Multiple sequence alignment - TraesCS2A01G113700

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 TraesCS2A01G113700 chr2A 100.000 3398 0 0 1 3398 65176223 65179620 0.000000e+00 6276.0
1 TraesCS2A01G113700 chr2A 88.346 1759 160 27 678 2408 65091133 65089392 0.000000e+00 2071.0
2 TraesCS2A01G113700 chr2A 100.000 30 0 0 297 326 369215770 369215799 4.740000e-04 56.5
3 TraesCS2A01G113700 chr2D 93.448 2732 127 24 1 2699 63561461 63564173 0.000000e+00 4006.0
4 TraesCS2A01G113700 chr2D 87.957 1752 174 25 678 2408 63548915 63547180 0.000000e+00 2032.0
5 TraesCS2A01G113700 chr2D 85.820 1763 200 35 675 2407 63530594 63532336 0.000000e+00 1825.0
6 TraesCS2A01G113700 chr2D 87.805 246 25 5 410 650 63553463 63553708 2.000000e-72 283.0
7 TraesCS2A01G113700 chr2D 93.182 44 3 0 283 326 63555583 63555626 7.870000e-07 65.8
8 TraesCS2A01G113700 chr2B 90.671 2294 162 34 410 2679 98432901 98435166 0.000000e+00 3003.0
9 TraesCS2A01G113700 chr2B 92.564 2071 114 18 628 2679 99247073 99249122 0.000000e+00 2935.0
10 TraesCS2A01G113700 chr2B 92.233 2073 121 21 628 2679 98816946 98818999 0.000000e+00 2900.0
11 TraesCS2A01G113700 chr2B 95.904 1538 50 7 999 2533 98914591 98916118 0.000000e+00 2479.0
12 TraesCS2A01G113700 chr2B 87.881 1741 182 22 679 2408 98812504 98810782 0.000000e+00 2019.0
13 TraesCS2A01G113700 chr2B 91.351 185 13 3 598 780 98914412 98914595 2.020000e-62 250.0
14 TraesCS2A01G113700 chr2B 91.489 47 4 0 283 329 364948337 364948291 7.870000e-07 65.8
15 TraesCS2A01G113700 chr6A 97.944 681 11 3 2721 3398 549730859 549730179 0.000000e+00 1177.0
16 TraesCS2A01G113700 chr1D 90.789 684 45 11 2721 3398 487201478 487200807 0.000000e+00 898.0
17 TraesCS2A01G113700 chr7D 90.337 683 39 14 2721 3398 564906966 564907626 0.000000e+00 870.0
18 TraesCS2A01G113700 chr5A 89.181 684 52 18 2721 3395 554691909 554691239 0.000000e+00 833.0
19 TraesCS2A01G113700 chr5A 97.143 35 0 1 3188 3221 111902868 111902902 1.320000e-04 58.4
20 TraesCS2A01G113700 chr6D 89.593 615 51 11 2792 3398 266416720 266416111 0.000000e+00 769.0
21 TraesCS2A01G113700 chr6D 97.345 113 3 0 2721 2833 266416834 266416722 3.460000e-45 193.0
22 TraesCS2A01G113700 chr1A 81.421 549 85 14 2824 3362 297255446 297255987 1.870000e-117 433.0
23 TraesCS2A01G113700 chr3B 77.000 200 33 9 2964 3156 189662620 189662427 6.000000e-18 102.0
24 TraesCS2A01G113700 chr5D 86.207 58 8 0 54 111 504724185 504724128 2.830000e-06 63.9


