Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold508
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: 522420
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36
File 3 of 3
Found at i:420767 original size:28 final size:28
Alignment explanation
Indices: 420688--420770 Score: 139
Period size: 28 Copynumber: 3.0 Consensus size: 28
420678 CAAATGCCAC
*
420688 CCTTTGTATTTGTCAAATATGGTAGTTT
1 CCTTTGTATTTGTCAAATATGGTGGTTT
*
420716 TCTTTGTATTTGTCAAATATGGTGGTTT
1 CCTTTGTATTTGTCAAATATGGTGGTTT
*
420744 CCTTTATATTTGTCAAATATGGTGGTT
1 CCTTTGTATTTGTCAAATATGGTGGTT
420771 ATTTTTGTTT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 51 1.00
ACGTcount: A:0.20, C:0.10, G:0.19, T:0.51
Consensus pattern (28 bp):
CCTTTGTATTTGTCAAATATGGTGGTTT
Found at i:420812 original size:24 final size:24
Alignment explanation
Indices: 420775--420820 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
420765 GTGGTTATTT
420775 TTGTTTGTACAAATTGGTGGCTTG
1 TTGTTTGTACAAATTGGTGGCTTG
420799 TTGTTTGT-CAAAATTGGTGGCT
1 TTGTTTGTAC-AAATTGGTGGCT
420821 AATTTTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.17, C:0.09, G:0.28, T:0.46
Consensus pattern (24 bp):
TTGTTTGTACAAATTGGTGGCTTG
Found at i:422427 original size:39 final size:40
Alignment explanation
Indices: 422349--422459 Score: 119
Period size: 39 Copynumber: 2.9 Consensus size: 40
422339 TTAACATAAA
*
422349 TTAAATTATTATT-TAAATAAT-A-A-AAAATATTTATTTT
1 TTAAA-TATTATTATAAATAATAATATAAAATATTTATATT
*
422386 TTAAAT-TTAATTATAAATATTAATATAAAATATTT-TATT
1 TTAAATATT-ATTATAAATAATAATATAAAATATTTATATT
* *
422425 TTAAATATTATTTTAAATAATAAAATAAAAT-TTTA
1 TTAAATATTATTATAAATAATAATATAAAATATTTA
422460 CATCAAGTCG
Statistics
Matches: 62, Mismatches: 5, Indels: 12
0.78 0.06 0.15
Matches are distributed among these distances:
35 2 0.03
36 4 0.06
37 12 0.19
38 4 0.06
39 29 0.47
40 11 0.18
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (40 bp):
TTAAATATTATTATAAATAATAATATAAAATATTTATATT
Found at i:422432 original size:14 final size:12
Alignment explanation
Indices: 422380--422443 Score: 51
Period size: 12 Copynumber: 5.2 Consensus size: 12
422370 AAAAAATATT
422380 TATT-TTTTAAA
1 TATTATTTTAAA
*
422391 T-TTAATTATAAA
1 TATT-ATTTTAAA
* *
422403 TATTAATATAAAA
1 TATT-ATTTTAAA
422416 TATTTTATTTTAAA
1 TA--TTATTTTAAA
422430 TATTATTTTAAA
1 TATTATTTTAAA
422442 TA
1 TA
422444 ATAAAATAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 9
0.74 0.11 0.16
Matches are distributed among these distances:
10 2 0.05
11 1 0.02
12 19 0.45
13 10 0.24
14 8 0.19
15 2 0.05
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
TATTATTTTAAA
Found at i:422441 original size:27 final size:26
Alignment explanation
Indices: 422373--422441 Score: 66
Period size: 27 Copynumber: 2.6 Consensus size: 26
422363 AAATAATAAA
**
422373 AAATATTTATTTTTTAAATTTAATTAT
1 AAATA-TTATTTTAAAAATTTAATTAT
* * * *
422400 AAATATTAATATAAAATATTTTATTTT
1 AAATATTATTTTAAAA-ATTTAATTAT
422427 AAATATTATTTTAAA
1 AAATATTATTTTAAA
422442 TAATAAAATA
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
26 7 0.21
27 26 0.79
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (26 bp):
AAATATTATTTTAAAAATTTAATTAT
Found at i:426399 original size:2 final size:2
Alignment explanation
Indices: 426387--426419 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
426377 TTTCATGTGT
*
426387 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
426420 GTTATAGTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:428622 original size:276 final size:278
Alignment explanation
Indices: 428120--428836 Score: 855
Period size: 279 Copynumber: 2.6 Consensus size: 278
428110 TGAAATATGA
* ** *
428120 TAGAATACAAGGAGAAAAAGAAA-AG--TAAATAAATTTATTCTAAGCTACAGTTTATGGTACAA
1 TAGAAT-CAAAGAGAAAAAGAAAGAGAATAAATAAATTTATTCTAAGCTACAACTTATGATACAA
* ** * * *
428182 GTCGTGAGTAATTAAACTTGCTTTTCGAGGT-TAGATGGTAGATTTTGATGATACAAGTCAAAAA
65 GTCTTGAGTAATTAAACTTATTTTTC-AAGTCTAGATGATAGATTTTGATGATACAAGTCAAAAG
* * * * *
428246 TAAGCCACAATCTTTTTAATTGTAAATAAATTATTCAAGAAAGTATTTTATCTTTTAAGATTAAA
129 TAAACCATAATCTTTTCAATTGTAAATAAATTATTCAAGAAAGTATTTTATCTTTTAAAACTAAA
* * *
428311 GTCATATGTGGCTAATTTATTTATTTTGCTTTCGAGTCTTGATCTCGTAAACGT-GTTAACAGTT
194 GTCATATGTGGCTAATTTATTTAGTTTACTTTCGAGTCTTGATCTCGTAAACGTAGTTAACAGCT
*
428375 TTGCTTTTTAAATTAAGTCT
259 TTGCTTTTTAAATTAAATCT
* * *
428395 TAGAAT--ATGAGGAAAAAGAAAGAGAATAAATAAATTTATTCCAAGCTACAACTTGTGATACAA
1 TAGAATCAAAGA-GAAAAAGAAAGAGAATAAATAAATTTATTCTAAGCTACAACTTATGATACAA
* *
428458 GTCTTGAGTAATTAAACTTATTTTTCAAGTCTAGATGATAGATTTTGATTATATAAGTCAAAAGT
65 GTCTTGAGTAATTAAACTTATTTTTCAAGTCTAGATGATAGATTTTGATGATACAAGTCAAAAGT
* * * * * * *
428523 AAATCATAATC-TTCCAACTGTAAATAAATTATTTAGGAAAGTGTTTTGTCTTTTAAAACTAAAG
130 AAACCATAATCTTTTCAATTGTAAATAAATTATTCAAGAAAGTATTTTATCTTTTAAAACTAAAG
* * ** *
428587 TCATATGTGGCTAATTTATTTAGTTTACTTTTCGAGTCTTGATTTCGTAAAGGTAGTTTTCTGCT
195 TCATATGTGGCTAATTTATTTAGTTTAC-TTTCGAGTCTTGATCTCGTAAACGTAGTTAACAGCT
428652 TTGCTTTTTAAATTAAATCT
259 TTGCTTTTTAAATTAAATCT
* * * *
428672 TAGAATCCAAAGAGAAAAAAAAAG-GAAATAAATAAAGTTATTTTAAGCTATAACTTATGATACA
1 TAGAAT-CAAAGAGAAAAAGAAAGAG-AATAAATAAATTTATTCTAAGCTACAACTTATGATACA
* * * * * * *
428736 AGTTTTGAGTAATTAAACTTGCTTTTT-AAGTCTAAATAATAAATTTTAATGACACAAGTCAAAA
64 AGTCTTGAGTAATTAAACTT-ATTTTTCAAGTCTAGATGATAGATTTTGATGATACAAGTCAAAA
428800 GTAAACCACT-ATCTTTTC-ATTGTAAATAAATTATTCA
128 GTAAACCA-TAATCTTTTCAATTGTAAATAAATTATTCA
428837 TTGTAAATAA
Statistics
Matches: 373, Mismatches: 55, Indels: 24
0.83 0.12 0.05
Matches are distributed among these distances:
272 3 0.01
273 10 0.03
274 2 0.01
275 79 0.21
276 116 0.31
277 31 0.08
278 1 0.00
279 119 0.32
280 12 0.03
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (278 bp):
TAGAATCAAAGAGAAAAAGAAAGAGAATAAATAAATTTATTCTAAGCTACAACTTATGATACAAG
TCTTGAGTAATTAAACTTATTTTTCAAGTCTAGATGATAGATTTTGATGATACAAGTCAAAAGTA
AACCATAATCTTTTCAATTGTAAATAAATTATTCAAGAAAGTATTTTATCTTTTAAAACTAAAGT
CATATGTGGCTAATTTATTTAGTTTACTTTCGAGTCTTGATCTCGTAAACGTAGTTAACAGCTTT
GCTTTTTAAATTAAATCT
Found at i:428826 original size:279 final size:277
Alignment explanation
Indices: 428134--428968 Score: 896
Period size: 276 Copynumber: 2.9 Consensus size: 277
428124 ATACAAGGAG
* ** * *
428134 AAAAAGAAAAGTAAATAAATTTATTCTAAGCTACAGTTTATGGTACAAGTCGTGAGTAATTAAAC
1 AAAAAGGAAA-TAAATAAATTTATTCTAAGCTACAACTTATGATACAAGTCTTGAGTAATTAAAC
* * * * * *
428199 TTGCTTTTCGAGGT-TAGATGGTAGATTTTGATGATACAAGTCAAAAATAAGCCACAATCTTTTT
65 TTGCTTTT-TAAGTCTAGATGATAGATTTTGATGATACAAGTCAAAAGTAAACCACTATC-TTTT
* * * *
428263 AATTGTAAATAAATTATTCAAGAAAGTATTTTATCTTTTAAGATTAAAGTCATATGTGGCTAATT
128 CATTGTAAATAAATTATTTAAGAAAGTGTTTTATCTTTTAAGACTAAAGTCATATGTGGCTAATT
* * ** *
428328 TATTTATTTTGC-TTTCGAGTCTTGATCTCGTAAACGT-GTTAACAGTTTTGCTTTTTAAATTAA
193 TATTTAGTTTACTTTTCGAGTCTTGATCTCGTAAACGTAGTTTTCTGTTTTGCTTTTTAAATTAA
* *
428391 GTCTTAGAATATGAGGAAAA
258 ATCTTAGAATAAGAGGAAAA
* * *
428411 AGAAA-GAGAATAAATAAATTTATTCCAAGCTACAACTTGTGATACAAGTCTTGAGTAATTAAAC
1 AAAAAGGA-AATAAATAAATTTATTCTAAGCTACAACTTATGATACAAGTCTTGAGTAATTAAAC
* * * * *
428475 TT-ATTTTTCAAGTCTAGATGATAGATTTTGATTATATAAGTCAAAAGTAAATCA-TAATC-TTC
65 TTGCTTTTT-AAGTCTAGATGATAGATTTTGATGATACAAGTCAAAAGTAAACCACT-ATCTTTT
* * * *
428537 CAACTGTAAATAAATTATTTAGGAAAGTGTTTTGTCTTTTAAAACTAAAGTCATATGTGGCTAAT
128 C-ATTGTAAATAAATTATTTAAGAAAGTGTTTTATCTTTTAAGACTAAAGTCATATGTGGCTAAT
* * *
428602 TTATTTAGTTTACTTTTCGAGTCTTGATTTCGTAAAGGTAGTTTTCTGCTTTGCTTTTTAAATTA
192 TTATTTAGTTTACTTTTCGAGTCTTGATCTCGTAAACGTAGTTTTCTGTTTTGCTTTTTAAATTA
428667 AATCTTAGAATCCAA-AGAGAAAA
257 AATCTTAGAAT--AAGAG-GAAAA
* * * *
428690 AAAAAGGAAATAAATAAAGTTATTTTAAGCTATAACTTATGATACAAGTTTTGAGTAATTAAACT
