Multiple sequence alignment - TraesCS2B01G372900

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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 TraesCS2B01G372900 chr2B 100.000 3176 0 0 1 3176 531465716 531468891 0.000000e+00 5866.0
1 TraesCS2B01G372900 chr2D 93.316 1870 77 27 561 2392 451287345 451289204 0.000000e+00 2717.0
2 TraesCS2B01G372900 chr2D 90.476 525 14 15 1 523 451286781 451287271 0.000000e+00 660.0
3 TraesCS2B01G372900 chr2D 92.784 194 9 2 2519 2711 451289638 451289827 3.120000e-70 276.0
4 TraesCS2B01G372900 chr2D 88.017 242 14 8 2773 3008 451289896 451290128 4.040000e-69 272.0
5 TraesCS2B01G372900 chr2D 85.294 102 11 2 3079 3176 451290265 451290366 5.600000e-18 102.0
6 TraesCS2B01G372900 chr2D 100.000 36 0 0 3023 3058 451290176 451290211 2.040000e-07 67.6
7 TraesCS2B01G372900 chr2A 93.918 1447 69 10 959 2392 598162405 598160965 0.000000e+00 2167.0
8 TraesCS2B01G372900 chr2A 93.069 404 12 9 564 958 598162834 598162438 7.640000e-161 577.0
9 TraesCS2B01G372900 chr2A 80.723 498 41 31 2514 3008 598160892 598160447 1.410000e-88 337.0
10 TraesCS2B01G372900 chr2A 90.717 237 8 3 1 237 598163361 598163139 1.430000e-78 303.0
11 TraesCS2B01G372900 chr6B 80.827 991 188 2 1015 2004 446836288 446837277 0.000000e+00 776.0
12 TraesCS2B01G372900 chr6B 82.877 146 18 4 613 752 446835883 446836027 1.200000e-24 124.0
13 TraesCS2B01G372900 chr6A 80.704 995 182 8 1015 2004 407085617 407086606 0.000000e+00 765.0
14 TraesCS2B01G372900 chr6A 82.877 146 18 4 613 752 407085211 407085355 1.200000e-24 124.0
15 TraesCS2B01G372900 chr6D 81.285 903 169 0 1015 1917 285869734 285870636 0.000000e+00 732.0
16 TraesCS2B01G372900 chr6D 82.192 146 19 4 613 752 285869329 285869473 5.570000e-23 119.0


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 TraesCS2B01G372900 chr2B 531465716 531468891 3175 False 5866.000000 5866 100.000000 1 3176 1 chr2B.!!$F1 3175
1 TraesCS2B01G372900 chr2D 451286781 451290366 3585 False 682.433333 2717 91.647833 1 3176 6 chr2D.!!$F1 3175
2 TraesCS2B01G372900 chr2A 598160447 598163361 2914 True 846.000000 2167 89.606750 1 3008 4 chr2A.!!$R1 3007
3 TraesCS2B01G372900 chr6B 446835883 446837277 1394 False 450.000000 776 81.852000 613 2004 2 chr6B.!!$F1 1391
4 TraesCS2B01G372900 chr6A 407085211 407086606 1395 False 444.500000 765 81.790500 613 2004 2 chr6A.!!$F1 1391
5 TraesCS2B01G372900 chr6D 285869329 285870636 1307 False 425.500000 732 81.738500 613 1917 2 chr6D.!!$F1 1304

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
770 843 1.545706 AAGGACGAGACCCAAGAGCC 61.546 60.0 0.0 0.0 0.0 4.7 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2535 3028 0.436913 CACGCGCAGTTCGTTATTCA 59.563 50.0 5.73 0.0 38.19 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
156 157 6.483307 TCTCTTGTTTCTAGGTCATGTTGTTG 59.517 38.462 0.00 0.00 0.00 3.33
200 201 2.135139 ACCGTATGATTATGTGCGCTG 58.865 47.619 9.73 0.00 0.00 5.18
265 266 5.226194 AGTTTGCATCTAGATCTGGGATC 57.774 43.478 5.18 0.00 0.00 3.36
267 268 4.886496 TTGCATCTAGATCTGGGATCTG 57.114 45.455 17.23 9.33 0.00 2.90
