Multiple sequence alignment - TraesCS7A01G345800

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS7A01G345800 chr7A 100.000 2375 0 0 1 2375 508610813 508608439 0.000000e+00 4386
1 TraesCS7A01G345800 chr7D 88.831 1155 64 17 593 1708 424658515 424659643 0.000000e+00 1358
2 TraesCS7A01G345800 chr7D 86.528 527 27 18 1799 2319 424659815 424660303 7.470000e-150 540
3 TraesCS7A01G345800 chr7D 82.011 189 18 7 353 525 424658071 424658259 1.900000e-31 147
4 TraesCS7A01G345800 chr7B 80.549 1275 110 54 526 1702 442363469 442364703 0.000000e+00 854
5 TraesCS7A01G345800 chr7B 85.866 283 26 6 1974 2248 442365340 442365616 2.990000e-74 289
6 TraesCS7A01G345800 chr7B 78.327 263 37 12 1725 1973 442364817 442365073 4.090000e-33 152
7 TraesCS7A01G345800 chr7B 77.444 266 29 19 69 332 442362713 442362949 1.920000e-26 130


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7A01G345800 chr7A 508608439 508610813 2374 True 4386.000000 4386 100.0000 1 2375 1 chr7A.!!$R1 2374
1 TraesCS7A01G345800 chr7D 424658071 424660303 2232 False 681.666667 1358 85.7900 353 2319 3 chr7D.!!$F1 1966
2 TraesCS7A01G345800 chr7B 442362713 442365616 2903 False 356.250000 854 80.5465 69 2248 4 chr7B.!!$F1 2179

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
150 151 0.036105 AGCAGACCATCACGCATTCA 60.036 50.0 0.0 0.0 0.0 2.57 F
151 152 0.097674 GCAGACCATCACGCATTCAC 59.902 55.0 0.0 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1337 1791 0.108329 GCCGCATGTGTAGTACTGGT 60.108 55.0 5.39 0.00 0.00 4.00 R
1899 2557 0.165079 GCAGCTTACGCGTTGCTTAA 59.835 50.0 28.38 12.94 42.32 1.85 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 2.850060 TCGACTAGCAAAAGAATACGCG 59.150 45.455 3.53 3.53 0.00 6.01
23 24 2.597305 CGACTAGCAAAAGAATACGCGT 59.403 45.455 19.17 19.17 0.00 6.01
24 25 3.301007 CGACTAGCAAAAGAATACGCGTC 60.301 47.826 18.63 0.16 0.00 5.19
25 26 2.597305 ACTAGCAAAAGAATACGCGTCG 59.403 45.455 18.63 0.00 0.00 5.12
26 27 0.719465 AGCAAAAGAATACGCGTCGG 59.281 50.000 18.63 0.00 0.00 4.79
27 28 0.717224 GCAAAAGAATACGCGTCGGA 59.283 50.000 18.63 0.00 0.00 4.55
28 29 1.127213 GCAAAAGAATACGCGTCGGAA 59.873 47.619 18.63 0.00 0.00 4.30
29 30 2.411806 GCAAAAGAATACGCGTCGGAAA 60.412 45.455 18.63 0.00 0.00 3.13
30 31 3.404564 CAAAAGAATACGCGTCGGAAAG 58.595 45.455 18.63 0.00 0.00 2.62
31 32 2.642139 AAGAATACGCGTCGGAAAGA 57.358 45.000 18.63 0.00 0.00 2.52
32 33 2.642139 AGAATACGCGTCGGAAAGAA 57.358 45.000 18.63 0.00 0.00 2.52
33 34 2.950433 AGAATACGCGTCGGAAAGAAA 58.050 42.857 18.63 0.00 0.00 2.52
34 35 3.518590 AGAATACGCGTCGGAAAGAAAT 58.481 40.909 18.63 0.00 0.00 2.17
35 36 4.675510 AGAATACGCGTCGGAAAGAAATA 58.324 39.130 18.63 0.00 0.00 1.40
36 37 5.104374 AGAATACGCGTCGGAAAGAAATAA 58.896 37.500 18.63 0.00 0.00 1.40
37 38 5.231568 AGAATACGCGTCGGAAAGAAATAAG 59.768 40.000 18.63 0.00 0.00 1.73
38 39 2.950433 ACGCGTCGGAAAGAAATAAGA 58.050 42.857 5.58 0.00 0.00 2.10
39 40 2.921754 ACGCGTCGGAAAGAAATAAGAG 59.078 45.455 5.58 0.00 0.00 2.85
40 41 2.921754 CGCGTCGGAAAGAAATAAGAGT 59.078 45.455 0.00 0.00 0.00 3.24
41 42 3.367025 CGCGTCGGAAAGAAATAAGAGTT 59.633 43.478 0.00 0.00 0.00 3.01
42 43 4.490479 CGCGTCGGAAAGAAATAAGAGTTC 60.490 45.833 0.00 0.00 0.00 3.01
43 44 4.490479 GCGTCGGAAAGAAATAAGAGTTCG 60.490 45.833 0.00 0.00 0.00 3.95
44 45 4.620184 CGTCGGAAAGAAATAAGAGTTCGT 59.380 41.667 0.00 0.00 0.00 3.85
45 46 5.796935 CGTCGGAAAGAAATAAGAGTTCGTA 59.203 40.000 0.00 0.00 0.00 3.43
46 47 6.021626 CGTCGGAAAGAAATAAGAGTTCGTAG 60.022 42.308 0.00 0.00 0.00 3.51
47 48 6.805760 GTCGGAAAGAAATAAGAGTTCGTAGT 59.194 38.462 0.00 0.00 0.00 2.73
48 49 7.328005 GTCGGAAAGAAATAAGAGTTCGTAGTT 59.672 37.037 0.00 0.00 0.00 2.24
49 50 7.869429 TCGGAAAGAAATAAGAGTTCGTAGTTT 59.131 33.333 0.00 0.00 0.00 2.66
50 51 8.160976 CGGAAAGAAATAAGAGTTCGTAGTTTC 58.839 37.037 0.00 0.00 0.00 2.78
51 52 8.441608 GGAAAGAAATAAGAGTTCGTAGTTTCC 58.558 37.037 0.00 0.00 0.00 3.13
52 53 7.578169 AAGAAATAAGAGTTCGTAGTTTCCG 57.422 36.000 0.00 0.00 0.00 4.30
53 54 6.917533 AGAAATAAGAGTTCGTAGTTTCCGA 58.082 36.000 0.00 0.00 0.00 4.55
54 55 7.545489 AGAAATAAGAGTTCGTAGTTTCCGAT 58.455 34.615 0.00 0.00 33.81 4.18
55 56 7.488471 AGAAATAAGAGTTCGTAGTTTCCGATG 59.512 37.037 0.00 0.00 33.81 3.84
56 57 4.778534 AAGAGTTCGTAGTTTCCGATGA 57.221 40.909 0.00 0.00 33.81 2.92
57 58 4.778534 AGAGTTCGTAGTTTCCGATGAA 57.221 40.909 0.00 0.00 33.81 2.57
58 59 4.734917 AGAGTTCGTAGTTTCCGATGAAG 58.265 43.478 0.00 0.00 33.81 3.02
59 60 4.458295 AGAGTTCGTAGTTTCCGATGAAGA 59.542 41.667 0.00 0.00 33.81 2.87
