Multiple sequence alignment - TraesCS4D01G077100

Loading Multiple Alignment...

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 TraesCS4D01G077100 chr4D 100.000 2276 0 0 1 2276 51316234 51313959 0.000000e+00 4204
1 TraesCS4D01G077100 chr4D 88.048 661 41 8 900 1531 51456031 51455380 0.000000e+00 749
2 TraesCS4D01G077100 chr4D 84.189 740 68 28 900 1622 51348377 51347670 0.000000e+00 673
3 TraesCS4D01G077100 chr4D 84.977 213 18 5 1524 1726 51349465 51349257 1.070000e-48 204
4 TraesCS4D01G077100 chr4D 96.491 114 3 1 795 907 51456233 51456120 1.070000e-43 187
5 TraesCS4D01G077100 chr3D 97.985 546 10 1 1731 2276 69653805 69653261 0.000000e+00 946
6 TraesCS4D01G077100 chr5D 97.830 507 10 1 1771 2276 410199221 410198715 0.000000e+00 874
7 TraesCS4D01G077100 chr1B 94.698 547 26 3 1731 2276 484225796 484225252 0.000000e+00 846
8 TraesCS4D01G077100 chr1B 94.516 547 27 3 1731 2276 484158801 484158257 0.000000e+00 841
9 TraesCS4D01G077100 chr5A 94.505 546 28 2 1731 2276 672737169 672736626 0.000000e+00 841
10 TraesCS4D01G077100 chr4A 93.967 547 32 1 1730 2276 621696187 621696732 0.000000e+00 826
11 TraesCS4D01G077100 chr4A 90.692 419 26 5 949 1358 545192953 545193367 1.540000e-151 545
12 TraesCS4D01G077100 chr4A 93.842 341 13 3 959 1291 545124416 545124756 7.250000e-140 507
13 TraesCS4D01G077100 chr4A 91.700 253 9 3 1322 1563 545124756 545125007 7.790000e-90 340
14 TraesCS4D01G077100 chr4A 91.250 160 13 1 1441 1599 545193446 545193605 1.370000e-52 217
15 TraesCS4D01G077100 chr4A 82.883 222 27 8 561 781 545192478 545192689 2.980000e-44 189
16 TraesCS4D01G077100 chr4A 96.491 114 3 1 795 907 545192670 545192783 1.070000e-43 187
17 TraesCS4D01G077100 chr3A 90.958 553 28 3 1724 2276 749673778 749674308 0.000000e+00 725
18 TraesCS4D01G077100 chr3B 91.078 538 23 9 1730 2244 154225249 154225784 0.000000e+00 704
19 TraesCS4D01G077100 chr4B 93.570 451 27 2 1726 2176 419658207 419658655 0.000000e+00 671
20 TraesCS4D01G077100 chr4B 91.981 424 21 2 900 1311 75652598 75652176 1.170000e-162 582
21 TraesCS4D01G077100 chr4B 93.607 219 12 2 1365 1581 75652154 75651936 2.180000e-85 326
22 TraesCS4D01G077100 chr4B 79.109 359 64 11 10 362 75653253 75652900 1.050000e-58 237
23 TraesCS4D01G077100 chr4B 78.846 364 45 12 546 907 75653001 75652668 1.370000e-52 217
24 TraesCS4D01G077100 chrUn 95.050 404 19 1 1838 2241 478403272 478403674 3.190000e-178 634
25 TraesCS4D01G077100 chrUn 79.279 333 59 10 36 362 249140032 249139704 8.180000e-55 224
26 TraesCS4D01G077100 chrUn 78.846 364 45 12 546 907 249139805 249139472 1.370000e-52 217


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 TraesCS4D01G077100 chr4D 51313959 51316234 2275 True 4204.0 4204 100.00000 1 2276 1 chr4D.!!$R1 2275
1 TraesCS4D01G077100 chr4D 51455380 51456233 853 True 468.0 749 92.26950 795 1531 2 chr4D.!!$R3 736
2 TraesCS4D01G077100 chr4D 51347670 51349465 1795 True 438.5 673 84.58300 900 1726 2 chr4D.!!$R2 826
3 TraesCS4D01G077100 chr3D 69653261 69653805 544 True 946.0 946 97.98500 1731 2276 1 chr3D.!!$R1 545
4 TraesCS4D01G077100 chr5D 410198715 410199221 506 True 874.0 874 97.83000 1771 2276 1 chr5D.!!$R1 505
5 TraesCS4D01G077100 chr1B 484225252 484225796 544 True 846.0 846 94.69800 1731 2276 1 chr1B.!!$R2 545
6 TraesCS4D01G077100 chr1B 484158257 484158801 544 True 841.0 841 94.51600 1731 2276 1 chr1B.!!$R1 545
7 TraesCS4D01G077100 chr5A 672736626 672737169 543 True 841.0 841 94.50500 1731 2276 1 chr5A.!!$R1 545
8 TraesCS4D01G077100 chr4A 621696187 621696732 545 False 826.0 826 93.96700 1730 2276 1 chr4A.!!$F1 546
9 TraesCS4D01G077100 chr4A 545124416 545125007 591 False 423.5 507 92.77100 959 1563 2 chr4A.!!$F2 604
10 TraesCS4D01G077100 chr4A 545192478 545193605 1127 False 284.5 545 90.32900 561 1599 4 chr4A.!!$F3 1038
11 TraesCS4D01G077100 chr3A 749673778 749674308 530 False 725.0 725 90.95800 1724 2276 1 chr3A.!!$F1 552
12 TraesCS4D01G077100 chr3B 154225249 154225784 535 False 704.0 704 91.07800 1730 2244 1 chr3B.!!$F1 514
13 TraesCS4D01G077100 chr4B 75651936 75653253 1317 True 340.5 582 85.88575 10 1581 4 chr4B.!!$R1 1571
14 TraesCS4D01G077100 chrUn 249139472 249140032 560 True 220.5 224 79.06250 36 907 2 chrUn.!!$R1 871

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
56 57 0.036765 TAGCTAAAGTGCACCCACCG 60.037 55.0 14.63 0.0 43.09 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1667 1953 0.035458 CGCTGGACAACCCTCTCTTT 59.965 55.0 0.0 0.0 35.38 2.52 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
21 22 3.393800 AGTTCTGTGACATGTTCTTCCG 58.606 45.455 0.00 0.00 0.00 4.30
22 23 3.131396 GTTCTGTGACATGTTCTTCCGT 58.869 45.455 0.00 0.00 0.00 4.69
34 35 6.479660 ACATGTTCTTCCGTTTTTACGAGTTA 59.520 34.615 0.00 0.00 34.64 2.24
39 40 7.801547 TCTTCCGTTTTTACGAGTTATGTAG 57.198 36.000 0.00 0.00 34.64 2.74
50 51 4.863131 ACGAGTTATGTAGCTAAAGTGCAC 59.137 41.667 9.40 9.40 34.99 4.57
56 57 0.036765 TAGCTAAAGTGCACCCACCG 60.037 55.000 14.63 0.00 43.09 4.94
63 64 4.947147 TGCACCCACCGGACAAGC 62.947 66.667 9.46 6.05 0.00 4.01
65 66 3.065306 CACCCACCGGACAAGCTA 58.935 61.111 9.46 0.00 0.00 3.32
68 69 1.153168 CCCACCGGACAAGCTATGG 60.153 63.158 9.46 1.59 0.00 2.74
69 70 1.819632 CCACCGGACAAGCTATGGC 60.820 63.158 9.46 0.00 35.73 4.40
