Multiple sequence alignment - TraesCS2A01G127000

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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 TraesCS2A01G127000 chr2A 100.000 2201 0 0 1 2201 74969900 74967700 0.000000e+00 4065
1 TraesCS2A01G127000 chr2D 92.113 2257 104 32 8 2201 75260491 75258246 0.000000e+00 3114
2 TraesCS2A01G127000 chr2B 95.686 1414 55 4 791 2201 115217650 115216240 0.000000e+00 2268
3 TraesCS2A01G127000 chr2B 85.885 503 41 10 241 733 115218134 115217652 1.950000e-140 508
4 TraesCS2A01G127000 chr2B 95.706 163 7 0 8 170 115218561 115218399 1.680000e-66 263


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 TraesCS2A01G127000 chr2A 74967700 74969900 2200 True 4065 4065 100.000000 1 2201 1 chr2A.!!$R1 2200
1 TraesCS2A01G127000 chr2D 75258246 75260491 2245 True 3114 3114 92.113000 8 2201 1 chr2D.!!$R1 2193
2 TraesCS2A01G127000 chr2B 115216240 115218561 2321 True 1013 2268 92.425667 8 2201 3 chr2B.!!$R1 2193

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
548 770 0.105778 TCATCACCGTGCACTGAACA 59.894 50.0 15.72 1.21 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1489 1749 0.107945 CTAAGCTCCTGTGCTGGGTC 60.108 60.0 0.0 0.0 43.24 4.46 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
21 22 4.143333 CGACGAGGGGTGGCGAAT 62.143 66.667 0.00 0.00 0.00 3.34
24 25 2.202932 CGAGGGGTGGCGAATGAG 60.203 66.667 0.00 0.00 0.00 2.90
72 73 0.669318 TTGATGGTCGAAGGTGACGC 60.669 55.000 0.00 0.00 39.83 5.19
160 165 1.669440 CGGGGAGTGGTTCGAAAGA 59.331 57.895 0.00 0.00 39.20 2.52
272 484 4.008074 TGTTTTCAGGTGAGGATGAGAC 57.992 45.455 0.00 0.00 0.00 3.36
275 487 0.684479 TCAGGTGAGGATGAGACCGG 60.684 60.000 0.00 0.00 34.73 5.28
303 516 1.413767 CCGGCGTTTGTCAGAGATCG 61.414 60.000 6.01 0.00 0.00 3.69
378 594 1.003866 GCAAGACACCAACGACAGTTC 60.004 52.381 0.00 0.00 38.79 3.01
425 643 2.181521 GCATGAGAGCTCTGCTGGC 61.182 63.158 23.91 15.18 39.88 4.85
505 727 2.738521 CACCAGCCAACCGACGAG 60.739 66.667 0.00 0.00 0.00 4.18
506 728 3.231736 ACCAGCCAACCGACGAGT 61.232 61.111 0.00 0.00 0.00 4.18
507 729 2.030562 CCAGCCAACCGACGAGTT 59.969 61.111 0.00 0.00 0.00 3.01
508 730 1.597027 CCAGCCAACCGACGAGTTT 60.597 57.895 0.00 0.00 0.00 2.66
548 770 0.105778 TCATCACCGTGCACTGAACA 59.894 50.000 15.72 1.21 0.00 3.18
559 781 2.048503 CTGAACACCCCGACGGTC 60.049 66.667 13.94 3.69 43.58 4.79
578 800 1.081840 GCGGCAGTTCAAAGTCAGC 60.082 57.895 0.00 0.00 0.00 4.26
