Multiple sequence alignment - TraesCS5D01G400600

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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 TraesCS5D01G400600 chr5D 100.000 3600 0 0 1 3600 465714830 465711231 0.000000e+00 6649
1 TraesCS5D01G400600 chr5B 96.209 3614 77 29 1 3587 572947183 572943603 0.000000e+00 5860
2 TraesCS5D01G400600 chr5A 95.171 3624 107 35 1 3600 586145224 586141645 0.000000e+00 5661
3 TraesCS5D01G400600 chr7D 76.569 478 60 28 1248 1707 58140942 58141385 7.830000e-52 215
4 TraesCS5D01G400600 chr1A 73.720 586 86 43 1139 1707 465248725 465248191 2.220000e-37 167
5 TraesCS5D01G400600 chr2D 84.564 149 18 3 1818 1963 565858161 565858015 3.750000e-30 143
6 TraesCS5D01G400600 chr4A 83.562 146 22 1 1818 1963 37899831 37899688 6.270000e-28 135
7 TraesCS5D01G400600 chr2A 83.673 147 21 2 1818 1963 364404220 364404364 6.270000e-28 135


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 TraesCS5D01G400600 chr5D 465711231 465714830 3599 True 6649 6649 100.000 1 3600 1 chr5D.!!$R1 3599
1 TraesCS5D01G400600 chr5B 572943603 572947183 3580 True 5860 5860 96.209 1 3587 1 chr5B.!!$R1 3586
2 TraesCS5D01G400600 chr5A 586141645 586145224 3579 True 5661 5661 95.171 1 3600 1 chr5A.!!$R1 3599

