Multiple sequence alignment - TraesCS6A01G239300

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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 TraesCS6A01G239300 chr6A 100.000 3454 0 0 1 3454 449583382 449586835 0.000000e+00 6379.0
1 TraesCS6A01G239300 chr6D 90.444 2543 139 55 388 2886 312762645 312765127 0.000000e+00 3254.0
2 TraesCS6A01G239300 chr6B 88.508 2506 151 52 388 2807 514119851 514117397 0.000000e+00 2905.0
3 TraesCS6A01G239300 chr6B 87.342 79 6 4 243 319 25916852 25916928 1.710000e-13 87.9
4 TraesCS6A01G239300 chr3A 97.350 566 14 1 2890 3454 730689807 730690372 0.000000e+00 961.0
5 TraesCS6A01G239300 chr1A 94.025 569 28 5 2890 3454 16538901 16538335 0.000000e+00 857.0
6 TraesCS6A01G239300 chr1A 80.672 238 33 8 2 235 321187628 321187400 4.580000e-39 172.0
7 TraesCS6A01G239300 chr4B 91.237 388 31 2 2890 3274 258376239 258376626 3.050000e-145 525.0
8 TraesCS6A01G239300 chr4B 84.270 178 5 1 3277 3454 258377190 258377344 5.970000e-33 152.0
9 TraesCS6A01G239300 chr5B 95.000 320 14 2 3136 3454 648314407 648314725 5.150000e-138 501.0
10 TraesCS6A01G239300 chr5B 95.000 320 14 2 3136 3454 648340788 648340470 5.150000e-138 501.0
11 TraesCS6A01G239300 chr5B 95.327 214 9 1 2890 3103 648313255 648313467 4.270000e-89 339.0
12 TraesCS6A01G239300 chr5B 94.860 214 11 0 2890 3103 648341941 648341728 5.520000e-88 335.0
13 TraesCS6A01G239300 chr7B 94.654 318 15 2 3139 3454 371739583 371739266 3.100000e-135 492.0
14 TraesCS6A01G239300 chr7B 96.330 218 6 2 2889 3104 371740741 371740524 1.180000e-94 357.0
15 TraesCS6A01G239300 chr7B 80.184 217 31 8 1055 1270 521578088 521578293 5.970000e-33 152.0
16 TraesCS6A01G239300 chr7B 76.496 234 41 11 2 231 578679981 578680204 7.830000e-22 115.0
17 TraesCS6A01G239300 chr2D 80.030 661 76 34 1060 1683 491429579 491430220 4.090000e-119 438.0
18 TraesCS6A01G239300 chr2D 88.372 215 23 2 2890 3102 447686969 447687183 1.230000e-64 257.0
19 TraesCS6A01G239300 chr2D 85.246 183 17 7 3278 3453 447695048 447695227 2.740000e-41 180.0
20 TraesCS6A01G239300 chr2D 88.235 136 16 0 3139 3274 447694067 447694202 2.760000e-36 163.0
21 TraesCS6A01G239300 chr2D 78.512 242 40 11 2 239 73447266 73447499 7.720000e-32 148.0
22 TraesCS6A01G239300 chr2D 75.949 237 41 12 5 235 112312049 112311823 1.310000e-19 108.0
23 TraesCS6A01G239300 chr2A 79.939 653 82 31 1060 1683 635723011 635723643 5.290000e-118 435.0
24 TraesCS6A01G239300 chr2A 88.158 76 9 0 244 319 730619103 730619178 1.320000e-14 91.6
25 TraesCS6A01G239300 chr2B 78.792 679 89 31 1060 1695 575903796 575904462 4.150000e-109 405.0
26 TraesCS6A01G239300 chr2B 76.190 189 29 10 2 185 82075694 82075871 6.140000e-13 86.1
27 TraesCS6A01G239300 chr1B 83.120 391 32 14 2917 3274 612690502 612690113 3.320000e-85 326.0
28 TraesCS6A01G239300 chr5A 98.980 98 1 0 3357 3454 174797929 174798026 3.540000e-40 176.0
29 TraesCS6A01G239300 chr7D 80.645 217 30 8 1055 1270 492148813 492149018 1.280000e-34 158.0
30 TraesCS6A01G239300 chr7D 81.618 136 18 6 67 199 23707940 23708071 4.710000e-19 106.0
31 TraesCS6A01G239300 chr7D 89.610 77 8 0 243 319 19406970 19406894 7.890000e-17 99.0
32 TraesCS6A01G239300 chr7D 77.966 177 25 10 2 174 552185281 552185115 7.890000e-17 99.0
33 TraesCS6A01G239300 chr7D 89.474 76 8 0 244 319 626459220 626459295 2.840000e-16 97.1
34 TraesCS6A01G239300 chr7D 88.312 77 7 2 244 319 246838461 246838386 1.320000e-14 91.6
35 TraesCS6A01G239300 chr7D 87.013 77 8 2 244 319 41448532 41448457 6.140000e-13 86.1
36 TraesCS6A01G239300 chr7D 87.013 77 8 2 244 319 598162815 598162740 6.140000e-13 86.1
37 TraesCS6A01G239300 chr7A 80.645 217 30 8 1055 1270 558402766 558402971 1.280000e-34 158.0
38 TraesCS6A01G239300 chr7A 79.747 158 26 5 1062 1217 65970082 65970235 3.640000e-20 110.0
39 TraesCS6A01G239300 chr7A 75.107 233 47 11 2 231 714301798 714302022 7.890000e-17 99.0
40 TraesCS6A01G239300 chr3D 78.924 223 36 6 2 222 472944217 472944004 1.290000e-29 141.0
41 TraesCS6A01G239300 chr3D 78.355 231 35 10 4 231 47757848 47757630 6.010000e-28 135.0
42 TraesCS6A01G239300 chr3D 76.170 235 40 13 6 231 360327865 360327638 3.640000e-20 110.0
43 TraesCS6A01G239300 chrUn 94.186 86 5 0 3018 3103 480605403 480605488 7.780000e-27 132.0
44 TraesCS6A01G239300 chr4A 90.789 76 6 1 244 319 133374629 133374555 2.190000e-17 100.0
45 TraesCS6A01G239300 chr1D 77.246 167 32 6 67 231 120533276 120533114 3.670000e-15 93.5
46 TraesCS6A01G239300 chr5D 87.013 77 8 2 244 319 442958296 442958221 6.140000e-13 86.1


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 TraesCS6A01G239300 chr6A 449583382 449586835 3453 False 6379.0 6379 100.0000 1 3454 1 chr6A.!!$F1 3453
