Multiple sequence alignment - TraesCS5D01G004700

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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 TraesCS5D01G004700 chr5D 100.000 3569 0 0 1 3569 3661822 3658254 0.000000e+00 6591.0
1 TraesCS5D01G004700 chr5D 99.733 2624 7 0 551 3174 3632445 3635068 0.000000e+00 4807.0
2 TraesCS5D01G004700 chr5D 85.742 1564 214 4 1003 2566 93862946 93861392 0.000000e+00 1644.0
3 TraesCS5D01G004700 chr5D 92.504 587 37 5 2987 3569 3635587 3636170 0.000000e+00 833.0
4 TraesCS5D01G004700 chr5D 91.525 472 23 6 34 494 3615830 3616295 5.030000e-178 634.0
5 TraesCS5D01G004700 chr5D 93.061 245 13 3 2378 2621 3635069 3635310 4.380000e-94 355.0
6 TraesCS5D01G004700 chr5D 91.765 170 11 2 2742 2911 3635383 3635549 2.140000e-57 233.0
7 TraesCS5D01G004700 chr5A 91.553 2427 126 29 487 2867 2618010 2615617 0.000000e+00 3273.0
8 TraesCS5D01G004700 chr5A 92.380 1273 54 25 697 1968 2430493 2429263 0.000000e+00 1773.0
9 TraesCS5D01G004700 chr5A 87.716 521 49 7 3058 3569 2428309 2427795 8.530000e-166 593.0
10 TraesCS5D01G004700 chr5A 88.679 318 35 1 3252 3569 2543156 2542840 1.550000e-103 387.0
11 TraesCS5D01G004700 chr5A 87.372 293 20 3 1 277 2431247 2430956 1.600000e-83 320.0
12 TraesCS5D01G004700 chr5A 81.046 306 58 0 3264 3569 2617475 2617170 9.900000e-61 244.0
13 TraesCS5D01G004700 chr5A 85.030 167 4 2 487 632 2430686 2430520 2.220000e-32 150.0
14 TraesCS5D01G004700 chr5A 80.000 95 7 5 2914 2996 2614018 2613924 3.850000e-05 60.2
15 TraesCS5D01G004700 chr5B 90.533 2271 108 30 492 2730 5073418 5071223 0.000000e+00 2904.0
16 TraesCS5D01G004700 chr5B 83.732 418 32 12 2768 3171 5070797 5070402 2.620000e-96 363.0
17 TraesCS5D01G004700 chr5B 80.137 292 54 3 3254 3543 5060094 5060383 7.760000e-52 215.0
18 TraesCS5D01G004700 chr5B 80.137 292 54 3 3254 3543 5067231 5066942 7.760000e-52 215.0
19 TraesCS5D01G004700 chr7A 88.835 1648 162 9 1007 2653 700300326 700301952 0.000000e+00 2004.0
20 TraesCS5D01G004700 chr7A 88.592 1648 166 9 1007 2653 700338144 700339770 0.000000e+00 1982.0
21 TraesCS5D01G004700 chr7D 88.303 1650 159 10 1005 2653 610421486 610419870 0.000000e+00 1947.0
22 TraesCS5D01G004700 chr7D 80.667 1200 159 41 1465 2647 610708530 610709673 0.000000e+00 863.0
23 TraesCS5D01G004700 chr7D 84.615 208 20 9 2438 2645 610247064 610246869 2.810000e-46 196.0
24 TraesCS5D01G004700 chr7D 79.646 226 38 7 3348 3569 610404587 610404366 4.770000e-34 156.0
25 TraesCS5D01G004700 chr7B 87.697 1650 181 8 1005 2653 698682826 698684454 0.000000e+00 1903.0
26 TraesCS5D01G004700 chrUn 87.273 1650 176 13 1005 2653 77521436 77523052 0.000000e+00 1853.0
27 TraesCS5D01G004700 chrUn 84.034 1190 159 19 1465 2647 83464335 83463170 0.000000e+00 1116.0
28 TraesCS5D01G004700 chrUn 80.576 278 49 4 3256 3530 83474701 83474426 3.610000e-50 209.0
29 TraesCS5D01G004700 chr4A 81.649 1019 124 29 1634 2647 661998030 661997070 0.000000e+00 787.0


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 TraesCS5D01G004700 chr5D 3658254 3661822 3568 True 6591.000000 6591 100.000000 1 3569 1 chr5D.!!$R1 3568
1 TraesCS5D01G004700 chr5D 93861392 93862946 1554 True 1644.000000 1644 85.742000 1003 2566 1 chr5D.!!$R2 1563
2 TraesCS5D01G004700 chr5D 3632445 3636170 3725 False 1557.000000 4807 94.265750 551 3569 4 chr5D.!!$F2 3018
3 TraesCS5D01G004700 chr5A 2613924 2618010 4086 True 1192.400000 3273 84.199667 487 3569 3 chr5A.!!$R3 3082
4 TraesCS5D01G004700 chr5A 2427795 2431247 3452 True 709.000000 1773 88.124500 1 3569 4 chr5A.!!$R2 3568