268 269 3.171528 TGCATCTAGATCTGGGATCTGG 58.828 50.000 17.23 14.88 0.00 3.86
269 270 2.500910 GCATCTAGATCTGGGATCTGGG 59.499 54.545 17.23 11.15 0.00 4.45
270 271 3.820852 GCATCTAGATCTGGGATCTGGGA 60.821 52.174 17.23 14.84 0.00 4.37
272 273 4.058417 TCTAGATCTGGGATCTGGGATG 57.942 50.000 17.23 5.60 0.00 3.51
273 274 2.811322 AGATCTGGGATCTGGGATGT 57.189 50.000 8.96 0.00 0.00 3.06
274 275 3.931241 AGATCTGGGATCTGGGATGTA 57.069 47.619 8.96 0.00 0.00 2.29
275 276 3.788933 AGATCTGGGATCTGGGATGTAG 58.211 50.000 8.96 0.00 0.00 2.74
276 277 3.143741 AGATCTGGGATCTGGGATGTAGT 59.856 47.826 8.96 0.00 0.00 2.73
277 278 4.358310 AGATCTGGGATCTGGGATGTAGTA 59.642 45.833 8.96 0.00 0.00 1.82
278 279 4.119556 TCTGGGATCTGGGATGTAGTAG 57.880 50.000 0.00 0.00 0.00 2.57
279 280 3.467483 TCTGGGATCTGGGATGTAGTAGT 59.533 47.826 0.00 0.00 0.00 2.73
280 281 4.668335 TCTGGGATCTGGGATGTAGTAGTA 59.332 45.833 0.00 0.00 0.00 1.82
281 282 4.999310 TGGGATCTGGGATGTAGTAGTAG 58.001 47.826 0.00 0.00 0.00 2.57
282 283 4.419200 TGGGATCTGGGATGTAGTAGTAGT 59.581 45.833 0.00 0.00 0.00 2.73
283 284 5.103215 TGGGATCTGGGATGTAGTAGTAGTT 60.103 44.000 0.00 0.00 0.00 2.24
284 285 5.839606 GGGATCTGGGATGTAGTAGTAGTTT 59.160 44.000 0.00 0.00 0.00 2.66
285 286 6.239345 GGGATCTGGGATGTAGTAGTAGTTTG 60.239 46.154 0.00 0.00 0.00 2.93
286 287 6.239345 GGATCTGGGATGTAGTAGTAGTTTGG 60.239 46.154 0.00 0.00 0.00 3.28
287 288 5.834460 TCTGGGATGTAGTAGTAGTTTGGA 58.166 41.667 0.00 0.00 0.00 3.53
288 289 5.892119 TCTGGGATGTAGTAGTAGTTTGGAG 59.108 44.000 0.00 0.00 0.00 3.86
289 290 5.586877 TGGGATGTAGTAGTAGTTTGGAGT 58.413 41.667 0.00 0.00 0.00 3.85
290 291 6.734532 TGGGATGTAGTAGTAGTTTGGAGTA 58.265 40.000 0.00 0.00 0.00 2.59
427 430 6.405508 GGCTTATGGCATCATGGATGATTTAG 60.406 42.308 1.65 2.15 45.23 1.85
494 497 4.124238 CCCGTAGAGTCACAAAGTTTCAA 58.876 43.478 0.00 0.00 0.00 2.69
496 499 5.238650 CCCGTAGAGTCACAAAGTTTCAAAT 59.761 40.000 0.00 0.00 0.00 2.32
499 502 6.238374 CGTAGAGTCACAAAGTTTCAAATGGT 60.238 38.462 0.00 0.00 0.00 3.55
524 529 6.744112 ACACATGTTCGTGGTTGAATTTTAT 58.256 32.000 0.00 0.00 41.38 1.40
525 530 7.206687 ACACATGTTCGTGGTTGAATTTTATT 58.793 30.769 0.00 0.00 41.38 1.40
527 532 8.849490 CACATGTTCGTGGTTGAATTTTATTAG 58.151 33.333 0.00 0.00 33.05 1.73
528 533 7.540745 ACATGTTCGTGGTTGAATTTTATTAGC 59.459 33.333 0.00 0.00 0.00 3.09
529 534 6.383415 TGTTCGTGGTTGAATTTTATTAGCC 58.617 36.000 0.00 0.00 0.00 3.93
530 535 6.016192 TGTTCGTGGTTGAATTTTATTAGCCA 60.016 34.615 0.00 0.00 0.00 4.75
531 536 6.767524 TCGTGGTTGAATTTTATTAGCCAT 57.232 33.333 0.00 0.00 0.00 4.40
532 537 6.791303 TCGTGGTTGAATTTTATTAGCCATC 58.209 36.000 0.00 0.00 0.00 3.51
768 841 2.943449 GTAAGGACGAGACCCAAGAG 57.057 55.000 0.00 0.00 0.00 2.85
770 843 1.545706 AAGGACGAGACCCAAGAGCC 61.546 60.000 0.00 0.00 0.00 4.70
771 844 1.985116 GGACGAGACCCAAGAGCCT 60.985 63.158 0.00 0.00 0.00 4.58
989 1134 2.366590 TCTGCTCTGCTTTCTGACTCAA 59.633 45.455 0.00 0.00 0.00 3.02
1050 1195 2.184579 GGCTACGAGAAGCGCCTT 59.815 61.111 2.29 0.00 46.04 4.35
1197 1342 3.493503 CCAACAAGGACTTTGACTCGTAC 59.506 47.826 4.05 0.00 41.22 3.67
