Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168037.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_29, 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: 14313602
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 50000 characters in sequence are not A, C, G, or T
File 24 of 74
Found at i:5669079 original size:74 final size:73
Alignment explanation
Indices: 5668906--5669101 Score: 173
Period size: 74 Copynumber: 2.6 Consensus size: 73
5668896 TCTTTATTGA
* * * * * *
5668906 AAAGATGATATTTCTAAGATAAAAACATATTCTTTATTAAAAACATG-AAAAGATATATTTTTTG
1 AAAGATGAT-TTTATAAGATAAAAACATATTATTTGTTAAAAACATGAAAAAAATATAGTTTTTA
** *
5668970 GTATCTAAC
65 AAATCCAAC
* * * *
5668979 AAAGATAACATTTTA-AAAATATAAAACATAATT-TTTGTTGAAAATATGAAAAAAATATAGTTT
1 AAAGAT--GATTTTATAAGATA-AAAACAT-ATTATTTGTTAAAAACATGAAAAAAATATAGTTT
*
5669042 TTAAAATCCAAT
62 TTAAAATCCAAC
* *
5669054 AAAGATGATGTTTATAAGATAAAAACGTATTATTTGTTAAAAAGATGA
1 AAAGATGAT-TTTATAAGATAAAAACATATTATTTGTTAAAAACATGA
5669102 CATTTCTAAT
Statistics
Matches: 97, Mismatches: 18, Indels: 15
0.75 0.14 0.12
Matches are distributed among these distances:
73 16 0.16
74 46 0.47
75 35 0.36
ACGTcount: A:0.49, C:0.06, G:0.10, T:0.35
Consensus pattern (73 bp):
AAAGATGATTTTATAAGATAAAAACATATTATTTGTTAAAAACATGAAAAAAATATAGTTTTTAA
AATCCAAC
Found at i:5669116 original size:40 final size:41
Alignment explanation
Indices: 5669054--5669158 Score: 106
Period size: 40 Copynumber: 2.6 Consensus size: 41
5669044 AAAATCCAAT
** * ** *
5669054 AAAGATGATGTTTATAAGATAAAAACGTATTATTTGTT-AA
1 AAAGATGAAATTTCTAAGATAAAAACACAGTATTTGTTGAA
* * * *
5669094 AAAGATGACATTTCTAATATAAAAATACAGTCTTTGTTGAA
1 AAAGATGAAATTTCTAAGATAAAAACACAGTATTTGTTGAA
5669135 AAA-ATGAAATTTCTAAGATAAAAA
1 AAAGATGAAATTTCTAAGATAAAAA
5669159 TGTTGTTTTT
Statistics
Matches: 53, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
40 48 0.91
41 5 0.09
ACGTcount: A:0.49, C:0.06, G:0.12, T:0.33
Consensus pattern (41 bp):
AAAGATGAAATTTCTAAGATAAAAACACAGTATTTGTTGAA
Found at i:5669170 original size:40 final size:40
Alignment explanation
Indices: 5669068--5669183 Score: 110
Period size: 40 Copynumber: 2.9 Consensus size: 40
5669058 ATGATGTTTA
* *
5669068 TAAGATAAAAACGTAT-TATTTGTT-AAAAAGATGACATTTC
1 TAAGATAAAAATGT-TGTATTTGTTGAAAAA-ATGAAATTTC
* *** *
5669108 TAATATAAAAATACAGTCTTTGTTGAAAAAATGAAATTTC
1 TAAGATAAAAATGTTGTATTTGTTGAAAAAATGAAATTTC
* * *
5669148 TAAGATAAAAATGTTGTTTTTGTTGTAAACATGAAA
1 TAAGATAAAAATGTTGTATTTGTTGAAAAAATGAAA
5669184 AAAAAAATTT
Statistics
Matches: 60, Mismatches: 14, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
40 55 0.92
41 5 0.08
ACGTcount: A:0.45, C:0.06, G:0.13, T:0.36
Consensus pattern (40 bp):
TAAGATAAAAATGTTGTATTTGTTGAAAAAATGAAATTTC
Found at i:5669283 original size:40 final size:41
Alignment explanation
Indices: 5669204--5669294 Score: 105
Period size: 43 Copynumber: 2.2 Consensus size: 41
5669194 AGGATGCAAC
* *
5669204 AAAAATGATGTTTGTAAGATTAAAAAAATGCAATCTTTATTGA
1 AAAAATGATGTTTCTAAGATTAAAAAAAT-CAATATTTATT-A
* *
5669247 AAAAATGATGTTTCTAAGA-TAAAAAACT-AGTATTTATTA
1 AAAAATGATGTTTCTAAGATTAAAAAAATCAATATTTATTA
5669286 AAAACATGA
1 AAAA-ATGA
5669295 AATAAATAGT
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
39 5 0.12
40 12 0.28
42 8 0.19
43 18 0.42
ACGTcount: A:0.49, C:0.05, G:0.12, T:0.33
Consensus pattern (41 bp):
AAAAATGATGTTTCTAAGATTAAAAAAATCAATATTTATTA
Found at i:5669354 original size:23 final size:22
Alignment explanation
Indices: 5669323--5669385 Score: 65
Period size: 23 Copynumber: 2.8 Consensus size: 22
5669313 TTTAACAAAG
*
5669323 AAAATATTTTT-AAGATAGAAA
1 AAAATATTTTTGAAAATAGAAA
*
5669344 ACATAATATTTGTTGAAAATATAAA
1 A-A-AATATTT-TTGAAAATAGAAA
*
5669369 AAAATATTTTTCAAAAT
1 AAAATATTTTTGAAAAT
5669386 TCAATAAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
21 1 0.03
22 8 0.23
23 14 0.40
24 3 0.09
25 9 0.26
ACGTcount: A:0.54, C:0.03, G:0.06, T:0.37
Consensus pattern (22 bp):
AAAATATTTTTGAAAATAGAAA
Found at i:5669374 original size:72 final size:72
Alignment explanation
Indices: 5669247--5669438 Score: 192
Period size: 72 Copynumber: 2.7 Consensus size: 72
5669237 TCTTTATTGA
* * * * * * *
5669247 AAAAATGATGTTTCTAAGATAAAAA-ACTAGTATTTATTAAAAACATGAAATAAATAGTTTTCAG
1 AAAAATAATATTTCTAAGATAAAAACA-TAATATTTGTTGAAAACATGAAAAAAATAGTTTTCAA
*
5669311 AATTTAAC
65 AATTCAAC
* * *
5669319 AAAGAA-AATATTTTTAAGATAGAAAACATAATATTTGTTGAAAATAT-AAAAAAATATTTTTCA
1 AAA-AATAATATTTCTAAGATA-AAAACATAATATTTGTTGAAAACATGAAAAAAATAGTTTTCA
*
5669382 AAATTCAAT
64 AAATTCAAC
* * * *
5669391 AAAAATGATGTTTCTAAGATAAAAACATAATTTTTGTTGAAAAGATGA
1 AAAAATAATATTTCTAAGATAAAAACATAATATTTGTTGAAAACATGA
5669439 CGTTTCTAAT
Statistics
Matches: 98, Mismatches: 17, Indels: 10
0.78 0.14 0.08
Matches are distributed among these distances:
71 25 0.26
72 51 0.52
73 21 0.21
74 1 0.01
ACGTcount: A:0.51, C:0.05, G:0.10, T:0.34
Consensus pattern (72 bp):
AAAAATAATATTTCTAAGATAAAAACATAATATTTGTTGAAAACATGAAAAAAATAGTTTTCAAA
ATTCAAC
Found at i:5669444 original size:40 final size:39
Alignment explanation
Indices: 5669391--5669478 Score: 104
Period size: 40 Copynumber: 2.2 Consensus size: 39
5669381 AAAATTCAAT
* * *
5669391 AAAAATGATGTTTCTAAGATAAAAACATAATTTTTGTTG
1 AAAAATGACGTTTCTAAGATAAAAACACAATATTTGTTG
* **
5669430 AAAAGATGACGTTTCTAATATAAAAATGCAATATTTGTTG
1 AAAA-ATGACGTTTCTAAGATAAAAACACAATATTTGTTG
5669470 AAAACATGA
1 AAAA-ATGA
5669479 AAAAATATTT
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
39 4 0.10
40 37 0.90
ACGTcount: A:0.45, C:0.07, G:0.14, T:0.34
Consensus pattern (39 bp):
AAAAATGACGTTTCTAAGATAAAAACACAATATTTGTTG
Found at i:5669455 original size:184 final size:185
Alignment explanation
Indices: 5669204--5669548 Score: 430
Period size: 184 Copynumber: 1.9 Consensus size: 185
5669194 AGGATGCAAC
* *
5669204 AAAAATGATGTTTGTAAGATTAAAAAAATGCAATCTTTATTGAAAAAATGATGTTTCTAAGATAA
1 AAAAATGATGTTTCTAAGATTAAAAAAAT-CAATCTTTATTGAAAAAATGACGTTTCTAAGATAA
* * *
5669269 AAA-ACTAGTATTTATTAAAAACATGAAATAAATA-GTTTTCAGAATTTAACAAAGAA-AATATT
65 AAATAC-AATATTTATTAAAAACATGAAA-AAATATGTTTTCAGAATTCAACAAA-AATAATAGT
* *
5669331 TTTAAGATAGAAAACATAATATTTGTTGAAAATATAAAAAAATATTTTTCAAAATTCAAT
127 TCTAAAATA-AAAACATAATATTTGTTGAAAATATAAAAAAATATTTTTCAAAATTCAAT
* * * * *
5669391 AAAAATGATGTTTCTAAGA-TAAAAACAT-AATTTTTGTTGAAAAGATGACGTTTCTAATATAAA
1 AAAAATGATGTTTCTAAGATTAAAAAAATCAATCTTTATTGAAAAAATGACGTTTCTAAGATAAA
* * * * * * *
5669454 AATGCAATATTTGTTGAAAACATGAAAAAATATTTTTTTAGAATTCAATAAAAATAATGGTTCTA
66 AATACAATATTTATTAAAAACATGAAAAAATATGTTTTCAGAATTCAACAAAAATAATAGTTCTA
*
5669519 AAATAAAAACATAATTTTTGTTGAAAATAT
131 AAATAAAAACATAATATTTGTTGAAAATAT
5669549 GACTTTTCAA
Statistics
Matches: 135, Mismatches: 20, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
183 31 0.23
184 77 0.57
185 1 0.01
186 8 0.06
187 18 0.13
ACGTcount: A:0.49, C:0.06, G:0.10, T:0.35
Consensus pattern (185 bp):
AAAAATGATGTTTCTAAGATTAAAAAAATCAATCTTTATTGAAAAAATGACGTTTCTAAGATAAA
AATACAATATTTATTAAAAACATGAAAAAATATGTTTTCAGAATTCAACAAAAATAATAGTTCTA
AAATAAAAACATAATATTTGTTGAAAATATAAAAAAATATTTTTCAAAATTCAAT
Found at i:5669465 original size:111 final size:112
Alignment explanation
Indices: 5669348--5669567 Score: 334
Period size: 112 Copynumber: 2.0 Consensus size: 112
5669338 TAGAAAACAT
* * * *
5669348 AATATTTGTTGAAAATATAAAAAAATA-TTTTTCAAAATTCAATAAAAATGATGTTTCTAAGATA
1 AATATTTGTTGAAAACATAAAAAAATATTTTTTCAAAATTCAATAAAAATAATGGTTCTAAAATA
* *
5669412 AAAACATAATTTTTGTTGAAAAGATGACGTTTCTAATATAAAAATGC
66 AAAACATAATTTTTGTTGAAAAGATGACGTTTCAAAGATAAAAATGC
* * *
5669459 AATATTTGTTGAAAACATGAAAAAATATTTTTTTAGAATTCAATAAAAATAATGGTTCTAAAATA
1 AATATTTGTTGAAAACATAAAAAAATATTTTTTCAAAATTCAATAAAAATAATGGTTCTAAAATA
* *
5669524 AAAACATAATTTTTGTTGAAAATATGACTTTTCAAAGATAAAAA
66 AAAACATAATTTTTGTTGAAAAGATGACGTTTCAAAGATAAAAA
5669568 AATACACTTT
Statistics
Matches: 97, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
111 25 0.26
112 72 0.74
ACGTcount: A:0.49, C:0.06, G:0.10, T:0.36
Consensus pattern (112 bp):
AATATTTGTTGAAAACATAAAAAAATATTTTTTCAAAATTCAATAAAAATAATGGTTCTAAAATA
AAAACATAATTTTTGTTGAAAAGATGACGTTTCAAAGATAAAAATGC
Found at i:5669643 original size:37 final size:37
Alignment explanation
Indices: 5669609--5669680 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 37
5669599 AATTAAAACA
* * *
5669609 TAAAAAATTTTTACTTGATATTATTACATATAAAATC
1 TAAAAAATATTTACTTAATATTATTACACATAAAATC
* *
5669646 TAAAATATATTTACTTAATATTATTGCACATAAAA
1 TAAAAAATATTTACTTAATATTATTACACATAAAA
5669681 GGTCAATCCG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.42
Consensus pattern (37 bp):
TAAAAAATATTTACTTAATATTATTACACATAAAATC
Found at i:5671618 original size:21 final size:19
Alignment explanation
Indices: 5671587--5671625 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
5671577 CAAAACTAAA
5671587 ATTCTTTTTTATTATTTCT
1 ATTCTTTTTTATTATTTCT
*
5671606 ATTCATTTATTTATTTTTTC
1 ATTC-TTT-TTTATTATTTC
5671626 CTAACAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 3 0.18
21 10 0.59
ACGTcount: A:0.18, C:0.10, G:0.00, T:0.72
Consensus pattern (19 bp):
ATTCTTTTTTATTATTTCT
Found at i:5674772 original size:11 final size:11
Alignment explanation
Indices: 5674758--5674789 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
5674748 GAAGTATAAT
5674758 TGTATTAAAGA
1 TGTATTAAAGA
5674769 TGTATTAAAGA
1 TGTATTAAAGA
*
5674780 TGTATAAAAG
1 TGTATTAAAG
5674790 TATGAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.47, C:0.00, G:0.19, T:0.34
Consensus pattern (11 bp):
TGTATTAAAGA
Found at i:5678160 original size:74 final size:71
Alignment explanation
Indices: 5678046--5678234 Score: 218
Period size: 74 Copynumber: 2.6 Consensus size: 71
5678036 ATTTATTGAA
* * * * *
5678046 AAAAATATATTTCTAAGATAAAAATACAGTTGTTGTTGAAAATATTAAAAGATATATTTTTTAAA
1 AAAAATATGTTTCTAAGATAAAAATATAGTT-TTATTGAAAATATGAAAAAATATATTTTTTAAA
5678111 ATTTAAC
65 ATTTAAC
* * *
5678118 AAAAATAATGTTTCTAAGATAGAAAATGTAGTATTTTTTGAAAATATGAAAAAATATATTTTTTT
1 AAAAAT-ATGTTTCTAAGATA-AAAATATAGT-TTTATTGAAAATATGAAAAAATATATTTTTTA
*
5678183 AAATTTAAT
63 AAATTTAAC
*
5678192 AAAAATGATGTTT-TAAAAATAAAAATATAGTCTTTATTGAAAA
1 AAAAAT-ATGTTTCT-AAGATAAAAATATAGT-TTTATTGAAAA
5678235 AACGATGTTT
Statistics
Matches: 100, Mismatches: 13, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
72 6 0.06
73 33 0.33
74 60 0.60
75 1 0.01
ACGTcount: A:0.49, C:0.03, G:0.09, T:0.39
Consensus pattern (71 bp):
AAAAATATGTTTCTAAGATAAAAATATAGTTTTATTGAAAATATGAAAAAATATATTTTTTAAAA
TTTAAC
Found at i:5678178 original size:25 final size:24
Alignment explanation
Indices: 5678084--5678186 Score: 75
Period size: 25 Copynumber: 4.2 Consensus size: 24
5678074 GTTGTTGTTG
* *
5678084 AAAATATTAAAAGATATATTTTTT
1 AAAATATGAAAAAATATATTTTTT
* * *
5678108 AAAATTTAACAAAAATA-ATGTTTCT
1 AAAATATGA-AAAAATATAT-TTTTT
* **
5678133 AAGATA-GAAAATGTAGTATTTTTT
1 AAAATATGAAAAAATA-TATTTTTT
5678157 GAAAATATGAAAAAATATATTTTTT
1 -AAAATATGAAAAAATATATTTTTT
*
5678182 TAAAT
1 AAAAT
5678187 TTAATAAAAA
Statistics
Matches: 59, Mismatches: 14, Indels: 12
0.69 0.16 0.14
Matches are distributed among these distances:
23 5 0.08
24 18 0.31
25 29 0.49
26 7 0.12
ACGTcount: A:0.50, C:0.02, G:0.08, T:0.41
Consensus pattern (24 bp):
AAAATATGAAAAAATATATTTTTT
Found at i:5678254 original size:40 final size:40
Alignment explanation
Indices: 5678192--5678298 Score: 108
Period size: 40 Copynumber: 2.7 Consensus size: 40
5678182 TAAATTTAAT
* * * *
5678192 AAAAATGATGTTT-TAAAAATAAAAATATAGTCTTTATTGA
1 AAAAACGATGTTTCT-AAGATAAAAATATAGTCCTTATTCA
** *
5678232 AAAAACGATGTTTCTAAGATAAAAACGTAGTCCTTGTTCA
1 AAAAACGATGTTTCTAAGATAAAAATATAGTCCTTATTCA
* * *
5678272 ATAAACAATATTTCTAAGATAAAAATA
