Multiple sequence alignment - TraesCS3D01G142900

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 TraesCS3D01G142900 chr3D 100.000 2726 0 0 1 2726 104817873 104820598 0.000000e+00 5035
1 TraesCS3D01G142900 chr3D 81.183 186 22 2 2543 2724 120288149 120288325 1.320000e-28 137
2 TraesCS3D01G142900 chr5D 95.245 2734 116 7 1 2724 480486667 480483938 0.000000e+00 4316
3 TraesCS3D01G142900 chr5D 94.799 2730 129 7 5 2724 235111353 235114079 0.000000e+00 4242
4 TraesCS3D01G142900 chr1D 95.175 2736 118 6 1 2724 421876302 421879035 0.000000e+00 4309
5 TraesCS3D01G142900 chr1D 94.952 2734 125 6 1 2724 412874353 412871623 0.000000e+00 4272
6 TraesCS3D01G142900 chr1D 94.952 2734 122 8 1 2724 107139065 107141792 0.000000e+00 4270
7 TraesCS3D01G142900 chr1D 94.696 2734 128 10 1 2724 467352677 467355403 0.000000e+00 4229
8 TraesCS3D01G142900 chr2D 95.137 2735 119 7 1 2724 126961990 126964721 0.000000e+00 4301
9 TraesCS3D01G142900 chr2D 94.879 2734 127 6 1 2724 593404237 593401507 0.000000e+00 4261
10 TraesCS3D01G142900 chr7D 94.843 2734 128 6 1 2724 413876046 413873316 0.000000e+00 4255
11 TraesCS3D01G142900 chr6D 94.115 2736 146 8 1 2726 411716067 411718797 0.000000e+00 4146
12 TraesCS3D01G142900 chr6D 93.821 2735 152 8 1 2724 95884842 95887570 0.000000e+00 4098
13 TraesCS3D01G142900 chr6D 94.300 2158 109 7 578 2724 97237901 97240055 0.000000e+00 3291
14 TraesCS3D01G142900 chr7B 84.444 180 14 6 2549 2724 124734382 124734551 6.040000e-37 165
15 TraesCS3D01G142900 chr4D 83.217 143 8 4 2589 2724 36845181 36845314 1.720000e-22 117


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 TraesCS3D01G142900 chr3D 104817873 104820598 2725 False 5035 5035 100.000 1 2726 1 chr3D.!!$F1 2725
1 TraesCS3D01G142900 chr5D 480483938 480486667 2729 True 4316 4316 95.245 1 2724 1 chr5D.!!$R1 2723
2 TraesCS3D01G142900 chr5D 235111353 235114079 2726 False 4242 4242 94.799 5 2724 1 chr5D.!!$F1 2719
3 TraesCS3D01G142900 chr1D 421876302 421879035 2733 False 4309 4309 95.175 1 2724 1 chr1D.!!$F2 2723
4 TraesCS3D01G142900 chr1D 412871623 412874353 2730 True 4272 4272 94.952 1 2724 1 chr1D.!!$R1 2723
5 TraesCS3D01G142900 chr1D 107139065 107141792 2727 False 4270 4270 94.952 1 2724 1 chr1D.!!$F1 2723
6 TraesCS3D01G142900 chr1D 467352677 467355403 2726 False 4229 4229 94.696 1 2724 1 chr1D.!!$F3 2723
7 TraesCS3D01G142900 chr2D 126961990 126964721 2731 False 4301 4301 95.137 1 2724 1 chr2D.!!$F1 2723
