Multiple sequence alignment - TraesCS7D01G231200

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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 TraesCS7D01G231200 chr7D 100.000 4016 0 0 1 4016 192366131 192370146 0.000000e+00 7417.0
1 TraesCS7D01G231200 chr7D 94.872 468 23 1 36 503 564180341 564180807 0.000000e+00 730.0
2 TraesCS7D01G231200 chr7D 87.791 172 20 1 504 674 570442101 570442272 2.450000e-47 200.0
3 TraesCS7D01G231200 chr7D 90.845 142 10 2 553 693 564181785 564181924 1.910000e-43 187.0
4 TraesCS7D01G231200 chr7D 90.780 141 10 3 363 503 570441799 570441936 6.850000e-43 185.0
5 TraesCS7D01G231200 chr7D 93.220 59 4 0 504 562 564180973 564181031 1.990000e-13 87.9
6 TraesCS7D01G231200 chr7D 94.595 37 1 1 329 365 570441775 570441810 5.610000e-04 56.5
7 TraesCS7D01G231200 chr7B 95.820 3349 96 14 696 4016 155466511 155469843 0.000000e+00 5369.0
8 TraesCS7D01G231200 chr7A 96.660 3084 78 6 948 4016 201982606 201985679 0.000000e+00 5101.0
9 TraesCS7D01G231200 chr7A 74.775 222 35 15 65 278 603358421 603358213 3.330000e-11 80.5
10 TraesCS7D01G231200 chr4D 94.453 631 23 2 3301 3930 167197868 167197249 0.000000e+00 961.0
11 TraesCS7D01G231200 chr4D 95.200 250 12 0 36 285 10392847 10393096 2.910000e-106 396.0
12 TraesCS7D01G231200 chr4D 93.846 65 3 1 2 65 461360073 461360009 3.300000e-16 97.1
13 TraesCS7D01G231200 chr3D 97.661 513 9 3 1 512 562639863 562639353 0.000000e+00 878.0
14 TraesCS7D01G231200 chr3D 95.812 191 7 1 504 693 562639193 562639003 1.400000e-79 307.0
15 TraesCS7D01G231200 chr3A 97.421 504 9 4 1 503 38421772 38422272 0.000000e+00 856.0
16 TraesCS7D01G231200 chr3A 96.875 192 4 2 504 693 38422441 38422632 1.800000e-83 320.0
17 TraesCS7D01G231200 chr3A 87.919 149 15 3 145 292 699291119 699291265 5.340000e-39 172.0
18 TraesCS7D01G231200 chr3A 94.805 77 3 1 699 774 32127494 32127570 7.050000e-23 119.0
19 TraesCS7D01G231200 chr3A 89.610 77 3 3 65 137 699290481 699290556 4.270000e-15 93.5
20 TraesCS7D01G231200 chr3A 89.855 69 5 2 704 771 120165583 120165650 1.990000e-13 87.9
21 TraesCS7D01G231200 chr3A 97.500 40 1 0 576 615 185164978 185165017 7.200000e-08 69.4
22 TraesCS7D01G231200 chr1D 93.617 470 27 3 36 503 211711667 211712135 0.000000e+00 699.0
23 TraesCS7D01G231200 chr1D 94.922 256 12 1 36 290 487590912 487591167 2.250000e-107 399.0
24 TraesCS7D01G231200 chr1D 91.099 191 15 2 504 693 211712303 211712492 1.430000e-64 257.0
25 TraesCS7D01G231200 chr1D 92.424 66 5 0 2 67 9729170 9729105 1.190000e-15 95.3
