Multiple sequence alignment - TraesCS3B01G288500

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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 TraesCS3B01G288500 chr3B 100.000 4880 0 0 1 4880 463114313 463109434 0.000000e+00 9012.0
1 TraesCS3B01G288500 chr3B 95.215 209 10 0 1232 1440 464610213 464610421 1.010000e-86 331.0
2 TraesCS3B01G288500 chr3B 100.000 43 0 0 4760 4802 463109498 463109456 4.050000e-11 80.5
3 TraesCS3B01G288500 chr3B 100.000 43 0 0 4816 4858 463109554 463109512 4.050000e-11 80.5
4 TraesCS3B01G288500 chr3A 98.539 2259 12 6 1 2242 477591473 477589219 0.000000e+00 3969.0
5 TraesCS3B01G288500 chr3A 97.848 2138 15 12 2752 4880 477586516 477584401 0.000000e+00 3664.0
6 TraesCS3B01G288500 chr3A 98.966 387 3 1 2365 2750 477589221 477588835 0.000000e+00 691.0
7 TraesCS3B01G288500 chr3A 100.000 43 0 0 4760 4802 477584465 477584423 4.050000e-11 80.5
8 TraesCS3B01G288500 chr6B 86.875 320 40 2 2366 2683 41992751 41993070 1.670000e-94 357.0
9 TraesCS3B01G288500 chr6B 93.981 216 13 0 1225 1440 583189240 583189025 1.310000e-85 327.0
10 TraesCS3B01G288500 chr6B 80.941 404 49 17 2803 3186 41993227 41993622 1.330000e-75 294.0
11 TraesCS3B01G288500 chr6B 96.992 133 4 0 2237 2369 172239628 172239760 1.770000e-54 224.0
12 TraesCS3B01G288500 chr6B 95.000 140 6 1 2231 2370 502311220 502311358 8.220000e-53 219.0
13 TraesCS3B01G288500 chr6B 85.567 194 19 5 1009 1200 41991732 41991918 1.390000e-45 195.0
14 TraesCS3B01G288500 chr6D 86.562 320 41 2 2366 2683 25782497 25782816 7.770000e-93 351.0
15 TraesCS3B01G288500 chr6D 95.215 209 10 0 1232 1440 151317473 151317265 1.010000e-86 331.0
16 TraesCS3B01G288500 chr6D 80.893 403 51 14 2803 3186 25782970 25783365 1.330000e-75 294.0
17 TraesCS3B01G288500 chr6D 85.659 258 37 0 1828 2085 25782114 25782371 6.220000e-69 272.0
18 TraesCS3B01G288500 chr6A 86.562 320 41 2 2366 2683 23888768 23889087 7.770000e-93 351.0
19 TraesCS3B01G288500 chr6A 81.141 403 49 15 2803 3186 23889242 23889636 1.030000e-76 298.0
20 TraesCS3B01G288500 chr6A 86.434 258 35 0 1828 2085 23888385 23888642 2.880000e-72 283.0
21 TraesCS3B01G288500 chr2A 94.495 218 11 1 1223 1440 29592017 29591801 7.830000e-88 335.0
22 TraesCS3B01G288500 chr2A 94.366 142 8 0 2236 2377 738175105 738174964 8.220000e-53 219.0
23 TraesCS3B01G288500 chr7B 95.215 209 10 0 1232 1440 464539692 464539900 1.010000e-86 331.0
24 TraesCS3B01G288500 chr7B 77.804 419 60 20 2803 3196 126778702 126779112 1.370000e-55 228.0
25 TraesCS3B01G288500 chr7B 82.812 256 39 2 1828 2083 126777815 126778065 1.770000e-54 224.0
26 TraesCS3B01G288500 chr7B 96.992 133 4 0 2239 2371 678552456 678552324 1.770000e-54 224.0
27 TraesCS3B01G288500 chr4A 93.953 215 13 0 1226 1440 723602265 723602479 4.710000e-85 326.0
28 TraesCS3B01G288500 chr4A 92.411 224 15 2 1217 1440 494702796 494702575 7.880000e-83 318.0
29 TraesCS3B01G288500 chr4A 91.518 224 17 2 1217 1440 494733914 494733693 1.710000e-79 307.0
30 TraesCS3B01G288500 chr2B 92.889 225 14 2 1216 1440 496538375 496538153 4.710000e-85 326.0
31 TraesCS3B01G288500 chr1D 93.548 217 12 1 1226 1440 153918993 153918777 6.090000e-84 322.0
32 TraesCS3B01G288500 chr1D 91.855 221 17 1 1221 1440 491899368 491899148 1.710000e-79 307.0
