Multiple sequence alignment - TraesCS3A01G421100

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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 TraesCS3A01G421100 chr3A 100.000 3280 0 0 1 3280 662561348 662564627 0.000000e+00 6058.0
1 TraesCS3A01G421100 chr3D 91.097 1786 82 25 1521 3277 528132575 528134312 0.000000e+00 2346.0
2 TraesCS3A01G421100 chr3D 90.926 1080 63 18 626 1682 528131633 528132700 0.000000e+00 1419.0
3 TraesCS3A01G421100 chr3D 95.760 283 7 3 324 606 528131366 528131643 4.990000e-123 451.0
4 TraesCS3A01G421100 chr3D 92.917 240 15 2 1 239 528130921 528131159 6.740000e-92 348.0
5 TraesCS3A01G421100 chr3B 90.657 974 57 15 626 1585 698231600 698232553 0.000000e+00 1264.0
6 TraesCS3A01G421100 chr3B 93.298 746 23 16 1521 2249 698232519 698233254 0.000000e+00 1075.0
7 TraesCS3A01G421100 chr3B 95.053 283 10 3 324 606 698231332 698231610 3.000000e-120 442.0
8 TraesCS3A01G421100 chr3B 87.632 380 45 2 2611 2988 698233259 698233638 1.080000e-119 440.0
9 TraesCS3A01G421100 chr3B 85.862 290 26 7 2974 3262 698234547 698234822 8.900000e-76 294.0
10 TraesCS3A01G421100 chr3B 89.177 231 19 4 5 229 698230732 698230962 1.930000e-72 283.0
11 TraesCS3A01G421100 chr7D 89.333 75 7 1 236 309 400165787 400165861 3.480000e-15 93.5


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 TraesCS3A01G421100 chr3A 662561348 662564627 3279 False 6058 6058 100.000000 1 3280 1 chr3A.!!$F1 3279
1 TraesCS3A01G421100 chr3D 528130921 528134312 3391 False 1141 2346 92.675000 1 3277 4 chr3D.!!$F1 3276
2 TraesCS3A01G421100 chr3B 698230732 698234822 4090 False 633 1264 90.279833 5 3262 6 chr3B.!!$F1 3257

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
723 1043 0.255033 AAGCTTCGGGTATGGTTCCC 59.745 55.0 0.0 0.0 41.41 3.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2458 2868 0.031515 TCATAAGCCCCCGGAAGAGA 60.032 55.0 0.73 0.0 0.0 3.1 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
147 149 4.154347 CTGGCGAGGTCCTGGAGC 62.154 72.222 17.93 17.93 0.00 4.70
178 186 3.117171 CGTCGTCTCCGTCTCCGT 61.117 66.667 0.00 0.00 35.01 4.69
183 191 1.575576 CGTCTCCGTCTCCGTTGAGT 61.576 60.000 0.00 0.00 39.75 3.41
239 437 3.593794 GTCGCTCCCGTATCGGCT 61.594 66.667 2.41 0.00 46.86 5.52
240 438 3.592814 TCGCTCCCGTATCGGCTG 61.593 66.667 2.41 0.00 46.86 4.85
241 439 3.592814 CGCTCCCGTATCGGCTGA 61.593 66.667 0.00 0.00 46.86 4.26
242 440 2.812499 GCTCCCGTATCGGCTGAA 59.188 61.111 0.00 0.00 46.86 3.02
243 441 1.143183 GCTCCCGTATCGGCTGAAA 59.857 57.895 0.00 0.00 46.86 2.69
244 442 0.461339 GCTCCCGTATCGGCTGAAAA 60.461 55.000 0.00 0.00 46.86 2.29
245 443 1.810412 GCTCCCGTATCGGCTGAAAAT 60.810 52.381 0.00 0.00 46.86 1.82
246 444 2.135933 CTCCCGTATCGGCTGAAAATC 58.864 52.381 0.00 0.00 46.86 2.17
247 445 1.483004 TCCCGTATCGGCTGAAAATCA 59.517 47.619 0.00 0.00 46.86 2.57
249 447 2.878406 CCCGTATCGGCTGAAAATCAAT 59.122 45.455 0.00 0.00 46.86 2.57
250 448 3.303990 CCCGTATCGGCTGAAAATCAATG 60.304 47.826 0.00 0.00 46.86 2.82
251 449 3.303990 CCGTATCGGCTGAAAATCAATGG 60.304 47.826 0.00 0.00 41.17 3.16
