Multiple sequence alignment - TraesCS3A01G168500

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 TraesCS3A01G168500 chr3A 100.000 2798 0 0 1 2798 175861129 175858332 0.000000e+00 5168
1 TraesCS3A01G168500 chr3A 87.225 1816 219 10 509 2318 110813118 110811310 0.000000e+00 2056
2 TraesCS3A01G168500 chr3A 91.777 1058 83 4 723 1778 102077334 102078389 0.000000e+00 1469
3 TraesCS3A01G168500 chr3A 88.060 536 61 3 1772 2306 102089647 102090180 1.410000e-177 632
4 TraesCS3A01G168500 chr3A 80.822 511 62 21 4 512 102076678 102077154 4.400000e-98 368
5 TraesCS3A01G168500 chr4A 97.018 2783 76 4 20 2796 70770302 70773083 0.000000e+00 4673
6 TraesCS3A01G168500 chr7A 96.570 2799 84 12 1 2796 16994591 16991802 0.000000e+00 4626
7 TraesCS3A01G168500 chr7A 96.724 2778 79 9 20 2796 67817968 67820734 0.000000e+00 4615
8 TraesCS3A01G168500 chr1A 96.655 2242 68 5 559 2796 255737944 255740182 0.000000e+00 3718
9 TraesCS3A01G168500 chr1A 95.907 562 23 0 1 562 255725371 255725932 0.000000e+00 911
10 TraesCS3A01G168500 chr2B 94.964 1688 82 3 509 2195 495227319 495225634 0.000000e+00 2643
11 TraesCS3A01G168500 chr2B 92.643 367 27 0 146 512 495227721 495227355 1.910000e-146 529
12 TraesCS3A01G168500 chr2B 93.952 248 15 0 2 249 495227925 495227678 2.630000e-100 375
13 TraesCS3A01G168500 chr5B 92.384 1707 107 18 509 2195 600375062 600373359 0.000000e+00 2410
14 TraesCS3A01G168500 chr5B 88.000 400 31 7 5 399 600375619 600375232 9.130000e-125 457
15 TraesCS3A01G168500 chr3B 86.099 1115 145 8 985 2095 783217202 783216094 0.000000e+00 1192


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 TraesCS3A01G168500 chr3A 175858332 175861129 2797 True 5168.000000 5168 100.0000 1 2798 1 chr3A.!!$R2 2797
1 TraesCS3A01G168500 chr3A 110811310 110813118 1808 True 2056.000000 2056 87.2250 509 2318 1 chr3A.!!$R1 1809
2 TraesCS3A01G168500 chr3A 102076678 102078389 1711 False 918.500000 1469 86.2995 4 1778 2 chr3A.!!$F2 1774
3 TraesCS3A01G168500 chr3A 102089647 102090180 533 False 632.000000 632 88.0600 1772 2306 1 chr3A.!!$F1 534
4 TraesCS3A01G168500 chr4A 70770302 70773083 2781 False 4673.000000 4673 97.0180 20 2796 1 chr4A.!!$F1 2776
5 TraesCS3A01G168500 chr7A 16991802 16994591 2789 True 4626.000000 4626 96.5700 1 2796 1 chr7A.!!$R1 2795
6 TraesCS3A01G168500 chr7A 67817968 67820734 2766 False 4615.000000 4615 96.7240 20 2796 1 chr7A.!!$F1 2776
7 TraesCS3A01G168500 chr1A 255737944 255740182 2238 False 3718.000000 3718 96.6550 559 2796 1 chr1A.!!$F2 2237
8 TraesCS3A01G168500 chr1A 255725371 255725932 561 False 911.000000 911 95.9070 1 562 1 chr1A.!!$F1 561
9 TraesCS3A01G168500 chr2B 495225634 495227925 2291 True 1182.333333 2643 93.8530 2 2195 3 chr2B.!!$R1 2193
10 TraesCS3A01G168500 chr5B 600373359 600375619 2260 True 1433.500000 2410 90.1920 5 2195 2 chr5B.!!$R1 2190
11 TraesCS3A01G168500 chr3B 783216094 783217202 1108 True 1192.000000 1192 86.0990 985 2095 1 chr3B.!!$R1 1110