92 93 0.179468 GCCGGTGCCATTTACTCCTA 59.821 55.000 1.90 0.00 0.00 2.94
120 121 2.916269 TGGACCACAATATCTGGGAACA 59.084 45.455 0.00 0.00 39.59 3.18
123 124 4.956075 GGACCACAATATCTGGGAACATTT 59.044 41.667 4.75 0.00 41.51 2.32
126 127 4.498009 CCACAATATCTGGGAACATTTCGC 60.498 45.833 0.00 0.00 41.51 4.70
128 129 1.948104 TATCTGGGAACATTTCGCGG 58.052 50.000 6.13 5.64 46.86 6.46
132 133 1.376812 GGGAACATTTCGCGGGAGT 60.377 57.895 6.13 0.00 32.80 3.85
139 140 2.287368 ACATTTCGCGGGAGTGTTTTTC 60.287 45.455 6.13 0.00 42.08 2.29
140 141 1.670791 TTTCGCGGGAGTGTTTTTCT 58.329 45.000 6.13 0.00 42.08 2.52
142 143 0.942410 TCGCGGGAGTGTTTTTCTCG 60.942 55.000 6.13 0.00 41.38 4.04
143 144 1.866925 GCGGGAGTGTTTTTCTCGG 59.133 57.895 0.00 0.00 38.92 4.63
144 145 0.883370 GCGGGAGTGTTTTTCTCGGT 60.883 55.000 0.00 0.00 38.92 4.69
145 146 0.865769 CGGGAGTGTTTTTCTCGGTG 59.134 55.000 0.00 0.00 34.96 4.94
148 149 2.289820 GGGAGTGTTTTTCTCGGTGAAC 59.710 50.000 0.00 0.00 33.88 3.18
151 152 2.606272 AGTGTTTTTCTCGGTGAACGTC 59.394 45.455 0.00 0.00 44.69 4.34
158 159 4.886247 TTCTCGGTGAACGTCAAATTTT 57.114 36.364 0.00 0.00 44.69 1.82
165 166 4.298332 GTGAACGTCAAATTTTCCATGCT 58.702 39.130 0.00 0.00 0.00 3.79
169 170 6.419413 TGAACGTCAAATTTTCCATGCTAAAC 59.581 34.615 0.00 0.00 0.00 2.01
211 212 6.532826 ACAATTTTGTAAGATTGGCCATGTT 58.467 32.000 6.09 4.49 40.16 2.71
216 217 4.188462 TGTAAGATTGGCCATGTTCGTAG 58.812 43.478 6.09 0.00 0.00 3.51
217 218 3.627395 AAGATTGGCCATGTTCGTAGA 57.373 42.857 6.09 0.00 0.00 2.59
231 232 2.333926 TCGTAGACGAAAACTGCCATG 58.666 47.619 1.51 0.00 46.30 3.66
237 238 2.484264 GACGAAAACTGCCATGTTAGCT 59.516 45.455 0.00 0.00 0.00 3.32
243 244 6.129194 CGAAAACTGCCATGTTAGCTAAAAAC 60.129 38.462 7.99 0.00 0.00 2.43
246 247 2.554462 TGCCATGTTAGCTAAAAACGCA 59.446 40.909 7.99 11.81 0.00 5.24
289 290 2.981400 AAAAATGCCGTTCGTTCGAT 57.019 40.000 0.00 0.00 0.00 3.59
291 292 1.434555 AAATGCCGTTCGTTCGATCA 58.565 45.000 0.00 2.76 0.00 2.92
292 293 1.651987 AATGCCGTTCGTTCGATCAT 58.348 45.000 0.00 4.54 0.00 2.45
295 296 1.209128 GCCGTTCGTTCGATCATGAT 58.791 50.000 8.25 8.25 0.00 2.45
297 298 2.459934 CCGTTCGTTCGATCATGATCA 58.540 47.619 30.13 17.21 37.69 2.92
298 299 2.469147 CCGTTCGTTCGATCATGATCAG 59.531 50.000 30.13 22.85 37.69 2.90
300 301 3.178618 CGTTCGTTCGATCATGATCAGAC 59.821 47.826 30.13 24.83 37.69 3.51
301 302 2.987046 TCGTTCGATCATGATCAGACG 58.013 47.619 33.34 33.34 42.23 4.18
302 303 2.047040 CGTTCGATCATGATCAGACGG 58.953 52.381 32.44 22.05 39.72 4.79
306 307 1.791204 CGATCATGATCAGACGGCTTG 59.209 52.381 30.13 10.88 37.69 4.01
307 308 2.141517 GATCATGATCAGACGGCTTGG 58.858 52.381 27.30 0.00 37.74 3.61
308 309 0.178767 TCATGATCAGACGGCTTGGG 59.821 55.000 0.09 0.00 0.00 4.12
309 310 0.816825 CATGATCAGACGGCTTGGGG 60.817 60.000 0.09 0.00 0.00 4.96
319 320 3.984732 GCTTGGGGCCCTTCCTGT 61.985 66.667 25.93 0.00 34.39 4.00
320 321 2.036256 CTTGGGGCCCTTCCTGTG 59.964 66.667 25.93 1.29 34.39 3.66
321 322 2.451493 TTGGGGCCCTTCCTGTGA 60.451 61.111 25.93 0.00 34.39 3.58
322 323 2.771328 CTTGGGGCCCTTCCTGTGAC 62.771 65.000 25.93 1.06 34.39 3.67
323 324 4.048470 GGGGCCCTTCCTGTGACC 62.048 72.222 24.38 0.00 34.39 4.02
324 325 2.936032 GGGCCCTTCCTGTGACCT 60.936 66.667 17.04 0.00 34.39 3.85
325 326 2.671682 GGCCCTTCCTGTGACCTC 59.328 66.667 0.00 0.00 0.00 3.85
328 329 2.660064 CCCTTCCTGTGACCTCCCG 61.660 68.421 0.00 0.00 0.00 5.14
329 330 2.266055 CTTCCTGTGACCTCCCGC 59.734 66.667 0.00 0.00 0.00 6.13
330 331 3.316573 CTTCCTGTGACCTCCCGCC 62.317 68.421 0.00 0.00 0.00 6.13
331 332 4.631740 TCCTGTGACCTCCCGCCA 62.632 66.667 0.00 0.00 0.00 5.69
333 334 4.087892 CTGTGACCTCCCGCCAGG 62.088 72.222 0.00 0.00 39.80 4.45
356 357 6.068473 GGAAACATTCCCCGTTATCATTAC 57.932 41.667 0.00 0.00 44.30 1.89
358 359 4.094830 ACATTCCCCGTTATCATTACCC 57.905 45.455 0.00 0.00 0.00 3.69
359 360 3.181437 ACATTCCCCGTTATCATTACCCC 60.181 47.826 0.00 0.00 0.00 4.95
360 361 2.500269 TCCCCGTTATCATTACCCCT 57.500 50.000 0.00 0.00 0.00 4.79
361 362 2.779163 TCCCCGTTATCATTACCCCTT 58.221 47.619 0.00 0.00 0.00 3.95
364 365 4.533311 TCCCCGTTATCATTACCCCTTATC 59.467 45.833 0.00 0.00 0.00 1.75
365 366 4.534897 CCCCGTTATCATTACCCCTTATCT 59.465 45.833 0.00 0.00 0.00 1.98
366 367 5.722923 CCCCGTTATCATTACCCCTTATCTA 59.277 44.000 0.00 0.00 0.00 1.98
368 369 6.127140 CCCGTTATCATTACCCCTTATCTAGG 60.127 46.154 0.00 0.00 44.33 3.02
380 381 5.796350 CCTTATCTAGGGAACGTTTTGTG 57.204 43.478 0.46 0.00 40.67 3.33
381 382 4.634443 CCTTATCTAGGGAACGTTTTGTGG 59.366 45.833 0.46 0.00 40.67 4.17
382 383 2.554370 TCTAGGGAACGTTTTGTGGG 57.446 50.000 0.46 0.00 0.00 4.61
383 384 2.048601 TCTAGGGAACGTTTTGTGGGA 58.951 47.619 0.46 0.00 0.00 4.37
384 385 2.038033 TCTAGGGAACGTTTTGTGGGAG 59.962 50.000 0.46 0.00 0.00 4.30
385 386 0.822121 AGGGAACGTTTTGTGGGAGC 60.822 55.000 0.46 0.00 0.00 4.70
386 387 1.281656 GGAACGTTTTGTGGGAGCG 59.718 57.895 0.46 0.00 0.00 5.03
387 388 1.441732 GGAACGTTTTGTGGGAGCGT 61.442 55.000 0.46 0.00 37.38 5.07
388 389 0.379316 GAACGTTTTGTGGGAGCGTT 59.621 50.000 0.46 0.00 46.34 4.84
389 390 0.812549 AACGTTTTGTGGGAGCGTTT 59.187 45.000 0.00 0.00 42.03 3.60
390 391 0.812549 ACGTTTTGTGGGAGCGTTTT 59.187 45.000 0.00 0.00 31.37 2.43
393 394 2.478879 CGTTTTGTGGGAGCGTTTTTCT 60.479 45.455 0.00 0.00 0.00 2.52