8 TraesCS3D01G142900 chr2D 593401507 593404237 2730 True 4261 4261 94.879 1 2724 1 chr2D.!!$R1 2723
9 TraesCS3D01G142900 chr7D 413873316 413876046 2730 True 4255 4255 94.843 1 2724 1 chr7D.!!$R1 2723
10 TraesCS3D01G142900 chr6D 411716067 411718797 2730 False 4146 4146 94.115 1 2726 1 chr6D.!!$F3 2725
11 TraesCS3D01G142900 chr6D 95884842 95887570 2728 False 4098 4098 93.821 1 2724 1 chr6D.!!$F1 2723
12 TraesCS3D01G142900 chr6D 97237901 97240055 2154 False 3291 3291 94.300 578 2724 1 chr6D.!!$F2 2146

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
508 509 1.064685 TCTCCGGATGCTGACTACTGA 60.065 52.381 3.57 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2362 2370 0.803117 GCCTTGTAGAAGTTTCGCCC 59.197 55.0 0.0 0.0 0.0 6.13 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
301 302 9.658799 CAAATCACTTCTAGACTGGAATCTAAA 57.341 33.333 1.27 0.00 30.76 1.85
309 310 5.828299 AGACTGGAATCTAAAGAGACTCG 57.172 43.478 0.00 0.00 33.41 4.18
433 434 6.347696 TGCAAAGTCTTTTGGTGATGATTTT 58.652 32.000 0.00 0.00 43.12 1.82
508 509 1.064685 TCTCCGGATGCTGACTACTGA 60.065 52.381 3.57 0.00 0.00 3.41
520 521 2.301870 TGACTACTGAAAGGATGCGGTT 59.698 45.455 0.00 0.00 39.30 4.44
581 582 5.010933 GGGAGATCACTGATCGTCCTTATA 58.989 45.833 23.19 0.00 43.17 0.98
706 707 6.948309 CCCAAAAGGAAGAAGAGGATTTCTTA 59.052 38.462 1.36 0.00 45.00 2.10
708 709 7.121907 CCAAAAGGAAGAAGAGGATTTCTTAGG 59.878 40.741 1.36 0.00 46.12 2.69
717 718 6.628644 AGAGGATTTCTTAGGCACTTACTT 57.371 37.500 0.00 0.00 41.75 2.24
718 719 6.410540 AGAGGATTTCTTAGGCACTTACTTG 58.589 40.000 0.00 0.00 41.75 3.16
720 721 4.944317 GGATTTCTTAGGCACTTACTTGCT 59.056 41.667 0.00 0.00 42.56 3.91
1018 1020 7.148950 GCTGACAAATGTGTATACTATCGCTAC 60.149 40.741 4.17 0.00 38.41 3.58
1048 1051 4.142447 GCGAAGGAGTTATACTGTGTCTGA 60.142 45.833 0.00 0.00 0.00 3.27
1122 1125 6.158695 AGGTCAAGGCCTTTCTATCTCATAAA 59.841 38.462 17.61 0.00 34.71 1.40
1233 1236 7.872113 ATCCCACTATGTTGAGAAGATTTTC 57.128 36.000 0.00 0.00 0.00 2.29
1254 1257 2.287915 CAGCCGTTTTGGATATTCGGAG 59.712 50.000 6.09 0.00 43.22 4.63
1262 1265 3.627395 TGGATATTCGGAGTGCAAACT 57.373 42.857 0.00 0.00 0.00 2.66
1385 1388 0.737715 GCTTGTGCTACTCGTCCTGG 60.738 60.000 0.00 0.00 36.03 4.45
1416 1419 1.153269 TGTGTGCAAACTGAGCCGA 60.153 52.632 8.83 0.00 0.00 5.54
1469 1473 0.867746 GTTGTTGAGCGAGTGATGCA 59.132 50.000 0.00 0.00 33.85 3.96
1473 1477 2.672874 TGTTGAGCGAGTGATGCATTAC 59.327 45.455 13.46 13.46 33.85 1.89