252 450 3.303990 CGTATCGGCTGAAAATCAATGGG 60.304 47.826 0.00 0.00 0.00 4.00
254 452 0.461135 CGGCTGAAAATCAATGGGGG 59.539 55.000 0.00 0.00 0.00 5.40
255 453 1.864669 GGCTGAAAATCAATGGGGGA 58.135 50.000 0.00 0.00 0.00 4.81
256 454 1.758862 GGCTGAAAATCAATGGGGGAG 59.241 52.381 0.00 0.00 0.00 4.30
257 455 2.624029 GGCTGAAAATCAATGGGGGAGA 60.624 50.000 0.00 0.00 0.00 3.71
258 456 3.099141 GCTGAAAATCAATGGGGGAGAA 58.901 45.455 0.00 0.00 0.00 2.87
260 458 4.382362 GCTGAAAATCAATGGGGGAGAAAG 60.382 45.833 0.00 0.00 0.00 2.62
261 459 5.009436 TGAAAATCAATGGGGGAGAAAGA 57.991 39.130 0.00 0.00 0.00 2.52
262 460 5.592795 TGAAAATCAATGGGGGAGAAAGAT 58.407 37.500 0.00 0.00 0.00 2.40
263 461 6.024893 TGAAAATCAATGGGGGAGAAAGATT 58.975 36.000 0.00 0.00 0.00 2.40
264 462 7.188381 TGAAAATCAATGGGGGAGAAAGATTA 58.812 34.615 0.00 0.00 0.00 1.75
266 464 6.347061 AATCAATGGGGGAGAAAGATTAGT 57.653 37.500 0.00 0.00 0.00 2.24
267 465 5.796502 TCAATGGGGGAGAAAGATTAGTT 57.203 39.130 0.00 0.00 0.00 2.24
269 467 6.900194 TCAATGGGGGAGAAAGATTAGTTAG 58.100 40.000 0.00 0.00 0.00 2.34
270 468 6.447084 TCAATGGGGGAGAAAGATTAGTTAGT 59.553 38.462 0.00 0.00 0.00 2.24
271 469 6.910259 ATGGGGGAGAAAGATTAGTTAGTT 57.090 37.500 0.00 0.00 0.00 2.24
272 470 6.062258 TGGGGGAGAAAGATTAGTTAGTTG 57.938 41.667 0.00 0.00 0.00 3.16
273 471 5.788533 TGGGGGAGAAAGATTAGTTAGTTGA 59.211 40.000 0.00 0.00 0.00 3.18
274 472 6.273730 TGGGGGAGAAAGATTAGTTAGTTGAA 59.726 38.462 0.00 0.00 0.00 2.69
277 475 7.549842 GGGGAGAAAGATTAGTTAGTTGAAGAC 59.450 40.741 0.00 0.00 0.00 3.01
279 477 7.549842 GGAGAAAGATTAGTTAGTTGAAGACCC 59.450 40.741 0.00 0.00 0.00 4.46
282 480 6.936968 AGATTAGTTAGTTGAAGACCCTGT 57.063 37.500 0.00 0.00 0.00 4.00
286 484 9.668497 GATTAGTTAGTTGAAGACCCTGTAAAT 57.332 33.333 0.00 0.00 0.00 1.40
287 485 9.668497 ATTAGTTAGTTGAAGACCCTGTAAATC 57.332 33.333 0.00 0.00 0.00 2.17
288 486 6.164176 AGTTAGTTGAAGACCCTGTAAATCG 58.836 40.000 0.00 0.00 0.00 3.34
289 487 4.618920 AGTTGAAGACCCTGTAAATCGT 57.381 40.909 0.00 0.00 0.00 3.73
290 488 4.566987 AGTTGAAGACCCTGTAAATCGTC 58.433 43.478 0.00 0.00 0.00 4.20
291 489 3.604875 TGAAGACCCTGTAAATCGTCC 57.395 47.619 0.00 0.00 0.00 4.79
292 490 2.094390 TGAAGACCCTGTAAATCGTCCG 60.094 50.000 0.00 0.00 0.00 4.79
293 491 1.553706 AGACCCTGTAAATCGTCCGT 58.446 50.000 0.00 0.00 0.00 4.69
295 493 3.091545 AGACCCTGTAAATCGTCCGTAA 58.908 45.455 0.00 0.00 0.00 3.18
296 494 3.119352 AGACCCTGTAAATCGTCCGTAAC 60.119 47.826 0.00 0.00 0.00 2.50
297 495 2.562298 ACCCTGTAAATCGTCCGTAACA 59.438 45.455 0.00 0.00 0.00 2.41
298 496 3.184541 CCCTGTAAATCGTCCGTAACAG 58.815 50.000 0.00 0.00 35.29 3.16
300 498 3.367703 CCTGTAAATCGTCCGTAACAGGT 60.368 47.826 10.46 0.00 45.74 4.00
301 499 3.836949 TGTAAATCGTCCGTAACAGGTC 58.163 45.455 0.00 0.00 0.00 3.85
302 500 2.375173 AAATCGTCCGTAACAGGTCC 57.625 50.000 0.00 0.00 0.00 4.46
304 502 0.962356 ATCGTCCGTAACAGGTCCGT 60.962 55.000 0.00 0.00 0.00 4.69
306 504 1.662044 GTCCGTAACAGGTCCGTGT 59.338 57.895 0.00 0.00 0.00 4.49
308 506 1.108727 TCCGTAACAGGTCCGTGTGT 61.109 55.000 0.00 0.00 0.00 3.72
309 507 0.665369 CCGTAACAGGTCCGTGTGTC 60.665 60.000 0.00 0.00 0.00 3.67