1206 1351 2.838386 TTGACTCGTACGTGCTATCC 57.162 50.000 16.05 1.88 0.00 2.59
1216 1361 1.777030 CGTGCTATCCGAGTCGAGCT 61.777 60.000 21.04 6.50 35.89 4.09
1293 1438 2.948315 GCTCACCATTCCAAGGATTCTC 59.052 50.000 0.00 0.00 0.00 2.87
1299 1444 2.680312 TTCCAAGGATTCTCGAGCTG 57.320 50.000 7.81 0.00 0.00 4.24
1365 1510 0.546598 GGATGTTCATCTTCCCCGGT 59.453 55.000 11.73 0.00 35.21 5.28
1560 1705 0.107312 AGATGTGCATGACTGGGCTC 60.107 55.000 0.00 0.00 0.00 4.70
1581 1726 2.421619 GACAAGAAGAAGGCCTCTGTG 58.578 52.381 5.23 7.37 33.37 3.66
1608 1753 0.917533 AGACTTCTGCTGATGGCCAT 59.082 50.000 20.96 20.96 40.92 4.40
1611 1756 1.022735 CTTCTGCTGATGGCCATGTC 58.977 55.000 26.56 11.82 40.92 3.06
1620 1765 1.569030 ATGGCCATGTCTCCTGTGCT 61.569 55.000 20.04 0.00 0.00 4.40
1806 1951 2.514592 ATGGGCATGGACGCTTCG 60.515 61.111 0.00 0.00 0.00 3.79
1869 2014 1.434188 TTGGCCCTTCAGAGTTCTCA 58.566 50.000 0.00 0.00 0.00 3.27
2075 2220 2.202676 CTGCTTCGAGGCCGAGAC 60.203 66.667 17.65 0.00 46.39 3.36
2080 2225 2.549611 CTTCGAGGCCGAGACTGTGG 62.550 65.000 0.00 0.00 46.39 4.17
2159 2307 1.002274 ATTCTCTGGAGGAGGGCGT 59.998 57.895 0.00 0.00 42.10 5.68
2186 2342 0.319469 TGCGAGTGATTTGCTGTCGA 60.319 50.000 0.00 0.00 37.09 4.20
2187 2343 0.790207 GCGAGTGATTTGCTGTCGAA 59.210 50.000 0.00 0.00 33.06 3.71
2193 2349 3.814842 AGTGATTTGCTGTCGAATGTTCA 59.185 39.130 0.00 0.00 0.00 3.18
2208 2364 3.988379 TGTTCAGTCTGTGGAATTTGC 57.012 42.857 0.00 0.00 0.00 3.68
2218 2374 4.040339 TCTGTGGAATTTGCTCTGACTGTA 59.960 41.667 0.00 0.00 0.00 2.74
2219 2375 4.910195 TGTGGAATTTGCTCTGACTGTAT 58.090 39.130 0.00 0.00 0.00 2.29
2221 2377 4.697352 GTGGAATTTGCTCTGACTGTATGT 59.303 41.667 0.00 0.00 0.00 2.29
2222 2378 4.937620 TGGAATTTGCTCTGACTGTATGTC 59.062 41.667 0.00 0.00 45.54 3.06
2223 2379 5.181748 GGAATTTGCTCTGACTGTATGTCT 58.818 41.667 0.00 0.00 45.54 3.41
2319 2476 2.327343 GCGTCTGCCACAATGAGCA 61.327 57.895 3.13 3.13 37.46 4.26
2324 2481 2.353889 GTCTGCCACAATGAGCATACTG 59.646 50.000 9.75 0.00 38.56 2.74
2325 2482 2.026915 TCTGCCACAATGAGCATACTGT 60.027 45.455 3.52 0.00 38.56 3.55
2326 2483 2.751259 CTGCCACAATGAGCATACTGTT 59.249 45.455 3.52 0.00 38.56 3.16
2397 2556 7.864307 ACGAGTGTCACTTTGTTATTACTAC 57.136 36.000 7.00 0.00 0.00 2.73
2398 2557 7.655490 ACGAGTGTCACTTTGTTATTACTACT 58.345 34.615 7.00 0.00 0.00 2.57
2399 2558 7.594015 ACGAGTGTCACTTTGTTATTACTACTG 59.406 37.037 7.00 0.00 0.00 2.74
2400 2559 7.806487 CGAGTGTCACTTTGTTATTACTACTGA 59.194 37.037 7.00 0.00 0.00 3.41
2401 2560 9.472361 GAGTGTCACTTTGTTATTACTACTGAA 57.528 33.333 7.00 0.00 0.00 3.02
2402 2561 9.998106 AGTGTCACTTTGTTATTACTACTGAAT 57.002 29.630 0.00 0.00 0.00 2.57
2412 2571 9.162764 TGTTATTACTACTGAATTCCTTTCTGC 57.837 33.333 2.27 0.00 36.91 4.26
2413 2572 8.613482 GTTATTACTACTGAATTCCTTTCTGCC 58.387 37.037 2.27 0.00 36.91 4.85
2414 2573 4.917906 ACTACTGAATTCCTTTCTGCCT 57.082 40.909 2.27 0.00 36.91 4.75
2415 2574 4.583871 ACTACTGAATTCCTTTCTGCCTG 58.416 43.478 2.27 0.00 36.91 4.85
2428 2587 8.206126 TCCTTTCTGCCTGTATCATATTCATA 57.794 34.615 0.00 0.00 0.00 2.15
