Multiple sequence alignment - TraesCS5B01G410500

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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 TraesCS5B01G410500 chr5B 100.000 3216 0 0 1 3216 585836965 585833750 0.000000e+00 5939.0
1 TraesCS5B01G410500 chr5B 85.612 139 20 0 1001 1139 391144731 391144869 2.590000e-31 147.0
2 TraesCS5B01G410500 chr5D 96.546 2577 81 7 644 3216 478223291 478220719 0.000000e+00 4259.0
3 TraesCS5B01G410500 chr5D 92.956 653 26 10 4 640 478224049 478223401 0.000000e+00 933.0
4 TraesCS5B01G410500 chr5A 95.092 1732 65 11 1499 3216 597329516 597327791 0.000000e+00 2710.0
5 TraesCS5B01G410500 chr5A 94.625 1507 58 5 1 1500 597331167 597329677 0.000000e+00 2313.0
6 TraesCS5B01G410500 chr5A 84.892 139 21 0 1001 1139 436089151 436089289 1.200000e-29 141.0
7 TraesCS5B01G410500 chr6A 91.549 142 12 0 998 1139 578887722 578887581 2.530000e-46 196.0
8 TraesCS5B01G410500 chr6D 90.141 142 14 0 998 1139 432710583 432710442 5.480000e-43 185.0
9 TraesCS5B01G410500 chr3B 82.353 136 16 7 1000 1131 478323394 478323263 9.430000e-21 111.0
10 TraesCS5B01G410500 chr3A 82.353 136 16 7 1000 1131 489311964 489311833 9.430000e-21 111.0
11 TraesCS5B01G410500 chr3D 81.618 136 17 7 1000 1131 367236965 367236834 4.390000e-19 106.0
12 TraesCS5B01G410500 chr2B 83.871 93 15 0 1545 1637 45735367 45735275 4.420000e-14 89.8


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 TraesCS5B01G410500 chr5B 585833750 585836965 3215 True 5939.0 5939 100.0000 1 3216 1 chr5B.!!$R1 3215
1 TraesCS5B01G410500 chr5D 478220719 478224049 3330 True 2596.0 4259 94.7510 4 3216 2 chr5D.!!$R1 3212
2 TraesCS5B01G410500 chr5A 597327791 597331167 3376 True 2511.5 2710 94.8585 1 3216 2 chr5A.!!$R1 3215

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
157 158 0.105246 AAAAAGGATGGGTGCCACCA 60.105 50.0 17.22 2.09 46.24 4.17 F
710 833 0.546122 TCATGAATAGGCCGGCAACT 59.454 50.0 30.85 19.77 0.00 3.16 F
1948 2239 0.185175 ACGGGGAAGCTCCAAACTTT 59.815 50.0 0.00 0.00 38.64 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1801 2092 0.187117 TGCCTTCCACCATTGAACCA 59.813 50.000 0.00 0.0 0.00 3.67 R
2184 2475 0.323178 AAGGTCGACCGGCTCTTCTA 60.323 55.000 28.26 0.0 42.08 2.10 R
3054 3357 2.679837 AGTATGAACGCTGGAAATGCAG 59.320 45.455 0.00 0.0 0.00 4.41 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