310 508 0.313043 CGTAACAGGTCCGTGTGTCT 59.687 55.000 0.00 0.00 0.00 3.41
311 509 1.536766 CGTAACAGGTCCGTGTGTCTA 59.463 52.381 0.00 0.00 0.00 2.59
312 510 2.413765 CGTAACAGGTCCGTGTGTCTAG 60.414 54.545 0.00 0.00 0.00 2.43
313 511 1.991121 AACAGGTCCGTGTGTCTAGA 58.009 50.000 0.00 0.00 0.00 2.43
315 513 2.526432 ACAGGTCCGTGTGTCTAGAAT 58.474 47.619 0.00 0.00 0.00 2.40
316 514 2.897969 ACAGGTCCGTGTGTCTAGAATT 59.102 45.455 0.00 0.00 0.00 2.17
317 515 4.084287 ACAGGTCCGTGTGTCTAGAATTA 58.916 43.478 0.00 0.00 0.00 1.40
318 516 4.710375 ACAGGTCCGTGTGTCTAGAATTAT 59.290 41.667 0.00 0.00 0.00 1.28
319 517 5.163540 ACAGGTCCGTGTGTCTAGAATTATC 60.164 44.000 0.00 0.00 0.00 1.75
487 807 6.239887 GGCTAATGGGATAAGGATGAGTGTAA 60.240 42.308 0.00 0.00 0.00 2.41
489 809 5.832539 ATGGGATAAGGATGAGTGTAAGG 57.167 43.478 0.00 0.00 0.00 2.69
490 810 4.890988 TGGGATAAGGATGAGTGTAAGGA 58.109 43.478 0.00 0.00 0.00 3.36
491 811 4.901849 TGGGATAAGGATGAGTGTAAGGAG 59.098 45.833 0.00 0.00 0.00 3.69
492 812 4.902448 GGGATAAGGATGAGTGTAAGGAGT 59.098 45.833 0.00 0.00 0.00 3.85
606 926 2.572556 ACCGGTCCATAATACACCACAA 59.427 45.455 0.00 0.00 0.00 3.33
607 927 3.201266 ACCGGTCCATAATACACCACAAT 59.799 43.478 0.00 0.00 0.00 2.71
608 928 3.563808 CCGGTCCATAATACACCACAATG 59.436 47.826 0.00 0.00 0.00 2.82
609 929 3.003275 CGGTCCATAATACACCACAATGC 59.997 47.826 0.00 0.00 0.00 3.56
610 930 4.207165 GGTCCATAATACACCACAATGCT 58.793 43.478 0.00 0.00 0.00 3.79
611 931 4.644685 GGTCCATAATACACCACAATGCTT 59.355 41.667 0.00 0.00 0.00 3.91
612 932 5.221048 GGTCCATAATACACCACAATGCTTC 60.221 44.000 0.00 0.00 0.00 3.86
613 933 4.887071 TCCATAATACACCACAATGCTTCC 59.113 41.667 0.00 0.00 0.00 3.46
614 934 4.889409 CCATAATACACCACAATGCTTCCT 59.111 41.667 0.00 0.00 0.00 3.36
615 935 5.009010 CCATAATACACCACAATGCTTCCTC 59.991 44.000 0.00 0.00 0.00 3.71
616 936 3.719268 ATACACCACAATGCTTCCTCA 57.281 42.857 0.00 0.00 0.00 3.86
617 937 2.363306 ACACCACAATGCTTCCTCAA 57.637 45.000 0.00 0.00 0.00 3.02
618 938 2.233271 ACACCACAATGCTTCCTCAAG 58.767 47.619 0.00 0.00 0.00 3.02
619 939 2.158623 ACACCACAATGCTTCCTCAAGA 60.159 45.455 0.00 0.00 0.00 3.02
620 940 2.886523 CACCACAATGCTTCCTCAAGAA 59.113 45.455 0.00 0.00 0.00 2.52
621 941 3.318839 CACCACAATGCTTCCTCAAGAAA 59.681 43.478 0.00 0.00 32.88 2.52
622 942 3.960102 ACCACAATGCTTCCTCAAGAAAA 59.040 39.130 0.00 0.00 32.88 2.29
623 943 4.405358 ACCACAATGCTTCCTCAAGAAAAA 59.595 37.500 0.00 0.00 32.88 1.94
676 996 4.568956 CCCTGCCCACTTTGAATTAAAAG 58.431 43.478 13.02 13.02 41.91 2.27
682 1002 7.286313 TGCCCACTTTGAATTAAAAGGAATTT 58.714 30.769 17.89 0.00 40.74 1.82
712 1032 3.067106 ACTACAATGTGTGAAGCTTCGG 58.933 45.455 21.11 7.21 0.00 4.30
723 1043 0.255033 AAGCTTCGGGTATGGTTCCC 59.745 55.000 0.00 0.00 41.41 3.97
798 1118 6.319405 TGATGATGCTCTTTAATTTAGCTGCA 59.681 34.615 1.02 0.00 37.16 4.41
854 1174 2.556622 ACGCAGTTACAAGGGAAAATGG 59.443 45.455 0.00 0.00 37.78 3.16
916 1236 5.446143 TTTATTGCACAAACGATGACCTT 57.554 34.783 0.00 0.00 0.00 3.50
931 1251 3.659786 TGACCTTTGTTGGATAGACACG 58.340 45.455 0.00 0.00 0.00 4.49
