Multiple sequence alignment - TraesCS1D01G149500

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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 TraesCS1D01G149500 chr1D 100.000 2933 0 0 1 2933 205765436 205762504 0.000000e+00 5417.0
1 TraesCS1D01G149500 chr1D 89.302 215 22 1 2196 2410 160828547 160828334 4.820000e-68 268.0
2 TraesCS1D01G149500 chr1D 100.000 29 0 0 650 678 205764747 205764719 1.000000e-03 54.7
3 TraesCS1D01G149500 chr1B 94.886 2190 93 12 3 2177 301567949 301565764 0.000000e+00 3406.0
4 TraesCS1D01G149500 chr1B 100.000 29 0 0 650 678 301567256 301567228 1.000000e-03 54.7
5 TraesCS1D01G149500 chr1A 96.820 1541 44 4 645 2181 262289764 262291303 0.000000e+00 2569.0
6 TraesCS1D01G149500 chr1A 91.150 452 32 5 160 607 262284594 262285041 8.990000e-170 606.0
7 TraesCS1D01G149500 chr1A 90.798 163 11 4 1 160 262283157 262283318 6.370000e-52 215.0
8 TraesCS1D01G149500 chr3D 92.505 507 37 1 2427 2933 416395646 416395141 0.000000e+00 725.0
9 TraesCS1D01G149500 chr3D 88.511 235 26 1 2177 2410 21575673 21575907 1.720000e-72 283.0
10 TraesCS1D01G149500 chr3D 88.085 235 26 2 2178 2410 600494585 600494351 8.010000e-71 278.0
11 TraesCS1D01G149500 chr5B 89.727 477 35 3 2457 2933 471125590 471125128 5.410000e-167 597.0
12 TraesCS1D01G149500 chr5B 88.945 398 31 5 2502 2899 78092885 78092501 2.040000e-131 479.0
13 TraesCS1D01G149500 chr3B 89.167 480 38 4 2455 2933 220789801 220790267 1.170000e-163 586.0
14 TraesCS1D01G149500 chr3B 87.660 235 24 5 2178 2410 521415178 521414947 4.820000e-68 268.0
15 TraesCS1D01G149500 chr2B 87.377 507 35 7 2427 2933 709421692 709422169 3.300000e-154 555.0
16 TraesCS1D01G149500 chr2B 89.310 449 29 7 2427 2875 37603271 37602842 1.990000e-151 545.0
17 TraesCS1D01G149500 chr2B 89.038 447 31 8 2427 2866 711998180 711998615 3.330000e-149 538.0
18 TraesCS1D01G149500 chr4B 89.333 450 34 5 2427 2875 276395002 276395438 1.190000e-153 553.0
19 TraesCS1D01G149500 chr4B 88.667 450 37 5 2427 2875 276426688 276427124 1.200000e-148 536.0
20 TraesCS1D01G149500 chr6B 89.950 398 27 3 2502 2899 621512649 621513033 4.360000e-138 501.0
21 TraesCS1D01G149500 chr6B 87.554 233 28 1 2178 2410 34216366 34216597 4.820000e-68 268.0
22 TraesCS1D01G149500 chr4A 85.010 507 47 13 2427 2923 730385230 730385717 3.400000e-134 488.0
23 TraesCS1D01G149500 chr5D 89.316 234 24 1 2178 2410 247754467 247754700 2.860000e-75 292.0
24 TraesCS1D01G149500 chr2D 88.333 240 20 7 2178 2413 462257935 462258170 6.190000e-72 281.0
25 TraesCS1D01G149500 chr7A 87.660 235 23 6 2177 2410 299306008 299305779 4.820000e-68 268.0
26 TraesCS1D01G149500 chr4D 87.179 234 28 2 2178 2410 172272105 172272337 6.230000e-67 265.0


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 TraesCS1D01G149500 chr1D 205762504 205765436 2932 True 2735.85 5417 100.000 1 2933 2 chr1D.!!$R2 2932
1 TraesCS1D01G149500 chr1B 301565764 301567949 2185 True 1730.35 3406 97.443 3 2177 2 chr1B.!!$R1 2174
2 TraesCS1D01G149500 chr1A 262289764 262291303 1539 False 2569.00 2569 96.820 645 2181 1 chr1A.!!$F1 1536
3 TraesCS1D01G149500 chr1A 262283157 262285041 1884 False 410.50 606 90.974 1 607 2 chr1A.!!$F2 606
4 TraesCS1D01G149500 chr3D 416395141 416395646 505 True 725.00 725 92.505 2427 2933 1 chr3D.!!$R1 506

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