60 61 5.048224 AGAGTTCGTAGTTTCCGATGAAGAA 60.048 40.000 0.00 0.00 33.81 2.52
61 62 5.535333 AGTTCGTAGTTTCCGATGAAGAAA 58.465 37.500 0.00 0.00 33.81 2.52
62 63 5.987347 AGTTCGTAGTTTCCGATGAAGAAAA 59.013 36.000 0.00 0.00 35.13 2.29
63 64 6.145696 AGTTCGTAGTTTCCGATGAAGAAAAG 59.854 38.462 0.00 0.00 35.13 2.27
64 65 5.775686 TCGTAGTTTCCGATGAAGAAAAGA 58.224 37.500 0.00 0.00 35.13 2.52
65 66 6.218019 TCGTAGTTTCCGATGAAGAAAAGAA 58.782 36.000 0.00 0.00 35.13 2.52
66 67 6.702723 TCGTAGTTTCCGATGAAGAAAAGAAA 59.297 34.615 0.00 0.00 35.13 2.52
67 68 6.790825 CGTAGTTTCCGATGAAGAAAAGAAAC 59.209 38.462 0.00 0.00 42.00 2.78
72 73 7.928908 TTCCGATGAAGAAAAGAAACATTTG 57.071 32.000 0.00 0.00 0.00 2.32
73 74 7.270757 TCCGATGAAGAAAAGAAACATTTGA 57.729 32.000 0.00 0.00 0.00 2.69
97 98 8.968969 TGATTGATAATTTTGGTCATGTCATCA 58.031 29.630 0.00 0.00 0.00 3.07
105 106 2.551887 TGGTCATGTCATCAAACCAACG 59.448 45.455 8.23 0.00 39.12 4.10
117 118 0.882927 AACCAACGGACCATCACACG 60.883 55.000 0.00 0.00 0.00 4.49
129 130 5.123186 GGACCATCACACGATTATTTCACAA 59.877 40.000 0.00 0.00 0.00 3.33
130 131 6.183360 GGACCATCACACGATTATTTCACAAT 60.183 38.462 0.00 0.00 0.00 2.71
132 133 7.919690 ACCATCACACGATTATTTCACAATAG 58.080 34.615 0.00 0.00 0.00 1.73
144 145 2.892374 TCACAATAGCAGACCATCACG 58.108 47.619 0.00 0.00 0.00 4.35
146 147 1.066215 ACAATAGCAGACCATCACGCA 60.066 47.619 0.00 0.00 0.00 5.24
147 148 2.216046 CAATAGCAGACCATCACGCAT 58.784 47.619 0.00 0.00 0.00 4.73
148 149 2.615447 CAATAGCAGACCATCACGCATT 59.385 45.455 0.00 0.00 0.00 3.56
150 151 0.036105 AGCAGACCATCACGCATTCA 60.036 50.000 0.00 0.00 0.00 2.57
151 152 0.097674 GCAGACCATCACGCATTCAC 59.902 55.000 0.00 0.00 0.00 3.18
152 153 0.371301 CAGACCATCACGCATTCACG 59.629 55.000 0.00 0.00 39.50 4.35
153 154 1.060937 GACCATCACGCATTCACGC 59.939 57.895 0.00 0.00 36.19 5.34
154 155 1.361668 GACCATCACGCATTCACGCT 61.362 55.000 0.00 0.00 36.19 5.07
155 156 1.061411 CCATCACGCATTCACGCTG 59.939 57.895 0.00 0.00 36.19 5.18
156 157 1.061411 CATCACGCATTCACGCTGG 59.939 57.895 0.00 0.00 36.19 4.85
157 158 1.375908 ATCACGCATTCACGCTGGT 60.376 52.632 0.00 0.00 36.19 4.00
158 159 1.638388 ATCACGCATTCACGCTGGTG 61.638 55.000 0.00 0.00 45.78 4.17
176 177 1.817099 GTTCAGGATCGCTGGCTGG 60.817 63.158 10.23 0.00 0.00 4.85
181 182 1.599240 GGATCGCTGGCTGGGAATC 60.599 63.158 14.70 11.94 41.04 2.52
185 186 0.677731 TCGCTGGCTGGGAATCAAAG 60.678 55.000 8.67 0.00 34.56 2.77
198 199 4.336713 GGGAATCAAAGCTGGATCTAACAC 59.663 45.833 1.94 0.00 0.00 3.32
199 200 4.943705 GGAATCAAAGCTGGATCTAACACA 59.056 41.667 1.94 0.00 0.00 3.72
200 201 5.065731 GGAATCAAAGCTGGATCTAACACAG 59.934 44.000 1.94 0.00 35.40 3.66
202 203 4.569943 TCAAAGCTGGATCTAACACAGAC 58.430 43.478 0.00 0.00 35.62 3.51
204 205 4.833478 AAGCTGGATCTAACACAGACAT 57.167 40.909 0.00 0.00 35.62 3.06
205 206 5.939764 AAGCTGGATCTAACACAGACATA 57.060 39.130 0.00 0.00 35.62 2.29
208 209 4.502259 GCTGGATCTAACACAGACATAGGG 60.502 50.000 0.00 0.00 35.62 3.53
209 210 3.388024 TGGATCTAACACAGACATAGGGC 59.612 47.826 0.00 0.00 35.62 5.19
210 211 3.553096 GGATCTAACACAGACATAGGGCG 60.553 52.174 0.00 0.00 35.62 6.13
212 213 0.177141 TAACACAGACATAGGGCGCC 59.823 55.000 21.18 21.18 0.00 6.53
213 214 1.553690 AACACAGACATAGGGCGCCT 61.554 55.000 28.56 15.07 37.71 5.52
214 215 1.522355 CACAGACATAGGGCGCCTG 60.522 63.158 28.56 19.78 34.61 4.85
215 216 2.590007 CAGACATAGGGCGCCTGC 60.590 66.667 28.56 11.04 41.71 4.85
241 242 1.382522 CGGCTGGTTGATGTTATGCT 58.617 50.000 0.00 0.00 0.00 3.79
249 250 5.242434 TGGTTGATGTTATGCTTAGTTCGT 58.758 37.500 0.00 0.00 0.00 3.85
250 251 6.399743 TGGTTGATGTTATGCTTAGTTCGTA 58.600 36.000 0.00 0.00 0.00 3.43
251 252 6.311935 TGGTTGATGTTATGCTTAGTTCGTAC 59.688 38.462 0.00 0.00 0.00 3.67
254 255 5.969435 TGATGTTATGCTTAGTTCGTACTCG 59.031 40.000 0.00 0.00 35.78 4.18
255 256 5.300969 TGTTATGCTTAGTTCGTACTCGT 57.699 39.130 0.00 0.00 35.78 4.18
256 257 6.421377 TGTTATGCTTAGTTCGTACTCGTA 57.579 37.500 0.00 0.00 35.78 3.43
258 259 6.092670 TGTTATGCTTAGTTCGTACTCGTAGT 59.907 38.462 0.00 0.00 35.78 2.73
261 262 5.149273 TGCTTAGTTCGTACTCGTAGTTTG 58.851 41.667 0.00 0.00 35.78 2.93
263 264 5.058977 GCTTAGTTCGTACTCGTAGTTTGTG 59.941 44.000 0.00 0.00 35.78 3.33
264 265 3.893720 AGTTCGTACTCGTAGTTTGTGG 58.106 45.455 0.00 0.00 38.33 4.17
265 266 3.316308 AGTTCGTACTCGTAGTTTGTGGT 59.684 43.478 0.00 0.00 38.33 4.16
268 269 2.154389 CGTACTCGTAGTTTGTGGTTGC 59.846 50.000 0.00 0.00 0.00 4.17
287 288 2.312722 CTGTTCTGCAGCATAGCTCT 57.687 50.000 9.47 0.00 36.40 4.09