1071 1394 3.191371 CCTCCTCCTTGATTGTTTTTCCG 59.809 47.826 0.00 0.00 0.00 4.30
1076 1399 4.616953 TCCTTGATTGTTTTTCCGCTTTC 58.383 39.130 0.00 0.00 0.00 2.62
1220 1551 8.687824 AACTAATTTCAGAAGTTTTGTGTGTG 57.312 30.769 0.00 0.00 29.25 3.82
1221 1552 8.050778 ACTAATTTCAGAAGTTTTGTGTGTGA 57.949 30.769 0.00 0.00 0.00 3.58
1233 1564 0.529773 GTGTGTGAGTTGCTCGACCA 60.530 55.000 0.00 0.00 32.35 4.02
1292 1623 4.481930 TGAAGTTCATTTTGGTGTAGCG 57.518 40.909 0.08 0.00 0.00 4.26
1398 1734 3.878519 GGACTCGAGCTCCGACGG 61.879 72.222 13.61 7.84 43.23 4.79
1580 1961 1.218875 CTCGTACAGCAACGGCAACA 61.219 55.000 6.45 0.00 44.61 3.33
1765 2149 3.527533 GCCGATGTACATAAACACCAGA 58.472 45.455 8.71 0.00 30.75 3.86
1915 2302 2.754658 AGGTTCGGCCTCGACGAT 60.755 61.111 0.00 0.00 46.96 3.73
1995 2382 2.350852 GATGCTCGCGACGATCGAC 61.351 63.158 24.34 15.51 43.74 4.20
2096 2488 0.441533 CAGTTCTGCGCAGTGATGTC 59.558 55.000 34.70 19.02 0.00 3.06
2195 2589 9.921637 ACTTAATTACTTCTTGTTCTCTCTCAG 57.078 33.333 0.00 0.00 0.00 3.35
2222 2620 3.923017 ACTTGGTTACTTCTTGCATGC 57.077 42.857 11.82 11.82 0.00 4.06
2223 2621 3.221771 ACTTGGTTACTTCTTGCATGCA 58.778 40.909 18.46 18.46 0.00 3.96
2227 2625 4.331108 TGGTTACTTCTTGCATGCACATA 58.669 39.130 22.58 4.90 0.00 2.29
2229 2627 4.396166 GGTTACTTCTTGCATGCACATACT 59.604 41.667 22.58 5.73 0.00 2.12
2230 2628 5.447818 GGTTACTTCTTGCATGCACATACTC 60.448 44.000 22.58 7.10 0.00 2.59
2231 2629 3.012518 ACTTCTTGCATGCACATACTCC 58.987 45.455 22.58 0.00 0.00 3.85
2245 2648 5.125356 CACATACTCCATGGCAACTTATGA 58.875 41.667 6.96 0.00 39.13 2.15
2250 2653 6.212888 ACTCCATGGCAACTTATGATTTTC 57.787 37.500 6.96 0.00 37.61 2.29
2251 2654 5.127682 ACTCCATGGCAACTTATGATTTTCC 59.872 40.000 6.96 0.00 37.61 3.13
2321 2731 7.712639 AGTCCATCTAAGTGCACATATTAAGTG 59.287 37.037 21.04 9.81 39.92 3.16
2378 2788 9.677567 TTTTAAGTTTGTCAGATGTAGAATTGC 57.322 29.630 0.00 0.00 0.00 3.56
2379 2789 8.621532 TTAAGTTTGTCAGATGTAGAATTGCT 57.378 30.769 0.00 0.00 0.00 3.91
2380 2790 6.734104 AGTTTGTCAGATGTAGAATTGCTC 57.266 37.500 0.00 0.00 0.00 4.26
2381 2791 6.233434 AGTTTGTCAGATGTAGAATTGCTCA 58.767 36.000 0.00 0.00 0.00 4.26
2382 2792 6.712095 AGTTTGTCAGATGTAGAATTGCTCAA 59.288 34.615 0.00 0.00 0.00 3.02
2383 2793 7.229306 AGTTTGTCAGATGTAGAATTGCTCAAA 59.771 33.333 0.00 0.00 0.00 2.69
2384 2794 7.692460 TTGTCAGATGTAGAATTGCTCAAAT 57.308 32.000 0.00 0.00 0.00 2.32
2385 2795 7.692460 TGTCAGATGTAGAATTGCTCAAATT 57.308 32.000 0.00 0.00 41.33 1.82
2386 2796 8.114331 TGTCAGATGTAGAATTGCTCAAATTT 57.886 30.769 0.00 0.00 38.64 1.82
2387 2797 8.024865 TGTCAGATGTAGAATTGCTCAAATTTG 58.975 33.333 12.15 12.15 38.64 2.32
2388 2798 7.487189 GTCAGATGTAGAATTGCTCAAATTTGG 59.513 37.037 17.90 9.84 38.64 3.28
2389 2799 7.394077 TCAGATGTAGAATTGCTCAAATTTGGA 59.606 33.333 17.90 4.50 38.64 3.53
2414 2824 5.550290 CACCAAAATTTCTGTATTGGGCTT 58.450 37.500 8.75 0.00 45.22 4.35
2454 2864 9.834628 CTTTTCATTTCATTCCATTCAATTTGG 57.165 29.630 0.00 0.00 35.45 3.28
2458 2868 7.937942 TCATTTCATTCCATTCAATTTGGTTGT 59.062 29.630 0.00 0.00 38.95 3.32