1 AAAAAGGAAATAAATAAATTTATTCTAAGCTACAACTTATGATACAAGTCTTGAGTAATTAAACT
* * * * *
428755 TGCTTTTTAAGTCTAAATAATAAATTTTAATGACACAAGTCAAAAGTAAACCACTATCTTTTCAT
66 TGCTTTTTAAGTCTAGATGATAGATTTTGATGATACAAGTCAAAAGTAAACCACTATCTTTTCAT
* *
428820 TGTAAATAAATTATTCATTGTAAATAAATTATTCAAGGATGTGTTCTATCTTTTAAGACTAAATT
131 TGTAAAT-AA--ATT-A-T-T---T-AA-GA---AA-G-TGT-TT-TATCTTTTAAGACTAAAGT
* *
428885 CATATGTGACTAATTTATTTAGTTTACTTTTCGAGTCTTGATCTCGTAAACGTA-TTTTTTGTTT
178 CATATGTGGCTAATTTATTTAGTTTACTTTTCGAGTCTTGATCTCGTAAACGTAGTTTTCTGTTT
*
428949 TGCTTTTTAAATTATATCTT
243 TGCTTTTTAAATTAAATCTT
428969 GTTGCTAGGT
Statistics
Matches: 460, Mismatches: 66, Indels: 45
0.81 0.12 0.08
Matches are distributed among these distances:
274 2 0.00
275 74 0.16
276 111 0.24
277 37 0.08
278 2 0.00
279 110 0.24
280 13 0.03
282 3 0.01
283 1 0.00
284 1 0.00
285 1 0.00
288 1 0.00
289 1 0.00
290 1 0.00
293 2 0.00
294 1 0.00
295 3 0.01
296 29 0.06
297 67 0.15
ACGTcount: A:0.36, C:0.10, G:0.14, T:0.40
Consensus pattern (277 bp):
AAAAAGGAAATAAATAAATTTATTCTAAGCTACAACTTATGATACAAGTCTTGAGTAATTAAACT
TGCTTTTTAAGTCTAGATGATAGATTTTGATGATACAAGTCAAAAGTAAACCACTATCTTTTCAT
TGTAAATAAATTATTTAAGAAAGTGTTTTATCTTTTAAGACTAAAGTCATATGTGGCTAATTTAT
TTAGTTTACTTTTCGAGTCTTGATCTCGTAAACGTAGTTTTCTGTTTTGCTTTTTAAATTAAATC
TTAGAATAAGAGGAAAA
Found at i:428838 original size:18 final size:18
Alignment explanation
Indices: 428815--428854 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
428805 CCACTATCTT
428815 TTCATTGTAAATAAATTA
1 TTCATTGTAAATAAATTA
428833 TTCATTGTAAATAAATTA
1 TTCATTGTAAATAAATTA
428851 TTCA
1 TTCA
428855 AGGATGTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.45
Consensus pattern (18 bp):
TTCATTGTAAATAAATTA
Found at i:429464 original size:17 final size:18
Alignment explanation
Indices: 429442--429475 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
429432 TCGTATTTTT
429442 ATTTAA-AAATTAATTAA
1 ATTTAAGAAATTAATTAA
*
429459 ATTTAAGAAATTTATTA
1 ATTTAAGAAATTAATTA
429476 CTACATCTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (18 bp):
ATTTAAGAAATTAATTAA
Found at i:432899 original size:358 final size:356
Alignment explanation
Indices: 431349--436353 Score: 4212
Period size: 358 Copynumber: 13.9 Consensus size: 356
431339 ATTTTCAAGC
* * * * *
431349 GAGAATTTCATAAC-AAAAATTTAAACATTTACTTATAAACACTATATCAACTAATTATTTTTAT
1 GAGAATTTGATAACAAAAAATTAAAAC-TTTACTTATAAACA-TGTATCAACTAGTTTTTTTTAT
* * * *
431413 CATTTGAGAGTTATAGATTTGAGATT-GATCAGTATAATAAA-AAAA-TCATTTAAAACTT-TCA
64 CATTT--GAGCTATAAATTTGAGATTCG-TC---ATAATAAATAAAACT-ATTT-GAAGTTGTC-
* *
431474 TAATTAAATATTATAAAAATAAATAGAAGTTGGATG--TT----AA-AAAA-AATAATAAAATTG
120 --A-TAAATATTATAAAAATAAATAGAAGTTGGATGTTTTAAAAAAGAAAAGAAAAATAAAATAG
* * * * * * * * * *
431531 AAGCCTATAGCGCTAAAGAAATAAATTAAGTTTTGAATTGTAAGGGATTTAATTCAATGTTTTAA
182 ACGCTTATAGCACTCAAGAAATAAATTAAGTTTTGACTT-T-TGAGATTTAATTTAATGTTTCAG
* * * * ** * * * * ** * * * * *
431596 GTAAAATTTCATCAAT-TTTTTGAAACCTGATTTCTCTCGAGTATTTTTATTTTTCTAGTAATAA
245 GTGAAATTCCA-C-CTGTTATTGAAAATTAACTTCTCTCAATTACCTTGATCTTTGTAATAACAA
*
431660 CTTAATAGGTATAATTTCATCTTTCTTCTACTTTTCTCAATTTTTTAGGT
308 CTTAACAGGTATAATTTCATCTTTCTTCTACTTTTCTCAA-TTTTTAGGT
* * * *
431710 AAAAATTTGATAACAAAAAAAATTAAAACTTTACTTATAACCATGTATCAACTAGAGTTTTTTTA
1 GAGAATTTGATAAC--AAAAAATTAAAACTTTACTTATAAACATGTATCAACTAG-TTTTTTTTA
* * * * * * * * *
431775 TTATCTGAGTTATAAGTTTGAGATTCGTCATATTAATTAAAACCACTT-AGAGTTGTCATAAGTA
63 TCATTTGAGCTATAAATTTGAGATTCGTCATAATAAATAAAACTATTTGA-AGTTGTCATAAATA
*
431839 TTATAAAAATAAATAGAAGTTGGATGTTTT----AA-AAAAG-AAAA-AAAATAGACGCCTATAG
127 TTATAAAAATAAATAGAAGTTGGATGTTTTAAAAAAGAAAAGAAAAATAAAATAGACGCTTATAG
* * * * *
431897 CACGT-AAGCACTAAATTTAACTTTTGACTTTTGCGAATTTCATTTAATGTTTCAGGTGAAATTC
192 CAC-TCAAGAAATAAA-TTAAGTTTTGACTTTTGAG-ATTTAATTTAATGTTTCAGGTGAAATTC
* * *
431961 CACTTGTTATTGGAAAATTAACTTCTCTCTATTACCTTGATCTTTGTACTAACAACTTAACAGGT
254 CACCTGTTATT-GAAAATTAACTTCTCTCAATTACCTTGATCTTTGTAATAACAACTTAACAGGT
* * * *
432026 ATAATTTCGTCTTTCTTCAACTTGTCTCAATTTTTTGGT
318 ATAATTTCATCTTTCTTCTACTTTTCTCAATTTTTAGGT
432065 GAGAATTTGATAACAAAAAATTAAAACTTTACTT-TAAACATGTATCAACTAGTTTTTTTTTTAA
1 GAGAATTTGATAACAAAAAATTAAAACTTTACTTATAAACATGTATCAACTAG--TTTTTTTT-A
* * * * * * *
432129 CCGTTTGAGCTATAAATTTGAGATTGGTCATAA-GAATAAAAATTATTTGAAGCTATCATAATTA
63 TCATTTGAGCTATAAATTTGAGATTCGTCATAATAAAT-AAAACTATTTGAAGTTGTCAT-A--A
* * * *
432193 AGTATTATAAAAATAAATAGAAGTTGGATGTTTTAAAAAATAAAAGAAAAATACAATAGATGCTA
124 A-TATTATAAAAATAAATAGAAGTTGGATGTTTTAAAAAAGAAAAGAAAAATAAAATAGACGCTT
* * * * * * *
432258 ATAACACTTAAGAAATAAATTAAGTTTTCACTTGTGATGGACTTACTTCAATGTTTCAGGTGAAA
188 ATAGCACTCAAGAAATAAATTAAGTTTTGACTTTTGA--GATTTAATTTAATGTTTCAGGTGAAA
* * * ** ** * *
432323 TTCCAGCAGATATTGGAAACCTAACTTCTCTCAATTACCTTTTTCTTTGTAATAATAACTTAAAA
251 TTCCACCTGTTATT-GAAAATTAACTTCTCTCAATTACCTTGATCTTTGTAATAACAACTTAACA
* *
432388 GGTATAATTTCATCTTTCTTCTACTTTTCTTAAATTTTTGGGT
315 GGTATAATTTCATCTTTCTTCTACTTTTC-TCAATTTTTAGGT
* * * *
432431 TAAAATTTGATAACAAAAAATTAAAACTTTTCTTATAAGCATGTATCAACTAG-TTTTTTTATCA
1 GAGAATTTGATAACAAAAAATTAAAACTTTACTTATAAACATGTATCAACTAGTTTTTTTTATCA
** * * * *
432495 TCCGAGCTATAAATTTGAGGTTCGTCAT-ATTAATAAAACCATTTGAAGTTTTCATAAATATTAT
66 TTTGAGCTATAAATTTGAGATTCGTCATAATAAATAAAACTATTTGAAGTTGTCATAAATATTAT
** * * *
432559 AAAAATAAGCAGAAGTTGGATGTTTTAGAAAAGAAAAGAAAATTAAAATAGATGCTTATAGCACT
131 AAAAATAAATAGAAGTTGGATGTTTTAAAAAAGAAAAGAAAAATAAAATAGACGCTTATAGCACT
* * * * * *
432624 TAAGAAATAAATTAAGTTTTAACTTTTGTAGATTTAATTTAATGTTTGAGGTGAAATTTCACATT
196 CAAGAAATAAATTAAGTTTTGACTTTTG-AGATTTAATTTAATGTTTCAGGTGAAATTCCACCTG
* * * * *
432689 TTATTAAAAAGTTGACTTCTTTCAATTA-CTTGATCTTTGTACTAATAACTTAACAGGTATAATT
260 TTATTGAAAA-TTAACTTCTCTCAATTACCTTGATCTTTGTAATAACAACTTAACAGGTATAATT
* * * *
432753 TCATCTTTCTTTTATTTTTATCAAATTTTAGGT
324 TCATCTTTCTTCTACTTTTCTCAATTTTTAGGT
* ** * * *
432786 GAGAATTTGATAACAAAATATTAAATTTTTATTTATAAACATGTATCAGCTAGTTTTTTTTATTA
1 GAGAATTTGATAACAAAAAATTAAAACTTTACTTATAAACATGTATCAACTAGTTTTTTTTATCA
* * * *
432851 TTTTAGCTATAAATTTAAGATTTGTCATAATAAATAAGAACTATTTGAAGCTAGTCATAATTAGG
66 TTTGAGCTATAAATTTGAGATTCGTCATAATAAATAA-AACTATTTGAAG-TTGTCATAA--A--
* * * * *
432916 TATTATTAAAGTAGAT-GTCATAATTAGGTAT-TATAAAAGTAGATAGAAGTTGCATGTTAAAA-
125 TATTATAAAAATAAATAG--A-AGTT-GG-ATGT-T----TTA-A-A-AA-----A-G--AAAAG
* * * * * * *
432978 AAATAATAAAATATATGCTTATAACGCTCAAGAAATAAATTAAATTTTAACTTGTGAGAAATTTA
169 AAA-AATAAAATAGACGCTTATAGCACTCAAGAAATAAATTAAGTTTTGACTTTTGAG--ATTTA
* * * * **
433043 ATTTAATATTTCAGGTAAAATTCCA-CTAGTTATTGAAAATTTGACTTCTCTC-ATCAGCCTTTC
231 ATTTAATGTTTCAGGTGAAATTCCACCT-GTTATTGAAAA-TTAACTTCTCTCAATTA-CCTTGA
* ** * * *
433106 TCTTTCTAATAACAACTTAACAGGTATGCTTTCGTATTTCTT-TCACTTTTATCAATTTTTAGGT
293 TCTTTGTAATAACAACTTAACAGGTATAATTTCATCTTTCTTCT-ACTTTTCTCAATTTTTAGGT
* * * *
433170 AAGAATTTGATAACAAAAAATTAAAACTTTACTTATAAACATGTATCAACTAATTTTTTTAATTA
1 GAGAATTTGATAACAAAAAATTAAAACTTTACTTATAAACATGTATCAACTAGTTTTTTTTATCA
* * * * *
433235 TTTGAGCTATAAATTTGAGATTGGTCATAACAACA-AAAATTATTTGAAGCTGTCATAATTAAGT
66 TTTGAGCTATAAATTTGAGATTCGTCATAATAA-ATAAAACTATTTGAAGTTGTCATAAAT-A-T
* * * * *
433299 ATATAAAAATAAATAGAAGTTAGATGTTTCAAAAAAG---A-AAAAATAAAATAAACACCTATAG
128 -TATAAAAATAAATAGAAGTTGGATGTTTTAAAAAAGAAAAGAAAAATAAAATAGACGCTTATAG
* * *
433360 CA-TGCAAGAAATAAATTTAAGTGTTGACTTTTGCGGATTTAATTCAATGTTTCAGGTGAAATTC
192 CACT-CAAGAAATAAA-TTAAGTTTTGACTTTTG-AGATTTAATTTAATGTTTCAGGTGAAATTC
* * * * * *
433424 CACCCGATATTGGAAAATTAACCTCTCTCAATTACCTTGATTTTTGTACTAACCACTTAACAGGT
254 CACCTGTTATT-GAAAATTAACTTCTCTCAATTACCTTGATCTTTGTAATAACAACTTAACAGGT
* * *
433489 ATAATTTTATCTTTCTTCAACTTTTCTCAATTTTTGGGT
318 ATAATTTCATCTTTCTTCTACTTTTCTCAATTTTTAGGT
