Multiple sequence alignment - TraesCS5A01G329800

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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 TraesCS5A01G329800 chr5A 100.000 2913 0 0 1 2913 539077772 539074860 0.000000e+00 5380
1 TraesCS5A01G329800 chr5A 92.398 1618 88 12 304 1903 139476653 139475053 0.000000e+00 2274
2 TraesCS5A01G329800 chr5A 93.271 431 25 4 2007 2434 139472297 139471868 1.470000e-177 632
3 TraesCS5A01G329800 chr2A 98.028 2434 45 3 1 2434 605005105 605002675 0.000000e+00 4226
4 TraesCS5A01G329800 chr2A 97.593 457 9 2 2429 2884 605002600 605002145 0.000000e+00 782
5 TraesCS5A01G329800 chr2A 92.098 367 25 4 2526 2890 364416100 364416464 5.570000e-142 514
6 TraesCS5A01G329800 chr6D 97.336 2140 43 6 304 2434 433251086 433253220 0.000000e+00 3624
7 TraesCS5A01G329800 chr6D 97.152 2142 46 7 304 2434 32038880 32036743 0.000000e+00 3603
8 TraesCS5A01G329800 chr6D 97.064 1158 24 3 304 1452 420713556 420714712 0.000000e+00 1941
9 TraesCS5A01G329800 chr6D 96.663 869 25 4 1511 2376 420714702 420715569 0.000000e+00 1441
10 TraesCS5A01G329800 chr6D 95.614 456 19 1 2429 2884 433253295 433253749 0.000000e+00 730
11 TraesCS5A01G329800 chr6D 95.561 428 18 1 2429 2856 32036668 32036242 0.000000e+00 684
12 TraesCS5A01G329800 chr2B 96.684 2141 52 9 304 2434 616459530 616461661 0.000000e+00 3542
13 TraesCS5A01G329800 chr2B 93.407 455 29 1 2429 2883 616461736 616462189 0.000000e+00 673
14 TraesCS5A01G329800 chr2B 96.333 300 10 1 1 300 616458179 616458477 2.610000e-135 492
15 TraesCS5A01G329800 chr2D 92.645 1618 83 13 304 1903 644817950 644819549 0.000000e+00 2296
16 TraesCS5A01G329800 chr2D 93.287 432 24 5 2007 2434 644822341 644822771 1.470000e-177 632
17 TraesCS5A01G329800 chr2D 93.151 365 23 2 2521 2883 644823076 644823440 4.270000e-148 534
18 TraesCS5A01G329800 chr2D 93.266 297 18 2 4 298 60006708 60007004 1.240000e-118 436
19 TraesCS5A01G329800 chr4D 92.460 1618 86 13 304 1903 403009182 403010781 0.000000e+00 2279
20 TraesCS5A01G329800 chr7D 92.331 1617 88 13 304 1903 29571537 29569940 0.000000e+00 2266
21 TraesCS5A01G329800 chr7D 93.533 433 22 5 2007 2434 29567148 29566717 8.800000e-180 640
22 TraesCS5A01G329800 chr7D 92.877 365 25 1 2521 2884 29566412 29566048 1.990000e-146 529
23 TraesCS5A01G329800 chr1D 91.899 1617 95 13 304 1903 187808656 187810253 0.000000e+00 2228
24 TraesCS5A01G329800 chr1D 93.056 432 25 5 2007 2434 187813044 187813474 6.850000e-176 627
25 TraesCS5A01G329800 chr1D 92.857 364 25 1 2521 2883 187813779 187814142 7.150000e-146 527
26 TraesCS5A01G329800 chr6A 92.580 1186 65 8 304 1473 615073658 615072480 0.000000e+00 1681
