Multiple sequence alignment - TraesCS3B01G358100

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 TraesCS3B01G358100 chr3B 100.000 2315 0 0 1 2315 571018237 571020551 0 4276
1 TraesCS3B01G358100 chr3B 91.463 1347 108 6 1 1345 808035096 808036437 0 1844
2 TraesCS3B01G358100 chr6B 95.387 1344 60 1 1 1344 564308499 564309840 0 2137
3 TraesCS3B01G358100 chr7A 94.866 1344 67 1 1 1344 29988487 29987146 0 2098
4 TraesCS3B01G358100 chr1B 94.866 1344 67 1 1 1344 41706533 41705192 0 2098
5 TraesCS3B01G358100 chr1B 93.318 1347 87 3 1 1346 31660987 31662331 0 1986
6 TraesCS3B01G358100 chr7B 94.420 1344 73 1 1 1344 722949209 722947868 0 2065
7 TraesCS3B01G358100 chr4D 88.205 1348 151 7 1 1345 482768188 482769530 0 1602
8 TraesCS3B01G358100 chr7D 88.178 1345 149 9 1 1342 139749773 139748436 0 1594
9 TraesCS3B01G358100 chrUn 85.979 1348 175 10 3 1345 298402290 298403628 0 1430
10 TraesCS3B01G358100 chr3D 92.797 833 25 11 1364 2174 434956963 434957782 0 1173
11 TraesCS3B01G358100 chr3A 89.117 974 41 28 1364 2304 573969437 573970378 0 1151


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 TraesCS3B01G358100 chr3B 571018237 571020551 2314 False 4276 4276 100.000 1 2315 1 chr3B.!!$F1 2314
1 TraesCS3B01G358100 chr3B 808035096 808036437 1341 False 1844 1844 91.463 1 1345 1 chr3B.!!$F2 1344
2 TraesCS3B01G358100 chr6B 564308499 564309840 1341 False 2137 2137 95.387 1 1344 1 chr6B.!!$F1 1343
3 TraesCS3B01G358100 chr7A 29987146 29988487 1341 True 2098 2098 94.866 1 1344 1 chr7A.!!$R1 1343
4 TraesCS3B01G358100 chr1B 41705192 41706533 1341 True 2098 2098 94.866 1 1344 1 chr1B.!!$R1 1343
5 TraesCS3B01G358100 chr1B 31660987 31662331 1344 False 1986 1986 93.318 1 1346 1 chr1B.!!$F1 1345
6 TraesCS3B01G358100 chr7B 722947868 722949209 1341 True 2065 2065 94.420 1 1344 1 chr7B.!!$R1 1343
7 TraesCS3B01G358100 chr4D 482768188 482769530 1342 False 1602 1602 88.205 1 1345 1 chr4D.!!$F1 1344
8 TraesCS3B01G358100 chr7D 139748436 139749773 1337 True 1594 1594 88.178 1 1342 1 chr7D.!!$R1 1341
9 TraesCS3B01G358100 chrUn 298402290 298403628 1338 False 1430 1430 85.979 3 1345 1 chrUn.!!$F1 1342
10 TraesCS3B01G358100 chr3D 434956963 434957782 819 False 1173 1173 92.797 1364 2174 1 chr3D.!!$F1 810
11 TraesCS3B01G358100 chr3A 573969437 573970378 941 False 1151 1151 89.117 1364 2304 1 chr3A.!!$F1 940

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
787 789 0.88649 GCCATCTTCGGCGATTCCAT 60.886 55.0 11.76 0.0 43.52 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2236 2299 0.037882 GCGCTGCATGGAGCTAGATA 60.038 55.0 32.53 0.0 45.94 1.98 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
87 88 1.614711 GGGCATGGAGGGTTGATCA 59.385 57.895 0.00 0.00 0.00 2.92
171 172 5.052481 CCAAGACAGCGATCTGATTTCATA 58.948 41.667 0.00 0.00 42.95 2.15
210 211 1.139058 AGTGGCGTTTTCTCTGTCAGT 59.861 47.619 0.00 0.00 0.00 3.41