2453 2612 8.894768 ATTCTGTAATTGGAGTTACTAGATGC 57.105 34.615 0.00 0.00 35.94 3.91
2455 2614 6.382859 TCTGTAATTGGAGTTACTAGATGCCA 59.617 38.462 0.00 0.00 35.94 4.92
2456 2615 6.953101 TGTAATTGGAGTTACTAGATGCCAA 58.047 36.000 5.19 5.19 39.45 4.52
2457 2616 7.047891 TGTAATTGGAGTTACTAGATGCCAAG 58.952 38.462 8.17 0.00 38.62 3.61
2459 2618 5.499004 TTGGAGTTACTAGATGCCAAGTT 57.501 39.130 0.00 0.00 32.19 2.66
2460 2619 5.499004 TGGAGTTACTAGATGCCAAGTTT 57.501 39.130 0.00 0.00 0.00 2.66
2461 2620 5.876357 TGGAGTTACTAGATGCCAAGTTTT 58.124 37.500 0.00 0.00 0.00 2.43
2462 2621 5.705441 TGGAGTTACTAGATGCCAAGTTTTG 59.295 40.000 0.00 0.00 0.00 2.44
2463 2622 5.392057 GGAGTTACTAGATGCCAAGTTTTGC 60.392 44.000 0.00 0.00 0.00 3.68
2465 2624 5.412904 AGTTACTAGATGCCAAGTTTTGCTC 59.587 40.000 0.00 0.00 0.00 4.26
2466 2625 3.084786 ACTAGATGCCAAGTTTTGCTCC 58.915 45.455 0.00 0.00 0.00 4.70
2467 2626 1.999648 AGATGCCAAGTTTTGCTCCA 58.000 45.000 0.00 0.00 0.00 3.86
2468 2627 2.532843 AGATGCCAAGTTTTGCTCCAT 58.467 42.857 0.00 0.00 0.00 3.41
2469 2628 2.901839 AGATGCCAAGTTTTGCTCCATT 59.098 40.909 0.00 0.00 0.00 3.16
2470 2629 4.088634 AGATGCCAAGTTTTGCTCCATTA 58.911 39.130 0.00 0.00 0.00 1.90
2471 2630 3.940209 TGCCAAGTTTTGCTCCATTAG 57.060 42.857 0.00 0.00 0.00 1.73
2473 2632 3.255642 TGCCAAGTTTTGCTCCATTAGTC 59.744 43.478 0.00 0.00 0.00 2.59
2474 2633 3.255642 GCCAAGTTTTGCTCCATTAGTCA 59.744 43.478 0.00 0.00 0.00 3.41
2475 2634 4.082026 GCCAAGTTTTGCTCCATTAGTCAT 60.082 41.667 0.00 0.00 0.00 3.06
2476 2635 5.404946 CCAAGTTTTGCTCCATTAGTCATG 58.595 41.667 0.00 0.00 0.00 3.07
2477 2636 5.047802 CCAAGTTTTGCTCCATTAGTCATGT 60.048 40.000 0.00 0.00 0.00 3.21
2478 2637 6.449698 CAAGTTTTGCTCCATTAGTCATGTT 58.550 36.000 0.00 0.00 0.00 2.71
2480 2639 7.944729 AGTTTTGCTCCATTAGTCATGTTAT 57.055 32.000 0.00 0.00 0.00 1.89
2481 2640 9.461312 AAGTTTTGCTCCATTAGTCATGTTATA 57.539 29.630 0.00 0.00 0.00 0.98
2482 2641 9.632638 AGTTTTGCTCCATTAGTCATGTTATAT 57.367 29.630 0.00 0.00 0.00 0.86
2499 2789 7.139896 TGTTATATTACTTGCAGTGTGTTGG 57.860 36.000 4.92 0.00 0.00 3.77
2514 2804 2.424474 TTGGCAAGCGACCAATGTT 58.576 47.368 0.00 0.00 42.23 2.71
2529 3022 5.595885 ACCAATGTTCTGATCATCTCGTAG 58.404 41.667 0.00 0.00 0.00 3.51
2535 3028 0.961753 TGATCATCTCGTAGGCGCAT 59.038 50.000 10.83 3.98 38.14 4.73
2542 3035 2.739292 TCTCGTAGGCGCATGAATAAC 58.261 47.619 10.83 0.00 38.14 1.89
2543 3036 1.452025 CTCGTAGGCGCATGAATAACG 59.548 52.381 10.83 9.11 38.14 3.18
2562 3056 1.006832 GAACTGCGCGTGGAATACAT 58.993 50.000 8.43 0.00 0.00 2.29
2594 3089 9.485206 AATCATTCTTTTGTTTGATTGAAGAGG 57.515 29.630 0.00 0.00 37.41 3.69
2657 3152 7.055378 AGCTTATCTTCTGCATTTCTGATTCT 58.945 34.615 0.00 0.00 0.00 2.40
2676 3171 6.211184 TGATTCTTGCAACCACTCCAATAATT 59.789 34.615 0.00 0.00 0.00 1.40
2719 3239 6.681368 GCCTCAATAATTCATTCAAGGTGTCC 60.681 42.308 0.00 0.00 32.51 4.02
2756 3276 7.575532 CGTGAGTTATTGGGTGTAGTAGTAACA 60.576 40.741 0.00 0.00 0.00 2.41
2764 3284 5.409214 TGGGTGTAGTAGTAACATTTTTCGC 59.591 40.000 0.00 0.00 0.00 4.70
2805 3325 1.368850 GTTCGTTCTTGCGTGTGCC 60.369 57.895 0.00 0.00 41.78 5.01
