Multiple sequence alignment - TraesCS7D01G362500

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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 TraesCS7D01G362500 chr7D 100.000 2372 0 0 1 2372 465836808 465834437 0.000000e+00 4381
1 TraesCS7D01G362500 chr7D 92.569 1090 47 13 578 1666 214764737 214765793 0.000000e+00 1533
2 TraesCS7D01G362500 chr7D 95.937 763 15 7 1624 2372 214765785 214766545 0.000000e+00 1223
3 TraesCS7D01G362500 chr7D 87.079 534 54 13 1 527 83170202 83170727 7.300000e-165 590
4 TraesCS7D01G362500 chr7D 93.798 258 12 4 572 827 219288431 219288686 3.700000e-103 385
5 TraesCS7D01G362500 chr2A 92.664 1813 84 27 581 2372 84206499 84208283 0.000000e+00 2566
6 TraesCS7D01G362500 chr2A 94.575 811 39 4 858 1666 766619140 766618333 0.000000e+00 1249
7 TraesCS7D01G362500 chr2A 89.036 757 43 14 1624 2372 766618341 766617617 0.000000e+00 902
8 TraesCS7D01G362500 chr2A 86.486 592 57 12 1 581 84019206 84019785 1.550000e-176 628
9 TraesCS7D01G362500 chr4A 92.374 1508 79 26 885 2372 485007460 485008951 0.000000e+00 2115
10 TraesCS7D01G362500 chr4A 82.612 1271 133 51 581 1814 465258946 465257727 0.000000e+00 1042
11 TraesCS7D01G362500 chr3D 95.111 1084 36 8 583 1666 460901749 460900683 0.000000e+00 1692
12 TraesCS7D01G362500 chr3D 96.461 763 12 6 1624 2372 460900691 460899930 0.000000e+00 1245
13 TraesCS7D01G362500 chr2D 93.028 1090 49 9 579 1666 643052215 643053279 0.000000e+00 1567
14 TraesCS7D01G362500 chr2D 91.041 1105 62 16 583 1666 648110768 648109680 0.000000e+00 1458
15 TraesCS7D01G362500 chr2D 85.577 624 55 16 582 1201 47287742 47288334 2.590000e-174 621
16 TraesCS7D01G362500 chr2D 96.584 322 8 3 2052 2372 648109397 648109078 4.490000e-147 531
17 TraesCS7D01G362500 chr2D 96.273 322 9 3 2052 2372 643053562 643053881 2.090000e-145 525
18 TraesCS7D01G362500 chr2D 97.619 294 7 0 1624 1917 648109688 648109395 2.720000e-139 505
19 TraesCS7D01G362500 chr2D 96.939 294 9 0 1624 1917 643053271 643053564 5.890000e-136 494
20 TraesCS7D01G362500 chr5D 90.698 1118 47 19 581 1666 367799725 367800817 0.000000e+00 1435
21 TraesCS7D01G362500 chr5D 96.894 322 7 3 2052 2372 367801139 367801458 9.650000e-149 536
22 TraesCS7D01G362500 chr5D 97.324 299 8 0 1624 1922 367800809 367801107 2.100000e-140 508
23 TraesCS7D01G362500 chr7B 86.997 1292 82 28 581 1814 455230274 455231537 0.000000e+00 1376
24 TraesCS7D01G362500 chr2B 93.096 898 50 6 786 1674 1903829 1904723 0.000000e+00 1304
25 TraesCS7D01G362500 chr2B 94.267 750 26 4 1623 2372 1904706 1905438 0.000000e+00 1131
26 TraesCS7D01G362500 chr1A 86.019 1266 109 34 576 1814 330088628 330089852 0.000000e+00 1295
27 TraesCS7D01G362500 chr1A 88.657 767 60 13 974 1735 481627501 481626757 0.000000e+00 909
28 TraesCS7D01G362500 chr1A 85.950 605 58 12 1 588 168336471 168335877 2.590000e-174 621
29 TraesCS7D01G362500 chr1A 88.327 257 28 2 583 837 481627827 481627571 8.240000e-80 307
30 TraesCS7D01G362500 chr7A 82.927 1271 111 44 580 1814 182686818 182688018 0.000000e+00 1048
31 TraesCS7D01G362500 chr7A 90.476 588 45 7 1 582 36206271 36205689 0.000000e+00 765
32 TraesCS7D01G362500 chr6D 94.632 503 23 2 583 1082 113904170 113904671 0.000000e+00 776
33 TraesCS7D01G362500 chr6D 86.555 595 58 15 1 582 160394167 160393582 9.250000e-179 636
34 TraesCS7D01G362500 chr3A 85.331 634 68 11 582 1209 487474702 487474088 1.200000e-177 632
35 TraesCS7D01G362500 chr3A 85.026 581 66 16 11 582 603024844 603024276 2.640000e-159 571
36 TraesCS7D01G362500 chr3A 84.228 596 66 17 1 582 276103843 276103262 2.660000e-154 555
37 TraesCS7D01G362500 chr6A 85.810 599 57 10 1 582 191297702 191297115 5.610000e-171 610
38 TraesCS7D01G362500 chr4B 85.738 596 62 15 1 582 169140971 169140385 2.020000e-170 608


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 TraesCS7D01G362500 chr7D 465834437 465836808 2371 True 4381.000000 4381 100.000000 1 2372 1 chr7D.!!$R1 2371
1 TraesCS7D01G362500 chr7D 214764737 214766545 1808 False 1378.000000 1533 94.253000 578 2372 2 chr7D.!!$F3 1794
