Multiple sequence alignment - TraesCS7A01G043300

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 TraesCS7A01G043300 chr7A 100.000 4298 0 0 1 4298 20050807 20046510 0.000000e+00 7938.0
1 TraesCS7A01G043300 chr7A 90.426 94 9 0 233 326 714613305 714613398 1.620000e-24 124.0
2 TraesCS7A01G043300 chrUn 96.117 3786 134 6 515 4298 50621727 50625501 0.000000e+00 6165.0
3 TraesCS7A01G043300 chrUn 84.872 390 56 3 995 1381 15550325 15550714 1.450000e-104 390.0
4 TraesCS7A01G043300 chrUn 84.615 390 57 3 995 1381 241628319 241628708 6.740000e-103 385.0
5 TraesCS7A01G043300 chrUn 84.359 390 57 4 995 1381 15774530 15774918 3.140000e-101 379.0
6 TraesCS7A01G043300 chrUn 84.359 390 58 3 995 1381 410124109 410124498 3.140000e-101 379.0
7 TraesCS7A01G043300 chrUn 84.359 390 57 4 995 1381 424221565 424221953 3.140000e-101 379.0
8 TraesCS7A01G043300 chrUn 94.531 128 6 1 1 127 50620732 50620859 3.390000e-46 196.0
9 TraesCS7A01G043300 chrUn 90.667 150 5 2 358 503 50621089 50621233 1.580000e-44 191.0
10 TraesCS7A01G043300 chr4A 84.062 3269 465 31 1000 4250 658968366 658965136 0.000000e+00 3099.0
11 TraesCS7A01G043300 chr7B 82.514 3317 541 26 996 4298 31799042 31795751 0.000000e+00 2876.0
12 TraesCS7A01G043300 chr7B 81.153 3295 569 32 1014 4298 746076182 746072930 0.000000e+00 2597.0
13 TraesCS7A01G043300 chr7B 81.262 3106 541 26 1012 4099 746387119 746384037 0.000000e+00 2473.0
14 TraesCS7A01G043300 chr7B 83.223 2712 436 11 1449 4144 746321869 746324577 0.000000e+00 2470.0
15 TraesCS7A01G043300 chr7B 81.973 2818 460 34 1501 4298 744652212 744649423 0.000000e+00 2346.0
16 TraesCS7A01G043300 chr7B 87.675 357 42 2 1014 1369 744652669 744652314 8.600000e-112 414.0
17 TraesCS7A01G043300 chr7B 88.636 88 9 1 240 326 665975941 665976028 5.880000e-19 106.0
18 TraesCS7A01G043300 chr7D 81.559 3297 578 21 1012 4296 633206016 633202738 0.000000e+00 2693.0
19 TraesCS7A01G043300 chr7D 81.267 3299 579 24 1012 4296 633033987 633030714 0.000000e+00 2632.0
20 TraesCS7A01G043300 chr7D 80.797 3312 589 27 1012 4293 633147752 633151046 0.000000e+00 2549.0
21 TraesCS7A01G043300 chr7D 79.835 1701 294 31 996 2676 631677252 631675581 0.000000e+00 1195.0
22 TraesCS7A01G043300 chr7D 87.798 377 41 4 3926 4298 19947361 19946986 1.840000e-118 436.0
23 TraesCS7A01G043300 chr7D 84.615 104 15 1 234 337 7499560 7499662 7.600000e-18 102.0
24 TraesCS7A01G043300 chr7D 88.679 53 3 2 3950 3999 71535938 71535990 1.290000e-05 62.1
25 TraesCS7A01G043300 chr5B 80.439 3328 568 59 1017 4296 663111857 663115149 0.000000e+00 2462.0
26 TraesCS7A01G043300 chr5B 89.773 88 8 1 240 326 347954116 347954203 1.260000e-20 111.0
27 TraesCS7A01G043300 chr5B 86.598 97 12 1 231 326 405706529 405706625 5.880000e-19 106.0
28 TraesCS7A01G043300 chr3B 82.583 999 165 8 3302 4298 30284409 30285400 0.000000e+00 872.0
29 TraesCS7A01G043300 chr2B 76.207 290 62 6 4009 4296 8633426 8633142 3.460000e-31 147.0
30 TraesCS7A01G043300 chr2B 76.207 290 62 6 4009 4296 8669261 8669545 3.460000e-31 147.0
31 TraesCS7A01G043300 chr2B 89.773 88 8 1 240 326 725998572 725998485 1.260000e-20 111.0
32 TraesCS7A01G043300 chr3D 88.889 90 10 0 237 326 98561909 98561998 1.260000e-20 111.0