33 TraesCS3B01G288500 chr1D 78.378 407 59 18 2803 3186 347397237 347397637 2.270000e-58 237.0
34 TraesCS3B01G288500 chr1D 96.063 127 5 0 2240 2366 368493811 368493685 1.780000e-49 207.0
35 TraesCS3B01G288500 chr1D 82.796 186 29 3 1011 1194 347395726 347395910 3.910000e-36 163.0
36 TraesCS3B01G288500 chr1A 91.892 222 18 0 1219 1440 13941442 13941663 1.320000e-80 311.0
37 TraesCS3B01G288500 chr1A 82.946 258 43 1 1828 2085 448009633 448009889 1.060000e-56 231.0
38 TraesCS3B01G288500 chr1A 80.526 190 32 5 1010 1196 448008368 448008555 1.830000e-29 141.0
39 TraesCS3B01G288500 chr7A 91.228 228 18 1 1215 1440 2222117 2222344 4.740000e-80 309.0
40 TraesCS3B01G288500 chr4D 91.593 226 14 4 1216 1440 43773890 43773669 1.710000e-79 307.0
41 TraesCS3B01G288500 chr1B 83.721 258 42 0 1828 2085 468503709 468503966 1.360000e-60 244.0
42 TraesCS3B01G288500 chr1B 78.676 408 56 18 2803 3186 468504602 468505002 4.880000e-60 243.0
43 TraesCS3B01G288500 chr1B 96.970 132 4 0 2240 2371 518809548 518809679 6.360000e-54 222.0
44 TraesCS3B01G288500 chr1B 96.970 132 4 0 2240 2371 623687580 623687711 6.360000e-54 222.0
45 TraesCS3B01G288500 chr1B 93.617 141 9 0 2233 2373 277456292 277456432 1.380000e-50 211.0
46 TraesCS3B01G288500 chr1B 82.812 192 30 3 1011 1200 468503051 468503241 8.400000e-38 169.0
47 TraesCS3B01G288500 chrUn 78.272 405 59 21 2803 3184 16579941 16580339 2.940000e-57 233.0
48 TraesCS3B01G288500 chrUn 82.186 247 44 0 1828 2074 16579048 16579294 3.830000e-51 213.0
49 TraesCS3B01G288500 chr5B 96.269 134 5 0 2240 2373 555175729 555175596 2.290000e-53 220.0


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 TraesCS3B01G288500 chr3B 463109434 463114313 4879 True 9012.000000 9012 100.000000 1 4880 1 chr3B.!!$R1 4879
1 TraesCS3B01G288500 chr3A 477588835 477591473 2638 True 2330.000000 3969 98.752500 1 2750 2 chr3A.!!$R2 2749
2 TraesCS3B01G288500 chr3A 477584401 477586516 2115 True 1872.250000 3664 98.924000 2752 4880 2 chr3A.!!$R1 2128
3 TraesCS3B01G288500 chr6B 41991732 41993622 1890 False 282.000000 357 84.461000 1009 3186 3 chr6B.!!$F3 2177
4 TraesCS3B01G288500 chr6D 25782114 25783365 1251 False 305.666667 351 84.371333 1828 3186 3 chr6D.!!$F1 1358
5 TraesCS3B01G288500 chr6A 23888385 23889636 1251 False 310.666667 351 84.712333 1828 3186 3 chr6A.!!$F1 1358
6 TraesCS3B01G288500 chr7B 126777815 126779112 1297 False 226.000000 228 80.308000 1828 3196 2 chr7B.!!$F2 1368
7 TraesCS3B01G288500 chr1B 468503051 468505002 1951 False 218.666667 244 81.736333 1011 3186 3 chr1B.!!$F4 2175
8 TraesCS3B01G288500 chrUn 16579048 16580339 1291 False 223.000000 233 80.229000 1828 3184 2 chrUn.!!$F1 1356

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
907 925 0.878523 TGCTTTTGGACGACGGACAG 60.879 55.0 0.0 0.0 0.0 3.51 F
2255 2644 0.038744 AGTTACTCCCTCCGTCCGAA 59.961 55.0 0.0 0.0 0.0 4.30 F
2256 2645 0.890683 GTTACTCCCTCCGTCCGAAA 59.109 55.0 0.0 0.0 0.0 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2350 2739 1.005569 ACATGTACTCCCTCTGTCCGA 59.994 52.381 0.00 0.00 0.00 4.55 R
3871 4364 0.179073 GTCGCAGGTGGCTATGATGT 60.179 55.000 0.00 0.00 41.67 3.06 R
4153 4646 3.384668 GCTCAGAATAGAATAGTGCGCA 58.615 45.455 5.66 5.66 0.00 6.09 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
211 212 5.173131 GCTCAAATTTTGGTACGACAAGTTG 59.827 40.000 9.71 9.71 0.00 3.16
