Multiple sequence alignment - TraesCS5A01G228700

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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 TraesCS5A01G228700 chr5A 100.000 2807 0 0 1 2807 444785446 444788252 0.000000e+00 5184.0
1 TraesCS5A01G228700 chr5A 90.965 2612 200 28 1 2590 101170153 101167556 0.000000e+00 3483.0
2 TraesCS5A01G228700 chr7A 95.101 2817 111 13 1 2807 592894522 592897321 0.000000e+00 4412.0
3 TraesCS5A01G228700 chr7A 91.560 2808 189 38 12 2797 404880253 404877472 0.000000e+00 3829.0
4 TraesCS5A01G228700 chr7A 90.381 2838 206 29 1 2797 385236363 385233552 0.000000e+00 3666.0
5 TraesCS5A01G228700 chr7A 86.525 2679 283 47 62 2712 582571278 582573906 0.000000e+00 2876.0
6 TraesCS5A01G228700 chr3A 92.540 2815 179 26 12 2807 211304574 211307376 0.000000e+00 4006.0
7 TraesCS5A01G228700 chr3A 88.806 2832 236 43 9 2797 46667160 46664367 0.000000e+00 3398.0
8 TraesCS5A01G228700 chr4A 90.436 2823 201 36 17 2797 344969657 344966862 0.000000e+00 3653.0
9 TraesCS5A01G228700 chr4A 90.343 2827 205 30 1 2785 344965166 344962366 0.000000e+00 3646.0
10 TraesCS5A01G228700 chr3B 85.353 2806 314 63 9 2797 289834833 289837558 0.000000e+00 2815.0
11 TraesCS5A01G228700 chr3B 85.714 119 15 2 1 117 69561782 69561664 1.060000e-24 124.0
12 TraesCS5A01G228700 chr6A 89.325 1630 150 20 1182 2797 335914745 335916364 0.000000e+00 2025.0
13 TraesCS5A01G228700 chr1A 92.345 1241 82 10 1558 2796 58160822 58159593 0.000000e+00 1753.0
14 TraesCS5A01G228700 chr7B 87.871 1245 105 26 1558 2797 456123302 456124505 0.000000e+00 1421.0
15 TraesCS5A01G228700 chr4B 86.116 1174 109 35 1630 2797 379116472 379115347 0.000000e+00 1216.0
16 TraesCS5A01G228700 chr2A 100.000 28 0 0 6 33 300378160 300378187 5.000000e-03 52.8


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 TraesCS5A01G228700 chr5A 444785446 444788252 2806 False 5184.0 5184 100.0000 1 2807 1 chr5A.!!$F1 2806
1 TraesCS5A01G228700 chr5A 101167556 101170153 2597 True 3483.0 3483 90.9650 1 2590 1 chr5A.!!$R1 2589
2 TraesCS5A01G228700 chr7A 592894522 592897321 2799 False 4412.0 4412 95.1010 1 2807 1 chr7A.!!$F2 2806
3 TraesCS5A01G228700 chr7A 404877472 404880253 2781 True 3829.0 3829 91.5600 12 2797 1 chr7A.!!$R2 2785
4 TraesCS5A01G228700 chr7A 385233552 385236363 2811 True 3666.0 3666 90.3810 1 2797 1 chr7A.!!$R1 2796
5 TraesCS5A01G228700 chr7A 582571278 582573906 2628 False 2876.0 2876 86.5250 62 2712 1 chr7A.!!$F1 2650
