Multiple sequence alignment - TraesCS5A01G293100

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS5A01G293100 chr5A 100.000 3434 0 0 776 4209 502847331 502850764 0.000000e+00 6342.0
1 TraesCS5A01G293100 chr5A 100.000 501 0 0 1 501 502846556 502847056 0.000000e+00 926.0
2 TraesCS5A01G293100 chr5A 90.680 676 48 2 1798 2458 486769528 486768853 0.000000e+00 885.0
3 TraesCS5A01G293100 chr5A 92.913 508 25 7 1 499 153399363 153398858 0.000000e+00 728.0
4 TraesCS5A01G293100 chr5A 92.323 508 28 7 1 499 137850423 137850928 0.000000e+00 712.0
5 TraesCS5A01G293100 chr5A 97.867 375 8 0 3835 4209 33145062 33145436 0.000000e+00 649.0
6 TraesCS5A01G293100 chr5A 85.838 579 46 7 2111 2689 699209173 699209715 2.180000e-162 582.0
7 TraesCS5A01G293100 chr7A 93.126 3244 157 20 777 3988 61450517 61447308 0.000000e+00 4695.0
8 TraesCS5A01G293100 chr7A 93.110 508 25 6 1 499 305167747 305167241 0.000000e+00 736.0
9 TraesCS5A01G293100 chr7A 97.333 375 9 1 3835 4209 118989911 118989538 1.650000e-178 636.0
10 TraesCS5A01G293100 chr7A 97.067 375 10 1 3835 4209 655224899 655225272 7.680000e-177 630.0
11 TraesCS5A01G293100 chr1B 92.318 3046 172 11 776 3790 502573174 502576188 0.000000e+00 4272.0
12 TraesCS5A01G293100 chr1B 97.115 416 12 0 3792 4207 502584475 502584890 0.000000e+00 702.0
13 TraesCS5A01G293100 chr1B 88.713 505 52 3 776 1275 484304733 484304229 2.780000e-171 612.0
14 TraesCS5A01G293100 chr1B 95.568 361 16 0 1713 2073 103084522 103084162 2.820000e-161 579.0
15 TraesCS5A01G293100 chr6A 94.981 2052 76 4 1370 3418 595721326 595723353 0.000000e+00 3193.0
16 TraesCS5A01G293100 chr6A 91.535 508 33 6 1 499 595720040 595720546 0.000000e+00 691.0
17 TraesCS5A01G293100 chr6A 92.823 418 14 5 3437 3838 97554388 97553971 3.620000e-165 592.0
18 TraesCS5A01G293100 chr3B 92.897 2126 111 6 776 2898 815998874 816000962 0.000000e+00 3053.0
19 TraesCS5A01G293100 chr3B 93.656 1198 46 8 3040 4209 816000960 816002155 0.000000e+00 1764.0
20 TraesCS5A01G293100 chr3B 97.105 760 21 1 3450 4209 765026409 765027167 0.000000e+00 1280.0
21 TraesCS5A01G293100 chr3B 94.692 471 21 2 1 467 713383093 713383563 0.000000e+00 728.0
22 TraesCS5A01G293100 chr3B 92.143 420 15 5 3435 3838 16520907 16521324 1.010000e-160 577.0
23 TraesCS5A01G293100 chr3B 88.814 447 48 2 830 1275 601207423 601207868 7.960000e-152 547.0
24 TraesCS5A01G293100 chr3B 92.742 124 9 0 1626 1749 777994698 777994575 3.340000e-41 180.0
25 TraesCS5A01G293100 chr3B 89.600 125 4 2 1504 1619 777994921 777994797 2.620000e-32 150.0
26 TraesCS5A01G293100 chr5D 88.889 2295 108 41 1798 3988 481667475 481665224 0.000000e+00 2689.0
27 TraesCS5A01G293100 chr5D 92.105 456 20 3 1798 2238 366924825 366925279 2.760000e-176 628.0
