 AAGATCCGTC
Statistics
Matches: 347, Mismatches: 60, Indels: 16
0.82 0.14 0.04
Matches are distributed among these distances:
51 47 0.14
54 3 0.01
55 293 0.84
56 4 0.01
ACGTcount: A:0.28, C:0.15, G:0.25, T:0.32
Consensus pattern (55 bp):
TCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACACGTTTGTTGAAGATTGT
Found at i:6240229 original size:59 final size:59
Alignment explanation
Indices: 6240132--6240259 Score: 175
Period size: 59 Copynumber: 2.2 Consensus size: 59
6240122 TAGCAGGCTG
* ** *
6240132 CATATTCAGGAATACACTAAAGGATACCTAGTGTATATGGTGGGCACGACCTTATGTGT
1 CATATTCGGGAATACACTAAAGGATACCTAGTACATATGGTGGACACGACCTTATGTGT
* * * *
6240191 CATATTCGGGACTATACTTAAGGATACCTAGTACATATGGTGGACATGACCTTATGTGT
1 CATATTCGGGAATACACTAAAGGATACCTAGTACATATGGTGGACACGACCTTATGTGT
*
6240250 CATACTCGGG
1 CATATTCGGG
6240260 TTAGCACTAC
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
59 60 1.00
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.30
Consensus pattern (59 bp):
CATATTCGGGAATACACTAAAGGATACCTAGTACATATGGTGGACACGACCTTATGTGT
Found at i:6240397 original size:45 final size:45
Alignment explanation
Indices: 6240343--6240520 Score: 295
Period size: 45 Copynumber: 4.0 Consensus size: 45
6240333 GTTTATGGTT
* *
6240343 TATTGGTAAAATAAGCTTACGAGTTTAAGGAATAAATGGTAAGTA
1 TATTGGTAAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTA
*
6240388 TATTGGTAAAATAAGCTTATGAGCTTATGGAATAAATGGTAAGTA
1 TATTGGTAAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTA
6240433 TATTGGTAAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTA
1 TATTGGTAAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTA
* *
6240478 TATTGGTAAAATAAGCTTACGAGCTCATAGG-ATAAATGATAAG
1 TATTGGTAAAATAAGCTTACGAGCTTAT-GGAATAAATGGTAAG
6240521 AAATTTTATA
Statistics
Matches: 126, Mismatches: 6, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
45 124 0.98
46 2 0.02
ACGTcount: A:0.41, C:0.06, G:0.22, T:0.31
Consensus pattern (45 bp):
TATTGGTAAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTA
Found at i:6240400 original size:24 final size:24
Alignment explanation
Indices: 6240373--6240446 Score: 59
Period size: 24 Copynumber: 3.2 Consensus size: 24
6240363 GAGTTTAAGG
6240373 AATAAATGGTAAGTATATTGGTAA
1 AATAAATGGTAAGTATATTGGTAA
* ** *
6240397 AATAAGCTTATGAGCT-TA-TGG---
1 AATAA-ATGGTAAG-TATATTGGTAA
6240418 AATAAATGGTAAGTATATTGGTAA
1 AATAAATGGTAAGTATATTGGTAA
6240442 AATAA
1 AATAA
6240447 GCTTACGAGC
Statistics
Matches: 35, Mismatches: 8, Indels: 14
0.61 0.14 0.25
Matches are distributed among these distances:
19 1 0.03
20 6 0.17
21 8 0.23
24 13 0.37
25 6 0.17
26 1 0.03
ACGTcount: A:0.45, C:0.03, G:0.20, T:0.32
Consensus pattern (24 bp):
AATAAATGGTAAGTATATTGGTAA
Found at i:6243358 original size:15 final size:14
Alignment explanation
Indices: 6243340--6243435 Score: 68
Period size: 15 Copynumber: 6.4 Consensus size: 14
6243330 AATATAATAT
6243340 AAGAAAAAACAGAAA
1 AAGAAAAAA-AGAAA
*
6243355 AAG-AAAGAAGAAA
1 AAGAAAAAAAGAAA
*
6243368 AAGAAAAGGAAGAAA
1 AAGAAAA-AAAGAAA
* **
6243383 AAGAAAACATTAAA
1 AAGAAAAAAAGAAA
*
6243397 AAGAAAAAGAAAACGAAG
1 AAG--AAA-AAAA-GAAA
6243415 AAGAAAAAATAGAAA
1 AAGAAAAAA-AGAAA
6243430 AAGAAA
1 AAGAAA
6243436 CGAAAAGAGA
Statistics
Matches: 65, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
13 8 0.12
14 14 0.22
15 29 0.45
16 7 0.11
17 2 0.03
18 5 0.08
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03
Consensus pattern (14 bp):
AAGAAAAAAAGAAA
Found at i:6243371 original size:6 final size:6
Alignment explanation
Indices: 6243345--6243449 Score: 68
Period size: 6 Copynumber: 15.8 Consensus size: 6
6243335 AATATAAGAA
*
6243345 AAAACAG AAAAAG AAAGAAG AAAAAG AAAAGGAAG AAAAAG AAAACATT
1 AAAA-AG AAAAAG AAA-AAG AAAAAG -AAA--AAG AAAAAG AAAA-A-G
* * *
6243394 AAAAAG AAAAAG AAAACG AAGAAGAA AAAATAG AAAAAG -AAACG AAAAGAG
1 AAAAAG AAAAAG AAAAAG AA-AA-AG AAAA-AG AAAAAG AAAAAG AAAA-AG
6243445 AAAAA
1 AAAAA
6243450 AATTATGAGA
Statistics
Matches: 79, Mismatches: 9, Indels: 21
0.72 0.08 0.19
Matches are distributed among these distances:
5 4 0.05
6 34 0.43
7 29 0.37
8 9 0.11
9 3 0.04
ACGTcount: A:0.75, C:0.04, G:0.18, T:0.03
Consensus pattern (6 bp):
AAAAAG
Found at i:6243435 original size:27 final size:26
Alignment explanation
Indices: 6243394--6243451 Score: 82
Period size: 26 Copynumber: 2.2 Consensus size: 26
6243384 AGAAAACATT
6243394 AAAAAGAAAAAGAAAACGAAGAAGA-AA
1 AAAAAGAAAAAG-AAACGAA-AAGAGAA
*
6243421 AAATAGAAAAAGAAACGAAAAGAGAA
1 AAAAAGAAAAAGAAACGAAAAGAGAA
6243447 AAAAA
1 AAAAA
6243452 TTATGAGAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 4 0.14
26 13 0.46
27 11 0.39
ACGTcount: A:0.78, C:0.03, G:0.17, T:0.02
Consensus pattern (26 bp):
AAAAAGAAAAAGAAACGAAAAGAGAA
Found at i:6243473 original size:2 final size:2
Alignment explanation
Indices: 6243468--6243499 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
6243458 GAGATGATTA
6243468 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
6243500 TCACTTGTGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6247512 original size:22 final size:22
Alignment explanation
Indices: 6247487--6247557 Score: 71
Period size: 22 Copynumber: 3.4 Consensus size: 22
6247477 TTGTAGCAGG
*
6247487 ATGATTTAACTGTCATTGTTAA
1 ATGATTTAACTGTCATTGTCAA
* *
6247509 ATGATTT-AC--T-ATAG-CAGG
1 ATGATTTAACTGTCATTGTCA-A
6247527 ATGATTTAACTGTCATTGTCAA
1 ATGATTTAACTGTCATTGTCAA
6247549 ATGATTTAA
1 ATGATTTAA
6247558 AGTATTTAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 12
0.69 0.09 0.22
Matches are distributed among these distances:
17 1 0.03
18 10 0.26
19 3 0.08
21 3 0.08
22 19 0.50
23 2 0.05
ACGTcount: A:0.34, C:0.10, G:0.15, T:0.41
Consensus pattern (22 bp):
ATGATTTAACTGTCATTGTCAA
Found at i:6247524 original size:40 final size:40
Alignment explanation
Indices: 6247480--6247556 Score: 145
Period size: 40 Copynumber: 1.9 Consensus size: 40
6247470 CTAATGGTTG
*
6247480 TAGCAGGATGATTTAACTGTCATTGTTAAATGATTTACTA
1 TAGCAGGATGATTTAACTGTCATTGTCAAATGATTTACTA
6247520 TAGCAGGATGATTTAACTGTCATTGTCAAATGATTTA
1 TAGCAGGATGATTTAACTGTCATTGTCAAATGATTTA
6247557 AAGTATTTAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.32, C:0.10, G:0.18, T:0.39
Consensus pattern (40 bp):
TAGCAGGATGATTTAACTGTCATTGTCAAATGATTTACTA
Found at i:6248405 original size:20 final size:21
Alignment explanation
Indices: 6248380--6248431 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
6248370 TTTTCCCAAT
*
6248380 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
6248400 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
6248421 TCGCAATGCGA
1 TCGCAATGCGA
6248432 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:6248445 original size:20 final size:20
Alignment explanation
Indices: 6248420--6248520 Score: 105
Period size: 20 Copynumber: 5.0 Consensus size: 20
6248410 AATTGGGAAA
6248420 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
6248440 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
6248460 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
6248481 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* * *
6248501 TTCGCAACGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
6248521 TTCATTTCGC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
19 2 0.03
20 51 0.75
21 13 0.19
22 2 0.03
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:6248605 original size:39 final size:35
Alignment explanation
Indices: 6248522--6248609 Score: 103
Period size: 33 Copynumber: 2.5 Consensus size: 35
6248512 ATTCTGACTT
6248522 TCATTTCGCGTTGCGA-TTTCATTTCGCATTGCGA
1 TCATTTCGCGTTGCGATTTTCATTTCGCATTGCGA
6248556 T--TTT-GTCGTTGCGATTTTCATTTCGCATTGCGA
1 TCATTTCG-CGTTGCGATTTTCATTTCGCATTGCGA
6248589 TAGCCATTTCCGCGTTGCGAT
1 T---CATTT-CGCGTTGCGAT
6248610 AGTCATTTTC
Statistics
Matches: 45, Mismatches: 0, Indels: 13
0.78 0.00 0.22
Matches are distributed among these distances:
31 1 0.02
32 11 0.24
33 19 0.42
34 1 0.02
38 3 0.07
39 9 0.20
40 1 0.02
ACGTcount: A:0.14, C:0.23, G:0.22, T:0.42
Consensus pattern (35 bp):
TCATTTCGCGTTGCGATTTTCATTTCGCATTGCGA
Found at i:6248608 original size:20 final size:19
Alignment explanation
Indices: 6248574--6248628 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
6248564 TTGCGATTTT
*
6248574 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
6248593 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
6248613 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
6248629 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:6249136 original size:18 final size:18
Alignment explanation
Indices: 6249110--6249154 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
6249100 GTCGATCAGA
*
6249110 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
6249128 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
6249146 TGATGGCTC
1 TGATGGCTC
6249155 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:6250495 original size:20 final size:20
Alignment explanation
Indices: 6250470--6250507 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
6250460 AATAGTTTCT
6250470 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
6250490 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
6250508 GAGAGAATCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:6250801 original size:22 final size:22
Alignment explanation
Indices: 6250771--6250814 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
6250761 GATGGAGATA
*
6250771 GACGGATTTCGCCGGAGATGGG
1 GACGAATTTCGCCGGAGATGGG
*
6250793 GACGAATTTCGTCGGAGATGGG
1 GACGAATTTCGCCGGAGATGGG
6250815 TGAGAGAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.16, G:0.43, T:0.20
Consensus pattern (22 bp):
GACGAATTTCGCCGGAGATGGG
Found at i:6251105 original size:41 final size:41
Alignment explanation
Indices: 6250988--6251117 Score: 156
Period size: 41 Copynumber: 3.2 Consensus size: 41
6250978 GAAAATCGTA
*
6250988 TTGCGATTATGTATTATCGCGTTGCGAAAGTCAGAATCGCG
1 TTGCGATTATGTATTATCGCGTTGCGAAAGTCAGTATCGCG
* * * *
6251029 TTGCGA--AAGTCAGTATCGCGTTGCGAAAGTAAGTATCTCG
1 TTGCGATTATGT-ATTATCGCGTTGCGAAAGTCAGTATCGCG
* * * *
6251069 TTGCGATTTTGTATTATCGCATTGCGATAGTCAGTATCGCA
1 TTGCGATTATGTATTATCGCGTTGCGAAAGTCAGTATCGCG
6251110 TTGCGATT
1 TTGCGATT
6251118 TTCCCAATTC
Statistics
Matches: 73, Mismatches: 13, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
39 3 0.04
40 31 0.42
41 37 0.51
42 2 0.03
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.34
Consensus pattern (41 bp):
TTGCGATTATGTATTATCGCGTTGCGAAAGTCAGTATCGCG
Found at i:6251116 original size:20 final size:20
Alignment explanation
Indices: 6251002--6251115 Score: 122
Period size: 20 Copynumber: 5.7 Consensus size: 20
6250992 GATTATGTAT