309 310 2.430332 CCCAACAGCTCCAGTTCAAAAA 59.570 45.455 0.00 0.00 0.00 1.94
491 492 5.180271 CCAGTTAAACTTCTAATGCCCGTA 58.820 41.667 0.00 0.00 0.00 4.02
532 533 9.762933 ACACTAGTATTTGCAAAATTTTGACAT 57.237 25.926 30.40 20.03 40.55 3.06
907 925 0.878523 TGCTTTTGGACGACGGACAG 60.879 55.000 0.00 0.00 0.00 3.51
1257 1282 5.030147 TCCCTCTATTCCACAATGTAGTGT 58.970 41.667 0.00 0.00 37.82 3.55
1407 1432 8.148351 TGCATTTGGTATTCTAGATGTACCTAC 58.852 37.037 24.31 14.77 38.89 3.18
1556 1581 2.552315 TGAGTTGTCCGGATTCTTTTGC 59.448 45.455 7.81 0.00 0.00 3.68
1557 1582 2.552315 GAGTTGTCCGGATTCTTTTGCA 59.448 45.455 7.81 0.00 0.00 4.08
2239 2628 1.103398 GTGACTTGCACCTGCCAGTT 61.103 55.000 5.56 0.00 45.50 3.16
2240 2629 0.472044 TGACTTGCACCTGCCAGTTA 59.528 50.000 5.56 0.00 45.50 2.24
2241 2630 0.875059 GACTTGCACCTGCCAGTTAC 59.125 55.000 5.56 0.00 45.50 2.50
2242 2631 0.474184 ACTTGCACCTGCCAGTTACT 59.526 50.000 0.00 0.00 43.42 2.24
2243 2632 1.160137 CTTGCACCTGCCAGTTACTC 58.840 55.000 0.00 0.00 41.18 2.59
2244 2633 0.250727 TTGCACCTGCCAGTTACTCC 60.251 55.000 0.00 0.00 41.18 3.85
2245 2634 1.377333 GCACCTGCCAGTTACTCCC 60.377 63.158 0.00 0.00 34.31 4.30
2246 2635 1.842381 GCACCTGCCAGTTACTCCCT 61.842 60.000 0.00 0.00 34.31 4.20
2247 2636 0.250513 CACCTGCCAGTTACTCCCTC 59.749 60.000 0.00 0.00 0.00 4.30
2248 2637 0.910088 ACCTGCCAGTTACTCCCTCC 60.910 60.000 0.00 0.00 0.00 4.30
2249 2638 1.517832 CTGCCAGTTACTCCCTCCG 59.482 63.158 0.00 0.00 0.00 4.63
2250 2639 1.229082 TGCCAGTTACTCCCTCCGT 60.229 57.895 0.00 0.00 0.00 4.69
2251 2640 1.255667 TGCCAGTTACTCCCTCCGTC 61.256 60.000 0.00 0.00 0.00 4.79
2252 2641 1.957765 GCCAGTTACTCCCTCCGTCC 61.958 65.000 0.00 0.00 0.00 4.79
2253 2642 1.664321 CCAGTTACTCCCTCCGTCCG 61.664 65.000 0.00 0.00 0.00 4.79
2254 2643 0.679002 CAGTTACTCCCTCCGTCCGA 60.679 60.000 0.00 0.00 0.00 4.55
2255 2644 0.038744 AGTTACTCCCTCCGTCCGAA 59.961 55.000 0.00 0.00 0.00 4.30
2256 2645 0.890683 GTTACTCCCTCCGTCCGAAA 59.109 55.000 0.00 0.00 0.00 3.46
2257 2646 1.273327 GTTACTCCCTCCGTCCGAAAA 59.727 52.381 0.00 0.00 0.00 2.29
2258 2647 1.856629 TACTCCCTCCGTCCGAAAAT 58.143 50.000 0.00 0.00 0.00 1.82
2259 2648 1.856629 ACTCCCTCCGTCCGAAAATA 58.143 50.000 0.00 0.00 0.00 1.40
2260 2649 1.479730 ACTCCCTCCGTCCGAAAATAC 59.520 52.381 0.00 0.00 0.00 1.89
2261 2650 1.755380 CTCCCTCCGTCCGAAAATACT 59.245 52.381 0.00 0.00 0.00 2.12
2262 2651 2.167900 CTCCCTCCGTCCGAAAATACTT 59.832 50.000 0.00 0.00 0.00 2.24
2263 2652 2.093869 TCCCTCCGTCCGAAAATACTTG 60.094 50.000 0.00 0.00 0.00 3.16
2264 2653 2.354403 CCCTCCGTCCGAAAATACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
2265 2654 2.928116 CCTCCGTCCGAAAATACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
2266 2655 3.581755 CTCCGTCCGAAAATACTTGTCA 58.418 45.455 0.00 0.00 0.00 3.58
2267 2656 4.181578 CTCCGTCCGAAAATACTTGTCAT 58.818 43.478 0.00 0.00 0.00 3.06
2268 2657 4.178540 TCCGTCCGAAAATACTTGTCATC 58.821 43.478 0.00 0.00 0.00 2.92
2269 2658 3.930229 CCGTCCGAAAATACTTGTCATCA 59.070 43.478 0.00 0.00 0.00 3.07
2270 2659 4.390603 CCGTCCGAAAATACTTGTCATCAA 59.609 41.667 0.00 0.00 0.00 2.57
2271 2660 5.106869 CCGTCCGAAAATACTTGTCATCAAA 60.107 40.000 0.00 0.00 32.87 2.69
2272 2661 6.367421 CGTCCGAAAATACTTGTCATCAAAA 58.633 36.000 0.00 0.00 32.87 2.44
