Multiple sequence alignment - TraesCS5D01G063400

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 TraesCS5D01G063400 chr5D 100.000 2347 0 0 1 2347 58912554 58914900 0 4335
1 TraesCS5D01G063400 chrUn 96.766 2350 68 6 1 2347 45100792 45098448 0 3912
2 TraesCS5D01G063400 chrUn 96.681 2350 72 5 1 2347 261513064 261515410 0 3903
3 TraesCS5D01G063400 chr5B 96.679 2349 72 5 1 2347 130609877 130607533 0 3901
4 TraesCS5D01G063400 chr5B 96.681 2350 71 5 1 2347 130614901 130612556 0 3901
5 TraesCS5D01G063400 chr5B 96.429 2352 77 5 1 2347 130568755 130571104 0 3871
6 TraesCS5D01G063400 chr3A 96.681 2350 71 6 1 2347 66030313 66032658 0 3901
7 TraesCS5D01G063400 chr7B 96.430 2353 74 6 1 2347 743033700 743036048 0 3871
8 TraesCS5D01G063400 chr2B 96.426 2350 76 7 1 2347 112869113 112866769 0 3868
9 TraesCS5D01G063400 chr5A 96.383 2350 77 6 1 2347 238828027 238830371 0 3862


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 TraesCS5D01G063400 chr5D 58912554 58914900 2346 False 4335 4335 100.000 1 2347 1 chr5D.!!$F1 2346
1 TraesCS5D01G063400 chrUn 45098448 45100792 2344 True 3912 3912 96.766 1 2347 1 chrUn.!!$R1 2346
2 TraesCS5D01G063400 chrUn 261513064 261515410 2346 False 3903 3903 96.681 1 2347 1 chrUn.!!$F1 2346
3 TraesCS5D01G063400 chr5B 130607533 130614901 7368 True 3901 3901 96.680 1 2347 2 chr5B.!!$R1 2346
4 TraesCS5D01G063400 chr5B 130568755 130571104 2349 False 3871 3871 96.429 1 2347 1 chr5B.!!$F1 2346
5 TraesCS5D01G063400 chr3A 66030313 66032658 2345 False 3901 3901 96.681 1 2347 1 chr3A.!!$F1 2346
6 TraesCS5D01G063400 chr7B 743033700 743036048 2348 False 3871 3871 96.430 1 2347 1 chr7B.!!$F1 2346
7 TraesCS5D01G063400 chr2B 112866769 112869113 2344 True 3868 3868 96.426 1 2347 1 chr2B.!!$R1 2346
8 TraesCS5D01G063400 chr5A 238828027 238830371 2344 False 3862 3862 96.383 1 2347 1 chr5A.!!$F1 2346