6251002 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
6251022 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
6251042 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* ** *
6251062 TATCTCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
* *
6251083 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
6251103 TATCGCATTGCGA
1 TATCGCGTTGCGA
6251116 TTTTCCCAAT
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
19 3 0.04
20 63 0.79
21 12 0.15
22 2 0.03
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.31
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:6251135 original size:41 final size:41
Alignment explanation
Indices: 6251002--6251137 Score: 105
Period size: 41 Copynumber: 3.3 Consensus size: 41
6250992 GATTATGTAT
* * * * *** *
6251002 TATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGT-CAG
1 TATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCAA
* * * ** *
6251042 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTTGTAT
1 TATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCAA
* *
6251083 TATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAA
1 TATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTT-CCAA
6251125 T-TCGCGTTGCGAT
1 TATCGCGTTGCGAT
6251138 TTACTTATTC
Statistics
Matches: 77, Mismatches: 17, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
40 31 0.40
41 44 0.57
42 2 0.03
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.32
Consensus pattern (41 bp):
TATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCAA
Found at i:6252213 original size:31 final size:31
Alignment explanation
Indices: 6252143--6252218 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
6252133 TGAAGTTCAA
*
6252143 TTTTTTAATTTAATTACTTAACATTCAAATC
1 TTTTTTAATTTAATCACTTAACATTCAAATC
** * *
6252174 ACTCTTAATTTAATCACTATAACTTTCAAAT-
1 TTTTTTAATTTAATCACT-TAACATTCAAATC
*
6252205 TTTTTTAATATAAT
1 TTTTTTAATTTAAT
6252219 TATATATTAA
Statistics
Matches: 35, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
31 24 0.69
32 11 0.31
ACGTcount: A:0.37, C:0.13, G:0.00, T:0.50
Consensus pattern (31 bp):
TTTTTTAATTTAATCACTTAACATTCAAATC
Found at i:6259095 original size:29 final size:27
Alignment explanation
Indices: 6259003--6259101 Score: 74
Period size: 29 Copynumber: 3.5 Consensus size: 27
6258993 TATCTTAAAT
* *
6259003 TTTAAAAATATATTTTATTTTTGTCTTAA
1 TTTAAAAATATATTTTATTTTT-TCAT-G
* * *
6259032 CTTATTAAATATATTATA-TTTTTCAATG
1 TTTA-AAAATATATTTTATTTTTTC-ATG
**
6259060 TAAAAAAATATATTTTATTTTTATCATCG
1 TTTAAAAATATATTTTATTTTT-TCAT-G
6259089 TTTAAAAATATAT
1 TTTAAAAATATAT
6259102 ATTTTTTATC
Statistics
Matches: 53, Mismatches: 12, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
27 11 0.21
28 9 0.17
29 22 0.42
30 11 0.21
ACGTcount: A:0.39, C:0.05, G:0.03, T:0.53
Consensus pattern (27 bp):
TTTAAAAATATATTTTATTTTTTCATG
Found at i:6259327 original size:23 final size:23
Alignment explanation
Indices: 6259301--6259346 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
6259291 ATATCAACTT
*
6259301 TAAAATATTTTTTAACTTAAGAA
1 TAAAATATATTTTAACTTAAGAA
*
6259324 TAAAATATATTTTAAGTTAAGAA
1 TAAAATATATTTTAACTTAAGAA
6259347 ATTTAAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.50, C:0.02, G:0.07, T:0.41
Consensus pattern (23 bp):
TAAAATATATTTTAACTTAAGAA
Found at i:6259392 original size:29 final size:29
Alignment explanation
Indices: 6259360--6259525 Score: 106
Period size: 30 Copynumber: 5.6 Consensus size: 29
6259350 TAAAAAAATA
*
6259360 AAGTTAAGATTAAAATAAAATATATTTTT
1 AAGTTAAAATTAAAATAAAATATATTTTT
* *
6259389 AAGTTAAAA--ATAATCAAATATATTTTT
1 AAGTTAAAATTAAAATAAAATATATTTTT
* * * * *
6259416 ATGTGAAAAATAAGCATAAACATAT-TTTAT
1 AAGTTAAAATTAA-AATAAA-ATATATTTTT
* *
6259446 ATA-TTAAAATAAAAATAAAATATATTTAAT
1 A-AGTTAAAATTAAAATAAAATATATTT-TT
* ** *
6259476 AAGTTAATACAAAAATAAAATATATTTCTAA
1 AAGTTAAAATTAAAATAAAATATATTT-T-T
6259507 AAGTTAAGAATATAAAATA
1 AAGTTAA-AAT-TAAAATA
6259526 TTATGAATTT
Statistics
Matches: 104, Mismatches: 22, Indels: 18
0.72 0.15 0.12
Matches are distributed among these distances:
27 23 0.22
28 4 0.04
29 18 0.17
30 41 0.39
31 11 0.11
32 1 0.01
33 6 0.06
ACGTcount: A:0.56, C:0.03, G:0.05, T:0.36
Consensus pattern (29 bp):
AAGTTAAAATTAAAATAAAATATATTTTT
Found at i:6259395 original size:23 final size:24
Alignment explanation
Indices: 6259301--6259428 Score: 91
Period size: 27 Copynumber: 5.1 Consensus size: 24
6259291 ATATCAACTT
* *
6259301 TAAAATAT-TTTTTAACTTAAGAA
1 TAAAATATATTTTTAAGTTAAAAA
6259324 TAAAATATA-TTTTAAGTTAAGAAA
1 TAAAATATATTTTTAAGTTAA-AAA
* ***
6259348 TTTAAAAAAATAAAGTTAAGATT-AAAA
1 --T-AAAATATATTTTTAAG-TTAAAAA
6259375 TAAAATATATTTTTAAGTTAAAAA
1 TAAAATATATTTTTAAGTTAAAAA
* *
6259399 TAATCAAATATATTTTTATGTGAAAAA
1 T-A--AAATATATTTTTAAGTTAAAAA
6259426 TAA
1 TAA
6259429 GCATAAACAT
Statistics
Matches: 83, Mismatches: 11, Indels: 21
0.72 0.10 0.18
Matches are distributed among these distances:
23 20 0.24
24 20 0.24
25 2 0.02
26 2 0.02
27 31 0.37
28 6 0.07
29 2 0.02
ACGTcount: A:0.54, C:0.02, G:0.06, T:0.38
Consensus pattern (24 bp):
TAAAATATATTTTTAAGTTAAAAA
Found at i:6264793 original size:15 final size:15
Alignment explanation
Indices: 6264773--6264825 Score: 88
Period size: 15 Copynumber: 3.5 Consensus size: 15
6264763 ATATTTAGCT
*
6264773 GGGCGGGTGGATGCG
1 GGGCGGGTGGATGCA
*
6264788 GGGCGGGCGGATGCA
1 GGGCGGGTGGATGCA
6264803 GGGCGGGTGGATGCA
1 GGGCGGGTGGATGCA
6264818 GGGCGGGT
1 GGGCGGGT
6264826 AAAGTCTCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 35 1.00
ACGTcount: A:0.09, C:0.15, G:0.64, T:0.11
Consensus pattern (15 bp):
GGGCGGGTGGATGCA
Found at i:6265755 original size:16 final size:16
Alignment explanation
Indices: 6265713--6265755 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
6265703 TATTATTTTC
*
6265713 TTCTTTATCTTCTATT
1 TTCTTTATTTTCTATT
*
6265729 TTTTTTATTTTCTA-T
1 TTCTTTATTTTCTATT
6265744 TTCTTTAGTTTT
1 TTCTTTA-TTTT
6265756 TTTCCTTCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 7 0.30
16 16 0.70
ACGTcount: A:0.12, C:0.12, G:0.02, T:0.74
Consensus pattern (16 bp):
TTCTTTATTTTCTATT
Found at i:6266657 original size:16 final size:16
Alignment explanation
Indices: 6266636--6266667 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
6266626 ATTCCGTTGT
6266636 TTTAAAATTAAATTAA
1 TTTAAAATTAAATTAA
*
6266652 TTTAAATTTAAATTAA
1 TTTAAAATTAAATTAA
6266668 ATTTTTCTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TTTAAAATTAAATTAA
Found at i:6269859 original size:19 final size:19
Alignment explanation
Indices: 6269770--6269860 Score: 60
Period size: 19 Copynumber: 4.6 Consensus size: 19
6269760 TTTTTTACAC
*
6269770 TATATAT-TA-TTATTATC
1 TATATATATATTTATTATT
* *
6269787 TATACATATATTTTTTATT
1 TATATATATATTTATTATT
* *
6269806 TATTTATATTCATTTGGTTATTT
1 TATATATA-T-ATTT-ATTA-TT
*
6269829 TTTAATACTATATTTATTATT
1 TAT-ATA-TATATTTATTATT
6269850 TATATATATAT
1 TATATATATAT
6269861 ATATACTTTT
Statistics
Matches: 56, Mismatches: 10, Indels: 14
0.70 0.12 0.17
Matches are distributed among these distances:
17 6 0.11
18 2 0.04
19 17 0.30
20 4 0.07
21 8 0.14
22 6 0.11
23 8 0.14
24 3 0.05
25 2 0.04
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (19 bp):
TATATATATATTTATTATT
Found at i:6274664 original size:16 final size:16
Alignment explanation
Indices: 6274638--6274678 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
6274628 AGATCCAATC
6274638 AAGAACAAAAAAG-AA
1 AAGAACAAAAAAGCAA
6274653 AAGAAGCAAAAAAGCAA
1 AAGAA-CAAAAAAGCAA
*
6274670 AACAACAAA
1 AAGAACAAA
6274679 GGAAAAAGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 5 0.22
16 12 0.52
17 6 0.26
ACGTcount: A:0.76, C:0.12, G:0.12, T:0.00
Consensus pattern (16 bp):
AAGAACAAAAAAGCAA
Found at i:6275585 original size:22 final size:22
Alignment explanation
Indices: 6275490--6275588 Score: 144
Period size: 22 Copynumber: 4.5 Consensus size: 22
6275480 GCTACCCCAT
*
6275490 CAAACCGTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
* *
6275512 CAAACCTATGAGCATCAAATTC
1 CAAACCTTTGAGCATCAAATGC
* *
6275534 GAAACCTATGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
*
6275556 TAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
6275578 CAAACCTTTGA
1 CAAACCTTTGA
6275589 CCAAACATAA
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 69 1.00
ACGTcount: A:0.38, C:0.25, G:0.14, T:0.22
Consensus pattern (22 bp):
CAAACCTTTGAGCATCAAATGC
Found at i:6276554 original size:106 final size:105
Alignment explanation
Indices: 6276396--6278087 Score: 2415
Period size: 106 Copynumber: 16.0 Consensus size: 105
6276386 GTGCCACTCA
* * * * * *
6276396 AGACAACACAAGTTCAACTTCACAATGAAGGGACCGCTGGTTATCAACAAACAACTTCTCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTT
6276461 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACCC
66 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACCC
* *
6276501 TAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCTCAATT
1 -AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATT
*
6276566 TCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
65 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC-CC
* * * *
6276608 AGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACGACTTCTCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTT
6276673 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
66 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC-CC
*
6276714 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTT
* *
6276779 CAGAGACAATTTCAACTTCACAACGAAGGATATTGGACTCA
66 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC-CC
* *
6276820 AGACAACACAAGTTCAACTTCACGACAAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTT
* *
6276885 CAGAGCCAATTTTAACTTCACAGCGAAGGATATTGGACTCC
66 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC-CC
* *
6276926 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTT
*
6276991 CAGAGCCAATTTCAACTTTACAACGAAGGATATTGGACTCC
66 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC-CC
* * * *
6277032 AGACAACGCAAGTTCAACTTCACGACGAAGGGACAGCTGTTTGTCAATAAATAATTTCCCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTT
* * * * * *
6277097 TATAGCCAATTTCAACTTCACAGCGTAGGATATTAGACTCA
66 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC-CC
*
6277138 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAATAACTTCCCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTT
* * *
6277203 CAGAGCCAATTTCAAATTCACAGCGAAGGATATTGGACTCT
66 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC-CC
* * * *
6277244 AGACAACACAAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTT
6277309 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
66 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC-CC