394 395 3.113322 GTTTTGTGGGAGCGTTTTTCTC 58.887 45.455 0.00 0.00 0.00 2.87
396 397 0.179067 TGTGGGAGCGTTTTTCTCGT 60.179 50.000 0.00 0.00 0.00 4.18
397 398 0.511653 GTGGGAGCGTTTTTCTCGTC 59.488 55.000 0.00 0.00 0.00 4.20
398 399 0.942410 TGGGAGCGTTTTTCTCGTCG 60.942 55.000 0.00 0.00 0.00 5.12
399 400 0.665369 GGGAGCGTTTTTCTCGTCGA 60.665 55.000 0.00 0.00 0.00 4.20
400 401 1.134226 GGAGCGTTTTTCTCGTCGAA 58.866 50.000 0.00 0.00 0.00 3.71
401 402 1.725164 GGAGCGTTTTTCTCGTCGAAT 59.275 47.619 0.00 0.00 0.00 3.34
402 403 2.472397 GGAGCGTTTTTCTCGTCGAATG 60.472 50.000 0.00 0.00 0.00 2.67
403 404 2.132762 AGCGTTTTTCTCGTCGAATGT 58.867 42.857 0.00 0.00 0.00 2.71
404 405 2.155155 AGCGTTTTTCTCGTCGAATGTC 59.845 45.455 0.00 0.00 0.00 3.06
406 407 3.602946 GCGTTTTTCTCGTCGAATGTCAA 60.603 43.478 0.00 0.00 0.00 3.18
408 409 5.137403 CGTTTTTCTCGTCGAATGTCAAAT 58.863 37.500 0.00 0.00 0.00 2.32
410 411 6.140108 CGTTTTTCTCGTCGAATGTCAAATTT 59.860 34.615 0.00 0.00 0.00 1.82
411 412 7.305190 CGTTTTTCTCGTCGAATGTCAAATTTT 60.305 33.333 0.00 0.00 0.00 1.82
412 413 7.603297 TTTTCTCGTCGAATGTCAAATTTTC 57.397 32.000 0.00 0.00 0.00 2.29
413 414 5.277601 TCTCGTCGAATGTCAAATTTTCC 57.722 39.130 0.00 0.00 0.00 3.13
414 415 4.752604 TCTCGTCGAATGTCAAATTTTCCA 59.247 37.500 0.00 0.00 0.00 3.53
415 416 5.411361 TCTCGTCGAATGTCAAATTTTCCAT 59.589 36.000 0.00 0.00 0.00 3.41
416 417 5.389778 TCGTCGAATGTCAAATTTTCCATG 58.610 37.500 0.00 0.00 0.00 3.66
417 418 4.030529 CGTCGAATGTCAAATTTTCCATGC 59.969 41.667 0.00 0.00 0.00 4.06
420 421 4.689812 CGAATGTCAAATTTTCCATGCCAA 59.310 37.500 0.00 0.00 0.00 4.52
422 423 5.945466 ATGTCAAATTTTCCATGCCAAAC 57.055 34.783 0.00 0.00 0.00 2.93
424 425 4.133078 GTCAAATTTTCCATGCCAAACCA 58.867 39.130 0.00 0.00 0.00 3.67
425 426 4.578105 GTCAAATTTTCCATGCCAAACCAA 59.422 37.500 0.00 0.00 0.00 3.67
426 427 4.578105 TCAAATTTTCCATGCCAAACCAAC 59.422 37.500 0.00 0.00 0.00 3.77
427 428 4.436113 AATTTTCCATGCCAAACCAACT 57.564 36.364 0.00 0.00 0.00 3.16
428 429 5.559148 AATTTTCCATGCCAAACCAACTA 57.441 34.783 0.00 0.00 0.00 2.24
429 430 5.559148 ATTTTCCATGCCAAACCAACTAA 57.441 34.783 0.00 0.00 0.00 2.24
430 431 5.359194 TTTTCCATGCCAAACCAACTAAA 57.641 34.783 0.00 0.00 0.00 1.85
431 432 4.599047 TTCCATGCCAAACCAACTAAAG 57.401 40.909 0.00 0.00 0.00 1.85
432 433 3.571590 TCCATGCCAAACCAACTAAAGT 58.428 40.909 0.00 0.00 0.00 2.66
433 434 3.964031 TCCATGCCAAACCAACTAAAGTT 59.036 39.130 0.00 0.00 39.12 2.66
436 437 4.911514 TGCCAAACCAACTAAAGTTCTC 57.088 40.909 0.00 0.00 35.83 2.87
437 438 4.274147 TGCCAAACCAACTAAAGTTCTCA 58.726 39.130 0.00 0.00 35.83 3.27
438 439 4.892934 TGCCAAACCAACTAAAGTTCTCAT 59.107 37.500 0.00 0.00 35.83 2.90
439 440 5.221224 TGCCAAACCAACTAAAGTTCTCATG 60.221 40.000 0.00 0.00 35.83 3.07
440 441 5.009610 GCCAAACCAACTAAAGTTCTCATGA 59.990 40.000 0.00 0.00 35.83 3.07
442 443 7.094377 GCCAAACCAACTAAAGTTCTCATGATA 60.094 37.037 0.00 0.00 35.83 2.15
443 444 8.792633 CCAAACCAACTAAAGTTCTCATGATAA 58.207 33.333 0.00 0.00 35.83 1.75
460 461 9.806203 CTCATGATAATTTTGTAAGATTTGCCA 57.194 29.630 0.00 0.00 0.00 4.92
464 465 9.941325 TGATAATTTTGTAAGATTTGCCATGTT 57.059 25.926 0.00 0.00 0.00 2.71
466 467 6.949578 ATTTTGTAAGATTTGCCATGTTCG 57.050 33.333 0.00 0.00 0.00 3.95
467 468 3.485947 TGTAAGATTTGCCATGTTCGC 57.514 42.857 0.00 0.00 0.00 4.70
469 470 2.642139 AAGATTTGCCATGTTCGCAG 57.358 45.000 0.00 0.00 37.57 5.18
470 471 0.813184 AGATTTGCCATGTTCGCAGG 59.187 50.000 0.00 0.00 37.57 4.85
482 483 2.635079 TCGCAGGCGAAAATTTCCA 58.365 47.368 14.68 0.00 46.01 3.53
483 484 1.173043 TCGCAGGCGAAAATTTCCAT 58.827 45.000 14.68 0.00 46.01 3.41
484 485 1.135431 TCGCAGGCGAAAATTTCCATG 60.135 47.619 14.68 2.88 46.01 3.66
486 487 2.670789 CGCAGGCGAAAATTTCCATGAA 60.671 45.455 8.15 0.00 42.83 2.57
488 489 2.925563 CAGGCGAAAATTTCCATGAAGC 59.074 45.455 0.00 0.00 0.00 3.86
489 490 2.827921 AGGCGAAAATTTCCATGAAGCT 59.172 40.909 0.00 0.00 0.00 3.74
490 491 3.119352 AGGCGAAAATTTCCATGAAGCTC 60.119 43.478 0.00 0.00 0.00 4.09
491 492 3.367292 GGCGAAAATTTCCATGAAGCTCA 60.367 43.478 0.00 0.00 0.00 4.26
492 493 4.236935 GCGAAAATTTCCATGAAGCTCAA 58.763 39.130 0.00 0.00 0.00 3.02
493 494 4.685628 GCGAAAATTTCCATGAAGCTCAAA 59.314 37.500 0.00 0.00 0.00 2.69
494 495 5.177327 GCGAAAATTTCCATGAAGCTCAAAA 59.823 36.000 0.00 0.00 0.00 2.44
527 528 5.917541 TTTTGCCACGTTTTGTAAAAACA 57.082 30.435 14.11 0.00 0.00 2.83
528 529 5.917541 TTTGCCACGTTTTGTAAAAACAA 57.082 30.435 14.11 0.00 0.00 2.83
529 530 5.917541 TTGCCACGTTTTGTAAAAACAAA 57.082 30.435 14.11 0.00 37.77 2.83
530 531 6.481954 TTGCCACGTTTTGTAAAAACAAAT 57.518 29.167 14.11 0.00 39.07 2.32
531 532 6.481954 TGCCACGTTTTGTAAAAACAAATT 57.518 29.167 14.11 0.00 39.07 1.82
533 534 7.453838 TGCCACGTTTTGTAAAAACAAATTAC 58.546 30.769 14.11 1.26 39.07 1.89
534 535 6.900828 GCCACGTTTTGTAAAAACAAATTACC 59.099 34.615 14.11 0.00 39.07 2.85
535 536 7.111768 CCACGTTTTGTAAAAACAAATTACCG 58.888 34.615 14.11 7.55 39.07 4.02
537 538 8.160976 CACGTTTTGTAAAAACAAATTACCGTT 58.839 29.630 14.11 0.00 39.07 4.44
539 540 8.976584 CGTTTTGTAAAAACAAATTACCGTTTG 58.023 29.630 14.11 0.00 43.11 2.93
551 552 8.665685 ACAAATTACCGTTTGTTTATTTGCAAA 58.334 25.926 15.44 15.44 46.96 3.68
576 577 7.790861 AAAAATTACCGTTTGTTCGATCATC 57.209 32.000 0.00 0.00 0.00 2.92
589 590 1.791204 CGATCATCATCAGACGGCTTG 59.209 52.381 0.00 0.00 0.00 4.01