* * * *
433528 GAGAATTTGATAACAAAAAATTAAAATTTTACTT-TCAAAAATGTAACAACTAGGTTTTTTTAAT
1 GAGAATTTGATAACAAAAAATTAAAACTTTACTTAT-AAACATGTATCAACTA-GTTTTTTTTAT
* * * * *
433592 CATTTAAGCTATAAATTTGAGATTGGTCATAA-GAATAAAAATCATTTGAAGCTGTCAGAATTAA
64 CATTTGAGCTATAAATTTGAGATTCGTCATAATAAATAAAACT-ATTTGAAGTTGTC---A-TAA
* * * ** * * **
433656 GTATTATAAAAATAAATAAAAGTTAGATACTTTAAAAAATAAAAGAAAAATAAAATAGATGCCAA
124 ATATTATAAAAATAAATAGAAGTTGGATGTTTTAAAAAAGAAAAGAAAAATAAAATAGACGCTTA
* * * *
433721 TAACACTCAAGAAATAAATTAAGTTTTAACTTGTGAGGGACTTAATTTAATGTTTCAGGTGAAAT
189 TAGCACTCAAGAAATAAATTAAGTTTTGACTTTTGA--GATTTAATTTAATGTTTCAGGTGAAAT
* * ** * ** * *
433786 TCCACCGGTTATTGGAAACTTGGCTTCTCTCAACTACCTTTTTCTTTGTAAAAACAACTTAAAAG
252 TCCACCTGTTATT-GAAAATTAACTTCTCTCAATTACCTTGATCTTTGTAATAACAACTTAACAG
* *
433851 GTATAATTTCATCTTTTTTCTACTTTTCTCAATTTTTTGGAT
316 GTATAATTTCATCTTTCTTCTACTTTTCTCAATTTTTAGG-T
* *
433893 GAGAATTTGATAACAAAAAAAATTAAAATTTTACTTATAAGCATGTATCAACTAGTTTTTTTTTT
1 GAGAATTTGATAAC--AAAAAATTAAAACTTTACTTATAAACATGTATCAACTAG--TTTTTTTT
* * * * * * *
433958 ATCATCTGAGCTATAAATTTAAAATTCATCAT-ATTAATAAAACCATTTGAAGTTGTCATAAGTA
62 ATCATTTGAGCTATAAATTTGAGATTCGTCATAATAAATAAAACTATTTGAAGTTGTCATAAATA
* * * * *
434022 TTATAAAAATAAATAGAAATTGGATGTTTTAAAAAAGAAAAGAAAAATAAAATAAACACCTATAA
127 TTATAAAAATAAATAGAAGTTGGATGTTTTAAAAAAGAAAAGAAAAATAAAATAGACGCTTATAG
* * * *
434087 CA-TGCAAGAAATAAATTTAACTCTTT-ACTTTTTACGGGTTTAATTTAATATTTCAGGTGAAAT
192 CACT-CAAGAAATAAA-TTAAGT-TTTGACTTTTGA--GATTTAATTTAATGTTTCAGGTGAAAT
* ** * * ** *
434150 TCCGCCCATTATTGGAAAATTAACTTCTCTCCATTACCTTGATCTCTGTGTTAACAGCTTAACAG
252 TCCACCTGTTATT-GAAAATTAACTTCTCTCAATTACCTTGATCTTTGTAATAACAACTTAACAG
* ** * ***
434215 GTATATTTTTGTTTTTCTT-TAACTTTTCTCAATTTAGGGGT
316 GTATAATTTCATCTTTCTTCT-ACTTTTCTCAATTTTTAGGT
* * * * *
434256 AAGAATTTGAT---AAAAAATTAAAACTTTACTTATAAACATATATCAATTAGGTTTTTTTACTG
1 GAGAATTTGATAACAAAAAATTAAAACTTTACTTATAAACATGTATCAACTAGTTTTTTTTA-TC
* * *
434318 ATTTGAGCTATAAATTTGAGATTGGTCATAAT-AATAAAATTCATTTGAAGCTT-TTATAATTAA
65 ATTTGAGCTATAAATTTGAGATTCGTCATAATAAATAAAACT-ATTTGAAG-TTGTCAT-A--AA
* * * *
434381 GTATTATAAAAATAAATAAAAGTTAGATGTTTTAAAAAATAAAAGAAAAATAAAATAGACGCTTG
125 -TATTATAAAAATAAATAGAAGTTGGATGTTTTAAAAAAGAAAAGAAAAATAAAATAGACGCTTA
* * * * *
434446 TAGCATTCAAGAAATAAATTAAGTTTTGACTTGTGAGAGACTTAATTCAATATTTCAGGTGAAAT
189 TAGCACTCAAGAAATAAATTAAGTTTTGACTT-T-TGAGATTTAATTTAATGTTTCAGGTGAAAT
* * * * ** *
434511 TCCATCAGTTATTGGAAACTTGACTTCTCTCAA-TAGCCTTTTTCTTTGTAATAACAATTTAACA
252 TCCACCTGTTATT-GAAAATTAACTTCTCTCAATTA-CCTTGATCTTTGTAATAACAACTTAACA
* * * * *
434575 GGTATAGTTTCATCTTTTTTCTACGTTTCTCGATTTTTTGGGT
315 GGTATAATTTCATCTTTCTTCTACTTTTCTC-AATTTTTAGGT
* * * *
434618 GAGATTTTGATAACAAAAAATTAAAATTTTACTTATAAACGTGTATTAACTAG-TTTTTTTATCA
1 GAGAATTTGATAACAAAAAATTAAAACTTTACTTATAAACATGTATCAACTAGTTTTTTTTATCA
* * * ** * * *
434682 TTCGAGCTATAAATTTGAGATTCGTTATATTAGTTAAAACCATTTAAAGTTGT--TAAGTATTAT
66 TTTGAGCTATAAATTTGAGATTCGTCATAATAAATAAAACTATTTGAAGTTGTCATAAATATTAT
* * * * *
434745 AAAAATAAATAGAAGTTAGATGTTTTAAAAAAGAAAAGAAAAATAAAATAAACGCCTATAACACG
131 AAAAATAAATAGAAGTTGGATGTTTTAAAAAAGAAAAGAAAAATAAAATAGACGCTTATAGCACT
* * *
434810 CAAGAAATAAATTTAACTTTTGACTTTTTACGAATTTAATTCAATGTTTCAGGTGAAATTCCACC
196 CAAGAAATAAA-TTAAGTTTTGACTTTTGA-G-ATTTAATTTAATGTTTCAGGTGAAATTCCACC
* ** *
434875 TGTTATTGGAAAATTAACTTCTCTCCATTACCTTGATCTTTGTGTTAACAGCTTAACAGGTATAA
258 TGTTATT-GAAAATTAACTTCTCTCAATTACCTTGATCTTTGTAATAACAACTTAACAGGTATAA
** * * *
434940 TTTTGTCTTTTTTCAACTTTTCTCAATTTTTGGGT
322 TTTCATCTTTCTTCTACTTTTCTCAATTTTTAGGT
* * *
434975 GAGAATTTGAT---AAAAAATTAAAACTTTACTTATAAACATATATCGATTAGTTTTTTTTTAAT
1 GAGAATTTGATAACAAAAAATTAAAACTTTACTTATAAACATGTATCAACTAG-TTTTTTTT-AT
* * * ** *
435037 CATTTGAGCTATAAATTTGAGATTGGTCATAA-CAATAAAATTCATACGAAGCTGTCATAATTAA
64 CATTTGAGCTATAAATTTGAGATTCGTCATAATAAATAAAACT-ATTTGAAGTTGTCAT-A--AA
* **
435101 GTATTATAAAAATAAATAGAAGTTAGATGTTTTAAAAAAAGAAAAGAAAAATAAAATAGACATTT
125 -TATTATAAAAATAAATAGAAGTTGGATGTTTT-AAAAAAGAAAAGAAAAATAAAATAGACGCTT
** * * *
435166 ATAGTTCTCAAGAAGTAAATTAAGTTTTGACTTGTGAGACATTTAATTCAATGTTTCAGGTGAAA
188 ATAGCACTCAAGAAATAAATTAAGTTTTGACTTTTGAG--ATTTAATTTAATGTTTCAGGTGAAA
* ** * * * ** * *
435231 TTCCACCGGTTATTGGAAACCTGACTTTTCTTC-ATAACCTTTTTCTTTGTAAAAATAACTTAAC
251 TTCCACCTGTTATT-GAAAATTAACTTCTC-TCAATTACCTTGATCTTTGTAATAACAACTTAAC
*
435295 AGGTATAATTTCATCTTTCTTCTACTTTTCTCAATTTTTGGGT
314 AGGTATAATTTCATCTTTCTTCTACTTTTCTCAATTTTTAGGT
*
435338 GAGAATTTGATAAC-AAAAATTAAAACTTTACTTAAAAACATGTATCAACTAG-TTTTTTTATCA
1 GAGAATTTGATAACAAAAAATTAAAACTTTACTTATAAACATGTATCAACTAGTTTTTTTTATCA
** * * * * *
435401 TCCGAGCCATAAATTTGAGATTCGTCATATTAATTAAAACTATTTGAAGTTGTTATAAGTATTAT
66 TTTGAGCTATAAATTTGAGATTCGTCATAATAAATAAAACTATTTGAAGTTGTCATAAATATTAT
435466 AAAAATAAATAGAAGTTGGATGTTTTAAAAAAGAAAAGAAAAGAAAAATAAAATTA-ACGCTTAT
131 AAAAATAAATAGAAGTTGGATGTTTT----AA-AAAAGAAAAGAAAAATAAAA-TAGACGCTTAT
* * * * * *
435530 AGCACTTAAAAAATAAATTAAGTTTTAACTTTTGCGGATTTAATTTAATGCTTAAGGTGAAATTC
190 AGCACTCAAGAAATAAATTAAGTTTTGACTTTTG-AGATTTAATTTAATGTTTCAGGTGAAATTC
* * * * * *
435595 CACCTTTTATTGGAAAATTAACTTCTCTCATTTACCTTGATCTTTCTCATAACAACTTAATAAGT
254 CACCTGTTATT-GAAAATTAACTTCTCTCAATTACCTTGATCTTTGTAATAACAACTTAACAGGT
* *
435660 ATAATTTCATCTTTCTTCTACTTTTGTCAATTTTTAGCT
318 ATAATTTCATCTTTCTTCTACTTTTCTCAATTTTTAGGT
* * *
435699 GAGAATTTGATAACAAAATATTAAAACTTTGCTTATAAACATGTATCAACTAG-GTTTTTTATCA
1 GAGAATTTGATAACAAAAAATTAAAACTTTACTTATAAACATGTATCAACTAGTTTTTTTTATCA
* * ** *
435763 TTTGAGCTAT-AA----A-ATTCGTAAGAATAAATAAGAA-TCATTTGAAACTGTTATAATTAGT
66 TTTGAGCTATAAATTTGAGATTCGTCATAATAAATAA-AACT-ATTTGAAGTTGTCATAA--A--
* * * * * *
435821 TATTATAAAAATAGATAGAAGTTGCA--ATTT-AAAAA-AAAA-TAAAATAAAATATACACTTAT
125 TATTATAAAAATAAATAGAAGTTGGATGTTTTAAAAAAGAAAAGAAAAATAAAATAGACGCTTAT
**** * *
435881 AATGTTCAAGAAATAAATTCAA-TTTTGACTTATGAGGGATTTAATTTAATGTTTTAGGTGAAAT
190 AGCACTCAAGAAATAAATT-AAGTTTTGACTTTTGA--GATTTAATTTAATGTTTCAGGTGAAAT
* * * * * * * * *
435945 TTCACCAGTTATTGGAAATTTGACTTCTCTCAAGTGCCTTTATCTTTTTAATAACAATTTAACAG
252 TCCACCTGTTATT-GAAAATTAACTTCTCTCAATTACCTTGATCTTTGTAATAACAACTTAACAG
* *
436010 GTATACTTTTATCTTTCTTCTACTTTTCTCAATTTTTAGGT
316 GTATAATTTCATCTTTCTTCTACTTTTCTCAATTTTTAGGT
* * *
436051 GAGAATTTGATACCAAAAAATTAAAACTTTATTTATAAATATGTATCAACTA-TTTTTTTTATCA
1 GAGAATTTGATAACAAAAAATTAAAACTTTACTTATAAACATGTATCAACTAGTTTTTTTTATCA
* * * *
436115 TTTGAGCTATAAATTTGAGATTTGTCATAATAATTAAAACCATTTGAAGTTGTCATAAGTATTAT
66 TTTGAGCTATAAATTTGAGATTCGTCATAATAAATAAAACTATTTGAAGTTGTCATAAATATTAT
* * * * * ** *
436180 ACAAATAAATAAAAGCTGTAAGTTTT--------TTA-AAAAATAAAATAGACGCCTATTATG--
131 AAAAATAAATAGAAGTTGGATGTTTTAAAAAAGAAAAGAAAAATAAAATAGACGCTTA-TA-GCA
* * * * * *
436234 CTTAAGAAATAAATTATGTTTTGACTTTTGAGTGATTTAATTCAATATTTCAAGTGAAATTTCAC
194 CTCAAGAAATAAATTAAGTTTTGACTTTTGA--GATTTAATTTAATGTTTCAGGTGAAATTCCAC
* * *** * * * *
436299 TTGTTATTGAAAACGTGTTTTCTCTCAATTAACTTGCTCTTTCTCATAACAACTT
257 CTGTTATTGAAAA-TTAACTTCTCTCAATTACCTTGATCTTTGTAATAACAACTT
436354 GGCATGTATA
Statistics
Matches: 3785, Mismatches: 671, Indels: 388
0.78 0.14 0.08
Matches are distributed among these distances:
348 5 0.00
349 107 0.03
350 4 0.00
351 39 0.01
352 203 0.05
353 56 0.01
354 75 0.02
355 117 0.03
356 237 0.06
357 281 0.07
358 524 0.14
359 108 0.03
360 41 0.01
361 289 0.08
362 274 0.07
363 400 0.11
364 354 0.09
365 214 0.06
366 47 0.01
367 66 0.02
368 41 0.01
370 2 0.00
371 3 0.00
372 1 0.00
373 2 0.00
374 2 0.00
377 3 0.00
378 3 0.00
379 5 0.00
380 3 0.00
381 15 0.00
382 61 0.02
383 58 0.02
384 144 0.04
385 1 0.00
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.39
Consensus pattern (356 bp):