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
84 85 1.636340 GCGTGGTACTATGCAAGCG 59.364 57.895 17.66 0.0 32.85 4.68 F
395 485 3.278574 CGGTTCATCCAAGCAATTCCTA 58.721 45.455 0.00 0.0 35.57 2.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1553 1708 0.534877 TCCGTGATTTGCACTGCTGT 60.535 50.000 1.98 0.0 45.49 4.40 R
2389 2548 8.028938 TCTTTTGGAAAGTTGAATATGCTAAGC 58.971 33.333 0.87 0.0 0.00 3.09 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
41 42 2.169769 GTCAAATCCATCCCGTAGACCA 59.830 50.000 0.00 0.0 0.00 4.02
84 85 1.636340 GCGTGGTACTATGCAAGCG 59.364 57.895 17.66 0.0 32.85 4.68
148 149 4.464069 GAGAAGCACTCAACTAGGACAT 57.536 45.455 0.00 0.0 44.36 3.06
395 485 3.278574 CGGTTCATCCAAGCAATTCCTA 58.721 45.455 0.00 0.0 35.57 2.94
1206 1361 7.972832 TCCACAAATAAACAAGTTAGATCGT 57.027 32.000 0.00 0.0 0.00 3.73
1353 1508 4.065088 CGAACTTGTTGAGAGGATTGGAA 58.935 43.478 0.00 0.0 0.00 3.53
1388 1543 9.017509 AGTAGATGAGAAAATTGAATTCTTGCA 57.982 29.630 7.05 0.0 37.26 4.08
1447 1602 3.569194 TGAACAGTTTGAAGGTGGCTA 57.431 42.857 0.00 0.0 0.00 3.93
1876 2032 3.399330 TCGTTTTGGACAGTCTCAATCC 58.601 45.455 0.00 0.0 0.00 3.01
1930 2086 6.538742 GTGCCTACTATTTCTGCATTTGACTA 59.461 38.462 0.00 0.0 34.04 2.59
2796 2959 8.440059 CAAACATGTTGTGTAGTTACGTATCAT 58.560 33.333 12.82 0.0 41.14 2.45
2797 2960 9.642327 AAACATGTTGTGTAGTTACGTATCATA 57.358 29.630 12.82 0.0 41.14 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
84 85 1.960689 GCAGAGGTAGTGGGAGAGATC 59.039 57.143 0.00 0.0 0.00 2.75
148 149 2.497273 TCAATGGCGAATGTCTGAGAGA 59.503 45.455 0.00 0.0 0.00 3.10
234 235 5.276440 AGATTGGAAGAGAGCTAGAAGGAA 58.724 41.667 0.00 0.0 0.00 3.36
395 485 4.081476 GGGTAAGTGGTGGTCGTAGTAAAT 60.081 45.833 0.00 0.0 0.00 1.40
494 584 8.332996 TCTAGTAGCTATAACCGAAACTATGG 57.667 38.462 0.00 0.0 0.00 2.74
704 834 4.518590 TGTATGCACACAACACATTTAGCT 59.481 37.500 0.00 0.0 0.00 3.32
1206 1361 1.140852 AGCACCAGCACTGTGAACTTA 59.859 47.619 12.86 0.0 45.49 2.24
1338 1493 2.726821 TGGCATTCCAATCCTCTCAAC 58.273 47.619 0.00 0.0 39.99 3.18
1353 1508 7.558807 TCAATTTTCTCATCTACTGATTGGCAT 59.441 33.333 0.00 0.0 32.10 4.40
1368 1523 7.094631 CCAGATGCAAGAATTCAATTTTCTCA 58.905 34.615 8.44 0.0 32.33 3.27
1388 1543 3.202818 TGTAACAGATCCCATTGCCAGAT 59.797 43.478 0.00 0.0 0.00 2.90
1447 1602 7.949690 GGTACTCCCTGGTTATTATTGTTTT 57.050 36.000 0.00 0.0 0.00 2.43
1553 1708 0.534877 TCCGTGATTTGCACTGCTGT 60.535 50.000 1.98 0.0 45.49 4.40
1930 2086 9.545105 GTTCTATCATCTTTGACATCTTCTCAT 57.455 33.333 0.00 0.0 33.85 2.90
2196 2355 8.801715 TTCATCTTTTGCAAACTTGAATACTC 57.198 30.769 12.39 0.0 0.00 2.59
2389 2548 8.028938 TCTTTTGGAAAGTTGAATATGCTAAGC 58.971 33.333 0.87 0.0 0.00 3.09


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

AutoCloner maintained by Alex Coulton.