2462 2872 6.494491 TCATTCCATTCAATTTGGTTGTCTCT 59.506 34.615 0.00 0.00 38.95 3.10
2466 2876 4.829064 TTCAATTTGGTTGTCTCTTCCG 57.171 40.909 0.00 0.00 38.95 4.30
2593 3003 5.779241 AATCCTTTCTCAGGGTGTCATTA 57.221 39.130 0.00 0.00 44.12 1.90
2594 3004 5.983333 ATCCTTTCTCAGGGTGTCATTAT 57.017 39.130 0.00 0.00 44.12 1.28
2595 3005 7.451731 AATCCTTTCTCAGGGTGTCATTATA 57.548 36.000 0.00 0.00 44.12 0.98
2596 3006 7.639062 ATCCTTTCTCAGGGTGTCATTATAT 57.361 36.000 0.00 0.00 44.12 0.86
2597 3007 7.451731 TCCTTTCTCAGGGTGTCATTATATT 57.548 36.000 0.00 0.00 44.12 1.28
2617 3027 9.699410 TTATATTTCTTGATGTGGACTCCAATT 57.301 29.630 0.00 0.00 34.18 2.32
2689 3100 2.123248 TTGAGATCCAACCGCTGCCA 62.123 55.000 0.00 0.00 0.00 4.92
2695 3106 1.152984 CCAACCGCTGCCATGGATA 60.153 57.895 18.40 1.89 34.82 2.59
2747 3159 2.287274 TGTTTGATCGGCGGGGAGA 61.287 57.895 7.21 0.00 0.00 3.71
2749 3161 0.463833 GTTTGATCGGCGGGGAGATT 60.464 55.000 7.21 0.00 0.00 2.40
2751 3163 0.254747 TTGATCGGCGGGGAGATTTT 59.745 50.000 7.21 0.00 0.00 1.82
2857 3269 2.052782 AATACTCCCCGTCAATTGCC 57.947 50.000 0.00 0.00 0.00 4.52
2870 3282 4.670621 CGTCAATTGCCGCAAGATATAAAC 59.329 41.667 12.16 2.50 43.02 2.01
2875 3287 4.983215 TGCCGCAAGATATAAACATACG 57.017 40.909 0.00 0.00 43.02 3.06
2895 3307 2.222420 CGCGGTGTTTAGACATGTTACG 60.222 50.000 0.00 0.00 38.23 3.18
2929 3341 8.554528 AGATGTAATTCTGATGATTGCTTTACG 58.445 33.333 0.00 0.00 0.00 3.18
3046 4381 9.660180 AGTCAAAGTTTAGAGATATTCTTGGAC 57.340 33.333 0.00 0.00 36.61 4.02
3053 4388 4.698575 AGAGATATTCTTGGACGCTTTCC 58.301 43.478 0.00 0.00 46.13 3.13
3062 4397 2.246719 GGACGCTTTCCATATGAGCT 57.753 50.000 3.65 0.00 45.10 4.09
3204 4540 7.449086 ACATAATTCCTTTAAAACCGTCTTCCA 59.551 33.333 0.00 0.00 0.00 3.53
3242 4578 5.769484 AGCATGATAGATTTGAAGGCAAG 57.231 39.130 0.00 0.00 35.04 4.01
3258 4594 3.055094 AGGCAAGAACATAGACGTGGATT 60.055 43.478 0.00 0.00 0.00 3.01
3265 4601 5.127845 AGAACATAGACGTGGATTGATCTGT 59.872 40.000 0.00 0.00 0.00 3.41
3277 4613 7.112009 CGTGGATTGATCTGTTAAATTTATGCG 59.888 37.037 0.00 0.00 0.00 4.73
3278 4614 6.917477 TGGATTGATCTGTTAAATTTATGCGC 59.083 34.615 0.00 0.00 0.00 6.09
3279 4615 6.917477 GGATTGATCTGTTAAATTTATGCGCA 59.083 34.615 14.96 14.96 0.00 6.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
178 186 3.558931 TGAGGCAAGTCAAGAACTCAA 57.441 42.857 0.00 0.00 37.17 3.02
239 437 5.009436 TCTTTCTCCCCCATTGATTTTCA 57.991 39.130 0.00 0.00 0.00 2.69
240 438 6.550938 AATCTTTCTCCCCCATTGATTTTC 57.449 37.500 0.00 0.00 0.00 2.29
241 439 7.191918 ACTAATCTTTCTCCCCCATTGATTTT 58.808 34.615 0.00 0.00 0.00 1.82
242 440 6.745857 ACTAATCTTTCTCCCCCATTGATTT 58.254 36.000 0.00 0.00 0.00 2.17
243 441 6.347061 ACTAATCTTTCTCCCCCATTGATT 57.653 37.500 0.00 0.00 0.00 2.57
244 442 6.347061 AACTAATCTTTCTCCCCCATTGAT 57.653 37.500 0.00 0.00 0.00 2.57
245 443 5.796502 AACTAATCTTTCTCCCCCATTGA 57.203 39.130 0.00 0.00 0.00 2.57
246 444 6.663734 ACTAACTAATCTTTCTCCCCCATTG 58.336 40.000 0.00 0.00 0.00 2.82
247 445 6.910259 ACTAACTAATCTTTCTCCCCCATT 57.090 37.500 0.00 0.00 0.00 3.16
249 447 5.788533 TCAACTAACTAATCTTTCTCCCCCA 59.211 40.000 0.00 0.00 0.00 4.96