1 AAAAACGATGTTTCTAAGATAAAAATA
5678299 AATTTTTTAT
Statistics
Matches: 54, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
40 53 0.98
41 1 0.02
ACGTcount: A:0.49, C:0.08, G:0.10, T:0.33
Consensus pattern (40 bp):
AAAAACGATGTTTCTAAGATAAAAATATAGTCCTTATTCA
Found at i:5678395 original size:115 final size:114
Alignment explanation
Indices: 5678276--5678489 Score: 270
Period size: 115 Copynumber: 1.9 Consensus size: 114
5678266 TGTTCAATAA
* * *
5678276 ACAATATTTCTAAGATAAAAAT-AAAT-TTTTTATTACAAATATAAAAAAATACATTTTTTAAAA
1 ACAATATTTCTAAGATAAAAATGAAATATTTGT-TTA-AAACATAAAAAAAAACATTTTTTAAAA
*
5678339 TTTAATAAAAATGACGTTTATAAGATAGAAAAATGCAATTTTTATTGAAAAG
64 TTTAATAAAAATAACGTTTATAAGATAG-AAAATGCAATTTTTATTGAAAAG
* * * * * *
5678391 ACAATGTTTTTAATATAAAAATGCAGTATTTGTTTAAAACATAAAAAAAAATATTTTTTAAAATT
1 ACAATATTTCTAAGATAAAAATGAAATATTTGTTTAAAACATAAAAAAAAACATTTTTTAAAATT
* * *
5678456 TAATAAAGATAATGTTTCTAAGATAGAAAATGCA
66 TAATAAAAATAACGTTTATAAGATAGAAAATGCA
5678490 GCATTTGTTG
Statistics
Matches: 84, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
114 8 0.10
115 67 0.80
116 5 0.06
117 4 0.05
ACGTcount: A:0.50, C:0.05, G:0.08, T:0.36
Consensus pattern (114 bp):
ACAATATTTCTAAGATAAAAATGAAATATTTGTTTAAAACATAAAAAAAAACATTTTTTAAAATT
TAATAAAAATAACGTTTATAAGATAGAAAATGCAATTTTTATTGAAAAG
Found at i:5678496 original size:74 final size:74
Alignment explanation
Indices: 5678387--5678558 Score: 215
Period size: 75 Copynumber: 2.3 Consensus size: 74
5678377 TTTTTATTGA
* * * * *
5678387 AAAGACAATGTTTTTAATATAAAAATGCAGTATTTGTTTAAAACAT-AAAAAAA-AATATTTTTT
1 AAAGAAAATGTTTCTAAGATAAAAATGCAGCATTTGTTGAAAACATGAAAAAAATAA-ATTTTTT
*
5678450 AAAATTTAAT
65 AAAATTCAAT
* *
5678460 AAAGATAATGTTTCTAAGATAGAAAATGCAGCATTTGTTGAAAATATGAAAAAAATAAATTTTTT
1 AAAGAAAATGTTTCTAAGATA-AAAATGCAGCATTTGTTGAAAACATGAAAAAAATAAATTTTTT
5678525 AAAATTCAAT
65 AAAATTCAAT
*
5678535 AAA-AAAGATGTTTCTAAAATAAAA
1 AAAGAAA-ATGTTTCTAAGATAAAA
5678559 TCATAATTTT
Statistics
Matches: 86, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
73 18 0.21
74 27 0.31
75 39 0.45
76 2 0.02
ACGTcount: A:0.52, C:0.05, G:0.09, T:0.34
Consensus pattern (74 bp):
AAAGAAAATGTTTCTAAGATAAAAATGCAGCATTTGTTGAAAACATGAAAAAAATAAATTTTTTA
AAATTCAAT
Found at i:5678582 original size:188 final size:184
Alignment explanation
Indices: 5678312--5678671 Score: 456
Period size: 188 Copynumber: 1.9 Consensus size: 184
5678302 TTTTTATTAC
* * * *
5678312 AAATATAAAAAAATACATTTTTTAAAATTTAATAAAAATGACGTTTATAAGATAGAAAAATGCAA
1 AAATATAAAAAAATAAATTTTTTAAAATTCAATAAAAAAGACGTTTATAAAATAGAAAAAT-CAA
* ** * * * * *
5678377 TTTTTATTGAAAAGACAATGTTTTTAATATAAAAATGCAGTATTTGTTTAAAACATAAAAAAAAA
65 TTTTTATTAAAAAGACAACATTTATAACATAAAAATGCAATATTTATTGAAAACAT-AAAAAAAA
*
5678442 TATTTTTTAAAATTTAATAAAGAT-AATGTTTCTAAGATAGAAAATGCAGCATTTGTTGA
129 -A-TTTTTAAAATTCAATAAAG-TCAATGTTTCTAAGATA-AAAATGCAGCATTTGTTGA
* * *
5678501 AAATATGAAAAAAATAAATTTTTTAAAATTCAATAAAAAAGATGTTTCTAAAATA-AAATCAT-A
1 AAATAT-AAAAAAATAAATTTTTTAAAATTCAATAAAAAAGACGTTTATAAAATAGAAA-AATCA
*
5678564 ATTTTTATTAAAAAGACAACATTTATAACATAAAAATGCAATCTTTATTGAAAACATAAAAAAAA
64 ATTTTTATTAAAAAGACAACATTTATAACATAAAAATGCAATATTTATTGAAAACATAAAAAAAA
* *
5678629 ATTTTTATAATTCAATAAAGTCGATGTTTCTAAGATAAAAATG
129 ATTTTTAAAATTCAATAAAGTCAATGTTTCTAAGATAAAAATG
5678672 TAATTTTGTC
Statistics
Matches: 149, Mismatches: 19, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
184 7 0.05
185 31 0.21
186 1 0.01
187 8 0.05
188 49 0.33
189 9 0.06
190 44 0.30
ACGTcount: A:0.51, C:0.06, G:0.08, T:0.35
Consensus pattern (184 bp):
AAATATAAAAAAATAAATTTTTTAAAATTCAATAAAAAAGACGTTTATAAAATAGAAAAATCAAT
TTTTATTAAAAAGACAACATTTATAACATAAAAATGCAATATTTATTGAAAACATAAAAAAAAAT
TTTTAAAATTCAATAAAGTCAATGTTTCTAAGATAAAAATGCAGCATTTGTTGA
Found at i:5678735 original size:110 final size:112
Alignment explanation
Indices: 5678497--5678740 Score: 248
Period size: 109 Copynumber: 2.2 Consensus size: 112
5678487 GCAGCATTTG
5678497 TTGAAAATATGAAAAAAATAAATTTTTTAAAATTCAATAAAAAAGATGTTTCTAAAATAAAATCA
1 TTGAAAATAT-AAAAAAA-AAATTTTTTAAAATTCAATAAAAAAGATGTTTCTAAAATAAAATCA
* **
5678562 TAATTTTTATTAAAAAGACAACATTTATAACATAAAAATGCAATCTTTA
64 TAATTTTTATCAAAAAGACAACATTTATAACATAAAAACACAATCTTTA
* * *** * *
5678611 TTGAAAACAT-AAAAAAAAA-TTTTTATAATTCAATAAAGTCGATGTTTCTAAGATAAAAAT-GT
1 TTGAAAATATAAAAAAAAAATTTTTTAAAATTCAATAAAAAAGATGTTTCTAAAAT-AAAATCAT
* * * * * *
5678673 AA-TTTTGTCAAAAATA-AGAC-TTCTCTAAGATAAAGACACAATCTTTT
65 AATTTTTATCAAAAAGACA-ACATT-TATAACATAAAAACACAATCTTTA
5678720 TTGAAAATATAAAAAATAAAA
1 TTGAAAATATAAAAAA-AAAA
5678741 CATAAAATAT
Statistics
Matches: 108, Mismatches: 17, Indels: 13
0.78 0.12 0.09
Matches are distributed among these distances:
108 3 0.03
109 40 0.37
110 38 0.35
111 12 0.11
112 6 0.06
114 9 0.08
ACGTcount: A:0.52, C:0.08, G:0.07, T:0.33
Consensus pattern (112 bp):
TTGAAAATATAAAAAAAAAATTTTTTAAAATTCAATAAAAAAGATGTTTCTAAAATAAAATCATA
ATTTTTATCAAAAAGACAACATTTATAACATAAAAACACAATCTTTA
Found at i:5678966 original size:18 final size:17
Alignment explanation
Indices: 5678943--5679002 Score: 61
Period size: 18 Copynumber: 3.5 Consensus size: 17
5678933 GAAGACAACA
*
5678943 TATTATTTATATGTCATG
1 TATTATTCA-ATGTCATG
*
5678961 TATTATTCACATGTCA-A
1 TATTATTCA-ATGTCATG
*
5678978 TATTA-TGAATGTCATG
1 TATTATTCAATGTCATG
5678994 TATTATTCA
1 TATTATTCA
5679003 CGTATTATTA
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
15 6 0.18
16 7 0.21
17 7 0.21
18 14 0.41
ACGTcount: A:0.32, C:0.10, G:0.10, T:0.48
Consensus pattern (17 bp):
TATTATTCAATGTCATG
Found at i:5679281 original size:21 final size:20
Alignment explanation
Indices: 5679235--5679275 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
5679225 GAACTCTCAA
5679235 AAAC-AAGCTTTATAAAAGT
1 AAACAAAGCTTTATAAAAGT
*
5679254 AAACAAAGCTATTTTAAAAGT
1 AAACAAAGCT-TTATAAAAGT
5679275 A
1 A
5679276 GCCAAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 4 0.21
20 5 0.26
21 10 0.53
ACGTcount: A:0.54, C:0.10, G:0.10, T:0.27
Consensus pattern (20 bp):
AAACAAAGCTTTATAAAAGT
Found at i:5681127 original size:7 final size:7
Alignment explanation
Indices: 5681111--5681163 Score: 52
Period size: 7 Copynumber: 7.6 Consensus size: 7
5681101 GCATGCATGA
5681111 ATGCTAT
1 ATGCTAT
*
5681118 ATGCTGT
1 ATGCTAT
5681125 ATGCTAT
1 ATGCTAT
*
5681132 ATGATAT
1 ATGCTAT
*
5681139 ATGATAT
1 ATGCTAT
* *
5681146 ATGATGT
1 ATGCTAT
*
5681153 ATGATAT
1 ATGCTAT
5681160 ATGC
1 ATGC
5681164 ATGCACAGTC
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
7 40 1.00
ACGTcount: A:0.32, C:0.08, G:0.19, T:0.42
Consensus pattern (7 bp):
ATGCTAT
Found at i:5681130 original size:14 final size:14
Alignment explanation
Indices: 5681115--5681162 Score: 69
Period size: 14 Copynumber: 3.4 Consensus size: 14
5681105 GCATGAATGC
* *
5681115 TATATGCTGTATGC
1 TATATGATGTATGA
*
5681129 TATATGATATATGA
1 TATATGATGTATGA
5681143 TATATGATGTATGA
1 TATATGATGTATGA
5681157 TATATG
1 TATATG
5681163 CATGCACAGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.33, C:0.04, G:0.19, T:0.44
Consensus pattern (14 bp):
TATATGATGTATGA
Found at i:5681139 original size:21 final size:21
Alignment explanation
Indices: 5681115--5681163 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
5681105 GCATGAATGC
* *
5681115 TATATGCTGTATGCTATATGA
1 TATATGCTATATGATATATGA
* *
5681136 TATATGATATATGATGTATGA
1 TATATGCTATATGATATATGA
5681157 TATATGC
1 TATATGC
5681164 ATGCACAGTC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.33, C:0.06, G:0.18, T:0.43
Consensus pattern (21 bp):
TATATGCTATATGATATATGA
Found at i:5684797 original size:106 final size:106
Alignment explanation
Indices: 5684612--5684825 Score: 419
Period size: 106 Copynumber: 2.0 Consensus size: 106
5684602 TAAGTATTTT
*
5684612 CCTTTACTTACCTTATTGCTTGCTTCAATCATTTTTTGTTGGTAGCGATTAGATGGGCTCAAGCT
1 CCTTTACTTACCTTATTGCTTGCTTCAATCAATTTTTGTTGGTAGCGATTAGATGGGCTCAAGCT
5684677 CATGTGAGCTTGGGTGATGAAAGTGCCAGCTCGCTGTTAGA
66 CATGTGAGCTTGGGTGATGAAAGTGCCAGCTCGCTGTTAGA
5684718 CCTTTACTTACCTTATTGCTTGCTTCAATCAATTTTTGTTGGTAGCGATTAGATGGGCTCAAGCT
1 CCTTTACTTACCTTATTGCTTGCTTCAATCAATTTTTGTTGGTAGCGATTAGATGGGCTCAAGCT
5684783 CATGTGAGCTTGGGTGATGAAAGTGCCAGCTCGCTGTTAGA
66 CATGTGAGCTTGGGTGATGAAAGTGCCAGCTCGCTGTTAGA
5684824 CC
1 CC
5684826 ATTTTGTAAT
Statistics
Matches: 107, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
106 107 1.00
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.36
Consensus pattern (106 bp):
CCTTTACTTACCTTATTGCTTGCTTCAATCAATTTTTGTTGGTAGCGATTAGATGGGCTCAAGCT
CATGTGAGCTTGGGTGATGAAAGTGCCAGCTCGCTGTTAGA
Found at i:5688060 original size:13 final size:13
Alignment explanation
Indices: 5688024--5688065 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
5688014 GTGATGAGAT
*
5688024 TTTTTAATTTATCAA
1 TTTTTAATTT-T-TA
5688039 TTTTT-ATTTTTA
1 TTTTTAATTTTTA
5688051 TTTTTAATTTTTA
1 TTTTTAATTTTTA
5688064 TT
1 TT
5688066 AACTCTCTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
12 6 0.24
13 10 0.40
14 4 0.16
15 5 0.20
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (13 bp):
TTTTTAATTTTTA
Found at i:5700132 original size:6 final size:6
Alignment explanation
Indices: 5700121--5700152 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
5700111 AAAATATTTT
5700121 TAAATA TAAATA TAAATA TAAATA TAAA-A TAA
1 TAAATA TAAATA TAAATA TAAATA TAAATA TAA
5700153 TTAAAAATAC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.15
6 22 0.85
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
TAAATA
Found at i:5700511 original size:16 final size:17
Alignment explanation
Indices: 5700490--5700523 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
5700480 AATAAATATT
5700490 AGTAAAATAAA-AAAAA
1 AGTAAAATAAATAAAAA
*
5700506 AGTAAAGTAAATAAAAA
1 AGTAAAATAAATAAAAA
5700523 A
1 A
5700524 AAAGTTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (17 bp):
AGTAAAATAAATAAAAA
Found at i:5702721 original size:34 final size:33
Alignment explanation
Indices: 5702683--5702757 Score: 96
Period size: 34 Copynumber: 2.2 Consensus size: 33
5702673 TTTAGTGACG
*
5702683 TTTGTATAAGAAAAACATCACTAATCTAGTGGCA
1 TTTGTATAA-AAAAACATCACTAATATAGTGGCA
** *
5702717 TTTGTATTAAAAAAACATCGTTAATATAGTGGTA
1 TTTGTA-TAAAAAAACATCACTAATATAGTGGCA
5702751 TTTGTAT
1 TTTGTAT
5702758 CATAAAATGT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
33 1 0.03
34 32 0.89
35 3 0.08
ACGTcount: A:0.39, C:0.09, G:0.15, T:0.37
Consensus pattern (33 bp):
TTTGTATAAAAAAACATCACTAATATAGTGGCA
Found at i:5702847 original size:33 final size:33
Alignment explanation
Indices: 5702803--5702874 Score: 92
Period size: 33 Copynumber: 2.2 Consensus size: 33
5702793 GACAATTGCT
* * *
5702803 GCTAAATTAACGGGA-TTGTATCAAAAAAATGTC
1 GCTAAAATAACGGCATTTGTAT-AAAAAAATGCC
*
5702836 GCTAAAATAACGGCATTTGTATAGAAAAATGCC
1 GCTAAAATAACGGCATTTGTATAAAAAAATGCC
5702869 GCTAAA
1 GCTAAA
5702875 TTTAGTCATG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
33 28 0.82
34 6 0.18
ACGTcount: A:0.43, C:0.14, G:0.18, T:0.25
Consensus pattern (33 bp):
GCTAAAATAACGGCATTTGTATAAAAAAATGCC
Found at i:5704556 original size:161 final size:161
Alignment explanation
Indices: 5704179--5705132 Score: 845
Period size: 161 Copynumber: 5.9 Consensus size: 161
5704169 CATTTTGGCA
* * * * *
5704179 TTTCACACATATCAA-TCATGAAAACCAAATTCAATTATTTGAACAAA-TATAATATCATGTATT
1 TTTCACACATATCAACT-GTGAAAACCAAGTTCAATTA-TTCAAAAAAGTTTAATATCATGTATT
* * * * *
5704242 GAAACCATCCAAACTGTTAAAATAGAATAATAATAGCAACTTTGTATTTTTACCTTTTAATTGCA
64 GAAGCTATCCAAACTGTTAAAACAGAACAATAATAGCAAATTTGTATTTTTACCTTTTAA---CA
* * * **
5704307 A-A-AAAAAGTCCTAAACAGAGGTAAAC---AACTT
126 ACACAAAAAGTCTTAAATAAACATAAACATTAACTT