592 593 0.816825 CATCATCAGACGGCTTGGGG 60.817 60.000 0.00 0.00 0.00 4.96
613 614 1.639298 GCGTTCATGTGACCTGCCTC 61.639 60.000 0.00 0.00 0.00 4.70
617 618 0.915872 TCATGTGACCTGCCTCCCAT 60.916 55.000 0.00 0.00 0.00 4.00
643 645 3.181418 ACATTCCCCATTATCATGTCCCC 60.181 47.826 0.00 0.00 0.00 4.81
644 646 2.531177 TCCCCATTATCATGTCCCCT 57.469 50.000 0.00 0.00 0.00 4.79
645 647 2.800656 TCCCCATTATCATGTCCCCTT 58.199 47.619 0.00 0.00 0.00 3.95
646 648 3.138518 TCCCCATTATCATGTCCCCTTT 58.861 45.455 0.00 0.00 0.00 3.11
647 649 3.535590 TCCCCATTATCATGTCCCCTTTT 59.464 43.478 0.00 0.00 0.00 2.27
649 651 5.196779 TCCCCATTATCATGTCCCCTTTTTA 59.803 40.000 0.00 0.00 0.00 1.52
650 652 5.902431 CCCCATTATCATGTCCCCTTTTTAA 59.098 40.000 0.00 0.00 0.00 1.52
651 653 6.558394 CCCCATTATCATGTCCCCTTTTTAAT 59.442 38.462 0.00 0.00 0.00 1.40
685 687 5.526111 ACTCGAATGAAGAAAACGAAAAGGA 59.474 36.000 0.00 0.00 32.85 3.36
689 691 6.303259 CGAATGAAGAAAACGAAAAGGACATC 59.697 38.462 0.00 0.00 0.00 3.06
722 724 5.593095 ACGACCTGTTTCACATATAGCTCTA 59.407 40.000 0.00 0.00 0.00 2.43
737 739 0.658897 CTCTACGAGCGGAGAACTCC 59.341 60.000 6.26 10.51 46.18 3.85
777 779 0.392706 ACAGGACGTGCATGAACTGA 59.607 50.000 28.39 0.00 31.50 3.41
778 780 0.792640 CAGGACGTGCATGAACTGAC 59.207 55.000 21.76 0.00 0.00 3.51
779 781 0.681733 AGGACGTGCATGAACTGACT 59.318 50.000 14.17 0.00 0.00 3.41
781 783 1.873591 GGACGTGCATGAACTGACTTT 59.126 47.619 14.17 0.00 0.00 2.66
783 785 3.243068 GGACGTGCATGAACTGACTTTTT 60.243 43.478 14.17 0.00 0.00 1.94
1003 1232 0.871722 CAGGACGCGAACCAAAATGA 59.128 50.000 15.93 0.00 0.00 2.57
1023 1252 2.437343 CGCTGCTTTCGTCTCGTCC 61.437 63.158 0.00 0.00 0.00 4.79
1298 1527 1.795768 CAAGCACTTCCGCTGACTTA 58.204 50.000 0.00 0.00 42.89 2.24
1305 1534 2.271800 CTTCCGCTGACTTACATCCAC 58.728 52.381 0.00 0.00 0.00 4.02
1313 1542 3.512496 TGACTTACATCCACCCAGTGTA 58.488 45.455 0.00 0.00 0.00 2.90
1314 1543 3.259876 TGACTTACATCCACCCAGTGTAC 59.740 47.826 0.00 0.00 0.00 2.90
1315 1544 2.232941 ACTTACATCCACCCAGTGTACG 59.767 50.000 0.00 0.00 0.00 3.67
1316 1545 1.927487 TACATCCACCCAGTGTACGT 58.073 50.000 0.00 0.00 0.00 3.57
1385 1621 1.654023 GGACGGGCTTTGGATTTCGG 61.654 60.000 0.00 0.00 0.00 4.30
1473 1753 7.301054 ACAGATTCTTTGTCGCTATTTTCAAG 58.699 34.615 0.00 0.00 0.00 3.02
1559 1845 1.689813 TGAACCGAGGCAAGACTGTAA 59.310 47.619 0.00 0.00 0.00 2.41
1563 1849 3.074412 ACCGAGGCAAGACTGTAATTTG 58.926 45.455 0.00 0.00 0.00 2.32
1619 1905 3.156293 TCTACACAATTGCATGCAACCT 58.844 40.909 34.10 21.51 38.88 3.50
1622 1908 3.543665 ACACAATTGCATGCAACCTTTT 58.456 36.364 34.10 21.56 38.88 2.27
1623 1909 3.946558 ACACAATTGCATGCAACCTTTTT 59.053 34.783 34.10 21.19 38.88 1.94
1648 1934 9.905713 TTTTTCTATCTAGAATACCACAAGCAT 57.094 29.630 0.00 0.00 41.52 3.79
1649 1935 8.893219 TTTCTATCTAGAATACCACAAGCATG 57.107 34.615 0.00 0.00 41.52 4.06
1650 1936 6.459066 TCTATCTAGAATACCACAAGCATGC 58.541 40.000 10.51 10.51 0.00 4.06
1651 1937 4.486125 TCTAGAATACCACAAGCATGCA 57.514 40.909 21.98 0.00 0.00 3.96
1652 1938 4.842574 TCTAGAATACCACAAGCATGCAA 58.157 39.130 21.98 0.00 0.00 4.08
1653 1939 5.252547 TCTAGAATACCACAAGCATGCAAA 58.747 37.500 21.98 0.00 0.00 3.68
1654 1940 5.887598 TCTAGAATACCACAAGCATGCAAAT 59.112 36.000 21.98 2.20 0.00 2.32
1655 1941 5.002464 AGAATACCACAAGCATGCAAATC 57.998 39.130 21.98 4.75 0.00 2.17
1656 1942 4.463539 AGAATACCACAAGCATGCAAATCA 59.536 37.500 21.98 0.00 0.00 2.57
1657 1943 5.128171 AGAATACCACAAGCATGCAAATCAT 59.872 36.000 21.98 3.53 35.31 2.45
1658 1944 6.321945 AGAATACCACAAGCATGCAAATCATA 59.678 34.615 21.98 5.83 33.19 2.15
1659 1945 6.659745 ATACCACAAGCATGCAAATCATAT 57.340 33.333 21.98 7.96 33.19 1.78
1660 1946 7.764141 ATACCACAAGCATGCAAATCATATA 57.236 32.000 21.98 2.86 33.19 0.86
1661 1947 6.659745 ACCACAAGCATGCAAATCATATAT 57.340 33.333 21.98 0.00 33.19 0.86
1662 1948 7.058023 ACCACAAGCATGCAAATCATATATT 57.942 32.000 21.98 0.00 33.19 1.28
1663 1949 7.149973 ACCACAAGCATGCAAATCATATATTC 58.850 34.615 21.98 0.00 33.19 1.75
1664 1950 7.149307 CCACAAGCATGCAAATCATATATTCA 58.851 34.615 21.98 0.00 33.19 2.57
1665 1951 7.817478 CCACAAGCATGCAAATCATATATTCAT 59.183 33.333 21.98 0.00 33.19 2.57
1666 1952 9.849166 CACAAGCATGCAAATCATATATTCATA 57.151 29.630 21.98 0.00 33.19 2.15
1683 1969 5.576563 TTCATAAAAGAGAGGGTTGTCCA 57.423 39.130 0.00 0.00 38.24 4.02
1684 1970 5.165961 TCATAAAAGAGAGGGTTGTCCAG 57.834 43.478 0.00 0.00 38.24 3.86
1685 1971 2.278332 AAAAGAGAGGGTTGTCCAGC 57.722 50.000 0.00 0.00 38.24 4.85
1686 1972 0.035458 AAAGAGAGGGTTGTCCAGCG 59.965 55.000 0.00 0.00 38.24 5.18
1687 1973 2.435059 GAGAGGGTTGTCCAGCGC 60.435 66.667 0.00 0.00 38.24 5.92
1688 1974 3.240134 GAGAGGGTTGTCCAGCGCA 62.240 63.158 11.47 0.00 38.24 6.09
1689 1975 2.045926 GAGGGTTGTCCAGCGCAT 60.046 61.111 11.47 0.00 38.24 4.73
1690 1976 1.675641 GAGGGTTGTCCAGCGCATT 60.676 57.895 11.47 0.00 38.24 3.56
1691 1977 0.392461 GAGGGTTGTCCAGCGCATTA 60.392 55.000 11.47 0.00 38.24 1.90
1692 1978 0.676782 AGGGTTGTCCAGCGCATTAC 60.677 55.000 11.47 4.43 38.24 1.89
1693 1979 0.958382 GGGTTGTCCAGCGCATTACA 60.958 55.000 11.47 7.46 35.00 2.41
1694 1980 1.094785 GGTTGTCCAGCGCATTACAT 58.905 50.000 11.47 0.00 0.00 2.29
1695 1981 1.064060 GGTTGTCCAGCGCATTACATC 59.936 52.381 11.47 9.15 0.00 3.06