** * * *
6277350 AGACAACGCAAGTTCAACTTCACGACGAAGGGATTGCTGGTTGTCAACAAATAATTTCCCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTT
* *
6277415 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCA
66 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC-CC
*
6277456 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGTTGGTTGTCAATAAACAACTTCCCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTT
**
6277521 CAGAGCCAATTTCAACTTCACAGTGAAGGATATTGGACTCC
66 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC-CC
* * *
6277562 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTCTCAACAAACAACTTCTCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTT
* *
6277627 TAGAGCCAATTTTAACTTCACAACGAAGGATATTGGACTCC
66 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC-CC
*
6277668 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTT
* * * * *
6277733 CAGAGCCAATTTCAACTTTACAGCGTAGGATATTAGACTCA
66 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC-CC
* *
6277774 AGACAACTCAAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTT
* * *
6277839 TAGAGCCAATTTCAACTTCTCAACGAAGGATCTTGGACCC
66 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACCC
* * * * * *
6277879 AAGACAACACAAGCTCAACTTCACGACGAAGGGGCGGCTGATTGTCAAT-AA-AA-TTTCC---T
1 -AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATT
* * * *
6277938 TCAGAGTCAATTTCAACTTCACAGCGATGGATATTGGACTCG
65 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC-CC
* * * * * * * **
6277980 AGACAACACAAGTTTAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAATAATTTCCCGGTTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTT
* *
6278045 CAGAGCCAATTTCAACTTCACAACGGAGGATATTGGACTC
66 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACCC
6278085 AGA
1 AGA
6278088 ACAATGCTAC
Statistics
Matches: 1440, Mismatches: 137, Indels: 19
0.90 0.09 0.01
Matches are distributed among these distances:
100 76 0.05
101 3 0.00
102 2 0.00
103 8 0.01
104 2 0.00
105 6 0.00
106 1341 0.93
107 2 0.00
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (105 bp):
AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTT
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACCC
Found at i:6276973 original size:318 final size:318
Alignment explanation
Indices: 6276391--6278085 Score: 2684
Period size: 318 Copynumber: 5.3 Consensus size: 318
6276381 ATATCGTGCC
* * * * * * *
6276391 ACTCAAGACAACACAAGTTCAACTTCACAATGAAGGGACCGCTGGTTATCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
* *
6276456 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACCCTAGACAACGCAAGTTCAACT
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACGCAAGTTCAACT
* *
6276521 TCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCTCAATTTCAGAGCCAATTTCAACTTC
131 TCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTC
*
6276586 ACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGGTTG
196 ACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTG
*
6276651 TCAACAAACGACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
261 TCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
*
6276709 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
* *
6276774 AATTTCAGAGACAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGTTCAACT
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACGCAAGTTCAACT
* *
6276839 TCACGACAAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTTAACTTC
131 TCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTC
6276904 ACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTG
196 ACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTG
*
6276969 TCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTTACAACGAAGGATATTGG
261 TCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * *
6277027 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACAGCTGTTTGTCAATAAATAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
* * * * *
6277092 AATTTTATAGCCAATTTCAACTTCACAGCGTAGGATATTAGACTCAAGACAACGCAAGTTCAACT
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACGCAAGTTCAACT
* *
6277157 TCACGACGAAGGGACCGCTGGTTGTCAATAAATAACTTCCCAATTTCAGAGCCAATTTCAAATTC
131 TCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTC
* * *
6277222 ACAGCGAAGGATATTGGACTCTAGACAACACAAGTTCAACTTCACGATGAAGGGACCGCTGGTTG
196 ACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTG
6277287 TCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
261 TCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
** *
6277345 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGATTGCTGGTTGTCAACAAATAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
*
6277410 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACT
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACGCAAGTTCAACT
*
6277475 TCACGACGAAGGGACCGTTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTC
131 TCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTC
* *
6277540 ACAGTGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTC
196 ACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTG
* *
6277605 TCAACAAACAACTTCTCAATTTTAGAGCCAATTTTAACTTCACAACGAAGGATATTGG
261 TCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
*
6277663 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
* * * * *
6277728 AATTTCAGAGCCAATTTCAACTTTACAGCGTAGGATATTAGACTCAAGACAACTCAAGTTCAACT
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACGCAAGTTCAACT
* *
6277793 TCACGATGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTTAGAGCCAATTTCAACTTC
131 TCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTC
* * * * * * * *
6277858 TCAACGAAGGATCTTGGAC-CCAAGACAACACAAGCTCAACTTCACGACGAAGGGGCGGCTGATT
196 ACAGCGAAGGATATTGGACTCC-AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTT
* * * * *
6277922 GTCAA-TAA-AA-TT-TC--CTTCAGAGTCAATTTCAACTTCACAGCGATGGATATTGG
260 GTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * * * *
6277975 ACTCGAGACAACACAAGTTTAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAATAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
** *
6278040 GGTTTCAGAGCCAATTTCAACTTCACAACGGAGGATATTGGACTCA
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCA
6278086 GAACAATGCT
Statistics
Matches: 1280, Mismatches: 96, Indels: 8
0.92 0.07 0.01
Matches are distributed among these distances:
312 131 0.10
314 2 0.00
315 2 0.00
316 2 0.00
317 4 0.00
318 1139 0.89
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (318 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACGCAAGTTCAACT
TCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTC
ACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTG
TCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
Found at i:6278868 original size:37 final size:37
Alignment explanation
Indices: 6278813--6278919 Score: 135
Period size: 37 Copynumber: 2.9 Consensus size: 37
6278803 CACCTTTTCG
*
6278813 TTCTACTAGGATTCAAACTCCTAAAAATAGGATGGAAC
1 TTCTACTAGGATTCAAACTCCTAAAAATAGGATAG-AC
* * *
6278851 TT-TGCTAGGATTCAAACTCCTAAAAATATGATAGAG
1 TTCTACTAGGATTCAAACTCCTAAAAATAGGATAGAC
* * *
6278887 TTCTACTATGATTTAAACTCCTAAAGATAGGAT
1 TTCTACTAGGATTCAAACTCCTAAAAATAGGAT
6278920 CCACAAGCAC
Statistics
Matches: 59, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
36 3 0.05
37 54 0.92
38 2 0.03
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.31
Consensus pattern (37 bp):
TTCTACTAGGATTCAAACTCCTAAAAATAGGATAGAC
Found at i:6281512 original size:16 final size:17
Alignment explanation
Indices: 6281483--6281514 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
6281473 AAGTTTTTAT
6281483 TTTTATTTTATTTTAAG
1 TTTTATTTTATTTTAAG
6281500 TTTTATTTT-TTTTAA
1 TTTTATTTTATTTTAA
6281515 AATGCTAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.75
Consensus pattern (17 bp):
TTTTATTTTATTTTAAG
Found at i:6289991 original size:20 final size:20
Alignment explanation
Indices: 6289952--6289992 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
6289942 CATTGCAGGA
*
6289952 ATTTATGGCCTCGACGAAAG
1 ATTTATGGCCTCCACGAAAG
6289972 ATTTCATGGCCTCCAC-AAAG
1 ATTT-ATGGCCTCCACGAAAG
6289992 A
1 A
6289993 CCTTGATGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (20 bp):
ATTTATGGCCTCCACGAAAG
Found at i:6298962 original size:16 final size:16
Alignment explanation
Indices: 6298941--6298972 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
6298931 CATTTTCTTG
*
6298941 CATTTCATATTGCATT
1 CATTTCATAATGCATT
6298957 CATTTCATAATGCATT
1 CATTTCATAATGCATT
6298973 GTATTAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.28, C:0.19, G:0.06, T:0.47
Consensus pattern (16 bp):
CATTTCATAATGCATT
Found at i:6301787 original size:258 final size:253
Alignment explanation
Indices: 6301324--6301798 Score: 630
Period size: 258 Copynumber: 1.9 Consensus size: 253
6301314 AGTTCGTCCA
* * * * * *
6301324 TTTCAGGTTCTTTTTCAATTCCTTATTGTTATTTAGCTTATTTTCATAAAAAAAATAAAGGGAAA
1 TTTCAGCTTCTTTTTCAATTCCATATTGTTATGTAGCTTATTTACATAAAAAAAAAAAAAGGAAA
* * * *
6301389 AAGGGGGGAAATGAGAAAAAAAAACAAAAAAAATCCAGAAATTCAAAACGAATGAATTCAGAGCT
66 AAAGGGGGAAA-GACAAAAAAAAACAAAAAAAATCCAAAAATTCAAAACAAATGAATTCAGAGCT
** * *
6301454 TATTGTTTATGGGAATATTCTTTACCCTAAGAGAGATCTACAGTTCAAAATCCAGATCAATCAGA
130 TATTGTTTACAGGAATATTCTTCACCCTAAGAGAGATCTACAGTTCAAAATCCAAATCAATCAGA
*
6301519 CAACAATAGACCCCATCTGATCCTTCATTCAAGATTGTTCTATAGAATTTAGAGCTTATT
195 CAAAAATAGACCCC-TCTGATCCTTCATTCAAGATTGTTCTATAGAATTTAGAGCTTATT
6301579 TTTCAGCTTCTTTTTCAATTCCATATTGTTATGTAGCTTATTTACATTAAAAATAAAGGAAAAAA
1 TTTCAGCTTCTTTTTCAATTCCATATTGTTATGTAGCTTATTTACA-T-AAAA-AAA--AAAAAA
* * * * * **
6301644 GGAAAAAATGGGGAAA-ACAAGAAAAAGCCAAAAGAATCCAAAAATTCAAAGTAAATGAATTC-G
61 GGAAAAAAGGGGGAAAGACAAAAAAAAACAAAAAAAATCCAAAAATTCAAAACAAATGAATTCAG
*
6301707 AAGCTTATTTTTTACAGGAATATTCTTCACCCTAAGAGAGATCTACAGTTCAAAATCCAAATCAA
126 -AGCTTATTGTTTACAGGAATATTCTTCACCCTAAGAGAGATCTACAGTTCAAAATCCAAATCAA
* * *
6301772 TCGGATAAAAATAGACCCCTCTTATCC
190 TCAGACAAAAATAGACCCCTCTGATCC
6301799 ATTTAAATAA
Statistics
Matches: 188, Mismatches: 26, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
255 42 0.22
256 1 0.01
257 12 0.06
258 115 0.61
260 18 0.10
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.30
Consensus pattern (253 bp):
TTTCAGCTTCTTTTTCAATTCCATATTGTTATGTAGCTTATTTACATAAAAAAAAAAAAAGGAAA
AAAGGGGGAAAGACAAAAAAAAACAAAAAAAATCCAAAAATTCAAAACAAATGAATTCAGAGCTT
ATTGTTTACAGGAATATTCTTCACCCTAAGAGAGATCTACAGTTCAAAATCCAAATCAATCAGAC
AAAAATAGACCCCTCTGATCCTTCATTCAAGATTGTTCTATAGAATTTAGAGCTTATT
Found at i:6301826 original size:15 final size:15
Alignment explanation
Indices: 6301795--6301833 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
6301785 GACCCCTCTT
*
6301795 ATCCATTTAAATAAA
1 ATCCATTGAAATAAA
