Multiple sequence alignment - TraesCS7D01G355200

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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 TraesCS7D01G355200 chr7D 100.000 3191 0 0 1 3191 459396776 459399966 0.000000e+00 5893.0
1 TraesCS7D01G355200 chr7D 95.850 771 28 2 2424 3191 580126696 580127465 0.000000e+00 1243.0
2 TraesCS7D01G355200 chr7B 95.781 2394 62 15 1 2394 481308495 481310849 0.000000e+00 3825.0
3 TraesCS7D01G355200 chr7B 95.238 42 0 2 2385 2424 481310919 481310960 7.390000e-07 65.8
4 TraesCS7D01G355200 chr7A 92.794 2165 125 11 286 2422 540881539 540879378 0.000000e+00 3105.0
5 TraesCS7D01G355200 chr3B 87.326 1578 160 23 855 2413 606657757 606656201 0.000000e+00 1770.0
6 TraesCS7D01G355200 chr3A 86.552 1621 173 25 803 2398 601412852 601411252 0.000000e+00 1744.0
7 TraesCS7D01G355200 chr3D 87.084 1564 162 20 855 2398 459224249 459222706 0.000000e+00 1733.0
8 TraesCS7D01G355200 chr3D 97.013 770 20 1 2425 3191 591890450 591891219 0.000000e+00 1291.0
9 TraesCS7D01G355200 chr2D 96.895 773 19 3 2424 3191 481539208 481538436 0.000000e+00 1290.0
10 TraesCS7D01G355200 chr2D 95.714 770 23 3 2425 3191 411678308 411677546 0.000000e+00 1230.0
11 TraesCS7D01G355200 chr1D 96.632 772 20 4 2425 3191 421656132 421655362 0.000000e+00 1277.0
12 TraesCS7D01G355200 chrUn 96.263 776 23 4 2419 3191 110710209 110710981 0.000000e+00 1267.0
13 TraesCS7D01G355200 chrUn 95.984 772 26 3 2425 3191 219607464 219606693 0.000000e+00 1249.0
14 TraesCS7D01G355200 chr4D 96.248 773 25 2 2423 3191 82035773 82036545 0.000000e+00 1264.0
15 TraesCS7D01G355200 chr5D 96.248 773 22 3 2425 3191 319429566 319430337 0.000000e+00 1260.0


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 TraesCS7D01G355200 chr7D 459396776 459399966 3190 False 5893.0 5893 100.0000 1 3191 1 chr7D.!!$F1 3190
1 TraesCS7D01G355200 chr7D 580126696 580127465 769 False 1243.0 1243 95.8500 2424 3191 1 chr7D.!!$F2 767
2 TraesCS7D01G355200 chr7B 481308495 481310960 2465 False 1945.4 3825 95.5095 1 2424 2 chr7B.!!$F1 2423
3 TraesCS7D01G355200 chr7A 540879378 540881539 2161 True 3105.0 3105 92.7940 286 2422 1 chr7A.!!$R1 2136
4 TraesCS7D01G355200 chr3B 606656201 606657757 1556 True 1770.0 1770 87.3260 855 2413 1 chr3B.!!$R1 1558
5 TraesCS7D01G355200 chr3A 601411252 601412852 1600 True 1744.0 1744 86.5520 803 2398 1 chr3A.!!$R1 1595
6 TraesCS7D01G355200 chr3D 459222706 459224249 1543 True 1733.0 1733 87.0840 855 2398 1 chr3D.!!$R1 1543
7 TraesCS7D01G355200 chr3D 591890450 591891219 769 False 1291.0 1291 97.0130 2425 3191 1 chr3D.!!$F1 766
8 TraesCS7D01G355200 chr2D 481538436 481539208 772 True 1290.0 1290 96.8950 2424 3191 1 chr2D.!!$R2 767
9 TraesCS7D01G355200 chr2D 411677546 411678308 762 True 1230.0 1230 95.7140 2425 3191 1 chr2D.!!$R1 766
10 TraesCS7D01G355200 chr1D 421655362 421656132 770 True 1277.0 1277 96.6320 2425 3191 1 chr1D.!!$R1 766
11 TraesCS7D01G355200 chrUn 110710209 110710981 772 False 1267.0 1267 96.2630 2419 3191 1 chrUn.!!$F1 772
12 TraesCS7D01G355200 chrUn 219606693 219607464 771 True 1249.0 1249 95.9840 2425 3191 1 chrUn.!!$R1 766
13 TraesCS7D01G355200 chr4D 82035773 82036545 772 False 1264.0 1264 96.2480 2423 3191 1 chr4D.!!$F1 768
14 TraesCS7D01G355200 chr5D 319429566 319430337 771 False 1260.0 1260 96.2480 2425 3191 1 chr5D.!!$F1 766

