Multiple sequence alignment - TraesCS2A01G319400

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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 TraesCS2A01G319400 chr2A 100.000 2918 0 0 1 2918 545799393 545802310 0.000000e+00 5389.0
1 TraesCS2A01G319400 chr2A 80.309 518 53 26 2415 2916 453102008 453102492 2.150000e-91 346.0
2 TraesCS2A01G319400 chr2A 80.916 131 19 6 2380 2507 227832756 227832629 6.650000e-17 99.0
3 TraesCS2A01G319400 chr2D 93.073 2281 132 14 1 2271 406409182 406411446 0.000000e+00 3314.0
4 TraesCS2A01G319400 chr2B 89.570 1975 166 13 421 2384 482337706 482339651 0.000000e+00 2470.0
5 TraesCS2A01G319400 chr2B 89.051 274 28 2 441 712 482337706 482337433 3.600000e-89 339.0
6 TraesCS2A01G319400 chr2B 88.288 222 21 4 1 218 482337195 482337415 8.020000e-66 261.0
7 TraesCS2A01G319400 chr2B 95.238 42 2 0 2382 2423 162945122 162945081 1.880000e-07 67.6
8 TraesCS2A01G319400 chr3D 78.504 842 160 19 1360 2193 68036814 68035986 1.540000e-147 532.0
9 TraesCS2A01G319400 chr3D 75.561 847 172 24 1358 2193 127904371 127905193 4.560000e-103 385.0
10 TraesCS2A01G319400 chr3D 73.111 569 116 29 739 1300 68037367 68036829 5.000000e-38 169.0
11 TraesCS2A01G319400 chr3B 78.092 849 170 13 1349 2193 113983965 113984801 9.270000e-145 523.0
12 TraesCS2A01G319400 chr3B 77.647 255 52 5 1053 1304 182203524 182203776 1.810000e-32 150.0
13 TraesCS2A01G319400 chr3B 76.305 249 56 3 1053 1299 113983713 113983960 2.360000e-26 130.0
14 TraesCS2A01G319400 chr3A 77.831 839 168 18 1360 2193 79875356 79874531 1.210000e-138 503.0
15 TraesCS2A01G319400 chr3A 77.003 861 173 22 1340 2193 79802126 79801284 1.220000e-128 470.0
16 TraesCS2A01G319400 chr3A 77.133 844 166 22 1360 2192 79904914 79904087 5.700000e-127 464.0
17 TraesCS2A01G319400 chr3A 80.990 505 50 19 2414 2904 614444870 614445342 2.760000e-95 359.0
18 TraesCS2A01G319400 chr3A 77.689 251 51 4 1053 1300 79875619 79875371 6.520000e-32 148.0
19 TraesCS2A01G319400 chr3A 77.381 252 50 6 1053 1300 79905177 79904929 3.030000e-30 143.0
20 TraesCS2A01G319400 chr3A 76.587 252 52 6 1053 1300 79802371 79802123 6.560000e-27 132.0
21 TraesCS2A01G319400 chr6A 81.748 515 49 22 2414 2916 104130174 104130655 3.530000e-104 388.0
22 TraesCS2A01G319400 chr6A 85.714 140 14 6 2398 2532 425307669 425307807 3.030000e-30 143.0
23 TraesCS2A01G319400 chr1A 81.359 515 51 19 2415 2916 25822215 25822697 7.630000e-101 377.0
24 TraesCS2A01G319400 chr1A 80.374 535 54 26 2399 2916 238186997 238187497 2.760000e-95 359.0
25 TraesCS2A01G319400 chr1A 74.621 264 59 7 2415 2674 506563429 506563170 3.070000e-20 110.0
26 TraesCS2A01G319400 chr7A 73.258 531 100 30 2415 2917 616050321 616049805 3.890000e-34 156.0
27 TraesCS2A01G319400 chr5A 82.558 172 20 6 2384 2547 546900908 546901077 3.030000e-30 143.0
28 TraesCS2A01G319400 chr5A 81.461 178 26 7 2398 2570 367492633 367492808 3.920000e-29 139.0
29 TraesCS2A01G319400 chr1D 72.348 528 111 21 2416 2917 382539744 382539226 1.820000e-27 134.0
30 TraesCS2A01G319400 chr7B 77.632 152 30 4 2384 2532 544047973 544047823 4.010000e-14 89.8
31 TraesCS2A01G319400 chr5D 76.786 168 16 8 2381 2527 556743050 556743215 4.030000e-09 73.1
32 TraesCS2A01G319400 chr5D 93.182 44 3 0 2380 2423 126587013 126587056 6.750000e-07 65.8