33 TraesCS7A01G043300 chr6D 86.000 100 12 2 229 326 10417971 10418070 5.880000e-19 106.0
34 TraesCS7A01G043300 chr1B 88.043 92 6 2 240 326 263183900 263183991 2.110000e-18 104.0
35 TraesCS7A01G043300 chr1B 96.875 32 1 0 324 355 290861589 290861620 2.000000e-03 54.7
36 TraesCS7A01G043300 chr5D 97.143 35 1 0 321 355 184428596 184428562 4.640000e-05 60.2
37 TraesCS7A01G043300 chr2A 94.444 36 2 0 320 355 191318167 191318132 6.000000e-04 56.5


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 TraesCS7A01G043300 chr7A 20046510 20050807 4297 True 7938 7938 100.000000 1 4298 1 chr7A.!!$R1 4297
1 TraesCS7A01G043300 chrUn 50620732 50625501 4769 False 2184 6165 93.771667 1 4298 3 chrUn.!!$F6 4297
2 TraesCS7A01G043300 chr4A 658965136 658968366 3230 True 3099 3099 84.062000 1000 4250 1 chr4A.!!$R1 3250
3 TraesCS7A01G043300 chr7B 31795751 31799042 3291 True 2876 2876 82.514000 996 4298 1 chr7B.!!$R1 3302
4 TraesCS7A01G043300 chr7B 746072930 746076182 3252 True 2597 2597 81.153000 1014 4298 1 chr7B.!!$R2 3284
5 TraesCS7A01G043300 chr7B 746384037 746387119 3082 True 2473 2473 81.262000 1012 4099 1 chr7B.!!$R3 3087
6 TraesCS7A01G043300 chr7B 746321869 746324577 2708 False 2470 2470 83.223000 1449 4144 1 chr7B.!!$F2 2695
7 TraesCS7A01G043300 chr7B 744649423 744652669 3246 True 1380 2346 84.824000 1014 4298 2 chr7B.!!$R4 3284
8 TraesCS7A01G043300 chr7D 633202738 633206016 3278 True 2693 2693 81.559000 1012 4296 1 chr7D.!!$R4 3284
9 TraesCS7A01G043300 chr7D 633030714 633033987 3273 True 2632 2632 81.267000 1012 4296 1 chr7D.!!$R3 3284
10 TraesCS7A01G043300 chr7D 633147752 633151046 3294 False 2549 2549 80.797000 1012 4293 1 chr7D.!!$F3 3281
11 TraesCS7A01G043300 chr7D 631675581 631677252 1671 True 1195 1195 79.835000 996 2676 1 chr7D.!!$R2 1680
12 TraesCS7A01G043300 chr5B 663111857 663115149 3292 False 2462 2462 80.439000 1017 4296 1 chr5B.!!$F3 3279
13 TraesCS7A01G043300 chr3B 30284409 30285400 991 False 872 872 82.583000 3302 4298 1 chr3B.!!$F1 996

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
161 268 0.041535 TTGCTCCATGGGGATGCTTT 59.958 50.0 18.46 0.0 43.91 3.51 F
590 1184 0.107643 TCACAAAGCCACCATGACGA 59.892 50.0 0.00 0.0 0.00 4.20 F
713 1308 0.172352 CTCAGCAGACGACTTCCCTC 59.828 60.0 0.00 0.0 0.00 4.30 F
1550 2370 1.386533 GTCAGTGGATGCATTCCCAG 58.613 55.0 7.35 0.0 44.77 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1338 1933 0.671472 CAGTGTGGCGAGCATTGAGA 60.671 55.000 0.0 0.0 0.00 3.27 R
1550 2370 0.903236 AAGGAGGAGTTTACCGAGCC 59.097 55.000 0.0 0.0 34.73 4.70 R
2067 2920 1.000274 CTGCCAACTTTTTCCCCTTCG 60.000 52.381 0.0 0.0 0.00 3.79 R
3436 4305 0.957888 GCCAAGCTCCCTCAGTTCAC 60.958 60.000 0.0 0.0 0.00 3.18 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 1.448540 CAGCCACCACCACGAGATC 60.449 63.158 0.00 0.00 0.00 2.75
27 28 2.614481 GCCACCACCACGAGATCTAAAA 60.614 50.000 0.00 0.00 0.00 1.52
33 34 4.315803 CACCACGAGATCTAAAACCAAGT 58.684 43.478 0.00 0.00 0.00 3.16
35 36 5.577164 CACCACGAGATCTAAAACCAAGTAG 59.423 44.000 0.00 0.00 0.00 2.57
38 39 6.750963 CCACGAGATCTAAAACCAAGTAGTAC 59.249 42.308 0.00 0.00 0.00 2.73