GAGAATTTGATAACAAAAAATTAAAACTTTACTTATAAACATGTATCAACTAGTTTTTTTTATCA
TTTGAGCTATAAATTTGAGATTCGTCATAATAAATAAAACTATTTGAAGTTGTCATAAATATTAT
AAAAATAAATAGAAGTTGGATGTTTTAAAAAAGAAAAGAAAAATAAAATAGACGCTTATAGCACT
CAAGAAATAAATTAAGTTTTGACTTTTGAGATTTAATTTAATGTTTCAGGTGAAATTCCACCTGT
TATTGAAAATTAACTTCTCTCAATTACCTTGATCTTTGTAATAACAACTTAACAGGTATAATTTC
ATCTTTCTTCTACTTTTCTCAATTTTTAGGT
Found at i:432939 original size:28 final size:28
Alignment explanation
Indices: 432904--432959 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
432894 TTTGAAGCTA
*
432904 GTCATAATTAGGTATTATTAAAGTAGAT
1 GTCATAATTAGGTATTATAAAAGTAGAT
432932 GTCATAATTAGGTATTATAAAAGTAGAT
1 GTCATAATTAGGTATTATAAAAGTAGAT
432960 AGAAGTTGCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.41, C:0.04, G:0.18, T:0.38
Consensus pattern (28 bp):
GTCATAATTAGGTATTATAAAAGTAGAT
Found at i:435358 original size:719 final size:718
Alignment explanation
Indices: 431349--436190 Score: 5149
Period size: 721 Copynumber: 6.7 Consensus size: 718
431339 ATTTTCAAGC
* * * * *
431349 GAGAATTTCATAACAAAAATTTAAACATTTACTTATAAACACTATATCAACTAATTATTTTT-AT
1 GAGAATTTGATAA-AAAAATTAAAAC-TTTACTTATAAACA-TGTATCAACTAGTTTTTTTTAAT
* * * * * * * *
431413 CATTTGAGAGTTATAGATTTGAGATTGATCAGTATA-ATAAAAAAATCATTTAAAACTTTCATAA
63 CATTT--GAGCTATAAATTTGAGATTGGTCA-TA-AGA-ATAAAATTCATTTGAAGCTGTCATAA
* * * *
431477 TTAAATATTATAAAAATAAATAGAAGTTGGATG--TT----AA-AAAA-AATAATAAAATTGA-A
123 TTAAGTATTATAAAAATAAATAGAAGTTAGATGTTTTAAAAAATAAAAGAAAAATAAAATAGACA
* * * * * * * * *
431533 GCCTATAGCGCTAAAGAAATAAATTAAGTTTTGAATTGTAAGGGATTTAATTCAATGTTTTAAGT
188 -CTTATAACTCTCAAGAAATAAATTAAGTTTTGACTTGTGAGAGATTTAATTCAATGTTTCAGGT
* * * * * * * * * * * * *
431598 AAAATTTCATCAATTTTTTGAAACCTGATTTCTCTCGAGT-A-TTTTTATTTTTCTAGTAATAAC
252 GAAATTCCACCAGTTATTGGAAACTTGACTTCTCTC-A-TAACCTTTT-TCTTTGTAATAACAAC
* * * *
431661 TTAATAGGTATAATTTCATCTTTCTTCTACTTTTCTCAATTTTTTAGGTAAAAATTTGATAACAA
314 TTAACAGGTATAATTTCATCTTTCTTCTACTTTTCTCAA-TTTTTGGGTGAGAATTTGATAAC--
* * *
431726 AAAAAATTAAAACTTTACTTATAACCATGTATCAACTAGAGTTTTTTTATTA-TCTGAGTTATAA
376 AAAAAATTAAAACTTTACTTATAAACATGTATCAACT--AGTTTTTTTATCATTC-GAGCTATAA
* *
431790 GTTTGAGATTCGTCATATTAATTAAAACCACTT-AGAGTTGTCATAAGTATTATAAAAATAAATA
438 ATTTGAGATTCGTCATATTAATTAAAACCATTTGA-AGTTGT-ATAAGTATTATAAAAATAAATA
* * * *
431854 GAAGTTGGATGTTTT----AA-AAAAG-AAAA-AAAATAGACGCCTATAGCACGTAAGCACTAAA
501 GAAGTTGGATGTTTTAAAAAAGAAAAGAAAAATAAAATAAACGCCTATAGCACGCAAGAAATAAA
* * * *
431912 TTTAACTTTTGACTTTTGCGAATTTCATTTAATGTTTCAGGTGAAATTCCACTTGTTATTGGAAA
566 TTTAACTTTTGACTTTTACGGATTTAATTTAATGTTTCAGGTGAAATTCCACCTGTTATTGGAAA
* *
431977 ATTAACTTCTCTCTATTACCTTGATCTTTGTACTAACAACTTAACAGGTATAATTTCGTCTTTCT
631 ATTAACTTCTCTCCATTACCTTGATCTTTGTACTAACAACTTAACAGGTATAATTTCATCTTTCT
* *
432042 TCAACTTGTCTCAATTTTTTGGT
696 TCAACTTTTCTCAATTTTTGGGT
432065 GAGAATTTGATAACAAAAAATTAAAACTTTACTT-TAAACATGTATCAACTAGTTTTTTTTTTAA
1 GAGAATTTGAT-A-AAAAAATTAAAACTTTACTTATAAACATGTATCAACTAG--TTTTTTTTAA
* * *
432129 CCGTTTGAGCTATAAATTTGAGATTGGTCATAAGAATAAAAATT-ATTTGAAGCTATCATAATTA
62 TCATTTGAGCTATAAATTTGAGATTGGTCATAAGAAT-AAAATTCATTTGAAGCTGTCATAATTA
* * ** *
432193 AGTATTATAAAAATAAATAGAAGTTGGATGTTTTAAAAAATAAAAGAAAAATACAATAGATGCTA
126 AGTATTATAAAAATAAATAGAAGTTAGATGTTTTAAAAAATAAAAGAAAAATAAAATAGACACTT
* * * * *
432258 ATAACACTTAAGAAATAAATTAAGTTTTCACTTGTGATG-GACTTACTTCAATGTTTCAGGTGAA
191 ATAACTCTCAAGAAATAAATTAAGTTTTGACTTGTGA-GAGATTTAATTCAATGTTTCAGGTGAA
* * * * * * *
432322 ATTCCAGCAGATATTGGAAACCTAACTTCTCTCAATTACCTTTTTCTTTGTAATAATAACTTAAA
255 ATTCCACCAGTTATTGGAAACTTGACTTCTCTC-ATAACCTTTTTCTTTGTAATAACAACTTAAC
* * *
432387 AGGTATAATTTCATCTTTCTTCTACTTTTCTTAAATTTTTGGGTTAAAATTTGATAACAAAAAAT
319 AGGTATAATTTCATCTTTCTTCTACTTTTC-TCAATTTTTGGGTGAGAATTTGATAACAAAAAAT
* * * *
432452 TAAAACTTTTCTTATAAGCATGTATCAACTAGTTTTTTTATCATCCGAGCTATAAATTTGAGGTT
383 TAAAACTTTACTTATAAACATGTATCAACTAGTTTTTTTATCATTCGAGCTATAAATTTGAGATT
* * **
432517 CGTCATATTAA-TAAAACCATTTGAAGTTTTCATAAATATTATAAAAATAAGCAGAAGTTGGATG
448 CGTCATATTAATTAAAACCATTTGAAGTTGT-ATAAGTATTATAAAAATAAATAGAAGTTGGATG
* * * * * ** * *
432581 TTTTAGAAAAGAAAAGAAAATTAAAATAGATGCTTATAGCACTTAAGAAATAAA-TTAAGTTTTA
512 TTTTAAAAAAGAAAAGAAAAATAAAATAAACGCCTATAGCACGCAAGAAATAAATTTAACTTTTG
*** * * * * * *
432645 ACTTTTGTAGATTTAATTTAATGTTTGAGGTGAAATTTCACATTTTATT-AAAAAGTTGACTTCT
577 ACTTTTACGGATTTAATTTAATGTTTCAGGTGAAATTCCACCTGTTATTGGAAAA-TTAACTTCT
* * * ** * *
432709 TTCAATTA-CTTGATCTTTGTACTAATAACTTAACAGGTATAATTTCATCTTTCTTTTATTTTTA
641 CTCCATTACCTTGATCTTTGTACTAACAACTTAACAGGTATAATTTCATCTTTCTTCAACTTTTC
* *
432773 TCAAATTTTAGGT
706 TCAATTTTTGGGT
** * * *
432786 GAGAATTTGATAACAAAATATTAAATTTTTATTTATAAACATGTATCAGCTAGTTTTTTTT-ATT
1 GAGAATTTGATAA-AAAA-ATTAAAACTTTACTTATAAACATGTATCAACTAGTTTTTTTTAATC
* * * * *
432850 ATTTTAGCTATAAATTTAAGATTTGTCATAATAAATAAGAACT-ATTTGAAGCTAGTCATAATTA
64 ATTTGAGCTATAAATTTGAGATTGGTCATAA-GAATAA-AATTCATTTGAAGCT-GTCATAATTA
* * * * * * * *
432914 GGTATTATTAAAGTAGAT-GTCATAATTAGGTATTATAAAAGTAGATAGAAGTTGCATGTTAAAA
126 AGTATTATAAAAATAAATAG--A-AGTTAGATGTTTTAAAA--A-ATA-AA-----A-G------
* ** * * * *
432978 AAATAATAAAATATATGCTTATAACGCTCAAGAAATAAATTAAATTTTAACTTGTGAGAAATTTA
172 AAA-AATAAAATAGACACTTATAACTCTCAAGAAATAAATTAAGTTTTGACTTGTGAGAGATTTA
* * * * * * * *
433043 ATTTAATATTTCAGGTAAAATTCCACTAGTTATTGAAAATTTGACTTCTCTCATCAGCCTTTCTC
236 ATTCAATGTTTCAGGTGAAATTCCACCAGTTATTGGAAACTTGACTTCTCTCAT-AACCTTTTTC
* ** * * * * *
433108 TTTCTAATAACAACTTAACAGGTATGCTTTCGTATTTCTT-TCACTTTTATCAATTTTTAGGTAA
300 TTTGTAATAACAACTTAACAGGTATAATTTCATCTTTCTTCT-ACTTTTCTCAATTTTTGGGTGA
* *
433172 GAATTTGATAACAAAAAATTAAAACTTTACTTATAAACATGTATCAACTAATTTTTTTAATTATT
364 GAATTTGATAACAAAAAATTAAAACTTTACTTATAAACATGTATCAACTAGTTTTTTT-ATCATT
* * ** ** ** * *
433237 TGAGCTATAAATTTGAGATTGGTCATAACAACAAAAATTATTTGAAGCTGTCATAATTAAGTATA
428 CGAGCTATAAATTTGAGATTCGTCATATTAATTAAAACCATTTGAAGTTGT-ATAAGT-A-T-TA
* * * *
433302 TAAAAATAAATAGAAGTTAGATGTTTCAAAAAAG---A-AAAAATAAAATAAACACCTATAGCAT
489 TAAAAATAAATAGAAGTTGGATGTTTTAAAAAAGAAAAGAAAAATAAAATAAACGCCTATAGCAC
* * * *
433363 GCAAGAAATAAATTTAAGTGTTGACTTTTGCGGATTTAATTCAATGTTTCAGGTGAAATTCCACC
554 GCAAGAAATAAATTTAACTTTTGACTTTTACGGATTTAATTTAATGTTTCAGGTGAAATTCCACC
* * * * * *
433428 CGATATTGGAAAATTAACCTCTCTCAATTACCTTGATTTTTGTACTAACCACTTAACAGGTATAA
619 TGTTATTGGAAAATTAACTTCTCTCCATTACCTTGATCTTTGTACTAACAACTTAACAGGTATAA
*
433493 TTTTATCTTTCTTCAACTTTTCTCAATTTTTGGGT
684 TTTCATCTTTCTTCAACTTTTCTCAATTTTTGGGT
* * * *
433528 GAGAATTTGATAACAAAAAATTAAAATTTTACTT-TCAAAAATGTAACAACTAGGTTTTTTTAAT
1 GAGAATTTGAT-A-AAAAAATTAAAACTTTACTTAT-AAACATGTATCAACTAGTTTTTTTTAAT
* * *
433592 CATTTAAGCTATAAATTTGAGATTGGTCATAAGAATAAAAATCATTTGAAGCTGTCAGAATTAAG
63 CATTTGAGCTATAAATTTGAGATTGGTCATAAGAATAAAATTCATTTGAAGCTGTCATAATTAAG
* ** ** **
433657 TATTATAAAAATAAATAAAAGTTAGATACTTTAAAAAATAAAAGAAAAATAAAATAGATGCCAAT
128 TATTATAAAAATAAATAGAAGTTAGATGTTTTAAAAAATAAAAGAAAAATAAAATAGACACTTAT
* * * * *
433722 AACACTCAAGAAATAAATTAAGTTTTAACTTGTGAGGGACTTAATTTAATGTTTCAGGTGAAATT
193 AACTCTCAAGAAATAAATTAAGTTTTGACTTGTGAGAGATTTAATTCAATGTTTCAGGTGAAATT
* * * *
433787 CCACCGGTTATTGGAAACTTGGCTTCTCTCA-ACTACCTTTTTCTTTGTAAAAACAACTTAAAAG
258 CCACCAGTTATTGGAAACTTGACTTCTCTCATA--ACCTTTTTCTTTGTAATAACAACTTAACAG
* *
433851 GTATAATTTCATCTTTTTTCTACTTTTCTCAATTTTTTGGATGAGAATTTGATAACAAAAAAAAT
321 GTATAATTTCATCTTTCTTCTACTTTTCTCAA-TTTTTGGGTGAGAATTTGATAAC--AAAAAAT
* * *
433916 TAAAATTTTACTTATAAGCATGTATCAACTAGTTTTTTTTTTATCA-TCTGAGCTATAAATTTAA
383 TAAAACTTTACTTATAAACATGTATCAACTAG---TTTTTTTATCATTC-GAGCTATAAATTTGA
* * *
433980 AATTCATCATATTAA-TAAAACCATTTGAAGTTGTCATAAGTATTATAAAAATAAATAGAAATTG
444 GATTCGTCATATTAATTAAAACCATTTGAAGTTGT-ATAAGTATTATAAAAATAAATAGAAGTTG