288 289 1.934525 CTGTTCTGCAGCATAGCTCTG 59.065 52.381 9.47 0.00 36.40 3.35
289 290 1.551883 TGTTCTGCAGCATAGCTCTGA 59.448 47.619 9.47 0.00 36.40 3.27
290 291 2.203401 GTTCTGCAGCATAGCTCTGAG 58.797 52.381 9.47 0.00 36.40 3.35
291 292 0.751452 TCTGCAGCATAGCTCTGAGG 59.249 55.000 9.47 0.00 36.40 3.86
292 293 0.881159 CTGCAGCATAGCTCTGAGGC 60.881 60.000 0.00 5.94 36.40 4.70
293 294 1.335882 TGCAGCATAGCTCTGAGGCT 61.336 55.000 6.83 3.61 45.29 4.58
294 295 0.179051 GCAGCATAGCTCTGAGGCTT 60.179 55.000 6.83 0.00 42.97 4.35
295 296 1.868469 CAGCATAGCTCTGAGGCTTC 58.132 55.000 6.83 0.00 42.97 3.86
296 297 0.388659 AGCATAGCTCTGAGGCTTCG 59.611 55.000 6.83 1.17 42.97 3.79
297 298 0.103937 GCATAGCTCTGAGGCTTCGT 59.896 55.000 6.83 0.00 42.97 3.85
332 333 5.977129 AGTTGCAGCATAACTTTGTTTGTAC 59.023 36.000 2.55 0.00 34.91 2.90
333 334 5.766150 TGCAGCATAACTTTGTTTGTACT 57.234 34.783 0.00 0.00 0.00 2.73
334 335 5.518812 TGCAGCATAACTTTGTTTGTACTG 58.481 37.500 0.00 0.00 0.00 2.74
335 336 4.382754 GCAGCATAACTTTGTTTGTACTGC 59.617 41.667 0.00 0.00 39.85 4.40
336 337 4.917415 CAGCATAACTTTGTTTGTACTGCC 59.083 41.667 0.00 0.00 0.00 4.85
337 338 4.827284 AGCATAACTTTGTTTGTACTGCCT 59.173 37.500 0.00 0.00 0.00 4.75
338 339 5.301805 AGCATAACTTTGTTTGTACTGCCTT 59.698 36.000 0.00 0.00 0.00 4.35
339 340 5.402270 GCATAACTTTGTTTGTACTGCCTTG 59.598 40.000 0.00 0.00 0.00 3.61
340 341 6.503524 CATAACTTTGTTTGTACTGCCTTGT 58.496 36.000 0.00 0.00 0.00 3.16
341 342 7.644490 CATAACTTTGTTTGTACTGCCTTGTA 58.356 34.615 0.00 0.00 0.00 2.41
342 343 5.751243 ACTTTGTTTGTACTGCCTTGTAG 57.249 39.130 0.00 0.00 0.00 2.74
343 344 4.036380 ACTTTGTTTGTACTGCCTTGTAGC 59.964 41.667 0.00 0.00 0.00 3.58
344 345 3.485463 TGTTTGTACTGCCTTGTAGCT 57.515 42.857 0.00 0.00 0.00 3.32
345 346 3.138304 TGTTTGTACTGCCTTGTAGCTG 58.862 45.455 0.00 0.00 37.68 4.24
346 347 3.139077 GTTTGTACTGCCTTGTAGCTGT 58.861 45.455 0.00 1.74 45.50 4.40
347 348 4.202274 TGTTTGTACTGCCTTGTAGCTGTA 60.202 41.667 0.00 0.00 43.61 2.74
348 349 3.868757 TGTACTGCCTTGTAGCTGTAG 57.131 47.619 0.00 0.00 44.58 2.74
349 350 3.162666 TGTACTGCCTTGTAGCTGTAGT 58.837 45.455 0.00 0.00 44.58 2.73
350 351 3.576982 TGTACTGCCTTGTAGCTGTAGTT 59.423 43.478 0.00 0.00 44.58 2.24
351 352 3.320673 ACTGCCTTGTAGCTGTAGTTC 57.679 47.619 0.00 0.00 42.34 3.01
352 353 2.263077 CTGCCTTGTAGCTGTAGTTCG 58.737 52.381 0.00 0.00 0.00 3.95
353 354 1.000145 GCCTTGTAGCTGTAGTTCGC 59.000 55.000 0.00 0.00 0.00 4.70
354 355 1.641577 CCTTGTAGCTGTAGTTCGCC 58.358 55.000 0.00 0.00 0.00 5.54
401 402 1.419374 CCGTCTGTGCAGTCTGTAAC 58.581 55.000 0.93 1.53 0.00 2.50
404 405 2.218759 CGTCTGTGCAGTCTGTAACAAC 59.781 50.000 0.93 7.17 0.00 3.32
429 437 1.514087 CATGGTTGATGTGCTGGGC 59.486 57.895 0.00 0.00 0.00 5.36
461 469 3.477530 GCTGTAAGGTGGTCTTTTGAGT 58.522 45.455 0.00 0.00 36.93 3.41
468 476 2.495084 GTGGTCTTTTGAGTCCTGGAC 58.505 52.381 19.20 19.20 0.00 4.02
469 477 1.420138 TGGTCTTTTGAGTCCTGGACC 59.580 52.381 22.81 14.59 42.27 4.46
525 705 7.542890 TGTTGCTGTTTTATCAGTTTTCAGAA 58.457 30.769 0.00 0.00 37.70 3.02
591 954 1.202818 AGACCCAAGAGGCACACTTTC 60.203 52.381 0.00 0.00 37.08 2.62
604 983 5.533528 AGGCACACTTTCTTTAAATTACGGT 59.466 36.000 0.00 0.00 0.00 4.83
606 985 7.229106 AGGCACACTTTCTTTAAATTACGGTAA 59.771 33.333 2.62 2.62 0.00 2.85
634 1013 5.296813 AGAATGGCATTCGAACTAAACAC 57.703 39.130 28.96 6.77 43.92 3.32
640 1019 3.972502 GCATTCGAACTAAACACAACACC 59.027 43.478 0.00 0.00 0.00 4.16
641 1020 4.496673 GCATTCGAACTAAACACAACACCA 60.497 41.667 0.00 0.00 0.00 4.17
645 1024 4.273969 TCGAACTAAACACAACACCAATCC 59.726 41.667 0.00 0.00 0.00 3.01
656 1035 3.683365 ACACCAATCCAAAGAAATGCC 57.317 42.857 0.00 0.00 0.00 4.40
658 1037 2.302445 CACCAATCCAAAGAAATGCCCA 59.698 45.455 0.00 0.00 0.00 5.36
699 1079 1.154338 GCGCTGTGAATGTGAGTGC 60.154 57.895 0.00 0.00 36.18 4.40
703 1083 2.416747 GCTGTGAATGTGAGTGCAGTA 58.583 47.619 0.00 0.00 0.00 2.74
706 1104 4.612259 GCTGTGAATGTGAGTGCAGTAAAG 60.612 45.833 0.00 0.00 0.00 1.85
709 1107 2.496899 ATGTGAGTGCAGTAAAGGGG 57.503 50.000 0.00 0.00 0.00 4.79
783 1184 2.690497 TCACTCGAGCCTGAATCTAAGG 59.310 50.000 13.61 0.00 37.91 2.69
933 1345 2.676822 TCGACGCCAGCTTCTCCT 60.677 61.111 0.00 0.00 0.00 3.69
934 1346 2.202676 CGACGCCAGCTTCTCCTC 60.203 66.667 0.00 0.00 0.00 3.71
935 1347 2.202676 GACGCCAGCTTCTCCTCG 60.203 66.667 0.00 0.00 0.00 4.63
936 1348 4.443266 ACGCCAGCTTCTCCTCGC 62.443 66.667 0.00 0.00 0.00 5.03
937 1349 4.441695 CGCCAGCTTCTCCTCGCA 62.442 66.667 0.00 0.00 0.00 5.10
938 1350 2.511145 GCCAGCTTCTCCTCGCAG 60.511 66.667 0.00 0.00 0.00 5.18