2806 3326 2.876879 TTCGTTCTTGCGTGTGCCG 61.877 57.895 0.00 0.00 41.78 5.69
2807 3327 4.368808 CGTTCTTGCGTGTGCCGG 62.369 66.667 0.00 0.00 41.78 6.13
2808 3328 3.276846 GTTCTTGCGTGTGCCGGT 61.277 61.111 1.90 0.00 41.78 5.28
2809 3329 3.276091 TTCTTGCGTGTGCCGGTG 61.276 61.111 1.90 0.00 41.78 4.94
2810 3330 4.539083 TCTTGCGTGTGCCGGTGT 62.539 61.111 1.90 0.00 41.78 4.16
2811 3331 4.312231 CTTGCGTGTGCCGGTGTG 62.312 66.667 1.90 0.00 41.78 3.82
2884 3409 5.049405 CGTATCTAATCTTTTGGGATGCACC 60.049 44.000 0.00 0.00 38.08 5.01
2885 3410 3.278574 TCTAATCTTTTGGGATGCACCG 58.721 45.455 0.00 0.00 40.11 4.94
2899 3424 0.947244 GCACCGGATTGATGGATGAC 59.053 55.000 9.46 0.00 0.00 3.06
3018 3543 0.320050 TTGCCGATAGATATGCCGCA 59.680 50.000 0.00 0.00 39.76 5.69
3019 3544 0.320050 TGCCGATAGATATGCCGCAA 59.680 50.000 0.00 0.00 39.76 4.85
3021 3546 1.328680 GCCGATAGATATGCCGCAATG 59.671 52.381 0.00 0.00 39.76 2.82
3058 3620 2.668212 CTTGTTTCTCGCCGGCCA 60.668 61.111 23.46 7.41 0.00 5.36
3059 3621 2.203224 TTGTTTCTCGCCGGCCAA 60.203 55.556 23.46 15.32 0.00 4.52
3060 3622 2.187599 CTTGTTTCTCGCCGGCCAAG 62.188 60.000 23.46 22.08 0.00 3.61
3062 3624 2.668212 TTTCTCGCCGGCCAAGTG 60.668 61.111 23.46 6.36 0.00 3.16
3063 3625 3.171828 TTTCTCGCCGGCCAAGTGA 62.172 57.895 23.46 11.12 0.00 3.41
3064 3626 2.668185 TTTCTCGCCGGCCAAGTGAA 62.668 55.000 23.46 16.27 0.00 3.18
3065 3627 3.423154 CTCGCCGGCCAAGTGAAC 61.423 66.667 23.46 0.00 0.00 3.18
3066 3628 4.243008 TCGCCGGCCAAGTGAACA 62.243 61.111 23.46 0.00 0.00 3.18
3085 3680 4.572571 AAAAGGCCGGCCACACGA 62.573 61.111 45.13 0.00 38.92 4.35
3116 3711 2.550855 GCATCTCCCTTGGCATATTCGA 60.551 50.000 0.00 0.00 0.00 3.71
3117 3712 2.910688 TCTCCCTTGGCATATTCGAC 57.089 50.000 0.00 0.00 0.00 4.20
3121 3716 3.885297 CTCCCTTGGCATATTCGACAATT 59.115 43.478 0.00 0.00 32.16 2.32
3154 3749 4.151798 CGACCAAAGAAATTTCGCTCTTC 58.848 43.478 12.42 7.18 30.57 2.87
3157 3756 4.584743 ACCAAAGAAATTTCGCTCTTCCTT 59.415 37.500 12.42 0.00 30.57 3.36
3166 3765 1.469308 TCGCTCTTCCTTCTCTCGTTC 59.531 52.381 0.00 0.00 0.00 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
156 157 1.493311 GAGCACAACTACAGCGCAC 59.507 57.895 11.47 0.00 0.00 5.34
265 266 5.657302 ACTCCAAACTACTACTACATCCCAG 59.343 44.000 0.00 0.00 0.00 4.45
267 268 7.504911 TCATACTCCAAACTACTACTACATCCC 59.495 40.741 0.00 0.00 0.00 3.85
268 269 8.461249 TCATACTCCAAACTACTACTACATCC 57.539 38.462 0.00 0.00 0.00 3.51
269 270 8.077386 GCTCATACTCCAAACTACTACTACATC 58.923 40.741 0.00 0.00 0.00 3.06
270 271 7.780745 AGCTCATACTCCAAACTACTACTACAT 59.219 37.037 0.00 0.00 0.00 2.29
272 273 7.571080 AGCTCATACTCCAAACTACTACTAC 57.429 40.000 0.00 0.00 0.00 2.73
273 274 9.286170 CATAGCTCATACTCCAAACTACTACTA 57.714 37.037 0.00 0.00 0.00 1.82
274 275 7.255660 GCATAGCTCATACTCCAAACTACTACT 60.256 40.741 0.00 0.00 0.00 2.57
275 276 6.864165 GCATAGCTCATACTCCAAACTACTAC 59.136 42.308 0.00 0.00 0.00 2.73
276 277 6.015350 GGCATAGCTCATACTCCAAACTACTA 60.015 42.308 0.00 0.00 0.00 1.82
277 278 5.221541 GGCATAGCTCATACTCCAAACTACT 60.222 44.000 0.00 0.00 0.00 2.57