124 125 3.701241 CTCGAGATCTGAAGCCAAGTAC 58.299 50.000 6.58 0.00 0.00 2.73
146 253 6.724893 ACTATTGTTTTTGTAGGGTTTGCT 57.275 33.333 0.00 0.00 0.00 3.91
161 268 0.041535 TTGCTCCATGGGGATGCTTT 59.958 50.000 18.46 0.00 43.91 3.51
188 295 1.267806 GCAGACAGTTGTGTTGGATGG 59.732 52.381 0.00 0.00 36.88 3.51
211 319 0.880278 CCGGCGTATGGTCCATCAAG 60.880 60.000 7.92 2.24 0.00 3.02
219 327 2.061509 TGGTCCATCAAGATGCATGG 57.938 50.000 2.46 0.00 41.04 3.66
241 349 5.530915 TGGCTGGCACATGATAATTAACTAC 59.469 40.000 0.00 0.00 38.20 2.73
243 351 6.073003 GGCTGGCACATGATAATTAACTACTC 60.073 42.308 0.00 0.00 38.20 2.59
244 352 6.708054 GCTGGCACATGATAATTAACTACTCT 59.292 38.462 0.00 0.00 38.20 3.24
245 353 7.095439 GCTGGCACATGATAATTAACTACTCTC 60.095 40.741 0.00 0.00 38.20 3.20
247 355 8.144478 TGGCACATGATAATTAACTACTCTCTC 58.856 37.037 0.00 0.00 0.00 3.20
249 357 7.327275 GCACATGATAATTAACTACTCTCTCCG 59.673 40.741 0.00 0.00 0.00 4.63
250 358 8.353684 CACATGATAATTAACTACTCTCTCCGT 58.646 37.037 0.00 0.00 0.00 4.69
251 359 8.915036 ACATGATAATTAACTACTCTCTCCGTT 58.085 33.333 0.00 0.00 0.00 4.44
252 360 9.400638 CATGATAATTAACTACTCTCTCCGTTC 57.599 37.037 0.00 0.00 0.00 3.95
253 361 7.938715 TGATAATTAACTACTCTCTCCGTTCC 58.061 38.462 0.00 0.00 0.00 3.62
254 362 7.778853 TGATAATTAACTACTCTCTCCGTTCCT 59.221 37.037 0.00 0.00 0.00 3.36
255 363 9.282569 GATAATTAACTACTCTCTCCGTTCCTA 57.717 37.037 0.00 0.00 0.00 2.94
256 364 7.951347 AATTAACTACTCTCTCCGTTCCTAA 57.049 36.000 0.00 0.00 0.00 2.69
257 365 7.951347 ATTAACTACTCTCTCCGTTCCTAAA 57.049 36.000 0.00 0.00 0.00 1.85
258 366 7.951347 TTAACTACTCTCTCCGTTCCTAAAT 57.049 36.000 0.00 0.00 0.00 1.40
259 367 9.638176 ATTAACTACTCTCTCCGTTCCTAAATA 57.362 33.333 0.00 0.00 0.00 1.40
260 368 9.638176 TTAACTACTCTCTCCGTTCCTAAATAT 57.362 33.333 0.00 0.00 0.00 1.28
262 370 9.638176 AACTACTCTCTCCGTTCCTAAATATAA 57.362 33.333 0.00 0.00 0.00 0.98
263 371 9.638176 ACTACTCTCTCCGTTCCTAAATATAAA 57.362 33.333 0.00 0.00 0.00 1.40
296 404 7.429633 AGAGATTTCAATCTGGACTACATACG 58.570 38.462 6.79 0.00 45.39 3.06
297 405 6.516718 AGATTTCAATCTGGACTACATACGG 58.483 40.000 1.04 0.00 43.81 4.02
298 406 5.925506 TTTCAATCTGGACTACATACGGA 57.074 39.130 0.00 0.00 0.00 4.69
299 407 5.925506 TTCAATCTGGACTACATACGGAA 57.074 39.130 0.00 0.00 0.00 4.30
300 408 5.258456 TCAATCTGGACTACATACGGAAC 57.742 43.478 0.00 0.00 0.00 3.62
301 409 4.707934 TCAATCTGGACTACATACGGAACA 59.292 41.667 0.00 0.00 0.00 3.18
302 410 5.186215 TCAATCTGGACTACATACGGAACAA 59.814 40.000 0.00 0.00 0.00 2.83
303 411 5.670792 ATCTGGACTACATACGGAACAAA 57.329 39.130 0.00 0.00 0.00 2.83
304 412 5.471556 TCTGGACTACATACGGAACAAAA 57.528 39.130 0.00 0.00 0.00 2.44
305 413 6.045072 TCTGGACTACATACGGAACAAAAT 57.955 37.500 0.00 0.00 0.00 1.82
306 414 5.872617 TCTGGACTACATACGGAACAAAATG 59.127 40.000 0.00 0.00 0.00 2.32
307 415 5.795972 TGGACTACATACGGAACAAAATGA 58.204 37.500 0.00 0.00 0.00 2.57
308 416 5.872617 TGGACTACATACGGAACAAAATGAG 59.127 40.000 0.00 0.00 0.00 2.90
309 417 5.873164 GGACTACATACGGAACAAAATGAGT 59.127 40.000 0.00 0.00 0.00 3.41
310 418 7.037438 GGACTACATACGGAACAAAATGAGTA 58.963 38.462 0.00 0.00 0.00 2.59
