Multiple sequence alignment - TraesCS5A01G533400

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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 TraesCS5A01G533400 chr5A 100.000 2454 0 0 1 2454 690643316 690640863 0.000000e+00 4532
1 TraesCS5A01G533400 chr5A 99.588 729 3 0 1 729 698852993 698853721 0.000000e+00 1330
2 TraesCS5A01G533400 chr7A 96.611 2272 73 3 185 2454 435733425 435731156 0.000000e+00 3766
3 TraesCS5A01G533400 chr7A 94.753 2306 79 16 185 2454 563493576 563495875 0.000000e+00 3550
4 TraesCS5A01G533400 chr7A 95.641 1560 61 5 896 2454 87693040 87691487 0.000000e+00 2497
5 TraesCS5A01G533400 chr7A 96.111 720 22 2 185 898 87693791 87693072 0.000000e+00 1170
6 TraesCS5A01G533400 chr7A 89.945 726 48 11 185 898 139135763 139135051 0.000000e+00 913
7 TraesCS5A01G533400 chr7A 89.405 538 45 7 895 1431 139135020 139134494 0.000000e+00 667
8 TraesCS5A01G533400 chr2B 96.611 1623 47 6 185 1807 338729284 338727670 0.000000e+00 2686
9 TraesCS5A01G533400 chr2B 94.444 162 3 5 1 162 186924704 186924549 6.780000e-61 244
10 TraesCS5A01G533400 chr2B 94.444 162 3 5 1 162 783423176 783423021 6.780000e-61 244
11 TraesCS5A01G533400 chr1D 96.159 1562 54 4 893 2454 34022519 34020964 0.000000e+00 2547
12 TraesCS5A01G533400 chr1D 97.361 720 13 2 185 898 34023267 34022548 0.000000e+00 1219
13 TraesCS5A01G533400 chr1D 91.004 667 38 12 1802 2454 123675626 123674968 0.000000e+00 880
14 TraesCS5A01G533400 chr3B 96.701 1273 39 3 185 1457 395707642 395706373 0.000000e+00 2115
15 TraesCS5A01G533400 chr3B 96.062 965 33 3 1492 2454 395706372 395705411 0.000000e+00 1567
16 TraesCS5A01G533400 chr5D 87.957 930 76 15 1540 2443 448014875 448015794 0.000000e+00 1064
17 TraesCS5A01G533400 chr5D 89.819 717 52 10 185 889 448013526 448014233 0.000000e+00 900
18 TraesCS5A01G533400 chr5D 88.555 533 49 8 900 1431 448014285 448014806 9.570000e-179 636
19 TraesCS5A01G533400 chr5B 91.278 665 38 11 1802 2454 102916548 102917204 0.000000e+00 889
20 TraesCS5A01G533400 chr5B 90.196 102 7 2 1414 1513 166379180 166379080 1.980000e-26 130
21 TraesCS5A01G533400 chr2D 91.114 664 38 11 1802 2454 5789776 5789123 0.000000e+00 880
22 TraesCS5A01G533400 chr4D 91.654 635 35 9 1802 2425 294681649 294682276 0.000000e+00 863
23 TraesCS5A01G533400 chr4D 91.000 100 5 3 1414 1510 414999564 414999662 5.510000e-27 132
24 TraesCS5A01G533400 chr1A 88.848 538 48 9 895 1431 291624927 291624401 0.000000e+00 651
25 TraesCS5A01G533400 chr1A 94.444 162 3 5 1 162 107526330 107526175 6.780000e-61 244
26 TraesCS5A01G533400 chr1A 93.827 162 4 5 1 162 111978802 111978647 3.150000e-59 239
27 TraesCS5A01G533400 chr7B 95.679 162 1 5 1 162 611669130 611669285 3.130000e-64 255
28 TraesCS5A01G533400 chr6B 94.444 162 3 5 1 162 335089921 335090076 6.780000e-61 244
29 TraesCS5A01G533400 chr1B 94.444 162 3 5 1 162 559582868 559582713 6.780000e-61 244
30 TraesCS5A01G533400 chr1B 94.444 162 3 5 1 162 627882067 627881912 6.780000e-61 244
31 TraesCS5A01G533400 chr4A 88.021 192 20 2 1674 1865 718087277 718087089 8.830000e-55 224
32 TraesCS5A01G533400 chr3D 91.089 101 5 3 1414 1512 9066348 9066250 1.530000e-27 134
33 TraesCS5A01G533400 chr4B 90.909 99 6 2 1414 1510 511163711 511163808 1.980000e-26 130