33 TraesCS2A01G319400 chr5B 97.436 39 1 0 2385 2423 305041516 305041478 1.880000e-07 67.6


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 TraesCS2A01G319400 chr2A 545799393 545802310 2917 False 5389.0 5389 100.0000 1 2918 1 chr2A.!!$F2 2917
1 TraesCS2A01G319400 chr2D 406409182 406411446 2264 False 3314.0 3314 93.0730 1 2271 1 chr2D.!!$F1 2270
2 TraesCS2A01G319400 chr2B 482337195 482339651 2456 False 1365.5 2470 88.9290 1 2384 2 chr2B.!!$F1 2383
3 TraesCS2A01G319400 chr3D 127904371 127905193 822 False 385.0 385 75.5610 1358 2193 1 chr3D.!!$F1 835
4 TraesCS2A01G319400 chr3D 68035986 68037367 1381 True 350.5 532 75.8075 739 2193 2 chr3D.!!$R1 1454
5 TraesCS2A01G319400 chr3B 113983713 113984801 1088 False 326.5 523 77.1985 1053 2193 2 chr3B.!!$F2 1140
6 TraesCS2A01G319400 chr3A 79874531 79875619 1088 True 325.5 503 77.7600 1053 2193 2 chr3A.!!$R2 1140
7 TraesCS2A01G319400 chr3A 79904087 79905177 1090 True 303.5 464 77.2570 1053 2192 2 chr3A.!!$R3 1139
8 TraesCS2A01G319400 chr3A 79801284 79802371 1087 True 301.0 470 76.7950 1053 2193 2 chr3A.!!$R1 1140
9 TraesCS2A01G319400 chr1A 238186997 238187497 500 False 359.0 359 80.3740 2399 2916 1 chr1A.!!$F2 517

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
246 252 2.495669 GGAGGGAGAGAAGACTTGACAG 59.504 54.545 0.00 0.0 0.0 3.51 F
1168 1314 0.911769 TTCCATGGCGAACTCCTCAT 59.088 50.000 6.96 0.0 0.0 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1538 1685 0.111061 ATGTATGGCGGGCATGTCAT 59.889 50.0 25.4 23.09 37.96 3.06 R
2706 2865 0.030638 CACAAAAAGCCCACGTCAGG 59.969 55.0 0.0 0.00 0.00 3.86 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
136 140 8.627487 GAATTTGAATTCACACAAGTTGTACA 57.373 30.769 7.89 0.00 43.29 2.90
137 141 9.248291 GAATTTGAATTCACACAAGTTGTACAT 57.752 29.630 7.89 0.00 43.29 2.29
174 178 8.779354 AAAGGAAATCTATCACACTTGAGTAC 57.221 34.615 0.00 0.00 34.35 2.73
184 188 4.754618 TCACACTTGAGTACGCATTGAAAT 59.245 37.500 13.43 0.00 0.00 2.17
229 235 4.301628 GTGCAATTTGTTCAAAGAGGAGG 58.698 43.478 0.00 0.00 0.00 4.30
239 245 3.436243 TCAAAGAGGAGGGAGAGAAGAC 58.564 50.000 0.00 0.00 0.00 3.01
246 252 2.495669 GGAGGGAGAGAAGACTTGACAG 59.504 54.545 0.00 0.00 0.00 3.51
254 361 6.760770 GGAGAGAAGACTTGACAGAATAATGG 59.239 42.308 0.00 0.00 0.00 3.16
268 375 6.155049 ACAGAATAATGGAATGGAAAAGTGGG 59.845 38.462 0.00 0.00 0.00 4.61
323 430 3.681593 AGACGACATAGATAGCCTCTCC 58.318 50.000 0.00 0.00 35.28 3.71
345 475 3.885297 CGAGGGTATTTCTTGATGGCATT 59.115 43.478 0.00 0.00 0.00 3.56
347 477 5.049405 CGAGGGTATTTCTTGATGGCATTAC 60.049 44.000 0.00 0.00 0.00 1.89
478 608 7.087007 ACGTGTGCTATCTTGTATCATCATAG 58.913 38.462 0.00 0.00 0.00 2.23
521 651 5.476091 ACAAAAGAAGGTGTGTTGGAAAA 57.524 34.783 0.00 0.00 0.00 2.29
693 825 5.779806 ATATTAGATGACGCCATTAACGC 57.220 39.130 0.00 0.00 32.09 4.84
707 839 6.848812 GCCATTAACGCGAAATTGTATTAAC 58.151 36.000 15.93 0.00 0.00 2.01
713 845 9.691795 TTAACGCGAAATTGTATTAACACATAG 57.308 29.630 15.93 0.00 34.61 2.23
723 855 6.894682 TGTATTAACACATAGGGCAAGATCA 58.105 36.000 0.00 0.00 0.00 2.92
730 862 4.646040 CACATAGGGCAAGATCAAATTCCA 59.354 41.667 0.00 0.00 0.00 3.53
1023 1169 1.909986 GATCCTAATGGCTCCTACCCC 59.090 57.143 0.00 0.00 0.00 4.95
1034 1180 3.079578 GCTCCTACCCCAACAAAGTTAC 58.920 50.000 0.00 0.00 0.00 2.50
