Multiple sequence alignment - TraesCS6B01G365400

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 TraesCS6B01G365400 chr6B 100.000 1969 0 0 1 1969 637145542 637143574 0.000000e+00 3637
1 TraesCS6B01G365400 chr6B 100.000 301 0 0 2270 2570 637143273 637142973 8.030000e-155 556
2 TraesCS6B01G365400 chr4D 92.208 1078 82 2 893 1969 639020 637944 0.000000e+00 1524
3 TraesCS6B01G365400 chr4D 90.676 858 78 2 1 857 658335 657479 0.000000e+00 1140
4 TraesCS6B01G365400 chr2B 91.261 1110 95 2 861 1969 784891054 784889946 0.000000e+00 1511
5 TraesCS6B01G365400 chr2B 89.431 1107 105 10 858 1960 773662255 773661157 0.000000e+00 1386
6 TraesCS6B01G365400 chr2B 90.316 1012 90 7 960 1969 693431517 693432522 0.000000e+00 1319
7 TraesCS6B01G365400 chr2B 90.105 859 81 3 2 857 784891992 784891135 0.000000e+00 1112
8 TraesCS6B01G365400 chr2B 87.485 839 97 7 22 857 773663166 773662333 0.000000e+00 961
9 TraesCS6B01G365400 chr2B 87.869 305 32 4 2270 2570 693432523 693432826 1.130000e-93 353
10 TraesCS6B01G365400 chr5B 89.630 1109 110 5 858 1963 660222097 660223203 0.000000e+00 1406
11 TraesCS6B01G365400 chr5B 86.176 1114 146 7 858 1969 577863004 577861897 0.000000e+00 1197
12 TraesCS6B01G365400 chr5B 86.033 852 115 4 2 851 660221164 660222013 0.000000e+00 911
13 TraesCS6B01G365400 chr5B 83.019 848 131 11 17 857 577863923 577863082 0.000000e+00 756
14 TraesCS6B01G365400 chr5B 87.417 302 36 2 2270 2570 660223210 660223510 1.890000e-91 346
15 TraesCS6B01G365400 chr3B 87.376 1109 134 6 858 1963 699289766 699290871 0.000000e+00 1267
16 TraesCS6B01G365400 chr5D 93.124 858 57 2 1 857 444076465 444075609 0.000000e+00 1256
17 TraesCS6B01G365400 chr5D 92.384 302 22 1 2270 2570 444074208 444073907 1.830000e-116 429
18 TraesCS6B01G365400 chr1D 87.047 1104 141 2 858 1960 72612948 72614050 0.000000e+00 1245
19 TraesCS6B01G365400 chr2D 86.355 1114 136 5 858 1969 36077686 36076587 0.000000e+00 1201
20 TraesCS6B01G365400 chr2D 82.827 856 139 8 6 857 619579325 619580176 0.000000e+00 760
21 TraesCS6B01G365400 chr2D 82.506 846 139 9 15 857 36078603 36077764 0.000000e+00 734
22 TraesCS6B01G365400 chr7D 84.928 836 114 9 24 857 501785051 501784226 0.000000e+00 835


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 TraesCS6B01G365400 chr6B 637142973 637145542 2569 True 2096.500000 3637 100.000000 1 2570 2 chr6B.!!$R1 2569
