Multiple sequence alignment - TraesCS2B01G271300

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 TraesCS2B01G271300 chr2B 100.000 4202 0 0 1 4202 371168492 371164291 0.000000e+00 7760.0
1 TraesCS2B01G271300 chr2B 100.000 33 0 0 2400 2432 772635071 772635039 1.260000e-05 62.1
2 TraesCS2B01G271300 chr2D 95.006 1702 64 12 2506 4199 299889387 299891075 0.000000e+00 2652.0
3 TraesCS2B01G271300 chr2D 96.799 1187 25 6 994 2170 299888088 299889271 0.000000e+00 1969.0
4 TraesCS2B01G271300 chr2D 94.782 824 24 6 196 1007 299887253 299888069 0.000000e+00 1266.0
5 TraesCS2B01G271300 chr2D 98.551 138 2 0 1 138 299886793 299886930 1.170000e-60 244.0
6 TraesCS2B01G271300 chr2D 97.500 120 2 1 2286 2405 299889270 299889388 1.980000e-48 204.0
7 TraesCS2B01G271300 chr2D 92.248 129 10 0 2165 2293 519130930 519131058 2.580000e-42 183.0
8 TraesCS2B01G271300 chr2D 90.625 64 5 1 4137 4199 449065492 449065555 2.690000e-12 84.2
9 TraesCS2B01G271300 chr2A 97.371 1179 29 1 994 2170 376076766 376077944 0.000000e+00 2004.0
10 TraesCS2B01G271300 chr2A 94.892 1018 33 6 1 1007 376075737 376076746 0.000000e+00 1574.0
11 TraesCS2B01G271300 chr2A 95.981 821 23 4 3385 4202 376081680 376082493 0.000000e+00 1325.0
12 TraesCS2B01G271300 chr2A 94.845 679 19 9 2643 3306 376079761 376080438 0.000000e+00 1046.0
13 TraesCS2B01G271300 chr2A 94.771 153 6 1 2506 2656 376078223 376078375 1.950000e-58 237.0
14 TraesCS2B01G271300 chr2A 95.370 108 4 1 2288 2395 376077944 376078050 2.010000e-38 171.0
15 TraesCS2B01G271300 chr2A 94.030 67 3 1 4137 4202 593656000 593655934 2.670000e-17 100.0
16 TraesCS2B01G271300 chr2A 94.915 59 3 0 4144 4202 1378702 1378644 4.470000e-15 93.5
17 TraesCS2B01G271300 chr5B 87.388 1784 123 37 1 1758 689487868 689486161 0.000000e+00 1954.0
18 TraesCS2B01G271300 chr5B 95.000 120 6 0 2166 2285 173271596 173271477 5.550000e-44 189.0
19 TraesCS2B01G271300 chr5B 92.308 39 1 2 2394 2432 453278692 453278728 2.000000e-03 54.7
20 TraesCS2B01G271300 chr5D 87.647 1020 57 20 1 1007 546366589 546365626 0.000000e+00 1122.0
21 TraesCS2B01G271300 chr5D 92.435 423 29 3 1106 1526 546359035 546358614 6.010000e-168 601.0
22 TraesCS2B01G271300 chr5D 93.651 126 8 0 2168 2293 565900906 565900781 5.550000e-44 189.0
23 TraesCS2B01G271300 chr5D 93.701 127 4 4 2168 2291 352456282 352456407 1.990000e-43 187.0
24 TraesCS2B01G271300 chr5D 95.455 66 3 0 1043 1108 546361566 546361501 5.750000e-19 106.0
25 TraesCS2B01G271300 chr5D 91.228 57 3 2 2399 2455 66982698 66982644 4.500000e-10 76.8
26 TraesCS2B01G271300 chr3A 82.955 616 64 25 384 979 724300903 724300309 6.230000e-143 518.0
27 TraesCS2B01G271300 chr3A 89.952 209 15 4 62 267 724301243 724301038 8.960000e-67 265.0
28 TraesCS2B01G271300 chr3A 91.667 60 5 0 4140 4199 646737345 646737286 2.690000e-12 84.2
29 TraesCS2B01G271300 chr3A 90.323 62 5 1 4139 4199 652027626 652027565 3.480000e-11 80.5
30 TraesCS2B01G271300 chrUn 95.763 118 5 0 2168 2285 22143708 22143591 1.540000e-44 191.0
31 TraesCS2B01G271300 chr3B 95.041 121 6 0 2168 2288 637086328 637086448 1.540000e-44 191.0
32 TraesCS2B01G271300 chr3B 94.355 124 7 0 2165 2288 744209695 744209818 1.540000e-44 191.0
33 TraesCS2B01G271300 chr3B 95.000 40 1 1 2394 2432 52459752 52459791 1.260000e-05 62.1
34 TraesCS2B01G271300 chr7D 93.600 125 7 1 2169 2293 610248165 610248288 7.170000e-43 185.0
35 TraesCS2B01G271300 chr4B 93.600 125 7 1 2168 2292 467274873 467274996 7.170000e-43 185.0
36 TraesCS2B01G271300 chr4B 93.182 44 2 1 2390 2432 187091052 187091095 3.510000e-06 63.9
37 TraesCS2B01G271300 chr5A 95.082 61 2 1 4142 4202 383880550 383880491 1.240000e-15 95.3