621 843 2.594592 GTCACCACCACCAGCACC 60.595 66.667 0.00 0.00 0.00 5.01
630 852 1.029681 CCACCAGCACCATGATGATG 58.970 55.000 0.00 0.00 35.45 3.07
641 863 2.636403 CCATGATGATGAGGCACCTCTA 59.364 50.000 17.34 4.97 43.12 2.43
659 884 0.325602 TACCGGCCATTCCTTTCGTT 59.674 50.000 0.00 0.00 0.00 3.85
769 1000 2.113774 CCACCCAGAGTGCAGCAA 59.886 61.111 0.00 0.00 45.83 3.91
802 1033 3.777106 AGGCACTGAAACTTGATCTGA 57.223 42.857 0.00 0.00 37.18 3.27
1051 1283 1.729586 TAGAAGCACTGGGGAACACT 58.270 50.000 0.00 0.00 0.00 3.55
1052 1284 0.846693 AGAAGCACTGGGGAACACTT 59.153 50.000 0.00 0.00 0.00 3.16
1090 1322 1.447643 ACTGGTCAGTCTGGTGCAC 59.552 57.895 8.80 8.80 36.92 4.57
1166 1398 1.200716 CGGTAGCAAGTGGTTCGTCTA 59.799 52.381 0.00 0.00 0.00 2.59
1184 1416 4.142160 CGTCTATGTCTCCATCCTGTTCAA 60.142 45.833 0.00 0.00 32.29 2.69
1358 1590 4.201657 TCCCACTGCTTCAACATGATATG 58.798 43.478 0.00 0.00 0.00 1.78
1379 1611 8.873215 ATATGGTACTCGTAACTCATTCTTTG 57.127 34.615 0.00 0.00 0.00 2.77
1474 1734 8.253113 AGTATTTTCATCACTTTTGGCCTATTG 58.747 33.333 3.32 0.00 0.00 1.90
1489 1749 6.233434 TGGCCTATTGCTAAGAACATGATAG 58.767 40.000 3.32 0.00 40.92 2.08
1496 1756 4.061596 GCTAAGAACATGATAGACCCAGC 58.938 47.826 0.00 0.00 0.00 4.85
1528 1789 2.438021 AGTGTGAACCTTTGCTAGACCA 59.562 45.455 0.00 0.00 0.00 4.02
1595 1856 5.922544 CACAGCAGGAAAGGAAAATTGTTAG 59.077 40.000 0.00 0.00 0.00 2.34
1715 1976 1.405391 GCAGCACAACCAAAAACCAGT 60.405 47.619 0.00 0.00 0.00 4.00
1804 2066 2.232208 CCAGAAAGCATGGGAAGGAAAC 59.768 50.000 0.00 0.00 33.94 2.78
1808 2070 2.052104 GCATGGGAAGGAAACGGGG 61.052 63.158 0.00 0.00 0.00 5.73
1831 2093 4.263243 GCCCAGATATTTCCTATGTCAGCT 60.263 45.833 0.00 0.00 0.00 4.24
1844 2106 1.348696 TGTCAGCTCAGCCAAGAATGA 59.651 47.619 0.00 0.00 0.00 2.57
1845 2107 2.224597 TGTCAGCTCAGCCAAGAATGAA 60.225 45.455 0.00 0.00 0.00 2.57
1866 2128 9.487790 AATGAAAACCATAATAAACACTTGTGG 57.512 29.630 5.72 0.00 39.85 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 4.143333 ATTCGCCACCCCTCGTCG 62.143 66.667 0.00 0.00 0.00 5.12
5 6 2.511600 CATTCGCCACCCCTCGTC 60.512 66.667 0.00 0.00 0.00 4.20
6 7 3.000819 TCATTCGCCACCCCTCGT 61.001 61.111 0.00 0.00 0.00 4.18
160 165 0.541863 CAGGGTAGAATCGCCAACCT 59.458 55.000 0.00 0.00 32.38 3.50
378 594 2.490328 TCGCCAAAACTTTTGCTGAG 57.510 45.000 8.53 0.00 0.00 3.35
425 643 6.183360 GCTTACTGCTTCCTCTACAAAATGAG 60.183 42.308 0.00 0.00 38.95 2.90