292 1574 0.036164 TGTAACCTGCCATCGCAAGT 59.964 50.0 0.0 0.0 46.66 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2022 3314 0.179225 GTACGCGGACTTGCAACATG 60.179 55.0 15.95 0.0 34.15 3.21 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
175 1455 5.450818 TTCCCTATACAGAGGTTTTGCAT 57.549 39.130 0.00 0.00 34.45 3.96
212 1494 2.002586 GAAGCATATCACTGCACACGT 58.997 47.619 0.00 0.00 44.77 4.49
292 1574 0.036164 TGTAACCTGCCATCGCAAGT 59.964 50.000 0.00 0.00 46.66 3.16
338 1620 5.048013 TGTGATGTCTGATACGTCTCAAACT 60.048 40.000 8.62 0.00 42.01 2.66
342 1624 8.251026 TGATGTCTGATACGTCTCAAACTTATT 58.749 33.333 8.62 0.00 43.47 1.40
446 1729 8.058847 TCTAACATATTAAGCCAATTCCAAGGT 58.941 33.333 0.00 0.00 0.00 3.50
447 1730 7.494922 AACATATTAAGCCAATTCCAAGGTT 57.505 32.000 0.00 0.00 0.00 3.50
449 1732 4.718940 ATTAAGCCAATTCCAAGGTTCG 57.281 40.909 0.00 0.00 0.00 3.95
459 1742 6.215845 CAATTCCAAGGTTCGATTTCTGTTT 58.784 36.000 0.00 0.00 0.00 2.83
506 1790 3.529533 TGTTCTCAAACGGACCGTAAAA 58.470 40.909 22.06 2.18 39.99 1.52
542 1826 9.921637 TTTTCAGATTGTAATGGACCATAAAAC 57.078 29.630 7.59 7.43 0.00 2.43
567 1854 8.410912 ACTTTAGGGTTTTTCAGATTGTACAAC 58.589 33.333 11.22 5.31 0.00 3.32
925 2215 3.181480 CCTTGGAATGGACACGTGTTTTT 60.181 43.478 24.26 16.07 31.60 1.94
946 2236 0.951040 CACTTTCTCAGCCACCGACC 60.951 60.000 0.00 0.00 0.00 4.79
1452 2742 1.372623 AAGAACGGACGAACGCCTC 60.373 57.895 0.00 0.00 37.37 4.70
1505 2795 1.457009 GCCGCTAGGTACCTCCAGAG 61.457 65.000 20.32 13.02 40.50 3.35
1605 2895 0.325296 TGCTGGACTCCGGGAACTAT 60.325 55.000 0.00 0.00 0.00 2.12
1659 2949 1.472728 GCGTTGTCCAAGATACGGGAT 60.473 52.381 0.00 0.00 35.25 3.85
1685 2975 4.101448 GCGGTGCATGGAGGAGGT 62.101 66.667 0.00 0.00 0.00 3.85
1955 3245 4.737765 GCTGCGTTTCAACAAACATTCTTA 59.262 37.500 0.00 0.00 41.94 2.10
2022 3314 2.740981 CTCCATGACAAACAGAGCTCAC 59.259 50.000 17.77 0.00 0.00 3.51
2029 3321 2.033801 ACAAACAGAGCTCACATGTTGC 59.966 45.455 17.77 11.46 37.24 4.17
2115 3411 7.227049 TCTCTTTTGAAAAACACCCCATATC 57.773 36.000 0.00 0.00 0.00 1.63
2184 3480 3.681705 CACAGCGGTGCTTAACATG 57.318 52.632 15.82 0.00 36.40 3.21
2185 3481 0.874390 CACAGCGGTGCTTAACATGT 59.126 50.000 15.82 0.00 36.40 3.21
2186 3482 1.266718 CACAGCGGTGCTTAACATGTT 59.733 47.619 16.68 16.68 36.40 2.71
2187 3483 1.953686 ACAGCGGTGCTTAACATGTTT 59.046 42.857 17.78 0.95 36.40 2.83
2188 3484 3.058570 CACAGCGGTGCTTAACATGTTTA 60.059 43.478 17.78 6.77 36.40 2.01
2189 3485 3.566322 ACAGCGGTGCTTAACATGTTTAA 59.434 39.130 17.78 8.15 36.40 1.52
2190 3486 3.911964 CAGCGGTGCTTAACATGTTTAAC 59.088 43.478 17.78 9.79 36.40 2.01
2191 3487 3.057806 AGCGGTGCTTAACATGTTTAACC 60.058 43.478 17.78 16.65 33.89 2.85
2192 3488 3.304794 GCGGTGCTTAACATGTTTAACCA 60.305 43.478 17.78 6.61 0.00 3.67
2193 3489 4.472286 CGGTGCTTAACATGTTTAACCAG 58.528 43.478 17.78 11.15 0.00 4.00
2194 3490 4.214545 CGGTGCTTAACATGTTTAACCAGA 59.785 41.667 17.78 0.00 0.00 3.86
2195 3491 5.278071 CGGTGCTTAACATGTTTAACCAGAA 60.278 40.000 17.78 1.88 0.00 3.02
2196 3492 6.569610 CGGTGCTTAACATGTTTAACCAGAAT 60.570 38.462 17.78 0.00 0.00 2.40
2197 3493 7.151976 GGTGCTTAACATGTTTAACCAGAATT 58.848 34.615 17.78 0.00 0.00 2.17
2198 3494 7.655732 GGTGCTTAACATGTTTAACCAGAATTT 59.344 33.333 17.78 0.00 0.00 1.82
2199 3495 9.040939 GTGCTTAACATGTTTAACCAGAATTTT 57.959 29.630 17.78 0.00 0.00 1.82
2200 3496 9.039870 TGCTTAACATGTTTAACCAGAATTTTG 57.960 29.630 17.78 0.00 0.00 2.44