2 TraesCS7D01G362500 chr7D 83170202 83170727 525 False 590.000000 590 87.079000 1 527 1 chr7D.!!$F1 526
3 TraesCS7D01G362500 chr2A 84206499 84208283 1784 False 2566.000000 2566 92.664000 581 2372 1 chr2A.!!$F2 1791
4 TraesCS7D01G362500 chr2A 766617617 766619140 1523 True 1075.500000 1249 91.805500 858 2372 2 chr2A.!!$R1 1514
5 TraesCS7D01G362500 chr2A 84019206 84019785 579 False 628.000000 628 86.486000 1 581 1 chr2A.!!$F1 580
6 TraesCS7D01G362500 chr4A 485007460 485008951 1491 False 2115.000000 2115 92.374000 885 2372 1 chr4A.!!$F1 1487
7 TraesCS7D01G362500 chr4A 465257727 465258946 1219 True 1042.000000 1042 82.612000 581 1814 1 chr4A.!!$R1 1233
8 TraesCS7D01G362500 chr3D 460899930 460901749 1819 True 1468.500000 1692 95.786000 583 2372 2 chr3D.!!$R1 1789
9 TraesCS7D01G362500 chr2D 643052215 643053881 1666 False 862.000000 1567 95.413333 579 2372 3 chr2D.!!$F2 1793
10 TraesCS7D01G362500 chr2D 648109078 648110768 1690 True 831.333333 1458 95.081333 583 2372 3 chr2D.!!$R1 1789
11 TraesCS7D01G362500 chr2D 47287742 47288334 592 False 621.000000 621 85.577000 582 1201 1 chr2D.!!$F1 619
12 TraesCS7D01G362500 chr5D 367799725 367801458 1733 False 826.333333 1435 94.972000 581 2372 3 chr5D.!!$F1 1791
13 TraesCS7D01G362500 chr7B 455230274 455231537 1263 False 1376.000000 1376 86.997000 581 1814 1 chr7B.!!$F1 1233
14 TraesCS7D01G362500 chr2B 1903829 1905438 1609 False 1217.500000 1304 93.681500 786 2372 2 chr2B.!!$F1 1586
15 TraesCS7D01G362500 chr1A 330088628 330089852 1224 False 1295.000000 1295 86.019000 576 1814 1 chr1A.!!$F1 1238
16 TraesCS7D01G362500 chr1A 168335877 168336471 594 True 621.000000 621 85.950000 1 588 1 chr1A.!!$R1 587
17 TraesCS7D01G362500 chr1A 481626757 481627827 1070 True 608.000000 909 88.492000 583 1735 2 chr1A.!!$R2 1152
18 TraesCS7D01G362500 chr7A 182686818 182688018 1200 False 1048.000000 1048 82.927000 580 1814 1 chr7A.!!$F1 1234
19 TraesCS7D01G362500 chr7A 36205689 36206271 582 True 765.000000 765 90.476000 1 582 1 chr7A.!!$R1 581
20 TraesCS7D01G362500 chr6D 113904170 113904671 501 False 776.000000 776 94.632000 583 1082 1 chr6D.!!$F1 499
21 TraesCS7D01G362500 chr6D 160393582 160394167 585 True 636.000000 636 86.555000 1 582 1 chr6D.!!$R1 581
22 TraesCS7D01G362500 chr3A 487474088 487474702 614 True 632.000000 632 85.331000 582 1209 1 chr3A.!!$R2 627
23 TraesCS7D01G362500 chr3A 603024276 603024844 568 True 571.000000 571 85.026000 11 582 1 chr3A.!!$R3 571
24 TraesCS7D01G362500 chr3A 276103262 276103843 581 True 555.000000 555 84.228000 1 582 1 chr3A.!!$R1 581
25 TraesCS7D01G362500 chr6A 191297115 191297702 587 True 610.000000 610 85.810000 1 582 1 chr6A.!!$R1 581
26 TraesCS7D01G362500 chr4B 169140385 169140971 586 True 608.000000 608 85.738000 1 582 1 chr4B.!!$R1 581

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
335 369 0.033109 ATTGCCTAGCCTTTGACCCC 60.033 55.0 0.0 0.0 0.0 4.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1690 2353 7.47998 CAAACTGGAAACTACATCAACTTCAA 58.52 34.615 0.0 0.0 0.0 2.69 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
275 309 0.109153 TTAGCCCATGCGCATGATCT 59.891 50.000 43.71 36.71 44.33 2.75
276 310 0.109153 TAGCCCATGCGCATGATCTT 59.891 50.000 43.71 28.69 44.33 2.40
277 311 0.754217 AGCCCATGCGCATGATCTTT 60.754 50.000 43.71 24.27 44.33 2.52
278 312 0.103572 GCCCATGCGCATGATCTTTT 59.896 50.000 43.71 11.32 41.20 2.27
279 313 1.472026 GCCCATGCGCATGATCTTTTT 60.472 47.619 43.71 10.50 41.20 1.94
280 314 2.466846 CCCATGCGCATGATCTTTTTC 58.533 47.619 43.71 0.00 41.20 2.29
281 315 2.159212 CCCATGCGCATGATCTTTTTCA 60.159 45.455 43.71 4.63 41.20 2.69
282 316 3.513662 CCATGCGCATGATCTTTTTCAA 58.486 40.909 43.71 4.12 41.20 2.69
283 317 3.927758 CCATGCGCATGATCTTTTTCAAA 59.072 39.130 43.71 3.37 41.20 2.69
284 318 4.569162 CCATGCGCATGATCTTTTTCAAAT 59.431 37.500 43.71 7.62 41.20 2.32
285 319 5.064198 CCATGCGCATGATCTTTTTCAAATT 59.936 36.000 43.71 7.19 41.20 1.82
286 320 6.402766 CCATGCGCATGATCTTTTTCAAATTT 60.403 34.615 43.71 6.80 41.20 1.82
287 321 5.918082 TGCGCATGATCTTTTTCAAATTTG 58.082 33.333 5.66 12.15 0.00 2.32