5 TraesCS5D01G004700 chr5B 5066942 5073418 6476 True 1160.666667 2904 84.800667 492 3543 3 chr5B.!!$R1 3051
6 TraesCS5D01G004700 chr7A 700300326 700301952 1626 False 2004.000000 2004 88.835000 1007 2653 1 chr7A.!!$F1 1646
7 TraesCS5D01G004700 chr7A 700338144 700339770 1626 False 1982.000000 1982 88.592000 1007 2653 1 chr7A.!!$F2 1646
8 TraesCS5D01G004700 chr7D 610419870 610421486 1616 True 1947.000000 1947 88.303000 1005 2653 1 chr7D.!!$R3 1648
9 TraesCS5D01G004700 chr7D 610708530 610709673 1143 False 863.000000 863 80.667000 1465 2647 1 chr7D.!!$F1 1182
10 TraesCS5D01G004700 chr7B 698682826 698684454 1628 False 1903.000000 1903 87.697000 1005 2653 1 chr7B.!!$F1 1648
11 TraesCS5D01G004700 chrUn 77521436 77523052 1616 False 1853.000000 1853 87.273000 1005 2653 1 chrUn.!!$F1 1648
12 TraesCS5D01G004700 chrUn 83463170 83464335 1165 True 1116.000000 1116 84.034000 1465 2647 1 chrUn.!!$R1 1182
13 TraesCS5D01G004700 chr4A 661997070 661998030 960 True 787.000000 787 81.649000 1634 2647 1 chr4A.!!$R1 1013

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
370 386 0.033011 ACCATCGAGTAGCCAGAGGT 60.033 55.0 0.0 0.0 0.0 3.85 F
385 401 0.321653 GAGGTTGAGGTTGATGGCGT 60.322 55.0 0.0 0.0 0.0 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2334 2493 2.965147 CAAACACAAATCAGGGTCCCTT 59.035 45.455 8.08 0.0 0.00 3.95 R
2999 5864 4.214986 TCAGATTTGGGTCGCTTAATCA 57.785 40.909 13.65 0.0 31.12 2.57 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
27 28 3.426615 TCAACAACAAACACCACCTCTT 58.573 40.909 0.00 0.00 0.00 2.85
96 97 2.856760 TCCTCCTATCCTGCTCAGTT 57.143 50.000 0.00 0.00 0.00 3.16
120 121 3.741476 CTTCCAAGCTGCACGGCC 61.741 66.667 1.02 0.00 0.00 6.13
162 163 5.012046 TGACTGAATCACCACACACTATCTT 59.988 40.000 0.00 0.00 29.99 2.40
186 202 1.207488 ACTGCCATGCCACCCTCTAA 61.207 55.000 0.00 0.00 0.00 2.10
194 210 1.049289 GCCACCCTCTAACCGGAGAT 61.049 60.000 9.46 0.00 35.52 2.75
239 255 1.965643 GTCCCACCCCAAACCTTAAAC 59.034 52.381 0.00 0.00 0.00 2.01
265 281 2.621526 CACCACAACCTAAAACCTCCAC 59.378 50.000 0.00 0.00 0.00 4.02
267 283 3.146847 CCACAACCTAAAACCTCCACTC 58.853 50.000 0.00 0.00 0.00 3.51
270 286 3.244112 ACAACCTAAAACCTCCACTCTCG 60.244 47.826 0.00 0.00 0.00 4.04
271 287 1.275573 ACCTAAAACCTCCACTCTCGC 59.724 52.381 0.00 0.00 0.00 5.03
277 293 2.752238 CTCCACTCTCGCCTCCGT 60.752 66.667 0.00 0.00 35.54 4.69
279 295 2.752238 CCACTCTCGCCTCCGTCT 60.752 66.667 0.00 0.00 35.54 4.18
280 296 2.344203 CCACTCTCGCCTCCGTCTT 61.344 63.158 0.00 0.00 35.54 3.01
281 297 1.030488 CCACTCTCGCCTCCGTCTTA 61.030 60.000 0.00 0.00 35.54 2.10
283 299 0.252479 ACTCTCGCCTCCGTCTTAGA 59.748 55.000 0.00 0.00 35.54 2.10
284 300 0.658897 CTCTCGCCTCCGTCTTAGAC 59.341 60.000 1.64 1.64 35.54 2.59
285 301 0.252479 TCTCGCCTCCGTCTTAGACT 59.748 55.000 10.83 0.00 35.54 3.24
286 302 0.658897 CTCGCCTCCGTCTTAGACTC 59.341 60.000 10.83 0.00 35.54 3.36
287 303 1.088340 TCGCCTCCGTCTTAGACTCG 61.088 60.000 10.83 6.24 35.54 4.18
288 304 1.728672 GCCTCCGTCTTAGACTCGG 59.271 63.158 10.83 7.82 44.76 4.63
289 305 1.031029 GCCTCCGTCTTAGACTCGGT 61.031 60.000 10.83 0.00 43.94 4.69
290 306 1.015868 CCTCCGTCTTAGACTCGGTC 58.984 60.000 10.83 0.00 43.94 4.79
291 307 1.015868 CTCCGTCTTAGACTCGGTCC 58.984 60.000 10.83 0.00 43.94 4.46
292 308 0.325933 TCCGTCTTAGACTCGGTCCA 59.674 55.000 10.83 0.00 43.94 4.02
293 309 1.064906 TCCGTCTTAGACTCGGTCCAT 60.065 52.381 10.83 0.00 43.94 3.41
295 311 2.290093 CCGTCTTAGACTCGGTCCATAC 59.710 54.545 10.83 0.00 39.51 2.39