250 448 6.309389 TCAACTAACTAATCTTTCTCCCCC 57.691 41.667 0.00 0.00 0.00 5.40
251 449 7.549842 GTCTTCAACTAACTAATCTTTCTCCCC 59.450 40.741 0.00 0.00 0.00 4.81
252 450 7.549842 GGTCTTCAACTAACTAATCTTTCTCCC 59.450 40.741 0.00 0.00 0.00 4.30
254 452 8.315482 AGGGTCTTCAACTAACTAATCTTTCTC 58.685 37.037 0.00 0.00 0.00 2.87
255 453 8.097662 CAGGGTCTTCAACTAACTAATCTTTCT 58.902 37.037 0.00 0.00 0.00 2.52
256 454 7.878644 ACAGGGTCTTCAACTAACTAATCTTTC 59.121 37.037 0.00 0.00 0.00 2.62
257 455 7.746703 ACAGGGTCTTCAACTAACTAATCTTT 58.253 34.615 0.00 0.00 0.00 2.52
258 456 7.317722 ACAGGGTCTTCAACTAACTAATCTT 57.682 36.000 0.00 0.00 0.00 2.40
260 458 9.668497 ATTTACAGGGTCTTCAACTAACTAATC 57.332 33.333 0.00 0.00 0.00 1.75
261 459 9.668497 GATTTACAGGGTCTTCAACTAACTAAT 57.332 33.333 0.00 0.00 0.00 1.73
262 460 7.816031 CGATTTACAGGGTCTTCAACTAACTAA 59.184 37.037 0.00 0.00 0.00 2.24
263 461 7.039504 ACGATTTACAGGGTCTTCAACTAACTA 60.040 37.037 0.00 0.00 0.00 2.24
264 462 6.164176 CGATTTACAGGGTCTTCAACTAACT 58.836 40.000 0.00 0.00 0.00 2.24
266 464 6.105397 ACGATTTACAGGGTCTTCAACTAA 57.895 37.500 0.00 0.00 0.00 2.24
267 465 5.337009 GGACGATTTACAGGGTCTTCAACTA 60.337 44.000 0.00 0.00 0.00 2.24
269 467 3.683340 GGACGATTTACAGGGTCTTCAAC 59.317 47.826 0.00 0.00 0.00 3.18
270 468 3.615592 CGGACGATTTACAGGGTCTTCAA 60.616 47.826 0.00 0.00 0.00 2.69
271 469 2.094390 CGGACGATTTACAGGGTCTTCA 60.094 50.000 0.00 0.00 0.00 3.02
272 470 2.094338 ACGGACGATTTACAGGGTCTTC 60.094 50.000 0.00 0.00 0.00 2.87
273 471 1.897802 ACGGACGATTTACAGGGTCTT 59.102 47.619 0.00 0.00 0.00 3.01
274 472 1.553706 ACGGACGATTTACAGGGTCT 58.446 50.000 0.00 0.00 0.00 3.85
277 475 3.184541 CTGTTACGGACGATTTACAGGG 58.815 50.000 0.00 0.00 31.69 4.45
279 477 3.841643 ACCTGTTACGGACGATTTACAG 58.158 45.455 0.00 6.11 34.32 2.74
282 480 2.159393 CGGACCTGTTACGGACGATTTA 60.159 50.000 0.00 0.00 32.61 1.40
286 484 1.600636 ACGGACCTGTTACGGACGA 60.601 57.895 15.66 0.00 34.13 4.20
287 485 1.443194 CACGGACCTGTTACGGACG 60.443 63.158 0.00 3.70 35.35 4.79
288 486 0.665369 CACACGGACCTGTTACGGAC 60.665 60.000 0.00 0.00 0.00 4.79
289 487 1.108727 ACACACGGACCTGTTACGGA 61.109 55.000 0.00 0.00 0.00 4.69
290 488 0.665369 GACACACGGACCTGTTACGG 60.665 60.000 0.00 0.00 0.00 4.02
291 489 0.313043 AGACACACGGACCTGTTACG 59.687 55.000 0.00 0.00 0.00 3.18
292 490 2.816087 TCTAGACACACGGACCTGTTAC 59.184 50.000 0.00 0.00 0.00 2.50
293 491 3.144657 TCTAGACACACGGACCTGTTA 57.855 47.619 0.00 0.00 0.00 2.41
295 493 1.991121 TTCTAGACACACGGACCTGT 58.009 50.000 0.00 0.00 0.00 4.00
296 494 3.594603 AATTCTAGACACACGGACCTG 57.405 47.619 0.00 0.00 0.00 4.00
297 495 4.954202 TGATAATTCTAGACACACGGACCT 59.046 41.667 0.00 0.00 0.00 3.85
298 496 5.258456 TGATAATTCTAGACACACGGACC 57.742 43.478 0.00 0.00 0.00 4.46
300 498 6.465439 ACATGATAATTCTAGACACACGGA 57.535 37.500 0.00 0.00 0.00 4.69
301 499 7.539712 AAACATGATAATTCTAGACACACGG 57.460 36.000 0.00 0.00 0.00 4.94
328 648 0.036388 CTTTCGTGCTCCCTGGCTAA 60.036 55.000 0.00 0.00 0.00 3.09
336 656 2.281140 GAGTACCTCTTTCGTGCTCC 57.719 55.000 0.00 0.00 37.09 4.70
