Multiple sequence alignment - TraesCS5B01G499400

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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 TraesCS5B01G499400 chr5B 100.000 3101 0 0 1 3101 665938237 665941337 0.000000e+00 5727
1 TraesCS5B01G499400 chr5B 86.467 1803 189 23 295 2079 665958156 665959921 0.000000e+00 1927
2 TraesCS5B01G499400 chr5B 82.114 492 67 11 2621 3100 665961225 665961707 4.820000e-108 401
3 TraesCS5B01G499400 chr5B 80.892 157 13 9 148 301 665912772 665912914 1.180000e-19 108
4 TraesCS5B01G499400 chr5D 93.141 1385 65 9 846 2212 528762730 528764102 0.000000e+00 2004
5 TraesCS5B01G499400 chr5D 86.724 1288 136 18 834 2100 528803240 528804513 0.000000e+00 1399
6 TraesCS5B01G499400 chr5D 84.177 1403 184 22 713 2095 528747679 528749063 0.000000e+00 1327
7 TraesCS5B01G499400 chr5D 92.222 720 46 6 1 716 528761877 528762590 0.000000e+00 1011
8 TraesCS5B01G499400 chr5D 92.135 712 30 8 2393 3101 528764111 528764799 0.000000e+00 981
9 TraesCS5B01G499400 chr5D 85.895 631 55 18 25 646 528745475 528746080 2.610000e-180 641
10 TraesCS5B01G499400 chr5D 81.166 669 104 11 2441 3100 528805275 528805930 4.580000e-143 518
11 TraesCS5B01G499400 chr5D 87.654 405 36 2 309 713 528802717 528803107 2.820000e-125 459
12 TraesCS5B01G499400 chr5D 81.404 570 92 8 2532 3100 528753028 528753584 1.310000e-123 453
13 TraesCS5B01G499400 chr5D 79.008 262 19 15 52 290 528760908 528761156 2.490000e-31 147
14 TraesCS5B01G499400 chr6B 82.199 1264 192 18 851 2095 106509354 106510603 0.000000e+00 1057
15 TraesCS5B01G499400 chr6B 80.500 400 56 11 2722 3101 106511585 106511982 1.410000e-73 287
16 TraesCS5B01G499400 chr6B 97.059 170 5 0 2217 2386 190675878 190676047 1.410000e-73 287
17 TraesCS5B01G499400 chrUn 81.205 1261 198 22 857 2095 97782359 97783602 0.000000e+00 979
18 TraesCS5B01G499400 chrUn 80.100 402 54 15 2722 3101 97784586 97784983 3.050000e-70 276
19 TraesCS5B01G499400 chr1D 82.335 985 158 11 1100 2076 476570488 476569512 0.000000e+00 841
20 TraesCS5B01G499400 chr1D 80.750 400 55 12 2722 3101 476568595 476568198 3.020000e-75 292
21 TraesCS5B01G499400 chr1D 86.395 147 20 0 2614 2760 476568736 476568590 8.900000e-36 161
22 TraesCS5B01G499400 chr1B 83.056 903 141 6 1180 2076 662843672 662842776 0.000000e+00 809
23 TraesCS5B01G499400 chr1B 94.915 177 9 0 2214 2390 136883777 136883601 8.470000e-71 278
24 TraesCS5B01G499400 chr1B 72.175 823 208 16 1173 1983 641198234 641199047 6.690000e-57 231
25 TraesCS5B01G499400 chr1B 78.295 258 36 10 2863 3101 662836822 662836566 6.930000e-32 148
26 TraesCS5B01G499400 chr4B 96.023 176 7 0 2214 2389 485923108 485922933 1.410000e-73 287
27 TraesCS5B01G499400 chr4B 93.889 180 10 1 2214 2392 89264374 89264195 1.420000e-68 270
28 TraesCS5B01G499400 chr4B 95.808 167 7 0 2214 2380 413088337 413088503 1.420000e-68 270
29 TraesCS5B01G499400 chr4B 94.798 173 9 0 2214 2386 490279330 490279502 1.420000e-68 270
30 TraesCS5B01G499400 chr4B 94.798 173 9 0 2217 2389 494592775 494592603 1.420000e-68 270
31 TraesCS5B01G499400 chr2B 95.954 173 7 0 2214 2386 634840179 634840351 6.550000e-72 281