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
636 655 0.450983 GCAGCTTCAGGAGAATGTGC 59.549 55.0 0.00 0.0 36.08 4.57 F
1794 1831 0.177836 TGTCATCGACGCATTGGGAT 59.822 50.0 7.82 0.0 34.95 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1848 1885 1.757118 GCTACACTCAGTGGGCTATCA 59.243 52.381 10.28 0.0 37.94 2.15 R
3030 3166 2.080693 TGGCAAGCGATCATAAACGTT 58.919 42.857 0.00 0.0 0.00 3.99 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
50 51 3.573229 TGCCCTTGCAGTGGAGCT 61.573 61.111 7.71 0.00 44.23 4.09
51 52 3.855503 TGCCCTTGCAGTGGAGCTG 62.856 63.158 7.71 0.00 44.23 4.24
174 175 3.007940 TGAAGGTCCAGATACACACTTGG 59.992 47.826 0.00 0.00 0.00 3.61
236 237 0.959372 AGTGCTGCTCATGACTTGGC 60.959 55.000 0.00 0.00 0.00 4.52
636 655 0.450983 GCAGCTTCAGGAGAATGTGC 59.549 55.000 0.00 0.00 36.08 4.57
669 688 3.555956 GCAACATATTCTGTAGGTGTCGG 59.444 47.826 0.00 0.00 36.98 4.79
671 690 5.680408 GCAACATATTCTGTAGGTGTCGGTA 60.680 44.000 0.00 0.00 36.98 4.02
772 791 5.521735 GTGGTGTAGCATGAGTGAGATAAAG 59.478 44.000 0.00 0.00 0.00 1.85
826 849 1.990563 GATGCTGATTGTGTTGCTTGC 59.009 47.619 0.00 0.00 0.00 4.01
926 952 6.647212 TCAGCAGTTAGACATTGTTATTCG 57.353 37.500 0.00 0.00 0.00 3.34
1111 1148 4.008074 TCTACCAAAGTTCAGGAAGCTG 57.992 45.455 0.00 0.00 0.00 4.24
1247 1284 2.228582 TGAACGAAATGGTGCCATTGAG 59.771 45.455 16.24 14.70 44.86 3.02
1317 1354 2.820787 TCTCAAGGTTCTCGAGAAGTCC 59.179 50.000 27.70 24.20 32.96 3.85
1320 1357 3.256136 TCAAGGTTCTCGAGAAGTCCTTC 59.744 47.826 32.06 19.72 37.87 3.46
1322 1359 3.231818 AGGTTCTCGAGAAGTCCTTCAA 58.768 45.455 27.70 0.30 41.84 2.69
1497 1534 4.443978 ACCATTTCAGGAGATGTATGGG 57.556 45.455 0.00 0.00 41.98 4.00
1509 1546 5.221722 GGAGATGTATGGGATACTTGAAGCA 60.222 44.000 0.00 0.00 36.70 3.91
1559 1596 0.965363 ACTTGGGCTGCCAATAACCG 60.965 55.000 22.05 3.59 0.00 4.44
1634 1671 5.541845 TCAGTTTGTTGAGATACTCACCAG 58.458 41.667 0.74 0.00 40.46 4.00
1693 1730 3.080158 TTGGTGCCCTTTGCCTCCA 62.080 57.895 0.00 0.00 39.88 3.86
1794 1831 0.177836 TGTCATCGACGCATTGGGAT 59.822 50.000 7.82 0.00 34.95 3.85
1848 1885 3.626930 CAGCCTCTTAGGTCAGTCTAGT 58.373 50.000 0.00 0.00 37.80 2.57
1870 1907 1.320344 TAGCCCACTGAGTGTAGCCG 61.320 60.000 17.82 0.71 33.35 5.52
1911 1948 2.226674 GCTACCAACCTTGTTGAAGCTC 59.773 50.000 18.69 0.00 0.00 4.09
2191 2228 4.082895 AGTGCAAGCAGCTTCATTTCTAAG 60.083 41.667 4.07 0.00 45.94 2.18
2348 2392 9.040939 GTAGCAAATTCCACTGTGTTAAAAATT 57.959 29.630 7.08 2.63 0.00 1.82
2503 2630 4.212636 CCGATTTTTATTAGCCGTCCGATT 59.787 41.667 0.00 0.00 0.00 3.34
2568 2695 1.494721 GAAGGGCATAATGGTCCAGGA 59.505 52.381 0.00 0.00 34.02 3.86