* *
6301810 ATCTATTGAAATCAA
1 ATCCATTGAAATAAA
6301825 ATCCATTGA
1 ATCCATTGA
6301834 TAAACGTCCA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.46, C:0.15, G:0.05, T:0.33
Consensus pattern (15 bp):
ATCCATTGAAATAAA
Found at i:6321868 original size:18 final size:18
Alignment explanation
Indices: 6321845--6321897 Score: 79
Period size: 18 Copynumber: 2.9 Consensus size: 18
6321835 AGGGATTATC
*
6321845 AGTGGTCATTCGGGACAT
1 AGTGGTCATTTGGGACAT
*
6321863 AGTGGTCCTTTGGGACAT
1 AGTGGTCATTTGGGACAT
*
6321881 AATGGTCATTTGGGACA
1 AGTGGTCATTTGGGACA
6321898 AATATTCATT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.23, C:0.15, G:0.32, T:0.30
Consensus pattern (18 bp):
AGTGGTCATTTGGGACAT
Found at i:6328713 original size:18 final size:18
Alignment explanation
Indices: 6328690--6328754 Score: 94
Period size: 18 Copynumber: 3.6 Consensus size: 18
6328680 ATTATCAGTT
*
6328690 GTCCTTCGGGACATACTG
1 GTCCTTCGGGACATAGTG
*
6328708 GTCCTTCGGGACTTAGTG
1 GTCCTTCGGGACATAGTG
* *
6328726 GTCTTTCCGGACATAGTG
1 GTCCTTCGGGACATAGTG
6328744 GTCCTTCGGGA
1 GTCCTTCGGGA
6328755 AAAATATTCA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 40 1.00
ACGTcount: A:0.14, C:0.25, G:0.31, T:0.31
Consensus pattern (18 bp):
GTCCTTCGGGACATAGTG
Found at i:6332280 original size:22 final size:20
Alignment explanation
Indices: 6332238--6332280 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 20
6332228 ATATTATCAT
*
6332238 CATTTCATTTCCACAATATC
1 CATTTCATTTCCACAACATC
*
6332258 CATTTCATCTTGCCACGACATC
1 CATTTCAT-TT-CCACAACATC
6332280 C
1 C
6332281 TCATCTGTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 8 0.42
21 2 0.11
22 9 0.47
ACGTcount: A:0.26, C:0.35, G:0.05, T:0.35
Consensus pattern (20 bp):
CATTTCATTTCCACAACATC
Found at i:6344867 original size:2 final size:2
Alignment explanation
Indices: 6344862--6344912 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
6344852 TCTCTAACAT
6344862 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6344904 TA TA TA TA T
1 TA TA TA TA T
6344913 GTGTGTGTGT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:6357777 original size:63 final size:64
Alignment explanation
Indices: 6357700--6357826 Score: 168
Period size: 63 Copynumber: 2.0 Consensus size: 64
6357690 AAAAAGTACT
** * ** *
6357700 TCGTTTAGGATGAAAACCCGAGAA-GGCGTCCTAAGTTGAAAAAAA-AGGAAAAAAACAAAAAAA
1 TCGTTTAGGATGAAAACCCGA-AAGGGCACCCTAAATTGAAAAAAATAAAAAAAAAAAAAAAAAA
*
6357763 TCGTTTAGGGTGAAAACCCGAAAGGGCACCCTAAATTGAAAAAAATAAAAAAAAAAAAAAAAAA
1 TCGTTTAGGATGAAAACCCGAAAGGGCACCCTAAATTGAAAAAAATAAAAAAAAAAAAAAAAAA
6357827 AAAAAAAAAA
Statistics
Matches: 55, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
62 2 0.04
63 38 0.69
64 15 0.27
ACGTcount: A:0.55, C:0.13, G:0.18, T:0.14
Consensus pattern (64 bp):
TCGTTTAGGATGAAAACCCGAAAGGGCACCCTAAATTGAAAAAAATAAAAAAAAAAAAAAAAAA
Found at i:6357807 original size:1 final size:1
Alignment explanation
Indices: 6357801--6357841 Score: 64
Period size: 1 Copynumber: 41.0 Consensus size: 1
6357791 CCCTAAATTG
* *
6357801 AAAAAAATAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
6357842 GAATGTGGGT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:0.95, C:0.00, G:0.02, T:0.02
Consensus pattern (1 bp):
A
Found at i:6359145 original size:106 final size:105
Alignment explanation
Indices: 6358927--6359236 Score: 452
Period size: 106 Copynumber: 3.0 Consensus size: 105
6358917 ATCGTGCACA
*
6358927 CAAGACAACACAAGCTCAACTTCACAGCGAAGGGGCGGCTGACTGT---C-AAC--TTTCCAATT
1 CAAGACAACACAAGCTCAACTTCACGGCGAAGGGGCGGCTGACTGTCAACAAACAATTTCCAATT
* * ** *
6358986 TCATAGCCAATTTCAACTTCACAATGAAGGATATTGGACT
66 TCAGAACCAATTTCAACTTCACAGCGAAGGATATTGGACC
6359026 CAAGACAACACAAGCTCAACTTCACGGCGAAGGGGCGGCTGACTGTCAACAAACAATTTCCCAAT
1 CAAGACAACACAAGCTCAACTTCACGGCGAAGGGGCGGCTGACTGTCAACAAACAATTT-CCAAT
* * *
6359091 TTCAGATCCAATTTCAACTTCGCAGCAAAGGATATTGGACC
65 TTCAGAACCAATTTCAACTTCACAGCGAAGGATATTGGACC
*
6359132 CAAGACAGCACAAGCTCAACTTCACGGCGAAGGGGCGGCTGACTGTCAACAAACAATTTTCCAAT
1 CAAGACAACACAAGCTCAACTTCACGGCGAAGGGGCGGCTGACTGTCAACAAACAA-TTTCCAAT
* *
6359197 TCCAGAACCAATTTCAACTTCACGGCGAAGGATATTGGAC
65 TTCAGAACCAATTTCAACTTCACAGCGAAGGATATTGGAC
6359237 TCGGAGCAAT
Statistics
Matches: 189, Mismatches: 14, Indels: 9
0.89 0.07 0.04
Matches are distributed among these distances:
99 45 0.24
102 1 0.01
103 3 0.02
105 3 0.02
106 134 0.71
107 3 0.02
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.21
Consensus pattern (105 bp):
CAAGACAACACAAGCTCAACTTCACGGCGAAGGGGCGGCTGACTGTCAACAAACAATTTCCAATT
TCAGAACCAATTTCAACTTCACAGCGAAGGATATTGGACC
Found at i:6361444 original size:4 final size:4
Alignment explanation
Indices: 6361435--6361459 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
6361425 TTTCTTCCCC
6361435 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
6361460 TTCATTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:6364933 original size:37 final size:37
Alignment explanation
Indices: 6364902--6364974 Score: 130
Period size: 37 Copynumber: 2.0 Consensus size: 37
6364892 AATATATTTG
6364902 AATT-TAAAATATGTATTTAATATATATAATATTTAA
1 AATTATAAAATATGTATTTAATATATATAATATTTAA
*
6364938 AATTATTAAATATGTATTTAATATATATAATATTTAA
1 AATTATAAAATATGTATTTAATATATATAATATTTAA
6364975 TATTTAACAA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
36 4 0.11
37 31 0.89
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (37 bp):
AATTATAAAATATGTATTTAATATATATAATATTTAA
Found at i:6365234 original size:22 final size:22
Alignment explanation
Indices: 6365206--6365247 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
6365196 AATGTTTATT
6365206 AATATTA-AATATATATTTGGGG
1 AATATTAGAAT-TATATTTGGGG
*
6365228 AATATTAGAATTATCTTTGG
1 AATATTAGAATTATATTTGG
6365248 TCTGTATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.38, C:0.02, G:0.17, T:0.43
Consensus pattern (22 bp):
AATATTAGAATTATATTTGGGG
Found at i:6366151 original size:97 final size:98
Alignment explanation
Indices: 6366041--6366232 Score: 241
Period size: 97 Copynumber: 2.0 Consensus size: 98
6366031 TGAAAATATT
* * * * *
6366041 TATTTTATCTTTATATTCACT-TAAAAATATATTTTATTCTTCTA-TTAATTTTTAAAAA-ATAT
1 TATTTTATCTTTATATT-AATATAAAAAAATATTTTATTATT-AACTTAAATTTTAAAAATATA-
* *
6366103 TTTTTTGAAATATCTTAAC-TTAAAATATATTTAAA
63 TCTTTTAAAATATCTTAACTTTAAAATATATTTAAA
*
6366138 TATTTTAAT-TTTATCTTAATATAAAAAAATATTTTATTATTAACTTAAATTTTAAAAATATATC
1 TATTTT-ATCTTTATATTAATATAAAAAAATATTTTATTATTAACTTAAATTTTAAAAATATATC
6366202 TTTTAAAATATCTTAACTTTAAAATATATTT
65 TTTTAAAATATCTTAACTTTAAAATATATTT
6366233 TAACTTAAGA
Statistics
Matches: 82, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
96 3 0.04
97 61 0.74
98 18 0.22
ACGTcount: A:0.42, C:0.06, G:0.01, T:0.52
Consensus pattern (98 bp):
TATTTTATCTTTATATTAATATAAAAAAATATTTTATTATTAACTTAAATTTTAAAAATATATCT
TTTAAAATATCTTAACTTTAAAATATATTTAAA
Found at i:6366160 original size:29 final size:29
Alignment explanation
Indices: 6366117--6366193 Score: 70
Period size: 29 Copynumber: 2.7 Consensus size: 29
6366107 TTGAAATATC
6366117 TTAACTTAAAATATATTTAAATATTTTAATT-
1 TTAACTT--AATATATTTAAATATTTT-ATTA
* ***
6366148 TTATCTTAATATAAAAAAATATTTTATTA
1 TTAACTTAATATATTTAAATATTTTATTA
6366177 TTAACTTAA-AT-TTTAAA
1 TTAACTTAATATATTTAAA
6366194 AATATATCTT
Statistics
Matches: 37, Mismatches: 8, Indels: 6
0.73 0.16 0.12
Matches are distributed among these distances:
27 3 0.08
28 5 0.14
29 23 0.62
31 6 0.16
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (29 bp):
TTAACTTAATATATTTAAATATTTTATTA
Found at i:6366356 original size:29 final size:28
Alignment explanation
Indices: 6366285--6366429 Score: 134
Period size: 29 Copynumber: 5.0 Consensus size: 28
6366275 AAAAAGTTAA
*
6366285 AAGTTAACATAAGAATAAAACATATATTTT
1 AAGTTAAAATAAGAAT-AAA-ATATATTTT
*
6366315 CAGTTAAAATAAGAATAAAATATACTTTT
1 AAGTTAAAATAAGAATAAAATATA-TTTT
* * * *
6366344 AAGTGAATATAAGATTAAAACATATATTT
1 AAGTTAAAATAAGAATAAAATATAT-TTT
*
6366373 ATA-TTAAAATAAGACTAAAATATATTTAAT
1 A-AGTTAAAATAAGAATAAAATATATTT--T
6366403 AAGTTAAGAA-AA-AATAAAATATATTTT
1 AAGTTAA-AATAAGAATAAAATATATTTT
6366430 TAAAAGTTAT
Statistics
Matches: 96, Mismatches: 12, Indels: 17
0.77 0.10 0.14
Matches are distributed among these distances:
27 1 0.01
28 8 0.08
29 62 0.65
30 23 0.24
31 2 0.02
ACGTcount: A:0.54, C:0.04, G:0.07, T:0.34
Consensus pattern (28 bp):
AAGTTAAAATAAGAATAAAATATATTTT
Found at i:6366421 original size:58 final size:62
Alignment explanation
Indices: 6366281--6366431 Score: 174
Period size: 58 Copynumber: 2.6 Consensus size: 62
6366271 TTAAAAAAAG
6366281 TTAA-AAGTTAACATAAGAATAAAACATATATTT-TCAGTTAAAATAAGAATAAAATATACT
1 TTAATAAGTTAACATAAGAATAAAACATATATTTATCAGTTAAAATAAGAATAAAATATACT
* * * *
6366341 TT--TAAGTGAATATAAGATTAAAACATATATTTAT-A-TTAAAATAAGACTAAAATATA-T
1 TTAATAAGTTAACATAAGAATAAAACATATATTTATCAGTTAAAATAAGAATAAAATATACT
* * * *
6366398 TTAATAAGTTAAGA-AAAAATAAAATATATTTTTA
1 TTAATAAGTTAACATAAGAATAAAACATATATTTA
6366432 AAAGTTATTA
Statistics
Matches: 77, Mismatches: 10, Indels: 10
0.79 0.10 0.10
Matches are distributed among these distances:
57 3 0.04
58 36 0.47
59 35 0.45
60 3 0.04
ACGTcount: A:0.54, C:0.04, G:0.07, T:0.35
Consensus pattern (62 bp):
TTAATAAGTTAACATAAGAATAAAACATATATTTATCAGTTAAAATAAGAATAAAATATACT
Found at i:6368140 original size:20 final size:20
Alignment explanation
Indices: 6368117--6368166 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
6368107 CTAACAAGTG
*
6368117 AGTATCGATACCAAGGGTTC
1 AGTATCGATACCAAGGGGTC
* **
6368137 AGTATCAATACTGAGGGGTC
1 AGTATCGATACCAAGGGGTC
*
6368157 AATATCGATA
1 AGTATCGATA
6368167 TTGATAGGCA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.26
Consensus pattern (20 bp):
AGTATCGATACCAAGGGGTC
Found at i:6371927 original size:35 final size:35
Alignment explanation
Indices: 6371878--6371945 Score: 109
Period size: 35 Copynumber: 1.9 Consensus size: 35
6371868 AACAGTCCTT
* *
6371878 AATTTCATTATAAACCCCAAATTCCAAAATAATTC
1 AATTACATTATAAACCCCAAATTACAAAATAATTC
*
6371913 AATTACATTCTAAACCCCAAATTACAAAATAAT
1 AATTACATTATAAACCCCAAATTACAAAATAAT
6371946 CAAAATAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.29
Consensus pattern (35 bp):
AATTACATTATAAACCCCAAATTACAAAATAATTC
Found at i:6373763 original size:23 final size:23
Alignment explanation
Indices: 6373736--6373793 Score: 107
Period size: 23 Copynumber: 2.5 Consensus size: 23
6373726 TTACCAAAAG
6373736 ACAGAGATAAACGTGTCAGAAAT
1 ACAGAGATAAACGTGTCAGAAAT
6373759 ACAGAGATAAACGTGTCAGAAAT
1 ACAGAGATAAACGTGTCAGAAAT
*
6373782 ACATAGATAAAC
1 ACAGAGATAAAC
6373794 TAACATCTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.50, C:0.14, G:0.19, T:0.17
Consensus pattern (23 bp):
ACAGAGATAAACGTGTCAGAAAT