1696 1982 1.737236 GTTGTCCAGCGCATTACATCA 59.263 47.619 11.47 0.00 0.00 3.07
1697 1983 2.330440 TGTCCAGCGCATTACATCAT 57.670 45.000 11.47 0.00 0.00 2.45
1698 1984 2.642427 TGTCCAGCGCATTACATCATT 58.358 42.857 11.47 0.00 0.00 2.57
1699 1985 3.016031 TGTCCAGCGCATTACATCATTT 58.984 40.909 11.47 0.00 0.00 2.32
1700 1986 3.181498 TGTCCAGCGCATTACATCATTTG 60.181 43.478 11.47 0.00 0.00 2.32
1701 1987 3.016031 TCCAGCGCATTACATCATTTGT 58.984 40.909 11.47 0.00 42.62 2.83
1702 1988 3.110358 CCAGCGCATTACATCATTTGTG 58.890 45.455 11.47 0.00 39.48 3.33
1703 1989 3.427909 CCAGCGCATTACATCATTTGTGT 60.428 43.478 11.47 0.00 39.48 3.72
1704 1990 3.787634 CAGCGCATTACATCATTTGTGTC 59.212 43.478 11.47 0.00 39.48 3.67
1705 1991 3.108144 GCGCATTACATCATTTGTGTCC 58.892 45.455 0.30 0.00 39.48 4.02
1706 1992 3.427368 GCGCATTACATCATTTGTGTCCA 60.427 43.478 0.30 0.00 39.48 4.02
1707 1993 4.731720 CGCATTACATCATTTGTGTCCAA 58.268 39.130 0.00 0.00 39.48 3.53
1708 1994 5.159925 CGCATTACATCATTTGTGTCCAAA 58.840 37.500 0.00 0.00 44.27 3.28
1719 2005 5.731599 TTTGTGTCCAAATGCAAACATTC 57.268 34.783 0.00 0.00 45.90 2.67
1720 2006 4.397481 TGTGTCCAAATGCAAACATTCA 57.603 36.364 0.00 0.00 45.90 2.57
1721 2007 4.958509 TGTGTCCAAATGCAAACATTCAT 58.041 34.783 0.00 0.00 45.90 2.57
1722 2008 4.989797 TGTGTCCAAATGCAAACATTCATC 59.010 37.500 0.00 0.00 45.90 2.92
1725 2011 4.389687 GTCCAAATGCAAACATTCATCCAC 59.610 41.667 0.00 0.00 45.90 4.02
1974 2283 5.907866 TTAAAATGGCCTAAGTAAGCACC 57.092 39.130 3.32 0.00 0.00 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 3.469008 ACGGAAGAACATGTCACAGAA 57.531 42.857 0.00 0.00 0.00 3.02
3 4 3.469008 AACGGAAGAACATGTCACAGA 57.531 42.857 0.00 0.00 0.00 3.41
4 5 4.552166 AAAACGGAAGAACATGTCACAG 57.448 40.909 0.00 0.00 0.00 3.66
6 7 4.901881 CGTAAAAACGGAAGAACATGTCAC 59.098 41.667 0.00 0.00 0.00 3.67
9 10 4.812626 ACTCGTAAAAACGGAAGAACATGT 59.187 37.500 0.00 0.00 0.00 3.21
10 11 5.338614 ACTCGTAAAAACGGAAGAACATG 57.661 39.130 0.00 0.00 0.00 3.21
11 12 5.996669 AACTCGTAAAAACGGAAGAACAT 57.003 34.783 0.00 0.00 0.00 2.71
14 15 7.148755 GCTACATAACTCGTAAAAACGGAAGAA 60.149 37.037 0.00 0.00 0.00 2.52
16 17 6.309737 AGCTACATAACTCGTAAAAACGGAAG 59.690 38.462 0.00 0.00 0.00 3.46
17 18 6.158598 AGCTACATAACTCGTAAAAACGGAA 58.841 36.000 0.00 0.00 0.00 4.30
18 19 5.713025 AGCTACATAACTCGTAAAAACGGA 58.287 37.500 0.00 0.00 0.00 4.69
19 20 7.510428 TTAGCTACATAACTCGTAAAAACGG 57.490 36.000 0.00 0.00 0.00 4.44
21 22 9.737025 CACTTTAGCTACATAACTCGTAAAAAC 57.263 33.333 0.00 0.00 0.00 2.43
22 23 8.437742 GCACTTTAGCTACATAACTCGTAAAAA 58.562 33.333 0.00 0.00 0.00 1.94
34 35 2.618045 GGTGGGTGCACTTTAGCTACAT 60.618 50.000 17.98 0.00 34.99 2.29
39 40 2.332654 CCGGTGGGTGCACTTTAGC 61.333 63.158 17.98 11.57 0.00 3.09
50 51 1.153168 CCATAGCTTGTCCGGTGGG 60.153 63.158 0.00 0.00 0.00 4.61
56 57 2.101700 GCAGTGCCATAGCTTGTCC 58.898 57.895 2.85 0.00 40.80 4.02
75 76 6.877611 ATAAAATAGGAGTAAATGGCACCG 57.122 37.500 0.00 0.00 0.00 4.94
92 93 7.361438 TCCCAGATATTGTGGTCCAATAAAAT 58.639 34.615 0.00 0.00 46.36 1.82
115 116 0.953960 ACACTCCCGCGAAATGTTCC 60.954 55.000 8.23 0.00 0.00 3.62
120 121 2.225727 GAGAAAAACACTCCCGCGAAAT 59.774 45.455 8.23 0.00 0.00 2.17
123 124 0.942410 CGAGAAAAACACTCCCGCGA 60.942 55.000 8.23 0.00 0.00 5.87
126 127 0.865769 CACCGAGAAAAACACTCCCG 59.134 55.000 0.00 0.00 0.00 5.14
128 129 2.033151 CGTTCACCGAGAAAAACACTCC 60.033 50.000 0.00 0.00 38.13 3.85
132 133 2.619147 TGACGTTCACCGAGAAAAACA 58.381 42.857 0.00 0.00 38.13 2.83
139 140 3.002862 TGGAAAATTTGACGTTCACCGAG 59.997 43.478 0.00 0.00 40.70 4.63
140 141 2.943690 TGGAAAATTTGACGTTCACCGA 59.056 40.909 0.00 0.00 40.70 4.69
142 143 3.428534 GCATGGAAAATTTGACGTTCACC 59.571 43.478 0.00 0.00 0.00 4.02
143 144 4.298332 AGCATGGAAAATTTGACGTTCAC 58.702 39.130 0.00 0.00 0.00 3.18
144 145 4.582701 AGCATGGAAAATTTGACGTTCA 57.417 36.364 0.00 0.00 0.00 3.18
145 146 6.128929 GGTTTAGCATGGAAAATTTGACGTTC 60.129 38.462 0.00 0.00 0.00 3.95
148 149 5.226396 TGGTTTAGCATGGAAAATTTGACG 58.774 37.500 0.00 0.00 0.00 4.35
151 152 8.600449 TTAGTTGGTTTAGCATGGAAAATTTG 57.400 30.769 0.00 0.00 0.00 2.32
211 212 4.559099 TAACATGGCAGTTTTCGTCTACGA 60.559 41.667 0.14 0.14 38.51 3.43
216 217 2.484264 AGCTAACATGGCAGTTTTCGTC 59.516 45.455 0.00 0.00 33.07 4.20
217 218 2.504367 AGCTAACATGGCAGTTTTCGT 58.496 42.857 0.00 0.00 33.07 3.85
271 272 1.801771 TGATCGAACGAACGGCATTTT 59.198 42.857 0.12 0.00 0.00 1.82
272 273 1.434555 TGATCGAACGAACGGCATTT 58.565 45.000 0.12 0.00 0.00 2.32
273 274 1.327460 CATGATCGAACGAACGGCATT 59.673 47.619 0.12 0.00 31.04 3.56
276 277 1.190323 GATCATGATCGAACGAACGGC 59.810 52.381 19.55 0.00 0.00 5.68
277 278 2.459934 TGATCATGATCGAACGAACGG 58.540 47.619 26.52 0.00 40.63 4.44
280 281 3.363178 CGTCTGATCATGATCGAACGAA 58.637 45.455 35.56 18.71 44.19 3.85
281 282 2.287009 CCGTCTGATCATGATCGAACGA 60.287 50.000 37.91 25.85 44.19 3.85
283 284 1.789464 GCCGTCTGATCATGATCGAAC 59.211 52.381 26.52 23.81 40.63 3.95
284 285 1.683385 AGCCGTCTGATCATGATCGAA 59.317 47.619 26.52 16.30 40.63 3.71
285 286 1.322442 AGCCGTCTGATCATGATCGA 58.678 50.000 26.52 22.68 40.63 3.59
287 288 2.141517 CCAAGCCGTCTGATCATGATC 58.858 52.381 25.91 25.91 38.29 2.92
289 290 0.178767 CCCAAGCCGTCTGATCATGA 59.821 55.000 0.00 0.00 0.00 3.07