2201 3497 9.255304 GCTTAACATGTTTAACCAGAATTTTGA 57.745 29.630 17.78 0.00 0.00 2.69
2304 3600 9.725019 TCTTAATCAATAATGCATTATCCGTCT 57.275 29.630 27.77 12.52 32.08 4.18
2308 3604 8.627208 ATCAATAATGCATTATCCGTCTTTCT 57.373 30.769 27.77 9.91 32.08 2.52
2309 3605 7.864686 TCAATAATGCATTATCCGTCTTTCTG 58.135 34.615 27.77 19.37 32.08 3.02
2310 3606 7.498900 TCAATAATGCATTATCCGTCTTTCTGT 59.501 33.333 27.77 8.79 32.08 3.41
2311 3607 5.741388 AATGCATTATCCGTCTTTCTGTC 57.259 39.130 11.02 0.00 0.00 3.51
2312 3608 4.200838 TGCATTATCCGTCTTTCTGTCA 57.799 40.909 0.00 0.00 0.00 3.58
2313 3609 4.769688 TGCATTATCCGTCTTTCTGTCAT 58.230 39.130 0.00 0.00 0.00 3.06
2314 3610 5.912892 TGCATTATCCGTCTTTCTGTCATA 58.087 37.500 0.00 0.00 0.00 2.15
2315 3611 6.524734 TGCATTATCCGTCTTTCTGTCATAT 58.475 36.000 0.00 0.00 0.00 1.78
2316 3612 6.646653 TGCATTATCCGTCTTTCTGTCATATC 59.353 38.462 0.00 0.00 0.00 1.63
2317 3613 6.183360 GCATTATCCGTCTTTCTGTCATATCG 60.183 42.308 0.00 0.00 0.00 2.92
2318 3614 3.710326 TCCGTCTTTCTGTCATATCGG 57.290 47.619 0.00 0.00 38.36 4.18
2319 3615 3.021695 TCCGTCTTTCTGTCATATCGGT 58.978 45.455 0.00 0.00 38.21 4.69
2320 3616 4.201657 TCCGTCTTTCTGTCATATCGGTA 58.798 43.478 0.00 0.00 38.21 4.02
2321 3617 4.275196 TCCGTCTTTCTGTCATATCGGTAG 59.725 45.833 0.00 0.00 38.21 3.18
2322 3618 4.036498 CCGTCTTTCTGTCATATCGGTAGT 59.964 45.833 0.00 0.00 33.39 2.73
2323 3619 4.970611 CGTCTTTCTGTCATATCGGTAGTG 59.029 45.833 0.00 0.00 0.00 2.74
2324 3620 5.220796 CGTCTTTCTGTCATATCGGTAGTGA 60.221 44.000 0.00 0.00 0.00 3.41
2325 3621 6.513556 CGTCTTTCTGTCATATCGGTAGTGAT 60.514 42.308 0.00 0.00 0.00 3.06
2326 3622 7.203910 GTCTTTCTGTCATATCGGTAGTGATT 58.796 38.462 0.00 0.00 0.00 2.57
2327 3623 7.380065 GTCTTTCTGTCATATCGGTAGTGATTC 59.620 40.741 0.00 0.00 0.00 2.52
2328 3624 5.358298 TCTGTCATATCGGTAGTGATTCG 57.642 43.478 0.00 0.00 0.00 3.34
2329 3625 4.215613 TCTGTCATATCGGTAGTGATTCGG 59.784 45.833 0.00 0.00 0.00 4.30
2330 3626 4.139038 TGTCATATCGGTAGTGATTCGGA 58.861 43.478 0.00 0.00 0.00 4.55
2331 3627 4.765339 TGTCATATCGGTAGTGATTCGGAT 59.235 41.667 0.00 0.00 0.00 4.18
2332 3628 5.243060 TGTCATATCGGTAGTGATTCGGATT 59.757 40.000 0.00 0.00 0.00 3.01
2333 3629 5.573282 GTCATATCGGTAGTGATTCGGATTG 59.427 44.000 0.00 0.00 0.00 2.67
2334 3630 2.882927 TCGGTAGTGATTCGGATTGG 57.117 50.000 0.00 0.00 0.00 3.16
2335 3631 1.411246 TCGGTAGTGATTCGGATTGGG 59.589 52.381 0.00 0.00 0.00 4.12
2336 3632 1.540363 CGGTAGTGATTCGGATTGGGG 60.540 57.143 0.00 0.00 0.00 4.96
2337 3633 1.766496 GGTAGTGATTCGGATTGGGGA 59.234 52.381 0.00 0.00 0.00 4.81
2338 3634 2.372172 GGTAGTGATTCGGATTGGGGAT 59.628 50.000 0.00 0.00 0.00 3.85
2339 3635 2.645838 AGTGATTCGGATTGGGGATG 57.354 50.000 0.00 0.00 0.00 3.51
2340 3636 2.126882 AGTGATTCGGATTGGGGATGA 58.873 47.619 0.00 0.00 0.00 2.92
2341 3637 2.509548 AGTGATTCGGATTGGGGATGAA 59.490 45.455 0.00 0.00 0.00 2.57
2342 3638 2.618709 GTGATTCGGATTGGGGATGAAC 59.381 50.000 0.00 0.00 0.00 3.18
2343 3639 2.240921 TGATTCGGATTGGGGATGAACA 59.759 45.455 0.00 0.00 0.00 3.18
2344 3640 2.122783 TTCGGATTGGGGATGAACAC 57.877 50.000 0.00 0.00 0.00 3.32
2345 3641 0.254747 TCGGATTGGGGATGAACACC 59.745 55.000 0.00 0.00 43.64 4.16
2346 3642 0.255890 CGGATTGGGGATGAACACCT 59.744 55.000 0.00 0.00 43.74 4.00
2347 3643 1.747206 CGGATTGGGGATGAACACCTC 60.747 57.143 0.00 0.00 43.74 3.85
