Multiple sequence alignment - TraesCS5A01G119400

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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 TraesCS5A01G119400 chr5A 100.000 2800 0 0 1 2800 248531921 248534720 0.000000e+00 5171
1 TraesCS5A01G119400 chr5D 94.737 2831 85 18 1 2800 193511923 193509126 0.000000e+00 4344
2 TraesCS5A01G119400 chr5B 92.695 1410 56 18 1 1387 216400069 216398684 0.000000e+00 1989
3 TraesCS5A01G119400 chr5B 96.604 795 18 4 2011 2800 216395420 216394630 0.000000e+00 1310
4 TraesCS5A01G119400 chr5B 98.787 577 6 1 1443 2019 216397014 216396439 0.000000e+00 1026
5 TraesCS5A01G119400 chr5B 96.774 62 1 1 1376 1437 216397138 216397078 4.930000e-18 102


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 TraesCS5A01G119400 chr5A 248531921 248534720 2799 False 5171.00 5171 100.000 1 2800 1 chr5A.!!$F1 2799
1 TraesCS5A01G119400 chr5D 193509126 193511923 2797 True 4344.00 4344 94.737 1 2800 1 chr5D.!!$R1 2799
2 TraesCS5A01G119400 chr5B 216394630 216400069 5439 True 1106.75 1989 96.215 1 2800 4 chr5B.!!$R1 2799