38 TraesCS2B01G271300 chr3D 92.982 57 3 1 4143 4198 571120534 571120590 9.680000e-12 82.4
39 TraesCS2B01G271300 chr1A 94.872 39 0 2 2393 2431 497318139 497318175 4.540000e-05 60.2
40 TraesCS2B01G271300 chr4D 97.143 35 0 1 2399 2432 14838095 14838129 1.630000e-04 58.4
41 TraesCS2B01G271300 chr7B 84.127 63 5 4 2404 2461 742569433 742569495 5.870000e-04 56.5
42 TraesCS2B01G271300 chr6B 90.698 43 3 1 2391 2432 37927397 37927439 5.870000e-04 56.5


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 TraesCS2B01G271300 chr2B 371164291 371168492 4201 True 7760.0 7760 100.000000 1 4202 1 chr2B.!!$R1 4201
1 TraesCS2B01G271300 chr2D 299886793 299891075 4282 False 1267.0 2652 96.527600 1 4199 5 chr2D.!!$F3 4198
2 TraesCS2B01G271300 chr2A 376075737 376082493 6756 False 1059.5 2004 95.538333 1 4202 6 chr2A.!!$F1 4201
3 TraesCS2B01G271300 chr5B 689486161 689487868 1707 True 1954.0 1954 87.388000 1 1758 1 chr5B.!!$R2 1757
4 TraesCS2B01G271300 chr5D 546365626 546366589 963 True 1122.0 1122 87.647000 1 1007 1 chr5D.!!$R2 1006
5 TraesCS2B01G271300 chr5D 546358614 546361566 2952 True 353.5 601 93.945000 1043 1526 2 chr5D.!!$R4 483
6 TraesCS2B01G271300 chr3A 724300309 724301243 934 True 391.5 518 86.453500 62 979 2 chr3A.!!$R3 917

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
280 608 0.110295 CACCACCCAATCAGTGTCCA 59.89 55.000 0.0 0.0 33.2 4.02 F
1568 4441 1.069978 GCCTATCTCTGGTCTTCCTGC 59.93 57.143 0.0 0.0 33.5 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1570 4443 0.863119 GAGCGCAATCATCAAACCGC 60.863 55.0 11.47 0.0 41.51 5.68 R
3369 7837 0.638746 CGTATGTTCGTTCGTGCCTC 59.361 55.0 0.00 0.0 0.00 4.70 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
280 608 0.110295 CACCACCCAATCAGTGTCCA 59.890 55.000 0.00 0.00 33.20 4.02
453 781 1.669115 GACTTGGAAGCAGCGCTCA 60.669 57.895 7.13 0.00 38.25 4.26
488 816 4.845580 CTTCTCCGCCGCCTGCAT 62.846 66.667 0.00 0.00 41.33 3.96
555 887 1.078426 GTACAGGCAGAACCCGCAT 60.078 57.895 0.00 0.00 40.58 4.73
611 949 4.124351 CACCGCTTCTACCGCCGA 62.124 66.667 0.00 0.00 0.00 5.54
1017 1409 4.596212 AGTAGGGGATAAGGAAATTACCCG 59.404 45.833 0.00 0.00 36.40 5.28
1108 3970 2.047274 CCGCCTTCCGCTCTTTCA 60.047 61.111 0.00 0.00 35.03 2.69
1480 4353 1.449246 ACTGCAGCATTCTCCGAGC 60.449 57.895 15.27 0.00 0.00 5.03
1530 4403 3.056962 TCGCAAGCTAAATGCAATCCAAA 60.057 39.130 9.42 0.00 44.01 3.28
1568 4441 1.069978 GCCTATCTCTGGTCTTCCTGC 59.930 57.143 0.00 0.00 33.50 4.85
1570 4443 2.364970 CCTATCTCTGGTCTTCCTGCAG 59.635 54.545 6.78 6.78 33.50 4.41
1975 4862 0.108615 ACTCAAGACGGCATTCGAGG 60.109 55.000 0.00 0.00 42.43 4.63
2047 4934 0.861155 TTCCAGGGGGTTTGGCTTTA 59.139 50.000 0.00 0.00 35.62 1.85
2170 5058 6.119536 TCACTTCATTGGATTACCATGGTAC 58.880 40.000 24.52 13.63 46.34 3.34
2171 5059 6.069673 TCACTTCATTGGATTACCATGGTACT 60.070 38.462 24.52 19.23 46.34 2.73
2172 5060 6.260936 CACTTCATTGGATTACCATGGTACTC 59.739 42.308 26.49 26.49 46.34 2.59
2173 5061 5.304686 TCATTGGATTACCATGGTACTCC 57.695 43.478 37.17 37.17 46.34 3.85
2174 5062 4.104102 TCATTGGATTACCATGGTACTCCC 59.896 45.833 38.76 30.14 44.71 4.30
2175 5063 3.431411 TGGATTACCATGGTACTCCCT 57.569 47.619 38.76 19.15 44.71 4.20
2176 5064 3.314693 TGGATTACCATGGTACTCCCTC 58.685 50.000 38.76 24.55 44.71 4.30
2177 5065 2.299297 GGATTACCATGGTACTCCCTCG 59.701 54.545 35.41 3.73 41.63 4.63
2178 5066 1.784358 TTACCATGGTACTCCCTCGG 58.216 55.000 24.52 0.00 0.00 4.63
2179 5067 0.632835 TACCATGGTACTCCCTCGGT 59.367 55.000 21.05 0.00 40.37 4.69
2180 5068 0.686769 ACCATGGTACTCCCTCGGTC 60.687 60.000 18.10 0.00 34.45 4.79