2348 3644 1.284785 GGATTGGGGATGAACACCTCA 59.715 52.381 0.00 0.00 43.74 3.86
2349 3645 2.648059 GATTGGGGATGAACACCTCAG 58.352 52.381 0.00 0.00 43.74 3.35
2350 3646 0.038166 TTGGGGATGAACACCTCAGC 59.962 55.000 0.00 0.00 43.74 4.26
2351 3647 1.133181 TGGGGATGAACACCTCAGCA 61.133 55.000 0.00 0.00 42.55 4.41
2352 3648 0.038166 GGGGATGAACACCTCAGCAA 59.962 55.000 0.00 0.00 42.55 3.91
2353 3649 1.547675 GGGGATGAACACCTCAGCAAA 60.548 52.381 0.00 0.00 42.55 3.68
2354 3650 2.238521 GGGATGAACACCTCAGCAAAA 58.761 47.619 0.00 0.00 42.55 2.44
2355 3651 2.827921 GGGATGAACACCTCAGCAAAAT 59.172 45.455 0.00 0.00 42.55 1.82
2356 3652 3.119352 GGGATGAACACCTCAGCAAAATC 60.119 47.826 0.00 0.00 42.55 2.17
2357 3653 3.507233 GGATGAACACCTCAGCAAAATCA 59.493 43.478 0.00 0.00 42.55 2.57
2358 3654 4.022068 GGATGAACACCTCAGCAAAATCAA 60.022 41.667 0.00 0.00 42.55 2.57
2359 3655 4.572985 TGAACACCTCAGCAAAATCAAG 57.427 40.909 0.00 0.00 0.00 3.02
2360 3656 4.206375 TGAACACCTCAGCAAAATCAAGA 58.794 39.130 0.00 0.00 0.00 3.02
2361 3657 4.828939 TGAACACCTCAGCAAAATCAAGAT 59.171 37.500 0.00 0.00 0.00 2.40
2362 3658 5.302568 TGAACACCTCAGCAAAATCAAGATT 59.697 36.000 0.00 0.00 0.00 2.40
2363 3659 6.489700 TGAACACCTCAGCAAAATCAAGATTA 59.510 34.615 0.00 0.00 0.00 1.75
2364 3660 6.506500 ACACCTCAGCAAAATCAAGATTAG 57.493 37.500 0.00 0.00 0.00 1.73
2365 3661 5.105997 ACACCTCAGCAAAATCAAGATTAGC 60.106 40.000 10.41 10.41 34.30 3.09
2366 3662 4.400567 ACCTCAGCAAAATCAAGATTAGCC 59.599 41.667 13.26 0.00 34.50 3.93
2367 3663 4.400251 CCTCAGCAAAATCAAGATTAGCCA 59.600 41.667 13.26 4.16 34.50 4.75
2368 3664 5.068723 CCTCAGCAAAATCAAGATTAGCCAT 59.931 40.000 13.26 0.00 34.50 4.40
2369 3665 5.898174 TCAGCAAAATCAAGATTAGCCATG 58.102 37.500 13.26 8.63 34.50 3.66
2370 3666 5.653330 TCAGCAAAATCAAGATTAGCCATGA 59.347 36.000 13.26 10.15 34.50 3.07
2371 3667 6.153170 TCAGCAAAATCAAGATTAGCCATGAA 59.847 34.615 13.26 0.00 34.50 2.57
2372 3668 6.814644 CAGCAAAATCAAGATTAGCCATGAAA 59.185 34.615 13.26 0.00 34.50 2.69
2373 3669 7.494625 CAGCAAAATCAAGATTAGCCATGAAAT 59.505 33.333 13.26 0.00 34.50 2.17
2374 3670 8.044908 AGCAAAATCAAGATTAGCCATGAAATT 58.955 29.630 13.26 0.00 34.50 1.82
2375 3671 8.120465 GCAAAATCAAGATTAGCCATGAAATTG 58.880 33.333 0.00 0.00 0.00 2.32
2376 3672 9.373603 CAAAATCAAGATTAGCCATGAAATTGA 57.626 29.630 0.00 0.00 0.00 2.57
2377 3673 9.947433 AAAATCAAGATTAGCCATGAAATTGAA 57.053 25.926 0.00 0.00 0.00 2.69
2378 3674 9.595823 AAATCAAGATTAGCCATGAAATTGAAG 57.404 29.630 0.00 0.00 0.00 3.02
2379 3675 7.943079 TCAAGATTAGCCATGAAATTGAAGA 57.057 32.000 0.00 0.00 0.00 2.87
2380 3676 8.529424 TCAAGATTAGCCATGAAATTGAAGAT 57.471 30.769 0.00 0.00 0.00 2.40
2381 3677 9.631257 TCAAGATTAGCCATGAAATTGAAGATA 57.369 29.630 0.00 0.00 0.00 1.98
2388 3684 8.205131 AGCCATGAAATTGAAGATAAATTTGC 57.795 30.769 0.00 0.00 37.35 3.68
2389 3685 8.044908 AGCCATGAAATTGAAGATAAATTTGCT 58.955 29.630 0.00 0.00 37.35 3.91
2390 3686 9.316730 GCCATGAAATTGAAGATAAATTTGCTA 57.683 29.630 0.00 0.00 37.35 3.49
2398 3694 7.849804 TGAAGATAAATTTGCTAGAGACACC 57.150 36.000 0.00 0.00 0.00 4.16
2399 3695 7.624549 TGAAGATAAATTTGCTAGAGACACCT 58.375 34.615 0.00 0.00 0.00 4.00
2400 3696 8.758829 TGAAGATAAATTTGCTAGAGACACCTA 58.241 33.333 0.00 0.00 0.00 3.08
2401 3697 9.601217 GAAGATAAATTTGCTAGAGACACCTAA 57.399 33.333 0.00 0.00 0.00 2.69
2412 3708 9.642343 TGCTAGAGACACCTAATAAATAAGAGA 57.358 33.333 0.00 0.00 0.00 3.10
