Multiple sequence alignment - TraesCS4B01G333900

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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 TraesCS4B01G333900 chr4B 100.000 3344 0 0 1 3344 625071843 625075186 0.000000e+00 6176.0
1 TraesCS4B01G333900 chr7A 88.980 2550 198 43 1 2499 731125096 731127613 0.000000e+00 3075.0
2 TraesCS4B01G333900 chr7A 88.680 2553 202 47 1 2499 731156533 731159052 0.000000e+00 3033.0
3 TraesCS4B01G333900 chr7A 88.676 2552 201 51 1 2499 731185498 731188014 0.000000e+00 3031.0
4 TraesCS4B01G333900 chr7A 90.485 2186 127 34 369 2502 731095392 731097548 0.000000e+00 2809.0
5 TraesCS4B01G333900 chr7A 85.470 1576 180 17 957 2499 731571412 731569853 0.000000e+00 1596.0
6 TraesCS4B01G333900 chr7A 85.066 1587 203 18 932 2497 675021899 675023472 0.000000e+00 1587.0
7 TraesCS4B01G333900 chr7A 84.779 1603 183 31 949 2497 731000676 731002271 0.000000e+00 1552.0
8 TraesCS4B01G333900 chr7A 92.663 995 69 3 1513 2505 731506620 731505628 0.000000e+00 1430.0
9 TraesCS4B01G333900 chr7A 91.790 1011 80 3 1490 2499 731220342 731221350 0.000000e+00 1404.0
10 TraesCS4B01G333900 chr7A 88.667 1050 105 6 1454 2502 731397762 731396726 0.000000e+00 1267.0
11 TraesCS4B01G333900 chr7A 87.370 768 48 20 2575 3333 731012437 731013164 0.000000e+00 835.0
12 TraesCS4B01G333900 chr7A 84.670 848 81 26 2498 3333 731013279 731014089 0.000000e+00 800.0
13 TraesCS4B01G333900 chr7A 84.316 848 85 23 2498 3333 731097411 731098222 0.000000e+00 785.0
14 TraesCS4B01G333900 chr7A 89.013 628 42 13 897 1517 731539520 731538913 0.000000e+00 752.0
15 TraesCS4B01G333900 chr7A 83.112 829 92 27 2515 3333 731221233 731222023 0.000000e+00 712.0
16 TraesCS4B01G333900 chr7A 85.333 600 49 14 2515 3107 731505753 731505186 4.810000e-163 584.0
17 TraesCS4B01G333900 chr7A 87.413 429 43 8 2913 3333 731188526 731188951 1.800000e-132 483.0
18 TraesCS4B01G333900 chr7A 86.713 429 46 8 2913 3333 731129860 731130285 1.820000e-127 466.0
19 TraesCS4B01G333900 chr7A 86.713 429 46 8 2913 3333 731159564 731159989 1.820000e-127 466.0
20 TraesCS4B01G333900 chr7A 82.323 594 50 24 2753 3333 731396646 731396095 6.530000e-127 464.0
21 TraesCS4B01G333900 chr7A 89.231 325 18 10 18 333 731095084 731095400 1.120000e-104 390.0
22 TraesCS4B01G333900 chr7A 78.085 470 76 21 17 476 731092615 731093067 4.250000e-69 272.0
23 TraesCS4B01G333900 chr7A 94.512 164 9 0 3170 3333 731505187 731505024 1.540000e-63 254.0
24 TraesCS4B01G333900 chr7A 82.759 116 11 3 2515 2630 730882776 730882882 9.880000e-16 95.3
25 TraesCS4B01G333900 chr7D 90.096 1565 134 12 897 2443 634659448 634661009 0.000000e+00 2012.0
26 TraesCS4B01G333900 chr7D 90.301 1464 112 15 916 2366 634751476 634750030 0.000000e+00 1890.0
27 TraesCS4B01G333900 chr7D 89.540 717 50 9 2619 3333 634661014 634661707 0.000000e+00 885.0
28 TraesCS4B01G333900 chr7D 86.441 590 68 7 951 1533 634454611 634455195 1.310000e-178 636.0
29 TraesCS4B01G333900 chr7D 86.299 489 42 11 2631 3116 634759501 634759035 2.980000e-140 508.0
30 TraesCS4B01G333900 chr7D 92.241 116 9 0 2515 2630 583549997 583550112 7.420000e-37 165.0