Found at i:6375233 original size:20 final size:20
Alignment explanation
Indices: 6375210--6375361 Score: 91
Period size: 20 Copynumber: 7.7 Consensus size: 20
6375200 GCTTTCTGAA
*
6375210 TTCGCAACGCAAA-TTTCTTT
1 TTCGCAACACAAATTTTC-TT
*
6375230 TTCGCAACACAAGTTTTCTT
1 TTCGCAACACAAATTTTCTT
* *
6375250 TTCGCAACA-AGATTTTCTAA
1 TTCGCAACACAAATTTTCT-T
* * *
6375270 ATCGCAACACGAATTTTGTT
1 TTCGCAACACAAATTTTCTT
* * **
6375290 TTCGCAACTC-GATTTTCAAA
1 TTCGCAACACAAATTTTC-TT
* **
6375310 TTCGCAACACGAATTTTAAT
1 TTCGCAACACAAATTTTCTT
*
6375330 TTCGCAACAGC---TTTTATT
1 TTCGCAACA-CAAATTTTCTT
6375348 TTCGCAACACAAAT
1 TTCGCAACACAAAT
6375362 GTTTTGGGTA
Statistics
Matches: 102, Mismatches: 21, Indels: 18
0.72 0.15 0.13
Matches are distributed among these distances:
17 1 0.01
18 15 0.15
19 12 0.12
20 58 0.57
21 16 0.16
ACGTcount: A:0.30, C:0.23, G:0.11, T:0.36
Consensus pattern (20 bp):
TTCGCAACACAAATTTTCTT
Found at i:6375267 original size:40 final size:39
Alignment explanation
Indices: 6375230--6375357 Score: 136
Period size: 40 Copynumber: 3.3 Consensus size: 39
6375220 AAATTTCTTT
*
6375230 TTCGCAACAC-AAGTTTTCTTTTCGCAACAAGATTTTCTAAA
1 TTCGCAACACGAA-TTTTATTTTCGCAAC-AGATTTTC-AAA
* *
6375271 -TCGCAACACGAATTTTGTTTTCGCAACTCGATTTTCAAA
1 TTCGCAACACGAATTTTATTTTCGCAAC-AGATTTTCAAA
* * **
6375310 TTCGCAACACGAATTTTAATTTCGCAACAGCTTTT-ATT
1 TTCGCAACACGAATTTTATTTTCGCAACAGATTTTCAAA
6375348 TTCGCAACAC
1 TTCGCAACAC
6375358 AAATGTTTTG
Statistics
Matches: 76, Mismatches: 9, Indels: 7
0.83 0.10 0.08
Matches are distributed among these distances:
38 11 0.14
39 8 0.11
40 55 0.72
41 2 0.03
ACGTcount: A:0.30, C:0.23, G:0.11, T:0.36
Consensus pattern (39 bp):
TTCGCAACACGAATTTTATTTTCGCAACAGATTTTCAAA
Found at i:6375515 original size:15 final size:16
Alignment explanation
Indices: 6375495--6375532 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
6375485 TCCCCATCTC
6375495 TAATTTTATTT-TACA
1 TAATTTTATTTCTACA
*
6375510 TAATTTTATTTCTATA
1 TAATTTTATTTCTACA
6375526 TAATTTT
1 TAATTTT
6375533 TCAATGATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 11 0.52
16 10 0.48
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (16 bp):
TAATTTTATTTCTACA
Found at i:6378609 original size:18 final size:18
Alignment explanation
Indices: 6378586--6378621 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
6378576 AAGCAAAAGG
*
6378586 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
6378604 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
6378622 CAACTGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:6378909 original size:20 final size:20
Alignment explanation
Indices: 6378823--6378951 Score: 111
Period size: 20 Copynumber: 6.5 Consensus size: 20
6378813 GTTTTCCTTG
6378823 AATTCGCAACGC-AAAAGTCA
1 AATTCGCAACGCGAAAA-TCA
* *** *
6378843 AATTTGCGTTGCGAAAGTCA
1 AATTCGCAACGCGAAAATCA
* *
6378863 AATTCG-AATTGCGAAAGTCA
1 AATTCGCAA-CGCGAAAATCA
6378883 AATTCGCAACGCGAAAATCA
1 AATTCGCAACGCGAAAATCA
* *
6378903 AATTCGCAACACGAAAATCG
1 AATTCGCAACGCGAAAATCA
*
6378923 AATTCG-ACACGCGAAAATAA
1 AATTCGCA-ACGCGAAAATCA
*
6378943 AAATCGCAA
1 AATTCGCAA
6378952 TGAAAATTTG
Statistics
Matches: 88, Mismatches: 16, Indels: 10
0.77 0.14 0.09
Matches are distributed among these distances:
19 1 0.01
20 81 0.92
21 6 0.07
ACGTcount: A:0.43, C:0.21, G:0.17, T:0.19
Consensus pattern (20 bp):
AATTCGCAACGCGAAAATCA
Found at i:6381077 original size:42 final size:42
Alignment explanation
Indices: 6381018--6381115 Score: 169
Period size: 42 Copynumber: 2.3 Consensus size: 42
6381008 GTGATGGAAT
* * *
6381018 AGGTGATGGCTCTCGGTGTGGAGGTGTATAATCGGCTCGATC
1 AGGTGATGGCTCTCGGTGTCGAGCTGTAGAATCGGCTCGATC
6381060 AGGTGATGGCTCTCGGTGTCGAGCTGTAGAATCGGCTCGATC
1 AGGTGATGGCTCTCGGTGTCGAGCTGTAGAATCGGCTCGATC
6381102 AGGTGATGGCTCTC
1 AGGTGATGGCTCTC
6381116 AAAGTGGAGG
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 53 1.00
ACGTcount: A:0.16, C:0.19, G:0.37, T:0.28
Consensus pattern (42 bp):
AGGTGATGGCTCTCGGTGTCGAGCTGTAGAATCGGCTCGATC
Found at i:6382636 original size:20 final size:20
Alignment explanation
Indices: 6382613--6382688 Score: 100
Period size: 20 Copynumber: 3.9 Consensus size: 20
6382603 TTTGAAACTT
*
6382613 AAATTCGCAACATGAAAATG
1 AAATTCGCAACGTGAAAATG
* *
6382633 AAATTCACAACGCGAAAAT-
1 AAATTCGCAACGTGAAAATG
*
6382652 AAAATCGCAACGTGAAAATG
1 AAATTCGCAACGTGAAAATG
*
6382672 AAATTCGCAACGCGAAA
1 AAATTCGCAACGTGAAA
6382689 CTAAAATCGC
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
19 16 0.34
20 31 0.66
ACGTcount: A:0.50, C:0.18, G:0.16, T:0.16
Consensus pattern (20 bp):
AAATTCGCAACGTGAAAATG
Found at i:6382706 original size:39 final size:39
Alignment explanation
Indices: 6382612--6382698 Score: 138
Period size: 39 Copynumber: 2.2 Consensus size: 39
6382602 TTTTGAAACT
* *
6382612 TAAATTCGCAACATGAAAATGAAATTCACAACGCGAAAA
1 TAAAATCGCAACGTGAAAATGAAATTCACAACGCGAAAA
* *
6382651 TAAAATCGCAACGTGAAAATGAAATTCGCAACGCGAAAC
1 TAAAATCGCAACGTGAAAATGAAATTCACAACGCGAAAA
6382690 TAAAATCGC
1 TAAAATCGC
6382699 GTTGTGAATT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.48, C:0.20, G:0.15, T:0.17
Consensus pattern (39 bp):
TAAAATCGCAACGTGAAAATGAAATTCACAACGCGAAAA
Found at i:6382748 original size:20 final size:20
Alignment explanation
Indices: 6382725--6382763 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
6382715 TCGCGTTGCG
*
6382725 ATTTTCGTGTCGCGAATTTT
1 ATTTTCGTATCGCGAATTTT
*
6382745 ATTTTCGTATTGCGAATTT
1 ATTTTCGTATCGCGAATTT
6382764 ACGTTTAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.13, G:0.18, T:0.51
Consensus pattern (20 bp):
ATTTTCGTATCGCGAATTTT
Found at i:6383337 original size:20 final size:20
Alignment explanation
Indices: 6383314--6383401 Score: 104
Period size: 20 Copynumber: 4.3 Consensus size: 20
6383304 TGAATTCTGT
6383314 GTTGCGATTTATAAATTCGC
1 GTTGCGATTTATAAATTCGC
6383334 GTTGCGATTTATAAATTCGC
1 GTTGCGATTTATAAATTCGC
* * *
6383354 GTTGCGAATTACAGATTCGC
1 GTTGCGATTTATAAATTCGC
* * * *
6383374 GTTACGAATTTAGAAAATCAC
1 GTTGCG-ATTTATAAATTCGC
6383395 GTTGCGA
1 GTTGCGA
6383402 AAAAGAAATT
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
20 43 0.75
21 14 0.25
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.34
Consensus pattern (20 bp):
GTTGCGATTTATAAATTCGC
Found at i:6383358 original size:40 final size:41
Alignment explanation
Indices: 6383314--6383472 Score: 117
Period size: 41 Copynumber: 3.9 Consensus size: 41
6383304 TGAATTCTGT
* * * * * *
6383314 GTTGCGATTTATAAATTCGCGTTGCG-ATTTATAAATTCGC
1 GTTGCGAATTACAAATTCGCGTTACGAATTTAGAAAATCAC
*
6383354 GTTGCGAATTACAGATTCGCGTTACGAATTTAGAAAATCAC
1 GTTGCGAATTACAAATTCGCGTTACGAATTTAGAAAATCAC
** * * * * *
6383395 GTTGCGAAAAAGAAATTCGAGTTGCGAATTTCA-AAACTGA-
1 GTTGCGAATTACAAATTCGCGTTACGAATTT-AGAAAATCAC
* * *
6383435 GTTGTGAATATGAGAAATTCGCGTTACGAATTTGGAAA
1 GTTGCGAAT-T-ACAAATTCGCGTTACGAATTTAGAAA
6383473 TTATGTTACG
Statistics
Matches: 93, Mismatches: 21, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
40 29 0.31
41 41 0.44
42 23 0.25
ACGTcount: A:0.33, C:0.13, G:0.22, T:0.31
Consensus pattern (41 bp):
GTTGCGAATTACAAATTCGCGTTACGAATTTAGAAAATCAC
Found at i:6383629 original size:13 final size:14
Alignment explanation
Indices: 6383611--6383640 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
6383601 ATTTTCTCAA
6383611 AAAAAATAAAA-AT
1 AAAAAATAAAACAT
6383624 AAAAAATAAAACAT
1 AAAAAATAAAACAT
6383638 AAA
1 AAA
6383641 CGCTTCTCCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.83, C:0.03, G:0.00, T:0.13
Consensus pattern (14 bp):
AAAAAATAAAACAT
Found at i:6386526 original size:14 final size:16
Alignment explanation
Indices: 6386495--6386534 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
6386485 AAAGGGGAAG
6386495 AAATGTAAAATGCTAA
1 AAATGTAAAATGCTAA
*
6386511 AAAT-TAAATTGC-AA
1 AAATGTAAAATGCTAA
6386525 AAATGTAAAA
1 AAATGTAAAA
6386535 ATAGAAAACT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
14 6 0.29
15 11 0.52
16 4 0.19
ACGTcount: A:0.60, C:0.05, G:0.10, T:0.25
Consensus pattern (16 bp):
AAATGTAAAATGCTAA
Found at i:6386571 original size:31 final size:29
Alignment explanation
Indices: 6386510--6386617 Score: 105
Period size: 31 Copynumber: 3.6 Consensus size: 29
6386500 TAAAATGCTA
* *
6386510 AAAATTAAATTGCAAAAATGT-AAAAATAG
1 AAAA-TAAAGTGCATAAATGTAAAAAATAG
*
6386539 AAAACTAAAG-GGATGAAATGTAAACAAATAG
1 AAAA-TAAAGTGCAT-AAATGTAAA-AAATAG
6386570 AAATATAAAGTGCATAAATGTAAATAAAT-G
1 AAA-ATAAAGTGCATAAATGTAAA-AAATAG
6386600 AAAAATAAAGTGCATAAA
1 -AAAATAAAGTGCATAAA
6386618 CATAAATAAC
Statistics
Matches: 67, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
28 2 0.03
29 14 0.21
30 17 0.25
31 30 0.45
32 4 0.06
ACGTcount: A:0.60, C:0.05, G:0.14, T:0.21
Consensus pattern (29 bp):
AAAATAAAGTGCATAAATGTAAAAAATAG
Found at i:6386610 original size:30 final size:31
Alignment explanation
Indices: 6386509--6386626 Score: 118
Period size: 30 Copynumber: 3.9 Consensus size: 31
6386499 GTAAAATGCT
* *
6386509 AAAAATTAAATTGCAAAAATGT-AA-AAATAG
1 AAAAA-TAAAGTGCATAAATGTAAATAAATAG
* * *
6386539 AAAACTAAAG-GGATGAAATGTAAACAAATAG
1 AAAAATAAAGTGCAT-AAATGTAAATAAATAG
*
6386570 AAATATAAAGTGCATAAATGTAAATAAAT-G
1 AAAAATAAAGTGCATAAATGTAAATAAATAG
**
6386600 AAAAATAAAGTGCATAAACATAAATAA
1 AAAAATAAAGTGCATAAATGTAAATAA
6386627 CATAAATGTA
Statistics
Matches: 73, Mismatches: 11, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
28 2 0.03
29 10 0.14
30 31 0.42
31 27 0.37
32 3 0.04
ACGTcount: A:0.61, C:0.05, G:0.13, T:0.21
Consensus pattern (31 bp):
AAAAATAAAGTGCATAAATGTAAATAAATAG
Found at i:6399301 original size:23 final size:21
Alignment explanation
Indices: 6399258--6399309 Score: 59
Period size: 23 Copynumber: 2.4 Consensus size: 21
6399248 GTACGTGGTT
*
6399258 CTTCGGGATATATATGTGGTC
1 CTTCGGGATATATATGAGGTC
*
6399279 CTTCGGGATAATTCTATGAGGTC
1 CTTCGGGAT-A-TATATGAGGTC
*
6399302 GTTCGGGA
1 CTTCGGGA
6399310 CATTTTATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 9 0.35
22 1 0.04
23 16 0.62
ACGTcount: A:0.19, C:0.15, G:0.31, T:0.35
Consensus pattern (21 bp):
CTTCGGGATATATATGAGGTC
Found at i:6400565 original size:23 final size:24
Alignment explanation
Indices: 6400523--6400597 Score: 75
Period size: 23 Copynumber: 3.2 Consensus size: 24
6400513 GAGTCGAGGG
* *
6400523 TTCTAC-GTGGTCCTTTGGGACAT
1 TTCTACTGCGGTCCTTCGGGACAT
* *
6400546 TTCTACT-CGGTTCTTCGGGACAA
1 TTCTACTGCGGTCCTTCGGGACAT
* *
6400569 TTCTA-TGTGGTCCTTTGGGACAT
1 TTCTACTGCGGTCCTTCGGGACAT
6400592 TTCTAC
1 TTCTAC
6400598 ATGGCACTTC
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
22 1 0.02
23 40 0.98
ACGTcount: A:0.15, C:0.23, G:0.23, T:0.40
Consensus pattern (24 bp):
TTCTACTGCGGTCCTTCGGGACAT
Found at i:6402084 original size:39 final size:39
