Multiple sequence alignment - TraesCS2D01G224400

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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 TraesCS2D01G224400 chr2D 100.000 2631 0 0 1 2631 192157923 192155293 0.000000e+00 4859
1 TraesCS2D01G224400 chr2A 91.750 2715 118 40 1 2630 206116067 206118760 0.000000e+00 3675
2 TraesCS2D01G224400 chr2B 91.319 2373 102 34 1 2300 248155428 248157769 0.000000e+00 3145
3 TraesCS2D01G224400 chr2B 91.640 311 14 6 2321 2630 248157906 248158205 1.130000e-113 420
4 TraesCS2D01G224400 chr1D 85.354 198 29 0 1125 1322 412023168 412023365 3.430000e-49 206
5 TraesCS2D01G224400 chr1B 85.354 198 29 0 1125 1322 555293857 555294054 3.430000e-49 206
6 TraesCS2D01G224400 chr1A 83.796 216 35 0 1125 1340 508527372 508527587 3.430000e-49 206


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 TraesCS2D01G224400 chr2D 192155293 192157923 2630 True 4859.0 4859 100.0000 1 2631 1 chr2D.!!$R1 2630
1 TraesCS2D01G224400 chr2A 206116067 206118760 2693 False 3675.0 3675 91.7500 1 2630 1 chr2A.!!$F1 2629
2 TraesCS2D01G224400 chr2B 248155428 248158205 2777 False 1782.5 3145 91.4795 1 2630 2 chr2B.!!$F1 2629

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
220 238 0.886563 TCTCGTTCTCTTTCGACCCC 59.113 55.0 0.0 0.0 32.65 4.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2211 2300 1.131126 GTGCATCAACGGTCAATGAGG 59.869 52.381 0.0 0.0 0.0 3.86 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
28 29 3.164269 CGCCTCCCAGGGTATGCT 61.164 66.667 5.01 0.00 35.37 3.79
29 30 2.832498 GCCTCCCAGGGTATGCTC 59.168 66.667 5.01 0.00 35.37 4.26
81 84 4.065088 GGTCTGTTGTTGATCTGCAGTTA 58.935 43.478 14.67 0.00 0.00 2.24
97 100 6.990349 TCTGCAGTTAAGTTATGTATTAGGGC 59.010 38.462 14.67 0.00 0.00 5.19
107 110 2.986050 TGTATTAGGGCCCCCTTCTAG 58.014 52.381 21.43 0.00 45.70 2.43
165 181 4.053295 CGTCTTCCGTGGTTCTTTCTTAA 58.947 43.478 0.00 0.00 0.00 1.85
220 238 0.886563 TCTCGTTCTCTTTCGACCCC 59.113 55.000 0.00 0.00 32.65 4.95
233 251 5.427481 TCTTTCGACCCCTATTGATAAGGTT 59.573 40.000 0.00 0.00 31.70 3.50
318 336 9.462606 TTTTAAGAAGAAGATTAGGGATTCCAC 57.537 33.333 4.80 0.00 34.83 4.02
320 338 6.245890 AGAAGAAGATTAGGGATTCCACTG 57.754 41.667 4.80 0.00 34.83 3.66
370 400 7.283127 AGCTCCATACATGTATTTTCATTTCGT 59.717 33.333 15.85 0.00 0.00 3.85