31 TraesCS4B01G333900 chr7B 85.054 1773 192 36 765 2502 741625155 741623421 0.000000e+00 1738.0
32 TraesCS4B01G333900 chr7B 89.076 595 46 11 2517 3108 741542792 741543370 0.000000e+00 721.0
33 TraesCS4B01G333900 chr7B 88.108 555 45 8 2516 3066 741623540 741623003 1.010000e-179 640.0
34 TraesCS4B01G333900 chr7B 92.377 446 29 3 958 1399 741482130 741482574 6.090000e-177 630.0
35 TraesCS4B01G333900 chr7B 87.238 572 35 20 1 569 741625746 741625210 4.740000e-173 617.0
36 TraesCS4B01G333900 chr7B 83.333 480 55 15 2825 3299 741483934 741484393 1.430000e-113 420.0
37 TraesCS4B01G333900 chr7B 80.866 439 50 16 2835 3267 651142241 651142651 6.960000e-82 315.0
38 TraesCS4B01G333900 chr7B 92.079 202 16 0 619 820 741625206 741625005 5.460000e-73 285.0
39 TraesCS4B01G333900 chr7B 92.241 116 9 0 2515 2630 651135887 651136002 7.420000e-37 165.0
40 TraesCS4B01G333900 chr7B 79.904 209 24 10 2631 2836 651141934 651142127 1.620000e-28 137.0
41 TraesCS4B01G333900 chr7B 94.118 68 4 0 2515 2582 741483523 741483590 1.640000e-18 104.0
42 TraesCS4B01G333900 chr7B 84.211 95 13 2 418 511 741481578 741481671 1.280000e-14 91.6


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 TraesCS4B01G333900 chr4B 625071843 625075186 3343 False 6176.0 6176 100.00000 1 3344 1 chr4B.!!$F1 3343
1 TraesCS4B01G333900 chr7A 731125096 731130285 5189 False 1770.5 3075 87.84650 1 3333 2 chr7A.!!$F6 3332
2 TraesCS4B01G333900 chr7A 731185498 731188951 3453 False 1757.0 3031 88.04450 1 3333 2 chr7A.!!$F8 3332
3 TraesCS4B01G333900 chr7A 731156533 731159989 3456 False 1749.5 3033 87.69650 1 3333 2 chr7A.!!$F7 3332
4 TraesCS4B01G333900 chr7A 731569853 731571412 1559 True 1596.0 1596 85.47000 957 2499 1 chr7A.!!$R2 1542
5 TraesCS4B01G333900 chr7A 675021899 675023472 1573 False 1587.0 1587 85.06600 932 2497 1 chr7A.!!$F1 1565
6 TraesCS4B01G333900 chr7A 731000676 731002271 1595 False 1552.0 1552 84.77900 949 2497 1 chr7A.!!$F3 1548
7 TraesCS4B01G333900 chr7A 731092615 731098222 5607 False 1064.0 2809 85.52925 17 3333 4 chr7A.!!$F5 3316
8 TraesCS4B01G333900 chr7A 731220342 731222023 1681 False 1058.0 1404 87.45100 1490 3333 2 chr7A.!!$F9 1843
9 TraesCS4B01G333900 chr7A 731396095 731397762 1667 True 865.5 1267 85.49500 1454 3333 2 chr7A.!!$R3 1879
10 TraesCS4B01G333900 chr7A 731012437 731014089 1652 False 817.5 835 86.02000 2498 3333 2 chr7A.!!$F4 835
11 TraesCS4B01G333900 chr7A 731505024 731506620 1596 True 756.0 1430 90.83600 1513 3333 3 chr7A.!!$R4 1820
12 TraesCS4B01G333900 chr7A 731538913 731539520 607 True 752.0 752 89.01300 897 1517 1 chr7A.!!$R1 620
13 TraesCS4B01G333900 chr7D 634750030 634751476 1446 True 1890.0 1890 90.30100 916 2366 1 chr7D.!!$R1 1450
14 TraesCS4B01G333900 chr7D 634659448 634661707 2259 False 1448.5 2012 89.81800 897 3333 2 chr7D.!!$F3 2436
15 TraesCS4B01G333900 chr7D 634454611 634455195 584 False 636.0 636 86.44100 951 1533 1 chr7D.!!$F2 582
16 TraesCS4B01G333900 chr7B 741623003 741625746 2743 True 820.0 1738 88.11975 1 3066 4 chr7B.!!$R1 3065
17 TraesCS4B01G333900 chr7B 741542792 741543370 578 False 721.0 721 89.07600 2517 3108 1 chr7B.!!$F2 591