27 TraesCS5A01G329800 chr1A 84.527 1312 160 28 724 2024 50508945 50510224 0.000000e+00 1258
28 TraesCS5A01G329800 chr5B 92.500 360 26 1 2526 2884 691750779 691750420 5.570000e-142 514
29 TraesCS5A01G329800 chr5B 94.352 301 15 2 1 300 545167413 545167712 7.360000e-126 460
30 TraesCS5A01G329800 chr1B 84.502 271 30 8 24 291 121208790 121209051 1.040000e-64 257
31 TraesCS5A01G329800 chr4B 84.133 271 31 8 24 291 483740151 483740412 4.820000e-63 252
32 TraesCS5A01G329800 chr7B 83.142 261 37 5 24 282 559151409 559151154 6.280000e-57 231
33 TraesCS5A01G329800 chr7A 95.146 103 5 0 1 103 322623251 322623149 2.320000e-36 163


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 TraesCS5A01G329800 chr5A 539074860 539077772 2912 True 5380.000000 5380 100.000000 1 2913 1 chr5A.!!$R1 2912
1 TraesCS5A01G329800 chr5A 139471868 139476653 4785 True 1453.000000 2274 92.834500 304 2434 2 chr5A.!!$R2 2130
2 TraesCS5A01G329800 chr2A 605002145 605005105 2960 True 2504.000000 4226 97.810500 1 2884 2 chr2A.!!$R1 2883
3 TraesCS5A01G329800 chr6D 433251086 433253749 2663 False 2177.000000 3624 96.475000 304 2884 2 chr6D.!!$F2 2580
4 TraesCS5A01G329800 chr6D 32036242 32038880 2638 True 2143.500000 3603 96.356500 304 2856 2 chr6D.!!$R1 2552
5 TraesCS5A01G329800 chr6D 420713556 420715569 2013 False 1691.000000 1941 96.863500 304 2376 2 chr6D.!!$F1 2072
6 TraesCS5A01G329800 chr2B 616458179 616462189 4010 False 1569.000000 3542 95.474667 1 2883 3 chr2B.!!$F1 2882
7 TraesCS5A01G329800 chr2D 644817950 644823440 5490 False 1154.000000 2296 93.027667 304 2883 3 chr2D.!!$F2 2579
8 TraesCS5A01G329800 chr4D 403009182 403010781 1599 False 2279.000000 2279 92.460000 304 1903 1 chr4D.!!$F1 1599
9 TraesCS5A01G329800 chr7D 29566048 29571537 5489 True 1145.000000 2266 92.913667 304 2884 3 chr7D.!!$R1 2580
10 TraesCS5A01G329800 chr1D 187808656 187814142 5486 False 1127.333333 2228 92.604000 304 2883 3 chr1D.!!$F1 2579
11 TraesCS5A01G329800 chr6A 615072480 615073658 1178 True 1681.000000 1681 92.580000 304 1473 1 chr6A.!!$R1 1169
12 TraesCS5A01G329800 chr1A 50508945 50510224 1279 False 1258.000000 1258 84.527000 724 2024 1 chr1A.!!$F1 1300


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
928 2005 2.667318 CGGTCACGAGCGCATTGTT 61.667 57.895 11.47 0.0 45.38 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2424 6222 0.90158 AAGCTTGGACAAGGCCATGG 60.902 55.0 13.45 7.63 37.86 3.66 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
633 1697 6.045955 GGACTTTACATGGTTTCTTGCAAAA 58.954 36.000 0.00 0.00 0.00 2.44
795 1870 5.566826 GCTGACTATACACACAAGAACCTCA 60.567 44.000 0.00 0.00 0.00 3.86
879 1956 8.506437 CAGTATGCTTACTGTTTCTTCATTCAA 58.494 33.333 24.61 0.00 46.84 2.69