28 TraesCS5A01G293100 chr5D 93.770 305 18 1 1798 2102 28572452 28572755 1.380000e-124 457.0
29 TraesCS5A01G293100 chr5D 91.237 194 15 2 802 995 28570925 28571116 3.230000e-66 263.0
30 TraesCS5A01G293100 chr1D 88.685 1255 76 8 2172 3394 475431666 475430446 0.000000e+00 1471.0
31 TraesCS5A01G293100 chr1D 94.458 794 24 4 3436 4209 475430343 475429550 0.000000e+00 1205.0
32 TraesCS5A01G293100 chr1D 89.668 784 49 4 2641 3392 69688371 69687588 0.000000e+00 970.0
33 TraesCS5A01G293100 chr1D 93.148 613 39 3 776 1387 123236969 123237579 0.000000e+00 896.0
34 TraesCS5A01G293100 chr1D 93.294 507 26 4 1 499 123236467 123236973 0.000000e+00 741.0
35 TraesCS5A01G293100 chr1D 91.886 456 21 3 1798 2238 41783060 41783514 1.290000e-174 623.0
36 TraesCS5A01G293100 chr1D 91.556 450 22 3 1804 2238 79840615 79840167 1.290000e-169 606.0
37 TraesCS5A01G293100 chr1D 90.385 312 25 5 1192 1500 49708157 49707848 5.070000e-109 405.0
38 TraesCS5A01G293100 chr3D 87.872 907 68 19 2521 3394 160281841 160280944 0.000000e+00 1027.0
39 TraesCS5A01G293100 chr3D 90.619 501 37 7 1005 1500 580718528 580719023 0.000000e+00 656.0
40 TraesCS5A01G293100 chr3D 90.952 420 19 4 3435 3838 426385721 426385305 7.960000e-152 547.0
41 TraesCS5A01G293100 chr3D 89.744 312 27 5 1192 1500 134372808 134373117 1.100000e-105 394.0
42 TraesCS5A01G293100 chr7B 87.597 903 75 17 2519 3394 68915797 68916689 0.000000e+00 1013.0
43 TraesCS5A01G293100 chr7B 90.818 501 45 1 776 1275 734671348 734671848 0.000000e+00 669.0
44 TraesCS5A01G293100 chr7B 95.430 372 16 1 1713 2084 543522170 543521800 3.620000e-165 592.0
45 TraesCS5A01G293100 chr2D 87.917 869 62 21 2560 3396 508406948 508407805 0.000000e+00 983.0
46 TraesCS5A01G293100 chr2D 90.097 414 24 4 3442 3838 50815997 50815584 4.820000e-144 521.0
47 TraesCS5A01G293100 chr6B 87.788 868 64 22 2560 3394 208853688 208852830 0.000000e+00 977.0
48 TraesCS5A01G293100 chr6B 95.291 361 17 0 1713 2073 47005707 47006067 1.310000e-159 573.0
49 TraesCS5A01G293100 chr2B 95.775 497 20 1 1378 1874 759372551 759372056 0.000000e+00 800.0
50 TraesCS5A01G293100 chr2B 92.520 508 27 7 1 499 159127008 159126503 0.000000e+00 717.0
51 TraesCS5A01G293100 chr2B 88.812 581 28 9 2111 2689 320514956 320514411 0.000000e+00 678.0
52 TraesCS5A01G293100 chr2B 89.057 530 56 2 776 1304 759388847 759388319 0.000000e+00 656.0
53 TraesCS5A01G293100 chr2B 94.505 364 20 0 1710 2073 60930131 60930494 2.840000e-156 562.0
54 TraesCS5A01G293100 chr2A 92.126 508 30 6 1 499 538686869 538686363 0.000000e+00 708.0
55 TraesCS5A01G293100 chr2A 97.600 375 9 0 3835 4209 740534925 740535299 0.000000e+00 643.0
56 TraesCS5A01G293100 chr2A 95.455 44 2 0 776 819 538686367 538686324 2.100000e-08 71.3