18 TraesCS4B01G333900 chr7B 741481578 741484393 2815 False 311.4 630 88.50975 418 3299 4 chr7B.!!$F4 2881
19 TraesCS4B01G333900 chr7B 651141934 651142651 717 False 226.0 315 80.38500 2631 3267 2 chr7B.!!$F3 636

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
476 2962 0.036294 GAACACCTCTAAGCCCGCTT 60.036 55.0 7.19 7.19 39.83 4.68 F
1674 4547 0.469705 TTGCTCCCAACACCAGCAAT 60.470 50.0 1.48 0.00 45.91 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1583 4456 0.034089 GGGTATGGTTGGAAGCAGCT 60.034 55.0 0.00 0.0 40.07 4.24 R
2511 5430 0.038435 CAACGCATGCACCCAATTGA 60.038 50.0 19.57 0.0 0.00 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
320 2801 1.917782 GCGCGTTTGCACAATCCCTA 61.918 55.000 8.43 0.00 42.97 3.53
346 2831 2.418692 CACCGCACCAAATAGTGTGTA 58.581 47.619 4.71 0.00 44.89 2.90
394 2879 3.061905 GCCCCCTCCCCAATCTCAC 62.062 68.421 0.00 0.00 0.00 3.51
476 2962 0.036294 GAACACCTCTAAGCCCGCTT 60.036 55.000 7.19 7.19 39.83 4.68
573 3062 6.293626 CGACAGAAAGATTCCAACAAGTGATT 60.294 38.462 0.00 0.00 0.00 2.57
590 3079 9.578576 ACAAGTGATTTATATATGGATGTTGCT 57.421 29.630 0.00 0.00 0.00 3.91
775 3566 3.486375 GGTCGCCCTAATTTTCTAAACGC 60.486 47.826 0.00 0.00 0.00 4.84
832 3635 9.726232 CCATGAAATTTAACAGACAGATGTATG 57.274 33.333 6.07 6.07 42.49 2.39
905 3709 4.094887 CGACAATTTTCGAATCCATGGAGT 59.905 41.667 21.33 18.83 41.78 3.85
914 3723 3.569701 CGAATCCATGGAGTTAAATGGGG 59.430 47.826 21.33 0.00 43.09 4.96
941 3756 1.612950 AGCTCACTGTCTCACTCACTG 59.387 52.381 0.00 0.00 0.00 3.66
988 3813 0.691078 CCTCGATCCCCTTCCTCCAA 60.691 60.000 0.00 0.00 0.00 3.53
1131 3983 2.813474 CGCGTCATCAAAGGCCGA 60.813 61.111 0.00 0.00 0.00 5.54
1392 4259 2.771639 CCGCGTCCTCCTCGATTGA 61.772 63.158 4.92 0.00 0.00 2.57
1672 4545 1.529010 CTTGCTCCCAACACCAGCA 60.529 57.895 0.00 0.00 41.45 4.41
1674 4547 0.469705 TTGCTCCCAACACCAGCAAT 60.470 50.000 1.48 0.00 45.91 3.56
1777 4651 4.357918 ACTATGCAATGGTCTATGGTCC 57.642 45.455 0.00 0.00 28.92 4.46
2363 5271 6.115446 TCTGATCAACTGGTAAGCCTAATTG 58.885 40.000 0.00 0.00 35.27 2.32
2391 5310 1.863325 TATGTTGCCATTGGGTGCAT 58.137 45.000 4.53 0.00 37.33 3.96
2395 5314 1.481901 TTGCCATTGGGTGCATGCTT 61.482 50.000 20.33 0.00 37.33 3.91
2409 5328 3.255969 CATGCTTTGCTTGCCCTATTT 57.744 42.857 0.00 0.00 0.00 1.40
2410 5329 2.747396 TGCTTTGCTTGCCCTATTTG 57.253 45.000 0.00 0.00 0.00 2.32
2411 5330 1.338011 TGCTTTGCTTGCCCTATTTGC 60.338 47.619 0.00 0.00 0.00 3.68
2412 5331 1.338011 GCTTTGCTTGCCCTATTTGCA 60.338 47.619 0.00 0.00 36.84 4.08
2413 5332 2.678769 GCTTTGCTTGCCCTATTTGCAT 60.679 45.455 0.00 0.00 38.76 3.96
2414 5333 2.676632 TTGCTTGCCCTATTTGCATG 57.323 45.000 0.00 0.00 38.76 4.06
2415 5334 0.825410 TGCTTGCCCTATTTGCATGG 59.175 50.000 0.00 0.00 38.76 3.66
2416 5335 0.826062 GCTTGCCCTATTTGCATGGT 59.174 50.000 0.00 0.00 38.76 3.55
2417 5336 1.207811 GCTTGCCCTATTTGCATGGTT 59.792 47.619 0.00 0.00 38.76 3.67
2418 5337 2.430332 GCTTGCCCTATTTGCATGGTTA 59.570 45.455 0.00 0.00 38.76 2.85
2419 5338 3.070015 GCTTGCCCTATTTGCATGGTTAT 59.930 43.478 0.00 0.00 38.76 1.89
2420 5339 4.280677 GCTTGCCCTATTTGCATGGTTATA 59.719 41.667 0.00 0.00 38.76 0.98