1 TraesCS6A01G239300 chr6D 312762645 312765127 2482 False 3254.0 3254 90.4440 388 2886 1 chr6D.!!$F1 2498
2 TraesCS6A01G239300 chr6B 514117397 514119851 2454 True 2905.0 2905 88.5080 388 2807 1 chr6B.!!$R1 2419
3 TraesCS6A01G239300 chr3A 730689807 730690372 565 False 961.0 961 97.3500 2890 3454 1 chr3A.!!$F1 564
4 TraesCS6A01G239300 chr1A 16538335 16538901 566 True 857.0 857 94.0250 2890 3454 1 chr1A.!!$R1 564
5 TraesCS6A01G239300 chr4B 258376239 258377344 1105 False 338.5 525 87.7535 2890 3454 2 chr4B.!!$F1 564
6 TraesCS6A01G239300 chr5B 648313255 648314725 1470 False 420.0 501 95.1635 2890 3454 2 chr5B.!!$F1 564
7 TraesCS6A01G239300 chr5B 648340470 648341941 1471 True 418.0 501 94.9300 2890 3454 2 chr5B.!!$R1 564
8 TraesCS6A01G239300 chr7B 371739266 371740741 1475 True 424.5 492 95.4920 2889 3454 2 chr7B.!!$R1 565
9 TraesCS6A01G239300 chr2D 491429579 491430220 641 False 438.0 438 80.0300 1060 1683 1 chr2D.!!$F3 623
10 TraesCS6A01G239300 chr2A 635723011 635723643 632 False 435.0 435 79.9390 1060 1683 1 chr2A.!!$F1 623
11 TraesCS6A01G239300 chr2B 575903796 575904462 666 False 405.0 405 78.7920 1060 1695 1 chr2B.!!$F2 635

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
670 690 0.036765 AAAATGCATGGCAGCCACAG 60.037 50.0 19.1 14.12 43.65 3.66 F
1315 1370 0.106918 TGTCCCTTGTTTCTTGCCGT 60.107 50.0 0.0 0.00 0.00 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1732 1849 0.465460 GTTCAGTGGCACCAACCTGA 60.465 55.0 15.27 8.27 30.52 3.86 R
2709 2863 0.315886 ACTTCACATCGTGTACCGCA 59.684 50.0 0.00 0.00 34.79 5.69 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
19 20 1.945580 TTGGTTTATTGGCCCCCTTC 58.054 50.000 0.00 0.00 0.00 3.46
20 21 0.787084 TGGTTTATTGGCCCCCTTCA 59.213 50.000 0.00 0.00 0.00 3.02
21 22 1.364328 TGGTTTATTGGCCCCCTTCAT 59.636 47.619 0.00 0.00 0.00 2.57
22 23 2.587777 TGGTTTATTGGCCCCCTTCATA 59.412 45.455 0.00 0.00 0.00 2.15
23 24 3.208692 TGGTTTATTGGCCCCCTTCATAT 59.791 43.478 0.00 0.00 0.00 1.78
24 25 4.231273 GGTTTATTGGCCCCCTTCATATT 58.769 43.478 0.00 0.00 0.00 1.28
25 26 4.658435 GGTTTATTGGCCCCCTTCATATTT 59.342 41.667 0.00 0.00 0.00 1.40
26 27 5.131977 GGTTTATTGGCCCCCTTCATATTTT 59.868 40.000 0.00 0.00 0.00 1.82
27 28 6.327887 GGTTTATTGGCCCCCTTCATATTTTA 59.672 38.462 0.00 0.00 0.00 1.52
28 29 7.017155 GGTTTATTGGCCCCCTTCATATTTTAT 59.983 37.037 0.00 0.00 0.00 1.40
29 30 7.552050 TTATTGGCCCCCTTCATATTTTATG 57.448 36.000 0.00 0.00 0.00 1.90
30 31 4.551215 TGGCCCCCTTCATATTTTATGT 57.449 40.909 0.00 0.00 0.00 2.29
31 32 4.479158 TGGCCCCCTTCATATTTTATGTC 58.521 43.478 0.00 0.00 0.00 3.06
32 33 4.078922 TGGCCCCCTTCATATTTTATGTCA 60.079 41.667 0.00 0.00 0.00 3.58
33 34 4.898861 GGCCCCCTTCATATTTTATGTCAA 59.101 41.667 0.00 0.00 0.00 3.18
34 35 5.365314 GGCCCCCTTCATATTTTATGTCAAA 59.635 40.000 0.00 0.00 0.00 2.69
35 36 6.043127 GGCCCCCTTCATATTTTATGTCAAAT 59.957 38.462 0.00 0.00 0.00 2.32
36 37 7.420097 GGCCCCCTTCATATTTTATGTCAAATT 60.420 37.037 0.00 0.00 0.00 1.82
37 38 7.992608 GCCCCCTTCATATTTTATGTCAAATTT 59.007 33.333 0.00 0.00 0.00 1.82
38 39 9.904198 CCCCCTTCATATTTTATGTCAAATTTT 57.096 29.630 0.00 0.00 0.00 1.82
104 105 9.850628 ATCATAAAAAGCATATCATTGGATTCG 57.149 29.630 0.00 0.00 34.89 3.34
105 106 8.849168 TCATAAAAAGCATATCATTGGATTCGT 58.151 29.630 0.00 0.00 34.89 3.85
113 114 9.283768 AGCATATCATTGGATTCGTATAAAACA 57.716 29.630 0.00 0.00 34.89 2.83
118 119 9.793259 ATCATTGGATTCGTATAAAACATAGGT 57.207 29.630 0.00 0.00 0.00 3.08
119 120 9.621629 TCATTGGATTCGTATAAAACATAGGTT 57.378 29.630 0.00 0.00 39.43 3.50
200 201 8.604640 TGGTCAAAATACAACTGTAAATACGA 57.395 30.769 0.00 0.00 33.76 3.43
201 202 8.714179 TGGTCAAAATACAACTGTAAATACGAG 58.286 33.333 0.00 0.00 33.76 4.18
202 203 8.173130 GGTCAAAATACAACTGTAAATACGAGG 58.827 37.037 0.00 0.00 33.76 4.63
203 204 8.173130 GTCAAAATACAACTGTAAATACGAGGG 58.827 37.037 0.00 0.00 33.76 4.30
204 205 7.879160 TCAAAATACAACTGTAAATACGAGGGT 59.121 33.333 0.00 0.00 33.76 4.34
205 206 9.153721 CAAAATACAACTGTAAATACGAGGGTA 57.846 33.333 0.00 0.00 33.76 3.69
206 207 8.707938 AAATACAACTGTAAATACGAGGGTAC 57.292 34.615 0.00 0.00 33.76 3.34
207 208 5.990120 ACAACTGTAAATACGAGGGTACT 57.010 39.130 0.00 0.00 0.00 2.73
208 209 8.752005 ATACAACTGTAAATACGAGGGTACTA 57.248 34.615 0.00 0.00 33.76 1.82
209 210 7.466746 ACAACTGTAAATACGAGGGTACTAA 57.533 36.000 0.00 0.00 0.00 2.24
210 211 8.071177 ACAACTGTAAATACGAGGGTACTAAT 57.929 34.615 0.00 0.00 0.00 1.73
211 212 9.189156 ACAACTGTAAATACGAGGGTACTAATA 57.811 33.333 0.00 0.00 0.00 0.98