288 322 5.695363 TGCGCATGATCTTTTTCAAATTTGA 59.305 32.000 16.91 16.91 34.92 2.69
289 323 6.369340 TGCGCATGATCTTTTTCAAATTTGAT 59.631 30.769 21.10 5.58 37.00 2.57
290 324 6.898189 GCGCATGATCTTTTTCAAATTTGATC 59.102 34.615 21.10 14.48 37.00 2.92
291 325 7.201496 GCGCATGATCTTTTTCAAATTTGATCT 60.201 33.333 21.10 3.53 37.00 2.75
292 326 8.108172 CGCATGATCTTTTTCAAATTTGATCTG 58.892 33.333 21.10 13.84 37.00 2.90
293 327 7.903431 GCATGATCTTTTTCAAATTTGATCTGC 59.097 33.333 21.10 18.19 37.00 4.26
294 328 7.571089 TGATCTTTTTCAAATTTGATCTGCG 57.429 32.000 21.10 9.50 37.00 5.18
295 329 7.147312 TGATCTTTTTCAAATTTGATCTGCGT 58.853 30.769 21.10 7.38 37.00 5.24
296 330 8.296000 TGATCTTTTTCAAATTTGATCTGCGTA 58.704 29.630 21.10 2.09 37.00 4.42
297 331 7.851822 TCTTTTTCAAATTTGATCTGCGTAC 57.148 32.000 21.10 0.00 37.00 3.67
298 332 6.577055 TCTTTTTCAAATTTGATCTGCGTACG 59.423 34.615 21.10 11.84 37.00 3.67
299 333 5.351233 TTTCAAATTTGATCTGCGTACGT 57.649 34.783 21.10 0.00 37.00 3.57
300 334 6.469139 TTTCAAATTTGATCTGCGTACGTA 57.531 33.333 21.10 12.02 37.00 3.57
301 335 6.656314 TTCAAATTTGATCTGCGTACGTAT 57.344 33.333 21.10 8.30 37.00 3.06
302 336 7.758613 TTCAAATTTGATCTGCGTACGTATA 57.241 32.000 21.10 5.40 37.00 1.47
303 337 7.389603 TCAAATTTGATCTGCGTACGTATAG 57.610 36.000 16.91 12.77 31.01 1.31
304 338 6.419710 TCAAATTTGATCTGCGTACGTATAGG 59.580 38.462 16.91 0.59 31.01 2.57
305 339 4.906065 TTTGATCTGCGTACGTATAGGT 57.094 40.909 17.90 9.32 0.00 3.08
306 340 4.906065 TTGATCTGCGTACGTATAGGTT 57.094 40.909 17.90 5.08 0.00 3.50
307 341 4.906065 TGATCTGCGTACGTATAGGTTT 57.094 40.909 17.90 2.89 0.00 3.27
308 342 6.375945 TTGATCTGCGTACGTATAGGTTTA 57.624 37.500 17.90 1.24 0.00 2.01
309 343 5.993891 TGATCTGCGTACGTATAGGTTTAG 58.006 41.667 17.90 0.00 0.00 1.85
310 344 5.528690 TGATCTGCGTACGTATAGGTTTAGT 59.471 40.000 17.90 0.00 0.00 2.24
311 345 5.409643 TCTGCGTACGTATAGGTTTAGTC 57.590 43.478 17.90 0.00 0.00 2.59
312 346 4.273480 TCTGCGTACGTATAGGTTTAGTCC 59.727 45.833 17.90 0.00 0.00 3.85
313 347 3.315191 TGCGTACGTATAGGTTTAGTCCC 59.685 47.826 17.90 0.00 0.00 4.46
314 348 3.315191 GCGTACGTATAGGTTTAGTCCCA 59.685 47.826 17.90 0.00 0.00 4.37
315 349 4.789802 GCGTACGTATAGGTTTAGTCCCAC 60.790 50.000 17.90 0.00 0.00 4.61
316 350 4.335315 CGTACGTATAGGTTTAGTCCCACA 59.665 45.833 7.22 0.00 0.00 4.17
317 351 5.009010 CGTACGTATAGGTTTAGTCCCACAT 59.991 44.000 7.22 0.00 0.00 3.21
318 352 5.945144 ACGTATAGGTTTAGTCCCACATT 57.055 39.130 0.00 0.00 0.00 2.71
319 353 5.667466 ACGTATAGGTTTAGTCCCACATTG 58.333 41.667 0.00 0.00 0.00 2.82
320 354 4.510340 CGTATAGGTTTAGTCCCACATTGC 59.490 45.833 0.00 0.00 0.00 3.56
321 355 2.215942 AGGTTTAGTCCCACATTGCC 57.784 50.000 0.00 0.00 0.00 4.52
322 356 1.710809 AGGTTTAGTCCCACATTGCCT 59.289 47.619 0.00 0.00 0.00 4.75
323 357 2.916934 AGGTTTAGTCCCACATTGCCTA 59.083 45.455 0.00 0.00 0.00 3.93
324 358 3.054361 AGGTTTAGTCCCACATTGCCTAG 60.054 47.826 0.00 0.00 0.00 3.02
325 359 2.683362 GTTTAGTCCCACATTGCCTAGC 59.317 50.000 0.00 0.00 0.00 3.42
326 360 0.837272 TAGTCCCACATTGCCTAGCC 59.163 55.000 0.00 0.00 0.00 3.93
327 361 0.916358 AGTCCCACATTGCCTAGCCT 60.916 55.000 0.00 0.00 0.00 4.58
328 362 0.034089 GTCCCACATTGCCTAGCCTT 60.034 55.000 0.00 0.00 0.00 4.35
329 363 0.704076 TCCCACATTGCCTAGCCTTT 59.296 50.000 0.00 0.00 0.00 3.11
330 364 0.819582 CCCACATTGCCTAGCCTTTG 59.180 55.000 0.00 0.00 0.00 2.77
331 365 1.616725 CCCACATTGCCTAGCCTTTGA 60.617 52.381 0.00 0.00 0.00 2.69
332 366 1.474077 CCACATTGCCTAGCCTTTGAC 59.526 52.381 0.00 0.00 0.00 3.18
333 367 1.474077 CACATTGCCTAGCCTTTGACC 59.526 52.381 0.00 0.00 0.00 4.02
334 368 1.106285 CATTGCCTAGCCTTTGACCC 58.894 55.000 0.00 0.00 0.00 4.46
335 369 0.033109 ATTGCCTAGCCTTTGACCCC 60.033 55.000 0.00 0.00 0.00 4.95
336 370 1.140134 TTGCCTAGCCTTTGACCCCT 61.140 55.000 0.00 0.00 0.00 4.79
337 371 0.252974 TGCCTAGCCTTTGACCCCTA 60.253 55.000 0.00 0.00 0.00 3.53
338 372 0.916809 GCCTAGCCTTTGACCCCTAA 59.083 55.000 0.00 0.00 0.00 2.69
339 373 1.283905 GCCTAGCCTTTGACCCCTAAA 59.716 52.381 0.00 0.00 0.00 1.85