6 TraesCS5A01G228700 chr3A 211304574 211307376 2802 False 4006.0 4006 92.5400 12 2807 1 chr3A.!!$F1 2795
7 TraesCS5A01G228700 chr3A 46664367 46667160 2793 True 3398.0 3398 88.8060 9 2797 1 chr3A.!!$R1 2788
8 TraesCS5A01G228700 chr4A 344962366 344969657 7291 True 3649.5 3653 90.3895 1 2797 2 chr4A.!!$R1 2796
9 TraesCS5A01G228700 chr3B 289834833 289837558 2725 False 2815.0 2815 85.3530 9 2797 1 chr3B.!!$F1 2788
10 TraesCS5A01G228700 chr6A 335914745 335916364 1619 False 2025.0 2025 89.3250 1182 2797 1 chr6A.!!$F1 1615
11 TraesCS5A01G228700 chr1A 58159593 58160822 1229 True 1753.0 1753 92.3450 1558 2796 1 chr1A.!!$R1 1238
12 TraesCS5A01G228700 chr7B 456123302 456124505 1203 False 1421.0 1421 87.8710 1558 2797 1 chr7B.!!$F1 1239
13 TraesCS5A01G228700 chr4B 379115347 379116472 1125 True 1216.0 1216 86.1160 1630 2797 1 chr4B.!!$R1 1167

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
130 133 2.265904 CGACACTCACAGTCCGGGA 61.266 63.158 0.0 0.0 32.41 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1851 6439 0.741326 GCTCTCTATCCTCGTGCACA 59.259 55.0 18.64 3.15 0.0 4.57 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
130 133 2.265904 CGACACTCACAGTCCGGGA 61.266 63.158 0.00 0.0 32.41 5.14
242 254 8.503196 GGTTTCTTGTTTTCTTTTTGTGACATT 58.497 29.630 0.00 0.0 0.00 2.71
542 556 5.535783 TCCTACATGCCATATTTGTGGATTG 59.464 40.000 0.00 0.0 42.02 2.67
608 622 2.437651 TCCCGATTGTTATGGCATGAGA 59.562 45.455 10.98 0.0 0.00 3.27
759 775 2.957402 ACAATGAGGAGAGCCACAAA 57.043 45.000 0.00 0.0 38.29 2.83
874 890 2.410322 ATCAACTCCAGCAACCGCCA 62.410 55.000 0.00 0.0 39.83 5.69
970 986 4.844420 CTTGGAGTGCCGAGGATC 57.156 61.111 0.00 0.0 41.37 3.36
1318 1334 7.280356 AGTAAAAGAAGCTCCTGTAGTTGAAA 58.720 34.615 0.00 0.0 0.00 2.69
1345 1361 5.391312 AGAACCAGAAATTCATTTTCCCG 57.609 39.130 0.00 0.0 44.06 5.14
1512 6036 0.810648 ATACTGTTGGTGGCATTGCG 59.189 50.000 1.91 0.0 0.00 4.85
1813 6370 5.455899 GGATTTAGAGCATGGTGAAGAGGAT 60.456 44.000 0.00 0.0 0.00 3.24
1822 6379 4.574674 TGGTGAAGAGGATAAGCAATGT 57.425 40.909 0.00 0.0 0.00 2.71
1851 6439 3.137360 ACAAGGAAGAGAAAAGCTGGAGT 59.863 43.478 0.00 0.0 0.00 3.85
1867 6485 1.066303 GGAGTGTGCACGAGGATAGAG 59.934 57.143 13.13 0.0 36.20 2.43
1868 6486 2.017782 GAGTGTGCACGAGGATAGAGA 58.982 52.381 13.13 0.0 36.20 3.10
1869 6487 2.020720 AGTGTGCACGAGGATAGAGAG 58.979 52.381 13.13 0.0 36.20 3.20
1870 6488 0.741326 TGTGCACGAGGATAGAGAGC 59.259 55.000 13.13 0.0 0.00 4.09