110 111 8.931775 CGTGTATGCTAATGCCAACTTATTATA 58.068 33.333 0.00 0.00 38.71 0.98
157 158 0.105246 AAAAAGGATGGGTGCCACCA 60.105 50.000 17.22 2.09 46.24 4.17
168 169 2.358737 GCCACCAACCGTCCAGAG 60.359 66.667 0.00 0.00 0.00 3.35
539 550 2.424302 CGGGTCACAAGGAACGGT 59.576 61.111 0.00 0.00 32.36 4.83
612 629 4.398988 TGCAAGTGAAGTATAGCCAAATGG 59.601 41.667 0.00 0.00 38.53 3.16
635 652 3.799281 AATAACGCATGAACCAATGGG 57.201 42.857 3.55 0.00 43.95 4.00
640 657 0.819582 GCATGAACCAATGGGACCAG 59.180 55.000 3.55 0.00 38.05 4.00
642 659 2.951787 GCATGAACCAATGGGACCAGAT 60.952 50.000 3.55 0.00 38.05 2.90
688 811 0.670546 CTACGGTGCACCAAGACCAG 60.671 60.000 34.16 18.73 35.14 4.00
696 819 1.545428 GCACCAAGACCAGGTTCATGA 60.545 52.381 0.00 0.00 37.23 3.07
710 833 0.546122 TCATGAATAGGCCGGCAACT 59.454 50.000 30.85 19.77 0.00 3.16
779 902 5.011023 ACAATTAGAAAGAAAGCAACCCAGG 59.989 40.000 0.00 0.00 0.00 4.45
790 913 2.516888 AACCCAGGTCAGACCACCG 61.517 63.158 22.31 10.00 41.95 4.94
841 964 1.593265 CAGCCACCTTTTCCCATGC 59.407 57.895 0.00 0.00 0.00 4.06
1047 1170 4.394712 AGCGTGAAGAAGGGCCCG 62.395 66.667 18.44 2.17 0.00 6.13
1178 1301 4.038042 GCTGAGTACCATGTAGTGATGCTA 59.962 45.833 0.00 0.00 0.00 3.49
1197 1320 2.961526 ACCAGTAAGCGGTAGTGATG 57.038 50.000 6.82 0.00 35.41 3.07
1247 1376 0.617413 CTTGTGTCTCTGGGGCATCT 59.383 55.000 0.00 0.00 0.00 2.90
1406 1535 1.148273 GCACAGTTGGTCTCACCCA 59.852 57.895 0.00 0.00 37.50 4.51
1418 1547 3.691609 GGTCTCACCCATCTTGTCAATTC 59.308 47.826 0.00 0.00 30.04 2.17
1432 1561 9.676861 ATCTTGTCAATTCTATGATCAACTCAA 57.323 29.630 0.00 0.00 37.44 3.02
1633 1924 3.786368 AGGCTCAAGAAGAAGCTCTTT 57.214 42.857 0.00 0.00 36.73 2.52
1822 2113 1.000843 GGTTCAATGGTGGAAGGCAAC 59.999 52.381 0.00 0.00 0.00 4.17
1867 2158 1.351017 TCCATCCGGAAGCTTCTGTTT 59.649 47.619 29.04 15.92 38.83 2.83
1891 2182 2.275318 CTAGGAGGAAGCTCTTTTGCG 58.725 52.381 0.00 0.00 38.13 4.85
1899 2190 3.752339 CTCTTTTGCGGCCCTGCC 61.752 66.667 0.00 0.00 46.75 4.85
1948 2239 0.185175 ACGGGGAAGCTCCAAACTTT 59.815 50.000 0.00 0.00 38.64 2.66
2047 2338 2.354203 GGACGAGAGCTTCCAGTTCAAT 60.354 50.000 0.00 0.00 32.89 2.57
2128 2419 0.779997 ATGAAGTGAGCCCCTTGGTT 59.220 50.000 0.00 0.00 0.00 3.67
2194 2485 1.064946 CTGCCTCGTAGAAGAGCCG 59.935 63.158 0.00 0.00 36.95 5.52
2217 2508 0.464554 GACCTTGGGATGCAGTAGCC 60.465 60.000 0.00 0.00 41.13 3.93
2338 2629 8.619546 AGAGCTCTGAATTAAGAACAATAATGC 58.380 33.333 17.42 0.00 0.00 3.56