340 374 2.944542 GCCTAGCCTTTGACCCCTAAAC 60.945 54.545 0.00 0.00 0.00 2.01
341 375 2.356844 CCTAGCCTTTGACCCCTAAACC 60.357 54.545 0.00 0.00 0.00 3.27
342 376 1.456919 AGCCTTTGACCCCTAAACCT 58.543 50.000 0.00 0.00 0.00 3.50
343 377 1.354705 AGCCTTTGACCCCTAAACCTC 59.645 52.381 0.00 0.00 0.00 3.85
344 378 1.616187 GCCTTTGACCCCTAAACCTCC 60.616 57.143 0.00 0.00 0.00 4.30
345 379 1.993301 CCTTTGACCCCTAAACCTCCT 59.007 52.381 0.00 0.00 0.00 3.69
346 380 2.378886 CCTTTGACCCCTAAACCTCCTT 59.621 50.000 0.00 0.00 0.00 3.36
347 381 3.181422 CCTTTGACCCCTAAACCTCCTTT 60.181 47.826 0.00 0.00 0.00 3.11
348 382 3.801307 TTGACCCCTAAACCTCCTTTC 57.199 47.619 0.00 0.00 0.00 2.62
349 383 1.990327 TGACCCCTAAACCTCCTTTCC 59.010 52.381 0.00 0.00 0.00 3.13
350 384 1.990327 GACCCCTAAACCTCCTTTCCA 59.010 52.381 0.00 0.00 0.00 3.53
351 385 1.709115 ACCCCTAAACCTCCTTTCCAC 59.291 52.381 0.00 0.00 0.00 4.02
352 386 1.005569 CCCCTAAACCTCCTTTCCACC 59.994 57.143 0.00 0.00 0.00 4.61
353 387 1.993301 CCCTAAACCTCCTTTCCACCT 59.007 52.381 0.00 0.00 0.00 4.00
354 388 3.187112 CCCTAAACCTCCTTTCCACCTA 58.813 50.000 0.00 0.00 0.00 3.08
355 389 3.786450 CCCTAAACCTCCTTTCCACCTAT 59.214 47.826 0.00 0.00 0.00 2.57
356 390 4.973211 CCCTAAACCTCCTTTCCACCTATA 59.027 45.833 0.00 0.00 0.00 1.31
357 391 5.430745 CCCTAAACCTCCTTTCCACCTATAA 59.569 44.000 0.00 0.00 0.00 0.98
358 392 6.069264 CCCTAAACCTCCTTTCCACCTATAAA 60.069 42.308 0.00 0.00 0.00 1.40
359 393 7.367459 CCCTAAACCTCCTTTCCACCTATAAAT 60.367 40.741 0.00 0.00 0.00 1.40
360 394 8.720537 CCTAAACCTCCTTTCCACCTATAAATA 58.279 37.037 0.00 0.00 0.00 1.40
364 398 9.684702 AACCTCCTTTCCACCTATAAATATAGA 57.315 33.333 8.68 0.00 38.30 1.98
365 399 9.102453 ACCTCCTTTCCACCTATAAATATAGAC 57.898 37.037 8.68 0.00 38.30 2.59
366 400 9.327731 CCTCCTTTCCACCTATAAATATAGACT 57.672 37.037 8.68 0.00 38.30 3.24
368 402 9.892444 TCCTTTCCACCTATAAATATAGACTCA 57.108 33.333 8.68 0.00 38.30 3.41
386 420 7.443302 AGACTCATAGATCCTCCAAAAATCA 57.557 36.000 0.00 0.00 0.00 2.57
387 421 8.043429 AGACTCATAGATCCTCCAAAAATCAT 57.957 34.615 0.00 0.00 0.00 2.45
388 422 8.156165 AGACTCATAGATCCTCCAAAAATCATC 58.844 37.037 0.00 0.00 0.00 2.92
389 423 8.043429 ACTCATAGATCCTCCAAAAATCATCT 57.957 34.615 0.00 0.00 0.00 2.90
390 424 7.937942 ACTCATAGATCCTCCAAAAATCATCTG 59.062 37.037 0.00 0.00 0.00 2.90
391 425 8.037723 TCATAGATCCTCCAAAAATCATCTGA 57.962 34.615 0.00 0.00 0.00 3.27
392 426 8.666821 TCATAGATCCTCCAAAAATCATCTGAT 58.333 33.333 0.00 0.00 36.07 2.90
393 427 9.298250 CATAGATCCTCCAAAAATCATCTGATT 57.702 33.333 0.00 0.00 45.91 2.57
394 428 7.820578 AGATCCTCCAAAAATCATCTGATTC 57.179 36.000 5.92 0.00 43.41 2.52
395 429 6.485984 AGATCCTCCAAAAATCATCTGATTCG 59.514 38.462 5.92 0.00 43.41 3.34
396 430 4.883585 TCCTCCAAAAATCATCTGATTCGG 59.116 41.667 5.92 7.50 43.41 4.30
397 431 4.037208 CCTCCAAAAATCATCTGATTCGGG 59.963 45.833 5.92 8.05 43.41 5.14
398 432 4.599041 TCCAAAAATCATCTGATTCGGGT 58.401 39.130 5.92 0.00 43.41 5.28
399 433 5.016173 TCCAAAAATCATCTGATTCGGGTT 58.984 37.500 5.92 0.00 43.41 4.11
400 434 6.184068 TCCAAAAATCATCTGATTCGGGTTA 58.816 36.000 5.92 0.00 43.41 2.85
401 435 6.661377 TCCAAAAATCATCTGATTCGGGTTAA 59.339 34.615 5.92 0.00 43.41 2.01
402 436 7.177568 TCCAAAAATCATCTGATTCGGGTTAAA 59.822 33.333 5.92 0.00 43.41 1.52
403 437 7.981225 CCAAAAATCATCTGATTCGGGTTAAAT 59.019 33.333 5.92 0.00 43.41 1.40
404 438 9.023967 CAAAAATCATCTGATTCGGGTTAAATC 57.976 33.333 5.92 0.00 43.41 2.17
405 439 7.880160 AAATCATCTGATTCGGGTTAAATCA 57.120 32.000 5.92 0.00 43.41 2.57
406 440 7.880160 AATCATCTGATTCGGGTTAAATCAA 57.120 32.000 0.00 0.00 40.49 2.57
407 441 8.469309 AATCATCTGATTCGGGTTAAATCAAT 57.531 30.769 0.00 0.00 40.49 2.57
408 442 9.573166 AATCATCTGATTCGGGTTAAATCAATA 57.427 29.630 0.00 0.00 40.49 1.90
409 443 9.745018 ATCATCTGATTCGGGTTAAATCAATAT 57.255 29.630 0.80 0.00 41.31 1.28
410 444 9.573166 TCATCTGATTCGGGTTAAATCAATATT 57.427 29.630 0.80 0.00 41.31 1.28
414 448 9.248291 CTGATTCGGGTTAAATCAATATTTTGG 57.752 33.333 0.80 0.00 41.31 3.28
415 449 8.754080 TGATTCGGGTTAAATCAATATTTTGGT 58.246 29.630 0.00 0.00 39.52 3.67