* * * * *
5704338 TTTTACATATATCAACTGTGAAAGCCAAGTTCAATCATTCAAAAAAGTTTAATATCATGTTTTGA
1 TTTCACACATATCAACTGTGAAAACCAAGTTCAATTATTCAAAAAAGTTTAATATCATGTATTGA
* *
5704403 AGCTATCCAAACTATAAAAACAGAACAATAATAGCAAATTTGTATTTTTACCTTTTAACAACACG
66 AGCTATCCAAACTGTTAAAACAGAACAATAATAGCAAATTTGTATTTTTACCTTTTAACAACAC-
** *
5704468 AAAAA-TCTTAAATAAAGGTAAACAGTAACTT
130 AAAAAGTCTTAAATAAACATAAACATTAACTT
* * * *
5704499 TTTCACATATATCAACTATGAAAATCAAGTTCAATTATTCAAAAAAGTTTAATATCATATATTGA
1 TTTCACACATATCAACTGTGAAAACCAAGTTCAATTATTCAAAAAAGTTTAATATCATGTATTGA
* * * * *
5704564 AGCCATCCAAACTGTTAAAATAGAATAATAATAGCAAATTTGTTTTTTTTTCCTTTT-ACAACA-
66 AGCTATCCAAACTGTTAAAACAGAACAATAATAGCAAATTTG-TATTTTTACCTTTTAACAACAC
* * *
5704627 AAAATAGTTTTAAATAAACATAAACAATAATTT
130 AAAA-AGTCTTAAATAAACATAAACATTAACTT
* * * * * * * *
5704660 TTTCACACATATCAATTGTAAAAATCAAGTTTAATTATTCAGACAAGTTTAACATTATGTATTGA
1 TTTCACACATATCAACTGTGAAAACCAAGTTCAATTATTCAAAAAAGTTTAATATCATGTATTGA
* * * * ** **
5704725 AGCTATCCAAACTGTTAAAACAAAACAATAATATCAAATTTTTA-TTTTGCCTTTTAATGACGTA
66 AGCTATCCAAACTGTTAAAACAGAACAATAATAGCAAATTTGTATTTTTACCTTTTAACAACACA
* * * *
5704789 AAAAGTCTTAAACATATATAAACATTAGCTT
131 AAAAGTCTTAAATAAACATAAACATTAACTT
* ** * *
5704820 TTTCACACATATCAACTGTGAATACCAAGTTCAATTATTCTGACAAGTTTAATATCATGTATTAA
1 TTTCACACATATCAACTGTGAAAACCAAGTTCAATTATTCAAAAAAGTTTAATATCATGTATTGA
* ** * * * * ** * * *
5704885 AGCTTTGTATACTGTTAAAATATAACAATAACAAAAAATTTGTATTTTTACCTATTAACAGCATA
66 AGCTATCCAAACTGTTAAAACAGAACAATAATAGCAAATTTGTATTTTTACCTTTTAACAACACA
* *
5704950 AAAAGTCCTAAATAGACATAAACATTAACTT
131 AAAAGTCTTAAATAAACATAAACATTAACTT
* ** * * *** * * * *
5704981 TTTCATACATATTGACTGTGAAAACTAAGTTCAATAATTTGGATAAGTTAAATATCATATATTAA
1 TTTCACACATATCAACTGTGAAAACCAAGTTCAATTATTCAAAAAAGTTTAATATCATGTATTGA
* * * * * ** * *
5705046 AACTAT-CAAGACTATTAAAACAAAATAATAATTGTTAATTTGTATTTTTATCTTTTAACGACAC
66 AGCTATCCAA-ACTGTTAAAACAGAACAATAATAGCAAATTTGTATTTTTACCTTTTAACAACAC
*
5705110 AAAAAGT-TGTAAATAGACATAAA
130 AAAAAGTCT-TAAATAAACATAAA
5705133 TTGCAAATTA
Statistics
Matches: 652, Mismatches: 127, Indels: 30
0.81 0.16 0.04
Matches are distributed among these distances:
156 3 0.00
157 1 0.00
158 22 0.03
159 115 0.18
160 118 0.18
161 381 0.58
162 12 0.02
ACGTcount: A:0.44, C:0.14, G:0.08, T:0.34
Consensus pattern (161 bp):
TTTCACACATATCAACTGTGAAAACCAAGTTCAATTATTCAAAAAAGTTTAATATCATGTATTGA
AGCTATCCAAACTGTTAAAACAGAACAATAATAGCAAATTTGTATTTTTACCTTTTAACAACACA
AAAAGTCTTAAATAAACATAAACATTAACTT
Found at i:5704901 original size:321 final size:320
Alignment explanation
Indices: 5704179--5705114 Score: 906
Period size: 321 Copynumber: 2.9 Consensus size: 320
5704169 CATTTTGGCA
* * *
5704179 TTTCACACATATCAA-TCATGAAAACCAAATTCAATTATT-TGAACAAATATAATATCATGTATT
1 TTTCACACATATCAACT-ATGAAAACCAAGTTCAATTATTCTG-ACAAGTTTAATATCATGTATT
*
5704242 GAAA-CCATCCAAACTGTTAAAATAGAATAATAATAGCAACTTTGTATTTTTACCTTTTAATTGC
64 -AAAGCCATCCAAACTGTTAAAATAGAATAATAATAGCAAATTTGTATTTTTACCTTTT-A---C
* ** * * * *
5704306 AA-AAAAAAGTCCTAAACAGAGGTAAAC-A-ACTTTTTT-ACATATATCAACTGTGAAAGCCAAG
124 AACAAAAAAGTCCTAAATAGACATAAACAATAATTTTTTCACACATATCAACTGTAAAAACCAAG
* * *
5704367 TTCAATCATTCAAAAAAGTTTAATATCATGTTTTGAAGCTATCCAAACTATAAAAACAGAACAAT
189 TTCAATCATTCAAAAAAGTTTAACATCATGTATTGAAGCTATCCAAACTATAAAAACAAAACAAT
* *
5704432 AATAGCAAATTTGTATTTTTACCTTTTAACAACACGAAAAATCTTAAATAAAGGTAAACAGTAAC
254 AATAGCAAATTTGTATTTTTACCTTTTAACAACACGAAAAATCTTAAACAAAGATAAACAGTAAC
5704497 TT
319 TT
* * ** * * *
5704499 TTTCACATATATCAACTATGAAAATCAAGTTCAATTATTCAAAAAAGTTTAATATCATATATTGA
1 TTTCACACATATCAACTATGAAAACCAAGTTCAATTATTCTGACAAGTTTAATATCATGTATTAA
* *
5704564 AGCCATCCAAACTGTTAAAATAGAATAATAATAGCAAATTTGTTTTTTTTTCCTTTTACAACAAA
66 AGCCATCCAAACTGTTAAAATAGAATAATAATAGCAAATTTG-TATTTTTACCTTTTACAACAAA
** * * * *
5704629 AATAGTTTTAAATAAACATAAACAATAATTTTTTCACACATATCAATTGTAAAAATCAAGTTTAA
130 AA-AGTCCTAAATAGACATAAACAATAATTTTTTCACACATATCAACTGTAAAAACCAAGTTCAA
* * * * * * *
5704694 TTATTCAGACAAGTTTAACATTATGTATTGAAGCTATCCAAACTGTTAAAACAAAACAATAATAT
194 TCATTCAAAAAAGTTTAACATCATGTATTGAAGCTATCCAAACTATAAAAACAAAACAATAATAG
* * ** * * * *
5704759 CAAATTTTTA-TTTTGCCTTTT-A-ATGACGTAAAAAGTCTTAAACATATATAAACATTAGCTT
259 CAAATTTGTATTTTTACCTTTTAACAACACG-AAAAA-TCTTAAACAAAGATAAACAGTAACTT
* *
5704820 TTTCACACATATCAACTGTGAATACCAAGTTCAATTATTCTGACAAGTTTAATATCATGTATTAA
1 TTTCACACATATCAACTATGAAAACCAAGTTCAATTATTCTGACAAGTTTAATATCATGTATTAA
** ** * * * * ** * *
5704885 AGCTTTGTATACTGTTAAAATATAACAATAACAAAAAATTTGTATTTTTACCTATTAACAGCATA
66 AGCCATCCAAACTGTTAAAATAGAATAATAATAGCAAATTTGTATTTTTACCT-TTTACAACA-A
* * * ** * *
5704950 AAAAGTCCTAAATAGACATAAACATTAACTTTTTCATACATATTGACTGTGAAAACTAAGTTCAA
129 AAAAGTCCTAAATAGACATAAACAATAATTTTTTCACACATATCAACTGTAAAAACCAAGTTCAA
* *** * * * * * * * * *
5705015 TAATTTGGATAAGTTAAATATCATATATTAAAACTAT-CAAGACTATTAAAACAAAATAATAATT
194 TCATTCAAAAAAGTTTAACATCATGTATTGAAGCTATCCAA-ACTATAAAAACAAAACAATAATA
** * *
5705079 GTTAATTTGTATTTTTATCTTTTAACGACAC-AAAAA
258 GCAAATTTGTATTTTTACCTTTTAACAACACGAAAAA
5705115 GTTGTAAATA
Statistics
Matches: 495, Mismatches: 104, Indels: 32
0.78 0.16 0.05
Matches are distributed among these distances:
317 3 0.01
318 5 0.01
319 20 0.04
320 110 0.22
321 248 0.50
322 106 0.21
323 1 0.00
324 2 0.00
ACGTcount: A:0.44, C:0.14, G:0.08, T:0.35
Consensus pattern (320 bp):
TTTCACACATATCAACTATGAAAACCAAGTTCAATTATTCTGACAAGTTTAATATCATGTATTAA
AGCCATCCAAACTGTTAAAATAGAATAATAATAGCAAATTTGTATTTTTACCTTTTACAACAAAA
AAGTCCTAAATAGACATAAACAATAATTTTTTCACACATATCAACTGTAAAAACCAAGTTCAATC
ATTCAAAAAAGTTTAACATCATGTATTGAAGCTATCCAAACTATAAAAACAAAACAATAATAGCA
AATTTGTATTTTTACCTTTTAACAACACGAAAAATCTTAAACAAAGATAAACAGTAACTT
Found at i:5704933 original size:482 final size:481
Alignment explanation
Indices: 5704235--5705132 Score: 1040
Period size: 482 Copynumber: 1.9 Consensus size: 481
5704225 ATATAATATC
* * * *
5704235 ATGTATTGAAACCATCCAAACTGTTAAAATAGAATAATAATAGCAACTTTGTATTTTTACCTTTT
1 ATGTATTGAAACCATCCAAACTGTTAAAACAAAACAATAATAGCAAATTTGTATTTTTACCTTTT
* * *
5704300 AATTGCAAAAAAAAGTCCTAAACAGAGGTAAACAACTTTTTTACATATATCAACTGTGAAAGCCA
66 AATTGCAAAAAAAAGTCCTAAACAGAGATAAACAACTTTTTCACACATATCAACTGTGAAAGCCA
* *
5704365 AGTTCAATCATTCAAAAAAGTTTAATATCATGTTTTGAAGCTATCCAAACTATAAAAACAGAACA
131 AGTTCAATCATTCAAAAAAGTTTAATATCATGTATTAAAGCTATCCAAACTATAAAAACAGAACA
* ** * * **
5704430 ATAATAGCAAATTTGTATTTTTACCTTTTAACAACACGAAAAA-TCTTAAATAAAGGTAAACAGT
196 ATAACAAAAAATTTGTATTTTTACCTATTAACAACA-GAAAAAGTCCTAAATAAACATAAACAGT
* * *
5704494 AACTTTTTCACATATATCAACTATGAAAA-TCAAGTTCAATTATTCAAAAAAGTTTAATATCATA
260 AACTTTTTCACACATATCAACTATGAAAACT-AAGTTCAATAATTCAAAAAAGTTAAATATCATA
* * * * * * *
5704558 TATTGAAGCCATCCAA-ACTGTTAAAATAGAATAATAATAGCAAATTTGTTTTTTTTTCCTTTT-
324 TATTAAAACCAT-CAAGACTATTAAAACAAAATAATAATAGCAAATTTGTATTTTTAT-CTTTTA
*
5704621 ACAACA-AAAATAGTTTTAAATAAACATAAACAATAATTTTTTCACACATATCAATTGTAAAAAT
387 ACAACACAAAA-AGTTGTAAATAAACATAAACAATAATTTTTTCACACATATCAATTGTAAAAAT
5704685 CAAGTTTAATTATTCAGACAAGTTTAACATT
451 CAAGTTTAATTATTCAGACAAGTTTAACATT
* * * * *
5704716 ATGTATTGAAGCTATCCAAACTGTTAAAACAAAACAATAATATCAAATTTTTA-TTTTGCCTTTT
1 ATGTATTGAAACCATCCAAACTGTTAAAACAAAACAATAATAGCAAATTTGTATTTTTACCTTTT
** * * *
5704780 AA-TG-ACGTAAAAAGTCTTAAACATATATAAACATTAGCTTTTTCACACATATCAACTGTGAAT
66 AATTGCA-AAAAAAAGTCCTAAACAGAGATAAACA--A-CTTTTTCACACATATCAACTGTGAA-
* ** * * ** * * * *
5704843 A-CCAAGTTCAATTATTCTGACAAGTTTAATATCATGTATTAAAGCTTTGTATACTGTTAAAATA
126 AGCCAAGTTCAATCATTCAAAAAAGTTTAATATCATGTATTAAAGCTATCCAAACTATAAAAACA
* * * *
5704907 TAACAATAACAAAAAATTTGTATTTTTACCTATTAACAGCATAAAAAGTCCTAAATAGACATAAA
191 GAACAATAACAAAAAATTTGTATTTTTACCTATTAACAACAGAAAAAGTCCTAAATAAACATAAA
* * ** * *** *
5704972 CATTAACTTTTTCATACATATTGACTGTGAAAACTAAGTTCAATAATTTGGATAAGTTAAATATC
256 CAGTAACTTTTTCACACATATCAACTATGAAAACTAAGTTCAATAATTCAAAAAAGTTAAATATC
* * **
5705037 ATATATTAAAACTATCAAGACTATTAAAACAAAATAATAATTGTTAATTTGTATTTTTATCTTTT
321 ATATATTAAAACCATCAAGACTATTAAAACAAAATAATAATAGCAAATTTGTATTTTTATCTTTT
* *
5705102 AACGACACAAAAAGTTGTAAATAGACATAAA
386 AACAACACAAAAAGTTGTAAATAAACATAAA
5705133 TTGCAAATTA
Statistics
Matches: 340, Mismatches: 67, Indels: 19
0.80 0.16 0.04
Matches are distributed among these distances:
478 1 0.00
479 23 0.07
480 12 0.04
481 59 0.17
482 239 0.70
483 6 0.02
ACGTcount: A:0.44, C:0.13, G:0.08, T:0.35
Consensus pattern (481 bp):
ATGTATTGAAACCATCCAAACTGTTAAAACAAAACAATAATAGCAAATTTGTATTTTTACCTTTT
AATTGCAAAAAAAAGTCCTAAACAGAGATAAACAACTTTTTCACACATATCAACTGTGAAAGCCA
AGTTCAATCATTCAAAAAAGTTTAATATCATGTATTAAAGCTATCCAAACTATAAAAACAGAACA
ATAACAAAAAATTTGTATTTTTACCTATTAACAACAGAAAAAGTCCTAAATAAACATAAACAGTA
ACTTTTTCACACATATCAACTATGAAAACTAAGTTCAATAATTCAAAAAAGTTAAATATCATATA
TTAAAACCATCAAGACTATTAAAACAAAATAATAATAGCAAATTTGTATTTTTATCTTTTAACAA
CACAAAAAGTTGTAAATAAACATAAACAATAATTTTTTCACACATATCAATTGTAAAAATCAAGT
TTAATTATTCAGACAAGTTTAACATT
Found at i:5706313 original size:13 final size:13
Alignment explanation
Indices: 5706278--5706314 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
5706268 ATAAAAGTGA
*
5706278 ATATATAAAAAAC
1 ATATATAAAGAAC
*
5706291 ATATGTAAAGAAC
1 ATATATAAAGAAC
5706304 ATATATAAAGA
1 ATATATAAAGA
5706315 CATTGAGAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.62, C:0.05, G:0.08, T:0.24
Consensus pattern (13 bp):
ATATATAAAGAAC
Found at i:5712478 original size:14 final size:14
Alignment explanation
Indices: 5712459--5712492 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
5712449 ATATGTAGTT
5712459 TGGTTTAAATATTG
1 TGGTTTAAATATTG
5712473 TGGTTTAAATATTG
1 TGGTTTAAATATTG
5712487 TGGTTT
1 TGGTTT
5712493 GCTAAATTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.53
Consensus pattern (14 bp):
TGGTTTAAATATTG
Found at i:5712584 original size:28 final size:28
Alignment explanation
Indices: 5712487--5712584 Score: 126
Period size: 28 Copynumber: 3.5 Consensus size: 28
5712477 TTAAATATTG
* *
5712487 TGGTTTGCTAAATTG-TATTATATGATAT
1 TGGTTTGCTGAA-TGATATTGTATGATAT
* *
5712515 TGGTTTACTGAATGGTATTGTATGATAT
1 TGGTTTGCTGAATGATATTGTATGATAT
*
5712543 TAGTTTGCTGAATGATATTGTATGATAT
1 TGGTTTGCTGAATGATATTGTATGATAT
*
5712571 TGGTTTGTTGAATG
1 TGGTTTGCTGAATG
5712585 GTTTACTGAA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
27 2 0.03
28 59 0.97
ACGTcount: A:0.26, C:0.03, G:0.23, T:0.48
Consensus pattern (28 bp):
TGGTTTGCTGAATGATATTGTATGATAT
Found at i:5712588 original size:12 final size:12
Alignment explanation
Indices: 5712579--5712636 Score: 64
Period size: 12 Copynumber: 4.7 Consensus size: 12
5712569 ATTGGTTTGT
5712579 TGAATGGTTTAC
1 TGAATGGTTTAC
*
5712591 TGAATGGTGTTTC
1 TGAATGGT-TTAC
5712604 TGAATGATGTTT-C
1 TGAATG--GTTTAC
5712617 TGAATGGTTTAC
1 TGAATGGTTTAC
*
5712629 CGAATGGT
1 TGAATGGT
5712637 GTTTCTAAAC
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
11 4 0.10
12 16 0.40
13 16 0.40
14 2 0.05
15 2 0.05
ACGTcount: A:0.22, C:0.09, G:0.28, T:0.41
Consensus pattern (12 bp):
TGAATGGTTTAC
Found at i:5712608 original size:13 final size:13
Alignment explanation
Indices: 5712579--5712642 Score: 78
Period size: 13 Copynumber: 5.1 Consensus size: 13
5712569 ATTGGTTTGT
*
5712579 TGAATGGT-TTAC
1 TGAATGGTGTTTC
5712591 TGAATGGTGTTTC
1 TGAATGGTGTTTC
*
5712604 TGAATGATGTTTC
1 TGAATGGTGTTTC
*
5712617 TGAATGGT-TTAC
1 TGAATGGTGTTTC
*
5712629 CGAATGGTGTTTC
1 TGAATGGTGTTTC
5712642 T
1 T
5712643 AAACACATTG
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
12 18 0.42
13 25 0.58
ACGTcount: A:0.20, C:0.09, G:0.27, T:0.44
Consensus pattern (13 bp):
TGAATGGTGTTTC
Found at i:5712633 original size:25 final size:26
Alignment explanation
Indices: 5712585--5712642 Score: 73
Period size: 25 Copynumber: 2.2 Consensus size: 26