218 219 8.953368 AAATACGAGGGTACTAATAAACAAGG 57.047 34.615 0.00 0.00 0.00 3.61
219 220 7.902920 ATACGAGGGTACTAATAAACAAGGA 57.097 36.000 0.00 0.00 0.00 3.36
220 221 5.970592 ACGAGGGTACTAATAAACAAGGAC 58.029 41.667 0.00 0.00 0.00 3.85
221 222 5.481473 ACGAGGGTACTAATAAACAAGGACA 59.519 40.000 0.00 0.00 0.00 4.02
222 223 6.014327 ACGAGGGTACTAATAAACAAGGACAA 60.014 38.462 0.00 0.00 0.00 3.18
223 224 6.875195 CGAGGGTACTAATAAACAAGGACAAA 59.125 38.462 0.00 0.00 0.00 2.83
224 225 7.388500 CGAGGGTACTAATAAACAAGGACAAAA 59.612 37.037 0.00 0.00 0.00 2.44
225 226 8.631480 AGGGTACTAATAAACAAGGACAAAAG 57.369 34.615 0.00 0.00 0.00 2.27
226 227 8.222637 AGGGTACTAATAAACAAGGACAAAAGT 58.777 33.333 0.00 0.00 0.00 2.66
227 228 9.506018 GGGTACTAATAAACAAGGACAAAAGTA 57.494 33.333 0.00 0.00 0.00 2.24
259 260 9.998106 AGTTAACAGTAAATACATGTCTCAACT 57.002 29.630 0.00 0.00 0.00 3.16
315 316 8.996024 AAATTAAGACATTTATTTTGGGACGG 57.004 30.769 0.00 0.00 26.18 4.79
316 317 7.948034 ATTAAGACATTTATTTTGGGACGGA 57.052 32.000 0.00 0.00 0.00 4.69
317 318 5.897377 AAGACATTTATTTTGGGACGGAG 57.103 39.130 0.00 0.00 0.00 4.63
318 319 4.270008 AGACATTTATTTTGGGACGGAGG 58.730 43.478 0.00 0.00 0.00 4.30
319 320 4.014406 GACATTTATTTTGGGACGGAGGT 58.986 43.478 0.00 0.00 0.00 3.85
320 321 5.045432 AGACATTTATTTTGGGACGGAGGTA 60.045 40.000 0.00 0.00 0.00 3.08
321 322 5.572252 ACATTTATTTTGGGACGGAGGTAA 58.428 37.500 0.00 0.00 0.00 2.85
322 323 6.192044 ACATTTATTTTGGGACGGAGGTAAT 58.808 36.000 0.00 0.00 0.00 1.89
323 324 6.096282 ACATTTATTTTGGGACGGAGGTAATG 59.904 38.462 0.00 0.00 0.00 1.90
324 325 3.732048 ATTTTGGGACGGAGGTAATGT 57.268 42.857 0.00 0.00 0.00 2.71
325 326 3.512219 TTTTGGGACGGAGGTAATGTT 57.488 42.857 0.00 0.00 0.00 2.71
326 327 4.637387 TTTTGGGACGGAGGTAATGTTA 57.363 40.909 0.00 0.00 0.00 2.41
327 328 3.899052 TTGGGACGGAGGTAATGTTAG 57.101 47.619 0.00 0.00 0.00 2.34
328 329 2.823959 TGGGACGGAGGTAATGTTAGT 58.176 47.619 0.00 0.00 0.00 2.24
329 330 3.175594 TGGGACGGAGGTAATGTTAGTT 58.824 45.455 0.00 0.00 0.00 2.24
330 331 4.352009 TGGGACGGAGGTAATGTTAGTTA 58.648 43.478 0.00 0.00 0.00 2.24
331 332 4.776837 TGGGACGGAGGTAATGTTAGTTAA 59.223 41.667 0.00 0.00 0.00 2.01
332 333 5.111989 GGGACGGAGGTAATGTTAGTTAAC 58.888 45.833 0.00 0.00 36.74 2.01
357 358 9.350951 ACACTAAATATAAGAGCCCAATAAACC 57.649 33.333 0.00 0.00 0.00 3.27
358 359 9.574516 CACTAAATATAAGAGCCCAATAAACCT 57.425 33.333 0.00 0.00 0.00 3.50
363 364 8.935614 ATATAAGAGCCCAATAAACCTAAACC 57.064 34.615 0.00 0.00 0.00 3.27
364 365 3.977312 AGAGCCCAATAAACCTAAACCC 58.023 45.455 0.00 0.00 0.00 4.11
365 366 3.596500 AGAGCCCAATAAACCTAAACCCT 59.403 43.478 0.00 0.00 0.00 4.34
366 367 3.699538 GAGCCCAATAAACCTAAACCCTG 59.300 47.826 0.00 0.00 0.00 4.45
367 368 3.335484 AGCCCAATAAACCTAAACCCTGA 59.665 43.478 0.00 0.00 0.00 3.86
368 369 3.446161 GCCCAATAAACCTAAACCCTGAC 59.554 47.826 0.00 0.00 0.00 3.51
369 370 4.021229 CCCAATAAACCTAAACCCTGACC 58.979 47.826 0.00 0.00 0.00 4.02
370 371 3.692593 CCAATAAACCTAAACCCTGACCG 59.307 47.826 0.00 0.00 0.00 4.79
371 372 4.566070 CCAATAAACCTAAACCCTGACCGA 60.566 45.833 0.00 0.00 0.00 4.69
372 373 4.914177 ATAAACCTAAACCCTGACCGAA 57.086 40.909 0.00 0.00 0.00 4.30
373 374 2.853235 AACCTAAACCCTGACCGAAG 57.147 50.000 0.00 0.00 0.00 3.79
374 375 1.725803 ACCTAAACCCTGACCGAAGT 58.274 50.000 0.00 0.00 0.00 3.01
375 376 2.893424 ACCTAAACCCTGACCGAAGTA 58.107 47.619 0.00 0.00 0.00 2.24
376 377 2.830321 ACCTAAACCCTGACCGAAGTAG 59.170 50.000 0.00 0.00 0.00 2.57
377 378 2.418334 CCTAAACCCTGACCGAAGTAGC 60.418 54.545 0.00 0.00 0.00 3.58
378 379 1.349067 AAACCCTGACCGAAGTAGCT 58.651 50.000 0.00 0.00 0.00 3.32
379 380 0.608640 AACCCTGACCGAAGTAGCTG 59.391 55.000 0.00 0.00 0.00 4.24
380 381 1.258445 ACCCTGACCGAAGTAGCTGG 61.258 60.000 0.00 0.00 0.00 4.85
381 382 1.153549 CCTGACCGAAGTAGCTGGC 60.154 63.158 0.00 0.00 0.00 4.85
382 383 1.591703 CTGACCGAAGTAGCTGGCA 59.408 57.895 0.00 0.00 0.00 4.92
383 384 0.737715 CTGACCGAAGTAGCTGGCAC 60.738 60.000 0.00 0.00 0.00 5.01
384 385 1.292223 GACCGAAGTAGCTGGCACA 59.708 57.895 0.00 0.00 0.00 4.57
385 386 1.004918 ACCGAAGTAGCTGGCACAC 60.005 57.895 0.00 0.00 0.00 3.82
386 387 1.741770 CCGAAGTAGCTGGCACACC 60.742 63.158 0.00 0.00 0.00 4.16
387 388 2.094659 CGAAGTAGCTGGCACACCG 61.095 63.158 0.00 0.00 39.70 4.94
388 389 2.358737 AAGTAGCTGGCACACCGC 60.359 61.111 0.00 0.00 39.70 5.68
389 390 3.177194 AAGTAGCTGGCACACCGCA 62.177 57.895 0.00 0.00 45.17 5.69
390 391 3.121030 GTAGCTGGCACACCGCAG 61.121 66.667 0.00 0.00 45.17 5.18
437 438 5.098211 ACTACGCTATAGACACGGAAAAAC 58.902 41.667 3.21 0.00 0.00 2.43