2181 5069 1.400530 CCATGGTACTCCCTCGGTCC 61.401 65.000 2.57 0.00 0.00 4.46
2182 5070 1.075450 ATGGTACTCCCTCGGTCCC 60.075 63.158 0.00 0.00 0.00 4.46
2183 5071 2.832201 GGTACTCCCTCGGTCCCG 60.832 72.222 0.00 0.00 41.35 5.14
2184 5072 2.273449 GTACTCCCTCGGTCCCGA 59.727 66.667 8.34 8.34 46.87 5.14
2194 5082 2.660189 TCGGTCCCGAAATACTTGTC 57.340 50.000 5.84 0.00 46.01 3.18
2195 5083 1.135315 TCGGTCCCGAAATACTTGTCG 60.135 52.381 5.84 0.00 46.01 4.35
2204 5092 5.143916 CGAAATACTTGTCGGAAGAATGG 57.856 43.478 2.55 0.00 45.01 3.16
2205 5093 4.868171 CGAAATACTTGTCGGAAGAATGGA 59.132 41.667 2.55 0.00 45.01 3.41
2206 5094 5.523916 CGAAATACTTGTCGGAAGAATGGAT 59.476 40.000 2.55 0.00 45.01 3.41
2207 5095 6.510157 CGAAATACTTGTCGGAAGAATGGATG 60.510 42.308 2.55 0.00 45.01 3.51
2208 5096 3.703001 ACTTGTCGGAAGAATGGATGT 57.297 42.857 2.55 0.00 45.01 3.06
2209 5097 4.819105 ACTTGTCGGAAGAATGGATGTA 57.181 40.909 2.55 0.00 45.01 2.29
2210 5098 5.359194 ACTTGTCGGAAGAATGGATGTAT 57.641 39.130 2.55 0.00 45.01 2.29
2211 5099 5.360591 ACTTGTCGGAAGAATGGATGTATC 58.639 41.667 2.55 0.00 45.01 2.24
2212 5100 5.129485 ACTTGTCGGAAGAATGGATGTATCT 59.871 40.000 2.55 0.00 45.01 1.98
2213 5101 6.323996 ACTTGTCGGAAGAATGGATGTATCTA 59.676 38.462 2.55 0.00 45.01 1.98
2214 5102 6.332735 TGTCGGAAGAATGGATGTATCTAG 57.667 41.667 0.00 0.00 45.01 2.43
2215 5103 6.068670 TGTCGGAAGAATGGATGTATCTAGA 58.931 40.000 0.00 0.00 45.01 2.43
2216 5104 6.721668 TGTCGGAAGAATGGATGTATCTAGAT 59.278 38.462 10.73 10.73 45.01 1.98
2217 5105 7.032580 GTCGGAAGAATGGATGTATCTAGATG 58.967 42.308 15.79 0.00 45.01 2.90
2218 5106 6.721668 TCGGAAGAATGGATGTATCTAGATGT 59.278 38.462 15.79 1.25 37.03 3.06
2219 5107 7.888546 TCGGAAGAATGGATGTATCTAGATGTA 59.111 37.037 15.79 4.44 37.03 2.29
2220 5108 8.690884 CGGAAGAATGGATGTATCTAGATGTAT 58.309 37.037 15.79 9.11 0.00 2.29
2258 5146 7.042797 ACATCCATTTTTATCCATTTCTCCG 57.957 36.000 0.00 0.00 0.00 4.63
2259 5147 6.833416 ACATCCATTTTTATCCATTTCTCCGA 59.167 34.615 0.00 0.00 0.00 4.55
2260 5148 6.693315 TCCATTTTTATCCATTTCTCCGAC 57.307 37.500 0.00 0.00 0.00 4.79
2261 5149 6.184068 TCCATTTTTATCCATTTCTCCGACA 58.816 36.000 0.00 0.00 0.00 4.35
2262 5150 6.661377 TCCATTTTTATCCATTTCTCCGACAA 59.339 34.615 0.00 0.00 0.00 3.18
2263 5151 6.974622 CCATTTTTATCCATTTCTCCGACAAG 59.025 38.462 0.00 0.00 0.00 3.16
2264 5152 7.362920 CCATTTTTATCCATTTCTCCGACAAGT 60.363 37.037 0.00 0.00 0.00 3.16
2265 5153 8.673711 CATTTTTATCCATTTCTCCGACAAGTA 58.326 33.333 0.00 0.00 0.00 2.24
2266 5154 8.801882 TTTTTATCCATTTCTCCGACAAGTAT 57.198 30.769 0.00 0.00 0.00 2.12
2267 5155 8.801882 TTTTATCCATTTCTCCGACAAGTATT 57.198 30.769 0.00 0.00 0.00 1.89
2268 5156 8.801882 TTTATCCATTTCTCCGACAAGTATTT 57.198 30.769 0.00 0.00 0.00 1.40
2269 5157 8.801882 TTATCCATTTCTCCGACAAGTATTTT 57.198 30.769 0.00 0.00 0.00 1.82
2270 5158 6.737254 TCCATTTCTCCGACAAGTATTTTC 57.263 37.500 0.00 0.00 0.00 2.29
2271 5159 5.350365 TCCATTTCTCCGACAAGTATTTTCG 59.650 40.000 0.00 0.00 0.00 3.46
2277 5165 2.598589 CGACAAGTATTTTCGGACGGA 58.401 47.619 0.00 0.00 0.00 4.69
2278 5166 2.597305 CGACAAGTATTTTCGGACGGAG 59.403 50.000 0.00 0.00 0.00 4.63
2279 5167 2.928116 GACAAGTATTTTCGGACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
2280 5168 2.277084 CAAGTATTTTCGGACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
2281 5169 1.856629 AGTATTTTCGGACGGAGGGA 58.143 50.000 0.00 0.00 0.00 4.20
2282 5170 1.755380 AGTATTTTCGGACGGAGGGAG 59.245 52.381 0.00 0.00 0.00 4.30
2283 5171 1.479730 GTATTTTCGGACGGAGGGAGT 59.520 52.381 0.00 0.00 0.00 3.85
2284 5172 1.856629 ATTTTCGGACGGAGGGAGTA 58.143 50.000 0.00 0.00 0.00 2.59