296 312 3.204526 CGTCTTAGACTCGGTCCATACT 58.795 50.000 10.83 0.00 32.18 2.12
297 313 3.248125 CGTCTTAGACTCGGTCCATACTC 59.752 52.174 10.83 0.00 32.18 2.59
299 315 1.590932 TAGACTCGGTCCATACTCGC 58.409 55.000 1.06 0.00 32.18 5.03
301 317 2.331805 CTCGGTCCATACTCGCCG 59.668 66.667 0.00 0.00 44.95 6.46
303 319 3.900892 CGGTCCATACTCGCCGCT 61.901 66.667 0.00 0.00 37.69 5.52
304 320 2.279517 GGTCCATACTCGCCGCTG 60.280 66.667 0.00 0.00 0.00 5.18
305 321 2.494918 GTCCATACTCGCCGCTGT 59.505 61.111 0.00 0.00 0.00 4.40
306 322 1.589196 GTCCATACTCGCCGCTGTC 60.589 63.158 0.00 0.00 0.00 3.51
307 323 2.655364 CCATACTCGCCGCTGTCG 60.655 66.667 0.00 0.00 0.00 4.35
308 324 2.102357 CATACTCGCCGCTGTCGT 59.898 61.111 0.00 0.00 0.00 4.34
318 334 4.702826 GCTGTCGTCGCACGCAAC 62.703 66.667 4.15 0.27 42.21 4.17
319 335 3.030308 CTGTCGTCGCACGCAACT 61.030 61.111 4.15 0.00 42.21 3.16
320 336 2.988549 CTGTCGTCGCACGCAACTC 61.989 63.158 4.15 0.00 42.21 3.01
322 338 4.273257 TCGTCGCACGCAACTCCA 62.273 61.111 4.15 0.00 42.21 3.86
323 339 3.112075 CGTCGCACGCAACTCCAT 61.112 61.111 0.00 0.00 33.65 3.41
324 340 2.476051 GTCGCACGCAACTCCATG 59.524 61.111 0.00 0.00 0.00 3.66
326 342 4.465512 CGCACGCAACTCCATGCC 62.466 66.667 0.00 0.00 43.47 4.40
329 345 1.885157 CACGCAACTCCATGCCAAT 59.115 52.632 0.00 0.00 43.47 3.16
330 346 0.457166 CACGCAACTCCATGCCAATG 60.457 55.000 0.00 0.00 43.47 2.82
332 348 1.895238 GCAACTCCATGCCAATGCT 59.105 52.632 5.00 0.00 40.49 3.79
333 349 1.105457 GCAACTCCATGCCAATGCTA 58.895 50.000 5.00 0.00 40.49 3.49
334 350 1.684983 GCAACTCCATGCCAATGCTAT 59.315 47.619 5.00 0.00 40.49 2.97
335 351 2.288030 GCAACTCCATGCCAATGCTATC 60.288 50.000 5.00 0.00 40.49 2.08
336 352 3.220110 CAACTCCATGCCAATGCTATCT 58.780 45.455 0.00 0.00 38.71 1.98
338 354 2.709934 ACTCCATGCCAATGCTATCTCT 59.290 45.455 0.00 0.00 38.71 3.10
340 356 1.540267 CCATGCCAATGCTATCTCTGC 59.460 52.381 0.00 0.00 38.71 4.26
341 357 1.540267 CATGCCAATGCTATCTCTGCC 59.460 52.381 0.00 0.00 38.71 4.85
342 358 0.841961 TGCCAATGCTATCTCTGCCT 59.158 50.000 0.00 0.00 38.71 4.75
343 359 1.213678 TGCCAATGCTATCTCTGCCTT 59.786 47.619 0.00 0.00 38.71 4.35
346 362 3.752665 CCAATGCTATCTCTGCCTTGAT 58.247 45.455 0.00 0.00 37.95 2.57
349 365 1.487558 TGCTATCTCTGCCTTGATGCA 59.512 47.619 0.00 0.00 39.37 3.96
350 366 1.872313 GCTATCTCTGCCTTGATGCAC 59.128 52.381 0.00 0.00 36.04 4.57
351 367 2.744166 GCTATCTCTGCCTTGATGCACA 60.744 50.000 0.00 0.00 36.04 4.57
352 368 1.747709 ATCTCTGCCTTGATGCACAC 58.252 50.000 0.00 0.00 36.04 3.82
353 369 0.321919 TCTCTGCCTTGATGCACACC 60.322 55.000 0.00 0.00 36.04 4.16
354 370 0.607217 CTCTGCCTTGATGCACACCA 60.607 55.000 0.00 0.00 36.04 4.17
355 371 0.038599 TCTGCCTTGATGCACACCAT 59.961 50.000 0.00 0.00 36.04 3.55
363 379 1.212616 GATGCACACCATCGAGTAGC 58.787 55.000 0.00 0.00 40.84 3.58
366 382 0.807667 GCACACCATCGAGTAGCCAG 60.808 60.000 0.00 0.00 0.00 4.85
367 383 0.817654 CACACCATCGAGTAGCCAGA 59.182 55.000 0.00 0.00 0.00 3.86
368 384 1.107114 ACACCATCGAGTAGCCAGAG 58.893 55.000 0.00 0.00 0.00 3.35
369 385 0.387202 CACCATCGAGTAGCCAGAGG 59.613 60.000 0.00 0.00 0.00 3.69
370 386 0.033011 ACCATCGAGTAGCCAGAGGT 60.033 55.000 0.00 0.00 0.00 3.85
371 387 1.115467 CCATCGAGTAGCCAGAGGTT 58.885 55.000 0.00 0.00 0.00 3.50
372 388 1.202463 CCATCGAGTAGCCAGAGGTTG 60.202 57.143 0.00 0.00 0.00 3.77
373 389 1.751351 CATCGAGTAGCCAGAGGTTGA 59.249 52.381 0.00 0.00 0.00 3.18
374 390 1.464734 TCGAGTAGCCAGAGGTTGAG 58.535 55.000 0.00 0.00 0.00 3.02