1495 1499 3.694043 TGCAAGGCACTGTGAACTATA 57.306 42.857 12.86 0.00 40.86 1.31
1623 1627 1.827789 TGGTGGTGCTGTTTCCTGC 60.828 57.895 0.00 0.00 36.19 4.85
1729 1736 2.224523 TGGTTCGAGAGCTTTTGATGGT 60.225 45.455 0.00 0.00 0.00 3.55
1788 1795 8.154203 TCCTTATGAACTGTGACAATCAAACTA 58.846 33.333 5.06 0.00 0.00 2.24
1792 1799 7.425577 TGAACTGTGACAATCAAACTATGAG 57.574 36.000 0.00 0.00 42.53 2.90
1803 1810 4.507710 TCAAACTATGAGTGCTAAGGCTG 58.492 43.478 0.00 0.00 34.90 4.85
1830 1837 7.066284 AGAGTTCAAAGGACAATATGAAATCCG 59.934 37.037 10.14 0.00 43.87 4.18
1886 1893 4.757149 AGAAAATCAAGAAACTCCGGAGTG 59.243 41.667 36.87 23.52 41.58 3.51
1895 1902 2.048444 ACTCCGGAGTGATAGCGTTA 57.952 50.000 35.89 0.00 40.75 3.18
2054 2061 4.402056 GGAGATCCCGTGAATTAGAACA 57.598 45.455 0.00 0.00 0.00 3.18
2075 2082 0.966179 GGGAAAACAATCCAGCGGTT 59.034 50.000 0.00 0.00 41.55 4.44
2079 2086 3.571571 GAAAACAATCCAGCGGTTAACC 58.428 45.455 15.13 15.13 0.00 2.85
2181 2189 7.446931 TGTCTTAATGTGTTCCAAAGCTTATGA 59.553 33.333 0.00 0.00 0.00 2.15
2241 2249 2.811410 ACACCTATGTGAACCCGACTA 58.189 47.619 5.05 0.00 45.76 2.59
2247 2255 0.963962 TGTGAACCCGACTACTGGTC 59.036 55.000 0.00 0.00 41.28 4.02
2248 2256 0.963962 GTGAACCCGACTACTGGTCA 59.036 55.000 0.00 0.00 44.70 4.02
2362 2370 1.328680 GCCACGTATCAGCTGACAATG 59.671 52.381 20.97 17.49 0.00 2.82
2378 2386 3.482436 ACAATGGGCGAAACTTCTACAA 58.518 40.909 0.00 0.00 0.00 2.41
2380 2388 2.178912 TGGGCGAAACTTCTACAAGG 57.821 50.000 0.00 0.00 33.37 3.61
2435 2443 5.794894 TCAGTTGTGAAGAAGTCTAATCCC 58.205 41.667 0.00 0.00 0.00 3.85
2542 2551 0.547471 TGCCTTGAGATCTGGTGGGA 60.547 55.000 0.00 0.00 0.00 4.37
2653 2663 3.975312 TGGGAAGTGTGGGAAGTTTAGTA 59.025 43.478 0.00 0.00 0.00 1.82
2660 2670 5.544948 AGTGTGGGAAGTTTAGTACCATACA 59.455 40.000 10.68 0.00 43.23 2.29
2661 2671 6.043474 AGTGTGGGAAGTTTAGTACCATACAA 59.957 38.462 10.68 0.00 43.23 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
301 302 0.827925 TGGCAGGTTCACGAGTCTCT 60.828 55.000 0.00 0.00 0.00 3.10
309 310 1.747355 CCATCAGAATGGCAGGTTCAC 59.253 52.381 3.86 0.00 45.88 3.18
433 434 3.012934 TCATCCATGAGGTACACGAGA 57.987 47.619 0.00 0.00 35.89 4.04
508 509 1.082117 CGCTACGAACCGCATCCTTT 61.082 55.000 0.00 0.00 0.00 3.11
520 521 1.687563 TGGAATCCATCTCGCTACGA 58.312 50.000 0.00 0.00 0.00 3.43
706 707 1.609208 CCACAAGCAAGTAAGTGCCT 58.391 50.000 0.00 0.00 46.14 4.75
708 709 3.479255 GCCACAAGCAAGTAAGTGC 57.521 52.632 0.00 0.00 45.28 4.40