993 1405 2.909006 TCTTCATCTTCCTCCTGCTGTT 59.091 45.455 0.00 0.00 0.00 3.16
994 1406 4.096681 TCTTCATCTTCCTCCTGCTGTTA 58.903 43.478 0.00 0.00 0.00 2.41
995 1407 4.718774 TCTTCATCTTCCTCCTGCTGTTAT 59.281 41.667 0.00 0.00 0.00 1.89
996 1408 4.412796 TCATCTTCCTCCTGCTGTTATG 57.587 45.455 0.00 0.00 0.00 1.90
997 1409 3.135348 TCATCTTCCTCCTGCTGTTATGG 59.865 47.826 0.00 0.00 0.00 2.74
998 1410 1.210478 TCTTCCTCCTGCTGTTATGGC 59.790 52.381 0.00 0.00 0.00 4.40
999 1411 1.211457 CTTCCTCCTGCTGTTATGGCT 59.789 52.381 0.00 0.00 0.00 4.75
1012 1424 3.201930 TGTTATGGCTATGGCTTCTTCCA 59.798 43.478 0.00 0.00 40.97 3.53
1081 1493 0.616111 TCTTCTGCTGTCCTCCTCCC 60.616 60.000 0.00 0.00 0.00 4.30
1087 1499 3.931631 CTGTCCTCCTCCCCTGCCA 62.932 68.421 0.00 0.00 0.00 4.92
1343 1797 4.201679 CGCCGCCGATGACCAGTA 62.202 66.667 0.00 0.00 36.29 2.74
1401 1855 0.748367 GAAGGATCCGGTTCTTGCCC 60.748 60.000 12.19 0.00 0.00 5.36
1472 1928 9.620660 CAAGTGTAAATATGGTGAGGTTTTAAC 57.379 33.333 0.00 0.00 0.00 2.01
1555 2011 2.882777 CGATGCACGCGAGCTCTT 60.883 61.111 27.94 13.68 34.99 2.85
1556 2012 2.699809 GATGCACGCGAGCTCTTG 59.300 61.111 27.94 8.95 34.99 3.02
1557 2013 2.047844 ATGCACGCGAGCTCTTGT 60.048 55.556 27.94 7.03 34.99 3.16
1568 2024 3.354397 CGAGCTCTTGTTGTTGTTGTTC 58.646 45.455 12.85 0.00 0.00 3.18
1708 2174 6.037391 AGTCGAAAACATTTGTTTAGTTCGGA 59.963 34.615 20.07 10.31 46.47 4.55
1711 2177 7.224362 TCGAAAACATTTGTTTAGTTCGGAGTA 59.776 33.333 20.07 6.43 46.47 2.59
1712 2178 7.319615 CGAAAACATTTGTTTAGTTCGGAGTAC 59.680 37.037 15.72 0.00 46.47 2.73
1713 2179 5.834239 ACATTTGTTTAGTTCGGAGTACG 57.166 39.130 0.00 0.00 46.11 3.67
1714 2180 5.291971 ACATTTGTTTAGTTCGGAGTACGT 58.708 37.500 0.00 0.00 44.69 3.57
1716 2182 3.559238 TGTTTAGTTCGGAGTACGTCC 57.441 47.619 0.00 2.28 44.69 4.79
1718 2184 3.569701 TGTTTAGTTCGGAGTACGTCCTT 59.430 43.478 0.00 0.00 44.35 3.36
1719 2185 4.037923 TGTTTAGTTCGGAGTACGTCCTTT 59.962 41.667 0.00 0.00 44.35 3.11
1721 2187 1.543358 AGTTCGGAGTACGTCCTTTCC 59.457 52.381 0.00 0.00 44.35 3.13
1723 2189 1.171308 TCGGAGTACGTCCTTTCCTG 58.829 55.000 0.00 0.00 44.35 3.86
1740 2373 1.550327 CTGTACCTGTGAGCAGAGGA 58.450 55.000 19.25 1.89 44.04 3.71
1746 2379 3.837355 ACCTGTGAGCAGAGGAAATTTT 58.163 40.909 19.25 0.00 44.04 1.82
1747 2380 3.823304 ACCTGTGAGCAGAGGAAATTTTC 59.177 43.478 19.25 0.24 44.04 2.29
1748 2381 3.822735 CCTGTGAGCAGAGGAAATTTTCA 59.177 43.478 7.87 0.00 44.04 2.69
1749 2382 4.461781 CCTGTGAGCAGAGGAAATTTTCAT 59.538 41.667 7.87 3.65 44.04 2.57
1752 2385 5.302568 TGTGAGCAGAGGAAATTTTCATTGT 59.697 36.000 11.09 0.00 0.00 2.71
1768 2401 5.756195 TCATTGTTCCTGTCTTTGTTCTG 57.244 39.130 0.00 0.00 0.00 3.02
1781 2417 1.896220 TGTTCTGAACACCAGCATCC 58.104 50.000 18.69 0.00 42.62 3.51
1788 2424 2.224426 TGAACACCAGCATCCGTTAAGT 60.224 45.455 0.00 0.00 0.00 2.24
1790 2426 2.858745 ACACCAGCATCCGTTAAGTTT 58.141 42.857 0.00 0.00 0.00 2.66
1794 2430 4.693566 CACCAGCATCCGTTAAGTTTCTTA 59.306 41.667 0.00 0.00 0.00 2.10
1795 2431 4.694037 ACCAGCATCCGTTAAGTTTCTTAC 59.306 41.667 0.00 0.00 0.00 2.34
1796 2432 4.693566 CCAGCATCCGTTAAGTTTCTTACA 59.306 41.667 0.00 0.00 0.00 2.41
1798 2434 5.408604 CAGCATCCGTTAAGTTTCTTACACT 59.591 40.000 0.00 0.00 0.00 3.55
1799 2435 5.995897 AGCATCCGTTAAGTTTCTTACACTT 59.004 36.000 0.00 0.00 38.13 3.16
1800 2436 7.117236 CAGCATCCGTTAAGTTTCTTACACTTA 59.883 37.037 0.00 0.00 35.95 2.24
1801 2437 7.117379 AGCATCCGTTAAGTTTCTTACACTTAC 59.883 37.037 0.00 0.00 36.63 2.34
1802 2438 7.095523 GCATCCGTTAAGTTTCTTACACTTACA 60.096 37.037 0.00 0.00 36.63 2.41
1804 2440 8.891671 TCCGTTAAGTTTCTTACACTTACATT 57.108 30.769 0.00 0.00 36.63 2.71
1805 2441 9.328845 TCCGTTAAGTTTCTTACACTTACATTT 57.671 29.630 0.00 0.00 36.63 2.32
1818 2471 5.008316 ACACTTACATTTCCTCGTTTCAACC 59.992 40.000 0.00 0.00 0.00 3.77
1830 2483 2.480419 CGTTTCAACCTACTGCTTGGAG 59.520 50.000 0.00 0.00 0.00 3.86
1845 2503 1.377202 GGAGCCGAGAAATGCACCA 60.377 57.895 0.00 0.00 38.03 4.17
1857 2515 5.540911 AGAAATGCACCAATGGTAAACTTG 58.459 37.500 3.85 0.00 32.11 3.16
1859 2517 6.266558 AGAAATGCACCAATGGTAAACTTGTA 59.733 34.615 3.85 0.00 32.11 2.41
1861 2519 5.446143 TGCACCAATGGTAAACTTGTAAG 57.554 39.130 3.85 0.00 32.11 2.34
1899 2557 7.039714 GGAGTTTCTTGGAGTAATTCATGGTTT 60.040 37.037 0.00 0.00 0.00 3.27
1900 2558 8.250143 AGTTTCTTGGAGTAATTCATGGTTTT 57.750 30.769 0.00 0.00 0.00 2.43
1929 2587 2.009774 CGTAAGCTGCATGTAAAGCCT 58.990 47.619 1.02 4.22 40.42 4.58
1955 2613 0.984230 TCGGAGTTTCTTGGGAGCAT 59.016 50.000 0.00 0.00 0.00 3.79