497 529 8.055279 TGTGATCTTGAAGTTGAAAGAAAACT 57.945 30.769 0.00 0.00 39.55 2.66
732 777 5.024785 TGTGGTGTAAGTGTGTTGTCATA 57.975 39.130 0.00 0.00 0.00 2.15
775 820 8.485578 TGTTCCTTGGTTTTGGTATAGAAATT 57.514 30.769 0.00 0.00 0.00 1.82
776 821 8.364142 TGTTCCTTGGTTTTGGTATAGAAATTG 58.636 33.333 0.00 0.00 0.00 2.32
780 825 6.189677 TGGTTTTGGTATAGAAATTGCTCG 57.810 37.500 0.00 0.00 0.00 5.03
795 840 3.476295 TGCTCGCTGATTTGTTGATTC 57.524 42.857 0.00 0.00 0.00 2.52
871 916 1.153524 AGTGGTCAAAGCCATGGCA 59.846 52.632 37.18 15.37 44.88 4.92
911 956 6.169419 TGAGAAATTACGAAGCTGTCATTG 57.831 37.500 0.00 0.00 0.00 2.82
1123 1168 7.374272 TGCTTAATTGTTTTGCTGCTACATAA 58.626 30.769 0.00 0.00 0.00 1.90
1241 1286 2.348998 CTGACCACTGTCCAGGGC 59.651 66.667 0.00 0.00 41.01 5.19
1353 1398 2.477189 GGACAGGTGTGTTGAAACAACG 60.477 50.000 9.49 0.00 42.82 4.10
1380 1425 5.359194 AACTCGTCATCCCTTATCATGTT 57.641 39.130 0.00 0.00 0.00 2.71
1386 1431 6.483307 TCGTCATCCCTTATCATGTTCATTTC 59.517 38.462 0.00 0.00 0.00 2.17
1428 1473 5.106396 GCAAGCTAGTTGTCTTGATCATTGT 60.106 40.000 10.85 0.00 41.50 2.71
1441 1486 5.988310 TGATCATTGTTGCTCTTTTCCAT 57.012 34.783 0.00 0.00 0.00 3.41
1582 1632 7.277174 AGATGTCTAATATGATGTGTCGACA 57.723 36.000 15.76 15.76 36.22 4.35
1631 1681 6.491062 ACACATCAAGATTCATGGTTTCTGAA 59.509 34.615 0.00 0.00 37.06 3.02
1713 1763 1.872388 TTTAGTTGTGTGCTAGCGCA 58.128 45.000 26.57 26.57 45.60 6.09
1749 1799 0.591488 TTGCGCGCTCTGAGTATACG 60.591 55.000 33.29 6.49 0.00 3.06
1794 1844 1.396996 CTGCGTGTATGCTTGTTACCC 59.603 52.381 0.00 0.00 35.36 3.69
1963 2013 6.689241 GTCGATACATCTAGTCTTGAACTGTG 59.311 42.308 0.00 0.00 39.11 3.66
1974 2030 4.060900 TCTTGAACTGTGTCTGCTTGATC 58.939 43.478 0.00 0.00 0.00 2.92
1985 2041 6.486320 TGTGTCTGCTTGATCACTGAATTAAA 59.514 34.615 0.00 0.00 32.14 1.52
1997 2053 3.256631 ACTGAATTAAACTGCCTGCTTGG 59.743 43.478 0.00 0.00 39.35 3.61
2176 2265 0.734253 CACACTGTGCGGCTCTCTAC 60.734 60.000 7.90 0.00 0.00 2.59
2211 2300 1.481871 TCCCATCTTACGTCAGACCC 58.518 55.000 0.61 0.00 0.00 4.46
2253 2343 0.982852 TTGATCCACGGAGGGCATCT 60.983 55.000 0.00 0.00 38.24 2.90
2287 2386 1.303561 TGGTCCAGCAAGGCATGTC 60.304 57.895 0.00 0.00 37.29 3.06
2412 2627 1.080705 GGTCTGACCTGGACGAACG 60.081 63.158 19.53 0.00 34.73 3.95