57 TraesCS5A01G293100 chr4B 89.501 581 25 8 2111 2689 219273568 219273022 0.000000e+00 702.0
58 TraesCS5A01G293100 chr4A 91.339 508 32 8 1 499 80963876 80964380 0.000000e+00 684.0
59 TraesCS5A01G293100 chr5B 88.256 579 32 8 2113 2689 37322193 37322737 0.000000e+00 660.0
60 TraesCS5A01G293100 chrUn 91.685 457 20 5 1798 2238 154748711 154749165 5.980000e-173 617.0
61 TraesCS5A01G293100 chr4D 95.467 375 17 0 3835 4209 271102517 271102891 2.170000e-167 599.0
62 TraesCS5A01G293100 chr7D 91.686 421 18 7 3435 3838 8617876 8618296 6.110000e-158 568.0
63 TraesCS5A01G293100 chr7D 82.018 228 17 10 3628 3838 548184984 548184764 5.590000e-39 172.0
64 TraesCS5A01G293100 chr6D 90.385 312 25 5 1192 1500 298385110 298384801 5.070000e-109 405.0
65 TraesCS5A01G293100 chr6D 89.744 312 27 5 1192 1500 9670294 9669985 1.100000e-105 394.0
66 TraesCS5A01G293100 chr6D 90.847 295 11 3 1960 2238 42385176 42384882 8.540000e-102 381.0


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 TraesCS5A01G293100 chr5A 502846556 502850764 4208 False 3634.00 6342 100.0000 1 4209 2 chr5A.!!$F4 4208
1 TraesCS5A01G293100 chr5A 486768853 486769528 675 True 885.00 885 90.6800 1798 2458 1 chr5A.!!$R2 660
2 TraesCS5A01G293100 chr5A 153398858 153399363 505 True 728.00 728 92.9130 1 499 1 chr5A.!!$R1 498
3 TraesCS5A01G293100 chr5A 137850423 137850928 505 False 712.00 712 92.3230 1 499 1 chr5A.!!$F2 498
4 TraesCS5A01G293100 chr5A 699209173 699209715 542 False 582.00 582 85.8380 2111 2689 1 chr5A.!!$F3 578
5 TraesCS5A01G293100 chr7A 61447308 61450517 3209 True 4695.00 4695 93.1260 777 3988 1 chr7A.!!$R1 3211
6 TraesCS5A01G293100 chr7A 305167241 305167747 506 True 736.00 736 93.1100 1 499 1 chr7A.!!$R3 498
7 TraesCS5A01G293100 chr1B 502573174 502576188 3014 False 4272.00 4272 92.3180 776 3790 1 chr1B.!!$F1 3014
8 TraesCS5A01G293100 chr1B 484304229 484304733 504 True 612.00 612 88.7130 776 1275 1 chr1B.!!$R2 499
9 TraesCS5A01G293100 chr6A 595720040 595723353 3313 False 1942.00 3193 93.2580 1 3418 2 chr6A.!!$F1 3417
10 TraesCS5A01G293100 chr3B 815998874 816002155 3281 False 2408.50 3053 93.2765 776 4209 2 chr3B.!!$F5 3433
11 TraesCS5A01G293100 chr3B 765026409 765027167 758 False 1280.00 1280 97.1050 3450 4209 1 chr3B.!!$F4 759
12 TraesCS5A01G293100 chr5D 481665224 481667475 2251 True 2689.00 2689 88.8890 1798 3988 1 chr5D.!!$R1 2190
13 TraesCS5A01G293100 chr5D 28570925 28572755 1830 False 360.00 457 92.5035 802 2102 2 chr5D.!!$F2 1300
14 TraesCS5A01G293100 chr1D 475429550 475431666 2116 True 1338.00 1471 91.5715 2172 4209 2 chr1D.!!$R4 2037
15 TraesCS5A01G293100 chr1D 69687588 69688371 783 True 970.00 970 89.6680 2641 3392 1 chr1D.!!$R2 751
