Multiple sequence alignment - TraesCS1A01G259300

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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 TraesCS1A01G259300 chr1A 100.000 3502 0 0 1 3502 452296787 452293286 0.000000e+00 6468
1 TraesCS1A01G259300 chr1A 96.226 3127 88 16 63 3172 452455088 452451975 0.000000e+00 5094
2 TraesCS1A01G259300 chr1A 98.438 64 1 0 1 64 452455313 452455250 2.860000e-21 113
3 TraesCS1A01G259300 chr1D 95.572 3320 132 12 1 3315 351917702 351914393 0.000000e+00 5302
4 TraesCS1A01G259300 chr1D 96.601 3177 84 9 1 3172 351545005 351541848 0.000000e+00 5247
5 TraesCS1A01G259300 chr1D 95.045 222 9 2 3279 3500 351914046 351913827 7.190000e-92 348
6 TraesCS1A01G259300 chr1B 94.868 3215 116 23 1 3172 474262208 474259000 0.000000e+00 4977
7 TraesCS1A01G259300 chr1B 88.197 305 24 4 2645 2938 399623245 399622942 1.550000e-93 353
8 TraesCS1A01G259300 chr3B 88.852 305 20 6 2645 2938 511819249 511818948 2.570000e-96 363
9 TraesCS1A01G259300 chr2B 88.079 302 24 4 2642 2932 535564908 535565208 7.190000e-92 348


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 TraesCS1A01G259300 chr1A 452293286 452296787 3501 True 6468.0 6468 100.0000 1 3502 1 chr1A.!!$R1 3501
1 TraesCS1A01G259300 chr1A 452451975 452455313 3338 True 2603.5 5094 97.3320 1 3172 2 chr1A.!!$R2 3171
2 TraesCS1A01G259300 chr1D 351541848 351545005 3157 True 5247.0 5247 96.6010 1 3172 1 chr1D.!!$R1 3171
3 TraesCS1A01G259300 chr1D 351913827 351917702 3875 True 2825.0 5302 95.3085 1 3500 2 chr1D.!!$R2 3499
4 TraesCS1A01G259300 chr1B 474259000 474262208 3208 True 4977.0 4977 94.8680 1 3172 1 chr1B.!!$R2 3171

