Multiple sequence alignment - TraesCS4A01G499600

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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 TraesCS4A01G499600 chr4A 100.000 3613 0 0 1 3613 744459084 744455472 0 6673
1 TraesCS4A01G499600 chr6B 93.874 3624 205 14 1 3613 571754539 571750922 0 5446
2 TraesCS4A01G499600 chr1B 93.102 3624 224 21 1 3613 547571303 547567695 0 5284
3 TraesCS4A01G499600 chr5B 92.942 3627 235 19 1 3613 638656554 638660173 0 5260
4 TraesCS4A01G499600 chr5B 91.469 3634 269 30 1 3613 541106400 541110013 0 4955
5 TraesCS4A01G499600 chr3B 92.964 3624 228 19 1 3613 46768168 46771775 0 5254
6 TraesCS4A01G499600 chr3B 92.973 3501 229 15 1 3489 675590976 675594471 0 5086
7 TraesCS4A01G499600 chr2B 92.316 3631 253 21 1 3613 621621244 621617622 0 5136
8 TraesCS4A01G499600 chr2B 92.130 3507 241 22 1 3493 687305066 687301581 0 4915
9 TraesCS4A01G499600 chr7B 92.914 3500 230 14 1 3489 26274894 26271402 0 5073


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 TraesCS4A01G499600 chr4A 744455472 744459084 3612 True 6673 6673 100.000 1 3613 1 chr4A.!!$R1 3612
1 TraesCS4A01G499600 chr6B 571750922 571754539 3617 True 5446 5446 93.874 1 3613 1 chr6B.!!$R1 3612
2 TraesCS4A01G499600 chr1B 547567695 547571303 3608 True 5284 5284 93.102 1 3613 1 chr1B.!!$R1 3612
3 TraesCS4A01G499600 chr5B 638656554 638660173 3619 False 5260 5260 92.942 1 3613 1 chr5B.!!$F2 3612
4 TraesCS4A01G499600 chr5B 541106400 541110013 3613 False 4955 4955 91.469 1 3613 1 chr5B.!!$F1 3612
5 TraesCS4A01G499600 chr3B 46768168 46771775 3607 False 5254 5254 92.964 1 3613 1 chr3B.!!$F1 3612
6 TraesCS4A01G499600 chr3B 675590976 675594471 3495 False 5086 5086 92.973 1 3489 1 chr3B.!!$F2 3488
7 TraesCS4A01G499600 chr2B 621617622 621621244 3622 True 5136 5136 92.316 1 3613 1 chr2B.!!$R1 3612
8 TraesCS4A01G499600 chr2B 687301581 687305066 3485 True 4915 4915 92.130 1 3493 1 chr2B.!!$R2 3492
9 TraesCS4A01G499600 chr7B 26271402 26274894 3492 True 5073 5073 92.914 1 3489 1 chr7B.!!$R1 3488