2273 2662 7.021196 CGTCCGAAAATACTTGTCATCAAAAT 58.979 34.615 0.00 0.00 32.87 1.82
2274 2663 7.007367 CGTCCGAAAATACTTGTCATCAAAATG 59.993 37.037 0.00 0.00 32.87 2.32
2275 2664 8.020819 GTCCGAAAATACTTGTCATCAAAATGA 58.979 33.333 0.00 0.00 39.63 2.57
2276 2665 8.572185 TCCGAAAATACTTGTCATCAAAATGAA 58.428 29.630 0.00 0.00 43.42 2.57
2277 2666 9.357652 CCGAAAATACTTGTCATCAAAATGAAT 57.642 29.630 0.00 0.00 43.42 2.57
2285 2674 8.096414 ACTTGTCATCAAAATGAATAAAAGGGG 58.904 33.333 0.00 0.00 43.42 4.79
2286 2675 7.789202 TGTCATCAAAATGAATAAAAGGGGA 57.211 32.000 0.00 0.00 43.42 4.81
2287 2676 7.610865 TGTCATCAAAATGAATAAAAGGGGAC 58.389 34.615 0.00 0.00 43.42 4.46
2288 2677 6.751888 GTCATCAAAATGAATAAAAGGGGACG 59.248 38.462 0.00 0.00 43.42 4.79
2289 2678 6.435904 TCATCAAAATGAATAAAAGGGGACGT 59.564 34.615 0.00 0.00 38.97 4.34
2290 2679 7.612244 TCATCAAAATGAATAAAAGGGGACGTA 59.388 33.333 0.00 0.00 38.97 3.57
2291 2680 7.948034 TCAAAATGAATAAAAGGGGACGTAT 57.052 32.000 0.00 0.00 0.00 3.06
2292 2681 7.992008 TCAAAATGAATAAAAGGGGACGTATC 58.008 34.615 0.00 0.00 0.00 2.24
2293 2682 7.832187 TCAAAATGAATAAAAGGGGACGTATCT 59.168 33.333 0.00 0.00 0.00 1.98
2294 2683 9.116067 CAAAATGAATAAAAGGGGACGTATCTA 57.884 33.333 0.00 0.00 0.00 1.98
2295 2684 8.904099 AAATGAATAAAAGGGGACGTATCTAG 57.096 34.615 0.00 0.00 0.00 2.43
2296 2685 7.850935 ATGAATAAAAGGGGACGTATCTAGA 57.149 36.000 0.00 0.00 0.00 2.43
2297 2686 7.850935 TGAATAAAAGGGGACGTATCTAGAT 57.149 36.000 10.73 10.73 0.00 1.98
2298 2687 7.667557 TGAATAAAAGGGGACGTATCTAGATG 58.332 38.462 15.79 1.92 0.00 2.90
2299 2688 7.289317 TGAATAAAAGGGGACGTATCTAGATGT 59.711 37.037 15.79 5.44 0.00 3.06
2300 2689 8.716674 AATAAAAGGGGACGTATCTAGATGTA 57.283 34.615 15.79 0.00 0.00 2.29
2301 2690 8.896722 ATAAAAGGGGACGTATCTAGATGTAT 57.103 34.615 15.79 0.00 0.00 2.29
2302 2691 7.613551 AAAAGGGGACGTATCTAGATGTATT 57.386 36.000 15.79 0.00 0.00 1.89
2303 2692 7.613551 AAAGGGGACGTATCTAGATGTATTT 57.386 36.000 15.79 3.36 0.00 1.40
2304 2693 7.613551 AAGGGGACGTATCTAGATGTATTTT 57.386 36.000 15.79 0.00 0.00 1.82
2305 2694 8.716674 AAGGGGACGTATCTAGATGTATTTTA 57.283 34.615 15.79 0.00 0.00 1.52
2306 2695 8.350852 AGGGGACGTATCTAGATGTATTTTAG 57.649 38.462 15.79 0.78 0.00 1.85
2307 2696 7.949006 AGGGGACGTATCTAGATGTATTTTAGT 59.051 37.037 15.79 3.72 0.00 2.24
2308 2697 8.583296 GGGGACGTATCTAGATGTATTTTAGTT 58.417 37.037 15.79 0.00 0.00 2.24
2309 2698 9.623350 GGGACGTATCTAGATGTATTTTAGTTC 57.377 37.037 15.79 2.83 0.00 3.01
2348 2737 9.829507 TTTTTGTCCATTTTGATGACAAGTATT 57.170 25.926 0.00 0.00 37.13 1.89
2349 2738 9.829507 TTTTGTCCATTTTGATGACAAGTATTT 57.170 25.926 0.00 0.00 37.13 1.40
2350 2739 9.829507 TTTGTCCATTTTGATGACAAGTATTTT 57.170 25.926 0.00 0.00 37.13 1.82
2351 2740 9.474920 TTGTCCATTTTGATGACAAGTATTTTC 57.525 29.630 0.00 0.00 37.32 2.29
2352 2741 7.807433 TGTCCATTTTGATGACAAGTATTTTCG 59.193 33.333 0.00 0.00 37.32 3.46
2353 2742 7.273381 GTCCATTTTGATGACAAGTATTTTCGG 59.727 37.037 0.00 0.00 37.32 4.30
2354 2743 7.175816 TCCATTTTGATGACAAGTATTTTCGGA 59.824 33.333 0.00 0.00 37.32 4.55
2355 2744 7.273381 CCATTTTGATGACAAGTATTTTCGGAC 59.727 37.037 0.00 0.00 37.32 4.79
2356 2745 6.869315 TTTGATGACAAGTATTTTCGGACA 57.131 33.333 0.00 0.00 37.32 4.02
2357 2746 6.480524 TTGATGACAAGTATTTTCGGACAG 57.519 37.500 0.00 0.00 0.00 3.51