439 440 3.056322 ACGCTATAGACACGGAAAAACCT 60.056 43.478 3.21 0.00 36.31 3.50
445 454 7.279313 GCTATAGACACGGAAAAACCTCATAAA 59.721 37.037 3.21 0.00 36.31 1.40
455 464 6.212589 GGAAAAACCTCATAAATCCCCAGAAA 59.787 38.462 0.00 0.00 35.41 2.52
501 511 0.253610 AACACCCGAACAACCACAGA 59.746 50.000 0.00 0.00 0.00 3.41
569 580 5.262588 AGTTCTTTCCAATCAACACAACC 57.737 39.130 0.00 0.00 0.00 3.77
575 586 4.399004 TCCAATCAACACAACCCTTTTG 57.601 40.909 0.00 0.00 0.00 2.44
600 611 4.468510 AGGTCCGTACTATCATCAAAACCA 59.531 41.667 0.00 0.00 0.00 3.67
602 613 5.465724 GGTCCGTACTATCATCAAAACCATC 59.534 44.000 0.00 0.00 0.00 3.51
605 616 5.051039 CCGTACTATCATCAAAACCATCACG 60.051 44.000 0.00 0.00 0.00 4.35
608 619 6.903883 ACTATCATCAAAACCATCACGTAC 57.096 37.500 0.00 0.00 0.00 3.67
620 631 2.054687 TCACGTACTACAAAGCCACG 57.945 50.000 0.00 0.00 39.27 4.94
642 653 2.277084 CCGAAACCTAGCACATGTACC 58.723 52.381 0.00 0.00 0.00 3.34
666 686 3.493213 GCAAAATGCATGGCAGCC 58.507 55.556 3.66 3.66 43.65 4.85
667 687 1.376166 GCAAAATGCATGGCAGCCA 60.376 52.632 18.99 18.99 43.65 4.75
668 688 1.641123 GCAAAATGCATGGCAGCCAC 61.641 55.000 19.10 5.54 43.65 5.01
669 689 0.320858 CAAAATGCATGGCAGCCACA 60.321 50.000 19.10 12.29 43.65 4.17
670 690 0.036765 AAAATGCATGGCAGCCACAG 60.037 50.000 19.10 14.12 43.65 3.66
671 691 2.515996 AAATGCATGGCAGCCACAGC 62.516 55.000 26.66 26.66 43.65 4.40
908 940 1.924524 ACGTTTATCTTCCACGCATCG 59.075 47.619 0.00 0.00 37.44 3.84
912 944 2.724977 TATCTTCCACGCATCGATCC 57.275 50.000 0.00 0.00 0.00 3.36
918 950 1.541588 TCCACGCATCGATCCATCTAG 59.458 52.381 0.00 0.00 0.00 2.43
919 951 1.344458 CACGCATCGATCCATCTAGC 58.656 55.000 0.00 0.00 0.00 3.42
921 953 1.547820 ACGCATCGATCCATCTAGCAT 59.452 47.619 0.00 0.00 0.00 3.79
924 956 3.675502 CGCATCGATCCATCTAGCATTCT 60.676 47.826 0.00 0.00 0.00 2.40
930 962 5.946377 TCGATCCATCTAGCATTCTAGCTAA 59.054 40.000 0.00 0.00 45.69 3.09
931 963 6.094742 TCGATCCATCTAGCATTCTAGCTAAG 59.905 42.308 0.00 0.00 45.69 2.18
932 964 5.398603 TCCATCTAGCATTCTAGCTAAGC 57.601 43.478 0.00 0.00 45.69 3.09
933 965 4.221703 TCCATCTAGCATTCTAGCTAAGCC 59.778 45.833 0.00 0.00 45.69 4.35
955 987 3.142796 GTGTACAGTTGCAACACGC 57.857 52.632 30.11 21.37 42.89 5.34
1040 1072 0.323908 GGAGGGGGAGATCGATCGAT 60.324 60.000 29.76 29.76 37.59 3.59
1281 1316 1.070445 CTGCCAGGTCAGGATCAGATC 59.930 57.143 1.18 1.18 0.00 2.75
1282 1317 1.126488 GCCAGGTCAGGATCAGATCA 58.874 55.000 12.66 0.00 0.00 2.92
1284 1319 2.744494 GCCAGGTCAGGATCAGATCAAC 60.744 54.545 12.66 6.95 0.00 3.18
1289 1324 5.990386 CAGGTCAGGATCAGATCAACATAAG 59.010 44.000 12.66 0.00 0.00 1.73
1295 1346 8.756927 TCAGGATCAGATCAACATAAGGATATC 58.243 37.037 12.66 0.00 0.00 1.63
1299 1350 9.585099 GATCAGATCAACATAAGGATATCTGTC 57.415 37.037 5.44 0.00 40.62 3.51
1304 1355 6.830912 TCAACATAAGGATATCTGTCCCTTG 58.169 40.000 2.05 0.00 40.26 3.61
1306 1361 6.831664 ACATAAGGATATCTGTCCCTTGTT 57.168 37.500 2.05 0.00 40.26 2.83
1308 1363 7.283329 ACATAAGGATATCTGTCCCTTGTTTC 58.717 38.462 2.05 0.00 40.26 2.78
1313 1368 1.981256 TCTGTCCCTTGTTTCTTGCC 58.019 50.000 0.00 0.00 0.00 4.52
1315 1370 0.106918 TGTCCCTTGTTTCTTGCCGT 60.107 50.000 0.00 0.00 0.00 5.68
1316 1371 1.029681 GTCCCTTGTTTCTTGCCGTT 58.970 50.000 0.00 0.00 0.00 4.44
1317 1372 1.001706 GTCCCTTGTTTCTTGCCGTTC 60.002 52.381 0.00 0.00 0.00 3.95
1318 1373 1.028905 CCCTTGTTTCTTGCCGTTCA 58.971 50.000 0.00 0.00 0.00 3.18
1732 1849 1.982660 TCTCTTCAGGCGGATCGTAT 58.017 50.000 0.00 0.00 0.00 3.06
1768 1885 4.284829 TGAACATTGGTGCAGATGAGTA 57.715 40.909 10.62 0.00 0.00 2.59
1777 1894 5.419542 TGGTGCAGATGAGTAGATGTTTAC 58.580 41.667 0.00 0.00 0.00 2.01
1780 1897 6.540189 GGTGCAGATGAGTAGATGTTTACAAT 59.460 38.462 0.00 0.00 0.00 2.71
1835 1952 2.406616 GCGGCAATGTTCCGGTCAT 61.407 57.895 0.00 5.15 46.51 3.06
1889 2007 5.009436 CCATTCCATTATGGGGATGGTTA 57.991 43.478 25.62 1.36 42.00 2.85
1892 2010 6.240438 CCATTCCATTATGGGGATGGTTAGTA 60.240 42.308 25.62 0.00 42.00 1.82
1895 2013 5.546499 TCCATTATGGGGATGGTTAGTAGTC 59.454 44.000 11.76 0.00 43.64 2.59
1933 2051 2.645281 TTTCGCAGCTTGCACACACG 62.645 55.000 8.52 0.00 45.36 4.49
1949 2067 2.113139 CGCTGGTCCAGGGTGTTT 59.887 61.111 24.44 0.00 39.17 2.83
2019 2137 5.863935 GGACACAAGCAAAATTTACATCTCC 59.136 40.000 0.00 0.00 0.00 3.71
2020 2138 6.294731 GGACACAAGCAAAATTTACATCTCCT 60.295 38.462 0.00 0.00 0.00 3.69
2021 2139 6.681777 ACACAAGCAAAATTTACATCTCCTC 58.318 36.000 0.00 0.00 0.00 3.71
2080 2219 0.462047 AGTAGCTCCCAATTTCGCGG 60.462 55.000 6.13 0.00 0.00 6.46
2143 2282 2.118233 TTGGGTGCCGCAGATGTACA 62.118 55.000 0.00 0.00 0.00 2.90