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
38 39 0.318441 GTGCAGTGAGGTGACAGCTA 59.682 55.0 7.24 0.0 30.13 3.32 F
1737 1761 0.763652 CCAGTAGGCATGAGAGGCAT 59.236 55.0 0.00 0.0 37.85 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1874 1900 0.106708 TGCGAACTTGACAGCCTTCT 59.893 50.0 0.00 0.0 0.0 2.85 R
3050 3093 0.609957 ATCACCCAGGTCGACGTACA 60.610 55.0 10.91 0.0 0.0 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
38 39 0.318441 GTGCAGTGAGGTGACAGCTA 59.682 55.000 7.24 0.00 30.13 3.32
179 182 0.979187 GTCCAACACCGGGGATCCTA 60.979 60.000 12.96 0.00 35.25 2.94
370 373 3.429822 CCCTTTTATGAGTGCATGGCAAG 60.430 47.826 0.00 0.00 41.47 4.01
591 602 2.505407 ACTGCTAACTATGCCACATGGA 59.495 45.455 0.87 0.00 37.39 3.41
790 812 3.184581 ACTCGAACGTCTTCATTCAAAGC 59.815 43.478 0.00 0.00 0.00 3.51
883 905 2.033675 CACACAAACTCTGATGCAAGCA 59.966 45.455 0.00 0.00 0.00 3.91
901 923 3.224324 GCCGACCATCTCCGCCTA 61.224 66.667 0.00 0.00 0.00 3.93
982 1004 2.012673 CTGCCAGGACAGCTGAAATAC 58.987 52.381 23.35 0.00 0.00 1.89
988 1010 1.009829 GACAGCTGAAATACTGCCCG 58.990 55.000 23.35 0.00 43.01 6.13
1017 1039 2.019249 GCAATGAAGGATGCTGCTGTA 58.981 47.619 0.00 0.00 39.46 2.74
1141 1163 2.034879 GCCACTCATGTGTCCACGG 61.035 63.158 0.00 0.00 42.34 4.94
1157 1179 2.753029 GGCAGAAGTGGCTGAGGT 59.247 61.111 0.00 0.00 45.85 3.85
1202 1224 1.356124 ACAGGTGAGAGTCTTGGCAT 58.644 50.000 0.00 0.00 0.00 4.40
1211 1233 2.836981 AGAGTCTTGGCATAACAGCTCT 59.163 45.455 0.00 0.00 34.17 4.09
1251 1273 2.356665 TTGCTAAGGCCACTGTTTCA 57.643 45.000 5.01 0.00 37.74 2.69
1276 1298 2.100989 CTAGTCTTCCACCTAGGCGTT 58.899 52.381 9.30 0.00 37.29 4.84
1359 1383 1.822990 GATGAGTCTGGTTACGTCCCA 59.177 52.381 6.69 6.69 0.00 4.37
1463 1487 1.215382 CGGGCACGAGTGATGAAGA 59.785 57.895 0.00 0.00 44.60 2.87
1473 1497 3.428180 CGAGTGATGAAGATGAACGTCCT 60.428 47.826 0.00 0.00 0.00 3.85
1474 1498 4.109050 GAGTGATGAAGATGAACGTCCTC 58.891 47.826 0.00 0.00 0.00 3.71
1510 1534 2.677228 CCGCAGTGGAAATCCCCT 59.323 61.111 0.00 0.00 42.00 4.79
1579 1603 1.272147 ACAGCCCCAACAAGAGGATTC 60.272 52.381 0.00 0.00 0.00 2.52
1737 1761 0.763652 CCAGTAGGCATGAGAGGCAT 59.236 55.000 0.00 0.00 37.85 4.40
1874 1900 3.548793 AACCAATGGTTGAGGGCAA 57.451 47.368 18.01 0.00 45.07 4.52
1899 1925 0.601046 CTGTCAAGTTCGCAGAGCCA 60.601 55.000 0.00 0.00 39.04 4.75
1921 1949 5.391950 CCAATCGTCCAAGGTACATTTCTTG 60.392 44.000 0.00 0.00 39.83 3.02
2068 2097 6.921486 TTTACTACACCATCTCACCTACAA 57.079 37.500 0.00 0.00 0.00 2.41
2094 2123 1.533625 TGCCATGCTGTAGTTTCCAC 58.466 50.000 0.00 0.00 0.00 4.02
2242 2276 2.028876 CCATGCTGCATTTCTCATCCA 58.971 47.619 13.38 0.00 0.00 3.41
2566 2607 0.618968 ACCCCTGAGGAGATTTCGCT 60.619 55.000 0.00 0.00 39.89 4.93
2587 2628 4.825422 CTGTCTCTTGATGAAGCTTACCA 58.175 43.478 0.00 0.00 0.00 3.25
2712 2753 1.073706 ACCCCTGGTTCTGTGAGGT 60.074 57.895 0.00 0.00 27.29 3.85
2724 2765 2.245028 TCTGTGAGGTAGCAGAGGGTAT 59.755 50.000 0.00 0.00 36.89 2.73
2781 2822 3.947834 AGTCAGGAACACAAAGGAACAAG 59.052 43.478 0.00 0.00 0.00 3.16
2787 2828 1.064017 ACACAAAGGAACAAGCCCAGA 60.064 47.619 0.00 0.00 0.00 3.86
2825 2866 1.680338 GATTTGGTAATGCGAGGGCT 58.320 50.000 0.00 0.00 40.82 5.19
2953 2996 5.410439 ACATGATCCGCTTACGTTTTAGTTT 59.590 36.000 0.00 0.00 37.70 2.66
3050 3093 5.066893 CCAAGGTCATTCAATGTGAATCGAT 59.933 40.000 0.00 0.00 43.03 3.59
3163 3206 4.598807 ACAAGCATATGGATATGTCTCCCA 59.401 41.667 4.56 0.00 41.63 4.37
3419 3468 5.537674 ACTGACTTTCTGATTTTTGCATCCT 59.462 36.000 0.00 0.00 0.00 3.24
3421 3470 5.535783 TGACTTTCTGATTTTTGCATCCTGA 59.464 36.000 0.00 0.00 0.00 3.86