2358 2747 5.789521 TGATGACAAGTATTTTCGGACAGA 58.210 37.500 0.00 0.00 0.00 3.41
2359 2748 5.869344 TGATGACAAGTATTTTCGGACAGAG 59.131 40.000 0.00 0.00 0.00 3.35
2360 2749 4.566004 TGACAAGTATTTTCGGACAGAGG 58.434 43.478 0.00 0.00 0.00 3.69
2361 2750 3.933332 GACAAGTATTTTCGGACAGAGGG 59.067 47.826 0.00 0.00 0.00 4.30
2362 2751 3.581332 ACAAGTATTTTCGGACAGAGGGA 59.419 43.478 0.00 0.00 0.00 4.20
2363 2752 4.184629 CAAGTATTTTCGGACAGAGGGAG 58.815 47.826 0.00 0.00 0.00 4.30
3378 3868 7.732025 TCACATCACGATATAATTGGTTAGGT 58.268 34.615 0.00 0.00 0.00 3.08
3871 4364 0.888736 CCGTGTTTGCCAGGACATCA 60.889 55.000 0.00 0.00 0.00 3.07
4145 4638 4.095782 AGTGAAAGCGCACTTGTTTTCTTA 59.904 37.500 11.47 0.00 46.42 2.10
4146 4639 4.976116 GTGAAAGCGCACTTGTTTTCTTAT 59.024 37.500 11.47 0.00 35.85 1.73
4147 4640 4.975502 TGAAAGCGCACTTGTTTTCTTATG 59.024 37.500 11.47 0.00 35.85 1.90
4148 4641 2.933769 AGCGCACTTGTTTTCTTATGC 58.066 42.857 11.47 0.00 0.00 3.14
4149 4642 2.554032 AGCGCACTTGTTTTCTTATGCT 59.446 40.909 11.47 0.00 0.00 3.79
4150 4643 3.751175 AGCGCACTTGTTTTCTTATGCTA 59.249 39.130 11.47 0.00 0.00 3.49
4151 4644 4.215399 AGCGCACTTGTTTTCTTATGCTAA 59.785 37.500 11.47 0.00 0.00 3.09
4152 4645 5.095490 GCGCACTTGTTTTCTTATGCTAAT 58.905 37.500 0.30 0.00 0.00 1.73
4153 4646 5.572896 GCGCACTTGTTTTCTTATGCTAATT 59.427 36.000 0.30 0.00 0.00 1.40
4179 4672 5.363939 GCACTATTCTATTCTGAGCCTGTT 58.636 41.667 0.00 0.00 0.00 3.16
4259 4752 4.035792 GCACCATGTTACGGCACATATTTA 59.964 41.667 1.75 0.00 35.51 1.40
4417 4910 7.201884 GGCTAACCTCGCAAGGATATACATATA 60.202 40.741 0.00 0.00 46.67 0.86
4418 4911 8.195436 GCTAACCTCGCAAGGATATACATATAA 58.805 37.037 0.00 0.00 46.67 0.98
4419 4912 9.517609 CTAACCTCGCAAGGATATACATATAAC 57.482 37.037 0.00 0.00 46.67 1.89
4420 4913 7.476540 ACCTCGCAAGGATATACATATAACA 57.523 36.000 0.00 0.00 46.67 2.41
4421 4914 8.079211 ACCTCGCAAGGATATACATATAACAT 57.921 34.615 0.00 0.00 46.67 2.71
4422 4915 9.197306 ACCTCGCAAGGATATACATATAACATA 57.803 33.333 0.00 0.00 46.67 2.29
4546 5039 2.159382 TCCCGAGAAAAATTGAGCACC 58.841 47.619 0.00 0.00 0.00 5.01
4763 5256 2.763039 TCATCATCTGGCTGGGTCTTA 58.237 47.619 0.00 0.00 0.00 2.10
4765 5258 0.824109 TCATCTGGCTGGGTCTTACG 59.176 55.000 0.00 0.00 0.00 3.18
4766 5259 0.537188 CATCTGGCTGGGTCTTACGT 59.463 55.000 0.00 0.00 0.00 3.57
4767 5260 1.066143 CATCTGGCTGGGTCTTACGTT 60.066 52.381 0.00 0.00 0.00 3.99
4768 5261 1.927487 TCTGGCTGGGTCTTACGTTA 58.073 50.000 0.00 0.00 0.00 3.18
4769 5262 1.547372 TCTGGCTGGGTCTTACGTTAC 59.453 52.381 0.00 0.00 0.00 2.50
4770 5263 1.274167 CTGGCTGGGTCTTACGTTACA 59.726 52.381 0.00 0.00 0.00 2.41
4771 5264 1.693062 TGGCTGGGTCTTACGTTACAA 59.307 47.619 0.00 0.00 0.00 2.41
4772 5265 2.289195 TGGCTGGGTCTTACGTTACAAG 60.289 50.000 0.00 0.00 0.00 3.16
4773 5266 2.289257 GGCTGGGTCTTACGTTACAAGT 60.289 50.000 0.00 0.00 0.00 3.16
4777 5270 5.021033 TGGGTCTTACGTTACAAGTCAAA 57.979 39.130 0.00 0.00 0.00 2.69
4778 5271 4.810491 TGGGTCTTACGTTACAAGTCAAAC 59.190 41.667 0.00 0.00 0.00 2.93
4779 5272 5.052481 GGGTCTTACGTTACAAGTCAAACT 58.948 41.667 0.00 0.00 0.00 2.66
4780 5273 6.183360 TGGGTCTTACGTTACAAGTCAAACTA 60.183 38.462 0.00 0.00 0.00 2.24
4781 5274 6.364435 GGGTCTTACGTTACAAGTCAAACTAG 59.636 42.308 0.00 0.00 0.00 2.57
4782 5275 6.128982 GGTCTTACGTTACAAGTCAAACTAGC 60.129 42.308 0.00 0.00 0.00 3.42