375 391 0.457851 CGAGTAGCCAGAGGTTGAGG 59.542 60.000 0.00 0.00 0.00 3.86
377 393 1.903183 GAGTAGCCAGAGGTTGAGGTT 59.097 52.381 0.00 0.00 0.00 3.50
378 394 1.625818 AGTAGCCAGAGGTTGAGGTTG 59.374 52.381 0.00 0.00 0.00 3.77
379 395 1.623811 GTAGCCAGAGGTTGAGGTTGA 59.376 52.381 0.00 0.00 0.00 3.18
380 396 1.366319 AGCCAGAGGTTGAGGTTGAT 58.634 50.000 0.00 0.00 0.00 2.57
382 398 1.952367 GCCAGAGGTTGAGGTTGATGG 60.952 57.143 0.00 0.00 0.00 3.51
383 399 1.457346 CAGAGGTTGAGGTTGATGGC 58.543 55.000 0.00 0.00 0.00 4.40
385 401 0.321653 GAGGTTGAGGTTGATGGCGT 60.322 55.000 0.00 0.00 0.00 5.68
386 402 0.981183 AGGTTGAGGTTGATGGCGTA 59.019 50.000 0.00 0.00 0.00 4.42
387 403 1.559682 AGGTTGAGGTTGATGGCGTAT 59.440 47.619 0.00 0.00 0.00 3.06
388 404 2.026262 AGGTTGAGGTTGATGGCGTATT 60.026 45.455 0.00 0.00 0.00 1.89
389 405 3.199071 AGGTTGAGGTTGATGGCGTATTA 59.801 43.478 0.00 0.00 0.00 0.98
390 406 3.942748 GGTTGAGGTTGATGGCGTATTAA 59.057 43.478 0.00 0.00 0.00 1.40
391 407 4.578928 GGTTGAGGTTGATGGCGTATTAAT 59.421 41.667 0.00 0.00 0.00 1.40
392 408 5.761234 GGTTGAGGTTGATGGCGTATTAATA 59.239 40.000 0.00 0.00 0.00 0.98
393 409 6.261381 GGTTGAGGTTGATGGCGTATTAATAA 59.739 38.462 0.00 0.00 0.00 1.40
394 410 7.201750 GGTTGAGGTTGATGGCGTATTAATAAA 60.202 37.037 0.00 0.00 0.00 1.40
396 412 7.276658 TGAGGTTGATGGCGTATTAATAAAGA 58.723 34.615 0.00 0.00 0.00 2.52
398 414 6.710744 AGGTTGATGGCGTATTAATAAAGAGG 59.289 38.462 0.00 0.00 0.00 3.69
399 415 6.708949 GGTTGATGGCGTATTAATAAAGAGGA 59.291 38.462 0.00 0.00 0.00 3.71
400 416 7.227910 GGTTGATGGCGTATTAATAAAGAGGAA 59.772 37.037 0.00 0.00 0.00 3.36
401 417 8.617809 GTTGATGGCGTATTAATAAAGAGGAAA 58.382 33.333 0.00 0.00 0.00 3.13
403 419 9.179909 TGATGGCGTATTAATAAAGAGGAAAAA 57.820 29.630 0.00 0.00 0.00 1.94
428 444 5.089970 AGATAGTTGCATGTTGTCTAGCA 57.910 39.130 0.00 0.00 34.79 3.49
429 445 5.491070 AGATAGTTGCATGTTGTCTAGCAA 58.509 37.500 0.00 0.00 43.90 3.91
433 449 8.279970 ATAGTTGCATGTTGTCTAGCAAATAA 57.720 30.769 9.64 0.00 46.16 1.40
434 450 8.739039 ATAGTTGCATGTTGTCTAGCAAATAAA 58.261 29.630 9.64 0.00 46.16 1.40
436 452 7.815398 TTGCATGTTGTCTAGCAAATAAATG 57.185 32.000 0.00 5.53 43.24 2.32
437 453 5.806502 TGCATGTTGTCTAGCAAATAAATGC 59.193 36.000 18.31 18.31 46.78 3.56
452 468 8.905702 GCAAATAAATGCGAAGATAAGTATTGG 58.094 33.333 0.00 0.00 36.45 3.16
453 469 9.398170 CAAATAAATGCGAAGATAAGTATTGGG 57.602 33.333 0.00 0.00 0.00 4.12
454 470 8.918202 AATAAATGCGAAGATAAGTATTGGGA 57.082 30.769 0.00 0.00 0.00 4.37
455 471 9.520515 AATAAATGCGAAGATAAGTATTGGGAT 57.479 29.630 0.00 0.00 0.00 3.85
457 473 4.556233 TGCGAAGATAAGTATTGGGATCG 58.444 43.478 0.00 0.00 0.00 3.69
458 474 4.279922 TGCGAAGATAAGTATTGGGATCGA 59.720 41.667 0.00 0.00 0.00 3.59
460 476 5.565045 GCGAAGATAAGTATTGGGATCGACT 60.565 44.000 0.00 0.00 0.00 4.18
461 477 6.349115 GCGAAGATAAGTATTGGGATCGACTA 60.349 42.308 0.00 0.00 0.00 2.59
466 482 9.756571 AGATAAGTATTGGGATCGACTATTAGT 57.243 33.333 0.00 0.00 0.00 2.24
470 486 8.937207 AGTATTGGGATCGACTATTAGTAAGT 57.063 34.615 0.00 0.00 0.00 2.24
471 487 9.364653 AGTATTGGGATCGACTATTAGTAAGTT 57.635 33.333 0.00 0.00 0.00 2.66
472 488 9.408069 GTATTGGGATCGACTATTAGTAAGTTG 57.592 37.037 0.00 0.00 0.00 3.16
473 489 5.839621 TGGGATCGACTATTAGTAAGTTGC 58.160 41.667 0.00 0.00 0.00 4.17
474 490 5.221382 TGGGATCGACTATTAGTAAGTTGCC 60.221 44.000 0.00 5.23 0.00 4.52
475 491 5.010820 GGGATCGACTATTAGTAAGTTGCCT 59.989 44.000 0.00 0.00 0.00 4.75
477 493 5.258456 TCGACTATTAGTAAGTTGCCTGG 57.742 43.478 0.00 0.00 0.00 4.45