3445 3494 4.808364 GCAAACTATGTGGCAACTTCAAAA 59.192 37.500 0.00 0.00 37.61 2.44
3489 3538 6.224584 TGTTCATACATGGACGACAACTTTA 58.775 36.000 0.00 0.00 39.20 1.85
3510 3561 9.676861 ACTTTATTTCAACTACCCACTATAACC 57.323 33.333 0.00 0.00 0.00 2.85
3530 3583 6.877611 AACCAAACATTCTACGTGATTCTT 57.122 33.333 0.00 0.00 0.00 2.52
3599 3655 5.385198 TCCTTCATTTTTACTTGCAGGTCT 58.615 37.500 4.04 0.00 29.63 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 0.313987 CTGTCACCTCACTGCACGTA 59.686 55.000 0.00 0.00 0.00 3.57
38 39 2.826128 TCTTCGTAACTGCTCATCCACT 59.174 45.455 0.00 0.00 0.00 4.00
179 182 0.036952 CTCAGGTCTGGCAACACGAT 60.037 55.000 0.00 0.00 46.17 3.73
262 265 2.372264 AGCTGAACGGATGCATTGAAT 58.628 42.857 0.00 0.00 0.00 2.57
370 373 5.699097 TGCCATGTAAAAACAAGTAGGAC 57.301 39.130 0.00 0.00 0.00 3.85
591 602 5.140454 GCCATGTAAGGGGAATATGAGTTT 58.860 41.667 0.00 0.00 38.99 2.66
790 812 0.947244 GAGTTGCCACCTGTTGACAG 59.053 55.000 4.15 4.15 43.40 3.51
988 1010 2.119801 TCCTTCATTGCCAGAAGAGC 57.880 50.000 10.41 0.00 44.00 4.09
1017 1039 2.042639 GATGGGGTGGCATGGCTT 60.043 61.111 21.08 0.00 0.00 4.35
1141 1163 1.673665 CCACCTCAGCCACTTCTGC 60.674 63.158 0.00 0.00 34.19 4.26
1251 1273 2.093106 CTAGGTGGAAGACTAGCACGT 58.907 52.381 0.00 0.00 31.29 4.49
1276 1298 3.280938 ATTGCTTGCGGGGGCTACA 62.281 57.895 0.00 0.00 0.00 2.74
1359 1383 2.426023 GGGAACAGTGTGGACGCT 59.574 61.111 0.00 0.00 37.13 5.07
1399 1423 1.608283 CCGGTCTTCTGGTTTCTCCAC 60.608 57.143 0.00 0.00 41.93 4.02
1463 1487 1.067283 CAGTCTGCTGAGGACGTTCAT 60.067 52.381 0.00 0.00 45.28 2.57
1510 1534 1.468520 GGAAGTGCGCAGATTTAAGCA 59.531 47.619 12.22 0.00 37.26 3.91
1579 1603 1.659098 GACGGGCGTAGATTTGTTGAG 59.341 52.381 0.00 0.00 0.00 3.02
1737 1761 2.166346 TGGGGTGAAGGCCATTGGA 61.166 57.895 5.01 0.00 0.00 3.53
1857 1883 0.482446 TCTTGCCCTCAACCATTGGT 59.518 50.000 1.37 1.37 37.65 3.67
1874 1900 0.106708 TGCGAACTTGACAGCCTTCT 59.893 50.000 0.00 0.00 0.00 2.85
1899 1925 5.181245 CACAAGAAATGTACCTTGGACGATT 59.819 40.000 12.38 0.00 41.46 3.34
2242 2276 1.466025 CCAGTTGCCATGTGGTTGCT 61.466 55.000 0.35 0.00 37.57 3.91
2566 2607 4.890158 TGGTAAGCTTCATCAAGAGACA 57.110 40.909 0.00 0.00 0.00 3.41
2587 2628 1.811778 TGCTGCCTCCTCAATCCTAT 58.188 50.000 0.00 0.00 0.00 2.57
2766 2807 1.756538 CTGGGCTTGTTCCTTTGTGTT 59.243 47.619 0.00 0.00 0.00 3.32
2767 2808 1.064017 TCTGGGCTTGTTCCTTTGTGT 60.064 47.619 0.00 0.00 0.00 3.72
2781 2822 3.990092 TGACAATATCGTACATCTGGGC 58.010 45.455 0.00 0.00 0.00 5.36
2787 2828 6.292865 CCAAATCGCTTGACAATATCGTACAT 60.293 38.462 0.00 0.00 37.17 2.29
2825 2866 2.477845 TCTTCATGTGCTTGCTGCTA 57.522 45.000 0.00 0.00 43.37 3.49
2844 2885 3.412386 AGGTCATTTACGCTTTCAGCTT 58.588 40.909 0.00 0.00 39.60 3.74
2918 2959 5.537300 AGCGGATCATGTCTACAAAGTAT 57.463 39.130 0.00 0.00 0.00 2.12
2925 2966 3.351020 ACGTAAGCGGATCATGTCTAC 57.649 47.619 0.00 0.00 43.45 2.59
3050 3093 0.609957 ATCACCCAGGTCGACGTACA 60.610 55.000 10.91 0.00 0.00 2.90
3093 3136 5.472148 ACTACATTCGTCGACATTTTACCA 58.528 37.500 17.16 0.00 0.00 3.25
3163 3206 6.985645 ACACTGTAATGCATGATTGTTTTGTT 59.014 30.769 0.00 0.00 0.00 2.83
3419 3468 2.862541 AGTTGCCACATAGTTTGCTCA 58.137 42.857 0.00 0.00 0.00 4.26
3421 3470 3.221771 TGAAGTTGCCACATAGTTTGCT 58.778 40.909 0.00 0.00 0.00 3.91
3489 3538 7.945664 TGTTTGGTTATAGTGGGTAGTTGAAAT 59.054 33.333 0.00 0.00 0.00 2.17
3510 3561 9.450807 AAAAAGAAGAATCACGTAGAATGTTTG 57.549 29.630 0.00 0.00 0.00 2.93
3539 3593 4.687901 TCACATGAAGAACAACAGAGGA 57.312 40.909 0.00 0.00 0.00 3.71


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

AutoCloner maintained by Alex Coulton.