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
115 116 0.635009 ACTGGATCCCTTCGGACCTA 59.365 55.0 9.9 0.0 42.48 3.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1501 6525 0.694771 TTCAGGAAGGCACATGAGCT 59.305 50.0 14.91 0.0 32.42 4.09 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
31 32 0.872388 CGGTGAAAAGTGGTAGGTGC 59.128 55.000 0.00 0.00 0.00 5.01
42 43 1.259840 GGTAGGTGCCCACTAACGGA 61.260 60.000 0.00 0.00 0.00 4.69
115 116 0.635009 ACTGGATCCCTTCGGACCTA 59.365 55.000 9.90 0.00 42.48 3.08
249 250 1.700186 GGATTTCGCTCTATTCCCCCT 59.300 52.381 0.00 0.00 0.00 4.79
326 327 0.651124 ACCCATACCATAGGACCCCA 59.349 55.000 0.00 0.00 0.00 4.96
350 351 2.620115 TCCCGTATCTTATCTTTCGCGT 59.380 45.455 5.77 0.00 0.00 6.01
361 362 6.653740 TCTTATCTTTCGCGTATAGGAGATCA 59.346 38.462 5.77 0.00 0.00 2.92
368 369 3.556513 GCGTATAGGAGATCAAGACACG 58.443 50.000 0.00 0.00 0.00 4.49
497 498 3.854286 GTCGCACCCGAACAATAATAG 57.146 47.619 0.00 0.00 46.34 1.73
564 565 5.860611 TCCGTGGAAAATTCAGACTTTCTA 58.139 37.500 4.78 0.00 33.06 2.10
749 750 3.695830 ACACATCGAAATGGTACCAGT 57.304 42.857 21.41 15.91 37.19 4.00
851 852 1.609501 TTAGGAGAGGTGCGCCAGT 60.610 57.895 20.59 4.28 39.21 4.00
998 999 4.768968 TCACTAAGTGGTTAGTACCTCCAC 59.231 45.833 18.16 18.16 46.01 4.02
1187 1188 1.555533 CTACCGCCCTTTCTTTCCTCT 59.444 52.381 0.00 0.00 0.00 3.69
1198 1199 2.821437 TCTTTCCTCTCGTCCCTTCAT 58.179 47.619 0.00 0.00 0.00 2.57
1225 1226 7.116805 GCATGAAGATCATCGTATGTATGTTCA 59.883 37.037 0.00 14.08 34.28 3.18
1389 6413 1.005037 CTAGGTTGCAGCACGTCCA 60.005 57.895 2.05 0.00 0.00 4.02
1404 6428 1.538512 CGTCCAGTCGTTAACTCCTCA 59.461 52.381 3.71 0.00 35.45 3.86
1405 6429 2.163815 CGTCCAGTCGTTAACTCCTCAT 59.836 50.000 3.71 0.00 35.45 2.90
1406 6430 3.376234 CGTCCAGTCGTTAACTCCTCATA 59.624 47.826 3.71 0.00 35.45 2.15
1414 6438 3.430929 CGTTAACTCCTCATAAGCTGCCT 60.431 47.826 3.71 0.00 0.00 4.75
1453 6477 3.807538 GCCTCACCTGCATGCACG 61.808 66.667 18.46 15.99 0.00 5.34
1496 6520 4.507756 GTCAGTCGCACATTCATAATAGCA 59.492 41.667 0.00 0.00 0.00 3.49
1501 6525 4.987912 TCGCACATTCATAATAGCATTCGA 59.012 37.500 0.00 0.00 0.00 3.71
1502 6526 5.119125 TCGCACATTCATAATAGCATTCGAG 59.881 40.000 0.00 0.00 0.00 4.04
1544 6568 3.987594 GGAATTCCCTTGCTCCTGT 57.012 52.632 14.03 0.00 0.00 4.00
1595 6619 0.043637 AAGGATTAGGACGTCCCCCA 59.956 55.000 30.82 15.46 35.00 4.96
1670 6694 3.764160 CTCCTCCGCATCCCAAGCC 62.764 68.421 0.00 0.00 0.00 4.35
1815 6839 8.421784 AGGTTGCGTTAATGATAAAGATCTCTA 58.578 33.333 0.00 0.00 32.79 2.43
1827 6852 9.300422 TGATAAAGATCTCTAGGGAAACCGCTG 62.300 44.444 0.00 0.00 43.98 5.18
1976 7002 6.036926 TCTAATTCCCTTCTCAGATCCTCT 57.963 41.667 0.00 0.00 0.00 3.69
2097 7126 1.750193 ACACTTCACACCCACACAAG 58.250 50.000 0.00 0.00 0.00 3.16
2141 7170 1.318576 TTCCAGATAGCGAGCGATCA 58.681 50.000 17.80 0.00 31.80 2.92
2158 7187 3.722147 GATCACTCAGCAATGATACCGT 58.278 45.455 0.00 0.00 35.67 4.83
2160 7189 2.233676 TCACTCAGCAATGATACCGTGT 59.766 45.455 0.00 0.00 0.00 4.49
2268 7300 3.255395 TGTGTTCATGTTGGCGATTTCAT 59.745 39.130 0.00 0.00 0.00 2.57
2289 7321 1.252215 TGTGAATGAGGCCGGTCGTA 61.252 55.000 1.90 0.00 0.00 3.43
2327 7359 1.527034 CCCAGTGACACATCAACCAG 58.473 55.000 8.59 0.00 36.31 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 2.550208 GCCAGGAATATCCGTTAGTGGG 60.550 54.545 0.00 0.00 42.75 4.61