1 TraesCS6B01G365400 chr4D 637944 639020 1076 True 1524.000000 1524 92.208000 893 1969 1 chr4D.!!$R1 1076
2 TraesCS6B01G365400 chr4D 657479 658335 856 True 1140.000000 1140 90.676000 1 857 1 chr4D.!!$R2 856
3 TraesCS6B01G365400 chr2B 784889946 784891992 2046 True 1311.500000 1511 90.683000 2 1969 2 chr2B.!!$R2 1967
4 TraesCS6B01G365400 chr2B 773661157 773663166 2009 True 1173.500000 1386 88.458000 22 1960 2 chr2B.!!$R1 1938
5 TraesCS6B01G365400 chr2B 693431517 693432826 1309 False 836.000000 1319 89.092500 960 2570 2 chr2B.!!$F1 1610
6 TraesCS6B01G365400 chr5B 577861897 577863923 2026 True 976.500000 1197 84.597500 17 1969 2 chr5B.!!$R1 1952
7 TraesCS6B01G365400 chr5B 660221164 660223510 2346 False 887.666667 1406 87.693333 2 2570 3 chr5B.!!$F1 2568
8 TraesCS6B01G365400 chr3B 699289766 699290871 1105 False 1267.000000 1267 87.376000 858 1963 1 chr3B.!!$F1 1105
9 TraesCS6B01G365400 chr5D 444073907 444076465 2558 True 842.500000 1256 92.754000 1 2570 2 chr5D.!!$R1 2569
10 TraesCS6B01G365400 chr1D 72612948 72614050 1102 False 1245.000000 1245 87.047000 858 1960 1 chr1D.!!$F1 1102
11 TraesCS6B01G365400 chr2D 36076587 36078603 2016 True 967.500000 1201 84.430500 15 1969 2 chr2D.!!$R1 1954
12 TraesCS6B01G365400 chr2D 619579325 619580176 851 False 760.000000 760 82.827000 6 857 1 chr2D.!!$F1 851
13 TraesCS6B01G365400 chr7D 501784226 501785051 825 True 835.000000 835 84.928000 24 857 1 chr7D.!!$R1 833


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
101 107 0.494095 AAGGAGAAGGAGGAGTGGGT 59.506 55.0 0.0 0.0 0.0 4.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1593 1901 1.810755 TCAGCTTCAGATTGCTTGCTG 59.189 47.619 0.0 0.0 46.21 4.41 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
36 38 1.685224 GGTGATCAGGTGGGCTTCA 59.315 57.895 0.00 0.00 0.00 3.02
55 57 3.843422 TCAAAGAAATCTGGCCCAAGAA 58.157 40.909 0.00 0.00 0.00 2.52
101 107 0.494095 AAGGAGAAGGAGGAGTGGGT 59.506 55.000 0.00 0.00 0.00 4.51
184 190 2.415426 CAAAAACTTGGCGGCGGT 59.585 55.556 9.78 2.67 0.00 5.68
294 307 2.003548 GGAAGAGGGGCCAGTCCAT 61.004 63.158 4.39 0.00 36.21 3.41
333 346 5.143369 TCTATGGCAGATCTGAGAGCTTTA 58.857 41.667 27.04 6.39 0.00 1.85
431 448 2.365941 GGGATCAGGGACTAACAGTAGC 59.634 54.545 0.00 0.00 36.02 3.58
492 509 1.398692 TGGAGACAACAAGTTTGGCC 58.601 50.000 0.00 0.00 37.44 5.36
585 603 6.431234 GGAAAGTGGGTCTATGGCTAATAATG 59.569 42.308 0.00 0.00 0.00 1.90