* * *
434044 GATGTTTTAAAAAAGAAAAGAAAAATAAAATAAACACCTATAACATGCAAGAAATAAATTTAACT
508 GATGTTTTAAAAAAGAAAAGAAAAATAAAATAAACGCCTATAGCACGCAAGAAATAAATTTAACT
* * * **
434109 CTTT-ACTTTTTACGGGTTTAATTTAATATTTCAGGTGAAATTCCGCCCATTATTGGAAAATTAA
573 -TTTGAC-TTTTACGGATTTAATTTAATGTTTCAGGTGAAATTCCACCTGTTATTGGAAAATTAA
* ** * * ** * *
434173 CTTCTCTCCATTACCTTGATCTCTGTGTTAACAGCTTAACAGGTATATTTTTGTTTTTCTTTAAC
636 CTTCTCTCCATTACCTTGATCTTTGTACTAACAACTTAACAGGTATAATTTCATCTTTCTTCAAC
**
434238 TTTTCTCAATTTAGGGGT
701 TTTTCTCAATTTTTGGGT
* * * * * *
434256 AAGAATTTGAT-AAAAAATTAAAACTTTACTTATAAACATATATCAATTAGGTTTTTTTACTGAT
1 GAGAATTTGATAAAAAAATTAAAACTTTACTTATAAACATGTATCAACTAGTTTTTTTTAATCAT
* * *
434320 TTGAGCTATAAATTTGAGATTGGTCATAATAATAAAATTCATTTGAAGCTTTTATAATTAAGTAT
66 TTGAGCTATAAATTTGAGATTGGTCATAAGAATAAAATTCATTTGAAGCTGTCATAATTAAGTAT
* * * *
434385 TATAAAAATAAATAAAAGTTAGATGTTTTAAAAAATAAAAGAAAAATAAAATAGACGCTTGTAGC
131 TATAAAAATAAATAGAAGTTAGATGTTTTAAAAAATAAAAGAAAAATAAAATAGACACTTATAAC
* *
434450 AT-TCAAGAAATAAATTAAGTTTTGACTTGTGAGAGACTTAATTCAATATTTCAGGTGAAATTCC
196 -TCTCAAGAAATAAATTAAGTTTTGACTTGTGAGAGATTTAATTCAATGTTTCAGGTGAAATTCC
* * *
434514 ATCAGTTATTGGAAACTTGACTTCTCTCAATAGCCTTTTTCTTTGTAATAACAATTTAACAGGTA
260 ACCAGTTATTGGAAACTTGACTTCTCTC-ATAACCTTTTTCTTTGTAATAACAACTTAACAGGTA
* * * * *
434579 TAGTTTCATCTTTTTTCTACGTTTCTCGATTTTTTGGGTGAGATTTTGATAACAAAAAATTAAAA
324 TAATTTCATCTTTCTTCTACTTTTCTC-AATTTTTGGGTGAGAATTTGATAACAAAAAATTAAAA
* * * *
434644 TTTTACTTATAAACGTGTATTAACTAGTTTTTTTATCATTCGAGCTATAAATTTGAGATTCGTTA
388 CTTTACTTATAAACATGTATCAACTAGTTTTTTTATCATTCGAGCTATAAATTTGAGATTCGTCA
* * *
434709 TATTAGTTAAAACCATTTAAAGTTGT-TAAGTATTATAAAAATAAATAGAAGTTAGATGTTTTAA
453 TATTAATTAAAACCATTTGAAGTTGTATAAGTATTATAAAAATAAATAGAAGTTGGATGTTTTAA
*
434773 AAAAGAAAAGAAAAATAAAATAAACGCCTATAACACGCAAGAAATAAATTTAACTTTTGACTTTT
518 AAAAGAAAAGAAAAATAAAATAAACGCCTATAGCACGCAAGAAATAAATTTAACTTTTGAC-TTT
* *
434838 TACGAATTTAATTCAATGTTTCAGGTGAAATTCCACCTGTTATTGGAAAATTAACTTCTCTCCAT
582 TACGGATTTAATTTAATGTTTCAGGTGAAATTCCACCTGTTATTGGAAAATTAACTTCTCTCCAT
** * ** *
434903 TACCTTGATCTTTGTGTTAACAGCTTAACAGGTATAATTTTGTCTTTTTTCAACTTTTCTCAATT
647 TACCTTGATCTTTGTACTAACAACTTAACAGGTATAATTTCATCTTTCTTCAACTTTTCTCAATT
434968 TTTGGGT
712 TTTGGGT
* * *
434975 GAGAATTTGAT-AAAAAATTAAAACTTTACTTATAAACATATATCGATTAGTTTTTTTTTAATCA
1 GAGAATTTGATAAAAAAATTAAAACTTTACTTATAAACATGTATCAACTAG-TTTTTTTTAATCA
* **
435039 TTTGAGCTATAAATTTGAGATTGGTCATAACAATAAAATTCATACGAAGCTGTCATAATTAAGTA
65 TTTGAGCTATAAATTTGAGATTGGTCATAAGAATAAAATTCATTTGAAGCTGTCATAATTAAGTA
* *
435104 TTATAAAAATAAATAGAAGTTAGATGTTTTAAAAAAAGAAAAGAAAAATAAAATAGACATTTATA
130 TTATAAAAATAAATAGAAGTTAGATGTTTT-AAAAAATAAAAGAAAAATAAAATAGACACTTATA
** * *
435169 GTTCTCAAGAAGTAAATTAAGTTTTGACTTGTGAGACATTTAATTCAATGTTTCAGGTGAAATTC
194 ACTCTCAAGAAATAAATTAAGTTTTGACTTGTGAGAGATTTAATTCAATGTTTCAGGTGAAATTC
* * * * *
435234 CACCGGTTATTGGAAACCTGACTTTTCTTCATAACCTTTTTCTTTGTAAAAATAACTTAACAGGT
259 CACCAGTTATTGGAAACTTGACTTCTC-TCATAACCTTTTTCTTTGTAATAACAACTTAACAGGT
435299 ATAATTTCATCTTTCTTCTACTTTTCTCAATTTTTGGGTGAGAATTTGATAAC-AAAAATTAAAA
323 ATAATTTCATCTTTCTTCTACTTTTCTCAATTTTTGGGTGAGAATTTGATAACAAAAAATTAAAA
* * *
435363 CTTTACTTAAAAACATGTATCAACTAGTTTTTTTATCATCCGAGCCATAAATTTGAGATTCGTCA
388 CTTTACTTATAAACATGTATCAACTAGTTTTTTTATCATTCGAGCTATAAATTTGAGATTCGTCA
*
435428 TATTAATTAAAACTATTTGAAGTTGTTATAAGTATTATAAAAATAAATAGAAGTTGGATGTTTTA
453 TATTAATTAAAACCATTTGAAGTTG-TATAAGTATTATAAAAATAAATAGAAGTTGGATGTTTT-
* * ** * * *
435493 AAAAAGAAAAGAAAAGAAAAATAAAATTAACGCTTATAGCACTTAAAAAATAAA-TTAAGTTTTA
516 ---AA-AAAAGAAAAGAAAAATAAAATAAACGCCTATAGCACGCAAGAAATAAATTTAACTTTTG
* * * *
435557 ACTTTTGCGGATTTAATTTAATGCTTAAGGTGAAATTCCACCTTTTATTGGAAAATTAACTTCTC
577 ACTTTTACGGATTTAATTTAATGTTTCAGGTGAAATTCCACCTGTTATTGGAAAATTAACTTCTC
* * * *
435622 T-CATTTACCTTGATCTTTCT-CATAACAACTTAATAAGTATAATTTCATCTTTCTTCTACTTTT
642 TCCA-TTACCTTGATCTTTGTAC-TAACAACTTAACAGGTATAATTTCATCTTTCTTCAACTTTT
* * *
435685 GTCAATTTTTAGCT
705 CTCAATTTTTGGGT
* *
435699 GAGAATTTGATAACAAAATATTAAAACTTTGCTTATAAACATGTATCAACTAG-GTTTTTT-ATC
1 GAGAATTTGATAA-AAAA-ATTAAAACTTTACTTATAAACATGTATCAACTAGTTTTTTTTAATC
* * ** * * *
435762 ATTTGAGCTATAAAATT-CG-TAAG-AAT-A-AATAAGAA-TCATTTGAAACTGTTATAATT-AG
64 ATTTGAGCTATAAATTTGAGATTGGTCATAAGAATAA-AATTCATTTGAAGCTGTCATAATTAAG
* * * *
435820 TTATTATAAAAATAGATAGAAGTT-GCA--ATTT-AAAAA-AAAA-TAAAATAAAATATACACTT
128 -TATTATAAAAATAAATAGAAGTTAG-ATGTTTTAAAAAATAAAAGAAAAATAAAATAGACACTT
* * * * *
435879 ATAA-TGTTCAAGAAATAAATTCAA-TTTTGACTTATGAGGGATTTAATTTAATGTTTTAGGTGA
191 ATAACT-CTCAAGAAATAAATT-AAGTTTTGACTTGTGAGAGATTTAATTCAATGTTTCAGGTGA
* * * * * *
435942 AATTTCACCAGTTATTGGAAATTTGACTTCTCTCA-AGTGCCTTTATCTTTTTAATAACAATTTA
254 AATTCCACCAGTTATTGGAAACTTGACTTCTCTCATA--ACCTTTTTCTTTGTAATAACAACTTA
* * * *
436006 ACAGGTATACTTTTATCTTTCTTCTACTTTTCTCAATTTTTAGGTGAGAATTTGATACCAAAAAA
317 ACAGGTATAATTTCATCTTTCTTCTACTTTTCTCAATTTTTGGGTGAGAATTTGATAACAAAAAA
* * * *
436071 TTAAAACTTTATTTATAAATATGTATCAACTATTTTTTTTATCATTTGAGCTATAAATTTGAGAT
382 TTAAAACTTTACTTATAAACATGTATCAACTAGTTTTTTTATCATTCGAGCTATAAATTTGAGAT
* * *
436136 TTGTCATAATAATTAAAACCATTTGAAGTTGTCATAAGTATTATACAAATAAATA
447 TCGTCATATTAATTAAAACCATTTGAAGTTGT-ATAAGTATTATAAAAATAAATA
436191 AAAGCTGTAA
Statistics
Matches: 3520, Mismatches: 484, Indels: 246
0.83 0.11 0.06
Matches are distributed among these distances:
711 1 0.00
712 4 0.00
713 217 0.06
714 136 0.04
715 34 0.01
716 74 0.02
717 60 0.02
718 8 0.00
719 470 0.13
720 201 0.06
721 497 0.14
722 244 0.07
723 135 0.04
724 149 0.04
725 376 0.11
726 75 0.02
727 105 0.03
728 138 0.04
729 1 0.00
730 1 0.00
732 1 0.00
733 1 0.00
735 2 0.00
736 3 0.00
737 1 0.00
739 86 0.02
740 198 0.06
741 110 0.03
742 124 0.04
743 36 0.01
744 32 0.01
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.39
Consensus pattern (718 bp):
GAGAATTTGATAAAAAAATTAAAACTTTACTTATAAACATGTATCAACTAGTTTTTTTTAATCAT
TTGAGCTATAAATTTGAGATTGGTCATAAGAATAAAATTCATTTGAAGCTGTCATAATTAAGTAT
TATAAAAATAAATAGAAGTTAGATGTTTTAAAAAATAAAAGAAAAATAAAATAGACACTTATAAC
TCTCAAGAAATAAATTAAGTTTTGACTTGTGAGAGATTTAATTCAATGTTTCAGGTGAAATTCCA
CCAGTTATTGGAAACTTGACTTCTCTCATAACCTTTTTCTTTGTAATAACAACTTAACAGGTATA
ATTTCATCTTTCTTCTACTTTTCTCAATTTTTGGGTGAGAATTTGATAACAAAAAATTAAAACTT
TACTTATAAACATGTATCAACTAGTTTTTTTATCATTCGAGCTATAAATTTGAGATTCGTCATAT
TAATTAAAACCATTTGAAGTTGTATAAGTATTATAAAAATAAATAGAAGTTGGATGTTTTAAAAA
AGAAAAGAAAAATAAAATAAACGCCTATAGCACGCAAGAAATAAATTTAACTTTTGACTTTTACG
GATTTAATTTAATGTTTCAGGTGAAATTCCACCTGTTATTGGAAAATTAACTTCTCTCCATTACC
TTGATCTTTGTACTAACAACTTAACAGGTATAATTTCATCTTTCTTCAACTTTTCTCAATTTTTG
GGT
Found at i:440288 original size:14 final size:15
Alignment explanation
Indices: 440260--440298 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
440250 GTTAGTTTTA
440260 AAATTTTTTAAATTC
1 AAATTTTTTAAATTC
*
440275 AAATTTTTT-TATTC
1 AAATTTTTTAAATTC
*
440289 GAATTTTTTA
1 AAATTTTTTA
440299 TTTTCTAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.33, C:0.05, G:0.03, T:0.59
Consensus pattern (15 bp):
AAATTTTTTAAATTC
Found at i:442506 original size:19 final size:19
Alignment explanation
Indices: 442457--442502 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
442447 GTTCAATCTA
*
442457 ATTTAAATTATTATTTATT
1 ATTTAAATTAATATTTATT
* *
442476 AATTAAAATAATATTT-TT
1 ATTTAAATTAATATTTATT
442494 ATTTAAATT
1 ATTTAAATT
442503 TAATTATAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
18 9 0.41
19 13 0.59
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
ATTTAAATTAATATTTATT
Found at i:443696 original size:7 final size:7
Alignment explanation
Indices: 443678--443717 Score: 71
Period size: 7 Copynumber: 5.6 Consensus size: 7
443668 AAATTACTTA