2453 3749 5.415701 ACAAGTGCCAAAATACCACTATGAG 59.584 40.000 0.00 0.00 38.77 2.90
2459 3755 5.417580 GCCAAAATACCACTATGAGAAACCA 59.582 40.000 0.00 0.00 0.00 3.67
2501 3797 7.123547 ACTCAAGTTCAGGTTTTTCATACCAAA 59.876 33.333 0.00 0.00 38.16 3.28
2507 3803 7.531857 TCAGGTTTTTCATACCAAAATAGCA 57.468 32.000 0.00 0.00 38.16 3.49
2511 3807 8.520351 AGGTTTTTCATACCAAAATAGCACTAC 58.480 33.333 0.00 0.00 38.16 2.73
2514 3810 4.124238 TCATACCAAAATAGCACTACCGC 58.876 43.478 0.00 0.00 0.00 5.68
2528 3824 3.370978 CACTACCGCCTATTGTCAAACAG 59.629 47.826 0.00 0.00 0.00 3.16
2530 3826 3.350219 ACCGCCTATTGTCAAACAGAT 57.650 42.857 0.00 0.00 0.00 2.90
2552 3848 2.894765 TCTGTTAGTCAACGGTGGATGA 59.105 45.455 0.00 0.00 41.15 2.92
2560 3856 0.670546 AACGGTGGATGAAGCTGTCG 60.671 55.000 0.00 0.00 0.00 4.35
2597 3893 4.043561 TGCCAAAAGTACCCTTCATCCTAA 59.956 41.667 0.00 0.00 0.00 2.69
2602 3898 5.941555 AAGTACCCTTCATCCTAACTCTG 57.058 43.478 0.00 0.00 0.00 3.35
2654 3950 2.851195 CTTGTACTGGTCAAAGTGGCT 58.149 47.619 0.00 0.00 0.00 4.75
2739 4035 4.830765 GCCGCCGCTGTATCCACA 62.831 66.667 0.00 0.00 0.00 4.17
2741 4037 2.184322 CGCCGCTGTATCCACACT 59.816 61.111 0.00 0.00 0.00 3.55
2845 4141 3.160047 CAGCTCCTCCCCGCATCT 61.160 66.667 0.00 0.00 0.00 2.90
2875 4171 3.068881 CCCCACTGTGGATGACGT 58.931 61.111 27.94 0.00 40.96 4.34
2881 4177 1.068816 CACTGTGGATGACGTCGTGTA 60.069 52.381 16.54 0.30 0.00 2.90
2892 4188 1.448013 GTCGTGTAGCCTCCTTGCC 60.448 63.158 0.00 0.00 0.00 4.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 65 7.388460 TCATGTGCAAAACATCACATACATA 57.612 32.000 7.43 0.00 45.56 2.29
98 102 6.183360 TGCAATGATACATTACATGCACACAT 60.183 34.615 0.00 0.00 36.79 3.21
150 154 5.191722 TGCAAAACCTCTGTATAGGGAATCT 59.808 40.000 0.00 0.00 41.32 2.40
175 1455 5.809719 TGCTTCATCAACACGCATATTTA 57.190 34.783 0.00 0.00 0.00 1.40
183 1464 4.784394 GCAGTGATATGCTTCATCAACACG 60.784 45.833 0.00 0.00 43.07 4.49
212 1494 7.441890 TCACACACAGTTAGACTTTTGAAAA 57.558 32.000 0.00 0.00 0.00 2.29
311 1593 4.399303 TGAGACGTATCAGACATCACACAT 59.601 41.667 9.19 0.00 0.00 3.21
474 1757 3.653344 GTTTGAGAACATTCAAAGCCCC 58.347 45.455 1.74 0.00 45.00 5.80
542 1826 8.630037 AGTTGTACAATCTGAAAAACCCTAAAG 58.370 33.333 12.26 0.00 0.00 1.85
567 1854 4.692625 CGCCTCCAGAATACATTTCCATAG 59.307 45.833 0.00 0.00 0.00 2.23
576 1863 0.616395 TGGTCCGCCTCCAGAATACA 60.616 55.000 0.00 0.00 35.27 2.29
582 1869 0.251916 TGTTTATGGTCCGCCTCCAG 59.748 55.000 0.00 0.00 38.42 3.86
658 1948 0.608640 AAGCAACGAATCTCCCGTCT 59.391 50.000 0.00 0.00 39.57 4.18
742 2032 0.321996 AAGACGGGACAGAAAGGCTC 59.678 55.000 0.00 0.00 0.00 4.70
777 2067 3.548214 GGAAAGACGCAGGTGACTTTTTC 60.548 47.826 10.60 4.82 40.21 2.29
925 2215 1.597854 CGGTGGCTGAGAAAGTGCA 60.598 57.895 0.00 0.00 0.00 4.57
946 2236 3.209410 GTCACATTTATGGGCAGAGAGG 58.791 50.000 0.00 0.00 0.00 3.69
1432 2722 2.170273 GCGTTCGTCCGTTCTTGC 59.830 61.111 0.00 0.00 0.00 4.01
1505 2795 0.798776 CAGGAAGAACACCATGTCGC 59.201 55.000 0.00 0.00 0.00 5.19
1621 2911 0.662085 GCCTCCTCGTAGAACCGTAG 59.338 60.000 0.00 0.00 34.09 3.51
1701 2991 4.147449 CGCACTCTCCATCCGGCA 62.147 66.667 0.00 0.00 0.00 5.69
1955 3245 3.474806 GCATGCTGCGTTACGACT 58.525 55.556 11.37 0.00 31.71 4.18
2022 3314 0.179225 GTACGCGGACTTGCAACATG 60.179 55.000 15.95 0.00 34.15 3.21