291 292 1.528824 CCCCAAGCCGTCTGATCAT 59.471 57.895 0.00 0.00 0.00 2.45
292 293 2.989639 CCCCAAGCCGTCTGATCA 59.010 61.111 0.00 0.00 0.00 2.92
302 303 3.984732 ACAGGAAGGGCCCCAAGC 61.985 66.667 21.43 5.03 42.60 4.01
306 307 4.048470 GGTCACAGGAAGGGCCCC 62.048 72.222 21.43 3.11 37.37 5.80
307 308 2.936032 AGGTCACAGGAAGGGCCC 60.936 66.667 16.46 16.46 37.37 5.80
308 309 2.671682 GAGGTCACAGGAAGGGCC 59.328 66.667 0.00 0.00 0.00 5.80
309 310 2.671682 GGAGGTCACAGGAAGGGC 59.328 66.667 0.00 0.00 0.00 5.19
312 313 2.266055 GCGGGAGGTCACAGGAAG 59.734 66.667 0.00 0.00 0.00 3.46
314 315 4.631740 TGGCGGGAGGTCACAGGA 62.632 66.667 0.00 0.00 0.00 3.86
315 316 4.087892 CTGGCGGGAGGTCACAGG 62.088 72.222 0.00 0.00 0.00 4.00
316 317 4.087892 CCTGGCGGGAGGTCACAG 62.088 72.222 6.48 0.00 37.23 3.66
334 335 5.009310 GGGTAATGATAACGGGGAATGTTTC 59.991 44.000 0.00 0.00 0.00 2.78
336 337 4.466827 GGGTAATGATAACGGGGAATGTT 58.533 43.478 0.00 0.00 0.00 2.71
337 338 3.181437 GGGGTAATGATAACGGGGAATGT 60.181 47.826 0.00 0.00 0.00 2.71
338 339 3.073946 AGGGGTAATGATAACGGGGAATG 59.926 47.826 0.00 0.00 0.00 2.67
339 340 3.332968 AGGGGTAATGATAACGGGGAAT 58.667 45.455 0.00 0.00 0.00 3.01
340 341 2.779163 AGGGGTAATGATAACGGGGAA 58.221 47.619 0.00 0.00 0.00 3.97
341 342 2.500269 AGGGGTAATGATAACGGGGA 57.500 50.000 0.00 0.00 0.00 4.81
342 343 4.534897 AGATAAGGGGTAATGATAACGGGG 59.465 45.833 0.00 0.00 0.00 5.73
343 344 5.757099 AGATAAGGGGTAATGATAACGGG 57.243 43.478 0.00 0.00 0.00 5.28
344 345 6.875076 CCTAGATAAGGGGTAATGATAACGG 58.125 44.000 0.00 0.00 42.32 4.44
358 359 4.634443 CCACAAAACGTTCCCTAGATAAGG 59.366 45.833 0.00 0.00 46.09 2.69
359 360 4.634443 CCCACAAAACGTTCCCTAGATAAG 59.366 45.833 0.00 0.00 0.00 1.73
360 361 4.286549 TCCCACAAAACGTTCCCTAGATAA 59.713 41.667 0.00 0.00 0.00 1.75
361 362 3.839490 TCCCACAAAACGTTCCCTAGATA 59.161 43.478 0.00 0.00 0.00 1.98
364 365 2.423577 CTCCCACAAAACGTTCCCTAG 58.576 52.381 0.00 0.00 0.00 3.02
365 366 1.543871 GCTCCCACAAAACGTTCCCTA 60.544 52.381 0.00 0.00 0.00 3.53
366 367 0.822121 GCTCCCACAAAACGTTCCCT 60.822 55.000 0.00 0.00 0.00 4.20
368 369 1.281656 CGCTCCCACAAAACGTTCC 59.718 57.895 0.00 0.00 0.00 3.62
369 370 0.379316 AACGCTCCCACAAAACGTTC 59.621 50.000 0.00 0.00 42.77 3.95
371 372 0.812549 AAAACGCTCCCACAAAACGT 59.187 45.000 0.00 0.00 38.88 3.99
372 373 1.849829 GAAAAACGCTCCCACAAAACG 59.150 47.619 0.00 0.00 0.00 3.60
373 374 3.113322 GAGAAAAACGCTCCCACAAAAC 58.887 45.455 0.00 0.00 0.00 2.43
374 375 2.223386 CGAGAAAAACGCTCCCACAAAA 60.223 45.455 0.00 0.00 0.00 2.44
375 376 1.332375 CGAGAAAAACGCTCCCACAAA 59.668 47.619 0.00 0.00 0.00 2.83
376 377 0.941542 CGAGAAAAACGCTCCCACAA 59.058 50.000 0.00 0.00 0.00 3.33
380 381 0.665369 TCGACGAGAAAAACGCTCCC 60.665 55.000 0.00 0.00 0.00 4.30
381 382 1.134226 TTCGACGAGAAAAACGCTCC 58.866 50.000 0.00 0.00 35.61 4.70
382 383 2.155155 ACATTCGACGAGAAAAACGCTC 59.845 45.455 0.00 0.00 42.91 5.03
383 384 2.132762 ACATTCGACGAGAAAAACGCT 58.867 42.857 0.00 0.00 42.91 5.07
384 385 2.097104 TGACATTCGACGAGAAAAACGC 60.097 45.455 0.00 0.00 42.91 4.84
385 386 3.763756 TGACATTCGACGAGAAAAACG 57.236 42.857 0.00 0.00 42.91 3.60
386 387 6.969669 AATTTGACATTCGACGAGAAAAAC 57.030 33.333 0.00 0.00 42.91 2.43
387 388 7.166804 GGAAAATTTGACATTCGACGAGAAAAA 59.833 33.333 0.00 0.00 42.91 1.94
388 389 6.635239 GGAAAATTTGACATTCGACGAGAAAA 59.365 34.615 0.00 0.00 42.91 2.29
389 390 6.140110 GGAAAATTTGACATTCGACGAGAAA 58.860 36.000 0.00 0.00 42.91 2.52
390 391 5.237561 TGGAAAATTTGACATTCGACGAGAA 59.762 36.000 0.00 0.00 43.93 2.87
393 394 5.389778 CATGGAAAATTTGACATTCGACGA 58.610 37.500 0.00 0.00 0.00 4.20
394 395 4.030529 GCATGGAAAATTTGACATTCGACG 59.969 41.667 5.41 0.00 0.00 5.12
396 397 4.021632 TGGCATGGAAAATTTGACATTCGA 60.022 37.500 5.41 0.00 0.00 3.71
397 398 4.244066 TGGCATGGAAAATTTGACATTCG 58.756 39.130 5.41 0.00 0.00 3.34
398 399 6.372981 GTTTGGCATGGAAAATTTGACATTC 58.627 36.000 5.41 2.06 0.00 2.67
399 400 5.241285 GGTTTGGCATGGAAAATTTGACATT 59.759 36.000 5.41 0.00 0.00 2.71
400 401 4.761227 GGTTTGGCATGGAAAATTTGACAT 59.239 37.500 0.00 0.00 0.00 3.06
401 402 4.133078 GGTTTGGCATGGAAAATTTGACA 58.867 39.130 0.00 0.00 0.00 3.58
402 403 4.133078 TGGTTTGGCATGGAAAATTTGAC 58.867 39.130 0.00 0.00 0.00 3.18
403 404 4.428294 TGGTTTGGCATGGAAAATTTGA 57.572 36.364 0.00 0.00 0.00 2.69
404 405 4.579753 AGTTGGTTTGGCATGGAAAATTTG 59.420 37.500 0.00 0.00 0.00 2.32
406 407 4.436113 AGTTGGTTTGGCATGGAAAATT 57.564 36.364 0.00 0.00 0.00 1.82
408 409 5.104735 ACTTTAGTTGGTTTGGCATGGAAAA 60.105 36.000 0.00 0.00 0.00 2.29
410 411 3.964031 ACTTTAGTTGGTTTGGCATGGAA 59.036 39.130 0.00 0.00 0.00 3.53
411 412 3.571590 ACTTTAGTTGGTTTGGCATGGA 58.428 40.909 0.00 0.00 0.00 3.41
412 413 4.039124 AGAACTTTAGTTGGTTTGGCATGG 59.961 41.667 0.00 0.00 38.56 3.66
413 414 5.200368 AGAACTTTAGTTGGTTTGGCATG 57.800 39.130 0.00 0.00 38.56 4.06
414 415 4.892934 TGAGAACTTTAGTTGGTTTGGCAT 59.107 37.500 0.00 0.00 38.56 4.40
415 416 4.274147 TGAGAACTTTAGTTGGTTTGGCA 58.726 39.130 0.00 0.00 38.56 4.92
416 417 4.911514 TGAGAACTTTAGTTGGTTTGGC 57.088 40.909 0.00 0.00 38.56 4.52
417 418 6.633500 TCATGAGAACTTTAGTTGGTTTGG 57.367 37.500 0.00 0.00 38.56 3.28
438 439 9.941325 AACATGGCAAATCTTACAAAATTATCA 57.059 25.926 0.00 0.00 0.00 2.15
440 441 9.086336 CGAACATGGCAAATCTTACAAAATTAT 57.914 29.630 0.00 0.00 0.00 1.28