2418 2633 1.000060 TGACCTGGACGAACGTTTAGG 60.000 52.381 20.52 20.52 37.46 2.69
2443 2658 1.832912 GATTGGATGACCGGCTCCT 59.167 57.895 16.68 1.55 39.42 3.69
2491 2706 2.011222 TCGTTTTGGAAGTCAGCGTTT 58.989 42.857 0.00 0.00 0.00 3.60
2557 2773 9.974980 AATATTTTTACCAACGACAAAATCACT 57.025 25.926 0.00 0.00 32.42 3.41
2630 2846 2.301346 CACCAAAAACTGAGGCTGAGT 58.699 47.619 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 0.914644 CCAAGAATCAGAGCAGGGGA 59.085 55.000 0.00 0.00 0.00 4.81
29 30 0.622665 ACCAAGAATCAGAGCAGGGG 59.377 55.000 0.00 0.00 0.00 4.79
81 84 3.688196 AGGGGGCCCTAATACATAACTT 58.312 45.455 24.38 0.00 46.14 2.66
107 110 5.960811 TCCATAATCATACAGATCCTCTCCC 59.039 44.000 0.00 0.00 35.39 4.30
165 181 2.577593 GCTCGACCCTAAACGGCT 59.422 61.111 0.00 0.00 0.00 5.52
248 266 7.962964 CAATCAATACCCGATTGTACAGTAT 57.037 36.000 0.00 0.00 44.66 2.12
295 313 7.403231 ACAGTGGAATCCCTAATCTTCTTCTTA 59.597 37.037 0.00 0.00 0.00 2.10
296 314 6.216456 ACAGTGGAATCCCTAATCTTCTTCTT 59.784 38.462 0.00 0.00 0.00 2.52
297 315 5.728741 ACAGTGGAATCCCTAATCTTCTTCT 59.271 40.000 0.00 0.00 0.00 2.85
385 416 3.947834 ACAAATTTATCCCCTTCGCTCAG 59.052 43.478 0.00 0.00 0.00 3.35
517 555 6.168389 TCAATTTTTCTTAGGTAGTCCGGAC 58.832 40.000 27.67 27.67 39.05 4.79
685 730 5.359009 AGCAATCATCACTGTTCTAATTGGG 59.641 40.000 0.00 0.00 0.00 4.12
732 777 4.494484 GAACAACAGTCAAAGCCAAACTT 58.506 39.130 0.00 0.00 41.70 2.66
775 820 3.076621 AGAATCAACAAATCAGCGAGCA 58.923 40.909 0.00 0.00 0.00 4.26
776 821 3.754188 AGAATCAACAAATCAGCGAGC 57.246 42.857 0.00 0.00 0.00 5.03
780 825 9.852091 AAAGAAAGATAGAATCAACAAATCAGC 57.148 29.630 0.00 0.00 0.00 4.26
871 916 6.403866 TTTCTCATTTGTACAACCAAGCAT 57.596 33.333 8.07 0.00 0.00 3.79
911 956 2.028567 GGGCATGCAGTATAGAGAGGTC 60.029 54.545 21.36 0.00 0.00 3.85
1068 1113 3.246699 CCAAACAGTGCAAGCAATTTCAG 59.753 43.478 0.00 0.00 0.00 3.02
1123 1168 2.757077 CCTCGGCAAAGGGGTCTT 59.243 61.111 0.00 0.00 32.35 3.01
1241 1286 3.259374 TGTAGCTGAACTCCTTCTTCAGG 59.741 47.826 0.00 0.00 43.34 3.86
1353 1398 2.100605 AAGGGATGACGAGTTTGCTC 57.899 50.000 0.00 0.00 38.35 4.26
1365 1410 7.859377 CGAAAGAAATGAACATGATAAGGGATG 59.141 37.037 0.00 0.00 0.00 3.51
1380 1425 6.089820 GCATGAGAAAATTGCGAAAGAAATGA 59.910 34.615 0.00 0.00 38.81 2.57
1386 1431 4.433805 GCTTGCATGAGAAAATTGCGAAAG 60.434 41.667 3.33 0.00 39.23 2.62