26 TraesCS7D01G231200 chr1D 95.000 60 3 0 1 60 211711606 211711665 1.190000e-15 95.3
27 TraesCS7D01G231200 chr1D 97.917 48 1 0 1 48 487590851 487590898 2.570000e-12 84.2
28 TraesCS7D01G231200 chr5A 84.071 226 15 11 283 502 477545065 477544855 8.800000e-47 198.0
29 TraesCS7D01G231200 chr5A 95.588 68 2 1 1 67 32945097 32945164 1.530000e-19 108.0
30 TraesCS7D01G231200 chr5A 91.781 73 4 2 702 773 539904640 539904711 2.550000e-17 100.0
31 TraesCS7D01G231200 chr2B 82.243 214 17 4 297 502 790218498 790218298 8.930000e-37 165.0
32 TraesCS7D01G231200 chr2B 91.892 74 5 1 701 774 13918160 13918088 7.100000e-18 102.0
33 TraesCS7D01G231200 chr2D 80.995 221 17 5 291 503 645732947 645733150 6.950000e-33 152.0
34 TraesCS7D01G231200 chr6D 83.439 157 14 9 290 444 89332107 89331961 7.000000e-28 135.0
35 TraesCS7D01G231200 chr2A 94.595 74 3 1 701 773 10724409 10724482 3.280000e-21 113.0
36 TraesCS7D01G231200 chr4A 96.970 66 2 0 2 67 102839929 102839864 1.180000e-20 111.0
37 TraesCS7D01G231200 chr4A 95.522 67 3 0 703 769 733934387 733934453 1.530000e-19 108.0
38 TraesCS7D01G231200 chr4A 92.958 71 5 0 699 769 739825554 739825484 1.970000e-18 104.0
39 TraesCS7D01G231200 chr3B 93.333 75 4 1 700 773 422559747 422559673 4.240000e-20 110.0
40 TraesCS7D01G231200 chr4B 93.939 66 3 1 1 65 582954245 582954180 9.190000e-17 99.0


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 TraesCS7D01G231200 chr7D 192366131 192370146 4015 False 7417.000000 7417 100.000000 1 4016 1 chr7D.!!$F1 4015
1 TraesCS7D01G231200 chr7D 564180341 564181924 1583 False 334.966667 730 92.979000 36 693 3 chr7D.!!$F2 657
2 TraesCS7D01G231200 chr7B 155466511 155469843 3332 False 5369.000000 5369 95.820000 696 4016 1 chr7B.!!$F1 3320
3 TraesCS7D01G231200 chr7A 201982606 201985679 3073 False 5101.000000 5101 96.660000 948 4016 1 chr7A.!!$F1 3068
4 TraesCS7D01G231200 chr4D 167197249 167197868 619 True 961.000000 961 94.453000 3301 3930 1 chr4D.!!$R1 629
5 TraesCS7D01G231200 chr3D 562639003 562639863 860 True 592.500000 878 96.736500 1 693 2 chr3D.!!$R1 692
6 TraesCS7D01G231200 chr3A 38421772 38422632 860 False 588.000000 856 97.148000 1 693 2 chr3A.!!$F4 692
7 TraesCS7D01G231200 chr1D 211711606 211712492 886 False 350.433333 699 93.238667 1 693 3 chr1D.!!$F1 692

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
547 745 0.180406 GGGAGGAGCCAAATCGCTAA 59.820 55.0 0.00 0.0 39.87 3.09 F