326 327 1.473965 CGTATGGCAAGCATCAGTCCT 60.474 52.381 0.00 0.00 0.00 3.85
436 437 5.128827 ACATCTACTTGTCGGTTATGTGGAT 59.871 40.000 0.00 0.00 30.84 3.41
445 446 4.094442 GTCGGTTATGTGGATTGGAAGAAC 59.906 45.833 0.00 0.00 0.00 3.01
496 497 3.211963 ATGCGCGAGGGATTTGGC 61.212 61.111 12.10 0.00 0.00 4.52
705 706 1.026718 CGGTGGAATTCCTGGACAGC 61.027 60.000 24.73 12.68 36.82 4.40
787 789 0.886490 GCCATCTTCGGCGATTCCAT 60.886 55.000 11.76 0.00 43.52 3.41
789 791 1.270518 CCATCTTCGGCGATTCCATCT 60.271 52.381 11.76 0.00 34.01 2.90
912 914 4.230002 GCGGCCGGTATGGTGCTA 62.230 66.667 29.38 0.00 41.21 3.49
977 979 3.414700 CCACTGCAACGACGCTCC 61.415 66.667 0.00 0.00 0.00 4.70
996 998 2.035442 GGAGGCTGAACTTCACGCC 61.035 63.158 17.80 17.80 39.41 5.68
1033 1035 0.321564 CTTGGCCATCCAACACTCGA 60.322 55.000 6.09 0.00 46.89 4.04
1299 1301 1.557099 TGTGGCCTCTCGACTGTAAT 58.443 50.000 3.32 0.00 0.00 1.89
1328 1330 7.687941 TGACATCTTGAATAAAACTCCCTTC 57.312 36.000 0.00 0.00 0.00 3.46
1406 1408 3.987868 GGAAGAAACAAAATTTCCTCGGC 59.012 43.478 0.00 0.00 36.88 5.54
1434 1436 1.135333 GTTTGCCAAACCGAGGAACAA 59.865 47.619 9.18 0.00 35.35 2.83
1450 1452 0.621862 ACAACCTCTCCATCCCTCCC 60.622 60.000 0.00 0.00 0.00 4.30
1602 1612 4.008933 GACCGCAGTGACTGGCCT 62.009 66.667 15.24 0.00 31.21 5.19
1631 1651 0.394488 TGGCTACCTCCTCAGACTCG 60.394 60.000 0.00 0.00 0.00 4.18
1727 1747 3.386237 GCGAGACAGACCCAGCCT 61.386 66.667 0.00 0.00 0.00 4.58
1744 1772 4.328041 TCTGCGTGAGAGAGAGGG 57.672 61.111 0.00 0.00 0.00 4.30
1754 1782 1.421646 GAGAGAGAGGGAGAGAGAGGG 59.578 61.905 0.00 0.00 0.00 4.30
1772 1800 1.232119 GGAGTAGGAGTAGCTCGCTC 58.768 60.000 9.11 9.11 0.00 5.03
1977 2037 1.557188 CCTTGGTAAGGGAGGGAAGGA 60.557 57.143 0.00 0.00 45.27 3.36
1984 2044 2.647949 GGGAGGGAAGGAGAGGGGA 61.648 68.421 0.00 0.00 0.00 4.81
2151 2214 2.495409 CCTCGCCCGTATGTGCCTA 61.495 63.158 0.00 0.00 0.00 3.93
2155 2218 1.299926 GCCCGTATGTGCCTACTCG 60.300 63.158 0.00 0.00 0.00 4.18
2167 2230 1.227664 CTACTCGCTCTCTCCCCCA 59.772 63.158 0.00 0.00 0.00 4.96
2169 2232 2.888464 TACTCGCTCTCTCCCCCACG 62.888 65.000 0.00 0.00 0.00 4.94
2202 2265 1.633852 CTCGCTGCTCCTGCTTGTTC 61.634 60.000 0.00 0.00 40.48 3.18
2203 2266 1.670406 CGCTGCTCCTGCTTGTTCT 60.670 57.895 0.00 0.00 40.48 3.01
2204 2267 1.233285 CGCTGCTCCTGCTTGTTCTT 61.233 55.000 0.00 0.00 40.48 2.52
2205 2268 0.520847 GCTGCTCCTGCTTGTTCTTC 59.479 55.000 0.00 0.00 40.48 2.87
2211 2274 5.804639 TGCTCCTGCTTGTTCTTCTTATTA 58.195 37.500 0.00 0.00 40.48 0.98
2243 2306 4.127726 GCCGTACGCGTATCTAGC 57.872 61.111 23.56 17.89 36.15 3.42
2244 2307 1.573436 GCCGTACGCGTATCTAGCT 59.427 57.895 23.56 0.00 36.15 3.32
2245 2308 0.452452 GCCGTACGCGTATCTAGCTC 60.452 60.000 23.56 6.48 36.15 4.09
2283 2346 4.402155 GGTGGCCACTGATTTGATTGATTA 59.598 41.667 33.91 0.00 0.00 1.75