4784 5277 6.639686 TCTTACGTTACAAGTCAAACTAGCAG 59.360 38.462 0.00 0.00 0.00 4.24
4787 5280 5.989777 ACGTTACAAGTCAAACTAGCAGAAT 59.010 36.000 0.00 0.00 0.00 2.40
4788 5281 6.482308 ACGTTACAAGTCAAACTAGCAGAATT 59.518 34.615 0.00 0.00 0.00 2.17
4789 5282 6.792250 CGTTACAAGTCAAACTAGCAGAATTG 59.208 38.462 14.39 14.39 41.51 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
211 212 4.615912 GCACATCTGTTTTATGGGTGTCAC 60.616 45.833 0.00 0.00 30.08 3.67
532 533 6.983474 TTCAAGATGCGTAGAATCAAATGA 57.017 33.333 0.00 0.00 0.00 2.57
807 824 0.181824 AAAGTACGCAACACCCAGGT 59.818 50.000 0.00 0.00 0.00 4.00
948 966 7.093771 CCTGTATCTGCATACCTTTTTCCTTTT 60.094 37.037 0.00 0.00 34.89 2.27
2239 2628 1.856629 ATTTTCGGACGGAGGGAGTA 58.143 50.000 0.00 0.00 0.00 2.59
2240 2629 1.479730 GTATTTTCGGACGGAGGGAGT 59.520 52.381 0.00 0.00 0.00 3.85
2241 2630 1.755380 AGTATTTTCGGACGGAGGGAG 59.245 52.381 0.00 0.00 0.00 4.30
2242 2631 1.856629 AGTATTTTCGGACGGAGGGA 58.143 50.000 0.00 0.00 0.00 4.20
2243 2632 2.277084 CAAGTATTTTCGGACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
2244 2633 2.928116 GACAAGTATTTTCGGACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
2245 2634 3.581755 TGACAAGTATTTTCGGACGGAG 58.418 45.455 0.00 0.00 0.00 4.63
2246 2635 3.663995 TGACAAGTATTTTCGGACGGA 57.336 42.857 0.00 0.00 0.00 4.69
2247 2636 3.930229 TGATGACAAGTATTTTCGGACGG 59.070 43.478 0.00 0.00 0.00 4.79
2248 2637 5.524511 TTGATGACAAGTATTTTCGGACG 57.475 39.130 0.00 0.00 0.00 4.79
2249 2638 8.020819 TCATTTTGATGACAAGTATTTTCGGAC 58.979 33.333 0.00 0.00 37.32 4.79
2250 2639 8.105097 TCATTTTGATGACAAGTATTTTCGGA 57.895 30.769 0.00 0.00 37.32 4.55
2251 2640 8.741101 TTCATTTTGATGACAAGTATTTTCGG 57.259 30.769 0.00 0.00 37.32 4.30
2259 2648 8.096414 CCCCTTTTATTCATTTTGATGACAAGT 58.904 33.333 0.00 0.00 37.32 3.16
2260 2649 8.313292 TCCCCTTTTATTCATTTTGATGACAAG 58.687 33.333 0.00 0.00 37.32 3.16
2261 2650 8.093927 GTCCCCTTTTATTCATTTTGATGACAA 58.906 33.333 0.00 0.00 0.00 3.18
2262 2651 7.576666 CGTCCCCTTTTATTCATTTTGATGACA 60.577 37.037 0.00 0.00 0.00 3.58
2263 2652 6.751888 CGTCCCCTTTTATTCATTTTGATGAC 59.248 38.462 0.00 0.00 0.00 3.06
2264 2653 6.435904 ACGTCCCCTTTTATTCATTTTGATGA 59.564 34.615 0.00 0.00 0.00 2.92
2265 2654 6.630071 ACGTCCCCTTTTATTCATTTTGATG 58.370 36.000 0.00 0.00 0.00 3.07
2266 2655 6.850752 ACGTCCCCTTTTATTCATTTTGAT 57.149 33.333 0.00 0.00 0.00 2.57
2267 2656 7.832187 AGATACGTCCCCTTTTATTCATTTTGA 59.168 33.333 0.00 0.00 0.00 2.69
2268 2657 7.996385 AGATACGTCCCCTTTTATTCATTTTG 58.004 34.615 0.00 0.00 0.00 2.44
2269 2658 9.338622 CTAGATACGTCCCCTTTTATTCATTTT 57.661 33.333 0.00 0.00 0.00 1.82
2270 2659 8.711170 TCTAGATACGTCCCCTTTTATTCATTT 58.289 33.333 0.00 0.00 0.00 2.32
2271 2660 8.258850 TCTAGATACGTCCCCTTTTATTCATT 57.741 34.615 0.00 0.00 0.00 2.57
2272 2661 7.850935 TCTAGATACGTCCCCTTTTATTCAT 57.149 36.000 0.00 0.00 0.00 2.57
2273 2662 7.289317 ACATCTAGATACGTCCCCTTTTATTCA 59.711 37.037 4.54 0.00 0.00 2.57
2274 2663 7.668492 ACATCTAGATACGTCCCCTTTTATTC 58.332 38.462 4.54 0.00 0.00 1.75
2275 2664 7.613551 ACATCTAGATACGTCCCCTTTTATT 57.386 36.000 4.54 0.00 0.00 1.40
2276 2665 8.896722 ATACATCTAGATACGTCCCCTTTTAT 57.103 34.615 4.54 0.00 0.00 1.40
2277 2666 8.716674 AATACATCTAGATACGTCCCCTTTTA 57.283 34.615 4.54 0.00 0.00 1.52