508 730 4.142578 TGACTTGCTGCGTCAAAGTAAAAA 60.143 37.500 7.74 0.00 38.36 1.94
512 734 2.232756 TGACTTGCTGCGTCAAAGTA 57.767 45.000 7.74 0.00 38.36 2.24
559 781 1.205064 CTGACTTTGAACTGCCGCG 59.795 57.895 0.00 0.00 0.00 6.46
570 792 1.680735 TGCAATGGTTTCGCTGACTTT 59.319 42.857 0.00 0.00 0.00 2.66
578 800 0.109597 GCTGGTCTGCAATGGTTTCG 60.110 55.000 0.00 0.00 0.00 3.46
607 829 1.792757 ATCATGGTGCTGGTGGTGGT 61.793 55.000 0.00 0.00 0.00 4.16
621 843 2.932855 AGAGGTGCCTCATCATCATG 57.067 50.000 19.22 0.00 44.99 3.07
630 852 3.851128 GGCCGGTAGAGGTGCCTC 61.851 72.222 10.12 10.12 40.77 4.70
641 863 0.958876 GAACGAAAGGAATGGCCGGT 60.959 55.000 1.90 0.00 43.43 5.28
648 873 4.040461 TCCTGAGTTCAGAACGAAAGGAAT 59.960 41.667 22.55 0.84 46.59 3.01
679 904 1.301479 GGTGTCCCGTCTGTGTTCC 60.301 63.158 0.00 0.00 0.00 3.62
680 905 0.878961 GTGGTGTCCCGTCTGTGTTC 60.879 60.000 0.00 0.00 0.00 3.18
681 906 1.145377 GTGGTGTCCCGTCTGTGTT 59.855 57.895 0.00 0.00 0.00 3.32
682 907 2.803817 GGTGGTGTCCCGTCTGTGT 61.804 63.158 0.00 0.00 0.00 3.72
769 1000 2.282391 TGCCTTGCCGCAGTGAAT 60.282 55.556 0.00 0.00 33.92 2.57
823 1054 3.207669 CGAGGCTGCCAGCATTCC 61.208 66.667 22.65 0.18 44.75 3.01
1051 1283 3.742369 GTCGACCTGACGTTCCATTTTAA 59.258 43.478 3.51 0.00 37.96 1.52
1052 1284 3.319755 GTCGACCTGACGTTCCATTTTA 58.680 45.455 3.51 0.00 37.96 1.52
1184 1416 9.206690 TGTATCTGATCTAGTTCATTCTCCTTT 57.793 33.333 3.98 0.00 0.00 3.11
1214 1446 0.250467 TTTCTCCAGCTGGCACTCAC 60.250 55.000 28.91 0.00 34.44 3.51
1358 1590 4.329256 GCCAAAGAATGAGTTACGAGTACC 59.671 45.833 0.00 0.00 0.00 3.34
1474 1734 4.061596 GCTGGGTCTATCATGTTCTTAGC 58.938 47.826 0.00 0.00 0.00 3.09
1489 1749 0.107945 CTAAGCTCCTGTGCTGGGTC 60.108 60.000 0.00 0.00 43.24 4.46
1496 1756 2.037772 AGGTTCACACTAAGCTCCTGTG 59.962 50.000 10.66 10.66 37.27 3.66
1715 1976 4.346709 TGGGATGTCTTTGAGTACAAGTGA 59.653 41.667 0.00 0.00 37.32 3.41
1804 2066 1.358152 TAGGAAATATCTGGGCCCCG 58.642 55.000 22.27 14.56 0.00 5.73
1808 2070 4.006319 GCTGACATAGGAAATATCTGGGC 58.994 47.826 0.00 0.00 0.00 5.36
1831 2093 6.855763 ATTATGGTTTTCATTCTTGGCTGA 57.144 33.333 0.00 0.00 37.30 4.26
1844 2106 7.213678 CCACCACAAGTGTTTATTATGGTTTT 58.786 34.615 0.00 0.00 45.74 2.43
1845 2107 6.740122 GCCACCACAAGTGTTTATTATGGTTT 60.740 38.462 0.00 0.00 45.74 3.27
1866 2128 3.475566 TGGAGCTATTGACTATGCCAC 57.524 47.619 0.00 0.00 0.00 5.01


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

AutoCloner maintained by Alex Coulton.