Multiple sequence alignment - TraesCS3D01G315100

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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 TraesCS3D01G315100 chr3D 100.000 2917 0 0 1 2917 428895608 428892692 0.000000e+00 5387.0
1 TraesCS3D01G315100 chr3B 98.694 2526 28 3 24 2549 560874850 560872330 0.000000e+00 4477.0
2 TraesCS3D01G315100 chr3B 98.046 307 6 0 2577 2883 560872333 560872027 4.280000e-148 534.0
3 TraesCS3D01G315100 chr3B 100.000 39 0 0 1 39 560874885 560874847 4.030000e-09 73.1
4 TraesCS3D01G315100 chr2A 91.794 2559 136 23 373 2883 773283980 773281448 0.000000e+00 3494.0
5 TraesCS3D01G315100 chr2A 85.309 388 20 10 1 378 773284396 773284036 1.650000e-97 366.0
6 TraesCS3D01G315100 chr3A 96.548 869 28 2 1998 2864 556989747 556990615 0.000000e+00 1437.0
7 TraesCS3D01G315100 chr3A 89.855 138 5 3 3 137 556989602 556989733 5.000000e-38 169.0
8 TraesCS3D01G315100 chr2D 90.045 884 67 11 1678 2556 646216347 646215480 0.000000e+00 1125.0
9 TraesCS3D01G315100 chr2D 86.148 758 64 15 374 1122 646353324 646354049 0.000000e+00 780.0
10 TraesCS3D01G315100 chr2D 89.664 387 24 9 1 378 646352888 646353267 2.030000e-131 479.0
11 TraesCS3D01G315100 chr2D 79.832 714 67 28 966 1641 646217427 646216753 1.590000e-122 449.0
12 TraesCS3D01G315100 chr2D 98.101 158 2 1 2727 2883 646361490 646361647 1.030000e-69 274.0
13 TraesCS3D01G315100 chr2D 85.036 274 11 7 2215 2481 646354153 646354403 4.830000e-63 252.0
14 TraesCS3D01G315100 chr2D 95.604 91 4 0 2553 2643 646361331 646361421 2.340000e-31 147.0
15 TraesCS3D01G315100 chr2B 83.607 183 22 3 2656 2833 357379315 357379494 6.470000e-37 165.0
16 TraesCS3D01G315100 chr2B 96.154 52 2 0 475 526 5086355 5086406 5.180000e-13 86.1
17 TraesCS3D01G315100 chr7B 83.616 177 21 4 2662 2833 54060959 54060786 3.010000e-35 159.0
18 TraesCS3D01G315100 chr7B 83.616 177 21 4 2662 2833 644444230 644444057 3.010000e-35 159.0
19 TraesCS3D01G315100 chr7A 83.616 177 21 3 2662 2833 211375424 211375251 3.010000e-35 159.0
20 TraesCS3D01G315100 chr1D 83.616 177 21 5 2662 2833 212456659 212456486 3.010000e-35 159.0
21 TraesCS3D01G315100 chr7D 84.466 103 13 2 833 935 618235748 618235649 6.650000e-17 99.0
22 TraesCS3D01G315100 chr6B 84.848 99 13 2 837 935 239367842 239367938 6.650000e-17 99.0


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 TraesCS3D01G315100 chr3D 428892692 428895608 2916 True 5387.000000 5387 100.000000 1 2917 1 chr3D.!!$R1 2916
1 TraesCS3D01G315100 chr3B 560872027 560874885 2858 True 1694.700000 4477 98.913333 1 2883 3 chr3B.!!$R1 2882
2 TraesCS3D01G315100 chr2A 773281448 773284396 2948 True 1930.000000 3494 88.551500 1 2883 2 chr2A.!!$R1 2882
3 TraesCS3D01G315100 chr3A 556989602 556990615 1013 False 803.000000 1437 93.201500 3 2864 2 chr3A.!!$F1 2861
4 TraesCS3D01G315100 chr2D 646215480 646217427 1947 True 787.000000 1125 84.938500 966 2556 2 chr2D.!!$R1 1590
5 TraesCS3D01G315100 chr2D 646352888 646354403 1515 False 503.666667 780 86.949333 1 2481 3 chr2D.!!$F1 2480