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
453 454 1.610522 ACTTGCGTAGTTCCACGTACT 59.389 47.619 0.0 0.0 43.79 2.73 F
1622 1635 1.422402 TCAACTGTAACCTTGACCCCC 59.578 52.381 0.0 0.0 0.00 5.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2121 2135 0.658244 CTTGTGTGTGTGATGCGTGC 60.658 55.0 0.00 0.0 0.00 5.34 R
2987 3018 0.389391 ATTGTAGAGATCGGGCACGG 59.611 55.0 9.32 0.0 41.39 4.94 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
159 160 3.681417 TGTCGATGAAGAGCAGTTGAATG 59.319 43.478 0.00 0.00 0.00 2.67
453 454 1.610522 ACTTGCGTAGTTCCACGTACT 59.389 47.619 0.00 0.00 43.79 2.73
995 1005 7.015877 TGTTAAGGTGCTAGGAGTAGAAAGAAA 59.984 37.037 0.00 0.00 0.00 2.52
1064 1074 3.269178 GCTATCTGAAGAAGCAAGCAGT 58.731 45.455 0.00 0.00 36.26 4.40
1178 1188 4.678287 CCAAAATGCTCATGCGCTATTTAG 59.322 41.667 9.73 0.00 43.34 1.85
1179 1189 5.276270 CAAAATGCTCATGCGCTATTTAGT 58.724 37.500 9.73 0.00 43.34 2.24
1328 1338 2.957006 CCGTATGGTAGCTTGGTAGAGT 59.043 50.000 0.00 0.00 0.00 3.24
1370 1380 8.367911 TCTGAAATAGCATATACCGAGTGATTT 58.632 33.333 0.00 0.00 0.00 2.17
1420 1430 5.010213 TGCAGACTTTAAACCATGTAAACCC 59.990 40.000 0.00 0.00 0.00 4.11
1486 1496 8.097038 AGTTACATAAGCAGATTTCTGTCAGAA 58.903 33.333 11.36 11.36 45.45 3.02
1521 1533 9.944376 GGGTATATTTATTGCTCTTGAGATACA 57.056 33.333 1.30 0.00 0.00 2.29
1622 1635 1.422402 TCAACTGTAACCTTGACCCCC 59.578 52.381 0.00 0.00 0.00 5.40
1697 1710 9.458727 ACTGAAATAGTGTGATCTGAATTCATT 57.541 29.630 8.96 0.00 38.49 2.57
1721 1734 7.630242 TTGTCTCCCAGATAAATCAATGAAC 57.370 36.000 0.00 0.00 0.00 3.18
1725 1738 5.200483 TCCCAGATAAATCAATGAACCACC 58.800 41.667 0.00 0.00 0.00 4.61
2023 2036 2.270257 GCAGCTGCAATGGTCACCA 61.270 57.895 33.36 0.00 41.59 4.17
2121 2135 3.190744 AGATCAAACATGCAGAGCACAAG 59.809 43.478 0.00 0.00 43.04 3.16
2128 2142 2.974489 GCAGAGCACAAGCACGCAT 61.974 57.895 0.00 0.00 45.49 4.73
2180 2194 4.918060 CACACACACGCACGCACG 62.918 66.667 0.00 0.00 39.50 5.34
2520 2547 9.747898 TGACAGGGAGTATACAAAAACATTATT 57.252 29.630 5.50 0.00 0.00 1.40
2572 2599 2.853159 TGCCAATGCAGGTCGTAAG 58.147 52.632 0.00 0.00 44.23 2.34
2590 2617 7.281484 GTCGTAAGTCATGTAACTTTGAAGTG 58.719 38.462 5.23 0.00 40.01 3.16
2650 2677 3.056322 GCATGCATTCCTGGTTTTCTTCT 60.056 43.478 14.21 0.00 0.00 2.85
2896 2925 2.183679 AGAGACCCAAACAGCTAGGAG 58.816 52.381 0.00 0.00 0.00 3.69
3112 3144 3.056250 TGGAAGCAGAGAGATTGACAGAC 60.056 47.826 0.00 0.00 0.00 3.51
3113 3145 3.056250 GGAAGCAGAGAGATTGACAGACA 60.056 47.826 0.00 0.00 0.00 3.41
3114 3146 3.872511 AGCAGAGAGATTGACAGACAG 57.127 47.619 0.00 0.00 0.00 3.51
3115 3147 3.429492 AGCAGAGAGATTGACAGACAGA 58.571 45.455 0.00 0.00 0.00 3.41
3170 3202 1.134280 AGAGCCAAGATCCCGTGATTG 60.134 52.381 0.00 0.00 0.00 2.67
3272 3304 4.148128 AGCAGGATGTACAAATGAGGAG 57.852 45.455 0.00 0.00 39.31 3.69
3276 3308 2.945668 GGATGTACAAATGAGGAGGTGC 59.054 50.000 0.00 0.00 0.00 5.01
3536 3571 3.935203 CCACAGTGTAGCACCTAGAAATG 59.065 47.826 0.00 0.00 34.49 2.32
3588 3623 2.097629 TCATTCCAAACAACGCAAACGA 59.902 40.909 0.00 0.00 43.93 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
159 160 2.726351 CCTCTGCTTCCCGTCCCTC 61.726 68.421 0.00 0.00 0.00 4.30