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 TraesCS2A01G113700 chr2A 65176223 65179620 3397 False 6276.0 6276 100.0000 1 3398 1 chr2A.!!$F1 3397
1 TraesCS2A01G113700 chr2A 65089392 65091133 1741 True 2071.0 2071 88.3460 678 2408 1 chr2A.!!$R1 1730
2 TraesCS2A01G113700 chr2D 63561461 63564173 2712 False 4006.0 4006 93.4480 1 2699 1 chr2D.!!$F2 2698
3 TraesCS2A01G113700 chr2D 63547180 63548915 1735 True 2032.0 2032 87.9570 678 2408 1 chr2D.!!$R1 1730
4 TraesCS2A01G113700 chr2D 63530594 63532336 1742 False 1825.0 1825 85.8200 675 2407 1 chr2D.!!$F1 1732
5 TraesCS2A01G113700 chr2B 98432901 98435166 2265 False 3003.0 3003 90.6710 410 2679 1 chr2B.!!$F1 2269
6 TraesCS2A01G113700 chr2B 99247073 99249122 2049 False 2935.0 2935 92.5640 628 2679 1 chr2B.!!$F3 2051
7 TraesCS2A01G113700 chr2B 98816946 98818999 2053 False 2900.0 2900 92.2330 628 2679 1 chr2B.!!$F2 2051
8 TraesCS2A01G113700 chr2B 98810782 98812504 1722 True 2019.0 2019 87.8810 679 2408 1 chr2B.!!$R1 1729
9 TraesCS2A01G113700 chr2B 98914412 98916118 1706 False 1364.5 2479 93.6275 598 2533 2 chr2B.!!$F4 1935
10 TraesCS2A01G113700 chr6A 549730179 549730859 680 True 1177.0 1177 97.9440 2721 3398 1 chr6A.!!$R1 677
11 TraesCS2A01G113700 chr1D 487200807 487201478 671 True 898.0 898 90.7890 2721 3398 1 chr1D.!!$R1 677
12 TraesCS2A01G113700 chr7D 564906966 564907626 660 False 870.0 870 90.3370 2721 3398 1 chr7D.!!$F1 677
13 TraesCS2A01G113700 chr5A 554691239 554691909 670 True 833.0 833 89.1810 2721 3395 1 chr5A.!!$R1 674
14 TraesCS2A01G113700 chr6D 266416111 266416834 723 True 481.0 769 93.4690 2721 3398 2 chr6D.!!$R1 677
15 TraesCS2A01G113700 chr1A 297255446 297255987 541 False 433.0 433 81.4210 2824 3362 1 chr1A.!!$F1 538

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
179 180 1.005037 CAACGGTGCAGAGCCTGTA 60.005 57.895 0.00 0.00 33.43 2.74 F
301 305 1.208776 AGTGGCGACAATAAGGGGTAC 59.791 52.381 0.00 0.00 46.06 3.34 F
831 862 1.801913 CTGAGCTCCGTGCACGTAC 60.802 63.158 34.81 23.67 45.94 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1731 2041 1.668101 CGGAGCCACTGGAGTCTACC 61.668 65.000 0.0 0.0 0.0 3.18 R
1741 2051 3.764466 CTTCGCCTCGGAGCCACT 61.764 66.667 0.0 0.0 0.0 4.00 R
2673 3010 1.687297 GGAGGAGGCCGAGGTTTAGG 61.687 65.000 0.0 0.0 0.0 2.69 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
17 18 4.043168 CGACAAGACACCCACCAC 57.957 61.111 0.00 0.00 0.00 4.16