443678 ATATATTT
1 ATATA-TT
443686 ATATATT
1 ATATATT
443693 ATATATT
1 ATATATT
443700 ATATATT
1 ATATATT
443707 ATATATT
1 ATATATT
443714 ATAT
1 ATAT
443718 TAAAAATGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
7 27 0.84
8 5 0.16
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
ATATATT
Found at i:445452 original size:25 final size:25
Alignment explanation
Indices: 445424--445472 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
445414 TTACAAACAA
*
445424 AAAGGAATCATCATTTTTGACAAAT
1 AAAGGAATCACCATTTTTGACAAAT
* *
445449 AAAGTAATCACCATTTTTTACAAA
1 AAAGGAATCACCATTTTTGACAAA
445473 CACAAAAGGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.45, C:0.14, G:0.08, T:0.33
Consensus pattern (25 bp):
AAAGGAATCACCATTTTTGACAAAT
Found at i:449113 original size:15 final size:15
Alignment explanation
Indices: 449095--449136 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
449085 AAAATTTTTA
449095 TAATTTAAATTAAAT
1 TAATTTAAATTAAAT
*
449110 TAATTAAAATTAAAT
1 TAATTTAAATTAAAT
449125 TATTATTTAAAT
1 TA--ATTTAAAT
449137 AATAAATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 16 0.70
17 7 0.30
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TAATTTAAATTAAAT
Found at i:451753 original size:26 final size:26
Alignment explanation
Indices: 451717--451768 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
451707 TGCCCCTCTC
451717 TGTATCTCTTTCTTTCTTAAGAGATA
1 TGTATCTCTTTCTTTCTTAAGAGATA
451743 TGTATCTCTTTCTTTCTTAAGAGATA
1 TGTATCTCTTTCTTTCTTAAGAGATA
451769 CAAAGTACTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.23, C:0.15, G:0.12, T:0.50
Consensus pattern (26 bp):
TGTATCTCTTTCTTTCTTAAGAGATA
Found at i:460581 original size:17 final size:15
Alignment explanation
Indices: 460561--460611 Score: 52
Period size: 14 Copynumber: 3.4 Consensus size: 15
460551 TTAAGTAAAA
460561 AAGAAAGAAAGAAGATG
1 AAGAAAGAAAGAA-A-G
460578 AAG-AAGAAAGAAAG
1 AAGAAAGAAAGAAAG
* *
460592 AA-AAAGAAAAAAAA
1 AAGAAAGAAAGAAAG
460606 AAGAAA
1 AAGAAA
460612 AAAATATGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
14 14 0.47
15 4 0.13
16 9 0.30
17 3 0.10
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (15 bp):
AAGAAAGAAAGAAAG
Found at i:460612 original size:17 final size:17
Alignment explanation
Indices: 460558--460613 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 17
460548 AAGTTAAGTA
* *
460558 AAAAAGAAAGAAAGAAG
1 AAAAAGAAAAAAAAAAG
** * *
460575 ATGAAGAAGAAAGAAAG
1 AAAAAGAAAAAAAAAAG
460592 AAAAAGAAAAAAAAAAG
1 AAAAAGAAAAAAAAAAG
460609 AAAAA
1 AAAAA
460614 AATATGAAAT
Statistics
Matches: 29, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.79, C:0.00, G:0.20, T:0.02
Consensus pattern (17 bp):
AAAAAGAAAAAAAAAAG
Found at i:466954 original size:13 final size:15
Alignment explanation
Indices: 466922--466967 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
466912 AAAAAAAGTC
466922 AAAA-GCAAAAGCACAA
1 AAAATGCAAAAG--CAA
466938 AAAATG-AAAAG-AA
1 AAAATGCAAAAGCAA
466951 AAAATGCAAAAGCAA
1 AAAATGCAAAAGCAA
466966 AA
1 AA
466968 TAAAAAAAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
13 8 0.30
14 5 0.19
15 4 0.15
16 9 0.33
17 1 0.04
ACGTcount: A:0.72, C:0.11, G:0.13, T:0.04
Consensus pattern (15 bp):
AAAATGCAAAAGCAA
Found at i:468362 original size:27 final size:27
Alignment explanation
Indices: 468319--468974 Score: 970
Period size: 27 Copynumber: 24.0 Consensus size: 27
468309 GTGGCATTTT
* *
468319 CTTTTAAAGTCCACAACTCTGTGGCATC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
*
468347 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
468374 CTTTTAAAGTCCATAACTCCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
* *
468402 CTTTTTAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
468429 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
468456 CTTTTAAGCCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
468483 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
** *
468510 CTTTTAAAAACCACAACTTCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
468538 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
468565 CTTTTAAGTCCATAACTCCGTGGCATCT
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
468593 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
468620 CTTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
* **
468648 CTTTTTAGTCCACAACTATGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
468675 CTTTTAAGTCCACAACTCCATGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
468702 CTTTTAAGACCACAACTCCGTGGTACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
468729 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
468756 CTTTTAAGTCCATAACTCCGTGGCATCT
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
* *
468784 TTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
468811 CTTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
* *
468839 CTTTTTAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
468866 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
468893 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
**
468920 CTTTTAAGTCCACAACTCCGTGGCGTC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
468947 CTTTTAAATCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
468974 C
1 C
468975 ATTTCAAAGC
Statistics
Matches: 568, Mismatches: 54, Indels: 13
0.89 0.09 0.02
Matches are distributed among these distances:
27 415 0.73
28 153 0.27
ACGTcount: A:0.23, C:0.34, G:0.14, T:0.29
Consensus pattern (27 bp):
CTTTTAAGTCCACAACTCCGTGGCACC
Found at i:468716 original size:191 final size:192
Alignment explanation
Indices: 468319--468971 Score: 1062
Period size: 191 Copynumber: 3.4 Consensus size: 192
468309 GTGGCATTTT
* * * *
468319 CTTTTAAAGTCCACAACTCTGTGGCATCCTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAAGT
1 CTTTTAAAGACCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTT-AAGT
* *
468384 CCATAACTCCGTGGCA-CCCTTTTTAGTCCACAACTCTGTGGCACCCTTTT-AAGTCCACAACTC
65 CCATAACTCCGTGGCATCTCTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAAGTCCACAACTC
* * *
468447 CGTGGCACCCTTTTAAGCCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
130 CGTGGCACCCTTTTTAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
* *
468510 CTTTTAAAAACCACAACTTCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
1 CTTTTAAAGACCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
468575 CATAACTCCGTGGCATCTCTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAAGTCCACAACTCC
66 CATAACTCCGTGGCATCTCTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAAGTCCACAACTCC
* *
468640 GTGGCACCCTTTTTAGTCCACAACTATGTGGCACCCTTTTAAGTCCACAACTCCATGGCACC
131 GTGGCACCCTTTTTAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
* *
468702 CTTTT-AAGACCACAACTCCGTGGTACCCTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAGTC
1 CTTTTAAAGACCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
*
468766 CATAACTCCGTGGCATCTTTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAAGTCCACAACTCC
66 CATAACTCCGTGGCATCTCTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAAGTCCACAACTCC
*
468831 GTGGCACCCTTTTTAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCTGTGGCACC
131 GTGGCACCCTTTTTAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
* ** *
468893 CTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCGTCCTTTTAAATC
1 CTTTTAAAGACCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
* *
468957 CACAACTCTGTGGCA
66 CATAACTCCGTGGCA
468972 CCCATTTCAA
Statistics
Matches: 431, Mismatches: 29, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
190 20 0.05
191 335 0.78
192 76 0.18
ACGTcount: A:0.23, C:0.33, G:0.14, T:0.29