453 454 8.856153 TTTCAGCATACAACTTTGATACCTTA 57.144 30.769 0.00 0.00 0.00 2.69
509 511 8.149647 TCATGGTTGATGCTTTAAAAAGTTGAT 58.850 29.630 4.50 0.00 38.28 2.57
995 1005 6.661377 TGGTGGTAAGTATGTATGCATTTTGT 59.339 34.615 3.54 0.00 36.58 2.83
1064 1074 5.677319 AAGTAGCAGTATCAGCCTTGTTA 57.323 39.130 0.00 0.00 0.00 2.41
1210 1220 7.020827 AGAAGAAACACTGGGATGATTAGAA 57.979 36.000 0.00 0.00 0.00 2.10
1328 1338 7.767659 GCTATTTCAGATATGCACATATCCTCA 59.232 37.037 21.49 7.89 46.77 3.86
1436 1446 1.842562 AGCAGTGGATCTGGCAATAGT 59.157 47.619 0.00 0.00 43.78 2.12
1521 1533 6.877236 TGATTTCTCAGGCTCAAAAGTTTTT 58.123 32.000 0.00 0.00 0.00 1.94
1697 1710 6.603201 GGTTCATTGATTTATCTGGGAGACAA 59.397 38.462 0.00 0.00 0.00 3.18
1721 1734 5.047660 TCAAATTCCTTAAATGGTTCGGTGG 60.048 40.000 0.00 0.00 0.00 4.61
1725 1738 8.810652 TTTCTTCAAATTCCTTAAATGGTTCG 57.189 30.769 0.00 0.00 0.00 3.95
2023 2036 9.185680 GGTTATGAACATACTTGGATTTAGGTT 57.814 33.333 0.00 0.00 0.00 3.50
2121 2135 0.658244 CTTGTGTGTGTGATGCGTGC 60.658 55.000 0.00 0.00 0.00 5.34
2128 2142 1.606994 GCGGGTATCTTGTGTGTGTGA 60.607 52.381 0.00 0.00 0.00 3.58
2180 2194 1.066136 GAACTTCCTTACGTCCGTGC 58.934 55.000 1.98 0.00 0.00 5.34
2184 2198 6.427974 CAAAGAAAAGAACTTCCTTACGTCC 58.572 40.000 0.00 0.00 0.00 4.79
2185 2199 6.259387 TCCAAAGAAAAGAACTTCCTTACGTC 59.741 38.462 0.00 0.00 0.00 4.34
2296 2319 8.715191 AAAAATGTTTGACTAGCACAAATTCA 57.285 26.923 15.36 11.39 39.01 2.57
2457 2483 2.934553 GCCTAGACCATTTACACGGTTC 59.065 50.000 0.00 0.00 34.99 3.62
2520 2547 3.076621 GTGAATGACATGGCTGAGAACA 58.923 45.455 0.00 0.00 0.00 3.18
2572 2599 4.537015 GCACCACTTCAAAGTTACATGAC 58.463 43.478 0.00 0.00 37.08 3.06
2627 2654 2.250031 AGAAAACCAGGAATGCATGCA 58.750 42.857 25.04 25.04 0.00 3.96
2687 2714 2.034053 TCCACAAAGACGGAAAATGTGC 59.966 45.455 0.00 0.00 39.93 4.57
2696 2723 0.392998 CATCCCCTCCACAAAGACGG 60.393 60.000 0.00 0.00 0.00 4.79
2987 3018 0.389391 ATTGTAGAGATCGGGCACGG 59.611 55.000 9.32 0.00 41.39 4.94
2988 3019 1.202417 ACATTGTAGAGATCGGGCACG 60.202 52.381 0.00 0.00 42.74 5.34
2989 3020 2.604046 ACATTGTAGAGATCGGGCAC 57.396 50.000 0.00 0.00 0.00 5.01
2990 3021 4.746535 TTAACATTGTAGAGATCGGGCA 57.253 40.909 0.00 0.00 0.00 5.36
2991 3022 7.724305 TTATTTAACATTGTAGAGATCGGGC 57.276 36.000 0.00 0.00 0.00 6.13
3035 3067 3.818121 TTGGTTCACCGTGCTCCCG 62.818 63.158 0.00 0.00 39.43 5.14
3112 3144 4.778534 AACATGGTCAGCTTGATTTCTG 57.221 40.909 0.00 0.00 0.00 3.02
3113 3145 4.560108 GCAAACATGGTCAGCTTGATTTCT 60.560 41.667 0.00 0.00 0.00 2.52
3114 3146 3.676646 GCAAACATGGTCAGCTTGATTTC 59.323 43.478 0.00 0.00 0.00 2.17
3115 3147 3.069872 TGCAAACATGGTCAGCTTGATTT 59.930 39.130 9.25 0.00 0.00 2.17
3170 3202 8.770438 TTTAATGCCAATACTTTTTCCATGAC 57.230 30.769 0.00 0.00 0.00 3.06
3272 3304 1.068541 GTTCCCTTGATGTTTCGCACC 60.069 52.381 0.00 0.00 0.00 5.01
3276 3308 4.568152 AAACAGTTCCCTTGATGTTTCG 57.432 40.909 0.00 0.00 40.82 3.46
3311 3343 5.879223 ACACATCTTTCTCATGCCTTTAGAG 59.121 40.000 0.00 0.00 0.00 2.43
3536 3571 4.092383 GCACAATGATTGTTGCTCATTTCC 59.908 41.667 8.30 0.00 43.23 3.13


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

AutoCloner maintained by Alex Coulton.