311 419 7.546667 GGACTACATACGGAACAAAATGAGTAA 59.453 37.037 0.00 0.00 0.00 2.24
312 420 8.836268 ACTACATACGGAACAAAATGAGTAAA 57.164 30.769 0.00 0.00 0.00 2.01
313 421 9.444600 ACTACATACGGAACAAAATGAGTAAAT 57.555 29.630 0.00 0.00 0.00 1.40
314 422 9.916397 CTACATACGGAACAAAATGAGTAAATC 57.084 33.333 0.00 0.00 0.00 2.17
315 423 8.561738 ACATACGGAACAAAATGAGTAAATCT 57.438 30.769 0.00 0.00 0.00 2.40
316 424 9.661563 ACATACGGAACAAAATGAGTAAATCTA 57.338 29.630 0.00 0.00 0.00 1.98
317 425 9.916397 CATACGGAACAAAATGAGTAAATCTAC 57.084 33.333 0.00 0.00 0.00 2.59
318 426 7.972832 ACGGAACAAAATGAGTAAATCTACA 57.027 32.000 0.00 0.00 0.00 2.74
319 427 7.803724 ACGGAACAAAATGAGTAAATCTACAC 58.196 34.615 0.00 0.00 0.00 2.90
320 428 7.660208 ACGGAACAAAATGAGTAAATCTACACT 59.340 33.333 0.00 0.00 0.00 3.55
321 429 8.169268 CGGAACAAAATGAGTAAATCTACACTC 58.831 37.037 0.00 0.00 41.31 3.51
322 430 9.220767 GGAACAAAATGAGTAAATCTACACTCT 57.779 33.333 3.65 0.00 41.46 3.24
331 439 8.235226 TGAGTAAATCTACACTCTAAACAGACG 58.765 37.037 3.65 0.00 41.46 4.18
332 440 8.108551 AGTAAATCTACACTCTAAACAGACGT 57.891 34.615 0.00 0.00 0.00 4.34
333 441 9.224267 AGTAAATCTACACTCTAAACAGACGTA 57.776 33.333 0.00 0.00 0.00 3.57
342 450 9.182214 ACACTCTAAACAGACGTATATTTAGGA 57.818 33.333 18.05 6.92 35.99 2.94
346 454 9.976511 TCTAAACAGACGTATATTTAGGAATGG 57.023 33.333 18.05 0.00 35.99 3.16
347 455 9.976511 CTAAACAGACGTATATTTAGGAATGGA 57.023 33.333 12.10 0.00 33.08 3.41
348 456 8.888579 AAACAGACGTATATTTAGGAATGGAG 57.111 34.615 0.00 0.00 0.00 3.86
349 457 6.994221 ACAGACGTATATTTAGGAATGGAGG 58.006 40.000 0.00 0.00 0.00 4.30
350 458 6.014499 ACAGACGTATATTTAGGAATGGAGGG 60.014 42.308 0.00 0.00 0.00 4.30
351 459 6.210784 CAGACGTATATTTAGGAATGGAGGGA 59.789 42.308 0.00 0.00 0.00 4.20
352 460 6.437793 AGACGTATATTTAGGAATGGAGGGAG 59.562 42.308 0.00 0.00 0.00 4.30
353 461 6.082707 ACGTATATTTAGGAATGGAGGGAGT 58.917 40.000 0.00 0.00 0.00 3.85
354 462 7.243824 ACGTATATTTAGGAATGGAGGGAGTA 58.756 38.462 0.00 0.00 0.00 2.59
355 463 7.731688 ACGTATATTTAGGAATGGAGGGAGTAA 59.268 37.037 0.00 0.00 0.00 2.24
356 464 8.033626 CGTATATTTAGGAATGGAGGGAGTAAC 58.966 40.741 0.00 0.00 0.00 2.50
398 506 2.715749 TAGTGTTGCTCCATGGGATG 57.284 50.000 13.02 3.90 0.00 3.51
408 520 2.836372 CTCCATGGGATGCTATGCTCTA 59.164 50.000 13.02 0.00 0.00 2.43
426 538 4.568760 GCTCTACTGGCAGTTGATAAGTTC 59.431 45.833 27.42 11.04 30.18 3.01
439 551 6.465894 AGTTGATAAGTTCAGCTTTACTGGGT 60.466 38.462 0.00 0.00 42.63 4.51
440 552 8.438047 AGTTGATAAGTTCAGCTTTACTGGGTG 61.438 40.741 0.00 0.00 42.63 4.61
480 592 5.570589 GTGAAATTGCTAGCAAAGTAAGCAG 59.429 40.000 32.35 0.00 46.17 4.24
503 615 3.357079 CGTGGCCACCAAGACAGC 61.357 66.667 29.95 1.81 35.05 4.40
506 618 0.674895 GTGGCCACCAAGACAGCTAG 60.675 60.000 26.31 0.00 34.18 3.42
508 620 0.902531 GGCCACCAAGACAGCTAGTA 59.097 55.000 0.00 0.00 0.00 1.82
509 621 1.486726 GGCCACCAAGACAGCTAGTAT 59.513 52.381 0.00 0.00 0.00 2.12
510 622 2.092914 GGCCACCAAGACAGCTAGTATT 60.093 50.000 0.00 0.00 30.24 1.89
512 624 3.375299 GCCACCAAGACAGCTAGTATTTG 59.625 47.826 0.00 0.00 26.83 2.32
548 1142 5.616270 TGTTGTGATTAGTTACAGGCTCAA 58.384 37.500 0.00 0.00 0.00 3.02