1039 1185 4.700213 CCTACCCCAACAAAGTTACATCTG 59.300 45.833 0.00 0.00 0.00 2.90
1044 1190 4.216257 CCCAACAAAGTTACATCTGGTGAG 59.784 45.833 0.00 0.00 0.00 3.51
1046 1192 5.530915 CCAACAAAGTTACATCTGGTGAGAA 59.469 40.000 0.00 0.00 0.00 2.87
1168 1314 0.911769 TTCCATGGCGAACTCCTCAT 59.088 50.000 6.96 0.00 0.00 2.90
1236 1382 1.006281 AGTTCCATGATGCCACACCAT 59.994 47.619 0.00 0.00 0.00 3.55
1248 1394 2.356125 GCCACACCATGAGAATGTAGGT 60.356 50.000 0.00 0.00 0.00 3.08
1407 1553 2.579410 ACCCTTTGTGGAATTACGCT 57.421 45.000 2.29 0.00 38.35 5.07
1425 1571 4.145052 ACGCTGACTCCTATCATCATACA 58.855 43.478 0.00 0.00 0.00 2.29
1538 1685 4.166725 AGCAATGGAGGATGGTTCAATCTA 59.833 41.667 0.00 0.00 0.00 1.98
1549 1696 2.549754 GGTTCAATCTATGACATGCCCG 59.450 50.000 0.00 0.00 37.92 6.13
1554 1701 1.347062 TCTATGACATGCCCGCCATA 58.653 50.000 0.00 0.00 31.47 2.74
1592 1741 7.990886 GGTAAACTCACTACCATATGGATTTCA 59.009 37.037 28.77 7.89 38.98 2.69
1741 1890 5.248640 CAACCTCACATGTACCAAGAGAAT 58.751 41.667 10.81 0.00 0.00 2.40
2273 2429 8.998277 TTTCTAGAGCTAGGTAAGATGTATGT 57.002 34.615 7.17 0.00 34.06 2.29
2276 2432 9.069082 TCTAGAGCTAGGTAAGATGTATGTTTC 57.931 37.037 0.00 0.00 34.06 2.78
2280 2436 8.548880 AGCTAGGTAAGATGTATGTTTCCTAA 57.451 34.615 0.00 0.00 34.36 2.69
2344 2500 8.649591 TCCAAATAATGTGCCATATAAAATGCT 58.350 29.630 0.00 0.00 0.00 3.79
2364 2520 8.776376 AATGCTAAACCATCTAAACCATTTTG 57.224 30.769 0.00 0.00 0.00 2.44
2365 2521 6.162777 TGCTAAACCATCTAAACCATTTTGC 58.837 36.000 0.00 0.00 0.00 3.68
2384 2540 9.035607 CATTTTGCTTAACGAGTAGTATCATCT 57.964 33.333 0.00 0.00 0.00 2.90
2386 2542 9.731819 TTTTGCTTAACGAGTAGTATCATCTAG 57.268 33.333 0.00 0.00 0.00 2.43
2387 2543 7.436430 TGCTTAACGAGTAGTATCATCTAGG 57.564 40.000 0.00 0.00 0.00 3.02
2388 2544 6.430308 TGCTTAACGAGTAGTATCATCTAGGG 59.570 42.308 0.00 0.00 0.00 3.53
2389 2545 6.127952 GCTTAACGAGTAGTATCATCTAGGGG 60.128 46.154 0.00 0.00 0.00 4.79
2390 2546 4.997545 ACGAGTAGTATCATCTAGGGGT 57.002 45.455 0.00 0.00 0.00 4.95
2391 2547 4.653868 ACGAGTAGTATCATCTAGGGGTG 58.346 47.826 0.00 0.00 0.00 4.61
2392 2548 4.011023 CGAGTAGTATCATCTAGGGGTGG 58.989 52.174 0.00 0.00 0.00 4.61
2393 2549 4.345854 GAGTAGTATCATCTAGGGGTGGG 58.654 52.174 0.00 0.00 0.00 4.61
2394 2550 2.031495 AGTATCATCTAGGGGTGGGC 57.969 55.000 0.00 0.00 0.00 5.36
2395 2551 1.223077 AGTATCATCTAGGGGTGGGCA 59.777 52.381 0.00 0.00 0.00 5.36
2396 2552 2.157942 AGTATCATCTAGGGGTGGGCAT 60.158 50.000 0.00 0.00 0.00 4.40
2397 2553 2.741159 ATCATCTAGGGGTGGGCATA 57.259 50.000 0.00 0.00 0.00 3.14
2406 2562 0.528924 GGGTGGGCATAAAAACCGAC 59.471 55.000 0.00 0.00 34.22 4.79
2407 2563 0.169451 GGTGGGCATAAAAACCGACG 59.831 55.000 0.00 0.00 35.67 5.12
2408 2564 1.158434 GTGGGCATAAAAACCGACGA 58.842 50.000 0.00 0.00 0.00 4.20
2409 2565 1.536331 GTGGGCATAAAAACCGACGAA 59.464 47.619 0.00 0.00 0.00 3.85
2410 2566 1.536331 TGGGCATAAAAACCGACGAAC 59.464 47.619 0.00 0.00 0.00 3.95
2413 2569 2.481185 GGCATAAAAACCGACGAACTGA 59.519 45.455 0.00 0.00 0.00 3.41
2422 2580 1.071041 CCGACGAACTGAAAACCGAAC 60.071 52.381 0.00 0.00 0.00 3.95
2427 2585 3.437741 ACGAACTGAAAACCGAACAAACT 59.562 39.130 0.00 0.00 0.00 2.66
2428 2586 4.630940 ACGAACTGAAAACCGAACAAACTA 59.369 37.500 0.00 0.00 0.00 2.24
2487 2646 2.040939 TCCTGTCCACTAACCGAACAA 58.959 47.619 0.00 0.00 0.00 2.83