2285 5173 1.856629 TTTTCGGACGGAGGGAGTAT 58.143 50.000 0.00 0.00 0.00 2.12
2286 5174 2.734755 TTTCGGACGGAGGGAGTATA 57.265 50.000 0.00 0.00 0.00 1.47
2349 5237 4.836125 ACGGACGAGTACTTGAAAACTA 57.164 40.909 17.37 0.00 0.00 2.24
2409 5461 9.933723 TTTCTTGTTATAGTTGTAAGTACTCCC 57.066 33.333 0.00 0.00 0.00 4.30
2410 5462 8.890410 TCTTGTTATAGTTGTAAGTACTCCCT 57.110 34.615 0.00 0.00 0.00 4.20
2411 5463 8.964772 TCTTGTTATAGTTGTAAGTACTCCCTC 58.035 37.037 0.00 0.00 0.00 4.30
2412 5464 7.651027 TGTTATAGTTGTAAGTACTCCCTCC 57.349 40.000 0.00 0.00 0.00 4.30
2413 5465 6.319658 TGTTATAGTTGTAAGTACTCCCTCCG 59.680 42.308 0.00 0.00 0.00 4.63
2414 5466 3.166560 AGTTGTAAGTACTCCCTCCGT 57.833 47.619 0.00 0.00 0.00 4.69
2415 5467 3.087781 AGTTGTAAGTACTCCCTCCGTC 58.912 50.000 0.00 0.00 0.00 4.79
2416 5468 2.134789 TGTAAGTACTCCCTCCGTCC 57.865 55.000 0.00 0.00 0.00 4.79
2417 5469 1.341383 TGTAAGTACTCCCTCCGTCCC 60.341 57.143 0.00 0.00 0.00 4.46
2418 5470 1.002069 TAAGTACTCCCTCCGTCCCA 58.998 55.000 0.00 0.00 0.00 4.37
2419 5471 0.338814 AAGTACTCCCTCCGTCCCAT 59.661 55.000 0.00 0.00 0.00 4.00
2420 5472 1.229131 AGTACTCCCTCCGTCCCATA 58.771 55.000 0.00 0.00 0.00 2.74
2421 5473 1.572415 AGTACTCCCTCCGTCCCATAA 59.428 52.381 0.00 0.00 0.00 1.90
2422 5474 2.179424 AGTACTCCCTCCGTCCCATAAT 59.821 50.000 0.00 0.00 0.00 1.28
2423 5475 1.424638 ACTCCCTCCGTCCCATAATG 58.575 55.000 0.00 0.00 0.00 1.90
2424 5476 1.344087 ACTCCCTCCGTCCCATAATGT 60.344 52.381 0.00 0.00 0.00 2.71
2425 5477 2.090943 ACTCCCTCCGTCCCATAATGTA 60.091 50.000 0.00 0.00 0.00 2.29
2426 5478 2.969950 CTCCCTCCGTCCCATAATGTAA 59.030 50.000 0.00 0.00 0.00 2.41
2427 5479 3.386063 TCCCTCCGTCCCATAATGTAAA 58.614 45.455 0.00 0.00 0.00 2.01
2428 5480 3.781407 TCCCTCCGTCCCATAATGTAAAA 59.219 43.478 0.00 0.00 0.00 1.52
2429 5481 3.881089 CCCTCCGTCCCATAATGTAAAAC 59.119 47.826 0.00 0.00 0.00 2.43
2430 5482 3.558418 CCTCCGTCCCATAATGTAAAACG 59.442 47.826 0.00 0.00 0.00 3.60
2431 5483 4.186159 CTCCGTCCCATAATGTAAAACGT 58.814 43.478 0.00 0.00 0.00 3.99
2432 5484 3.933955 TCCGTCCCATAATGTAAAACGTG 59.066 43.478 0.00 0.00 0.00 4.49
2433 5485 3.685756 CCGTCCCATAATGTAAAACGTGT 59.314 43.478 0.00 0.00 0.00 4.49
2434 5486 4.869297 CCGTCCCATAATGTAAAACGTGTA 59.131 41.667 0.00 0.00 0.00 2.90
2435 5487 5.005971 CCGTCCCATAATGTAAAACGTGTAG 59.994 44.000 0.00 0.00 0.00 2.74
2436 5488 5.806502 CGTCCCATAATGTAAAACGTGTAGA 59.193 40.000 0.00 0.00 0.00 2.59
2437 5489 6.020121 CGTCCCATAATGTAAAACGTGTAGAG 60.020 42.308 0.00 0.00 0.00 2.43
2438 5490 6.815142 GTCCCATAATGTAAAACGTGTAGAGT 59.185 38.462 0.00 0.00 0.00 3.24
2439 5491 7.009907 GTCCCATAATGTAAAACGTGTAGAGTC 59.990 40.741 0.00 0.00 0.00 3.36
2440 5492 6.814644 CCCATAATGTAAAACGTGTAGAGTCA 59.185 38.462 0.00 0.00 0.00 3.41
2441 5493 7.332430 CCCATAATGTAAAACGTGTAGAGTCAA 59.668 37.037 0.00 0.00 0.00 3.18
2442 5494 8.714179 CCATAATGTAAAACGTGTAGAGTCAAA 58.286 33.333 0.00 0.00 0.00 2.69
2476 5528 4.967084 TGGGACAGCACTAGAGTAAAAA 57.033 40.909 0.00 0.00 0.00 1.94
2499 5551 8.442660 AAAAAGGTTTTACATTATGGGATGGA 57.557 30.769 0.00 0.00 0.00 3.41
2500 5552 7.660030 AAAGGTTTTACATTATGGGATGGAG 57.340 36.000 0.00 0.00 0.00 3.86
2501 5553 5.705400 AGGTTTTACATTATGGGATGGAGG 58.295 41.667 0.00 0.00 0.00 4.30
2502 5554 4.832823 GGTTTTACATTATGGGATGGAGGG 59.167 45.833 0.00 0.00 0.00 4.30
2503 5555 5.399727 GGTTTTACATTATGGGATGGAGGGA 60.400 44.000 0.00 0.00 0.00 4.20
2504 5556 6.133356 GTTTTACATTATGGGATGGAGGGAA 58.867 40.000 0.00 0.00 0.00 3.97
2505 5557 6.544327 TTTACATTATGGGATGGAGGGAAT 57.456 37.500 0.00 0.00 0.00 3.01
2506 5558 7.655819 TTTACATTATGGGATGGAGGGAATA 57.344 36.000 0.00 0.00 0.00 1.75