2029 3321 1.640428 ATGTCATGTACGCGGACTTG 58.360 50.000 26.80 26.80 32.84 3.16
2143 3439 8.030106 TGTGTGTGAAGTATGATGTAACGAATA 58.970 33.333 0.00 0.00 0.00 1.75
2254 3550 9.678260 AGATTGCATCTTAGATAGTGTTTTTCT 57.322 29.630 0.00 0.00 35.76 2.52
2278 3574 9.725019 AGACGGATAATGCATTATTGATTAAGA 57.275 29.630 28.16 3.69 33.37 2.10
2282 3578 9.071276 AGAAAGACGGATAATGCATTATTGATT 57.929 29.630 28.16 19.80 33.37 2.57
2283 3579 8.509690 CAGAAAGACGGATAATGCATTATTGAT 58.490 33.333 28.16 17.96 33.37 2.57
2284 3580 7.498900 ACAGAAAGACGGATAATGCATTATTGA 59.501 33.333 28.16 7.70 33.37 2.57
2285 3581 7.642669 ACAGAAAGACGGATAATGCATTATTG 58.357 34.615 28.16 24.49 33.37 1.90
2286 3582 7.498900 TGACAGAAAGACGGATAATGCATTATT 59.501 33.333 28.16 15.82 33.37 1.40
2287 3583 6.992123 TGACAGAAAGACGGATAATGCATTAT 59.008 34.615 27.95 27.95 35.77 1.28
2288 3584 6.345298 TGACAGAAAGACGGATAATGCATTA 58.655 36.000 20.95 20.95 0.00 1.90
2289 3585 5.185454 TGACAGAAAGACGGATAATGCATT 58.815 37.500 17.56 17.56 0.00 3.56
2290 3586 4.769688 TGACAGAAAGACGGATAATGCAT 58.230 39.130 0.00 0.00 0.00 3.96
2291 3587 4.200838 TGACAGAAAGACGGATAATGCA 57.799 40.909 0.00 0.00 0.00 3.96
2292 3588 6.183360 CGATATGACAGAAAGACGGATAATGC 60.183 42.308 0.00 0.00 0.00 3.56
2293 3589 6.309009 CCGATATGACAGAAAGACGGATAATG 59.691 42.308 0.00 0.00 41.30 1.90
2294 3590 6.015350 ACCGATATGACAGAAAGACGGATAAT 60.015 38.462 0.00 0.00 41.30 1.28
2295 3591 5.301045 ACCGATATGACAGAAAGACGGATAA 59.699 40.000 0.00 0.00 41.30 1.75
2296 3592 4.825634 ACCGATATGACAGAAAGACGGATA 59.174 41.667 0.00 0.00 41.30 2.59
2297 3593 3.637229 ACCGATATGACAGAAAGACGGAT 59.363 43.478 0.00 0.00 41.30 4.18
2298 3594 3.021695 ACCGATATGACAGAAAGACGGA 58.978 45.455 0.00 0.00 41.30 4.69
2299 3595 3.438297 ACCGATATGACAGAAAGACGG 57.562 47.619 0.00 0.00 43.79 4.79
2300 3596 4.970611 CACTACCGATATGACAGAAAGACG 59.029 45.833 0.00 0.00 0.00 4.18
2301 3597 6.132791 TCACTACCGATATGACAGAAAGAC 57.867 41.667 0.00 0.00 0.00 3.01
2302 3598 6.961360 ATCACTACCGATATGACAGAAAGA 57.039 37.500 0.00 0.00 0.00 2.52
2303 3599 6.360947 CGAATCACTACCGATATGACAGAAAG 59.639 42.308 0.00 0.00 0.00 2.62
2304 3600 6.206498 CGAATCACTACCGATATGACAGAAA 58.794 40.000 0.00 0.00 0.00 2.52
2305 3601 5.278315 CCGAATCACTACCGATATGACAGAA 60.278 44.000 0.00 0.00 0.00 3.02
2306 3602 4.215613 CCGAATCACTACCGATATGACAGA 59.784 45.833 0.00 0.00 0.00 3.41
2307 3603 4.215613 TCCGAATCACTACCGATATGACAG 59.784 45.833 0.00 0.00 0.00 3.51
2308 3604 4.139038 TCCGAATCACTACCGATATGACA 58.861 43.478 0.00 0.00 0.00 3.58
2309 3605 4.761235 TCCGAATCACTACCGATATGAC 57.239 45.455 0.00 0.00 0.00 3.06
2310 3606 5.336451 CCAATCCGAATCACTACCGATATGA 60.336 44.000 0.00 0.00 0.00 2.15
2311 3607 4.864806 CCAATCCGAATCACTACCGATATG 59.135 45.833 0.00 0.00 0.00 1.78
2312 3608 4.081642 CCCAATCCGAATCACTACCGATAT 60.082 45.833 0.00 0.00 0.00 1.63
2313 3609 3.257375 CCCAATCCGAATCACTACCGATA 59.743 47.826 0.00 0.00 0.00 2.92
2314 3610 2.037251 CCCAATCCGAATCACTACCGAT 59.963 50.000 0.00 0.00 0.00 4.18
2315 3611 1.411246 CCCAATCCGAATCACTACCGA 59.589 52.381 0.00 0.00 0.00 4.69
2316 3612 1.540363 CCCCAATCCGAATCACTACCG 60.540 57.143 0.00 0.00 0.00 4.02
2317 3613 1.766496 TCCCCAATCCGAATCACTACC 59.234 52.381 0.00 0.00 0.00 3.18
2318 3614 3.071023 TCATCCCCAATCCGAATCACTAC 59.929 47.826 0.00 0.00 0.00 2.73
2319 3615 3.313791 TCATCCCCAATCCGAATCACTA 58.686 45.455 0.00 0.00 0.00 2.74