2532 2824 3.102204 GAGTACCAACCCTAGTGGCTAA 58.898 50.000 0.00 0.00 37.83 3.09
2539 2831 6.127101 ACCAACCCTAGTGGCTAAATATTTC 58.873 40.000 3.39 0.00 37.83 2.17
2673 2965 5.762825 ATAAGGCATGTCTGTAAAGCATG 57.237 39.130 0.00 11.05 41.89 4.06
2687 2979 7.064134 TCTGTAAAGCATGAAAATCGTCGTTAT 59.936 33.333 0.00 0.00 0.00 1.89
2753 3045 1.608590 ACACGTCTTTTTGGAGCATGG 59.391 47.619 0.00 0.00 0.00 3.66
2830 3122 9.815936 CTTTGAAATTCAAATTAATGTTCCAGC 57.184 29.630 19.84 0.00 44.37 4.85
2982 3285 6.037940 CAGTACTGTGGAATGATGAAATGGAG 59.962 42.308 15.06 0.00 0.00 3.86
3054 3357 5.126061 ACTTCACCTGTTTGATTCCATATGC 59.874 40.000 0.00 0.00 0.00 3.14
3161 3464 7.119699 TCCACAGAAAAACTATAGTCATTGCTG 59.880 37.037 24.65 24.65 36.89 4.41
3162 3465 7.119699 CCACAGAAAAACTATAGTCATTGCTGA 59.880 37.037 29.16 0.00 35.57 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 55 7.272978 ACAACCACACCATCTTACTGATATAC 58.727 38.462 0.00 0.00 33.36 1.47
110 111 9.877178 TGTTTTGACATAACATTTGGTAAAAGT 57.123 25.926 7.30 0.00 30.96 2.66
157 158 1.430992 TTTTCCTCCTCTGGACGGTT 58.569 50.000 0.00 0.00 35.58 4.44
161 162 6.659824 TGGTAAATATTTTCCTCCTCTGGAC 58.340 40.000 20.59 3.77 35.58 4.02
336 347 7.881142 TGTTTTAAGAAGTCATGTGTTATGGG 58.119 34.615 0.00 0.00 0.00 4.00
471 482 4.730966 TGGTCTGGGTGCAAATTTTACTA 58.269 39.130 0.00 0.00 0.00 1.82
523 534 1.599797 CCACCGTTCCTTGTGACCC 60.600 63.158 0.00 0.00 34.37 4.46
579 596 9.261180 GCTATACTTCACTTGCATATTCTGTTA 57.739 33.333 0.00 0.00 0.00 2.41
612 629 3.306703 CCATTGGTTCATGCGTTATTTGC 59.693 43.478 0.00 0.00 0.00 3.68
613 630 3.864583 CCCATTGGTTCATGCGTTATTTG 59.135 43.478 1.20 0.00 0.00 2.32
635 652 9.077885 AGTGAGATCTTCTTATCTAATCTGGTC 57.922 37.037 0.00 0.00 36.33 4.02
688 811 0.465460 TGCCGGCCTATTCATGAACC 60.465 55.000 26.77 6.52 0.00 3.62
696 819 0.463833 GCACTAGTTGCCGGCCTATT 60.464 55.000 26.77 10.38 46.63 1.73
710 833 0.823460 TCATGCGTCCATCAGCACTA 59.177 50.000 0.00 0.00 46.83 2.74
779 902 3.561503 GTTTAATTTGCGGTGGTCTGAC 58.438 45.455 0.00 0.00 0.00 3.51
841 964 4.585162 AGGAGAGACGAGGTGTATTATTGG 59.415 45.833 0.00 0.00 0.00 3.16
1178 1301 2.453521 TCATCACTACCGCTTACTGGT 58.546 47.619 0.00 0.00 43.62 4.00
1197 1320 8.254508 CACACCTAATTAGCTTCTCCCTATATC 58.745 40.741 6.99 0.00 0.00 1.63
1247 1376 1.152247 ACACCTCCTCAGACCTGCA 60.152 57.895 0.00 0.00 0.00 4.41