2592 5646 7.233348 TGTGTACTCTATGCATGGATAGATCAA 59.767 37.037 30.10 18.55 34.98 2.57
2659 7112 3.846588 ACCCTAAGATCTCACCAACATGT 59.153 43.478 0.00 0.00 0.00 3.21
3051 7507 2.731572 CAGAAGTGGGATTTCAGCCAT 58.268 47.619 0.00 0.00 0.00 4.40
3055 7511 1.572415 AGTGGGATTTCAGCCATGGAT 59.428 47.619 18.40 6.18 0.00 3.41
3110 7572 4.818546 AGAAATATCTGGATCCAAAGTGCG 59.181 41.667 17.00 2.72 33.59 5.34
3111 7573 3.845781 ATATCTGGATCCAAAGTGCGT 57.154 42.857 17.00 0.00 0.00 5.24
3112 7574 2.029838 ATCTGGATCCAAAGTGCGTC 57.970 50.000 17.00 0.00 0.00 5.19
3113 7575 0.684535 TCTGGATCCAAAGTGCGTCA 59.315 50.000 17.00 0.00 0.00 4.35
3114 7576 1.278985 TCTGGATCCAAAGTGCGTCAT 59.721 47.619 17.00 0.00 0.00 3.06
3115 7577 1.399440 CTGGATCCAAAGTGCGTCATG 59.601 52.381 17.00 0.00 0.00 3.07
3116 7578 1.271325 TGGATCCAAAGTGCGTCATGT 60.271 47.619 13.46 0.00 0.00 3.21
3191 7659 4.148079 TGGATTGACTAATTGGTTGTGCA 58.852 39.130 0.00 0.00 0.00 4.57
3270 7738 4.744795 TTAGGCTCTTAGCTCCTTTCTG 57.255 45.455 0.00 0.00 41.99 3.02
3369 7837 8.896744 TGGAAATAATCTGCACTTTAATCTCTG 58.103 33.333 0.00 0.00 0.00 3.35
3375 7843 3.338249 TGCACTTTAATCTCTGAGGCAC 58.662 45.455 4.59 0.00 0.00 5.01
3379 7847 4.092091 CACTTTAATCTCTGAGGCACGAAC 59.908 45.833 4.59 0.00 0.00 3.95
3393 9024 1.917955 CACGAACGAACATACGATGCT 59.082 47.619 0.14 0.00 37.03 3.79
3522 9153 6.259608 ACAATTCACTCTGCATTATCAGCTAC 59.740 38.462 0.00 0.00 34.19 3.58
3615 9246 1.488393 GCCTGCAGGGTAGAAAGATCT 59.512 52.381 33.46 0.00 36.25 2.75
3667 9298 3.576648 ACGTTAGTAGCAAAGCTCTGTC 58.423 45.455 0.00 0.00 40.44 3.51
3703 9334 7.527568 AACCTAGCCATATTAGAGTGTCTAC 57.472 40.000 0.00 0.00 0.00 2.59
3894 9529 6.052840 AGAGTCACATGCAAATATTTAGCG 57.947 37.500 0.00 0.00 0.00 4.26
3930 9566 2.105821 AGAAGTCAATTTCCGGTCCACA 59.894 45.455 0.00 0.00 0.00 4.17
3948 9584 6.016276 GGTCCACAAACAGTTGATTACAGATT 60.016 38.462 0.00 0.00 38.20 2.40
3951 9587 6.857964 CCACAAACAGTTGATTACAGATTGTC 59.142 38.462 0.00 0.00 37.22 3.18
4080 9717 5.049543 GCATGGCAGAAAACTTTAATTGCAA 60.050 36.000 0.00 0.00 0.00 4.08
4081 9718 6.595794 CATGGCAGAAAACTTTAATTGCAAG 58.404 36.000 4.94 0.00 0.00 4.01
4082 9719 5.669477 TGGCAGAAAACTTTAATTGCAAGT 58.331 33.333 4.94 4.58 35.94 3.16
4083 9720 5.523188 TGGCAGAAAACTTTAATTGCAAGTG 59.477 36.000 10.14 0.00 34.59 3.16
4084 9721 5.050159 GGCAGAAAACTTTAATTGCAAGTGG 60.050 40.000 10.14 2.42 34.59 4.00
4085 9722 5.523552 GCAGAAAACTTTAATTGCAAGTGGT 59.476 36.000 10.14 3.06 34.59 4.16
4086 9723 6.037062 GCAGAAAACTTTAATTGCAAGTGGTT 59.963 34.615 10.14 8.95 34.59 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
138 141 4.567747 GGGAGGGTTAGATTTTTCAGCTCA 60.568 45.833 0.00 0.00 0.00 4.26
280 608 2.446802 GGAATCCGCTCCCTCCCT 60.447 66.667 0.00 0.00 0.00 4.20
342 670 4.735132 TCCGACCAAGCCGAAGCG 62.735 66.667 0.00 0.00 46.67 4.68
453 781 2.670148 GGAGGGCTCCGACATGGTT 61.670 63.158 0.00 0.00 40.36 3.67
488 816 2.523168 TGTCGTGGGAGGAGTGCA 60.523 61.111 0.00 0.00 0.00 4.57
555 887 0.914417 ATGCGGAGGAAGAAGGGGAA 60.914 55.000 0.00 0.00 0.00 3.97
693 1034 1.851021 TTGCAATGGCGTCCGAAGTG 61.851 55.000 0.00 0.00 45.35 3.16
850 1211 3.119637 CCGAGGACAAGTCTTCTCTTCTC 60.120 52.174 10.08 1.74 34.03 2.87
851 1212 2.823154 CCGAGGACAAGTCTTCTCTTCT 59.177 50.000 10.08 0.00 34.03 2.85
852 1213 2.820787 TCCGAGGACAAGTCTTCTCTTC 59.179 50.000 10.08 0.00 34.03 2.87
853 1214 2.559231 GTCCGAGGACAAGTCTTCTCTT 59.441 50.000 16.75 0.00 44.02 2.85
854 1215 2.164338 GTCCGAGGACAAGTCTTCTCT 58.836 52.381 16.75 0.00 44.02 3.10
952 1313 3.417601 GGCTTAAACGGGCCGATC 58.582 61.111 35.78 8.68 38.91 3.69