416 450 9.594478 GATTCGGGTTAAATCAATATTTTGGTT 57.406 29.630 0.00 0.00 37.79 3.67
417 451 9.952030 ATTCGGGTTAAATCAATATTTTGGTTT 57.048 25.926 11.20 11.20 45.71 3.27
418 452 8.764524 TCGGGTTAAATCAATATTTTGGTTTG 57.235 30.769 15.00 1.42 44.07 2.93
419 453 8.585881 TCGGGTTAAATCAATATTTTGGTTTGA 58.414 29.630 15.00 6.27 44.07 2.69
420 454 8.652463 CGGGTTAAATCAATATTTTGGTTTGAC 58.348 33.333 16.22 16.22 45.06 3.18
421 455 9.719355 GGGTTAAATCAATATTTTGGTTTGACT 57.281 29.630 20.71 1.09 45.10 3.41
435 469 9.621629 TTTTGGTTTGACTAGATTCACTAAAGA 57.378 29.630 0.00 0.00 0.00 2.52
436 470 9.621629 TTTGGTTTGACTAGATTCACTAAAGAA 57.378 29.630 0.00 0.00 0.00 2.52
437 471 9.621629 TTGGTTTGACTAGATTCACTAAAGAAA 57.378 29.630 0.00 0.00 0.00 2.52
438 472 9.621629 TGGTTTGACTAGATTCACTAAAGAAAA 57.378 29.630 0.00 0.00 0.00 2.29
457 491 8.910351 AAGAAAAATATATTTCTCCTCTCCGG 57.090 34.615 11.08 0.00 46.25 5.14
458 492 6.937465 AGAAAAATATATTTCTCCTCTCCGGC 59.063 38.462 11.08 0.00 44.28 6.13
459 493 4.457834 AATATATTTCTCCTCTCCGGCG 57.542 45.455 0.00 0.00 0.00 6.46
460 494 0.969894 ATATTTCTCCTCTCCGGCGG 59.030 55.000 22.51 22.51 0.00 6.13
461 495 1.113517 TATTTCTCCTCTCCGGCGGG 61.114 60.000 27.98 17.02 0.00 6.13
462 496 2.873557 ATTTCTCCTCTCCGGCGGGA 62.874 60.000 27.98 20.38 41.08 5.14
463 497 4.816984 TCTCCTCTCCGGCGGGAC 62.817 72.222 27.98 0.00 37.43 4.46
464 498 4.824515 CTCCTCTCCGGCGGGACT 62.825 72.222 27.98 0.00 37.43 3.85
465 499 4.377760 TCCTCTCCGGCGGGACTT 62.378 66.667 27.98 0.00 37.43 3.01
466 500 3.839432 CCTCTCCGGCGGGACTTC 61.839 72.222 27.98 0.00 37.43 3.01
467 501 2.756283 CTCTCCGGCGGGACTTCT 60.756 66.667 27.98 0.00 37.43 2.85
468 502 3.068691 TCTCCGGCGGGACTTCTG 61.069 66.667 27.98 7.84 37.43 3.02
469 503 4.148825 CTCCGGCGGGACTTCTGG 62.149 72.222 27.98 0.00 37.43 3.86
470 504 4.689549 TCCGGCGGGACTTCTGGA 62.690 66.667 27.98 0.00 37.43 3.86
471 505 3.702048 CCGGCGGGACTTCTGGAA 61.702 66.667 20.56 0.00 34.06 3.53
472 506 2.125512 CGGCGGGACTTCTGGAAG 60.126 66.667 0.00 8.59 43.79 3.46
486 520 6.538189 CTTCTGGAAGTTGTCTTTTCTCTC 57.462 41.667 2.47 0.00 33.64 3.20
487 521 4.962155 TCTGGAAGTTGTCTTTTCTCTCC 58.038 43.478 0.00 0.00 33.64 3.71
488 522 3.728845 TGGAAGTTGTCTTTTCTCTCCG 58.271 45.455 0.00 0.00 33.64 4.63
489 523 3.386726 TGGAAGTTGTCTTTTCTCTCCGA 59.613 43.478 0.00 0.00 33.64 4.55
490 524 4.141801 TGGAAGTTGTCTTTTCTCTCCGAA 60.142 41.667 0.00 0.00 33.64 4.30
491 525 4.449405 GGAAGTTGTCTTTTCTCTCCGAAG 59.551 45.833 0.00 0.00 33.64 3.79
492 526 4.674281 AGTTGTCTTTTCTCTCCGAAGT 57.326 40.909 0.00 0.00 32.21 3.01
493 527 4.623002 AGTTGTCTTTTCTCTCCGAAGTC 58.377 43.478 0.00 0.00 32.21 3.01
494 528 4.099573 AGTTGTCTTTTCTCTCCGAAGTCA 59.900 41.667 0.00 0.00 32.21 3.41
495 529 4.873746 TGTCTTTTCTCTCCGAAGTCAT 57.126 40.909 0.00 0.00 32.21 3.06
496 530 5.215252 TGTCTTTTCTCTCCGAAGTCATT 57.785 39.130 0.00 0.00 32.21 2.57
497 531 5.611374 TGTCTTTTCTCTCCGAAGTCATTT 58.389 37.500 0.00 0.00 32.21 2.32
498 532 6.055588 TGTCTTTTCTCTCCGAAGTCATTTT 58.944 36.000 0.00 0.00 32.21 1.82
499 533 6.542370 TGTCTTTTCTCTCCGAAGTCATTTTT 59.458 34.615 0.00 0.00 32.21 1.94
545 579 9.298250 TCTTTCTTCATATATACTTCCGTAGCT 57.702 33.333 0.00 0.00 0.00 3.32
546 580 9.915629 CTTTCTTCATATATACTTCCGTAGCTT 57.084 33.333 0.00 0.00 0.00 3.74
690 724 8.029522 ACTCAATACGCCTACATGTGATTATAG 58.970 37.037 9.11 0.00 0.00 1.31
847 911 6.528321 TGAAATATCAGTGCTGAATCCCTAG 58.472 40.000 5.95 0.00 43.58 3.02
964 1131 2.725312 CGCCCTCTTCCAGCAGCTA 61.725 63.158 0.00 0.00 0.00 3.32
1061 1243 0.748005 GTGGTGGTGCCGCTCATAAT 60.748 55.000 1.58 0.00 44.20 1.28
1086 1268 0.385390 CTTTTTGCCCTGCTCGTGTT 59.615 50.000 0.00 0.00 0.00 3.32
1936 2624 8.845227 TGAAGTTAATGTTTGAAGCTGTTGATA 58.155 29.630 0.00 0.00 0.00 2.15
2114 2835 5.833131 ACCAACAATTCAGAACATAACCAGT 59.167 36.000 0.00 0.00 0.00 4.00
2145 2866 5.255397 ACAAAATGATCTGGGAAGTACCA 57.745 39.130 0.00 0.00 41.20 3.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 49 6.313744 ACAGAAAGGAAAACTGAATAACGG 57.686 37.500 0.00 0.00 35.85 4.44
163 179 2.618794 CTGGCCCATCTAGGAGAGAAT 58.381 52.381 0.00 0.00 41.22 2.40