1983 2641 3.795041 AGCTGCTGGCCTGCCTAG 61.795 66.667 29.35 21.86 43.05 3.02
2117 3049 0.038251 TATCCATGCGAGCGGTGATC 60.038 55.000 0.00 0.00 0.00 2.92
2126 3058 4.278956 GCGGTGATCGGTGAGTTT 57.721 55.556 0.00 0.00 39.69 2.66
2189 3121 2.753043 TCTGGTCCCGTAGCGTCC 60.753 66.667 0.00 0.00 0.00 4.79
2262 3194 2.104967 TCGACCGGGACTAATGATTGT 58.895 47.619 6.32 0.00 0.00 2.71
2272 3204 5.125417 GGGACTAATGATTGTGCAAGCTTAA 59.875 40.000 0.00 0.00 0.00 1.85
2274 3206 7.013274 GGGACTAATGATTGTGCAAGCTTAATA 59.987 37.037 0.00 0.00 0.00 0.98
2275 3207 8.405531 GGACTAATGATTGTGCAAGCTTAATAA 58.594 33.333 0.00 0.00 0.00 1.40
2276 3208 9.787532 GACTAATGATTGTGCAAGCTTAATAAA 57.212 29.630 0.00 0.00 0.00 1.40
2319 3251 8.046708 TCATAGTAGTTTGTATTGCATTGAGGT 58.953 33.333 0.00 0.00 0.00 3.85
2320 3252 9.325198 CATAGTAGTTTGTATTGCATTGAGGTA 57.675 33.333 0.00 0.00 0.00 3.08
2321 3253 9.899661 ATAGTAGTTTGTATTGCATTGAGGTAA 57.100 29.630 0.00 0.00 0.00 2.85
2322 3254 8.630054 AGTAGTTTGTATTGCATTGAGGTAAA 57.370 30.769 0.00 0.00 0.00 2.01
2323 3255 9.073475 AGTAGTTTGTATTGCATTGAGGTAAAA 57.927 29.630 0.00 0.00 0.00 1.52
2324 3256 9.685828 GTAGTTTGTATTGCATTGAGGTAAAAA 57.314 29.630 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.486108 CGCGTATTCTTTTGCTAGTCGAT 59.514 43.478 0.00 0.00 0.00 3.59
1 2 2.850060 CGCGTATTCTTTTGCTAGTCGA 59.150 45.455 0.00 0.00 0.00 4.20
2 3 2.597305 ACGCGTATTCTTTTGCTAGTCG 59.403 45.455 11.67 0.00 0.00 4.18
3 4 3.301007 CGACGCGTATTCTTTTGCTAGTC 60.301 47.826 13.97 0.00 0.00 2.59
4 5 2.597305 CGACGCGTATTCTTTTGCTAGT 59.403 45.455 13.97 0.00 0.00 2.57
5 6 2.034842 CCGACGCGTATTCTTTTGCTAG 60.035 50.000 13.97 0.00 0.00 3.42
6 7 1.921887 CCGACGCGTATTCTTTTGCTA 59.078 47.619 13.97 0.00 0.00 3.49
7 8 0.719465 CCGACGCGTATTCTTTTGCT 59.281 50.000 13.97 0.00 0.00 3.91
8 9 0.717224 TCCGACGCGTATTCTTTTGC 59.283 50.000 13.97 0.00 0.00 3.68
9 10 3.122278 TCTTTCCGACGCGTATTCTTTTG 59.878 43.478 13.97 0.00 0.00 2.44
10 11 3.319755 TCTTTCCGACGCGTATTCTTTT 58.680 40.909 13.97 0.00 0.00 2.27
11 12 2.950433 TCTTTCCGACGCGTATTCTTT 58.050 42.857 13.97 0.00 0.00 2.52
12 13 2.642139 TCTTTCCGACGCGTATTCTT 57.358 45.000 13.97 0.00 0.00 2.52
13 14 2.642139 TTCTTTCCGACGCGTATTCT 57.358 45.000 13.97 0.00 0.00 2.40
14 15 3.920112 ATTTCTTTCCGACGCGTATTC 57.080 42.857 13.97 0.00 0.00 1.75
15 16 5.104374 TCTTATTTCTTTCCGACGCGTATT 58.896 37.500 13.97 0.00 0.00 1.89
16 17 4.675510 TCTTATTTCTTTCCGACGCGTAT 58.324 39.130 13.97 0.21 0.00 3.06
17 18 4.095410 TCTTATTTCTTTCCGACGCGTA 57.905 40.909 13.97 0.00 0.00 4.42
18 19 2.921754 CTCTTATTTCTTTCCGACGCGT 59.078 45.455 13.85 13.85 0.00 6.01
19 20 2.921754 ACTCTTATTTCTTTCCGACGCG 59.078 45.455 3.53 3.53 0.00 6.01
20 21 4.490479 CGAACTCTTATTTCTTTCCGACGC 60.490 45.833 0.00 0.00 0.00 5.19
21 22 4.620184 ACGAACTCTTATTTCTTTCCGACG 59.380 41.667 0.00 0.00 0.00 5.12
22 23 6.805760 ACTACGAACTCTTATTTCTTTCCGAC 59.194 38.462 0.00 0.00 0.00 4.79
23 24 6.917533 ACTACGAACTCTTATTTCTTTCCGA 58.082 36.000 0.00 0.00 0.00 4.55
24 25 7.578169 AACTACGAACTCTTATTTCTTTCCG 57.422 36.000 0.00 0.00 0.00 4.30
25 26 8.441608 GGAAACTACGAACTCTTATTTCTTTCC 58.558 37.037 0.00 0.00 31.65 3.13
26 27 8.160976 CGGAAACTACGAACTCTTATTTCTTTC 58.839 37.037 0.00 0.00 0.00 2.62
27 28 7.869429 TCGGAAACTACGAACTCTTATTTCTTT 59.131 33.333 0.00 0.00 37.42 2.52
28 29 7.373493 TCGGAAACTACGAACTCTTATTTCTT 58.627 34.615 0.00 0.00 37.42 2.52
29 30 6.917533 TCGGAAACTACGAACTCTTATTTCT 58.082 36.000 0.00 0.00 37.42 2.52
30 31 7.487189 TCATCGGAAACTACGAACTCTTATTTC 59.513 37.037 0.00 0.00 44.20 2.17
31 32 7.318141 TCATCGGAAACTACGAACTCTTATTT 58.682 34.615 0.00 0.00 44.20 1.40
32 33 6.860080 TCATCGGAAACTACGAACTCTTATT 58.140 36.000 0.00 0.00 44.20 1.40
33 34 6.446781 TCATCGGAAACTACGAACTCTTAT 57.553 37.500 0.00 0.00 44.20 1.73
34 35 5.885230 TCATCGGAAACTACGAACTCTTA 57.115 39.130 0.00 0.00 44.20 2.10
35 36 4.778534 TCATCGGAAACTACGAACTCTT 57.221 40.909 0.00 0.00 44.20 2.85
36 37 4.458295 TCTTCATCGGAAACTACGAACTCT 59.542 41.667 0.00 0.00 44.20 3.24
37 38 4.730657 TCTTCATCGGAAACTACGAACTC 58.269 43.478 0.00 0.00 44.20 3.01
38 39 4.778534 TCTTCATCGGAAACTACGAACT 57.221 40.909 0.00 0.00 44.20 3.01
39 40 5.834239 TTTCTTCATCGGAAACTACGAAC 57.166 39.130 0.00 0.00 44.20 3.95
40 41 6.218019 TCTTTTCTTCATCGGAAACTACGAA 58.782 36.000 0.00 0.00 44.20 3.85
41 42 5.775686 TCTTTTCTTCATCGGAAACTACGA 58.224 37.500 0.00 0.00 45.19 3.43
42 43 6.462073 TTCTTTTCTTCATCGGAAACTACG 57.538 37.500 0.00 0.00 33.22 3.51
43 44 7.636326 TGTTTCTTTTCTTCATCGGAAACTAC 58.364 34.615 14.45 0.00 41.39 2.73
