Multiple sequence alignment - TraesCS2A01G439300

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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 TraesCS2A01G439300 chr2A 100.000 3103 0 0 1 3103 690715653 690718755 0 5731
1 TraesCS2A01G439300 chr2D 98.521 3110 33 8 1 3103 547144642 547147745 0 5476


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 TraesCS2A01G439300 chr2A 690715653 690718755 3102 False 5731 5731 100.000 1 3103 1 chr2A.!!$F1 3102
1 TraesCS2A01G439300 chr2D 547144642 547147745 3103 False 5476 5476 98.521 1 3103 1 chr2D.!!$F1 3102

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
839 846 0.249120 TCCGATGTTTCATGCCGACT 59.751 50.0 0.0 0.0 0.0 4.18 F
1396 1403 0.251209 AGGAGCACTACGACAGACCA 60.251 55.0 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
1908 1915 0.109226 GTAGTCGGGTGCTGTCTGTC 60.109 60.000 0.00 0.0 0.00 3.51 R
2478 2485 3.252974 AGGCTACAGAGTTGCATACAC 57.747 47.619 5.99 0.0 36.13 2.90 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
70 71 5.900437 AGATCATGCATAATTTCATCCCCT 58.100 37.500 0.00 0.00 0.00 4.79
143 145 2.482839 CGAAATTGGAGAGGGAGCTCTC 60.483 54.545 14.64 10.30 46.67 3.20
146 148 2.334006 TTGGAGAGGGAGCTCTCTTT 57.666 50.000 19.43 12.97 46.61 2.52
147 149 3.474798 TTGGAGAGGGAGCTCTCTTTA 57.525 47.619 19.43 1.60 46.61 1.85
148 150 3.697190 TGGAGAGGGAGCTCTCTTTAT 57.303 47.619 19.43 7.12 46.61 1.40
149 151 3.571590 TGGAGAGGGAGCTCTCTTTATC 58.428 50.000 19.43 15.70 46.61 1.75
150 152 3.052566 TGGAGAGGGAGCTCTCTTTATCA 60.053 47.826 19.43 11.23 46.61 2.15
177 179 3.625745 AGTTTGGGGTACAAGCTCG 57.374 52.632 0.00 0.00 46.04 5.03
269 271 6.397272 GCCCAAATGACAGTCAATGATAAAA 58.603 36.000 17.29 0.00 0.00 1.52
270 272 6.532657 GCCCAAATGACAGTCAATGATAAAAG 59.467 38.462 17.29 3.94 0.00 2.27
272 274 7.972277 CCCAAATGACAGTCAATGATAAAAGAG 59.028 37.037 17.29 2.87 0.00 2.85
377 384 1.518367 AACTCAGACCCCCTGTTTCA 58.482 50.000 0.00 0.00 43.38 2.69
395 402 2.359975 CGCTCCCCTGTTTCACCC 60.360 66.667 0.00 0.00 0.00 4.61
396 403 2.895424 CGCTCCCCTGTTTCACCCT 61.895 63.158 0.00 0.00 0.00 4.34
471 478 2.042435 CTCTCCCCCTTCCTCGCT 60.042 66.667 0.00 0.00 0.00 4.93
563 570 2.742116 GCTTCTCCCCCGCCATACA 61.742 63.158 0.00 0.00 0.00 2.29
622 629 1.143183 GAGCGATTCGGCCACCTTA 59.857 57.895 2.24 0.00 0.00 2.69
708 715 1.414181 AGTCTGTATGCGATTGAGGGG 59.586 52.381 0.00 0.00 0.00 4.79
839 846 0.249120 TCCGATGTTTCATGCCGACT 59.751 50.000 0.00 0.00 0.00 4.18
1085 1092 5.654603 TCAGTTAAAGATCTAGGCGTCAA 57.345 39.130 0.00 0.00 0.00 3.18
1240 1247 4.990426 ACTTTAGGCATTCAAATGTTGTGC 59.010 37.500 4.76 0.00 38.65 4.57
1287 1294 3.885297 CAGGCTATCCCAGGTTTGTATTG 59.115 47.826 0.00 0.00 35.39 1.90
1387 1394 1.740025 GCATTCCAACAGGAGCACTAC 59.260 52.381 0.00 0.00 31.86 2.73