589 1183 0.518636 CTCACAAAGCCACCATGACG 59.481 55.000 0.00 0.00 0.00 4.35
590 1184 0.107643 TCACAAAGCCACCATGACGA 59.892 50.000 0.00 0.00 0.00 4.20
591 1185 0.238289 CACAAAGCCACCATGACGAC 59.762 55.000 0.00 0.00 0.00 4.34
617 1211 7.121168 CAGTCATCTCTCTGTAGATATCTTCCC 59.879 44.444 11.25 0.34 34.40 3.97
618 1212 7.018550 AGTCATCTCTCTGTAGATATCTTCCCT 59.981 40.741 11.25 0.00 34.40 4.20
641 1235 1.226101 CTGCAGTTAACGCGCCATG 60.226 57.895 5.73 0.00 0.00 3.66
651 1245 2.393768 CGCGCCATGCCATATCTCC 61.394 63.158 0.00 0.00 42.08 3.71
652 1246 1.302752 GCGCCATGCCATATCTCCA 60.303 57.895 0.00 0.00 37.76 3.86
653 1247 0.679002 GCGCCATGCCATATCTCCAT 60.679 55.000 0.00 0.00 37.76 3.41
654 1248 1.092348 CGCCATGCCATATCTCCATG 58.908 55.000 0.00 0.00 36.87 3.66
713 1308 0.172352 CTCAGCAGACGACTTCCCTC 59.828 60.000 0.00 0.00 0.00 4.30
787 1382 2.195615 CGCGTCTACGTGCATACTG 58.804 57.895 0.00 0.00 43.06 2.74
795 1390 4.446385 GTCTACGTGCATACTGTTTGTTCA 59.554 41.667 0.00 0.00 0.00 3.18
803 1398 5.412594 TGCATACTGTTTGTTCATTCCTCTC 59.587 40.000 0.40 0.00 0.00 3.20
809 1404 4.690748 TGTTTGTTCATTCCTCTCGTGATC 59.309 41.667 0.00 0.00 0.00 2.92
858 1453 7.878477 TTGCAATCACAATCAATTTTCTCTC 57.122 32.000 0.00 0.00 0.00 3.20
881 1476 7.012138 TCTCTAGTGAGTACTTATTTACCGCTG 59.988 40.741 0.00 0.00 40.98 5.18
913 1508 7.047891 TGGTGTGCATTAATAACCAAACAAAA 58.952 30.769 8.33 0.00 37.96 2.44
1338 1933 2.288763 GGGTTGCGTCCATGATTTTTGT 60.289 45.455 0.00 0.00 0.00 2.83
1550 2370 1.386533 GTCAGTGGATGCATTCCCAG 58.613 55.000 7.35 0.00 44.77 4.45
1669 2510 3.920841 AGTACTGGGGTTTCATAGGGTTT 59.079 43.478 0.00 0.00 0.00 3.27
2067 2920 7.621796 AGATTAAAACATATATCCCTCGGGTC 58.378 38.462 1.18 0.00 36.47 4.46
2409 3265 7.217906 AGACCGGAGATAAGATAATGGAAAAC 58.782 38.462 9.46 0.00 0.00 2.43
3147 4006 1.679139 TTTCAGCACTTGTCCACCTG 58.321 50.000 0.00 0.00 0.00 4.00
3414 4283 8.806146 TCAATAAAGAAAGGGAAGGATTTGAAG 58.194 33.333 0.00 0.00 0.00 3.02
3436 4305 5.947443 AGCAAAGCAACTAGAGCATTTAAG 58.053 37.500 12.97 0.24 0.00 1.85
3533 4402 8.651589 TGATAGAGAAAAACTACTTGGAGAGA 57.348 34.615 0.00 0.00 0.00 3.10
3680 4549 1.702401 TGTCCAACATGGCTAGGTGAA 59.298 47.619 0.00 0.00 37.47 3.18
3838 4707 3.352648 AGCAAAGCTTTATCGGGCTAAA 58.647 40.909 16.78 0.00 33.89 1.85
3959 4828 5.497474 GACTGCCCTAAAATCTTGGAGTTA 58.503 41.667 0.00 0.00 0.00 2.24
4077 4958 7.496920 CAGAATTCTTGTTAGTGCCTCATATCA 59.503 37.037 4.86 0.00 0.00 2.15
4091 4972 4.115516 CTCATATCACCTGGACTGAAACG 58.884 47.826 0.00 0.00 0.00 3.60
4188 5075 6.833933 AGTAGGACTGAAAATTGTTGGAAAGT 59.166 34.615 0.00 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 9.443365 ACCACCATAATAATAGTACTACTTGGT 57.557 33.333 4.31 2.12 34.21 3.67
33 34 7.731235 TGGAGCACCACCATAATAATAGTACTA 59.269 37.037 4.77 4.77 41.77 1.82
35 36 6.765403 TGGAGCACCACCATAATAATAGTAC 58.235 40.000 0.00 0.00 41.77 2.73
52 53 3.499737 CGACGCCCAATGGAGCAC 61.500 66.667 0.00 0.00 34.24 4.40
124 125 6.156519 GGAGCAAACCCTACAAAAACAATAG 58.843 40.000 0.00 0.00 0.00 1.73
188 295 1.745320 ATGGACCATACGCCGGACTC 61.745 60.000 5.05 0.00 0.00 3.36
194 301 2.146342 CATCTTGATGGACCATACGCC 58.854 52.381 7.05 0.00 0.00 5.68