5712575 TTGTTGAATG
* *
5712585 GTTTACTGAATGGTGTTTCTGAATGAT
1 GTTT-CTGAATGGTGTTACCGAATGAT
*
5712612 GTTTCTGAATGGT-TTACCGAATGGT
1 GTTTCTGAATGGTGTTACCGAATGAT
5712637 GTTTCT
1 GTTTCT
5712643 AAACACATTG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 15 0.54
26 9 0.32
27 4 0.14
ACGTcount: A:0.19, C:0.10, G:0.26, T:0.45
Consensus pattern (26 bp):
GTTTCTGAATGGTGTTACCGAATGAT
Found at i:5715863 original size:35 final size:35
Alignment explanation
Indices: 5715809--5715877 Score: 120
Period size: 35 Copynumber: 2.0 Consensus size: 35
5715799 TATATAAACT
*
5715809 AAATGTTTTGTGGGTATAAACCTACAACTGACTTC
1 AAATGTTTTGTGGGCATAAACCTACAACTGACTTC
*
5715844 AAATGTTTTTTGGGCATAAACCTACAACTGACTT
1 AAATGTTTTGTGGGCATAAACCTACAACTGACTT
5715878 TACATATATA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Consensus pattern (35 bp):
AAATGTTTTGTGGGCATAAACCTACAACTGACTTC
Found at i:5716409 original size:62 final size:62
Alignment explanation
Indices: 5716343--5716474 Score: 146
Period size: 61 Copynumber: 2.1 Consensus size: 62
5716333 AAATGCTTGA
* * *
5716343 AATAATCCCATT-CAATT-TTTGTAAGGGATTATT-TAAGACATTTTTTGGTCAAAAATACCTTC
1 AATAATCCCATTCCAATTATTT-CAAGGGAGTATTGAAAG-CA-TTTTTGGTCAAAAATACCTTC
* * * *
5716405 AATAAT-CCATTCCCATTATTTCAGGGGAGTATTGAAAGCATTTTTGGTCAGAAATACCTTG
1 AATAATCCCATTCCAATTATTTCAAGGGAGTATTGAAAGCATTTTTGGTCAAAAATACCTTC
5716466 AATAATCCC
1 AATAATCCC
5716475 TTACAAATAA
Statistics
Matches: 59, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
61 30 0.51
62 23 0.39
63 6 0.10
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (62 bp):
AATAATCCCATTCCAATTATTTCAAGGGAGTATTGAAAGCATTTTTGGTCAAAAATACCTTC
Found at i:5718349 original size:13 final size:13
Alignment explanation
Indices: 5718333--5718357 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5718323 TTTTGTGTAA
5718333 TTTCAATAATATC
1 TTTCAATAATATC
5718346 TTTCAATAATAT
1 TTTCAATAATAT
5718358 TTTAGCAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.48
Consensus pattern (13 bp):
TTTCAATAATATC
Found at i:5723290 original size:2 final size:2
Alignment explanation
Indices: 5723283--5723310 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5723273 GATTTTCAAG
5723283 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
5723311 CAACACATGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5725420 original size:21 final size:21
Alignment explanation
Indices: 5725387--5725445 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
5725377 ATATAATATT
*
5725387 TATAAAAATATTATTTTTA-A
1 TATAAATATATTATTTTTATA
**
5725407 TATAAATTATATTATAATTATA
1 TATAAA-TATATTATTTTTATA
*
5725429 TATAAATATAATATTTT
1 TATAAATATATTATTTT
5725446 ATTAAATTAA
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
20 6 0.19
21 18 0.58
22 7 0.23
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TATAAATATATTATTTTTATA
Found at i:5725514 original size:42 final size:41
Alignment explanation
Indices: 5725422--5725514 Score: 102
Period size: 42 Copynumber: 2.2 Consensus size: 41
5725412 ATTATATTAT
*
5725422 AATTATATATAAATATAATATTTTATTAAATTAACATCATA
1 AATTAAATATAAATATAATATTTTATTAAATTAACATCATA
*
5725463 AATTAAAATATCAAATA-ATTATTTTATTAATATATAA-AT-ATAA
1 AATT-AAATAT-AAATATAATATTTTATTAA-AT-TAACATCAT-A
5725506 AATTAAATA
1 AATTAAATA
5725515 AATAATAAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
41 4 0.09
42 24 0.53
43 14 0.31
44 3 0.07
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (41 bp):
AATTAAATATAAATATAATATTTTATTAAATTAACATCATA
Found at i:5725522 original size:42 final size:41
Alignment explanation
Indices: 5725430--5725527 Score: 98
Period size: 43 Copynumber: 2.4 Consensus size: 41
5725420 ATAATTATAT
5725430 ATAAAT-ATAA-TATTTTATTAAATTAACATCATAAATTAA
1 ATAAATAATAATTATTTTATTAAATTAACATCATAAATTAA
*
5725469 A-ATATCAAATAATTATTTTATTAATATATAA-AT-ATAAAATTAA
1 ATAAAT--AATAATTATTTTATTAA-AT-TAACATCAT-AAATTAA
5725512 ATAAATAATAAATTAT
1 ATAAATAAT-AATTAT
5725528 ATATTTTTAT
Statistics
Matches: 48, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
38 3 0.06
39 1 0.02
41 4 0.08
42 16 0.33
43 18 0.38
44 6 0.12
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (41 bp):
ATAAATAATAATTATTTTATTAAATTAACATCATAAATTAA
Found at i:5725950 original size:20 final size:19
Alignment explanation
Indices: 5725915--5725953 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
5725905 CTCATATTAT
5725915 TTTAATTTTATAATTTTAA
1 TTTAATTTTATAATTTTAA
5725934 TTTAATTATTA-ATATTTTAA
1 TTTAATT-TTATA-ATTTTAA
5725954 AAATTTATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTAATTTTATAATTTTAA
Found at i:5727217 original size:21 final size:21
Alignment explanation
Indices: 5727193--5727244 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
5727183 ATAAATTAAA
5727193 ATATCAATCAA-TTAAAATATT
1 ATATCAATCAAGTTAAAA-ATT
* **
5727214 ATATTAAAAAAGTTAAAAATT
1 ATATCAATCAAGTTAAAAATT
5727235 ATATC-ATCAA
1 ATATCAATCAA
5727245 ATCTACAATC
Statistics
Matches: 24, Mismatches: 6, Indels: 3
0.73 0.18 0.09
Matches are distributed among these distances:
20 3 0.12
21 15 0.62
22 6 0.25
ACGTcount: A:0.56, C:0.08, G:0.02, T:0.35
Consensus pattern (21 bp):
ATATCAATCAAGTTAAAAATT
Found at i:5727799 original size:22 final size:20
Alignment explanation
Indices: 5727771--5727810 Score: 62
Period size: 22 Copynumber: 1.9 Consensus size: 20
5727761 TTATAAGATT
5727771 AAATTATTAATTATTTATTAAC
1 AAATTATT-ATTA-TTATTAAC
5727793 AAATTATTATTATTATTA
1 AAATTATTATTATTATTA
5727811 TTAAACATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.33
21 4 0.22
22 8 0.44
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (20 bp):
AAATTATTATTATTATTAAC
Found at i:5728771 original size:26 final size:26
Alignment explanation
Indices: 5728717--5728774 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 26
5728707 TTATTTATGA
*
5728717 AATTAAA-AATTTTTATTGATAATGT
1 AATTAAATAATTTTTATTGATAATCT
*
5728742 -ATTAAATAATTTTT-TTGATTCATCT
1 AATTAAATAATTTTTATTGA-TAATCT
5728767 AATTAAAT
1 AATTAAAT
5728775 TATAAATCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
24 10 0.36
25 11 0.39
26 7 0.25
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.50
Consensus pattern (26 bp):
AATTAAATAATTTTTATTGATAATCT
Found at i:5735032 original size:71 final size:71
Alignment explanation
Indices: 5734906--5735040 Score: 164
Period size: 71 Copynumber: 1.9 Consensus size: 71
5734896 AGTTAGTGTT
* * ** * *
5734906 AATTAAATTCAAAATGTAATTCAGTTAATTAATATAAAAAGTGGCATTTAGTAAGTATGAGATTT
1 AATTAAATCCAAAATGTAATTCAATTAATTAATATAAAAAGTAACATTTAATAAGTAAGAGATTT
5734971 AAGATC
66 AAGATC
* * * *
5734977 AATTGAATCCAAAATTTAATTTAATTAATTAATATAAACAA-TAATATTTAATAAGTAAGAGATT
1 AATTAAATCCAAAATGTAATTCAATTAATTAATATAAA-AAGTAACATTTAATAAGTAAGAGATT
5735041 CAAATCCAAA
Statistics
Matches: 53, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
71 51 0.96
72 2 0.04
ACGTcount: A:0.48, C:0.05, G:0.10, T:0.36
Consensus pattern (71 bp):
AATTAAATCCAAAATGTAATTCAATTAATTAATATAAAAAGTAACATTTAATAAGTAAGAGATTT
AAGATC
Found at i:5736017 original size:2 final size:2
Alignment explanation
Indices: 5736010--5736065 Score: 85
Period size: 2 Copynumber: 28.0 Consensus size: 2
5736000 TTACAATCTT
* *
5736010 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
5736052 TT TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
5736066 AAAGCATGAA
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:5736638 original size:17 final size:17
Alignment explanation
Indices: 5736616--5736656 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
5736606 CTACTGAAAT
*
5736616 AATATTTATTTATTATC
1 AATATTTATTAATTATC
*
5736633 AATATTAATTAATTATC
1 AATATTTATTAATTATC
5736650 AA-ATTTA
1 AATATTTA
5736657 AACCCATTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
16 4 0.19
17 17 0.81
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (17 bp):
AATATTTATTAATTATC
Found at i:5750721 original size:11 final size:11
Alignment explanation
Indices: 5750705--5750729 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5750695 CTCCTTATCA
5750705 TAAAGACATGT
1 TAAAGACATGT
5750716 TAAAGACATGT
1 TAAAGACATGT
5750727 TAA
1 TAA
5750730 GTGTCCATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.08, G:0.16, T:0.28
Consensus pattern (11 bp):
TAAAGACATGT
Found at i:5753532 original size:71 final size:71
Alignment explanation
Indices: 5753444--5753577 Score: 268
Period size: 71 Copynumber: 1.9 Consensus size: 71
5753434 GTAGAAGGAA
5753444 GCAGTGCTAACCTGACGGGCTGTGACCATGAACGACATGGCTGTAACCGAAACAGCCATGCACTA
1 GCAGTGCTAACCTGACGGGCTGTGACCATGAACGACATGGCTGTAACCGAAACAGCCATGCACTA
5753509 CGGGAT
66 CGGGAT
5753515 GCAGTGCTAACCTGACGGGCTGTGACCATGAACGACATGGCTGTAACCGAAACAGCCATGCAC
1 GCAGTGCTAACCTGACGGGCTGTGACCATGAACGACATGGCTGTAACCGAAACAGCCATGCAC
5753578 AACAGCCTGA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 63 1.00
ACGTcount: A:0.28, C:0.28, G:0.28, T:0.16
Consensus pattern (71 bp):
GCAGTGCTAACCTGACGGGCTGTGACCATGAACGACATGGCTGTAACCGAAACAGCCATGCACTA
CGGGAT
Found at i:5762958 original size:13 final size:13
Alignment explanation
Indices: 5762940--5762964 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5762930 TCACGGGTTG
5762940 TCTAACTTCTGGA
1 TCTAACTTCTGGA
5762953 TCTAACTTCTGG
1 TCTAACTTCTGG
5762965 GTTGCAGATC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.24, G:0.16, T:0.40
Consensus pattern (13 bp):
TCTAACTTCTGGA
Found at i:5764720 original size:15 final size:15
Alignment explanation
Indices: 5764692--5764722 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5764682 TAGGGTTTCA
5764692 GATTTTGGAGTTTTG
1 GATTTTGGAGTTTTG
*
5764707 GATTTTGGGGTTTTG
1 GATTTTGGAGTTTTG
5764722 G
1 G
5764723 TTTGAGTTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.10, C:0.00, G:0.39, T:0.52
Consensus pattern (15 bp):
GATTTTGGAGTTTTG
Found at i:5764818 original size:14 final size:14
Alignment explanation
Indices: 5764799--5764850 Score: 59
Period size: 14 Copynumber: 3.7 Consensus size: 14
5764789 ATTTGAAAAG
5764799 TTTAGGGTTTTGAT
1 TTTAGGGTTTTGAT
* **
5764813 TTTAGGGTTTGGGG
1 TTTAGGGTTTTGAT
* *
5764827 ATTAGGTTTTTGAT
1 TTTAGGGTTTTGAT
5764841 TTTAGGGTTT
1 TTTAGGGTTT
5764851 ACATGGTTTA
Statistics
Matches: 28, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.13, C:0.00, G:0.33, T:0.54
Consensus pattern (14 bp):
TTTAGGGTTTTGAT
Found at i:5764889 original size:30 final size:31
Alignment explanation
Indices: 5764837--5764920 Score: 86
Period size: 30 Copynumber: 2.8 Consensus size: 31
5764827 ATTAGGTTTT
* ** *
5764837 TGATTTTAGGGTTTACATGGTTTAAGATTT-
1 TGATTTTAGAGTTTGGAGGGTTTAAGATTTC
5764867 T-AGTTTTACG-GTTTGGAGGGTTT-AGATTTC
1 TGA-TTTTA-GAGTTTGGAGGGTTTAAGATTTC
5764897 TGATTTTAGAGTTTGGAGGGTTTA
1 TGATTTTAGAGTTTGGAGGGTTTA
5764921 TGGTTTCGAT
Statistics
Matches: 45, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
29 8 0.18
30 35 0.78
31 2 0.04
ACGTcount: A:0.20, C:0.04, G:0.29, T:0.48
Consensus pattern (31 bp):
TGATTTTAGAGTTTGGAGGGTTTAAGATTTC
Found at i:5764932 original size:30 final size:29
Alignment explanation
Indices: 5764877--5764940 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 29
5764867 TAGTTTTACG
5764877 GTTTGGAGGGTTTAGATTTCTGATTTTAGA
1 GTTTGGAGGGTTTAGATTTCTGA-TTTAGA
* *
5764907 GTTTGGAGGGTTTATGGTTTC-GATTTAGG
1 GTTTGGAGGGTTTA-GATTTCTGATTTAGA
5764936 GTTTG
1 GTTTG
5764941 AAAAGTTTAG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
29 10 0.32
30 16 0.52
31 5 0.16
ACGTcount: A:0.16, C:0.03, G:0.34, T:0.47
Consensus pattern (29 bp):
GTTTGGAGGGTTTAGATTTCTGATTTAGA
Found at i:5765142 original size:11 final size:11
Alignment explanation
Indices: 5765111--5765151 Score: 59