2203 2342 2.093306 CAGTCCGCACTGGTGAAATA 57.907 50.000 0.00 0.00 45.75 1.40
2317 2459 3.554129 GGCTTAATTTCTGGGTTTTGCGT 60.554 43.478 0.00 0.00 0.00 5.24
2336 2478 1.497309 TTCCCTGGGCGTCCTCATTT 61.497 55.000 7.97 0.00 0.00 2.32
2356 2498 2.046314 CGGGATGTTTGGGAGCGT 60.046 61.111 0.00 0.00 0.00 5.07
2373 2515 0.660300 CGTTCGTGCTTTTTGAGGCC 60.660 55.000 0.00 0.00 0.00 5.19
2375 2517 1.098712 TTCGTGCTTTTTGAGGCCGT 61.099 50.000 0.00 0.00 0.00 5.68
2399 2541 5.665381 GAGAAAATCTCCGCTCCTTTATG 57.335 43.478 0.00 0.00 37.55 1.90
2499 2653 4.567959 AGTTGAATTTCTGCAGTTGTTTGC 59.432 37.500 14.67 0.00 44.33 3.68
2546 2700 5.334802 CGGTTGCTTGATTGACTGTAAATGA 60.335 40.000 0.00 0.00 0.00 2.57
2560 2714 4.998788 TGTAAATGACGTGGAGAGATCAG 58.001 43.478 0.00 0.00 0.00 2.90
2576 2730 5.067674 AGAGATCAGACTGAAGCTATGTGAC 59.932 44.000 9.70 0.00 0.00 3.67
2665 2819 1.762957 ACATAATCGGACACCCTCCAG 59.237 52.381 0.00 0.00 39.39 3.86
2690 2844 4.666105 GGGCAAACCTCCCTCATC 57.334 61.111 0.00 0.00 40.66 2.92
2708 2862 2.444624 CGTCCGATCAGGTGCAACG 61.445 63.158 0.00 0.00 41.99 4.10
2709 2863 1.374252 GTCCGATCAGGTGCAACGT 60.374 57.895 0.00 0.00 41.99 3.99
2738 2892 5.779922 ACACGATGTGAAGTACTACAACAT 58.220 37.500 14.52 14.52 36.96 2.71
2747 2901 5.820423 TGAAGTACTACAACATGCAACAAGT 59.180 36.000 0.00 0.00 0.00 3.16
2768 2922 2.371306 TGCATCAGTGTTGCAGCATAT 58.629 42.857 22.04 0.00 44.73 1.78
2823 2977 8.908786 ACCAGTACACCATCAATAATAAGATG 57.091 34.615 0.00 0.00 40.94 2.90
2854 3008 3.503363 ACGTCATTGCAATCACATCAACT 59.497 39.130 14.13 0.00 0.00 3.16
2863 3017 4.266157 CAATCACATCAACTAACGCATCG 58.734 43.478 0.00 0.00 0.00 3.84
2868 3022 1.017177 TCAACTAACGCATCGCCCAC 61.017 55.000 0.00 0.00 0.00 4.61
2886 3040 4.685030 GCCCACGACCTTTCTTTATGGATA 60.685 45.833 0.00 0.00 0.00 2.59
2887 3041 5.057149 CCCACGACCTTTCTTTATGGATAG 58.943 45.833 0.00 0.00 0.00 2.08
3040 3196 1.247567 GGGGCATAATCATCAACCGG 58.752 55.000 0.00 0.00 0.00 5.28
3110 3967 9.905713 ATGATTTTCCTGTTCAAACTATAGCTA 57.094 29.630 0.00 0.00 0.00 3.32
3111 3968 9.383519 TGATTTTCCTGTTCAAACTATAGCTAG 57.616 33.333 0.00 0.00 0.00 3.42
3229 4308 3.265791 GCACATAGTCCAACTCTCAAGG 58.734 50.000 0.00 0.00 0.00 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.150135 TGAAGGGGGCCAATAAACCAA 59.850 47.619 4.39 0.00 0.00 3.67
1 2 0.787084 TGAAGGGGGCCAATAAACCA 59.213 50.000 4.39 0.00 0.00 3.67
2 3 2.174685 ATGAAGGGGGCCAATAAACC 57.825 50.000 4.39 0.00 0.00 3.27
4 5 7.570607 ACATAAAATATGAAGGGGGCCAATAAA 59.429 33.333 4.39 0.00 0.00 1.40
5 6 7.079048 ACATAAAATATGAAGGGGGCCAATAA 58.921 34.615 4.39 0.00 0.00 1.40
6 7 6.629156 ACATAAAATATGAAGGGGGCCAATA 58.371 36.000 4.39 0.00 0.00 1.90
7 8 5.476054 ACATAAAATATGAAGGGGGCCAAT 58.524 37.500 4.39 0.00 0.00 3.16
8 9 4.889780 ACATAAAATATGAAGGGGGCCAA 58.110 39.130 4.39 0.00 0.00 4.52
9 10 4.078922 TGACATAAAATATGAAGGGGGCCA 60.079 41.667 4.39 0.00 0.00 5.36
11 12 6.478512 TTTGACATAAAATATGAAGGGGGC 57.521 37.500 4.47 0.00 0.00 5.80
12 13 9.904198 AAAATTTGACATAAAATATGAAGGGGG 57.096 29.630 4.47 0.00 0.00 5.40
78 79 9.850628 CGAATCCAATGATATGCTTTTTATGAT 57.149 29.630 0.00 0.00 0.00 2.45
79 80 8.849168 ACGAATCCAATGATATGCTTTTTATGA 58.151 29.630 0.00 0.00 0.00 2.15
87 88 9.283768 TGTTTTATACGAATCCAATGATATGCT 57.716 29.630 0.00 0.00 0.00 3.79
92 93 9.793259 ACCTATGTTTTATACGAATCCAATGAT 57.207 29.630 0.00 0.00 0.00 2.45
93 94 9.621629 AACCTATGTTTTATACGAATCCAATGA 57.378 29.630 0.00 0.00 0.00 2.57
174 175 9.221933 TCGTATTTACAGTTGTATTTTGACCAT 57.778 29.630 0.00 0.00 0.00 3.55
175 176 8.604640 TCGTATTTACAGTTGTATTTTGACCA 57.395 30.769 0.00 0.00 0.00 4.02
176 177 8.173130 CCTCGTATTTACAGTTGTATTTTGACC 58.827 37.037 0.00 0.00 0.00 4.02
177 178 8.173130 CCCTCGTATTTACAGTTGTATTTTGAC 58.827 37.037 0.00 0.00 0.00 3.18
178 179 7.879160 ACCCTCGTATTTACAGTTGTATTTTGA 59.121 33.333 0.00 0.00 0.00 2.69
179 180 8.036273 ACCCTCGTATTTACAGTTGTATTTTG 57.964 34.615 0.00 0.00 0.00 2.44
180 181 9.154847 GTACCCTCGTATTTACAGTTGTATTTT 57.845 33.333 0.00 0.00 0.00 1.82
181 182 8.534496 AGTACCCTCGTATTTACAGTTGTATTT 58.466 33.333 0.00 0.00 0.00 1.40
182 183 8.071177 AGTACCCTCGTATTTACAGTTGTATT 57.929 34.615 0.00 0.00 0.00 1.89
183 184 7.651027 AGTACCCTCGTATTTACAGTTGTAT 57.349 36.000 0.00 0.00 0.00 2.29
184 185 8.574251 TTAGTACCCTCGTATTTACAGTTGTA 57.426 34.615 0.00 0.00 0.00 2.41
185 186 5.990120 AGTACCCTCGTATTTACAGTTGT 57.010 39.130 0.00 0.00 0.00 3.32
193 194 8.761689 TCCTTGTTTATTAGTACCCTCGTATTT 58.238 33.333 0.00 0.00 0.00 1.40
194 195 8.200120 GTCCTTGTTTATTAGTACCCTCGTATT 58.800 37.037 0.00 0.00 0.00 1.89
195 196 7.342799 TGTCCTTGTTTATTAGTACCCTCGTAT 59.657 37.037 0.00 0.00 0.00 3.06