16 TraesCS5A01G293100 chr1D 123236467 123237579 1112 False 818.50 896 93.2210 1 1387 2 chr1D.!!$F2 1386
17 TraesCS5A01G293100 chr3D 160280944 160281841 897 True 1027.00 1027 87.8720 2521 3394 1 chr3D.!!$R1 873
18 TraesCS5A01G293100 chr7B 68915797 68916689 892 False 1013.00 1013 87.5970 2519 3394 1 chr7B.!!$F1 875
19 TraesCS5A01G293100 chr7B 734671348 734671848 500 False 669.00 669 90.8180 776 1275 1 chr7B.!!$F2 499
20 TraesCS5A01G293100 chr2D 508406948 508407805 857 False 983.00 983 87.9170 2560 3396 1 chr2D.!!$F1 836
21 TraesCS5A01G293100 chr6B 208852830 208853688 858 True 977.00 977 87.7880 2560 3394 1 chr6B.!!$R1 834
22 TraesCS5A01G293100 chr2B 159126503 159127008 505 True 717.00 717 92.5200 1 499 1 chr2B.!!$R1 498
23 TraesCS5A01G293100 chr2B 320514411 320514956 545 True 678.00 678 88.8120 2111 2689 1 chr2B.!!$R2 578
24 TraesCS5A01G293100 chr2B 759388319 759388847 528 True 656.00 656 89.0570 776 1304 1 chr2B.!!$R4 528
25 TraesCS5A01G293100 chr2A 538686324 538686869 545 True 389.65 708 93.7905 1 819 2 chr2A.!!$R1 818
26 TraesCS5A01G293100 chr4B 219273022 219273568 546 True 702.00 702 89.5010 2111 2689 1 chr4B.!!$R1 578
27 TraesCS5A01G293100 chr4A 80963876 80964380 504 False 684.00 684 91.3390 1 499 1 chr4A.!!$F1 498
28 TraesCS5A01G293100 chr5B 37322193 37322737 544 False 660.00 660 88.2560 2113 2689 1 chr5B.!!$F1 576

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
475 480 0.322975 CCATCCTCCCCATCATCGAC 59.677 60.0 0.00 0.0 0.0 4.20 F
476 481 0.322975 CATCCTCCCCATCATCGACC 59.677 60.0 0.00 0.0 0.0 4.79 F
1373 1755 0.451783 GTGCGCATCTAAGGTTTGGG 59.548 55.0 15.91 0.0 0.0 4.12 F
2024 3357 0.036010 CACTTGGATCGAAGGTGGCT 60.036 55.0 19.98 0.0 0.0 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2006 3339 0.036010 CAGCCACCTTCGATCCAAGT 60.036 55.0 0.0 0.0 0.00 3.16 R
2024 3357 0.251209 AGACCTCGTACCAGTGCTCA 60.251 55.0 0.0 0.0 0.00 4.26 R
2411 3768 0.611714 AGGGCCGTTGTATTCGTCTT 59.388 50.0 0.0 0.0 0.00 3.01 R
3606 5071 0.392193 CCTGCCCTGCACACTCTTAG 60.392 60.0 0.0 0.0 33.79 2.18 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
71 72 1.532868 CCGAGTTGGCTGTTTCTCAAG 59.467 52.381 0.00 0.00 0.00 3.02
120 121 9.196552 CAATCAAATTGATGATCATCCATGAAG 57.803 33.333 28.61 17.29 42.83 3.02
124 125 4.362470 TGATGATCATCCATGAAGGGTC 57.638 45.455 28.61 5.52 40.69 4.46
253 255 4.096984 GCTCATTTTCGAACCAATCAGGAT 59.903 41.667 0.00 0.00 41.22 3.24
318 320 3.688702 GCCTCCTACTGATCCAGTGTCTA 60.689 52.174 9.64 0.00 45.01 2.59
325 327 4.366267 ACTGATCCAGTGTCTATCCCTTT 58.634 43.478 0.00 0.00 43.63 3.11
344 346 3.742248 CTCCCTCGACCCCCTCCTC 62.742 73.684 0.00 0.00 0.00 3.71
368 370 1.275573 GAGAAACCCTAGGTCAAGCGT 59.724 52.381 8.29 0.00 33.12 5.07