1871 6489 0.741326 GTGCACGAGGATAGAGAGCA 59.259 55.000 0.00 0.0 0.00 4.26
1872 6490 1.339610 GTGCACGAGGATAGAGAGCAT 59.660 52.381 0.00 0.0 32.75 3.79
1873 6491 1.339291 TGCACGAGGATAGAGAGCATG 59.661 52.381 0.00 0.0 0.00 4.06
1874 6492 1.611006 GCACGAGGATAGAGAGCATGA 59.389 52.381 0.00 0.0 0.00 3.07
1875 6493 2.351641 GCACGAGGATAGAGAGCATGAG 60.352 54.545 0.00 0.0 0.00 2.90
1876 6494 2.228582 CACGAGGATAGAGAGCATGAGG 59.771 54.545 0.00 0.0 0.00 3.86
1877 6495 2.107378 ACGAGGATAGAGAGCATGAGGA 59.893 50.000 0.00 0.0 0.00 3.71
1878 6496 3.245229 ACGAGGATAGAGAGCATGAGGAT 60.245 47.826 0.00 0.0 0.00 3.24
1879 6497 4.018870 ACGAGGATAGAGAGCATGAGGATA 60.019 45.833 0.00 0.0 0.00 2.59
1880 6498 4.576053 CGAGGATAGAGAGCATGAGGATAG 59.424 50.000 0.00 0.0 0.00 2.08
1881 6499 5.628899 CGAGGATAGAGAGCATGAGGATAGA 60.629 48.000 0.00 0.0 0.00 1.98
1922 6546 0.935898 CGATGCAAGAGGATGTGAGC 59.064 55.000 0.00 0.0 0.00 4.26
1951 6576 5.331876 AGCGAGTTCTACTTCATAAAGCT 57.668 39.130 0.00 0.0 35.81 3.74
1955 6580 5.448768 CGAGTTCTACTTCATAAAGCTCGGA 60.449 44.000 0.00 0.0 36.91 4.55
2022 6654 7.452880 ACAAGCTGAAATCAATTGCTAGTTA 57.547 32.000 0.00 0.0 33.28 2.24
2101 6736 4.341806 TGCTTGATGTGAATTTGTGACCTT 59.658 37.500 0.00 0.0 0.00 3.50
2270 6907 8.420222 TCACCATGTTTAGATGTTGAATTTGTT 58.580 29.630 0.00 0.0 0.00 2.83
2312 6949 4.716784 AGAGCAATCACCTAACCACTATGA 59.283 41.667 0.00 0.0 0.00 2.15
2322 6959 6.992123 CACCTAACCACTATGAATTAGCATGA 59.008 38.462 0.00 0.0 0.00 3.07
2405 7044 4.679197 TGTGCTTATGCGTTGTTCATTTTC 59.321 37.500 0.00 0.0 43.34 2.29
2577 7233 1.958579 CTCGGGATCGGTGGTATGTTA 59.041 52.381 0.00 0.0 36.95 2.41
2642 7308 4.202326 GGTGTATACCATGTTCTCGGGATT 60.202 45.833 3.35 0.0 46.71 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
259 271 5.846868 ACTAGTACAGTGGTTAGGGGTTAT 58.153 41.667 0.00 0.00 35.62 1.89
351 365 1.747206 GCTCGCATATCCTTGGTGGTT 60.747 52.381 0.00 0.00 37.07 3.67
353 367 0.179048 TGCTCGCATATCCTTGGTGG 60.179 55.000 0.00 0.00 37.10 4.61
542 556 3.070576 GTGGGTGAATGGCCCTGC 61.071 66.667 0.00 0.00 46.22 4.85
608 622 2.911143 CTAGGCTGTGGGGCGAAT 59.089 61.111 0.00 0.00 45.89 3.34
759 775 7.255381 GCTGAATAAATCTGTTGTGGAGCATAT 60.255 37.037 0.00 0.00 0.00 1.78
874 890 2.352421 GCACTTGCACATGAGATTGCTT 60.352 45.455 0.00 0.00 39.62 3.91
904 920 8.969260 AGCTTGTCTATATCATCAAATTCACA 57.031 30.769 0.00 0.00 0.00 3.58
905 921 9.049523 TGAGCTTGTCTATATCATCAAATTCAC 57.950 33.333 0.00 0.00 0.00 3.18