44 45 7.795482 TGTTTCTTTTCTTCATCGGAAACTA 57.205 32.000 14.45 2.85 41.39 2.24
45 46 6.693315 TGTTTCTTTTCTTCATCGGAAACT 57.307 33.333 14.45 0.00 41.39 2.66
46 47 7.930513 AATGTTTCTTTTCTTCATCGGAAAC 57.069 32.000 0.00 0.00 41.28 2.78
47 48 8.194104 TCAAATGTTTCTTTTCTTCATCGGAAA 58.806 29.630 0.00 0.00 31.35 3.13
48 49 7.711846 TCAAATGTTTCTTTTCTTCATCGGAA 58.288 30.769 0.00 0.00 0.00 4.30
49 50 7.270757 TCAAATGTTTCTTTTCTTCATCGGA 57.729 32.000 0.00 0.00 0.00 4.55
50 51 8.430063 CAATCAAATGTTTCTTTTCTTCATCGG 58.570 33.333 0.00 0.00 0.00 4.18
51 52 9.184062 TCAATCAAATGTTTCTTTTCTTCATCG 57.816 29.630 0.00 0.00 0.00 3.84
66 67 9.947433 ACATGACCAAAATTATCAATCAAATGT 57.053 25.926 0.00 0.00 0.00 2.71
72 73 9.806203 TTGATGACATGACCAAAATTATCAATC 57.194 29.630 0.00 0.00 29.93 2.67
80 81 5.804944 TGGTTTGATGACATGACCAAAAT 57.195 34.783 0.00 0.00 38.61 1.82
81 82 5.355596 GTTGGTTTGATGACATGACCAAAA 58.644 37.500 20.69 6.11 45.23 2.44
97 98 1.314730 GTGTGATGGTCCGTTGGTTT 58.685 50.000 0.00 0.00 0.00 3.27
105 106 4.634004 TGTGAAATAATCGTGTGATGGTCC 59.366 41.667 0.00 0.00 34.24 4.46
117 118 8.072567 GTGATGGTCTGCTATTGTGAAATAATC 58.927 37.037 0.00 0.00 0.00 1.75
129 130 2.158914 TGAATGCGTGATGGTCTGCTAT 60.159 45.455 0.00 0.00 0.00 2.97
130 131 1.206849 TGAATGCGTGATGGTCTGCTA 59.793 47.619 0.00 0.00 0.00 3.49
132 133 0.097674 GTGAATGCGTGATGGTCTGC 59.902 55.000 0.00 0.00 0.00 4.26
144 145 0.110056 CTGAACACCAGCGTGAATGC 60.110 55.000 0.00 0.00 43.14 3.56
146 147 0.396435 TCCTGAACACCAGCGTGAAT 59.604 50.000 0.00 0.00 43.14 2.57
147 148 0.396435 ATCCTGAACACCAGCGTGAA 59.604 50.000 0.00 0.00 43.14 3.18
148 149 0.037326 GATCCTGAACACCAGCGTGA 60.037 55.000 0.00 0.00 43.14 4.35
150 151 1.079819 CGATCCTGAACACCAGCGT 60.080 57.895 0.00 0.00 41.57 5.07
151 152 2.456119 GCGATCCTGAACACCAGCG 61.456 63.158 0.00 0.00 41.57 5.18
152 153 1.078848 AGCGATCCTGAACACCAGC 60.079 57.895 0.00 0.00 41.57 4.85
153 154 0.742281 CCAGCGATCCTGAACACCAG 60.742 60.000 11.48 0.00 44.64 4.00
154 155 1.296392 CCAGCGATCCTGAACACCA 59.704 57.895 11.48 0.00 44.64 4.17
155 156 2.109126 GCCAGCGATCCTGAACACC 61.109 63.158 11.48 0.00 44.64 4.16
156 157 1.078848 AGCCAGCGATCCTGAACAC 60.079 57.895 11.48 1.21 44.64 3.32
157 158 1.078918 CAGCCAGCGATCCTGAACA 60.079 57.895 11.48 0.00 44.64 3.18
158 159 1.817099 CCAGCCAGCGATCCTGAAC 60.817 63.158 11.48 5.02 44.64 3.18
176 177 4.943705 TGTGTTAGATCCAGCTTTGATTCC 59.056 41.667 0.00 0.00 0.00 3.01
181 182 4.318332 TGTCTGTGTTAGATCCAGCTTTG 58.682 43.478 0.00 0.00 37.83 2.77
185 186 4.502259 CCCTATGTCTGTGTTAGATCCAGC 60.502 50.000 0.00 0.00 37.83 4.85
198 199 2.590007 GCAGGCGCCCTATGTCTG 60.590 66.667 26.15 14.51 29.64 3.51
219 220 1.714899 ATAACATCAACCAGCCGCGC 61.715 55.000 0.00 0.00 0.00 6.86
220 221 0.027979 CATAACATCAACCAGCCGCG 59.972 55.000 0.00 0.00 0.00 6.46
221 222 0.248621 GCATAACATCAACCAGCCGC 60.249 55.000 0.00 0.00 0.00 6.53
222 223 1.382522 AGCATAACATCAACCAGCCG 58.617 50.000 0.00 0.00 0.00 5.52
223 224 3.947834 ACTAAGCATAACATCAACCAGCC 59.052 43.478 0.00 0.00 0.00 4.85
224 225 5.567138 AACTAAGCATAACATCAACCAGC 57.433 39.130 0.00 0.00 0.00 4.85
225 226 5.351465 ACGAACTAAGCATAACATCAACCAG 59.649 40.000 0.00 0.00 0.00 4.00
226 227 5.242434 ACGAACTAAGCATAACATCAACCA 58.758 37.500 0.00 0.00 0.00 3.67
235 236 6.668541 ACTACGAGTACGAACTAAGCATAA 57.331 37.500 0.00 0.00 42.66 1.90
241 242 5.008613 ACCACAAACTACGAGTACGAACTAA 59.991 40.000 0.00 0.00 42.66 2.24
249 250 3.181473 ACAGCAACCACAAACTACGAGTA 60.181 43.478 0.00 0.00 0.00 2.59
250 251 2.210116 CAGCAACCACAAACTACGAGT 58.790 47.619 0.00 0.00 0.00 4.18
251 252 2.210116 ACAGCAACCACAAACTACGAG 58.790 47.619 0.00 0.00 0.00 4.18
254 255 3.792124 GCAGAACAGCAACCACAAACTAC 60.792 47.826 0.00 0.00 0.00 2.73
255 256 2.357637 GCAGAACAGCAACCACAAACTA 59.642 45.455 0.00 0.00 0.00 2.24
256 257 1.134946 GCAGAACAGCAACCACAAACT 59.865 47.619 0.00 0.00 0.00 2.66
258 259 1.134753 CTGCAGAACAGCAACCACAAA 59.865 47.619 8.42 0.00 45.13 2.83
281 282 2.299013 TCAAAACGAAGCCTCAGAGCTA 59.701 45.455 0.00 0.00 44.11 3.32
283 284 1.462670 CTCAAAACGAAGCCTCAGAGC 59.537 52.381 0.00 0.00 0.00 4.09
287 288 1.939934 CACACTCAAAACGAAGCCTCA 59.060 47.619 0.00 0.00 0.00 3.86
288 289 2.210116 TCACACTCAAAACGAAGCCTC 58.790 47.619 0.00 0.00 0.00 4.70
289 290 2.213499 CTCACACTCAAAACGAAGCCT 58.787 47.619 0.00 0.00 0.00 4.58
290 291 1.940613 ACTCACACTCAAAACGAAGCC 59.059 47.619 0.00 0.00 0.00 4.35
291 292 3.354397 CAACTCACACTCAAAACGAAGC 58.646 45.455 0.00 0.00 0.00 3.86