442 443 6.128580 GCGAACATGGCAAATCTTACAAAATT 60.129 34.615 0.00 0.00 0.00 1.82
443 444 5.348451 GCGAACATGGCAAATCTTACAAAAT 59.652 36.000 0.00 0.00 0.00 1.82
445 446 4.233789 GCGAACATGGCAAATCTTACAAA 58.766 39.130 0.00 0.00 0.00 2.83
446 447 3.254411 TGCGAACATGGCAAATCTTACAA 59.746 39.130 0.00 0.00 37.49 2.41
448 449 3.429085 CTGCGAACATGGCAAATCTTAC 58.571 45.455 0.00 0.00 40.39 2.34
449 450 2.423185 CCTGCGAACATGGCAAATCTTA 59.577 45.455 0.00 0.00 40.39 2.10
450 451 1.203052 CCTGCGAACATGGCAAATCTT 59.797 47.619 0.00 0.00 40.39 2.40
451 452 0.813184 CCTGCGAACATGGCAAATCT 59.187 50.000 0.00 0.00 40.39 2.40
454 455 2.650196 GCCTGCGAACATGGCAAA 59.350 55.556 0.00 0.00 45.46 3.68
455 456 3.736100 CGCCTGCGAACATGGCAA 61.736 61.111 5.43 0.00 46.39 4.52
456 457 4.695993 TCGCCTGCGAACATGGCA 62.696 61.111 12.40 0.00 46.01 4.92
465 466 1.135431 TCATGGAAATTTTCGCCTGCG 60.135 47.619 4.92 4.92 41.35 5.18
466 467 2.652941 TCATGGAAATTTTCGCCTGC 57.347 45.000 3.17 0.00 0.00 4.85
467 468 2.925563 GCTTCATGGAAATTTTCGCCTG 59.074 45.455 3.17 1.56 0.00 4.85
469 470 3.182182 GAGCTTCATGGAAATTTTCGCC 58.818 45.455 3.17 0.00 0.00 5.54
470 471 3.836949 TGAGCTTCATGGAAATTTTCGC 58.163 40.909 3.17 0.56 0.00 4.70
471 472 6.768029 TTTTGAGCTTCATGGAAATTTTCG 57.232 33.333 3.17 0.00 0.00 3.46
505 506 5.917541 TGTTTTTACAAAACGTGGCAAAA 57.082 30.435 7.42 0.00 33.05 2.44
506 507 5.917541 TTGTTTTTACAAAACGTGGCAAA 57.082 30.435 7.42 0.00 33.05 3.68
507 508 5.917541 TTTGTTTTTACAAAACGTGGCAA 57.082 30.435 7.42 0.00 36.75 4.52
508 509 6.481954 AATTTGTTTTTACAAAACGTGGCA 57.518 29.167 7.45 0.00 42.04 4.92
509 510 6.900828 GGTAATTTGTTTTTACAAAACGTGGC 59.099 34.615 7.45 0.00 42.04 5.01
510 511 7.111768 CGGTAATTTGTTTTTACAAAACGTGG 58.888 34.615 7.45 0.00 42.04 4.94
511 512 7.664567 ACGGTAATTTGTTTTTACAAAACGTG 58.335 30.769 16.98 8.64 42.04 4.49
512 513 7.809226 ACGGTAATTTGTTTTTACAAAACGT 57.191 28.000 7.45 11.68 42.04 3.99
526 527 9.490663 TTTTGCAAATAAACAAACGGTAATTTG 57.509 25.926 13.65 0.00 43.81 2.32
559 560 3.595173 TGATGATGATCGAACAAACGGT 58.405 40.909 0.00 0.00 0.00 4.83
565 566 2.799562 GCCGTCTGATGATGATCGAACA 60.800 50.000 0.00 0.00 0.00 3.18
576 577 2.124570 CCCCCAAGCCGTCTGATG 60.125 66.667 0.00 0.00 0.00 3.07
592 593 2.690778 GCAGGTCACATGAACGCCC 61.691 63.158 0.00 0.00 36.72 6.13
594 595 1.639298 GAGGCAGGTCACATGAACGC 61.639 60.000 0.00 5.53 36.72 4.84
595 596 1.021390 GGAGGCAGGTCACATGAACG 61.021 60.000 0.00 0.00 36.72 3.95
603 604 0.038166 GTTTCATGGGAGGCAGGTCA 59.962 55.000 0.00 0.00 0.00 4.02
613 614 4.900652 TGATAATGGGGAATGTTTCATGGG 59.099 41.667 0.00 0.00 0.00 4.00
617 618 5.598005 GGACATGATAATGGGGAATGTTTCA 59.402 40.000 0.00 0.00 31.82 2.69
668 670 5.588648 ACAGATGTCCTTTTCGTTTTCTTCA 59.411 36.000 0.00 0.00 0.00 3.02
689 691 3.485216 GTGAAACAGGTCGTGTGAAACAG 60.485 47.826 0.00 0.00 43.55 3.16
786 788 3.318839 CAGTTCATGCACTCCCTCAAAAA 59.681 43.478 0.00 0.00 0.00 1.94
787 789 2.886523 CAGTTCATGCACTCCCTCAAAA 59.113 45.455 0.00 0.00 0.00 2.44
788 790 2.106338 TCAGTTCATGCACTCCCTCAAA 59.894 45.455 0.00 0.00 0.00 2.69
789 791 1.699083 TCAGTTCATGCACTCCCTCAA 59.301 47.619 0.00 0.00 0.00 3.02
790 792 1.002430 GTCAGTTCATGCACTCCCTCA 59.998 52.381 0.00 0.00 0.00 3.86
793 795 2.191128 AAGTCAGTTCATGCACTCCC 57.809 50.000 0.00 0.00 0.00 4.30
794 796 5.886960 AATTAAGTCAGTTCATGCACTCC 57.113 39.130 0.00 0.00 0.00 3.85
795 797 7.413438 CCACTAATTAAGTCAGTTCATGCACTC 60.413 40.741 0.00 0.00 35.76 3.51
1003 1232 2.430921 CGAGACGAAAGCAGCGGT 60.431 61.111 0.00 0.00 0.00 5.68
1023 1252 4.729918 GTGGTGGCCAGGCTCCTG 62.730 72.222 5.11 8.93 43.26 3.86
1298 1527 2.754648 ACGTACACTGGGTGGATGT 58.245 52.632 2.26 2.26 41.27 3.06
1305 1534 0.942410 CACCAACGACGTACACTGGG 60.942 60.000 18.13 8.66 0.00 4.45
1313 1542 4.224274 TTCGGCCACCAACGACGT 62.224 61.111 2.24 0.00 39.04 4.34
1314 1543 3.708734 GTTCGGCCACCAACGACG 61.709 66.667 2.24 0.00 39.04 5.12
1315 1544 3.351416 GGTTCGGCCACCAACGAC 61.351 66.667 7.38 0.00 39.04 4.34
1316 1545 3.862991 TGGTTCGGCCACCAACGA 61.863 61.111 12.46 1.35 44.30 3.85
1337 1571 1.336795 ACGCAGCAAATTAACAAGGCC 60.337 47.619 0.00 0.00 0.00 5.19
1451 1728 8.507470 AAACTTGAAAATAGCGACAAAGAATC 57.493 30.769 0.00 0.00 0.00 2.52
1622 1908 9.905713 ATGCTTGTGGTATTCTAGATAGAAAAA 57.094 29.630 6.40 0.00 44.63 1.94
1623 1909 9.330063 CATGCTTGTGGTATTCTAGATAGAAAA 57.670 33.333 6.40 0.00 44.63 2.29
1624 1910 7.442364 GCATGCTTGTGGTATTCTAGATAGAAA 59.558 37.037 11.37 0.00 44.63 2.52
1625 1911 6.931281 GCATGCTTGTGGTATTCTAGATAGAA 59.069 38.462 11.37 4.84 45.43 2.10
1626 1912 6.041979 TGCATGCTTGTGGTATTCTAGATAGA 59.958 38.462 20.33 0.00 0.00 1.98
1627 1913 6.226052 TGCATGCTTGTGGTATTCTAGATAG 58.774 40.000 20.33 0.00 0.00 2.08
1628 1914 6.173427 TGCATGCTTGTGGTATTCTAGATA 57.827 37.500 20.33 0.00 0.00 1.98
1629 1915 5.039920 TGCATGCTTGTGGTATTCTAGAT 57.960 39.130 20.33 0.00 0.00 1.98
1630 1916 4.486125 TGCATGCTTGTGGTATTCTAGA 57.514 40.909 20.33 0.00 0.00 2.43
1631 1917 5.565592 TTTGCATGCTTGTGGTATTCTAG 57.434 39.130 20.33 0.00 0.00 2.43
1632 1918 5.651576 TGATTTGCATGCTTGTGGTATTCTA 59.348 36.000 20.33 0.00 0.00 2.10
1633 1919 4.463539 TGATTTGCATGCTTGTGGTATTCT 59.536 37.500 20.33 0.00 0.00 2.40
1634 1920 4.746729 TGATTTGCATGCTTGTGGTATTC 58.253 39.130 20.33 3.80 0.00 1.75