1582 2565 0.388907 GCACCGTGATGCAGCAATTT 60.389 50.0 6.05 0.0 45.39 1.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1875 2858 1.329292 TCACGAAAGTTCCAAACTGCG 59.671 47.619 11.42 11.42 46.4 5.18 R
3126 4109 0.762418 TTCCCAGACATGACAACCGT 59.238 50.000 0.00 0.00 0.0 4.83 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
186 213 2.030027 TGGGAAGGAGAGCTCTTTCA 57.970 50.000 23.29 11.88 44.47 2.69
547 745 0.180406 GGGAGGAGCCAAATCGCTAA 59.820 55.000 0.00 0.00 39.87 3.09
562 1523 0.941542 GCTAACGACAAGGTTGTGCA 59.058 50.000 0.00 0.00 42.43 4.57
582 1543 1.910580 ATGTGGGATCGTTCGGGCTT 61.911 55.000 0.00 0.00 0.00 4.35
693 1656 2.360767 CGGGGGTTATCGGTGTCCA 61.361 63.158 0.00 0.00 0.00 4.02
694 1657 1.901654 CGGGGGTTATCGGTGTCCAA 61.902 60.000 0.00 0.00 0.00 3.53
717 1680 7.437267 CCAATGTCTGATTTTATTTCTCATGCC 59.563 37.037 0.00 0.00 0.00 4.40
718 1681 7.893124 ATGTCTGATTTTATTTCTCATGCCT 57.107 32.000 0.00 0.00 0.00 4.75
730 1693 5.643379 TTCTCATGCCTTTGTAAATGACC 57.357 39.130 0.00 0.00 0.00 4.02
736 1699 2.227865 GCCTTTGTAAATGACCTTGCGA 59.772 45.455 0.00 0.00 0.00 5.10
840 1803 2.352715 GCCATTGCTTGTGTTTCCTACC 60.353 50.000 0.00 0.00 33.53 3.18
846 1816 2.226674 GCTTGTGTTTCCTACCTTCAGC 59.773 50.000 0.00 0.00 0.00 4.26
1122 2105 1.729586 ACCTCTGCAACAACCTCCTA 58.270 50.000 0.00 0.00 0.00 2.94
1582 2565 0.388907 GCACCGTGATGCAGCAATTT 60.389 50.000 6.05 0.00 45.39 1.82
1789 2772 1.406069 GCGGTGGAGTGAATGAGATGT 60.406 52.381 0.00 0.00 0.00 3.06
1806 2789 1.045407 TGTCTAGGTTGTCTTGCCGT 58.955 50.000 0.00 0.00 0.00 5.68
1875 2858 1.066002 CGGAATGGATGCAACATGGAC 59.934 52.381 7.88 4.04 0.00 4.02
1978 2961 4.933505 TCATCATTAGGACAGCTGAGAG 57.066 45.455 23.35 2.82 0.00 3.20
2157 3140 3.541711 GGCATTATTAACTTGCTACGCG 58.458 45.455 3.53 3.53 36.62 6.01
2320 3303 1.067071 CGAGGGTGGTGAAGTTAGGAC 60.067 57.143 0.00 0.00 0.00 3.85
2337 3320 2.947652 AGGACTTGATGATGCCAATTCG 59.052 45.455 0.00 0.00 0.00 3.34
2358 3341 2.029020 GGTTGAGAATGCCCTTTTGACC 60.029 50.000 0.00 0.00 0.00 4.02
2691 3674 1.060937 CCGCGCTGGAAGATTTTCG 59.939 57.895 12.11 0.00 42.00 3.46
2927 3910 2.346766 ACTGTGTTTGATGTCCAGCA 57.653 45.000 0.00 0.00 0.00 4.41
3126 4109 1.072806 AGATTGACTGACTGCTTGCCA 59.927 47.619 0.00 0.00 0.00 4.92
3263 4255 8.824756 ATCTTAAGGTGAGATACTCTGTTACA 57.175 34.615 1.85 0.00 32.27 2.41
3542 4537 7.310664 CAAAGAAGACACAATGCTAATGTCAT 58.689 34.615 6.40 0.00 44.26 3.06
3572 4567 6.105657 TGCAACATCAACAATCTGTATACG 57.894 37.500 0.00 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