1318 1334 7.879677 GGGAAAATGAATTTCTGGTTCTTCATT 59.120 33.333 4.08 4.08 45.45 2.57
1345 1361 2.257974 TCACGCTCTTGTATGACGAC 57.742 50.000 0.00 0.00 0.00 4.34
1649 6173 8.783660 ACCCTCTAAATGATGAATAGAGTACA 57.216 34.615 0.00 0.00 40.56 2.90
1813 6370 4.331108 TCCTTGTATGTGCACATTGCTTA 58.669 39.130 35.45 16.16 45.31 3.09
1822 6379 4.216257 GCTTTTCTCTTCCTTGTATGTGCA 59.784 41.667 0.00 0.00 0.00 4.57
1851 6439 0.741326 GCTCTCTATCCTCGTGCACA 59.259 55.000 18.64 3.15 0.00 4.57
1867 6485 6.482973 CCTTTTTCTTCTCTATCCTCATGCTC 59.517 42.308 0.00 0.00 0.00 4.26
1868 6486 6.157645 TCCTTTTTCTTCTCTATCCTCATGCT 59.842 38.462 0.00 0.00 0.00 3.79
1869 6487 6.352516 TCCTTTTTCTTCTCTATCCTCATGC 58.647 40.000 0.00 0.00 0.00 4.06
1870 6488 7.790027 TCTCCTTTTTCTTCTCTATCCTCATG 58.210 38.462 0.00 0.00 0.00 3.07
1871 6489 7.071071 CCTCTCCTTTTTCTTCTCTATCCTCAT 59.929 40.741 0.00 0.00 0.00 2.90
1872 6490 6.382570 CCTCTCCTTTTTCTTCTCTATCCTCA 59.617 42.308 0.00 0.00 0.00 3.86
1873 6491 6.609616 TCCTCTCCTTTTTCTTCTCTATCCTC 59.390 42.308 0.00 0.00 0.00 3.71
1874 6492 6.507568 TCCTCTCCTTTTTCTTCTCTATCCT 58.492 40.000 0.00 0.00 0.00 3.24
1875 6493 6.382859 ACTCCTCTCCTTTTTCTTCTCTATCC 59.617 42.308 0.00 0.00 0.00 2.59
1876 6494 7.123547 TGACTCCTCTCCTTTTTCTTCTCTATC 59.876 40.741 0.00 0.00 0.00 2.08
1877 6495 6.957020 TGACTCCTCTCCTTTTTCTTCTCTAT 59.043 38.462 0.00 0.00 0.00 1.98
1878 6496 6.209788 GTGACTCCTCTCCTTTTTCTTCTCTA 59.790 42.308 0.00 0.00 0.00 2.43
1879 6497 5.011635 GTGACTCCTCTCCTTTTTCTTCTCT 59.988 44.000 0.00 0.00 0.00 3.10
1880 6498 5.234752 GTGACTCCTCTCCTTTTTCTTCTC 58.765 45.833 0.00 0.00 0.00 2.87
1881 6499 4.262249 CGTGACTCCTCTCCTTTTTCTTCT 60.262 45.833 0.00 0.00 0.00 2.85
1922 6546 3.064134 TGAAGTAGAACTCGCTCGATCAG 59.936 47.826 0.00 0.00 0.00 2.90
1951 6576 1.066858 GGTCATGAAACAGCTCTCCGA 60.067 52.381 0.00 0.00 0.00 4.55
1955 6580 1.067295 TGGGGTCATGAAACAGCTCT 58.933 50.000 0.00 0.00 0.00 4.09
2022 6654 2.887151 ATAACTGGCTCAAGCAACCT 57.113 45.000 4.13 0.00 44.36 3.50
2101 6736 9.515226 ACTAGTTTACAAGGCATTTAGAAATCA 57.485 29.630 0.00 0.00 0.00 2.57
2312 6949 6.204852 TCCAGGGAACATATCATGCTAATT 57.795 37.500 0.00 0.00 0.00 1.40
2322 6959 2.567615 GCTACCGATCCAGGGAACATAT 59.432 50.000 0.00 0.00 35.02 1.78
2369 7006 4.324402 GCATAAGCACAAAAACAGGAATCG 59.676 41.667 0.00 0.00 41.58 3.34
2642 7308 3.454447 CTCACCATAGGAACATACCACCA 59.546 47.826 0.00 0.00 0.00 4.17


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

AutoCloner maintained by Alex Coulton.