196 303 2.837498 TGCATCTTGATGGACCATACG 58.163 47.619 7.05 0.00 0.00 3.06
211 319 1.067416 CATGTGCCAGCCATGCATC 59.933 57.895 0.00 0.00 41.46 3.91
219 327 6.708054 AGAGTAGTTAATTATCATGTGCCAGC 59.292 38.462 0.00 0.00 0.00 4.85
270 378 8.568794 CGTATGTAGTCCAGATTGAAATCTCTA 58.431 37.037 2.50 0.32 43.65 2.43
271 379 7.429633 CGTATGTAGTCCAGATTGAAATCTCT 58.570 38.462 2.50 1.19 43.65 3.10
272 380 6.642950 CCGTATGTAGTCCAGATTGAAATCTC 59.357 42.308 2.50 0.00 43.65 2.75
273 381 6.323996 TCCGTATGTAGTCCAGATTGAAATCT 59.676 38.462 0.00 0.00 46.30 2.40
274 382 6.513180 TCCGTATGTAGTCCAGATTGAAATC 58.487 40.000 0.00 0.00 35.64 2.17
275 383 6.479972 TCCGTATGTAGTCCAGATTGAAAT 57.520 37.500 0.00 0.00 0.00 2.17
276 384 5.925506 TCCGTATGTAGTCCAGATTGAAA 57.074 39.130 0.00 0.00 0.00 2.69
277 385 5.186215 TGTTCCGTATGTAGTCCAGATTGAA 59.814 40.000 0.00 0.00 0.00 2.69
278 386 4.707934 TGTTCCGTATGTAGTCCAGATTGA 59.292 41.667 0.00 0.00 0.00 2.57
279 387 5.006153 TGTTCCGTATGTAGTCCAGATTG 57.994 43.478 0.00 0.00 0.00 2.67
280 388 5.670792 TTGTTCCGTATGTAGTCCAGATT 57.329 39.130 0.00 0.00 0.00 2.40
281 389 5.670792 TTTGTTCCGTATGTAGTCCAGAT 57.329 39.130 0.00 0.00 0.00 2.90
282 390 5.471556 TTTTGTTCCGTATGTAGTCCAGA 57.528 39.130 0.00 0.00 0.00 3.86
283 391 5.872617 TCATTTTGTTCCGTATGTAGTCCAG 59.127 40.000 0.00 0.00 0.00 3.86
284 392 5.795972 TCATTTTGTTCCGTATGTAGTCCA 58.204 37.500 0.00 0.00 0.00 4.02
285 393 5.873164 ACTCATTTTGTTCCGTATGTAGTCC 59.127 40.000 0.00 0.00 0.00 3.85
286 394 6.963049 ACTCATTTTGTTCCGTATGTAGTC 57.037 37.500 0.00 0.00 0.00 2.59
287 395 8.836268 TTTACTCATTTTGTTCCGTATGTAGT 57.164 30.769 0.00 0.00 0.00 2.73
288 396 9.916397 GATTTACTCATTTTGTTCCGTATGTAG 57.084 33.333 0.00 0.00 0.00 2.74
289 397 9.661563 AGATTTACTCATTTTGTTCCGTATGTA 57.338 29.630 0.00 0.00 0.00 2.29
290 398 8.561738 AGATTTACTCATTTTGTTCCGTATGT 57.438 30.769 0.00 0.00 0.00 2.29
291 399 9.916397 GTAGATTTACTCATTTTGTTCCGTATG 57.084 33.333 0.00 0.00 0.00 2.39
292 400 9.661563 TGTAGATTTACTCATTTTGTTCCGTAT 57.338 29.630 0.00 0.00 0.00 3.06
293 401 8.928733 GTGTAGATTTACTCATTTTGTTCCGTA 58.071 33.333 0.00 0.00 0.00 4.02
294 402 7.660208 AGTGTAGATTTACTCATTTTGTTCCGT 59.340 33.333 0.00 0.00 0.00 4.69
295 403 8.029642 AGTGTAGATTTACTCATTTTGTTCCG 57.970 34.615 0.00 0.00 0.00 4.30
296 404 9.220767 AGAGTGTAGATTTACTCATTTTGTTCC 57.779 33.333 7.09 0.00 44.41 3.62
305 413 8.235226 CGTCTGTTTAGAGTGTAGATTTACTCA 58.765 37.037 7.09 0.00 44.41 3.41
306 414 8.235905 ACGTCTGTTTAGAGTGTAGATTTACTC 58.764 37.037 0.00 0.00 42.77 2.59
307 415 8.108551 ACGTCTGTTTAGAGTGTAGATTTACT 57.891 34.615 0.00 0.00 32.48 2.24
316 424 9.182214 TCCTAAATATACGTCTGTTTAGAGTGT 57.818 33.333 23.05 0.00 36.66 3.55
320 428 9.976511 CCATTCCTAAATATACGTCTGTTTAGA 57.023 33.333 23.05 10.87 36.66 2.10
321 429 9.976511 TCCATTCCTAAATATACGTCTGTTTAG 57.023 33.333 17.70 17.70 35.15 1.85
322 430 9.976511 CTCCATTCCTAAATATACGTCTGTTTA 57.023 33.333 0.00 0.00 0.00 2.01
323 431 7.931948 CCTCCATTCCTAAATATACGTCTGTTT 59.068 37.037 0.00 0.00 0.00 2.83
324 432 7.442656 CCTCCATTCCTAAATATACGTCTGTT 58.557 38.462 0.00 0.00 0.00 3.16
325 433 6.014499 CCCTCCATTCCTAAATATACGTCTGT 60.014 42.308 0.00 0.00 0.00 3.41