58 59 2.123428 GGCAATTGCGGCATCTCCT 61.123 57.895 23.48 0.00 43.26 3.69
111 112 3.797331 CTGACCACCAGCTCCAGA 58.203 61.111 0.00 0.00 35.89 3.86
176 177 2.281070 CACAACGGTGCAGAGCCT 60.281 61.111 0.00 0.00 38.37 4.58
177 178 2.281070 ACAACGGTGCAGAGCCTG 60.281 61.111 0.00 0.00 34.12 4.85
178 179 2.281070 CAACGGTGCAGAGCCTGT 60.281 61.111 0.00 0.00 33.43 4.00
179 180 1.005037 CAACGGTGCAGAGCCTGTA 60.005 57.895 0.00 0.00 33.43 2.74
230 234 1.772063 GCTGTCGCAACCGAACTTGT 61.772 55.000 0.00 0.00 46.34 3.16
301 305 1.208776 AGTGGCGACAATAAGGGGTAC 59.791 52.381 0.00 0.00 46.06 3.34
326 330 2.751837 CCAAAGGCGGGCTCTTCC 60.752 66.667 3.91 0.00 0.00 3.46
366 370 6.183360 TGTGTGTGCAATTTCATCACAAAAAG 60.183 34.615 13.20 0.00 41.66 2.27
485 489 8.542497 TTGTGAATAGTACATGTGGTAGAAAC 57.458 34.615 9.11 0.00 31.13 2.78
550 557 4.020396 TGGCCATGATACTTTGCAAACAAT 60.020 37.500 8.05 4.47 35.21 2.71
563 570 8.846211 ACTTTGCAAACAATTAGTAGTACACAT 58.154 29.630 8.05 0.00 35.21 3.21
647 657 4.688021 TGTAACAAAAATGGAGTTGTGCC 58.312 39.130 0.00 0.00 37.99 5.01
669 679 2.537128 CCGTCTTAGATCGAGTCACACG 60.537 54.545 5.95 0.00 0.00 4.49
830 861 2.265904 ACTGAGCTCCGTGCACGTA 61.266 57.895 34.81 21.56 45.94 3.57
831 862 1.801913 CTGAGCTCCGTGCACGTAC 60.802 63.158 34.81 23.67 45.94 3.67
832 863 2.874780 GAGCTCCGTGCACGTACG 60.875 66.667 34.81 23.23 45.94 3.67
914 972 2.544694 GCCGGAGTAGATCACATCACAG 60.545 54.545 5.05 0.00 0.00 3.66
928 986 3.056250 ACATCACAGAGCACGAAGAAGAT 60.056 43.478 0.00 0.00 0.00 2.40
966 1043 2.560542 CGAATCAGTAGATCCTCCCAGG 59.439 54.545 0.00 0.00 36.46 4.45
986 1063 2.745100 TCCCTCGTCACCGACTCG 60.745 66.667 0.00 0.00 38.40 4.18
1741 2051 1.541310 CCCGTTGCTGGTAGACTCCA 61.541 60.000 0.00 0.00 36.00 3.86
2037 2347 2.335011 CGCATCCTATCGCACCGA 59.665 61.111 0.00 0.00 41.13 4.69
2154 2464 3.726517 CCGCTGAACGCCAACCTG 61.727 66.667 0.00 0.00 41.76 4.00
2496 2813 3.957586 CTGCCACAGCCCACCTGA 61.958 66.667 0.00 0.00 44.64 3.86
2560 2896 3.372554 GACTGCCCGGGTGACTAGC 62.373 68.421 24.63 5.93 0.00 3.42
2587 2923 5.449177 CGGCCTTTCCAGAATGAACTAATTC 60.449 44.000 0.00 0.00 39.69 2.17
2595 2931 5.420104 CCAGAATGAACTAATTCCAGCCTTT 59.580 40.000 0.00 0.00 39.69 3.11
2673 3010 4.989279 TTCTATCAAAAAGCCCATCAGC 57.011 40.909 0.00 0.00 0.00 4.26
2699 3036 3.532155 CGGCCTCCTCCTCTTCCG 61.532 72.222 0.00 0.00 0.00 4.30
2700 3037 3.157949 GGCCTCCTCCTCTTCCGG 61.158 72.222 0.00 0.00 0.00 5.14