196 197 6.663093 TGTCCTTGTTTATTAGTACCCTCGTA 59.337 38.462 0.00 0.00 0.00 3.43
197 198 5.481473 TGTCCTTGTTTATTAGTACCCTCGT 59.519 40.000 0.00 0.00 0.00 4.18
198 199 5.969423 TGTCCTTGTTTATTAGTACCCTCG 58.031 41.667 0.00 0.00 0.00 4.63
199 200 8.625786 TTTTGTCCTTGTTTATTAGTACCCTC 57.374 34.615 0.00 0.00 0.00 4.30
200 201 8.222637 ACTTTTGTCCTTGTTTATTAGTACCCT 58.777 33.333 0.00 0.00 0.00 4.34
201 202 8.400184 ACTTTTGTCCTTGTTTATTAGTACCC 57.600 34.615 0.00 0.00 0.00 3.69
233 234 9.998106 AGTTGAGACATGTATTTACTGTTAACT 57.002 29.630 7.22 0.00 0.00 2.24
289 290 9.430623 CCGTCCCAAAATAAATGTCTTAATTTT 57.569 29.630 0.00 0.00 32.16 1.82
290 291 8.808092 TCCGTCCCAAAATAAATGTCTTAATTT 58.192 29.630 0.00 0.00 34.24 1.82
291 292 8.356000 TCCGTCCCAAAATAAATGTCTTAATT 57.644 30.769 0.00 0.00 0.00 1.40
292 293 7.068226 CCTCCGTCCCAAAATAAATGTCTTAAT 59.932 37.037 0.00 0.00 0.00 1.40
293 294 6.376018 CCTCCGTCCCAAAATAAATGTCTTAA 59.624 38.462 0.00 0.00 0.00 1.85
294 295 5.883673 CCTCCGTCCCAAAATAAATGTCTTA 59.116 40.000 0.00 0.00 0.00 2.10
295 296 4.705023 CCTCCGTCCCAAAATAAATGTCTT 59.295 41.667 0.00 0.00 0.00 3.01
296 297 4.263771 ACCTCCGTCCCAAAATAAATGTCT 60.264 41.667 0.00 0.00 0.00 3.41
297 298 4.014406 ACCTCCGTCCCAAAATAAATGTC 58.986 43.478 0.00 0.00 0.00 3.06
298 299 4.042271 ACCTCCGTCCCAAAATAAATGT 57.958 40.909 0.00 0.00 0.00 2.71
299 300 6.096282 ACATTACCTCCGTCCCAAAATAAATG 59.904 38.462 0.00 0.00 0.00 2.32
300 301 6.192044 ACATTACCTCCGTCCCAAAATAAAT 58.808 36.000 0.00 0.00 0.00 1.40
301 302 5.572252 ACATTACCTCCGTCCCAAAATAAA 58.428 37.500 0.00 0.00 0.00 1.40
302 303 5.182169 ACATTACCTCCGTCCCAAAATAA 57.818 39.130 0.00 0.00 0.00 1.40
303 304 4.847990 ACATTACCTCCGTCCCAAAATA 57.152 40.909 0.00 0.00 0.00 1.40
304 305 3.732048 ACATTACCTCCGTCCCAAAAT 57.268 42.857 0.00 0.00 0.00 1.82
305 306 3.512219 AACATTACCTCCGTCCCAAAA 57.488 42.857 0.00 0.00 0.00 2.44
306 307 3.583966 ACTAACATTACCTCCGTCCCAAA 59.416 43.478 0.00 0.00 0.00 3.28
307 308 3.175594 ACTAACATTACCTCCGTCCCAA 58.824 45.455 0.00 0.00 0.00 4.12
308 309 2.823959 ACTAACATTACCTCCGTCCCA 58.176 47.619 0.00 0.00 0.00 4.37
309 310 3.900966 AACTAACATTACCTCCGTCCC 57.099 47.619 0.00 0.00 0.00 4.46
310 311 5.578336 GTGTTAACTAACATTACCTCCGTCC 59.422 44.000 7.22 0.00 46.56 4.79
311 312 6.393171 AGTGTTAACTAACATTACCTCCGTC 58.607 40.000 7.22 0.00 46.56 4.79
312 313 6.350629 AGTGTTAACTAACATTACCTCCGT 57.649 37.500 7.22 0.00 46.56 4.69
313 314 8.761575 TTTAGTGTTAACTAACATTACCTCCG 57.238 34.615 7.22 0.00 46.24 4.63
331 332 9.350951 GGTTTATTGGGCTCTTATATTTAGTGT 57.649 33.333 0.00 0.00 0.00 3.55
332 333 9.574516 AGGTTTATTGGGCTCTTATATTTAGTG 57.425 33.333 0.00 0.00 0.00 2.74
337 338 9.363401 GGTTTAGGTTTATTGGGCTCTTATATT 57.637 33.333 0.00 0.00 0.00 1.28
338 339 7.948447 GGGTTTAGGTTTATTGGGCTCTTATAT 59.052 37.037 0.00 0.00 0.00 0.86
339 340 7.129816 AGGGTTTAGGTTTATTGGGCTCTTATA 59.870 37.037 0.00 0.00 0.00 0.98
340 341 6.068438 AGGGTTTAGGTTTATTGGGCTCTTAT 60.068 38.462 0.00 0.00 0.00 1.73
341 342 5.254501 AGGGTTTAGGTTTATTGGGCTCTTA 59.745 40.000 0.00 0.00 0.00 2.10
342 343 4.045462 AGGGTTTAGGTTTATTGGGCTCTT 59.955 41.667 0.00 0.00 0.00 2.85
343 344 3.596500 AGGGTTTAGGTTTATTGGGCTCT 59.403 43.478 0.00 0.00 0.00 4.09
344 345 3.699538 CAGGGTTTAGGTTTATTGGGCTC 59.300 47.826 0.00 0.00 0.00 4.70
345 346 3.335484 TCAGGGTTTAGGTTTATTGGGCT 59.665 43.478 0.00 0.00 0.00 5.19
346 347 3.446161 GTCAGGGTTTAGGTTTATTGGGC 59.554 47.826 0.00 0.00 0.00 5.36
347 348 4.021229 GGTCAGGGTTTAGGTTTATTGGG 58.979 47.826 0.00 0.00 0.00 4.12
348 349 3.692593 CGGTCAGGGTTTAGGTTTATTGG 59.307 47.826 0.00 0.00 0.00 3.16
349 350 4.581868 TCGGTCAGGGTTTAGGTTTATTG 58.418 43.478 0.00 0.00 0.00 1.90
350 351 4.914177 TCGGTCAGGGTTTAGGTTTATT 57.086 40.909 0.00 0.00 0.00 1.40
351 352 4.287845 ACTTCGGTCAGGGTTTAGGTTTAT 59.712 41.667 0.00 0.00 0.00 1.40
352 353 3.647590 ACTTCGGTCAGGGTTTAGGTTTA 59.352 43.478 0.00 0.00 0.00 2.01
353 354 2.440627 ACTTCGGTCAGGGTTTAGGTTT 59.559 45.455 0.00 0.00 0.00 3.27
354 355 2.052468 ACTTCGGTCAGGGTTTAGGTT 58.948 47.619 0.00 0.00 0.00 3.50
355 356 1.725803 ACTTCGGTCAGGGTTTAGGT 58.274 50.000 0.00 0.00 0.00 3.08
356 357 2.418334 GCTACTTCGGTCAGGGTTTAGG 60.418 54.545 0.00 0.00 0.00 2.69
357 358 2.496470 AGCTACTTCGGTCAGGGTTTAG 59.504 50.000 0.00 0.00 0.00 1.85
358 359 2.232941 CAGCTACTTCGGTCAGGGTTTA 59.767 50.000 0.00 0.00 0.00 2.01
359 360 1.002087 CAGCTACTTCGGTCAGGGTTT 59.998 52.381 0.00 0.00 0.00 3.27
360 361 0.608640 CAGCTACTTCGGTCAGGGTT 59.391 55.000 0.00 0.00 0.00 4.11
361 362 1.258445 CCAGCTACTTCGGTCAGGGT 61.258 60.000 0.00 0.00 0.00 4.34