278 279 4.991687 GGCATAGCTCATACTCCAAACTAC 59.008 45.833 0.00 0.00 0.00 2.73
279 280 4.901849 AGGCATAGCTCATACTCCAAACTA 59.098 41.667 0.00 0.00 0.00 2.24
280 281 3.713764 AGGCATAGCTCATACTCCAAACT 59.286 43.478 0.00 0.00 0.00 2.66
281 282 4.078639 AGGCATAGCTCATACTCCAAAC 57.921 45.455 0.00 0.00 0.00 2.93
282 283 4.080356 ACAAGGCATAGCTCATACTCCAAA 60.080 41.667 0.00 0.00 0.00 3.28
283 284 3.455910 ACAAGGCATAGCTCATACTCCAA 59.544 43.478 0.00 0.00 0.00 3.53
284 285 3.041211 ACAAGGCATAGCTCATACTCCA 58.959 45.455 0.00 0.00 0.00 3.86
285 286 3.760580 ACAAGGCATAGCTCATACTCC 57.239 47.619 0.00 0.00 0.00 3.85
286 287 5.713792 TCTACAAGGCATAGCTCATACTC 57.286 43.478 0.00 0.00 0.00 2.59
287 288 5.046735 CCATCTACAAGGCATAGCTCATACT 60.047 44.000 0.00 0.00 0.00 2.12
288 289 5.047021 TCCATCTACAAGGCATAGCTCATAC 60.047 44.000 0.00 0.00 0.00 2.39
289 290 5.086621 TCCATCTACAAGGCATAGCTCATA 58.913 41.667 0.00 0.00 0.00 2.15
290 291 3.906218 TCCATCTACAAGGCATAGCTCAT 59.094 43.478 0.00 0.00 0.00 2.90
494 497 3.134574 ACCACGAACATGTGTACCATT 57.865 42.857 0.00 0.00 38.20 3.16
496 499 2.158943 TCAACCACGAACATGTGTACCA 60.159 45.455 0.00 0.00 38.20 3.25
499 502 5.759506 AAATTCAACCACGAACATGTGTA 57.240 34.783 0.00 0.00 38.20 2.90
543 592 8.611654 AGCAAAACTAAGGAAACGTTTCTATA 57.388 30.769 33.23 25.01 37.35 1.31
556 605 7.389053 AGACAACAGATTCTAGCAAAACTAAGG 59.611 37.037 0.00 0.00 0.00 2.69
558 607 9.772973 TTAGACAACAGATTCTAGCAAAACTAA 57.227 29.630 0.00 0.00 0.00 2.24
757 830 0.980423 AGTGAAGGCTCTTGGGTCTC 59.020 55.000 0.00 0.00 0.00 3.36
759 832 1.349357 AGAAGTGAAGGCTCTTGGGTC 59.651 52.381 0.00 0.00 0.00 4.46
760 833 1.072965 CAGAAGTGAAGGCTCTTGGGT 59.927 52.381 0.00 0.00 0.00 4.51
762 835 2.557920 ACAGAAGTGAAGGCTCTTGG 57.442 50.000 0.00 0.00 0.00 3.61
766 839 3.063485 GTCTGAACAGAAGTGAAGGCTC 58.937 50.000 6.08 0.00 39.48 4.70
768 841 2.838736 TGTCTGAACAGAAGTGAAGGC 58.161 47.619 6.08 0.00 39.48 4.35
770 843 8.997323 AGATAAAATGTCTGAACAGAAGTGAAG 58.003 33.333 6.08 0.00 39.20 3.02
771 844 8.908786 AGATAAAATGTCTGAACAGAAGTGAA 57.091 30.769 6.08 0.00 39.20 3.18
989 1134 3.294079 GCAGCCATTGTTGCAGTTT 57.706 47.368 0.48 0.00 46.76 2.66
1026 1171 1.471676 CGCTTCTCGTAGCCCTCAAAT 60.472 52.381 0.00 0.00 37.90 2.32
1050 1195 2.106566 GCCTCAGAGAAGGTGATCTCA 58.893 52.381 0.00 0.00 46.73 3.27
1197 1342 1.369448 GCTCGACTCGGATAGCACG 60.369 63.158 5.89 0.00 35.05 5.34
1206 1351 4.911053 AGTAGATAAACAAGCTCGACTCG 58.089 43.478 0.00 0.00 0.00 4.18
1216 1361 9.645059 CACAATCTTCTGAGAGTAGATAAACAA 57.355 33.333 0.00 0.00 32.20 2.83
1560 1705 1.001406 ACAGAGGCCTTCTTCTTGTCG 59.999 52.381 6.77 0.00 32.41 4.35
1581 1726 4.153835 CCATCAGCAGAAGTCTTGAAGAAC 59.846 45.833 0.00 0.00 0.00 3.01
1620 1765 3.703556 CAGAGAGCTTGGTCATCTCCTTA 59.296 47.826 2.64 0.00 40.29 2.69
1770 1915 1.020861 TGACCTCGTAGCTCGCGTAA 61.021 55.000 5.77 0.00 39.67 3.18
1869 2014 1.296715 GAAGATGGTGACCGCCACT 59.703 57.895 4.21 2.23 45.03 4.00
2091 2236 1.871126 GCTTGCCTTCCTTGACCAGC 61.871 60.000 0.00 0.00 0.00 4.85
2133 2278 0.758685 CCTCCAGAGAATCCTCCGCT 60.759 60.000 0.00 0.00 40.30 5.52