275 309 6.202937 ACGTACGCAGATCAAATTTGAAAAA 58.797 32.000 23.91 2.26 41.13 1.94
276 310 5.753744 ACGTACGCAGATCAAATTTGAAAA 58.246 33.333 23.91 2.65 41.13 2.29
277 311 5.351233 ACGTACGCAGATCAAATTTGAAA 57.649 34.783 23.91 3.41 41.13 2.69
278 312 6.656314 ATACGTACGCAGATCAAATTTGAA 57.344 33.333 23.91 8.65 41.13 2.69
279 313 6.419710 CCTATACGTACGCAGATCAAATTTGA 59.580 38.462 22.52 22.52 42.14 2.69
280 314 6.200286 ACCTATACGTACGCAGATCAAATTTG 59.800 38.462 16.72 12.15 0.00 2.32
281 315 6.278363 ACCTATACGTACGCAGATCAAATTT 58.722 36.000 16.72 0.00 0.00 1.82
282 316 5.839621 ACCTATACGTACGCAGATCAAATT 58.160 37.500 16.72 0.00 0.00 1.82
283 317 5.449107 ACCTATACGTACGCAGATCAAAT 57.551 39.130 16.72 0.00 0.00 2.32
284 318 4.906065 ACCTATACGTACGCAGATCAAA 57.094 40.909 16.72 0.00 0.00 2.69
285 319 4.906065 AACCTATACGTACGCAGATCAA 57.094 40.909 16.72 0.00 0.00 2.57
286 320 4.906065 AAACCTATACGTACGCAGATCA 57.094 40.909 16.72 0.00 0.00 2.92
287 321 5.995055 ACTAAACCTATACGTACGCAGATC 58.005 41.667 16.72 0.00 0.00 2.75
288 322 5.049129 GGACTAAACCTATACGTACGCAGAT 60.049 44.000 16.72 9.09 0.00 2.90
289 323 4.273480 GGACTAAACCTATACGTACGCAGA 59.727 45.833 16.72 0.00 0.00 4.26
290 324 4.531332 GGACTAAACCTATACGTACGCAG 58.469 47.826 16.72 10.04 0.00 5.18
291 325 3.315191 GGGACTAAACCTATACGTACGCA 59.685 47.826 16.72 1.76 0.00 5.24
292 326 3.315191 TGGGACTAAACCTATACGTACGC 59.685 47.826 16.72 0.00 0.00 4.42
293 327 4.335315 TGTGGGACTAAACCTATACGTACG 59.665 45.833 15.01 15.01 0.00 3.67
294 328 5.835113 TGTGGGACTAAACCTATACGTAC 57.165 43.478 0.00 0.00 0.00 3.67
295 329 6.683610 GCAATGTGGGACTAAACCTATACGTA 60.684 42.308 0.00 0.00 0.00 3.57
296 330 5.667466 CAATGTGGGACTAAACCTATACGT 58.333 41.667 0.00 0.00 0.00 3.57
297 331 4.510340 GCAATGTGGGACTAAACCTATACG 59.490 45.833 0.00 0.00 0.00 3.06
298 332 4.820173 GGCAATGTGGGACTAAACCTATAC 59.180 45.833 0.00 0.00 0.00 1.47
299 333 4.724798 AGGCAATGTGGGACTAAACCTATA 59.275 41.667 0.00 0.00 0.00 1.31
300 334 3.527665 AGGCAATGTGGGACTAAACCTAT 59.472 43.478 0.00 0.00 0.00 2.57
301 335 2.916934 AGGCAATGTGGGACTAAACCTA 59.083 45.455 0.00 0.00 0.00 3.08
302 336 1.710809 AGGCAATGTGGGACTAAACCT 59.289 47.619 0.00 0.00 0.00 3.50
303 337 2.215942 AGGCAATGTGGGACTAAACC 57.784 50.000 0.00 0.00 0.00 3.27
304 338 2.683362 GCTAGGCAATGTGGGACTAAAC 59.317 50.000 0.00 0.00 0.00 2.01
305 339 2.356741 GGCTAGGCAATGTGGGACTAAA 60.357 50.000 12.16 0.00 0.00 1.85
306 340 1.211949 GGCTAGGCAATGTGGGACTAA 59.788 52.381 12.16 0.00 0.00 2.24
307 341 0.837272 GGCTAGGCAATGTGGGACTA 59.163 55.000 12.16 0.00 0.00 2.59
308 342 0.916358 AGGCTAGGCAATGTGGGACT 60.916 55.000 19.70 0.00 0.00 3.85
309 343 0.034089 AAGGCTAGGCAATGTGGGAC 60.034 55.000 19.70 0.00 0.00 4.46
310 344 0.704076 AAAGGCTAGGCAATGTGGGA 59.296 50.000 19.70 0.00 0.00 4.37
311 345 0.819582 CAAAGGCTAGGCAATGTGGG 59.180 55.000 19.70 0.00 0.00 4.61
312 346 1.474077 GTCAAAGGCTAGGCAATGTGG 59.526 52.381 19.70 1.83 0.00 4.17
313 347 1.474077 GGTCAAAGGCTAGGCAATGTG 59.526 52.381 19.70 10.20 0.00 3.21
314 348 1.616994 GGGTCAAAGGCTAGGCAATGT 60.617 52.381 19.70 0.00 0.00 2.71
315 349 1.106285 GGGTCAAAGGCTAGGCAATG 58.894 55.000 19.70 15.96 0.00 2.82
316 350 0.033109 GGGGTCAAAGGCTAGGCAAT 60.033 55.000 19.70 3.76 0.00 3.56
317 351 1.140134 AGGGGTCAAAGGCTAGGCAA 61.140 55.000 19.70 0.00 0.00 4.52
318 352 0.252974 TAGGGGTCAAAGGCTAGGCA 60.253 55.000 19.70 0.00 0.00 4.75
319 353 0.916809 TTAGGGGTCAAAGGCTAGGC 59.083 55.000 8.55 8.55 0.00 3.93
320 354 2.356844 GGTTTAGGGGTCAAAGGCTAGG 60.357 54.545 0.00 0.00 0.00 3.02
321 355 2.576648 AGGTTTAGGGGTCAAAGGCTAG 59.423 50.000 0.00 0.00 0.00 3.42
322 356 2.574824 GAGGTTTAGGGGTCAAAGGCTA 59.425 50.000 0.00 0.00 0.00 3.93
323 357 1.354705 GAGGTTTAGGGGTCAAAGGCT 59.645 52.381 0.00 0.00 0.00 4.58
324 358 1.616187 GGAGGTTTAGGGGTCAAAGGC 60.616 57.143 0.00 0.00 0.00 4.35
325 359 1.993301 AGGAGGTTTAGGGGTCAAAGG 59.007 52.381 0.00 0.00 0.00 3.11
326 360 3.808834 AAGGAGGTTTAGGGGTCAAAG 57.191 47.619 0.00 0.00 0.00 2.77
327 361 3.181426 GGAAAGGAGGTTTAGGGGTCAAA 60.181 47.826 0.00 0.00 0.00 2.69