Period size: 11 Copynumber: 3.9 Consensus size: 11
5765101 CTTTTAGGAG
5765111 ATTTATTATT-
1 ATTTATTATTA
*
5765121 A-TTATTGTTA
1 ATTTATTATTA
5765131 ATTTATTATTA
1 ATTTATTATTA
5765142 ATTTATTATT
1 ATTTATTATT
5765152 TATTATCTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
9 7 0.26
10 2 0.07
11 18 0.67
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (11 bp):
ATTTATTATTA
Found at i:5766976 original size:37 final size:37
Alignment explanation
Indices: 5766917--5767014 Score: 115
Period size: 37 Copynumber: 2.6 Consensus size: 37
5766907 ACGACGCAAC
* *
5766917 AAGTTGAGAAATAAAGAATCGATCGGGATAAAACTGT
1 AAGTCGAGAAATAAAGAATCGATCGGGACAAAACTGT
* * * *
5766954 AAGTCGAGGAATAAATAATCGATTGGGACAACACTGT
1 AAGTCGAGAAATAAAGAATCGATCGGGACAAAACTGT
** *
5766991 AAGTTAAAAAATAAAGAATCGATC
1 AAGTCGAGAAATAAAGAATCGATC
5767015 AAGATAACAC
Statistics
Matches: 49, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
37 49 1.00
ACGTcount: A:0.47, C:0.10, G:0.21, T:0.21
Consensus pattern (37 bp):
AAGTCGAGAAATAAAGAATCGATCGGGACAAAACTGT
Found at i:5767468 original size:131 final size:129
Alignment explanation
Indices: 5767247--5767644 Score: 431
Period size: 131 Copynumber: 3.0 Consensus size: 129
5767237 GGTCTTATAG
* * * * *
5767247 AATCGACTGAGATAACACCGTAAGTCAAAAAATAAGAAATCAATTGGGATAATA-CTGCGAATTG
1 AATCGACTGGGATAACACCGCAAGTCAAAAAATAA-AAATCAATCGGGATAACATC-ACGAATTG
* * * *
5767311 AAAGTATGCCTAGAGGTCTTAAAGATTATGCTCGGAGTTCTTAGAAATCATGCCTGAAGGTTTTA
64 AAATTATGCCTAGAGGTCTTAAAGATTATGCTCAGAGGTCTTAGAAATCATG-CTGGAGGTTTTA
5767376 CAA
128 -AA
*
5767379 AATCGACTGGGATAACACCGCAAGTCAAAAAATAAAAATCAATCGGGACAACATCACGAATTGAA
1 AATCGACTGGGATAACACCGCAAGTCAAAAAATAAAAATCAATCGGGATAACATCACGAATTGAA
* ** * ** * * *
5767444 ATTATGCCCAGAAATCTTAAAGATTATACTTTGAGGTCTTAAAAATCATGTTCGGAGGTTTTGGA
66 ATTATGCCTAGAGGTCTTAAAGATTATGCTCAGAGGTCTTAGAAATCATGCT-GGAGGTTTT-AA
*
5767509 G
129 A
* * * ** *
5767510 AATCGATTGGGACAACACTGCAAGTCAAAAAATAAAGAATTGATCAGGATAACATCACGAATTGA
1 AATCGACTGGGATAACACCGCAAGTCAAAAAATAAA-AATCAATCGGGATAACATCACGAATTGA
* * * *
5767575 AATTATGCCTGGAGGTTTTAAAGATCATGC-CTAGAGGTCTTAGAAATCATGTCTGGAGGTATTA
65 AATTATGCCTAGAGGTCTTAAAGATTATGCTC-AGAGGTCTTAGAAATCATG-CTGGAGGTTTTA
5767639 AA
128 AA
5767641 AATC
1 AATC
5767645 ATGCTCGGAG
Statistics
Matches: 220, Mismatches: 40, Indels: 13
0.81 0.15 0.05
Matches are distributed among these distances:
130 1 0.00
131 112 0.51
132 106 0.48
133 1 0.00
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.26
Consensus pattern (129 bp):
AATCGACTGGGATAACACCGCAAGTCAAAAAATAAAAATCAATCGGGATAACATCACGAATTGAA
ATTATGCCTAGAGGTCTTAAAGATTATGCTCAGAGGTCTTAGAAATCATGCTGGAGGTTTTAAA
Found at i:5767611 original size:22 final size:21
Alignment explanation
Indices: 5767574--5767656 Score: 78
Period size: 22 Copynumber: 3.8 Consensus size: 21
5767564 TCACGAATTG
* *
5767574 AAATTATGCCTGGAGGTTTTA
1 AAATCATGCCTGGAGGTATTA
* *
5767595 AAGATCATGCCTAGAGGTCTTA
1 AA-ATCATGCCTGGAGGTATTA
*
5767617 GAAATCATGTCTGGAGGTATTAA
1 -AAATCATGCCTGGAGGTATT-A
5767640 AAATCATG-CTCGGAGGT
1 AAATCATGCCT-GGAGGT
5767657 CTTACAGAAT
Statistics
Matches: 52, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
21 4 0.08
22 45 0.87
23 3 0.06
ACGTcount: A:0.31, C:0.13, G:0.25, T:0.30
Consensus pattern (21 bp):
AAATCATGCCTGGAGGTATTA
Found at i:5767622 original size:132 final size:132
Alignment explanation
Indices: 5767181--5767634 Score: 452
Period size: 132 Copynumber: 3.4 Consensus size: 132
5767171 ATTCTCGAAG
* * * * * * * * *
5767181 ATTATGCTTAGAAGTTTTAAAAATCATGCCTGGAGGTATTAAAAATCATAT-TCAGAGGTCTTAT
1 ATTATGCCTAGAGGTCTTAAAGATCATGCCTGGAGGTCTTAAAAATCATGTCT-GGAGGTTTTAC
* * * * *
5767245 AGAATCGACTGAGATAACACCGTAAGTCAAAAAAT-AAGAAATCAATTGGGATAATA-CTGCGAA
65 AGAATCGACTGGGATAACACCGCAAGTCAAAAAATAAAG-AATCAATCGGGATAACATC-ACGAA
5767308 TTGAA
128 TTGAA
* * * * * *
5767313 AGTATGCCTAGAGGTCTTAAAGATTATG-CTCGGAGTTCTTAGAAATCATGCCTGAAGGTTTTAC
1 ATTATGCCTAGAGGTCTTAAAGATCATGCCT-GGAGGTCTTAAAAATCATGTCTGGAGGTTTTAC
* *
5767377 AAAATCGACTGGGATAACACCGCAAGTCAAAAAATAAA-AATCAATCGGGACAACATCACGAATT
65 AGAATCGACTGGGATAACACCGCAAGTCAAAAAATAAAGAATCAATCGGGATAACATCACGAATT
5767441 GAA
130 GAA
* ** * * * * **
5767444 ATTATGCCCAGAAATCTTAAAGATTATACTTTGAGGTCTTAAAAATCATGT-TCGGAGGTTTTGG
1 ATTATGCCTAGAGGTCTTAAAGATCATGCCTGGAGGTCTTAAAAATCATGTCT-GGAGGTTTTAC
* * * ** *
5767508 AGAATCGATTGGGACAACACTGCAAGTCAAAAAATAAAGAATTGATCAGGATAACATCACGAATT
65 AGAATCGACTGGGATAACACCGCAAGTCAAAAAATAAAGAATCAATCGGGATAACATCACGAATT
5767573 GAA
130 GAA
* * * *
5767576 ATTATGCCTGGAGGTTTTAAAGATCATGCCTAGAGGTCTTAGAAATCATGTCTGGAGGT
1 ATTATGCCTAGAGGTCTTAAAGATCATGCCTGGAGGTCTTAAAAATCATGTCTGGAGGT
5767635 ATTAAAAATC
Statistics
Matches: 261, Mismatches: 53, Indels: 16
0.79 0.16 0.05
Matches are distributed among these distances:
130 1 0.00
131 106 0.41
132 150 0.57
133 4 0.02
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.27
Consensus pattern (132 bp):
ATTATGCCTAGAGGTCTTAAAGATCATGCCTGGAGGTCTTAAAAATCATGTCTGGAGGTTTTACA
GAATCGACTGGGATAACACCGCAAGTCAAAAAATAAAGAATCAATCGGGATAACATCACGAATTG
AA
Found at i:5767732 original size:154 final size:153
Alignment explanation
Indices: 5767476--5767780 Score: 380
Period size: 154 Copynumber: 2.0 Consensus size: 153
5767466 ATTATACTTT
* * * ** *
5767476 GAGGTCTTAAAAATCATGTTCGGAGGTTTTGGAGAATCGATTGGGACAACACTGCAAGTCAAAAA
1 GAGGTATTAAAAATCATGCTCGGAGGTCTTACAGAATCGACTGGGACAACACT-CAAGTCAAAAA
* * * ** ** *
5767541 ATAAAGAATTGATCAGGATAACATCACGAATTGAAATTATGCCTGGAGGTTTTAAAGATCATGCC
65 ATAAAGAATCGATCAGAACAACATCACGAATCAAAATTATGCCCAGAGGTCTTAAAGATCATGCC
5767606 TAGAGGTCTTAGAAATCATGTCTG
130 TAGAGGTCTTAGAAATCATGTCTG
5767630 GAGGTATTAAAAATCATGCTCGGAGGTCTTACAGAATCGACTGGGACAACAACAT-AAGTCAAAA
1 GAGGTATTAAAAATCATGCTCGGAGGTCTTACAGAATCGACTGGGACAAC-AC-TCAAGTCAAAA
* * * *
5767694 AATAAGGAATCGATC-GAAACAACATCGCGAATCAAAATTATGCCCAGATGTCTTAAAGATTATG
64 AATAAAGAATCGATCAG-AACAACATCACGAATCAAAATTATGCCCAGAGGTCTTAAAGATCATG
* *
5767758 CCTGGAGGTCTTAGAAATTATGT
128 CCTAGAGGTCTTAGAAATCATGT
5767781 TCGAAGGTCT
Statistics
Matches: 128, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
153 1 0.01
154 124 0.97
155 2 0.02
156 1 0.01
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.26
Consensus pattern (153 bp):
GAGGTATTAAAAATCATGCTCGGAGGTCTTACAGAATCGACTGGGACAACACTCAAGTCAAAAAA
TAAAGAATCGATCAGAACAACATCACGAATCAAAATTATGCCCAGAGGTCTTAAAGATCATGCCT
AGAGGTCTTAGAAATCATGTCTG
Found at i:5767827 original size:286 final size:282
Alignment explanation
Indices: 5767316--5768188 Score: 914
Period size: 286 Copynumber: 3.1 Consensus size: 282
5767306 AATTGAAAGT
* * * *
5767316 ATGCCTAGAGGTCTTAAAGATTATG-CTCGGAGTTCTTAGAAATCATGCCTGAAGGTTTTACAAA
1 ATGCCTAGAGGTCTTAAAGATTATGTCT-GGAGGTATTAGAAATCATGCC-GAAGGTCTTACAGA
* * ** * * **
5767380 ATCGACTGGGATAACACCGCAAGTCAAAAAATAAAAATCAATCGGGACAACATCACGAATTGAAA
64 ATCGACTGGGACAACAACATAAGTCAAAAAATAAGAATCAATCGGGACAACATCGCGAATCAAAA
* * * * *
5767445 TTATGCCCAGAAATCTTAAAGATTATACTTTGAGGTCTTAAAAATCATGTTCGGAGGTTTTGGAG
129 TTATGCCCAG-AGTCTTAAAGATTATGCTTGGAGGTCTTAAAAATCATGTTCGGAGGTCTTAGAG
* * * * **
5767510 AATCGATTGGGACAACACTGCAAGTCAAAAAATAAAGAATTGATCAGGATAACA-TCACGAATTG
193 AATCGACTGGGATAACAC-GTAAGTCAAAAAATAAAGAATTGATCAGGATAACATTCA-AAATCA
*
5767574 AAATTATGC-CTGGAGGTTTTAAAGATC
256 AAATTATGCTC-GGAGGTCTTAAAGATC
* * *
5767601 ATGCCTAGAGGTCTTAGAA-ATCATGTCTGGAGGTATTAAAAATCATGCTCGGAGGTCTTACAGA
1 ATGCCTAGAGGTCTTA-AAGATTATGTCTGGAGGTATTAGAAATCATGC-CGAAGGTCTTACAGA
* **
5767665 ATCGACTGGGACAACAACATAAGTCAAAAAATAAGGAATCGATCGAAACAACATCGCGAATCAAA
64 ATCGACTGGGACAACAACATAAGTCAAAAAATAA-GAATCAATCGGGACAACATCGCGAATCAAA
* * * *
5767730 ATTATGCCCAGATGTCTTAAAGATTATGCCTGGAGGTCTTAGAAATTATGTTCGAAGGTCTTAGA
128 ATTATGCCCAGA-GTCTTAAAGATTATGCTTGGAGGTCTTAAAAATCATGTTCGGAGGTCTTAGA
* ** * *
5767795 GAATCGACTGGGATAACATCGTAAGTCAAAAAATAAAGAATTAATTGGGACAACATTGAAAATCA
192 GAATCGACTGGGATAACA-CGTAAGTCAAAAAATAAAGAATTGATCAGGATAACATTCAAAATCA
*
5767860 AAATTATGCTCGGAGGTCTTAAAGATT
256 AAATTATGCTCGGAGGTCTTAAAGATC
* * * ** * * *
5767887 ATGCTTGGAAGTCTTAAAGATTATGTCAAGAGGTTTTAGAAATCATTCCCGAAGGTCTTATAGAA
1 ATGCCTAGAGGTCTTAAAGATTATGTCTGGAGGTATTAGAAATCA-TGCCGAAGGTCTTACAGAA
* * * * * **
5767952 TCGACTAGGACAAC-ACAGTAAGCCAAAAAATAAAGAATCAATTGGGATAACACCGTAAATCAAA
65 TCGACTGGGACAACAACA-TAAGTCAAAAAAT-AAGAATCAATCGGGACAACATCGCGAATCAAA
* *
5768016 ATTATGCCTAGAGATCTTAAAGATTATG-TTCGAAGGTCTTAAAAATCATGCTT-GGAGGTCTTA
128 ATTATGCCCAGAG-TCTTAAAGATTATGCTT-GGAGGTCTTAAAAATCATG-TTCGGAGGTCTTA
* * * * **
5768079 GAGAATCGACTAGGATAACACCGTAAGTCAAAAAATAAAGAATTGATCTGGATAATACTGTAAAT
190 GAGAATCGACTGGGATAACA-CGTAAGTCAAAAAATAAAGAATTGATCAGGATAACATTCAAAAT
* * * *
5768144 CAAAATTATGTTCAGAGGTATTAAAGATT
254 CAAAATTATGCTCGGAGGTCTTAAAGATC
* *
5768173 ATACCTGGAGGTCTTA
1 ATGCCTAGAGGTCTTA
5768189 GAAATCATAT
Statistics
Matches: 491, Mismatches: 82, Indels: 29
0.82 0.14 0.05
Matches are distributed among these distances:
285 87 0.18
286 394 0.80
287 10 0.02
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.26
Consensus pattern (282 bp):
ATGCCTAGAGGTCTTAAAGATTATGTCTGGAGGTATTAGAAATCATGCCGAAGGTCTTACAGAAT
CGACTGGGACAACAACATAAGTCAAAAAATAAGAATCAATCGGGACAACATCGCGAATCAAAATT
ATGCCCAGAGTCTTAAAGATTATGCTTGGAGGTCTTAAAAATCATGTTCGGAGGTCTTAGAGAAT
CGACTGGGATAACACGTAAGTCAAAAAATAAAGAATTGATCAGGATAACATTCAAAATCAAAATT
ATGCTCGGAGGTCTTAAAGATC
Found at i:5767848 original size:132 final size:132
Alignment explanation
Indices: 5767601--5768304 Score: 420
Period size: 132 Copynumber: 5.2 Consensus size: 132
5767591 TTTAAAGATC
* * * * * * *
5767601 ATGCCTAGAGGTCTTAGAA-ATCATGTCTGGAGGTATTAAAAATCATGCTCGGAGGTCTTACAGA
1 ATGCCCAGAGGTCTTA-AAGATTATGCCTGGAGGTCTTAAAAATCATGTTCGAAGGTCTTAGAGA
* * * * ** *
5767665 ATCGACTGGGACAACAACATAAGTCAAAAAATAAGGAATCGATC-GAAACAACATCGCGAATCAA
65 ATCGACTGGGATAACACCGTAAGTCAAAAAATAAAGAATTAATCAG-GACAACATCGCGAATCAA
5767729 AATT
129 AATT
* * *
5767733 ATGCCCAGATGTCTTAAAGATTATGCCTGGAGGTCTTAGAAATTATGTTCGAAGGTCTTAGAGAA
1 ATGCCCAGAGGTCTTAAAGATTATGCCTGGAGGTCTTAAAAATCATGTTCGAAGGTCTTAGAGAA
* ** * **
5767798 TCGACTGGGATAACATCGTAAGTCAAAAAATAAAGAATTAATTGGGACAACATTGAAAATCAAAA
66 TCGACTGGGATAACACCGTAAGTCAAAAAATAAAGAATTAATCAGGACAACATCGCGAATCAAAA
5767863 TT
131 TT
* * * * * * * *
5767865 ATGCTCGGAGGTCTTAAAGATTATGCTTGGAAGTCTTAAAGATTATG-TCAAGAGGTTTTAGA-A
1 ATGCCCAGAGGTCTTAAAGATTATGCCTGGAGGTCTTAAAAATCATGTTCGA-AGGTCTTAGAGA
* * * * * * ** * *
5767928 ATC-ATTCCCGAAGGTCTTATAGA-ATCGACTAGGACAACACAGT-AAGCCAAAAAATAAAGAAT
65 ATCGA---CTG--GG----ATA-ACACCG--TAAGTCAA-AAAATAAAG--AATTAAT-CAGGA-
* *
5767990 CAATTGGGATAACACCGTAAATCAAAATT
113 CAA----CAT--C-GCG--AATCAAAATT
* * * * *
5768019 ATGCCTAGAGATCTTAAAGATTATG-TTCGAAGGTCTTAAAAATCATGCTT-GGAGGTCTTAGAG
1 ATGCCCAGAGGTCTTAAAGATTATGCCT-GGAGGTCTTAAAAATCATG-TTCGAAGGTCTTAGAG
* * * * * **
5768082 AATCGACTAGGATAACACCGTAAGTCAAAAAATAAAGAATTGATCTGGATAATA-CTGTAAATCA
64 AATCGACTGGGATAACACCGTAAGTCAAAAAATAAAGAATTAATCAGGACAACATC-GCGAATCA
5768146 AAATT
128 AAATT
** * * * * *
5768151 ATGTTCAGAGGTATTAAAGATTATACCTGGAGGTCTTAGAAATCATATCCGAAGGTCTTAGAGAA
1 ATGCCCAGAGGTCTTAAAGATTATGCCTGGAGGTCTTAAAAATCATGTTCGAAGGTCTTAGAGAA
* * * * *
5768216 TCGACTGAGACAATACCGCAAGTCAAAAAATAAAGAATTAATCAGGACAATATCGCGAATCAAAA
66 TCGACTGGGATAACACCGTAAGTCAAAAAATAAAGAATTAATCAGGACAACATCGCGAATCAAAA
5768281 TT
131 TT
** *
5768283 ATGCTTAGAGGTCTAAAAGATT
1 ATGCCCAGAGGTCTTAAAGATT
5768305 TCAAGATCTT
Statistics
Matches: 432, Mismatches: 101, Indels: 78
0.71 0.17 0.13
Matches are distributed among these distances:
130 1 0.00
131 10 0.02
132 287 0.66
133 5 0.01
134 1 0.00
135 2 0.00
137 1 0.00
139 7 0.02
140 1 0.00
141 11 0.03
142 5 0.01
143 9 0.02
144 5 0.01
145 12 0.03
146 1 0.00
147 6 0.01
149 2 0.00