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 TraesCS5A01G533400 chr5A 690640863 690643316 2453 True 4532.000000 4532 100.0000 1 2454 1 chr5A.!!$R1 2453
1 TraesCS5A01G533400 chr5A 698852993 698853721 728 False 1330.000000 1330 99.5880 1 729 1 chr5A.!!$F1 728
2 TraesCS5A01G533400 chr7A 435731156 435733425 2269 True 3766.000000 3766 96.6110 185 2454 1 chr7A.!!$R1 2269
3 TraesCS5A01G533400 chr7A 563493576 563495875 2299 False 3550.000000 3550 94.7530 185 2454 1 chr7A.!!$F1 2269
4 TraesCS5A01G533400 chr7A 87691487 87693791 2304 True 1833.500000 2497 95.8760 185 2454 2 chr7A.!!$R2 2269
5 TraesCS5A01G533400 chr7A 139134494 139135763 1269 True 790.000000 913 89.6750 185 1431 2 chr7A.!!$R3 1246
6 TraesCS5A01G533400 chr2B 338727670 338729284 1614 True 2686.000000 2686 96.6110 185 1807 1 chr2B.!!$R2 1622
7 TraesCS5A01G533400 chr1D 34020964 34023267 2303 True 1883.000000 2547 96.7600 185 2454 2 chr1D.!!$R2 2269
8 TraesCS5A01G533400 chr1D 123674968 123675626 658 True 880.000000 880 91.0040 1802 2454 1 chr1D.!!$R1 652
9 TraesCS5A01G533400 chr3B 395705411 395707642 2231 True 1841.000000 2115 96.3815 185 2454 2 chr3B.!!$R1 2269
10 TraesCS5A01G533400 chr5D 448013526 448015794 2268 False 866.666667 1064 88.7770 185 2443 3 chr5D.!!$F1 2258
11 TraesCS5A01G533400 chr5B 102916548 102917204 656 False 889.000000 889 91.2780 1802 2454 1 chr5B.!!$F1 652
12 TraesCS5A01G533400 chr2D 5789123 5789776 653 True 880.000000 880 91.1140 1802 2454 1 chr2D.!!$R1 652
13 TraesCS5A01G533400 chr4D 294681649 294682276 627 False 863.000000 863 91.6540 1802 2425 1 chr4D.!!$F1 623
14 TraesCS5A01G533400 chr1A 291624401 291624927 526 True 651.000000 651 88.8480 895 1431 1 chr1A.!!$R3 536

