Multiple sequence alignment - TraesCS5A01G453500

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 TraesCS5A01G453500 chr5A 100.000 2529 0 0 1 2529 634990915 634988387 0.000000e+00 4671
1 TraesCS5A01G453500 chr5A 95.156 2539 112 7 1 2529 635244689 635247226 0.000000e+00 3997
2 TraesCS5A01G453500 chr5A 88.267 2574 221 38 1 2529 634358819 634356282 0.000000e+00 3005
3 TraesCS5A01G453500 chr5A 86.809 1774 179 26 1 1755 638380826 638382563 0.000000e+00 1929
4 TraesCS5A01G453500 chr5A 85.792 549 72 6 1984 2527 638334274 638333727 6.070000e-161 577
5 TraesCS5A01G453500 chr5D 90.039 2570 182 33 1 2529 507519194 507516658 0.000000e+00 3260
6 TraesCS5A01G453500 chr5D 88.521 1873 155 30 680 2529 506739544 506737709 0.000000e+00 2213
7 TraesCS5A01G453500 chr5D 89.242 1320 124 10 1227 2529 506703341 506702023 0.000000e+00 1635
8 TraesCS5A01G453500 chr5D 89.105 927 74 19 1 911 506704242 506703327 0.000000e+00 1127
9 TraesCS5A01G453500 chr5D 88.726 683 59 12 1 670 506740202 506739525 0.000000e+00 819
10 TraesCS5A01G453500 chr5B 87.524 2557 236 37 1 2529 637216444 637213943 0.000000e+00 2878
11 TraesCS5A01G453500 chr5B 86.790 2218 188 46 1 2179 637729944 637727793 0.000000e+00 2375
12 TraesCS5A01G453500 chr5B 88.100 1605 144 19 954 2529 637804213 637802627 0.000000e+00 1862
13 TraesCS5A01G453500 chr5B 87.709 1611 145 23 954 2529 637783047 637781455 0.000000e+00 1829
14 TraesCS5A01G453500 chr5B 91.419 874 60 8 1 862 637783956 637783086 0.000000e+00 1184
15 TraesCS5A01G453500 chr5B 91.076 874 63 8 1 862 637805122 637804252 0.000000e+00 1168


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 TraesCS5A01G453500 chr5A 634988387 634990915 2528 True 4671.0 4671 100.0000 1 2529 1 chr5A.!!$R2 2528
1 TraesCS5A01G453500 chr5A 635244689 635247226 2537 False 3997.0 3997 95.1560 1 2529 1 chr5A.!!$F1 2528
2 TraesCS5A01G453500 chr5A 634356282 634358819 2537 True 3005.0 3005 88.2670 1 2529 1 chr5A.!!$R1 2528
3 TraesCS5A01G453500 chr5A 638380826 638382563 1737 False 1929.0 1929 86.8090 1 1755 1 chr5A.!!$F2 1754
4 TraesCS5A01G453500 chr5A 638333727 638334274 547 True 577.0 577 85.7920 1984 2527 1 chr5A.!!$R3 543
5 TraesCS5A01G453500 chr5D 507516658 507519194 2536 True 3260.0 3260 90.0390 1 2529 1 chr5D.!!$R1 2528
6 TraesCS5A01G453500 chr5D 506737709 506740202 2493 True 1516.0 2213 88.6235 1 2529 2 chr5D.!!$R3 2528
7 TraesCS5A01G453500 chr5D 506702023 506704242 2219 True 1381.0 1635 89.1735 1 2529 2 chr5D.!!$R2 2528
8 TraesCS5A01G453500 chr5B 637213943 637216444 2501 True 2878.0 2878 87.5240 1 2529 1 chr5B.!!$R1 2528
9 TraesCS5A01G453500 chr5B 637727793 637729944 2151 True 2375.0 2375 86.7900 1 2179 1 chr5B.!!$R2 2178
10 TraesCS5A01G453500 chr5B 637802627 637805122 2495 True 1515.0 1862 89.5880 1 2529 2 chr5B.!!$R4 2528
11 TraesCS5A01G453500 chr5B 637781455 637783956 2501 True 1506.5 1829 89.5640 1 2529 2 chr5B.!!$R3 2528