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
126 157 1.166129 CTTCTTCGTCGACTCCCAGA 58.834 55.000 14.7 6.39 0.00 3.86 F
315 348 8.966155 TGTATATCTACAGATCCCATTGGTTA 57.034 34.615 1.2 0.00 36.05 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1007 1131 1.377333 CCCGGGAAAGAGAACCAGC 60.377 63.158 18.48 0.0 0.0 4.85 R
2516 3071 3.998341 TCAGTCTACAAAATACGGGTTGC 59.002 43.478 0.00 0.0 0.0 4.17 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
126 157 1.166129 CTTCTTCGTCGACTCCCAGA 58.834 55.000 14.70 6.39 0.00 3.86
315 348 8.966155 TGTATATCTACAGATCCCATTGGTTA 57.034 34.615 1.20 0.00 36.05 2.85
1616 1789 3.293337 AGGTACGCAGATATGTGTGGTA 58.707 45.455 16.50 9.40 34.13 3.25
1617 1790 3.702548 AGGTACGCAGATATGTGTGGTAA 59.297 43.478 16.50 0.00 34.13 2.85
2625 3180 7.308951 CCTGTAGTTCTCTAATAGGAAGCTAGC 60.309 44.444 6.62 6.62 36.07 3.42
2883 3439 3.449737 AGTGGCATTGCAAATGAGCTATT 59.550 39.130 11.39 0.00 34.99 1.73
2884 3440 4.081309 AGTGGCATTGCAAATGAGCTATTT 60.081 37.500 11.39 0.00 39.55 1.40
2885 3441 4.632688 GTGGCATTGCAAATGAGCTATTTT 59.367 37.500 11.39 0.00 36.87 1.82
2886 3442 4.871557 TGGCATTGCAAATGAGCTATTTTC 59.128 37.500 11.39 0.00 36.87 2.29
2887 3443 4.026310 GGCATTGCAAATGAGCTATTTTCG 60.026 41.667 11.39 0.00 36.87 3.46
2888 3444 4.563976 GCATTGCAAATGAGCTATTTTCGT 59.436 37.500 1.71 0.00 36.87 3.85
2889 3445 5.062558 GCATTGCAAATGAGCTATTTTCGTT 59.937 36.000 1.71 0.00 36.87 3.85
2890 3446 6.401367 GCATTGCAAATGAGCTATTTTCGTTT 60.401 34.615 1.71 0.00 36.87 3.60
2891 3447 7.512297 CATTGCAAATGAGCTATTTTCGTTTT 58.488 30.769 1.71 0.00 36.87 2.43
2892 3448 6.450845 TGCAAATGAGCTATTTTCGTTTTG 57.549 33.333 0.00 0.00 36.87 2.44
2893 3449 5.982516 TGCAAATGAGCTATTTTCGTTTTGT 59.017 32.000 0.00 0.00 36.87 2.83
2894 3450 6.478344 TGCAAATGAGCTATTTTCGTTTTGTT 59.522 30.769 0.00 0.00 36.87 2.83
2895 3451 7.010923 TGCAAATGAGCTATTTTCGTTTTGTTT 59.989 29.630 0.00 0.00 36.87 2.83
2896 3452 8.484008 GCAAATGAGCTATTTTCGTTTTGTTTA 58.516 29.630 0.00 0.00 36.87 2.01
2897 3453 9.777843 CAAATGAGCTATTTTCGTTTTGTTTAC 57.222 29.630 0.00 0.00 36.87 2.01
2898 3454 9.522804 AAATGAGCTATTTTCGTTTTGTTTACA 57.477 25.926 0.00 0.00 35.47 2.41
2899 3455 7.901874 TGAGCTATTTTCGTTTTGTTTACAC 57.098 32.000 0.00 0.00 0.00 2.90
2900 3456 6.629649 TGAGCTATTTTCGTTTTGTTTACACG 59.370 34.615 0.00 0.00 35.18 4.49
2901 3457 6.717413 AGCTATTTTCGTTTTGTTTACACGA 58.283 32.000 0.00 0.00 41.05 4.35
2902 3458 6.849305 AGCTATTTTCGTTTTGTTTACACGAG 59.151 34.615 0.00 0.00 43.40 4.18