2701 3038 3.157949 GCCTCCTCCTCTTCCGGG 61.158 72.222 0.00 0.00 0.00 5.73
2702 3039 2.690452 CCTCCTCCTCTTCCGGGA 59.310 66.667 0.00 0.00 0.00 5.14
2704 3041 2.042843 TCCTCCTCTTCCGGGAGC 60.043 66.667 4.24 0.00 46.48 4.70
2705 3042 2.042435 CCTCCTCTTCCGGGAGCT 60.042 66.667 4.24 0.00 46.48 4.09
2706 3043 2.131067 CCTCCTCTTCCGGGAGCTC 61.131 68.421 4.24 4.71 46.48 4.09
2707 3044 2.042843 TCCTCTTCCGGGAGCTCC 60.043 66.667 25.59 25.59 32.43 4.70
2708 3045 2.042435 CCTCTTCCGGGAGCTCCT 60.042 66.667 31.36 0.00 35.95 3.69
2709 3046 1.230497 CCTCTTCCGGGAGCTCCTA 59.770 63.158 31.36 15.11 35.95 2.94
2710 3047 0.397254 CCTCTTCCGGGAGCTCCTAA 60.397 60.000 31.36 20.82 35.95 2.69
2711 3048 0.747852 CTCTTCCGGGAGCTCCTAAC 59.252 60.000 31.36 14.74 35.95 2.34
2712 3049 0.686769 TCTTCCGGGAGCTCCTAACC 60.687 60.000 31.36 14.37 35.95 2.85
2713 3050 2.017559 CTTCCGGGAGCTCCTAACCG 62.018 65.000 31.36 24.52 45.57 4.44
2715 3052 4.222847 CGGGAGCTCCTAACCGGC 62.223 72.222 31.36 12.50 42.48 6.13
2716 3053 4.222847 GGGAGCTCCTAACCGGCG 62.223 72.222 31.36 0.00 35.95 6.46
2717 3054 4.893601 GGAGCTCCTAACCGGCGC 62.894 72.222 26.25 0.00 43.98 6.53
2718 3055 4.893601 GAGCTCCTAACCGGCGCC 62.894 72.222 19.07 19.07 44.75 6.53
2893 3273 1.827394 GAGCCACCCCGCAGTATTA 59.173 57.895 0.00 0.00 0.00 0.98
3023 3405 9.311916 TGTGAAATATTTTTGAAAGTTCACAGG 57.688 29.630 11.98 0.00 44.93 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 2.179517 GCCAGACTCTCCACGACG 59.820 66.667 0.00 0.00 0.00 5.12
103 104 2.210013 TCGCACTGGTTCTGGAGCT 61.210 57.895 0.00 0.00 0.00 4.09
166 167 3.181967 CGCGTACAGGCTCTGCAC 61.182 66.667 0.00 0.00 34.37 4.57
172 173 4.530857 GATGGGCGCGTACAGGCT 62.531 66.667 8.43 0.00 0.00 4.58
195 199 2.364056 GCATTGGGGTCCATGCCA 60.364 61.111 1.91 0.00 34.44 4.92
219 223 0.878961 GCGTCTCCACAAGTTCGGTT 60.879 55.000 0.00 0.00 0.00 4.44
220 224 1.300697 GCGTCTCCACAAGTTCGGT 60.301 57.895 0.00 0.00 0.00 4.69
225 229 1.956170 CTTGCGCGTCTCCACAAGT 60.956 57.895 8.43 0.00 35.81 3.16
285 289 3.255969 TCTTGTACCCCTTATTGTCGC 57.744 47.619 0.00 0.00 0.00 5.19
326 330 5.236263 TGCACACACATTTAGTACAAGTCTG 59.764 40.000 0.00 0.00 0.00 3.51
421 425 5.590530 TTTACAGCTCACACCAAAATGTT 57.409 34.783 0.00 0.00 0.00 2.71
521 528 4.099266 TGCAAAGTATCATGGCCAAATACC 59.901 41.667 26.37 16.94 0.00 2.73
563 570 9.295825 AGAAAGGAAATACACACATACATTGAA 57.704 29.630 0.00 0.00 0.00 2.69