2507 2666 4.223659 CAAAATTCGGTAGGTTCGGTTTG 58.776 43.478 0.00 0.00 0.00 2.93
2532 2691 5.640189 TCTCGGTTAACCAAACAAAAACA 57.360 34.783 24.14 0.00 40.08 2.83
2533 2692 6.022163 TCTCGGTTAACCAAACAAAAACAA 57.978 33.333 24.14 0.00 40.08 2.83
2536 2695 6.885247 TCGGTTAACCAAACAAAAACAAAAC 58.115 32.000 24.14 0.00 40.08 2.43
2537 2696 5.784139 CGGTTAACCAAACAAAAACAAAACG 59.216 36.000 24.14 0.35 40.08 3.60
2538 2697 6.346359 CGGTTAACCAAACAAAAACAAAACGA 60.346 34.615 24.14 0.00 40.08 3.85
2544 2703 5.332355 CCAAACAAAAACAAAACGAACGTGA 60.332 36.000 0.00 0.00 0.00 4.35
2555 2714 3.637998 ACGAACGTGACTGATTGTACT 57.362 42.857 0.00 0.00 0.00 2.73
2556 2715 3.305964 ACGAACGTGACTGATTGTACTG 58.694 45.455 0.00 0.00 0.00 2.74
2557 2716 3.243301 ACGAACGTGACTGATTGTACTGT 60.243 43.478 0.00 0.00 0.00 3.55
2558 2717 4.023792 ACGAACGTGACTGATTGTACTGTA 60.024 41.667 0.00 0.00 0.00 2.74
2559 2718 4.320164 CGAACGTGACTGATTGTACTGTAC 59.680 45.833 10.98 10.98 0.00 2.90
2560 2719 4.841443 ACGTGACTGATTGTACTGTACA 57.159 40.909 16.26 16.26 36.79 2.90
2561 2720 4.795268 ACGTGACTGATTGTACTGTACAG 58.205 43.478 21.44 21.44 40.24 2.74
2562 2721 3.608506 CGTGACTGATTGTACTGTACAGC 59.391 47.826 22.90 15.57 40.24 4.40
2563 2722 4.556233 GTGACTGATTGTACTGTACAGCA 58.444 43.478 22.90 18.58 40.24 4.41
2564 2723 4.386049 GTGACTGATTGTACTGTACAGCAC 59.614 45.833 22.90 20.20 40.24 4.40
2565 2724 4.038642 TGACTGATTGTACTGTACAGCACA 59.961 41.667 22.42 22.42 40.24 4.57
2566 2725 4.956085 ACTGATTGTACTGTACAGCACAA 58.044 39.130 33.21 33.21 45.55 3.33
2567 2726 5.364778 ACTGATTGTACTGTACAGCACAAA 58.635 37.500 34.18 22.68 44.89 2.83
2568 2727 5.820423 ACTGATTGTACTGTACAGCACAAAA 59.180 36.000 34.18 26.04 44.89 2.44
2569 2728 6.017934 ACTGATTGTACTGTACAGCACAAAAG 60.018 38.462 34.18 32.14 44.89 2.27
2570 2729 4.545823 TTGTACTGTACAGCACAAAAGC 57.454 40.909 30.65 11.27 40.59 3.51
2571 2730 3.536570 TGTACTGTACAGCACAAAAGCA 58.463 40.909 23.70 8.75 36.48 3.91
2572 2731 3.559655 TGTACTGTACAGCACAAAAGCAG 59.440 43.478 23.70 0.00 36.48 4.24
2573 2732 1.949525 ACTGTACAGCACAAAAGCAGG 59.050 47.619 22.90 0.00 36.48 4.85
2574 2733 0.667993 TGTACAGCACAAAAGCAGGC 59.332 50.000 0.00 0.00 36.85 4.85
2575 2734 0.385974 GTACAGCACAAAAGCAGGCG 60.386 55.000 0.00 0.00 36.85 5.52
2576 2735 0.817634 TACAGCACAAAAGCAGGCGT 60.818 50.000 0.00 0.00 36.85 5.68
2577 2736 0.817634 ACAGCACAAAAGCAGGCGTA 60.818 50.000 0.00 0.00 36.85 4.42
2578 2737 0.110056 CAGCACAAAAGCAGGCGTAG 60.110 55.000 0.00 0.00 36.85 3.51
2579 2738 1.210155 GCACAAAAGCAGGCGTAGG 59.790 57.895 0.00 0.00 0.00 3.18
2598 2757 4.134623 GTGCAACGTTGTCTCCCA 57.865 55.556 27.78 14.85 0.00 4.37
2607 2766 1.048601 GTTGTCTCCCAGGAGTCACA 58.951 55.000 12.37 8.35 39.29 3.58
2610 2769 2.262915 CTCCCAGGAGTCACACGC 59.737 66.667 5.47 0.00 37.47 5.34
2614 2773 2.425592 CAGGAGTCACACGCCCAA 59.574 61.111 0.00 0.00 39.00 4.12
2617 2776 3.041940 GAGTCACACGCCCAACCG 61.042 66.667 0.00 0.00 0.00 4.44
2633 2792 3.891400 CGCCCACAATCGCCCATG 61.891 66.667 0.00 0.00 0.00 3.66
2634 2793 2.440065 GCCCACAATCGCCCATGA 60.440 61.111 0.00 0.00 0.00 3.07
2635 2794 2.051518 GCCCACAATCGCCCATGAA 61.052 57.895 0.00 0.00 0.00 2.57
2636 2795 1.394266 GCCCACAATCGCCCATGAAT 61.394 55.000 0.00 0.00 0.00 2.57
2637 2796 0.386476 CCCACAATCGCCCATGAATG 59.614 55.000 0.00 0.00 0.00 2.67