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
317 481 5.227238 CAAGATTTTGGACTCCTCGATTG 57.773 43.478 0.00 0.0 0.00 2.67 F
1781 1947 4.498850 CGTATGGATCAGACTGGAACTGAG 60.499 50.000 1.81 0.0 45.49 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2089 2255 1.006998 TGGGGGCATGCTGAAATAAGT 59.993 47.619 18.92 0.0 0.0 2.24 R
2643 2811 0.325933 CATGCCAGGTCTGAAGGTGA 59.674 55.000 0.00 0.0 0.0 4.02 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
77 241 8.144478 GGCTTCACTTCTAGTATCATATCAACA 58.856 37.037 0.00 0.00 0.00 3.33
317 481 5.227238 CAAGATTTTGGACTCCTCGATTG 57.773 43.478 0.00 0.00 0.00 2.67
1584 1750 9.828852 CATACTCTTCGTCTAGAATATGTTACC 57.171 37.037 0.00 0.00 38.34 2.85
1781 1947 4.498850 CGTATGGATCAGACTGGAACTGAG 60.499 50.000 1.81 0.00 45.49 3.35
2321 2487 5.292589 TGAAGTAGTTGGTTTGTTCGACTTC 59.707 40.000 0.00 0.00 40.35 3.01
2419 2585 2.076863 CGACAAGGGATTGGACAGAAC 58.923 52.381 0.00 0.00 0.00 3.01
2597 2765 8.082242 ACATTAAAGTAGGTTCAGTTTTCATGC 58.918 33.333 0.00 0.00 0.00 4.06
2655 2823 4.946478 ATAGCAGTATCACCTTCAGACC 57.054 45.455 0.00 0.00 0.00 3.85
2752 2931 7.041372 TGCCTTTAGTTGACTTTGAGATAACAC 60.041 37.037 0.00 0.00 0.00 3.32
2787 2966 3.740832 TCTGAGCATGAACGTGTTTGTAG 59.259 43.478 0.00 0.00 0.00 2.74
2803 2982 7.904977 CGTGTTTGTAGAAGATGAACATATTGG 59.095 37.037 0.00 0.00 33.39 3.16
2846 3040 8.008513 ACTCCAGTTCAGTATTATGAATACGT 57.991 34.615 0.00 0.00 46.51 3.57
2877 3071 1.598130 GCAGGTCAACTTCGCCACT 60.598 57.895 0.00 0.00 0.00 4.00
2932 3126 3.258971 GGATCAAGTCCAACCTCTGAG 57.741 52.381 0.00 0.00 46.96 3.35
2966 3160 2.943033 GACCATTGGAAGGAACGGTATG 59.057 50.000 10.37 0.00 0.00 2.39
3046 3241 2.739379 GACACAAGCTCTGAAGTTAGGC 59.261 50.000 0.00 0.00 0.00 3.93
3072 3267 3.328931 ACAGGCATGAGTTATCCCCATAG 59.671 47.826 4.84 0.00 0.00 2.23
3168 3392 8.925700 GTCAAAGTTCAGAAAGAAAATGTTTGT 58.074 29.630 0.00 0.00 38.13 2.83
3172 3396 6.753744 AGTTCAGAAAGAAAATGTTTGTCAGC 59.246 34.615 0.00 0.00 38.13 4.26
3180 3404 7.992180 AGAAAATGTTTGTCAGCTTAACTTG 57.008 32.000 0.00 0.00 0.00 3.16
3182 3406 7.489113 AGAAAATGTTTGTCAGCTTAACTTGTG 59.511 33.333 0.00 0.00 0.00 3.33
3235 3459 6.027025 TGGGTACTCTCAGTGTATTCCTAT 57.973 41.667 0.00 0.00 0.00 2.57
3241 3465 4.878968 TCTCAGTGTATTCCTATGGGTCA 58.121 43.478 0.00 0.00 0.00 4.02
3243 3467 4.620723 TCAGTGTATTCCTATGGGTCACT 58.379 43.478 0.00 3.96 34.71 3.41
3252 3476 2.966516 CCTATGGGTCACTTAGGTCCTC 59.033 54.545 5.97 0.00 40.43 3.71
3338 3946 0.524862 TCCAGTAACTCGCGGTCTTC 59.475 55.000 6.13 0.00 0.00 2.87
3404 4012 2.618442 TTGCATCTCACACACACAGA 57.382 45.000 0.00 0.00 0.00 3.41
3405 4013 2.159327 TGCATCTCACACACACAGAG 57.841 50.000 0.00 0.00 0.00 3.35
3413 4021 5.111989 TCTCACACACACAGAGAGAAAAAG 58.888 41.667 0.00 0.00 33.75 2.27
3427 4035 2.029020 AGAAAAAGGAAATTGGCCGCTC 60.029 45.455 0.00 0.00 0.00 5.03
3429 4037 1.177401 AAAGGAAATTGGCCGCTCTC 58.823 50.000 0.00 0.00 0.00 3.20
3442 4050 1.845266 CGCTCTCGGTCGTACTACTA 58.155 55.000 0.00 0.00 0.00 1.82
3462 4070 6.347859 ACTAGAAGTTCTTCAGTCGGATTT 57.652 37.500 11.40 0.00 0.00 2.17
3464 4072 4.570930 AGAAGTTCTTCAGTCGGATTTCC 58.429 43.478 13.85 0.00 0.00 3.13