2304 2367 1.086696 CGCCTAATCCTGTGTGTTGG 58.913 55.000 0.00 0.00 0.00 3.77
2305 2368 1.610624 CGCCTAATCCTGTGTGTTGGT 60.611 52.381 0.00 0.00 0.00 3.67
2306 2369 2.514803 GCCTAATCCTGTGTGTTGGTT 58.485 47.619 0.00 0.00 0.00 3.67
2307 2370 2.488153 GCCTAATCCTGTGTGTTGGTTC 59.512 50.000 0.00 0.00 0.00 3.62
2308 2371 3.081804 CCTAATCCTGTGTGTTGGTTCC 58.918 50.000 0.00 0.00 0.00 3.62
2309 2372 3.244911 CCTAATCCTGTGTGTTGGTTCCT 60.245 47.826 0.00 0.00 0.00 3.36
2310 2373 2.568623 ATCCTGTGTGTTGGTTCCTC 57.431 50.000 0.00 0.00 0.00 3.71
2311 2374 0.105964 TCCTGTGTGTTGGTTCCTCG 59.894 55.000 0.00 0.00 0.00 4.63
2312 2375 0.179056 CCTGTGTGTTGGTTCCTCGT 60.179 55.000 0.00 0.00 0.00 4.18
2313 2376 0.937304 CTGTGTGTTGGTTCCTCGTG 59.063 55.000 0.00 0.00 0.00 4.35
2314 2377 1.092921 TGTGTGTTGGTTCCTCGTGC 61.093 55.000 0.00 0.00 0.00 5.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
111 112 6.270695 TCTTGAGGATATGCTGAACATCCATA 59.729 38.462 0.00 0.00 40.67 2.74
171 172 2.900546 ACTCTTCTCTGGAAACCACGAT 59.099 45.455 0.00 0.00 0.00 3.73
210 211 9.243105 TCATATGTAGCTAATCTGTATGCACTA 57.757 33.333 1.90 0.00 0.00 2.74
326 327 2.897436 CCGTGATCTTCATCTTCTGCA 58.103 47.619 0.00 0.00 0.00 4.41
436 437 0.555769 AAGGTGCCCTGTTCTTCCAA 59.444 50.000 0.00 0.00 32.13 3.53
445 446 2.036098 TGCATGGAAGGTGCCCTG 59.964 61.111 0.00 0.00 41.83 4.45
489 490 1.588139 GCGCATCTGCAGCCAAATC 60.588 57.895 9.47 0.00 42.21 2.17
496 497 1.881709 ATCTGTCGCGCATCTGCAG 60.882 57.895 7.63 7.63 42.21 4.41
705 706 7.434307 CCAGCAAGCTTGATTGATTTGTAATAG 59.566 37.037 30.39 6.74 31.55 1.73
912 914 1.079819 CTGTCCTTGATGGTCGCGT 60.080 57.895 5.77 0.00 37.07 6.01
977 979 2.383527 GCGTGAAGTTCAGCCTCCG 61.384 63.158 5.62 7.12 0.00 4.63
1033 1035 1.111116 TGAACGACGACTGGGGACTT 61.111 55.000 0.00 0.00 0.00 3.01
1244 1246 4.072088 GAACCGAGCGCAACCACG 62.072 66.667 11.47 7.07 0.00 4.94
1299 1301 9.832445 GGGAGTTTTATTCAAGATGTCATAGTA 57.168 33.333 0.00 0.00 0.00 1.82
1345 1347 5.655893 ATTTGCGGTTCTTGTTTGAATTG 57.344 34.783 0.00 0.00 0.00 2.32
1346 1348 6.238347 GGAAATTTGCGGTTCTTGTTTGAATT 60.238 34.615 0.00 0.00 0.00 2.17
1347 1349 5.236263 GGAAATTTGCGGTTCTTGTTTGAAT 59.764 36.000 0.00 0.00 0.00 2.57
1348 1350 4.568760 GGAAATTTGCGGTTCTTGTTTGAA 59.431 37.500 0.00 0.00 0.00 2.69
1349 1351 4.116238 GGAAATTTGCGGTTCTTGTTTGA 58.884 39.130 0.00 0.00 0.00 2.69
1350 1352 3.247411 GGGAAATTTGCGGTTCTTGTTTG 59.753 43.478 3.43 0.00 0.00 2.93
1351 1353 3.462982 GGGAAATTTGCGGTTCTTGTTT 58.537 40.909 3.43 0.00 0.00 2.83
1352 1354 2.544903 CGGGAAATTTGCGGTTCTTGTT 60.545 45.455 8.79 0.00 0.00 2.83
1353 1355 1.000717 CGGGAAATTTGCGGTTCTTGT 60.001 47.619 8.79 0.00 0.00 3.16
1354 1356 1.268352 TCGGGAAATTTGCGGTTCTTG 59.732 47.619 15.17 0.00 0.00 3.02
1355 1357 1.539827 CTCGGGAAATTTGCGGTTCTT 59.460 47.619 15.17 0.00 0.00 2.52
1356 1358 1.165270 CTCGGGAAATTTGCGGTTCT 58.835 50.000 15.17 0.00 0.00 3.01