2638 2797 0.249155 CCACAATCGCCCATGAATGC 60.249 55.000 0.00 0.00 0.00 3.56
2639 2798 0.456628 CACAATCGCCCATGAATGCA 59.543 50.000 0.00 0.00 0.00 3.96
2640 2799 1.067974 CACAATCGCCCATGAATGCAT 59.932 47.619 0.00 0.00 34.29 3.96
2641 2800 1.338973 ACAATCGCCCATGAATGCATC 59.661 47.619 0.00 0.00 30.68 3.91
2642 2801 1.338655 CAATCGCCCATGAATGCATCA 59.661 47.619 0.00 0.00 43.67 3.07
2661 2820 3.469739 TCATGCACGCATCTCACATAAT 58.530 40.909 0.44 0.00 33.90 1.28
2672 2831 2.118132 CACATAATGTGGGCCTGCC 58.882 57.895 4.53 0.00 44.27 4.85
2679 2838 4.052518 GTGGGCCTGCCTGACCAT 62.053 66.667 4.53 0.00 35.13 3.55
2680 2839 3.267233 TGGGCCTGCCTGACCATT 61.267 61.111 4.53 0.00 36.10 3.16
2681 2840 2.440980 GGGCCTGCCTGACCATTC 60.441 66.667 8.29 0.00 36.10 2.67
2689 2848 0.610232 GCCTGACCATTCAAGTGCCT 60.610 55.000 0.00 0.00 0.00 4.75
2709 2868 3.325135 CCTACAAGGATAAGGCCTACCTG 59.675 52.174 21.54 17.67 41.70 4.00
2736 2899 1.555477 CTTTTTGTGAACGGTGTGCC 58.445 50.000 0.00 0.00 0.00 5.01
2737 2900 0.173708 TTTTTGTGAACGGTGTGCCC 59.826 50.000 0.00 0.00 0.00 5.36
2766 2937 3.009723 CGAATAGCTGACCACACCATTT 58.990 45.455 0.00 0.00 0.00 2.32
2767 2938 3.063997 CGAATAGCTGACCACACCATTTC 59.936 47.826 0.00 0.00 0.00 2.17
2768 2939 2.093306 TAGCTGACCACACCATTTCG 57.907 50.000 0.00 0.00 0.00 3.46
2769 2940 1.210155 GCTGACCACACCATTTCGC 59.790 57.895 0.00 0.00 0.00 4.70
2770 2941 1.237285 GCTGACCACACCATTTCGCT 61.237 55.000 0.00 0.00 0.00 4.93
2771 2942 0.518636 CTGACCACACCATTTCGCTG 59.481 55.000 0.00 0.00 0.00 5.18
2772 2943 1.210155 GACCACACCATTTCGCTGC 59.790 57.895 0.00 0.00 0.00 5.25
2774 2945 1.237285 ACCACACCATTTCGCTGCTC 61.237 55.000 0.00 0.00 0.00 4.26
2791 2962 3.528370 CTAGTCCCACCTCGCCCG 61.528 72.222 0.00 0.00 0.00 6.13
2855 3026 1.688735 AGCTAGTGCAATCGGAGCATA 59.311 47.619 9.79 0.00 44.79 3.14
2856 3027 2.064762 GCTAGTGCAATCGGAGCATAG 58.935 52.381 2.67 0.00 44.79 2.23
2860 3031 3.919216 AGTGCAATCGGAGCATAGATAC 58.081 45.455 0.00 0.00 44.79 2.24
2865 3036 4.991056 GCAATCGGAGCATAGATACTTGAA 59.009 41.667 0.00 0.00 0.00 2.69
2878 3049 1.523758 ACTTGAAGCGTGGTCATTCC 58.476 50.000 0.00 0.00 0.00 3.01
2880 3051 0.250124 TTGAAGCGTGGTCATTCCGT 60.250 50.000 0.00 0.00 39.52 4.69
2889 3060 3.933955 CGTGGTCATTCCGTATAAAACCA 59.066 43.478 0.00 0.00 39.52 3.67
2897 3068 6.206243 TCATTCCGTATAAAACCAAAAACCGA 59.794 34.615 0.00 0.00 0.00 4.69
2900 3071 4.916831 CCGTATAAAACCAAAAACCGAACC 59.083 41.667 0.00 0.00 0.00 3.62
2901 3072 4.612198 CGTATAAAACCAAAAACCGAACCG 59.388 41.667 0.00 0.00 0.00 4.44
2904 3075 3.804786 AAACCAAAAACCGAACCGAAT 57.195 38.095 0.00 0.00 0.00 3.34
2905 3076 4.915158 AAACCAAAAACCGAACCGAATA 57.085 36.364 0.00 0.00 0.00 1.75
2907 3078 6.572167 AAACCAAAAACCGAACCGAATATA 57.428 33.333 0.00 0.00 0.00 0.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
161 165 3.378911 TCAATGCGTACTCAAGTGTGA 57.621 42.857 0.00 0.00 0.00 3.58
174 178 3.563508 TGTGCACACTTATTTCAATGCG 58.436 40.909 17.42 0.00 35.83 4.73
184 188 2.299013 CCCTGTAGACTGTGCACACTTA 59.701 50.000 17.42 5.78 0.00 2.24
229 235 6.760770 CCATTATTCTGTCAAGTCTTCTCTCC 59.239 42.308 0.00 0.00 0.00 3.71
239 245 8.526147 ACTTTTCCATTCCATTATTCTGTCAAG 58.474 33.333 0.00 0.00 0.00 3.02
246 252 6.544928 ACCCACTTTTCCATTCCATTATTC 57.455 37.500 0.00 0.00 0.00 1.75
254 361 9.150348 CAATAATTACAACCCACTTTTCCATTC 57.850 33.333 0.00 0.00 0.00 2.67