Alignment explanation
Indices: 6401960--6402095 Score: 191
Period size: 39 Copynumber: 3.5 Consensus size: 39
6401950 AGCCAAGGTT
* *
6401960 GAACAAGTTATTCTCATTAGGAACTTCTTCTCCCTCATC
1 GAACGAGTTCTTCTCATTAGGAACTTCTTCTCCCTCATC
** *
6401999 GAAAAAGTTCTTCTGATTAGGAACTTCTTCTCCCTCATC
1 GAACGAGTTCTTCTCATTAGGAACTTCTTCTCCCTCATC
*
6402038 GAACGAGTTCTTCTCATTAGGAACTTCTTCTCCCTCGTC
1 GAACGAGTTCTTCTCATTAGGAACTTCTTCTCCCTCATC
** *
6402077 GGGCGAGTTCTTGTCATTA
1 GAACGAGTTCTTCTCATTA
6402096 TGGACTCTCT
Statistics
Matches: 87, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 87 1.00
ACGTcount: A:0.22, C:0.26, G:0.15, T:0.36
Consensus pattern (39 bp):
GAACGAGTTCTTCTCATTAGGAACTTCTTCTCCCTCATC
Found at i:6406366 original size:14 final size:14
Alignment explanation
Indices: 6406347--6406381 Score: 61
Period size: 14 Copynumber: 2.4 Consensus size: 14
6406337 ATCGAGGCAA
6406347 CAACAACCCCTATT
1 CAACAACCCCTATT
6406361 CAACAACCCCTATT
1 CAACAACCCCTATT
6406375 CTAACAA
1 C-AACAA
6406382 TCTTGGATGG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 15 0.75
15 5 0.25
ACGTcount: A:0.40, C:0.40, G:0.00, T:0.20
Consensus pattern (14 bp):
CAACAACCCCTATT
Found at i:6408313 original size:8 final size:9
Alignment explanation
Indices: 6408298--6408331 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
6408288 AAAAACCCAC
6408298 TAAAAAAAT
1 TAAAAAAAT
6408307 TAAAAAAAT
1 TAAAAAAAT
*
6408316 TGAAAAAAT
1 TAAAAAAAT
*
6408325 GAAAAAA
1 TAAAAAA
6408332 TGAAGTTGTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.18
Consensus pattern (9 bp):
TAAAAAAAT
Found at i:6413833 original size:20 final size:21
Alignment explanation
Indices: 6413808--6413856 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
6413798 ACTTAAGGAT
* *
6413808 ATTTTTAACCGCAACCCAGTG
1 ATTTTCAACCGCAACCCAATG
*
6413829 ATTTTCACCCGCAACCCAATG
1 ATTTTCAACCGCAACCCAATG
6413850 ATTTTCA
1 ATTTTCA
6413857 CCAGGGTTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.29, C:0.31, G:0.10, T:0.31
Consensus pattern (21 bp):
ATTTTCAACCGCAACCCAATG
Found at i:6413857 original size:21 final size:21
Alignment explanation
Indices: 6413816--6413858 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
6413806 ATATTTTTAA
*
6413816 CCGCAACCCAGTGATTTTCAC
1 CCGCAACCCAATGATTTTCAC
6413837 CCGCAACCCAATGATTTTCAC
1 CCGCAACCCAATGATTTTCAC
6413858 C
1 C
6413859 AGGGTTTGCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.26, C:0.40, G:0.12, T:0.23
Consensus pattern (21 bp):
CCGCAACCCAATGATTTTCAC
Found at i:6415676 original size:23 final size:23
Alignment explanation
Indices: 6415646--6415710 Score: 112
Period size: 23 Copynumber: 2.8 Consensus size: 23
6415636 AAGCACAGTT
**
6415646 AGGTATTTAGTCTTTCATCCCTA
1 AGGTATTTAACCTTTCATCCCTA
6415669 AGGTATTTAACCTTTCATCCCTA
1 AGGTATTTAACCTTTCATCCCTA
6415692 AGGTATTTAACCTTTCATC
1 AGGTATTTAACCTTTCATC
6415711 TAACTTGCAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.25, C:0.23, G:0.11, T:0.42
Consensus pattern (23 bp):
AGGTATTTAACCTTTCATCCCTA
Found at i:6415826 original size:81 final size:80
Alignment explanation
Indices: 6415691--6416656 Score: 1346
Period size: 81 Copynumber: 11.9 Consensus size: 80
6415681 TTTCATCCCT
* *
6415691 AAGGTATTTAACCTTTCATCTAACTTGCATGATTGACACATTTTTGTCAAATGCACAGTGAGGCA
1 AAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACATTTCTGTCAAATGCACAGT-AGGCA
6415756 TTTAATCTTTTACTCA
65 TTTAATCTTTTACTCA
* * *
6415772 AAGGTATTTAATCTTTTATCTAACTGGCATGATTGACATC-TTTCTGTCAAATGCACAACTAGGC
1 AAGGTATTTAACCTTTCATCTAACTGGCATGATTGACA-CATTTCTGTCAAATGCAC-AGTAGGC
6415836 ATTTAATCTTTTACTCA
64 ATTTAATCTTTTACTCA
* * * *
6415853 AAGGTATTTAACCTTTCATCTAACTAGCATGATTAACAC-TTTCTGTCAAATGCACAACTATGCA
1 AAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACATTTCTGTCAAATGCAC-AGTAGGCA
6415917 TTTAATCTTTTACTCA
65 TTTAATCTTTTACTCA
*
6415933 AAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGCTAGGCA
1 AAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACATTTCTGTCAAATGCACAG-TAGGCA
6415998 TTTAATCTTTTACTCA
65 TTTAATCTTTTACTCA
* * * * * *
6416014 AGGGTAGTTACCCTTTCATCTAACTGGCATGATTGACACCTTTATGTCAAATGCACACCTAGGCA
1 AAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACATTTCTGTCAAATGCACA-GTAGGCA
6416079 TTTAATCTTTTACTCA
65 TTTAATCTTTTACTCA
* * * *
6416095 AAGATATTTAACTTTTCATCTAACTGTCATGATTGACACATTTCTGTCAAATACACAGCTAGGCA
1 AAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACATTTCTGTCAAATGCACAG-TAGGCA
*
6416160 TATAATCTTTTACTCA
65 TTTAATCTTTTACTCA
* * * * * *
6416176 AAGGTATTTAACCTTTCATTTAACTGGCATGATTGACACTTTTATGTCAAATGTACAACTAGACA
1 AAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACATTTCTGTCAAATGCAC-AGTAGGCA
6416241 TTTAATCTTTTACTCA
65 TTTAATCTTTTACTCA
* * *
6416257 AAAGTATTTAACCTTTTATCTAATTGGCATGATTGACATC-TTTCTGTCAAATGCACAGCTAGGC
1 AAGGTATTTAACCTTTCATCTAACTGGCATGATTGACA-CATTTCTGTCAAATGCACAG-TAGGC
*
6416321 ATTTAATATTTTACTCA
64 ATTTAATCTTTTACTCA
* *
6416338 AAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACATTTCTGTCAAATGCACCGCTAAGCA
1 AAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACATTTCTGTCAAATGCACAG-TAGGCA
6416403 TTTAA-CTTTTACTCA
65 TTTAATCTTTTACTCA
* * *
6416418 AAGGTATTGAACCTTTCATCTAACTGGCATGATTGACACATTTCTATCAAATGCACAACTAGGCA
1 AAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACATTTCTGTCAAATGCAC-AGTAGGCA
*
6416483 TTTAATCTTTTACGCA
65 TTTAATCTTTTACTCA
* *
6416499 AAGGTATTTAACCTTTCATCTAACTGCCATGATTGACACATTTCTGTCAAATGCACAATTAGGCA
1 AAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACATTTCTGTCAAATGCAC-AGTAGGCA
6416564 TTTAATCTTTTACTCA
65 TTTAATCTTTTACTCA
* * * * * * * *
6416580 AAGGTATTTAACCTTTAATCTAACTGGCATTATTGAAACCTTTTTGTAAAATGCATAGCTAGACA
1 AAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACATTTCTGTCAAATGCACAG-TAGGCA
*
6416645 TTTAGTCTTTTA
65 TTTAATCTTTTA
6416657 TTTTAAAATA
Statistics
Matches: 794, Mismatches: 78, Indels: 26
0.88 0.09 0.03
Matches are distributed among these distances:
80 155 0.20
81 634 0.80
82 5 0.01
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (80 bp):
AAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACATTTCTGTCAAATGCACAGTAGGCAT
TTAATCTTTTACTCA
Found at i:6416603 original size:485 final size:485
Alignment explanation
Indices: 6415691--6416656 Score: 1506
Period size: 485 Copynumber: 2.0 Consensus size: 485
6415681 TTTCATCCCT
* * *
6415691 AAGGTATTTAACCTTTCATCTAACTTGCATGATTGACACATTTTTGTCAAATGCACAGTGAGGCA
1 AAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACATTTTTGTCAAATGCACACTGAGACA
* *
6415756 TTTAATCTTTTACTCAAAGGTATTTAATCTTTTATCTAACTGGCATGATTGACATCTTTCTGTCA
66 TTTAATCTTTTACTCAAAAGTATTTAACCTTTTATCTAACTGGCATGATTGACATCTTTCTGTCA
*
6415821 AATGCACAACTAGGCATTTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTAGCATGAT
131 AATGCACAACTAGGCATTTAATATTTTACTCAAAGGTATTTAACCTTTCATCTAACTAGCATGAT
* *
6415886 TAACACTTTCTGTCAAATGCACAACTATGCATTTAATCTTTTACTCAAAGGTATTTAACCTTTCA
196 TAACACTTTCTGTCAAATGCACAACTAAGCATTTAATCTTTTACTCAAAGGTATTGAACCTTTCA
* * * * *
6415951 TCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGCTAGGCATTTAATCTTTTACTCAAG
261 TCTAACTGGCATGATTGACACATTTCTATCAAATGCACAACTAGGCATTTAATCTTTTACGCAAA
* * * *
6416016 GGTAGTTACCCTTTCATCTAACTGGCATGATTGACACCTTTATGTCAAATGCACACCTAGGCATT
326 GGTAGTTAACCTTTCATCTAACTGCCATGATTGACACATTTATGTCAAATGCACAACTAGGCATT
* * * * *
6416081 TAATCTTTTACTCAAAGATATTTAACTTTTCATCTAACTGTCATGATTGACACATTTCTGTCAAA
391 TAATCTTTTACTCAAAGATATTTAACCTTTAATCTAACTGGCATGATTGAAACATTTCTGTAAAA
*
6416146 TACACAGCTAGGCATATAATCTTTTACTCA
456 TACACAGCTAGACATATAATCTTTTACTCA
* *
6416176 AAGGTATTTAACCTTTCATTTAACTGGCATGATTGACAC-TTTTATGTCAAATGTACAACT-AGA
1 AAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACATTTT-TGTCAAATGCAC-ACTGAGA
*
6416239 CATTTAATCTTTTACTCAAAAGTATTTAACCTTTTATCTAATTGGCATGATTGACATCTTTCTGT
64 CATTTAATCTTTTACTCAAAAGTATTTAACCTTTTATCTAACTGGCATGATTGACATCTTTCTGT
* *
6416304 CAAATGCACAGCTAGGCATTTAATATTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATG
129 CAAATGCACAACTAGGCATTTAATATTTTACTCAAAGGTATTTAACCTTTCATCTAACTAGCATG
* **
6416369 ATTGACACATTTCTGTCAAATGCACCGCTAAGCATTTAA-CTTTTACTCAAAGGTATTGAACCTT
194 ATTAACAC-TTTCTGTCAAATGCACAACTAAGCATTTAATCTTTTACTCAAAGGTATTGAACCTT
6416433 TCATCTAACTGGCATGATTGACACATTTCTATCAAATGCACAACTAGGCATTTAATCTTTTACGC
258 TCATCTAACTGGCATGATTGACACATTTCTATCAAATGCACAACTAGGCATTTAATCTTTTACGC
* * *
6416498 AAAGGTATTTAACCTTTCATCTAACTGCCATGATTGACACATTTCTGTCAAATGCACAATTAGGC
323 AAAGGTAGTTAACCTTTCATCTAACTGCCATGATTGACACATTTATGTCAAATGCACAACTAGGC
* * * *
6416563 ATTTAATCTTTTACTCAAAGGTATTTAACCTTTAATCTAACTGGCATTATTGAAACCTTTTTGTA
388 ATTTAATCTTTTACTCAAAGATATTTAACCTTTAATCTAACTGGCATGATTGAAACATTTCTGTA
* * * *
6416628 AAATGCATAGCTAGACATTTAGTCTTTTA
453 AAATACACAGCTAGACATATAATCTTTTA
6416657 TTTTAAAATA
Statistics
Matches: 436, Mismatches: 42, Indels: 6
0.90 0.09 0.01
Matches are distributed among these distances:
484 4 0.01
485 403 0.92
486 29 0.07
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (485 bp):
AAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACATTTTTGTCAAATGCACACTGAGACA
TTTAATCTTTTACTCAAAAGTATTTAACCTTTTATCTAACTGGCATGATTGACATCTTTCTGTCA
AATGCACAACTAGGCATTTAATATTTTACTCAAAGGTATTTAACCTTTCATCTAACTAGCATGAT
TAACACTTTCTGTCAAATGCACAACTAAGCATTTAATCTTTTACTCAAAGGTATTGAACCTTTCA
TCTAACTGGCATGATTGACACATTTCTATCAAATGCACAACTAGGCATTTAATCTTTTACGCAAA
GGTAGTTAACCTTTCATCTAACTGCCATGATTGACACATTTATGTCAAATGCACAACTAGGCATT
TAATCTTTTACTCAAAGATATTTAACCTTTAATCTAACTGGCATGATTGAAACATTTCTGTAAAA
TACACAGCTAGACATATAATCTTTTACTCA
Found at i:6416634 original size:242 final size:243
Alignment explanation
Indices: 6415691--6416656 Score: 1431
Period size: 242 Copynumber: 4.0 Consensus size: 243
6415681 TTTCATCCCT
* * *
6415691 AAGGTATTTAACCTTTCATCTAACTTGCATGATTGACACATTTTTGTCAAATGCAC-AGTGAGGC
1 AAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACATTTCTGTCAAATGCACAACT-AGGC
* *
6415755 ATTTAATCTTTTACTCAAAGGTATTTAATCTTTTATCTAACTGGCATGATTGACATCTTTCTGTC
65 ATTTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACATCTTTCTGTC
*
6415820 AAATGCACAACTAGGCATTTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTAGCATGA
130 AAATGCACAACTAGGCATTTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGA
* *
6415885 TT--AACACTTTCTGTCAAATGCACAACTATGCATTTAATCTTTTACTCA
195 TTGAAACA-TTTCTGTCAAATGCACAGCTAAGCATTTAATCTTTTACTCA
* *
6415933 AAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGCTAGGCA
1 AAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACATTTCTGTCAAATGCACAACTAGGCA
* * * * *
6415998 TTTAATCTTTTACTCAAGGGTAGTTACCCTTTCATCTAACTGGCATGATTGACACCTTTATGTCA
66 TTTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACATCTTTCTGTCA
* * * *
6416063 AATGCACACCTAGGCATTTAATCTTTTACTCAAAGATATTTAACTTTTCATCTAACTGTCATGAT
131 AATGCACAACTAGGCATTTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGAT
* * * *
6416128 TGACACATTTCTGTCAAATACACAGCTAGGCATATAATCTTTTACTCA
196 TGAAACATTTCTGTCAAATGCACAGCTAAGCATTTAATCTTTTACTCA
* * * * *
6416176 AAGGTATTTAACCTTTCATTTAACTGGCATGATTGACACTTTTATGTCAAATGTACAACTAGACA
1 AAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACATTTCTGTCAAATGCACAACTAGGCA
* * *
6416241 TTTAATCTTTTACTCAAAAGTATTTAACCTTTTATCTAATTGGCATGATTGACATCTTTCTGTCA
66 TTTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACATCTTTCTGTCA
* *
6416306 AATGCACAGCTAGGCATTTAATATTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGAT
131 AATGCACAACTAGGCATTTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGAT
* *
6416371 TGACACATTTCTGTCAAATGCACCGCTAAGCATTTAA-CTTTTACTCA
196 TGAAACATTTCTGTCAAATGCACAGCTAAGCATTTAATCTTTTACTCA
* *
6416418 AAGGTATTGAACCTTTCATCTAACTGGCATGATTGACACATTTCTATCAAATGCACAACTAGGCA
1 AAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACATTTCTGTCAAATGCACAACTAGGCA
* *
6416483 TTTAATCTTTTACGCAAAGGTATTTAACCTTTCATCTAACTGCCATGATTGACA-CATTTCTGTC
66 TTTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACATC-TTTCTGTC
* * *
6416547 AAATGCACAATTAGGCATTTAATCTTTTACTCAAAGGTATTTAACCTTTAATCTAACTGGCATTA
130 AAATGCACAACTAGGCATTTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGA
* * * * *
6416612 TTGAAACCTTTTTGTAAAATGCATAGCT-AGACATTTAGTCTTTTA
195 TTGAAACATTTCTGTCAAATGCACAGCTAAG-CATTTAATCTTTTA
6416657 TTTTAAAATA
Statistics
Matches: 649, Mismatches: 69, Indels: 11
0.89 0.09 0.02
Matches are distributed among these distances:
241 3 0.00
242 390 0.60
243 253 0.39
244 3 0.00
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (243 bp):
AAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACATTTCTGTCAAATGCACAACTAGGCA
TTTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACATCTTTCTGTCA
AATGCACAACTAGGCATTTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGAT
TGAAACATTTCTGTCAAATGCACAGCTAAGCATTTAATCTTTTACTCA
Found at i:6422439 original size:23 final size:23
Alignment explanation
Indices: 6422413--6422502 Score: 144
Period size: 23 Copynumber: 3.9 Consensus size: 23
6422403 TGCCGCATAA
*
6422413 TTGTCACGAAGGACCACATAGGT
1 TTGTCCCGAAGGACCACATAGGT
6422436 TTGTCCCGAAGGACCACATAGGT
1 TTGTCCCGAAGGACCACATAGGT
**
6422459 TTGTCCCGAAGGACCACATAATT
1 TTGTCCCGAAGGACCACATAGGT
*
6422482 TTGTCCCGAAGAACCACATAG
1 TTGTCCCGAAGGACCACATAG
6422503 AACCCTTAAC
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 62 1.00
ACGTcount: A:0.30, C:0.26, G:0.22, T:0.22
Consensus pattern (23 bp):
TTGTCCCGAAGGACCACATAGGT
Found at i:6429405 original size:30 final size:30
Alignment explanation
Indices: 6429369--6429430 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
6429359 CCCGCAGGAC
* *
6429369 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTAATAAAGATCCTCAGTAA
6429399 CTATCCAGAGGTAATAAAGATCCTCAGTAA
1 CTATCCAGAGGTAATAAAGATCCTCAGTAA
6429429 CT
1 CT
6429431 GTTCATAGGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (30 bp):
CTATCCAGAGGTAATAAAGATCCTCAGTAA
Found at i:6430617 original size:64 final size:62
Alignment explanation
Indices: 6430484--6430641 Score: 183
Period size: 64 Copynumber: 2.5 Consensus size: 62
6430474 TAATGAAGGT
* * *
6430484 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTGTATTTAATGGGG
1 ATGCATCGATGCACT-C-CTATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAAT-GGA
* *
6430549 ATGCATCGATGCACTCCTTATGCATCGATGCATAAATCCTATTCGATGTTTTCTTTTTAAAT-TA
1 ATGCATCGATGCACTCC-TATGCATCGATGCATAAATCCTATTCGATG-TTTCTATTT-AATGGA
* *
6430613 ATGCATCGATGCACTGCATGTGCATCGAT
1 ATGCATCGATGCACT-CCTATGCATCGAT
6430642 ACACCTTAAA
Statistics
Matches: 82, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
63 1 0.01
64 55 0.67
65 23 0.28
66 3 0.04
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.35
Consensus pattern (62 bp):
ATGCATCGATGCACTCCTATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAATGGA
Found at i:6435708 original size:32 final size:32
Alignment explanation
Indices: 6435637--6435696 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
6435627 TATTCTTTCA
* *
6435637 CAATAACAAATTGTAACAAAATTATTTAGTCT
1 CAATAAAAAATTATAACAAAATTATTTAGTCT
*
6435669 CAGTAAAAAATTATAA-AAAA-TATTTAGT
1 CAATAAAAAATTATAACAAAATTATTTAGT
6435697 GTCGAAATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 8 0.32
31 4 0.16
32 13 0.52
ACGTcount: A:0.52, C:0.08, G:0.07, T:0.33
Consensus pattern (32 bp):
CAATAAAAAATTATAACAAAATTATTTAGTCT
Found at i:6444483 original size:20 final size:21
Alignment explanation
Indices: 6444446--6444484 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
6444436 TTATAATGAA
*
6444446 AAATTACAAGGACTTAATTAC
1 AAATTAAAAGGACTTAATTAC
6444467 AAATTAAAAGG-CTTAATT
1 AAATTAAAAGGACTTAATT
6444485 TGAAGATTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.49, C:0.10, G:0.10, T:0.31
Consensus pattern (21 bp):
AAATTAAAAGGACTTAATTAC
Found at i:6445841 original size:226 final size:225
Alignment explanation
Indices: 6445434--6446044 Score: 904
Period size: 226 Copynumber: 2.7 Consensus size: 225
6445424 TAACATAACC
* * * *
6445434 GGTTAATTACTGGAAACATTATCAACCATAATAACATAACAGGTAGCGTTTATGTAACGTAATAT
1 GGTTAATTACTGGAAACATTATCAACCATAATAACATAACAAGTAGCGTTTATTTAATGTAATAG
* * *
6445499 GTAGCGCCT-TATTAAAGCTAATGGGTCCTTACAAATTCGATGATAACAAAATAGGTTAATTACT
66 GTAGCGCCTGT-TTAAAGCTAATGGGGCCTTAGAAATTCGACGATAACAAAATAGGTTAATTACT
* * * * *
6445563 TGATTTGTTATTAATATTATCAACATATTAGGTAGCGCCTAAAATTTTACCAAAGTTTAAGCTGA
130 TGATTTGTTATCAATATTATCAAAATATTAGGTAGCACCTAAAATGTTACCAAAGTTTAAGCTAA
6445628 TGGAGCCTTAGAAATCC-GACGATAACAAAATA
195 TGGAGCCTTAGAAA-CCAGA-GATAACAAAATA
* * * * *
6445660 TGTTAGTTACTGGAAACATTATCAACCATAATAAAATAACAAGTAACGGTTATTTAATGTAATAG
1 GGTTAATTACTGGAAACATTATCAACCATAATAACATAACAAGTAGCGTTTATTTAATGTAATAG
* * * * *
6445725 GTAGCGCATGTTTAAAACTGATGGGGCCTTAGAAA-TCTAACAATAACAAAATAGGTTAATTACT
66 GTAGCGCCTGTTTAAAGCTAATGGGGCCTTAGAAATTC-GACGATAACAAAATAGGTTAATTACT
6445789 TGATTTGTTATCAATATTATCAAAATATTAGGTAGCACCTAAAATGTTACCAAAGTTTAAGCTAA
130 TGATTTGTTATCAATATTATCAAAATATTAGGTAGCACCTAAAATGTTACCAAAGTTTAAGCTAA
*
6445854 TGGAGCCTTAGAAACCTAGAGATAACCAAATA
195 TGGAGCCTTAGAAACC-AGAGATAACAAAATA
*
6445886 GGTTAATTACTGAAAACATTATCAACCATAATAACATAACAAGTAGCGTTTATTTAATGTAATAG
1 GGTTAATTACTGGAAACATTATCAACCATAATAACATAACAAGTAGCGTTTATTTAATGTAATAG
* *
6445951 GTAGCGCCTGTTTAAAGCTAATGGAGCCTTAGAAATTCGACGATAACAAAAAAGGTTAATTACTT
66 GTAGCGCCTGTTTAAAGCTAATGGGGCCTTAGAAATTCGACGATAACAAAATAGGTTAATTACTT
* *
6446016 GATTTGTTTTCAATATTATCAATATATTA
131 GATTTGTTATCAATATTATCAAAATATTA
6446045 CCGTGTACAT
Statistics
Matches: 342, Mismatches: 38, Indels: 10
0.88 0.10 0.03
Matches are distributed among these distances:
225 4 0.01
226 333 0.97
227 5 0.01
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.32
Consensus pattern (225 bp):
GGTTAATTACTGGAAACATTATCAACCATAATAACATAACAAGTAGCGTTTATTTAATGTAATAG
GTAGCGCCTGTTTAAAGCTAATGGGGCCTTAGAAATTCGACGATAACAAAATAGGTTAATTACTT
GATTTGTTATCAATATTATCAAAATATTAGGTAGCACCTAAAATGTTACCAAAGTTTAAGCTAAT
GGAGCCTTAGAAACCAGAGATAACAAAATA
Found at i:6446581 original size:200 final size:199
Alignment explanation
Indices: 6446275--6446770 Score: 583
Period size: 199 Copynumber: 2.5 Consensus size: 199
6446265 ATATCGTTAT
* * * *
6446275 ACTTTTATCGTTTTCATTGTAAATTAACTTATTACTTTAAAGTAATAT-GTTTCAAAATTATAGG
1 ACTTTTATCGTTTACATTGTAAATTTACCTATTACTTTAAAGTAAT-TGGTTTCAAAATTACAGG
* * * ** * * *
6446339 TATTGATACTTTATATATGTGTATCGATGGCTTTTTCGTGCAAATTGCTTG-AGAAGCATACTGG
65 TATTGATACTTTGTACATGTGTATCGATGACTTTAGCGTGCAAATCG-TTGTA-AAACATAATGG
* * * * *
6446403 AATGAAAGTATCAATACATATATAGACAA-TATTGATACTTGGTATTTACTCCTATTATCAATAT
128 AATAAAAGTACCAATACATATATAGA-AAGTATCGATACTTGGTATATACACCTATTATCAATAT
6446467 ACCCGA-AA
192 A-CCGATAA
*
6446475 ACTTTTATCGTTTACATTGTAAATTTACCTATTACTTTAAAGTAATTGGTTTCAAAATTACGGGT
1 ACTTTTATCGTTTACATTGTAAATTTACCTATTACTTTAAAGTAATTGGTTTCAAAATTACAGGT
** *
6446540 ATTGATACTTTGTACATGTGTATTTAT-ACATTTAGCGTGCAAATCGTTGTAAAACATAATGGAC
66 ATTGATACTTTGTACATGTGTATCGATGAC-TTTAGCGTGCAAATCGTTGTAAAACATAATGGAA
* * *
6446604 TAAAAGTACCAATACCTATATATAAAGTATCGATACTTGGTATATACACCTATTATCATTATACC
130 TAAAAGTACCAATACATATATAGAAAGTATCGATACTTGGTATATACACCTATTATCAATATACC
6446669 GATAA
195 GATAA
* * * * * * *
6446674 ACTTTTACCCTTTACATTGTTAATTTACCTATTACTTTATAGTAATAGGTTTCGAAATT-CAAAG
1 ACTTTTATCGTTTACATTGTAAATTTACCTATTACTTTAAAGTAATTGGTTTCAAAATTAC-AGG
* *
6446738 TATCGATTCTTTGTACATGTGTATCGATG-CTTT
65 TATTGATACTTTGTACATGTGTATCGATGACTTT
6446771 GTACATGTGT
Statistics
Matches: 253, Mismatches: 36, Indels: 16
0.83 0.12 0.05
Matches are distributed among these distances:
198 10 0.04
199 148 0.58
200 95 0.38
ACGTcount: A:0.33, C:0.14, G:0.13, T:0.40
Consensus pattern (199 bp):
ACTTTTATCGTTTACATTGTAAATTTACCTATTACTTTAAAGTAATTGGTTTCAAAATTACAGGT
ATTGATACTTTGTACATGTGTATCGATGACTTTAGCGTGCAAATCGTTGTAAAACATAATGGAAT
AAAAGTACCAATACATATATAGAAAGTATCGATACTTGGTATATACACCTATTATCAATATACCG
ATAA
Found at i:6446763 original size:21 final size:21
Alignment explanation
Indices: 6446737--6446781 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
6446727 GAAATTCAAA
*
6446737 GTATCGATTCTTTGTACATGT
1 GTATCGATGCTTTGTACATGT
6446758 GTATCGATGCTTTGTACATGT
1 GTATCGATGCTTTGTACATGT
6446779 GTA
1 GTA
6446782 ATTGGTTTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.20, C:0.13, G:0.22, T:0.44
Consensus pattern (21 bp):
GTATCGATGCTTTGTACATGT
Found at i:6454647 original size:21 final size:21
Alignment explanation
Indices: 6454617--6454667 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
6454607 TATTGTCATG
*
6454617 TATCGATACATGTGTGTAAGC
1 TATCGATACATGTGTGAAAGC
* *
6454638 TATCGGTACATGTGTGAAAGG
1 TATCGATACATGTGTGAAAGC
6454659 TATCGATAC
1 TATCGATAC
6454668 TTTTGAGACG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.29, C:0.14, G:0.25, T:0.31
Consensus pattern (21 bp):
TATCGATACATGTGTGAAAGC
Found at i:6454823 original size:20 final size:20
Alignment explanation
Indices: 6454785--6454857 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
6454775 CTCTTTACTA
**
6454785 ATTTTGTCAAATTGAAATCG
1 ATTTTGTCAAATTTCAATCG
6454805 ATTTTGTCAAATTTCAATCG
1 ATTTTGTCAAATTTCAATCG
** * *
6454825 GCTTTGTTAATTTTCAATCG
1 ATTTTGTCAAATTTCAATCG
* *
6454845 GTTTAGTCAAATT
1 ATTTTGTCAAATT
6454858 CGTTACTTGT
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.29, C:0.12, G:0.14, T:0.45
Consensus pattern (20 bp):
ATTTTGTCAAATTTCAATCG
Found at i:6455801 original size:2 final size:2
Alignment explanation
Indices: 6455796--6455876 Score: 61
Period size: 2 Copynumber: 44.5 Consensus size: 2
6455786 TAATGGTGTG
* *