2421 5340 5.047092 GCTTGCCCTATTTGCATGGTTATAT 60.047 40.000 0.00 0.00 38.76 0.86
2422 5341 6.152661 GCTTGCCCTATTTGCATGGTTATATA 59.847 38.462 0.00 0.00 38.76 0.86
2423 5342 7.629222 GCTTGCCCTATTTGCATGGTTATATAG 60.629 40.741 0.00 0.00 38.76 1.31
2424 5343 6.186957 TGCCCTATTTGCATGGTTATATAGG 58.813 40.000 0.00 0.00 36.14 2.57
2429 5348 9.479549 CCTATTTGCATGGTTATATAGGGAATT 57.520 33.333 0.00 0.00 33.89 2.17
2448 5367 8.870116 AGGGAATTAATTATTGTTCTATTGGGC 58.130 33.333 0.00 0.00 0.00 5.36
2449 5368 8.870116 GGGAATTAATTATTGTTCTATTGGGCT 58.130 33.333 0.00 0.00 0.00 5.19
2454 5373 7.961326 AATTATTGTTCTATTGGGCTTGACT 57.039 32.000 0.00 0.00 0.00 3.41
2456 5375 7.859325 TTATTGTTCTATTGGGCTTGACTAC 57.141 36.000 0.00 0.00 0.00 2.73
2457 5376 4.216411 TGTTCTATTGGGCTTGACTACC 57.784 45.455 0.00 0.00 0.00 3.18
2458 5377 3.844211 TGTTCTATTGGGCTTGACTACCT 59.156 43.478 0.00 0.00 0.00 3.08
2459 5378 4.081087 TGTTCTATTGGGCTTGACTACCTC 60.081 45.833 0.00 0.00 0.00 3.85
2460 5379 2.693591 TCTATTGGGCTTGACTACCTCG 59.306 50.000 0.00 0.00 0.00 4.63
2461 5380 1.276622 ATTGGGCTTGACTACCTCGT 58.723 50.000 0.00 0.00 0.00 4.18
2462 5381 0.606604 TTGGGCTTGACTACCTCGTC 59.393 55.000 0.00 0.00 34.52 4.20
2463 5382 0.541063 TGGGCTTGACTACCTCGTCA 60.541 55.000 0.00 0.00 41.82 4.35
2470 5389 3.844577 TGACTACCTCGTCAAACTAGC 57.155 47.619 0.00 0.00 40.69 3.42
2471 5390 3.418995 TGACTACCTCGTCAAACTAGCT 58.581 45.455 0.00 0.00 40.69 3.32
2472 5391 4.582869 TGACTACCTCGTCAAACTAGCTA 58.417 43.478 0.00 0.00 40.69 3.32
2473 5392 4.634883 TGACTACCTCGTCAAACTAGCTAG 59.365 45.833 19.44 19.44 40.69 3.42
2474 5393 3.946558 ACTACCTCGTCAAACTAGCTAGG 59.053 47.826 24.35 8.72 0.00 3.02
2475 5394 3.083122 ACCTCGTCAAACTAGCTAGGA 57.917 47.619 24.35 9.69 0.00 2.94
2476 5395 2.754002 ACCTCGTCAAACTAGCTAGGAC 59.246 50.000 24.35 19.06 0.00 3.85
2477 5396 2.753452 CCTCGTCAAACTAGCTAGGACA 59.247 50.000 24.35 11.36 0.00 4.02
2478 5397 3.181495 CCTCGTCAAACTAGCTAGGACAG 60.181 52.174 24.35 17.84 0.00 3.51
2479 5398 2.753452 TCGTCAAACTAGCTAGGACAGG 59.247 50.000 24.35 10.70 0.00 4.00
2480 5399 2.492484 CGTCAAACTAGCTAGGACAGGT 59.508 50.000 24.35 0.18 38.84 4.00
2481 5400 3.673594 CGTCAAACTAGCTAGGACAGGTG 60.674 52.174 24.35 12.09 36.15 4.00
2482 5401 2.832129 TCAAACTAGCTAGGACAGGTGG 59.168 50.000 24.35 0.00 39.04 4.61
2483 5402 1.196012 AACTAGCTAGGACAGGTGGC 58.804 55.000 24.35 0.00 36.76 5.01
2484 5403 0.688087 ACTAGCTAGGACAGGTGGCC 60.688 60.000 24.35 0.00 46.16 5.36
2490 5409 4.841441 GGACAGGTGGCCAATTGA 57.159 55.556 21.15 0.00 44.76 2.57
2491 5410 3.288099 GGACAGGTGGCCAATTGAT 57.712 52.632 21.15 8.18 44.76 2.57
2492 5411 0.819582 GGACAGGTGGCCAATTGATG 59.180 55.000 21.15 12.19 44.76 3.07
2513 5432 9.693739 TTGATGGTTTTAAGCCTAATTATCTCA 57.306 29.630 0.00 0.00 0.00 3.27
2582 5501 9.213799 GAAAATTAATTGTTGTTCTATTGGGCA 57.786 29.630 0.39 0.00 0.00 5.36
2633 5786 7.686434 AGAGGTAGCTAGTTGATGGTTTTAAA 58.314 34.615 0.00 0.00 0.00 1.52
2657 5810 5.873712 ACTGATGTCTGAGCACTCTTTATTG 59.126 40.000 0.00 0.00 0.00 1.90
2674 5829 8.519799 TCTTTATTGACCTTGTTCTGTTTTCT 57.480 30.769 0.00 0.00 0.00 2.52
2742 7636 3.902261 TGCTTCACTGCAATAACTGTG 57.098 42.857 0.00 0.00 40.29 3.66