268 375 6.771076 TCGTGATCTGTGCAATAATTACAAC 58.229 36.000 0.00 0.00 0.00 3.32
323 430 2.917933 TGCCATCAAGAAATACCCTCG 58.082 47.619 0.00 0.00 0.00 4.63
358 488 6.622896 GCACCATGTGTCCAAACTACTATTTC 60.623 42.308 0.00 0.00 35.75 2.17
359 489 5.183140 GCACCATGTGTCCAAACTACTATTT 59.817 40.000 0.00 0.00 35.75 1.40
438 568 4.053295 GCACACGTCTTCCTAAACAAGTA 58.947 43.478 0.00 0.00 0.00 2.24
691 823 6.133392 CCCTATGTGTTAATACAATTTCGCG 58.867 40.000 9.23 0.00 35.69 5.87
693 825 7.022055 TGCCCTATGTGTTAATACAATTTCG 57.978 36.000 9.23 0.00 35.69 3.46
700 832 7.801716 TTGATCTTGCCCTATGTGTTAATAC 57.198 36.000 0.00 0.00 0.00 1.89
707 839 4.646040 TGGAATTTGATCTTGCCCTATGTG 59.354 41.667 0.00 0.00 0.00 3.21
712 844 3.173953 TGTGGAATTTGATCTTGCCCT 57.826 42.857 0.00 0.00 0.00 5.19
713 845 4.081531 TCAATGTGGAATTTGATCTTGCCC 60.082 41.667 0.00 0.00 0.00 5.36
723 855 7.443302 TCTAGGATCTCTCAATGTGGAATTT 57.557 36.000 0.00 0.00 0.00 1.82
730 862 7.888021 ACGAGATATTCTAGGATCTCTCAATGT 59.112 37.037 20.74 11.30 43.97 2.71
1023 1169 6.618287 TTCTCACCAGATGTAACTTTGTTG 57.382 37.500 0.00 0.00 0.00 3.33
1034 1180 3.210232 AGGCATCATTCTCACCAGATG 57.790 47.619 0.00 0.00 40.52 2.90
1039 1185 4.276926 GGAAATGTAGGCATCATTCTCACC 59.723 45.833 7.42 6.22 34.92 4.02
1044 1190 2.893489 GGGGGAAATGTAGGCATCATTC 59.107 50.000 7.42 3.17 34.92 2.67
1046 1192 2.146998 AGGGGGAAATGTAGGCATCAT 58.853 47.619 0.00 0.00 33.50 2.45
1236 1382 3.447586 GTGGTGCTAGACCTACATTCTCA 59.552 47.826 11.21 0.00 46.32 3.27
1248 1394 1.157513 TGGTGGGAGTGGTGCTAGA 59.842 57.895 0.00 0.00 0.00 2.43
1260 1406 3.684908 TGTATCAGACAATTGTGGTGGG 58.315 45.455 17.58 0.65 34.15 4.61
1323 1469 3.541242 TGGATTTCCTCATTGTTGGGT 57.459 42.857 0.00 0.00 36.82 4.51
1407 1553 7.241628 AGGTATGTGTATGATGATAGGAGTCA 58.758 38.462 0.00 0.00 0.00 3.41
1425 1571 2.032620 GACTCCATGGACGAGGTATGT 58.967 52.381 11.44 4.31 0.00 2.29
1538 1685 0.111061 ATGTATGGCGGGCATGTCAT 59.889 50.000 25.40 23.09 37.96 3.06
1549 1696 4.672587 TTACCTCAGAGACATGTATGGC 57.327 45.455 0.00 0.00 35.53 4.40
1592 1741 6.953520 TGGGTCAATATTTTCAGGAGAACAAT 59.046 34.615 0.00 0.00 32.39 2.71
1717 1866 2.744202 CTCTTGGTACATGTGAGGTTGC 59.256 50.000 9.11 0.00 39.30 4.17
1741 1890 4.264941 TGGACCAACTAGAGGGGTGTTATA 60.265 45.833 8.98 0.00 34.39 0.98
2004 2156 7.446001 AAAATTTCTCCACTTGAGCTAGAAG 57.554 36.000 0.00 3.84 41.18 2.85
2121 2273 8.855110 ACAACACATACCATTCAAACAAAGATA 58.145 29.630 0.00 0.00 0.00 1.98
2340 2496 6.818142 GCAAAATGGTTTAGATGGTTTAGCAT 59.182 34.615 0.00 0.00 0.00 3.79
2344 2500 9.699703 GTTAAGCAAAATGGTTTAGATGGTTTA 57.300 29.630 0.00 0.00 39.08 2.01
2364 2520 6.127952 CCCCTAGATGATACTACTCGTTAAGC 60.128 46.154 0.00 0.00 0.00 3.09
2365 2521 6.941436 ACCCCTAGATGATACTACTCGTTAAG 59.059 42.308 0.00 0.00 0.00 1.85
2384 2540 1.341187 CGGTTTTTATGCCCACCCCTA 60.341 52.381 0.00 0.00 0.00 3.53
2385 2541 0.613572 CGGTTTTTATGCCCACCCCT 60.614 55.000 0.00 0.00 0.00 4.79
2386 2542 0.612453 TCGGTTTTTATGCCCACCCC 60.612 55.000 0.00 0.00 0.00 4.95
2387 2543 0.528924 GTCGGTTTTTATGCCCACCC 59.471 55.000 0.00 0.00 0.00 4.61
2388 2544 0.169451 CGTCGGTTTTTATGCCCACC 59.831 55.000 0.00 0.00 0.00 4.61
2389 2545 1.158434 TCGTCGGTTTTTATGCCCAC 58.842 50.000 0.00 0.00 0.00 4.61
2390 2546 1.536331 GTTCGTCGGTTTTTATGCCCA 59.464 47.619 0.00 0.00 0.00 5.36