897 1974 4.868314 TCAATTTCATGTGGCAATGACA 57.132 36.364 10.52 0.00 36.31 3.58
928 2005 2.667318 CGGTCACGAGCGCATTGTT 61.667 57.895 11.47 0.00 45.38 2.83
1198 2275 1.156736 GACTTGACATTGTGGTCGGG 58.843 55.000 0.00 0.00 40.72 5.14
1312 2390 3.932710 GGCAGACATCGACAACTATTCAA 59.067 43.478 0.00 0.00 0.00 2.69
1484 2566 8.378565 ACTACAGATCCATTCCGATATTTTCAT 58.621 33.333 0.00 0.00 0.00 2.57
1764 2855 1.070309 GTGCGCGATCCATTCATTCTC 60.070 52.381 12.10 0.00 0.00 2.87
1876 2967 7.544511 CATTAATTGCAATGAGAAGTATCGC 57.455 36.000 13.82 0.00 38.01 4.58
2305 6097 5.718649 TGTTATCTCGAGCAATGCTTTAC 57.281 39.130 9.91 0.00 39.88 2.01
2354 6152 6.923199 ACACTAGGTTAAAAGCCTACTGTA 57.077 37.500 0.00 0.00 35.41 2.74
2424 6222 7.254252 CGAATGATCTTACTGAATGACTGTTCC 60.254 40.741 0.00 0.00 33.04 3.62
2483 6360 9.883142 GGGGAATGTTAAAATATTTTGTGATGA 57.117 29.630 21.19 0.00 0.00 2.92
2515 6392 2.665649 TGGTTAGGTATGTGTCGCAG 57.334 50.000 0.00 0.00 0.00 5.18
2790 6811 4.735369 ACAACCAACCCACAATGAATAGA 58.265 39.130 0.00 0.00 0.00 1.98
2884 6906 4.601084 ACACACAGGCACTCTACTAGTAT 58.399 43.478 2.33 0.00 35.76 2.12
2885 6907 4.399618 ACACACAGGCACTCTACTAGTATG 59.600 45.833 2.33 0.20 35.76 2.39
2886 6908 3.381908 ACACAGGCACTCTACTAGTATGC 59.618 47.826 15.61 15.61 35.76 3.14
2887 6909 3.381590 CACAGGCACTCTACTAGTATGCA 59.618 47.826 22.24 0.00 35.76 3.96
2888 6910 4.038522 CACAGGCACTCTACTAGTATGCAT 59.961 45.833 22.24 15.79 35.76 3.96
2889 6911 5.241728 CACAGGCACTCTACTAGTATGCATA 59.758 44.000 22.24 1.16 35.76 3.14
2890 6912 5.833667 ACAGGCACTCTACTAGTATGCATAA 59.166 40.000 22.24 0.00 35.76 1.90
2891 6913 6.323996 ACAGGCACTCTACTAGTATGCATAAA 59.676 38.462 22.24 0.00 35.76 1.40
2892 6914 6.642950 CAGGCACTCTACTAGTATGCATAAAC 59.357 42.308 22.24 0.00 35.76 2.01
2893 6915 6.323996 AGGCACTCTACTAGTATGCATAAACA 59.676 38.462 22.24 0.00 35.76 2.83
2894 6916 6.984474 GGCACTCTACTAGTATGCATAAACAA 59.016 38.462 22.24 0.00 35.76 2.83
2895 6917 7.042658 GGCACTCTACTAGTATGCATAAACAAC 60.043 40.741 22.24 0.00 35.76 3.32
2896 6918 7.491372 GCACTCTACTAGTATGCATAAACAACA 59.509 37.037 18.00 0.00 35.76 3.33
2897 6919 9.366216 CACTCTACTAGTATGCATAAACAACAA 57.634 33.333 8.28 0.00 35.76 2.83
2898 6920 9.367444 ACTCTACTAGTATGCATAAACAACAAC 57.633 33.333 8.28 0.00 36.36 3.32
2899 6921 8.712285 TCTACTAGTATGCATAAACAACAACC 57.288 34.615 8.28 0.00 0.00 3.77
2900 6922 8.315482 TCTACTAGTATGCATAAACAACAACCA 58.685 33.333 8.28 0.00 0.00 3.67
2901 6923 7.938140 ACTAGTATGCATAAACAACAACCAT 57.062 32.000 8.28 0.00 0.00 3.55
2902 6924 7.761409 ACTAGTATGCATAAACAACAACCATG 58.239 34.615 8.28 0.00 0.00 3.66
2903 6925 6.832520 AGTATGCATAAACAACAACCATGA 57.167 33.333 8.28 0.00 0.00 3.07