2159 2307 0.534877 AAATCACTCGCACAGCACCA 60.535 50.000 0.00 0.00 0.00 4.17
2186 2342 4.586001 AGCAAATTCCACAGACTGAACATT 59.414 37.500 10.08 0.00 0.00 2.71
2187 2343 4.147321 AGCAAATTCCACAGACTGAACAT 58.853 39.130 10.08 0.00 0.00 2.71
2193 2349 3.072184 AGTCAGAGCAAATTCCACAGACT 59.928 43.478 0.00 0.00 0.00 3.24
2218 2374 5.355910 ACAGTAACCAAACGACAAAAGACAT 59.644 36.000 0.00 0.00 0.00 3.06
2219 2375 4.696402 ACAGTAACCAAACGACAAAAGACA 59.304 37.500 0.00 0.00 0.00 3.41
2221 2377 4.936411 TCACAGTAACCAAACGACAAAAGA 59.064 37.500 0.00 0.00 0.00 2.52
2222 2378 5.224562 TCACAGTAACCAAACGACAAAAG 57.775 39.130 0.00 0.00 0.00 2.27
2223 2379 5.624344 TTCACAGTAACCAAACGACAAAA 57.376 34.783 0.00 0.00 0.00 2.44
2319 2476 5.454966 AGACAACTTTTCCCCAAACAGTAT 58.545 37.500 0.00 0.00 0.00 2.12
2324 2481 4.159693 AGTTGAGACAACTTTTCCCCAAAC 59.840 41.667 10.73 0.00 0.00 2.93
2325 2482 4.349365 AGTTGAGACAACTTTTCCCCAAA 58.651 39.130 10.73 0.00 0.00 3.28
2326 2483 3.976015 AGTTGAGACAACTTTTCCCCAA 58.024 40.909 10.73 0.00 0.00 4.12
2371 2529 5.924825 AGTAATAACAAAGTGACACTCGTCC 59.075 40.000 8.93 0.00 41.85 4.79
2389 2548 7.987458 CAGGCAGAAAGGAATTCAGTAGTAATA 59.013 37.037 7.93 0.00 40.72 0.98
2390 2549 6.825721 CAGGCAGAAAGGAATTCAGTAGTAAT 59.174 38.462 7.93 0.00 40.72 1.89
2391 2550 6.173339 CAGGCAGAAAGGAATTCAGTAGTAA 58.827 40.000 7.93 0.00 40.72 2.24
2392 2551 5.248477 ACAGGCAGAAAGGAATTCAGTAGTA 59.752 40.000 7.93 0.00 40.72 1.82
2393 2552 4.042187 ACAGGCAGAAAGGAATTCAGTAGT 59.958 41.667 7.93 0.00 40.72 2.73
2394 2553 4.583871 ACAGGCAGAAAGGAATTCAGTAG 58.416 43.478 7.93 0.00 40.72 2.57
2395 2554 4.640771 ACAGGCAGAAAGGAATTCAGTA 57.359 40.909 7.93 0.00 40.72 2.74
2396 2555 3.515602 ACAGGCAGAAAGGAATTCAGT 57.484 42.857 7.93 0.00 40.72 3.41
2397 2556 5.188434 TGATACAGGCAGAAAGGAATTCAG 58.812 41.667 7.93 0.00 40.72 3.02
2398 2557 5.178096 TGATACAGGCAGAAAGGAATTCA 57.822 39.130 7.93 0.00 40.72 2.57
2399 2558 7.992754 ATATGATACAGGCAGAAAGGAATTC 57.007 36.000 0.00 0.00 38.39 2.17
2400 2559 8.000709 TGAATATGATACAGGCAGAAAGGAATT 58.999 33.333 0.00 0.00 0.00 2.17
2401 2560 7.520798 TGAATATGATACAGGCAGAAAGGAAT 58.479 34.615 0.00 0.00 0.00 3.01
2402 2561 6.899089 TGAATATGATACAGGCAGAAAGGAA 58.101 36.000 0.00 0.00 0.00 3.36
2403 2562 6.499106 TGAATATGATACAGGCAGAAAGGA 57.501 37.500 0.00 0.00 0.00 3.36
2404 2563 9.458727 AATATGAATATGATACAGGCAGAAAGG 57.541 33.333 0.00 0.00 0.00 3.11
2407 2566 9.662947 CAGAATATGAATATGATACAGGCAGAA 57.337 33.333 0.00 0.00 0.00 3.02
2408 2567 8.819845 ACAGAATATGAATATGATACAGGCAGA 58.180 33.333 0.00 0.00 0.00 4.26
2428 2587 7.934120 GGCATCTAGTAACTCCAATTACAGAAT 59.066 37.037 0.00 0.00 37.49 2.40
2438 2597 5.499004 AAACTTGGCATCTAGTAACTCCA 57.501 39.130 0.00 0.00 0.00 3.86
2440 2599 5.412904 AGCAAAACTTGGCATCTAGTAACTC 59.587 40.000 0.00 0.00 0.00 3.01
2442 2601 5.392057 GGAGCAAAACTTGGCATCTAGTAAC 60.392 44.000 0.00 0.00 0.00 2.50
2443 2602 4.700213 GGAGCAAAACTTGGCATCTAGTAA 59.300 41.667 0.00 0.00 0.00 2.24
2448 2607 1.999648 TGGAGCAAAACTTGGCATCT 58.000 45.000 0.00 0.00 0.00 2.90