2720 2852 0.907486 TCGTTCTCGTCCTCCTCCTA 59.093 55.000 0.00 0.00 38.33 2.94
2960 3096 5.424252 TCATCGATTTAGGTTTCCCTAGTGT 59.576 40.000 0.00 0.00 44.21 3.55
3098 3235 9.672086 TTTAAAATTCCACACAAGATTTCGTAG 57.328 29.630 0.00 0.00 0.00 3.51
3172 3309 0.328926 TGATGCAGGAAGACATGGCA 59.671 50.000 0.00 0.00 0.00 4.92
3175 3312 0.035725 TGCAGGAAGACATGGCAGAG 60.036 55.000 0.00 0.00 0.00 3.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 4.025858 GCTCCCAGCTCCACTGCA 62.026 66.667 0.00 0.00 45.78 4.41
122 123 3.992260 ACTCTACCACATGTATCGAGC 57.008 47.619 0.00 0.00 29.17 5.03
174 175 4.791974 CTTGAACTTTGCAGATGGAGAAC 58.208 43.478 0.00 0.00 0.00 3.01
403 421 2.401583 AAGATGCCACATGCGTAAGA 57.598 45.000 0.00 0.00 45.60 2.10
404 422 3.373748 TGTTAAGATGCCACATGCGTAAG 59.626 43.478 0.00 0.00 45.60 2.34
406 424 2.979240 TGTTAAGATGCCACATGCGTA 58.021 42.857 0.00 0.00 45.60 4.42
407 425 1.819928 TGTTAAGATGCCACATGCGT 58.180 45.000 0.00 0.00 45.60 5.24
408 426 2.917701 TTGTTAAGATGCCACATGCG 57.082 45.000 0.00 0.00 45.60 4.73
409 427 5.170021 TCAATTTGTTAAGATGCCACATGC 58.830 37.500 0.00 0.00 41.77 4.06
410 428 7.837202 AATCAATTTGTTAAGATGCCACATG 57.163 32.000 0.00 0.00 0.00 3.21
411 429 8.095792 TGAAATCAATTTGTTAAGATGCCACAT 58.904 29.630 0.00 0.00 0.00 3.21
412 430 7.440198 TGAAATCAATTTGTTAAGATGCCACA 58.560 30.769 0.00 0.00 0.00 4.17
636 655 9.803130 CTACAGAATATGTTGCTAAATTGATCG 57.197 33.333 0.00 0.00 39.96 3.69
669 688 7.648510 GGCAAGACACATAGTACTATTCTGTAC 59.351 40.741 12.87 10.52 42.09 2.90
671 690 6.154534 TGGCAAGACACATAGTACTATTCTGT 59.845 38.462 12.87 15.66 0.00 3.41
772 791 9.979270 CATTGAAGACAGTATCTAACATTCAAC 57.021 33.333 0.00 0.00 36.27 3.18
985 1011 4.624015 CACTGCATGTCCAAGTCAAAAAT 58.376 39.130 0.00 0.00 0.00 1.82
1111 1148 8.948631 TTAACTTCATCCACTATCTGATCAAC 57.051 34.615 0.00 0.00 0.00 3.18
1497 1534 6.615088 TCTTGCTTTCATTGCTTCAAGTATC 58.385 36.000 0.00 0.00 34.30 2.24
1559 1596 4.574013 AGCTATTCTGCAACAGCTTATCAC 59.426 41.667 5.46 0.00 41.50 3.06
1794 1831 2.359981 TTAGCTCCTCGGCTAGCTTA 57.640 50.000 15.72 1.84 46.82 3.09
1848 1885 1.757118 GCTACACTCAGTGGGCTATCA 59.243 52.381 10.28 0.00 37.94 2.15
1870 1907 2.164422 GCCCTTGAAAACCAGCTGATAC 59.836 50.000 17.39 2.44 0.00 2.24
1911 1948 2.406616 GGCAGCCATTACCGTGGTG 61.407 63.158 6.55 0.00 41.47 4.17
2503 2630 4.683766 TTCATTCTTAATCCCCCACCAA 57.316 40.909 0.00 0.00 0.00 3.67
3030 3166 2.080693 TGGCAAGCGATCATAAACGTT 58.919 42.857 0.00 0.00 0.00 3.99
3098 3235 4.002316 ACATAAATGCATGCAAAACCCAC 58.998 39.130 26.68 0.00 0.00 4.61


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

AutoCloner maintained by Alex Coulton.