467 472 4.088351 TCCGCTCCATCCTCCCCA 62.088 66.667 0.00 0.00 0.00 4.96
469 474 2.746359 CGCTCCATCCTCCCCATC 59.254 66.667 0.00 0.00 0.00 3.51
470 475 2.142761 CGCTCCATCCTCCCCATCA 61.143 63.158 0.00 0.00 0.00 3.07
471 476 1.486997 CGCTCCATCCTCCCCATCAT 61.487 60.000 0.00 0.00 0.00 2.45
473 478 0.612229 CTCCATCCTCCCCATCATCG 59.388 60.000 0.00 0.00 0.00 3.84
475 480 0.322975 CCATCCTCCCCATCATCGAC 59.677 60.000 0.00 0.00 0.00 4.20
476 481 0.322975 CATCCTCCCCATCATCGACC 59.677 60.000 0.00 0.00 0.00 4.79
496 505 3.788766 GCGCACGTCCCACACATC 61.789 66.667 0.30 0.00 0.00 3.06
497 506 3.478394 CGCACGTCCCACACATCG 61.478 66.667 0.00 0.00 0.00 3.84
498 507 2.048597 GCACGTCCCACACATCGA 60.049 61.111 0.00 0.00 0.00 3.59
499 508 1.447838 GCACGTCCCACACATCGAT 60.448 57.895 0.00 0.00 0.00 3.59
500 509 1.421410 GCACGTCCCACACATCGATC 61.421 60.000 0.00 0.00 0.00 3.69
838 850 4.180946 CTCGTCTGACCTCGCCGG 62.181 72.222 0.00 0.00 39.35 6.13
995 1009 2.338984 GGACTTCCGTCTGCACGT 59.661 61.111 0.00 0.00 45.17 4.49
996 1010 1.300697 GGACTTCCGTCTGCACGTT 60.301 57.895 0.00 0.00 45.17 3.99
1174 1556 1.069090 GACTGCGTCCACAACCTCA 59.931 57.895 0.00 0.00 0.00 3.86
1275 1657 1.004918 CGTCGGCAAGTTCTTCCCT 60.005 57.895 0.00 0.00 0.00 4.20
1311 1693 1.186917 TCCCGTTGCTTTCCGTCCTA 61.187 55.000 0.00 0.00 0.00 2.94
1365 1747 1.016627 GATTGCTGGTGCGCATCTAA 58.983 50.000 23.25 14.41 43.34 2.10
1373 1755 0.451783 GTGCGCATCTAAGGTTTGGG 59.548 55.000 15.91 0.00 0.00 4.12
1659 2041 5.683681 TCTCATAATCAGTTGGCAGCATAA 58.316 37.500 3.63 0.00 0.00 1.90
1848 3181 7.445121 AGTGTAGTTTGTGATTGAGAGAATGA 58.555 34.615 0.00 0.00 0.00 2.57
1937 3270 3.376859 TGATGTTATTGTTGCCATCCGAC 59.623 43.478 0.00 0.00 34.22 4.79
2024 3357 0.036010 CACTTGGATCGAAGGTGGCT 60.036 55.000 19.98 0.00 0.00 4.75
2049 3382 2.163815 CACTGGTACGAGGTCTACAAGG 59.836 54.545 9.86 0.00 0.00 3.61
2086 3424 3.307762 GCCAACCTCTGGTTCATCTACTT 60.308 47.826 0.00 0.00 43.05 2.24
2102 3455 3.329300 CTTGTGGGAGGACAAGGTG 57.671 57.895 0.00 0.00 46.16 4.00
2176 3529 6.382859 AGTGTAAGGTTTTGGATTGGAAACTT 59.617 34.615 0.00 0.00 36.32 2.66
2243 3600 9.638239 TTTTATTGATGAATGCACTACCTTTTC 57.362 29.630 0.00 0.00 0.00 2.29
2276 3633 9.995003 GATCCAAAATGTCATCTTATCTCTAGT 57.005 33.333 0.00 0.00 0.00 2.57
2411 3768 2.035832 GCTTGCTTTTTCTGTGCCCTAA 59.964 45.455 0.00 0.00 0.00 2.69
2495 3852 2.354103 GCTCTCACTGTTGCCATCTACA 60.354 50.000 0.00 0.00 0.00 2.74
2496 3853 3.866066 GCTCTCACTGTTGCCATCTACAA 60.866 47.826 0.00 0.00 0.00 2.41
2497 3854 3.930336 TCTCACTGTTGCCATCTACAAG 58.070 45.455 0.00 0.00 0.00 3.16
2498 3855 3.324846 TCTCACTGTTGCCATCTACAAGT 59.675 43.478 0.00 0.00 0.00 3.16
2499 3856 4.067896 CTCACTGTTGCCATCTACAAGTT 58.932 43.478 0.00 0.00 0.00 2.66