326 434 6.210784 TCCCTCCATTCCTAAATATACGTCTG 59.789 42.308 0.00 0.00 0.00 3.51
327 435 6.320518 TCCCTCCATTCCTAAATATACGTCT 58.679 40.000 0.00 0.00 0.00 4.18
328 436 6.210984 ACTCCCTCCATTCCTAAATATACGTC 59.789 42.308 0.00 0.00 0.00 4.34
329 437 6.082707 ACTCCCTCCATTCCTAAATATACGT 58.917 40.000 0.00 0.00 0.00 3.57
330 438 6.607004 ACTCCCTCCATTCCTAAATATACG 57.393 41.667 0.00 0.00 0.00 3.06
331 439 8.033626 CGTTACTCCCTCCATTCCTAAATATAC 58.966 40.741 0.00 0.00 0.00 1.47
332 440 7.951806 TCGTTACTCCCTCCATTCCTAAATATA 59.048 37.037 0.00 0.00 0.00 0.86
333 441 6.785963 TCGTTACTCCCTCCATTCCTAAATAT 59.214 38.462 0.00 0.00 0.00 1.28
334 442 6.138263 TCGTTACTCCCTCCATTCCTAAATA 58.862 40.000 0.00 0.00 0.00 1.40
335 443 4.966805 TCGTTACTCCCTCCATTCCTAAAT 59.033 41.667 0.00 0.00 0.00 1.40
336 444 4.355549 TCGTTACTCCCTCCATTCCTAAA 58.644 43.478 0.00 0.00 0.00 1.85
337 445 3.958798 CTCGTTACTCCCTCCATTCCTAA 59.041 47.826 0.00 0.00 0.00 2.69
338 446 3.053095 ACTCGTTACTCCCTCCATTCCTA 60.053 47.826 0.00 0.00 0.00 2.94
339 447 2.292323 ACTCGTTACTCCCTCCATTCCT 60.292 50.000 0.00 0.00 0.00 3.36
340 448 2.108970 ACTCGTTACTCCCTCCATTCC 58.891 52.381 0.00 0.00 0.00 3.01
341 449 4.205587 TCTACTCGTTACTCCCTCCATTC 58.794 47.826 0.00 0.00 0.00 2.67
342 450 4.246712 TCTACTCGTTACTCCCTCCATT 57.753 45.455 0.00 0.00 0.00 3.16
343 451 3.947612 TCTACTCGTTACTCCCTCCAT 57.052 47.619 0.00 0.00 0.00 3.41
344 452 3.947612 ATCTACTCGTTACTCCCTCCA 57.052 47.619 0.00 0.00 0.00 3.86
345 453 5.375773 AGTTATCTACTCGTTACTCCCTCC 58.624 45.833 0.00 0.00 28.23 4.30
346 454 6.940831 AAGTTATCTACTCGTTACTCCCTC 57.059 41.667 0.00 0.00 35.54 4.30
347 455 7.118060 AGAAAGTTATCTACTCGTTACTCCCT 58.882 38.462 0.00 0.00 35.54 4.20
348 456 7.332213 AGAAAGTTATCTACTCGTTACTCCC 57.668 40.000 0.00 0.00 35.54 4.30
349 457 8.242739 ACAAGAAAGTTATCTACTCGTTACTCC 58.757 37.037 0.00 0.00 35.54 3.85
350 458 9.063739 CACAAGAAAGTTATCTACTCGTTACTC 57.936 37.037 0.00 0.00 35.54 2.59
351 459 8.574737 ACACAAGAAAGTTATCTACTCGTTACT 58.425 33.333 0.00 0.00 35.54 2.24
352 460 8.739649 ACACAAGAAAGTTATCTACTCGTTAC 57.260 34.615 0.00 0.00 35.54 2.50
353 461 9.754382 AAACACAAGAAAGTTATCTACTCGTTA 57.246 29.630 0.00 0.00 35.54 3.18
354 462 8.658499 AAACACAAGAAAGTTATCTACTCGTT 57.342 30.769 0.00 0.00 35.54 3.85
355 463 9.408069 CTAAACACAAGAAAGTTATCTACTCGT 57.592 33.333 0.00 0.00 35.54 4.18
356 464 9.408069 ACTAAACACAAGAAAGTTATCTACTCG 57.592 33.333 0.00 0.00 35.54 4.18
398 506 2.159043 TCAACTGCCAGTAGAGCATAGC 60.159 50.000 0.00 0.00 40.04 2.97
408 520 3.077359 GCTGAACTTATCAACTGCCAGT 58.923 45.455 0.00 0.00 37.67 4.00
426 538 1.683011 CCATCCCACCCAGTAAAGCTG 60.683 57.143 0.00 0.00 44.63 4.24
439 551 0.031111 CACTCCCTACTCCCATCCCA 60.031 60.000 0.00 0.00 0.00 4.37
440 552 0.264955 TCACTCCCTACTCCCATCCC 59.735 60.000 0.00 0.00 0.00 3.85
441 553 2.176247 TTCACTCCCTACTCCCATCC 57.824 55.000 0.00 0.00 0.00 3.51
442 554 4.455606 CAATTTCACTCCCTACTCCCATC 58.544 47.826 0.00 0.00 0.00 3.51
443 555 3.372025 GCAATTTCACTCCCTACTCCCAT 60.372 47.826 0.00 0.00 0.00 4.00
494 606 9.601217 AATACTAACAAATACTAGCTGTCTTGG 57.399 33.333 0.00 0.00 0.00 3.61
524 1118 5.804639 TGAGCCTGTAACTAATCACAACAT 58.195 37.500 0.00 0.00 0.00 2.71