32 TraesCS5B01G499400 chr3B 95.376 173 8 0 2214 2386 686030868 686031040 3.050000e-70 276
33 TraesCS5B01G499400 chr1A 82.323 198 31 4 1173 1368 584840466 584840661 5.320000e-38 169


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 TraesCS5B01G499400 chr5B 665938237 665941337 3100 False 5727.000000 5727 100.000000 1 3101 1 chr5B.!!$F2 3100
1 TraesCS5B01G499400 chr5B 665958156 665961707 3551 False 1164.000000 1927 84.290500 295 3100 2 chr5B.!!$F3 2805
2 TraesCS5B01G499400 chr5D 528760908 528764799 3891 False 1035.750000 2004 89.126500 1 3101 4 chr5D.!!$F2 3100
3 TraesCS5B01G499400 chr5D 528745475 528753584 8109 False 807.000000 1327 83.825333 25 3100 3 chr5D.!!$F1 3075
4 TraesCS5B01G499400 chr5D 528802717 528805930 3213 False 792.000000 1399 85.181333 309 3100 3 chr5D.!!$F3 2791
5 TraesCS5B01G499400 chr6B 106509354 106511982 2628 False 672.000000 1057 81.349500 851 3101 2 chr6B.!!$F2 2250
6 TraesCS5B01G499400 chrUn 97782359 97784983 2624 False 627.500000 979 80.652500 857 3101 2 chrUn.!!$F1 2244
7 TraesCS5B01G499400 chr1D 476568198 476570488 2290 True 431.333333 841 83.160000 1100 3101 3 chr1D.!!$R1 2001
8 TraesCS5B01G499400 chr1B 662842776 662843672 896 True 809.000000 809 83.056000 1180 2076 1 chr1B.!!$R3 896
9 TraesCS5B01G499400 chr1B 641198234 641199047 813 False 231.000000 231 72.175000 1173 1983 1 chr1B.!!$F1 810

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
800 3340 0.171007 GTGTTGGCCATCATGTTCCG 59.829 55.0 19.23 0.0 0.0 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2269 8557 0.108138 GTCTACCTTCCGCTGCATGT 60.108 55.0 0.0 0.0 0.0 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
99 1083 3.193479 AGATGCTTTAAGGGCCTTTTTCG 59.807 43.478 26.29 11.69 0.00 3.46
169 1153 1.150827 GTACCCACCAACTTGTACGC 58.849 55.000 0.00 0.00 0.00 4.42
182 1166 6.453396 CCAACTTGTACGCGTACTTTATTCTC 60.453 42.308 39.69 18.41 37.00 2.87
185 1169 4.414852 TGTACGCGTACTTTATTCTCACC 58.585 43.478 39.69 17.10 37.00 4.02
190 1174 3.302699 GCGTACTTTATTCTCACCGTCAC 59.697 47.826 0.00 0.00 0.00 3.67
212 1196 2.224426 TGATAGGCAGTTGTTGACCGTT 60.224 45.455 0.00 0.00 34.24 4.44
290 1274 1.380112 ACCAGGAGCTCGTCTACCC 60.380 63.158 5.82 0.00 0.00 3.69
301 1285 1.189524 CGTCTACCCCTTCACCCACA 61.190 60.000 0.00 0.00 0.00 4.17
318 1303 1.597302 CATCCTCGCAGCCATCAGG 60.597 63.158 0.00 0.00 38.23 3.86
389 1374 0.250166 CATCATCGCCTCTGCCATCA 60.250 55.000 0.00 0.00 0.00 3.07
392 1377 0.250166 CATCGCCTCTGCCATCATCA 60.250 55.000 0.00 0.00 0.00 3.07
427 1412 2.501261 CAGATCATGTCCGCCATCAAT 58.499 47.619 0.00 0.00 0.00 2.57
488 1473 1.336440 AGAAGATGAGATCGTCGCTGG 59.664 52.381 0.00 0.00 41.70 4.85
502 1487 2.681778 CTGGAGACGGTGGAGGCT 60.682 66.667 0.00 0.00 0.00 4.58
509 1494 3.385384 CGGTGGAGGCTCTGCTCA 61.385 66.667 15.23 0.25 0.00 4.26
522 1507 1.066914 CTGCTCAAAGACGCTGAGAC 58.933 55.000 10.11 3.80 42.51 3.36
525 1510 0.664466 CTCAAAGACGCTGAGACGCA 60.664 55.000 1.68 0.00 42.51 5.24
647 1632 1.270274 CTGCTGCACAAAAGGTATGCA 59.730 47.619 0.00 0.00 46.73 3.96
655 1640 3.069443 CACAAAAGGTATGCAAACCCAGT 59.931 43.478 0.00 0.00 40.71 4.00
661 1646 2.890945 GGTATGCAAACCCAGTTGACTT 59.109 45.455 0.00 0.00 33.02 3.01