2500 3857 3.814842 TCACTGTTGCCATCTACAAGTTG 59.185 43.478 0.00 0.00 0.00 3.16
2501 3858 2.554032 ACTGTTGCCATCTACAAGTTGC 59.446 45.455 1.81 0.00 0.00 4.17
2502 3859 2.816087 CTGTTGCCATCTACAAGTTGCT 59.184 45.455 1.81 0.00 0.00 3.91
2503 3860 2.553602 TGTTGCCATCTACAAGTTGCTG 59.446 45.455 1.81 0.00 0.00 4.41
2504 3861 2.813754 GTTGCCATCTACAAGTTGCTGA 59.186 45.455 1.81 1.72 0.00 4.26
2505 3862 2.703416 TGCCATCTACAAGTTGCTGAG 58.297 47.619 1.81 0.00 0.00 3.35
2506 3863 2.038952 TGCCATCTACAAGTTGCTGAGT 59.961 45.455 1.81 0.00 0.00 3.41
2507 3864 2.417933 GCCATCTACAAGTTGCTGAGTG 59.582 50.000 1.81 2.96 0.00 3.51
2508 3865 3.668447 CCATCTACAAGTTGCTGAGTGT 58.332 45.455 1.81 0.00 0.00 3.55
2509 3866 3.434641 CCATCTACAAGTTGCTGAGTGTG 59.565 47.826 1.81 2.94 0.00 3.82
2510 3867 3.819564 TCTACAAGTTGCTGAGTGTGT 57.180 42.857 1.81 0.00 0.00 3.72
2511 3868 4.929819 TCTACAAGTTGCTGAGTGTGTA 57.070 40.909 1.81 0.00 0.00 2.90
2512 3869 4.871513 TCTACAAGTTGCTGAGTGTGTAG 58.128 43.478 1.81 0.00 39.72 2.74
2513 3870 2.213499 ACAAGTTGCTGAGTGTGTAGC 58.787 47.619 1.81 0.00 40.29 3.58
2598 3959 1.200716 GCATTGCTGCTGAAACTGCTA 59.799 47.619 0.16 0.00 45.32 3.49
2775 4140 8.195436 GTGGCTTAGTGTAATTGATGTACTAGA 58.805 37.037 0.00 0.00 0.00 2.43
3124 4520 1.078848 GGAGGCAACGAGATGCTGT 60.079 57.895 11.18 1.67 45.68 4.40
3222 4618 2.092968 GCACATGACCCCTTCTACATCA 60.093 50.000 0.00 0.00 0.00 3.07
3347 4749 2.692557 TGTTTATTTGGCTGCACTGTGT 59.307 40.909 9.86 0.00 0.00 3.72
3349 4751 2.566833 TATTTGGCTGCACTGTGTCT 57.433 45.000 9.86 0.00 0.00 3.41
3355 4757 0.514691 GCTGCACTGTGTCTTACTGC 59.485 55.000 9.86 4.32 32.67 4.40
3408 4845 2.035632 AGTACTATGGCTGAGGCAGTC 58.964 52.381 15.56 0.00 42.43 3.51
3606 5071 7.822658 TGTGGAATGCAAGTTATTTTAGGTAC 58.177 34.615 0.00 0.00 0.00 3.34
3783 5248 2.994186 AGGCCATTTGATTGAATGCC 57.006 45.000 5.01 0.00 36.04 4.40
3790 5271 5.107133 CCATTTGATTGAATGCCTGAAGTC 58.893 41.667 0.00 0.00 36.04 3.01
3873 5365 4.478206 CTCTTGTGAGCTCTTCCCATTA 57.522 45.455 16.19 0.00 33.12 1.90
4087 5583 5.163416 TGCATCCTAATTGTCAATCTCGAGA 60.163 40.000 19.19 19.19 0.00 4.04
4088 5584 5.755375 GCATCCTAATTGTCAATCTCGAGAA 59.245 40.000 20.91 1.26 0.00 2.87
4096 5592 5.072040 TGTCAATCTCGAGAATGCACTTA 57.928 39.130 23.05 5.29 0.00 2.24
4197 5693 9.708092 GGAAACTTAGACTACAGACTGTTAAAT 57.292 33.333 14.50 1.07 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 8.154649 AGAAACGAGTCAAATTTGAACTACAT 57.845 30.769 22.07 8.23 39.21 2.29
55 56 4.327680 AGGTATCTTGAGAAACAGCCAAC 58.672 43.478 0.00 0.00 0.00 3.77
71 72 7.715265 TGCATTTTCGATCTTTCTAGGTATC 57.285 36.000 0.00 0.00 0.00 2.24
120 121 7.430992 AATTTTCACTTAAGTTAGACGACCC 57.569 36.000 5.07 0.00 0.00 4.46