2449 2608 3.323751 AATGGAGCAAAACTTGGCATC 57.676 42.857 0.00 0.00 0.00 3.91
2451 2610 3.230134 ACTAATGGAGCAAAACTTGGCA 58.770 40.909 0.00 0.00 0.00 4.92
2452 2611 3.255642 TGACTAATGGAGCAAAACTTGGC 59.744 43.478 0.00 0.00 0.00 4.52
2453 2612 5.047802 ACATGACTAATGGAGCAAAACTTGG 60.048 40.000 0.00 0.00 40.94 3.61
2455 2614 6.655078 AACATGACTAATGGAGCAAAACTT 57.345 33.333 0.00 0.00 40.94 2.66
2456 2615 7.944729 ATAACATGACTAATGGAGCAAAACT 57.055 32.000 0.00 0.00 40.94 2.66
2499 2789 0.874390 TCAGAACATTGGTCGCTTGC 59.126 50.000 0.00 0.00 0.00 4.01
2514 2804 0.593618 GCGCCTACGAGATGATCAGA 59.406 55.000 0.09 0.00 43.93 3.27
2529 3022 1.856014 GCAGTTCGTTATTCATGCGCC 60.856 52.381 4.18 0.00 0.00 6.53
2535 3028 0.436913 CACGCGCAGTTCGTTATTCA 59.563 50.000 5.73 0.00 38.19 2.57
2542 3035 1.343821 GTATTCCACGCGCAGTTCG 59.656 57.895 5.73 0.00 42.12 3.95
2543 3036 1.006832 ATGTATTCCACGCGCAGTTC 58.993 50.000 5.73 0.00 0.00 3.01
2562 3056 6.070897 TCAAACAAAAGAATGATTCGAGCA 57.929 33.333 0.00 0.00 34.02 4.26
2594 3089 8.860780 AGATAAGGATGAAGAATCAAATAGGC 57.139 34.615 0.00 0.00 39.49 3.93
2657 3152 4.321899 GCTGAATTATTGGAGTGGTTGCAA 60.322 41.667 0.00 0.00 41.61 4.08
2701 3196 3.438781 GCACGGACACCTTGAATGAATTA 59.561 43.478 0.00 0.00 0.00 1.40
2756 3276 5.336744 TGTCAAAAGAACGAAGCGAAAAAT 58.663 33.333 0.00 0.00 0.00 1.82
2764 3284 4.267357 TCCGTTTGTCAAAAGAACGAAG 57.733 40.909 12.18 0.00 46.47 3.79
2805 3325 2.794910 CCAAGATTAGATACGCACACCG 59.205 50.000 0.00 0.00 44.21 4.94
2806 3326 2.544267 GCCAAGATTAGATACGCACACC 59.456 50.000 0.00 0.00 0.00 4.16
2807 3327 2.218759 CGCCAAGATTAGATACGCACAC 59.781 50.000 0.00 0.00 0.00 3.82
2808 3328 2.159156 ACGCCAAGATTAGATACGCACA 60.159 45.455 0.00 0.00 0.00 4.57
2809 3329 2.470821 ACGCCAAGATTAGATACGCAC 58.529 47.619 0.00 0.00 0.00 5.34
2810 3330 2.882927 ACGCCAAGATTAGATACGCA 57.117 45.000 0.00 0.00 0.00 5.24
2811 3331 5.646467 TTTTACGCCAAGATTAGATACGC 57.354 39.130 0.00 0.00 0.00 4.42
2857 3382 5.409826 GCATCCCAAAAGATTAGATACGGAG 59.590 44.000 0.00 0.00 0.00 4.63
2859 3384 5.049405 GTGCATCCCAAAAGATTAGATACGG 60.049 44.000 0.00 0.00 0.00 4.02
2884 3409 1.560004 CGCCGTCATCCATCAATCCG 61.560 60.000 0.00 0.00 0.00 4.18
2885 3410 0.532862 ACGCCGTCATCCATCAATCC 60.533 55.000 0.00 0.00 0.00 3.01
2962 3487 4.264380 CGTCATCACGTGATAAAACGATGA 59.736 41.667 33.86 23.92 46.49 2.92
2963 3488 4.264380 TCGTCATCACGTGATAAAACGATG 59.736 41.667 34.75 28.37 46.49 3.84
2990 3515 5.482908 CATATCTATCGGCAAGCCTAAGTT 58.517 41.667 9.73 2.10 0.00 2.66
2992 3517 3.868077 GCATATCTATCGGCAAGCCTAAG 59.132 47.826 9.73 3.94 0.00 2.18
3129 3724 3.404899 AGCGAAATTTCTTTGGTCGGTA 58.595 40.909 15.92 0.00 0.00 4.02
3133 3728 4.216472 AGGAAGAGCGAAATTTCTTTGGTC 59.784 41.667 15.92 14.19 33.97 4.02
3134 3729 4.145052 AGGAAGAGCGAAATTTCTTTGGT 58.855 39.130 15.92 6.32 33.97 3.67
3148 3743 2.752903 AGAGAACGAGAGAAGGAAGAGC 59.247 50.000 0.00 0.00 0.00 4.09
3154 3749 2.289072 TGCCAAAGAGAACGAGAGAAGG 60.289 50.000 0.00 0.00 0.00 3.46


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

AutoCloner maintained by Alex Coulton.