292 293 3.181511 TGCAACTCACACTCAAAACGAAG 60.182 43.478 0.00 0.00 0.00 3.79
293 294 2.744741 TGCAACTCACACTCAAAACGAA 59.255 40.909 0.00 0.00 0.00 3.85
294 295 2.351418 CTGCAACTCACACTCAAAACGA 59.649 45.455 0.00 0.00 0.00 3.85
295 296 2.708514 CTGCAACTCACACTCAAAACG 58.291 47.619 0.00 0.00 0.00 3.60
296 297 2.159393 TGCTGCAACTCACACTCAAAAC 60.159 45.455 0.00 0.00 0.00 2.43
297 298 2.090760 TGCTGCAACTCACACTCAAAA 58.909 42.857 0.00 0.00 0.00 2.44
332 333 2.263077 CGAACTACAGCTACAAGGCAG 58.737 52.381 0.00 0.00 34.17 4.85
333 334 1.671850 GCGAACTACAGCTACAAGGCA 60.672 52.381 0.00 0.00 34.17 4.75
334 335 1.000145 GCGAACTACAGCTACAAGGC 59.000 55.000 0.00 0.00 0.00 4.35
335 336 1.641577 GGCGAACTACAGCTACAAGG 58.358 55.000 0.00 0.00 0.00 3.61
336 337 1.269166 CGGCGAACTACAGCTACAAG 58.731 55.000 0.00 0.00 0.00 3.16
337 338 0.599558 ACGGCGAACTACAGCTACAA 59.400 50.000 16.62 0.00 0.00 2.41
338 339 0.109458 CACGGCGAACTACAGCTACA 60.109 55.000 16.62 0.00 0.00 2.74
339 340 1.411493 GCACGGCGAACTACAGCTAC 61.411 60.000 16.62 0.00 0.00 3.58
340 341 1.153901 GCACGGCGAACTACAGCTA 60.154 57.895 16.62 0.00 0.00 3.32
341 342 2.432628 GCACGGCGAACTACAGCT 60.433 61.111 16.62 0.00 0.00 4.24
342 343 2.432628 AGCACGGCGAACTACAGC 60.433 61.111 16.62 5.61 0.00 4.40
343 344 1.073216 CAGAGCACGGCGAACTACAG 61.073 60.000 16.62 0.00 0.00 2.74
344 345 1.080772 CAGAGCACGGCGAACTACA 60.081 57.895 16.62 0.00 0.00 2.74
345 346 2.445438 GCAGAGCACGGCGAACTAC 61.445 63.158 16.62 4.77 0.00 2.73
346 347 2.126071 GCAGAGCACGGCGAACTA 60.126 61.111 16.62 0.00 0.00 2.24
347 348 3.521529 AAGCAGAGCACGGCGAACT 62.522 57.895 16.62 10.46 41.73 3.01
348 349 3.016474 GAAGCAGAGCACGGCGAAC 62.016 63.158 16.62 4.57 41.73 3.95
349 350 2.738521 GAAGCAGAGCACGGCGAA 60.739 61.111 16.62 0.00 41.73 4.70
350 351 3.989787 TGAAGCAGAGCACGGCGA 61.990 61.111 16.62 0.00 41.73 5.54
351 352 3.782244 GTGAAGCAGAGCACGGCG 61.782 66.667 4.80 4.80 41.73 6.46
352 353 2.666190 TGTGAAGCAGAGCACGGC 60.666 61.111 0.00 0.00 37.83 5.68
353 354 2.320587 GGTGTGAAGCAGAGCACGG 61.321 63.158 0.00 0.00 37.83 4.94
354 355 2.320587 GGGTGTGAAGCAGAGCACG 61.321 63.158 0.00 0.00 37.83 5.34
386 387 2.802816 GAGGTTGTTACAGACTGCACAG 59.197 50.000 1.25 0.00 0.00 3.66
404 405 1.135199 GCACATCAACCATGCAAGAGG 60.135 52.381 0.00 0.00 39.23 3.69
429 437 4.081420 ACCACCTTACAGCTAGAACATCTG 60.081 45.833 0.00 0.00 0.00 2.90
453 461 1.070134 TCACGGTCCAGGACTCAAAAG 59.930 52.381 19.57 6.82 32.47 2.27
482 490 2.596346 ACATCCAAAATGGTGTCTGCA 58.404 42.857 0.00 0.00 39.03 4.41
487 504 2.699846 ACAGCAACATCCAAAATGGTGT 59.300 40.909 5.09 3.85 46.27 4.16
554 910 3.442076 GGTCTTGACTTCCCCTCTTCTA 58.558 50.000 0.61 0.00 0.00 2.10
555 911 2.261729 GGTCTTGACTTCCCCTCTTCT 58.738 52.381 0.61 0.00 0.00 2.85
634 1013 3.747529 GGCATTTCTTTGGATTGGTGTTG 59.252 43.478 0.00 0.00 0.00 3.33
640 1019 6.578163 AAAAATGGGCATTTCTTTGGATTG 57.422 33.333 0.00 0.00 39.88 2.67
672 1052 2.715532 ATTCACAGCGCACGGACACT 62.716 55.000 11.47 0.00 0.00 3.55
727 1128 4.926238 ACAAGAGCTCATAAAACAGAGTCG 59.074 41.667 17.77 0.00 34.39 4.18
935 1347 2.395690 GTACGTGCATGCGACTGC 59.604 61.111 14.09 2.96 42.62 4.40
936 1348 2.689183 CGTACGTGCATGCGACTG 59.311 61.111 14.09 10.75 35.59 3.51
937 1349 3.179265 GCGTACGTGCATGCGACT 61.179 61.111 17.90 0.00 35.59 4.18
938 1350 4.204891 GGCGTACGTGCATGCGAC 62.205 66.667 17.90 11.32 36.28 5.19
970 1382 4.293494 ACAGCAGGAGGAAGATGAAGATA 58.707 43.478 0.00 0.00 0.00 1.98
971 1383 3.113824 ACAGCAGGAGGAAGATGAAGAT 58.886 45.455 0.00 0.00 0.00 2.40
977 1389 2.158696 GCCATAACAGCAGGAGGAAGAT 60.159 50.000 0.00 0.00 0.00 2.40
993 1405 2.106511 GGTGGAAGAAGCCATAGCCATA 59.893 50.000 0.00 0.00 40.68 2.74
994 1406 1.133668 GGTGGAAGAAGCCATAGCCAT 60.134 52.381 0.00 0.00 40.68 4.40
995 1407 0.255890 GGTGGAAGAAGCCATAGCCA 59.744 55.000 0.00 0.00 40.68 4.75
996 1408 0.815615 CGGTGGAAGAAGCCATAGCC 60.816 60.000 0.00 0.00 40.68 3.93
997 1409 1.440145 GCGGTGGAAGAAGCCATAGC 61.440 60.000 0.00 0.00 40.68 2.97
998 1410 2.695314 GCGGTGGAAGAAGCCATAG 58.305 57.895 0.00 0.00 40.68 2.23
999 1411 4.954933 GCGGTGGAAGAAGCCATA 57.045 55.556 0.00 0.00 40.68 2.74
1337 1791 0.108329 GCCGCATGTGTAGTACTGGT 60.108 55.000 5.39 0.00 0.00 4.00
1338 1792 1.145759 CGCCGCATGTGTAGTACTGG 61.146 60.000 5.39 0.00 0.00 4.00
1343 1797 4.082523 AGCCGCCGCATGTGTAGT 62.083 61.111 5.38 0.00 37.52 2.73
1401 1855 1.075425 CTTCTCAGTCGAAGCAGGCG 61.075 60.000 0.00 0.00 34.59 5.52
1472 1928 1.889530 AACCGGAGAAGAAGGCGAGG 61.890 60.000 9.46 0.00 0.00 4.63