678 1663 7.376072 CAGTTGACTTAACCAAGACGAAATTTC 59.624 37.037 8.20 8.20 40.24 2.17
682 1667 5.178809 ACTTAACCAAGACGAAATTTCTCCG 59.821 40.000 15.92 6.43 35.60 4.63
735 3272 6.141844 GCTTTTTGCGTCCTTAGTAAGAAAAC 59.858 38.462 11.66 5.87 0.00 2.43
741 3278 6.316890 TGCGTCCTTAGTAAGAAAACAAACTT 59.683 34.615 11.66 0.00 0.00 2.66
744 3281 7.165318 CGTCCTTAGTAAGAAAACAAACTTTGC 59.835 37.037 11.66 0.00 0.00 3.68
746 3283 8.188139 TCCTTAGTAAGAAAACAAACTTTGCTG 58.812 33.333 11.66 0.00 0.00 4.41
747 3284 7.043391 CCTTAGTAAGAAAACAAACTTTGCTGC 60.043 37.037 11.66 0.00 0.00 5.25
748 3285 5.965922 AGTAAGAAAACAAACTTTGCTGCT 58.034 33.333 0.00 0.00 0.00 4.24
749 3286 6.036470 AGTAAGAAAACAAACTTTGCTGCTC 58.964 36.000 0.00 0.00 0.00 4.26
751 3288 4.676546 AGAAAACAAACTTTGCTGCTCTC 58.323 39.130 0.00 0.00 0.00 3.20
800 3340 0.171007 GTGTTGGCCATCATGTTCCG 59.829 55.000 19.23 0.00 0.00 4.30
827 3367 9.389570 GACCACCGCATATTTACATTATAAAAC 57.610 33.333 0.00 0.00 0.00 2.43
831 3371 7.801315 ACCGCATATTTACATTATAAAACAGCG 59.199 33.333 0.00 0.00 35.56 5.18
869 3409 5.144100 TGTGTTGGGGTGTTTGATTTCTAT 58.856 37.500 0.00 0.00 0.00 1.98
971 3521 6.402222 TGAAATTGTTGCCTTTGTAGTGTTT 58.598 32.000 0.00 0.00 0.00 2.83
1007 3557 2.323999 TCCAGGTTGAAAATGGCCAT 57.676 45.000 14.09 14.09 33.92 4.40
1072 3622 1.886542 ACCGCATTCCTTTCACTTTCC 59.113 47.619 0.00 0.00 0.00 3.13
1105 3664 0.107456 CCCTCGCATGCAGGATAACT 59.893 55.000 27.62 0.00 31.91 2.24
1135 3694 2.253758 GCGGCTGTGACAGAAGCAA 61.254 57.895 18.18 0.00 41.36 3.91
1171 3730 4.816925 GGGATAAGGAAAAACAGGAGATCG 59.183 45.833 0.00 0.00 0.00 3.69
1186 3745 4.885907 AGGAGATCGTGGTTCGTTTATCTA 59.114 41.667 0.00 0.00 40.80 1.98
1286 3845 5.009911 TGGTTTTCAATGATCCACAGTTCAG 59.990 40.000 0.00 0.00 0.00 3.02
1625 4197 3.760684 GCTCCCTTGACAGATGACATTTT 59.239 43.478 0.00 0.00 0.00 1.82
1670 4242 4.583871 ACTTCCTTTGATGCTAGAACTGG 58.416 43.478 0.00 0.00 0.00 4.00
1679 4251 1.472878 TGCTAGAACTGGCAGAGTACG 59.527 52.381 23.66 7.46 42.20 3.67
1729 4301 1.834263 AGAAGTGTGGAGGTATGGCTC 59.166 52.381 0.00 0.00 0.00 4.70
1744 4316 3.003740 GCTCTAGCAGCCCAATCTG 57.996 57.895 0.00 0.00 43.17 2.90
1807 4379 0.582005 GTCGGTGAACAACAGTGAGC 59.418 55.000 0.00 0.00 0.00 4.26
1938 4510 5.435291 TGTGCAATTTTTCCAAAAGGTCAT 58.565 33.333 0.00 0.00 0.00 3.06
1959 4531 7.387397 GGTCATTGGATATCTAAAGAAGCTCTG 59.613 40.741 8.13 0.00 0.00 3.35
2082 4657 3.823304 GCTTCCTTGAACATCCAAAGTCT 59.177 43.478 0.00 0.00 0.00 3.24
2095 4670 3.907474 TCCAAAGTCTTCATGGGTGAGTA 59.093 43.478 3.89 0.00 35.39 2.59
2109 4796 5.766590 TGGGTGAGTAACTGATCTGATCTA 58.233 41.667 17.82 4.75 0.00 1.98
2168 5624 4.149598 ACTTCCAGTACACCAAAAATCCC 58.850 43.478 0.00 0.00 0.00 3.85
2175 5631 5.460748 CAGTACACCAAAAATCCCGAAAAAC 59.539 40.000 0.00 0.00 0.00 2.43
2189 5645 8.810990 ATCCCGAAAAACTTATAACCATTGTA 57.189 30.769 0.00 0.00 0.00 2.41
2191 5647 7.664731 TCCCGAAAAACTTATAACCATTGTACA 59.335 33.333 0.00 0.00 0.00 2.90
2192 5648 8.463607 CCCGAAAAACTTATAACCATTGTACAT 58.536 33.333 0.00 0.00 0.00 2.29
2218 8100 2.341257 ACACGCTAGCTCATGTGAAAG 58.659 47.619 22.29 2.92 36.25 2.62
2221 8103 2.232452 ACGCTAGCTCATGTGAAAGTCT 59.768 45.455 13.93 0.00 0.00 3.24