253 255 2.358615 GGTGATCCGTGTGCTGCA 60.359 61.111 0.00 0.00 0.00 4.41
318 320 0.691413 GGGTCGAGGGAGAAAGGGAT 60.691 60.000 0.00 0.00 0.00 3.85
325 327 3.752167 GGAGGGGGTCGAGGGAGA 61.752 72.222 0.00 0.00 0.00 3.71
344 346 0.616679 TGACCTAGGGTTTCTCGGGG 60.617 60.000 14.81 0.00 35.25 5.73
368 370 2.683933 GGGAGAGGGAGACGGCAA 60.684 66.667 0.00 0.00 0.00 4.52
408 410 0.994050 TCTGGATCGAGGAGAGGGGA 60.994 60.000 4.78 0.00 0.00 4.81
418 420 0.113385 GGAGGAGGGATCTGGATCGA 59.887 60.000 4.75 0.00 38.69 3.59
784 793 2.121506 ATGTGTGGGTGGGAGGGT 60.122 61.111 0.00 0.00 0.00 4.34
819 831 2.473760 CGGCGAGGTCAGACGAGAT 61.474 63.158 0.00 0.00 44.04 2.75
966 980 1.586564 GAAGTCCAGATCGACGCCG 60.587 63.158 0.00 0.00 37.85 6.46
1019 1034 1.227645 GATGCGAGCACCATAGCCA 60.228 57.895 0.00 0.00 34.23 4.75
1023 1038 2.421314 CCCGATGCGAGCACCATA 59.579 61.111 0.00 0.00 0.00 2.74
1077 1164 2.677542 AGTCGGAGCCTATCACCATA 57.322 50.000 0.00 0.00 0.00 2.74
1166 1544 1.139058 AGAAGTCGTTGCTGAGGTTGT 59.861 47.619 0.00 0.00 0.00 3.32
1174 1556 1.179814 AGGTCGGAGAAGTCGTTGCT 61.180 55.000 0.00 0.00 39.69 3.91
1253 1635 1.429463 GAAGAACTTGCCGACGACAT 58.571 50.000 0.00 0.00 0.00 3.06
1254 1636 0.599204 GGAAGAACTTGCCGACGACA 60.599 55.000 0.00 0.00 0.00 4.35
1311 1693 3.521126 CCGATAAATCCCAGGATGAGGAT 59.479 47.826 0.00 0.00 44.55 3.24
1360 1742 1.209747 GACTCGCCCCAAACCTTAGAT 59.790 52.381 0.00 0.00 0.00 1.98
1365 1747 0.322546 GAATGACTCGCCCCAAACCT 60.323 55.000 0.00 0.00 0.00 3.50
1659 2041 5.070001 TGTGCTAGCTTCCTTACAAAATGT 58.930 37.500 17.23 0.00 0.00 2.71
1768 2459 3.753434 CGAGCACGGCAGGAGAGT 61.753 66.667 0.00 0.00 35.72 3.24
1848 3181 1.822990 AGCACAAATAGCAGCAGCAAT 59.177 42.857 3.17 0.00 45.49 3.56
1886 3219 5.752892 AGAAATAGCAGCATGTCAATCAG 57.247 39.130 0.00 0.00 39.31 2.90
1937 3270 3.362986 GCTACGGATCACAACAATATGCG 60.363 47.826 0.00 0.00 39.88 4.73
2006 3339 0.036010 CAGCCACCTTCGATCCAAGT 60.036 55.000 0.00 0.00 0.00 3.16
2009 3342 1.900351 CTCAGCCACCTTCGATCCA 59.100 57.895 0.00 0.00 0.00 3.41
2024 3357 0.251209 AGACCTCGTACCAGTGCTCA 60.251 55.000 0.00 0.00 0.00 4.26
2086 3424 2.142220 GACACCTTGTCCTCCCACA 58.858 57.895 0.00 0.00 41.37 4.17
2102 3455 4.081420 TCCTAACATTCAGAGCCAGAAGAC 60.081 45.833 0.00 0.00 0.00 3.01
2176 3529 4.802918 GCCTAAGAGCCAAACTTCACACTA 60.803 45.833 0.00 0.00 0.00 2.74
2243 3600 6.710597 AGATGACATTTTGGATCAATCAGG 57.289 37.500 0.00 0.00 0.00 3.86
2276 3633 5.923204 ACAAACATTTTAACTCCCATTGCA 58.077 33.333 0.00 0.00 0.00 4.08
2345 3702 9.135189 TCCCATTACAGAATGAAAATTCCATAG 57.865 33.333 0.00 0.00 44.59 2.23
2356 3713 5.762179 ACTTCAGTCCCATTACAGAATGA 57.238 39.130 0.00 0.00 44.59 2.57
2411 3768 0.611714 AGGGCCGTTGTATTCGTCTT 59.388 50.000 0.00 0.00 0.00 3.01