1635 1921 4.804868 TGATTTGCATGCTTGTGGTATT 57.195 36.364 20.33 0.00 0.00 1.89
1636 1922 6.659745 ATATGATTTGCATGCTTGTGGTAT 57.340 33.333 20.33 8.10 37.87 2.73
1637 1923 7.764141 ATATATGATTTGCATGCTTGTGGTA 57.236 32.000 20.33 6.09 37.87 3.25
1638 1924 6.659745 ATATATGATTTGCATGCTTGTGGT 57.340 33.333 20.33 3.93 37.87 4.16
1639 1925 7.149307 TGAATATATGATTTGCATGCTTGTGG 58.851 34.615 20.33 0.00 37.87 4.17
1640 1926 8.757164 ATGAATATATGATTTGCATGCTTGTG 57.243 30.769 20.33 0.00 37.87 3.33
1657 1943 8.998814 TGGACAACCCTCTCTTTTATGAATATA 58.001 33.333 0.00 0.00 35.38 0.86
1658 1944 7.872138 TGGACAACCCTCTCTTTTATGAATAT 58.128 34.615 0.00 0.00 35.38 1.28
1659 1945 7.265599 TGGACAACCCTCTCTTTTATGAATA 57.734 36.000 0.00 0.00 35.38 1.75
1660 1946 6.139679 TGGACAACCCTCTCTTTTATGAAT 57.860 37.500 0.00 0.00 35.38 2.57
1661 1947 5.560724 CTGGACAACCCTCTCTTTTATGAA 58.439 41.667 0.00 0.00 35.38 2.57
1662 1948 4.565652 GCTGGACAACCCTCTCTTTTATGA 60.566 45.833 0.00 0.00 35.38 2.15
1663 1949 3.691609 GCTGGACAACCCTCTCTTTTATG 59.308 47.826 0.00 0.00 35.38 1.90
1664 1950 3.619979 CGCTGGACAACCCTCTCTTTTAT 60.620 47.826 0.00 0.00 35.38 1.40
1665 1951 2.289444 CGCTGGACAACCCTCTCTTTTA 60.289 50.000 0.00 0.00 35.38 1.52
1666 1952 1.543429 CGCTGGACAACCCTCTCTTTT 60.543 52.381 0.00 0.00 35.38 2.27
1667 1953 0.035458 CGCTGGACAACCCTCTCTTT 59.965 55.000 0.00 0.00 35.38 2.52
1668 1954 1.674057 CGCTGGACAACCCTCTCTT 59.326 57.895 0.00 0.00 35.38 2.85
1669 1955 2.948720 GCGCTGGACAACCCTCTCT 61.949 63.158 0.00 0.00 35.38 3.10
1670 1956 2.435059 GCGCTGGACAACCCTCTC 60.435 66.667 0.00 0.00 35.38 3.20
1671 1957 2.129555 AATGCGCTGGACAACCCTCT 62.130 55.000 9.73 0.00 35.38 3.69
1672 1958 0.392461 TAATGCGCTGGACAACCCTC 60.392 55.000 9.73 0.00 35.38 4.30
1673 1959 0.676782 GTAATGCGCTGGACAACCCT 60.677 55.000 9.73 0.00 35.38 4.34
1674 1960 0.958382 TGTAATGCGCTGGACAACCC 60.958 55.000 9.73 0.00 34.81 4.11
1675 1961 1.064060 GATGTAATGCGCTGGACAACC 59.936 52.381 9.73 2.99 0.00 3.77
1676 1962 1.737236 TGATGTAATGCGCTGGACAAC 59.263 47.619 9.73 9.02 0.00 3.32
1677 1963 2.106477 TGATGTAATGCGCTGGACAA 57.894 45.000 9.73 0.00 0.00 3.18
1678 1964 2.330440 ATGATGTAATGCGCTGGACA 57.670 45.000 9.73 10.18 0.00 4.02
1679 1965 3.181497 ACAAATGATGTAATGCGCTGGAC 60.181 43.478 9.73 3.91 41.63 4.02
1680 1966 3.016031 ACAAATGATGTAATGCGCTGGA 58.984 40.909 9.73 0.00 41.63 3.86
1681 1967 3.110358 CACAAATGATGTAATGCGCTGG 58.890 45.455 9.73 0.00 41.46 4.85
1682 1968 3.761657 ACACAAATGATGTAATGCGCTG 58.238 40.909 9.73 0.00 41.46 5.18
1683 1969 3.181497 GGACACAAATGATGTAATGCGCT 60.181 43.478 9.73 0.00 41.46 5.92
1684 1970 3.108144 GGACACAAATGATGTAATGCGC 58.892 45.455 0.00 0.00 41.46 6.09
1685 1971 4.354071 TGGACACAAATGATGTAATGCG 57.646 40.909 0.00 0.00 41.46 4.73
1698 1984 4.763073 TGAATGTTTGCATTTGGACACAA 58.237 34.783 0.00 0.00 44.61 3.33
1699 1985 4.397481 TGAATGTTTGCATTTGGACACA 57.603 36.364 0.00 0.00 44.61 3.72
1700 1986 4.389687 GGATGAATGTTTGCATTTGGACAC 59.610 41.667 0.00 0.00 44.61 3.67
1701 1987 4.040095 TGGATGAATGTTTGCATTTGGACA 59.960 37.500 0.00 0.00 44.61 4.02
1702 1988 4.389687 GTGGATGAATGTTTGCATTTGGAC 59.610 41.667 0.00 0.00 44.61 4.02
1703 1989 4.040095 TGTGGATGAATGTTTGCATTTGGA 59.960 37.500 0.00 0.00 44.61 3.53
1704 1990 4.316645 TGTGGATGAATGTTTGCATTTGG 58.683 39.130 0.00 0.00 44.61 3.28
1705 1991 5.467399 ACTTGTGGATGAATGTTTGCATTTG 59.533 36.000 0.00 0.00 44.61 2.32
1706 1992 5.613329 ACTTGTGGATGAATGTTTGCATTT 58.387 33.333 0.00 0.00 44.61 2.32
1707 1993 5.217978 ACTTGTGGATGAATGTTTGCATT 57.782 34.783 0.00 0.00 46.99 3.56
1708 1994 4.877378 ACTTGTGGATGAATGTTTGCAT 57.123 36.364 0.00 0.00 36.80 3.96
1709 1995 4.826733 AGTACTTGTGGATGAATGTTTGCA 59.173 37.500 0.00 0.00 0.00 4.08
1710 1996 5.376854 AGTACTTGTGGATGAATGTTTGC 57.623 39.130 0.00 0.00 0.00 3.68
1711 1997 7.905604 TCTAGTACTTGTGGATGAATGTTTG 57.094 36.000 0.00 0.00 0.00 2.93
1712 1998 7.492669 CGATCTAGTACTTGTGGATGAATGTTT 59.507 37.037 0.00 0.00 0.00 2.83
1713 1999 6.980978 CGATCTAGTACTTGTGGATGAATGTT 59.019 38.462 0.00 0.00 0.00 2.71
1714 2000 6.321435 TCGATCTAGTACTTGTGGATGAATGT 59.679 38.462 0.00 0.00 0.00 2.71
1715 2001 6.739112 TCGATCTAGTACTTGTGGATGAATG 58.261 40.000 0.00 0.00 0.00 2.67
1716 2002 6.773200 TCTCGATCTAGTACTTGTGGATGAAT 59.227 38.462 0.00 0.00 0.00 2.57
1717 2003 6.120220 TCTCGATCTAGTACTTGTGGATGAA 58.880 40.000 0.00 0.00 0.00 2.57
1718 2004 5.681639 TCTCGATCTAGTACTTGTGGATGA 58.318 41.667 0.00 0.00 0.00 2.92
1719 2005 6.567687 ATCTCGATCTAGTACTTGTGGATG 57.432 41.667 0.00 0.00 0.00 3.51
1720 2006 5.410132 CGATCTCGATCTAGTACTTGTGGAT 59.590 44.000 0.00 0.44 43.02 3.41
1721 2007 4.750598 CGATCTCGATCTAGTACTTGTGGA 59.249 45.833 0.00 0.00 43.02 4.02
1722 2008 4.611807 GCGATCTCGATCTAGTACTTGTGG 60.612 50.000 0.00 0.00 43.02 4.17
1725 2011 3.727518 CGCGATCTCGATCTAGTACTTG 58.272 50.000 0.00 0.00 43.02 3.16
1896 2182 2.224426 ACGGTTGATGGCTGAGTACAAA 60.224 45.455 0.00 0.00 0.00 2.83
1947 2256 9.863845 GTGCTTACTTAGGCCATTTTAATTTTA 57.136 29.630 5.01 0.00 0.00 1.52
1974 2283 6.127730 GGATTTTATGTATTGGATTAGGGCCG 60.128 42.308 0.00 0.00 0.00 6.13
2146 2457 5.163519 GGCTCCTTATTGTGTGCATACAAAT 60.164 40.000 29.18 19.93 43.13 2.32


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

AutoCloner maintained by Alex Coulton.