2743 7637 2.030893 TGCTTCACTGCAATAACTGTGC 60.031 45.455 0.00 0.00 40.29 4.57
2751 7645 2.001872 GCAATAACTGTGCAATTGGGC 58.998 47.619 7.72 0.00 41.80 5.36
2861 7880 1.895131 GATTCCCATTGCACCAACTGT 59.105 47.619 0.00 0.00 0.00 3.55
2874 7895 1.534595 CCAACTGTGCACTTGCTTCAC 60.535 52.381 19.41 0.00 42.66 3.18
2935 8251 5.363005 TGTTCTATAGGGCTTGACTACCTTC 59.637 44.000 0.00 0.00 35.84 3.46
2944 8262 4.930405 GGCTTGACTACCTTCTCAAACTAC 59.070 45.833 0.00 0.00 0.00 2.73
3009 8341 9.119418 CATGTTTAACTCCCATGTATGTGATTA 57.881 33.333 0.00 0.00 33.06 1.75
3023 8355 7.919690 TGTATGTGATTAAGAATGCTAACTGC 58.080 34.615 0.00 0.00 43.25 4.40
3066 8398 5.123344 AGTTTCGACAGCTAGTTTTTGTTGT 59.877 36.000 0.00 0.00 0.00 3.32
3117 8466 2.872245 GCGCTTGCATCTTTATGTAGGA 59.128 45.455 0.00 0.00 38.92 2.94
3140 8497 8.619546 AGGAAGTACATCGTTAGTCATACTTAC 58.380 37.037 0.00 0.00 34.85 2.34
3141 8498 7.859875 GGAAGTACATCGTTAGTCATACTTACC 59.140 40.741 0.00 0.00 34.00 2.85
3142 8499 7.870509 AGTACATCGTTAGTCATACTTACCA 57.129 36.000 0.00 0.00 0.00 3.25
3143 8500 7.928103 AGTACATCGTTAGTCATACTTACCAG 58.072 38.462 0.00 0.00 0.00 4.00
3144 8501 6.770746 ACATCGTTAGTCATACTTACCAGT 57.229 37.500 0.00 0.00 36.99 4.00
3145 8502 7.166691 ACATCGTTAGTCATACTTACCAGTT 57.833 36.000 0.00 0.00 34.06 3.16
3146 8503 8.284945 ACATCGTTAGTCATACTTACCAGTTA 57.715 34.615 0.00 0.00 34.06 2.24
3152 8509 6.210287 AGTCATACTTACCAGTTAGCACTC 57.790 41.667 0.00 0.00 34.06 3.51
3162 8520 3.928992 CCAGTTAGCACTCACTACACATG 59.071 47.826 0.00 0.00 0.00 3.21
3242 9528 2.155279 GTTTGAAGGCCCTGAGTCTTC 58.845 52.381 0.00 0.00 37.85 2.87
3329 9616 6.019779 TGGTCTGCCAATTTTTGTGTATAC 57.980 37.500 0.00 0.00 42.83 1.47
3333 9620 5.242615 TCTGCCAATTTTTGTGTATACTGCA 59.757 36.000 4.17 0.70 0.00 4.41
3334 9621 5.847304 TGCCAATTTTTGTGTATACTGCAA 58.153 33.333 4.17 6.86 0.00 4.08
3335 9622 6.283694 TGCCAATTTTTGTGTATACTGCAAA 58.716 32.000 16.55 16.55 0.00 3.68
3336 9623 6.763135 TGCCAATTTTTGTGTATACTGCAAAA 59.237 30.769 22.73 22.73 39.41 2.44
3337 9624 7.443575 TGCCAATTTTTGTGTATACTGCAAAAT 59.556 29.630 24.97 18.31 40.37 1.82
3338 9625 7.745594 GCCAATTTTTGTGTATACTGCAAAATG 59.254 33.333 24.97 21.89 40.37 2.32
3339 9626 8.986847 CCAATTTTTGTGTATACTGCAAAATGA 58.013 29.630 24.97 17.65 40.37 2.57
3341 9628 7.636259 TTTTTGTGTATACTGCAAAATGAGC 57.364 32.000 24.97 0.00 40.37 4.26
3342 9629 5.956068 TTGTGTATACTGCAAAATGAGCA 57.044 34.783 4.17 0.00 40.19 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
415 2900 1.866853 GCTTTCTTGGGCACGGGAAG 61.867 60.000 0.00 0.00 0.00 3.46
459 2944 2.986492 TAAGCGGGCTTAGAGGTGT 58.014 52.632 8.97 0.00 37.47 4.16
476 2962 0.469892 TCATGCTCAGGGATCCGCTA 60.470 55.000 5.45 0.00 0.00 4.26
596 3085 7.001674 GTGGGTTGGATAAAAAGGGAAAATTT 58.998 34.615 0.00 0.00 0.00 1.82
602 3091 3.399644 TCTGTGGGTTGGATAAAAAGGGA 59.600 43.478 0.00 0.00 0.00 4.20
678 3200 8.535690 AATTGTCGTTTTAACCTTCAAAAACA 57.464 26.923 10.28 0.00 42.85 2.83
775 3566 7.463469 AAATTGTCGCTTTAACCTTCAAAAG 57.537 32.000 0.00 0.00 36.09 2.27
887 3691 7.417797 CCCATTTAACTCCATGGATTCGAAAAT 60.418 37.037 16.63 13.07 42.49 1.82