1396 1403 0.251209 AGGAGCACTACGACAGACCA 60.251 55.000 0.00 0.00 0.00 4.02
1908 1915 5.248640 AGGTTCATCAACTATGTTGGAGTG 58.751 41.667 10.05 7.49 36.89 3.51
2026 2033 4.286032 TGGTAAGACCTAAACTGCATGTCT 59.714 41.667 0.00 0.00 39.58 3.41
2053 2060 5.278957 GGTGTGCCTATAATAAATTGGCCAG 60.279 44.000 5.11 0.00 42.62 4.85
2103 2110 3.057315 CACCATTTCAAGAGGCGTTTGAT 60.057 43.478 7.39 0.00 34.76 2.57
2491 2498 5.689383 ATTGTTTTCGTGTATGCAACTCT 57.311 34.783 0.00 0.00 0.00 3.24
2538 2545 6.515272 ACAGGGAATTGCTTATACAAACTG 57.485 37.500 0.00 0.00 32.27 3.16
2612 2619 7.598118 ACTGATTGATCATGATCTTAGTTAGCG 59.402 37.037 30.65 15.10 38.60 4.26
2688 2695 2.641815 AGGAATCCTGAGGATGTATGGC 59.358 50.000 15.97 0.91 42.27 4.40
2842 2849 2.230660 GTCCCCTTCTTGGAGTTGTTG 58.769 52.381 0.00 0.00 38.35 3.33
2869 2876 1.070758 TGTGGTCAAGAGGCTGAAGAC 59.929 52.381 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
165 167 0.971447 ACTCTCCCGAGCTTGTACCC 60.971 60.000 0.00 0.0 41.09 3.69
177 179 0.250901 TTTGGCTCTTGCACTCTCCC 60.251 55.000 0.00 0.0 41.91 4.30
293 300 3.041940 GTGGCTGCGCGTAACAGT 61.042 61.111 8.43 0.0 37.47 3.55
311 318 0.469917 AGTGGGTCTGTCTTGTGTGG 59.530 55.000 0.00 0.0 0.00 4.17
366 373 2.359975 GGAGCGTGAAACAGGGGG 60.360 66.667 0.00 0.0 35.74 5.40
377 384 2.430367 GGTGAAACAGGGGAGCGT 59.570 61.111 0.00 0.0 39.98 5.07
395 402 6.481313 TGAATGAGCATTTCCTTATTCGAGAG 59.519 38.462 0.00 0.0 39.40 3.20
396 403 6.348498 TGAATGAGCATTTCCTTATTCGAGA 58.652 36.000 0.00 0.0 39.40 4.04
471 478 3.992641 TCCCCGGAGAGGCAGACA 61.993 66.667 0.73 0.0 39.21 3.41
681 688 1.271856 TCGCATACAGACTCCCCAAA 58.728 50.000 0.00 0.0 0.00 3.28
688 695 1.414181 CCCCTCAATCGCATACAGACT 59.586 52.381 0.00 0.0 0.00 3.24
708 715 5.164954 GGCGATGACAAATAGAGATCCTAC 58.835 45.833 0.00 0.0 0.00 3.18
1240 1247 5.707298 ACACATCATAGAAGTTTTGGACAGG 59.293 40.000 0.00 0.0 0.00 4.00
1287 1294 1.671379 GCTTCCGTCCACCCAAGAC 60.671 63.158 0.00 0.0 0.00 3.01
1387 1394 0.459237 GCTCACAGGATGGTCTGTCG 60.459 60.000 0.00 0.0 45.24 4.35
1396 1403 0.842635 GGATTGAGGGCTCACAGGAT 59.157 55.000 0.00 0.0 39.66 3.24
1761 1768 1.998315 CCTGACAATCTCTCAACTGCG 59.002 52.381 0.00 0.0 0.00 5.18
1908 1915 0.109226 GTAGTCGGGTGCTGTCTGTC 60.109 60.000 0.00 0.0 0.00 3.51
2053 2060 0.243636 CGGTTGCCATTGGGAGTTTC 59.756 55.000 4.53 0.0 35.59 2.78
2103 2110 4.758251 CCACGTGCGGCCTGATGA 62.758 66.667 10.91 0.0 0.00 2.92
2478 2485 3.252974 AGGCTACAGAGTTGCATACAC 57.747 47.619 5.99 0.0 36.13 2.90
2491 2498 4.041567 TCTGAATCCAGTTTCAAGGCTACA 59.958 41.667 0.00 0.0 41.16 2.74
2688 2695 4.270084 TCAAGCTAGTTTGTCTCGTTGTTG 59.730 41.667 17.56 0.0 0.00 3.33
2869 2876 3.374988 ACAAGTGATGATTACATGCCACG 59.625 43.478 0.00 0.0 36.78 4.94


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

AutoCloner maintained by Alex Coulton.