151 2 0.00
153 3 0.01
154 55 0.13
155 4 0.01
156 2 0.00
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.26
Consensus pattern (132 bp):
ATGCCCAGAGGTCTTAAAGATTATGCCTGGAGGTCTTAAAAATCATGTTCGAAGGTCTTAGAGAA
TCGACTGGGATAACACCGTAAGTCAAAAAATAAAGAATTAATCAGGACAACATCGCGAATCAAAA
TT
Found at i:5767887 original size:22 final size:22
Alignment explanation
Indices: 5767862--5767911 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
5767852 GAAAATCAAA
*
5767862 ATTATGCTCGGAGGTCTTAAAG
1 ATTATGCTCGGAAGTCTTAAAG
*
5767884 ATTATGCTTGGAAGTCTTAAAG
1 ATTATGCTCGGAAGTCTTAAAG
5767906 ATTATG
1 ATTATG
5767912 TCAAGAGGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.30, C:0.10, G:0.24, T:0.36
Consensus pattern (22 bp):
ATTATGCTCGGAAGTCTTAAAG
Found at i:5768012 original size:154 final size:154
Alignment explanation
Indices: 5767743--5768085 Score: 406
Period size: 154 Copynumber: 2.2 Consensus size: 154
5767733 ATGCCCAGAT
** * * *
5767743 GTCTTAAAGATTATGCCTGGAGGTCTTAGAAATTATGTTCGAAGGTCTTAGAGAATCGACTGGGA
1 GTCTTAAAGATTATGCCAAGAGGTCTTAGAAATCATGTCCGAAGGTCTTAGAGAATCGACTAGGA
* * * ** *
5767808 TAACATCGTAAGTCAAAAAATAAAGAATTAATTGGGACAACATTGAAAATCAAAATTATG-CTCG
66 CAACATCGTAAGCCAAAAAATAAAGAATCAATTGGGACAACACCGAAAATCAAAATTATGCCT-A
* *
5767872 GAGGTCTTAAAGATTATGCTTGGAA-
130 GAGATCTTAAAGATTATG-TTCGAAG
* * *
5767897 GTCTTAAAGATTATGTCAAGAGGTTTTAGAAATCAT-TCCCGAAGGTCTTATAGAATCGACTAGG
1 GTCTTAAAGATTATGCCAAGAGGTCTTAGAAATCATGT-CCGAAGGTCTTAGAGAATCGACTAGG
* *
5767961 ACAACA-CAGTAAGCCAAAAAATAAAGAATCAATTGGGATAACACCGTAAATCAAAATTATGCCT
65 ACAACATC-GTAAGCCAAAAAATAAAGAATCAATTGGGACAACACCGAAAATCAAAATTATGCCT
5768025 AGAGATCTTAAAGATTATGTTCGAAG
129 AGAGATCTTAAAGATTATGTTCGAAG
* * ***
5768051 GTCTTAAAAATCATGCTTGGAGGTCTTAGAGAATC
1 GTCTTAAAGATTATGCCAAGAGGTCTTAGA-AATC
5768086 GACTAGGATA
Statistics
Matches: 159, Mismatches: 25, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
153 7 0.04
154 146 0.92
155 6 0.04
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.28
Consensus pattern (154 bp):
GTCTTAAAGATTATGCCAAGAGGTCTTAGAAATCATGTCCGAAGGTCTTAGAGAATCGACTAGGA
CAACATCGTAAGCCAAAAAATAAAGAATCAATTGGGACAACACCGAAAATCAAAATTATGCCTAG
AGATCTTAAAGATTATGTTCGAAG
Found at i:5768698 original size:18 final size:18
Alignment explanation
Indices: 5768671--5768706 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
5768661 CTCATCAAAT
*
5768671 GATGTTAATGAAAATGTC
1 GATGTGAATGAAAATGTC
*
5768689 GATGTGAATGTAAATGTC
1 GATGTGAATGAAAATGTC
5768707 AATGAAAGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.36, C:0.06, G:0.25, T:0.33
Consensus pattern (18 bp):
GATGTGAATGAAAATGTC
Found at i:5776972 original size:21 final size:20
Alignment explanation
Indices: 5776903--5776975 Score: 67
Period size: 22 Copynumber: 3.5 Consensus size: 20
5776893 ATTTTAAAGG
*
5776903 TTAGGGTTTCGGATTTTGGATT
1 TTAGGGTTTTGGA-TTTGG-TT
*
5776925 TTGGGGTTTTGG-TTTGAGTT
1 TTAGGGTTTTGGATTTG-GTT
*
5776945 TCAAGGGTTTTAGGATTTGGTT
1 T-TAGGGTTTT-GGATTTGGTT
5776967 TTAGGGTTT
1 TTAGGGTTT
5776976 AAAGAGTTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
20 7 0.17
21 15 0.36
22 16 0.38
23 4 0.10
ACGTcount: A:0.12, C:0.03, G:0.34, T:0.51
Consensus pattern (20 bp):
TTAGGGTTTTGGATTTGGTT
Found at i:5777012 original size:14 final size:14
Alignment explanation
Indices: 5776995--5777048 Score: 54
Period size: 14 Copynumber: 3.9 Consensus size: 14
5776985 TAAGGCTTAA
5776995 ATTTTAGGGTTTTG
1 ATTTTAGGGTTTTG
*
5777009 ATTTTAGGGTTTGG
1 ATTTTAGGGTTTTG
*** * *
5777023 GGATTAAGTTTTTG
1 ATTTTAGGGTTTTG
5777037 ATTTTAGGGTTT
1 ATTTTAGGGTTT
5777049 ACAAGGTTTA
Statistics
Matches: 28, Mismatches: 12, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.17, C:0.00, G:0.30, T:0.54
Consensus pattern (14 bp):
ATTTTAGGGTTTTG
Found at i:5777103 original size:14 final size:14
Alignment explanation
Indices: 5777069--5777140 Score: 67
Period size: 16 Copynumber: 4.9 Consensus size: 14
5777059 AGCTCTTAGT
*
5777069 TTTACGGTTTGGAGGG
1 TTTAGGGTTTGGA--G
5777085 TTTAGGGTTCT-GAG
1 TTTAGGGTT-TGGAG
5777099 TTTAGGGTTTGGAGAG
1 TTTAGGGTTT-G-GAG
*
5777115 TTTAGGGTTTCGA-
1 TTTAGGGTTTGGAG
5777128 TTTAGGGTTTGGA
1 TTTAGGGTTTGGA
5777141 AGGTTAAGGG
Statistics
Matches: 49, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
13 13 0.27
14 12 0.24
16 23 0.47
17 1 0.02
ACGTcount: A:0.15, C:0.04, G:0.39, T:0.42
Consensus pattern (14 bp):
TTTAGGGTTTGGAG
Found at i:5777108 original size:30 final size:29
Alignment explanation
Indices: 5777069--5777153 Score: 109
Period size: 29 Copynumber: 2.9 Consensus size: 29
5777059 AGCTCTTAGT
*
5777069 TTTACGGTTTGGAGGGTTTAGGG-TTCTGA
1 TTTAGGGTTTGGAGGGTTTAGGGTTTC-GA
*
5777098 GTTTAGGGTTTGGAGAGTTTAGGGTTTCGA
1 -TTTAGGGTTTGGAGGGTTTAGGGTTTCGA
* *
5777128 TTTAGGGTTTGGAAGGTTAAGGGTTT
1 TTTAGGGTTTGGAGGGTTTAGGGTTT
5777154 TAATTTTATG
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
29 23 0.47
30 23 0.47
31 3 0.06
ACGTcount: A:0.16, C:0.04, G:0.39, T:0.41
Consensus pattern (29 bp):
TTTAGGGTTTGGAGGGTTTAGGGTTTCGA
Found at i:5777150 original size:29 final size:31
Alignment explanation
Indices: 5776997--5777153 Score: 109
Period size: 30 Copynumber: 5.3 Consensus size: 31
5776987 AGGCTTAAAT
*
5776997 TTTAGGGTTT-TGATTTTAGGGTTTGG--GG
1 TTTAGGGTTTCTGAGTTTAGGGTTTGGAAGG
* * * * **
5777025 ATTA-AGTTTTTGATTTTAGGGTTTACAAGG
1 TTTAGGGTTTCTGAGTTTAGGGTTTGGAAGG
* * * * *
5777055 TTTA-AG-CTCTTAGTTTTACGGTTTGGAGGG
1 TTTAGGGTTTCTGAG-TTTAGGGTTTGGAAGG
5777085 TTTAGGG-TTCTGAGTTTAGGGTTTGG-AGAG
1 TTTAGGGTTTCTGAGTTTAGGGTTTGGAAG-G
5777115 TTTAGGGTTTC-GA-TTTAGGGTTTGGAAGG
1 TTTAGGGTTTCTGAGTTTAGGGTTTGGAAGG
*
5777144 TTAAGGGTTT
1 TTTAGGGTTT
5777154 TAATTTTATG
Statistics
Matches: 102, Mismatches: 19, Indels: 15
0.75 0.14 0.11
Matches are distributed among these distances:
27 4 0.04
28 17 0.17
29 26 0.25
30 46 0.45
31 9 0.09
ACGTcount: A:0.18, C:0.04, G:0.34, T:0.45
Consensus pattern (31 bp):
TTTAGGGTTTCTGAGTTTAGGGTTTGGAAGG
Found at i:5778292 original size:20 final size:20
Alignment explanation
Indices: 5778254--5778292 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
5778244 CGGTTAAGAC
**
5778254 TGTAGATATTTTTTTTTTTG
1 TGTAGATATTTTTAGTTTTG
5778274 TGTAGATATTTTTAGTTTT
1 TGTAGATATTTTTAGTTTT
5778293 TTGATAGGTA
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:0.00, G:0.15, T:0.67
Consensus pattern (20 bp):
TGTAGATATTTTTAGTTTTG
Found at i:5778749 original size:11 final size:11
Alignment explanation
Indices: 5778720--5778749 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
5778710 TGCAGGGTAG
5778720 GGATGGCTATA
1 GGATGGCTATA
5778731 GG-TGGCTATA
1 GGATGGCTATA
5778741 GGATGGCTA
1 GGATGGCTA
5778750 GTCCCAGGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.23, C:0.10, G:0.40, T:0.27
Consensus pattern (11 bp):
GGATGGCTATA
Found at i:5783199 original size:25 final size:25
Alignment explanation
Indices: 5783169--5783218 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
5783159 CATATGTAAG
5783169 TATGCATTCTTTTATTAAAGAATGT
1 TATGCATTCTTTTATTAAAGAATGT
5783194 TATGCATTCTTTTATTAAAGAATGT
1 TATGCATTCTTTTATTAAAGAATGT
5783219 CTCATTCAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.32, C:0.08, G:0.12, T:0.48
Consensus pattern (25 bp):
TATGCATTCTTTTATTAAAGAATGT
Found at i:5793330 original size:28 final size:28
Alignment explanation
Indices: 5793299--5793354 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
5793289 AACAGAACTT
5793299 AAAGAAAAGAAACTGACAGTGGAAGATG
1 AAAGAAAAGAAACTGACAGTGGAAGATG
* * *
5793327 AAAGAAATGAAATTGAGAGTGGAAGATG
1 AAAGAAAAGAAACTGACAGTGGAAGATG
5793355 CTCTTAATGC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.52, C:0.04, G:0.30, T:0.14
Consensus pattern (28 bp):
AAAGAAAAGAAACTGACAGTGGAAGATG
Found at i:5795773 original size:31 final size:30
Alignment explanation
Indices: 5795738--5795827 Score: 85
Period size: 31 Copynumber: 3.0 Consensus size: 30
5795728 ATGAATGTTT
5795738 TTTAAATTATAATAAAATATTTAATGTGATA
1 TTTAAATTATAATAAAATA-TTAATGTGATA
* *
5795769 TTTAAAATT-TAA-AAATTATTAATATGATA
1 TTT-AAATTATAATAAAATATTAATGTGATA
* * **
5795798 TATGAATTATAATTTAATAATTAATGTGAT
1 TTTAAATTATAATAAAAT-ATTAATGTGAT
5795828 TTATTTTTAA
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
28 4 0.09
29 15 0.32
30 7 0.15
31 16 0.34
32 5 0.11
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.46
Consensus pattern (30 bp):
TTTAAATTATAATAAAATATTAATGTGATA
Found at i:5798144 original size:8 final size:8
Alignment explanation
Indices: 5798130--5798159 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
5798120 TATACAAGAT
5798130 AAAAATAA
1 AAAAATAA
*
5798138 GAAAATAA
1 AAAAATAA
5798146 AAAAATAA
1 AAAAATAA
5798154 AAAAAT
1 AAAAAT
5798160 TTTAGTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.83, C:0.00, G:0.03, T:0.13
Consensus pattern (8 bp):
AAAAATAA
Found at i:5799297 original size:32 final size:29
Alignment explanation
Indices: 5799251--5799329 Score: 86
Period size: 29 Copynumber: 2.6 Consensus size: 29
5799241 TCTTATAAGT
* *
5799251 TTCAAATATTATATTAATTAACAAATTTATAA
1 TTCAAATATCATATTAA--AA-AAATTTAAAA
**
5799283 TTCAAATATCATATTAAAAATTTTTAAAA
1 TTCAAATATCATATTAAAAAAATTTAAAA
*
5799312 TTTAAATATCATATTAAA
1 TTCAAATATCATATTAAA
5799330 CATTTTATTA
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
29 24 0.57
30 2 0.05
32 16 0.38
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (29 bp):
TTCAAATATCATATTAAAAAAATTTAAAA
Found at i:5799318 original size:29 final size:29
Alignment explanation
Indices: 5799276--5799335 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
5799266 AATTAACAAA
*
5799276 TTTATAATTCAAATATCATATTAAAAATT
1 TTTAAAATTCAAATATCATATTAAAAATT
* *
5799305 TTTAAAATTTAAATATCATATTAAACATT
1 TTTAAAATTCAAATATCATATTAAAAATT
5799334 TT
1 TT
5799336 ATTATTACTC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (29 bp):
TTTAAAATTCAAATATCATATTAAAAATT
Found at i:5801116 original size:11 final size:11
Alignment explanation
Indices: 5801102--5801126 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5801092 ATTTTTTTCA
5801102 TAATTTTATTT
1 TAATTTTATTT
5801113 TAATTTTATTT
1 TAATTTTATTT
5801124 TAA
1 TAA
5801127 AATTCATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TAATTTTATTT
Found at i:5801151 original size:14 final size:15
Alignment explanation
Indices: 5801134--5801178 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 15
5801124 TAAAATTCAT
*
5801134 ATTTTT-TGAATAAC
1 ATTTTTATGAAAAAC
5801148 ATTTTTCATGAAAAAC
1 ATTTTT-ATGAAAAAC
5801164 ATTTTTATGCAAAAA
1 ATTTTTATG-AAAAA
5801179 ATGATGATGT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
14 6 0.22
15 3 0.11
16 18 0.67
ACGTcount: A:0.42, C:0.09, G:0.07, T:0.42
Consensus pattern (15 bp):
ATTTTTATGAAAAAC
Found at i:5801714 original size:19 final size:19
Alignment explanation
Indices: 5801671--5801714 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
5801661 CTAGGTTCTG
*
5801671 GGTTTAGGGTTTGATTTAT
1 GGTTTAGGGTTTGATTTAA
* *
5801690 GATTTAGGGTTTGGTTTAA
1 GGTTTAGGGTTTGATTTAA
5801709 GGTTTA
1 GGTTTA
5801715 AGGCAGGTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.18, C:0.00, G:0.32, T:0.50
Consensus pattern (19 bp):
GGTTTAGGGTTTGATTTAA
Found at i:5801935 original size:20 final size:20
Alignment explanation
Indices: 5801789--5801991 Score: 148
Period size: 20 Copynumber: 10.4 Consensus size: 20
5801779 TGTTAGGAGG
* *
5801789 TTGACTTTGGGATTTAGGGT
1 TTGACTTTGGGGTTTAAGGT
* * * *
5801809 TTAACTTTAGGATTTAAGAT
1 TTGACTTTGGGGTTTAAGGT
* *
5801829 TTTACTTTGGGGTTTAAGAT
1 TTGACTTTGGGGTTTAAGGT
* *
5801849 TTGACTTTAGGG-TTAGGGT
1 TTGACTTTGGGGTTTAAGGT
* *
5801868 TTGACTTTAGGGTTTAAAGT
1 TTGACTTTGGGGTTTAAGGT