620 638 4.452733 GGAACGCAGGGAGGACCG 62.453 72.222 0.00 0.00 46.96 4.79
821 839 4.405358 AGAGTGGAAGGAGCTAAAGAGATG 59.595 45.833 0.00 0.00 0.00 2.90
891 986 3.407424 ACTGAAGAATGCACTGTGCTA 57.593 42.857 30.43 18.50 45.31 3.49
907 1002 4.894784 TGTGCTAAAACAAACCAAACCAA 58.105 34.783 0.00 0.00 0.00 3.67
985 1081 4.463186 ACACCAAAGAGATCGTAGCTACTT 59.537 41.667 21.20 8.96 0.00 2.24
1075 1171 2.802247 GGCTTCAGCAAAATGTTTGACC 59.198 45.455 4.93 0.00 44.36 4.02
1142 1238 8.855804 TTCCTTATGAGATTTCCTAGTAAGGT 57.144 34.615 8.87 0.00 44.09 3.50
1436 1744 1.209019 ACCTGCTGGCACTGAGATAAG 59.791 52.381 9.95 0.00 36.63 1.73
1578 1886 6.043854 AGTTCTGAAACATAGAGGGAGAAC 57.956 41.667 0.00 0.00 38.62 3.01
1593 1901 3.120165 GGGAGAACGAGATGCAGAAAAAC 60.120 47.826 0.00 0.00 0.00 2.43
1613 1921 2.195741 AGCAAGCAATCTGAAGCTGA 57.804 45.000 8.46 0.00 41.70 4.26
1620 1928 3.261390 AGCAATCTGAAGCTGAGAAGTCT 59.739 43.478 7.11 0.00 40.13 3.24
1635 1944 4.678256 AGAAGTCTAATGTCAGTCTGGGA 58.322 43.478 0.00 0.00 0.00 4.37
1662 1972 5.011533 CCTGGGGTTGAACAATATGAACAAA 59.988 40.000 0.00 0.00 0.00 2.83
1691 2001 1.792757 AAGCAGGAGACATGGGCCAA 61.793 55.000 11.89 0.00 0.00 4.52
1845 2155 5.234466 TGGAGGAAAAGAAGAGGAAAGAG 57.766 43.478 0.00 0.00 0.00 2.85
1862 2172 8.378115 AGGAAAGAGATGGATATCATAAGGAG 57.622 38.462 4.83 0.00 35.97 3.69
2369 2682 2.202236 GATTGAGCAGGCTGTGGGGA 62.202 60.000 17.16 0.00 0.00 4.81
2431 2744 6.264067 AGGAGACTGAATCCTTTGAAACAAAG 59.736 38.462 14.76 14.76 45.13 2.77
2501 2814 3.446873 ACTGAGAAGATGCACTAGACTGG 59.553 47.826 0.00 0.00 0.00 4.00
2528 2842 5.473504 GGCAAGGAAGACAAAAAGATCACTA 59.526 40.000 0.00 0.00 0.00 2.74
2542 2856 8.691661 AAAAGATCACTAAACTGGCTAAAGAA 57.308 30.769 0.00 0.00 0.00 2.52
2551 2865 2.087646 CTGGCTAAAGAAAGAGTGGCC 58.912 52.381 0.00 0.00 38.67 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 21 1.815003 CTTTGAAGCCCACCTGATCAC 59.185 52.381 0.00 0.0 0.00 3.06
36 38 3.516700 CCATTCTTGGGCCAGATTTCTTT 59.483 43.478 6.23 0.0 39.56 2.52
73 75 3.014110 TCCTCCTTCTCCTTTATCTGGGT 59.986 47.826 0.00 0.0 0.00 4.51
88 92 6.068140 CCCTATATATAGACCCACTCCTCCTT 60.068 46.154 19.51 0.0 32.05 3.36
184 190 1.030488 CGCGTCCTCTCCTCCACTTA 61.030 60.000 0.00 0.0 0.00 2.24
289 302 4.468153 AGAAGTTACCTCTTCCTCATGGAC 59.532 45.833 0.00 0.0 43.06 4.02
294 307 4.406003 GCCATAGAAGTTACCTCTTCCTCA 59.594 45.833 3.32 0.0 43.17 3.86
333 346 4.832492 TCCTGCCTATTAAATCCTCTCCT 58.168 43.478 0.00 0.0 0.00 3.69