1017 1409 1.664965 AGTGTTCGGTCGCTCTTGC 60.665 57.895 0.00 0.00 0.00 4.01
1108 3970 1.682005 CAATGGCGGTGGGGTGAAT 60.682 57.895 0.00 0.00 0.00 2.57
1530 4403 7.753630 AGATAGGCACAAATTGAAGATAGGAT 58.246 34.615 0.00 0.00 0.00 3.24
1568 4441 1.135699 GCGCAATCATCAAACCGCTG 61.136 55.000 0.30 0.00 38.52 5.18
1570 4443 0.863119 GAGCGCAATCATCAAACCGC 60.863 55.000 11.47 0.00 41.51 5.68
1601 4487 3.118555 TCCGGTCGGTGATTTTGTCATAT 60.119 43.478 9.36 0.00 39.48 1.78
2047 4934 6.991531 GCATCTTCTATTGTCTGAAAGGAGAT 59.008 38.462 0.00 0.00 0.00 2.75
2109 4996 4.647424 TGTTCTAAGGTTGCAACAAAGG 57.353 40.909 29.55 16.52 0.00 3.11
2176 5064 1.274596 CGACAAGTATTTCGGGACCG 58.725 55.000 3.96 3.96 41.35 4.79
2182 5070 4.868171 TCCATTCTTCCGACAAGTATTTCG 59.132 41.667 0.00 0.00 34.93 3.46
2183 5071 6.316390 ACATCCATTCTTCCGACAAGTATTTC 59.684 38.462 0.00 0.00 0.00 2.17
2184 5072 6.180472 ACATCCATTCTTCCGACAAGTATTT 58.820 36.000 0.00 0.00 0.00 1.40
2185 5073 5.745227 ACATCCATTCTTCCGACAAGTATT 58.255 37.500 0.00 0.00 0.00 1.89
2186 5074 5.359194 ACATCCATTCTTCCGACAAGTAT 57.641 39.130 0.00 0.00 0.00 2.12
2187 5075 4.819105 ACATCCATTCTTCCGACAAGTA 57.181 40.909 0.00 0.00 0.00 2.24
2188 5076 3.703001 ACATCCATTCTTCCGACAAGT 57.297 42.857 0.00 0.00 0.00 3.16
2189 5077 5.605534 AGATACATCCATTCTTCCGACAAG 58.394 41.667 0.00 0.00 0.00 3.16
2190 5078 5.614324 AGATACATCCATTCTTCCGACAA 57.386 39.130 0.00 0.00 0.00 3.18
2191 5079 6.068670 TCTAGATACATCCATTCTTCCGACA 58.931 40.000 0.00 0.00 0.00 4.35
2192 5080 6.576662 TCTAGATACATCCATTCTTCCGAC 57.423 41.667 0.00 0.00 0.00 4.79
2193 5081 6.721668 ACATCTAGATACATCCATTCTTCCGA 59.278 38.462 4.54 0.00 0.00 4.55
2194 5082 6.929625 ACATCTAGATACATCCATTCTTCCG 58.070 40.000 4.54 0.00 0.00 4.30
2232 5120 8.796475 CGGAGAAATGGATAAAAATGGATGTAT 58.204 33.333 0.00 0.00 0.00 2.29
2233 5121 7.996066 TCGGAGAAATGGATAAAAATGGATGTA 59.004 33.333 0.00 0.00 0.00 2.29
2234 5122 6.833416 TCGGAGAAATGGATAAAAATGGATGT 59.167 34.615 0.00 0.00 0.00 3.06
2235 5123 7.141363 GTCGGAGAAATGGATAAAAATGGATG 58.859 38.462 0.00 0.00 39.69 3.51
2236 5124 6.833416 TGTCGGAGAAATGGATAAAAATGGAT 59.167 34.615 0.00 0.00 39.69 3.41
2237 5125 6.184068 TGTCGGAGAAATGGATAAAAATGGA 58.816 36.000 0.00 0.00 39.69 3.41
2238 5126 6.449635 TGTCGGAGAAATGGATAAAAATGG 57.550 37.500 0.00 0.00 39.69 3.16
2239 5127 7.538575 ACTTGTCGGAGAAATGGATAAAAATG 58.461 34.615 0.00 0.00 39.69 2.32
2240 5128 7.703058 ACTTGTCGGAGAAATGGATAAAAAT 57.297 32.000 0.00 0.00 39.69 1.82
2241 5129 8.801882 ATACTTGTCGGAGAAATGGATAAAAA 57.198 30.769 0.00 0.00 39.69 1.94
2242 5130 8.801882 AATACTTGTCGGAGAAATGGATAAAA 57.198 30.769 0.00 0.00 39.69 1.52
2243 5131 8.801882 AAATACTTGTCGGAGAAATGGATAAA 57.198 30.769 0.00 0.00 39.69 1.40
2244 5132 8.801882 AAAATACTTGTCGGAGAAATGGATAA 57.198 30.769 0.00 0.00 39.69 1.75
2245 5133 7.223971 CGAAAATACTTGTCGGAGAAATGGATA 59.776 37.037 0.00 0.00 39.69 2.59
2246 5134 6.037172 CGAAAATACTTGTCGGAGAAATGGAT 59.963 38.462 0.00 0.00 39.69 3.41
2247 5135 5.350365 CGAAAATACTTGTCGGAGAAATGGA 59.650 40.000 0.00 0.00 39.69 3.41
2248 5136 5.560148 CGAAAATACTTGTCGGAGAAATGG 58.440 41.667 0.00 0.00 39.69 3.16
2257 5145 2.597305 CTCCGTCCGAAAATACTTGTCG 59.403 50.000 0.00 0.00 34.58 4.35
2258 5146 2.928116 CCTCCGTCCGAAAATACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
2259 5147 2.354403 CCCTCCGTCCGAAAATACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
2260 5148 2.093869 TCCCTCCGTCCGAAAATACTTG 60.094 50.000 0.00 0.00 0.00 3.16
2261 5149 2.167900 CTCCCTCCGTCCGAAAATACTT 59.832 50.000 0.00 0.00 0.00 2.24
2262 5150 1.755380 CTCCCTCCGTCCGAAAATACT 59.245 52.381 0.00 0.00 0.00 2.12