478 494 4.951715 TCGACTATTAGTAAGTTGCCTGGA 59.048 41.667 0.00 0.00 0.00 3.86
479 495 5.419788 TCGACTATTAGTAAGTTGCCTGGAA 59.580 40.000 0.00 0.00 0.00 3.53
481 497 6.592607 CGACTATTAGTAAGTTGCCTGGAAAA 59.407 38.462 0.00 0.00 0.00 2.29
482 498 7.118680 CGACTATTAGTAAGTTGCCTGGAAAAA 59.881 37.037 0.00 0.00 0.00 1.94
831 933 2.868787 GGCGACGACGACGAAGAC 60.869 66.667 22.94 5.57 42.66 3.01
2398 2557 4.394712 AGGCCAAGGAAGACGCGG 62.395 66.667 12.47 0.00 0.00 6.46
2629 2804 1.145571 TGTTCACTAGTGCCCCCTTT 58.854 50.000 18.45 0.00 0.00 3.11
2630 2805 2.340731 TGTTCACTAGTGCCCCCTTTA 58.659 47.619 18.45 0.00 0.00 1.85
2960 5810 2.559668 TCGTCACAATCGGAACTTACCT 59.440 45.455 0.00 0.00 0.00 3.08
2961 5811 3.758023 TCGTCACAATCGGAACTTACCTA 59.242 43.478 0.00 0.00 0.00 3.08
2996 5861 8.359875 TGATTAAGCAACCCAAATCTGAATTA 57.640 30.769 0.00 0.00 31.16 1.40
2997 5862 8.811017 TGATTAAGCAACCCAAATCTGAATTAA 58.189 29.630 0.00 0.00 31.16 1.40
2998 5863 9.822185 GATTAAGCAACCCAAATCTGAATTAAT 57.178 29.630 0.00 0.00 0.00 1.40
3000 5865 7.910441 AAGCAACCCAAATCTGAATTAATTG 57.090 32.000 5.17 0.00 0.00 2.32
3001 5866 7.243604 AGCAACCCAAATCTGAATTAATTGA 57.756 32.000 5.17 0.00 0.00 2.57
3002 5867 7.854337 AGCAACCCAAATCTGAATTAATTGAT 58.146 30.769 5.17 0.31 0.00 2.57
3003 5868 8.323567 AGCAACCCAAATCTGAATTAATTGATT 58.676 29.630 5.17 6.67 0.00 2.57
3008 5873 8.971321 CCCAAATCTGAATTAATTGATTAAGCG 58.029 33.333 5.17 0.89 35.88 4.68
3012 5877 7.259290 TCTGAATTAATTGATTAAGCGACCC 57.741 36.000 5.17 0.00 35.88 4.46
3014 5879 7.338196 TCTGAATTAATTGATTAAGCGACCCAA 59.662 33.333 5.17 0.00 35.88 4.12
3015 5880 7.831753 TGAATTAATTGATTAAGCGACCCAAA 58.168 30.769 5.17 0.00 35.88 3.28
3020 5885 4.214986 TGATTAAGCGACCCAAATCTGA 57.785 40.909 0.00 0.00 31.16 3.27
3051 5916 9.438228 GCCCTTCTACCTAGTAATTAATTGATC 57.562 37.037 11.05 2.01 0.00 2.92
3135 6057 1.545614 CCGACGACAACAACGACCAG 61.546 60.000 0.00 0.00 34.70 4.00
3252 6177 0.387565 GAAGAAGAGAGCTAGCCGGG 59.612 60.000 12.13 0.00 0.00 5.73
3273 6198 0.040058 ATGGCAGCAATGGTGGAGAA 59.960 50.000 14.61 0.00 0.00 2.87
3280 6205 0.251297 CAATGGTGGAGAAGTGGGCA 60.251 55.000 0.00 0.00 0.00 5.36
3289 6214 3.110031 AAGTGGGCAGGGTTGGGT 61.110 61.111 0.00 0.00 0.00 4.51
3360 9411 2.356780 CGGTTACCCTCCGCCTCTT 61.357 63.158 0.00 0.00 41.48 2.85
3473 9524 0.167470 CGAGTTCTTCTACGCCGTCA 59.833 55.000 0.00 0.00 0.00 4.35
3530 9581 0.323451 TAGACTCAAGGCCGAGCTCA 60.323 55.000 15.40 0.00 36.42 4.26
3535 9586 2.284258 AAGGCCGAGCTCAGGAGT 60.284 61.111 23.26 9.94 0.00 3.85
3548 9599 2.560542 CTCAGGAGTGACAGCAGTAACT 59.439 50.000 0.00 0.00 42.39 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 3.631250 AGAGGTGGTGTTTGTTGTTGAT 58.369 40.909 0.00 0.00 0.00 2.57
96 97 0.106769 TGCAGCTTGGAAGACAACCA 60.107 50.000 0.00 0.00 34.76 3.67
125 126 4.008933 AGTCAGGTGAGGCCACGC 62.009 66.667 5.01 5.00 44.09 5.34
129 130 0.615331 TGATTCAGTCAGGTGAGGCC 59.385 55.000 0.00 0.00 37.58 5.19
135 136 1.768275 TGTGTGGTGATTCAGTCAGGT 59.232 47.619 0.00 0.00 37.56 4.00
162 163 1.568597 AGGGTGGCATGGCAGTAATTA 59.431 47.619 24.03 0.00 0.00 1.40
186 202 4.342665 GGAGAAGAAACTCATATCTCCGGT 59.657 45.833 0.00 0.00 44.72 5.28
194 210 1.485066 GGGCCGGAGAAGAAACTCATA 59.515 52.381 5.05 0.00 38.51 2.15
239 255 4.461198 AGGTTTTAGGTTGTGGTGAAGAG 58.539 43.478 0.00 0.00 0.00 2.85
265 281 0.658897 GTCTAAGACGGAGGCGAGAG 59.341 60.000 0.00 0.00 0.00 3.20
267 283 0.658897 GAGTCTAAGACGGAGGCGAG 59.341 60.000 0.00 0.00 37.67 5.03
277 293 3.464907 CGAGTATGGACCGAGTCTAAGA 58.535 50.000 4.41 0.00 32.47 2.10