622 942 3.336468 TCGCCGTATGTGGTGTATTTTT 58.664 40.909 0.00 0.00 40.48 1.94
623 943 2.975266 TCGCCGTATGTGGTGTATTTT 58.025 42.857 0.00 0.00 40.48 1.82
624 944 2.676632 TCGCCGTATGTGGTGTATTT 57.323 45.000 0.00 0.00 40.48 1.40
625 945 2.166870 TCTTCGCCGTATGTGGTGTATT 59.833 45.455 0.00 0.00 40.48 1.89
626 946 1.752498 TCTTCGCCGTATGTGGTGTAT 59.248 47.619 0.00 0.00 40.48 2.29
627 947 1.175654 TCTTCGCCGTATGTGGTGTA 58.824 50.000 0.00 0.00 40.48 2.90
628 948 0.535335 ATCTTCGCCGTATGTGGTGT 59.465 50.000 0.00 0.00 40.48 4.16
629 949 1.202417 AGATCTTCGCCGTATGTGGTG 60.202 52.381 0.00 0.00 40.98 4.17
630 950 1.112113 AGATCTTCGCCGTATGTGGT 58.888 50.000 0.00 0.00 0.00 4.16
631 951 3.502920 GATAGATCTTCGCCGTATGTGG 58.497 50.000 0.00 0.00 0.00 4.17
632 952 3.164358 CGATAGATCTTCGCCGTATGTG 58.836 50.000 0.00 0.00 39.76 3.21
633 953 3.473093 CGATAGATCTTCGCCGTATGT 57.527 47.619 0.00 0.00 39.76 2.29
682 1002 9.448438 AGCTTCACACATTGTAGTTAATTCATA 57.552 29.630 0.00 0.00 0.00 2.15
698 1018 1.338674 CCATACCCGAAGCTTCACACA 60.339 52.381 25.47 8.58 0.00 3.72
699 1019 1.338769 ACCATACCCGAAGCTTCACAC 60.339 52.381 25.47 0.00 0.00 3.82
723 1043 5.423015 ACTTAGGAGACTTGCATACATGTG 58.577 41.667 9.11 0.00 43.67 3.21
798 1118 2.019984 GACGTCCTGAAGGGTACGTAT 58.980 52.381 14.17 0.00 44.94 3.06
854 1174 3.174779 ACTTCCTCAGAGAACCTAACCC 58.825 50.000 0.00 0.00 0.00 4.11
916 1236 2.773487 CCAACCGTGTCTATCCAACAA 58.227 47.619 0.00 0.00 0.00 2.83
931 1251 0.248866 CACAACCGTTCAAGCCAACC 60.249 55.000 0.00 0.00 0.00 3.77
1046 1369 4.657814 AAAACAATCAAGGAGGAGGCTA 57.342 40.909 0.00 0.00 0.00 3.93
1071 1394 4.795278 CACAGTGAAAAGTGAACAGAAAGC 59.205 41.667 0.00 0.00 37.97 3.51
1076 1399 3.488047 CCAGCACAGTGAAAAGTGAACAG 60.488 47.826 4.15 0.00 37.97 3.16
1220 1551 1.149148 GGAAAGTGGTCGAGCAACTC 58.851 55.000 20.46 14.95 29.22 3.01
1221 1552 0.600255 CGGAAAGTGGTCGAGCAACT 60.600 55.000 20.46 15.40 31.20 3.16
1233 1564 0.527817 GCATCGATCGGACGGAAAGT 60.528 55.000 16.41 0.00 0.00 2.66
1292 1623 9.182933 CTTAATTCCTCTTCTTATACGTGCTAC 57.817 37.037 0.00 0.00 0.00 3.58
1298 1634 5.932883 GGGGCTTAATTCCTCTTCTTATACG 59.067 44.000 0.00 0.00 0.00 3.06
1300 1636 7.349859 TCTTGGGGCTTAATTCCTCTTCTTATA 59.650 37.037 0.00 0.00 0.00 0.98
1414 1750 2.180017 GACGGCGAGCGTTCCTTA 59.820 61.111 16.62 0.00 0.00 2.69
1432 1768 3.036577 TCGGACTTCTTGCGACGT 58.963 55.556 0.00 0.00 44.07 4.34
1765 2149 0.397254 CCCCATAGACGTGGACCTCT 60.397 60.000 0.00 0.00 42.02 3.69
1915 2302 1.337071 GGCGTGATCGATCAGTTCCTA 59.663 52.381 27.95 1.46 37.51 2.94
1983 2370 0.573987 TGTAGTAGTCGATCGTCGCG 59.426 55.000 15.94 0.00 40.21 5.87
2096 2488 2.462889 GATGCAACACAAACCACACAG 58.537 47.619 0.00 0.00 0.00 3.66
2220 2618 1.004628 AGTTGCCATGGAGTATGTGCA 59.995 47.619 18.40 0.00 39.54 4.57
2221 2619 1.755179 AGTTGCCATGGAGTATGTGC 58.245 50.000 18.40 0.00 34.87 4.57
2222 2620 5.125356 TCATAAGTTGCCATGGAGTATGTG 58.875 41.667 18.40 5.71 34.87 3.21
2223 2621 5.372343 TCATAAGTTGCCATGGAGTATGT 57.628 39.130 18.40 0.00 34.87 2.29
2227 2625 5.127682 GGAAAATCATAAGTTGCCATGGAGT 59.872 40.000 18.40 0.00 0.00 3.85