2263 5151 1.479730 ACTCCCTCCGTCCGAAAATAC 59.520 52.381 0.00 0.00 0.00 1.89
2264 5152 1.856629 ACTCCCTCCGTCCGAAAATA 58.143 50.000 0.00 0.00 0.00 1.40
2265 5153 1.856629 TACTCCCTCCGTCCGAAAAT 58.143 50.000 0.00 0.00 0.00 1.82
2266 5154 1.856629 ATACTCCCTCCGTCCGAAAA 58.143 50.000 0.00 0.00 0.00 2.29
2267 5155 2.734755 TATACTCCCTCCGTCCGAAA 57.265 50.000 0.00 0.00 0.00 3.46
2268 5156 2.734755 TTATACTCCCTCCGTCCGAA 57.265 50.000 0.00 0.00 0.00 4.30
2269 5157 2.965671 ATTATACTCCCTCCGTCCGA 57.034 50.000 0.00 0.00 0.00 4.55
2270 5158 6.764308 TTATTATTATACTCCCTCCGTCCG 57.236 41.667 0.00 0.00 0.00 4.79
2271 5159 8.358895 GCTATTATTATTATACTCCCTCCGTCC 58.641 40.741 0.00 0.00 0.00 4.79
2272 5160 8.910944 TGCTATTATTATTATACTCCCTCCGTC 58.089 37.037 0.00 0.00 0.00 4.79
2273 5161 8.834004 TGCTATTATTATTATACTCCCTCCGT 57.166 34.615 0.00 0.00 0.00 4.69
2307 5195 1.875514 TCTTATCATGCATGGCTTCGC 59.124 47.619 25.97 0.00 0.00 4.70
2349 5237 8.706322 AACCTTGTTCCTACATTTCATAGTTT 57.294 30.769 0.00 0.00 33.44 2.66
2405 5457 1.424638 ACATTATGGGACGGAGGGAG 58.575 55.000 0.00 0.00 0.00 4.30
2406 5458 2.779429 TACATTATGGGACGGAGGGA 57.221 50.000 0.00 0.00 0.00 4.20
2407 5459 3.849563 TTTACATTATGGGACGGAGGG 57.150 47.619 0.00 0.00 0.00 4.30
2408 5460 3.558418 CGTTTTACATTATGGGACGGAGG 59.442 47.826 0.00 0.00 0.00 4.30
2409 5461 4.033587 CACGTTTTACATTATGGGACGGAG 59.966 45.833 13.17 5.31 33.74 4.63
2410 5462 3.933955 CACGTTTTACATTATGGGACGGA 59.066 43.478 13.17 0.00 33.74 4.69
2411 5463 3.685756 ACACGTTTTACATTATGGGACGG 59.314 43.478 13.17 7.36 33.74 4.79
2412 5464 4.932268 ACACGTTTTACATTATGGGACG 57.068 40.909 0.00 4.11 35.39 4.79
2413 5465 6.815142 ACTCTACACGTTTTACATTATGGGAC 59.185 38.462 0.00 0.00 0.00 4.46
2414 5466 6.938507 ACTCTACACGTTTTACATTATGGGA 58.061 36.000 0.00 0.00 0.00 4.37
2415 5467 6.814644 TGACTCTACACGTTTTACATTATGGG 59.185 38.462 0.00 0.00 0.00 4.00
2416 5468 7.821595 TGACTCTACACGTTTTACATTATGG 57.178 36.000 0.00 0.00 0.00 2.74
2442 5494 3.823873 TGCTGTCCCATAATGACGTTTTT 59.176 39.130 0.00 0.00 35.46 1.94
2443 5495 3.190535 GTGCTGTCCCATAATGACGTTTT 59.809 43.478 0.00 0.00 35.46 2.43
2444 5496 2.747446 GTGCTGTCCCATAATGACGTTT 59.253 45.455 0.00 0.00 35.46 3.60
2445 5497 2.027192 AGTGCTGTCCCATAATGACGTT 60.027 45.455 0.00 0.00 35.46 3.99
2446 5498 1.555075 AGTGCTGTCCCATAATGACGT 59.445 47.619 0.00 0.00 35.46 4.34
2447 5499 2.315925 AGTGCTGTCCCATAATGACG 57.684 50.000 0.00 0.00 35.46 4.35
2448 5500 4.100189 ACTCTAGTGCTGTCCCATAATGAC 59.900 45.833 0.00 0.00 0.00 3.06
2449 5501 4.290093 ACTCTAGTGCTGTCCCATAATGA 58.710 43.478 0.00 0.00 0.00 2.57
2450 5502 4.679373 ACTCTAGTGCTGTCCCATAATG 57.321 45.455 0.00 0.00 0.00 1.90
2451 5503 6.808321 TTTACTCTAGTGCTGTCCCATAAT 57.192 37.500 0.00 0.00 0.00 1.28
2452 5504 6.614694 TTTTACTCTAGTGCTGTCCCATAA 57.385 37.500 0.00 0.00 0.00 1.90
2453 5505 6.614694 TTTTTACTCTAGTGCTGTCCCATA 57.385 37.500 0.00 0.00 0.00 2.74
2454 5506 5.499004 TTTTTACTCTAGTGCTGTCCCAT 57.501 39.130 0.00 0.00 0.00 4.00
2455 5507 4.967084 TTTTTACTCTAGTGCTGTCCCA 57.033 40.909 0.00 0.00 0.00 4.37
2474 5526 8.442660 TCCATCCCATAATGTAAAACCTTTTT 57.557 30.769 0.00 0.00 0.00 1.94
2475 5527 7.125659 CCTCCATCCCATAATGTAAAACCTTTT 59.874 37.037 0.00 0.00 0.00 2.27
2476 5528 6.611236 CCTCCATCCCATAATGTAAAACCTTT 59.389 38.462 0.00 0.00 0.00 3.11
2477 5529 6.136155 CCTCCATCCCATAATGTAAAACCTT 58.864 40.000 0.00 0.00 0.00 3.50
2478 5530 5.400189 CCCTCCATCCCATAATGTAAAACCT 60.400 44.000 0.00 0.00 0.00 3.50
2479 5531 4.832823 CCCTCCATCCCATAATGTAAAACC 59.167 45.833 0.00 0.00 0.00 3.27
2480 5532 5.701224 TCCCTCCATCCCATAATGTAAAAC 58.299 41.667 0.00 0.00 0.00 2.43