892 3696 3.569701 CCCCATTTAACTCCATGGATTCG 59.430 47.826 16.63 6.40 42.49 3.34
905 3709 3.101437 TGAGCTCTACGACCCCATTTAA 58.899 45.455 16.19 0.00 0.00 1.52
914 3723 2.077627 TGAGACAGTGAGCTCTACGAC 58.922 52.381 16.19 4.41 32.44 4.34
941 3756 1.048601 TGGGGATAGATGGAGCGAAC 58.951 55.000 0.00 0.00 0.00 3.95
1392 4259 3.032459 GGAACGAGGGTAGAAGGATCTT 58.968 50.000 0.00 0.00 37.10 2.40
1583 4456 0.034089 GGGTATGGTTGGAAGCAGCT 60.034 55.000 0.00 0.00 40.07 4.24
1672 4545 1.741770 GCTGTTCCTCGCCGTCATT 60.742 57.895 0.00 0.00 0.00 2.57
1674 4547 4.373116 GGCTGTTCCTCGCCGTCA 62.373 66.667 0.00 0.00 36.45 4.35
1777 4651 1.006400 AGAAGGGAAAATGGGAGGCTG 59.994 52.381 0.00 0.00 0.00 4.85
2391 5310 1.338011 GCAAATAGGGCAAGCAAAGCA 60.338 47.619 0.00 0.00 0.00 3.91
2395 5314 1.207570 CCATGCAAATAGGGCAAGCAA 59.792 47.619 0.00 0.00 45.60 3.91
2403 5322 9.479549 AATTCCCTATATAACCATGCAAATAGG 57.520 33.333 0.00 0.00 37.01 2.57
2422 5341 8.870116 GCCCAATAGAACAATAATTAATTCCCT 58.130 33.333 3.39 0.00 0.00 4.20
2423 5342 8.870116 AGCCCAATAGAACAATAATTAATTCCC 58.130 33.333 3.39 0.00 0.00 3.97
2428 5347 9.474313 AGTCAAGCCCAATAGAACAATAATTAA 57.526 29.630 0.00 0.00 0.00 1.40
2430 5349 7.961326 AGTCAAGCCCAATAGAACAATAATT 57.039 32.000 0.00 0.00 0.00 1.40
2431 5350 7.502561 GGTAGTCAAGCCCAATAGAACAATAAT 59.497 37.037 0.00 0.00 0.00 1.28
2432 5351 6.826741 GGTAGTCAAGCCCAATAGAACAATAA 59.173 38.462 0.00 0.00 0.00 1.40
2433 5352 6.157994 AGGTAGTCAAGCCCAATAGAACAATA 59.842 38.462 0.00 0.00 0.00 1.90
2434 5353 5.044846 AGGTAGTCAAGCCCAATAGAACAAT 60.045 40.000 0.00 0.00 0.00 2.71
2435 5354 4.288626 AGGTAGTCAAGCCCAATAGAACAA 59.711 41.667 0.00 0.00 0.00 2.83
2436 5355 3.844211 AGGTAGTCAAGCCCAATAGAACA 59.156 43.478 0.00 0.00 0.00 3.18
2437 5356 4.443621 GAGGTAGTCAAGCCCAATAGAAC 58.556 47.826 0.00 0.00 0.00 3.01
2438 5357 3.132289 CGAGGTAGTCAAGCCCAATAGAA 59.868 47.826 0.00 0.00 0.00 2.10
2439 5358 2.693591 CGAGGTAGTCAAGCCCAATAGA 59.306 50.000 0.00 0.00 0.00 1.98
2440 5359 2.431057 ACGAGGTAGTCAAGCCCAATAG 59.569 50.000 0.00 0.00 0.00 1.73
2441 5360 2.429610 GACGAGGTAGTCAAGCCCAATA 59.570 50.000 0.00 0.00 40.65 1.90
2442 5361 1.207329 GACGAGGTAGTCAAGCCCAAT 59.793 52.381 0.00 0.00 40.65 3.16
2443 5362 0.606604 GACGAGGTAGTCAAGCCCAA 59.393 55.000 0.00 0.00 40.65 4.12
2444 5363 0.541063 TGACGAGGTAGTCAAGCCCA 60.541 55.000 0.00 0.00 46.81 5.36
2445 5364 2.273908 TGACGAGGTAGTCAAGCCC 58.726 57.895 0.00 0.00 46.81 5.19
2450 5369 6.374352 CCTAGCTAGTTTGACGAGGTAGTCA 61.374 48.000 19.31 0.00 44.73 3.41
2451 5370 4.035441 CCTAGCTAGTTTGACGAGGTAGTC 59.965 50.000 19.31 0.00 44.73 2.59
2452 5371 3.946558 CCTAGCTAGTTTGACGAGGTAGT 59.053 47.826 19.31 0.00 44.73 2.73
2453 5372 4.035441 GTCCTAGCTAGTTTGACGAGGTAG 59.965 50.000 19.31 15.77 45.33 3.18
2454 5373 3.944015 GTCCTAGCTAGTTTGACGAGGTA 59.056 47.826 19.31 1.37 33.73 3.08
2455 5374 2.754002 GTCCTAGCTAGTTTGACGAGGT 59.246 50.000 19.31 0.00 35.76 3.85
2456 5375 2.753452 TGTCCTAGCTAGTTTGACGAGG 59.247 50.000 19.31 3.49 0.00 4.63
2457 5376 3.181495 CCTGTCCTAGCTAGTTTGACGAG 60.181 52.174 19.31 16.01 0.00 4.18
2458 5377 2.753452 CCTGTCCTAGCTAGTTTGACGA 59.247 50.000 19.31 5.59 0.00 4.20