2222 8104 3.257393 CGCTAGCTCATGTGAAAGTCTT 58.743 45.455 13.93 0.00 0.00 3.01
2225 8107 4.692625 GCTAGCTCATGTGAAAGTCTTCAA 59.307 41.667 7.70 0.00 43.18 2.69
2227 8109 6.293626 GCTAGCTCATGTGAAAGTCTTCAAAA 60.294 38.462 7.70 0.00 43.18 2.44
2228 8110 5.825507 AGCTCATGTGAAAGTCTTCAAAAC 58.174 37.500 0.00 0.00 43.18 2.43
2230 8112 5.684626 GCTCATGTGAAAGTCTTCAAAACAG 59.315 40.000 0.00 0.00 43.18 3.16
2231 8113 6.135290 TCATGTGAAAGTCTTCAAAACAGG 57.865 37.500 0.00 0.00 43.18 4.00
2232 8114 4.981806 TGTGAAAGTCTTCAAAACAGGG 57.018 40.909 0.00 0.00 43.18 4.45
2233 8115 4.594970 TGTGAAAGTCTTCAAAACAGGGA 58.405 39.130 0.00 0.00 43.18 4.20
2235 8117 5.067674 TGTGAAAGTCTTCAAAACAGGGATG 59.932 40.000 0.00 0.00 43.18 3.51
2238 8120 6.831353 TGAAAGTCTTCAAAACAGGGATGTTA 59.169 34.615 0.00 0.00 38.65 2.41
2241 8123 6.542821 AGTCTTCAAAACAGGGATGTTATGA 58.457 36.000 0.00 0.00 0.00 2.15
2244 8532 7.174946 GTCTTCAAAACAGGGATGTTATGAAGA 59.825 37.037 9.98 9.98 36.66 2.87
2250 8538 5.630121 ACAGGGATGTTATGAAGACAAACA 58.370 37.500 0.00 0.00 37.51 2.83
2253 8541 7.888021 ACAGGGATGTTATGAAGACAAACAATA 59.112 33.333 0.00 0.00 36.75 1.90
2254 8542 8.400947 CAGGGATGTTATGAAGACAAACAATAG 58.599 37.037 0.00 0.00 36.75 1.73
2264 8552 8.463930 TGAAGACAAACAATAGAAATGAACCT 57.536 30.769 0.00 0.00 0.00 3.50
2265 8553 8.912988 TGAAGACAAACAATAGAAATGAACCTT 58.087 29.630 0.00 0.00 0.00 3.50
2266 8554 9.750125 GAAGACAAACAATAGAAATGAACCTTT 57.250 29.630 0.00 0.00 0.00 3.11
2274 8562 8.462016 ACAATAGAAATGAACCTTTAGACATGC 58.538 33.333 0.00 0.00 0.00 4.06
2275 8563 8.461222 CAATAGAAATGAACCTTTAGACATGCA 58.539 33.333 0.00 0.00 0.00 3.96
2278 8566 2.076100 TGAACCTTTAGACATGCAGCG 58.924 47.619 0.00 0.00 0.00 5.18
2283 8571 1.667724 CTTTAGACATGCAGCGGAAGG 59.332 52.381 0.00 0.00 0.00 3.46
2287 8575 0.175760 GACATGCAGCGGAAGGTAGA 59.824 55.000 0.00 0.00 41.81 2.59
2288 8576 0.108138 ACATGCAGCGGAAGGTAGAC 60.108 55.000 0.00 0.00 41.81 2.59
2292 8580 0.815734 GCAGCGGAAGGTAGACTACA 59.184 55.000 14.48 0.00 41.81 2.74
2294 8582 2.093106 CAGCGGAAGGTAGACTACACT 58.907 52.381 14.48 6.41 41.81 3.55
2295 8583 3.276857 CAGCGGAAGGTAGACTACACTA 58.723 50.000 14.48 0.00 41.81 2.74
2298 8586 3.312146 GCGGAAGGTAGACTACACTAGAC 59.688 52.174 14.48 0.00 0.00 2.59
2301 8589 5.064962 CGGAAGGTAGACTACACTAGACAAG 59.935 48.000 14.48 0.00 0.00 3.16
2305 8593 4.645588 GGTAGACTACACTAGACAAGCCAT 59.354 45.833 14.48 0.00 0.00 4.40
2307 8595 6.016943 GGTAGACTACACTAGACAAGCCATAG 60.017 46.154 14.48 0.00 0.00 2.23
2310 8598 5.262009 ACTACACTAGACAAGCCATAGTCA 58.738 41.667 0.00 0.00 37.23 3.41
2333 8624 7.905493 GTCAAGTAAGCAATATAGTGAAAGCAC 59.095 37.037 3.96 0.00 45.49 4.40
2348 8639 2.575694 AGCACGAAGACTATCAGCAG 57.424 50.000 0.00 0.00 0.00 4.24
2352 8643 3.626977 CACGAAGACTATCAGCAGCTAG 58.373 50.000 0.00 0.00 0.00 3.42
2354 8645 2.621055 CGAAGACTATCAGCAGCTAGGT 59.379 50.000 0.00 0.00 0.00 3.08
2356 8647 4.083537 CGAAGACTATCAGCAGCTAGGTAG 60.084 50.000 0.00 2.65 0.00 3.18
2358 8649 5.570205 AGACTATCAGCAGCTAGGTAGTA 57.430 43.478 14.29 0.00 0.00 1.82
2359 8650 6.134535 AGACTATCAGCAGCTAGGTAGTAT 57.865 41.667 14.29 10.47 0.00 2.12