589 1183 8.621532 AAGATATCTACAGAGAGATGACTGTC 57.378 38.462 5.46 0.00 44.59 3.51
590 1184 7.665559 GGAAGATATCTACAGAGAGATGACTGT 59.334 40.741 5.46 0.00 46.81 3.55
591 1185 7.121168 GGGAAGATATCTACAGAGAGATGACTG 59.879 44.444 5.46 0.00 33.69 3.51
617 1211 1.745489 GCGTTAACTGCAGGGGGAG 60.745 63.158 19.93 7.51 38.63 4.30
618 1212 2.349755 GCGTTAACTGCAGGGGGA 59.650 61.111 19.93 0.00 0.00 4.81
641 1235 2.239150 AGAGGATGCATGGAGATATGGC 59.761 50.000 2.46 0.00 0.00 4.40
651 1245 2.141517 CGCTAAGGAAGAGGATGCATG 58.858 52.381 2.46 0.00 0.00 4.06
652 1246 2.540265 CGCTAAGGAAGAGGATGCAT 57.460 50.000 0.00 0.00 0.00 3.96
683 1278 2.669670 CGTCTGCTGAGAGTTGTGTAGG 60.670 54.545 0.00 0.00 0.00 3.18
781 1376 5.639506 ACGAGAGGAATGAACAAACAGTATG 59.360 40.000 0.00 0.00 46.00 2.39
782 1377 5.639506 CACGAGAGGAATGAACAAACAGTAT 59.360 40.000 0.00 0.00 0.00 2.12
787 1382 4.093556 GGATCACGAGAGGAATGAACAAAC 59.906 45.833 0.00 0.00 0.00 2.93
795 1390 0.387202 CGCAGGATCACGAGAGGAAT 59.613 55.000 0.00 0.00 0.00 3.01
858 1453 5.686397 GCAGCGGTAAATAAGTACTCACTAG 59.314 44.000 0.00 0.00 33.48 2.57
881 1476 6.983307 TGGTTATTAATGCACACCAATTATGC 59.017 34.615 0.00 0.00 34.49 3.14
913 1508 6.721208 TGAGGACCTGCAAAAATTAAGAGAAT 59.279 34.615 0.00 0.00 0.00 2.40
926 1521 0.106708 GTGAGTGTGAGGACCTGCAA 59.893 55.000 0.00 0.00 0.00 4.08
929 1524 1.620323 TGATGTGAGTGTGAGGACCTG 59.380 52.381 0.00 0.00 0.00 4.00
1338 1933 0.671472 CAGTGTGGCGAGCATTGAGA 60.671 55.000 0.00 0.00 0.00 3.27
1550 2370 0.903236 AAGGAGGAGTTTACCGAGCC 59.097 55.000 0.00 0.00 34.73 4.70
1660 2501 8.834465 CATTCTTTCAGAGACATAAACCCTATG 58.166 37.037 0.00 0.00 33.02 2.23
1669 2510 6.466812 TGCACTTCATTCTTTCAGAGACATA 58.533 36.000 0.00 0.00 33.02 2.29
2067 2920 1.000274 CTGCCAACTTTTTCCCCTTCG 60.000 52.381 0.00 0.00 0.00 3.79
2928 3787 6.102897 TGTCCCTTAAAGTTCTCTTGAGAG 57.897 41.667 1.51 1.51 43.36 3.20
3147 4006 4.579454 TGTACCCAGACATAAGTATCGC 57.421 45.455 0.00 0.00 0.00 4.58
3296 4164 6.540438 TCACTCAGGGTATAAAAACGATCT 57.460 37.500 0.00 0.00 0.00 2.75
3298 4166 6.884832 TCATCACTCAGGGTATAAAAACGAT 58.115 36.000 0.00 0.00 0.00 3.73
3387 4256 8.353423 TCAAATCCTTCCCTTTCTTTATTGAG 57.647 34.615 0.00 0.00 0.00 3.02
3414 4283 5.570589 CACTTAAATGCTCTAGTTGCTTTGC 59.429 40.000 10.68 0.00 0.00 3.68
3436 4305 0.957888 GCCAAGCTCCCTCAGTTCAC 60.958 60.000 0.00 0.00 0.00 3.18
3481 4350 4.432712 TGCTTTGGTTGCTTCTTCTTTTC 58.567 39.130 0.00 0.00 0.00 2.29
3533 4402 7.547227 GCTTACTGTCCCAATCAAATGTTAAT 58.453 34.615 0.00 0.00 0.00 1.40
3542 4411 0.981183 ACCGCTTACTGTCCCAATCA 59.019 50.000 0.00 0.00 0.00 2.57
3680 4549 2.565841 AGAGCTTCAACAACGAGCTTT 58.434 42.857 0.00 0.00 46.08 3.51
3838 4707 2.110578 AGCCAACAAGTTCAAGCCTTT 58.889 42.857 0.00 0.00 0.00 3.11
3959 4828 7.880713 GGGTTAATAATGTGGTTTGAAAATGGT 59.119 33.333 0.00 0.00 0.00 3.55
4077 4958 1.623811 ACATAGCGTTTCAGTCCAGGT 59.376 47.619 0.00 0.00 0.00 4.00
4091 4972 4.976731 CCTCGTATGTTGACAGTACATAGC 59.023 45.833 0.00 0.00 38.70 2.97
4188 5075 3.636764 TGATCTAAGCTCCGCAGTTCATA 59.363 43.478 0.00 0.00 0.00 2.15


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

AutoCloner maintained by Alex Coulton.