2320 3616 2.126882 TCATCCCCAATCCGAATCACT 58.873 47.619 0.00 0.00 0.00 3.41
2321 3617 2.618709 GTTCATCCCCAATCCGAATCAC 59.381 50.000 0.00 0.00 0.00 3.06
2322 3618 2.240921 TGTTCATCCCCAATCCGAATCA 59.759 45.455 0.00 0.00 0.00 2.57
2323 3619 2.618709 GTGTTCATCCCCAATCCGAATC 59.381 50.000 0.00 0.00 0.00 2.52
2324 3620 2.654863 GTGTTCATCCCCAATCCGAAT 58.345 47.619 0.00 0.00 0.00 3.34
2325 3621 1.340600 GGTGTTCATCCCCAATCCGAA 60.341 52.381 0.00 0.00 0.00 4.30
2326 3622 0.254747 GGTGTTCATCCCCAATCCGA 59.745 55.000 0.00 0.00 0.00 4.55
2327 3623 0.255890 AGGTGTTCATCCCCAATCCG 59.744 55.000 0.00 0.00 0.00 4.18
2328 3624 1.284785 TGAGGTGTTCATCCCCAATCC 59.715 52.381 0.00 0.00 0.00 3.01
2329 3625 2.648059 CTGAGGTGTTCATCCCCAATC 58.352 52.381 0.00 0.00 34.68 2.67
2330 3626 1.341383 GCTGAGGTGTTCATCCCCAAT 60.341 52.381 0.00 0.00 34.68 3.16
2331 3627 0.038166 GCTGAGGTGTTCATCCCCAA 59.962 55.000 0.00 0.00 34.68 4.12
2332 3628 1.133181 TGCTGAGGTGTTCATCCCCA 61.133 55.000 0.00 0.00 34.68 4.96
2333 3629 0.038166 TTGCTGAGGTGTTCATCCCC 59.962 55.000 0.00 0.00 34.68 4.81
2334 3630 1.909700 TTTGCTGAGGTGTTCATCCC 58.090 50.000 0.00 0.00 34.68 3.85
2335 3631 3.507233 TGATTTTGCTGAGGTGTTCATCC 59.493 43.478 0.00 0.00 34.68 3.51
2336 3632 4.771590 TGATTTTGCTGAGGTGTTCATC 57.228 40.909 0.00 0.00 34.68 2.92
2337 3633 4.828939 TCTTGATTTTGCTGAGGTGTTCAT 59.171 37.500 0.00 0.00 34.68 2.57
2338 3634 4.206375 TCTTGATTTTGCTGAGGTGTTCA 58.794 39.130 0.00 0.00 0.00 3.18
2339 3635 4.836125 TCTTGATTTTGCTGAGGTGTTC 57.164 40.909 0.00 0.00 0.00 3.18
2340 3636 5.796424 AATCTTGATTTTGCTGAGGTGTT 57.204 34.783 0.00 0.00 0.00 3.32
2341 3637 5.105997 GCTAATCTTGATTTTGCTGAGGTGT 60.106 40.000 0.95 0.00 0.00 4.16
2342 3638 5.338365 GCTAATCTTGATTTTGCTGAGGTG 58.662 41.667 0.95 0.00 0.00 4.00
2343 3639 4.400567 GGCTAATCTTGATTTTGCTGAGGT 59.599 41.667 15.11 0.00 0.00 3.85
2344 3640 4.400251 TGGCTAATCTTGATTTTGCTGAGG 59.600 41.667 15.11 0.00 0.00 3.86
2345 3641 5.571784 TGGCTAATCTTGATTTTGCTGAG 57.428 39.130 15.11 3.85 0.00 3.35
2346 3642 5.653330 TCATGGCTAATCTTGATTTTGCTGA 59.347 36.000 15.11 11.34 0.00 4.26
2347 3643 5.898174 TCATGGCTAATCTTGATTTTGCTG 58.102 37.500 15.11 9.97 0.00 4.41
2348 3644 6.534475 TTCATGGCTAATCTTGATTTTGCT 57.466 33.333 15.11 1.73 0.00 3.91
2349 3645 7.781548 ATTTCATGGCTAATCTTGATTTTGC 57.218 32.000 0.95 6.78 0.00 3.68
2350 3646 9.373603 TCAATTTCATGGCTAATCTTGATTTTG 57.626 29.630 0.95 0.00 0.00 2.44
2351 3647 9.947433 TTCAATTTCATGGCTAATCTTGATTTT 57.053 25.926 0.95 0.00 0.00 1.82
2352 3648 9.595823 CTTCAATTTCATGGCTAATCTTGATTT 57.404 29.630 0.95 0.00 0.00 2.17
2353 3649 8.974238 TCTTCAATTTCATGGCTAATCTTGATT 58.026 29.630 0.00 1.35 0.00 2.57
2354 3650 8.529424 TCTTCAATTTCATGGCTAATCTTGAT 57.471 30.769 0.00 0.00 0.00 2.57
2355 3651 7.943079 TCTTCAATTTCATGGCTAATCTTGA 57.057 32.000 0.00 0.00 0.00 3.02
2362 3658 9.316730 GCAAATTTATCTTCAATTTCATGGCTA 57.683 29.630 0.00 0.00 32.57 3.93
2363 3659 8.044908 AGCAAATTTATCTTCAATTTCATGGCT 58.955 29.630 0.00 0.00 32.57 4.75
2364 3660 8.205131 AGCAAATTTATCTTCAATTTCATGGC 57.795 30.769 0.00 0.00 32.57 4.40
2372 3668 8.897752 GGTGTCTCTAGCAAATTTATCTTCAAT 58.102 33.333 0.00 0.00 0.00 2.57
2373 3669 8.103305 AGGTGTCTCTAGCAAATTTATCTTCAA 58.897 33.333 0.00 0.00 0.00 2.69
2374 3670 7.624549 AGGTGTCTCTAGCAAATTTATCTTCA 58.375 34.615 0.00 0.00 0.00 3.02
2375 3671 9.601217 TTAGGTGTCTCTAGCAAATTTATCTTC 57.399 33.333 0.00 0.00 0.00 2.87