2904 6926 7.225784 AGTATGCATAAACAACAACCATGAA 57.774 32.000 8.28 0.00 0.00 2.57
2905 6927 7.665690 AGTATGCATAAACAACAACCATGAAA 58.334 30.769 8.28 0.00 0.00 2.69
2906 6928 8.147058 AGTATGCATAAACAACAACCATGAAAA 58.853 29.630 8.28 0.00 0.00 2.29
2907 6929 6.595772 TGCATAAACAACAACCATGAAAAC 57.404 33.333 0.00 0.00 0.00 2.43
2908 6930 6.344500 TGCATAAACAACAACCATGAAAACT 58.656 32.000 0.00 0.00 0.00 2.66
2909 6931 6.478344 TGCATAAACAACAACCATGAAAACTC 59.522 34.615 0.00 0.00 0.00 3.01
2910 6932 6.073819 GCATAAACAACAACCATGAAAACTCC 60.074 38.462 0.00 0.00 0.00 3.85
2911 6933 5.413309 AAACAACAACCATGAAAACTCCA 57.587 34.783 0.00 0.00 0.00 3.86
2912 6934 5.413309 AACAACAACCATGAAAACTCCAA 57.587 34.783 0.00 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 7.172703 GGGTATAAGTATGCTAACGCTTGAATT 59.827 37.037 0.00 0.00 36.97 2.17
855 1932 9.846248 AATTGAATGAAGAAACAGTAAGCATAC 57.154 29.630 0.00 0.00 0.00 2.39
879 1956 2.557924 ACGTGTCATTGCCACATGAAAT 59.442 40.909 0.00 0.00 35.17 2.17
897 1974 1.605451 TGACCGTCATCCTCCACGT 60.605 57.895 0.00 0.00 34.06 4.49
928 2005 4.020617 CCCTCCGGTGAGCTTGCA 62.021 66.667 4.76 0.00 37.29 4.08
1215 2293 0.677731 CGCCAGGCAAGAAATCTCCA 60.678 55.000 13.30 0.00 0.00 3.86
1312 2390 8.037758 TGTGTCAGAATTTTGTTGTGGTTATTT 58.962 29.630 0.00 0.00 0.00 1.40
1462 2544 8.102800 TCAATGAAAATATCGGAATGGATCTG 57.897 34.615 0.00 0.00 35.59 2.90
1764 2855 5.675538 AGGAATAAGGAAGGATCAAACGAG 58.324 41.667 0.00 0.00 0.00 4.18
1870 2961 7.891183 AGTGAAGTTTATGGATATGCGATAC 57.109 36.000 0.00 0.00 0.00 2.24
1876 2967 9.912634 AACAACAAAGTGAAGTTTATGGATATG 57.087 29.630 0.00 0.00 0.00 1.78
2205 5997 5.533154 CGACCACCTCATCTAGTAGATTCTT 59.467 44.000 10.09 0.00 31.32 2.52
2424 6222 0.901580 AAGCTTGGACAAGGCCATGG 60.902 55.000 13.45 7.63 37.86 3.66
2483 6360 7.556275 CACATACCTAACCATTTAGAACCATGT 59.444 37.037 0.00 0.00 37.49 3.21
2741 6761 5.648572 TGATTGCATATCAAATTTCGCACA 58.351 33.333 8.52 0.00 38.34 4.57
2864 6886 3.381908 GCATACTAGTAGAGTGCCTGTGT 59.618 47.826 13.70 0.00 39.39 3.72
2884 6906 6.344500 AGTTTTCATGGTTGTTGTTTATGCA 58.656 32.000 0.00 0.00 0.00 3.96
2885 6907 6.073819 GGAGTTTTCATGGTTGTTGTTTATGC 60.074 38.462 0.00 0.00 0.00 3.14
2886 6908 6.983307 TGGAGTTTTCATGGTTGTTGTTTATG 59.017 34.615 0.00 0.00 0.00 1.90
2887 6909 7.118496 TGGAGTTTTCATGGTTGTTGTTTAT 57.882 32.000 0.00 0.00 0.00 1.40
2888 6910 6.531503 TGGAGTTTTCATGGTTGTTGTTTA 57.468 33.333 0.00 0.00 0.00 2.01
2889 6911 5.413309 TGGAGTTTTCATGGTTGTTGTTT 57.587 34.783 0.00 0.00 0.00 2.83
2890 6912 5.413309 TTGGAGTTTTCATGGTTGTTGTT 57.587 34.783 0.00 0.00 0.00 2.83



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

AutoCloner maintained by Alex Coulton.