Consensus pattern (192 bp):
CTTTTAAAGACCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
CATAACTCCGTGGCATCTCTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAAGTCCACAACTCC
GTGGCACCCTTTTTAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
Found at i:469015 original size:32 final size:32
Alignment explanation
Indices: 468957--469207 Score: 351
Period size: 32 Copynumber: 7.8 Consensus size: 32
468947 CTTTTAAATC
* *
468957 CACAACTCTGTGGC-ACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
468988 CACAAGTCGGTGGCAACCCATTCCAAAGCCCAA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCC-A
469021 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
469053 CACAAGTCGGTGGCAACCCATTTAAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
469085 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
469117 CACAAGTCGGTGGCAACTCATTTCAAAGCGCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* * * *
469149 TATAAGTCGGTGGAAACCCATTTAAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
** * *
469181 TGCAAGTCAGTGGCAACCCTTTTCAAA
1 CACAAGTCGGTGGCAACCCATTTCAAA
469208 TCACCATTTT
Statistics
Matches: 196, Mismatches: 22, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
31 12 0.06
32 153 0.78
33 31 0.16
ACGTcount: A:0.32, C:0.32, G:0.18, T:0.18
Consensus pattern (32 bp):
CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
Found at i:470452 original size:11 final size:11
Alignment explanation
Indices: 470435--470497 Score: 57
Period size: 10 Copynumber: 6.0 Consensus size: 11
470425 AGAGGAGGTC
470435 GAAAAGAGTCTA
1 GAAAAGA-TCTA
470447 -AAAAGAATCTA
1 GAAAAG-ATCTA
470458 GAAAA-ATCTA
1 GAAAAGATCTA
470468 GAAAA-ATCTA
1 GAAAAGATCTA
470478 -AAAAGAAT-TA
1 GAAAAG-ATCTA
470488 GAAAA-ATCTA
1 GAAAAGATCTA
470498 ATTCCGGATT
Statistics
Matches: 45, Mismatches: 0, Indels: 14
0.76 0.00 0.24
Matches are distributed among these distances:
9 6 0.13
10 19 0.42
11 15 0.33
12 5 0.11
ACGTcount: A:0.60, C:0.08, G:0.13, T:0.19
Consensus pattern (11 bp):
GAAAAGATCTA
Found at i:470465 original size:10 final size:10
Alignment explanation
Indices: 470452--470497 Score: 67
Period size: 10 Copynumber: 4.6 Consensus size: 10
470442 GTCTAAAAAG
470452 AATCTAGAAA
1 AATCTAGAAA
470462 AATCTAGAAA
1 AATCTAGAAA
*
470472 AATCTAAAAA
1 AATCTAGAAA
470482 GAAT-TAGAAA
1 -AATCTAGAAA
470492 AATCTA
1 AATCTA
470498 ATTCCGGATT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
9 3 0.09
10 26 0.81
11 3 0.09
ACGTcount: A:0.61, C:0.09, G:0.09, T:0.22
Consensus pattern (10 bp):
AATCTAGAAA
Found at i:470695 original size:17 final size:15
Alignment explanation
Indices: 470675--470725 Score: 52
Period size: 14 Copynumber: 3.4 Consensus size: 15
470665 TTAAGTAAAA
470675 AAGAAAGAAAGAAGATG
1 AAGAAAGAAAGAA-A-G
470692 AAG-AAGAAAGAAAG
1 AAGAAAGAAAGAAAG
* *
470706 AA-AAAGAAAAAAAA
1 AAGAAAGAAAGAAAG
470720 AAGAAA
1 AAGAAA
470726 AAAATATGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
14 14 0.47
15 4 0.13
16 9 0.30
17 3 0.10
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (15 bp):
AAGAAAGAAAGAAAG
Found at i:470726 original size:17 final size:17
Alignment explanation
Indices: 470672--470727 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 17
470662 AAGTTAAGTA
* *
470672 AAAAAGAAAGAAAGAAG
1 AAAAAGAAAAAAAAAAG
** * *
470689 ATGAAGAAGAAAGAAAG
1 AAAAAGAAAAAAAAAAG
470706 AAAAAGAAAAAAAAAAG
1 AAAAAGAAAAAAAAAAG
470723 AAAAA
1 AAAAA
470728 AATATGAAAT
Statistics
Matches: 29, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.79, C:0.00, G:0.20, T:0.02
Consensus pattern (17 bp):
AAAAAGAAAAAAAAAAG
Found at i:471117 original size:14 final size:14
Alignment explanation
Indices: 471098--471130 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
471088 TTATTTTATT
471098 TATATGTATATATA
1 TATATGTATATATA
471112 TATATGTATATATA
1 TATATGTATATATA
471126 TATAT
1 TATAT
471131 TTTAAAAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (14 bp):
TATATGTATATATA
Found at i:476178 original size:2 final size:2
Alignment explanation
Indices: 476171--476204 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
476161 GGTATAAATT
*
476171 TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
476205 GCGATGGATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:478161 original size:245 final size:245
Alignment explanation
Indices: 477731--478223 Score: 977
Period size: 245 Copynumber: 2.0 Consensus size: 245
477721 TTTAATTAAT
477731 TTTATCTTATGTTTGCTTCTTATAGTCATGTTTGATCCAAAATTACAAAAGTATAATTTCTACCT
1 TTTATCTTATGTTTGCTTCTTATAGTCATGTTTGATCCAAAATTACAAAAGTATAATTTCTACCT
477796 GGGGATAATATATCATGAAACTTTTACAAATTTGTATTGCTTTAAGTATCTAAATCTTAACAATA
66 GGGGATAATATATCATGAAACTTTTACAAATTTGTATTGCTTTAAGTATCTAAATCTTAACAATA
*
477861 GATGTGACGATTTATGCATTCATGTCGAGTTTATATATTTTTAGATTTCATAATTATATTTGGAG
131 GATGTGACGATTTATGCATTCATGTCGAGTTTATATATATTTAGATTTCATAATTATATTTGGAG
477926 TATTATATATTTATAAAAAATTTGATATGTTAATAATCATATTATATAAC
196 TATTATATATTTATAAAAAATTTGATATGTTAATAATCATATTATATAAC
477976 TTTATCTTATGTTTGCTTCTTATAGTCATGTTTGATCCAAAATTACAAAAGTATAATTTCTACCT
1 TTTATCTTATGTTTGCTTCTTATAGTCATGTTTGATCCAAAATTACAAAAGTATAATTTCTACCT
478041 GGGGATAATATATCATGAAACTTTTACAAATTTGTATTGCTTTAAGTATCTAAATCTTAACAATA
66 GGGGATAATATATCATGAAACTTTTACAAATTTGTATTGCTTTAAGTATCTAAATCTTAACAATA
478106 GATGTGACGATTTATGCATTCATGTCGAGTTTATATATATTTAGATTTCATAATTATATTTGGAG
131 GATGTGACGATTTATGCATTCATGTCGAGTTTATATATATTTAGATTTCATAATTATATTTGGAG
478171 TATTATATATTTATAAAAAATTTGATATGTTAATAATCATATTATATAAC
196 TATTATATATTTATAAAAAATTTGATATGTTAATAATCATATTATATAAC
478221 TTT
1 TTT
478224 GATAATATCG
Statistics
Matches: 247, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
245 247 1.00
ACGTcount: A:0.35, C:0.10, G:0.11, T:0.44
Consensus pattern (245 bp):
TTTATCTTATGTTTGCTTCTTATAGTCATGTTTGATCCAAAATTACAAAAGTATAATTTCTACCT
GGGGATAATATATCATGAAACTTTTACAAATTTGTATTGCTTTAAGTATCTAAATCTTAACAATA
GATGTGACGATTTATGCATTCATGTCGAGTTTATATATATTTAGATTTCATAATTATATTTGGAG
TATTATATATTTATAAAAAATTTGATATGTTAATAATCATATTATATAAC
Found at i:485514 original size:4 final size:4
Alignment explanation
Indices: 485505--485531 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
485495 ATTTCAGATT
485505 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
485532 TCCAAGAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:486216 original size:19 final size:18
Alignment explanation
Indices: 486194--486232 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
486184 TATTATAATC
*
486194 ATATTTAAATATTACATAT
1 ATATATAAATATTA-ATAT
*
486213 ATATATAAATTTTAATAT
1 ATATATAAATATTAATAT
486231 AT
1 AT
486233 TAATAATTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (18 bp):
ATATATAAATATTAATAT
Found at i:493075 original size:23 final size:24
Alignment explanation
Indices: 493030--493075 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
493020 ACAGAAAAGG
**
493030 AGAATCTTCAAGCTGTTGGTGGTT
1 AGAATCTTCAAGCTGTTAATGGTT
*
493054 AGAAT-TTCAAGCTTTTAATGGT
1 AGAATCTTCAAGCTGTTAATGGT
493076 AATATATATA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.26, C:0.11, G:0.24, T:0.39
Consensus pattern (24 bp):
AGAATCTTCAAGCTGTTAATGGTT
Found at i:493946 original size:25 final size:23
Alignment explanation
Indices: 493918--493964 Score: 67
Period size: 25 Copynumber: 2.0 Consensus size: 23
493908 AAGAATTTTA
*
493918 TATATTATTTACAATTTTAATATTG
1 TATAATATTTA-AATTTT-ATATTG
493943 TATAATATTTAAATTTTATATT
1 TATAATATTTAAATTTTATATT
493965 TTCATACTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 5 0.24
24 6 0.29
25 10 0.48
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (23 bp):
TATAATATTTAAATTTTATATTG
Found at i:499013 original size:2 final size:2