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
818 848 0.035458 CAACCCCACTCTCACTCACC 59.965 60.0 0.0 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2104 4785 2.164422 GCAAAGCATCTCCTTGTAACCC 59.836 50.0 0.0 0.0 0.0 4.11 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
90 91 3.008835 AGCAGCAAAGCATTGGAGATA 57.991 42.857 3.55 0.0 37.02 1.98
121 122 1.891933 TATGACCCATGGCAGGAGAA 58.108 50.000 6.09 0.0 0.00 2.87
169 170 1.173913 GCAAACTATCCGGCAAAGGT 58.826 50.000 0.00 0.0 0.00 3.50
343 347 2.291741 CTGTCTGAGCAAAGGAAACACC 59.708 50.000 0.00 0.0 39.35 4.16
382 386 4.035675 GGCAGGCAGTTGTCTAAATATGTC 59.964 45.833 0.00 0.0 0.00 3.06
399 403 6.919775 ATATGTCATAGAGGTCAGGTTACC 57.080 41.667 0.00 0.0 40.06 2.85
403 407 1.033746 TAGAGGTCAGGTTACCGCCG 61.034 60.000 0.00 0.0 44.77 6.46
535 540 3.714144 AGTGGCATCTACTAGTGGAAGT 58.286 45.455 13.39 0.0 0.00 3.01
549 554 3.055094 AGTGGAAGTATGAATCGGCAAGT 60.055 43.478 0.00 0.0 0.00 3.16
565 570 2.095364 GCAAGTGATGAAGCAAGTGGAG 60.095 50.000 0.00 0.0 0.00 3.86
598 603 2.300437 CCTCCAAGAATCGGTAGGGATC 59.700 54.545 0.00 0.0 0.00 3.36
629 634 1.134461 CAGAAGCTCCATCACCTCAGG 60.134 57.143 0.00 0.0 0.00 3.86
650 655 0.304705 GAAGCGCTCTCTCTCTCTCG 59.695 60.000 12.06 0.0 0.00 4.04
737 763 3.917760 GCCTCGCCTCGCCACTAT 61.918 66.667 0.00 0.0 0.00 2.12
765 791 3.357079 CTCGGCTGGCCACACAAC 61.357 66.667 0.00 0.0 35.37 3.32
775 805 1.639534 CCACACAACGACAACGGAC 59.360 57.895 0.00 0.0 44.46 4.79
818 848 0.035458 CAACCCCACTCTCACTCACC 59.965 60.000 0.00 0.0 0.00 4.02
875 905 2.155732 CACCGTCTGTCGTCTTTCAATG 59.844 50.000 0.00 0.0 37.94 2.82
946 979 6.347806 GGTTCGATTTCTCTTCTCAAAGGAAC 60.348 42.308 0.00 0.0 32.95 3.62
989 1023 2.511145 GCGGCAGCAAGAGGAGAG 60.511 66.667 3.18 0.0 44.35 3.20
990 1024 2.186384 CGGCAGCAAGAGGAGAGG 59.814 66.667 0.00 0.0 0.00 3.69
991 1025 2.354401 CGGCAGCAAGAGGAGAGGA 61.354 63.158 0.00 0.0 0.00 3.71
1124 1158 1.023513 CCTTCTCTTGGCTCTTGCGG 61.024 60.000 0.00 0.0 40.82 5.69
1267 1301 4.889995 GGACCTAGGAAGAATTGGGATTTG 59.110 45.833 17.98 0.0 0.00 2.32
1312 1352 5.183228 CACGGTGGACTTCCTACATATTTT 58.817 41.667 0.00 0.0 36.82 1.82
1378 1418 3.568007 TGTGGCACTCCATGTTTAGTTTC 59.432 43.478 19.83 0.0 45.62 2.78
1460 3114 7.276218 CCTGTTTTATATGCTGGTGTTTTGATG 59.724 37.037 0.00 0.0 0.00 3.07
2059 4740 1.460504 AGATGGTGCTGCATTGTGAG 58.539 50.000 5.27 0.0 0.00 3.51
2104 4785 6.599437 ACGTCCTTTTTCGAATGTCTATTTG 58.401 36.000 0.00 0.0 0.00 2.32
2125 4806 2.164422 GGGTTACAAGGAGATGCTTTGC 59.836 50.000 0.00 0.0 37.10 3.68
2266 4947 6.349611 GCTTGTCTTCTTTGGCATCTCATTAA 60.350 38.462 0.00 0.0 0.00 1.40
2421 5102 8.518702 TGTAATCAACATAACTAAATTGCAGCA 58.481 29.630 0.00 0.0 31.43 4.41
2449 5130 0.745845 GCACATGGTCAGATTCGGCT 60.746 55.000 0.00 0.0 0.00 5.52
2544 5229 2.780010 AGAGTGGGCTAGCCATTATGTT 59.220 45.455 34.09 12.4 37.98 2.71
2545 5230 3.973973 AGAGTGGGCTAGCCATTATGTTA 59.026 43.478 34.09 7.5 37.98 2.41
2597 5282 9.062524 TGCTACTGACATACTGTTTTATGTTTT 57.937 29.630 0.00 0.0 41.78 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 62 1.958579 TGCTTTGCTGCTTTCACATCT 59.041 42.857 0.00 0.0 0.00 2.90
90 91 4.526970 CATGGGTCATAACAAGGTAAGCT 58.473 43.478 0.00 0.0 0.00 3.74
121 122 1.539929 GCTCGCATCCTCTATTGTGCT 60.540 52.381 0.00 0.0 35.52 4.40
201 202 1.671328 CGAGTCACGATGGAGCTTCTA 59.329 52.381 0.00 0.0 45.77 2.10
237 238 3.282374 AACCTGAATGGGGGTCGGC 62.282 63.158 0.00 0.0 41.11 5.54
343 347 0.979665 TGCCACTTCTCTCAGGAAGG 59.020 55.000 8.71 0.0 44.82 3.46
382 386 1.068741 GGCGGTAACCTGACCTCTATG 59.931 57.143 0.00 0.0 37.34 2.23
399 403 2.784505 TCTGTTTATACGTGTACGGCG 58.215 47.619 4.80 4.8 44.95 6.46
403 407 7.864307 AGTCTGTTTCTGTTTATACGTGTAC 57.136 36.000 0.00 0.0 0.00 2.90
535 540 3.561310 GCTTCATCACTTGCCGATTCATA 59.439 43.478 0.00 0.0 0.00 2.15
549 554 2.355108 GGTAGCTCCACTTGCTTCATCA 60.355 50.000 0.00 0.0 41.46 3.07
565 570 0.745468 CTTGGAGGTAGGACGGTAGC 59.255 60.000 0.00 0.0 0.00 3.58
608 613 0.907486 TGAGGTGATGGAGCTTCTGG 59.093 55.000 0.00 0.0 30.42 3.86
636 641 1.221414 GAGAGCGAGAGAGAGAGAGC 58.779 60.000 0.00 0.0 0.00 4.09
737 763 1.379176 CAGCCGAGACCCAGAGAGA 60.379 63.158 0.00 0.0 0.00 3.10
766 792 4.446413 ATCCCGCGGTCCGTTGTC 62.446 66.667 26.12 0.0 34.38 3.18
900 930 6.484364 ACCAACAAGTCAAAGAATCCAATT 57.516 33.333 0.00 0.0 0.00 2.32
904 936 4.274950 TCGAACCAACAAGTCAAAGAATCC 59.725 41.667 0.00 0.0 0.00 3.01
987 1021 2.733945 GCCATCTCGCTCCTCCTC 59.266 66.667 0.00 0.0 0.00 3.71
988 1022 3.222855 CGCCATCTCGCTCCTCCT 61.223 66.667 0.00 0.0 0.00 3.69
1124 1158 1.738030 GCATGAATCCCTTGCAGCAAC 60.738 52.381 2.83 0.0 43.22 4.17
1196 1230 0.186873 ATCCCAATCCCAGGACATGC 59.813 55.000 0.00 0.0 34.20 4.06
1267 1301 0.769873 ATGAGGTCATGATGGCTCCC 59.230 55.000 0.00 0.0 34.83 4.30
1378 1418 1.526887 CTGATACGCAATAAGCACCCG 59.473 52.381 0.00 0.0 46.13 5.28
1460 3114 9.453572 TCTTATGATGAATTAATAGGTGATGCC 57.546 33.333 0.00 0.0 37.58 4.40
1615 3269 4.863707 GCATCTTCGCCTCATCCA 57.136 55.556 0.00 0.0 0.00 3.41
1869 3523 9.082313 AGAAACATAGATGGAATTTGTGAACTT 57.918 29.630 0.00 0.0 0.00 2.66
1979 3633 3.568430 CCTTTCTTTTTCTGTAAGCGGGT 59.432 43.478 0.00 0.0 0.00 5.28
2059 4740 5.924825 ACGTCATTGTAACCAAAGTAGAGAC 59.075 40.000 0.00 0.0 33.44 3.36
2104 4785 2.164422 GCAAAGCATCTCCTTGTAACCC 59.836 50.000 0.00 0.0 0.00 4.11
2266 4947 9.661954 TTTCTCAAGGATATCTATACAGACCTT 57.338 33.333 2.05 0.0 35.96 3.50
2449 5130 7.124573 TGCTAATAAGAGGTTGATTCTGCTA 57.875 36.000 0.00 0.0 0.00 3.49
2620 5305 7.726033 AACATCCTCTGTCAACTAGATTACT 57.274 36.000 0.00 0.0 36.98 2.24


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

AutoCloner maintained by Alex Coulton.