2459 5378 2.492484 ACCTGTCCTAGCTAGTTTGACG 59.508 50.000 19.31 13.80 0.00 4.35
2460 5379 3.368531 CCACCTGTCCTAGCTAGTTTGAC 60.369 52.174 19.31 18.05 0.00 3.18
2461 5380 2.832129 CCACCTGTCCTAGCTAGTTTGA 59.168 50.000 19.31 7.03 0.00 2.69
2462 5381 2.678190 GCCACCTGTCCTAGCTAGTTTG 60.678 54.545 19.31 4.65 0.00 2.93
2463 5382 1.555533 GCCACCTGTCCTAGCTAGTTT 59.444 52.381 19.31 0.00 0.00 2.66
2464 5383 1.196012 GCCACCTGTCCTAGCTAGTT 58.804 55.000 19.31 0.00 0.00 2.24
2465 5384 0.688087 GGCCACCTGTCCTAGCTAGT 60.688 60.000 19.31 0.00 0.00 2.57
2466 5385 0.687757 TGGCCACCTGTCCTAGCTAG 60.688 60.000 14.20 14.20 0.00 3.42
2467 5386 0.252513 TTGGCCACCTGTCCTAGCTA 60.253 55.000 3.88 0.00 0.00 3.32
2468 5387 0.916358 ATTGGCCACCTGTCCTAGCT 60.916 55.000 3.88 0.00 0.00 3.32
2469 5388 0.034089 AATTGGCCACCTGTCCTAGC 60.034 55.000 3.88 0.00 0.00 3.42
2470 5389 1.281867 TCAATTGGCCACCTGTCCTAG 59.718 52.381 3.88 0.00 0.00 3.02
2471 5390 1.367346 TCAATTGGCCACCTGTCCTA 58.633 50.000 3.88 0.00 0.00 2.94
2472 5391 0.706433 ATCAATTGGCCACCTGTCCT 59.294 50.000 3.88 0.00 0.00 3.85
2473 5392 0.819582 CATCAATTGGCCACCTGTCC 59.180 55.000 3.88 0.00 0.00 4.02
2474 5393 0.819582 CCATCAATTGGCCACCTGTC 59.180 55.000 3.88 0.00 39.09 3.51
2475 5394 2.980541 CCATCAATTGGCCACCTGT 58.019 52.632 3.88 0.00 39.09 4.00
2487 5406 9.693739 TGAGATAATTAGGCTTAAAACCATCAA 57.306 29.630 0.00 0.00 0.00 2.57
2488 5407 9.693739 TTGAGATAATTAGGCTTAAAACCATCA 57.306 29.630 0.00 0.00 0.00 3.07
2492 5411 9.750125 CCAATTGAGATAATTAGGCTTAAAACC 57.250 33.333 7.12 0.00 0.00 3.27
2493 5412 9.750125 CCCAATTGAGATAATTAGGCTTAAAAC 57.250 33.333 7.12 0.00 0.00 2.43
2494 5413 9.487442 ACCCAATTGAGATAATTAGGCTTAAAA 57.513 29.630 7.12 0.00 0.00 1.52
2495 5414 8.912988 CACCCAATTGAGATAATTAGGCTTAAA 58.087 33.333 7.12 0.00 0.00 1.52
2496 5415 7.014230 GCACCCAATTGAGATAATTAGGCTTAA 59.986 37.037 7.12 0.00 0.00 1.85
2497 5416 6.490040 GCACCCAATTGAGATAATTAGGCTTA 59.510 38.462 7.12 0.00 0.00 3.09
2498 5417 5.302823 GCACCCAATTGAGATAATTAGGCTT 59.697 40.000 7.12 0.00 0.00 4.35
2499 5418 4.829492 GCACCCAATTGAGATAATTAGGCT 59.171 41.667 7.12 0.00 0.00 4.58
2500 5419 4.584325 TGCACCCAATTGAGATAATTAGGC 59.416 41.667 7.12 0.00 0.00 3.93
2501 5420 6.684686 CATGCACCCAATTGAGATAATTAGG 58.315 40.000 7.12 0.00 0.00 2.69
2502 5421 6.154445 GCATGCACCCAATTGAGATAATTAG 58.846 40.000 14.21 0.00 0.00 1.73
2503 5422 5.278414 CGCATGCACCCAATTGAGATAATTA 60.278 40.000 19.57 0.00 0.00 1.40
2504 5423 4.500205 CGCATGCACCCAATTGAGATAATT 60.500 41.667 19.57 0.00 0.00 1.40
2505 5424 3.005050 CGCATGCACCCAATTGAGATAAT 59.995 43.478 19.57 0.00 0.00 1.28
2506 5425 2.358582 CGCATGCACCCAATTGAGATAA 59.641 45.455 19.57 0.00 0.00 1.75
2507 5426 1.948834 CGCATGCACCCAATTGAGATA 59.051 47.619 19.57 0.00 0.00 1.98
2508 5427 0.742505 CGCATGCACCCAATTGAGAT 59.257 50.000 19.57 0.00 0.00 2.75
2509 5428 0.608856 ACGCATGCACCCAATTGAGA 60.609 50.000 19.57 0.00 0.00 3.27
2510 5429 0.244450 AACGCATGCACCCAATTGAG 59.756 50.000 19.57 0.00 0.00 3.02
2511 5430 0.038435 CAACGCATGCACCCAATTGA 60.038 50.000 19.57 0.00 0.00 2.57
2512 5431 2.447408 CAACGCATGCACCCAATTG 58.553 52.632 19.57 7.81 0.00 2.32