42 43 1.821061 CGGAGCCGAGCCAGGAATAT 61.821 60.000 2.00 0.00 42.83 1.28
115 116 0.389391 CCCAGTGTCACACGTTCTCT 59.611 55.000 1.22 0.00 39.64 3.10
249 250 2.669434 GCGTGGCGTAAAGTGAAGATTA 59.331 45.455 0.00 0.00 0.00 1.75
326 327 4.379603 CGCGAAAGATAAGATACGGGAGAT 60.380 45.833 0.00 0.00 36.20 2.75
350 351 2.891580 GGCCGTGTCTTGATCTCCTATA 59.108 50.000 0.00 0.00 0.00 1.31
497 498 4.703703 GTGCAGTTCCCTCTGGAC 57.296 61.111 3.01 3.01 45.94 4.02
509 510 7.646922 GCTCAAAATATTTGATCTTAGGTGCAG 59.353 37.037 0.39 0.00 0.00 4.41
564 565 5.503662 TTTATGTGATCGCAGCATCAAAT 57.496 34.783 15.24 12.47 35.30 2.32
749 750 9.485206 GCCAAATCCTTCTATTATTAAGTACGA 57.515 33.333 0.00 0.00 0.00 3.43
827 828 2.158943 GGCGCACCTCTCCTAACTATTT 60.159 50.000 10.83 0.00 0.00 1.40
851 852 0.685097 AACCTTGCTTCTACTCGCCA 59.315 50.000 0.00 0.00 0.00 5.69
858 859 7.828508 TCGGTATCTAATAACCTTGCTTCTA 57.171 36.000 0.00 0.00 33.34 2.10
998 999 2.426522 TCTGAAAAGGTTCGCTCATGG 58.573 47.619 0.00 0.00 36.46 3.66
1061 1062 3.138283 GGGGACATGATCAATAGAACCCA 59.862 47.826 21.08 0.00 36.85 4.51
1062 1063 3.395941 AGGGGACATGATCAATAGAACCC 59.604 47.826 0.00 7.44 34.66 4.11
1198 1199 6.458210 ACATACATACGATGATCTTCATGCA 58.542 36.000 9.10 0.00 37.20 3.96
1210 1211 5.657474 ACCGAAGTTGAACATACATACGAT 58.343 37.500 0.00 0.00 0.00 3.73
1249 1250 3.073209 TGCCATAATATACTCCCGCCAAA 59.927 43.478 0.00 0.00 0.00 3.28
1296 1297 4.019321 CACAATTCTTCTTGGAGGAGGGTA 60.019 45.833 0.00 0.00 0.00 3.69
1389 6413 4.678309 GCAGCTTATGAGGAGTTAACGACT 60.678 45.833 0.00 2.30 42.70 4.18
1404 6428 3.976654 TCCTAGAAATGGAGGCAGCTTAT 59.023 43.478 0.00 0.00 0.00 1.73
1405 6429 3.134804 GTCCTAGAAATGGAGGCAGCTTA 59.865 47.826 0.00 0.00 33.78 3.09
1406 6430 2.092699 GTCCTAGAAATGGAGGCAGCTT 60.093 50.000 0.00 0.00 33.78 3.74
1414 6438 1.108776 CGGTCGGTCCTAGAAATGGA 58.891 55.000 0.00 0.00 0.00 3.41
1463 6487 2.619646 TGTGCGACTGACACTACACTAA 59.380 45.455 0.00 0.00 38.86 2.24
1476 6500 5.107337 CGAATGCTATTATGAATGTGCGACT 60.107 40.000 0.00 0.00 0.00 4.18
1496 6520 1.661341 GAAGGCACATGAGCTCGAAT 58.339 50.000 14.91 0.00 34.17 3.34
1501 6525 0.694771 TTCAGGAAGGCACATGAGCT 59.305 50.000 14.91 0.00 32.42 4.09
1502 6526 0.807496 GTTCAGGAAGGCACATGAGC 59.193 55.000 6.57 6.57 32.42 4.26
1544 6568 1.879430 GCCGGCTAATCGTACGCAA 60.879 57.895 22.15 0.00 0.00 4.85
1762 6786 5.627499 TTTGCTCATTCATGGAGTTGTAC 57.373 39.130 0.00 0.00 34.83 2.90
1951 6977 6.036926 AGGATCTGAGAAGGGAATTAGAGA 57.963 41.667 0.00 0.00 0.00 3.10
1976 7002 5.670818 TGAGTAGGATAAGGAGGAGTAGTCA 59.329 44.000 0.00 0.00 0.00 3.41
2097 7126 7.617041 ATGGAGTGTTAGTTTCAAATAGAGC 57.383 36.000 0.00 0.00 0.00 4.09
2141 7170 2.735444 CGACACGGTATCATTGCTGAGT 60.735 50.000 0.00 0.00 34.12 3.41
2158 7187 2.092753 AGGATAGGTACTTCGTCCGACA 60.093 50.000 0.00 0.00 41.75 4.35
2160 7189 2.804572 CGAGGATAGGTACTTCGTCCGA 60.805 54.545 0.00 0.00 41.75 4.55
2179 7208 2.511900 AAAAAGCGTGGTCCCCGA 59.488 55.556 0.00 0.00 0.00 5.14
2268 7300 0.104120 CGACCGGCCTCATTCACATA 59.896 55.000 0.00 0.00 0.00 2.29
2327 7359 1.378646 CGGAGAAAAGGAAGGGGCC 60.379 63.158 0.00 0.00 0.00 5.80


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

AutoCloner maintained by Alex Coulton.