431 448 2.272146 CCATCCCCACCAGAACCG 59.728 66.667 0.00 0.0 0.00 4.44
492 509 1.580942 CCATGTCTGGTGCAAACCG 59.419 57.895 0.00 0.0 37.79 4.44
585 603 5.510671 CGTTCCCATCTGTTGTATATTTGC 58.489 41.667 0.00 0.0 0.00 3.68
637 655 5.163683 CCACTGTTGCTCATCATAGGAAAAG 60.164 44.000 0.00 0.0 37.95 2.27
700 718 2.102252 TCTTGTGGCATGAAACCAAACC 59.898 45.455 0.00 0.0 39.39 3.27
834 852 2.899900 GCTCCTTGGGATTTCCTGTTTT 59.100 45.455 0.00 0.0 36.20 2.43
891 986 4.082125 TGGCAATTGGTTTGGTTTGTTTT 58.918 34.783 7.72 0.0 35.75 2.43
907 1002 4.834496 CCCATATCCAACATACTTGGCAAT 59.166 41.667 0.00 0.0 39.38 3.56
975 1071 5.462398 GGGATTGATGTGTTAAGTAGCTACG 59.538 44.000 17.99 0.0 0.00 3.51
985 1081 3.668141 AGCCATGGGATTGATGTGTTA 57.332 42.857 15.13 0.0 0.00 2.41
1029 1125 1.815408 GCCACAGTGGTGTCATTCAGT 60.815 52.381 21.26 0.0 43.71 3.41
1056 1152 3.052036 CCGGTCAAACATTTTGCTGAAG 58.948 45.455 0.00 0.0 0.00 3.02
1075 1171 1.826024 CTCTCCAAGTCCATCCCCG 59.174 63.158 0.00 0.0 0.00 5.73
1142 1238 2.727123 TTTCAGCTCCACCAACTTGA 57.273 45.000 0.00 0.0 0.00 3.02
1436 1744 6.106673 TCATAAAGCAGCAGGTCTTTAGTAC 58.893 40.000 0.00 0.0 37.94 2.73
1567 1875 2.092375 TCTGCATCTCGTTCTCCCTCTA 60.092 50.000 0.00 0.0 0.00 2.43
1578 1886 2.975410 TGCTGTTTTTCTGCATCTCG 57.025 45.000 0.00 0.0 43.97 4.04
1593 1901 1.810755 TCAGCTTCAGATTGCTTGCTG 59.189 47.619 0.00 0.0 46.21 4.41
1613 1921 4.678256 TCCCAGACTGACATTAGACTTCT 58.322 43.478 3.32 0.0 0.00 2.85
1620 1928 2.551270 AGGCTTCCCAGACTGACATTA 58.449 47.619 3.32 0.0 36.79 1.90
1635 1944 2.990740 TATTGTTCAACCCCAGGCTT 57.009 45.000 0.00 0.0 0.00 4.35
1698 2008 2.919602 TGCCCTCTCCTTGGTTATTTCT 59.080 45.455 0.00 0.0 0.00 2.52
1845 2155 7.398618 TCCAGAGTTCTCCTTATGATATCCATC 59.601 40.741 0.00 0.0 36.71 3.51
1862 2172 1.978580 TGACCTCCCTTTCCAGAGTTC 59.021 52.381 0.00 0.0 0.00 3.01
2297 2608 0.823356 TGTTTGTCTTCTGCTGCCCC 60.823 55.000 0.00 0.0 0.00 5.80
2299 2610 0.595095 CCTGTTTGTCTTCTGCTGCC 59.405 55.000 0.00 0.0 0.00 4.85
2431 2744 3.009584 CCCCTATCCCAGCCTTCTTAATC 59.990 52.174 0.00 0.0 0.00 1.75
2501 2814 4.918810 TCTTTTTGTCTTCCTTGCCTTC 57.081 40.909 0.00 0.0 0.00 3.46
2528 2842 3.570125 GCCACTCTTTCTTTAGCCAGTTT 59.430 43.478 0.00 0.0 0.00 2.66
2542 2856 2.430694 GTTGTTTTTCTGGGCCACTCTT 59.569 45.455 0.00 0.0 0.00 2.85



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

AutoCloner maintained by Alex Coulton.