2495 3852 2.487934 CTGCTACACACTCAGCAACTT 58.512 47.619 0.00 0.00 46.55 2.66
2496 3853 2.160822 CTGCTACACACTCAGCAACT 57.839 50.000 0.00 0.00 46.55 3.16
2501 3858 2.375173 TGATGCTGCTACACACTCAG 57.625 50.000 0.00 0.00 0.00 3.35
2502 3859 2.027837 ACATGATGCTGCTACACACTCA 60.028 45.455 0.00 0.00 0.00 3.41
2503 3860 2.350804 CACATGATGCTGCTACACACTC 59.649 50.000 0.00 0.00 0.00 3.51
2504 3861 2.289882 ACACATGATGCTGCTACACACT 60.290 45.455 0.00 0.00 0.00 3.55
2505 3862 2.079158 ACACATGATGCTGCTACACAC 58.921 47.619 0.00 0.00 0.00 3.82
2506 3863 2.477845 ACACATGATGCTGCTACACA 57.522 45.000 0.00 0.00 0.00 3.72
2507 3864 5.490139 AATTACACATGATGCTGCTACAC 57.510 39.130 0.00 0.00 0.00 2.90
2508 3865 5.759763 CCTAATTACACATGATGCTGCTACA 59.240 40.000 0.00 1.34 0.00 2.74
2509 3866 5.991606 TCCTAATTACACATGATGCTGCTAC 59.008 40.000 0.00 0.00 0.00 3.58
2510 3867 6.173427 TCCTAATTACACATGATGCTGCTA 57.827 37.500 0.00 0.00 0.00 3.49
2511 3868 5.039920 TCCTAATTACACATGATGCTGCT 57.960 39.130 0.00 0.00 0.00 4.24
2512 3869 4.818546 ACTCCTAATTACACATGATGCTGC 59.181 41.667 0.00 0.00 0.00 5.25
2513 3870 6.648310 CCTACTCCTAATTACACATGATGCTG 59.352 42.308 0.00 0.00 0.00 4.41
2514 3871 6.554982 TCCTACTCCTAATTACACATGATGCT 59.445 38.462 0.00 0.00 0.00 3.79
2515 3872 6.647067 GTCCTACTCCTAATTACACATGATGC 59.353 42.308 0.00 0.00 0.00 3.91
2516 3873 7.726216 TGTCCTACTCCTAATTACACATGATG 58.274 38.462 0.00 0.00 0.00 3.07
2517 3874 7.914427 TGTCCTACTCCTAATTACACATGAT 57.086 36.000 0.00 0.00 0.00 2.45
2598 3959 2.264813 GCAATCGCAGCATCATGTTTT 58.735 42.857 0.00 0.00 38.36 2.43
3124 4520 1.891919 GAGGACACAACCGCAGCAA 60.892 57.895 0.00 0.00 34.73 3.91
3222 4618 4.963944 CTGGATCTCCTCCCGGAT 57.036 61.111 0.73 0.00 44.23 4.18
3347 4749 3.141398 CAGTTTTCAGCTGGCAGTAAGA 58.859 45.455 17.16 8.85 0.00 2.10
3349 4751 1.608590 GCAGTTTTCAGCTGGCAGTAA 59.391 47.619 17.16 5.70 34.73 2.24
3355 4757 1.952296 ACAGAAGCAGTTTTCAGCTGG 59.048 47.619 15.13 0.00 41.73 4.85
3606 5071 0.392193 CCTGCCCTGCACACTCTTAG 60.392 60.000 0.00 0.00 33.79 2.18
3783 5248 5.931146 AGACTTAGAAGCACATTGACTTCAG 59.069 40.000 19.20 13.66 43.84 3.02
3790 5271 6.815641 ACTACATGAGACTTAGAAGCACATTG 59.184 38.462 0.00 0.00 0.00 2.82
3824 5305 9.412460 AGACAAAGAAATGGATAAATGCATCTA 57.588 29.630 0.00 0.00 37.91 1.98
3826 5307 7.042925 GCAGACAAAGAAATGGATAAATGCATC 60.043 37.037 0.00 0.00 37.91 3.91
3873 5365 3.256281 GCAGCTAGCCAAGTTTCCT 57.744 52.632 12.13 0.00 37.23 3.36
4087 5583 9.357652 GACATCAAAAACATACATAAGTGCATT 57.642 29.630 0.00 0.00 0.00 3.56
4088 5584 8.522003 TGACATCAAAAACATACATAAGTGCAT 58.478 29.630 0.00 0.00 0.00 3.96


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

AutoCloner maintained by Alex Coulton.