2363 8654 4.119556 TCAGCAGCTAGGTAGTATGGAT 57.880 45.455 0.00 0.00 0.00 3.41
2364 8655 4.082845 TCAGCAGCTAGGTAGTATGGATC 58.917 47.826 0.00 0.00 0.00 3.36
2365 8656 3.829026 CAGCAGCTAGGTAGTATGGATCA 59.171 47.826 0.00 0.00 0.00 2.92
2367 8658 3.194542 GCAGCTAGGTAGTATGGATCAGG 59.805 52.174 0.00 0.00 0.00 3.86
2368 8659 4.667573 CAGCTAGGTAGTATGGATCAGGA 58.332 47.826 0.00 0.00 0.00 3.86
2370 8661 5.126869 CAGCTAGGTAGTATGGATCAGGATG 59.873 48.000 0.00 0.00 37.54 3.51
2372 8663 4.767000 AGGTAGTATGGATCAGGATGGA 57.233 45.455 0.00 0.00 36.16 3.41
2373 8664 5.093236 AGGTAGTATGGATCAGGATGGAA 57.907 43.478 0.00 0.00 36.16 3.53
2374 8665 5.090139 AGGTAGTATGGATCAGGATGGAAG 58.910 45.833 0.00 0.00 36.16 3.46
2376 8667 5.723887 GGTAGTATGGATCAGGATGGAAGAT 59.276 44.000 0.00 0.00 36.16 2.40
2377 8668 6.897966 GGTAGTATGGATCAGGATGGAAGATA 59.102 42.308 0.00 0.00 36.16 1.98
2378 8669 7.069331 GGTAGTATGGATCAGGATGGAAGATAG 59.931 44.444 0.00 0.00 36.16 2.08
2379 8670 6.569737 AGTATGGATCAGGATGGAAGATAGT 58.430 40.000 0.00 0.00 36.16 2.12
2380 8671 7.713518 AGTATGGATCAGGATGGAAGATAGTA 58.286 38.462 0.00 0.00 36.16 1.82
2381 8672 6.865834 ATGGATCAGGATGGAAGATAGTAC 57.134 41.667 0.00 0.00 36.16 2.73
2382 8673 4.767409 TGGATCAGGATGGAAGATAGTACG 59.233 45.833 0.00 0.00 36.16 3.67
2385 8676 6.349777 GGATCAGGATGGAAGATAGTACGAAG 60.350 46.154 0.00 0.00 36.16 3.79
2386 8677 5.691896 TCAGGATGGAAGATAGTACGAAGA 58.308 41.667 0.00 0.00 36.16 2.87
2389 8680 5.533154 AGGATGGAAGATAGTACGAAGACAG 59.467 44.000 0.00 0.00 0.00 3.51
2390 8681 4.634184 TGGAAGATAGTACGAAGACAGC 57.366 45.455 0.00 0.00 0.00 4.40
2391 8682 4.014406 TGGAAGATAGTACGAAGACAGCA 58.986 43.478 0.00 0.00 0.00 4.41
2420 8911 6.015519 CCGATGATGGATTTCTCTTCTACTCT 60.016 42.308 0.00 0.00 0.00 3.24
2451 9182 6.110033 TGTCCTTATATTTTTAGACAGCGCA 58.890 36.000 11.47 0.00 31.10 6.09
2489 9228 4.481930 TGTGTACAAGGCTTTTCGATTG 57.518 40.909 0.00 0.00 0.00 2.67
2515 9254 8.017946 GCCTTTTCTGTCTAGTTGTTAATGAAG 58.982 37.037 0.00 0.00 0.00 3.02
2555 9304 3.845781 ATAGCATGAAGGTGTTCCGAT 57.154 42.857 0.00 0.00 39.05 4.18
2558 9307 2.489329 AGCATGAAGGTGTTCCGATTTG 59.511 45.455 0.00 0.00 39.05 2.32
2594 9346 6.613233 ACTATGTATACTATTGACGCAGAGC 58.387 40.000 4.17 0.00 0.00 4.09
2649 9416 1.410517 ACCTGGTACATGATCTCGCAG 59.589 52.381 0.00 0.00 38.20 5.18
2791 9729 4.966366 GCATTTTCATGATCGTAGCAACTC 59.034 41.667 0.00 0.00 31.07 3.01
2935 9873 3.338250 TTCATGGGGCCGGAAGCT 61.338 61.111 5.05 0.00 43.05 3.74
3024 9980 1.306642 ATCACGTCGCGGAAGACTCT 61.307 55.000 6.13 0.00 38.90 3.24
3077 10033 8.842358 TCATGGAACTCCGGTATTTAAATATC 57.158 34.615 11.00 9.57 39.43 1.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 1031 8.102047 TCGGGTGGAGTTTATTTACTTATGAAA 58.898 33.333 0.00 0.00 0.00 2.69
60 1044 3.681594 GCATCTTCATCGGGTGGAGTTTA 60.682 47.826 0.00 0.00 34.78 2.01
68 1052 3.545703 CCTTAAAGCATCTTCATCGGGT 58.454 45.455 0.00 0.00 0.00 5.28
99 1083 4.929808 CCTACGCCAGAATATCATTACCAC 59.070 45.833 0.00 0.00 0.00 4.16
169 1153 4.557690 CAGTGACGGTGAGAATAAAGTACG 59.442 45.833 0.00 0.00 0.00 3.67
182 1166 3.352447 CTGCCTATCAGTGACGGTG 57.648 57.895 10.95 2.92 38.02 4.94
200 1184 1.533129 GCCAAGTCAACGGTCAACAAC 60.533 52.381 0.00 0.00 0.00 3.32