Alignment explanation
Indices: 499006--499054 Score: 80
Period size: 2 Copynumber: 24.5 Consensus size: 2
498996 AAGGGTGCAA
*
499006 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
499048 AT CT AT A
1 AT AT AT A
499055 GTGATGGATT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:499396 original size:33 final size:33
Alignment explanation
Indices: 499354--499469 Score: 169
Period size: 33 Copynumber: 3.5 Consensus size: 33
499344 TATTAAAGTG
* *
499354 TGTTGATTAAATGGTGATTTAGTAGTTTACCAT
1 TGTTGATTAAATGGTGATTTGGTAGTTTGCCAT
*
499387 TGTTGATTAAATGGGTGATTTGGTGGTTTGCCAT
1 TGTTGATTAAAT-GGTGATTTGGTAGTTTGCCAT
* * *
499421 TGTTGACTAAATGGAGATTTGGTAGGTTGCCAT
1 TGTTGATTAAATGGTGATTTGGTAGTTTGCCAT
499454 TGTTGATTAAATGGTG
1 TGTTGATTAAATGGTG
499470 GTTTTTACCA
Statistics
Matches: 73, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
33 44 0.60
34 29 0.40
ACGTcount: A:0.23, C:0.06, G:0.28, T:0.42
Consensus pattern (33 bp):
TGTTGATTAAATGGTGATTTGGTAGTTTGCCAT
Found at i:499828 original size:19 final size:19
Alignment explanation
Indices: 499772--499834 Score: 81
Period size: 19 Copynumber: 3.3 Consensus size: 19
499762 TGGTTGTCGA
**
499772 GGTACTATTCACGTATATA
1 GGTACTATTCACGTATACG
*
499791 TGTACTATTCACGTATACG
1 GGTACTATTCACGTATACG
*
499810 GGTACTATTCAAGTATACG
1 GGTACTATTCACGTATACG
*
499829 GTTACT
1 GGTACT
499835 GTACACGTGA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 38 1.00
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (19 bp):
GGTACTATTCACGTATACG
Found at i:503942 original size:33 final size:33
Alignment explanation
Indices: 503900--504017 Score: 173
Period size: 33 Copynumber: 3.5 Consensus size: 33
503890 AAGTGGGAGA
* *
503900 ATTGTTGATTAAATGGTGATTTAGTAGTTTACC
1 ATTGTTGATTAAATGGTGATTTGGTAGTTTGCC
*
503933 ATTGTTGATTAAATGGGTGATTTGGTGGTTTGCC
1 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTGCC
* * *
503967 ATTGTTGACTAAATGGAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGTGATTTGGTAGTTTGCC
504000 ATTGTTGATTAAATGGTG
1 ATTGTTGATTAAATGGTG
504018 GTTTTTACCA
Statistics
Matches: 75, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
33 46 0.61
34 29 0.39
ACGTcount: A:0.24, C:0.06, G:0.28, T:0.42
Consensus pattern (33 bp):
ATTGTTGATTAAATGGTGATTTGGTAGTTTGCC
Found at i:509389 original size:3 final size:3
Alignment explanation
Indices: 509383--509409 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
509373 AAATATAAAT
509383 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
509410 GTAGTAGTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:509723 original size:177 final size:182
Alignment explanation
Indices: 509423--509785 Score: 587
Period size: 177 Copynumber: 2.0 Consensus size: 182
509413 GTAGTAGTAG
509423 TATT-TTATTTTATTTTAAATTATTTAGACTTTTCAGATAGAAAAAATTACAACTCATCTAGAAA
1 TATTATTATTTTATTTTAAATTATTTAGACTTTTCAGATAGAAAAAATTACAACTCATCTAGAAA
* * *
509487 TAATTTCATGAATTTTATTTGTGAAAATGATTGATGCGACTGAAAAGAAAAAATTGTACCAT-TT
66 TAATTTCATGAATTTCATTTGTGAAAATAATTGATGCAACTGAAAAGAAAAAATTGTACC-TCTT
* *
509551 CTAGCAAGTTGTATATTTTCTACAGTAG-AAAAAAT-ATA-A-ATTTATT-AT
130 CTAGCAAGTTGTATATTGTCTACAATAGAAAAAAATGATAGAGATTTATTAAT
* *
509599 TATTATTATTTTGTTTTAAATTATTTAGACTTTTCAGATAGAAAAAATTACAACTCGTCTAGAAA
1 TATTATTATTTTATTTTAAATTATTTAGACTTTTCAGATAGAAAAAATTACAACTCATCTAGAAA
*
509664 TAATTTCATGAATTTCATTTGTGAAAATAATTGATGCAACTGAGAAGAAAAAATTGTACCTCTTC
66 TAATTTCATGAATTTCATTTGTGAAAATAATTGATGCAACTGAAAAGAAAAAATTGTACCTCTTC
*
509729 TAGCAAGTTGTATATTGTCTTCAATAGAAAAAAATGATAGAGATTTATTAAT
131 TAGCAAGTTGTATATTGTCTACAATAGAAAAAAATGATAGAGATTTATTAAT
509781 TATTA
1 TATTA
509786 CACTTTCACG
Statistics
Matches: 171, Mismatches: 9, Indels: 8
0.91 0.05 0.04
Matches are distributed among these distances:
176 5 0.03
177 141 0.82
178 7 0.04
179 3 0.02
180 1 0.01
181 7 0.04
182 7 0.04
ACGTcount: A:0.40, C:0.09, G:0.12, T:0.40
Consensus pattern (182 bp):
TATTATTATTTTATTTTAAATTATTTAGACTTTTCAGATAGAAAAAATTACAACTCATCTAGAAA
TAATTTCATGAATTTCATTTGTGAAAATAATTGATGCAACTGAAAAGAAAAAATTGTACCTCTTC
TAGCAAGTTGTATATTGTCTACAATAGAAAAAAATGATAGAGATTTATTAAT
Found at i:510162 original size:18 final size:17
Alignment explanation
Indices: 510130--510163 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
510120 ATTTTTTTCA
510130 TTTGAAAATTAATTAAG
1 TTTGAAAATTAATTAAG
*
510147 TTTGAGAAATTTATTAA
1 TTTGA-AAATTAATTAA
510164 TACATGTAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (17 bp):
TTTGAAAATTAATTAAG
Found at i:514750 original size:18 final size:17
Alignment explanation
Indices: 514688--514754 Score: 55
Period size: 18 Copynumber: 3.7 Consensus size: 17
514678 ATTTAGTTTT
514688 AAAAATATTTAAATAT-
1 AAAAATATTTAAATATC
*
514704 AAATTAGATAATTTTAATATC
1 AAA--A-AT-ATTTAAATATC
* *
514725 GAATATATATTAAATATC
1 AAAAATAT-TTAAATATC
514743 AAAAATATTTAA
1 AAAAATATTTAA
514755 TAAAAATATA
Statistics
Matches: 39, Mismatches: 6, Indels: 11
0.70 0.11 0.20
Matches are distributed among these distances:
16 3 0.08
17 6 0.15
18 17 0.44
19 2 0.05
20 9 0.23
21 2 0.05
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (17 bp):
AAAAATATTTAAATATC
Found at i:514767 original size:17 final size:17
Alignment explanation
Indices: 514726--514776 Score: 52
Period size: 16 Copynumber: 3.0 Consensus size: 17
514716 TTTAATATCG
* *
514726 AATATATATTAAATATCA
1 AATATATATTTAATA-AA
514744 AA-A-ATATTTAATAAA
1 AATATATATTTAATAAA
514759 AATATATATTTAACTAAA
1 AATATATATTTAA-TAAA
514777 TTGTATGATC
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
15 3 0.11
16 10 0.36
17 9 0.32
18 6 0.21
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (17 bp):
AATATATATTTAATAAA
Found at i:515328 original size:17 final size:17
Alignment explanation
Indices: 515302--515334 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
515292 TGTTCTGAGT
*
515302 AAGTTTAATATCACAAA
1 AAGTTAAATATCACAAA
515319 AAGTTAAATATCACAA
1 AAGTTAAATATCACAA
515335 GCTCGAGCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.55, C:0.12, G:0.06, T:0.27
Consensus pattern (17 bp):
AAGTTAAATATCACAAA
Found at i:518322 original size:27 final size:27
Alignment explanation
Indices: 518285--518362 Score: 93
Period size: 27 Copynumber: 2.9 Consensus size: 27
518275 AAAAGCCACC
* *
518285 CTTTGTGTTTGTCAACAATGGTGGTTA
1 CTTTGTATTTGTCAAAAATGGTGGTTA
*
518312 CTTTGTATTTGTCAAAAATGGTGGTTC
1 CTTTGTATTTGTCAAAAATGGTGGTTA
* * * *
518339 CTTTTTGTTTATCAAAAATTGTGG
1 CTTTGTATTTGTCAAAAATGGTGG
518363 CTTGTTGTTT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 44 1.00
ACGTcount: A:0.22, C:0.10, G:0.22, T:0.46
Consensus pattern (27 bp):
CTTTGTATTTGTCAAAAATGGTGGTTA
Found at i:518377 original size:24 final size:24
Alignment explanation
Indices: 518319--518388 Score: 70
Period size: 24 Copynumber: 2.8 Consensus size: 24
518309 TTACTTTGTA
* *
518319 TTTGTCAAAAATGGTGGTTCCTTTTTG
1 TTTGTCAAAAATTGTGG---CTTGTTG
*
518346 TTTATCAAAAATTGTGGCTTGTTG
1 TTTGTCAAAAATTGTGGCTTGTTG
518370 TTTGTC-AAAATTGGTGGCT
1 TTTGTCAAAAATT-GTGGCT
518389 AATTTTTATT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
23 6 0.16
24 17 0.45
27 15 0.39
ACGTcount: A:0.21, C:0.10, G:0.23, T:0.46
Consensus pattern (24 bp):
TTTGTCAAAAATTGTGGCTTGTTG
Found at i:520962 original size:21 final size:22
Alignment explanation
Indices: 520933--520978 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
520923 TGTTCAGATA
** *
520933 AGTAGTACTCCGCAGCAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
520955 AGTA-TACTCCAAAACAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
520976 AGT
1 AGT
520979 TTCAACAGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (22 bp):
AGTAGTACTCCAAAACAGGTGG
Done.