279 295 1.945394 GCGAGTATGGACCGAGTCTAA 59.055 52.381 4.41 0.00 32.47 2.10
280 296 1.590932 GCGAGTATGGACCGAGTCTA 58.409 55.000 4.41 0.00 32.47 2.59
281 297 1.102222 GGCGAGTATGGACCGAGTCT 61.102 60.000 4.41 0.00 32.47 3.24
283 299 3.522808 GGCGAGTATGGACCGAGT 58.477 61.111 0.00 0.00 0.00 4.18
287 303 2.279517 CAGCGGCGAGTATGGACC 60.280 66.667 12.98 0.00 0.00 4.46
288 304 1.589196 GACAGCGGCGAGTATGGAC 60.589 63.158 12.98 0.00 0.00 4.02
289 305 2.805546 GACAGCGGCGAGTATGGA 59.194 61.111 12.98 0.00 0.00 3.41
290 306 2.655364 CGACAGCGGCGAGTATGG 60.655 66.667 12.98 0.00 0.00 2.74
291 307 1.939785 GACGACAGCGGCGAGTATG 60.940 63.158 12.98 5.63 43.17 2.39
292 308 2.408022 GACGACAGCGGCGAGTAT 59.592 61.111 12.98 0.00 43.17 2.12
301 317 4.702826 GTTGCGTGCGACGACAGC 62.703 66.667 11.94 0.00 46.05 4.40
303 319 3.028019 GAGTTGCGTGCGACGACA 61.028 61.111 11.94 7.12 46.05 4.35
304 320 3.764049 GGAGTTGCGTGCGACGAC 61.764 66.667 11.94 5.48 46.05 4.34
305 321 3.567478 ATGGAGTTGCGTGCGACGA 62.567 57.895 11.94 0.00 46.05 4.20
306 322 3.112075 ATGGAGTTGCGTGCGACG 61.112 61.111 6.58 4.61 45.88 5.12
307 323 2.476051 CATGGAGTTGCGTGCGAC 59.524 61.111 3.98 3.98 0.00 5.19
308 324 3.422303 GCATGGAGTTGCGTGCGA 61.422 61.111 2.06 0.00 32.06 5.10
314 330 1.105457 TAGCATTGGCATGGAGTTGC 58.895 50.000 0.00 0.00 44.61 4.17
315 331 3.220110 AGATAGCATTGGCATGGAGTTG 58.780 45.455 0.00 0.00 44.61 3.16
316 332 3.137913 AGAGATAGCATTGGCATGGAGTT 59.862 43.478 0.00 0.00 44.61 3.01
317 333 2.709934 AGAGATAGCATTGGCATGGAGT 59.290 45.455 0.00 0.00 44.61 3.85
318 334 3.075148 CAGAGATAGCATTGGCATGGAG 58.925 50.000 0.00 0.00 44.61 3.86
319 335 2.812983 GCAGAGATAGCATTGGCATGGA 60.813 50.000 0.00 0.00 44.61 3.41
320 336 1.540267 GCAGAGATAGCATTGGCATGG 59.460 52.381 0.00 0.00 44.61 3.66
322 338 1.424302 AGGCAGAGATAGCATTGGCAT 59.576 47.619 10.13 0.00 44.61 4.40
323 339 0.841961 AGGCAGAGATAGCATTGGCA 59.158 50.000 10.13 0.00 44.61 4.92
324 340 1.607628 CAAGGCAGAGATAGCATTGGC 59.392 52.381 4.82 0.92 46.49 4.52
329 345 1.487558 TGCATCAAGGCAGAGATAGCA 59.512 47.619 0.00 0.00 39.25 3.49
330 346 1.872313 GTGCATCAAGGCAGAGATAGC 59.128 52.381 0.00 0.00 45.96 2.97
332 348 2.420547 GGTGTGCATCAAGGCAGAGATA 60.421 50.000 0.00 0.00 45.96 1.98
333 349 1.681166 GGTGTGCATCAAGGCAGAGAT 60.681 52.381 0.00 0.00 45.96 2.75
334 350 0.321919 GGTGTGCATCAAGGCAGAGA 60.322 55.000 0.00 0.00 45.96 3.10
335 351 0.607217 TGGTGTGCATCAAGGCAGAG 60.607 55.000 0.00 0.00 45.96 3.35
336 352 0.038599 ATGGTGTGCATCAAGGCAGA 59.961 50.000 0.00 0.00 45.96 4.26
338 354 1.307355 CGATGGTGTGCATCAAGGCA 61.307 55.000 0.00 0.00 42.53 4.75
340 356 1.012086 CTCGATGGTGTGCATCAAGG 58.988 55.000 0.00 0.00 0.00 3.61
341 357 1.730501 ACTCGATGGTGTGCATCAAG 58.269 50.000 0.00 0.00 0.00 3.02
342 358 2.892374 CTACTCGATGGTGTGCATCAA 58.108 47.619 0.00 0.00 0.00 2.57
343 359 1.471501 GCTACTCGATGGTGTGCATCA 60.472 52.381 0.00 0.00 0.00 3.07
346 362 1.218047 GGCTACTCGATGGTGTGCA 59.782 57.895 0.00 0.00 0.00 4.57
349 365 1.107114 CTCTGGCTACTCGATGGTGT 58.893 55.000 0.00 0.00 0.00 4.16
350 366 0.387202 CCTCTGGCTACTCGATGGTG 59.613 60.000 0.00 0.00 0.00 4.17
351 367 0.033011 ACCTCTGGCTACTCGATGGT 60.033 55.000 0.00 0.00 0.00 3.55
352 368 1.115467 AACCTCTGGCTACTCGATGG 58.885 55.000 0.00 0.00 0.00 3.51
353 369 1.751351 TCAACCTCTGGCTACTCGATG 59.249 52.381 0.00 0.00 0.00 3.84
354 370 2.028130 CTCAACCTCTGGCTACTCGAT 58.972 52.381 0.00 0.00 0.00 3.59
355 371 1.464734 CTCAACCTCTGGCTACTCGA 58.535 55.000 0.00 0.00 0.00 4.04