2481 5533 6.348478 TTCCCTCCATCCCATAATGTAAAA 57.652 37.500 0.00 0.00 0.00 1.52
2482 5534 6.544327 ATTCCCTCCATCCCATAATGTAAA 57.456 37.500 0.00 0.00 0.00 2.01
2483 5535 7.845537 ATATTCCCTCCATCCCATAATGTAA 57.154 36.000 0.00 0.00 0.00 2.41
2484 5536 7.845537 AATATTCCCTCCATCCCATAATGTA 57.154 36.000 0.00 0.00 0.00 2.29
2485 5537 6.741500 AATATTCCCTCCATCCCATAATGT 57.259 37.500 0.00 0.00 0.00 2.71
2486 5538 6.319658 CGAAATATTCCCTCCATCCCATAATG 59.680 42.308 0.00 0.00 0.00 1.90
2487 5539 6.011628 ACGAAATATTCCCTCCATCCCATAAT 60.012 38.462 0.00 0.00 0.00 1.28
2488 5540 5.312178 ACGAAATATTCCCTCCATCCCATAA 59.688 40.000 0.00 0.00 0.00 1.90
2489 5541 4.849810 ACGAAATATTCCCTCCATCCCATA 59.150 41.667 0.00 0.00 0.00 2.74
2490 5542 3.657727 ACGAAATATTCCCTCCATCCCAT 59.342 43.478 0.00 0.00 0.00 4.00
2491 5543 3.053077 ACGAAATATTCCCTCCATCCCA 58.947 45.455 0.00 0.00 0.00 4.37
2492 5544 3.790089 ACGAAATATTCCCTCCATCCC 57.210 47.619 0.00 0.00 0.00 3.85
2493 5545 5.480772 TCTCTACGAAATATTCCCTCCATCC 59.519 44.000 0.00 0.00 0.00 3.51
2494 5546 6.591750 TCTCTACGAAATATTCCCTCCATC 57.408 41.667 0.00 0.00 0.00 3.51
2495 5547 6.996180 TTCTCTACGAAATATTCCCTCCAT 57.004 37.500 0.00 0.00 0.00 3.41
2496 5548 6.801718 TTTCTCTACGAAATATTCCCTCCA 57.198 37.500 0.00 0.00 36.72 3.86
2497 5549 8.560374 CATTTTTCTCTACGAAATATTCCCTCC 58.440 37.037 0.00 0.00 41.04 4.30
2498 5550 9.326413 TCATTTTTCTCTACGAAATATTCCCTC 57.674 33.333 0.00 0.00 41.04 4.30
2499 5551 9.331282 CTCATTTTTCTCTACGAAATATTCCCT 57.669 33.333 0.00 0.00 41.04 4.20
2500 5552 9.110502 ACTCATTTTTCTCTACGAAATATTCCC 57.889 33.333 0.00 0.00 41.04 3.97
2554 5608 9.185680 TGCATAGAGTACACAGAGAAGTTATAA 57.814 33.333 0.00 0.00 0.00 0.98
2563 5617 4.926140 TCCATGCATAGAGTACACAGAG 57.074 45.455 0.00 0.00 0.00 3.35
2567 5621 7.163001 TGATCTATCCATGCATAGAGTACAC 57.837 40.000 11.90 2.77 38.50 2.90
2659 7112 7.232330 TCACCAGTGAATCCATGTCAAATTAAA 59.768 33.333 0.00 0.00 36.53 1.52
3113 7575 9.725019 TCTCTACTGAATTGAACATGTTTACAT 57.275 29.630 13.36 2.54 36.96 2.29
3114 7576 9.725019 ATCTCTACTGAATTGAACATGTTTACA 57.275 29.630 13.36 4.08 0.00 2.41
3115 7577 9.979270 CATCTCTACTGAATTGAACATGTTTAC 57.021 33.333 13.36 1.09 0.00 2.01
3116 7578 9.725019 ACATCTCTACTGAATTGAACATGTTTA 57.275 29.630 13.36 5.62 0.00 2.01
3356 7824 3.849911 TCGTGCCTCAGAGATTAAAGTG 58.150 45.455 0.00 0.00 0.00 3.16
3369 7837 0.638746 CGTATGTTCGTTCGTGCCTC 59.361 55.000 0.00 0.00 0.00 4.70
3375 7843 4.948864 AATAGCATCGTATGTTCGTTCG 57.051 40.909 0.00 0.00 0.00 3.95
3379 7847 5.651172 TTGGAAATAGCATCGTATGTTCG 57.349 39.130 0.00 0.00 0.00 3.95
3393 9024 9.558396 AATTTGACAAGCTTCAATTTGGAAATA 57.442 25.926 0.00 0.00 35.42 1.40
3703 9334 4.510167 AGGAAACATCATACCTTCCCTG 57.490 45.455 0.00 0.00 38.50 4.45
3866 9500 7.701539 AAATATTTGCATGTGACTCTTACCA 57.298 32.000 0.00 0.00 0.00 3.25
3879 9514 3.713858 TGCTGCGCTAAATATTTGCAT 57.286 38.095 9.73 0.00 34.66 3.96
3894 9529 5.869753 TGACTTCTCTATTCTTTTGCTGC 57.130 39.130 0.00 0.00 0.00 5.25
4080 9717 3.709653 TGAAGTTCTGACCACTAACCACT 59.290 43.478 4.17 0.00 0.00 4.00
4081 9718 4.067972 TGAAGTTCTGACCACTAACCAC 57.932 45.455 4.17 0.00 0.00 4.16
4082 9719 4.974645 ATGAAGTTCTGACCACTAACCA 57.025 40.909 4.17 0.00 0.00 3.67
4083 9720 5.763204 TCAAATGAAGTTCTGACCACTAACC 59.237 40.000 4.17 0.00 0.00 2.85
4084 9721 6.861065 TCAAATGAAGTTCTGACCACTAAC 57.139 37.500 4.17 0.00 0.00 2.34
4085 9722 9.567776 TTTATCAAATGAAGTTCTGACCACTAA 57.432 29.630 4.17 0.00 0.00 2.24
4086 9723 9.219603 CTTTATCAAATGAAGTTCTGACCACTA 57.780 33.333 4.17 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.