2391 2547 1.808343 AGTTCGTCGGTTTTTATGCCC 59.192 47.619 0.00 0.00 0.00 5.36
2392 2548 2.481185 TCAGTTCGTCGGTTTTTATGCC 59.519 45.455 0.00 0.00 0.00 4.40
2393 2549 3.799137 TCAGTTCGTCGGTTTTTATGC 57.201 42.857 0.00 0.00 0.00 3.14
2394 2550 5.397240 GGTTTTCAGTTCGTCGGTTTTTATG 59.603 40.000 0.00 0.00 0.00 1.90
2395 2551 5.513376 GGTTTTCAGTTCGTCGGTTTTTAT 58.487 37.500 0.00 0.00 0.00 1.40
2396 2552 4.493872 CGGTTTTCAGTTCGTCGGTTTTTA 60.494 41.667 0.00 0.00 0.00 1.52
2397 2553 3.728566 CGGTTTTCAGTTCGTCGGTTTTT 60.729 43.478 0.00 0.00 0.00 1.94
2406 2562 4.011058 AGTTTGTTCGGTTTTCAGTTCG 57.989 40.909 0.00 0.00 0.00 3.95
2407 2563 7.980742 ATTTAGTTTGTTCGGTTTTCAGTTC 57.019 32.000 0.00 0.00 0.00 3.01
2408 2564 8.766000 AAATTTAGTTTGTTCGGTTTTCAGTT 57.234 26.923 0.00 0.00 0.00 3.16
2409 2565 8.766000 AAAATTTAGTTTGTTCGGTTTTCAGT 57.234 26.923 0.00 0.00 0.00 3.41
2410 2566 8.047859 CGAAAATTTAGTTTGTTCGGTTTTCAG 58.952 33.333 0.00 0.00 35.28 3.02
2413 2569 7.224290 CCGAAAATTTAGTTTGTTCGGTTTT 57.776 32.000 14.30 0.00 41.78 2.43
2459 2618 5.012354 TCGGTTAGTGGACAGGAAAACTAAT 59.988 40.000 0.00 0.00 37.43 1.73
2461 2620 3.896888 TCGGTTAGTGGACAGGAAAACTA 59.103 43.478 0.00 0.00 0.00 2.24
2468 2627 2.536761 TTGTTCGGTTAGTGGACAGG 57.463 50.000 0.00 0.00 0.00 4.00
2469 2628 5.432885 AATTTTGTTCGGTTAGTGGACAG 57.567 39.130 0.00 0.00 0.00 3.51
2487 2646 2.227149 GCAAACCGAACCTACCGAATTT 59.773 45.455 0.00 0.00 0.00 1.82
2507 2666 3.907894 TTGTTTGGTTAACCGAGATGC 57.092 42.857 19.65 9.75 39.43 3.91
2532 2691 4.807304 AGTACAATCAGTCACGTTCGTTTT 59.193 37.500 0.00 0.00 0.00 2.43
2533 2692 4.208460 CAGTACAATCAGTCACGTTCGTTT 59.792 41.667 0.00 0.00 0.00 3.60
2536 2695 3.305964 ACAGTACAATCAGTCACGTTCG 58.694 45.455 0.00 0.00 0.00 3.95
2537 2696 5.217393 TGTACAGTACAATCAGTCACGTTC 58.783 41.667 11.21 0.00 35.38 3.95
2538 2697 5.190992 TGTACAGTACAATCAGTCACGTT 57.809 39.130 11.21 0.00 35.38 3.99
2555 2714 0.667993 GCCTGCTTTTGTGCTGTACA 59.332 50.000 0.00 0.00 37.56 2.90
2556 2715 0.385974 CGCCTGCTTTTGTGCTGTAC 60.386 55.000 0.00 0.00 0.00 2.90
2557 2716 0.817634 ACGCCTGCTTTTGTGCTGTA 60.818 50.000 0.00 0.00 0.00 2.74
2558 2717 0.817634 TACGCCTGCTTTTGTGCTGT 60.818 50.000 0.00 0.00 0.00 4.40
2559 2718 0.110056 CTACGCCTGCTTTTGTGCTG 60.110 55.000 0.00 0.00 0.00 4.41
2560 2719 1.237285 CCTACGCCTGCTTTTGTGCT 61.237 55.000 0.00 0.00 0.00 4.40
2561 2720 1.210155 CCTACGCCTGCTTTTGTGC 59.790 57.895 0.00 0.00 0.00 4.57
2562 2721 1.210155 GCCTACGCCTGCTTTTGTG 59.790 57.895 0.00 0.00 0.00 3.33
2563 2722 2.325082 CGCCTACGCCTGCTTTTGT 61.325 57.895 0.00 0.00 0.00 2.83
2564 2723 2.325082 ACGCCTACGCCTGCTTTTG 61.325 57.895 0.00 0.00 45.53 2.44
2565 2724 2.032071 ACGCCTACGCCTGCTTTT 59.968 55.556 0.00 0.00 45.53 2.27
2566 2725 2.742372 CACGCCTACGCCTGCTTT 60.742 61.111 0.00 0.00 45.53 3.51
2570 2729 3.788766 GTTGCACGCCTACGCCTG 61.789 66.667 0.00 0.00 45.53 4.85
2581 2740 1.507141 CCTGGGAGACAACGTTGCAC 61.507 60.000 27.61 20.64 0.00 4.57
2582 2741 1.227823 CCTGGGAGACAACGTTGCA 60.228 57.895 27.61 15.63 0.00 4.08
2583 2742 0.951040 CTCCTGGGAGACAACGTTGC 60.951 60.000 27.61 19.38 44.53 4.17
2584 2743 0.393077 ACTCCTGGGAGACAACGTTG 59.607 55.000 26.20 26.20 44.53 4.10
2585 2744 0.680061 GACTCCTGGGAGACAACGTT 59.320 55.000 21.86 0.00 44.53 3.99