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
83 88 2.781757 TCTCCCCCGATACTCTACTTCA 59.218 50.0 0.0 0.0 0.0 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2064 2125 2.634639 TGTGGGACTAGGAAAGGCTA 57.365 50.0 0.0 0.0 31.67 3.93 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
83 88 2.781757 TCTCCCCCGATACTCTACTTCA 59.218 50.000 0.00 0.00 0.00 3.02
84 89 3.203710 TCTCCCCCGATACTCTACTTCAA 59.796 47.826 0.00 0.00 0.00 2.69
239 246 6.048509 GGTTTGCCATATTTATTTGAGTGGG 58.951 40.000 0.00 0.00 34.09 4.61
242 249 5.523588 TGCCATATTTATTTGAGTGGGGAA 58.476 37.500 0.00 0.00 0.00 3.97
281 289 4.239428 TCATGAAGGCAATGGAGATTGA 57.761 40.909 0.00 0.00 41.49 2.57
324 332 3.323979 CCCTTCGGCCCGCTATATATAAT 59.676 47.826 0.00 0.00 0.00 1.28
1154 1178 6.128138 AGAAGCAGTTAACCTATTCCTTGT 57.872 37.500 0.88 0.00 0.00 3.16
1228 1252 1.552792 GTCCTGAGGTGCTTAGCTTCT 59.447 52.381 5.60 2.57 0.00 2.85
1231 1255 0.905357 TGAGGTGCTTAGCTTCTCCC 59.095 55.000 18.60 6.99 31.46 4.30
1245 1269 5.831103 AGCTTCTCCCTTGGATTTTCAATA 58.169 37.500 0.00 0.00 0.00 1.90
1550 1576 2.886523 CACAATCCAACTTCCTTGAGCA 59.113 45.455 0.00 0.00 30.42 4.26
1606 1632 9.669353 CTATGTTTTCTTATGTATGCATTGTCC 57.331 33.333 3.54 0.00 36.58 4.02
1770 1822 4.118410 GCAATGTTTTGTCCATTGTCACA 58.882 39.130 12.97 0.00 46.91 3.58
1911 1965 9.912634 AACATTTCGTGAGACATTGATTTTTAT 57.087 25.926 0.00 0.00 41.84 1.40
2064 2125 0.320374 TCGTTGCTCTTCGTCCCATT 59.680 50.000 0.00 0.00 0.00 3.16
2076 2138 2.698797 TCGTCCCATTAGCCTTTCCTAG 59.301 50.000 0.00 0.00 0.00 3.02
2127 2189 0.652592 CATCCCTTTGTCGTCGCATC 59.347 55.000 0.00 0.00 0.00 3.91
2281 2354 2.759114 CATGGGATATGCCGCCCT 59.241 61.111 8.92 0.00 44.96 5.19
2285 2358 1.152756 GGGATATGCCGCCCTGTTT 60.153 57.895 0.00 0.00 41.31 2.83
2294 2367 1.376812 CGCCCTGTTTCCCCTGTAC 60.377 63.158 0.00 0.00 0.00 2.90
2324 2397 2.116238 GGCATACTCAGGGTACAAGGA 58.884 52.381 0.00 0.00 32.72 3.36
2377 2450 4.904853 AGGAGGAAAGAGATCCATTCTACC 59.095 45.833 0.00 1.01 42.27 3.18
2429 2502 8.679344 TTCAGCCTACATATCCCTATTTCATA 57.321 34.615 0.00 0.00 0.00 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
83 88 1.347707 TGGACAGGAAGAAGCATCGTT 59.652 47.619 0.00 0.00 0.00 3.85
84 89 0.976641 TGGACAGGAAGAAGCATCGT 59.023 50.000 0.00 0.00 0.00 3.73
239 246 1.418373 GCAAAAATCTGCACCGTTCC 58.582 50.000 0.00 0.00 42.17 3.62
281 289 2.158696 GGAGAATTAGCTCATGGCCAGT 60.159 50.000 13.05 0.00 43.05 4.00
324 332 3.275143 CTTGTACCCCGATTATGTTGCA 58.725 45.455 0.00 0.00 0.00 4.08
911 934 5.045578 AGTTATTCCCTTACACACTCATGCT 60.046 40.000 0.00 0.00 0.00 3.79
981 1005 6.728200 TGCCATGATCAGATAAACGAATTTC 58.272 36.000 0.09 0.00 0.00 2.17
993 1017 1.478105 GCCTTGGATGCCATGATCAGA 60.478 52.381 0.09 0.00 31.53 3.27
1141 1165 3.265489 TCTTCCCCACAAGGAATAGGTT 58.735 45.455 0.00 0.00 44.87 3.50
1154 1178 7.610580 AAAATAATGTCAAACTTCTTCCCCA 57.389 32.000 0.00 0.00 0.00 4.96
1510 1536 3.580895 TGTGCTAGACCATGGTGTTCTTA 59.419 43.478 25.52 1.40 0.00 2.10
1550 1576 5.279657 GGAGCAGAAAAACATTTCCTCCATT 60.280 40.000 15.67 0.00 37.98 3.16
1606 1632 7.810766 ACAACACAATGAAACTAAACAACAG 57.189 32.000 0.00 0.00 0.00 3.16
1658 1684 3.067106 TCTTCTTGCTTAGAACAAGCGG 58.933 45.455 4.68 1.09 45.80 5.52
2064 2125 2.634639 TGTGGGACTAGGAAAGGCTA 57.365 50.000 0.00 0.00 31.67 3.93
2076 2138 3.393800 CACGAGATAATGGATGTGGGAC 58.606 50.000 0.00 0.00 0.00 4.46
2127 2189 7.711772 TCTTTGGAAATGCAATATTTATGGCTG 59.288 33.333 0.00 0.00 33.71 4.85
2277 2350 0.111639 TTGTACAGGGGAAACAGGGC 59.888 55.000 0.00 0.00 0.00 5.19
2281 2354 3.047115 TGGTACTTGTACAGGGGAAACA 58.953 45.455 10.04 0.73 0.00 2.83
2285 2358 2.193127 CCATGGTACTTGTACAGGGGA 58.807 52.381 10.04 0.00 32.77 4.81
2294 2367 3.470709 CCTGAGTATGCCATGGTACTTG 58.529 50.000 14.67 10.51 31.61 3.16
2324 2397 5.240844 GCTTCACTATTTTGGTGGTAGTGTT 59.759 40.000 10.48 0.00 43.51 3.32


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

AutoCloner maintained by Alex Coulton.