2903 3459 6.630045 GCTATTTTCGTTTTGTTTACACGAGT 59.370 34.615 0.00 0.00 43.40 4.18
2904 3460 6.784068 ATTTTCGTTTTGTTTACACGAGTG 57.216 33.333 1.13 1.13 43.40 3.51
2905 3461 5.527511 TTTCGTTTTGTTTACACGAGTGA 57.472 34.783 10.50 0.00 43.40 3.41
2906 3462 4.503767 TCGTTTTGTTTACACGAGTGAC 57.496 40.909 10.50 0.00 38.00 3.67
2907 3463 3.306703 TCGTTTTGTTTACACGAGTGACC 59.693 43.478 10.50 0.00 38.00 4.02
2908 3464 3.307782 CGTTTTGTTTACACGAGTGACCT 59.692 43.478 10.50 0.00 35.93 3.85
2909 3465 4.503734 CGTTTTGTTTACACGAGTGACCTA 59.496 41.667 10.50 0.00 35.93 3.08
2910 3466 5.555069 CGTTTTGTTTACACGAGTGACCTAC 60.555 44.000 10.50 3.53 35.93 3.18
2911 3467 4.652421 TTGTTTACACGAGTGACCTACA 57.348 40.909 10.50 5.85 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 75 1.846124 GAGTTGGTGGGTGGGAGGA 60.846 63.158 0.00 0.00 0.00 3.71
315 348 1.799181 CGTTGTCAAGATCGATCGCCT 60.799 52.381 19.33 7.14 0.00 5.52
1007 1131 1.377333 CCCGGGAAAGAGAACCAGC 60.377 63.158 18.48 0.00 0.00 4.85
2516 3071 3.998341 TCAGTCTACAAAATACGGGTTGC 59.002 43.478 0.00 0.00 0.00 4.17
2625 3180 1.597742 CCGGAGGCCATTCAAGTATG 58.402 55.000 5.01 0.00 46.14 2.39
2883 3439 5.315195 GTCACTCGTGTAAACAAAACGAAA 58.685 37.500 0.00 0.00 44.84 3.46
2884 3440 4.201705 GGTCACTCGTGTAAACAAAACGAA 60.202 41.667 0.00 0.00 44.84 3.85
2885 3441 3.306703 GGTCACTCGTGTAAACAAAACGA 59.693 43.478 0.00 0.00 43.50 3.85
2886 3442 3.307782 AGGTCACTCGTGTAAACAAAACG 59.692 43.478 0.00 0.00 38.64 3.60
2887 3443 4.870221 AGGTCACTCGTGTAAACAAAAC 57.130 40.909 0.00 0.00 0.00 2.43
2888 3444 5.291614 GTGTAGGTCACTCGTGTAAACAAAA 59.708 40.000 0.00 0.00 43.13 2.44
2889 3445 4.805192 GTGTAGGTCACTCGTGTAAACAAA 59.195 41.667 0.00 0.00 43.13 2.83
2890 3446 4.362279 GTGTAGGTCACTCGTGTAAACAA 58.638 43.478 0.00 0.00 43.13 2.83
2891 3447 3.243501 GGTGTAGGTCACTCGTGTAAACA 60.244 47.826 0.00 0.00 45.50 2.83
2892 3448 3.005155 AGGTGTAGGTCACTCGTGTAAAC 59.995 47.826 0.00 0.00 45.50 2.01
2893 3449 3.225104 AGGTGTAGGTCACTCGTGTAAA 58.775 45.455 0.00 0.00 45.50 2.01
2894 3450 2.867624 AGGTGTAGGTCACTCGTGTAA 58.132 47.619 0.00 0.00 45.50 2.41
2895 3451 2.574006 AGGTGTAGGTCACTCGTGTA 57.426 50.000 0.00 0.00 45.50 2.90
2896 3452 1.612463 GAAGGTGTAGGTCACTCGTGT 59.388 52.381 0.00 0.00 45.50 4.49
2897 3453 2.349297 GAAGGTGTAGGTCACTCGTG 57.651 55.000 0.00 0.00 45.50 4.35


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

AutoCloner maintained by Alex Coulton.