356 372 0.457851 CCTCAACCTCTGGCTACTCG 59.542 60.000 0.00 0.00 0.00 4.18
358 374 1.625818 CAACCTCAACCTCTGGCTACT 59.374 52.381 0.00 0.00 0.00 2.57
359 375 1.623811 TCAACCTCAACCTCTGGCTAC 59.376 52.381 0.00 0.00 0.00 3.58
360 376 2.024176 TCAACCTCAACCTCTGGCTA 57.976 50.000 0.00 0.00 0.00 3.93
361 377 1.004044 CATCAACCTCAACCTCTGGCT 59.996 52.381 0.00 0.00 0.00 4.75
363 379 1.952367 GCCATCAACCTCAACCTCTGG 60.952 57.143 0.00 0.00 0.00 3.86
366 382 0.321653 ACGCCATCAACCTCAACCTC 60.322 55.000 0.00 0.00 0.00 3.85
367 383 0.981183 TACGCCATCAACCTCAACCT 59.019 50.000 0.00 0.00 0.00 3.50
368 384 2.038387 ATACGCCATCAACCTCAACC 57.962 50.000 0.00 0.00 0.00 3.77
369 385 5.751243 ATTAATACGCCATCAACCTCAAC 57.249 39.130 0.00 0.00 0.00 3.18
370 386 7.771361 TCTTTATTAATACGCCATCAACCTCAA 59.229 33.333 0.00 0.00 0.00 3.02
371 387 7.276658 TCTTTATTAATACGCCATCAACCTCA 58.723 34.615 0.00 0.00 0.00 3.86
372 388 7.095187 CCTCTTTATTAATACGCCATCAACCTC 60.095 40.741 0.00 0.00 0.00 3.85
373 389 6.710744 CCTCTTTATTAATACGCCATCAACCT 59.289 38.462 0.00 0.00 0.00 3.50
374 390 6.708949 TCCTCTTTATTAATACGCCATCAACC 59.291 38.462 0.00 0.00 0.00 3.77
375 391 7.724305 TCCTCTTTATTAATACGCCATCAAC 57.276 36.000 0.00 0.00 0.00 3.18
377 393 8.740123 TTTTCCTCTTTATTAATACGCCATCA 57.260 30.769 0.00 0.00 0.00 3.07
403 419 6.430925 TGCTAGACAACATGCAACTATCTTTT 59.569 34.615 0.00 0.00 32.12 2.27
404 420 5.939883 TGCTAGACAACATGCAACTATCTTT 59.060 36.000 0.00 0.00 32.12 2.52
406 422 5.089970 TGCTAGACAACATGCAACTATCT 57.910 39.130 0.00 0.00 32.12 1.98
407 423 5.801350 TTGCTAGACAACATGCAACTATC 57.199 39.130 0.00 0.00 39.98 2.08
408 424 6.764308 ATTTGCTAGACAACATGCAACTAT 57.236 33.333 0.00 0.00 43.74 2.12
409 425 7.680442 TTATTTGCTAGACAACATGCAACTA 57.320 32.000 0.00 0.00 43.74 2.24
410 426 6.573664 TTATTTGCTAGACAACATGCAACT 57.426 33.333 0.00 0.00 43.74 3.16
411 427 7.669098 CATTTATTTGCTAGACAACATGCAAC 58.331 34.615 0.00 0.00 43.74 4.17
413 429 5.806502 GCATTTATTTGCTAGACAACATGCA 59.193 36.000 16.83 0.00 38.23 3.96
414 430 5.052172 CGCATTTATTTGCTAGACAACATGC 60.052 40.000 0.00 7.82 40.54 4.06
416 432 6.435430 TCGCATTTATTTGCTAGACAACAT 57.565 33.333 0.00 0.00 40.54 2.71
417 433 5.871465 TCGCATTTATTTGCTAGACAACA 57.129 34.783 0.00 0.00 40.54 3.33
418 434 6.542852 TCTTCGCATTTATTTGCTAGACAAC 58.457 36.000 0.00 0.00 40.54 3.32
419 435 6.735678 TCTTCGCATTTATTTGCTAGACAA 57.264 33.333 0.00 0.00 40.54 3.18
420 436 6.925610 ATCTTCGCATTTATTTGCTAGACA 57.074 33.333 0.00 0.00 40.54 3.41
421 437 8.552034 ACTTATCTTCGCATTTATTTGCTAGAC 58.448 33.333 0.00 0.00 40.54 2.59
425 441 9.669353 CAATACTTATCTTCGCATTTATTTGCT 57.331 29.630 0.00 0.00 40.54 3.91
428 444 9.349713 TCCCAATACTTATCTTCGCATTTATTT 57.650 29.630 0.00 0.00 0.00 1.40
429 445 8.918202 TCCCAATACTTATCTTCGCATTTATT 57.082 30.769 0.00 0.00 0.00 1.40
430 446 9.167311 GATCCCAATACTTATCTTCGCATTTAT 57.833 33.333 0.00 0.00 0.00 1.40
431 447 7.330946 CGATCCCAATACTTATCTTCGCATTTA 59.669 37.037 0.00 0.00 0.00 1.40
432 448 6.147821 CGATCCCAATACTTATCTTCGCATTT 59.852 38.462 0.00 0.00 0.00 2.32
433 449 5.639506 CGATCCCAATACTTATCTTCGCATT 59.360 40.000 0.00 0.00 0.00 3.56
434 450 5.047306 TCGATCCCAATACTTATCTTCGCAT 60.047 40.000 0.00 0.00 0.00 4.73
436 452 4.621886 GTCGATCCCAATACTTATCTTCGC 59.378 45.833 0.00 0.00 0.00 4.70
437 453 6.015027 AGTCGATCCCAATACTTATCTTCG 57.985 41.667 0.00 0.00 0.00 3.79
440 456 9.756571 ACTAATAGTCGATCCCAATACTTATCT 57.243 33.333 0.00 0.00 0.00 1.98
444 460 9.364653 ACTTACTAATAGTCGATCCCAATACTT 57.635 33.333 0.00 0.00 0.00 2.24