209 1193 2.051345 GGTTGCGCCAAGTCAACG 60.051 61.111 4.18 0.00 42.42 4.10
290 1274 1.450312 GCGAGGATGTGGGTGAAGG 60.450 63.158 0.00 0.00 0.00 3.46
301 1285 2.827423 CCTGATGGCTGCGAGGAT 59.173 61.111 0.00 0.00 0.00 3.24
318 1303 2.419851 CCTCTCTCAACTCCTCAATGGC 60.420 54.545 0.00 0.00 35.26 4.40
389 1374 1.878088 CTGCTTGCTCACAACACTGAT 59.122 47.619 0.00 0.00 0.00 2.90
392 1377 2.149578 GATCTGCTTGCTCACAACACT 58.850 47.619 0.00 0.00 0.00 3.55
427 1412 0.329261 ACTGCAGCTTAATCTGGCCA 59.671 50.000 15.27 4.71 34.74 5.36
436 1421 1.070134 ACGAAGTTCCACTGCAGCTTA 59.930 47.619 15.27 0.00 37.78 3.09
459 1444 3.562141 CGATCTCATCTTCTGTAGGTCGT 59.438 47.826 0.00 0.00 0.00 4.34
488 1473 2.888863 CAGAGCCTCCACCGTCTC 59.111 66.667 0.00 0.00 0.00 3.36
502 1487 0.961753 TCTCAGCGTCTTTGAGCAGA 59.038 50.000 0.00 0.00 41.41 4.26
509 1494 0.664767 GACTGCGTCTCAGCGTCTTT 60.665 55.000 2.10 0.00 46.76 2.52
647 1632 4.643334 GTCTTGGTTAAGTCAACTGGGTTT 59.357 41.667 0.00 0.00 37.30 3.27
648 1633 4.204799 GTCTTGGTTAAGTCAACTGGGTT 58.795 43.478 0.00 0.00 37.30 4.11
655 1640 7.255001 GGAGAAATTTCGTCTTGGTTAAGTCAA 60.255 37.037 12.42 0.00 35.38 3.18
661 1646 3.998341 CCGGAGAAATTTCGTCTTGGTTA 59.002 43.478 12.42 0.00 0.00 2.85
678 1663 0.532573 TTAGAGCTCAAGCACCGGAG 59.467 55.000 17.77 0.00 45.16 4.63
682 1667 4.006319 AGAACAATTAGAGCTCAAGCACC 58.994 43.478 17.77 0.00 45.16 5.01
726 3263 6.036470 AGAGCAGCAAAGTTTGTTTTCTTAC 58.964 36.000 16.70 0.00 0.00 2.34
767 3307 2.290641 GCCAACACTACCAACTCTTGTG 59.709 50.000 0.00 0.00 35.09 3.33
769 3309 1.880027 GGCCAACACTACCAACTCTTG 59.120 52.381 0.00 0.00 0.00 3.02
800 3340 7.675962 TTATAATGTAAATATGCGGTGGTCC 57.324 36.000 0.00 0.00 0.00 4.46
827 3367 6.991485 ACACAATGAACTTATTTTTCGCTG 57.009 33.333 0.00 0.00 0.00 5.18
831 3371 6.989759 ACCCCAACACAATGAACTTATTTTTC 59.010 34.615 0.00 0.00 0.00 2.29
948 3490 6.019075 GGAAACACTACAAAGGCAACAATTTC 60.019 38.462 0.00 0.00 41.41 2.17
971 3521 3.498481 CCTGGAAACACTGATTTGAGGGA 60.498 47.826 0.00 0.00 35.60 4.20
1007 3557 7.379059 TGCCCTCTCATATTCTTCATCTTAA 57.621 36.000 0.00 0.00 0.00 1.85
1072 3622 1.135575 GCGAGGGACATTTTCTTGCAG 60.136 52.381 0.00 0.00 37.73 4.41
1105 3664 2.192861 CAGCCGCTGTTGTTTCCCA 61.193 57.895 12.54 0.00 0.00 4.37
1135 3694 5.171541 TCCTTATCCCTCCCTATGACTTT 57.828 43.478 0.00 0.00 0.00 2.66
1171 3730 4.119442 TGCTCCTAGATAAACGAACCAC 57.881 45.455 0.00 0.00 0.00 4.16
1186 3745 4.260170 GTGATCTCTTTTGTGATGCTCCT 58.740 43.478 0.00 0.00 33.36 3.69
1426 3992 6.708285 TGATTAGGACCTTCTTACCAGAAAC 58.292 40.000 0.00 0.00 38.63 2.78
1670 4242 4.611807 CGATCATCTCTAACCGTACTCTGC 60.612 50.000 0.00 0.00 0.00 4.26
1679 4251 3.006003 GTCCTTCCCGATCATCTCTAACC 59.994 52.174 0.00 0.00 0.00 2.85
1744 4316 5.246203 TCATAGAGTCCAGCATATACCCAAC 59.754 44.000 0.00 0.00 0.00 3.77
1807 4379 2.743928 GGCAAGCACGTCCCAGAG 60.744 66.667 0.00 0.00 0.00 3.35
1938 4510 6.814954 ACCAGAGCTTCTTTAGATATCCAA 57.185 37.500 0.00 0.00 0.00 3.53
2082 4657 4.777366 TCAGATCAGTTACTCACCCATGAA 59.223 41.667 0.00 0.00 33.30 2.57
2095 4670 4.382470 GGTGCACACTAGATCAGATCAGTT 60.382 45.833 20.43 0.00 0.00 3.16