1477 1933 1.469423 GCGAGTAACCGGAGAAGAAGG 60.469 57.143 9.46 0.00 0.00 3.46
1555 2011 0.811915 CCACCGGAACAACAACAACA 59.188 50.000 9.46 0.00 0.00 3.33
1556 2012 0.526739 GCCACCGGAACAACAACAAC 60.527 55.000 9.46 0.00 0.00 3.32
1557 2013 1.668101 GGCCACCGGAACAACAACAA 61.668 55.000 9.46 0.00 0.00 2.83
1708 2174 2.824341 CAGGTACAGGAAAGGACGTACT 59.176 50.000 0.00 0.00 35.61 2.73
1711 2177 1.343465 CACAGGTACAGGAAAGGACGT 59.657 52.381 0.00 0.00 0.00 4.34
1712 2178 1.616865 TCACAGGTACAGGAAAGGACG 59.383 52.381 0.00 0.00 0.00 4.79
1713 2179 2.613223 GCTCACAGGTACAGGAAAGGAC 60.613 54.545 0.00 0.00 0.00 3.85
1714 2180 1.623811 GCTCACAGGTACAGGAAAGGA 59.376 52.381 0.00 0.00 0.00 3.36
1716 2182 2.300152 TCTGCTCACAGGTACAGGAAAG 59.700 50.000 0.00 0.00 44.59 2.62
1718 2184 1.895798 CTCTGCTCACAGGTACAGGAA 59.104 52.381 0.00 0.00 44.59 3.36
1719 2185 1.550327 CTCTGCTCACAGGTACAGGA 58.450 55.000 0.00 0.00 44.59 3.86
1721 2187 1.550327 TCCTCTGCTCACAGGTACAG 58.450 55.000 0.00 0.00 44.59 2.74
1723 2189 3.618690 ATTTCCTCTGCTCACAGGTAC 57.381 47.619 0.00 0.00 44.59 3.34
1740 2373 8.791327 AACAAAGACAGGAACAATGAAAATTT 57.209 26.923 0.00 0.00 0.00 1.82
1746 2379 5.436175 TCAGAACAAAGACAGGAACAATGA 58.564 37.500 0.00 0.00 0.00 2.57
1747 2380 5.756195 TCAGAACAAAGACAGGAACAATG 57.244 39.130 0.00 0.00 0.00 2.82
1748 2381 5.652014 TGTTCAGAACAAAGACAGGAACAAT 59.348 36.000 13.90 0.00 39.84 2.71
1749 2382 5.007034 TGTTCAGAACAAAGACAGGAACAA 58.993 37.500 13.90 0.00 39.84 2.83
1752 2385 3.945285 GGTGTTCAGAACAAAGACAGGAA 59.055 43.478 17.83 0.00 44.16 3.36
1768 2401 2.423577 ACTTAACGGATGCTGGTGTTC 58.576 47.619 0.00 0.00 0.00 3.18
1781 2417 9.590088 GGAAATGTAAGTGTAAGAAACTTAACG 57.410 33.333 0.00 0.00 40.75 3.18
1788 2424 8.441312 AAACGAGGAAATGTAAGTGTAAGAAA 57.559 30.769 0.00 0.00 0.00 2.52
1790 2426 7.211573 TGAAACGAGGAAATGTAAGTGTAAGA 58.788 34.615 0.00 0.00 0.00 2.10
1794 2430 5.008316 GGTTGAAACGAGGAAATGTAAGTGT 59.992 40.000 0.00 0.00 0.00 3.55
1795 2431 5.238650 AGGTTGAAACGAGGAAATGTAAGTG 59.761 40.000 0.00 0.00 0.00 3.16
1796 2432 5.374071 AGGTTGAAACGAGGAAATGTAAGT 58.626 37.500 0.00 0.00 0.00 2.24
1798 2434 6.425721 CAGTAGGTTGAAACGAGGAAATGTAA 59.574 38.462 0.00 0.00 0.00 2.41
1799 2435 5.929992 CAGTAGGTTGAAACGAGGAAATGTA 59.070 40.000 0.00 0.00 0.00 2.29
1800 2436 4.755123 CAGTAGGTTGAAACGAGGAAATGT 59.245 41.667 0.00 0.00 0.00 2.71
1801 2437 4.378459 GCAGTAGGTTGAAACGAGGAAATG 60.378 45.833 0.00 0.00 0.00 2.32
1802 2438 3.751698 GCAGTAGGTTGAAACGAGGAAAT 59.248 43.478 0.00 0.00 0.00 2.17
1804 2440 2.367567 AGCAGTAGGTTGAAACGAGGAA 59.632 45.455 0.00 0.00 0.00 3.36
1805 2441 1.968493 AGCAGTAGGTTGAAACGAGGA 59.032 47.619 0.00 0.00 0.00 3.71
1818 2471 0.532573 TTCTCGGCTCCAAGCAGTAG 59.467 55.000 0.86 0.00 44.75 2.57
1830 2483 0.179129 CCATTGGTGCATTTCTCGGC 60.179 55.000 0.00 0.00 0.00 5.54
1845 2503 7.284489 TGTGAAAGAGCTTACAAGTTTACCATT 59.716 33.333 0.00 0.00 0.00 3.16
1857 2515 5.760743 AGAAACTCCTTGTGAAAGAGCTTAC 59.239 40.000 0.00 0.00 0.00 2.34
1859 2517 4.786425 AGAAACTCCTTGTGAAAGAGCTT 58.214 39.130 0.00 0.00 0.00 3.74
1861 2519 4.261363 CCAAGAAACTCCTTGTGAAAGAGC 60.261 45.833 0.00 0.00 41.34 4.09
1899 2557 0.165079 GCAGCTTACGCGTTGCTTAA 59.835 50.000 28.38 12.94 42.32 1.85
1900 2558 0.946700 TGCAGCTTACGCGTTGCTTA 60.947 50.000 28.38 20.16 42.32 3.09
1929 2587 1.000607 CCAAGAAACTCCGAGACGTCA 60.001 52.381 19.50 0.00 0.00 4.35
1978 2636 1.884926 CGGCAAGCTAGCACTAGGC 60.885 63.158 18.83 13.92 45.30 3.93
1979 2637 0.249238 CTCGGCAAGCTAGCACTAGG 60.249 60.000 18.83 3.06 35.83 3.02
1980 2638 0.457851 ACTCGGCAAGCTAGCACTAG 59.542 55.000 18.83 7.93 35.83 2.57
1983 2641 0.460987 ATCACTCGGCAAGCTAGCAC 60.461 55.000 18.83 5.64 35.83 4.40
2029 2953 1.087202 TAAACAGCACGCCATAGCCG 61.087 55.000 0.00 0.00 34.57 5.52
2070 2994 5.919141 GCCATTCATGCTAATTGATCAACTC 59.081 40.000 11.07 0.94 0.00 3.01
2117 3049 3.119602 TCGAAGTCTATGGAAACTCACCG 60.120 47.826 0.00 0.00 0.00 4.94
2189 3121 1.386533 GTTGATGGAGCCATGGAGTG 58.613 55.000 18.40 0.00 36.70 3.51
2293 3225 8.046708 ACCTCAATGCAATACAAACTACTATGA 58.953 33.333 0.00 0.00 0.00 2.15
2294 3226 8.213518 ACCTCAATGCAATACAAACTACTATG 57.786 34.615 0.00 0.00 0.00 2.23
2295 3227 9.899661 TTACCTCAATGCAATACAAACTACTAT 57.100 29.630 0.00 0.00 0.00 2.12
2296 3228 9.727859 TTTACCTCAATGCAATACAAACTACTA 57.272 29.630 0.00 0.00 0.00 1.82
2297 3229 8.630054 TTTACCTCAATGCAATACAAACTACT 57.370 30.769 0.00 0.00 0.00 2.57
2298 3230 9.685828 TTTTTACCTCAATGCAATACAAACTAC 57.314 29.630 0.00 0.00 0.00 2.73


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.