* * * *
5801888 TTCAATTT-GGGTCT-AGGG
1 TTGACTTTGGGGTTTAAGGT
*
5801906 TT-AGTTTGGGGTTTAAGGT
1 TTGACTTTGGGGTTTAAGGT
5801925 TTGACTTTGGGG-TTAGAGG-
1 TTGACTTTGGGGTTTA-AGGT
* *
5801944 TTGACTTTGGGTTTTAATGT
1 TTGACTTTGGGGTTTAAGGT
* ** *
5801964 TTAACTTTAAGGTTTAGGGT
1 TTGACTTTGGGGTTTAAGGT
5801984 TTGACTTT
1 TTGACTTT
5801992 AGTTTTAAAG
Statistics
Matches: 145, Mismatches: 31, Indels: 14
0.76 0.16 0.07
Matches are distributed among these distances:
17 4 0.03
18 9 0.06
19 43 0.30
20 89 0.61
ACGTcount: A:0.20, C:0.05, G:0.29, T:0.46
Consensus pattern (20 bp):
TTGACTTTGGGGTTTAAGGT
Found at i:5804762 original size:56 final size:54
Alignment explanation
Indices: 5804694--5804801 Score: 162
Period size: 56 Copynumber: 2.0 Consensus size: 54
5804684 TTTCTTTTGA
* *
5804694 ATTTCTAAATTTTTCACCATTTGGACCTATTTAGAAATTCTCTTTTTATTTTTTTT
1 ATTTCTAAATTTTTCACAATTTGGACCTATTTAG-AATT-TCTTTTTAATTTTTTT
* *
5804750 ATTTCTAAATTTTTCACAATTTGGGCCTATTTAGAATTTTTTTTTAATTTTT
1 ATTTCTAAATTTTTCACAATTTGGACCTATTTAGAATTTCTTTTTAATTTTT
5804802 AAAATTTTCA
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
54 12 0.25
55 4 0.08
56 32 0.67
ACGTcount: A:0.24, C:0.12, G:0.06, T:0.57
Consensus pattern (54 bp):
ATTTCTAAATTTTTCACAATTTGGACCTATTTAGAATTTCTTTTTAATTTTTTT
Found at i:5804828 original size:46 final size:45
Alignment explanation
Indices: 5804742--5804840 Score: 114
Period size: 46 Copynumber: 2.2 Consensus size: 45
5804732 TCTCTTTTTA
*
5804742 TTTTTTTT-ATTTCTAAATTTTTCACAATTTGGGCCTATTTAGAAT
1 TTTTTTTTAATTTCTAAAATTTTCACAATTTGGGCCTATTTA-AAT
* * *
5804787 TTTTTTTTAATTTTTAAAATTTTCATC-ATTTGGG-TTAATTTAATT
1 TTTTTTTTAATTTCTAAAATTTTCA-CAATTTGGGCCT-ATTTAAAT
5804832 TTTTTTTTA
1 TTTTTTTTA
5804841 TCTTTGGGAA
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
45 20 0.43
46 26 0.55
47 1 0.02
ACGTcount: A:0.24, C:0.07, G:0.07, T:0.62
Consensus pattern (45 bp):
TTTTTTTTAATTTCTAAAATTTTCACAATTTGGGCCTATTTAAAT
Found at i:5805179 original size:24 final size:25
Alignment explanation
Indices: 5805111--5805169 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
5805101 ACAAATTCAG
*
5805111 ATAAAATTTTA-CATTTAGAAATTTT
1 ATAAAAATTTACCATTT-GAAATTTT
*
5805136 ATAGAAATTTACCATTTGAAATTTT
1 ATAAAAATTTACCATTTGAAATTTT
5805161 -TAAAAATTT
1 ATAAAAATTT
5805170 CATCATTGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
24 8 0.27
25 17 0.57
26 5 0.17
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (25 bp):
ATAAAAATTTACCATTTGAAATTTT
Found at i:5806012 original size:8 final size:8
Alignment explanation
Indices: 5806001--5806122 Score: 101
Period size: 8 Copynumber: 15.4 Consensus size: 8
5805991 ACATCAAAAC
*
5806001 AAATCAAT
1 AAATAAAT
5806009 AAAT-AAT
1 AAATAAAT
5806016 CAAAATAAAT
1 -A-AATAAAT
5806026 AAATAAAT
1 AAATAAAT
*
5806034 AAATCAAT
1 AAATAAAT
* *
5806042 CAATGAAAC
1 AAAT-AAAT
*
5806051 AAGTAAAAT
1 AAAT-AAAT
5806060 AAATAAAT
1 AAATAAAT
5806068 AAATAAAT
1 AAATAAAT
5806076 AAATAAAT
1 AAATAAAT
* *
5806084 AACTAAAC
1 AAATAAAT
5806092 AAAT-AAT
1 AAATAAAT
*
5806099 AAATGAA-
1 AAATAAAT
5806106 AAAT-AA-
1 AAATAAAT
5806112 AAATAAAT
1 AAATAAAT
5806120 AAA
1 AAA
5806123 AAACATAAAA
Statistics
Matches: 94, Mismatches: 13, Indels: 14
0.78 0.11 0.12
Matches are distributed among these distances:
6 6 0.06
7 15 0.16
8 56 0.60
9 14 0.15
10 3 0.03
ACGTcount: A:0.70, C:0.06, G:0.02, T:0.21
Consensus pattern (8 bp):
AAATAAAT
Found at i:5806019 original size:21 final size:22
Alignment explanation
Indices: 5805993--5806122 Score: 78
Period size: 21 Copynumber: 6.0 Consensus size: 22
5805983 AGAGATAAAC
*
5805993 ATCAAAACAAATCAATAAAT-A
1 ATCAAAACAAATAAATAAATAA
*
5806014 ATCAAAATAAATAAATAAATAA
1 ATCAAAACAAATAAATAAATAA
* * *
5806036 ATC-AATC-AATGAAACAAGTAA
1 ATCAAAACAAAT-AAATAAATAA
*
5806057 A--ATAAATAAATAAATAAATAA
1 ATCA-AAACAAATAAATAAATAA
* *
5806078 ATAAATAACTAAACAAAT-AATAA
1 ATCAA-AAC-AAATAAATAAATAA
*
5806101 ATGAAAA-ATAA-AAATAAATAA
1 ATCAAAACA-AATAAATAAATAA
5806122 A
1 A
5806123 AAACATAAAA
Statistics
Matches: 85, Mismatches: 13, Indels: 22
0.71 0.11 0.18
Matches are distributed among these distances:
20 8 0.09
21 48 0.56
22 10 0.12
23 12 0.14
24 7 0.08
ACGTcount: A:0.70, C:0.07, G:0.02, T:0.21
Consensus pattern (22 bp):
ATCAAAACAAATAAATAAATAA
Found at i:5806025 original size:4 final size:4
Alignment explanation
Indices: 5806018--5806122 Score: 101
Period size: 4 Copynumber: 26.8 Consensus size: 4
5806008 TAAATAATCA
* * * *
5806018 AAAT AAAT AAAT AAAT AAAT CAAT CAAT GAAAC AAGT AAAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT -AAAT AAAT -AAAT AAAT AAAT
* * *
5806068 AAAT AAAT AAAT AAAT AACT AAAC AAAT -AAT AAAT GAA- AAAT -AA-
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
5806112 AAAT AAAT AAA
1 AAAT AAAT AAA
5806123 AAACATAAAA
Statistics
Matches: 83, Mismatches: 12, Indels: 12
0.78 0.11 0.11
Matches are distributed among these distances:
3 9 0.11
4 69 0.83
5 5 0.06
ACGTcount: A:0.71, C:0.05, G:0.03, T:0.21
Consensus pattern (4 bp):
AAAT
Found at i:5806137 original size:17 final size:19
Alignment explanation
Indices: 5806092--5806137 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 19
5806082 ATAACTAAAC
5806092 AAATAATAAATGAAAAATAA
1 AAATAATAAA-GAAAAATAA
*
5806112 AAATAAATAAA-AAACAT-A
1 AAAT-AATAAAGAAAAATAA
5806130 AAATAATA
1 AAATAATA
5806138 TGTATTTAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
17 4 0.17
18 5 0.21
19 5 0.21
20 4 0.17
21 6 0.25
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (19 bp):
AAATAATAAAGAAAAATAA
Found at i:5806457 original size:88 final size:87
Alignment explanation
Indices: 5806347--5806634 Score: 274
Period size: 88 Copynumber: 3.3 Consensus size: 87
5806337 GAATAATACA
* * * * **
5806347 AAAACTCCTCTAAGTAAAGGCTCAATGACTTTCAAAAAATAAATAAAGTTTCTCTAAATTGAGGC
1 AAAACTCTTCTAA-TAGAGGCTCAATGACTTTCAAAAAATAAATAAAGCTCCTCTAAACAGAGGC
*
5806412 TTAACGACTTCTG-AAAAATAAAT
65 TTAACAACTT-TGAAAAAATAAAT
* **
5806435 AAAACTCTTCTAATCAGAGGCTCAATAACTTTTGAAAAATAAATAAAGCTCCTCTAAACAGAGGC
1 AAAACTCTTCTAAT-AGAGGCTCAATGACTTTCAAAAAATAAATAAAGCTCCTCTAAACAGAGGC
5806500 TTAACAACTTTGAAAAAATAAAT
65 TTAACAACTTTGAAAAAATAAAT
** * * * * * * * * *
5806523 -AAGGTTTCTCTAATTAGAAGCTTAATGACTTTGAGAAAATAAATAAAACTCCTATAAGCAAAGG
1 AAAACTCT-TCTAA-TAGAGGCTCAATGACTTTCAAAAAATAAATAAAGCTCCTCTAAACAGAGG
* *
5806587 CTTAACATCTTTGGAAAAATAAAT
64 CTTAACAACTTTGAAAAAATAAAT
** *
5806611 AAGGCTCATCTAATCAGAGGCTCA
1 AAAACTCTTCTAAT-AGAGGCTCA
5806635 TTTAAGCATA
Statistics
Matches: 163, Mismatches: 31, Indels: 12
0.79 0.15 0.06
Matches are distributed among these distances:
87 8 0.05
88 151 0.93
89 4 0.02
ACGTcount: A:0.44, C:0.16, G:0.12, T:0.27
Consensus pattern (87 bp):
AAAACTCTTCTAATAGAGGCTCAATGACTTTCAAAAAATAAATAAAGCTCCTCTAAACAGAGGCT
TAACAACTTTGAAAAAATAAAT
Found at i:5806516 original size:132 final size:132
Alignment explanation
Indices: 5806374--5806632 Score: 351
Period size: 132 Copynumber: 2.0 Consensus size: 132
5806364 AGGCTCAATG
*
5806374 ACTTTCAAAAAATAAATAAAGTTTCTCTAAATT-GAGGCTTAACGACTTCTGA-AAAATAAATAA
1 ACTTTCAAAAAATAAATAAAGTTTCTCT-AATTAGAAGCTTAACGACTT-TGAGAAAATAAATAA
* * * * * * *
5806437 AACTCTTCTAATCAGAGGCTCAATAACTTTTGAAAAATAAATAAAGCTCCTCTAAACAGAGGCTT
64 AACTCCTATAAGCAAAGGCTCAACAACTTTGGAAAAATAAATAAAGCTCATCTAAACAGAGGCTT
5806502 AACA
129 AACA
* * *
5806506 ACTTTGAAAAAATAAATAAGGTTTCTCTAATTAGAAGCTTAATGACTTTGAGAAAATAAATAAAA
1 ACTTTCAAAAAATAAATAAAGTTTCTCTAATTAGAAGCTTAACGACTTTGAGAAAATAAATAAAA
* * * *
5806571 CTCCTATAAGCAAAGGCTTAACATCTTTGGAAAAATAAATAAGGCTCATCTAATCAGAGGCT
66 CTCCTATAAGCAAAGGCTCAACAACTTTGGAAAAATAAATAAAGCTCATCTAAACAGAGGCT
5806633 CATTTAAGCA
Statistics
Matches: 110, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
131 7 0.06
132 103 0.94
ACGTcount: A:0.44, C:0.15, G:0.12, T:0.28
Consensus pattern (132 bp):
ACTTTCAAAAAATAAATAAAGTTTCTCTAATTAGAAGCTTAACGACTTTGAGAAAATAAATAAAA
CTCCTATAAGCAAAGGCTCAACAACTTTGGAAAAATAAATAAAGCTCATCTAAACAGAGGCTTAA
CA
Found at i:5806590 original size:44 final size:43
Alignment explanation
Indices: 5806347--5806612 Score: 185
Period size: 44 Copynumber: 6.0 Consensus size: 43
5806337 GAATAATACA
** * *
5806347 AAAACTCCTCTAAGTAAAGGCTCAATGACTTTCAAAAAATAAAT
1 AAAACTCCTCTAAACAAAGGCTTAATGACTTT-GAAAAATAAAT
** * *** *
5806391 AAAGTTTCTCTAAATTGAGGCTTAACGACTTCTGAAAAATAAAT
1 AAAACTCCTCTAAACAAAGGCTTAATGACTT-TGAAAAATAAAT
* * * * *
5806435 AAAACTCTTCTAATCAGAGGCTCAATAACTTTTGAAAAATAAAT
1 AAAACTCCTCTAAACAAAGGCTTAATGAC-TTTGAAAAATAAAT
* * **
5806479 AAAGCTCCTCTAAACAGAGGCTTAACAACTTTGAAAAAATAAAT
1 AAAACTCCTCTAAACAAAGGCTTAATGACTTTG-AAAAATAAAT
*** * **
5806523 AAGGTTTCTCTAATTAGAA-GCTTAATGACTTTGAGAAAATAAAT
1 AAAACTCCTCTAAACA-AAGGCTTAATGACTTTGA-AAAATAAAT
* * *
5806567 AAAACTCCTATAAGCAAAGGCTTAA-CATCTTTGGAAAAATAAAT
1 AAAACTCCTCTAAACAAAGGCTTAATGA-CTTT-GAAAAATAAAT
5806611 AA
1 AA
5806613 GGCTCATCTA
Statistics
Matches: 174, Mismatches: 40, Indels: 16
0.76 0.17 0.07
Matches are distributed among these distances:
43 8 0.05
44 160 0.92
45 6 0.03
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (43 bp):
AAAACTCCTCTAAACAAAGGCTTAATGACTTTGAAAAATAAAT
Found at i:5806632 original size:44 final size:42
Alignment explanation
Indices: 5806381--5806632 Score: 218
Period size: 44 Copynumber: 5.8 Consensus size: 42
5806371 ATGACTTTCA
* * *
5806381 AAAAATAAATAAAGTTTCTCTAAAT-TGAGGCTTAACGACTTCTG
1 AAAAATAAATAAAGCTCCTCT-AATCAGAGGCTTAAC-ACTT-TG
* * * *
5806425 AAAAATAAATAAAACTCTTCTAATCAGAGGCTCAATAACTTTTG
1 AAAAATAAATAAAGCTCCTCTAATCAGAGGCTTAA-CAC-TTTG
*
5806469 AAAAATAAATAAAGCTCCTCTAAACAGAGGCTTAACAACTTTG
1 AAAAATAAATAAAGCTCCTCTAATCAGAGGCTTAAC-ACTTTG
* * * * * *
5806512 AAAAAATAAATAAGGTTTCTCTAATTAGAAGCTTAATGACTTTG
1 -AAAAATAAATAAAGCTCCTCTAATCAGAGGCTTAA-CACTTTG
* * * *
5806556 AGAAAATAAATAAAACTCCTATAAGCAAAGGCTTAACATCTTTGG
1 A-AAAATAAATAAAGCTCCTCTAATCAGAGGCTTAACA-CTTT-G
* *
5806601 AAAAATAAATAAGGCTCATCTAATCAGAGGCT
1 AAAAATAAATAAAGCTCCTCTAATCAGAGGCT
5806633 CATTTAAGCA
Statistics
Matches: 164, Mismatches: 35, Indels: 18
0.76 0.16 0.08
Matches are distributed among these distances:
43 9 0.05
44 151 0.92
45 4 0.02
ACGTcount: A:0.45, C:0.15, G:0.13, T:0.28
Consensus pattern (42 bp):
AAAAATAAATAAAGCTCCTCTAATCAGAGGCTTAACACTTTG
Found at i:5806694 original size:44 final size:44
Alignment explanation
Indices: 5806637--5806777 Score: 185
Period size: 44 Copynumber: 3.2 Consensus size: 44
5806627 GAGGCTCATT
* * *
5806637 TAAGCATATGCTCAACAATTTTGGAAAAATAAATAAGGCTCCTC
1 TAAGCAGAGGCTCAACAATTTTGGAAAAATAAATAAAGCTCCTC
* *
5806681 TAAGCAGAGGCTCAACGACTTTGGAAAAATAAATAAAGCTCCTC
1 TAAGCAGAGGCTCAACAATTTTGGAAAAATAAATAAAGCTCCTC
* * * * *
5806725 TAACCAAAGGCTTAACAATTTT-GAAAAATAAACAAAGCTCCTT
1 TAAGCAGAGGCTCAACAATTTTGGAAAAATAAATAAAGCTCCTC
5806768 TAAGCAGAGG
1 TAAGCAGAGG
5806778 AGTCATAGAT
Statistics
Matches: 83, Mismatches: 14, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
43 27 0.33
44 56 0.67
ACGTcount: A:0.43, C:0.18, G:0.16, T:0.23
Consensus pattern (44 bp):
TAAGCAGAGGCTCAACAATTTTGGAAAAATAAATAAAGCTCCTC
Found at i:5807273 original size:14 final size:15
Alignment explanation
Indices: 5807256--5807292 Score: 60
Period size: 14 Copynumber: 2.6 Consensus size: 15
5807246 ATTCAAAGAC
5807256 AAAGATTCTC-ATTT
1 AAAGATTCTCTATTT
5807270 AAAGATT-TCTATTT
1 AAAGATTCTCTATTT
5807284 AAAGATTCT
1 AAAGATTCT
5807293 TCTTGAAAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 2 0.10
14 18 0.86
15 1 0.05
ACGTcount: A:0.38, C:0.11, G:0.08, T:0.43
Consensus pattern (15 bp):
AAAGATTCTCTATTT
Found at i:5807768 original size:79 final size:79
Alignment explanation
Indices: 5807636--5807788 Score: 209
Period size: 79 Copynumber: 1.9 Consensus size: 79