583 590 6.980051 AGGTGCGTAATAAAACTAGAAAGG 57.020 37.500 0.00 0.00 0.00 3.11
647 657 2.014857 TGTGACTCGATCTAAGACGGG 58.985 52.381 0.00 0.00 36.00 5.28
669 679 2.301505 CATCACGTTCGAGATGGCC 58.698 57.895 19.24 0.00 38.33 5.36
835 866 4.758251 TGGCGCTGACCATGGACG 62.758 66.667 21.47 16.78 33.75 4.79
865 896 0.782384 CGCGTGGATTTATAGACGGC 59.218 55.000 0.00 0.00 32.45 5.68
897 944 4.358851 GTGCTCTGTGATGTGATCTACTC 58.641 47.826 0.00 0.00 0.00 2.59
914 972 5.403246 TGACTAGAAATCTTCTTCGTGCTC 58.597 41.667 0.00 0.00 41.14 4.26
928 986 4.021456 TGATTCGGTTCAGCTGACTAGAAA 60.021 41.667 18.03 7.99 31.00 2.52
975 1052 4.773117 GGTCGGCGAGTCGGTGAC 62.773 72.222 11.20 0.00 0.00 3.67
1329 1639 3.071206 GGGCAGAGCTGGTCGAGA 61.071 66.667 0.00 0.00 0.00 4.04
1695 2005 3.637273 ACGACCTCCTTGCCCACC 61.637 66.667 0.00 0.00 0.00 4.61
1731 2041 1.668101 CGGAGCCACTGGAGTCTACC 61.668 65.000 0.00 0.00 0.00 3.18
1741 2051 3.764466 CTTCGCCTCGGAGCCACT 61.764 66.667 0.00 0.00 0.00 4.00
2439 2751 8.123445 TCTTATTTATTCTCGACTAAAACCGC 57.877 34.615 0.00 0.00 0.00 5.68
2496 2813 5.956642 TGTTTGCCTAAAGAAAAACGAGTT 58.043 33.333 0.00 0.00 35.71 3.01
2560 2896 2.113860 TCATTCTGGAAAGGCCGAAG 57.886 50.000 0.00 0.00 40.66 3.79
2587 2923 3.384467 TGAAGGAAACTGAAAAAGGCTGG 59.616 43.478 0.00 0.00 42.68 4.85
2629 2965 7.495934 AGAATATCAGACTGTTGTTATTTCCCG 59.504 37.037 1.59 0.00 0.00 5.14
2673 3010 1.687297 GGAGGAGGCCGAGGTTTAGG 61.687 65.000 0.00 0.00 0.00 2.69
2699 3036 4.222847 CGCCGGTTAGGAGCTCCC 62.223 72.222 29.54 14.04 45.00 4.30
2704 3041 3.458163 TCAGGCGCCGGTTAGGAG 61.458 66.667 26.04 7.56 45.00 3.69
2705 3042 3.766691 GTCAGGCGCCGGTTAGGA 61.767 66.667 26.04 12.51 45.00 2.94
2706 3043 4.832608 GGTCAGGCGCCGGTTAGG 62.833 72.222 26.04 10.36 44.97 2.69
2707 3044 3.310860 AAGGTCAGGCGCCGGTTAG 62.311 63.158 26.04 12.49 0.00 2.34
2708 3045 3.305177 GAAGGTCAGGCGCCGGTTA 62.305 63.158 26.04 5.02 0.00 2.85
2709 3046 4.699522 GAAGGTCAGGCGCCGGTT 62.700 66.667 26.04 13.47 0.00 4.44
2717 3054 4.785453 GGGCGCCAGAAGGTCAGG 62.785 72.222 30.85 0.00 37.19 3.86
2718 3055 4.020617 TGGGCGCCAGAAGGTCAG 62.021 66.667 30.85 0.00 37.19 3.51
2719 3056 4.329545 GTGGGCGCCAGAAGGTCA 62.330 66.667 30.85 12.44 37.19 4.02
2893 3273 4.485163 AGCTTTATCGCGCTGAAATTTTT 58.515 34.783 5.56 0.00 34.69 1.94
3275 3705 9.887406 GATGAACTTTTACTAAAATCCGTGAAA 57.113 29.630 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.