3477 4085 2.084546 GGATTTCCCAGGTCAAGTTCG 58.915 52.381 0.00 0.00 34.14 3.95
3484 4092 1.602377 CCAGGTCAAGTTCGGTTTGTC 59.398 52.381 0.00 0.00 0.00 3.18
3500 4108 0.740868 TGTCTACATTGGCTCTGCGC 60.741 55.000 0.00 0.00 38.13 6.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
101 265 6.939551 GCGAGGTATCTTTACGCATAATTA 57.060 37.500 0.00 0.00 46.75 1.40
317 481 9.856488 AAGAGTGTAAAACCTTTCTTTCTTTTC 57.144 29.630 0.00 0.00 0.00 2.29
1584 1750 2.812011 CCCTAAACTGTTTCCTTCCACG 59.188 50.000 9.38 0.00 0.00 4.94
2089 2255 1.006998 TGGGGGCATGCTGAAATAAGT 59.993 47.619 18.92 0.00 0.00 2.24
2153 2319 9.625747 TGGAAATTTATGATATGTAGCAAGTCA 57.374 29.630 0.00 0.00 0.00 3.41
2321 2487 2.032528 TCCGCAAAGGAGCCAGTG 59.967 61.111 0.00 0.00 45.98 3.66
2340 2506 7.607250 TCAAGTAAAAGTTTCAAGAAGCCAAA 58.393 30.769 0.00 0.00 0.00 3.28
2342 2508 6.767524 TCAAGTAAAAGTTTCAAGAAGCCA 57.232 33.333 0.00 0.00 0.00 4.75
2596 2764 4.864916 TGCAATTCTTCTACAGATTCGC 57.135 40.909 0.00 0.00 0.00 4.70
2643 2811 0.325933 CATGCCAGGTCTGAAGGTGA 59.674 55.000 0.00 0.00 0.00 4.02
2714 2893 6.200854 GTCAACTAAAGGCAAACTGAAATTGG 59.799 38.462 0.00 0.00 0.00 3.16
2752 2931 1.012841 GCTCAGAATTCTCCCTTGCG 58.987 55.000 4.57 0.00 0.00 4.85
2787 2966 9.807649 AAACAATTAGCCAATATGTTCATCTTC 57.192 29.630 6.12 0.00 33.39 2.87
2846 3040 1.342474 TGACCTGCCCAAGACCAAAAA 60.342 47.619 0.00 0.00 0.00 1.94
2932 3126 2.558359 CCAATGGTCTTGACTTGTTCCC 59.442 50.000 0.00 0.00 0.00 3.97
2966 3160 1.609072 GAGGTTCCCAACACAAGCTTC 59.391 52.381 0.00 0.00 30.50 3.86
3046 3241 4.532126 TGGGGATAACTCATGCCTGTATAG 59.468 45.833 0.00 0.00 44.44 1.31
3058 3253 6.657541 TCAACAACAAACTATGGGGATAACTC 59.342 38.462 0.00 0.00 0.00 3.01
3072 3267 3.129113 ACGGGGTAACTTCAACAACAAAC 59.871 43.478 0.00 0.00 0.00 2.93
3168 3392 3.673902 TGCATAGCACAAGTTAAGCTGA 58.326 40.909 10.55 0.00 39.30 4.26
3191 3415 6.880529 ACCCAGCATTCAAATTTGGAAATAAG 59.119 34.615 17.90 4.55 0.00 1.73
3235 3459 1.149288 ACAGAGGACCTAAGTGACCCA 59.851 52.381 0.00 0.00 0.00 4.51
3241 3465 5.833340 AGAGACATAACAGAGGACCTAAGT 58.167 41.667 0.00 0.00 0.00 2.24
3243 3467 5.105310 GCAAGAGACATAACAGAGGACCTAA 60.105 44.000 0.00 0.00 0.00 2.69
3252 3476 3.340814 ACCAGGCAAGAGACATAACAG 57.659 47.619 0.00 0.00 0.00 3.16
3338 3946 1.269051 GCGGGAACAGTTCAAAACAGG 60.269 52.381 15.36 0.00 0.00 4.00
3391 3999 4.272018 CCTTTTTCTCTCTGTGTGTGTGAG 59.728 45.833 0.00 0.00 0.00 3.51
3404 4012 2.029020 GCGGCCAATTTCCTTTTTCTCT 60.029 45.455 2.24 0.00 0.00 3.10
3405 4013 2.029020 AGCGGCCAATTTCCTTTTTCTC 60.029 45.455 2.24 0.00 0.00 2.87
3413 4021 3.102097 CGAGAGCGGCCAATTTCC 58.898 61.111 2.24 0.00 0.00 3.13
3427 4035 5.108517 AGAACTTCTAGTAGTACGACCGAG 58.891 45.833 2.07 1.33 0.00 4.63
3429 4037 5.349817 TGAAGAACTTCTAGTAGTACGACCG 59.650 44.000 14.31 0.00 40.14 4.79
3442 4050 4.563786 GGGAAATCCGACTGAAGAACTTCT 60.564 45.833 14.31 0.00 37.40 2.85
3462 4070 0.841289 AAACCGAACTTGACCTGGGA 59.159 50.000 0.00 0.00 0.00 4.37
3464 4072 1.602377 GACAAACCGAACTTGACCTGG 59.398 52.381 0.00 0.00 0.00 4.45
3477 4085 2.162408 GCAGAGCCAATGTAGACAAACC 59.838 50.000 0.00 0.00 0.00 3.27


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

AutoCloner maintained by Alex Coulton.