1357 1359 0.170339 CCTCGGGAAATTTGCGGTTC 59.830 55.000 15.17 0.00 0.00 3.62
1358 1360 0.250989 TCCTCGGGAAATTTGCGGTT 60.251 50.000 15.17 0.00 0.00 4.44
1359 1361 0.034477 ATCCTCGGGAAATTTGCGGT 60.034 50.000 15.17 0.00 34.34 5.68
1360 1362 0.381801 CATCCTCGGGAAATTTGCGG 59.618 55.000 10.45 10.45 34.34 5.69
1361 1363 0.248621 GCATCCTCGGGAAATTTGCG 60.249 55.000 3.43 0.00 34.34 4.85
1362 1364 0.103026 GGCATCCTCGGGAAATTTGC 59.897 55.000 0.22 0.22 34.40 3.68
1406 1408 1.362355 GTTTGGCAAACTGGGACGG 59.638 57.895 30.54 0.00 38.35 4.79
1434 1436 1.316266 CAGGGAGGGATGGAGAGGT 59.684 63.158 0.00 0.00 0.00 3.85
1444 1446 2.718073 CGTACCGTTCCAGGGAGGG 61.718 68.421 4.72 4.72 38.24 4.30
1450 1452 2.681064 TCCCCCGTACCGTTCCAG 60.681 66.667 0.00 0.00 0.00 3.86
1620 1640 0.393673 CTCTGCTCCGAGTCTGAGGA 60.394 60.000 12.83 9.34 34.93 3.71
1631 1651 3.191539 CGAAAGGCGCTCTGCTCC 61.192 66.667 7.64 0.00 45.43 4.70
1727 1747 0.393673 CTCCCTCTCTCTCACGCAGA 60.394 60.000 0.00 0.00 0.00 4.26
1744 1772 3.244457 GCTACTCCTACTCCCTCTCTCTC 60.244 56.522 0.00 0.00 0.00 3.20
1754 1782 0.863144 CGAGCGAGCTACTCCTACTC 59.137 60.000 9.95 0.00 0.00 2.59
1772 1800 2.027751 GGGCTAGTAGCTTCGCCG 59.972 66.667 21.20 0.00 43.38 6.46
1832 1865 3.486383 TCTTTTTGATCGCTTCTTGGGT 58.514 40.909 0.00 0.00 0.00 4.51
2151 2214 2.363147 GTGGGGGAGAGAGCGAGT 60.363 66.667 0.00 0.00 0.00 4.18
2155 2218 3.462678 GGTCGTGGGGGAGAGAGC 61.463 72.222 0.00 0.00 0.00 4.09
2167 2230 4.680537 AGCGAGGGAGGTGGTCGT 62.681 66.667 0.00 0.00 36.09 4.34
2169 2232 3.827898 CGAGCGAGGGAGGTGGTC 61.828 72.222 0.00 0.00 0.00 4.02
2188 2251 2.645838 AAGAAGAACAAGCAGGAGCA 57.354 45.000 0.00 0.00 45.49 4.26
2202 2265 4.254492 GCGGGGAGGCTAATAATAAGAAG 58.746 47.826 0.00 0.00 0.00 2.85
2203 2266 3.008704 GGCGGGGAGGCTAATAATAAGAA 59.991 47.826 0.00 0.00 42.90 2.52
2204 2267 2.570302 GGCGGGGAGGCTAATAATAAGA 59.430 50.000 0.00 0.00 42.90 2.10
2205 2268 2.677037 CGGCGGGGAGGCTAATAATAAG 60.677 54.545 0.00 0.00 44.22 1.73
2231 2294 0.039074 GCATGGAGCTAGATACGCGT 60.039 55.000 19.17 19.17 41.15 6.01
2232 2295 0.039165 TGCATGGAGCTAGATACGCG 60.039 55.000 3.53 3.53 45.94 6.01
2234 2297 1.707632 GCTGCATGGAGCTAGATACG 58.292 55.000 29.72 0.00 45.94 3.06
2235 2298 1.707632 CGCTGCATGGAGCTAGATAC 58.292 55.000 32.53 6.66 45.94 2.24
2236 2299 0.037882 GCGCTGCATGGAGCTAGATA 60.038 55.000 32.53 0.00 45.94 1.98
2239 2302 2.202974 TGCGCTGCATGGAGCTAG 60.203 61.111 32.53 21.02 45.94 3.42
2240 2303 2.202974 CTGCGCTGCATGGAGCTA 60.203 61.111 32.53 21.53 45.94 3.32
2261 2324 4.460948 AATCAATCAAATCAGTGGCCAC 57.539 40.909 29.22 29.22 0.00 5.01
2268 2331 7.805071 GGATTAGGCGTTAATCAATCAAATCAG 59.195 37.037 17.63 0.00 46.30 2.90
2283 2346 2.151202 CAACACACAGGATTAGGCGTT 58.849 47.619 0.00 0.00 0.00 4.84


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

AutoCloner maintained by Alex Coulton.