718 719 0.606401 TTGTCAGCCTAGCCACAAGC 60.606 55.000 0.00 0.00 44.25 4.01
720 721 0.250727 GGTTGTCAGCCTAGCCACAA 60.251 55.000 0.00 0.00 32.00 3.33
1018 1020 1.968050 ATAACTCCTTCGCCCCACCG 61.968 60.000 0.00 0.00 0.00 4.94
1122 1125 3.359950 GCCCAGGTCTTTCATCTCAAAT 58.640 45.455 0.00 0.00 0.00 2.32
1176 1179 6.316390 GTGTAATTCCACCCTCAGTATTTCTG 59.684 42.308 0.00 0.00 44.85 3.02
1233 1236 2.285083 TCCGAATATCCAAAACGGCTG 58.715 47.619 0.00 0.00 42.73 4.85
1262 1265 4.858850 AGGATCATATGGTGTTGCAGAAA 58.141 39.130 2.13 0.00 0.00 2.52
1385 1388 1.625616 GCACACAGCAAATGAGATGC 58.374 50.000 0.00 0.00 44.79 3.91
1451 1454 1.812235 ATGCATCACTCGCTCAACAA 58.188 45.000 0.00 0.00 0.00 2.83
1469 1473 2.862541 TCACAGTGCCTTGCAAGTAAT 58.137 42.857 24.35 10.09 41.47 1.89
1473 1477 1.027357 AGTTCACAGTGCCTTGCAAG 58.973 50.000 19.93 19.93 41.47 4.01
1623 1627 1.220529 TCGTCTGCTTGCAAGACTTG 58.779 50.000 30.39 11.02 41.60 3.16
1788 1795 2.465813 ACTCTCAGCCTTAGCACTCAT 58.534 47.619 0.00 0.00 43.56 2.90
1792 1799 2.751166 TGAACTCTCAGCCTTAGCAC 57.249 50.000 0.00 0.00 43.56 4.40
1796 1803 3.646162 TGTCCTTTGAACTCTCAGCCTTA 59.354 43.478 0.00 0.00 31.69 2.69
1803 1810 8.401709 GGATTTCATATTGTCCTTTGAACTCTC 58.598 37.037 0.00 0.00 31.92 3.20
1830 1837 8.970691 TTTAATCTTCTTCTTATGTGCTTTGC 57.029 30.769 0.00 0.00 0.00 3.68
1886 1893 7.133513 CCGTCTGGATATAATCTAACGCTATC 58.866 42.308 0.00 0.00 37.49 2.08
1895 1902 8.598041 AGATTTTTAGCCGTCTGGATATAATCT 58.402 33.333 9.68 9.68 39.96 2.40
2051 2058 2.029110 CGCTGGATTGTTTTCCCATGTT 60.029 45.455 0.00 0.00 34.67 2.71
2054 2061 1.185315 CCGCTGGATTGTTTTCCCAT 58.815 50.000 0.00 0.00 34.67 4.00
2247 2255 4.081476 TCACCCAATCTCATAGACTGTGTG 60.081 45.833 0.00 0.00 0.00 3.82
2248 2256 4.096681 TCACCCAATCTCATAGACTGTGT 58.903 43.478 0.00 0.00 0.00 3.72
2362 2370 0.803117 GCCTTGTAGAAGTTTCGCCC 59.197 55.000 0.00 0.00 0.00 6.13
2378 2386 2.036346 GCCTTGAATTGTCAGTTTGCCT 59.964 45.455 0.00 0.00 34.49 4.75
2380 2388 3.096489 TGCCTTGAATTGTCAGTTTGC 57.904 42.857 0.00 0.00 34.49 3.68
2435 2443 3.942829 TGAACTTCCACCTAGAGCAATG 58.057 45.455 0.00 0.00 0.00 2.82
2542 2551 4.294168 AGCCCATCCATAATCCATCAATCT 59.706 41.667 0.00 0.00 0.00 2.40
2602 2612 0.457035 GTACACATGCATGGGCCTTG 59.543 55.000 28.81 19.26 40.13 3.61
2653 2663 6.254522 AGGTCTCTTACTGTAGTTGTATGGT 58.745 40.000 0.00 0.00 0.00 3.55


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

AutoCloner maintained by Alex Coulton.