464 493 7.604545 TGAACAAAACTACCATACGATCATGAA 59.395 33.333 0.00 0.00 0.00 2.57
547 745 1.065401 CACATTGCACAACCTTGTCGT 59.935 47.619 0.00 0.00 39.91 4.34
562 1523 1.451387 GCCCGAACGATCCCACATT 60.451 57.895 0.00 0.00 0.00 2.71
582 1543 2.450476 GTTCGGTAGAAGTACCCCTCA 58.550 52.381 0.00 0.00 45.61 3.86
693 1656 8.302515 AGGCATGAGAAATAAAATCAGACATT 57.697 30.769 0.00 0.00 0.00 2.71
694 1657 7.893124 AGGCATGAGAAATAAAATCAGACAT 57.107 32.000 0.00 0.00 0.00 3.06
717 1680 8.586273 CAAATAATCGCAAGGTCATTTACAAAG 58.414 33.333 0.00 0.00 23.98 2.77
718 1681 8.300286 TCAAATAATCGCAAGGTCATTTACAAA 58.700 29.630 0.00 0.00 23.98 2.83
730 1693 9.994432 AGACTTTATTTCTCAAATAATCGCAAG 57.006 29.630 2.97 1.00 41.51 4.01
1100 2083 1.339151 GGAGGTTGTTGCAGAGGTAGG 60.339 57.143 0.00 0.00 0.00 3.18
1122 2105 0.684479 TGCCGCTGATGTAGGAGAGT 60.684 55.000 0.00 0.00 0.00 3.24
1253 2236 3.594134 AGCATGTCGGAGAAGAGAAAAG 58.406 45.455 0.00 0.00 39.69 2.27
1582 2565 3.012518 GCAGCATCTTCTTTAGCAAGGA 58.987 45.455 0.00 0.00 0.00 3.36
1743 2726 2.903784 ACCATACATCGCTATAAGGGCA 59.096 45.455 0.00 0.00 0.00 5.36
1789 2772 4.098960 CCTTATACGGCAAGACAACCTAGA 59.901 45.833 0.00 0.00 0.00 2.43
1875 2858 1.329292 TCACGAAAGTTCCAAACTGCG 59.671 47.619 11.42 11.42 46.40 5.18
2164 3147 3.172339 AGAGTGTCTCCAGAGCAAGATT 58.828 45.455 0.00 0.00 0.00 2.40
2320 3303 3.129113 TCAACCGAATTGGCATCATCAAG 59.871 43.478 0.00 0.00 43.94 3.02
2337 3320 2.029020 GGTCAAAAGGGCATTCTCAACC 60.029 50.000 0.00 0.00 0.00 3.77
2691 3674 4.553547 GCATCAATAAACTCGAGTGCATCC 60.554 45.833 20.85 0.00 0.00 3.51
2927 3910 7.746703 ACTACTTCCCACATCTTTTCTTACTT 58.253 34.615 0.00 0.00 0.00 2.24
3072 4055 5.133221 AGTCCATTATGCCTCAATACAACC 58.867 41.667 0.00 0.00 0.00 3.77
3126 4109 0.762418 TTCCCAGACATGACAACCGT 59.238 50.000 0.00 0.00 0.00 4.83
3209 4200 4.828939 ACATATTGCAACCATGTCCTATGG 59.171 41.667 18.32 4.45 44.54 2.74
3211 4202 6.835488 AGAAACATATTGCAACCATGTCCTAT 59.165 34.615 22.23 12.78 31.82 2.57
3263 4255 5.533482 TGTTTGCAGTTTACAACAGTGTTT 58.467 33.333 5.57 1.02 39.30 2.83
3481 4476 9.838975 TGTTCAAACATAGCATATTACAACTTG 57.161 29.630 0.00 0.00 33.17 3.16
3542 4537 6.183360 ACAGATTGTTGATGTTGCAGTTAACA 60.183 34.615 8.61 0.00 43.93 2.41
3572 4567 4.839668 AGTAAGCACATACGAGATCCTC 57.160 45.455 0.00 0.00 0.00 3.71
3809 4814 3.439857 AGCTCAACTAGGGATGCAAAA 57.560 42.857 0.00 0.00 0.00 2.44


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

AutoCloner maintained by Alex Coulton.