362 363 1.517832 CCAGCTACTTCGGTCAGGG 59.482 63.158 0.00 0.00 0.00 4.45
363 364 1.153549 GCCAGCTACTTCGGTCAGG 60.154 63.158 0.00 0.00 0.00 3.86
364 365 0.737715 GTGCCAGCTACTTCGGTCAG 60.738 60.000 0.00 0.00 0.00 3.51
365 366 1.292223 GTGCCAGCTACTTCGGTCA 59.708 57.895 0.00 0.00 0.00 4.02
366 367 1.014564 GTGTGCCAGCTACTTCGGTC 61.015 60.000 0.00 0.00 0.00 4.79
367 368 1.004918 GTGTGCCAGCTACTTCGGT 60.005 57.895 0.00 0.00 0.00 4.69
368 369 1.741770 GGTGTGCCAGCTACTTCGG 60.742 63.158 0.00 0.00 34.09 4.30
369 370 2.094659 CGGTGTGCCAGCTACTTCG 61.095 63.158 0.00 0.00 34.09 3.79
370 371 2.391389 GCGGTGTGCCAGCTACTTC 61.391 63.158 0.00 0.00 37.76 3.01
371 372 2.358737 GCGGTGTGCCAGCTACTT 60.359 61.111 0.00 0.00 37.76 2.24
372 373 3.596066 CTGCGGTGTGCCAGCTACT 62.596 63.158 0.00 0.00 45.60 2.57
373 374 3.121030 CTGCGGTGTGCCAGCTAC 61.121 66.667 0.00 0.00 45.60 3.58
391 392 3.266686 TTGACTGCCCCATGTCCGG 62.267 63.158 0.00 0.00 32.67 5.14
392 393 1.746615 CTTGACTGCCCCATGTCCG 60.747 63.158 0.00 0.00 32.67 4.79
393 394 1.379044 CCTTGACTGCCCCATGTCC 60.379 63.158 0.00 0.00 32.67 4.02
394 395 2.048603 GCCTTGACTGCCCCATGTC 61.049 63.158 0.00 0.00 0.00 3.06
395 396 2.036256 GCCTTGACTGCCCCATGT 59.964 61.111 0.00 0.00 0.00 3.21
396 397 3.136123 CGCCTTGACTGCCCCATG 61.136 66.667 0.00 0.00 0.00 3.66
397 398 3.329889 TCGCCTTGACTGCCCCAT 61.330 61.111 0.00 0.00 0.00 4.00
398 399 4.329545 GTCGCCTTGACTGCCCCA 62.330 66.667 0.00 0.00 44.58 4.96
428 429 4.021229 GGGGATTTATGAGGTTTTTCCGT 58.979 43.478 0.00 0.00 41.99 4.69
437 438 7.665974 GGTTACTATTTCTGGGGATTTATGAGG 59.334 40.741 0.00 0.00 0.00 3.86
439 440 8.344939 AGGTTACTATTTCTGGGGATTTATGA 57.655 34.615 0.00 0.00 0.00 2.15
445 454 6.895756 GGAAAAAGGTTACTATTTCTGGGGAT 59.104 38.462 0.00 0.00 33.42 3.85
501 511 1.187567 GGGCATGCCACTCCTGTTTT 61.188 55.000 36.56 0.00 37.98 2.43
575 586 3.728076 TTGATGATAGTACGGACCTGC 57.272 47.619 0.00 0.00 0.00 4.85
600 611 2.602878 CGTGGCTTTGTAGTACGTGAT 58.397 47.619 0.00 0.00 32.90 3.06
602 613 0.437295 GCGTGGCTTTGTAGTACGTG 59.563 55.000 0.00 0.00 36.85 4.49
605 616 1.356527 CGGGCGTGGCTTTGTAGTAC 61.357 60.000 0.00 0.00 0.00 2.73
608 619 1.231958 TTTCGGGCGTGGCTTTGTAG 61.232 55.000 0.00 0.00 0.00 2.74
620 631 0.676782 ACATGTGCTAGGTTTCGGGC 60.677 55.000 0.00 0.00 0.00 6.13
642 653 1.077645 CCATGCATTTTGCCGTTCGG 61.078 55.000 6.90 6.90 44.23 4.30
666 686 0.839277 TCATATCCCTGTGGGCTGTG 59.161 55.000 0.00 0.00 43.94 3.66
667 687 1.825105 ATCATATCCCTGTGGGCTGT 58.175 50.000 0.00 0.00 43.94 4.40
668 688 3.176411 TCTATCATATCCCTGTGGGCTG 58.824 50.000 0.00 0.00 43.94 4.85
669 689 3.567375 TCTATCATATCCCTGTGGGCT 57.433 47.619 0.00 0.00 43.94 5.19
670 690 5.211973 TCTATCTATCATATCCCTGTGGGC 58.788 45.833 0.00 0.00 43.94 5.36
671 691 7.071917 TGATCTATCTATCATATCCCTGTGGG 58.928 42.308 0.00 0.00 36.16 4.61
672 692 8.003629 TCTGATCTATCTATCATATCCCTGTGG 58.996 40.741 0.00 0.00 35.40 4.17
695 715 2.158340 TCTCCCTCCCTGATCTGATCTG 60.158 54.545 17.82 16.49 0.00 2.90
878 910 2.124860 ATAAACGTGAGGGGCCGC 60.125 61.111 12.88 12.88 0.00 6.53
908 940 6.042143 GCTTAGCTAGAATGCTAGATGGATC 58.958 44.000 12.36 0.00 45.71 3.36
912 944 4.172505 CGGCTTAGCTAGAATGCTAGATG 58.827 47.826 12.36 0.00 45.71 2.90
918 950 1.560860 CGGCGGCTTAGCTAGAATGC 61.561 60.000 7.61 0.00 37.29 3.56
919 951 0.249489 ACGGCGGCTTAGCTAGAATG 60.249 55.000 13.24 0.00 37.29 2.67
921 953 1.141019 CACGGCGGCTTAGCTAGAA 59.859 57.895 13.24 0.00 37.29 2.10
924 956 1.314534 TGTACACGGCGGCTTAGCTA 61.315 55.000 13.24 0.00 37.29 3.32
930 962 2.357034 CAACTGTACACGGCGGCT 60.357 61.111 13.24 0.00 0.00 5.52
931 963 4.084888 GCAACTGTACACGGCGGC 62.085 66.667 13.24 0.00 0.00 6.53
932 964 2.248135 TTGCAACTGTACACGGCGG 61.248 57.895 13.24 2.35 0.00 6.13
933 965 1.083015 GTTGCAACTGTACACGGCG 60.083 57.895 22.36 4.80 0.00 6.46
955 987 2.969238 GATGGATCGCCCGCAGTG 60.969 66.667 0.00 0.00 37.93 3.66
1022 1054 1.099689 GATCGATCGATCTCCCCCTC 58.900 60.000 38.45 19.96 45.42 4.30
1040 1072 0.725686 GTCGATGTCGGAACTCTCGA 59.274 55.000 2.25 0.00 37.68 4.04
1041 1073 0.248134 GGTCGATGTCGGAACTCTCG 60.248 60.000 2.25 0.00 40.29 4.04
1043 1075 1.135139 CATGGTCGATGTCGGAACTCT 59.865 52.381 2.25 0.00 40.29 3.24
1044 1076 1.134367 TCATGGTCGATGTCGGAACTC 59.866 52.381 2.25 0.00 40.29 3.01
1045 1077 1.182667 TCATGGTCGATGTCGGAACT 58.817 50.000 2.25 0.00 40.29 3.01
1046 1078 1.927174 CTTCATGGTCGATGTCGGAAC 59.073 52.381 2.25 0.00 40.29 3.62
1047 1079 1.134818 CCTTCATGGTCGATGTCGGAA 60.135 52.381 2.25 0.00 40.29 4.30
1048 1080 0.459899 CCTTCATGGTCGATGTCGGA 59.540 55.000 2.25 0.00 40.29 4.55