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
934 993 1.000843 TGAAGTGCTCTTTGCTAGCGA 59.999 47.619 10.77 5.12 43.11 4.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2403 2562 1.181098 ACCCCACATTGCTGCAGTTC 61.181 55.0 16.64 0.0 0.0 3.01 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
890 908 3.840078 AGTGGAAAAATGATTTGGGAGGG 59.160 43.478 0.00 0.00 0.00 4.30
925 984 3.072184 AGTCTTGACCATGAAGTGCTCTT 59.928 43.478 0.00 0.00 36.51 2.85
928 987 1.881973 TGACCATGAAGTGCTCTTTGC 59.118 47.619 2.00 0.00 43.25 3.68
934 993 1.000843 TGAAGTGCTCTTTGCTAGCGA 59.999 47.619 10.77 5.12 43.11 4.93
1146 1205 1.052617 GGCTTCCCTCTACTGGATCC 58.947 60.000 4.20 4.20 0.00 3.36
1233 1292 5.240403 GGAGATGAACTTTTGCTTCTCAAGT 59.760 40.000 0.00 0.00 37.17 3.16
1461 1521 4.133856 CAGCTTTGAACTAAGGTGTTCG 57.866 45.455 15.69 0.00 46.59 3.95
1574 1646 2.618709 GGATATGGGAGCAAAAGGTTCG 59.381 50.000 0.00 0.00 0.00 3.95
1577 1649 0.181587 TGGGAGCAAAAGGTTCGACA 59.818 50.000 0.00 0.00 0.00 4.35
1696 1776 1.336125 GCCTGCCATTATCAGTTGAGC 59.664 52.381 0.00 0.00 0.00 4.26
1718 1798 2.200337 GGGCCTGACCAGCGTTTTT 61.200 57.895 0.84 0.00 42.05 1.94
1797 1877 5.296748 ACCACATCACTAAAATTTGGTTGC 58.703 37.500 0.00 0.00 34.31 4.17
1865 1945 2.067013 GCCTCGTCAGGTTGTTTAGTC 58.933 52.381 0.00 0.00 42.74 2.59
1906 1986 1.633432 TCCCCCATCTTGTGTCGATTT 59.367 47.619 0.00 0.00 0.00 2.17
1956 2036 5.620206 AGTGACATTGTCTATTTGGTGTCA 58.380 37.500 17.26 2.22 42.35 3.58
2265 2415 8.662781 TTGTTAGATGATACATGCTTCTAACC 57.337 34.615 21.49 12.28 44.26 2.85
2280 2430 5.105716 GCTTCTAACCACAGTACAGATCAGA 60.106 44.000 0.00 0.00 0.00 3.27
2342 2493 0.036010 AAGTTGCTCGGGTGGATCTG 60.036 55.000 0.00 0.00 0.00 2.90
2362 2521 2.297701 GTTGTGGTTCAAGCTCCTCAA 58.702 47.619 3.30 3.30 36.66 3.02
2380 2539 5.960811 TCCTCAAGTGGATCTAATCAAGACT 59.039 40.000 0.00 0.00 36.93 3.24
2386 2545 9.522804 CAAGTGGATCTAATCAAGACTACTTAC 57.477 37.037 0.00 0.00 36.19 2.34
2387 2546 8.240267 AGTGGATCTAATCAAGACTACTTACC 57.760 38.462 0.00 0.00 36.93 2.85
2403 2562 4.261801 ACTTACCGACCATCTTCCATTTG 58.738 43.478 0.00 0.00 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
890 908 3.498777 GGTCAAGACTAAAGCAACCTCAC 59.501 47.826 0.00 0.0 0.00 3.51
1461 1521 3.558418 TGTCGCAGTTTTGAACTAAGGTC 59.442 43.478 0.00 0.0 40.46 3.85
1574 1646 8.817100 CCATCTCAGGTTTTAAAAGTTTTTGTC 58.183 33.333 6.10 0.0 0.00 3.18
1577 1649 9.599866 CTTCCATCTCAGGTTTTAAAAGTTTTT 57.400 29.630 6.10 0.0 0.00 1.94
1696 1776 2.109799 CGCTGGTCAGGCCCTATG 59.890 66.667 0.00 0.0 36.04 2.23
1797 1877 5.121611 TCGACTTAAACATGCAACCATAGTG 59.878 40.000 0.00 0.0 0.00 2.74
1865 1945 3.560636 ATGGATTTAGACCTCGTTGGG 57.439 47.619 2.69 0.0 41.11 4.12
1906 1986 6.964086 AGGGGAAACATTAGTACTAAGAAGGA 59.036 38.462 19.58 0.0 0.00 3.36
1971 2053 8.662781 TTAGCAGGATGAACATCATAAAGTAC 57.337 34.615 15.22 0.0 37.20 2.73
2235 2385 9.182214 AGAAGCATGTATCATCTAACAAAATGT 57.818 29.630 0.00 0.0 0.00 2.71
2265 2415 6.820152 TGATTTTGGATCTGATCTGTACTGTG 59.180 38.462 16.61 0.0 0.00 3.66
2280 2430 5.533903 GCTGTCATGTATCCTGATTTTGGAT 59.466 40.000 0.00 0.0 45.37 3.41
2342 2493 1.967319 TGAGGAGCTTGAACCACAAC 58.033 50.000 0.00 0.0 34.56 3.32
2362 2521 7.013464 CGGTAAGTAGTCTTGATTAGATCCACT 59.987 40.741 0.00 0.0 34.79 4.00
2380 2539 5.188163 TCAAATGGAAGATGGTCGGTAAGTA 59.812 40.000 0.00 0.0 0.00 2.24
2386 2545 3.127548 CAGTTCAAATGGAAGATGGTCGG 59.872 47.826 0.00 0.0 35.82 4.79
2387 2546 3.426695 GCAGTTCAAATGGAAGATGGTCG 60.427 47.826 0.00 0.0 35.82 4.79
2403 2562 1.181098 ACCCCACATTGCTGCAGTTC 61.181 55.000 16.64 0.0 0.00 3.01


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

AutoCloner maintained by Alex Coulton.