2278 2667 7.613551 AATACATCTAGATACGTCCCCTTTT 57.386 36.000 4.54 0.00 0.00 2.27
2279 2668 7.613551 AAATACATCTAGATACGTCCCCTTT 57.386 36.000 4.54 0.00 0.00 3.11
2280 2669 7.613551 AAAATACATCTAGATACGTCCCCTT 57.386 36.000 4.54 0.00 0.00 3.95
2281 2670 7.949006 ACTAAAATACATCTAGATACGTCCCCT 59.051 37.037 4.54 0.00 0.00 4.79
2282 2671 8.120140 ACTAAAATACATCTAGATACGTCCCC 57.880 38.462 4.54 0.00 0.00 4.81
2283 2672 9.623350 GAACTAAAATACATCTAGATACGTCCC 57.377 37.037 4.54 0.00 0.00 4.46
2322 2711 9.829507 AATACTTGTCATCAAAATGGACAAAAA 57.170 25.926 7.70 0.55 34.98 1.94
2323 2712 9.829507 AAATACTTGTCATCAAAATGGACAAAA 57.170 25.926 7.70 0.84 34.98 2.44
2324 2713 9.829507 AAAATACTTGTCATCAAAATGGACAAA 57.170 25.926 7.70 0.00 34.98 2.83
2325 2714 9.474920 GAAAATACTTGTCATCAAAATGGACAA 57.525 29.630 0.00 0.00 34.59 3.18
2326 2715 7.807433 CGAAAATACTTGTCATCAAAATGGACA 59.193 33.333 0.00 0.00 33.42 4.02
2327 2716 7.273381 CCGAAAATACTTGTCATCAAAATGGAC 59.727 37.037 0.00 0.00 33.42 4.02
2328 2717 7.175816 TCCGAAAATACTTGTCATCAAAATGGA 59.824 33.333 0.00 0.00 33.42 3.41
2329 2718 7.273381 GTCCGAAAATACTTGTCATCAAAATGG 59.727 37.037 0.00 0.00 33.42 3.16
2330 2719 7.807433 TGTCCGAAAATACTTGTCATCAAAATG 59.193 33.333 0.00 0.00 32.87 2.32
2331 2720 7.881142 TGTCCGAAAATACTTGTCATCAAAAT 58.119 30.769 0.00 0.00 32.87 1.82
2332 2721 7.227711 TCTGTCCGAAAATACTTGTCATCAAAA 59.772 33.333 0.00 0.00 32.87 2.44
2333 2722 6.708502 TCTGTCCGAAAATACTTGTCATCAAA 59.291 34.615 0.00 0.00 32.87 2.69
2334 2723 6.227522 TCTGTCCGAAAATACTTGTCATCAA 58.772 36.000 0.00 0.00 0.00 2.57
2335 2724 5.789521 TCTGTCCGAAAATACTTGTCATCA 58.210 37.500 0.00 0.00 0.00 3.07
2336 2725 5.292101 CCTCTGTCCGAAAATACTTGTCATC 59.708 44.000 0.00 0.00 0.00 2.92
2337 2726 5.178797 CCTCTGTCCGAAAATACTTGTCAT 58.821 41.667 0.00 0.00 0.00 3.06
2338 2727 4.562757 CCCTCTGTCCGAAAATACTTGTCA 60.563 45.833 0.00 0.00 0.00 3.58
2339 2728 3.933332 CCCTCTGTCCGAAAATACTTGTC 59.067 47.826 0.00 0.00 0.00 3.18
2340 2729 3.581332 TCCCTCTGTCCGAAAATACTTGT 59.419 43.478 0.00 0.00 0.00 3.16
2341 2730 4.184629 CTCCCTCTGTCCGAAAATACTTG 58.815 47.826 0.00 0.00 0.00 3.16
2342 2731 3.838903 ACTCCCTCTGTCCGAAAATACTT 59.161 43.478 0.00 0.00 0.00 2.24
2343 2732 3.442076 ACTCCCTCTGTCCGAAAATACT 58.558 45.455 0.00 0.00 0.00 2.12
2344 2733 3.889520 ACTCCCTCTGTCCGAAAATAC 57.110 47.619 0.00 0.00 0.00 1.89
2345 2734 4.346730 TGTACTCCCTCTGTCCGAAAATA 58.653 43.478 0.00 0.00 0.00 1.40
2346 2735 3.170717 TGTACTCCCTCTGTCCGAAAAT 58.829 45.455 0.00 0.00 0.00 1.82
2347 2736 2.600790 TGTACTCCCTCTGTCCGAAAA 58.399 47.619 0.00 0.00 0.00 2.29
2348 2737 2.297698 TGTACTCCCTCTGTCCGAAA 57.702 50.000 0.00 0.00 0.00 3.46
2349 2738 2.100197 CATGTACTCCCTCTGTCCGAA 58.900 52.381 0.00 0.00 0.00 4.30
2350 2739 1.005569 ACATGTACTCCCTCTGTCCGA 59.994 52.381 0.00 0.00 0.00 4.55
2351 2740 1.135139 CACATGTACTCCCTCTGTCCG 59.865 57.143 0.00 0.00 0.00 4.79
2352 2741 2.180276 ACACATGTACTCCCTCTGTCC 58.820 52.381 0.00 0.00 0.00 4.02
2353 2742 3.258372 TCAACACATGTACTCCCTCTGTC 59.742 47.826 0.00 0.00 0.00 3.51
2354 2743 3.239449 TCAACACATGTACTCCCTCTGT 58.761 45.455 0.00 0.00 0.00 3.41
2355 2744 3.961480 TCAACACATGTACTCCCTCTG 57.039 47.619 0.00 0.00 0.00 3.35
2356 2745 3.369892 GCATCAACACATGTACTCCCTCT 60.370 47.826 0.00 0.00 0.00 3.69