6455796 TA TA TA TA T- TA TA CA TA TA -A TA TA -A TA TG TA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
6455834 TA CA TA TA -A AA TA -A TA -A TG TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6455873 -A TA T
1 TA TA T
6455877 TTAATTTTCA
Statistics
Matches: 62, Mismatches: 9, Indels: 16
0.71 0.10 0.18
Matches are distributed among these distances:
1 8 0.13
2 54 0.87
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (2 bp):
TA
Found at i:6455828 original size:27 final size:27
Alignment explanation
Indices: 6455798--6455876 Score: 117
Period size: 27 Copynumber: 3.0 Consensus size: 27
6455788 ATGGTGTGTA
6455798 TATATATTATACATATAATATAATATG
1 TATATATTATACATATAATATAATATG
*
6455825 TATATATTATACATATAAAATAATAATG
1 TATATATTATACATATAATATAAT-ATG
*
6455853 TATATA-TATATATAT-ATATAATAT
1 TATATATTATACATATAATATAATAT
6455877 TTAATTTTCA
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
25 2 0.04
26 6 0.12
27 31 0.65
28 9 0.19
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.44
Consensus pattern (27 bp):
TATATATTATACATATAATATAATATG
Found at i:6457663 original size:18 final size:17
Alignment explanation
Indices: 6457640--6457674 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
6457630 TTAATACGAG
6457640 AATGATATAAAAAATAAT
1 AATGATA-AAAAAATAAT
*
6457658 AATGATAATAAAATAAT
1 AATGATAAAAAAATAAT
6457675 TATAAAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.29
Consensus pattern (17 bp):
AATGATAAAAAAATAAT
Found at i:6458179 original size:34 final size:34
Alignment explanation
Indices: 6458115--6458210 Score: 83
Period size: 34 Copynumber: 2.9 Consensus size: 34
6458105 ATCCAACCAT
*
6458115 ATATCTTTTAATATTCAACTTTAAATAGATAATA
1 ATATCTTTTAATATTCAAATTTAAATAGATAATA
*
6458149 ATATCTTTTAAT-TTGAAATATTCAAA-AGATAA-A
1 ATATCTTTTAATATTCAAAT-TT-AAATAGATAATA
* * ** *
6458182 CT-CCTTTTACCATTCAAACTTAAATAGAT
1 ATATCTTTTAATATTCAAATTTAAATAGAT
6458211 TTTATTTTAA
Statistics
Matches: 50, Mismatches: 8, Indels: 10
0.74 0.12 0.15
Matches are distributed among these distances:
31 3 0.06
32 12 0.24
33 12 0.24
34 20 0.40
35 3 0.06
ACGTcount: A:0.43, C:0.12, G:0.04, T:0.41
Consensus pattern (34 bp):
ATATCTTTTAATATTCAAATTTAAATAGATAATA
Found at i:6460462 original size:32 final size:32
Alignment explanation
Indices: 6460425--6460574 Score: 178
Period size: 32 Copynumber: 4.6 Consensus size: 32
6460415 TTTAGGTTAT
*
6460425 AACCATATTTTAGGTTGAAATTTGTTTAGTGC
1 AACCATATTTTAGGTTGAAACTTGTTTAGTGC
*
6460457 AACCATATTTTAGGTTGAAACTTGTTTTAGTTTTC
1 AACCATATTTTAGGTTGAAACTTG-TTTAG--TGC
* * *
6460492 AACCATATTGTAGGTTGTAACTTGTTTATTGC
1 AACCATATTTTAGGTTGAAACTTGTTTAGTGC
*
6460524 AACCATATTTTAGGTTGGAACTCT-TTTAGTG-
1 AACCATATTTTAGGTTGAAACT-TGTTTAGTGC
* *
6460555 TAGCATATTTTAGGTTGAAA
1 AACCATATTTTAGGTTGAAA
6460575 AATCAAACCT
Statistics
Matches: 102, Mismatches: 12, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
31 17 0.17
32 51 0.50
33 6 0.06
34 4 0.04
35 24 0.24
ACGTcount: A:0.27, C:0.11, G:0.18, T:0.44
Consensus pattern (32 bp):
AACCATATTTTAGGTTGAAACTTGTTTAGTGC
Found at i:6460518 original size:67 final size:66
Alignment explanation
Indices: 6460410--6460574 Score: 201
Period size: 67 Copynumber: 2.5 Consensus size: 66
6460400 TAAGAACTTG
* *
6460410 CTTGTTTTAGGTTATAACCATATTTTAGGTTGAAATTTGTTTAGTGCAACCATATTTTAGGTTGA
1 CTTGTTTTA-GTTATAACCATATTGTAGGTTGAAACTTGTTTAGTGCAACCATATTTTAGGTTGA
6460475 AA
65 AA
* * * *
6460477 CTTGTTTTAGTTTTCAACCATATTGTAGGTTGTAACTTGTTTATTGCAACCATATTTTAGGTTGG
1 CTTGTTTTAGTTAT-AACCATATTGTAGGTTGAAACTTGTTTAGTGCAACCATATTTTAGGTTGA
6460542 AA
65 AA
* * * *
6460544 C-TCTTTTAG-TGT-AGCATATTTTAGGTTGAAA
1 CTTGTTTTAGTTATAACCATATTGTAGGTTGAAA
6460575 AATCAAACCT
Statistics
Matches: 86, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
63 16 0.19
65 2 0.02
66 11 0.13
67 57 0.66
ACGTcount: A:0.26, C:0.10, G:0.18, T:0.45
Consensus pattern (66 bp):
CTTGTTTTAGTTATAACCATATTGTAGGTTGAAACTTGTTTAGTGCAACCATATTTTAGGTTGAA
A
Found at i:6460972 original size:80 final size:79
Alignment explanation
Indices: 6460805--6460997 Score: 251
Period size: 80 Copynumber: 2.4 Consensus size: 79
6460795 TTAGAATTTT
* ** * * * * *
6460805 TAAATATGAAAGTGGTGATATATTGTACAAGATACACACCTAACTATAGCAAGATGATGTATTAT
1 TAAATATGAAAGTGGTGATGTATTGTACGGGATAAACACCCAACTAAAACAAGATGATGTATGAT
6460870 ACGGGGTACACATC
66 ACGGGGTACACATC
* *
6460884 TAAATATGAAGGTGGTGATGTATTGTACGGGATAAACACCCAACTACAAACAAGATGATGTATGG
1 TAAATATGAAAGTGGTGATGTATTGTACGGGATAAACACCCAACTA-AAACAAGATGATGTATGA
*
6460949 TATGGGGTACACATC
65 TACGGGGTACACATC
** *
6460964 TAAATATGAAAGTTATAATGTATTGTACGGGATA
1 TAAATATGAAAGTGGTGATGTATTGTACGGGATA
6460998 CGAACCCAAT
Statistics
Matches: 98, Mismatches: 15, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
79 40 0.41
80 58 0.59
ACGTcount: A:0.38, C:0.12, G:0.22, T:0.28
Consensus pattern (79 bp):
TAAATATGAAAGTGGTGATGTATTGTACGGGATAAACACCCAACTAAAACAAGATGATGTATGAT
ACGGGGTACACATC
Found at i:6461023 original size:80 final size:80
Alignment explanation
Indices: 6460805--6461048 Score: 224
Period size: 80 Copynumber: 3.1 Consensus size: 80
6460795 TTAGAATTTT
* * * ** * * * * ***
6460805 TAAATATGAAAGTGGTGATATATTGTACAAGATACACACCTAACTA-TAGCAAGATGATGTATTA
1 TAAATATGAAAGTGATAATGTATTGTACGGGATAAACACCCAACTACAAACAAGATGATGTAACG
6460869 TACGGGGTACACATC
66 TACGGGGTACACATC
* * * **
6460884 TAAATATGAAGGTGGTGATGTATTGTACGGGATAAACACCCAACTACAAACAAGATGATGTATGG
1 TAAATATGAAAGTGATAATGTATTGTACGGGATAAACACCCAACTACAAACAAGATGATGTAACG
*
6460949 TATGGGGTACACATC
66 TACGGGGTACACATC
* * * * *
6460964 TAAATATGAAAGTTATAATGTATTGTACGGGATACGA-ACCCAATTATAAGCAATG-TGATGTAA
1 TAAATATGAAAGTGATAATGTATTGTACGGGATA-AACACCCAACTACAAACAA-GATGATGTAA
* *
6461027 CGTACGGTGTACACACC
64 CGTACGGGGTACACATC
6461044 TAAAT
1 TAAAT
6461049 TTATGAGTAG
Statistics
Matches: 138, Mismatches: 24, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
79 40 0.29
80 96 0.70
81 2 0.01
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.27
Consensus pattern (80 bp):
TAAATATGAAAGTGATAATGTATTGTACGGGATAAACACCCAACTACAAACAAGATGATGTAACG
TACGGGGTACACATC
Found at i:6462831 original size:20 final size:19
Alignment explanation
Indices: 6462787--6462840 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 19
6462777 CTATTCAAGC
*
6462787 GGTATCGATACCAAGAGGG
1 GGTATCGATACCATGAGGG
6462806 GAGTATCGATACCATG-GGG
1 G-GTATCGATACCATGAGGG
6462825 ATGGTATCGATACCAT
1 --GGTATCGATACCAT
6462841 TAATCACAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
19 4 0.13
20 26 0.84
21 1 0.03
ACGTcount: A:0.30, C:0.17, G:0.31, T:0.22
Consensus pattern (19 bp):
GGTATCGATACCATGAGGG
Found at i:6462868 original size:34 final size:34
Alignment explanation
Indices: 6462825--6462906 Score: 146
Period size: 34 Copynumber: 2.4 Consensus size: 34
6462815 TACCATGGGG
*
6462825 ATGGTATCGATACCATTAATCACAAAATGCAAAA
1 ATGGTATCGATACCATTAATCACAAAATGAAAAA
6462859 ATGGTATCGATACCATTAATCACAAAATGAAAAA
1 ATGGTATCGATACCATTAATCACAAAATGAAAAA
*
6462893 ATGGTATCGGTACC
1 ATGGTATCGATACC
6462907 GTAATAGAGT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
34 46 1.00
ACGTcount: A:0.44, C:0.17, G:0.15, T:0.24
Consensus pattern (34 bp):
ATGGTATCGATACCATTAATCACAAAATGAAAAA
Found at i:6462942 original size:22 final size:20
Alignment explanation
Indices: 6462896--6462966 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
6462886 TGAAAAAATG
* * *
6462896 GTATCGGTACCGTAATAG-A
1 GTATCGATACCATGATAGTA
6462915 GTATCGATACCATAGCATAGTA
1 GTATCGATACCAT-G-ATAGTA
* *
6462937 GTATCGATACCATGATGGTG
1 GTATCGATACCATGATAGTA
6462957 GTATCGATAC
1 GTATCGATAC
6462967 TTATAAGCTA
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
19 11 0.25
20 14 0.32
21 5 0.11
22 14 0.32
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.28
Consensus pattern (20 bp):
GTATCGATACCATGATAGTA
Found at i:6462962 original size:20 final size:22
Alignment explanation
Indices: 6462910--6462966 Score: 75
Period size: 20 Copynumber: 2.7 Consensus size: 22
6462900 CGGTACCGTA
6462910 ATAG-AGTATCGATACCATAGC
1 ATAGTAGTATCGATACCATAGC
6462931 ATAGTAGTATCGATACCAT-G-
1 ATAGTAGTATCGATACCATAGC
* *
6462951 ATGGTGGTATCGATAC
1 ATAGTAGTATCGATAC
6462967 TTATAAGCTA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
20 14 0.42
21 5 0.15
22 14 0.42
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (22 bp):
ATAGTAGTATCGATACCATAGC
Found at i:6463448 original size:54 final size:55
Alignment explanation
Indices: 6463300--6463450 Score: 232
Period size: 55 Copynumber: 2.7 Consensus size: 55
6463290 GACACTAAAC
* *
6463300 GTGCAAAAACTTAAGAAATTCATACTAAGTGTATGAATTTCGGTATGGGCACTTTGT
1 GTGC-AAAAC-TAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGGCACTATGT
*
6463357 GTGCAAAACTAAGAATTTCATACTAAGTGTATGAATTTCCGTATGGGCACTATGT
1 GTGCAAAACTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGGCACTATGT
* *
6463412 GTGC-AAACTAAGAAATCCATACTAAGTGTATTAATTTCC
1 GTGCAAAACTAAGAAATTCATACTAAGTGTATGAATTTCC
6463451 ATATAGGAAA
Statistics
Matches: 88, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
54 32 0.36
55 47 0.53
56 5 0.06
57 4 0.05
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.32
Consensus pattern (55 bp):
GTGCAAAACTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGGCACTATGT
Found at i:6465028 original size:21 final size:21
Alignment explanation
Indices: 6465004--6465057 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
6464994 TCAATACCAT
6465004 TATCGATACTCCAAACCTTAG
1 TATCGATACTCCAAACCTTAG
6465025 TATCGATACTCCAAACCTTAG
1 TATCGATACTCCAAACCTTAG
6465046 TATCGATACTCC
1 TATCGATACTCC
6465058 CTACCCAACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.31, C:0.30, G:0.09, T:0.30
Consensus pattern (21 bp):
TATCGATACTCCAAACCTTAG
Found at i:6467532 original size:14 final size:14
Alignment explanation
Indices: 6467513--6467566 Score: 63
Period size: 14 Copynumber: 3.9 Consensus size: 14
6467503 TTTGACCCAA
*
6467513 CTGAGTCAACTCGT
1 CTGAGTCAACCCGT
*
6467527 CTGAGTCAACCCAT
1 CTGAGTCAACCCGT
* *
6467541 CTGAGTGAACGCGT
1 CTGAGTCAACCCGT
*
6467555 CCGAGTCAACCC
1 CTGAGTCAACCC
6467567 AATGACCATT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 32 1.00
ACGTcount: A:0.24, C:0.33, G:0.22, T:0.20
Consensus pattern (14 bp):
CTGAGTCAACCCGT
Found at i:6467539 original size:28 final size:28
Alignment explanation
Indices: 6467507--6467568 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
6467497 GGTCTATTTG
* *
6467507 ACCCAACTGAGTCAACTCGTCTGAGTCA
1 ACCCAACTGAGTCAACGCGTCCGAGTCA
* *
6467535 ACCCATCTGAGTGAACGCGTCCGAGTCA
1 ACCCAACTGAGTCAACGCGTCCGAGTCA
6467563 ACCCAA
1 ACCCAA
6467569 TGACCATTGA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.29, C:0.34, G:0.19, T:0.18
Consensus pattern (28 bp):
ACCCAACTGAGTCAACGCGTCCGAGTCA
Done.