1428 1473 3.157087 GACCTGGAATGGAAAAGAGCAA 58.843 45.455 0.00 0.00 0.00 3.91
1441 1486 2.040278 CCTGGAGTTGAATGACCTGGAA 59.960 50.000 0.00 0.00 41.78 3.53
1582 1632 1.973281 CTTCACAATGCCGGCCTGT 60.973 57.895 26.77 24.00 0.00 4.00
1631 1681 1.561076 TGATATGGAGCTGGCAGTTGT 59.439 47.619 17.16 0.67 0.00 3.32
1749 1799 3.149981 GGTGGGCTATGCTAGATTTTCC 58.850 50.000 0.00 0.00 0.00 3.13
1794 1844 5.743872 GCTCCTTACAAAGTTTCAACACAAG 59.256 40.000 0.00 0.00 0.00 3.16
1883 1933 3.181465 GGATGATACGAAGGACACCACAT 60.181 47.826 0.00 0.00 0.00 3.21
1884 1934 2.167693 GGATGATACGAAGGACACCACA 59.832 50.000 0.00 0.00 0.00 4.17
1890 1940 4.881850 ACCAAAATGGATGATACGAAGGAC 59.118 41.667 2.85 0.00 40.96 3.85
1963 2013 7.020010 CAGTTTAATTCAGTGATCAAGCAGAC 58.980 38.462 0.00 0.00 0.00 3.51
1974 2030 4.232221 CAAGCAGGCAGTTTAATTCAGTG 58.768 43.478 0.00 0.00 0.00 3.66
1997 2053 2.804212 GCCCAGAATAATTGGTGCATGC 60.804 50.000 11.82 11.82 34.23 4.06
2080 2140 4.087892 AGTAGCCGCAGCACCAGG 62.088 66.667 0.00 0.00 43.56 4.45
2081 2141 2.510238 GAGTAGCCGCAGCACCAG 60.510 66.667 0.00 0.00 43.56 4.00
2167 2256 3.075148 GTTTCCCTGTTTGTAGAGAGCC 58.925 50.000 0.00 0.00 0.00 4.70
2176 2265 3.865700 GGAAGCGTTTCCCTGTTTG 57.134 52.632 19.49 0.00 46.03 2.93
2195 2284 2.100197 TGAGGGGTCTGACGTAAGATG 58.900 52.381 5.75 0.00 43.62 2.90
2211 2300 1.131126 GTGCATCAACGGTCAATGAGG 59.869 52.381 0.00 0.00 0.00 3.86
2253 2343 5.186256 TGGACCAGCTATCCAAAAATGTA 57.814 39.130 15.01 0.00 43.43 2.29
2287 2386 1.402787 ACCAAAACAGTCCCTGCAAG 58.597 50.000 0.00 0.00 34.37 4.01
2300 2399 8.474025 AGTTTTAATGTCTGATCACAACCAAAA 58.526 29.630 0.00 0.00 0.00 2.44
2301 2400 8.006298 AGTTTTAATGTCTGATCACAACCAAA 57.994 30.769 0.00 0.00 0.00 3.28
2302 2401 7.581213 AGTTTTAATGTCTGATCACAACCAA 57.419 32.000 0.00 0.00 0.00 3.67
2303 2402 8.862325 ATAGTTTTAATGTCTGATCACAACCA 57.138 30.769 0.00 0.00 0.00 3.67
2412 2627 2.341846 TCCAATCGCATCCCCTAAAC 57.658 50.000 0.00 0.00 0.00 2.01
2418 2633 1.230635 CGGTCATCCAATCGCATCCC 61.231 60.000 0.00 0.00 0.00 3.85
2443 2658 3.610619 CTGTCCGGGCAGTGATGCA 62.611 63.158 28.25 0.00 36.33 3.96
2505 2720 6.849151 ACTCCTCAATTTTTAGGGTAAGTGT 58.151 36.000 0.00 0.00 33.40 3.55


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

AutoCloner maintained by Alex Coulton.