2109 4796 0.316204 GGTACGTGTAGGTGCACACT 59.684 55.000 20.43 15.40 45.40 3.55
2189 5645 4.713824 TGAGCTAGCGTGTAGTTTATGT 57.286 40.909 9.55 0.00 0.00 2.29
2191 5647 5.043903 CACATGAGCTAGCGTGTAGTTTAT 58.956 41.667 18.56 0.00 36.31 1.40
2192 5648 4.157105 TCACATGAGCTAGCGTGTAGTTTA 59.843 41.667 18.56 0.00 36.31 2.01
2193 5649 3.056821 TCACATGAGCTAGCGTGTAGTTT 60.057 43.478 18.56 0.00 36.31 2.66
2195 5651 2.092323 TCACATGAGCTAGCGTGTAGT 58.908 47.619 18.56 9.33 36.31 2.73
2218 8100 6.817765 TCATAACATCCCTGTTTTGAAGAC 57.182 37.500 8.51 0.00 44.80 3.01
2222 8104 6.303054 TGTCTTCATAACATCCCTGTTTTGA 58.697 36.000 7.30 7.30 45.54 2.69
2225 8107 6.549364 TGTTTGTCTTCATAACATCCCTGTTT 59.451 34.615 0.00 0.00 43.05 2.83
2227 8109 5.630121 TGTTTGTCTTCATAACATCCCTGT 58.370 37.500 0.00 0.00 37.12 4.00
2228 8110 6.573664 TTGTTTGTCTTCATAACATCCCTG 57.426 37.500 0.00 0.00 32.39 4.45
2230 8112 8.506168 TCTATTGTTTGTCTTCATAACATCCC 57.494 34.615 0.00 0.00 32.39 3.85
2238 8120 9.082313 AGGTTCATTTCTATTGTTTGTCTTCAT 57.918 29.630 0.00 0.00 0.00 2.57
2250 8538 8.579850 TGCATGTCTAAAGGTTCATTTCTATT 57.420 30.769 0.00 0.00 0.00 1.73
2253 8541 5.105997 GCTGCATGTCTAAAGGTTCATTTCT 60.106 40.000 0.00 0.00 0.00 2.52
2254 8542 5.098211 GCTGCATGTCTAAAGGTTCATTTC 58.902 41.667 0.00 0.00 0.00 2.17
2262 8550 1.667724 CTTCCGCTGCATGTCTAAAGG 59.332 52.381 0.00 0.00 0.00 3.11
2263 8551 1.667724 CCTTCCGCTGCATGTCTAAAG 59.332 52.381 0.00 0.00 0.00 1.85
2264 8552 1.003118 ACCTTCCGCTGCATGTCTAAA 59.997 47.619 0.00 0.00 0.00 1.85
2265 8553 0.613260 ACCTTCCGCTGCATGTCTAA 59.387 50.000 0.00 0.00 0.00 2.10
2266 8554 1.409064 CTACCTTCCGCTGCATGTCTA 59.591 52.381 0.00 0.00 0.00 2.59
2267 8555 0.176680 CTACCTTCCGCTGCATGTCT 59.823 55.000 0.00 0.00 0.00 3.41
2268 8556 0.175760 TCTACCTTCCGCTGCATGTC 59.824 55.000 0.00 0.00 0.00 3.06
2269 8557 0.108138 GTCTACCTTCCGCTGCATGT 60.108 55.000 0.00 0.00 0.00 3.21
2270 8558 0.176680 AGTCTACCTTCCGCTGCATG 59.823 55.000 0.00 0.00 0.00 4.06
2271 8559 1.409427 GTAGTCTACCTTCCGCTGCAT 59.591 52.381 0.00 0.00 0.00 3.96
2273 8561 0.815734 TGTAGTCTACCTTCCGCTGC 59.184 55.000 7.56 0.00 0.00 5.25
2274 8562 2.093106 AGTGTAGTCTACCTTCCGCTG 58.907 52.381 7.56 0.00 0.00 5.18
2275 8563 2.510928 AGTGTAGTCTACCTTCCGCT 57.489 50.000 7.56 0.00 0.00 5.52
2278 8566 5.163632 GCTTGTCTAGTGTAGTCTACCTTCC 60.164 48.000 7.56 0.00 0.00 3.46
2283 8571 5.838531 ATGGCTTGTCTAGTGTAGTCTAC 57.161 43.478 2.81 2.81 0.00 2.59
2287 8575 5.262009 TGACTATGGCTTGTCTAGTGTAGT 58.738 41.667 0.00 0.00 34.57 2.73
2288 8576 5.836821 TGACTATGGCTTGTCTAGTGTAG 57.163 43.478 0.00 0.00 34.57 2.74
2292 8580 6.628398 GCTTACTTGACTATGGCTTGTCTAGT 60.628 42.308 18.48 18.48 45.64 2.57
2294 8582 5.186992 TGCTTACTTGACTATGGCTTGTCTA 59.813 40.000 0.00 0.00 34.57 2.59
2295 8583 4.020218 TGCTTACTTGACTATGGCTTGTCT 60.020 41.667 0.00 0.00 34.57 3.41
2298 8586 5.824904 ATTGCTTACTTGACTATGGCTTG 57.175 39.130 0.00 0.00 0.00 4.01
2301 8589 7.872993 TCACTATATTGCTTACTTGACTATGGC 59.127 37.037 0.00 0.00 0.00 4.40
2305 8593 9.314321 GCTTTCACTATATTGCTTACTTGACTA 57.686 33.333 0.00 0.00 0.00 2.59
2307 8595 7.905493 GTGCTTTCACTATATTGCTTACTTGAC 59.095 37.037 0.00 0.00 40.03 3.18