5807626 TTCCCTTTTA
* * ** *
5807636 GCTTCTCAGCATTAAAAATTTCAGAACATATTCCATCCATTGATTCATGTTATTTCCATTACTTG
1 GCTTCTCAGCACTAAAAATTTCAGAACAAATTCCATCCATTGATTCACATTATTTCCATCACTTG
5807701 ATCACAACTCACAG
66 ATCACAACTCACAG
** * *
5807715 GCTTCTCAGCACTAGTAATTTCAGAACAAATTTCATCCATTGA-TCGACATTATTTTCATCACTT
1 GCTTCTCAGCACTAAAAATTTCAGAACAAATTCCATCCATTGATTC-ACATTATTTCCATCACTT
5807779 GATCACAACT
65 GATCACAACT
5807789 TCCCAAGTTA
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
78 2 0.03
79 62 0.97
ACGTcount: A:0.31, C:0.24, G:0.09, T:0.35
Consensus pattern (79 bp):
GCTTCTCAGCACTAAAAATTTCAGAACAAATTCCATCCATTGATTCACATTATTTCCATCACTTG
ATCACAACTCACAG
Found at i:5808401 original size:10 final size:10
Alignment explanation
Indices: 5808381--5808475 Score: 83
Period size: 10 Copynumber: 9.6 Consensus size: 10
5808371 CTTTATTTCA
5808381 TTTTTCT-TT
1 TTTTTCTATT
5808390 TTTTTCTATT
1 TTTTTCTATT
5808400 TTTTTCTATT
1 TTTTTCTATT
5808410 TTTTTCT-TT
1 TTTTTCTATT
5808419 TTTTCTCT-TT
1 TTTT-TCTATT
***
5808429 CAATTCTCATT
1 TTTTTCT-ATT
5808440 GTTTTTC-ATT
1 -TTTTTCTATT
*
5808450 TTTTTCTTTT
1 TTTTTCTATT
5808460 ATTTTTC-ATT
1 -TTTTTCTATT
5808470 TTTTTC
1 TTTTTC
5808476 CATTATCGAT
Statistics
Matches: 71, Mismatches: 8, Indels: 14
0.76 0.09 0.15
Matches are distributed among these distances:
9 28 0.39
10 32 0.45
11 8 0.11
12 3 0.04
ACGTcount: A:0.08, C:0.14, G:0.01, T:0.77
Consensus pattern (10 bp):
TTTTTCTATT
Found at i:5808459 original size:8 final size:9
Alignment explanation
Indices: 5808362--5808475 Score: 76
Period size: 10 Copynumber: 12.1 Consensus size: 9
5808352 TTTCCTCTTA
5808362 CATTTTTTT
1 CATTTTTTT
*
5808371 C-TTTATTT
1 CATTTTTTT
5808379 CA--TTTTT
1 CATTTTTTT
*
5808386 CTTTTTTTT
1 CATTTTTTT
5808395 CTATTTTTTT
1 C-ATTTTTTT
5808405 CTATTTTTTT
1 C-ATTTTTTT
5808415 C-TTTTTTT
1 CATTTTTTT
5808423 C-TCTTTCAATTCT
1 CAT-TTT---TT-T
5808436 CATTGTTTTT
1 CATT-TTTTT
5808446 CATTTTTTT
1 CATTTTTTT
*
5808455 CTTTTATTTTT
1 C-ATT-TTTTT
5808466 CATTTTTTT
1 CATTTTTTT
5808475 C
1 C
5808476 CATTATCGAT
Statistics
Matches: 86, Mismatches: 6, Indels: 26
0.73 0.05 0.22
Matches are distributed among these distances:
7 5 0.06
8 16 0.19
9 22 0.26
10 27 0.31
11 8 0.09
12 2 0.02
13 3 0.03
14 3 0.03
ACGTcount: A:0.10, C:0.14, G:0.01, T:0.75
Consensus pattern (9 bp):
CATTTTTTT
Found at i:5813496 original size:25 final size:27
Alignment explanation
Indices: 5813455--5813511 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 27
5813445 AAACTGGAAA
*
5813455 TTTT-CCAAATAAATT-CCAGAAAAAC
1 TTTTACCAAATAAATTCCCAAAAAAAC
* *
5813480 TTTTACCAAA-AATTTCCCAAAAAAAG
1 TTTTACCAAATAAATTCCCAAAAAAAC
5813506 TTTTAC
1 TTTTAC
5813512 ACGTCCTAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 8 0.30
26 19 0.70
ACGTcount: A:0.46, C:0.19, G:0.04, T:0.32
Consensus pattern (27 bp):
TTTTACCAAATAAATTCCCAAAAAAAC
Found at i:5813837 original size:5 final size:4
Alignment explanation
Indices: 5813790--5813887 Score: 69
Period size: 4 Copynumber: 24.2 Consensus size: 4
5813780 ACATCAAAAC
* * *
5813790 AAAT CAAT AAAT AATCT AAAT AAAT AAAT AACT CAAA- AAAGT AAAGT
1 AAAT AAAT AAAT AA-AT AAAT AAAT AAAT AAAT -AAAT AAA-T AAA-T
* * *
5813837 AAAAT AAAT AAAT AAAT AAAC AAAT -AAT AAAT GAA- AAAT GAA- AAAT
1 -AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
5813883 AAAT A
1 AAAT A
5813888 GAAAAATATA
Statistics
Matches: 74, Mismatches: 12, Indels: 16
0.73 0.12 0.16
Matches are distributed among these distances:
3 10 0.14
4 50 0.68
5 11 0.15
6 3 0.04
ACGTcount: A:0.69, C:0.05, G:0.04, T:0.21
Consensus pattern (4 bp):
AAAT
Found at i:5813885 original size:18 final size:19
Alignment explanation
Indices: 5813862--5813903 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
5813852 ATAAACAAAT
5813862 AATAAAT-GAAAAATGA-AA
1 AATAAATAGAAAAAT-ATAA
5813880 AATAAATAGAAAAATATAA
1 AATAAATAGAAAAATATAA
5813899 AATAA
1 AATAA
5813904 TATGCACTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.36
19 14 0.64
ACGTcount: A:0.74, C:0.00, G:0.07, T:0.19
Consensus pattern (19 bp):
AATAAATAGAAAAATATAA
Found at i:5816420 original size:2 final size:2
Alignment explanation
Indices: 5816413--5816447 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
5816403 TATCAATAGT
5816413 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5816448 AGTGGATACT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5816995 original size:20 final size:21
Alignment explanation
Indices: 5816958--5816998 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
5816948 CTCTGCTCAT
* *
5816958 TTTTTTTTCTCCTCAAATTGC
1 TTTTCTTTCCCCTCAAATTGC
5816979 TTTTCTTTCCCCT-AAATTGC
1 TTTTCTTTCCCCTCAAATTGC
5816999 CAACTCCATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.15, C:0.27, G:0.05, T:0.54
Consensus pattern (21 bp):
TTTTCTTTCCCCTCAAATTGC
Found at i:5817687 original size:20 final size:21
Alignment explanation
Indices: 5817659--5817697 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
5817649 AGAAAAAGAA
5817659 AAGGAAATGAAGAAAGAAAGG
1 AAGGAAATGAAGAAAGAAAGG
*
5817680 AAGG-AATGAGGAAAGAAA
1 AAGGAAATGAAGAAAGAAA
5817698 AATAAGAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.62, C:0.00, G:0.33, T:0.05
Consensus pattern (21 bp):
AAGGAAATGAAGAAAGAAAGG
Found at i:5817865 original size:10 final size:10
Alignment explanation
Indices: 5817852--5817921 Score: 70
Period size: 10 Copynumber: 6.9 Consensus size: 10
5817842 GGAGAAAGAA
5817852 AAAAAAAAAG
1 AAAAAAAAAG
*
5817862 AAAAAAGAAG
1 AAAAAAAAAG
5817872 AAAAAAAAAG
1 AAAAAAAAAG
5817882 -AAAAAAAAG
1 AAAAAAAAAG
* * *
5817891 AAGAGAAGAG
1 AAAAAAAAAG
*
5817901 AAAGAAGAAAG
1 AAA-AAAAAAG
5817912 ATAAAAAAAA
1 A-AAAAAAAA
5817922 AGTTTGAAAA
Statistics
Matches: 47, Mismatches: 10, Indels: 5
0.76 0.16 0.08
Matches are distributed among these distances:
9 9 0.19
10 26 0.55
11 10 0.21
12 2 0.04
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.01
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:5817872 original size:22 final size:22
Alignment explanation
Indices: 5817847--5817894 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
5817837 AAGAAGGAGA
5817847 AAGAAAAAAAAA-AAGAAAAAAG
1 AAGAAAAAAAAAGAA-AAAAAAG
5817869 AAGAAAAAAAAAGAAAAAAAAG
1 AAGAAAAAAAAAGAAAAAAAAG
5817891 AAGA
1 AAGA
5817895 GAAGAGAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
22 23 0.92
23 2 0.08
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (22 bp):
AAGAAAAAAAAAGAAAAAAAAG
Found at i:5817882 original size:32 final size:36
Alignment explanation
Indices: 5817846--5817910 Score: 50
Period size: 32 Copynumber: 1.9 Consensus size: 36
5817836 TAAGAAGGAG
* * *
5817846 AAAGAAAAAAAAAAAGAAAAAAGAAGA-AA-AAAAAA
1 AAAGAAAAAAAAGAAGAGAAGAGAA-AGAAGAAAAAA
*
5817881 GAA-A-AAAA-AGAAGAGAAGAGAAAGAAGAAA
1 AAAGAAAAAAAAGAAGAGAAGAGAAAGAAGAAA
5817911 GATAAAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 6
0.71 0.12 0.18
Matches are distributed among these distances:
31 1 0.04
32 13 0.54
33 7 0.29
34 1 0.04
35 2 0.08
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (36 bp):
AAAGAAAAAAAAGAAGAGAAGAGAAAGAAGAAAAAA
Found at i:5817918 original size:32 final size:31
Alignment explanation
Indices: 5817844--5817923 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 31
5817834 TATAAGAAGG
5817844 AGAAAGAAAAAAAAAAAGAAAAAAGAAGAAAA
1 AGAAAG-AAAAAAAAAAGAAAAAAGAAGAAAA
* *
5817876 A-AAA-AGAAAAAAAAGAAGAGAAG-AGAAAGA
1 AGAAAGAAAAAAAAAAGAA-AAAAGAAGAAA-A
5817906 AGAAAGATAAAAAAAAAG
1 AGAAAGA-AAAAAAAAAG
5817924 TTTGAAAAGT
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
29 17 0.43
30 6 0.15
31 6 0.15
32 2 0.05
33 9 0.22
ACGTcount: A:0.80, C:0.00, G:0.19, T:0.01
Consensus pattern (31 bp):
AGAAAGAAAAAAAAAAGAAAAAAGAAGAAAA
Found at i:5833459 original size:49 final size:49
Alignment explanation
Indices: 5833322--5833565 Score: 150
Period size: 49 Copynumber: 4.9 Consensus size: 49
5833312 TACTTTTATC
* * *
5833322 TGAGACTTTTAAAGTTGTCAAGCCTTTGTTTAAAGGAG-TTTTCCCTAGA
1 TGAGACTTTTAAAGTTATCAAACCTTTGTTTAAAGGAGCTTTT-ACTAGA
* * * * ** * *
5833371 CGATATTTTTAAAGTTTTTGAACCTTTGTTTAAAAGAGCTTTTTCTAGA
1 TGAGACTTTTAAAGTTATCAAACCTTTGTTTAAAGGAGCTTTTACTAGA
* * * *
5833420 TGAGACTTTTAAAGTTATCAAACTTTTATCTAAAGGAGCTTTCTACAAGA
1 TGAGACTTTTAAAGTTATCAAACCTTTGTTTAAAGGAGCTTT-TACTAGA
* * * * * * * *
5833470 TGAGATTTTTTTAAAAGTTGTTAAGCCTTTGTTTAAAAGAGCCTTTTTCAAAA
1 TGAGA--CTTTT-AAAGTTATCAAACCTTTGTTTAAAGGAG-CTTTTACTAGA
* * * * * * *
5833523 TTAAAATTTTAAAATTGTCAAGCCTTTG-TTAAATGAGCTTTTA
1 TGAGACTTTTAAAGTTATCAAACCTTTGTTTAAAGGAGCTTTTA
5833566 GATTTATTTT
Statistics
Matches: 151, Mismatches: 38, Indels: 13
0.75 0.19 0.06
Matches are distributed among these distances:
48 5 0.03
49 75 0.50
50 30 0.20
51 4 0.03
52 4 0.03
53 29 0.19
54 4 0.03
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.42
Consensus pattern (49 bp):
TGAGACTTTTAAAGTTATCAAACCTTTGTTTAAAGGAGCTTTTACTAGA
Found at i:5835028 original size:14 final size:14
Alignment explanation
Indices: 5834977--5835031 Score: 58
Period size: 14 Copynumber: 3.9 Consensus size: 14
5834967 GAGTAAACAT
5834977 AAAGAAAAAAAAAGG
1 AAAGAAAAAAAAA-G
* *
5834992 AAA-AGAAGAAAAG
1 AAAGAAAAAAAAAG
* *
5835005 AGAGAGAAAAAAAG
1 AAAGAAAAAAAAAG
5835019 AAAGAAAAAAAAA
1 AAAGAAAAAAAAA
5835032 AGTTGTTAGG
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
13 3 0.09
14 27 0.82
15 3 0.09
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (14 bp):
AAAGAAAAAAAAAG
Found at i:5835080 original size:16 final size:15
Alignment explanation
Indices: 5835059--5835120 Score: 70
Period size: 16 Copynumber: 3.9 Consensus size: 15
5835049 TGTGAAAAGG
*
5835059 AGAAAGGGAAAGAATA
1 AGAAAGAGAAAGAA-A
5835075 AGAAAGAAGAAAGAAA
1 AGAAAG-AGAAAGAAA
5835091 AGAAAGAGAAAAGAAA
1 AGAAAGAG-AAAGAAA
* *
5835107 ATAAAGAAAAAGAA
1 AGAAAGAGAAAGAA
5835121 GAAAAAAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
15 8 0.20
16 26 0.63
17 7 0.17
ACGTcount: A:0.73, C:0.00, G:0.24, T:0.03
Consensus pattern (15 bp):
AGAAAGAGAAAGAAA
Found at i:5835125 original size:23 final size:22
Alignment explanation
Indices: 5835093--5835135 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
5835083 GAAAGAAAAG
* *
5835093 AAAGAGAAAAGAAAATAAAGAA
1 AAAGAGAAAAAAAAAAAAAGAA
5835115 AAAGAAGAAAAAAAAAAAAAG
1 AAAG-AGAAAAAAAAAAAAAG
5835136 GAAATTTGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.02
Consensus pattern (22 bp):
AAAGAGAAAAAAAAAAAAAGAA
Found at i:5835132 original size:16 final size:17
Alignment explanation
Indices: 5835077--5835135 Score: 64
Period size: 20 Copynumber: 3.2 Consensus size: 17
5835067 AAAGAATAAG
5835077 AAAGAAGAAAGAAAAGAA
1 AAAGAAGAAA-AAAAGAA
*
5835095 AGAGAAAAGAAAATAAAGAA
1 A-A-AGAAGAAAA-AAAGAA
*
5835115 AAAGAAGAAAAAAAAAA
1 AAAGAAGAAAAAAAGAA
5835132 AAAG
1 AAAG
5835136 GAAATTTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
17 9 0.26
18 9 0.26
19 3 0.09
20 14 0.40
ACGTcount: A:0.80, C:0.00, G:0.19, T:0.02
Consensus pattern (17 bp):
AAAGAAGAAAAAAAGAA
Found at i:5835139 original size:15 final size:16
Alignment explanation
Indices: 5835067--5835140 Score: 62
Period size: 16 Copynumber: 4.6 Consensus size: 16
5835057 GGAGAAAGGG
* *
5835067 AAAGAATAAGAAAGAAG
1 AAAGAA-AATAAAGAAA
* *
5835084 AAAGAAAAGAAAGAGA
1 AAAGAAAATAAAGAAA
5835100 AAAGAAAATAAAGAAAA
1 AAAGAAAATAAAG-AAA
5835117 AGAAGAAAA-AAA-AAA
1 A-AAGAAAATAAAGAAA
*
5835132 AAAGGAAAT
1 AAAGAAAAT
5835141 TTGAAAAGTC
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
14 6 0.12
15 4 0.08
16 20 0.41
17 12 0.24
18 7 0.14
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.04
Consensus pattern (16 bp):
AAAGAAAATAAAGAAA
Done.