1049 1081 2.977700 CCTTCATGGTCGATGTCGG 58.022 57.895 2.25 0.00 40.29 4.79
1095 1127 3.394836 AGCAGAAGACGGAGGCCC 61.395 66.667 0.00 0.00 0.00 5.80
1281 1316 6.595682 ACAAGGGACAGATATCCTTATGTTG 58.404 40.000 0.00 0.55 38.70 3.33
1282 1317 6.831664 ACAAGGGACAGATATCCTTATGTT 57.168 37.500 0.00 0.00 38.70 2.71
1284 1319 7.512992 AGAAACAAGGGACAGATATCCTTATG 58.487 38.462 0.00 0.00 38.70 1.90
1289 1324 4.336713 GCAAGAAACAAGGGACAGATATCC 59.663 45.833 0.00 0.00 38.13 2.59
1295 1346 0.593128 CGGCAAGAAACAAGGGACAG 59.407 55.000 0.00 0.00 0.00 3.51
1299 1350 1.028905 TGAACGGCAAGAAACAAGGG 58.971 50.000 0.00 0.00 0.00 3.95
1304 1355 2.663119 GCAATCATGAACGGCAAGAAAC 59.337 45.455 0.00 0.00 0.00 2.78
1306 1361 1.202114 GGCAATCATGAACGGCAAGAA 59.798 47.619 15.59 0.00 0.00 2.52
1308 1363 0.523968 CGGCAATCATGAACGGCAAG 60.524 55.000 17.73 8.65 0.00 4.01
1313 1368 2.095768 ACTTTCACGGCAATCATGAACG 60.096 45.455 0.00 5.22 32.21 3.95
1315 1370 2.228582 CCACTTTCACGGCAATCATGAA 59.771 45.455 0.00 0.00 0.00 2.57
1316 1371 1.811965 CCACTTTCACGGCAATCATGA 59.188 47.619 0.00 0.00 0.00 3.07
1317 1372 2.267188 CCACTTTCACGGCAATCATG 57.733 50.000 0.00 0.00 0.00 3.07
1732 1849 0.465460 GTTCAGTGGCACCAACCTGA 60.465 55.000 15.27 8.27 30.52 3.86
1835 1952 1.947212 GCAGTGATGTGGATGCAGACA 60.947 52.381 0.00 0.00 38.54 3.41
1889 2007 4.686972 TGAGCGTAGTACGTATGACTACT 58.313 43.478 22.81 9.40 44.72 2.57
1892 2010 3.875727 ACATGAGCGTAGTACGTATGACT 59.124 43.478 27.48 16.98 44.73 3.41
1895 2013 4.144221 CGAAACATGAGCGTAGTACGTATG 59.856 45.833 22.81 22.91 44.73 2.39
1933 2051 1.202891 ACTAAAACACCCTGGACCAGC 60.203 52.381 16.72 0.00 0.00 4.85
1934 2052 2.951229 ACTAAAACACCCTGGACCAG 57.049 50.000 15.15 15.15 0.00 4.00
1949 2067 4.014406 TCTGAGGATGTTGTCGCTACTAA 58.986 43.478 0.00 0.00 0.00 2.24
2019 2137 2.996621 CCGAAAGCCAAGTTAGTCAGAG 59.003 50.000 0.00 0.00 0.00 3.35
2020 2138 2.367567 ACCGAAAGCCAAGTTAGTCAGA 59.632 45.455 0.00 0.00 0.00 3.27
2021 2139 2.480419 CACCGAAAGCCAAGTTAGTCAG 59.520 50.000 0.00 0.00 0.00 3.51
2070 2209 2.553770 TCGTGCACCGCGAAATTG 59.446 55.556 8.23 0.00 43.38 2.32
2111 2250 2.233566 ACCCAATGCTCCTGCCTCA 61.234 57.895 0.00 0.00 38.71 3.86
2186 2325 4.034048 CACTTATATTTCACCAGTGCGGAC 59.966 45.833 0.00 0.00 38.63 4.79
2203 2342 2.125269 GCCGCCGGTGACACTTAT 60.125 61.111 18.79 0.00 0.00 1.73
2317 2459 1.497309 AAATGAGGACGCCCAGGGAA 61.497 55.000 10.89 0.00 33.88 3.97
2336 2478 1.602237 GCTCCCAAACATCCCGAGA 59.398 57.895 0.00 0.00 0.00 4.04
2356 2498 1.098712 ACGGCCTCAAAAAGCACGAA 61.099 50.000 0.00 0.00 0.00 3.85
2391 2533 6.779860 ACTTAGGAGAAAAGCACATAAAGGA 58.220 36.000 0.00 0.00 0.00 3.36
2399 2541 4.745125 GGCAAAAACTTAGGAGAAAAGCAC 59.255 41.667 0.00 0.00 0.00 4.40
2457 2611 5.465390 TCAACTTCTGACCAAACTGTTATCG 59.535 40.000 0.00 0.00 0.00 2.92
2492 2646 0.808125 ACACGCTCAAGTGCAAACAA 59.192 45.000 0.00 0.00 45.45 2.83
2528 2682 5.408299 TCCACGTCATTTACAGTCAATCAAG 59.592 40.000 0.00 0.00 0.00 3.02
2529 2683 5.301555 TCCACGTCATTTACAGTCAATCAA 58.698 37.500 0.00 0.00 0.00 2.57
2546 2700 2.498644 TCAGTCTGATCTCTCCACGT 57.501 50.000 0.00 0.00 0.00 4.49
2560 2714 2.263077 CACCGTCACATAGCTTCAGTC 58.737 52.381 0.00 0.00 0.00 3.51
2576 2730 2.052891 CAACATGTTCATTGCACACCG 58.947 47.619 8.48 0.00 0.00 4.94
2665 2819 4.621087 AGGTTTGCCCTGGGGTGC 62.621 66.667 16.03 0.00 44.08 5.01
2690 2844 2.444624 CGTTGCACCTGATCGGACG 61.445 63.158 2.08 0.32 36.31 4.79
2708 2862 0.713883 CTTCACATCGTGTACCGCAC 59.286 55.000 0.00 0.00 44.36 5.34
2709 2863 0.315886 ACTTCACATCGTGTACCGCA 59.684 50.000 0.00 0.00 34.79 5.69
2728 2882 4.854399 GCAACTTGTTGCATGTTGTAGTA 58.146 39.130 27.19 0.00 45.23 1.82
2768 2922 6.832900 TGATGGGTATTGCATCTTTGTATTCA 59.167 34.615 0.00 0.00 0.00 2.57
2816 2970 3.937814 TGACGTTTGCACTCCATCTTAT 58.062 40.909 0.00 0.00 0.00 1.73
2863 3017 1.743394 CCATAAAGAAAGGTCGTGGGC 59.257 52.381 0.00 0.00 0.00 5.36
2868 3022 5.360591 AGTGCTATCCATAAAGAAAGGTCG 58.639 41.667 0.00 0.00 0.00 4.79
2872 3026 7.500992 TGGTCTAGTGCTATCCATAAAGAAAG 58.499 38.462 0.00 0.00 0.00 2.62
3074 3230 7.499292 TGAACAGGAAAATCATGAACACAAAT 58.501 30.769 0.00 0.00 31.79 2.32
3110 3967 9.906660 CTGTCTATTTCTCGATTAGCTATTTCT 57.093 33.333 0.00 0.00 0.00 2.52
3111 3968 8.643752 GCTGTCTATTTCTCGATTAGCTATTTC 58.356 37.037 0.00 0.00 0.00 2.17
3229 4308 2.814336 GACATTCCACCCAAGAACTCAC 59.186 50.000 0.00 0.00 0.00 3.51
3319 4959 1.537202 GGAACCATGTCAACTCACTGC 59.463 52.381 0.00 0.00 0.00 4.40
3430 5093 3.019564 GACTTGAAGGAATGGGTCATGG 58.980 50.000 0.00 0.00 0.00 3.66


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

AutoCloner maintained by Alex Coulton.