2586 2745 0.469331 TGACTCCTGGGAGACAACGT 60.469 55.000 21.86 0.36 44.53 3.99
2587 2746 0.038159 GTGACTCCTGGGAGACAACG 60.038 60.000 21.86 0.00 45.15 4.10
2588 2747 1.048601 TGTGACTCCTGGGAGACAAC 58.951 55.000 21.86 15.61 45.15 3.32
2589 2748 1.048601 GTGTGACTCCTGGGAGACAA 58.951 55.000 21.86 10.47 45.15 3.18
2590 2749 1.179174 CGTGTGACTCCTGGGAGACA 61.179 60.000 21.86 18.49 44.53 3.41
2598 2757 2.426023 GTTGGGCGTGTGACTCCT 59.574 61.111 0.00 0.00 0.00 3.69
2610 2769 3.439540 CGATTGTGGGCGGTTGGG 61.440 66.667 0.00 0.00 0.00 4.12
2617 2776 1.394266 ATTCATGGGCGATTGTGGGC 61.394 55.000 0.00 0.00 0.00 5.36
2623 2782 1.694844 TGATGCATTCATGGGCGATT 58.305 45.000 0.00 0.00 31.96 3.34
2637 2796 0.316772 GTGAGATGCGTGCATGATGC 60.317 55.000 12.81 11.12 45.29 3.91
2638 2797 1.011333 TGTGAGATGCGTGCATGATG 58.989 50.000 12.81 0.00 36.70 3.07
2639 2798 1.963172 ATGTGAGATGCGTGCATGAT 58.037 45.000 12.81 0.15 36.70 2.45
2640 2799 2.600470 TATGTGAGATGCGTGCATGA 57.400 45.000 12.81 0.00 36.70 3.07
2641 2800 3.002965 ACATTATGTGAGATGCGTGCATG 59.997 43.478 12.81 0.09 36.70 4.06
2642 2801 3.208594 ACATTATGTGAGATGCGTGCAT 58.791 40.909 7.12 7.12 39.69 3.96
2672 2831 3.057969 TGTAGGCACTTGAATGGTCAG 57.942 47.619 0.00 0.00 41.75 3.51
2679 2838 4.843728 CCTTATCCTTGTAGGCACTTGAA 58.156 43.478 0.00 0.00 41.75 2.69
2680 2839 4.487714 CCTTATCCTTGTAGGCACTTGA 57.512 45.455 0.00 0.00 41.75 3.02
2689 2848 3.965347 GTCAGGTAGGCCTTATCCTTGTA 59.035 47.826 12.58 2.47 44.18 2.41
2704 2863 1.134037 ACAAAAAGCCCACGTCAGGTA 60.134 47.619 3.21 0.00 0.00 3.08
2706 2865 0.030638 CACAAAAAGCCCACGTCAGG 59.969 55.000 0.00 0.00 0.00 3.86
2709 2868 1.835121 GTTCACAAAAAGCCCACGTC 58.165 50.000 0.00 0.00 0.00 4.34
2716 2875 0.920664 GCACACCGTTCACAAAAAGC 59.079 50.000 0.00 0.00 0.00 3.51
2740 2903 1.066215 TGTGGTCAGCTATTCGCATGT 60.066 47.619 0.00 0.00 42.61 3.21
2760 2931 1.134670 GGACTAGAGCAGCGAAATGGT 60.135 52.381 0.00 0.00 0.00 3.55
2766 2937 2.052690 GGTGGGACTAGAGCAGCGA 61.053 63.158 0.00 0.00 0.00 4.93
2767 2938 2.010582 GAGGTGGGACTAGAGCAGCG 62.011 65.000 0.00 0.00 0.00 5.18
2768 2939 1.819905 GAGGTGGGACTAGAGCAGC 59.180 63.158 0.00 0.00 0.00 5.25
2769 2940 2.010582 GCGAGGTGGGACTAGAGCAG 62.011 65.000 0.00 0.00 0.00 4.24
2770 2941 2.052690 GCGAGGTGGGACTAGAGCA 61.053 63.158 0.00 0.00 0.00 4.26
2771 2942 2.787567 GGCGAGGTGGGACTAGAGC 61.788 68.421 0.00 0.00 0.00 4.09
2772 2943 2.128507 GGGCGAGGTGGGACTAGAG 61.129 68.421 0.00 0.00 0.00 2.43
2774 2945 3.528370 CGGGCGAGGTGGGACTAG 61.528 72.222 0.00 0.00 0.00 2.57
2791 2962 4.953940 AATCTGGCTAATCTCCTCAGTC 57.046 45.455 0.00 0.00 0.00 3.51
2848 3019 3.738282 CACGCTTCAAGTATCTATGCTCC 59.262 47.826 0.00 0.00 0.00 4.70
2855 3026 3.895232 ATGACCACGCTTCAAGTATCT 57.105 42.857 0.00 0.00 0.00 1.98
2856 3027 3.309954 GGAATGACCACGCTTCAAGTATC 59.690 47.826 0.00 0.00 38.79 2.24
2860 3031 0.443869 CGGAATGACCACGCTTCAAG 59.556 55.000 0.00 0.00 38.90 3.02
2865 3036 3.530265 TTTATACGGAATGACCACGCT 57.470 42.857 0.00 0.00 38.90 5.07
2878 3049 4.612198 CGGTTCGGTTTTTGGTTTTATACG 59.388 41.667 0.00 0.00 0.00 3.06
2880 3051 6.382869 TTCGGTTCGGTTTTTGGTTTTATA 57.617 33.333 0.00 0.00 0.00 0.98
2889 3060 4.863152 CCGTATATTCGGTTCGGTTTTT 57.137 40.909 12.28 0.00 44.77 1.94


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

AutoCloner maintained by Alex Coulton.