2357 2746 2.939103 GCATCAACACATGTACTCCCTC 59.061 50.000 0.00 0.00 0.00 4.30
2358 2747 2.356125 GGCATCAACACATGTACTCCCT 60.356 50.000 0.00 0.00 0.00 4.20
2359 2748 2.017049 GGCATCAACACATGTACTCCC 58.983 52.381 0.00 0.00 0.00 4.30
2360 2749 2.939103 GAGGCATCAACACATGTACTCC 59.061 50.000 0.00 0.00 30.19 3.85
2361 2750 3.599343 TGAGGCATCAACACATGTACTC 58.401 45.455 0.00 0.00 33.79 2.59
2362 2751 3.261643 TCTGAGGCATCAACACATGTACT 59.738 43.478 1.37 0.00 34.23 2.73
2363 2752 3.599343 TCTGAGGCATCAACACATGTAC 58.401 45.455 1.37 0.00 34.23 2.90
2425 2814 6.153340 TCCCTGCCAATAATCTTTCTTTTCTG 59.847 38.462 0.00 0.00 0.00 3.02
2725 3116 9.520515 AGTATAACACCTGATCAAGTTTGAATT 57.479 29.630 11.59 0.00 41.13 2.17
3871 4364 0.179073 GTCGCAGGTGGCTATGATGT 60.179 55.000 0.00 0.00 41.67 3.06
4145 4638 6.652481 AGAATAGAATAGTGCGCAATTAGCAT 59.348 34.615 18.32 0.00 46.96 3.79
4146 4639 5.991606 AGAATAGAATAGTGCGCAATTAGCA 59.008 36.000 18.32 0.00 46.13 3.49
4147 4640 6.146184 TCAGAATAGAATAGTGCGCAATTAGC 59.854 38.462 18.32 5.48 40.87 3.09
4148 4641 7.621013 GCTCAGAATAGAATAGTGCGCAATTAG 60.621 40.741 18.32 4.28 0.00 1.73
4149 4642 6.146184 GCTCAGAATAGAATAGTGCGCAATTA 59.854 38.462 18.32 10.75 0.00 1.40
4150 4643 5.049818 GCTCAGAATAGAATAGTGCGCAATT 60.050 40.000 18.32 11.95 0.00 2.32
4151 4644 4.450419 GCTCAGAATAGAATAGTGCGCAAT 59.550 41.667 17.03 17.03 0.00 3.56
4152 4645 3.804325 GCTCAGAATAGAATAGTGCGCAA 59.196 43.478 14.00 0.00 0.00 4.85
4153 4646 3.384668 GCTCAGAATAGAATAGTGCGCA 58.615 45.455 5.66 5.66 0.00 6.09
4418 4911 9.090692 GCAACAAAGCTTCAATAATCAATATGT 57.909 29.630 0.00 0.00 0.00 2.29
4419 4912 8.545420 GGCAACAAAGCTTCAATAATCAATATG 58.455 33.333 0.00 0.00 34.17 1.78
4420 4913 7.436080 CGGCAACAAAGCTTCAATAATCAATAT 59.564 33.333 0.00 0.00 34.17 1.28
4421 4914 6.751425 CGGCAACAAAGCTTCAATAATCAATA 59.249 34.615 0.00 0.00 34.17 1.90
4422 4915 5.577945 CGGCAACAAAGCTTCAATAATCAAT 59.422 36.000 0.00 0.00 34.17 2.57
4423 4916 4.922692 CGGCAACAAAGCTTCAATAATCAA 59.077 37.500 0.00 0.00 34.17 2.57
4546 5039 0.660300 TGTGCGCTAGACATATCGCG 60.660 55.000 9.73 0.00 46.72 5.87
4763 5256 4.940463 TCTGCTAGTTTGACTTGTAACGT 58.060 39.130 0.00 0.00 0.00 3.99
4765 5258 6.578919 GCAATTCTGCTAGTTTGACTTGTAAC 59.421 38.462 0.00 0.00 45.74 2.50
4766 5259 6.668323 GCAATTCTGCTAGTTTGACTTGTAA 58.332 36.000 0.00 0.00 45.74 2.41
4767 5260 6.241207 GCAATTCTGCTAGTTTGACTTGTA 57.759 37.500 0.00 0.00 45.74 2.41
4768 5261 5.113502 GCAATTCTGCTAGTTTGACTTGT 57.886 39.130 0.00 0.00 45.74 3.16
4782 5275 1.470098 CTGTTTCCGGGAGCAATTCTG 59.530 52.381 0.00 0.00 0.00 3.02
4784 5277 1.740025 CTCTGTTTCCGGGAGCAATTC 59.260 52.381 0.00 0.00 0.00 2.17
4787 5280 1.374947 CCTCTGTTTCCGGGAGCAA 59.625 57.895 0.00 0.00 0.00 3.91
4788 5281 1.827399 GACCTCTGTTTCCGGGAGCA 61.827 60.000 0.00 0.00 0.00 4.26
4789 5282 1.079057 GACCTCTGTTTCCGGGAGC 60.079 63.158 0.00 0.00 0.00 4.70
4791 5284 1.117142 AACGACCTCTGTTTCCGGGA 61.117 55.000 0.00 0.00 0.00 5.14
4792 5285 0.669625 GAACGACCTCTGTTTCCGGG 60.670 60.000 0.00 0.00 0.00 5.73
4793 5286 0.669625 GGAACGACCTCTGTTTCCGG 60.670 60.000 0.00 0.00 35.41 5.14
4794 5287 2.823628 GGAACGACCTCTGTTTCCG 58.176 57.895 0.00 0.00 35.41 4.30


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

AutoCloner maintained by Alex Coulton.