2229 2627 5.127519 CAGGAAAATCATAAGTTGCCATGGA 59.872 40.000 18.40 0.00 0.00 3.41
2230 2628 5.105228 ACAGGAAAATCATAAGTTGCCATGG 60.105 40.000 7.63 7.63 0.00 3.66
2231 2629 5.969423 ACAGGAAAATCATAAGTTGCCATG 58.031 37.500 0.00 0.00 0.00 3.66
2245 2648 5.831103 AGGACCACATCATTACAGGAAAAT 58.169 37.500 0.00 0.00 0.00 1.82
2250 2653 4.494091 AAGAGGACCACATCATTACAGG 57.506 45.455 0.00 0.00 0.00 4.00
2251 2654 6.824305 AAAAAGAGGACCACATCATTACAG 57.176 37.500 0.00 0.00 0.00 2.74
2299 2702 8.437360 TTCCACTTAATATGTGCACTTAGATG 57.563 34.615 19.41 12.02 34.38 2.90
2308 2711 7.650834 TTTTGCTTTTCCACTTAATATGTGC 57.349 32.000 1.23 0.00 34.38 4.57
2356 2766 6.712095 TGAGCAATTCTACATCTGACAAACTT 59.288 34.615 0.00 0.00 0.00 2.66
2358 2768 6.486253 TGAGCAATTCTACATCTGACAAAC 57.514 37.500 0.00 0.00 0.00 2.93
2386 2796 5.279406 CCAATACAGAAATTTTGGTGCTCCA 60.279 40.000 2.64 2.64 42.66 3.86
2387 2797 5.170748 CCAATACAGAAATTTTGGTGCTCC 58.829 41.667 0.00 0.00 35.07 4.70
2388 2798 5.170748 CCCAATACAGAAATTTTGGTGCTC 58.829 41.667 0.00 0.00 37.50 4.26
2389 2799 4.563374 GCCCAATACAGAAATTTTGGTGCT 60.563 41.667 0.00 0.00 37.50 4.40
2404 2814 5.468540 AAACAAGGAAGAAAGCCCAATAC 57.531 39.130 0.00 0.00 0.00 1.89
2414 2824 7.846066 TGAAATGAAAAGGAAACAAGGAAGAA 58.154 30.769 0.00 0.00 0.00 2.52
2454 2864 2.046217 GCCCCCGGAAGAGACAAC 60.046 66.667 0.73 0.00 0.00 3.32
2458 2868 0.031515 TCATAAGCCCCCGGAAGAGA 60.032 55.000 0.73 0.00 0.00 3.10
2462 2872 0.764890 CTCATCATAAGCCCCCGGAA 59.235 55.000 0.73 0.00 0.00 4.30
2466 2876 3.659183 ATATGCTCATCATAAGCCCCC 57.341 47.619 0.00 0.00 40.73 5.40
2539 2949 9.421399 CTGAAATTAGGTGGGTTATAAATTCCT 57.579 33.333 0.00 0.00 0.00 3.36
2593 3003 7.616935 ACAATTGGAGTCCACATCAAGAAATAT 59.383 33.333 12.69 0.00 30.78 1.28
2594 3004 6.947733 ACAATTGGAGTCCACATCAAGAAATA 59.052 34.615 12.69 0.00 30.78 1.40
2595 3005 5.776716 ACAATTGGAGTCCACATCAAGAAAT 59.223 36.000 12.69 0.00 30.78 2.17
2596 3006 5.139727 ACAATTGGAGTCCACATCAAGAAA 58.860 37.500 12.69 0.00 30.78 2.52
2597 3007 4.728772 ACAATTGGAGTCCACATCAAGAA 58.271 39.130 12.69 0.00 30.78 2.52
2617 3027 1.241165 CACTCAGCATGGAAGCAACA 58.759 50.000 0.00 0.00 36.16 3.33
2676 3087 1.631071 TATCCATGGCAGCGGTTGGA 61.631 55.000 6.96 9.07 42.18 3.53
2840 3252 1.219664 CGGCAATTGACGGGGAGTA 59.780 57.895 26.26 0.00 44.21 2.59
2857 3269 3.427528 ACCGCGTATGTTTATATCTTGCG 59.572 43.478 4.92 0.00 42.40 4.85
2870 3282 2.927477 ACATGTCTAAACACCGCGTATG 59.073 45.455 4.92 5.61 38.48 2.39
2875 3287 2.093152 CCGTAACATGTCTAAACACCGC 59.907 50.000 0.00 0.00 38.48 5.68
2895 3307 6.586344 TCATCAGAATTACATCTTGAGGACC 58.414 40.000 0.00 0.00 0.00 4.46
2988 4323 6.344500 CAGGCATACAGAGTTCTTGTAGATT 58.656 40.000 0.00 0.00 0.00 2.40
2989 4324 5.683509 GCAGGCATACAGAGTTCTTGTAGAT 60.684 44.000 0.00 0.00 0.00 1.98
3046 4381 9.155975 AGTATATAAAAGCTCATATGGAAAGCG 57.844 33.333 2.13 0.00 40.95 4.68
3204 4540 3.641436 TCATGCTATGTATGGAGAACCGT 59.359 43.478 0.00 0.00 39.42 4.83
3242 4578 5.352284 ACAGATCAATCCACGTCTATGTTC 58.648 41.667 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.