328 362 2.377531 GGAAAGGAGGTTTAGGGGTCAA 59.622 50.000 0.00 0.00 0.00 3.18
329 363 1.990327 GGAAAGGAGGTTTAGGGGTCA 59.010 52.381 0.00 0.00 0.00 4.02
330 364 1.990327 TGGAAAGGAGGTTTAGGGGTC 59.010 52.381 0.00 0.00 0.00 4.46
331 365 1.709115 GTGGAAAGGAGGTTTAGGGGT 59.291 52.381 0.00 0.00 0.00 4.95
332 366 1.005569 GGTGGAAAGGAGGTTTAGGGG 59.994 57.143 0.00 0.00 0.00 4.79
333 367 1.993301 AGGTGGAAAGGAGGTTTAGGG 59.007 52.381 0.00 0.00 0.00 3.53
334 368 6.570654 TTATAGGTGGAAAGGAGGTTTAGG 57.429 41.667 0.00 0.00 0.00 2.69
338 372 9.684702 TCTATATTTATAGGTGGAAAGGAGGTT 57.315 33.333 5.08 0.00 37.00 3.50
339 373 9.102453 GTCTATATTTATAGGTGGAAAGGAGGT 57.898 37.037 5.08 0.00 37.00 3.85
340 374 9.327731 AGTCTATATTTATAGGTGGAAAGGAGG 57.672 37.037 5.08 0.00 37.00 4.30
342 376 9.892444 TGAGTCTATATTTATAGGTGGAAAGGA 57.108 33.333 5.08 0.00 37.00 3.36
360 394 9.163894 TGATTTTTGGAGGATCTATGAGTCTAT 57.836 33.333 0.00 0.00 33.73 1.98
361 395 8.553085 TGATTTTTGGAGGATCTATGAGTCTA 57.447 34.615 0.00 0.00 33.73 2.59
362 396 7.443302 TGATTTTTGGAGGATCTATGAGTCT 57.557 36.000 0.00 0.00 33.73 3.24
363 397 8.156165 AGATGATTTTTGGAGGATCTATGAGTC 58.844 37.037 0.00 0.00 33.73 3.36
364 398 7.937942 CAGATGATTTTTGGAGGATCTATGAGT 59.062 37.037 0.00 0.00 33.73 3.41
365 399 8.155510 TCAGATGATTTTTGGAGGATCTATGAG 58.844 37.037 0.00 0.00 33.73 2.90
366 400 8.037723 TCAGATGATTTTTGGAGGATCTATGA 57.962 34.615 0.00 0.00 33.73 2.15
367 401 8.865420 ATCAGATGATTTTTGGAGGATCTATG 57.135 34.615 0.00 0.00 33.73 2.23
368 402 9.517868 GAATCAGATGATTTTTGGAGGATCTAT 57.482 33.333 9.33 0.00 44.14 1.98
369 403 7.658982 CGAATCAGATGATTTTTGGAGGATCTA 59.341 37.037 9.33 0.00 44.14 1.98
370 404 6.485984 CGAATCAGATGATTTTTGGAGGATCT 59.514 38.462 9.33 0.00 44.14 2.75
371 405 6.293845 CCGAATCAGATGATTTTTGGAGGATC 60.294 42.308 9.33 0.00 44.14 3.36
372 406 5.533903 CCGAATCAGATGATTTTTGGAGGAT 59.466 40.000 9.33 0.00 44.14 3.24
373 407 4.883585 CCGAATCAGATGATTTTTGGAGGA 59.116 41.667 9.33 0.00 44.14 3.71
374 408 4.037208 CCCGAATCAGATGATTTTTGGAGG 59.963 45.833 17.23 11.07 44.14 4.30
375 409 4.641989 ACCCGAATCAGATGATTTTTGGAG 59.358 41.667 18.20 12.76 44.14 3.86
376 410 4.599041 ACCCGAATCAGATGATTTTTGGA 58.401 39.130 18.20 0.00 44.14 3.53
377 411 4.989279 ACCCGAATCAGATGATTTTTGG 57.011 40.909 9.33 11.68 44.14 3.28
378 412 8.931385 ATTTAACCCGAATCAGATGATTTTTG 57.069 30.769 9.33 4.20 44.14 2.44
379 413 8.748412 TGATTTAACCCGAATCAGATGATTTTT 58.252 29.630 9.33 4.42 44.14 1.94
380 414 8.292444 TGATTTAACCCGAATCAGATGATTTT 57.708 30.769 9.33 3.16 44.14 1.82
381 415 7.880160 TGATTTAACCCGAATCAGATGATTT 57.120 32.000 9.33 0.00 44.14 2.17
382 416 7.880160 TTGATTTAACCCGAATCAGATGATT 57.120 32.000 7.77 7.77 46.54 2.57
383 417 9.745018 ATATTGATTTAACCCGAATCAGATGAT 57.255 29.630 0.00 0.00 42.54 2.45
384 418 9.573166 AATATTGATTTAACCCGAATCAGATGA 57.427 29.630 0.00 0.00 42.54 2.92
388 422 9.248291 CCAAAATATTGATTTAACCCGAATCAG 57.752 33.333 0.00 0.00 42.54 2.90
389 423 8.754080 ACCAAAATATTGATTTAACCCGAATCA 58.246 29.630 0.00 0.00 40.65 2.57
390 424 9.594478 AACCAAAATATTGATTTAACCCGAATC 57.406 29.630 0.00 0.00 38.94 2.52
391 425 9.952030 AAACCAAAATATTGATTTAACCCGAAT 57.048 25.926 0.00 0.00 38.94 3.34
392 426 9.209175 CAAACCAAAATATTGATTTAACCCGAA 57.791 29.630 0.00 0.00 38.94 4.30
393 427 8.585881 TCAAACCAAAATATTGATTTAACCCGA 58.414 29.630 0.00 0.00 38.94 5.14
394 428 8.652463 GTCAAACCAAAATATTGATTTAACCCG 58.348 33.333 0.00 0.00 38.94 5.28
395 429 9.719355 AGTCAAACCAAAATATTGATTTAACCC 57.281 29.630 0.00 0.00 38.94 4.11
409 443 9.621629 TCTTTAGTGAATCTAGTCAAACCAAAA 57.378 29.630 0.00 0.00 0.00 2.44
410 444 9.621629 TTCTTTAGTGAATCTAGTCAAACCAAA 57.378 29.630 0.00 0.00 0.00 3.28
411 445 9.621629 TTTCTTTAGTGAATCTAGTCAAACCAA 57.378 29.630 0.00 0.00 0.00 3.67
412 446 9.621629 TTTTCTTTAGTGAATCTAGTCAAACCA 57.378 29.630 0.00 0.00 0.00 3.67
431 465 9.343539 CCGGAGAGGAGAAATATATTTTTCTTT 57.656 33.333 21.58 13.72 44.04 2.52
432 466 7.445707 GCCGGAGAGGAGAAATATATTTTTCTT 59.554 37.037 21.58 16.98 44.04 2.52