2310 8598 6.816640 TCGTGCTTTCACTATATTGCTTACTT 59.183 34.615 0.00 0.00 40.99 2.24
2333 8624 2.621055 ACCTAGCTGCTGATAGTCTTCG 59.379 50.000 13.43 2.18 30.76 3.79
2334 8625 4.825085 ACTACCTAGCTGCTGATAGTCTTC 59.175 45.833 13.43 0.00 30.76 2.87
2340 8631 5.256806 TCCATACTACCTAGCTGCTGATA 57.743 43.478 13.43 0.92 0.00 2.15
2343 8634 3.829026 TGATCCATACTACCTAGCTGCTG 59.171 47.826 13.43 0.00 0.00 4.41
2348 8639 4.404073 CCATCCTGATCCATACTACCTAGC 59.596 50.000 0.00 0.00 0.00 3.42
2352 8643 5.087323 TCTTCCATCCTGATCCATACTACC 58.913 45.833 0.00 0.00 0.00 3.18
2354 8645 7.713518 ACTATCTTCCATCCTGATCCATACTA 58.286 38.462 0.00 0.00 0.00 1.82
2356 8647 6.865834 ACTATCTTCCATCCTGATCCATAC 57.134 41.667 0.00 0.00 0.00 2.39
2358 8649 5.420421 CGTACTATCTTCCATCCTGATCCAT 59.580 44.000 0.00 0.00 0.00 3.41
2359 8650 4.767409 CGTACTATCTTCCATCCTGATCCA 59.233 45.833 0.00 0.00 0.00 3.41
2363 8654 5.531659 GTCTTCGTACTATCTTCCATCCTGA 59.468 44.000 0.00 0.00 0.00 3.86
2364 8655 5.299531 TGTCTTCGTACTATCTTCCATCCTG 59.700 44.000 0.00 0.00 0.00 3.86
2365 8656 5.446860 TGTCTTCGTACTATCTTCCATCCT 58.553 41.667 0.00 0.00 0.00 3.24
2367 8658 5.216648 GCTGTCTTCGTACTATCTTCCATC 58.783 45.833 0.00 0.00 0.00 3.51
2368 8659 4.645136 TGCTGTCTTCGTACTATCTTCCAT 59.355 41.667 0.00 0.00 0.00 3.41
2370 8661 4.634184 TGCTGTCTTCGTACTATCTTCC 57.366 45.455 0.00 0.00 0.00 3.46
2372 8663 5.452077 GGGAATGCTGTCTTCGTACTATCTT 60.452 44.000 0.00 0.00 0.00 2.40
2373 8664 4.038162 GGGAATGCTGTCTTCGTACTATCT 59.962 45.833 0.00 0.00 0.00 1.98
2374 8665 4.299978 GGGAATGCTGTCTTCGTACTATC 58.700 47.826 0.00 0.00 0.00 2.08
2376 8667 2.098607 CGGGAATGCTGTCTTCGTACTA 59.901 50.000 0.00 0.00 0.00 1.82
2377 8668 1.135083 CGGGAATGCTGTCTTCGTACT 60.135 52.381 0.00 0.00 0.00 2.73
2378 8669 1.135199 TCGGGAATGCTGTCTTCGTAC 60.135 52.381 0.00 0.00 0.00 3.67
2379 8670 1.179152 TCGGGAATGCTGTCTTCGTA 58.821 50.000 0.00 0.00 0.00 3.43
2380 8671 0.537188 ATCGGGAATGCTGTCTTCGT 59.463 50.000 0.00 0.00 0.00 3.85
2381 8672 0.933097 CATCGGGAATGCTGTCTTCG 59.067 55.000 0.00 0.00 0.00 3.79
2382 8673 2.315925 TCATCGGGAATGCTGTCTTC 57.684 50.000 0.00 0.00 35.17 2.87
2385 8676 1.202687 TCCATCATCGGGAATGCTGTC 60.203 52.381 0.00 0.00 35.17 3.51
2386 8677 0.839277 TCCATCATCGGGAATGCTGT 59.161 50.000 0.00 0.00 35.17 4.40
2389 8680 3.152341 AGAAATCCATCATCGGGAATGC 58.848 45.455 0.00 0.00 38.09 3.56
2390 8681 4.649692 AGAGAAATCCATCATCGGGAATG 58.350 43.478 0.00 0.00 38.09 2.67
2391 8682 4.989875 AGAGAAATCCATCATCGGGAAT 57.010 40.909 0.00 0.00 38.09 3.01
2451 9182 6.877236 TGTACACATGATATCACACTGATGT 58.123 36.000 7.78 11.39 37.70 3.06
2489 9228 7.435068 TCATTAACAACTAGACAGAAAAGGC 57.565 36.000 0.00 0.00 0.00 4.35
2594 9346 6.073980 CCAAGAATTCAGTTTCAACTTGCATG 60.074 38.462 8.44 0.00 37.08 4.06
2649 9416 0.465705 TCATCGGCCAGAACAGATCC 59.534 55.000 2.24 0.00 0.00 3.36
2791 9729 1.718396 TGCTTCACGATCAAGCTGAG 58.282 50.000 15.06 0.00 45.59 3.35
2937 9875 1.337823 CCTTGTAGACTCCCACCGTTG 60.338 57.143 0.00 0.00 0.00 4.10
3024 9980 2.642311 TCATGACCTTTGGCAGTCCTAA 59.358 45.455 0.00 0.00 31.76 2.69
3077 10033 6.721571 AAATAATAACCGTGACAGTGTGAG 57.278 37.500 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.