1389 1518 1.349026 AGATGGGTGAGACCAACTGTG 59.651 52.381 0.00 0.00 45.13 3.66
1406 1535 9.676861 TTGAGTTGATCATAGAATTGACAAGAT 57.323 29.630 0.00 0.00 37.89 2.40
1418 1547 9.689976 CTAATCCTACAGTTGAGTTGATCATAG 57.310 37.037 0.00 0.00 37.89 2.23
1432 1561 4.256920 CAGTTTGCAGCTAATCCTACAGT 58.743 43.478 0.00 0.00 0.00 3.55
1633 1924 3.179869 CTTGCGCGACTGTTTGCCA 62.180 57.895 12.10 0.00 0.00 4.92
1801 2092 0.187117 TGCCTTCCACCATTGAACCA 59.813 50.000 0.00 0.00 0.00 3.67
1921 2212 1.653151 GAGCTTCCCCGTACATTGAC 58.347 55.000 0.00 0.00 0.00 3.18
1922 2213 0.539986 GGAGCTTCCCCGTACATTGA 59.460 55.000 0.00 0.00 0.00 2.57
2041 2332 2.485814 GTCCAGCTTGACCTGATTGAAC 59.514 50.000 6.68 0.00 34.77 3.18
2047 2338 2.583441 CCCGTCCAGCTTGACCTGA 61.583 63.158 12.05 0.00 34.77 3.86
2128 2419 1.337447 GCGACAGTAGTGTTAGGGCAA 60.337 52.381 4.32 0.00 36.88 4.52
2184 2475 0.323178 AAGGTCGACCGGCTCTTCTA 60.323 55.000 28.26 0.00 42.08 2.10
2188 2479 3.382832 CCAAGGTCGACCGGCTCT 61.383 66.667 28.26 8.32 42.08 4.09
2194 2485 1.450312 CTGCATCCCAAGGTCGACC 60.450 63.158 27.67 27.67 0.00 4.79
2217 2508 6.204688 TGAGAACAAACACCAATAGCTAGTTG 59.795 38.462 0.00 4.48 0.00 3.16
2338 2629 3.117701 TCTCATCTAGGAGTGGTGAGAGG 60.118 52.174 2.96 0.00 40.06 3.69
2487 2779 8.645814 TCGGTATAAATATCACACATAGACCT 57.354 34.615 0.00 0.00 0.00 3.85
2539 2831 5.679734 ATGCTGTTAGAGAACACACAAAG 57.320 39.130 0.00 0.00 40.72 2.77
2629 2921 2.015736 AGTCCACGAATGTCTCATGC 57.984 50.000 0.00 0.00 0.00 4.06
2673 2965 8.390854 TCTCTAACTTCATAACGACGATTTTC 57.609 34.615 0.00 0.00 0.00 2.29
2753 3045 8.555361 GGAAAGTCATTTTCTATCTATGTCTGC 58.445 37.037 0.00 0.00 43.81 4.26
2807 3099 7.374272 TCGCTGGAACATTAATTTGAATTTCA 58.626 30.769 0.00 0.00 38.20 2.69
2808 3100 7.810766 TCGCTGGAACATTAATTTGAATTTC 57.189 32.000 0.00 0.00 38.20 2.17
2809 3101 8.776376 AATCGCTGGAACATTAATTTGAATTT 57.224 26.923 0.00 0.00 38.20 1.82
2830 3122 7.579726 TGTAAAATCCATTTTTGCCAAAATCG 58.420 30.769 3.01 0.32 40.09 3.34
2900 3196 4.821260 TGACACAATGTGAGCAACTTACAT 59.179 37.500 21.34 0.00 41.38 2.29
2982 3285 7.604164 ACATATGATGACCGGATAAATGAAGTC 59.396 37.037 9.46 0.00 0.00 3.01
3023 3326 3.390135 TCAAACAGGTGAAGTAGAAGCG 58.610 45.455 0.00 0.00 0.00 4.68
3054 3357 2.679837 AGTATGAACGCTGGAAATGCAG 59.320 45.455 0.00 0.00 0.00 4.41
3122 3425 3.402628 TCTGTGGAAGGAGTTTAGTGC 57.597 47.619 0.00 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.