2513 5432 4.992515 CAACGCATGCACCCAATT 57.007 50.000 19.57 0.00 0.00 2.32
2567 5486 2.102578 AGCCATGCCCAATAGAACAAC 58.897 47.619 0.00 0.00 0.00 3.32
2582 5501 3.264450 AGCTAGTTTCACAAGGTAGCCAT 59.736 43.478 0.00 0.00 37.43 4.40
2633 5786 5.674052 ATAAAGAGTGCTCAGACATCAGT 57.326 39.130 1.82 0.00 0.00 3.41
2657 5810 5.057149 TGCTCTAGAAAACAGAACAAGGTC 58.943 41.667 0.00 0.00 0.00 3.85
2674 5829 7.069950 ACCATAACATGTGAACTCTATGCTCTA 59.930 37.037 0.00 0.00 0.00 2.43
2738 7632 1.448893 GCCATGCCCAATTGCACAG 60.449 57.895 0.00 0.00 45.48 3.66
2739 7633 0.614134 TAGCCATGCCCAATTGCACA 60.614 50.000 0.00 0.12 45.48 4.57
2740 7634 0.754472 ATAGCCATGCCCAATTGCAC 59.246 50.000 0.00 0.00 45.48 4.57
2741 7635 2.241160 CTATAGCCATGCCCAATTGCA 58.759 47.619 0.00 0.00 46.94 4.08
2742 7636 1.547372 CCTATAGCCATGCCCAATTGC 59.453 52.381 0.00 0.00 0.00 3.56
2743 7637 3.159213 TCCTATAGCCATGCCCAATTG 57.841 47.619 0.00 0.00 0.00 2.32
2744 7638 4.045079 AGAATCCTATAGCCATGCCCAATT 59.955 41.667 0.00 0.00 0.00 2.32
2745 7639 3.595138 AGAATCCTATAGCCATGCCCAAT 59.405 43.478 0.00 0.00 0.00 3.16
2746 7640 2.988859 AGAATCCTATAGCCATGCCCAA 59.011 45.455 0.00 0.00 0.00 4.12
2747 7641 2.636005 AGAATCCTATAGCCATGCCCA 58.364 47.619 0.00 0.00 0.00 5.36
2748 7642 3.350833 CAAGAATCCTATAGCCATGCCC 58.649 50.000 0.00 0.00 0.00 5.36
2749 7643 3.350833 CCAAGAATCCTATAGCCATGCC 58.649 50.000 0.00 0.00 0.00 4.40
2750 7644 3.009473 TCCCAAGAATCCTATAGCCATGC 59.991 47.826 0.00 0.00 0.00 4.06
2751 7645 4.916041 TCCCAAGAATCCTATAGCCATG 57.084 45.455 0.00 0.00 0.00 3.66
2819 7723 9.508567 GAATCTTTCCTATCTGCAAAATTACAC 57.491 33.333 0.00 0.00 0.00 2.90
2854 7871 0.740149 TGAAGCAAGTGCACAGTTGG 59.260 50.000 21.04 4.27 45.16 3.77
2861 7880 4.136796 AGTAGAAATGTGAAGCAAGTGCA 58.863 39.130 6.00 0.00 45.16 4.57
2862 7881 4.378874 GGAGTAGAAATGTGAAGCAAGTGC 60.379 45.833 0.00 0.00 42.49 4.40
2865 7886 4.326826 TGGGAGTAGAAATGTGAAGCAAG 58.673 43.478 0.00 0.00 0.00 4.01
2919 8208 2.327325 TGAGAAGGTAGTCAAGCCCT 57.673 50.000 0.00 0.00 0.00 5.19
3023 8355 8.761497 TCGAAACTAGTGTGTAATCTTTCTTTG 58.239 33.333 0.00 0.00 0.00 2.77
3066 8398 7.072961 AGCCATTTTCTCTCCTAAGATATGGAA 59.927 37.037 14.71 0.00 38.69 3.53
3117 8466 8.284945 TGGTAAGTATGACTAACGATGTACTT 57.715 34.615 0.00 0.00 36.61 2.24
3140 8497 3.660501 TGTGTAGTGAGTGCTAACTGG 57.339 47.619 0.00 0.00 36.52 4.00
3141 8498 4.809673 TCATGTGTAGTGAGTGCTAACTG 58.190 43.478 0.00 0.00 36.52 3.16
3142 8499 5.667539 ATCATGTGTAGTGAGTGCTAACT 57.332 39.130 0.00 0.00 40.21 2.24
3143 8500 5.869344 TGAATCATGTGTAGTGAGTGCTAAC 59.131 40.000 0.00 0.00 0.00 2.34
3144 8501 6.036577 TGAATCATGTGTAGTGAGTGCTAA 57.963 37.500 0.00 0.00 0.00 3.09
3145 8502 5.659440 TGAATCATGTGTAGTGAGTGCTA 57.341 39.130 0.00 0.00 0.00 3.49
3146 8503 4.541973 TGAATCATGTGTAGTGAGTGCT 57.458 40.909 0.00 0.00 0.00 4.40
3152 8509 7.368480 TCAACTGAATGAATCATGTGTAGTG 57.632 36.000 0.00 0.00 37.44 2.74
3242 9528 7.552687 TGGTAAATAAGGAGTGCTCACAAATAG 59.447 37.037 2.63 0.00 0.00 1.73
3293 9579 1.732259 GCAGACCATAACAGGTGAACG 59.268 52.381 0.00 0.00 43.38 3.95


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

AutoCloner maintained by Alex Coulton.