433 467 6.937465 GCCGGAGAGGAGAAATATATTTTTCT 59.063 38.462 21.58 17.76 46.08 2.52
434 468 6.128526 CGCCGGAGAGGAGAAATATATTTTTC 60.129 42.308 16.68 16.68 43.02 2.29
435 469 5.701290 CGCCGGAGAGGAGAAATATATTTTT 59.299 40.000 5.05 6.55 43.02 1.94
436 470 5.238583 CGCCGGAGAGGAGAAATATATTTT 58.761 41.667 5.05 2.96 43.02 1.82
437 471 4.322801 CCGCCGGAGAGGAGAAATATATTT 60.323 45.833 5.05 10.51 43.02 1.40
438 472 3.195825 CCGCCGGAGAGGAGAAATATATT 59.804 47.826 5.05 0.00 43.02 1.28
439 473 2.761208 CCGCCGGAGAGGAGAAATATAT 59.239 50.000 5.05 0.00 43.02 0.86
440 474 2.168496 CCGCCGGAGAGGAGAAATATA 58.832 52.381 5.05 0.00 43.02 0.86
441 475 0.969894 CCGCCGGAGAGGAGAAATAT 59.030 55.000 5.05 0.00 43.02 1.28
442 476 1.113517 CCCGCCGGAGAGGAGAAATA 61.114 60.000 5.05 0.00 43.02 1.40
443 477 2.435693 CCCGCCGGAGAGGAGAAAT 61.436 63.158 5.05 0.00 43.02 2.17
444 478 3.075005 CCCGCCGGAGAGGAGAAA 61.075 66.667 5.05 0.00 43.02 2.52
445 479 4.056584 TCCCGCCGGAGAGGAGAA 62.057 66.667 5.05 0.00 43.02 2.87
446 480 4.816984 GTCCCGCCGGAGAGGAGA 62.817 72.222 5.05 1.95 43.02 3.71
447 481 4.824515 AGTCCCGCCGGAGAGGAG 62.825 72.222 5.05 0.00 45.00 3.69
448 482 4.377760 AAGTCCCGCCGGAGAGGA 62.378 66.667 5.05 8.67 45.00 3.71
449 483 3.839432 GAAGTCCCGCCGGAGAGG 61.839 72.222 5.05 5.92 39.51 3.69
450 484 2.756283 AGAAGTCCCGCCGGAGAG 60.756 66.667 5.05 0.00 39.51 3.20
451 485 3.068691 CAGAAGTCCCGCCGGAGA 61.069 66.667 5.05 0.00 39.51 3.71
452 486 4.148825 CCAGAAGTCCCGCCGGAG 62.149 72.222 5.05 0.00 39.51 4.63
453 487 4.689549 TCCAGAAGTCCCGCCGGA 62.690 66.667 5.05 0.00 35.01 5.14
454 488 3.665675 CTTCCAGAAGTCCCGCCGG 62.666 68.421 0.00 0.00 33.87 6.13
455 489 2.125512 CTTCCAGAAGTCCCGCCG 60.126 66.667 0.00 0.00 33.87 6.46
463 497 5.468409 GGAGAGAAAAGACAACTTCCAGAAG 59.532 44.000 5.85 5.85 43.79 2.85
464 498 5.368989 GGAGAGAAAAGACAACTTCCAGAA 58.631 41.667 0.00 0.00 35.05 3.02
465 499 4.501571 CGGAGAGAAAAGACAACTTCCAGA 60.502 45.833 0.00 0.00 35.05 3.86
466 500 3.743396 CGGAGAGAAAAGACAACTTCCAG 59.257 47.826 0.00 0.00 35.05 3.86
467 501 3.386726 TCGGAGAGAAAAGACAACTTCCA 59.613 43.478 0.00 0.00 35.05 3.53
468 502 3.991367 TCGGAGAGAAAAGACAACTTCC 58.009 45.455 0.00 0.00 35.05 3.46
469 503 5.051153 ACTTCGGAGAGAAAAGACAACTTC 58.949 41.667 0.00 0.00 38.57 3.01
470 504 5.024785 ACTTCGGAGAGAAAAGACAACTT 57.975 39.130 0.00 0.00 38.57 2.66
471 505 4.099573 TGACTTCGGAGAGAAAAGACAACT 59.900 41.667 0.00 0.00 38.57 3.16
472 506 4.369182 TGACTTCGGAGAGAAAAGACAAC 58.631 43.478 0.00 0.00 38.57 3.32
473 507 4.665833 TGACTTCGGAGAGAAAAGACAA 57.334 40.909 0.00 0.00 38.57 3.18
474 508 4.873746 ATGACTTCGGAGAGAAAAGACA 57.126 40.909 0.00 0.00 38.57 3.41
475 509 6.546972 AAAATGACTTCGGAGAGAAAAGAC 57.453 37.500 0.00 0.00 38.57 3.01
572 606 8.571336 GCCAGTGCATTTTACTCATCTAATTAT 58.429 33.333 0.00 0.00 37.47 1.28
573 607 7.254761 CGCCAGTGCATTTTACTCATCTAATTA 60.255 37.037 0.00 0.00 37.32 1.40
574 608 6.458751 CGCCAGTGCATTTTACTCATCTAATT 60.459 38.462 0.00 0.00 37.32 1.40
575 609 5.008019 CGCCAGTGCATTTTACTCATCTAAT 59.992 40.000 0.00 0.00 37.32 1.73
576 610 4.332543 CGCCAGTGCATTTTACTCATCTAA 59.667 41.667 0.00 0.00 37.32 2.10
577 611 3.871006 CGCCAGTGCATTTTACTCATCTA 59.129 43.478 0.00 0.00 37.32 1.98
578 612 2.679837 CGCCAGTGCATTTTACTCATCT 59.320 45.455 0.00 0.00 37.32 2.90
690 724 0.665369 CGTACGGTGAACAGTGACCC 60.665 60.000 7.57 0.00 0.00 4.46
723 758 3.573967 GGTCAACAAGTGGTCAAATGGAT 59.426 43.478 0.00 0.00 0.00 3.41
847 911 3.015753 GGGGAGGGAGTGGGGAAC 61.016 72.222 0.00 0.00 0.00 3.62
1061 1243 0.252193 AGCAGGGCAAAAAGGGCATA 60.252 50.000 0.00 0.00 34.52 3.14
1086 1268 6.152154 TCTCCATGTTCGACACATAGAACTTA 59.848 38.462 11.26 0.00 45.06 2.24
1690 2353 7.479980 CAAACTGGAAACTACATCAACTTCAA 58.520 34.615 0.00 0.00 0.00 2.69
2064 2784 8.038862 ACTTCCCAGATATGTTATGTTCTGAT 57.961 34.615 0.00 0.00 38.25 2.90
2114 2835 9.177608 CTTCCCAGATCATTTTGTAACTGAATA 57.822 33.333 0.00 0.00 0.00 1.75
2145 2866 8.533657 TGAATGCTGGATATGTTCTGAATTTTT 58.466 29.630 0.00 0.00 0.00 1.94


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

AutoCloner maintained by Alex Coulton.