2386 3682 9.642343 TCTCTTATTTATTAGGTGTCTCTAGCA 57.358 33.333 0.00 0.00 0.00 3.49
2402 3698 9.998106 GGTATTGTGGCTATTCTCTCTTATTTA 57.002 33.333 0.00 0.00 0.00 1.40
2403 3699 8.494433 TGGTATTGTGGCTATTCTCTCTTATTT 58.506 33.333 0.00 0.00 0.00 1.40
2404 3700 7.934120 GTGGTATTGTGGCTATTCTCTCTTATT 59.066 37.037 0.00 0.00 0.00 1.40
2405 3701 7.071196 TGTGGTATTGTGGCTATTCTCTCTTAT 59.929 37.037 0.00 0.00 0.00 1.73
2406 3702 6.382859 TGTGGTATTGTGGCTATTCTCTCTTA 59.617 38.462 0.00 0.00 0.00 2.10
2407 3703 5.189736 TGTGGTATTGTGGCTATTCTCTCTT 59.810 40.000 0.00 0.00 0.00 2.85
2408 3704 4.716784 TGTGGTATTGTGGCTATTCTCTCT 59.283 41.667 0.00 0.00 0.00 3.10
2409 3705 5.023533 TGTGGTATTGTGGCTATTCTCTC 57.976 43.478 0.00 0.00 0.00 3.20
2410 3706 5.045578 ACTTGTGGTATTGTGGCTATTCTCT 60.046 40.000 0.00 0.00 0.00 3.10
2411 3707 5.065218 CACTTGTGGTATTGTGGCTATTCTC 59.935 44.000 0.00 0.00 0.00 2.87
2412 3708 4.943705 CACTTGTGGTATTGTGGCTATTCT 59.056 41.667 0.00 0.00 0.00 2.40
2413 3709 4.438744 GCACTTGTGGTATTGTGGCTATTC 60.439 45.833 2.81 0.00 0.00 1.75
2414 3710 3.443681 GCACTTGTGGTATTGTGGCTATT 59.556 43.478 2.81 0.00 0.00 1.73
2415 3711 3.016736 GCACTTGTGGTATTGTGGCTAT 58.983 45.455 2.81 0.00 0.00 2.97
2416 3712 2.432444 GCACTTGTGGTATTGTGGCTA 58.568 47.619 2.81 0.00 0.00 3.93
2417 3713 1.247567 GCACTTGTGGTATTGTGGCT 58.752 50.000 2.81 0.00 0.00 4.75
2418 3714 0.243636 GGCACTTGTGGTATTGTGGC 59.756 55.000 2.81 0.00 45.72 5.01
2419 3715 1.614996 TGGCACTTGTGGTATTGTGG 58.385 50.000 2.81 0.00 0.00 4.17
2420 3716 3.724508 TTTGGCACTTGTGGTATTGTG 57.275 42.857 2.81 0.00 0.00 3.33
2421 3717 4.953940 ATTTTGGCACTTGTGGTATTGT 57.046 36.364 2.81 0.00 0.00 2.71
2422 3718 5.167845 GGTATTTTGGCACTTGTGGTATTG 58.832 41.667 2.81 0.00 0.00 1.90
2423 3719 4.835615 TGGTATTTTGGCACTTGTGGTATT 59.164 37.500 2.81 0.00 0.00 1.89
2424 3720 4.219725 GTGGTATTTTGGCACTTGTGGTAT 59.780 41.667 2.81 0.00 0.00 2.73
2425 3721 3.570550 GTGGTATTTTGGCACTTGTGGTA 59.429 43.478 2.81 0.00 0.00 3.25
2453 3749 4.376146 TGCTATTTTGGCACTTTGGTTTC 58.624 39.130 0.00 0.00 34.56 2.78
2501 3797 3.386726 TGACAATAGGCGGTAGTGCTATT 59.613 43.478 0.00 0.00 29.25 1.73
2507 3803 3.259876 TCTGTTTGACAATAGGCGGTAGT 59.740 43.478 0.00 0.00 0.00 2.73
2511 3807 3.941483 AGAATCTGTTTGACAATAGGCGG 59.059 43.478 0.00 0.00 0.00 6.13
2528 3824 3.921677 TCCACCGTTGACTAACAGAATC 58.078 45.455 0.00 0.00 36.58 2.52
2530 3826 3.322541 TCATCCACCGTTGACTAACAGAA 59.677 43.478 0.00 0.00 36.58 3.02
2571 3867 4.381932 GGATGAAGGGTACTTTTGGCAATG 60.382 45.833 0.00 0.00 36.97 2.82
2572 3868 3.769300 GGATGAAGGGTACTTTTGGCAAT 59.231 43.478 0.00 0.00 36.97 3.56
2577 3873 6.595716 CAGAGTTAGGATGAAGGGTACTTTTG 59.404 42.308 0.00 0.00 36.97 2.44
2582 3878 4.202172 GCTCAGAGTTAGGATGAAGGGTAC 60.202 50.000 0.00 0.00 0.00 3.34
2654 3950 0.672401 GGCCGACGAAACAATCTCCA 60.672 55.000 0.00 0.00 0.00 3.86
2727 4023 4.560752 TGGGAACAGTGTGGATACAGCG 62.561 54.545 0.00 0.00 42.28 5.18
2741 4037 1.296392 CTCCATGTCGCTGGGAACA 59.704 57.895 0.00 0.00 36.89 3.18
2865 4161 0.801067 GGCTACACGACGTCATCCAC 60.801 60.000 17.16 0.00 0.00 4.02
2870 4166 0.892358 AAGGAGGCTACACGACGTCA 60.892 55.000 17.16 0.00 0.00 4.35
2875 4171 2.656069 GGGCAAGGAGGCTACACGA 61.656 63.158 0.00 0.00 43.56 4.35


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

AutoCloner maintained by Alex Coulton.