445 461 8.937207 ACTTACTAATAGTCGATCCCAATACT 57.063 34.615 0.00 0.00 0.00 2.12
446 462 9.408069 CAACTTACTAATAGTCGATCCCAATAC 57.592 37.037 0.00 0.00 0.00 1.89
448 464 6.929606 GCAACTTACTAATAGTCGATCCCAAT 59.070 38.462 0.00 0.00 0.00 3.16
449 465 6.278363 GCAACTTACTAATAGTCGATCCCAA 58.722 40.000 0.00 0.00 0.00 4.12
450 466 5.221382 GGCAACTTACTAATAGTCGATCCCA 60.221 44.000 0.00 0.00 0.00 4.37
451 467 5.228665 GGCAACTTACTAATAGTCGATCCC 58.771 45.833 0.00 0.00 0.00 3.85
481 497 1.826720 AGGATGCATGACGCCAATTTT 59.173 42.857 2.46 0.00 41.33 1.82
482 498 1.406539 GAGGATGCATGACGCCAATTT 59.593 47.619 2.46 0.00 41.33 1.82
483 499 1.027357 GAGGATGCATGACGCCAATT 58.973 50.000 2.46 0.00 41.33 2.32
484 500 0.107066 TGAGGATGCATGACGCCAAT 60.107 50.000 2.46 0.00 41.33 3.16
485 501 0.745486 CTGAGGATGCATGACGCCAA 60.745 55.000 2.46 0.00 41.33 4.52
828 930 3.653009 TCGTCGCCGTTGTCGTCT 61.653 61.111 0.00 0.00 35.01 4.18
829 931 2.498761 TAGTCGTCGCCGTTGTCGTC 62.499 60.000 0.00 0.00 35.01 4.20
830 932 2.606961 TAGTCGTCGCCGTTGTCGT 61.607 57.895 0.00 0.00 35.01 4.34
831 933 2.142239 GTAGTCGTCGCCGTTGTCG 61.142 63.158 0.00 0.00 35.01 4.35
832 934 1.081906 TGTAGTCGTCGCCGTTGTC 60.082 57.895 0.00 0.00 35.01 3.18
833 935 1.370900 GTGTAGTCGTCGCCGTTGT 60.371 57.895 0.00 0.00 35.01 3.32
834 936 2.423031 CGTGTAGTCGTCGCCGTTG 61.423 63.158 0.00 0.00 35.01 4.10
835 937 2.127118 CGTGTAGTCGTCGCCGTT 60.127 61.111 0.00 0.00 35.01 4.44
836 938 2.896801 AACGTGTAGTCGTCGCCGT 61.897 57.895 0.00 0.00 43.38 5.68
837 939 2.127118 AACGTGTAGTCGTCGCCG 60.127 61.111 0.00 0.00 43.38 6.46
838 940 2.713894 GCAACGTGTAGTCGTCGCC 61.714 63.158 0.00 0.00 43.38 5.54
839 941 1.273455 AAGCAACGTGTAGTCGTCGC 61.273 55.000 0.00 0.00 42.90 5.19
2334 2493 2.965147 CAAACACAAATCAGGGTCCCTT 59.035 45.455 8.08 0.00 0.00 3.95
2996 5861 5.652014 TCAGATTTGGGTCGCTTAATCAATT 59.348 36.000 13.65 0.00 31.12 2.32
2997 5862 5.192927 TCAGATTTGGGTCGCTTAATCAAT 58.807 37.500 13.65 0.00 31.12 2.57
2998 5863 4.584874 TCAGATTTGGGTCGCTTAATCAA 58.415 39.130 13.65 0.00 31.12 2.57
2999 5864 4.214986 TCAGATTTGGGTCGCTTAATCA 57.785 40.909 13.65 0.00 31.12 2.57
3000 5865 5.757850 ATTCAGATTTGGGTCGCTTAATC 57.242 39.130 7.01 7.01 0.00 1.75
3001 5866 6.332630 CAAATTCAGATTTGGGTCGCTTAAT 58.667 36.000 4.39 0.00 45.37 1.40
3002 5867 5.708948 CAAATTCAGATTTGGGTCGCTTAA 58.291 37.500 4.39 0.00 45.37 1.85
3003 5868 5.309323 CAAATTCAGATTTGGGTCGCTTA 57.691 39.130 4.39 0.00 45.37 3.09
3014 5879 5.198602 AGGTAGAAGGGCAAATTCAGATT 57.801 39.130 0.00 0.00 0.00 2.40
3015 5880 4.870021 AGGTAGAAGGGCAAATTCAGAT 57.130 40.909 0.00 0.00 0.00 2.90
3051 5916 2.295349 AGATGCAGAACTTGGTTGCTTG 59.705 45.455 0.00 0.00 38.60 4.01
3252 6177 2.185867 CCACCATTGCTGCCATGC 59.814 61.111 8.12 0.00 0.00 4.06
3262 6187 0.038744 CTGCCCACTTCTCCACCATT 59.961 55.000 0.00 0.00 0.00 3.16
3273 6198 3.110031 AACCCAACCCTGCCCACT 61.110 61.111 0.00 0.00 0.00 4.00
3280 6205 3.264845 ATGGCCGAACCCAACCCT 61.265 61.111 0.00 0.00 38.61 4.34
3289 6214 4.488136 ATGCTCGCCATGGCCGAA 62.488 61.111 30.79 17.18 37.98 4.30
3511 9562 0.323451 TGAGCTCGGCCTTGAGTCTA 60.323 55.000 9.64 0.00 38.28 2.59
3514 9565 2.654079 CCTGAGCTCGGCCTTGAGT 61.654 63.158 17.68 0.00 38.28 3.41
3530 9581 2.548920 GCAAGTTACTGCTGTCACTCCT 60.549 50.000 10.54 0.00 39.34 3.69
3535 9586 1.140852 ACCTGCAAGTTACTGCTGTCA 59.859 47.619 0.00 0.00 43.07 3.58
3548 9599 2.741092 GTCCACGGAGACCTGCAA 59.259 61.111 0.00 0.00 0.00 4.08


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

AutoCloner maintained by Alex Coulton.